From 1ecac9eab0e59d4624818f8f4c5e9b3334a4a32a Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Mon, 26 May 2014 23:54:30 +0100 Subject: [PATCH 001/154] Update README.md --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index febcf2f..6f9d8c8 100644 --- a/README.md +++ b/README.md @@ -14,13 +14,13 @@ There can be two keys in the root object: Elements are defined as key-value pairs, where the key is a description of the element, and the value is a dictionary of specifiers defining the element and its processing. Allowed keys in the specifier dictionary are: -- ***selector*** - an XPath selector targetting the content to be extracted -- ***download*** - a boolean flag: true if the element is a URL to a resource that must be downloaded +- ***selector*** - an XPath selector targetting the content to be extracted. **Required**. +- ***download*** - a boolean flag: true if the element is a URL to a resource that must be downloaded. **Optional** (omitting this key is equivalent to giving it a value of `false`). Example: ```json { - "url": "plosgenetics.org", + "url": "plos.*\\.org", "elements": { "fulltext_pdf": { "selector": "//meta[@name='citation_pdf_url']", @@ -32,4 +32,4 @@ Example: ### Usage -Currently these definitions can be used with the [quickscrape](http://github.com/ContentMine/quickscrape) tool. \ No newline at end of file +Currently these definitions can be used with the [quickscrape](http://github.com/ContentMine/quickscrape) tool. From a35fecda939b2c8f02b5e1cab99dd76736fa9065 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Tue, 27 May 2014 18:10:41 +0100 Subject: [PATCH 002/154] fix README formatting and typo --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index 4dae089..2b25de9 100644 --- a/README.md +++ b/README.md @@ -14,8 +14,7 @@ There can be two keys in the root object: Elements are defined as key-value pairs, where the key is a description of the element, and the value is a dictionary of specifiers defining the element and its processing. Allowed keys in the specifier dictionary are: -<<<<<<< HEAD -- ***selector*** - an XPath or CSS selector targetting the element to be selected. +- ***selector*** - an XPath selector targetting the element to be selected. - ***attribute*** - a string specifying the attribute to extract from the selected element. **Optional** (omitting this key is equivalent to giving it a value of 'text'). - ***download*** - a boolean flag: true if the element is a URL to a resource that must be downloaded. **Optional** (omitting this key is equivalent to giving it a value of `false`). From acb9e7cfbe255c42961fa19d7c35a2ce966717e0 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Thu, 29 May 2014 11:11:09 +0100 Subject: [PATCH 003/154] add html and text special attributes to README --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 2b25de9..45cbfc8 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,9 @@ There can be two keys in the root object: Elements are defined as key-value pairs, where the key is a description of the element, and the value is a dictionary of specifiers defining the element and its processing. Allowed keys in the specifier dictionary are: - ***selector*** - an XPath selector targetting the element to be selected. -- ***attribute*** - a string specifying the attribute to extract from the selected element. **Optional** (omitting this key is equivalent to giving it a value of 'text'). +- ***attribute*** - a string specifying the attribute to extract from the selected element. **Optional** (omitting this key is equivalent to giving it a value of `text`). In addition to html attributes there are two special attributes allowed: + - `text` - extracts any plaintext inside the selected element + - `html` - extracts the inner HTML of the selected element - ***download*** - a boolean flag: true if the element is a URL to a resource that must be downloaded. **Optional** (omitting this key is equivalent to giving it a value of `false`). Example: From a2a6d26aa10b6f96f630dd3b7e7e06ec846dc2b8 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 1 Jun 2014 22:37:30 +0100 Subject: [PATCH 004/154] Update README.md --- README.md | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 45cbfc8..ed995ee 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,21 @@ journal-scrapers ================ -Journal scraper definitions for the ContentMine framework +Journal scraper definitions for the ContentMine framework. -### Definition +This repo is a collection of ScraperJSON definitions targetting academic journals. They can be used to extract and download data from URLs of journal articles, such as: -Scrapers are defined in JSON, using a schema that is currently evolving: +- Title, author list, date +- Figures and their captions +- Fulltext PDF, HTML, XML, RDF +- Supplementary materials +- Reference lists + +### ScraperJSON definitions + +Scrapers are defined in JSON, using a schema called ScraperJSON which is currently evolving. + +The current schema is described below. There can be two keys in the root object: From ebea30a4c3f4b0e6377a973ef9e07976d7bc73ce Mon Sep 17 00:00:00 2001 From: ianthe Date: Thu, 19 Jun 2014 15:11:58 +0100 Subject: [PATCH 005/154] Create science_direct.json Initial work on science direct/elsevier scraper. --- science_direct.json | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 science_direct.json diff --git a/science_direct.json b/science_direct.json new file mode 100644 index 0000000..30659aa --- /dev/null +++ b/science_direct.json @@ -0,0 +1,43 @@ +{ + "url": "sciencedirect.com", + "elements": { + "fulltext_pdf": { + "selector": "//a[@id='pdfLink']", + "attribute": "href", + "download": true + }, + "fulltext_html": { + "selector": "//meta[@name='citation_fulltext_html_url']", + "attribute": "content", + "download": true + }, + "title": { + "selector": "//h1[@class='svTitle']" + }, + "author": { + "selector": "//a[@class='authorName']" + }, + "date": { + "selector": "//meta[@name='citation_date']", + "attribute": "content" + }, + "doi": { + "selector": "//dd[@class='doiLink']/dd[@class='doi']/span" + }, + "volume": { + "selector": "//p[@class='volIssue']/a", + "patternProperties": "/Volume: ([0-9]+)/g" + }, + "issue": { + "selector": "//meta[@name='citation_issue']", + "attribute": "content" + }, + "firstpage": { + "selector": "//meta[@name='citation_firstpage']", + "attribute": "content" + }, + "abstract": { + "selector": "//div[@class='abstract svAbstract ']/p" + } + } +} From 40b80a4f0b8edef80e6ecb0aee95ed7de115e945 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Sun, 22 Jun 2014 13:41:20 +0200 Subject: [PATCH 006/154] travis setup --- .travis.yml | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..a1aedcd --- /dev/null +++ b/.travis.yml @@ -0,0 +1,9 @@ +language: ruby +rvm: + - 2.1.0 +before_install: + - sudo apt-get update -qq +install: + - curl -sSL http://git.io/DAuTPQ | sudo bash +script: + - ruby test/test_all.rb From 13ef95b3d375353a5a9e34d65ce9714ad1cd9e86 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Sun, 22 Jun 2014 14:46:30 +0200 Subject: [PATCH 007/154] auto test generation script --- scripts/make_tests.rb | 86 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100755 scripts/make_tests.rb diff --git a/scripts/make_tests.rb b/scripts/make_tests.rb new file mode 100755 index 0000000..e426f1b --- /dev/null +++ b/scripts/make_tests.rb @@ -0,0 +1,86 @@ +#! /usr/bin/env ruby + +require 'trollop' +require 'digest' +require 'json' + +parser = Trollop::Parser.new do + banner <<-EOS +make_tests.rb - ScraperJSON test generator script +by Richard Smith-Unna for ContentMine.org + +This script generates a test file from a ScraperJSON scraper definition +and a list of URLs the scraper applies to. + +The test files record what the scraper extracts from each URL so that tests can detect when the scrapers break. + +Example use: +make_tests.rb --definition scraper.json --urls urls.txt + +Options: +EOS + + opt :definition, "Path to ScraperJSON definition", + :type => :string, + :required => true + opt :urls, "File containing a list of 5-10 URLs to test", + :type => :string, + :required => true +end + +opts = Trollop::with_standard_exception_handling parser do + parser.parse ARGV + raise Trollop::HelpNeeded if ARGV.empty? # show help screen +end + +urls = File.readlines(opts.urls) +if urls.length < 5 || urls.length > 10 + puts "ERROR: you must provide at least 5 and up to 10 URLS" +end + +puts "generating ScraperJSON test files for #{opts.definition}" +puts "using #{urls.length} urls" + +opts.definition = File.expand_path opts.definition + +Dir.mkdir('test') unless Dir.exist?('test') + +Dir.chdir('test') do + testobject = {} + # for each URL, run the scraper + urls.each_with_index do |url, index| + puts "running quickscrape for URL #{url}" + results = nil + # hash the url + hash = Digest::SHA256.hexdigest url + # run the scraper + cmd = "quickscrape" + cmd += " --url #{url}" + cmd += " --scraper #{opts.definition}" + cmd += " --output #{hash}" + cmd += " --loglevel silent" + puts `cmd` + # load the output + Dir.chdir(hash) do + results = JSON.load(File.open 'results.json') + filehashes = `md5sum !(results.json)` + filehashes.split("\n").each do |line| + filehash, filename = line.strip.split("\t") + results[filename] = filehash + end + end + if (index + 1) < urls.length + puts "waiting 15 seconds before next scrape" + sleep(15) + end + # store results for this URL + testobject[url] = results + end + + # write out the test JSON + File.open(File.basename(opts.definition), 'w') do |f| + f.write(JSON.pretty_generate(testobject)) + end +end + +puts "done! Test definition written to test/#{File.basename(opts.definition)}" From 073a4daae084e00b54d93611f0292104336c7580 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Sun, 22 Jun 2014 19:24:36 +0200 Subject: [PATCH 008/154] move scrapers to subdir --- generic_open.json => scrapers/generic_open.json | 0 scrapers/mdpi_figures.json | 17 +++++++++++++++++ peerj.json => scrapers/peerj.json | 0 plos.json => scrapers/plos.json | 0 scrapers/results.json | 0 5 files changed, 17 insertions(+) rename generic_open.json => scrapers/generic_open.json (100%) create mode 100644 scrapers/mdpi_figures.json rename peerj.json => scrapers/peerj.json (100%) rename plos.json => scrapers/plos.json (100%) create mode 100644 scrapers/results.json diff --git a/generic_open.json b/scrapers/generic_open.json similarity index 100% rename from generic_open.json rename to scrapers/generic_open.json diff --git a/scrapers/mdpi_figures.json b/scrapers/mdpi_figures.json new file mode 100644 index 0000000..055462a --- /dev/null +++ b/scrapers/mdpi_figures.json @@ -0,0 +1,17 @@ +{ + "url": "mdpi", + "elements": { + "dc.source": { + "selector": "//meta[@name='dc.source']", + "attribute": "content" + }, + "figure_img": { + "selector": "//div[contains(@id, 'fig')]/div/img", + "attribute": "src", + "download": true + }, + "figure_caption": { + "selector": "//div[contains(@class, 'html-fig_description')]" + } + } +} diff --git a/peerj.json b/scrapers/peerj.json similarity index 100% rename from peerj.json rename to scrapers/peerj.json diff --git a/plos.json b/scrapers/plos.json similarity index 100% rename from plos.json rename to scrapers/plos.json diff --git a/scrapers/results.json b/scrapers/results.json new file mode 100644 index 0000000..e69de29 From 4962babb888d78af4255a79c8ca2ac7f746370d1 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Sun, 22 Jun 2014 19:35:01 +0200 Subject: [PATCH 009/154] test generator script fixes --- scripts/make_tests.rb | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/scripts/make_tests.rb b/scripts/make_tests.rb index e426f1b..e419347 100755 --- a/scripts/make_tests.rb +++ b/scripts/make_tests.rb @@ -30,7 +30,7 @@ opts = Trollop::with_standard_exception_handling parser do parser.parse ARGV - raise Trollop::HelpNeeded if ARGV.empty? # show help screen + # raise Trollop::HelpNeeded if ARGV.empty? # show help screen end urls = File.readlines(opts.urls) @@ -38,35 +38,36 @@ puts "ERROR: you must provide at least 5 and up to 10 URLS" end -puts "generating ScraperJSON test files for #{opts.definition}" +definition = File.expand_path opts.definition +puts "generating ScraperJSON test files for #{definition}" puts "using #{urls.length} urls" -opts.definition = File.expand_path opts.definition - Dir.mkdir('test') unless Dir.exist?('test') Dir.chdir('test') do testobject = {} # for each URL, run the scraper urls.each_with_index do |url, index| + url = url.strip puts "running quickscrape for URL #{url}" results = nil # hash the url hash = Digest::SHA256.hexdigest url # run the scraper cmd = "quickscrape" - cmd += " --url #{url}" - cmd += " --scraper #{opts.definition}" - cmd += " --output #{hash}" - cmd += " --loglevel silent" - puts `cmd` + cmd << " --url #{url}" + cmd << " --scraper #{definition}" + cmd << " --output #{hash}" + cmd << " --loglevel silent" + `#{cmd}` + puts "scraping done - parsing results" # load the output Dir.chdir(hash) do results = JSON.load(File.open 'results.json') filehashes = `md5sum !(results.json)` filehashes.split("\n").each do |line| filehash, filename = line.strip.split("\t") - results[filename] = filehash + results += { filename => filehash } end end if (index + 1) < urls.length From cdb542b1c6e73209a327298f50e09ebaecf22f92 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Sun, 22 Jun 2014 19:36:14 +0200 Subject: [PATCH 010/154] self-populating tests and peerj example --- test/peerj_test_urls.txt | 6 ++++ test/test_all.rb | 73 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 test/peerj_test_urls.txt create mode 100644 test/test_all.rb diff --git a/test/peerj_test_urls.txt b/test/peerj_test_urls.txt new file mode 100644 index 0000000..05278e7 --- /dev/null +++ b/test/peerj_test_urls.txt @@ -0,0 +1,6 @@ +https://peerj.com/articles/50/ +https://peerj.com/articles/102/ +https://peerj.com/articles/234/ +https://peerj.com/articles/275/ +https://peerj.com/articles/311/ +https://peerj.com/articles/384/ diff --git a/test/test_all.rb b/test/test_all.rb new file mode 100644 index 0000000..d56a9a1 --- /dev/null +++ b/test/test_all.rb @@ -0,0 +1,73 @@ +require 'digest' +require 'json' + +testdir = File.expand_path(File.dirname(__FILE__)) +scrapers = Dir[File.join(thisdir, '..', '*.json')] + +scrapers = 0 +passed = 0 +warnings = 0 +errors = 0 + +Dir.mktmpdir do |tmpdir| + Dir.chdir(mktmpdir) do + scrapers.each do |scraper| + scrapers += 1 + basename = File.basename scraper + puts "scraper #{basename}" + testobjectpath = File.join(testdir, basename) + if File.exist? testobjectpath + # load expected output + testobject = JSON.load(File.open(testobjectpath)) + url = testobject.keys.shuffle.first + expected = testobject[url] + # run the scraper + puts "running quickscrape for URL #{url}" + results = nil + # hash the url + hash = Digest::SHA256.hexdigest url + # run the scraper + cmd = "quickscrape" + cmd += " --url #{url}" + cmd += " --scraper #{opts.definition}" + cmd += " --output #{hash}" + cmd += " --loglevel silent" + puts `cmd` + # load the output + unless File.exist? 'results.json' + puts "FAIL: no results from scraping" + errors += 1 + end + Dir.chdir(hash) do + results = JSON.load(File.open 'results.json') + filehashes = `md5sum !(results.json)` + filehashes.split("\n").each do |line| + filehash, filename = line.strip.split("\t") + results[filename] = filehash + end + end + # compare results to expected + expected.each_pair do |key, exp_val| + match = results.detect { |result| result[key] == exp_val } + if match + passed += 1 + else + puts "ERROR: #{key} not found in results" + puts "expected value: #{exp_val}" + errors += 1 + end + else + puts "WARN: no test found!" + warnings += 1 + end + end +end + +puts "-" * 25 +puts "tests completed for #{scrapers} scrapers" +puts " - #{passed} passed" +puts " - #{warnings} warnings" +puts " - #{errors} errors" + +exit(1) if errors > 0 +exit(0) From 0ee30be3af55ed95f3b3821c1d46a55420ca13ae Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Sun, 22 Jun 2014 19:38:15 +0200 Subject: [PATCH 011/154] move sciencedirect to scrapers --- science_direct.json => scrapers/science_direct.json | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename science_direct.json => scrapers/science_direct.json (100%) diff --git a/science_direct.json b/scrapers/science_direct.json similarity index 100% rename from science_direct.json rename to scrapers/science_direct.json From c1cafdda48e87534ea9e54b4073e460243cb231a Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Sun, 22 Jun 2014 19:57:13 +0200 Subject: [PATCH 012/154] fix tmpdir use --- scripts/make_tests.rb | 44 +++++++++++++++++++++------------------- test/peerj_test_urls.txt | 11 +++++----- test/test_all.rb | 1 + 3 files changed, 29 insertions(+), 27 deletions(-) diff --git a/scripts/make_tests.rb b/scripts/make_tests.rb index e419347..5a46418 100755 --- a/scripts/make_tests.rb +++ b/scripts/make_tests.rb @@ -3,6 +3,7 @@ require 'trollop' require 'digest' require 'json' +require 'tmpdir' parser = Trollop::Parser.new do banner <<-EOS @@ -51,29 +52,30 @@ url = url.strip puts "running quickscrape for URL #{url}" results = nil - # hash the url - hash = Digest::SHA256.hexdigest url - # run the scraper - cmd = "quickscrape" - cmd << " --url #{url}" - cmd << " --scraper #{definition}" - cmd << " --output #{hash}" - cmd << " --loglevel silent" - `#{cmd}` - puts "scraping done - parsing results" - # load the output - Dir.chdir(hash) do - results = JSON.load(File.open 'results.json') - filehashes = `md5sum !(results.json)` - filehashes.split("\n").each do |line| - filehash, filename = line.strip.split("\t") - results += { filename => filehash } + Dir.mktmpdir do |tmpdir| + Dir.chdir tmpdir do + # run the scraper + cmd = "quickscrape" + cmd << " --url #{url}" + cmd << " --scraper #{definition}" + cmd << " --loglevel silent" + `#{cmd}` + puts "scraping done - parsing results" + # load the output + Dir.chdir('output') do + results = JSON.load(File.open 'results.json') + filehashes = `md5sum !(results.json)` + filehashes.split("\n").each do |line| + filehash, filename = line.strip.split("\t") + results += { filename => filehash } + end + end + if (index + 1) < urls.length + puts "waiting 15 seconds before next scrape" + sleep(15) + end end end - if (index + 1) < urls.length - puts "waiting 15 seconds before next scrape" - sleep(15) - end # store results for this URL testobject[url] = results end diff --git a/test/peerj_test_urls.txt b/test/peerj_test_urls.txt index 05278e7..28a2118 100644 --- a/test/peerj_test_urls.txt +++ b/test/peerj_test_urls.txt @@ -1,6 +1,5 @@ -https://peerj.com/articles/50/ -https://peerj.com/articles/102/ -https://peerj.com/articles/234/ -https://peerj.com/articles/275/ -https://peerj.com/articles/311/ -https://peerj.com/articles/384/ + https://peerj.com/articles/102/ + https://peerj.com/articles/234/ + https://peerj.com/articles/275/ + https://peerj.com/articles/311/ + https://peerj.com/articles/384/ diff --git a/test/test_all.rb b/test/test_all.rb index d56a9a1..c03d6d9 100644 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -1,5 +1,6 @@ require 'digest' require 'json' +require 'tmpdir' testdir = File.expand_path(File.dirname(__FILE__)) scrapers = Dir[File.join(thisdir, '..', '*.json')] From 1cdbd3bb799e97367ae035410aee8b822bb39cca Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Sun, 22 Jun 2014 20:08:37 +0200 Subject: [PATCH 013/154] debug test generator tmpdir error --- scripts/make_tests.rb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/scripts/make_tests.rb b/scripts/make_tests.rb index 5a46418..afb403f 100755 --- a/scripts/make_tests.rb +++ b/scripts/make_tests.rb @@ -53,12 +53,13 @@ puts "running quickscrape for URL #{url}" results = nil Dir.mktmpdir do |tmpdir| + puts "using temporary directory #{tmpdir}" Dir.chdir tmpdir do # run the scraper cmd = "quickscrape" cmd << " --url #{url}" cmd << " --scraper #{definition}" - cmd << " --loglevel silent" + cmd << " --output output" `#{cmd}` puts "scraping done - parsing results" # load the output From 9c82fa01a7b1488ec7e3e74b70ce3bd34e0e213c Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 22 Jun 2014 18:28:39 -0400 Subject: [PATCH 014/154] test set for peerj scraper --- test/peerj.json | 297 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 297 insertions(+) create mode 100644 test/peerj.json diff --git a/test/peerj.json b/test/peerj.json new file mode 100644 index 0000000..506940c --- /dev/null +++ b/test/peerj.json @@ -0,0 +1,297 @@ +{ + "https://peerj.com/articles/102/": [ + { + "fulltext_pdf": "https://peerj.com/articles/102.pdf" + }, + { + "fulltext_html": "https://peerj.com/articles/102" + }, + { + "supplementary_material": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/S1_CONSORT_checklist.pdf" + }, + { + "supplementary_material": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/S2_trial_protocol.pdf" + }, + { + "title": "Affect-focused psychodynamic psychotherapy for depression and anxiety through the Internet: a randomized controlled trial" + }, + { + "author": "Robert Johansson" + }, + { + "author": "Martin Björklund" + }, + { + "author": "Christoffer Hornborg" + }, + { + "author": "Stina Karlsson" + }, + { + "author": "Hugo Hesser" + }, + { + "author": "Brjánn Ljótsson" + }, + { + "author": "Andréas Rousseau" + }, + { + "author": "Ronald J. Frederick" + }, + { + "author": "Gerhard Andersson" + }, + { + "date": "2013-07-09" + }, + { + "doi": "10.7717/peerj.102" + }, + { + "volume": "1" + }, + { + "firstpage": "e102" + }, + { + "description": "Background. Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base. Research has indicated an association between therapist-facilitated affective experience and outcome in psychodynamic therapy. Affect-phobia therapy (APT), as outlined by McCullough et al., is a psychodynamic treatment that emphasizes a strong focus on expression and experience of affect. This model has neither been evaluated for depression nor anxiety disorders in a randomized controlled trial. While Internet-delivered psychodynamic treatments for depression and generalized anxiety disorder exist, they have not been based on APT. The aim of this randomized controlled trial was to investigate the efficacy of an Internet-based, psychodynamic, guided self-help treatment based on APT for depression and anxiety disorders.Methods. One hundred participants with diagnoses of mood and anxiety disorders participated in a randomized (1:1 ratio) controlled trial of an active group versus a control condition. The treatment group received a 10-week, psychodynamic, guided self-help treatment based on APT that was delivered through the Internet. The treatment consisted of eight text-based treatment modules and included therapist contact (9.5 min per client and week, on average) in a secure online environment. Participants in the control group also received online therapist support and clinical monitoring of symptoms, but received no treatment modules. Outcome measures were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). Process measures were also included. All measures were administered weekly during the treatment period and at a 7-month follow-up.Results. Mixed models analyses using the full intention-to-treat sample revealed significant interaction effects of group and time on all outcome measures, when comparing treatment to the control group. A large between-group effect size of Cohen’s d = 0.77 (95% CI: 0.37–1.18) was found on the PHQ-9 and a moderately large between-group effect size d = 0.48 (95% CI: 0.08–0.87) was found on the GAD-7. The number of patients who recovered (had no diagnoses of depression and anxiety, and had less than 10 on both the PHQ-9 and the GAD-7) were at post-treatment 52% in the treatment group and 24% in the control group. This difference was significant, χ2(N = 100, d f = 1) = 8.3, p < .01. From post-treatment to follow-up, treatment gains were maintained on the PHQ-9, and significant improvements were seen on the GAD-7.Conclusion. This study provides initial support for the efficacy of Internet-delivered psychodynamic therapy based on the affect-phobia model in the treatment of depression and anxiety disorders. The results support the conclusion that psychodynamic treatment approaches may be transferred to the guided self-help format and delivered via the Internet." + }, + { + "S2_trial_protocol.pdf": "26787550a80a05fc451d245fb7107183" + }, + { + "rendered.html": "2db7d1ccd7a863ac9942dbb5ecc50825" + }, + { + "102": "aa2aac89c8379b5c67250a26a48ae58b" + }, + { + "S1_CONSORT_checklist.pdf": "eef414787965a937fc479d31f86a9541" + }, + { + "102.pdf": "8e2c1cb94b99943cc618c437f8fd1618" + } + ], + "https://peerj.com/articles/234/": [ + { + "fulltext_pdf": "https://peerj.com/articles/234.pdf" + }, + { + "fulltext_html": "https://peerj.com/articles/234" + }, + { + "title": "A new specimen of the Early Cretaceous bird Hongshanornis longicresta: insights into the aerodynamics and diet of a basal ornithuromorph" + }, + { + "author": "Luis M. Chiappe" + }, + { + "author": "Bo Zhao" + }, + { + "author": "Jingmai K. O’Connor" + }, + { + "author": "Gao Chunling" + }, + { + "author": "Xuri Wang" + }, + { + "author": "Michael Habib" + }, + { + "author": "Jesus Marugan-Lobon" + }, + { + "author": "Qingjin Meng" + }, + { + "author": "Xiaodong Cheng" + }, + { + "date": "2014-01-02" + }, + { + "doi": "10.7717/peerj.234" + }, + { + "volume": "2" + }, + { + "firstpage": "e234" + }, + { + "description": "The discovery of Hongshanornis longicresta, a small ornithuromorph bird with unusually long hindlimb proportions, was followed by the discovery of two closely related species, Longicrusavis houi and Parahongshanornis chaoyangensis. Together forming the Hongshanornithidae, these species reveal important information about the early diversity and morphological specialization of ornithuromorphs, the clade that contains all living birds. Here we report on a new specimen (DNHM D2945/6) referable to Hongshanornis longicresta that contributes significant information to better understand the morphology, trophic ecology, and aerodynamics of this species, as well as the taxonomy of the Hongshanornithidae. Most notable are the well-preserved wings and feathered tail of DNHM D2945/6, which afford an accurate reconstruction of aerodynamic parameters indicating that as early as 125 million years ago, basal ornithuromorphs had evolved aerodynamic surfaces comparable in size and design to those of many modern birds, and flight modes alike to those of some small living birds." + }, + { + "234.pdf": "3aa12392730333dd193322c7fb7ac72c" + }, + { + "234": "fa3274087243cf9e8b32b18f8d86d5c2" + }, + { + "rendered.html": "48d795fb6a0567b3b8f1ee529fd25bf5" + } + ], + "https://peerj.com/articles/275/": [ + { + "fulltext_pdf": "https://peerj.com/articles/275.pdf" + }, + { + "fulltext_html": "https://peerj.com/articles/275" + }, + { + "title": "Spectral characteristics of the mutant form GGBP/H152C of D-glucose/D-galactose-binding protein labeled with fluorescent dye BADAN: influence of external factors" + }, + { + "author": "Alexander V. Fonin" + }, + { + "author": "Olga V. Stepanenko" + }, + { + "author": "Olga I. Povarova" + }, + { + "author": "Catherine A. Volova" + }, + { + "author": "Elizaveta M. Philippova" + }, + { + "author": "Grigory S. Bublikov" + }, + { + "author": "Irina M. Kuznetsova" + }, + { + "author": "Alexander P. Demchenko" + }, + { + "author": "Konstantin K. Turoverov" + }, + { + "date": "2014-03-18" + }, + { + "doi": "10.7717/peerj.275" + }, + { + "volume": "2" + }, + { + "firstpage": "e275" + }, + { + "description": "The mutant form GGBP/H152C of the D-glucose/D-galactose-binding protein with the solvatochromic dye BADAN linked to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various external factors on the physical-chemical properties of GGBP/H152C-BADAN and its complex with glucose. The high affinity (Kd = 8.5 µM) and high binding rate of glucose make GGBP/H152C-BADAN a good candidate to determine the sugar content in biological fluids extracted using transdermal techniques. It was shown that changes in the ionic strength and pH of solution within the physiological range did not have a significant influence on the fluorescent characteristics of GGBP/H152C-BADAN. The mutant form GGBP/H152C has relatively low resistance to denaturation action of GdnHCl and urea. This result emphasizes the need to find more stable proteins for the creation of a sensitive element for a glucose biosensor system." + }, + { + "275": "67744f9749de75719601ef63718d28a8" + }, + { + "rendered.html": "14811027ddcf0230aed2aad5a0397347" + }, + { + "275.pdf": "6b554c704f1ed7a8129863a2869036eb" + } + ], + "https://peerj.com/articles/311/": [ + { + "fulltext_pdf": "https://peerj.com/articles/311.pdf" + }, + { + "fulltext_html": "https://peerj.com/articles/311" + }, + { + "title": "Religious attendance after elevated depressive symptoms: is selection bias at work?" + }, + { + "author": "Lloyd Balbuena" + }, + { + "author": "Marilyn Baetz" + }, + { + "author": "Rudy Bowen" + }, + { + "date": "2014-03-13" + }, + { + "doi": "10.7717/peerj.311" + }, + { + "volume": "2" + }, + { + "firstpage": "e311" + }, + { + "description": "In an attempt to determine if selection bias could be a reason that religious attendance and depression are related, the predictive value of elevated depressive symptoms for a decrease in future attendance at religious services was examined in a longitudinal panel of 1,673 Dutch adults. Religious attendance was assessed yearly over five years using the single question, “how often do you attend religious gatherings nowadays?” Depressive symptoms were assessed four times within the first year using the Depression subscale of the Brief Symptom Inventory. Logistic regression models of change in attendance were created, stratifying by baseline attendance status. Attenders who developed elevated symptoms were less likely to subsequently decrease their attendance (relative risk ratio: 0.55, 95% CI [0.38–0.79]) relative to baseline as compared to those without elevated symptoms. This inverse association remained significant after controlling for health and demographic covariates, and when using multiply imputed data to account for attrition. Non-attenders were unlikely to start attending after elevated depressive symptoms. This study provides counter evidence against previous findings that church attenders are a self-selected healthier group." + }, + { + "311": "daf380aa95bfd59264132483e46581d8" + }, + { + "311.pdf": "8aa4a538c24c0f3bfcc8b9fa5cd63d7c" + }, + { + "rendered.html": "f886abd9f8484ad4a4275719b1077f0c" + } + ], + "https://peerj.com/articles/384/": [ + { + "fulltext_pdf": "https://peerj.com/articles/384.pdf" + }, + { + "fulltext_html": "https://peerj.com/articles/384" + }, + { + "title": "Mutation analysis of the SLC26A4, FOXI1 and KCNJ10 genes in individuals with congenital hearing loss" + }, + { + "author": "Lynn M. Pique" + }, + { + "author": "Marie-Luise Brennan" + }, + { + "author": "Colin J. Davidson" + }, + { + "author": "Frederick Schaefer" + }, + { + "author": "John Greinwald Jr" + }, + { + "author": "Iris Schrijver" + }, + { + "date": "2014-05-08" + }, + { + "doi": "10.7717/peerj.384" + }, + { + "volume": "2" + }, + { + "firstpage": "e384" + }, + { + "description": "Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype." + }, + { + "384.pdf": "b2020a8f8037228e6face4a220751932" + }, + { + "384": "befa18960e439f737d1a4bee7f0f7ae4" + }, + { + "rendered.html": "28104961eb099d940b156396cac7d503" + } + ] +} \ No newline at end of file From 4e94869df52b6b857672afa59d6f9309fadbfc1c Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 22 Jun 2014 18:29:01 -0400 Subject: [PATCH 015/154] fix test generator - now working --- scripts/make_tests.rb | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/scripts/make_tests.rb b/scripts/make_tests.rb index afb403f..734bf2c 100755 --- a/scripts/make_tests.rb +++ b/scripts/make_tests.rb @@ -52,9 +52,9 @@ url = url.strip puts "running quickscrape for URL #{url}" results = nil - Dir.mktmpdir do |tmpdir| - puts "using temporary directory #{tmpdir}" - Dir.chdir tmpdir do + dir = Dir.mktmpdir + Dir.chdir dir do + puts "using temporary directory #{dir}" # run the scraper cmd = "quickscrape" cmd << " --url #{url}" @@ -63,19 +63,21 @@ `#{cmd}` puts "scraping done - parsing results" # load the output - Dir.chdir('output') do + cleanurl = url.gsub(/:?\/+/, '_') + Dir.chdir("output/#{cleanurl}") do results = JSON.load(File.open 'results.json') - filehashes = `md5sum !(results.json)` + files = Dir['*'] + files = files.keep_if { |f| f != 'results.json' } + filehashes = `md5sum #{files.join(' ')}` filehashes.split("\n").each do |line| - filehash, filename = line.strip.split("\t") - results += { filename => filehash } + filehash, filename = line.strip.split(" ") + results << { filename => filehash } end end if (index + 1) < urls.length puts "waiting 15 seconds before next scrape" sleep(15) end - end end # store results for this URL testobject[url] = results From ad734f34dc650811fa6e916df1a1aeae429c57fe Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 22 Jun 2014 18:29:10 -0400 Subject: [PATCH 016/154] fix test runner - now working --- test/test_all.rb | 59 ++++++++++++++++++++++++++++++------------------ 1 file changed, 37 insertions(+), 22 deletions(-) diff --git a/test/test_all.rb b/test/test_all.rb index c03d6d9..5274935 100644 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -3,17 +3,19 @@ require 'tmpdir' testdir = File.expand_path(File.dirname(__FILE__)) -scrapers = Dir[File.join(thisdir, '..', '*.json')] +scraperglob = File.join(testdir, '..', 'scrapers', '*.json') +scrapers = Dir[scraperglob] -scrapers = 0 +scrapercount = 0 passed = 0 warnings = 0 errors = 0 -Dir.mktmpdir do |tmpdir| - Dir.chdir(mktmpdir) do +tmpdir = Dir.mktmpdir +puts "using tmp dir #{tmpdir}" + Dir.chdir(tmpdir) do scrapers.each do |scraper| - scrapers += 1 + scrapercount += 1 basename = File.basename scraper puts "scraper #{basename}" testobjectpath = File.join(testdir, basename) @@ -25,47 +27,60 @@ # run the scraper puts "running quickscrape for URL #{url}" results = nil - # hash the url - hash = Digest::SHA256.hexdigest url # run the scraper cmd = "quickscrape" cmd += " --url #{url}" - cmd += " --scraper #{opts.definition}" - cmd += " --output #{hash}" + cmd += " --scraper #{scraper}" + cmd += " --output output" cmd += " --loglevel silent" - puts `cmd` + puts `#{cmd}` # load the output - unless File.exist? 'results.json' - puts "FAIL: no results from scraping" - errors += 1 - end - Dir.chdir(hash) do + cleanurl = url.gsub(/:?\/+/, '_') + Dir.chdir("output/#{cleanurl}") do + unless File.exist? 'results.json' + puts "FAIL: no results from scraping" + errors += 1 + end results = JSON.load(File.open 'results.json') - filehashes = `md5sum !(results.json)` + files = Dir['*'] + puts files + files = files.keep_if { |f| f != 'results.json' }.map{ |f| f.strip } + cmd = "md5sum #{files.join(' ')}" + puts cmd + filehashes = `#{cmd}` filehashes.split("\n").each do |line| - filehash, filename = line.strip.split("\t") - results[filename] = filehash + filehash, filename = line.strip.split(" ") + puts "#{filename} - #{filehash}" + results << { filename => filehash } end end # compare results to expected - expected.each_pair do |key, exp_val| + expected.each do |hash| + key = hash.keys.first + exp_val = hash[key] + exist = results.detect { |result| result.key? key } match = results.detect { |result| result[key] == exp_val } - if match + if exist && match + puts "PASS: #{key}" passed += 1 + elsif exist + puts "WARN: #{key} exists in results but is not exactly the same" + warnings += 1 else puts "ERROR: #{key} not found in results" puts "expected value: #{exp_val}" errors += 1 + end end else puts "WARN: no test found!" warnings += 1 + end end end -end puts "-" * 25 -puts "tests completed for #{scrapers} scrapers" +puts "tests completed for #{scrapercount} scrapers" puts " - #{passed} passed" puts " - #{warnings} warnings" puts " - #{errors} errors" From 86c37351ae64a0533c7d5e16bd40d911b46fd81e Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 22 Jun 2014 18:37:31 -0400 Subject: [PATCH 017/154] attempted fix for travis dependency install --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index a1aedcd..c7b9a21 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,6 +3,7 @@ rvm: - 2.1.0 before_install: - sudo apt-get update -qq + - sudo -H npm install --global phantomjs casperjs quickscrape install: - curl -sSL http://git.io/DAuTPQ | sudo bash script: From 1ce66d6efea636a04ad187301c26c65dd076d157 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 22 Jun 2014 18:40:08 -0400 Subject: [PATCH 018/154] remove unneeded prints from tests --- test/test_all.rb | 3 --- 1 file changed, 3 deletions(-) diff --git a/test/test_all.rb b/test/test_all.rb index 5274935..6f03a25 100644 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -43,14 +43,11 @@ end results = JSON.load(File.open 'results.json') files = Dir['*'] - puts files files = files.keep_if { |f| f != 'results.json' }.map{ |f| f.strip } cmd = "md5sum #{files.join(' ')}" - puts cmd filehashes = `#{cmd}` filehashes.split("\n").each do |line| filehash, filename = line.strip.split(" ") - puts "#{filename} - #{filehash}" results << { filename => filehash } end end From bf2c92631538ef3b078c306397976337e83876b1 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 22 Jun 2014 18:40:20 -0400 Subject: [PATCH 019/154] tests for plos scraper --- test/plos.json | 323 ++++++++++++++++++++++++++++++++++++++++ test/plos_test_urls.txt | 6 + 2 files changed, 329 insertions(+) create mode 100644 test/plos.json create mode 100644 test/plos_test_urls.txt diff --git a/test/plos.json b/test/plos.json new file mode 100644 index 0000000..5af0d7c --- /dev/null +++ b/test/plos.json @@ -0,0 +1,323 @@ +{ + "http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001874": [ + { + "fulltext_pdf": "http://dx.plos.org/10.1371/journal.pbio.1001874.pdf" + }, + { + "title": "Extracellular Vesicle-Mediated Transfer of Genetic Information between the Hematopoietic System and the Brain in Response to Inflammation" + }, + { + "author": "Kirsten Ridder" + }, + { + "author": "Sascha Keller" + }, + { + "author": "Maria Dams" + }, + { + "author": "Anne-Kathleen Rupp" + }, + { + "author": "Jessica Schlaudraff" + }, + { + "author": "Domenico Del Turco" + }, + { + "author": "Julia Starmann" + }, + { + "author": "Jadranka Macas" + }, + { + "author": "Darja Karpova" + }, + { + "author": "Kavi Devraj" + }, + { + "author": "Candan Depboylu" + }, + { + "author": "Britta Landfried" + }, + { + "author": "Bernd Arnold" + }, + { + "author": "Karl H. Plate" + }, + { + "author": "Günter Höglinger" + }, + { + "author": "Holger Sültmann" + }, + { + "author": "Peter Altevogt" + }, + { + "author": "Stefan Momma" + }, + { + "date": "2014/6/3" + }, + { + "doi": "10.1371/journal.pbio.1001874" + }, + { + "volume": "12" + }, + { + "issue": "6" + }, + { + "firstpage": "e1001874" + }, + { + "description": "PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines." + }, + { + "journal.pbio.1001874.pdf": "c730b7b2434f950ea409d74a78c30316" + }, + { + "rendered.html": "572e489fbe4397ba32e3820a738dba98" + } + ], + "http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001882": [ + { + "fulltext_pdf": "http://dx.plos.org/10.1371/journal.pbio.1001882.pdf" + }, + { + "title": "The Billion Cell Construct: Will Three-Dimensional Printing Get Us There?" + }, + { + "author": "Jordan S. Miller" + }, + { + "date": "2014/6/17" + }, + { + "doi": "10.1371/journal.pbio.1001882" + }, + { + "volume": "12" + }, + { + "issue": "6" + }, + { + "firstpage": "e1001882" + }, + { + "description": "PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines." + }, + { + "journal.pbio.1001882.pdf": "b1a6bb4e193cb39cc6aef1b1866dcb3b" + }, + { + "rendered.html": "3c9615f49fa85dd19c92d1cb5987be1c" + } + ], + "http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004441": [ + { + "fulltext_pdf": "http://dx.plos.org/10.1371/journal.pgen.1004441.pdf" + }, + { + "title": "An Operon of Three Transcriptional Regulators Controls Horizontal Gene Transfer of the Integrative and Conjugative Element ICEclc in Pseudomonas knackmussii B13" + }, + { + "author": "Nicolas Pradervand" + }, + { + "author": "Sandra Sulser" + }, + { + "author": "François Delavat" + }, + { + "author": "Ryo Miyazaki" + }, + { + "author": "Iker Lamas" + }, + { + "author": "Jan Roelof van der Meer" + }, + { + "date": "2014/6/19" + }, + { + "doi": "10.1371/journal.pgen.1004441" + }, + { + "volume": "10" + }, + { + "issue": "6" + }, + { + "firstpage": "e1004441" + }, + { + "description": "PLOS Genetics is an open-access" + }, + { + "journal.pgen.1004441.pdf": "037d0a292bcca909943daf27a1e51f77" + }, + { + "rendered.html": "7723036de0bd17afaa3be1f649f10e12" + } + ], + "http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004433": [ + { + "fulltext_pdf": "http://dx.plos.org/10.1371/journal.pgen.1004433.pdf" + }, + { + "title": "A Novel Peptidoglycan Binding Protein Crucial for PBP1A-Mediated Cell Wall Biogenesis in Vibrio cholerae" + }, + { + "author": "Tobias Dörr" + }, + { + "author": "Hubert Lam" + }, + { + "author": "Laura Alvarez" + }, + { + "author": "Felipe Cava" + }, + { + "author": "Brigid M. Davis" + }, + { + "author": "Matthew K. Waldor" + }, + { + "date": "2014/6/19" + }, + { + "doi": "10.1371/journal.pgen.1004433" + }, + { + "volume": "10" + }, + { + "issue": "6" + }, + { + "firstpage": "e1004433" + }, + { + "description": "PLOS Genetics is an open-access" + }, + { + "rendered.html": "7b4572e01def8bb477debc2a5d406a91" + }, + { + "journal.pgen.1004433.pdf": "890d664254554ae5142d7a8e0d10633e" + } + ], + "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0098781": [ + { + "fulltext_pdf": "http://dx.plos.org/10.1371/journal.pone.0098781.pdf" + }, + { + "title": "Foldscope: Origami-Based Paper Microscope" + }, + { + "author": "James S. Cybulski" + }, + { + "author": "James Clements" + }, + { + "author": "Manu Prakash" + }, + { + "date": "2014/6/18" + }, + { + "doi": "10.1371/journal.pone.0098781" + }, + { + "volume": "9" + }, + { + "issue": "6" + }, + { + "firstpage": "e98781" + }, + { + "description": "PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world." + }, + { + "journal.pone.0098781.pdf": "5dfa35bcba2f631b40673c498c62f64b" + }, + { + "rendered.html": "6ecb886b6ca79c5436a1c13ed66bf95e" + } + ], + "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099348": [ + { + "fulltext_pdf": "http://dx.plos.org/10.1371/journal.pone.0099348.pdf" + }, + { + "title": "Co-Infection of Blacklegged Ticks with Babesia microti and Borrelia burgdorferi Is Higher than Expected and Acquired from Small Mammal Hosts" + }, + { + "author": "Michelle H. Hersh" + }, + { + "author": "Richard S. Ostfeld" + }, + { + "author": "Diana J. McHenry" + }, + { + "author": "Michael Tibbetts" + }, + { + "author": "Jesse L. Brunner" + }, + { + "author": "Mary E. Killilea" + }, + { + "author": "Kathleen LoGiudice" + }, + { + "author": "Kenneth A. Schmidt" + }, + { + "author": "Felicia Keesing" + }, + { + "date": "2014/6/18" + }, + { + "doi": "10.1371/journal.pone.0099348" + }, + { + "volume": "9" + }, + { + "issue": "6" + }, + { + "firstpage": "e99348" + }, + { + "description": "PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world." + }, + { + "rendered.html": "1c315b137486fd9350c63c1193eb672b" + }, + { + "journal.pone.0099348.pdf": "71ff4b0cd5933789dbb0a38d756c6193" + } + ] +} \ No newline at end of file diff --git a/test/plos_test_urls.txt b/test/plos_test_urls.txt new file mode 100644 index 0000000..97e646b --- /dev/null +++ b/test/plos_test_urls.txt @@ -0,0 +1,6 @@ +http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001874 +http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001882 +http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004441 +http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004433 +http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0098781 +http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099348 From 9b1f20d3c92cac97091472e380591a974b267e36 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 00:47:09 +0200 Subject: [PATCH 020/154] another attempted travis install fix --- .travis.yml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index c7b9a21..c18548d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,8 +3,12 @@ rvm: - 2.1.0 before_install: - sudo apt-get update -qq - - sudo -H npm install --global phantomjs casperjs quickscrape + - sudo apt-get install -y software-properties-common python-software-properties + - sudo add-apt-repository -y ppa:chris-lea/node.js + - sudo apt-get update + - sudo apt-get install -y python g++ make nodejs + - curl --insecure https://www.npmjs.org/install.sh | bash install: - - curl -sSL http://git.io/DAuTPQ | sudo bash + - sudo -H npm install --global phantomjs casperjs quickscrape script: - ruby test/test_all.rb From aa0cfc6ed39a26a9e385605adba25940a2860a5e Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 00:47:34 +0200 Subject: [PATCH 021/154] delete wayward results file --- scrapers/results.json | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 scrapers/results.json diff --git a/scrapers/results.json b/scrapers/results.json deleted file mode 100644 index e69de29..0000000 From 998b0deb30ee39fc80f13e9433f9a911284efb46 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 00:48:03 +0200 Subject: [PATCH 022/154] add .gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..91a9c59 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +results.json From fb463a8fcb4542cf570233ccc2ab3daf78e48007 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 00:52:21 +0200 Subject: [PATCH 023/154] add travis badge and explanation to README --- README.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/README.md b/README.md index ed995ee..eb59061 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ journal-scrapers ================ + Journal scraper definitions for the ContentMine framework. This repo is a collection of ScraperJSON definitions targetting academic journals. They can be used to extract and download data from URLs of journal articles, such as: @@ -11,6 +12,14 @@ This repo is a collection of ScraperJSON definitions targetting academic journal - Supplementary materials - Reference lists +### Scraper collection status + +All the scrapers in the collection are automatically tested daily as well as every time any scraper is changed. If the badge is green and says 'build | passing', all the scrapers are OK. If the badge is red and says 'build | failing', one or more of the scrapers has stopped working. You can click on the badge to see the test report, to see which scrapers are failing and how. + +[![Build Status](https://secure.travis-ci.org/ContentMine/journal-scrapers.png?branch=master)][travis] + +[travis]: http://travis-ci.org/ContentMine/journal-scrapers + ### ScraperJSON definitions Scrapers are defined in JSON, using a schema called ScraperJSON which is currently evolving. From ab88faf2d919de51ad2e08d5c773f5e4a1510c56 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Mon, 23 Jun 2014 00:53:33 +0200 Subject: [PATCH 024/154] tidy formatting in README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index eb59061..b368930 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ This repo is a collection of ScraperJSON definitions targetting academic journal ### Scraper collection status -All the scrapers in the collection are automatically tested daily as well as every time any scraper is changed. If the badge is green and says 'build | passing', all the scrapers are OK. If the badge is red and says 'build | failing', one or more of the scrapers has stopped working. You can click on the badge to see the test report, to see which scrapers are failing and how. +All the scrapers in the collection are automatically tested daily as well as every time any scraper is changed. If the badge is green and says `build|passing`, all the scrapers are OK. If the badge is red and says `build|failing`, one or more of the scrapers has stopped working. You can click on the badge to see the test report, to see which scrapers are failing and how. [![Build Status](https://secure.travis-ci.org/ContentMine/journal-scrapers.png?branch=master)][travis] From 8e9d287171407883faaef351c3a37f03ab7e5ba1 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 22 Jun 2014 19:23:19 -0400 Subject: [PATCH 025/154] add science direct tests --- test/science_direct.json | 233 ++++++++++++++++++++++++++++++ test/science_direct_test_urls.txt | 6 + 2 files changed, 239 insertions(+) create mode 100644 test/science_direct.json create mode 100644 test/science_direct_test_urls.txt diff --git a/test/science_direct.json b/test/science_direct.json new file mode 100644 index 0000000..c86b7ec --- /dev/null +++ b/test/science_direct.json @@ -0,0 +1,233 @@ +{ + "http://www.sciencedirect.com/science/article/pii/S2211124714004343": [ + { + "fulltext_pdf": "http://www.sciencedirect.com/science/article/pii/S2211124714004343/pdfft?md5=82ec6328cc3285896d7ac5e5cebe8648&pid=1-s2.0-S2211124714004343-main.pdf" + }, + { + "title": "Diet-Induced Alterations in Gut Microflora Contribute to Lethal Pulmonary Damage in TLR2/TLR4-Deficient Mice " + }, + { + "author": "Yewei Ji" + }, + { + "author": "Shengyi Sun" + }, + { + "author": "Julia K. Goodrich" + }, + { + "author": "Hana Kim" + }, + { + "author": "Angela C. Poole" + }, + { + "author": "Gerald E. Duhamel" + }, + { + "author": "Ruth E. Ley" + }, + { + "author": "Ling Qi" + }, + { + "doi": " DOI: 10.1016/j.celrep.2014.05.040" + }, + { + "abstract": "Chronic intake of Western diet has driven an epidemic of obesity and metabolic syndrome, but how it induces mortality remains unclear. Here, we show that chronic intake of a high-fat diet (HFD), not a low-fat diet, leads to severe pulmonary damage and mortality in mice deficient in Toll-like receptors 2 and 4 (DKO). Diet-induced pulmonary lesions are blocked by antibiotic treatment and are transmissible to wild-type mice upon either cohousing or fecal transplantation, pointing to the existence of bacterial pathogens. Indeed, diet and innate deficiency exert significant impact on gut microbiota composition. Thus, chronic intake of HFD promotes severe pulmonary damage and mortality in DKO mice in part via gut dysbiosis, a finding that may be important for immunodeficient patients, particularly those on chemotherapy or radiotherapy, where gut-microbiota-caused conditions are often life threatening." + } + ], + "http://www.sciencedirect.com/science/article/pii/S1755436514000218": [ + { + "fulltext_pdf": "http://www.sciencedirect.com/science/article/pii/S1755436514000218/pdfft?md5=9d001518cb31c48d3609ab17d1be1163&pid=1-s2.0-S1755436514000218-main.pdf" + }, + { + "title": "Surveillance of gastrointestinal disease in France using drug sales data" + }, + { + "author": "Mathilde Pivette" + }, + { + "author": "Judith E. Mueller" + }, + { + "author": "Pascal Crépey" + }, + { + "author": "Avner Bar-Hen" + }, + { + "doi": " DOI: 10.1016/j.epidem.2014.05.001" + }, + { + "volume": "Volume 8" + }, + { + "abstract": "Drug sales data have increasingly been used for disease surveillance during recent years. Our objective was to assess the value of drug sales data as an operational early detection tool for gastroenteritis epidemics at national and regional level in France. For the period 2008–2013, we compared temporal trends of drug sales for the treatment of gastroenteritis with trends of cases reported by a Sentinel Network of general practitioners. We benchmarked detection models to select the one with the best sensitivity, false alert proportion and timeliness, and developed a prospective framework to assess the operational performance of the system. Drug sales data allowed the detection of seasonal gastrointestinal epidemics occurring in winter with a distinction between prescribed and non-prescribed drugs. Sales of non-prescribed drugs allowed epidemic detection on average 2.25 weeks earlier than Sentinel data. These results confirm the value of drug sales data for real-time monitoring of gastroenteritis epidemic activity." + } + ], + "http://www.sciencedirect.com/science/article/pii/S1755436514000206": [ + { + "fulltext_pdf": "http://www.sciencedirect.com/science/article/pii/S1755436514000206/pdfft?md5=1474e634a576549b859cea84bd8a18b2&pid=1-s2.0-S1755436514000206-main.pdf" + }, + { + "title": "OutbreakTools: A new platform for disease outbreak analysis using the R software" + }, + { + "author": "Thibaut Jombart" + }, + { + "author": "David M. Aanensen" + }, + { + "author": "Marc Baguelin" + }, + { + "author": "Paul Birrell" + }, + { + "author": "Simon Cauchemez" + }, + { + "author": "Anton Camacho" + }, + { + "author": "Caroline Colijn" + }, + { + "author": "Caitlin Collins" + }, + { + "author": "Anne Cori" + }, + { + "author": "Xavier Didelot" + }, + { + "author": "Christophe Fraser" + }, + { + "author": "Simon Frost" + }, + { + "author": "Niel Hens" + }, + { + "author": "Joseph Hugues" + }, + { + "author": "Michael Höhle" + }, + { + "author": "Lulla Opatowski" + }, + { + "author": "Andrew Rambaut" + }, + { + "author": "Oliver Ratmann" + }, + { + "author": "Samuel Soubeyrand" + }, + { + "author": "Marc A. Suchard" + }, + { + "author": "Jacco Wallinga" + }, + { + "author": "Rolf Ypma" + }, + { + "author": "Neil Ferguson" + }, + { + "doi": " DOI: 10.1016/j.epidem.2014.04.003" + }, + { + "volume": "Volume 7" + }, + { + "abstract": "The investigation of infectious disease outbreaks relies on the analysis of increasingly complex and diverse data, which offer new prospects for gaining insights into disease transmission processes and informing public health policies. However, the potential of such data can only be harnessed using a number of different, complementary approaches and tools, and a unified platform for the analysis of disease outbreaks is still lacking. In this paper, we present the new R package OutbreakTools, which aims to provide a basis for outbreak data management and analysis in R. OutbreakTools is developed by a community of epidemiologists, statisticians, modellers and bioinformaticians, and implements classes and methods for storing, handling and visualizing outbreak data. It includes real and simulated outbreak datasets. Together with a number of tools for infectious disease epidemiology recently made available in R, OutbreakTools contributes to the emergence of a new, free and open-source platform for the analysis of disease outbreaks." + } + ], + "http://www.sciencedirect.com/science/article/pii/S2211124714004355": [ + { + "fulltext_html": "http://www.cell.com/article/S2211124714004355/fulltext" + }, + { + "date": "" + }, + { + "issue": "0" + }, + { + "firstpage": "" + }, + { + "rendered.html": "0042073821eb617327b0bf833e11f7f9" + } + ], + "http://www.sciencedirect.com/science/article/pii/S2215016114200112": [ + { + "fulltext_pdf": "http://www.sciencedirect.com/science/article/pii/S2215016114200112/pdfft?md5=0b0f240cf90b0f595ce78cca6e8f340a&pid=1-s2.0-S2215016114200112-main.pdf" + }, + { + "title": "Macropinosome quantitation assay" + }, + { + "author": "Jack T.H. Wang" + }, + { + "author": "Rohan D. Teasdale" + }, + { + "author": "David Liebl" + }, + { + "doi": " DOI: 10.1016/j.mex.2014.05.002" + }, + { + "volume": "Volume 1" + }, + { + "abstract": "In contrast to phagocytosis, macropinocytosis is not directly initiated by interactions between cell surface receptors and cargo ligands, but is a result of constitutive membrane ruffling driven by dynamic remodelling of cortical actin cytoskeleton in response to stimulation of growth factor receptors. Wang et al. (2010) [13] developed a reliable assay that allows quantitative assessment of the efficiency and kinetics of macropinosome biogenesis and/or maturation in cells where the function of a targeted protein has been perturbed by pharmacological inhibitors or by knock-down or knock-out approaches. In this manuscript we describe a modified quantitative protocol to measure the rate and volume of fluid phase uptake in adherent cells. This assay:" + }, + { + "abstract": "" + }, + { + "rendered.html": "17e602d25e2a307fad746536bb2385c8" + } + ], + "http://www.sciencedirect.com/science/article/pii/S221501611400003X": [ + { + "fulltext_pdf": "http://www.sciencedirect.com/science/article/pii/S221501611400003X/pdfft?md5=7e5614118d66b8be106028e92f479c86&pid=1-s2.0-S221501611400003X-main.pdf" + }, + { + "title": "The Nav channel bench series: Plasmid preparation" + }, + { + "author": "Daniel H. Feldman" + }, + { + "author": "Christoph Lossin" + }, + { + "doi": " DOI: 10.1016/j.mex.2014.01.002" + }, + { + "volume": "Volume 1" + }, + { + "abstract": "Research involving recombinant voltage-gated sodium (Nav) channels has unique challenges. Multiple factors contribute, but undoubtedly at the top of the list is these channels’ DNA instability. Once introduced into bacterial hosts, Nav channel plasmid DNA will almost invariably emerge mutagenized and unusable, unless special conditions are adopted. This is particularly true for Nav1.1 (gene name SCN1A), Nav1.2 (SCN2A), and Nav1.6 (SCN8A), but less so for Nav1.4 (SCN4A) and Nav1.5 (SCN5A) while other Nav channel isoforms such as Nav1.7 (SCN9A) lie in between. The following recommendations for Nav plasmid DNA amplification and preparation address this problem. Three points are essential:" + }, + { + "abstract": "" + }, + { + "rendered.html": "27c831f847713528e12467b14b81eea2" + } + ] +} \ No newline at end of file diff --git a/test/science_direct_test_urls.txt b/test/science_direct_test_urls.txt new file mode 100644 index 0000000..46ca188 --- /dev/null +++ b/test/science_direct_test_urls.txt @@ -0,0 +1,6 @@ +http://www.sciencedirect.com/science/article/pii/S2211124714004343 +http://www.sciencedirect.com/science/article/pii/S1755436514000218 +http://www.sciencedirect.com/science/article/pii/S1755436514000206 +http://www.sciencedirect.com/science/article/pii/S2211124714004355 +http://www.sciencedirect.com/science/article/pii/S2215016114200112 +http://www.sciencedirect.com/science/article/pii/S221501611400003X From da2a0f25b17e6aefd1511f30c7f3166426a7134f Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Mon, 23 Jun 2014 02:16:52 +0200 Subject: [PATCH 026/154] add CC0 license --- README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/README.md b/README.md index b368930..f913eef 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,8 @@ journal-scrapers ================ +[![Build Status](https://secure.travis-ci.org/ContentMine/journal-scrapers.png?branch=master)][travis] +[![License](http://img.shields.io/badge/license-CC0-blue.svg)][license] Journal scraper definitions for the ContentMine framework. @@ -19,6 +21,7 @@ All the scrapers in the collection are automatically tested daily as well as eve [![Build Status](https://secure.travis-ci.org/ContentMine/journal-scrapers.png?branch=master)][travis] [travis]: http://travis-ci.org/ContentMine/journal-scrapers +[license]: https://creativecommons.org/publicdomain/zero/1.0/ ### ScraperJSON definitions @@ -59,3 +62,8 @@ Example: ### Usage Currently these definitions can be used with the [quickscrape](http://github.com/ContentMine/quickscrape) tool. + + +### License + +All scrapers are released under the [Creative Commons 0 (CC0)](https://creativecommons.org/publicdomain/zero/1.0/) license. From 5ce546e7b0e502d473120b1616eb8a3073fdfd60 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 09:53:04 +0200 Subject: [PATCH 027/154] matching badges --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index f913eef..fec0b15 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ journal-scrapers ================ -[![Build Status](https://secure.travis-ci.org/ContentMine/journal-scrapers.png?branch=master)][travis] +[![Build Status](http://img.shields.io/travis/joyent/node.svg)][travis] [![License](http://img.shields.io/badge/license-CC0-blue.svg)][license] Journal scraper definitions for the ContentMine framework. From d1f3ddfcffd4656d4c73ec6b79ab704e0608c447 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 09:53:49 +0200 Subject: [PATCH 028/154] fix badge address --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index fec0b15..c0d54d8 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ journal-scrapers ================ -[![Build Status](http://img.shields.io/travis/joyent/node.svg)][travis] +[![Build Status](http://img.shields.io/travis/ContentMine/journal-scrapers.svg)][travis] [![License](http://img.shields.io/badge/license-CC0-blue.svg)][license] Journal scraper definitions for the ContentMine framework. From d5f7b08c0f0d4940a8ac05ca2d93338fdf645d97 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 10:45:03 +0200 Subject: [PATCH 029/154] coverage reporting for scrapers --- .coveralls.yml | 2 + .gitignore | 1 + coverage.rb | 25 ++++++++ test/test_all.rb | 159 ++++++++++++++++++++++++++++++----------------- 4 files changed, 130 insertions(+), 57 deletions(-) create mode 100644 .coveralls.yml create mode 100644 coverage.rb diff --git a/.coveralls.yml b/.coveralls.yml new file mode 100644 index 0000000..2a2c114 --- /dev/null +++ b/.coveralls.yml @@ -0,0 +1,2 @@ +repo_token: vHHvsw3QKvjK7zPb9DcFgt6ivLVS8r5uP +service_name: travis diff --git a/.gitignore b/.gitignore index 91a9c59..10c192d 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ results.json +coverage.json diff --git a/coverage.rb b/coverage.rb new file mode 100644 index 0000000..b1c4389 --- /dev/null +++ b/coverage.rb @@ -0,0 +1,25 @@ +# generate coverage information for tests + +def coverage scraperjsonpath, results + lines = File.readlines scraperjsonpath + # get the element names + elements = JSON.load(File.open scraperjson)['elements'].keys + coverage = [] + lines.each do |line| + valid = false + elements.keys.each do |element| + if line ~= /"#{element}":/ + # calculate coverage for this line + if results.key? element + coverage << 1 + else + coverage << 0 + end + else + valid = false + end + end + coverage << nil unless valid + end + coverage +end diff --git a/test/test_all.rb b/test/test_all.rb index 6f03a25..8f668f6 100644 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -11,70 +11,115 @@ warnings = 0 errors = 0 +# generate coverage information for tests +def coverage scraperjsonpath, results + lines = File.readlines scraperjsonpath + # get the element names + elements = JSON.load(File.open scraperjson)['elements'].keys + coverage = [] + source = [] + lines.each do |line| + valid = true + elements.keys.each do |element| + if line =~ /"#{element}":/ + # calculate coverage for this line + if results.key? element + coverage << 1 + else + coverage << 0 + end + else + valid = false + end + end + coverage << nil unless valid + end + { :name => scraperjsonpath, + :source => lines, + :coverage => coverage } +end + +# run tests +coverage_files = [] tmpdir = Dir.mktmpdir puts "using tmp dir #{tmpdir}" - Dir.chdir(tmpdir) do - scrapers.each do |scraper| - scrapercount += 1 - basename = File.basename scraper - puts "scraper #{basename}" - testobjectpath = File.join(testdir, basename) - if File.exist? testobjectpath - # load expected output - testobject = JSON.load(File.open(testobjectpath)) - url = testobject.keys.shuffle.first - expected = testobject[url] - # run the scraper - puts "running quickscrape for URL #{url}" - results = nil - # run the scraper - cmd = "quickscrape" - cmd += " --url #{url}" - cmd += " --scraper #{scraper}" - cmd += " --output output" - cmd += " --loglevel silent" - puts `#{cmd}` - # load the output - cleanurl = url.gsub(/:?\/+/, '_') - Dir.chdir("output/#{cleanurl}") do - unless File.exist? 'results.json' - puts "FAIL: no results from scraping" - errors += 1 - end - results = JSON.load(File.open 'results.json') - files = Dir['*'] - files = files.keep_if { |f| f != 'results.json' }.map{ |f| f.strip } - cmd = "md5sum #{files.join(' ')}" - filehashes = `#{cmd}` - filehashes.split("\n").each do |line| - filehash, filename = line.strip.split(" ") - results << { filename => filehash } - end +Dir.chdir(tmpdir) do + scrapers.each do |scraper| + scrapercount += 1 + basename = File.basename scraper + puts "scraper #{basename}" + testobjectpath = File.join(testdir, basename) + if File.exist? testobjectpath + # load expected output + testobject = JSON.load(File.open(testobjectpath)) + url = testobject.keys.shuffle.first + expected = testobject[url] + # run the scraper + puts "running quickscrape for URL #{url}" + results = nil + # run the scraper + cmd = "quickscrape" + cmd += " --url #{url}" + cmd += " --scraper #{scraper}" + cmd += " --output output" + cmd += " --loglevel silent" + puts `#{cmd}` + # load the output + cleanurl = url.gsub(/:?\/+/, '_') + Dir.chdir("output/#{cleanurl}") do + unless File.exist? 'results.json' + puts "FAIL: no results from scraping" + errors += 1 + coverage_files << coverage(scraper, {}) end - # compare results to expected - expected.each do |hash| - key = hash.keys.first - exp_val = hash[key] - exist = results.detect { |result| result.key? key } - match = results.detect { |result| result[key] == exp_val } - if exist && match - puts "PASS: #{key}" - passed += 1 - elsif exist - puts "WARN: #{key} exists in results but is not exactly the same" - warnings += 1 - else - puts "ERROR: #{key} not found in results" - puts "expected value: #{exp_val}" - errors += 1 - end + results = JSON.load(File.open 'results.json') + files = Dir['*'] + files = files.keep_if { |f| f != 'results.json' }.map{ |f| f.strip } + cmd = "md5sum #{files.join(' ')}" + filehashes = `#{cmd}` + filehashes.split("\n").each do |line| + filehash, filename = line.strip.split(" ") + results << { filename => filehash } end - else - puts "WARN: no test found!" - warnings += 1 end + coverage_files << coverage(scraper, results) + # compare results to expected + expected.each do |hash| + key = hash.keys.first + exp_val = hash[key] + exist = results.detect { |result| result.key? key } + match = results.detect { |result| result[key] == exp_val } + if exist && match + puts "PASS: #{key}" + passed += 1 + elsif exist + puts "WARN: #{key} exists in results but is not exactly the same" + warnings += 1 + else + puts "ERROR: #{key} not found in results" + puts "expected value: #{exp_val}" + errors += 1 + end + end + else + puts "WARN: no test found!" + warnings += 1 end end +end + +# send coverage report to coveralls.io +cov_report = { + :service_name => 'travis-ci', + :source_files => coverage_files +} +File.open('coverage.json', 'w') do |f| + f.write JSON.dump(cov_report) +end +cmd = "curl -XPOST -H content-type:application/json" +cmd += "--data @coverage.json https://coveralls.io/api/v1/jobs" +puts "posting coverage data to coveralls.io" +puts `#{cmd}` puts "-" * 25 puts "tests completed for #{scrapercount} scrapers" From ac46bc23b794ce97126264d44c94932630ee99a2 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 10:51:04 +0200 Subject: [PATCH 030/154] fix coverage reporting --- test/test_all.rb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/test/test_all.rb b/test/test_all.rb index 8f668f6..a051e74 100644 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -12,12 +12,13 @@ errors = 0 # generate coverage information for tests -def coverage scraperjsonpath, results +def coverage(scraperjsonpath, results) lines = File.readlines scraperjsonpath # get the element names - elements = JSON.load(File.open scraperjson)['elements'].keys + elements = JSON.load(File.open scraperjsonpath)['elements'].keys coverage = [] source = [] + # calculate coverage lines.each do |line| valid = true elements.keys.each do |element| @@ -121,6 +122,7 @@ def coverage scraperjsonpath, results puts "posting coverage data to coveralls.io" puts `#{cmd}` +# report test results puts "-" * 25 puts "tests completed for #{scrapercount} scrapers" puts " - #{passed} passed" From 29b9cce1dd349ab1d56a78a549a8f9fe98ff6e29 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 11:05:36 +0200 Subject: [PATCH 031/154] another coveralls fix --- test/test_all.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/test_all.rb b/test/test_all.rb index a051e74..f563def 100644 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -21,7 +21,7 @@ def coverage(scraperjsonpath, results) # calculate coverage lines.each do |line| valid = true - elements.keys.each do |element| + elements.each do |element| if line =~ /"#{element}":/ # calculate coverage for this line if results.key? element From ed42173f5478836c665abdf497874accbcd1bfd9 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 11:12:17 +0200 Subject: [PATCH 032/154] another coveralls fix --- test/test_all.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/test_all.rb b/test/test_all.rb index f563def..68e821f 100644 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -24,7 +24,7 @@ def coverage(scraperjsonpath, results) elements.each do |element| if line =~ /"#{element}":/ # calculate coverage for this line - if results.key? element + if results.detect { |result| result.key? element } coverage << 1 else coverage << 0 From 622191ff3ad6afe0001d646792d5c616ad49eb4e Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 11:22:57 +0200 Subject: [PATCH 033/154] mend broken curl command --- test/test_all.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/test_all.rb b/test/test_all.rb index 68e821f..be141e4 100644 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -117,8 +117,8 @@ def coverage(scraperjsonpath, results) File.open('coverage.json', 'w') do |f| f.write JSON.dump(cov_report) end -cmd = "curl -XPOST -H content-type:application/json" -cmd += "--data @coverage.json https://coveralls.io/api/v1/jobs" +cmd = "curl -XPOST -H 'content-type:application/json'" +cmd += " --data @coverage.json https://coveralls.io/api/v1/jobs" puts "posting coverage data to coveralls.io" puts `#{cmd}` From 1a82584d79e3bc224a9db730198667ea6edee102 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 20:20:48 +0200 Subject: [PATCH 034/154] remove empty file --- coverage.rb | 25 ------------------------- 1 file changed, 25 deletions(-) delete mode 100644 coverage.rb diff --git a/coverage.rb b/coverage.rb deleted file mode 100644 index b1c4389..0000000 --- a/coverage.rb +++ /dev/null @@ -1,25 +0,0 @@ -# generate coverage information for tests - -def coverage scraperjsonpath, results - lines = File.readlines scraperjsonpath - # get the element names - elements = JSON.load(File.open scraperjson)['elements'].keys - coverage = [] - lines.each do |line| - valid = false - elements.keys.each do |element| - if line ~= /"#{element}":/ - # calculate coverage for this line - if results.key? element - coverage << 1 - else - coverage << 0 - end - else - valid = false - end - end - coverage << nil unless valid - end - coverage -end From 396b658b5980c7439643c6149cb2ea75fb2783c4 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 20:21:03 +0200 Subject: [PATCH 035/154] fix coveralls CURL command --- test/test_all.rb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/test_all.rb b/test/test_all.rb index be141e4..7c105d3 100644 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -36,7 +36,7 @@ def coverage(scraperjsonpath, results) coverage << nil unless valid end { :name => scraperjsonpath, - :source => lines, + :source => lines.join(''), :coverage => coverage } end @@ -111,14 +111,14 @@ def coverage(scraperjsonpath, results) # send coverage report to coveralls.io cov_report = { - :service_name => 'travis-ci', + :repo_token => 'vHHvsw3QKvjK7zPb9DcFgt6ivLVS8r5uP', :source_files => coverage_files } File.open('coverage.json', 'w') do |f| f.write JSON.dump(cov_report) end cmd = "curl -XPOST -H 'content-type:application/json'" -cmd += " --data @coverage.json https://coveralls.io/api/v1/jobs" +cmd += " --form json_file=@coverage.json https://coveralls.io/api/v1/jobs" puts "posting coverage data to coveralls.io" puts `#{cmd}` From 641c260232dc86fbb4522337edb755de637958ee Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 20:29:13 +0200 Subject: [PATCH 036/154] add coveralls to README --- README.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index c0d54d8..fe2d792 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,12 @@ journal-scrapers ================ +[travis]: http://img.shields.io/travis/ContentMine/journal-scrapers.svg +[license]: https://creativecommons.org/publicdomain/zero/1.0/ +[coverage]: https://coveralls.io/r/ContentMine/journal-scrapers + [![Build Status](http://img.shields.io/travis/ContentMine/journal-scrapers.svg)][travis] +[![Coverage](http://img.shields.io/coveralls/ContentMine/journal-scrapers.svg)][coverage] [![License](http://img.shields.io/badge/license-CC0-blue.svg)][license] Journal scraper definitions for the ContentMine framework. @@ -16,12 +21,13 @@ This repo is a collection of ScraperJSON definitions targetting academic journal ### Scraper collection status -All the scrapers in the collection are automatically tested daily as well as every time any scraper is changed. If the badge is green and says `build|passing`, all the scrapers are OK. If the badge is red and says `build|failing`, one or more of the scrapers has stopped working. You can click on the badge to see the test report, to see which scrapers are failing and how. +All the scrapers in the collection are automatically tested daily as well as every time any scraper is changed. The tests work by having the expected results for a set of URLs stored, and randomly selecting one of those URLs to re-scrape. If the results match those expected the test passes. If the badge is green and says `build|passing`, all the scrapers are OK. If the badge is red and says `build|failing`, one or more of the scrapers has stopped working. You can click on the badge to see the test report, to see which scrapers are failing and how. [![Build Status](https://secure.travis-ci.org/ContentMine/journal-scrapers.png?branch=master)][travis] -[travis]: http://travis-ci.org/ContentMine/journal-scrapers -[license]: https://creativecommons.org/publicdomain/zero/1.0/ +How well the scrapers are covered by the tests is also checked. Coverage should be 100% - this means every element of every scraper is checked at least once in the testing. If coverage is below 100%, you can see exactly which parts of which scrapers are not covered by clicking the `coverage` badge below. + +[![Coverage](http://img.shields.io/coveralls/ContentMine/journal-scrapers.svg)][coverage] ### ScraperJSON definitions From a443c184f7af872a0c3eb4ec354fb6557fb5d204 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 20:30:38 +0200 Subject: [PATCH 037/154] make travis badges consistent --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index fe2d792..5fc92f4 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ journal-scrapers ================ -[travis]: http://img.shields.io/travis/ContentMine/journal-scrapers.svg +[travis]: http://travis-ci.org/ContentMine/journal-scrapers [license]: https://creativecommons.org/publicdomain/zero/1.0/ [coverage]: https://coveralls.io/r/ContentMine/journal-scrapers @@ -23,7 +23,7 @@ This repo is a collection of ScraperJSON definitions targetting academic journal All the scrapers in the collection are automatically tested daily as well as every time any scraper is changed. The tests work by having the expected results for a set of URLs stored, and randomly selecting one of those URLs to re-scrape. If the results match those expected the test passes. If the badge is green and says `build|passing`, all the scrapers are OK. If the badge is red and says `build|failing`, one or more of the scrapers has stopped working. You can click on the badge to see the test report, to see which scrapers are failing and how. -[![Build Status](https://secure.travis-ci.org/ContentMine/journal-scrapers.png?branch=master)][travis] +[![Build Status](http://img.shields.io/travis/ContentMine/journal-scrapers.svg)][travis] How well the scrapers are covered by the tests is also checked. Coverage should be 100% - this means every element of every scraper is checked at least once in the testing. If coverage is below 100%, you can see exactly which parts of which scrapers are not covered by clicking the `coverage` badge below. From 09c6410f38b9793c8c902751db23960a75e8e4c7 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Mon, 23 Jun 2014 20:46:22 +0200 Subject: [PATCH 038/154] another CURL cmd fix --- test/test_all.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/test_all.rb b/test/test_all.rb index 7c105d3..3442485 100644 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -117,9 +117,9 @@ def coverage(scraperjsonpath, results) File.open('coverage.json', 'w') do |f| f.write JSON.dump(cov_report) end -cmd = "curl -XPOST -H 'content-type:application/json'" -cmd += " --form json_file=@coverage.json https://coveralls.io/api/v1/jobs" +cmd = "curl -XPOST --form json_file=@coverage.json https://coveralls.io/api/v1/jobs" puts "posting coverage data to coveralls.io" +puts cmd puts `#{cmd}` # report test results From 04d530009ee2e308d2e3f8d093d04e9c2d9fcb97 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Tue, 24 Jun 2014 01:05:18 +0200 Subject: [PATCH 039/154] add contribution instructions --- README.md | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 5fc92f4..bf3618d 100644 --- a/README.md +++ b/README.md @@ -65,11 +65,21 @@ Example: } ``` +### Contributing scrapers + +If your favourite publisher or journal is not covered by a scraper in our collection, we'd love you to submit a new scraper. + +We ask that all contributions follow some simple rules that help us maintain a high-quality collection. + +1. The scraper covers all [the data elements used in the ContentMine])(wiki/data_collected_for_ContentMine). +2. You must submit a set of 5-10 test URLs. +3. It comes with a regression test ([which can be auto-generated](wiki/Generating-tests-for-your-scrapers)). +4. You agree to release the scraper definition and tests under the [Creative Commons Zero license](https://creativecommons.org/publicdomain/zero/1.0/). + ### Usage Currently these definitions can be used with the [quickscrape](http://github.com/ContentMine/quickscrape) tool. - ### License All scrapers are released under the [Creative Commons 0 (CC0)](https://creativecommons.org/publicdomain/zero/1.0/) license. From 3d6e3a75bac3a187bfa705e4da41a5daaa68b438 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Tue, 24 Jun 2014 01:17:40 +0200 Subject: [PATCH 040/154] fix typo; finalise self-testing (fixes #4) --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index bf3618d..1e80eb0 100644 --- a/README.md +++ b/README.md @@ -71,7 +71,7 @@ If your favourite publisher or journal is not covered by a scraper in our collec We ask that all contributions follow some simple rules that help us maintain a high-quality collection. -1. The scraper covers all [the data elements used in the ContentMine])(wiki/data_collected_for_ContentMine). +1. The scraper covers all [the data elements used in the ContentMine](wiki/data_collected_for_ContentMine). 2. You must submit a set of 5-10 test URLs. 3. It comes with a regression test ([which can be auto-generated](wiki/Generating-tests-for-your-scrapers)). 4. You agree to release the scraper definition and tests under the [Creative Commons Zero license](https://creativecommons.org/publicdomain/zero/1.0/). From 2340fa36ba0dd4ff49c852fdd23111c4d325f300 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Tue, 24 Jun 2014 01:21:55 +0200 Subject: [PATCH 041/154] add TOC to README --- README.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/README.md b/README.md index 1e80eb0..fcf6ca4 100644 --- a/README.md +++ b/README.md @@ -11,6 +11,19 @@ journal-scrapers Journal scraper definitions for the ContentMine framework. + + +**Table of Contents** *generated with [DocToc](http://doctoc.herokuapp.com/)* + +- [journal-scrapers](#journal-scrapers) + - [Scraper collection status](#scraper-collection-status) + - [ScraperJSON definitions](#scraperjson-definitions) + - [Contributing scrapers](#contributing-scrapers) + - [Usage](#usage) + - [License](#license) + + + This repo is a collection of ScraperJSON definitions targetting academic journals. They can be used to extract and download data from URLs of journal articles, such as: - Title, author list, date From 222a00a7b536eb38eca74245ce22017d28df9466 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Tue, 24 Jun 2014 01:22:57 +0200 Subject: [PATCH 042/154] prettify TOC --- README.md | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index fcf6ca4..054a2cf 100644 --- a/README.md +++ b/README.md @@ -13,14 +13,13 @@ Journal scraper definitions for the ContentMine framework. -**Table of Contents** *generated with [DocToc](http://doctoc.herokuapp.com/)* - -- [journal-scrapers](#journal-scrapers) - - [Scraper collection status](#scraper-collection-status) - - [ScraperJSON definitions](#scraperjson-definitions) - - [Contributing scrapers](#contributing-scrapers) - - [Usage](#usage) - - [License](#license) +### Table of Contents + +- [Scraper collection status](#scraper-collection-status) +- [ScraperJSON definitions](#scraperjson-definitions) +- [Contributing scrapers](#contributing-scrapers) +- [Usage](#usage) +- [License](#license) From 9d189bc0e2dd1b8aa9c65f39763831795e291502 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Tue, 24 Jun 2014 01:24:07 +0200 Subject: [PATCH 043/154] tidy TOC --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 054a2cf..119706a 100644 --- a/README.md +++ b/README.md @@ -11,17 +11,16 @@ journal-scrapers Journal scraper definitions for the ContentMine framework. - - ### Table of Contents +- [Summary](#summary) - [Scraper collection status](#scraper-collection-status) - [ScraperJSON definitions](#scraperjson-definitions) - [Contributing scrapers](#contributing-scrapers) - [Usage](#usage) - [License](#license) - +### Summary This repo is a collection of ScraperJSON definitions targetting academic journals. They can be used to extract and download data from URLs of journal articles, such as: From 9ffe4381ac09fc53b6e11ac82fd9c919e43fe2f1 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Tue, 24 Jun 2014 06:59:44 +0200 Subject: [PATCH 044/154] coveralls submission recognises travis environment --- test/test_all.rb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/test/test_all.rb b/test/test_all.rb index 3442485..d770211 100644 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -72,6 +72,7 @@ def coverage(scraperjsonpath, results) puts "FAIL: no results from scraping" errors += 1 coverage_files << coverage(scraper, {}) + next end results = JSON.load(File.open 'results.json') files = Dir['*'] @@ -105,15 +106,21 @@ def coverage(scraperjsonpath, results) else puts "WARN: no test found!" warnings += 1 + coverage_files << coverage(scraper, {}) end end end # send coverage report to coveralls.io cov_report = { - :repo_token => 'vHHvsw3QKvjK7zPb9DcFgt6ivLVS8r5uP', :source_files => coverage_files } +if ENV['TRAVIS'] + cov_report[:service_job_id] = ENV['TRAVIS_JOB_ID'] + cov_report[:service_name] = 'travis-ci' +else + cov_report[:repo_token] = 'vHHvsw3QKvjK7zPb9DcFgt6ivLVS8r5uP', +end File.open('coverage.json', 'w') do |f| f.write JSON.dump(cov_report) end From 34c46069b75b2929a41cfcb35f904adc69fc8887 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Tue, 24 Jun 2014 07:04:32 +0200 Subject: [PATCH 045/154] typo --- test/test_all.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/test_all.rb b/test/test_all.rb index d770211..3e95600 100644 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -119,7 +119,7 @@ def coverage(scraperjsonpath, results) cov_report[:service_job_id] = ENV['TRAVIS_JOB_ID'] cov_report[:service_name] = 'travis-ci' else - cov_report[:repo_token] = 'vHHvsw3QKvjK7zPb9DcFgt6ivLVS8r5uP', + cov_report[:repo_token] = 'vHHvsw3QKvjK7zPb9DcFgt6ivLVS8r5uP' end File.open('coverage.json', 'w') do |f| f.write JSON.dump(cov_report) From e60fe56377b0febaaa528ea0fa4ba276f64121e5 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Wed, 2 Jul 2014 23:13:55 +0100 Subject: [PATCH 046/154] peerj scraper now implements all ContentMine fields --- scrapers/peerj.json | 59 +++++-- test/peerj.json | 399 ++++++++++++++++++++++++++++++++++++-------- 2 files changed, 374 insertions(+), 84 deletions(-) diff --git a/scrapers/peerj.json b/scrapers/peerj.json index 5cd9e34..6e53777 100644 --- a/scrapers/peerj.json +++ b/scrapers/peerj.json @@ -1,26 +1,19 @@ { "url": "peerj.com", "elements": { - "fulltext_pdf": { - "selector": "//meta[@name='citation_pdf_url']", - "attribute": "content", - "download": true - }, - "fulltext_html": { - "selector": "//meta[@name='citation_fulltext_html_url']", - "attribute": "content", - "download": true + "publisher": { + "selector": "//meta[@name='citation_publisher']", + "attribute": "content" }, - "supplementary_material": { - "selector": "//a[contains(concat(' ', normalize-space(@class), ' '), ' article-supporting-download ')]", - "attribute": "href", - "download": true + "journal": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" }, "title": { "selector": "//meta[@name='citation_title']", "attribute": "content" }, - "author": { + "authors": { "selector": "//meta[@name='citation_author']", "attribute": "content" }, @@ -47,6 +40,42 @@ "description": { "selector": "//meta[@name='description']", "attribute": "content" + }, + "abstract": { + "selector": "//meta[@name='description']", + "attribute": "content" + }, + "fulltext_html": { + "selector": "//meta[@name='citation_fulltext_html_url']", + "attribute": "content", + "download": true + }, + "fulltext_pdf": { + "selector": "//meta[@name='citation_pdf_url']", + "attribute": "content", + "download": true + }, + "supplementary_material": { + "selector": "//a[contains(concat(' ', normalize-space(@class), ' '), ' article-supporting-download ')]", + "attribute": "href", + "download": true + }, + "figure": { + "selector": "//div[contains(concat(' ', normalize-space(@class), ' '), ' article-image-download ')]/a", + "attribute": "href", + "download": true + }, + "figure_caption": { + "selector": "//figcaption", + "attribute": "text" + }, + "license": { + "selector": "//div[contains(concat(' ', normalize-space(@class), ' '), ' license-p ')]", + "attribute": "text" + }, + "copyright": { + "selector": "//div[contains(@class, 'copyright')]", + "attribute": "text" } } -} \ No newline at end of file +} diff --git a/test/peerj.json b/test/peerj.json index 506940c..75813d4 100644 --- a/test/peerj.json +++ b/test/peerj.json @@ -1,46 +1,40 @@ { "https://peerj.com/articles/102/": [ { - "fulltext_pdf": "https://peerj.com/articles/102.pdf" + "publisher": "PeerJ Inc." }, { - "fulltext_html": "https://peerj.com/articles/102" - }, - { - "supplementary_material": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/S1_CONSORT_checklist.pdf" - }, - { - "supplementary_material": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/S2_trial_protocol.pdf" + "journal": "PeerJ" }, { "title": "Affect-focused psychodynamic psychotherapy for depression and anxiety through the Internet: a randomized controlled trial" }, { - "author": "Robert Johansson" + "authors": "Robert Johansson" }, { - "author": "Martin Björklund" + "authors": "Martin Björklund" }, { - "author": "Christoffer Hornborg" + "authors": "Christoffer Hornborg" }, { - "author": "Stina Karlsson" + "authors": "Stina Karlsson" }, { - "author": "Hugo Hesser" + "authors": "Hugo Hesser" }, { - "author": "Brjánn Ljótsson" + "authors": "Brjánn Ljótsson" }, { - "author": "Andréas Rousseau" + "authors": "Andréas Rousseau" }, { - "author": "Ronald J. Frederick" + "authors": "Ronald J. Frederick" }, { - "author": "Gerhard Andersson" + "authors": "Gerhard Andersson" }, { "date": "2013-07-09" @@ -58,57 +52,99 @@ "description": "Background. Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base. Research has indicated an association between therapist-facilitated affective experience and outcome in psychodynamic therapy. Affect-phobia therapy (APT), as outlined by McCullough et al., is a psychodynamic treatment that emphasizes a strong focus on expression and experience of affect. This model has neither been evaluated for depression nor anxiety disorders in a randomized controlled trial. While Internet-delivered psychodynamic treatments for depression and generalized anxiety disorder exist, they have not been based on APT. The aim of this randomized controlled trial was to investigate the efficacy of an Internet-based, psychodynamic, guided self-help treatment based on APT for depression and anxiety disorders.Methods. One hundred participants with diagnoses of mood and anxiety disorders participated in a randomized (1:1 ratio) controlled trial of an active group versus a control condition. The treatment group received a 10-week, psychodynamic, guided self-help treatment based on APT that was delivered through the Internet. The treatment consisted of eight text-based treatment modules and included therapist contact (9.5 min per client and week, on average) in a secure online environment. Participants in the control group also received online therapist support and clinical monitoring of symptoms, but received no treatment modules. Outcome measures were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). Process measures were also included. All measures were administered weekly during the treatment period and at a 7-month follow-up.Results. Mixed models analyses using the full intention-to-treat sample revealed significant interaction effects of group and time on all outcome measures, when comparing treatment to the control group. A large between-group effect size of Cohen’s d = 0.77 (95% CI: 0.37–1.18) was found on the PHQ-9 and a moderately large between-group effect size d = 0.48 (95% CI: 0.08–0.87) was found on the GAD-7. The number of patients who recovered (had no diagnoses of depression and anxiety, and had less than 10 on both the PHQ-9 and the GAD-7) were at post-treatment 52% in the treatment group and 24% in the control group. This difference was significant, χ2(N = 100, d f = 1) = 8.3, p < .01. From post-treatment to follow-up, treatment gains were maintained on the PHQ-9, and significant improvements were seen on the GAD-7.Conclusion. This study provides initial support for the efficacy of Internet-delivered psychodynamic therapy based on the affect-phobia model in the treatment of depression and anxiety disorders. The results support the conclusion that psychodynamic treatment approaches may be transferred to the guided self-help format and delivered via the Internet." }, { - "S2_trial_protocol.pdf": "26787550a80a05fc451d245fb7107183" + "abstract": "Background. Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base. Research has indicated an association between therapist-facilitated affective experience and outcome in psychodynamic therapy. Affect-phobia therapy (APT), as outlined by McCullough et al., is a psychodynamic treatment that emphasizes a strong focus on expression and experience of affect. This model has neither been evaluated for depression nor anxiety disorders in a randomized controlled trial. While Internet-delivered psychodynamic treatments for depression and generalized anxiety disorder exist, they have not been based on APT. The aim of this randomized controlled trial was to investigate the efficacy of an Internet-based, psychodynamic, guided self-help treatment based on APT for depression and anxiety disorders.Methods. One hundred participants with diagnoses of mood and anxiety disorders participated in a randomized (1:1 ratio) controlled trial of an active group versus a control condition. The treatment group received a 10-week, psychodynamic, guided self-help treatment based on APT that was delivered through the Internet. The treatment consisted of eight text-based treatment modules and included therapist contact (9.5 min per client and week, on average) in a secure online environment. Participants in the control group also received online therapist support and clinical monitoring of symptoms, but received no treatment modules. Outcome measures were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). Process measures were also included. All measures were administered weekly during the treatment period and at a 7-month follow-up.Results. Mixed models analyses using the full intention-to-treat sample revealed significant interaction effects of group and time on all outcome measures, when comparing treatment to the control group. A large between-group effect size of Cohen’s d = 0.77 (95% CI: 0.37–1.18) was found on the PHQ-9 and a moderately large between-group effect size d = 0.48 (95% CI: 0.08–0.87) was found on the GAD-7. The number of patients who recovered (had no diagnoses of depression and anxiety, and had less than 10 on both the PHQ-9 and the GAD-7) were at post-treatment 52% in the treatment group and 24% in the control group. This difference was significant, χ2(N = 100, d f = 1) = 8.3, p < .01. From post-treatment to follow-up, treatment gains were maintained on the PHQ-9, and significant improvements were seen on the GAD-7.Conclusion. This study provides initial support for the efficacy of Internet-delivered psychodynamic therapy based on the affect-phobia model in the treatment of depression and anxiety disorders. The results support the conclusion that psychodynamic treatment approaches may be transferred to the guided self-help format and delivered via the Internet." + }, + { + "fulltext_html": "https://peerj.com/articles/102" + }, + { + "fulltext_pdf": "https://peerj.com/articles/102.pdf" + }, + { + "supplementary_material": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/S1_CONSORT_checklist.pdf" + }, + { + "supplementary_material": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/S2_trial_protocol.pdf" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/fig-1-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/fig-2-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/fig-3-full.png" }, { - "rendered.html": "2db7d1ccd7a863ac9942dbb5ecc50825" + "figure_caption": "\nFigure 1: CONSORT flowchart.\n\n  Download full-size image\nDOI: 10.7717/peerj.102/fig-1\n\n" }, { - "102": "aa2aac89c8379b5c67250a26a48ae58b" + "figure_caption": "\nFigure 2: Malan’s two triangles - the triangle of conflict and the triangle of person.\nThe two triangles (Malan, 1995) represent what David Malan called “the universal principle of psychodynamic psychotherapy”. That is, defenses (D) and anxieties (A) can block the expression of true feelings (F). These patterns began with past persons (P), are maintained with current persons (C), and are often enacted with the therapist (T).\n  Download full-size image\nDOI: 10.7717/peerj.102/fig-2\n\n" }, { - "S1_CONSORT_checklist.pdf": "eef414787965a937fc479d31f86a9541" + "figure_caption": "\nFigure 3: Weekly PHQ-9 and GAD-7 scores.\nWeekly scores on the PHQ-9 and the GAD-7 for both groups. Vertical bars denote 95% confidence intervals (CI). PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.\n  Download full-size image\nDOI: 10.7717/peerj.102/fig-3\n\n" }, { - "102.pdf": "8e2c1cb94b99943cc618c437f8fd1618" + "": "MD5 (102) = 3479bd71a51ffb3bd0f4847289a3ed35" + }, + { + "": "MD5 (102.pdf) = 8e2c1cb94b99943cc618c437f8fd1618" + }, + { + "": "MD5 (fig-1-full.png) = c72e8d96d4bda0fef5f986543c7a5970" + }, + { + "": "MD5 (fig-2-full.png) = 9072aa50632170a8558ee1bd2d086e38" + }, + { + "": "MD5 (fig-3-full.png) = 0146a2e575c584b50ab4832654e97a96" + }, + { + "": "MD5 (rendered.html) = cf8d7e33f443c16041243cb41025e787" + }, + { + "": "MD5 (S1_CONSORT_checklist.pdf) = eef414787965a937fc479d31f86a9541" + }, + { + "": "MD5 (S2_trial_protocol.pdf) = 26787550a80a05fc451d245fb7107183" } ], "https://peerj.com/articles/234/": [ { - "fulltext_pdf": "https://peerj.com/articles/234.pdf" + "publisher": "PeerJ Inc." }, { - "fulltext_html": "https://peerj.com/articles/234" + "journal": "PeerJ" }, { "title": "A new specimen of the Early Cretaceous bird Hongshanornis longicresta: insights into the aerodynamics and diet of a basal ornithuromorph" }, { - "author": "Luis M. Chiappe" + "authors": "Luis M. Chiappe" }, { - "author": "Bo Zhao" + "authors": "Bo Zhao" }, { - "author": "Jingmai K. O’Connor" + "authors": "Jingmai K. O’Connor" }, { - "author": "Gao Chunling" + "authors": "Gao Chunling" }, { - "author": "Xuri Wang" + "authors": "Xuri Wang" }, { - "author": "Michael Habib" + "authors": "Michael Habib" }, { - "author": "Jesus Marugan-Lobon" + "authors": "Jesus Marugan-Lobon" }, { - "author": "Qingjin Meng" + "authors": "Qingjin Meng" }, { - "author": "Xiaodong Cheng" + "authors": "Xiaodong Cheng" }, { "date": "2014-01-02" @@ -126,51 +162,159 @@ "description": "The discovery of Hongshanornis longicresta, a small ornithuromorph bird with unusually long hindlimb proportions, was followed by the discovery of two closely related species, Longicrusavis houi and Parahongshanornis chaoyangensis. Together forming the Hongshanornithidae, these species reveal important information about the early diversity and morphological specialization of ornithuromorphs, the clade that contains all living birds. Here we report on a new specimen (DNHM D2945/6) referable to Hongshanornis longicresta that contributes significant information to better understand the morphology, trophic ecology, and aerodynamics of this species, as well as the taxonomy of the Hongshanornithidae. Most notable are the well-preserved wings and feathered tail of DNHM D2945/6, which afford an accurate reconstruction of aerodynamic parameters indicating that as early as 125 million years ago, basal ornithuromorphs had evolved aerodynamic surfaces comparable in size and design to those of many modern birds, and flight modes alike to those of some small living birds." }, { - "234.pdf": "3aa12392730333dd193322c7fb7ac72c" + "abstract": "The discovery of Hongshanornis longicresta, a small ornithuromorph bird with unusually long hindlimb proportions, was followed by the discovery of two closely related species, Longicrusavis houi and Parahongshanornis chaoyangensis. Together forming the Hongshanornithidae, these species reveal important information about the early diversity and morphological specialization of ornithuromorphs, the clade that contains all living birds. Here we report on a new specimen (DNHM D2945/6) referable to Hongshanornis longicresta that contributes significant information to better understand the morphology, trophic ecology, and aerodynamics of this species, as well as the taxonomy of the Hongshanornithidae. Most notable are the well-preserved wings and feathered tail of DNHM D2945/6, which afford an accurate reconstruction of aerodynamic parameters indicating that as early as 125 million years ago, basal ornithuromorphs had evolved aerodynamic surfaces comparable in size and design to those of many modern birds, and flight modes alike to those of some small living birds." + }, + { + "fulltext_html": "https://peerj.com/articles/234" + }, + { + "fulltext_pdf": "https://peerj.com/articles/234.pdf" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-1-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-2-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-3-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-4-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-5-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-6-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-7-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-8-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-9-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-10-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-11-full.png" + }, + { + "figure_caption": "\nFigure 1: Photograph of DNHM D2945.\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-1\n\n" + }, + { + "figure_caption": "\nFigure 2: Interpretive drawing of DNHM D2945.\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pt, proximal tarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-2\n\n" + }, + { + "figure_caption": "\nFigure 3: Photograph of DNHM D2946.\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-3\n\n" + }, + { + "figure_caption": "\nFigure 4: Interpretive drawing of DNHM D2946.\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; st, sternum; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-4\n\n" + }, + { + "figure_caption": "\nFigure 5: Close up photograph of the skull of DNHM D2945 in right lateral view and detail (inset) of the central portion of its maxilla.\nAbbreviations: al, alveoli.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-5\n\n" + }, + { + "figure_caption": "\nFigure 6: Photograph (A) and interpretive drawing (B) of the thoracic girdle and vertebral series, rib cage, and humeri of DNHM D2946.\nAbbreviations: co, coracoid; fu, furcula; hu, humerus; lt, lateral trabecular; ra, radius; rb, ribs; sc, scapula; sp, supracondylar process; st, sternum; up, uncinate process.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-6\n\n" + }, + { + "figure_caption": "\nFigure 7: Photograph of the left manus of DNHM D2945/6 in ventral (A; DNHM D2945) and dorsal (B; DNHM D2946) views.\nAbbreviations: mc I-III, metacarpals I-III; p1-I, phalanx 1 (proximal) of digit I (alular digit); p2-I, phalanx 2 (ungual) of digit I (alular digit); p1-II, phalanx 1 (proximal) of digit II (major digit); p2-II, phalanx 2 (intermediate) of digit II (major digit); p3-II, phalanx 3 (ungual) of digit II (major digit); p1-III, phalanx 1 (proximal) of digit III (minor digit); p2-III, phalanx 2 of digit III (minor digit); ra, radius; sl, semilunate carpal; ul, ulna.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-7\n\n" + }, + { + "figure_caption": "\nFigure 8: Close up photograph of the right knee (medial view) and pubic symphysis (left laterocaudal view) of DNHM D2946.\nNote the detail of the gastroliths. Abbreviations: fe, femur; fi, fibula; gl, gastroliths, pu, pubis; ti, tibia. (l) and (r) refer to the left and right pubis, respectively.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-8\n\n" + }, + { + "figure_caption": "\nFigure 9: Close up photograph of the left knee (lateral view) of DNHM D2946.\nAbbreviations: cn, cnemial crest; fc, fibular condyle; fe, femur; fi, fibula; ld, lateral articular facet of tibia; md, medial articular facet of tibia; ti, tibia.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-9\n\n" + }, + { + "figure_caption": "\nFigure 10: Close up photograph of the feet and rectrices of DNHM D2945.\nAbbreviations: mt, metatarsals; re, rectrices; I-IV, digits I-IV.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-10\n\n" + }, + { + "figure_caption": "\nFigure 11: Interpretive drawing of the outline of the wings and feathered tail of DNHM D2945/6 (see Figs. 1 and 3 for the maximum extent of the primaries and secondaries).\nThe aerodynamic parameters used in this study were derived from this reconstruction (see Materials and Methods).\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-11\n\n" + }, + { + "": "MD5 (234) = 7a9d98efbd63cc8c88559b215e17f768" + }, + { + "": "MD5 (234.pdf) = 3aa12392730333dd193322c7fb7ac72c" + }, + { + "": "MD5 (fig-1-full.png) = 5870a310df205fb7216bd358568a11d9" + }, + { + "": "MD5 (fig-10-full.png) = d3d1eadb360073c696eef317130004e8" + }, + { + "": "MD5 (fig-11-full.png) = 0ce3c5edbe7822a1c6b5ea26f6cfd1c4" + }, + { + "": "MD5 (fig-2-full.png) = af0dbb6dbbdd9dc38ba8fdb5a4409d26" + }, + { + "": "MD5 (fig-3-full.png) = 165114a6bd917393af1c628e4f15cc23" + }, + { + "": "MD5 (fig-4-full.png) = 9e43600b181b87de53f52d1ee145aec8" + }, + { + "": "MD5 (fig-5-full.png) = 95ed20e2b3abffa642caccf50c73941d" + }, + { + "": "MD5 (fig-6-full.png) = 28860f72dcafe1bae43e29c49374e644" + }, + { + "": "MD5 (fig-7-full.png) = 7040496f9de9004852cf2bae90034fe7" + }, + { + "": "MD5 (fig-8-full.png) = 73da14b5d45b36d95a9fa8a206651336" }, { - "234": "fa3274087243cf9e8b32b18f8d86d5c2" + "": "MD5 (fig-9-full.png) = 3d3868736ac56e4f2e8e6395d05df051" }, { - "rendered.html": "48d795fb6a0567b3b8f1ee529fd25bf5" + "": "MD5 (rendered.html) = b46a53d7e3b3dcf68e35ef8991cf748d" } ], "https://peerj.com/articles/275/": [ { - "fulltext_pdf": "https://peerj.com/articles/275.pdf" + "publisher": "PeerJ Inc." }, { - "fulltext_html": "https://peerj.com/articles/275" + "journal": "PeerJ" }, { "title": "Spectral characteristics of the mutant form GGBP/H152C of D-glucose/D-galactose-binding protein labeled with fluorescent dye BADAN: influence of external factors" }, { - "author": "Alexander V. Fonin" + "authors": "Alexander V. Fonin" }, { - "author": "Olga V. Stepanenko" + "authors": "Olga V. Stepanenko" }, { - "author": "Olga I. Povarova" + "authors": "Olga I. Povarova" }, { - "author": "Catherine A. Volova" + "authors": "Catherine A. Volova" }, { - "author": "Elizaveta M. Philippova" + "authors": "Elizaveta M. Philippova" }, { - "author": "Grigory S. Bublikov" + "authors": "Grigory S. Bublikov" }, { - "author": "Irina M. Kuznetsova" + "authors": "Irina M. Kuznetsova" }, { - "author": "Alexander P. Demchenko" + "authors": "Alexander P. Demchenko" }, { - "author": "Konstantin K. Turoverov" + "authors": "Konstantin K. Turoverov" }, { "date": "2014-03-18" @@ -188,33 +332,105 @@ "description": "The mutant form GGBP/H152C of the D-glucose/D-galactose-binding protein with the solvatochromic dye BADAN linked to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various external factors on the physical-chemical properties of GGBP/H152C-BADAN and its complex with glucose. The high affinity (Kd = 8.5 µM) and high binding rate of glucose make GGBP/H152C-BADAN a good candidate to determine the sugar content in biological fluids extracted using transdermal techniques. It was shown that changes in the ionic strength and pH of solution within the physiological range did not have a significant influence on the fluorescent characteristics of GGBP/H152C-BADAN. The mutant form GGBP/H152C has relatively low resistance to denaturation action of GdnHCl and urea. This result emphasizes the need to find more stable proteins for the creation of a sensitive element for a glucose biosensor system." }, { - "275": "67744f9749de75719601ef63718d28a8" + "abstract": "The mutant form GGBP/H152C of the D-glucose/D-galactose-binding protein with the solvatochromic dye BADAN linked to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various external factors on the physical-chemical properties of GGBP/H152C-BADAN and its complex with glucose. The high affinity (Kd = 8.5 µM) and high binding rate of glucose make GGBP/H152C-BADAN a good candidate to determine the sugar content in biological fluids extracted using transdermal techniques. It was shown that changes in the ionic strength and pH of solution within the physiological range did not have a significant influence on the fluorescent characteristics of GGBP/H152C-BADAN. The mutant form GGBP/H152C has relatively low resistance to denaturation action of GdnHCl and urea. This result emphasizes the need to find more stable proteins for the creation of a sensitive element for a glucose biosensor system." + }, + { + "fulltext_html": "https://peerj.com/articles/275" + }, + { + "fulltext_pdf": "https://peerj.com/articles/275.pdf" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-1-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-2-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-3-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-4-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-5-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-6-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-7-full.png" + }, + { + "figure_caption": "\nFigure 1: Determination of the dissociation constant (Kd) of the complex of GGBP/H152C-BADAN with glucose (Glc).\nThe excitation wavelength was 387 nm, the emission wavelength was 545 nm.\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-1\n\n" + }, + { + "figure_caption": "\nFigure 2: The kinetics of Glc binding to GGBP/H152C-BADAN in solutions with different viscosities.\nGlc concentration was 20 mM. The excitation wavelength was 405 nm. Curve 1, 2 and 3 represents the control, Glc binding to GGBP/H152C-BADAN in a PBS solution, and in PBS-glycerol solution with viscosity equal to 4.0 cP. Inset: The kinetic curves 1 and 2 in interval from 0.01 to 0.08 s are given.\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-2\n\n" }, { - "rendered.html": "14811027ddcf0230aed2aad5a0397347" + "figure_caption": "\nFigure 3: The effect of solvent viscosity and temperature on the fluorescence quantum yield of the GGBP/H152C-BADAN in the open (circles) and closed (triangles) forms.\nThe excitation wavelength was 387 nm.\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-3\n\n" }, { - "275.pdf": "6b554c704f1ed7a8129863a2869036eb" + "figure_caption": "\nFigure 4: GdnHCl-induced (A, B) and urea-induced (C, D) conformational changing of GGBP/H152C-BADAN structure in open (circles) and closed forms (triangles).\n(A) and (C) represents the dependence of the fluorescence intensity (the excitation wavelength was 387 nm, the emission wavelength was 545 nm) on the denaturants concentration. (B) and (D) represents the dependence of the parameter A = I320/I365 (I320 and I365 fluorescence intensities recorded at 320 and 365 nm, respectively) on the denaturants concentration (the excitation wavelength was 297 nm).\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-4\n\n" + }, + { + "figure_caption": "\nFigure 5: Changes of ellipticity at 222 nm of GGBP/H152C-BADAN and GGBP/H152C-BADAN–Glc on the GdnHCl concentration.\n\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-5\n\n" + }, + { + "figure_caption": "\nFigure 6: The effect of the pH solution on the fluorescent characteristics of GGBP/H152C-BADAN in the open (the solid curves) and closed (the dashed curves) forms.\n(A) The excitation wavelength was 297 nm. (B) The excitation wavelength was 387 nm. The pH values of the solution were 2.8 (black curves), 4.2 (red curves), 6.4 (blue curves), 7.4 (dark green curves) and 9.6 (dark red curves).\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-6\n\n" + }, + { + "figure_caption": "\nFigure 7: The effect of NaCl and MgCl2 on the fluorescent characteristics of GGBP/H152C-BADAN in open (solid curves) and closed (dashed curves) forms.\n(A) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.8 M NaCl (red curve) and 2.5 M NaCl (blue curve). (B) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.1 M MgCl2 (red curve) and 0.5 M MgCl2 (blue curve). The fluorescence spectra of GGBP/H152C-BADAN in PBS solution appear in black. (The excitation wavelength was 387 nm.)\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-7\n\n" + }, + { + "": "MD5 (275) = 576a158c3b08a6d0764bd189828d5bd2" + }, + { + "": "MD5 (275.pdf) = 6b554c704f1ed7a8129863a2869036eb" + }, + { + "": "MD5 (fig-1-full.png) = 3698cf17a11ba9ef9183634bd3801b49" + }, + { + "": "MD5 (fig-2-full.png) = 90442c7e0490029e4d59193979537f6a" + }, + { + "": "MD5 (fig-3-full.png) = c41e4a8c837cfe6aeabff81982844a98" + }, + { + "": "MD5 (fig-4-full.png) = e3ea581b9d3ae478cc5c7e3c630576e8" + }, + { + "": "MD5 (fig-5-full.png) = 97904c56a6215db7065fd1830624f708" + }, + { + "": "MD5 (fig-6-full.png) = fff6b0de359e83441f6b5838d862fd93" + }, + { + "": "MD5 (fig-7-full.png) = b76d31a596a07e5ef4fe238d687c5729" + }, + { + "": "MD5 (rendered.html) = 0798f6f9153bd5208e0836d1456a9ad6" } ], "https://peerj.com/articles/311/": [ { - "fulltext_pdf": "https://peerj.com/articles/311.pdf" + "publisher": "PeerJ Inc." }, { - "fulltext_html": "https://peerj.com/articles/311" + "journal": "PeerJ" }, { "title": "Religious attendance after elevated depressive symptoms: is selection bias at work?" }, { - "author": "Lloyd Balbuena" + "authors": "Lloyd Balbuena" }, { - "author": "Marilyn Baetz" + "authors": "Marilyn Baetz" }, { - "author": "Rudy Bowen" + "authors": "Rudy Bowen" }, { "date": "2014-03-13" @@ -232,42 +448,69 @@ "description": "In an attempt to determine if selection bias could be a reason that religious attendance and depression are related, the predictive value of elevated depressive symptoms for a decrease in future attendance at religious services was examined in a longitudinal panel of 1,673 Dutch adults. Religious attendance was assessed yearly over five years using the single question, “how often do you attend religious gatherings nowadays?” Depressive symptoms were assessed four times within the first year using the Depression subscale of the Brief Symptom Inventory. Logistic regression models of change in attendance were created, stratifying by baseline attendance status. Attenders who developed elevated symptoms were less likely to subsequently decrease their attendance (relative risk ratio: 0.55, 95% CI [0.38–0.79]) relative to baseline as compared to those without elevated symptoms. This inverse association remained significant after controlling for health and demographic covariates, and when using multiply imputed data to account for attrition. Non-attenders were unlikely to start attending after elevated depressive symptoms. This study provides counter evidence against previous findings that church attenders are a self-selected healthier group." }, { - "311": "daf380aa95bfd59264132483e46581d8" + "abstract": "In an attempt to determine if selection bias could be a reason that religious attendance and depression are related, the predictive value of elevated depressive symptoms for a decrease in future attendance at religious services was examined in a longitudinal panel of 1,673 Dutch adults. Religious attendance was assessed yearly over five years using the single question, “how often do you attend religious gatherings nowadays?” Depressive symptoms were assessed four times within the first year using the Depression subscale of the Brief Symptom Inventory. Logistic regression models of change in attendance were created, stratifying by baseline attendance status. Attenders who developed elevated symptoms were less likely to subsequently decrease their attendance (relative risk ratio: 0.55, 95% CI [0.38–0.79]) relative to baseline as compared to those without elevated symptoms. This inverse association remained significant after controlling for health and demographic covariates, and when using multiply imputed data to account for attrition. Non-attenders were unlikely to start attending after elevated depressive symptoms. This study provides counter evidence against previous findings that church attenders are a self-selected healthier group." }, { - "311.pdf": "8aa4a538c24c0f3bfcc8b9fa5cd63d7c" + "fulltext_html": "https://peerj.com/articles/311" }, { - "rendered.html": "f886abd9f8484ad4a4275719b1077f0c" + "fulltext_pdf": "https://peerj.com/articles/311.pdf" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/311/1/fig-1-full.png" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/311/1/fig-2-full.png" + }, + { + "figure_caption": "\nFigure 1: Subjects.\n(A) LISS datasets used and participant flowchart; (B) schedule of religion and depression assessments.\n  Download full-size image\nDOI: 10.7717/peerj.311/fig-1\n\n" + }, + { + "figure_caption": "\nFigure 2: Probabilities.\nPredicted probabilities of a decrease, same, and increase in religious attendance (95% CI).\n  Download full-size image\nDOI: 10.7717/peerj.311/fig-2\n\n" + }, + { + "": "MD5 (311) = 81468d060387974711cec3b724a142ca" + }, + { + "": "MD5 (311.pdf) = 8aa4a538c24c0f3bfcc8b9fa5cd63d7c" + }, + { + "": "MD5 (fig-1-full.png) = 3ff19ca931ac3850d2e6d045efb5d213" + }, + { + "": "MD5 (fig-2-full.png) = b6a99fff0a72af9fde1e550f80d43799" + }, + { + "": "MD5 (rendered.html) = 9b8cedfb522b359d5715838a097a2ff8" } ], "https://peerj.com/articles/384/": [ { - "fulltext_pdf": "https://peerj.com/articles/384.pdf" + "publisher": "PeerJ Inc." }, { - "fulltext_html": "https://peerj.com/articles/384" + "journal": "PeerJ" }, { "title": "Mutation analysis of the SLC26A4, FOXI1 and KCNJ10 genes in individuals with congenital hearing loss" }, { - "author": "Lynn M. Pique" + "authors": "Lynn M. Pique" }, { - "author": "Marie-Luise Brennan" + "authors": "Marie-Luise Brennan" }, { - "author": "Colin J. Davidson" + "authors": "Colin J. Davidson" }, { - "author": "Frederick Schaefer" + "authors": "Frederick Schaefer" }, { - "author": "John Greinwald Jr" + "authors": "John Greinwald Jr" }, { - "author": "Iris Schrijver" + "authors": "Iris Schrijver" }, { "date": "2014-05-08" @@ -285,13 +528,31 @@ "description": "Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype." }, { - "384.pdf": "b2020a8f8037228e6face4a220751932" + "abstract": "Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype." + }, + { + "fulltext_html": "https://peerj.com/articles/384" + }, + { + "fulltext_pdf": "https://peerj.com/articles/384.pdf" + }, + { + "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/384/1/fig-1-full.png" + }, + { + "figure_caption": "\nFigure 1: Identification of the heterozygous SLC26A4 deletion g.8091T-22145Cdel in subject PDS41.\n(A) The SLC26A4 MLPA probe mix includes probes for the 21 SLC26A4 exons, 14 reference probes and three probes specific for the point mutations c.1001+1G>A (IV S8+1G>A), c.707T>C (p.Leu236Pro) and c.1246A>C (p.Thr416Pro). Subject PDS41 is heterozygous for a deletion (g.8091T-22145Cdel) spanning exons 4–6 in SLC26A4, as evidenced by the reproducible reduction in peak height for these three exon probes (peaks labeled 4, 5, 6) relative to the control. PDS41 also has a heterozygous c.1246A>C (p.Thr416Pro) mutation that was previously identified by sequencing and confirmed by these MLPA results (peak labeled p.T416P). (B) Sequencing chromatogram of the deletion breakpoints in SLC26A4 IVS3 and IVS6. The deletion removes a total of 14,053 bp. IVS, intervening sequence.\n  Download full-size image\nDOI: 10.7717/peerj.384/fig-1\n\n" + }, + { + "": "MD5 (384) = be322abd43c5c3a82883245d26fc0985" + }, + { + "": "MD5 (384.pdf) = b2020a8f8037228e6face4a220751932" }, { - "384": "befa18960e439f737d1a4bee7f0f7ae4" + "": "MD5 (fig-1-full.png) = 6ee6bf8676df1087e9d724bfdc9178e8" }, { - "rendered.html": "28104961eb099d940b156396cac7d503" + "": "MD5 (rendered.html) = ce8535e3c2971ad6cd724a42c9197470" } ] } \ No newline at end of file From 7317635057f10be5b543958e61ca9f560719f9db Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Thu, 3 Jul 2014 00:31:19 +0100 Subject: [PATCH 047/154] fix contributing doc links --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 119706a..0a1131c 100644 --- a/README.md +++ b/README.md @@ -82,9 +82,9 @@ If your favourite publisher or journal is not covered by a scraper in our collec We ask that all contributions follow some simple rules that help us maintain a high-quality collection. -1. The scraper covers all [the data elements used in the ContentMine](wiki/data_collected_for_ContentMine). +1. The scraper covers all [the data elements used in the ContentMine](https://github.com/ContentMine/journal-scrapers/wiki/data_collected_for_ContentMine). 2. You must submit a set of 5-10 test URLs. -3. It comes with a regression test ([which can be auto-generated](wiki/Generating-tests-for-your-scrapers)). +3. It comes with a regression test ([which can be auto-generated](https://github.com/ContentMine/journal-scrapers/wiki/Generating%20tests%20for%20your%20scrapers)). 4. You agree to release the scraper definition and tests under the [Creative Commons Zero license](https://creativecommons.org/publicdomain/zero/1.0/). ### Usage From 905c04cf727b154ec430950b18872708758a123c Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Thu, 3 Jul 2014 22:59:24 +0100 Subject: [PATCH 048/154] run tests in debug mode --- test/test_all.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/test_all.rb b/test/test_all.rb index 3e95600..5e8ebd4 100644 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -63,7 +63,7 @@ def coverage(scraperjsonpath, results) cmd += " --url #{url}" cmd += " --scraper #{scraper}" cmd += " --output output" - cmd += " --loglevel silent" + cmd += " --loglevel debug" puts `#{cmd}` # load the output cleanurl = url.gsub(/:?\/+/, '_') From 7198106818463374d81631d331fd961ceb439ea8 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Fri, 4 Jul 2014 01:53:29 +0100 Subject: [PATCH 049/154] install libfontconfig before running travis tests --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index c18548d..5b60593 100644 --- a/.travis.yml +++ b/.travis.yml @@ -6,9 +6,9 @@ before_install: - sudo apt-get install -y software-properties-common python-software-properties - sudo add-apt-repository -y ppa:chris-lea/node.js - sudo apt-get update - - sudo apt-get install -y python g++ make nodejs + - sudo apt-get install -y python g++ make nodejs libfontconfig1 - curl --insecure https://www.npmjs.org/install.sh | bash install: - - sudo -H npm install --global phantomjs casperjs quickscrape + - sudo -H npm install --global quickscrape script: - ruby test/test_all.rb From a5746a388b3ecc93a8a65ab46779d5824b25a3cd Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 13 Jul 2014 14:27:28 -0400 Subject: [PATCH 050/154] fix broken peerj tests --- test/peerj.json | 82 ++++++++++++++++++++++++------------------------- 1 file changed, 41 insertions(+), 41 deletions(-) diff --git a/test/peerj.json b/test/peerj.json index 75813d4..c62dfed 100644 --- a/test/peerj.json +++ b/test/peerj.json @@ -85,28 +85,28 @@ "figure_caption": "\nFigure 3: Weekly PHQ-9 and GAD-7 scores.\nWeekly scores on the PHQ-9 and the GAD-7 for both groups. Vertical bars denote 95% confidence intervals (CI). PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.\n  Download full-size image\nDOI: 10.7717/peerj.102/fig-3\n\n" }, { - "": "MD5 (102) = 3479bd71a51ffb3bd0f4847289a3ed35" + "fig-3-full.png": "0146a2e575c584b50ab4832654e97a96" }, { - "": "MD5 (102.pdf) = 8e2c1cb94b99943cc618c437f8fd1618" + "fig-1-full.png": "c72e8d96d4bda0fef5f986543c7a5970" }, { - "": "MD5 (fig-1-full.png) = c72e8d96d4bda0fef5f986543c7a5970" + "rendered.html": "4461035334376c3cc6b33d56467df660" }, { - "": "MD5 (fig-2-full.png) = 9072aa50632170a8558ee1bd2d086e38" + "102.pdf": "8e2c1cb94b99943cc618c437f8fd1618" }, { - "": "MD5 (fig-3-full.png) = 0146a2e575c584b50ab4832654e97a96" + "102": "460e830d7dd7a3f929828342b9b6f12b" }, { - "": "MD5 (rendered.html) = cf8d7e33f443c16041243cb41025e787" + "S2_trial_protocol.pdf": "26787550a80a05fc451d245fb7107183" }, { - "": "MD5 (S1_CONSORT_checklist.pdf) = eef414787965a937fc479d31f86a9541" + "S1_CONSORT_checklist.pdf": "eef414787965a937fc479d31f86a9541" }, { - "": "MD5 (S2_trial_protocol.pdf) = 26787550a80a05fc451d245fb7107183" + "fig-2-full.png": "9072aa50632170a8558ee1bd2d086e38" } ], "https://peerj.com/articles/234/": [ @@ -237,46 +237,46 @@ "figure_caption": "\nFigure 11: Interpretive drawing of the outline of the wings and feathered tail of DNHM D2945/6 (see Figs. 1 and 3 for the maximum extent of the primaries and secondaries).\nThe aerodynamic parameters used in this study were derived from this reconstruction (see Materials and Methods).\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-11\n\n" }, { - "": "MD5 (234) = 7a9d98efbd63cc8c88559b215e17f768" + "fig-4-full.png": "9e43600b181b87de53f52d1ee145aec8" }, { - "": "MD5 (234.pdf) = 3aa12392730333dd193322c7fb7ac72c" + "fig-3-full.png": "165114a6bd917393af1c628e4f15cc23" }, { - "": "MD5 (fig-1-full.png) = 5870a310df205fb7216bd358568a11d9" + "fig-7-full.png": "7040496f9de9004852cf2bae90034fe7" }, { - "": "MD5 (fig-10-full.png) = d3d1eadb360073c696eef317130004e8" + "fig-9-full.png": "3d3868736ac56e4f2e8e6395d05df051" }, { - "": "MD5 (fig-11-full.png) = 0ce3c5edbe7822a1c6b5ea26f6cfd1c4" + "fig-10-full.png": "d3d1eadb360073c696eef317130004e8" }, { - "": "MD5 (fig-2-full.png) = af0dbb6dbbdd9dc38ba8fdb5a4409d26" + "234": "9be160e6461eae366392ccc3945e7070" }, { - "": "MD5 (fig-3-full.png) = 165114a6bd917393af1c628e4f15cc23" + "fig-1-full.png": "5870a310df205fb7216bd358568a11d9" }, { - "": "MD5 (fig-4-full.png) = 9e43600b181b87de53f52d1ee145aec8" + "fig-6-full.png": "28860f72dcafe1bae43e29c49374e644" }, { - "": "MD5 (fig-5-full.png) = 95ed20e2b3abffa642caccf50c73941d" + "rendered.html": "9baf1d55e8d7429ee2d6349afd8ab221" }, { - "": "MD5 (fig-6-full.png) = 28860f72dcafe1bae43e29c49374e644" + "fig-11-full.png": "0ce3c5edbe7822a1c6b5ea26f6cfd1c4" }, { - "": "MD5 (fig-7-full.png) = 7040496f9de9004852cf2bae90034fe7" + "234.pdf": "3aa12392730333dd193322c7fb7ac72c" }, { - "": "MD5 (fig-8-full.png) = 73da14b5d45b36d95a9fa8a206651336" + "fig-8-full.png": "73da14b5d45b36d95a9fa8a206651336" }, { - "": "MD5 (fig-9-full.png) = 3d3868736ac56e4f2e8e6395d05df051" + "fig-5-full.png": "95ed20e2b3abffa642caccf50c73941d" }, { - "": "MD5 (rendered.html) = b46a53d7e3b3dcf68e35ef8991cf748d" + "fig-2-full.png": "af0dbb6dbbdd9dc38ba8fdb5a4409d26" } ], "https://peerj.com/articles/275/": [ @@ -383,34 +383,34 @@ "figure_caption": "\nFigure 7: The effect of NaCl and MgCl2 on the fluorescent characteristics of GGBP/H152C-BADAN in open (solid curves) and closed (dashed curves) forms.\n(A) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.8 M NaCl (red curve) and 2.5 M NaCl (blue curve). (B) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.1 M MgCl2 (red curve) and 0.5 M MgCl2 (blue curve). The fluorescence spectra of GGBP/H152C-BADAN in PBS solution appear in black. (The excitation wavelength was 387 nm.)\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-7\n\n" }, { - "": "MD5 (275) = 576a158c3b08a6d0764bd189828d5bd2" + "fig-4-full.png": "e3ea581b9d3ae478cc5c7e3c630576e8" }, { - "": "MD5 (275.pdf) = 6b554c704f1ed7a8129863a2869036eb" + "fig-3-full.png": "c41e4a8c837cfe6aeabff81982844a98" }, { - "": "MD5 (fig-1-full.png) = 3698cf17a11ba9ef9183634bd3801b49" + "fig-7-full.png": "b76d31a596a07e5ef4fe238d687c5729" }, { - "": "MD5 (fig-2-full.png) = 90442c7e0490029e4d59193979537f6a" + "275.pdf": "6b554c704f1ed7a8129863a2869036eb" }, { - "": "MD5 (fig-3-full.png) = c41e4a8c837cfe6aeabff81982844a98" + "fig-1-full.png": "3698cf17a11ba9ef9183634bd3801b49" }, { - "": "MD5 (fig-4-full.png) = e3ea581b9d3ae478cc5c7e3c630576e8" + "fig-6-full.png": "fff6b0de359e83441f6b5838d862fd93" }, { - "": "MD5 (fig-5-full.png) = 97904c56a6215db7065fd1830624f708" + "rendered.html": "30d93308f1f8fa6d21f202254c6fa516" }, { - "": "MD5 (fig-6-full.png) = fff6b0de359e83441f6b5838d862fd93" + "275": "c067c205f735cbb13d14a7771502cc30" }, { - "": "MD5 (fig-7-full.png) = b76d31a596a07e5ef4fe238d687c5729" + "fig-5-full.png": "97904c56a6215db7065fd1830624f708" }, { - "": "MD5 (rendered.html) = 0798f6f9153bd5208e0836d1456a9ad6" + "fig-2-full.png": "90442c7e0490029e4d59193979537f6a" } ], "https://peerj.com/articles/311/": [ @@ -469,19 +469,19 @@ "figure_caption": "\nFigure 2: Probabilities.\nPredicted probabilities of a decrease, same, and increase in religious attendance (95% CI).\n  Download full-size image\nDOI: 10.7717/peerj.311/fig-2\n\n" }, { - "": "MD5 (311) = 81468d060387974711cec3b724a142ca" + "311.pdf": "8aa4a538c24c0f3bfcc8b9fa5cd63d7c" }, { - "": "MD5 (311.pdf) = 8aa4a538c24c0f3bfcc8b9fa5cd63d7c" + "fig-1-full.png": "3ff19ca931ac3850d2e6d045efb5d213" }, { - "": "MD5 (fig-1-full.png) = 3ff19ca931ac3850d2e6d045efb5d213" + "311": "7c457cc73a24cb05df634e0d01dbe561" }, { - "": "MD5 (fig-2-full.png) = b6a99fff0a72af9fde1e550f80d43799" + "rendered.html": "9d3054adc95559f5e507e87f2c2f2ae0" }, { - "": "MD5 (rendered.html) = 9b8cedfb522b359d5715838a097a2ff8" + "fig-2-full.png": "b6a99fff0a72af9fde1e550f80d43799" } ], "https://peerj.com/articles/384/": [ @@ -543,16 +543,16 @@ "figure_caption": "\nFigure 1: Identification of the heterozygous SLC26A4 deletion g.8091T-22145Cdel in subject PDS41.\n(A) The SLC26A4 MLPA probe mix includes probes for the 21 SLC26A4 exons, 14 reference probes and three probes specific for the point mutations c.1001+1G>A (IV S8+1G>A), c.707T>C (p.Leu236Pro) and c.1246A>C (p.Thr416Pro). Subject PDS41 is heterozygous for a deletion (g.8091T-22145Cdel) spanning exons 4–6 in SLC26A4, as evidenced by the reproducible reduction in peak height for these three exon probes (peaks labeled 4, 5, 6) relative to the control. PDS41 also has a heterozygous c.1246A>C (p.Thr416Pro) mutation that was previously identified by sequencing and confirmed by these MLPA results (peak labeled p.T416P). (B) Sequencing chromatogram of the deletion breakpoints in SLC26A4 IVS3 and IVS6. The deletion removes a total of 14,053 bp. IVS, intervening sequence.\n  Download full-size image\nDOI: 10.7717/peerj.384/fig-1\n\n" }, { - "": "MD5 (384) = be322abd43c5c3a82883245d26fc0985" + "fig-1-full.png": "6ee6bf8676df1087e9d724bfdc9178e8" }, { - "": "MD5 (384.pdf) = b2020a8f8037228e6face4a220751932" + "rendered.html": "96b5f65a07b9df06ab331f682f347d53" }, { - "": "MD5 (fig-1-full.png) = 6ee6bf8676df1087e9d724bfdc9178e8" + "384.pdf": "b2020a8f8037228e6face4a220751932" }, { - "": "MD5 (rendered.html) = ce8535e3c2971ad6cd724a42c9197470" + "384": "003b6f777ee95fffaf497181c427420b" } ] } \ No newline at end of file From 2901ab4ebe68d077e1e73a6204c33d27e0192454 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Sun, 13 Jul 2014 20:32:04 +0200 Subject: [PATCH 051/154] link out to scraperJSON --- README.md | 36 ++---------------------------------- 1 file changed, 2 insertions(+), 34 deletions(-) diff --git a/README.md b/README.md index 0a1131c..315f02d 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ Journal scraper definitions for the ContentMine framework. ### Summary -This repo is a collection of ScraperJSON definitions targetting academic journals. They can be used to extract and download data from URLs of journal articles, such as: +This repo is a collection of scraperJSON definitions targeting academic journals. They can be used to extract and download data from URLs of journal articles, such as: - Title, author list, date - Figures and their captions @@ -42,39 +42,7 @@ How well the scrapers are covered by the tests is also checked. Coverage should ### ScraperJSON definitions -Scrapers are defined in JSON, using a schema called ScraperJSON which is currently evolving. - -The current schema is described below. - -There can be two keys in the root object: - -- ***url*** - a string-form regular expression specifying which URL(s) this scraper targets -- ***elements*** - a dictionary of elements to scrape - -Elements are defined as key-value pairs, where the key is a description of the element, and the value is a dictionary of specifiers defining the element and its processing. Allowed keys in the specifier dictionary are: - -- ***selector*** - an XPath selector targetting the element to be selected. -- ***attribute*** - a string specifying the attribute to extract from the selected element. **Optional** (omitting this key is equivalent to giving it a value of `text`). In addition to html attributes there are two special attributes allowed: - - `text` - extracts any plaintext inside the selected element - - `html` - extracts the inner HTML of the selected element -- ***download*** - a boolean flag: true if the element is a URL to a resource that must be downloaded. **Optional** (omitting this key is equivalent to giving it a value of `false`). - -Example: -```json -{ - "url": "plos.*\\.org", - "elements": { - "fulltext_pdf": { - "selector": "//meta[@name='citation_pdf_url']", - "attribute": "content", - "download": true - }, - "title": { - "selector": "//meta[@name='citation_title']" - } - } -} -``` +Scrapers are defined in JSON, using a schema called scraperJSON which is currently evolving. The current schema is described at [the scraperJSON repo](https://github.com/ContentMine/scraperJSON). ### Contributing scrapers From 3746fcc0f7769304c22baa777c39fc7c4c9648ac Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Sun, 13 Jul 2014 20:50:02 +0200 Subject: [PATCH 052/154] handle mac MD5hash --- scripts/make_tests.rb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/scripts/make_tests.rb b/scripts/make_tests.rb index 734bf2c..fd966be 100755 --- a/scripts/make_tests.rb +++ b/scripts/make_tests.rb @@ -70,7 +70,13 @@ files = files.keep_if { |f| f != 'results.json' } filehashes = `md5sum #{files.join(' ')}` filehashes.split("\n").each do |line| - filehash, filename = line.strip.split(" ") + if line =~ /MD5 \(/ + # OSX version of MD5 + filename, filehash = /\((.*)\) = (\w+)/.match(line)[1, 2] + else + # linux version + filehash, filename = line.strip.split(" ") + end results << { filename => filehash } end end From 187846b6af6cd0096583a8344aef2577ac4689f9 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Sun, 13 Jul 2014 20:53:29 +0200 Subject: [PATCH 053/154] MDPI full --- scrapers/mdpi.json | 80 ++++++ scrapers/mdpi_figures.json | 17 -- test/mdpi.json | 529 +++++++++++++++++++++++++++++++++++++ test/mdpi_test_urls.txt | 7 + 4 files changed, 616 insertions(+), 17 deletions(-) create mode 100644 scrapers/mdpi.json delete mode 100644 scrapers/mdpi_figures.json create mode 100644 test/mdpi.json create mode 100644 test/mdpi_test_urls.txt diff --git a/scrapers/mdpi.json b/scrapers/mdpi.json new file mode 100644 index 0000000..724afac --- /dev/null +++ b/scrapers/mdpi.json @@ -0,0 +1,80 @@ +{ + "url": "mdpi\\.com", + "elements": { + "publisher": { + "selector": "//meta[@name='citation_publisher']", + "attribute": "content" + }, + "journal": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" + }, + "title": { + "selector": "//meta[@name='citation_title']", + "attribute": "content" + }, + "authors": { + "selector": "//meta[@name='citation_author']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@name='citation_date']", + "attribute": "content" + }, + "doi": { + "selector": "//meta[@name='citation_doi']", + "attribute": "content" + }, + "volume": { + "selector": "//meta[@name='citation_volume']", + "attribute": "content" + }, + "issue": { + "selector": "//meta[@name='citation_issue']", + "attribute": "content" + }, + "firstpage": { + "selector": "//meta[@name='citation_firstpage']", + "attribute": "content" + }, + "description": { + "selector": "//meta[@name='description']", + "attribute": "content" + }, + "abstract": { + "selector": "//meta[@name='description']", + "attribute": "content" + }, + "fulltext_html": { + "selector": "//meta[@name='citation_fulltext_html_url']", + "attribute": "content", + "download": true + }, + "fulltext_pdf": { + "selector": "//meta[@name='citation_pdf_url']", + "attribute": "content", + "download": true + }, + "supplementary_material": { + "selector": "//a[contains(concat(' ', normalize-space(@class), ' '), ' article-supporting-download ')]", + "attribute": "href", + "download": true + }, + "figure": { + "selector": "//div[contains(@id, 'fig')]/div/img", + "attribute": "src", + "download": true + }, + "figure_caption": { + "selector": "//div[contains(@class, 'html-fig_description')]" + }, + "license": { + "selector": "//div[contains(concat(' ', normalize-space(@class), ' '), ' license-p ')]", + "attribute": "text" + }, + "copyright": { + "selector": "//div[contains(@class, 'copyright')]", + "attribute": "text" + } + } +} diff --git a/scrapers/mdpi_figures.json b/scrapers/mdpi_figures.json deleted file mode 100644 index 055462a..0000000 --- a/scrapers/mdpi_figures.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "url": "mdpi", - "elements": { - "dc.source": { - "selector": "//meta[@name='dc.source']", - "attribute": "content" - }, - "figure_img": { - "selector": "//div[contains(@id, 'fig')]/div/img", - "attribute": "src", - "download": true - }, - "figure_caption": { - "selector": "//div[contains(@class, 'html-fig_description')]" - } - } -} diff --git a/test/mdpi.json b/test/mdpi.json new file mode 100644 index 0000000..6fa4eeb --- /dev/null +++ b/test/mdpi.json @@ -0,0 +1,529 @@ +{ + "http://www.mdpi.com/1420-3049/19/4/5150/htm": [ + { + "publisher": "Multidisciplinary Digital Publishing Institute" + }, + { + "journal": "Molecules" + }, + { + "title": "Development of Simple Sequence Repeat (SSR) Markers of Sesame (Sesamum indicum) from a Genome Survey" + }, + { + "date": "2014-04-22" + }, + { + "doi": "10.3390/molecules19045150" + }, + { + "volume": "19" + }, + { + "issue": "4" + }, + { + "firstpage": "5150" + }, + { + "description": "Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world’s population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding." + }, + { + "abstract": "Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world’s population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding." + }, + { + "fulltext_html": "http://www.mdpi.com/1420-3049/19/4/5150/htm" + }, + { + "fulltext_pdf": "http://www.mdpi.com/1420-3049/19/4/5150/pdf" + }, + { + "figure": "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g001-1024.png" + }, + { + "figure": "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g002-1024.png" + }, + { + "figure": "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g003-1024.png" + }, + { + "figure": "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g004-1024.png" + }, + { + "figure": "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g005-1024.png" + }, + { + "figure_caption": "\n Figure 1.\n Distribution of various classes of simple repeat motifs with different numbers of repeats in the sesame genome.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 2.\n (a) Percentage of different dinucleotide repeat motifs in the sesame genome. and (b) Percentage of different motifs in trinucleotide repeat motifs in the sesame genome.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 3.\n Population structure of sesame accessions. STRUCTURE was constructed by all loci. K = 2. Clusters are indicated by different colours. Samples included in all clusters are listed in Table S3.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 4.\n Phylogenetic tree of 31 sesame accessions derived from NJ analysis based on 218 SSR markers. Bootstrap values >50 are shown.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 5.\n Dendrogram of 23 sesame varieties based on 20 high polymorphism markers. Samples are listed in Table S4.\n \n Click here to enlarge figure\n \n " + }, + { + "htm": "d7ea878e001ad40456f7694b4deebbaf" + }, + { + "molecules-19-05150-g001-1024.png": "a3c4dc0eb2508db7a66a9eacb4fb387c" + }, + { + "molecules-19-05150-g002-1024.png": "94703bfe8b0b62cf8548e84f0298dd32" + }, + { + "molecules-19-05150-g003-1024.png": "1e4034516b7343ad496f6b7105c512ec" + }, + { + "molecules-19-05150-g004-1024.png": "f8a819eeb997cb72ac2651f6a37c1f78" + }, + { + "molecules-19-05150-g005-1024.png": "62eb6d8e24dd966f32a6124e61a0de69" + }, + { + "pdf": "36fcc2bbb7d479c5542b09f6249cd262" + }, + { + "rendered.html": "fdda905ed712b6c4698bb3a986e7cdb3" + } + ], + "http://www.mdpi.com/1420-3049/19/7/9502": [ + { + "publisher": "Multidisciplinary Digital Publishing Institute" + }, + { + "journal": "Molecules" + }, + { + "title": "Effects of Icariin on Reproductive Functions in Male Rats" + }, + { + "date": "2014-07-03" + }, + { + "doi": "10.3390/molecules19079502" + }, + { + "volume": "19" + }, + { + "issue": "7" + }, + { + "firstpage": "9502" + }, + { + "description": "The present study investigated the effects and potential mechanism(s) of action of icariin on the reproductive functions of male rats. Adult rats were treated orally with icariin at doses of 0 (control), 50, 100, or 200 mg/kg body weight for 35 consecutive days. The results show that icariin had virtually no effect on the body weight or organ coefficients of the testes or epididymides. However, 100 mg/kg icariin significantly increased epididymal sperm counts. In addition, 50 and 100 mg/kg icariin significantly increased testosterone levels. Real-time PCR suggests icariin may be involved in testosterone production via mRNA expression regulation of genes such as peripheral type benzodiazepine receptor (PBR) and steroidogenic acute regulatory protein (StAR). Furthermore, 100 mg/kg icariin treatment also affected follicle stimulating hormone receptor (FSHR) and claudin-11 mRNA expression in Sertoli cells. Superoxide dismutase (SOD) activity and malondialdehyde (MDA) levels were measured in the testes; 50 and 100 mg/kg icariin treatment improved antioxidative capacity, while 200 mg/kg icariin treatment upregulated oxidative stress. These results collectively suggest that icariin within a certain dose range is beneficial to male reproductive functions; meanwhile, higher doses of icariin may damage reproductive functions by increasing oxidative stress in the testes." + }, + { + "abstract": "The present study investigated the effects and potential mechanism(s) of action of icariin on the reproductive functions of male rats. Adult rats were treated orally with icariin at doses of 0 (control), 50, 100, or 200 mg/kg body weight for 35 consecutive days. The results show that icariin had virtually no effect on the body weight or organ coefficients of the testes or epididymides. However, 100 mg/kg icariin significantly increased epididymal sperm counts. In addition, 50 and 100 mg/kg icariin significantly increased testosterone levels. Real-time PCR suggests icariin may be involved in testosterone production via mRNA expression regulation of genes such as peripheral type benzodiazepine receptor (PBR) and steroidogenic acute regulatory protein (StAR). Furthermore, 100 mg/kg icariin treatment also affected follicle stimulating hormone receptor (FSHR) and claudin-11 mRNA expression in Sertoli cells. Superoxide dismutase (SOD) activity and malondialdehyde (MDA) levels were measured in the testes; 50 and 100 mg/kg icariin treatment improved antioxidative capacity, while 200 mg/kg icariin treatment upregulated oxidative stress. These results collectively suggest that icariin within a certain dose range is beneficial to male reproductive functions; meanwhile, higher doses of icariin may damage reproductive functions by increasing oxidative stress in the testes." + }, + { + "fulltext_pdf": "http://www.mdpi.com/1420-3049/19/7/9502/pdf" + }, + { + "pdf": "04bad9a75a92c8fd28a47c83dfbd9caa" + }, + { + "rendered.html": "60852209eac7ffc82080199f27415ea3" + } + ], + "http://www.mdpi.com/1420-3049/12/3/290": [ + { + "publisher": "Molecular Diversity Preservation International" + }, + { + "journal": "Molecules" + }, + { + "title": "Modelingof Acetylene Pyrolysis under Steel Vacuum Carburizing Conditions in a Tubular Flow Reactor" + }, + { + "date": "2007-03-02" + }, + { + "doi": "10.3390/12030290" + }, + { + "volume": "12" + }, + { + "issue": "3" + }, + { + "firstpage": "290" + }, + { + "description": "In the present work, the pyrolysis of acetylene was studied under steel vacuumcarburizing conditions in a tubular flow reactor. The pyrolysis temperature ranged from650 °C to 1050 °C. The partial pressure of acetylene in the feed mixture was 10 and 20mbar, respectively, while the rest of the mixture consisted of nitrogen. The total pressureof the mixture was 1.6 bar. A kinetic mechanism which consists of seven species andnine reactions has been used in the commercial computational fluid dynamics (CFD)software Fluent. The species transport and reaction model of Fluent was used in thesimulations. A comparison of simulated and experimental results is presented in thispaper." + }, + { + "abstract": "In the present work, the pyrolysis of acetylene was studied under steel vacuumcarburizing conditions in a tubular flow reactor. The pyrolysis temperature ranged from650 °C to 1050 °C. The partial pressure of acetylene in the feed mixture was 10 and 20mbar, respectively, while the rest of the mixture consisted of nitrogen. The total pressureof the mixture was 1.6 bar. A kinetic mechanism which consists of seven species andnine reactions has been used in the commercial computational fluid dynamics (CFD)software Fluent. The species transport and reaction model of Fluent was used in thesimulations. A comparison of simulated and experimental results is presented in thispaper." + }, + { + "fulltext_pdf": "http://www.mdpi.com/1420-3049/12/3/290/pdf" + }, + { + "pdf": "f81f429b42f2cd8a752b50892d713ca0" + }, + { + "rendered.html": "b70fc9a13bf29ff7d6b97323f56bfded" + } + ], + "http://www.mdpi.com/2077-0472/4/2/199/htm": [ + { + "publisher": "Multidisciplinary Digital Publishing Institute" + }, + { + "journal": "Agriculture" + }, + { + "title": "Rapid Development of Microsatellite Markers for Plantago ovata Forsk.: Using Next Generation Sequencing and Their Cross-Species Transferability" + }, + { + "date": "2014-06-20" + }, + { + "doi": "10.3390/agriculture4020199" + }, + { + "volume": "4" + }, + { + "issue": "2" + }, + { + "firstpage": "199" + }, + { + "description": "Isabgol (Plantago ovata Forsk.) is an important medicinal plant having high pharmacological activity in its seed husk, which is substantially used in the food, beverages and packaging industries. Nevertheless, isabgol lags behind in research, particularly for genomic resources, like molecular markers, genetic maps, etc. Presently, molecular markers can be easily developed through next generation sequencing technologies, more efficiently, cost effectively and in less time than ever before. This study was framed keeping in view the need to develop molecular markers for this economically important crop by employing a microsatellite enrichment protocol using a next generation sequencing platform (ion torrent PGM™) to obtain simple sequence repeats (SSRs) for Plantago ovata for the very first time. A total of 3447 contigs were assembled, which contained 249 SSRs. Thirty seven loci were randomly selected for primer development; of which, 30 loci were successfully amplified. The developed microsatellite markers showed the amplification of the expected size and cross-amplification in another six species of Plantago. The SSR markers were unable to show polymorphism within P. ovata, suggesting that low variability exists within genotypes of P. ovata. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing SSR markers for non-model species, and the markers so-observed could be useful in the molecular breeding of P. ovata." + }, + { + "abstract": "Isabgol (Plantago ovata Forsk.) is an important medicinal plant having high pharmacological activity in its seed husk, which is substantially used in the food, beverages and packaging industries. Nevertheless, isabgol lags behind in research, particularly for genomic resources, like molecular markers, genetic maps, etc. Presently, molecular markers can be easily developed through next generation sequencing technologies, more efficiently, cost effectively and in less time than ever before. This study was framed keeping in view the need to develop molecular markers for this economically important crop by employing a microsatellite enrichment protocol using a next generation sequencing platform (ion torrent PGM™) to obtain simple sequence repeats (SSRs) for Plantago ovata for the very first time. A total of 3447 contigs were assembled, which contained 249 SSRs. Thirty seven loci were randomly selected for primer development; of which, 30 loci were successfully amplified. The developed microsatellite markers showed the amplification of the expected size and cross-amplification in another six species of Plantago. The SSR markers were unable to show polymorphism within P. ovata, suggesting that low variability exists within genotypes of P. ovata. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing SSR markers for non-model species, and the markers so-observed could be useful in the molecular breeding of P. ovata." + }, + { + "fulltext_html": "http://www.mdpi.com/2077-0472/4/2/199/htm" + }, + { + "fulltext_pdf": "http://www.mdpi.com/2077-0472/4/2/199/pdf" + }, + { + "figure": "/agriculture/agriculture-04-00199/article_deploy/html/images/agriculture-04-00199-g001-1024.png" + }, + { + "figure": "/agriculture/agriculture-04-00199/article_deploy/html/images/agriculture-04-00199-g002-1024.png" + }, + { + "figure": "/agriculture/agriculture-04-00199/article_deploy/html/images/agriculture-04-00199-g003-1024.png" + }, + { + "figure_caption": "\n Figure 1.\n Frequency distribution of microsatellites in P. ovata based on the di-repeat and tri-repeat motif sequence types.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 2.\n Agarose gel image showing amplification patterns of SSR markers, APOM 23 and APOM 25, among six genotypes of P. ovata and allied species. M, 100 bp plus ladder (Thermo Scientific); 1, GI-3; 2: GI-2; 3, RI-89; 4, DPO13; 5, DPO13; 6, EC124345; 7, Plantago arneria; 8, Plantago coronopus; 9, Plantago psyllium; 10, Plantago indica; 11, Plantago serraria, 12, Plantago lanceolata.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 3.\n Dendrogram based on UPGMA clustering of 12 genotypes of isabgol using SSR markers.\n \n Click here to enlarge figure\n \n " + }, + { + "agriculture-04-00199-g001-1024.png": "7be1acb663571046fae8d49eeda6eeba" + }, + { + "agriculture-04-00199-g002-1024.png": "3dee15bacd3d66f75d41d167cd833e85" + }, + { + "agriculture-04-00199-g003-1024.png": "3979c2a3fc22c8f8a04a4bd15ae55e05" + }, + { + "htm": "a37d92f2487441423d11442febf28340" + }, + { + "pdf": "3764be3556ed014d2221707bc860dba9" + }, + { + "rendered.html": "291bc3047833e742f02748be1f987622" + } + ], + "http://www.mdpi.com/1999-4893/7/3/363": [ + { + "publisher": "Multidisciplinary Digital Publishing Institute" + }, + { + "journal": "Algorithms" + }, + { + "title": "Pressure Model of Control Valve Based on LS-SVM with the Fruit Fly Algorithm" + }, + { + "date": "2014-07-11" + }, + { + "doi": "10.3390/a7030363" + }, + { + "volume": "7" + }, + { + "issue": "3" + }, + { + "firstpage": "363" + }, + { + "description": "Control valve is a kind of essential terminal control component which is hard to model by traditional methodologies because of its complexity and nonlinearity. This paper proposes a new modeling method for the upstream pressure of control valve using the least squares support vector machine (LS-SVM), which has been successfully used to identify nonlinear system. In order to improve the modeling performance, the fruit fly optimization algorithm (FOA) is used to optimize two critical parameters of LS-SVM. As an example, a set of actual production data from a controlling system of chlorine in a salt chemistry industry is applied. The validity of LS-SVM modeling method using FOA is verified by comparing the predicted results with the actual data with a value of MSE 2.474 × 10−3. Moreover, it is demonstrated that the initial position of FOA does not affect its optimal ability. By comparison, simulation experiments based on PSO algorithm and the grid search method are also carried out. The results show that LS-SVM based on FOA has equal performance in prediction accuracy. However, from the respect of calculation time, FOA has a significant advantage and is more suitable for the online prediction." + }, + { + "abstract": "Control valve is a kind of essential terminal control component which is hard to model by traditional methodologies because of its complexity and nonlinearity. This paper proposes a new modeling method for the upstream pressure of control valve using the least squares support vector machine (LS-SVM), which has been successfully used to identify nonlinear system. In order to improve the modeling performance, the fruit fly optimization algorithm (FOA) is used to optimize two critical parameters of LS-SVM. As an example, a set of actual production data from a controlling system of chlorine in a salt chemistry industry is applied. The validity of LS-SVM modeling method using FOA is verified by comparing the predicted results with the actual data with a value of MSE 2.474 × 10−3. Moreover, it is demonstrated that the initial position of FOA does not affect its optimal ability. By comparison, simulation experiments based on PSO algorithm and the grid search method are also carried out. The results show that LS-SVM based on FOA has equal performance in prediction accuracy. However, from the respect of calculation time, FOA has a significant advantage and is more suitable for the online prediction." + }, + { + "fulltext_pdf": "http://www.mdpi.com/1999-4893/7/3/363/pdf" + }, + { + "pdf": "78405ce3aa4ccb7de4eb283663b06101" + }, + { + "rendered.html": "51f396a8c4f582f22277a8d7be7579c5" + } + ], + "http://www.mdpi.com/2076-3425/2/3/347/htm": [ + { + "publisher": "Molecular Diversity Preservation International" + }, + { + "journal": "Brain Sciences" + }, + { + "title": "Internet and Gaming Addiction: A Systematic Literature Review of Neuroimaging Studies" + }, + { + "date": "2012-09-05" + }, + { + "doi": "10.3390/brainsci2030347" + }, + { + "volume": "2" + }, + { + "issue": "3" + }, + { + "firstpage": "347" + }, + { + "description": "In the past decade, research has accumulated suggesting that excessive Internet use can lead to the development of a behavioral addiction. Internet addiction has been considered as a serious threat to mental health and the excessive use of the Internet has been linked to a variety of negative psychosocial consequences. The aim of this review is to identify all empirical studies to date that used neuroimaging techniques to shed light upon the emerging mental health problem of Internet and gaming addiction from a neuroscientific perspective. Neuroimaging studies offer an advantage over traditional survey and behavioral research because with this method, it is possible to distinguish particular brain areas that are involved in the development and maintenance of addiction. A systematic literature search was conducted, identifying 18 studies. These studies provide compelling evidence for the similarities between different types of addictions, notably substance-related addictions and Internet and gaming addiction, on a variety of levels. On the molecular level, Internet addiction is characterized by an overall reward deficiency that entails decreased dopaminergic activity. On the level of neural circuitry, Internet and gaming addiction led to neuroadaptation and structural changes that occur as a consequence of prolonged increased activity in brain areas associated with addiction. On a behavioral level, Internet and gaming addicts appear to be constricted with regards to their cognitive functioning in various domains. The paper shows that understanding the neuronal correlates associated with the development of Internet and gaming addiction will promote future research and will pave the way for the development of addiction treatment approaches." + }, + { + "abstract": "In the past decade, research has accumulated suggesting that excessive Internet use can lead to the development of a behavioral addiction. Internet addiction has been considered as a serious threat to mental health and the excessive use of the Internet has been linked to a variety of negative psychosocial consequences. The aim of this review is to identify all empirical studies to date that used neuroimaging techniques to shed light upon the emerging mental health problem of Internet and gaming addiction from a neuroscientific perspective. Neuroimaging studies offer an advantage over traditional survey and behavioral research because with this method, it is possible to distinguish particular brain areas that are involved in the development and maintenance of addiction. A systematic literature search was conducted, identifying 18 studies. These studies provide compelling evidence for the similarities between different types of addictions, notably substance-related addictions and Internet and gaming addiction, on a variety of levels. On the molecular level, Internet addiction is characterized by an overall reward deficiency that entails decreased dopaminergic activity. On the level of neural circuitry, Internet and gaming addiction led to neuroadaptation and structural changes that occur as a consequence of prolonged increased activity in brain areas associated with addiction. On a behavioral level, Internet and gaming addicts appear to be constricted with regards to their cognitive functioning in various domains. The paper shows that understanding the neuronal correlates associated with the development of Internet and gaming addiction will promote future research and will pave the way for the development of addiction treatment approaches." + }, + { + "fulltext_html": "http://www.mdpi.com/2076-3425/2/3/347/htm" + }, + { + "fulltext_pdf": "http://www.mdpi.com/2076-3425/2/3/347/pdf" + }, + { + "htm": "a829954ab83878099d0b3e7d23c0eab4" + }, + { + "pdf": "f26da200c65aee82debda1b3f00dfb45" + }, + { + "rendered.html": "022bd9be411f343674d8382633657a08" + } + ], + "http://www.mdpi.com/2073-431X/2/4/152/htm": [ + { + "publisher": "Multidisciplinary Digital Publishing Institute" + }, + { + "journal": "Computers" + }, + { + "title": "Static Three-Dimensional Fuzzy Routing Based on the Receiving Probability in Wireless Sensor Networks" + }, + { + "date": "2013-11-12" + }, + { + "doi": "10.3390/computers2040152" + }, + { + "volume": "2" + }, + { + "issue": "4" + }, + { + "firstpage": "152" + }, + { + "description": "A Wireless Sensor Network (WSN) is a collection of low-cost, low-power and large-scale wireless sensor nodes. Routing protocols are an important topic in WSN. Every sensor node should use a proper mechanism to transmit the generated packets to its destination, usually a base station. In previous works, routing protocols use the global information of the network that causes the redundant packets to be increased. Moreover, it leads to an increase in the network traffic, to a decrease in the delivery ratio of data packets, and to a reduction in network life. In this paper, we propose a new inferential routing protocol called SFRRP (Static Three-Dimensional Fuzzy Routing based on the Receiving Probability). The proposed protocol solves the above mentioned problems considerably. The data packets are transmitted by hop-to-hop delivery to the base station. It uses a fuzzy procedure to transmit the sensed data or the buffered data packets to one of the neighbors called selected node. In the proposed fuzzy system, the distance and number of neighbors are input variables, while the receiving probability is the output variable. SFRRP just uses the local neighborhood information to forward the packets and is not needed by any redundant packet for route discovery. The proposed protocol has some advantages such as a high delivery ratio, less delay time, high network life, and less network traffic. The performance of the proposed protocol surpasses the performance of the Flooding routing protocol in terms of delivery ratio, delay time and network lifetime." + }, + { + "abstract": "A Wireless Sensor Network (WSN) is a collection of low-cost, low-power and large-scale wireless sensor nodes. Routing protocols are an important topic in WSN. Every sensor node should use a proper mechanism to transmit the generated packets to its destination, usually a base station. In previous works, routing protocols use the global information of the network that causes the redundant packets to be increased. Moreover, it leads to an increase in the network traffic, to a decrease in the delivery ratio of data packets, and to a reduction in network life. In this paper, we propose a new inferential routing protocol called SFRRP (Static Three-Dimensional Fuzzy Routing based on the Receiving Probability). The proposed protocol solves the above mentioned problems considerably. The data packets are transmitted by hop-to-hop delivery to the base station. It uses a fuzzy procedure to transmit the sensed data or the buffered data packets to one of the neighbors called selected node. In the proposed fuzzy system, the distance and number of neighbors are input variables, while the receiving probability is the output variable. SFRRP just uses the local neighborhood information to forward the packets and is not needed by any redundant packet for route discovery. The proposed protocol has some advantages such as a high delivery ratio, less delay time, high network life, and less network traffic. The performance of the proposed protocol surpasses the performance of the Flooding routing protocol in terms of delivery ratio, delay time and network lifetime." + }, + { + "fulltext_html": "http://www.mdpi.com/2073-431X/2/4/152/htm" + }, + { + "fulltext_pdf": "http://www.mdpi.com/2073-431X/2/4/152/pdf" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g001-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g002-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g003-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g004-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g005-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g006-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g007-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g008-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g009-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g010-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g011-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g012-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g013-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g014-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g015-1024.png" + }, + { + "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g016-1024.png" + }, + { + "figure_caption": "\n Figure 1.\n The fuzzy value for a room temperature.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 2.\n A fuzzy logic system.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 3.\n A network model to route the data packets by Static Three-Dimensional Fuzzy Routing Based on the Receiving Probability (SFRRP) in a typical Wireless Sensor Network (WSN).\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 4.\n Memberships of the input variable distance.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 5.\n Memberships of the input variable number of neighbors.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 6.\n Memberships of the output variable receiving probability.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 7.\n Schematic of the fuzzy rules, (a) rules based on receiving probability and distance; and (b) rules based on receiving probability and number of neighbors.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 8.\n Scheme of the SFRRP functionality to choose the selected node.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 9.\n Work flow of SFRRP.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 10.\n Impact of data generation rate, (a) average delivery rate; (b) average delay; and (c) network life.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 11.\n Impact of buffer size, (a) average delivery rate; (b) average delay; and (c) network life.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 12.\n Impact of node initial energy, (a) average delivery rate; (b) average delay; and (c) network life.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 13.\n Total energy consumption of the nodes.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 14.\n The residual energy of the nodes in the proposed protocol.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 15.\n Number of live nodes.\n \n Click here to enlarge figure\n \n " + }, + { + "figure_caption": "\n Figure 16.\n Percent of filled node buffer.\n \n Click here to enlarge figure\n \n " + }, + { + "computers-02-00152-g001-1024.png": "2ae71a48f49dee23127205d8c52628e7" + }, + { + "computers-02-00152-g002-1024.png": "ef45f1466a733db20859a2d81d8adbbe" + }, + { + "computers-02-00152-g003-1024.png": "e5814b3183dde01975554174095387c9" + }, + { + "computers-02-00152-g004-1024.png": "14aade47890186768c9fa855a00cb7a6" + }, + { + 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"54430cf36f2d6fae616220f268b3ee9b" + }, + { + "pdf": "639d60f2edf4a21b5eb4760f08c2ef18" + }, + { + "rendered.html": "f9960490e62f4f4afbee7e9f5ae61688" + } + ] +} \ No newline at end of file diff --git a/test/mdpi_test_urls.txt b/test/mdpi_test_urls.txt new file mode 100644 index 0000000..e5e86d4 --- /dev/null +++ b/test/mdpi_test_urls.txt @@ -0,0 +1,7 @@ +http://www.mdpi.com/1420-3049/19/4/5150/htm +http://www.mdpi.com/1420-3049/19/7/9502 +http://www.mdpi.com/1420-3049/12/3/290 +http://www.mdpi.com/2077-0472/4/2/199/htm +http://www.mdpi.com/1999-4893/7/3/363 +http://www.mdpi.com/2076-3425/2/3/347/htm +http://www.mdpi.com/2073-431X/2/4/152/htm From 4f239fabc4bfc0e8af6a432b890b627075c4b281 Mon Sep 17 00:00:00 2001 From: CristianCantoro Date: Wed, 16 Jul 2014 16:03:39 +0200 Subject: [PATCH 054/154] Extract abstract from PLOS pages --- scrapers/plos.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/scrapers/plos.json b/scrapers/plos.json index 4d00b50..f169b96 100644 --- a/scrapers/plos.json +++ b/scrapers/plos.json @@ -42,6 +42,10 @@ "description": { "selector": "//meta[@name='description']", "attribute": "content" + }, + "abstract":{ + "selector": "//div[contains(@class, 'abstract')]", + "attribute": "text" } } } \ No newline at end of file From f64dd8dc9b5d8675e7a7399fe2c879156cf1f300 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Thu, 17 Jul 2014 11:03:53 +0200 Subject: [PATCH 055/154] add renaming to all scrapers --- scrapers/generic_open.json | 10 +++++++--- scrapers/mdpi.json | 8 ++++++-- scrapers/peerj.json | 8 ++++++-- scrapers/plos.json | 10 +++++++--- 4 files changed, 26 insertions(+), 10 deletions(-) diff --git a/scrapers/generic_open.json b/scrapers/generic_open.json index 711f945..b11d433 100644 --- a/scrapers/generic_open.json +++ b/scrapers/generic_open.json @@ -4,12 +4,16 @@ "fulltext_pdf": { "selector": "//meta[@name='citation_pdf_url']", "attribute": "content", - "download": true + "download": { + "rename": "fulltext.pdf" + } }, "fulltext_html": { "selector": "//meta[@name='citation_fulltext_html_url']", "attribute": "content", - "download": true + "download": { + "rename": "fulltext.html" + } }, "title": { "selector": "//meta[@name='citation_title']", @@ -44,4 +48,4 @@ "attribute": "content" } } -} \ No newline at end of file +} diff --git a/scrapers/mdpi.json b/scrapers/mdpi.json index 724afac..db6d783 100644 --- a/scrapers/mdpi.json +++ b/scrapers/mdpi.json @@ -48,12 +48,16 @@ "fulltext_html": { "selector": "//meta[@name='citation_fulltext_html_url']", "attribute": "content", - "download": true + "download": { + "rename": "fulltext.html" + } }, "fulltext_pdf": { "selector": "//meta[@name='citation_pdf_url']", "attribute": "content", - "download": true + "download": { + "rename": "fulltext.pdf" + } }, "supplementary_material": { "selector": "//a[contains(concat(' ', normalize-space(@class), ' '), ' article-supporting-download ')]", diff --git a/scrapers/peerj.json b/scrapers/peerj.json index 6e53777..7a3333d 100644 --- a/scrapers/peerj.json +++ b/scrapers/peerj.json @@ -48,12 +48,16 @@ "fulltext_html": { "selector": "//meta[@name='citation_fulltext_html_url']", "attribute": "content", - "download": true + "download": { + "rename": "fulltext.html" + } }, "fulltext_pdf": { "selector": "//meta[@name='citation_pdf_url']", "attribute": "content", - "download": true + "download": { + "rename": "fulltext.pdf" + } }, "supplementary_material": { "selector": "//a[contains(concat(' ', normalize-space(@class), ' '), ' article-supporting-download ')]", diff --git a/scrapers/plos.json b/scrapers/plos.json index 4d00b50..ebdce33 100644 --- a/scrapers/plos.json +++ b/scrapers/plos.json @@ -4,12 +4,16 @@ "fulltext_pdf": { "selector": "//meta[@name='citation_pdf_url']", "attribute": "content", - "download": true + "download": { + "rename": "fulltext.pdf" + } }, "fulltext_html": { "selector": "//meta[@name='citation_fulltext_html_url']", "attribute": "content", - "download": true + "download": { + "rename": "fulltext.html" + } }, "title": { "selector": "//meta[@name='citation_title']", @@ -44,4 +48,4 @@ "attribute": "content" } } -} \ No newline at end of file +} From cec7cf356f2a19621090a90ef83a58c315b58d96 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Thu, 17 Jul 2014 11:04:16 +0200 Subject: [PATCH 056/154] make test line counting more accurate --- test/test_all.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) mode change 100644 => 100755 test/test_all.rb diff --git a/test/test_all.rb b/test/test_all.rb old mode 100644 new mode 100755 index 5e8ebd4..09b921f --- a/test/test_all.rb +++ b/test/test_all.rb @@ -22,7 +22,7 @@ def coverage(scraperjsonpath, results) lines.each do |line| valid = true elements.each do |element| - if line =~ /"#{element}":/ + if line =~ /"#{element}": \{/ # calculate coverage for this line if results.detect { |result| result.key? element } coverage << 1 From dd8f6e025ab87d5faa618a2d11bd7df6312f143b Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Thu, 17 Jul 2014 17:26:20 +0200 Subject: [PATCH 057/154] update PLOS with fulltext xml and new tests --- scrapers/peerj.json | 7 +++++ test/plos.json | 73 +++++++++++++++++++++++++++++---------------- 2 files changed, 54 insertions(+), 26 deletions(-) diff --git a/scrapers/peerj.json b/scrapers/peerj.json index 7a3333d..af35d02 100644 --- a/scrapers/peerj.json +++ b/scrapers/peerj.json @@ -59,6 +59,13 @@ "rename": "fulltext.pdf" } }, + "fulltext_xml": { + "selector": "//a[@title='Download article XML']", + "attribute": "href", + "download": { + "rename": "fulltext.xml" + } + }, "supplementary_material": { "selector": "//a[contains(concat(' ', normalize-space(@class), ' '), ' article-supporting-download ')]", "attribute": "href", diff --git a/test/plos.json b/test/plos.json index 5af0d7c..f6337e5 100644 --- a/test/plos.json +++ b/test/plos.json @@ -78,11 +78,17 @@ { "description": "PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines." }, + { + "abstract": "AbstractMechanisms behind how the immune system signals to the brain in response to systemic inflammation are not fully understood. Transgenic mice expressing Cre recombinase specifically in the hematopoietic lineage in a Cre reporter background display recombination and marker gene expression in Purkinje neurons. Here we show that reportergene expression in neurons is caused by intercellular transfer of functional Cre recombinase messenger RNA from immune cells into neurons in the absence of cell fusion. In vitro purified secreted extracellular vesicles (EVs) from blood cells contain Cre mRNA, which induces recombination in neurons when injected into the brain. Although Cre-mediated recombination events in the brain occur very rarely in healthy animals, their number increases considerably in different injury models, particularly under inflammatory conditions, and extend beyond Purkinje neurons to other neuronal populations in cortex, hippocampus, and substantia nigra. Recombined Purkinje neurons differ in their miRNA profile from their nonrecombined counterparts, indicating physiological significance. These observations reveal the existence of a previously unrecognized mechanism to communicate RNA-based signals between the hematopoietic system and various organs, including the brain, in response to inflammation.\n" + }, + { + "abstract": "\nAuthor Summary\nPeripheral infections leading to an inflammatory response can initiate signaling from the hematopoietic system to various organs including the brain. The traditional view of this communication between blood and brain is that individual factors are released by immune cells that in turn bind to neuronal or nonneuronal target cells in the brain where they exert their effects. By using a genetic tracing system, we now show that extracellular vesicles, small membrane structures that can contain a multitude of different molecules, can transfer functional RNA directly from blood cells to neurons. Although this type of signaling is highly restricted in the healthy animal, inflammatory injuries increase both the frequency of transfer and the range of the neuronal target populations in the brain. By showing altered miRNA profiles in neurons receiving extracellular vesicle cargo, we predict a complex regulation of gene expression in neural cells in response to peripheral inflammation.\n" + }, { "journal.pbio.1001874.pdf": "c730b7b2434f950ea409d74a78c30316" }, { - "rendered.html": "572e489fbe4397ba32e3820a738dba98" + "rendered.html": "264e78eb7494e3c8cffe3da98b88806b" } ], "http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001882": [ @@ -113,11 +119,14 @@ { "description": "PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines." }, + { + "abstract": "AbstractHow structure relates to function—across spatial scales, from the single molecule to the whole organism—is a central theme in biology. Bioengineers, however, wrestle with the converse question: will function follow form? That is, we struggle to approximate the architecture of living tissues experimentally, hoping that the structure we create will lead to the function we desire. A new means to explore the relationship between form and function in living tissue has arrived with three-dimensional printing, but the technology is not without limitations.\n" + }, { "journal.pbio.1001882.pdf": "b1a6bb4e193cb39cc6aef1b1866dcb3b" }, { - "rendered.html": "3c9615f49fa85dd19c92d1cb5987be1c" + "rendered.html": "3842a2f207852e476a6c31c7baeed87b" } ], "http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004441": [ @@ -163,11 +172,17 @@ { "description": "PLOS Genetics is an open-access" }, + { + "abstract": "AbstractThe integrative and conjugative element ICEclc is a mobile genetic element in Pseudomonas knackmussii B13, and an experimental model for a widely distributed group of elements in Proteobacteria. ICEclc is transferred from specialized transfer competent cells, which arise at a frequency of 3-5% in a population at stationary phase. Very little is known about the different factors that control the transfer frequency of this ICE family. Here we report the discovery of a three-gene operon encoded by ICEclc, which exerts global control on transfer initiation. The operon consists of three consecutive regulatory genes, encoding a TetR-type repressor MfsR, a MarR-type regulator and a LysR-type activator TciR. We show that MfsR autoregulates expression of the operon, whereas TciR is a global activator of ICEclc gene expression, but no clear role was yet found for MarR. Deletion of mfsR increases expression of tciR and marR, causing the proportion of transfer competent cells to reach almost 100% and transfer frequencies to approach 1 per donor. mfsR deletion also caused a two orders of magnitude loss in population viability, individual cell growth arrest and loss of ICEclc. This indicates that autoregulation is an important feature maintaining ICE transfer but avoiding fitness loss. Bioinformatic analysis showed that the mfsR-marR-tciR operon is unique for ICEclc and a few highly related ICE, whereas tciR orthologues occur more widely in a large variety of suspected ICE among Proteobacteria.\n" + }, + { + "abstract": "\nAuthor Summary\nIntegrative and conjugative elements (ICEs) are a relatively newly recognized class of mobile elements in bacteria, which integrate at one or more positions in a host chromosome, can be excised, circularized, and transfer by conjugation to a new recipient cell. Genome sequencing indicated that ICEs often carry genes with potential adaptive functions for the host. Various ICE-types have been described and ICEclc is a useful model for a wide class of elements found in Beta- and Gammaproteobacteria. Because ICEs normally remain “silent” in the host chromosome and often lack selectable markers, their lifestyle is difficult to study. One of the characteristics of ICEclc is that transfer is initiated in only 3-5% of donor cells in a population during stationary phase. Here, we describe an operon of three regulatory genes, two of which control the transfer initiation of ICEclc. Our findings suggest that the low transfer rate results from the repression of an activator and that this is essential to minimize the deleterious effect of hyper-activation of transfer initiation. While the individual regulatory genes are quite common on ICEs, they rarely occur in this configuration.\n" + }, { "journal.pgen.1004441.pdf": "037d0a292bcca909943daf27a1e51f77" }, { - "rendered.html": "7723036de0bd17afaa3be1f649f10e12" + "rendered.html": "7f62500dce027f9e941b755ba2b8eef3" } ], "http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004433": [ @@ -214,10 +229,16 @@ "description": "PLOS Genetics is an open-access" }, { - "rendered.html": "7b4572e01def8bb477debc2a5d406a91" + "abstract": "AbstractThe bacterial cell wall, which is comprised of a mesh of polysaccharide strands crosslinked via peptide bridges (peptidoglycan, PG), is critical for maintenance of cell shape and survival. PG assembly is mediated by a variety of Penicillin Binding Proteins (PBP) whose fundamental activities have been characterized in great detail; however, there is limited knowledge of the factors that modulate their activities in different environments or growth phases. In Vibrio cholerae, the cause of cholera, PG synthesis during the transition into stationary phase is primarily mediated by the bifunctional enzyme PBP1A. Here, we screened an ordered V. cholerae transposon library for mutants that are sensitive to growth inhibition by non-canonical D-amino acids (DAA), which prevent growth and maintenance of cell shape in PBP1A-deficient V. cholerae. In addition to PBP1A and its lipoprotein activator LpoA, we found that CsiV, a small periplasmic protein with no previously described function, is essential for growth in the presence of DAA. Deletion of csiV, like deletion of lpoA or the PBP1A–encoding gene mrcA, causes cells to lose their rod shape in the presence of DAA or the beta-lactam antibiotic cefsulodin, and all three mutations are synthetically lethal with deletion of mrcB, which encodes PBP1B, V. cholerae's second key bifunctional PBP. CsiV interacts with LpoA and PG but apparently not with PBP1A, supporting the hypothesis that CsiV promotes LpoA's role as an activator of PBP1A, and thereby modulates V. cholerae PG biogenesis. Finally, the requirement for CsiV in PBP1A-mediated growth of V. cholerae can be overcome either by augmenting PG synthesis or by reducing PG degradation, thereby highlighting the importance of balancing these two processes for bacterial survival.\n" + }, + { + "abstract": "\nAuthor Summary\nBacteria surround themselves with a mesh-like peptidoglycan (PG) cell wall, which is essential for maintenance of cell shape and survival. While the enzymes that catalyze the assembly of the cell wall (aka penicillin-binding proteins (PBPs)) have been extensively characterized, our understanding of the factors that modulate the activities of these enzymes is less developed. Here, using a genetic screen, we identified a gene of unknown function that plays a crucial role in PBP1A-mediated cell wall synthesis in Vibrio cholerae, the bacterium causing cholera. V. cholerae mutants lacking this gene, whose protein product was re-named CsiV (for Cell shape integrity Vibrio), share many phenotypes with PBP1A mutants, including becoming spherical during stationary phase. We show that CsiV interacts with LpoA, a lipoprotein activator of PBP1A, as well as with PG. CsiV, LpoA, or PBP1A are all required for survival of V. cholerae lacking PBP1B, and mutants lacking any of these factors show marked changes in PG content in stationary phase. Collectively, our data suggest that CsiV acts through LpoA to promote PG biogenesis in V. cholerae and other vibrio species as well as in the other genera where this protein is found.\n" }, { "journal.pgen.1004433.pdf": "890d664254554ae5142d7a8e0d10633e" + }, + { + "rendered.html": "1f0c36ede91377b79f56d7c81ced323f" } ], "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0098781": [ @@ -254,70 +275,70 @@ { "description": "PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world." }, + { + "abstract": "AbstractHere we describe an ultra-low-cost origami-based approach for large-scale manufacturing of microscopes, specifically demonstrating brightfield, darkfield, and fluorescence microscopes. Merging principles of optical design with origami enables high-volume fabrication of microscopes from 2D media. Flexure mechanisms created via folding enable a flat compact design. Structural loops in folded paper provide kinematic constraints as a means for passive self-alignment. This light, rugged instrument can survive harsh field conditions while providing a diversity of imaging capabilities, thus serving wide-ranging applications for cost-effective, portable microscopes in science and education.\n" + }, { "journal.pone.0098781.pdf": "5dfa35bcba2f631b40673c498c62f64b" }, { - "rendered.html": "6ecb886b6ca79c5436a1c13ed66bf95e" + "rendered.html": "7f91873f6353563e6ed11951ff5530c2" } ], "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099348": [ { - "fulltext_pdf": "http://dx.plos.org/10.1371/journal.pone.0099348.pdf" + "fulltext_pdf": "https://peerj.com/articles/384.pdf" }, { - "title": "Co-Infection of Blacklegged Ticks with Babesia microti and Borrelia burgdorferi Is Higher than Expected and Acquired from Small Mammal Hosts" + "fulltext_html": "https://peerj.com/articles/384" }, { - "author": "Michelle H. Hersh" + "title": "Mutation analysis of the SLC26A4, FOXI1 and KCNJ10 genes in individuals with congenital hearing loss" }, { - "author": "Richard S. Ostfeld" + "author": "Lynn M. Pique" }, { - "author": "Diana J. McHenry" + "author": "Marie-Luise Brennan" }, { - "author": "Michael Tibbetts" + "author": "Colin J. Davidson" }, { - "author": "Jesse L. Brunner" + "author": "Frederick Schaefer" }, { - "author": "Mary E. Killilea" + "author": "John Greinwald Jr" }, { - "author": "Kathleen LoGiudice" + "author": "Iris Schrijver" }, { - "author": "Kenneth A. Schmidt" + "date": "2014-05-08" }, { - "author": "Felicia Keesing" + "doi": "10.7717/peerj.384" }, { - "date": "2014/6/18" + "volume": "2" }, { - "doi": "10.1371/journal.pone.0099348" + "firstpage": "e384" }, { - "volume": "9" + "description": "Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype." }, { - "issue": "6" + "abstract": "Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype." }, { - "firstpage": "e99348" - }, - { - "description": "PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world." + "384": "72292ac92c4e073b47f2c50fb54dda67" }, { - "rendered.html": "1c315b137486fd9350c63c1193eb672b" + "384.pdf": "b2020a8f8037228e6face4a220751932" }, { - "journal.pone.0099348.pdf": "71ff4b0cd5933789dbb0a38d756c6193" + "rendered.html": "8ef2fb18332a90a7fbbe6d533affb0ac" } ] } \ No newline at end of file From f50850ea9111776d176c1eca0a4165989806d9ad Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Thu, 17 Jul 2014 17:30:55 +0200 Subject: [PATCH 058/154] add fulltext_xml to MDPI --- scrapers/mdpi.json | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/scrapers/mdpi.json b/scrapers/mdpi.json index db6d783..d6bb9a1 100644 --- a/scrapers/mdpi.json +++ b/scrapers/mdpi.json @@ -59,6 +59,13 @@ "rename": "fulltext.pdf" } }, + "fulltext_xml": { + "selector": "//meta[@name='fulltest_xml']", + "attribute": "content", + "download": { + "rename": "fulltext.pdf" + } + }, "supplementary_material": { "selector": "//a[contains(concat(' ', normalize-space(@class), ' '), ' article-supporting-download ')]", "attribute": "href", From edb76356b4169231979c65a2794d8f5b9914b358 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Thu, 17 Jul 2014 17:36:14 +0200 Subject: [PATCH 059/154] add fulltext xml to compatible scrapers --- scrapers/mdpi.json | 2 +- scrapers/peerj.json | 2 +- scrapers/plos.json | 7 +++++++ 3 files changed, 9 insertions(+), 2 deletions(-) diff --git a/scrapers/mdpi.json b/scrapers/mdpi.json index d6bb9a1..436cdf5 100644 --- a/scrapers/mdpi.json +++ b/scrapers/mdpi.json @@ -63,7 +63,7 @@ "selector": "//meta[@name='fulltest_xml']", "attribute": "content", "download": { - "rename": "fulltext.pdf" + "rename": "fulltext.xml" } }, "supplementary_material": { diff --git a/scrapers/peerj.json b/scrapers/peerj.json index af35d02..6d9b3ac 100644 --- a/scrapers/peerj.json +++ b/scrapers/peerj.json @@ -60,7 +60,7 @@ } }, "fulltext_xml": { - "selector": "//a[@title='Download article XML']", + "selector": "//a[@class='article-download-xml']", "attribute": "href", "download": { "rename": "fulltext.xml" diff --git a/scrapers/plos.json b/scrapers/plos.json index 5fecba2..f6bba67 100644 --- a/scrapers/plos.json +++ b/scrapers/plos.json @@ -15,6 +15,13 @@ "rename": "fulltext.html" } }, + "fulltext_xml": { + "selector": "//a[@title='Download article XML']", + "attribute": "href", + "download": { + "rename": "fulltext.xml" + } + }, "title": { "selector": "//meta[@name='citation_title']", "attribute": "content" From 0ecc002bb53a1ef8debec18d622f2f523cb33870 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Thu, 17 Jul 2014 11:54:47 -0400 Subject: [PATCH 060/154] generate tests for MDPI --- test/mdpi.json | 70 +++++++++++++++++++++++++------------------------- 1 file changed, 35 insertions(+), 35 deletions(-) diff --git a/test/mdpi.json b/test/mdpi.json index 6fa4eeb..b4f8307 100644 --- a/test/mdpi.json +++ b/test/mdpi.json @@ -67,25 +67,25 @@ "figure_caption": "\n Figure 5.\n Dendrogram of 23 sesame varieties based on 20 high polymorphism markers. Samples are listed in Table S4.\n \n Click here to enlarge figure\n \n " }, { - "htm": "d7ea878e001ad40456f7694b4deebbaf" + "molecules-19-05150-g004-1024.png": "f8a819eeb997cb72ac2651f6a37c1f78" }, { - "molecules-19-05150-g001-1024.png": "a3c4dc0eb2508db7a66a9eacb4fb387c" + "molecules-19-05150-g005-1024.png": "62eb6d8e24dd966f32a6124e61a0de69" }, { - "molecules-19-05150-g002-1024.png": "94703bfe8b0b62cf8548e84f0298dd32" + "htm": "9c6c990abc3132b88e83d0bd78f7f95b" }, { - "molecules-19-05150-g003-1024.png": "1e4034516b7343ad496f6b7105c512ec" + "molecules-19-05150-g002-1024.png": "94703bfe8b0b62cf8548e84f0298dd32" }, { - "molecules-19-05150-g004-1024.png": "f8a819eeb997cb72ac2651f6a37c1f78" + "pdf": "36fcc2bbb7d479c5542b09f6249cd262" }, { - "molecules-19-05150-g005-1024.png": "62eb6d8e24dd966f32a6124e61a0de69" + "molecules-19-05150-g003-1024.png": "1e4034516b7343ad496f6b7105c512ec" }, { - "pdf": "36fcc2bbb7d479c5542b09f6249cd262" + "molecules-19-05150-g001-1024.png": "a3c4dc0eb2508db7a66a9eacb4fb387c" }, { "rendered.html": "fdda905ed712b6c4698bb3a986e7cdb3" @@ -129,7 +129,7 @@ "pdf": "04bad9a75a92c8fd28a47c83dfbd9caa" }, { - "rendered.html": "60852209eac7ffc82080199f27415ea3" + "rendered.html": "026c9b22b4fa5f6dbe22c31a3435644a" } ], "http://www.mdpi.com/1420-3049/12/3/290": [ @@ -170,7 +170,7 @@ "pdf": "f81f429b42f2cd8a752b50892d713ca0" }, { - "rendered.html": "b70fc9a13bf29ff7d6b97323f56bfded" + "rendered.html": "0a598a2fd773a3873fe0667805a9d2a1" } ], "http://www.mdpi.com/2077-0472/4/2/199/htm": [ @@ -229,14 +229,11 @@ "figure_caption": "\n Figure 3.\n Dendrogram based on UPGMA clustering of 12 genotypes of isabgol using SSR markers.\n \n Click here to enlarge figure\n \n " }, { - "agriculture-04-00199-g001-1024.png": "7be1acb663571046fae8d49eeda6eeba" + "agriculture-04-00199-g003-1024.png": "3979c2a3fc22c8f8a04a4bd15ae55e05" }, { "agriculture-04-00199-g002-1024.png": "3dee15bacd3d66f75d41d167cd833e85" }, - { - 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-469,31 +469,28 @@ "figure_caption": "\n Figure 16.\n Percent of filled node buffer.\n \n Click here to enlarge figure\n \n " }, { - "computers-02-00152-g001-1024.png": "2ae71a48f49dee23127205d8c52628e7" - }, - { - "computers-02-00152-g002-1024.png": "ef45f1466a733db20859a2d81d8adbbe" + "computers-02-00152-g014-1024.png": "5b0efd717600f47404abf05be4a64965" }, { - "computers-02-00152-g003-1024.png": "e5814b3183dde01975554174095387c9" + "computers-02-00152-g012-1024.png": "4c856d5686ffd51727c0dd8e08610f6c" }, { - "computers-02-00152-g004-1024.png": "14aade47890186768c9fa855a00cb7a6" + "computers-02-00152-g016-1024.png": "a2ce86f98e0566497eef554a7629ff77" }, { - "computers-02-00152-g005-1024.png": "7c90363213d7fd98f5e7a20b08a19c80" + "computers-02-00152-g015-1024.png": "7e5a61c578e226758c2c5b3ad7e9689e" }, { - "computers-02-00152-g006-1024.png": "a30a231c7a2976768d0a5fc58f832c3b" + "computers-02-00152-g001-1024.png": "2ae71a48f49dee23127205d8c52628e7" }, { - "computers-02-00152-g007-1024.png": "4caf09516a4b4497b31ada9ee92761ac" + "htm": "f81fd6fb069ea7a2308235b67665fb29" }, { - "computers-02-00152-g008-1024.png": "c3bee75cde33eb4fe72b05a63510fd1a" + "computers-02-00152-g005-1024.png": "7c90363213d7fd98f5e7a20b08a19c80" }, { - "computers-02-00152-g009-1024.png": "8f41e4c7fcb10243ab992d7667f4da2a" + "pdf": "639d60f2edf4a21b5eb4760f08c2ef18" }, { "computers-02-00152-g010-1024.png": "9819440057f17feefe12b8763c3f97f7" @@ -502,28 +499,31 @@ "computers-02-00152-g011-1024.png": "3705c3ea855bb92556bff9587730ec98" }, { - "computers-02-00152-g012-1024.png": "4c856d5686ffd51727c0dd8e08610f6c" + "rendered.html": "c3304d0e156f1219d53a49c6f3bec52f" }, { "computers-02-00152-g013-1024.png": "00bf36ffe2dcb774498fadc260ca8f7e" }, { - "computers-02-00152-g014-1024.png": "5b0efd717600f47404abf05be4a64965" + "computers-02-00152-g006-1024.png": "a30a231c7a2976768d0a5fc58f832c3b" }, { - "computers-02-00152-g015-1024.png": "7e5a61c578e226758c2c5b3ad7e9689e" + "computers-02-00152-g004-1024.png": "14aade47890186768c9fa855a00cb7a6" }, { - "computers-02-00152-g016-1024.png": "a2ce86f98e0566497eef554a7629ff77" + "computers-02-00152-g008-1024.png": "c3bee75cde33eb4fe72b05a63510fd1a" }, { - "htm": "54430cf36f2d6fae616220f268b3ee9b" + "computers-02-00152-g009-1024.png": "8f41e4c7fcb10243ab992d7667f4da2a" }, { - "pdf": "639d60f2edf4a21b5eb4760f08c2ef18" + "computers-02-00152-g003-1024.png": "e5814b3183dde01975554174095387c9" + }, + { + "computers-02-00152-g002-1024.png": "ef45f1466a733db20859a2d81d8adbbe" }, { - "rendered.html": "f9960490e62f4f4afbee7e9f5ae61688" + "computers-02-00152-g007-1024.png": "4caf09516a4b4497b31ada9ee92761ac" } ] } \ No newline at end of file From fac1fdc16fe6a4986adf072e5f4d9a278f6e711b Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Thu, 17 Jul 2014 17:56:15 +0200 Subject: [PATCH 061/154] elife scraper --- scrapers/elife.json | 92 ++++++++++++++++++++++++++++++++++++++++ test/elife_test_urls.txt | 5 +++ 2 files changed, 97 insertions(+) create mode 100644 scrapers/elife.json create mode 100644 test/elife_test_urls.txt diff --git a/scrapers/elife.json b/scrapers/elife.json new file mode 100644 index 0000000..dfa1103 --- /dev/null +++ b/scrapers/elife.json @@ -0,0 +1,92 @@ +{ + "url": "elifesciences\\.org", + "elements": { + "publisher": { + "selector": "//meta[@name='citation_publisher']", + "attribute": "content" + }, + "journal": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" + }, + "title": { + "selector": "//meta[@name='citation_title']", + "attribute": "content" + }, + "authors": { + "selector": "//meta[@name='citation_author']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@name='citation_date']", + "attribute": "content" + }, + "doi": { + "selector": "//meta[@name='citation_doi']", + "attribute": "content" + }, + "volume": { + "selector": "//meta[@name='citation_volume']", + "attribute": "content" + }, + "issue": { + "selector": "//meta[@name='citation_issue']", + "attribute": "content" + }, + "firstpage": { + "selector": "//meta[@name='citation_firstpage']", + "attribute": "content" + }, + "description": { + "selector": "//meta[@name='description']", + "attribute": "content" + }, + "abstract": { + "selector": "//div[contains(class, 'abstract')]//p[1]", + "attribute": "content" + }, + "fulltext_html": { + "selector": "//meta[@name='citation_fulltext_html_url']", + "attribute": "content", + "download": { + "rename": "fulltext.html" + } + }, + "fulltext_pdf": { + "selector": "//meta[@name='citation_pdf_url']", + "attribute": "content", + "download": { + "rename": "fulltext.pdf" + } + }, + "fulltext_xml": { + "selector": "//meta[@name='citation_xml_url']", + "attribute": "content", + "download": { + "rename": "fulltext.xml" + } + }, + "supplementary_material": { + "selector": "//a[contains(concat(' ', normalize-space(@class), ' '), ' article-supporting-download ')]", + "attribute": "href", + "download": true + }, + "figure": { + "selector": "//div[contains(concat(' ', normalize-space(@class), ' '), ' elife-figure-link-download ')]/a", + "attribute": "href", + "download": true + }, + "figure_caption": { + "selector": "//div[contains(class, 'fig-caption')]", + "attribute": "text" + }, + "license": { + "selector": "//meta[@name='DC.Rights']", + "attribute": "text" + }, + "copyright": { + "selector": "//meta[@name='DC.Rights']", + "attribute": "text" + } + } +} diff --git a/test/elife_test_urls.txt b/test/elife_test_urls.txt new file mode 100644 index 0000000..6c4c5ac --- /dev/null +++ b/test/elife_test_urls.txt @@ -0,0 +1,5 @@ +http://elifesciences.org/content/3/e03080 +http://elifesciences.org/content/3/e02137 +http://elifesciences.org/content/3/e02349 +http://elifesciences.org/content/3/e00590 +http://elifesciences.org/content/2/e00747 From 1c3648c349a859fcaf73b76db27d2b5945c245af Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Thu, 17 Jul 2014 12:02:20 -0400 Subject: [PATCH 062/154] elife tests --- test/elife.json | 417 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 417 insertions(+) create mode 100644 test/elife.json diff --git a/test/elife.json b/test/elife.json new file mode 100644 index 0000000..0c53d39 --- /dev/null +++ b/test/elife.json @@ -0,0 +1,417 @@ +{ + "http://elifesciences.org/content/3/e03080": [ + { + "publisher": "eLife Sciences Publications Limited" + }, + { + "journal": "eLife" + }, + { + "title": "Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine" + }, + { + "authors": "Wilson Wong" + }, + { + "authors": "Xiao-chen Bai" + }, + { + "authors": "Alan Brown" + }, + { + "authors": "Israel S Fernandez" + }, + { + "authors": "Eric Hanssen" + }, + { + "authors": "Melanie Condron" + }, + { + "authors": "Yan Hong Tan" + }, + { + "authors": "Jake Baum" + }, + { + "authors": "Sjors HW Scheres" + }, + { + "doi": "10.7554/eLife.03080" + }, + { + "volume": "3" + }, + { + "firstpage": "e03080" + }, + { + "description": "eLife - Open access to the most promising advances in science" + }, + { + "fulltext_pdf": "http://elifesciences.org/content/3/e03080.full.pdf" + }, + { + "fulltext_xml": "http://elifesciences.org/content/3/e03080.source.xml" + }, + { + "license": "" + }, + { + "copyright": "" + }, + { + "e03080.full.pdf": "851eb256466737ecd1de664e99151b1e" + }, + { + "e03080.source.xml": "bdb94c3e403faee0b0fe20578b08d56e" + }, + { + "rendered.html": "b76c5cdcffc8a1e1456d4b0dfe6b3c72" + } + ], + "http://elifesciences.org/content/3/e02137": [ + { + "publisher": "eLife Sciences Publications Limited" + }, + { + "journal": "eLife" + }, + { + "title": "The quantitative architecture of centromeric chromatin" + }, + { + "authors": "Dani L Bodor" + }, + { + "authors": "João F Mata" + }, + { + "authors": "Mikhail Sergeev" + }, + { + "authors": "Ana Filipa David" + }, + { + "authors": "Kevan J Salimian" + }, + { + "authors": "Tanya Panchenko" + }, + { + "authors": "Don W Cleveland" + }, + { + "authors": "Ben E Black" + }, + { + "authors": "Jagesh V Shah" + }, + { + "authors": "Lars ET Jansen" + }, + { + "doi": "10.7554/eLife.02137" + }, + { + "volume": "3" + }, + { + "firstpage": "e02137" + }, + { + "description": "eLife - Open access to the most promising advances in science" + }, + { + "fulltext_pdf": "http://elifesciences.org/content/3/e02137.full.pdf" + }, + { + "fulltext_xml": "http://elifesciences.org/content/3/e02137.source.xml" + }, + { + "license": "" + }, + { + "copyright": "" + }, + { + "e02137.source.xml": "b068f04e09bc971ccdf1699ede94b6e3" + }, + { + "rendered.html": "3ec5d2e6078a15ebe5ef168656dfb359" + }, + { + "e02137.full.pdf": "99eeed6d3488672365d3ccaabcc828b0" + } + ], + "http://elifesciences.org/content/3/e02349": [ + { + "publisher": "eLife Sciences Publications Limited" + }, + { + "journal": "eLife" + }, + { + "title": "tRNA synthetase counteracts c-Myc to develop functional vasculature" + }, + { + "authors": "Yi Shi" + }, + { + "authors": "Xiaoling Xu" + }, + { + "authors": "Qian Zhang" + }, + { + "authors": "Guangsen Fu" + }, + { + "authors": "Zhongying Mo" + }, + { + "authors": "George S Wang" + }, + { + "authors": "Shuji Kishi" + }, + { + "authors": "Xiang-Lei Yang" + }, + { + "doi": "10.7554/eLife.02349" + }, + { + "volume": "3" + }, + { + "firstpage": "e02349" + }, + { + "description": "eLife - Open access to the most promising advances in science" + }, + { + "fulltext_pdf": "http://elifesciences.org/content/3/e02349.full.pdf" + }, + { + "fulltext_xml": "http://elifesciences.org/content/3/e02349.source.xml" + }, + { + "license": "" + }, + { + "copyright": "" + }, + { + "e02349.full.pdf": "7d8c1c8c30073ee4835035f0edab70a6" + }, + { + "e02349.source.xml": "9de87984f8608b2fa85d50cd99064194" + }, + { + "rendered.html": "632a13144ed7b6843aca6530dcb90e92" + } + ], + "http://elifesciences.org/content/3/e00590": [ + { + "publisher": "eLife Sciences Publications Limited" + }, + { + "journal": "eLife" + }, + { + "title": "Extinction risk and conservation of the world’s sharks and rays" + }, + { + "authors": "Nicholas K Dulvy" + }, + { + "authors": "Sarah L Fowler" + }, + { + "authors": "John A Musick" + }, + { + "authors": "Rachel D Cavanagh" + }, + { + "authors": "Peter M Kyne" + }, + { + "authors": "Lucy R Harrison" + }, + { + "authors": "John K Carlson" + }, + { + "authors": "Lindsay NK Davidson" + }, + { + "authors": "Sonja V Fordham" + }, + { + "authors": "Malcolm P Francis" + }, + { + "authors": "Caroline M Pollock" + }, + { + "authors": "Colin A Simpfendorfer" + }, + { + "authors": "George H Burgess" + }, + { + "authors": "Kent E Carpenter" + }, + { + "authors": "Leonard JV Compagno" + }, + { + "authors": "David A Ebert" + }, + { + "authors": "Claudine Gibson" + }, + { + "authors": "Michelle R Heupel" + }, + { + "authors": "Suzanne R Livingstone" + }, + { + "authors": "Jonnell C Sanciangco" + }, + { + "authors": "John D Stevens" + }, + { + "authors": "Sarah Valenti" + }, + { + "authors": "William T White" + }, + { + "doi": "10.7554/eLife.00590" + }, + { + "volume": "3" + }, + { + "firstpage": "e00590" + }, + { + "description": "eLife - Open access to the most promising advances in science" + }, + { + "fulltext_pdf": "http://elifesciences.org/content/3/e00590.full.pdf" + }, + { + "fulltext_xml": "http://elifesciences.org/content/3/e00590.source.xml" + }, + { + "license": "" + }, + { + "copyright": "" + }, + { + "rendered.html": "f896f10d724eb36c5733847a11c0b32d" + }, + { + "e00590.full.pdf": "0346be2f1154e0bd608459b19682a08b" + }, + { + "e00590.source.xml": "4890527e549d9f9ee3f8ec22ea06f414" + } + ], + "http://elifesciences.org/content/2/e00747": [ + { + "publisher": "eLife Sciences Publications Limited" + }, + { + "journal": "eLife" + }, + { + "title": "Evolutionary dynamics of cancer in response to targeted combination therapy" + }, + { + "authors": "Ivana Bozic" + }, + { + "authors": "Johannes G Reiter" + }, + { + "authors": "Benjamin Allen" + }, + { + "authors": "Tibor Antal" + }, + { + "authors": "Krishnendu Chatterjee" + }, + { + "authors": "Preya Shah" + }, + { + "authors": "Yo Sup Moon" + }, + { + "authors": "Amin Yaqubie" + }, + { + "authors": "Nicole Kelly" + }, + { + "authors": "Dung T Le" + }, + { + "authors": "Evan J Lipson" + }, + { + "authors": "Paul B Chapman" + }, + { + "authors": "Luis A Diaz, Jr" + }, + { + "authors": "Bert Vogelstein" + }, + { + "authors": "Martin A Nowak" + }, + { + "doi": "10.7554/eLife.00747" + }, + { + "volume": "2" + }, + { + "firstpage": "e00747" + }, + { + "description": "eLife - Open access to the most promising advances in science" + }, + { + "fulltext_pdf": "http://elifesciences.org/content/2/e00747.full.pdf" + }, + { + "fulltext_xml": "http://elifesciences.org/content/2/e00747.source.xml" + }, + { + "license": "" + }, + { + "copyright": "" + }, + { + "e00747.source.xml": "77ac1d3b2d9bb7ba0c55daa06bf63e3e" + }, + { + "rendered.html": "4b495cee9be666808f0d113d8fdbdc9f" + }, + { + "e00747.full.pdf": "c8e8c52362bbb1663c7d4c98cfbd0a56" + } + ] +} \ No newline at end of file From 0f25cdce48d984e7f329dfa70088387fda9b2238 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Thu, 17 Jul 2014 22:09:16 +0200 Subject: [PATCH 063/154] update test coverage calculation with element names only --- test/test_all.rb | 24 +++++++----------------- 1 file changed, 7 insertions(+), 17 deletions(-) diff --git a/test/test_all.rb b/test/test_all.rb index 09b921f..c2d5ae1 100755 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -13,30 +13,20 @@ # generate coverage information for tests def coverage(scraperjsonpath, results) - lines = File.readlines scraperjsonpath # get the element names elements = JSON.load(File.open scraperjsonpath)['elements'].keys coverage = [] - source = [] # calculate coverage - lines.each do |line| - valid = true - elements.each do |element| - if line =~ /"#{element}": \{/ - # calculate coverage for this line - if results.detect { |result| result.key? element } - coverage << 1 - else - coverage << 0 - end - else - valid = false - end + elements.each do |element| + # calculate coverage for this line + if results.detect { |result| result.key? element } + coverage << 1 + else + coverage << 0 end - coverage << nil unless valid end { :name => scraperjsonpath, - :source => lines.join(''), + :source => elements.join('\n'), :coverage => coverage } end From 34dafb009e8e8b151b5424d7367638b7cc7c39a8 Mon Sep 17 00:00:00 2001 From: Matt Swain Date: Tue, 22 Jul 2014 21:35:31 +0100 Subject: [PATCH 064/154] Use Ruby Digest::MD5 instead of md5sum The Ruby Digest::MD5 API is more consistent than trying to use the `md5sum` command line tool which has different names and response formats on different operating systems. --- scripts/make_tests.rb | 13 ++----------- test/test_all.rb | 7 ++----- 2 files changed, 4 insertions(+), 16 deletions(-) diff --git a/scripts/make_tests.rb b/scripts/make_tests.rb index fd966be..ed15cc7 100755 --- a/scripts/make_tests.rb +++ b/scripts/make_tests.rb @@ -68,18 +68,9 @@ results = JSON.load(File.open 'results.json') files = Dir['*'] files = files.keep_if { |f| f != 'results.json' } - filehashes = `md5sum #{files.join(' ')}` - filehashes.split("\n").each do |line| - if line =~ /MD5 \(/ - # OSX version of MD5 - filename, filehash = /\((.*)\) = (\w+)/.match(line)[1, 2] - else - # linux version - filehash, filename = line.strip.split(" ") - end - results << { filename => filehash } + files.each do |f| + results << { f => Digest::MD5.file(f).hexdigest } end - end if (index + 1) < urls.length puts "waiting 15 seconds before next scrape" sleep(15) diff --git a/test/test_all.rb b/test/test_all.rb index c2d5ae1..75635b6 100755 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -67,11 +67,8 @@ def coverage(scraperjsonpath, results) results = JSON.load(File.open 'results.json') files = Dir['*'] files = files.keep_if { |f| f != 'results.json' }.map{ |f| f.strip } - cmd = "md5sum #{files.join(' ')}" - filehashes = `#{cmd}` - filehashes.split("\n").each do |line| - filehash, filename = line.strip.split(" ") - results << { filename => filehash } + files.each do |f| + results << { f => Digest::MD5.file(f).hexdigest } end end coverage_files << coverage(scraper, results) From d0a3652ab5f612e4d5f7a77828f21829e0ec71bd Mon Sep 17 00:00:00 2001 From: Peter Murray-Rust Date: Tue, 22 Jul 2014 22:37:19 +0100 Subject: [PATCH 065/154] added Acta Cryst E scraper; probably works with other IUCr journals but not tested --- scrapers/acta_cryst_e.json | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 scrapers/acta_cryst_e.json diff --git a/scrapers/acta_cryst_e.json b/scrapers/acta_cryst_e.json new file mode 100644 index 0000000..5c4f079 --- /dev/null +++ b/scrapers/acta_cryst_e.json @@ -0,0 +1,34 @@ +{ + "url": "iucr", + "elements": { + "fulltext_html": { + "selector": "//a[@target='_parent']", + "attribute": "href", + "download": true + }, + "fulltext_pdf": { + "selector": "//a[img[@alt='pdf version']]", + "attribute": "href", + "download": true + }, + + "iucr:cif": { + "selector": "//a[img[@alt='cif file']]", + "attribute": "href", + "download": true + }, + + "iucr:supplementary": { + "selector": "//a[img[@alt='supplementary materials']]", + "attribute": "href", + "download": true + }, + + "iucr:cif_check": { + "selector": "//a[img[@alt='CIF check report']]", + "attribute": "href", + "download": true + } + } +} + From aa5a6dd1e5fa335b86d4716b618b615506929508 Mon Sep 17 00:00:00 2001 From: Peter Murray-Rust Date: Wed, 23 Jul 2014 11:00:00 +0100 Subject: [PATCH 066/154] added ACS(JACS) scraper; fails on resolving relative/absolute links --- scrapers/acs.json | 44 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 scrapers/acs.json diff --git a/scrapers/acs.json b/scrapers/acs.json new file mode 100644 index 0000000..fe79c12 --- /dev/null +++ b/scrapers/acs.json @@ -0,0 +1,44 @@ + +{ + "url": "pubs\\.acs\\.org", + "elements": { + +// "acs:active_view_pdf": { +// "selector": "//a[@title='View the ACS ActiveView PDF Full Text']", +// "attribute": "href", +// "download": true +// }, + + "fulltext_pdf": { + "selector": "//a[@title='Download the PDF Full Text']", + "attribute": "href", + "download": true + }, + + "acs:quick_pdf": { + "selector": "//a[@title='Download the quick PDF (Full Text with Links)']", + "attribute": "href", + "download": true + }, + + "fulltext_html": { + "selector": "//a[@title='View the Full Text HTML']", + "attribute": "href", + "download": true + }, + + "dc:abstract": { + "selector": "//a[@title='View the Abstract']", + "attribute": "href", + "download": true + }, + + "acs:supporting_info": { + "selector": "//a[@title='View Supporting Information']", + "attribute": "href", + "download": true + } + + } +} + From 1cf4191665c5f4a3b08867e6be7c34a452eb9058 Mon Sep 17 00:00:00 2001 From: Richard Smith Date: Thu, 24 Jul 2014 08:41:34 +0100 Subject: [PATCH 067/154] remove broken scrapers to PRs --- scrapers/acs.json | 44 -------------------------------------- scrapers/acta_cryst_e.json | 34 ----------------------------- 2 files changed, 78 deletions(-) delete mode 100644 scrapers/acs.json delete mode 100644 scrapers/acta_cryst_e.json diff --git a/scrapers/acs.json b/scrapers/acs.json deleted file mode 100644 index fe79c12..0000000 --- a/scrapers/acs.json +++ /dev/null @@ -1,44 +0,0 @@ - -{ - "url": "pubs\\.acs\\.org", - "elements": { - -// "acs:active_view_pdf": { -// "selector": "//a[@title='View the ACS ActiveView PDF Full Text']", -// "attribute": "href", -// "download": true -// }, - - "fulltext_pdf": { - "selector": "//a[@title='Download the PDF Full Text']", - "attribute": "href", - "download": true - }, - - "acs:quick_pdf": { - "selector": "//a[@title='Download the quick PDF (Full Text with Links)']", - "attribute": "href", - "download": true - }, - - "fulltext_html": { - "selector": "//a[@title='View the Full Text HTML']", - "attribute": "href", - "download": true - }, - - "dc:abstract": { - "selector": "//a[@title='View the Abstract']", - "attribute": "href", - "download": true - }, - - "acs:supporting_info": { - "selector": "//a[@title='View Supporting Information']", - "attribute": "href", - "download": true - } - - } -} - diff --git a/scrapers/acta_cryst_e.json b/scrapers/acta_cryst_e.json deleted file mode 100644 index 5c4f079..0000000 --- a/scrapers/acta_cryst_e.json +++ /dev/null @@ -1,34 +0,0 @@ -{ - "url": "iucr", - "elements": { - "fulltext_html": { - "selector": "//a[@target='_parent']", - "attribute": "href", - "download": true - }, - "fulltext_pdf": { - "selector": "//a[img[@alt='pdf version']]", - "attribute": "href", - "download": true - }, - - "iucr:cif": { - "selector": "//a[img[@alt='cif file']]", - "attribute": "href", - "download": true - }, - - "iucr:supplementary": { - "selector": "//a[img[@alt='supplementary materials']]", - "attribute": "href", - "download": true - }, - - "iucr:cif_check": { - "selector": "//a[img[@alt='CIF check report']]", - "attribute": "href", - "download": true - } - } -} - From 0803636f693950306d74ee198d264d107629182d Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Mon, 1 Sep 2014 13:55:39 -0400 Subject: [PATCH 068/154] ACS Scraper - requires relative URL parsing from quickscrape --- scrapers/acs.json | 83 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 scrapers/acs.json diff --git a/scrapers/acs.json b/scrapers/acs.json new file mode 100644 index 0000000..bb394a8 --- /dev/null +++ b/scrapers/acs.json @@ -0,0 +1,83 @@ +{ + "url": "pubs\\.acs\\.org", + "elements": { + "publisher": { + "selector": "//meta[@name='dc.Publisher']", + "attribute": "content" + }, + "title": { + "selector": "//meta[@name='dc.Title']", + "attribute": "content" + }, + "authors": { + "selector": "//meta[@name='dc.Creator']", + "attribute": "content" + }, + "date": { + "selector": "//div[@id='pubDate']", + "attribute": "text" + }, + "volume": { + "selector": "//span[@class='citation_volume']", + "attribute": "text" + }, + "doi": { + "selector": "//meta[@scheme='doi']", + "attribute": "content" + }, + "description": { + "selector": "//meta[@name='dc.Description']", + "attribute": "content" + }, + "journal": { + "selector": "//cite", + "attribute": "text" + }, + "abstract": { + "selector": "//p[@class='articleBody_abstractText']", + "attribute": "text" + }, + "abstract2": { + "selector": "//a[@title='View the Abstract']", + "attribute": "html", + "download": { + "rename": "abstract.pdf" + } + }, + "language": { + "selector": "//meta[@name='dc.Language']", + "attribute": "content" + }, + "fulltext_html": { + "selector": "//a[@title='View the Full Text HTML']", + "attribute": "href", + "download": { + "rename": "fulltext.html" + } + }, + "fulltext_pdf": { + "selector": "//a[@title='Download the PDF Full Text']", + "attribute": "href", + "download": { + "rename": "fulltext.pdf" + } + }, + "supplementary_material": { + "selector": "//a[title='View Supporting Information']", + "attribute": "href", + "download": true + }, + "figure": { + "selector": "//img[@alt='Abstract Image']", + "attribute": "src", + "download": { + "rename": "graphical_abstract.gif" + } + }, + "copyright": { + "selector": "//div[contains(@id, 'artCopyright')]", + "attribute": "text" + } + } +} + From db82379080d6070415ebd0255f190d96ca630e83 Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Mon, 1 Sep 2014 13:56:04 -0400 Subject: [PATCH 069/154] AAAS (Science) Scraper - requires relative URL parsing from quickscrape --- scrapers/aaas.json | 70 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 scrapers/aaas.json diff --git a/scrapers/aaas.json b/scrapers/aaas.json new file mode 100644 index 0000000..2a624a7 --- /dev/null +++ b/scrapers/aaas.json @@ -0,0 +1,70 @@ +{ + "url": "sciencemag\\.org", + "elements": { + "publisher": { + "selector": "//meta[@name='DC.Publisher']", + "attribute": "content" + }, + "title": { + "selector": "//meta[@name='DC.Title']", + "attribute": "content" + }, + "authors": { + "selector": "//meta[@name='DC.Contributor']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@name='citation_date']", + "attribute": "content" + }, + "volume": { + "selector": "//meta[@name='citation_volume']", + "attribute": "content" + }, + "issue": { + "selector": "//meta[@name='citation_issue']", + "attribute": "content" + }, + "firstpage": { + "selector": "//meta[@name='citation_firstpage']", + "attribute": "content" + }, + "doi": { + "selector": "//meta[@name='citation_doi']", + "attribute": "content" + }, + "journal": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" + }, + "abstract": { + "selector": "//div[@class='section abstract']", + "attribute": "text" + }, + "language": { + "selector": "//meta[@name='DC.Language']", + "attribute": "content" + }, + "fulltext_pdf": { + "selector": "//a[@rel='view-full-text.pdf']", + "attribute": "href", + "download": { + "rename": "fulltext.pdf" + } + }, + "fulltext_html": { + "selector": "//a[@rel='view-full-text']", + "attribute": "href", + "download": { + "rename": "fulltext.html" + } + }, + "supplementary_material": { + "selector": "//a[@rel='supplemental-data']", + "attribute": "href", + "download": { + "rename": "supplemental_data.html" + } + } + } +} From a9e20aaa76e7b8884823f063119a06c8f1f6c53c Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Mon, 1 Sep 2014 13:56:29 -0400 Subject: [PATCH 070/154] Nature Scraper - requires relative URL parsing from quickscrape --- scrapers/nature.json | 64 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 scrapers/nature.json diff --git a/scrapers/nature.json b/scrapers/nature.json new file mode 100644 index 0000000..c13ec85 --- /dev/null +++ b/scrapers/nature.json @@ -0,0 +1,64 @@ +{ + "url": "nature\\.com", + "elements": { + "publisher": { + "selector": "//meta[@name='DC.publisher']", + "attribute": "content" + }, + "title": { + "selector": "//meta[@name='citation_title']", + "attribute": "content" + }, + "authors": { + "selector": "//meta[@name='citation_author']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@id='citation_date']", + "attribute": "content" + }, + "volume": { + "selector": "//meta[@class='citation_volume']", + "attribute": "content" + }, + "issue": { + "selector": "//meta[@name='citation_issue']", + "attribute": "content" + }, + "firstpage": { + "selector": "//meta[@name='citation_firstpage']", + "attribute": "content" + }, + "doi": { + "selector": "//meta[@name='citation_doi']", + "attribute": "content" + }, + "journal": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" + }, + "abstract": { + "selector": "//div[@id='abstract']", + "attribute": "text" + }, + "language": { + "selector": "//meta[@name='DC.language']", + "attribute": "content" + }, + "fulltext_pdf": { + "selector": "//a[@id='download-pdf']", + "attribute": "href", + "download": { + "rename": "fulltext.pdf" + } + }, + "copyright": { + "selector": "//div[@name='prism.copyright']", + "attribute": "content" + }, + "license": { + "selector": "//div[@name='DC.rights']", + "attribute": "content" + } + } +} From 6c721ff2fdf0efc2d7640002bbf3e771aef7cbb2 Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Mon, 1 Sep 2014 15:56:58 -0400 Subject: [PATCH 071/154] Additional use of meta tags --- scrapers/aaas.json | 15 +++++++++++---- scrapers/nature.json | 17 +++++++++++++---- 2 files changed, 24 insertions(+), 8 deletions(-) diff --git a/scrapers/aaas.json b/scrapers/aaas.json index 2a624a7..9c9b115 100644 --- a/scrapers/aaas.json +++ b/scrapers/aaas.json @@ -46,15 +46,22 @@ "attribute": "content" }, "fulltext_pdf": { - "selector": "//a[@rel='view-full-text.pdf']", - "attribute": "href", + "selector": "//meta[@name='citation_pdf_url']", + "attribute": "content", "download": { "rename": "fulltext.pdf" } }, + "abstract_html": { + "selector": "//meta[@name='citation_abstract_html_url']", + "attribute": "content", + "download": { + "rename": "abstract.html" + } + }, "fulltext_html": { - "selector": "//a[@rel='view-full-text']", - "attribute": "href", + "selector": "//meta[@name='citation_fulltext_html_url']", + "attribute": "content", "download": { "rename": "fulltext.html" } diff --git a/scrapers/nature.json b/scrapers/nature.json index c13ec85..a7aa4eb 100644 --- a/scrapers/nature.json +++ b/scrapers/nature.json @@ -1,6 +1,6 @@ { - "url": "nature\\.com", - "elements": { + "url": "nature", + "elements": { "publisher": { "selector": "//meta[@name='DC.publisher']", "attribute": "content" @@ -52,12 +52,21 @@ "rename": "fulltext.pdf" } }, + "figure": { + "selector": "//img[@data-media-id='figure']", + "attribute": "src", + "download": true + }, + "caption": { + "selector": "//figcaption", + "attribute": "text" + }, "copyright": { - "selector": "//div[@name='prism.copyright']", + "selector": "//meta[@name='prism.copyright']", "attribute": "content" }, "license": { - "selector": "//div[@name='DC.rights']", + "selector": "//meta[@name='DC.rights']", "attribute": "content" } } From 79bbf529694df48b77ca8d6fdd28e56c19077c5a Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Mon, 1 Sep 2014 15:57:42 -0400 Subject: [PATCH 072/154] Wiley Scraper --- scrapers/wiley.json | 86 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 scrapers/wiley.json diff --git a/scrapers/wiley.json b/scrapers/wiley.json new file mode 100644 index 0000000..b9af69d --- /dev/null +++ b/scrapers/wiley.json @@ -0,0 +1,86 @@ +{ + "url": "onlinelibrary\\.wiley\\.com", + "elements": { + "publisher": { + "selector": "//meta[@name='citation_publisher']", + "attribute": "content" + }, + "title": { + "selector": "//meta[@name='citation_title']", + "attribute": "content" + }, + "authors": { + "selector": "//meta[@name='citation_author']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@name='citation_publication_date']", + "attribute": "content" + }, + "volume": { + "selector": "//meta[@name='citation_volume']", + "attribute": "content" + }, + "issue": { + "selector": "//meta[@name='citation_issue']", + "attribute": "content" + }, + "firstpage": { + "selector": "//meta[@name='citation_firstpage']", + "attribute": "content" + }, + "doi": { + "selector": "//meta[@name='citation_doi']", + "attribute": "content" + }, + "journal": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" + }, + "abstract_html": { + "selector": "//meta[@class='citation_abstract_html_url']", + "attribute": "content", + "download": { + "rename": "abstract.html" + } + }, + "abstract": { + "selector": "//div[@id='abstract']", + "attribute": "text" + }, + "abstract": { + "selector": "//div[@class='para']", + "attribute": "text" + }, + "figure": { + "selector": "//a[@title='Link to full-size graphical abstract']", + "attribute": "href", + "download": true + }, + "language": { + "selector": "//meta[@name='citation_language']", + "attribute": "content" + }, + "fulltext_pdf": { + "selector": "//meta[@name='citation_pdf_url']", + "attribute": "content", + "download": { + "rename": "fulltext.pdf" + } + }, + "fulltext_html": { + "selector": "//meta[@name='citation_fulltext_html_url']", + "attribute": "content", + "download": { + "rename": "fulltext.html" + } + }, + "supplementary_material": { + "selector": "//a[@title='Link to supporting information']", + "attribute": "href", + "download": { + "rename": "supplemental_data.html" + } + } + } +} From 6194072c07feb16c897b30dca402984caf5724ad Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Mon, 1 Sep 2014 20:56:38 -0400 Subject: [PATCH 073/154] removed renames from download - doesn't properly work in urllist cases --- scrapers/aaas.json | 16 ++++------------ scrapers/acs.json | 16 ++++------------ scrapers/nature.json | 4 +--- scrapers/wiley.json | 16 ++++------------ 4 files changed, 13 insertions(+), 39 deletions(-) diff --git a/scrapers/aaas.json b/scrapers/aaas.json index 9c9b115..f52090a 100644 --- a/scrapers/aaas.json +++ b/scrapers/aaas.json @@ -48,30 +48,22 @@ "fulltext_pdf": { "selector": "//meta[@name='citation_pdf_url']", "attribute": "content", - "download": { - "rename": "fulltext.pdf" - } + "download": true }, "abstract_html": { "selector": "//meta[@name='citation_abstract_html_url']", "attribute": "content", - "download": { - "rename": "abstract.html" - } + "download": true }, "fulltext_html": { "selector": "//meta[@name='citation_fulltext_html_url']", "attribute": "content", - "download": { - "rename": "fulltext.html" - } + "download": true }, "supplementary_material": { "selector": "//a[@rel='supplemental-data']", "attribute": "href", - "download": { - "rename": "supplemental_data.html" - } + "download": true } } } diff --git a/scrapers/acs.json b/scrapers/acs.json index bb394a8..b32dca3 100644 --- a/scrapers/acs.json +++ b/scrapers/acs.json @@ -40,9 +40,7 @@ "abstract2": { "selector": "//a[@title='View the Abstract']", "attribute": "html", - "download": { - "rename": "abstract.pdf" - } + "download": true }, "language": { "selector": "//meta[@name='dc.Language']", @@ -51,16 +49,12 @@ "fulltext_html": { "selector": "//a[@title='View the Full Text HTML']", "attribute": "href", - "download": { - "rename": "fulltext.html" - } + "download": true }, "fulltext_pdf": { "selector": "//a[@title='Download the PDF Full Text']", "attribute": "href", - "download": { - "rename": "fulltext.pdf" - } + "download": true }, "supplementary_material": { "selector": "//a[title='View Supporting Information']", @@ -70,9 +64,7 @@ "figure": { "selector": "//img[@alt='Abstract Image']", "attribute": "src", - "download": { - "rename": "graphical_abstract.gif" - } + "download": true }, "copyright": { "selector": "//div[contains(@id, 'artCopyright')]", diff --git a/scrapers/nature.json b/scrapers/nature.json index a7aa4eb..146155f 100644 --- a/scrapers/nature.json +++ b/scrapers/nature.json @@ -48,9 +48,7 @@ "fulltext_pdf": { "selector": "//a[@id='download-pdf']", "attribute": "href", - "download": { - "rename": "fulltext.pdf" - } + "download": true }, "figure": { "selector": "//img[@data-media-id='figure']", diff --git a/scrapers/wiley.json b/scrapers/wiley.json index b9af69d..f0f2a67 100644 --- a/scrapers/wiley.json +++ b/scrapers/wiley.json @@ -40,9 +40,7 @@ "abstract_html": { "selector": "//meta[@class='citation_abstract_html_url']", "attribute": "content", - "download": { - "rename": "abstract.html" - } + "download": true }, "abstract": { "selector": "//div[@id='abstract']", @@ -64,23 +62,17 @@ "fulltext_pdf": { "selector": "//meta[@name='citation_pdf_url']", "attribute": "content", - "download": { - "rename": "fulltext.pdf" - } + "download": true }, "fulltext_html": { "selector": "//meta[@name='citation_fulltext_html_url']", "attribute": "content", - "download": { - "rename": "fulltext.html" - } + "download": true }, "supplementary_material": { "selector": "//a[@title='Link to supporting information']", "attribute": "href", - "download": { - "rename": "supplemental_data.html" - } + "download": true } } } From 16da68f99bf522b8dfa5b4c46597350c29c30570 Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Mon, 1 Sep 2014 20:56:58 -0400 Subject: [PATCH 074/154] Added Springer Scraper --- scrapers/springer.json | 78 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 scrapers/springer.json diff --git a/scrapers/springer.json b/scrapers/springer.json new file mode 100644 index 0000000..9dc4ddb --- /dev/null +++ b/scrapers/springer.json @@ -0,0 +1,78 @@ +{ + "url": "link\\.springer\\.com", + "elements": { + "publisher": { + "selector": "//meta[@name='citation_publisher']", + "attribute": "content" + }, + "title": { + "selector": "//meta[@name='citation_title']", + "attribute": 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+ "attribute": "href", + "download": true + }, + "fulltext_html": { + "selector": "//a[@class='txt']", + "attribute": "href", + "download": true + }, + "supplementary_material": { + "selector": "//a[@class='suppl']", + "attribute": "href", + "download": true + } + } +} From f124a0a429c77bcd9c4c7d04766722bbc4f63fdd Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Mon, 1 Sep 2014 23:51:42 -0400 Subject: [PATCH 076/154] URLLists for written scrapers --- test/aaas_test_urls.txt | 8 ++++++++ test/acs_test_urls.txt | 7 +++++++ test/springer_test_urls.txt | 8 ++++++++ test/tandf_test_urls.txt | 8 ++++++++ test/wiley_test_urls.txt | 10 ++++++++++ 5 files changed, 41 insertions(+) create mode 100644 test/aaas_test_urls.txt create mode 100644 test/acs_test_urls.txt create mode 100644 test/springer_test_urls.txt create mode 100644 test/tandf_test_urls.txt create mode 100644 test/wiley_test_urls.txt diff --git a/test/aaas_test_urls.txt b/test/aaas_test_urls.txt new file mode 100644 index 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at end of file diff --git a/test/springer_test_urls.txt b/test/springer_test_urls.txt new file mode 100644 index 0000000..9a1560b --- /dev/null +++ b/test/springer_test_urls.txt @@ -0,0 +1,8 @@ +http://link.springer.com/article/10.1007/s00894-014-2429-8 +http://link.springer.com/article/10.1007/s00216-014-7672-4 +http://link.springer.com/article/10.1007/s00216-013-7560-3 +http://link.springer.com/article/10.1007/BF01024715 +http://link.springer.com/article/10.1007/s40333-014-0028-2 +http://link.springer.com/article/10.1007/s40069-014-0084-1 +http://link.springer.com/article/10.1007/BF02896800 +http://link.springer.com/article/10.1007/s10719-014-9555-5 \ No newline at end of file diff --git a/test/tandf_test_urls.txt b/test/tandf_test_urls.txt new file mode 100644 index 0000000..ea5f30b --- /dev/null +++ b/test/tandf_test_urls.txt @@ -0,0 +1,8 @@ +http://www.tandfonline.com/doi/abs/10.1080/02757540.2013.878336 +http://www.tandfonline.com/doi/abs/10.1080/1747423X.2013.786151 +http://www.tandfonline.com/doi/abs/10.1080/19376812.2013.838660 +http://www.tandfonline.com/doi/abs/10.1080/13647830.2014.923116 +http://www.tandfonline.com/doi/abs/10.1080/16841360802338738 +http://www.tandfonline.com/doi/abs/10.1207/S15326926CLP0701_04 +http://www.tandfonline.com/doi/abs/10.1080/02630672.1992.9689834 +http://www.tandfonline.com/doi/abs/10.1080/03085147.2012.760347 \ No newline at end of file diff --git a/test/wiley_test_urls.txt b/test/wiley_test_urls.txt new file mode 100644 index 0000000..a8f08b2 --- /dev/null +++ b/test/wiley_test_urls.txt @@ -0,0 +1,10 @@ +http://onlinelibrary.wiley.com/doi/10.1002/anie.201403615/abstract +http://onlinelibrary.wiley.com/doi/10.1002/anie.201404164/abstract +http://onlinelibrary.wiley.com/doi/10.1002/anie.200501671/abstract +http://onlinelibrary.wiley.com/doi/10.1002/cbic.201300780/abstract +http://onlinelibrary.wiley.com/doi/10.1002/open.201300039/abstract +http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12175/abstract +http://onlinelibrary.wiley.com/doi/10.1002/j.2161-007X.2012.00017.x/abstract +http://onlinelibrary.wiley.com/doi/10.1002/mma.2929/abstract +http://onlinelibrary.wiley.com/doi/10.1002/nem.1840/abstract +http://onlinelibrary.wiley.com/doi/10.1002/anie.197205681/abstract \ No newline at end of file From c9ef71423108e86d22971b030e49e47bf071ae3e Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Tue, 2 Sep 2014 10:22:38 -0400 Subject: [PATCH 077/154] Built test .json files --- test/aaas.json | 834 +++++++++++++++++++++++++++++++++++++++++++++ test/acs.json | 745 ++++++++++++++++++++++++++++++++++++++++ test/springer.json | 609 +++++++++++++++++++++++++++++++++ test/tandf.json | 357 +++++++++++++++++++ test/wiley.json | 556 ++++++++++++++++++++++++++++++ 5 files changed, 3101 insertions(+) create mode 100644 test/aaas.json create mode 100644 test/acs.json create mode 100644 test/springer.json create mode 100644 test/tandf.json create mode 100644 test/wiley.json diff --git a/test/aaas.json b/test/aaas.json new file mode 100644 index 0000000..012f251 --- /dev/null +++ b/test/aaas.json @@ -0,0 +1,834 @@ +{ + "http://www.sciencemag.org/content/345/6197/1255215": [ + { + "publisher": "American Association for the Advancement of Science" + }, + { + "title": "Integration of growth and patterning during vascular tissue formation in Arabidopsis" + }, + { + "authors": "Bert De Rybel" + }, + { + "authors": "Milad Adibi" + }, + { + "authors": "Alice S. Breda" + }, + { + "authors": "Jos R. Wendrich" + }, + { + "authors": "Margot E. Smit" + }, + { + "authors": "Ondřej Novák" + }, + { + "authors": "Nobutoshi Yamaguchi" + }, + { + "authors": "Saiko Yoshida" + }, + { + "authors": "Gert Van Isterdael" + }, + { + "authors": "Joakim Palovaara" + }, + { + "authors": "Bart Nijsse" + }, + { + "authors": "Mark V. Boekschoten" + }, + { + "authors": "Guido Hooiveld" + }, + { + "authors": "Tom Beeckman" + }, + { + "authors": "Doris Wagner" + }, + { + "authors": "Karin Ljung" + }, + { + "authors": "Christian Fleck" + }, + { + "authors": "Dolf Weijers" + }, + { + "date": "08/08/2014" + }, + { + "volume": "345" + }, + { + "issue": "6197" + }, + { + "firstpage": "1255215" + }, + { + "doi": "10.1126/science.1255215" + }, + { + "journal": "Science" + }, + { + "abstract": "\n Abstract\n \n Coordination of cell division and pattern formation is central to tissue and organ development, particularly in plants where\n walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these\n hormones converge upon tissue development. We identify a genetic network that reinforces an early embryonic bias in auxin\n distribution to create a local, nonresponding cytokinin source within the root vascular tissue. Experimental and theoretical\n evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions. We further\n demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate\n distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue.\n \n \n " + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://www.sciencemag.org/content/345/6197/1255215.full.pdf" + }, + { + "abstract_html": "http://www.sciencemag.org/content/345/6197/1255215.abstract" + }, + { + "fulltext_html": "http://www.sciencemag.org/content/345/6197/1255215.full" + }, + { + "supplementary_material": "/content/345/6197/1255215/suppl/DC1" + }, + { + "DC1": "5fe7fe941e2881406b05c65f393a22d6" + }, + { + "rendered.html": "c4c922d70fe40f9f0e6866c7d1f69aba" + } + ], + "http://www.sciencemag.org/content/338/6113/1440": [ + { + "publisher": "American Association for the Advancement of Science" + }, + { + "title": "Aggravating Genetic Interactions Allow a Solution to Redundancy in a Bacterial Pathogen" + }, + { + "authors": "Tamara J. O’Connor" + }, + { + "authors": "Dana Boyd" + }, + { + "authors": "Marion S. Dorer" + }, + { + "authors": "Ralph R. Isberg" + }, + { + "date": "12/14/2012" + }, + { + "volume": "338" + }, + { + "issue": "6113" + }, + { + "firstpage": "1440" + }, + { + "doi": "10.1126/science.1229556" + }, + { + "journal": "Science" + }, + { + "abstract": "\n Abstract\n \n Interactions between hosts and pathogens are complex, so understanding the events that govern these interactions requires\n the analysis of molecular mechanisms operating in both organisms. Many pathogens use multiple strategies to target a single\n event in the disease process, confounding the identification of the important determinants of virulence. We developed a genetic\n screening strategy called insertional mutagenesis and depletion (iMAD) that combines bacterial mutagenesis and RNA interference,\n to systematically dissect the interplay between a pathogen and its host. We used this technique to resolve the network of\n proteins secreted by the bacterium Legionella pneumophila to promote intracellular growth, a critical determinant of pathogenicity of this organism. This strategy is broadly applicable,\n allowing the dissection of any interface between two organisms involving numerous interactions.\n \n \n " + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://www.sciencemag.org/content/338/6113/1440.full.pdf" + }, + { + "abstract_html": "http://www.sciencemag.org/content/338/6113/1440.abstract" + }, + { + "fulltext_html": "http://www.sciencemag.org/content/338/6113/1440.full" + }, + { + "supplementary_material": "/content/338/6113/1440/suppl/DC1" + }, + { + "DC1": "6096f22eb0cb20ca7243635aa84967fd" + }, + { + "rendered.html": "ecf22f2fc7b2e6be762b907a96ddbcd6" + } + ], + "http://www.sciencemag.org/content/338/6106/514": [ + { + "publisher": "American Association for the Advancement of Science" + }, + { + "title": "Australopithecus afarensis Scapular Ontogeny, Function, and the Role of Climbing in Human Evolution" + }, + { + "authors": "David J. Green" + }, + { + "authors": "Zeresenay Alemseged" + }, + { + "date": "10/26/2012" + }, + { + "volume": "338" + }, + { + "issue": "6106" + }, + { + "firstpage": "514" + }, + { + "doi": "10.1126/science.1227123" + }, + { + "journal": "Science" + }, + { + "abstract": "\n Abstract\n \n Scapular morphology is predictive of locomotor adaptations among primates, but this skeletal element is scarce in the hominin\n fossil record. Notably, both scapulae of the juvenile Australopithecus afarensis skeleton from Dikika, Ethiopia, have been recovered. These scapulae display several traits characteristic of suspensory apes,\n as do the few known fragmentary adult australopith representatives. Many of these traits change significantly throughout modern\n human ontogeny, but remain stable in apes. Thus, the similarity of juvenile and adult fossil morphologies implies that A. afarensis development was apelike. Additionally, changes in other scapular traits throughout African ape development are associated\n with shifts in locomotor behavior. This affirms the functional relevance of those characteristics, and their presence in australopith\n fossils supports the hypothesis that their locomotor repertoire included a substantial amount of climbing.\n \n \n " + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://www.sciencemag.org/content/338/6106/514.full.pdf" + }, + { + "abstract_html": "http://www.sciencemag.org/content/338/6106/514.abstract" + }, + { + "fulltext_html": "http://www.sciencemag.org/content/338/6106/514.full" + }, + { + "supplementary_material": "/content/338/6106/549.2/suppl/DC1" + }, + { + "supplementary_material": "/content/338/6106/514/suppl/DC1" + }, + { + "supplementary_material": "/content/338/6106/514/suppl/DC2" + }, + { + "DC1": "29be2f1dd06f0f6c6dc84dec8d213102" + }, + { + "rendered.html": "7a753746eeeea3d944ca7191481f7c6e" + } + ], + "http://stke.sciencemag.org/content/7/340/ra82": [ + { + "publisher": "Science Signaling" + }, + { + "title": "Diacylglycerol kinase α establishes T cell polarity by shaping diacylglycerol accumulation at the immunological synapse" + }, + { + "authors": "Anne Chauveau" + }, + { + "authors": "Audrey Le Floc’h" + }, + { + "authors": "Niels S. Bantilan" + }, + { + "authors": "Gary A. Koretzky" + }, + { + "authors": "Morgan Huse" + }, + { + "volume": "7" + }, + { + "issue": "340" + }, + { + "firstpage": "ra82" + }, + { + "doi": "10.1126/scisignal.2005287" + }, + { + "journal": "Science Signaling" + }, + { + "abstract": "Abstract\nPolarization of the T cell microtubule–organizing center (MTOC) to the immunological synapse between the T cell and an antigen-presenting cell (APC) maintains the specificity of T cell effector responses by enabling directional secretion toward the APC. The reorientation of the MTOC is guided by a sharp gradient of the second messenger diacylglycerol (DAG), which is centered at the immunological synapse. We used a single-cell photoactivation approach to demonstrate that diacylglycerol kinase α (DGK-α), which catalyzes the conversion of DAG to phosphatidic acid, determined T cell polarity by limiting the diffusion of DAG. DGK-α–deficient T cells exhibited enlarged accumulations of DAG at the immunological synapse, as well as impaired reorientation of the MTOC. In contrast, T cells lacking the related isoform DGK-ζ did not display polarization defects. We also found that DGK-α localized preferentially to the periphery of the immunological synapse, suggesting that it constrained the area over which DAG accumulated. Phosphoinositide 3-kinase activity was required for the peripheral localization pattern of DGK-α, which suggests a link between DAG and phosphatidylinositol signaling during T cell activation. These results reveal a previously unappreciated function of DGK-α and provide insight into the mechanisms that determine lymphocyte polarity.\n" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://stke.sciencemag.org/content/sigtrans/7/340/ra82.full.pdf" + }, + { + "abstract_html": "http://stke.sciencemag.org/content/7/340/ra82.abstract" + }, + { + "ra82.abstract": "2cce9d016f9aed794f0ace73c4dc9464" + }, + { + "rendered.html": "b8f8b262bec8fd970f2df04ec9aca44a" + } + ], + "http://stm.sciencemag.org/content/6/251/251ra119": [ + { + "publisher": "American Association for the Advancement of Science" + }, + { + "title": "Adult human neural crest–derived cells for articular cartilage repair" + }, + { + "authors": "Karoliina Pelttari" + }, + { + "authors": "Benjamin Pippenger" + }, + { + "authors": "Marcus Mumme" + }, + { + "authors": "Sandra Feliciano" + }, + { + "authors": "Celeste Scotti" + }, + { + "authors": "Pierre Mainil-Varlet" + }, + { + "authors": "Alfredo Procino" + }, + { + "authors": "Brigitte von Rechenberg" + }, + { + "authors": "Thomas Schwamborn" + }, + { + "authors": "Marcel Jakob" + }, + { + "authors": "Clemente Cillo" + }, + { + "authors": "Andrea Barbero" + }, + { + "authors": "Ivan Martin" + }, + { + "date": "08/27/2014" + }, + { + "volume": "6" + }, + { + "issue": "251" + }, + { + "firstpage": "251ra119" + }, + { + "doi": "10.1126/scitranslmed.3009688" + }, + { + "journal": "Science Translational Medicine" + }, + { + "abstract": "\n Abstract\n \n In embryonic models and stem cell systems, mesenchymal cells derived from the neuroectoderm can be distinguished from mesoderm-derived\n cells by their Hox-negative profile—a phenotype associated with enhanced capacity of tissue regeneration. We investigated\n whether developmental origin and Hox negativity correlated with self-renewal and environmental plasticity also in differentiated\n cells from adults. Using hyaline cartilage as a model, we showed that adult human neuroectoderm-derived nasal chondrocytes\n (NCs) can be constitutively distinguished from mesoderm-derived articular chondrocytes (ACs) by lack of expression of specific\n HOX genes, including HOXC4 and HOXD8. In contrast to ACs, serially cloned NCs could be continuously reverted from differentiated to dedifferentiated states, conserving\n the ability to form cartilage tissue in vitro and in vivo. NCs could also be reprogrammed to stably express Hox genes typical of ACs upon implantation into goat articular cartilage defects, directly contributing to cartilage repair.\n Our findings identify previously unrecognized regenerative properties of HOX-negative differentiated neuroectoderm cells in adults, implying a role for NCs in the unmet clinical challenge of articular\n cartilage repair. An ongoing phase 1 clinical trial preliminarily indicated the safety and feasibility of autologous NC–based\n engineered tissues for the treatment of traumatic articular cartilage lesions.\n \n \n " + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://stm.sciencemag.org/content/6/251/251ra119.full.pdf" + }, + { + "abstract_html": "http://stm.sciencemag.org/content/6/251/251ra119.abstract" + }, + { + "fulltext_html": "http://stm.sciencemag.org/content/6/251/251ra119.full" + }, + { + "supplementary_material": "/content/6/232/232fs16/suppl/DC1" + }, + { + "supplementary_material": "/content/5/167/167ra6/suppl/DC1" + }, + { + "supplementary_material": "/content/4/132/132ra55/suppl/DC1" + }, + { + "supplementary_material": "/content/3/101/101ra93/suppl/DC1" + }, + { + "supplementary_material": "/content/6/251/251ra119/suppl/DC1" + }, + { + "251ra119.abstract": "64437cb3e1cb715f20332be915b76772" + }, + { + "rendered.html": "fd0af991de23407282300fea49bc47ed" + } + ], + "http://stm.sciencemag.org/content/1/7/7ra17": [ + { + "publisher": "American Association for the Advancement of Science" + }, + { + "title": "Restoration of Norepinephrine-Modulated Contextual Memory in a Mouse Model of Down Syndrome" + }, + { + "authors": "A. Salehi" + }, + { + "authors": "M. Faizi" + }, + { + "authors": "D. Colas" + }, + { + "authors": "J. Valletta" + }, + { + "authors": "J. Laguna" + }, + { + "authors": "R. Takimoto-Kimura" + }, + { + "authors": "A. Kleschevnikov" + }, + { + "authors": "S. L. Wagner" + }, + { + "authors": "P. Aisen" + }, + { + "authors": "M. Shamloo" + }, + { + "authors": "W. C. Mobley" + }, + { + "date": "11/18/2009" + }, + { + "volume": "1" + }, + { + "issue": "7" + }, + { + "firstpage": "7ra17" + }, + { + "doi": "10.1126/scitranslmed.3000258" + }, + { + "journal": "Science Translational Medicine" + }, + { + "abstract": "\n Abstract\n \n Down syndrome (trisomy 21) is the most common cause of mental retardation in children and leads to marked deficits in contextual\n learning and memory. In rodents, these tasks require the hippocampus and are mediated by several inputs, particularly those\n originating in the locus coeruleus. These afferents mainly use norepinephrine as a transmitter. To explore the basis for contextual\n learning defects in Down syndrome, we examined the Ts65Dn mouse model. These mice, which have three copies of a fragment of\n mouse chromosome 16, exhibited significant deficits in contextual learning together with dysfunction and degeneration of locus\n coeruleus neurons. However, the postsynaptic targets of innervation remained responsive to noradrenergic receptor agonists.\n Indeed, despite advanced locus coeruleus degeneration, we were able to reverse contextual learning failure by using a prodrug\n for norepinephrine called l-threo-3,4-dihydroxyphenylserine, or xamoterol, a β1-adrenergic receptor partial agonist. Moreover, an increased gene dosage of App, in the context of Down syndrome, was necessary for locus coeruleus degeneration. Our findings raise the possibility that\n restoring norepinephrine-mediated neurotransmission could reverse cognitive dysfunction in Down syndrome.\n \n \n " + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://stm.sciencemag.org/content/1/7/7ra17.full.pdf" + }, + { + "abstract_html": "http://stm.sciencemag.org/content/1/7/7ra17.abstract" + }, + { + "fulltext_html": "http://stm.sciencemag.org/content/1/7/7ra17.full" + }, + { + "supplementary_material": "http://www.sciencemag.org/content/343/6174/964/suppl/DC1" + }, + { + "supplementary_material": "/content/5/201/201ra120/suppl/DC1" + }, + { + "supplementary_material": "/content/1/7/7ra17/suppl/DC1" + }, + { + "DC1": "0ad45234188c98efdec1acc4b3033e2b" + }, + { + "rendered.html": "050ac6b02761e37c5e685377391fc791" + } + ], + "http://stke.sciencemag.org/content/1/8/pe11": [ + { + "publisher": "Science Signaling" + }, + { + "title": "A Cytoskeletal Platform for Local Translation in Axons" + }, + { + "authors": "Francisca P. G. Van Horck" + }, + { + "authors": "Christine E. Holt" + }, + { + "volume": "1" + }, + { + "issue": "8" + }, + { + "firstpage": "pe11" + }, + { + "doi": "10.1126/stke.18pe11" + }, + { + "journal": "Science Signaling" + }, + { + "abstract": "Abstract\n Recent data indicate that local translation in growth cones is critical for axon guidance. Evidence from the Drosophila midline axon guidance system suggests that the F-actin-microtubule cross-linker Short stop (Shot) might link the translation machinery to the cytoskeleton in the growth cone. The identification of a complex of translation factors attached to the actin and microtubule networks points to a mechanism by which cytoskeletal dynamics regulate translation in axons and vice versa.\n " + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://stke.sciencemag.org/content/sigtrans/1/8/pe11.full.pdf" + }, + { + "abstract_html": "http://stke.sciencemag.org/content/1/8/pe11.abstract" + }, + { + "pe11.abstract": "4e554ccd229f2d1d25137a18ef8b12b4" + }, + { + "rendered.html": "e0fb49a47083530a38b9076d7df0d03d" + } + ], + "http://www.sciencemag.org/content/298/5601/2157": [ + { + "publisher": "American Association for the Advancement of Science" + }, + { + "title": "The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins" + }, + { + "authors": "Paramvir Dehal" + }, + { + "authors": "Yutaka Satou" + }, + { + "authors": "Robert K. Campbell" + }, + { + "authors": "Jarrod Chapman" + }, + { + "authors": "Bernard Degnan" + }, + { + "authors": "Anthony De Tomaso" + }, + { + "authors": "Brad Davidson" + }, + { + "authors": "Anna Di Gregorio" + }, + { + "authors": "Maarten Gelpke" + }, + { + "authors": "David M. Goodstein" + }, + { + "authors": "Naoe Harafuji" + }, + { + "authors": "Kenneth E. M. Hastings" + }, + { + "authors": "Isaac Ho" + }, + { + "authors": "Kohji Hotta" + }, + { + "authors": "Wayne Huang" + }, + { + "authors": "Takeshi Kawashima" + }, + { + "authors": "Patrick Lemaire" + }, + { + "authors": "Diego Martinez" + }, + { + "authors": "Ian A. Meinertzhagen" + }, + { + "authors": "Simona Necula" + }, + { + "authors": "Masaru Nonaka" + }, + { + "authors": "Nik Putnam" + }, + { + "authors": "Sam Rash" + }, + { + "authors": "Hidetoshi Saiga" + }, + { + "authors": "Masanobu Satake" + }, + { + "authors": "Astrid Terry" + }, + { + "authors": "Lixy Yamada" + }, + { + "authors": "Hong-Gang Wang" + }, + { + "authors": "Satoko Awazu" + }, + { + "authors": "Kaoru Azumi" + }, + { + "authors": "Jeffrey Boore" + }, + { + "authors": "Margherita Branno" + }, + { + "authors": "Stephen Chin-bow" + }, + { + "authors": "Rosaria DeSantis" + }, + { + "authors": "Sharon Doyle" + }, + { + "authors": "Pilar Francino" + }, + { + "authors": "David N. Keys" + }, + { + "authors": "Shinobu Haga" + }, + { + "authors": "Hiroko Hayashi" + }, + { + "authors": "Kyosuke Hino" + }, + { + "authors": "Kaoru S. Imai" + }, + { + "authors": "Kazuo Inaba" + }, + { + "authors": "Shungo Kano" + }, + { + "authors": "Kenji Kobayashi" + }, + { + "authors": "Mari Kobayashi" + }, + { + "authors": "Byung-In Lee" + }, + { + "authors": "Kazuhiro W. Makabe" + }, + { + "authors": "Chitra Manohar" + }, + { + "authors": "Giorgio Matassi" + }, + { + "authors": "Monica Medina" + }, + { + "authors": "Yasuaki Mochizuki" + }, + { + "authors": "Steve Mount" + }, + { + "authors": "Tomomi Morishita" + }, + { + "authors": "Sachiko Miura" + }, + { + "authors": "Akie Nakayama" + }, + { + "authors": "Satoko Nishizaka" + }, + { + "authors": "Hisayo Nomoto" + }, + { + "authors": "Fumiko Ohta" + }, + { + "authors": "Kazuko Oishi" + }, + { + "authors": "Isidore Rigoutsos" + }, + { + "authors": "Masako Sano" + }, + { + "authors": "Akane Sasaki" + }, + { + "authors": "Yasunori Sasakura" + }, + { + "authors": "Eiichi Shoguchi" + }, + { + "authors": "Tadasu Shin-i" + }, + { + "authors": "Antoinetta Spagnuolo" + }, + { + "authors": "Didier Stainier" + }, + { + "authors": "Miho M. Suzuki" + }, + { + "authors": "Olivier Tassy" + }, + { + "authors": "Naohito Takatori" + }, + { + "authors": "Miki Tokuoka" + }, + { + "authors": "Kasumi Yagi" + }, + { + "authors": "Fumiko Yoshizaki" + }, + { + "authors": "Shuichi Wada" + }, + { + "authors": "Cindy Zhang" + }, + { + "authors": "P. Douglas Hyatt" + }, + { + "authors": "Frank Larimer" + }, + { + "authors": "Chris Detter" + }, + { + "authors": "Norman Doggett" + }, + { + "authors": "Tijana Glavina" + }, + { + "authors": "Trevor Hawkins" + }, + { + "authors": "Paul Richardson" + }, + { + "authors": "Susan Lucas" + }, + { + "authors": "Yuji Kohara" + }, + { + "authors": "Michael Levine" + }, + { + "authors": "Nori Satoh" + }, + { + "authors": "Daniel S. Rokhsar" + }, + { + "date": "12/13/2002" + }, + { + "volume": "298" + }, + { + "issue": "5601" + }, + { + "firstpage": "2157" + }, + { + "doi": "10.1126/science.1080049" + }, + { + "journal": "Science" + }, + { + "abstract": "\n Abstract\n The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern\n ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate\n and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. TheCiona genome contains ∼16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates.\n Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The\n ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose\n metabolism that are related to those in bacteria and fungi.\n \n " + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://www.sciencemag.org/content/298/5601/2157.full.pdf" + }, + { + "abstract_html": "http://www.sciencemag.org/content/298/5601/2157.abstract" + }, + { + "fulltext_html": "http://www.sciencemag.org/content/298/5601/2157.full" + }, + { + "supplementary_material": "/content/298/5601/2157/suppl/DC1" + }, + { + "2157.abstract": "45f763e9739badd9fc92e21116168ad9" + }, + { + "rendered.html": "308ecf9932204a34faabbcfa51cc7908" + } + ] +} \ No newline at end of file diff --git a/test/acs.json b/test/acs.json new file mode 100644 index 0000000..fbec5e7 --- /dev/null +++ b/test/acs.json @@ -0,0 +1,745 @@ +{ + "http://pubs.acs.org/doi/abs/10.1021/ic50161a007": [ + { + "publisher": " American Chemical Society " + }, + { + "title": "Metal complexes of cyclic triamines. 1. Complexes of 1,4,7-triazacyclononane ([9]aneN3) with nickel(II), copper(II), and zinc(II)" + }, + { + "authors": " Rita. Yang " + }, + { + "authors": " Leverett J. Zompa " + }, + { + "date": "Publication Date: July 1976" + }, + { + "volume": "15" + }, + { + "doi": "10.1021/ic50161a007" + }, + { + "journal": "Inorg. Chem." + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "The Journal of Organic Chemistry" + }, + { + "journal": "The Journal of Organic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "abstract2": "First Page" + }, + { + "language": "EN" + }, + { + "fulltext_html": "/doi/full/10.1021/ic400174r" + }, + { + "fulltext_html": "/doi/full/10.1021/ic101360d" + }, + { + "fulltext_html": "/doi/full/10.1021/ic101210d" + }, + { + "fulltext_html": "/doi/full/10.1021/jo902504d" + }, + { + "fulltext_html": "/doi/full/10.1021/ic8004079" + }, + { + "fulltext_pdf": "/doi/pdf/10.1021/ic50161a007" + }, + { + "rendered.html": "e1ff5b84d8faca6a1227827dd25d0548" + }, + { + "span%3E": "04fa87eedefd1f0728a8c6682379914d" + } + ], + "http://pubs.acs.org/doi/abs/10.1021/ic501196q": [ + { + "publisher": "American Chemical Society" + }, + { + "title": "Ring-Shaped Rhenium(I) Multinuclear Complexes: Improved Synthesis and Photoinduced Multielectron Accumulation" + }, + { + "authors": "Tsuyoshi Asatani" + }, + { + "authors": "Yuki Nakagawa" + }, + { + "authors": "Yusuke Funada" + }, + { + "authors": "Shuhei Sawa" + }, + { + "authors": "Hiroyuki Takeda" + }, + { + "authors": "Tatsuki Morimoto" + }, + { + "authors": "Kazuhide Koike" + }, + { + "authors": "Osamu Ishitani" + }, + { + "date": "Publication Date (Web): July 9, 2014" + }, + { + "volume": "53" + }, + { + "doi": "10.1021/ic501196q" + }, + { + "description": "We successfully developed selective synthesis of strongly emissive ring-shaped Re(I) multinuclear complexes (RnP(x)n+ in Chart 1) with much higher yields compared with the previously reported method. This improved method could also be employed to prepare a novel ring-shaped multinuclear complex composed of structurally different Re(I) units. Each Re unit in RnP(x)n+ could electrochemically accept one electron, and the multielectron reduced states of RnP(x)n+ were stable. In the presence of triethanolamine, the ring-shaped tetranuclear and hexanuclear complexes can be photochemically reduced and accumulate 2.9–3.6 and 4.4 electrons in one molecule, respectively." + }, + { + "description": "In the presence of triethanolamine, ring-shaped Re(I) tetranuclear and hexanuclear complexes can photochemically accumulate four and five electrons in a single molecule, respectively. We succeeded in much improving the synthetic yield for these complexes compared with the previously reported method." + }, + { + "description": "" + }, + { + "journal": "Inorg. Chem." + }, + { + "abstract": "We successfully developed selective synthesis of strongly emissive ring-shaped Re(I) multinuclear complexes (RnP(x)n+ in Chart 1) with much higher yields compared with the previously reported method. This improved method could also be employed to prepare a novel ring-shaped multinuclear complex composed of structurally different Re(I) units. Each Re unit in RnP(x)n+ could electrochemically accept one electron, and the multielectron reduced states of RnP(x)n+ were stable. In the presence of triethanolamine, the ring-shaped tetranuclear and hexanuclear complexes can be photochemically reduced and accumulate 2.9–3.6 and 4.4 electrons in one molecule, respectively." + }, + { + "abstract2": "Abstract" + }, + { + "language": "EN" + }, + { + "fulltext_html": "/doi/full/10.1021/ic501196q" + }, + { + "fulltext_pdf": "/doi/pdf/10.1021/ic501196q" + }, + { + "figure": "/appl/literatum/publisher/achs/journals/content/inocaj/2014/inocaj.2014.53.issue-14/ic501196q/production/images/medium/ic-2014-01196q_0009.gif" + }, + { + "copyright": "Copyright © 2014 American Chemical Society" + }, + { + "rendered.html": "159e464f7294d5bd8fa7a7bb8100a0e9" + }, + { + "span%3E": "61d99547e16199b6bd74628be706a224" + } + ], + "http://pubs.acs.org/doi/abs/10.1021/ic5007007": [ + { + "publisher": "American Chemical Society" + }, + { + "title": "Luminescence Modulations of Rhenium Tricarbonyl Complexes Induced by Structural Variations" + }, + { + "authors": "Hélène C. Bertrand" + }, + { + "authors": "Sylvain Clède" + }, + { + "authors": "Régis Guillot" + }, + { + "authors": "François Lambert" + }, + { + "authors": "Clotilde Policar" + }, + { + "date": "Publication Date (Web): June 6, 2014" + }, + { + "volume": "53" + }, + { + "doi": "10.1021/ic5007007" + }, + { + "description": "Octahedral d6 low-spin Re(I) tricarbonyl complexes are of considerable interest as noninvasive imaging probes and have been deeply studied owing to their biological stability, low toxicity, large Stokes shifts, and long luminescence lifetimes. We reported recently the bimodal IR and luminescence imaging of a Re(I) tricarbonyl complex with a Pyta ligand (4-(2-pyridyl)-1,2,3-triazole) in cells and labeled such metal–carbonyl complexes SCoMPIs for single-core multimodal probes for imaging. Re(I) tricarbonyl complexes have unique photophysical properties allowing for their unequivocal detection in cells but also present some weaknesses such as a very low luminescence quantum yield in aqueous medium. Further optimizations would thus be desirable. We therefore developed new Re(I) tricarbonyl complexes prepared from different ancillary ligands. Complexes with benzothiadiazole–triazole ligands show interesting luminescent quantum yields in acetonitrile and may constitute valuable luminescent metal complexes in or..." + }, + { + "description": "Re(I) tricarbonyl complexes are of considerable interest as bioimaging probes. Single-core multimodal probes for imaging (SCoMPIs) display unique photophysical properties enabling their unequivocal detection in cells. New SCoMPIs were prepared from an ancillary 1-(2-pyridyl)-1,2,3-triazole ligand, denoted Tapy, a regioisomer of the widely used Pyta ligand. When functionalized with long alkyl chains, they show impressive enhancement of their luminescent properties relative to the parent Pyta complex, both in solution and in MDA-MB231 breast cancer cells." + }, + { + "description": "" + }, + { + "journal": "Inorg. Chem." + }, + { + "abstract": "Octahedral d6 low-spin Re(I) tricarbonyl complexes are of considerable interest as noninvasive imaging probes and have been deeply studied owing to their biological stability, low toxicity, large Stokes shifts, and long luminescence lifetimes. We reported recently the bimodal IR and luminescence imaging of a Re(I) tricarbonyl complex with a Pyta ligand (4-(2-pyridyl)-1,2,3-triazole) in cells and labeled such metal–carbonyl complexes SCoMPIs for single-core multimodal probes for imaging. Re(I) tricarbonyl complexes have unique photophysical properties allowing for their unequivocal detection in cells but also present some weaknesses such as a very low luminescence quantum yield in aqueous medium. Further optimizations would thus be desirable. We therefore developed new Re(I) tricarbonyl complexes prepared from different ancillary ligands. Complexes with benzothiadiazole–triazole ligands show interesting luminescent quantum yields in acetonitrile and may constitute valuable luminescent metal complexes in organic media. A series of complexes with bidentate 1-(2-quinolinyl)-1,2,3-triazole (Taquin) and 1-(2-pyridyl)-1,2,3-triazole (Tapy) ligands bearing various 4-substituted alkyl side chains has been designed and synthesized with efficient procedures. Their photophysical properties have been characterized in acetonitrile and in a H2O/DMSO (98/2) mixture and compared with those of the parent Quinta- and Pyta-based complexes. Tapy complexes bearing long alkyl chains show impressive enhancement of their luminescent properties relative to the parent Pyta complex. Theoretical calculations have been performed to further characterize this new class of rhenium tricarbonyl complexes. Preliminary cellular imaging studies in MDA-MB231 breast cancer cells reveal a strong increase in the luminescence signal in cells incubated with the Tapy complex substituted with a C12 alkyl chain. This study points out the interesting potential of the Tapy ligand in coordination chemistry, which has been so far underexploited." + }, + { + "abstract2": "Abstract" + }, + { + "language": "EN" + }, + { + "fulltext_html": "/doi/full/10.1021/ic5007007" + }, + { + "fulltext_pdf": "/doi/pdf/10.1021/ic5007007" + }, + { + "figure": "/appl/literatum/publisher/achs/journals/content/inocaj/2014/inocaj.2014.53.issue-12/ic5007007/production/images/medium/ic-2014-007007_0014.gif" + }, + { + "copyright": "Copyright © 2014 American Chemical Society" + }, + { + "ic-2014-007007_0014.gif": "e67ff4fb6ea512f6ee9cba0aa40b39e1" + }, + { + "rendered.html": "c28639adfb2fb05847d4cdb2dfe92e56" + } + ], + "http://pubs.acs.org/doi/abs/10.1021/ja2105834": [ + { + "publisher": "American Chemical Society" + }, + { + "title": "Mechanisms for CO Production from CO2 Using Reduced Rhenium Tricarbonyl Catalysts" + }, + { + "authors": "Jay Agarwal" + }, + { + "authors": "Etsuko Fujita" + }, + { + "authors": "Henry F. Schaefer, III" + }, + { + "authors": "James T. Muckerman" + }, + { + "date": "Publication Date (Web): February 23, 2012" + }, + { + "volume": "134" + }, + { + "doi": "10.1021/ja2105834" + }, + { + "description": "The chemical conversion of CO2 has been studied by numerous experimental groups. Particularly the use of rhenium tricarbonyl-based molecular catalysts has attracted interest owing to their ability to absorb light, store redox equivalents, and convert CO2 into higher-energy products. The mechanism by which these catalysts mediate reduction, particularly to CO and HCOO–, is poorly understood, and studies aimed at elucidating the reaction pathway have likely been hindered by the large number of species present in solution. Herein the mechanism for carbon monoxide production using rhenium tricarbonyl catalysts has been investigated using density functional theory. The investigation presented proceeds from the experimental work of Meyer’s group (J. Chem. Soc., Chem. Commun.1985, 1414–1416) in DMSO and Fujita’s group (J. Am. Chem. Soc.2003, 125, 11976–11987) in dry DMF. The latter work with a simplified reaction mixture, one that removes the photo-induced reduction step with a sacrificial donor, is used for val..." + }, + { + "description": "" + }, + { + "journal": "J. Am. Chem. Soc." + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "journal": "ACS Catalysis" + }, + { + "journal": "ACS Catalysis" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "The Journal of Physical Chemistry A" + }, + { + "journal": "The Journal of Physical Chemistry A" + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "journal": "Accounts of Chemical Research" + }, + { + "journal": "Accounts of Chemical Research" + }, + { + "abstract": "The chemical conversion of CO2 has been studied by numerous experimental groups. Particularly the use of rhenium tricarbonyl-based molecular catalysts has attracted interest owing to their ability to absorb light, store redox equivalents, and convert CO2 into higher-energy products. The mechanism by which these catalysts mediate reduction, particularly to CO and HCOO–, is poorly understood, and studies aimed at elucidating the reaction pathway have likely been hindered by the large number of species present in solution. Herein the mechanism for carbon monoxide production using rhenium tricarbonyl catalysts has been investigated using density functional theory. The investigation presented proceeds from the experimental work of Meyer’s group (J. Chem. Soc., Chem. Commun.1985, 1414–1416) in DMSO and Fujita’s group (J. Am. Chem. Soc.2003, 125, 11976–11987) in dry DMF. The latter work with a simplified reaction mixture, one that removes the photo-induced reduction step with a sacrificial donor, is used for validation of the proposed mechanism, which involves formation of a rhenium carboxylate dimer, [Re(dmb)(CO)3]2(OCO), where dmb = 4,4′-dimethyl-2,2′-bipyridine. CO2 insertion into this species, and subsequent rearrangement, is proposed to yield CO and the carbonate-bridged [Re(dmb)(CO)3]2(OCO2). Structures and energies for the proposed reaction path are presented and compared to previously published experimental observations." + }, + { + "abstract2": "Abstract" + }, + { + "language": "EN" + }, + { + "fulltext_html": "/doi/full/10.1021/ja2105834" + }, + { + "fulltext_html": "/doi/full/10.1021/ja500403e" + }, + { + "fulltext_html": "/doi/full/10.1021/ic500050q" + }, + { + "fulltext_html": "/doi/full/10.1021/ja409271s" + }, + { + "fulltext_html": "/doi/full/10.1021/cs400332y" + }, + { + "fulltext_html": "/doi/full/10.1021/ic302663c" + }, + { + "fulltext_pdf": "/doi/pdf/10.1021/ja2105834" + }, + { + "figure": "/appl/literatum/publisher/achs/journals/content/jacsat/2012/jacsat.2012.134.issue-11/ja2105834/production/images/medium/ja-2011-105834_0003.gif" + }, + { + "copyright": "Copyright © 2012 American Chemical Society" + }, + { + "ja-2011-105834_0003.gif": "ef696f8cc86dbb4cecd51b1ff8036ec6" + }, + { + "rendered.html": "029bbc92f3e271398b30c340eed51a7e" + } + ], + "http://pubs.acs.org/doi/abs/10.1021/jz1010237": [ + { + "publisher": "American Chemical Society" + }, + { + "title": "New Directions for the Photocatalytic Reduction of CO2: Supramolecular, scCO2 or Biphasic Ionic Liquid−scCO2 Systems" + }, + { + "authors": "David C. Grills" + }, + { + "authors": "Etsuko Fujita" + }, + { + "date": "Publication Date (Web): September 2, 2010" + }, + { + "volume": "1" + }, + { + "doi": "10.1021/jz1010237" + }, + { + "description": "There is an urgent need for the discovery of carbon-neutral sources of energy to avoid the consequences of global warming caused by ever-increasing atmospheric CO2 levels. An attractive possibility is to use CO2 captured from industrial emissions as a feedstock for the production of useful fuels and precursors such as carbon monoxide and methanol. An active field of research to achieve this goal is the development of catalysts capable of harnessing solar energy for use in artificial photosynthetic processes for CO2 reduction. Transition-metal complexes are excellent candidates, and it has already been shown that they can be used to reduce CO2 with high quantum efficiency. However, they generally suffer from poor visible light absorption, short catalyst lifetimes, and poor reaction rates. In this Perspective, the field of photocatalytic CO2 reduction is introduced, and recent developments that seek to improve the efficiency of such catalytic processes are highlighted, especially CO2 reduction with supramol..." + }, + { + "description": "" + }, + { + "journal": "J. Phys. Chem." + }, + { + "journal": "J. Phys. Chem. Lett." + }, + { + "journal": "ACS Catalysis" + }, + { + "journal": "ACS Catalysis" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "The Journal of Physical Chemistry Letters" + }, + { + "journal": "The Journal of Physical Chemistry Letters" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "ACS Catalysis" + }, + { + "journal": "ACS Catalysis" + }, + { + "journal": "Accounts of Chemical Research" + }, + { + "journal": "Accounts of Chemical Research" + }, + { + "journal": "ACS Nano" + }, + { + "journal": "ACS Nano" + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "abstract": "There is an urgent need for the discovery of carbon-neutral sources of energy to avoid the consequences of global warming caused by ever-increasing atmospheric CO2 levels. An attractive possibility is to use CO2 captured from industrial emissions as a feedstock for the production of useful fuels and precursors such as carbon monoxide and methanol. An active field of research to achieve this goal is the development of catalysts capable of harnessing solar energy for use in artificial photosynthetic processes for CO2 reduction. Transition-metal complexes are excellent candidates, and it has already been shown that they can be used to reduce CO2 with high quantum efficiency. However, they generally suffer from poor visible light absorption, short catalyst lifetimes, and poor reaction rates. In this Perspective, the field of photocatalytic CO2 reduction is introduced, and recent developments that seek to improve the efficiency of such catalytic processes are highlighted, especially CO2 reduction with supramolecules and molecular systems in supercritical CO2 (scCO2) or biphasic ionic liquid−scCO2 mixtures." + }, + { + "abstract2": "Abstract" + }, + { + "language": "EN" + }, + { + "fulltext_html": "/doi/full/10.1021/jz1010237" + }, + { + "fulltext_html": "/doi/full/10.1021/cs500730w" + }, + { + "fulltext_html": "/doi/full/10.1021/ic500829p" + }, + { + "fulltext_html": "/doi/full/10.1021/jz500759x" + }, + { + "fulltext_html": "/doi/full/10.1021/ic401031j" + }, + { + "fulltext_html": "/doi/full/10.1021/cs400332y" + }, + { + "fulltext_pdf": "/doi/pdf/10.1021/jz1010237" + }, + { + "figure": "/appl/literatum/publisher/achs/journals/content/jpclcd/2010/jpclcd.2010.1.issue-18/jz1010237/production/images/medium/jz-2010-010237_0004.gif" + }, + { + "copyright": "Copyright © 2010 American Chemical Society" + }, + { + "rendered.html": "58d347ee8062d84c7f90f225d31a9dcc" + }, + { + "span%3E": "5e4c63f805bed5b3336b974c401fccca" + } + ], + "http://pubs.acs.org/doi/abs/10.1021/ar700111a": [ + { + "publisher": " American Chemical Society" + }, + { + "title": "Density Functionals with Broad Applicability in Chemistry" + }, + { + "authors": "Yan Zhao" + }, + { + "authors": "Donald G. Truhlar" + }, + { + "date": "Publication Date (Web): January 11, 2008" + }, + { + "volume": "41" + }, + { + "doi": "10.1021/ar700111a" + }, + { + "description": "Although density functional theory is widely used in the computational chemistry community, the most popular density functional, B3LYP, has some serious shortcomings: (i) it is better for main-group chemistry than for transition metals; (ii) it systematically underestimates reaction barrier heights; (iii) it is inaccurate for interactions dominated by medium-range correlation energy, such as van der Waals attraction, aromatic−aromatic stacking, and alkane isomerization energies. We have developed a variety of databases for testing and designing new density functionals. We used these data to design new density functionals, called M06-class (and, earlier, M05-class) functionals, for which we enforced some fundamental exact constraints such as the uniform-electron-gas limit and the absence of self-correlation energy. Our M06-class functionals depend on spin-up and spin-down electron densities (i.e., spin densities), spin density gradients, spin kinetic energy densities, and, for nonlocal (also called hybrid)..." + }, + { + "journal": "Acc. Chem. Res." + }, + { + "journal": "Environmental Science & Technology" + }, + { + "journal": "Environmental Science & Technology" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "The Journal of Physical Chemistry A" + }, + { + "journal": "The Journal of Physical Chemistry A" + }, + { + "journal": "The Journal of Physical Chemistry B" + }, + { + "journal": "The Journal of Physical Chemistry B" + }, + { + "journal": "The Journal of Physical Chemistry A" + }, + { + "journal": "The Journal of Physical Chemistry A" + }, + { + "journal": "Accounts of Chemical Research" + }, + { + "journal": "Accounts of Chemical Research" + }, + { + "journal": "Nano Letters" + }, + { + "journal": "Nano Letters" + }, + { + "journal": "Nano Letters" + }, + { + "journal": "Nano Letters" + }, + { + "abstract": " Although density functional theory is widely used in the computational chemistry community, the most popular density functional, B3LYP, has some serious shortcomings: (i) it is better for main-group chemistry than for transition metals; (ii) it systematically underestimates reaction barrier heights; (iii) it is inaccurate for interactions dominated by medium-range correlation energy, such as van der Waals attraction, aromatic−aromatic stacking, and alkane isomerization energies. We have developed a variety of databases for testing and designing new density functionals. We used these data to design new density functionals, called M06-class (and, earlier, M05-class) functionals, for which we enforced some fundamental exact constraints such as the uniform-electron-gas limit and the absence of self-correlation energy. Our M06-class functionals depend on spin-up and spin-down electron densities (i.e., spin densities), spin density gradients, spin kinetic energy densities, and, for nonlocal (also called hybrid) functionals, Hartree−Fock exchange. We have developed four new functionals that overcome the above-mentioned difficulties: (a) M06, a hybrid meta functional, is a functional with good accuracy “across-the-board” for transition metals, main group thermochemistry, medium-range correlation energy, and barrier heights; (b) M06-2X, another hybrid meta functional, is not good for transition metals but has excellent performance for main group chemistry, predicts accurate valence and Rydberg electronic excitation energies, and is an excellent functional for aromatic−aromatic stacking interactions; (c) M06-L is not as accurate as M06 for barrier heights but is the most accurate functional for transition metals and is the only local functional (no Hartree−Fock exchange) with better across-the-board average performance than B3LYP; this is very important because only local functionals are affordable for many demanding applications on very large systems; (d) M06-HF has good performance for valence, Rydberg, and charge transfer excited states with minimal sacrifice of ground-state accuracy. In this Account, we compared the performance of the M06-class functionals and one M05-class functional (M05-2X) to that of some popular functionals for diverse databases and their performance on several difficult cases. The tests include barrier heights, conformational energy, and the trend in bond dissociation energies of Grubbsʼ ruthenium catalysts for olefin metathesis. Based on these tests, we recommend (1) the M06-2X, BMK, and M05-2X functionals for main-group thermochemistry and kinetics, (2) M06-2X and M06 for systems where main-group thermochemistry, kinetics, and noncovalent interactions are all important, (3) M06-L and M06 for transition metal thermochemistry, (4) M06 for problems involving multireference rearrangements or reactions where both organic and transition-metal bonds are formed or broken, (5) M06-2X, M05-2X, M06-HF, M06, and M06-L for the study of noncovalent interactions, (6) M06-HF when the use of full Hartree−Fock exchange is important, for example, to avoid the error of self-interaction at long-range, (7) M06-L when a local functional is required, because a local functional has much lower cost for large systems." + }, + { + "abstract2": "Abstract" + }, + { + "language": "EN" + }, + { + "fulltext_html": "/doi/full/10.1021/ar700111a" + }, + { + "fulltext_html": "/doi/full/10.1021/es5026678" + }, + { + "fulltext_html": "/doi/full/10.1021/ic5006659" + }, + { + "fulltext_html": "/doi/full/10.1021/jp5035568" + }, + { + "fulltext_html": "/doi/full/10.1021/jp501408e" + }, + { + "fulltext_html": "/doi/full/10.1021/jp502558p" + }, + { + "fulltext_pdf": "/doi/pdf/10.1021/ar700111a" + }, + { + "copyright": "Copyright © 2008 American Chemical Society" + }, + { + "rendered.html": "c3e74598bb87024ea3ec2d7f2aae2a54" + }, + { + "span%3E": "61d99547e16199b6bd74628be706a224" + } + ], + "http://pubs.acs.org/doi/abs/10.1021/om960044%2B": [ + { + "publisher": " American Chemical Society " + }, + { + "title": "Electrocatalytic Reduction of CO2 Using the Complexes [Re(bpy)(CO)3L]n (n = +1, L = P(OEt)3, CH3CN; n = 0, L = Cl-, Otf-; bpy = 2,2‘-Bipyridine; Otf- = CF3SO3) as Catalyst Precursors:  Infrared Spectroelectrochemical Investigation" + }, + { + "authors": "Frank P. A. Johnson,*,†" + }, + { + "authors": "Michael W. George,†" + }, + { + "authors": "Frantisek Hartl,*,‡ and" + }, + { + "authors": "James J. Turner†" + }, + { + "date": "Publication Date (Web): July 23, 1996" + }, + { + "volume": "15" + }, + { + "doi": "10.1021/om960044+" + }, + { + "description": "This article describes the results of an IR spectroelectrochemical study of the electrocatalytic reduction of carbon dioxide using the complexes [Re(CO)3(bpy)L]n (bpy = 2,2‘-bipyridine; n = 0, L = Cl-, CF3SO3-; n = +1, L = CH3CN, P(OEt)3) as catalyst precursors. The study was performed for the first time with an optically transparent thin-layer electrochemical (OTTLE) cell. The results confirm unambiguously the catalytic activity of the reduced five-coordinate complexes, the radical [Re(CO)3(bpy)]• and the anion [Re(CO)3(bpy)]-. The catalytic behavior of these species could be investigated separately for the first time due to the application of complexes other than those with L = halide, whose catalytic routes may involve simultaneously both radical and anionic catalysis depending on the solvent used. The complex [Re(CO)3(bpy)Cl], so far the most studied catalyst precursor, upon one-electron reduction gives the corresponding radical-anion [Re(CO)3(bpy)Cl]•-, which was previously believed to react directly..." + }, + { + "description": "Electrocatalytic reduction of carbon dioxide has been investigated by IR spectroelectrochemistry using the complexes [Re(CO)3(bpy)L]n (n = 0, L = Cl-, CF3SO3-; n = +1, L = CH3CN, P(OEt)3) as catalyst precursors. Variation of the axial ligand L and the solvent used made it possible to discriminate between the 1e and 2e catalytic routes and, hence, to provide independent spectroscopic evidence for the catalytic activity of the five-coordinate radicals [Re(CO)3(bpy)]• and anions [Re(CO)3(bpy)]-." + }, + { + "description": "" + }, + { + "journal": "Organometallics" + }, + { + "journal": "Organometallics" + }, + { + "journal": "Organometallics" + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Organometallics" + }, + { + "journal": "Organometallics" + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "journal": "Journal of the American Chemical Society" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "journal": "Inorganic Chemistry" + }, + { + "abstract": "This article describes the results of an IR spectroelectrochemical study of the electrocatalytic reduction of carbon dioxide using the complexes [Re(CO)3(bpy)L]n (bpy = 2,2‘-bipyridine; n = 0, L = Cl-, CF3SO3-; n = +1, L = CH3CN, P(OEt)3) as catalyst precursors. The study was performed for the first time with an optically transparent thin-layer electrochemical (OTTLE) cell. The results confirm unambiguously the catalytic activity of the reduced five-coordinate complexes, the radical [Re(CO)3(bpy)]• and the anion [Re(CO)3(bpy)]-. The catalytic behavior of these species could be investigated separately for the first time due to the application of complexes other than those with L = halide, whose catalytic routes may involve simultaneously both radical and anionic catalysis depending on the solvent used. The complex [Re(CO)3(bpy)Cl], so far the most studied catalyst precursor, upon one-electron reduction gives the corresponding radical-anion [Re(CO)3(bpy)Cl]•-, which was previously believed to react directly with CO2. By contrast, this study demonstrates its stability toward attack by CO2, which may only take place after dissociation of the chloride ligand. This conclusion also applies to other six-coordinate radicals [Re(CO)3(bpy)L]• (L = CH3CN (in CH3CN) and P(OEt)3) whose catalytic route requires subsequent one-electron reduction to produce the anionic catalyst [Re(CO)3(bpy)]- (the 2e pathway). The catalytic route of [Re(CO)3(bpy)Cl] in CH3CN therefore deviates from that of the related [Re(CO)3(dmbpy)Cl], the other complex studied by IR (reflectance) spectroelectrochemistry, with the more basic ligand, 4,4‘-dimethyl-2,2‘-bipyridine (dmbpy). The latter complex tends to form the five-coordinate radicals [Re(CO)3(dmbpy)]•, capable of CO2 reduction (the 1e pathway), even in CH3CN, hence eliminating the possibility of the 2e pathway via the anion [Re(CO)3(dmbpy)]-, which operates in the case of the 2,2‘-bipyridine complex. For [Re(CO)3(bpy)L]n (n = 0, L = Cl-, CF3SO3-; n = +1, L = CH3CN), the 1e catalytic route becomes possible in weakly coordinating THF, due to the instability of the radical [Re(CO)3(bpy)(THF)]•. The inherent stability of the radical [Re(CO)3(bpy){P(OEt)3}]• was found convenient for the investigation of the 2e pathway via [Re(CO)3(bpy)]-. The main, spectroscopically observed products of the CO2 reduction are, independent of the 1e and 2e catalytic routes, CO, CO32-, and free CO2H-. The latter product is formed via one-electron reduction of the radical anion [Re(CO)3(bpy)(CO2H)]•-, which is the main byproduct in the catalytic cycle. " + }, + { + "abstract2": "Abstract" + }, + { + "language": "en" + }, + { + "fulltext_html": "/doi/full/10.1021/om960044%2B" + }, + { + "fulltext_html": "/doi/full/10.1021/om500389y" + }, + { + "fulltext_html": "/doi/full/10.1021/ja500403e" + }, + { + "fulltext_html": "/doi/full/10.1021/ic500025k" + }, + { + "fulltext_html": "/doi/full/10.1021/om500044a" + }, + { + "fulltext_html": "/doi/full/10.1021/ja501051s" + }, + { + "fulltext_pdf": "/doi/pdf/10.1021/om960044%2B" + }, + { + "figure": "/appl/literatum/publisher/achs/journals/content/orgnd7/1996/orgnd7.1996.15.issue-15/om960044%2B/production/images/medium/om9600441n00001.gif" + }, + { + "copyright": "Copyright © 1996 American Chemical Society" + }, + { + "om9600441n00001.gif": "d3cd6a0e739ff29fdc972fd8c1360306" + }, + { + "rendered.html": "2b85c69bf2247835acae8dfc33d95ca8" + } + ] +} \ No newline at end of file diff --git a/test/springer.json b/test/springer.json new file mode 100644 index 0000000..84b0f3c --- /dev/null +++ b/test/springer.json @@ -0,0 +1,609 @@ +{ + "http://link.springer.com/article/10.1007/s00894-014-2429-8": [ + { + "publisher": "Springer Berlin Heidelberg" + }, + { + "title": "Construction and conformational behavior of peptoids with cis-amide bond geometry: design of a peptoid with alternate φ, ψ values of inverse PP-II/PP-II and PP-I structures" + }, + { + "authors": "Fateh Singh Nandel" + }, + { + "authors": "Radhika Rani Jaswal" + }, + { + "authors": "Avneet Saini" + }, + { + "authors": "Vibhuti Nandel" + }, + { + "authors": "Mohd Shafique" + }, + { + "date": "2014/09/01" + }, + { + "volume": "20" + }, + { + "issue": "9" + }, + { + "firstpage": "1" + }, + { + "doi": "10.1007/s00894-014-2429-8" + }, + { + "journal": "Journal of Molecular Modeling" + }, + { + "description": "In peptoids due to the absence of amide protons, the backbone is devoid of hydrogen bond donor, linked by tertiary amide, which can be iso-energetic between cis and trans-amide bond geometry. The pept" + }, + { + "abstract": "In peptoids due to the absence of amide protons, the backbone is devoid of hydrogen bond donor, linked by tertiary amide, which can be iso-energetic between cis and trans-amide bond geometry. The peptoids can be realized with cis amide bond if the side chain of ith residue can engage the carbonyl group of ith-1 residue in CH--O interactions. Simulations studies both in water and DMSO have been carried out. The peptoid Ac-(Ntle)7 -NMe2 can adopt degenerate conformations with alternate φ, ψ values of inverse PP-I and PP-I type structure’s, or vice versa in water. In DMSO, Ac-(Ntle)7-NMe2 also adopts inverse PP-I type structure. Like polyproline, molecule adopting a rigid structure can be used as molecular markers or spacers in biological studies." + }, + { + "abstract": "The peptoid Ac-(Nala-Ntle)3-NMe2 with alternate trans and cis amide bond geometry for Nala and Ntle residue corresponding to inverse PP-II/PP-II type and for Ntle residue of PP-I type." + }, + { + "abstract_html": "http://link.springer.com/article/10.1007/s00894-014-2429-8" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2Fs00894-014-2429-8.pdf" + }, + { + "fulltext_html": "http://link.springer.com/article/10.1007/s00894-014-2429-8/fulltext.html" + }, + { + "supplementary_material": "/content/esm/art:10.1007/s00894-014-2429-8/file/MediaObjects/894_2014_2429_MOESM1_ESM.doc" + }, + { + "894_2014_2429_MOESM1_ESM.doc": "1de5071739e63c48055d35e4d826eecb" + }, + { + "rendered.html": "259cf9345c6fa9e043533b8ac52aa88b" + } + ], + "http://link.springer.com/article/10.1007/s00216-014-7672-4": [ + { + "publisher": "Springer Berlin Heidelberg" + }, + { + "title": "Suspect screening and target quantification of multi-class pharmaceuticals in surface water based on large-volume injection liquid chromatography and time-of-flight mass spectrometry" + }, + { + "authors": "Leendert Vergeynst" + }, + { + "authors": "Herman Van Langenhove" + }, + { + "authors": "Pieter Joos" + }, + { + "authors": "Kristof Demeestere" + }, + { + "date": "2014/04/01" + }, + { + "volume": "406" + }, + { + "issue": "11" + }, + { + "firstpage": "2533" + }, + { + "doi": "10.1007/s00216-014-7672-4" + }, + { + "journal": "Analytical and Bioanalytical Chemistry" + }, + { + "description": "The ever-growing number of emerging micropollutants such as pharmaceuticals requests rapid and sensitive full-spectrum analytical techniques. Time-of-flight high-resolution mass spectrometry (TOF-HRMS" + }, + { + "abstract": "The ever-growing number of emerging micropollutants such as pharmaceuticals requests rapid and sensitive full-spectrum analytical techniques. Time-of-flight high-resolution mass spectrometry (TOF-HRMS) is a promising alternative for the state-of-the-art tandem mass spectrometry instruments because of its ability to simultaneously screen for a virtually unlimited number of suspect analytes and to perform target quantification. The challenge for such suspect screening is to develop a strategy, which minimizes the false-negative rate without restraining numerous false-positives. At the same time, omitting laborious sample enrichment through large-volume injection ultra-performance liquid chromatography (LVI-UPLC) avoids selective preconcentration. A suspect screening strategy was developed using LVI-UPLC-TOF-MS aiming the detection of 69 multi-class pharmaceuticals in surface water without the a priori availability of analytical standards. As a novel approach, the screening takes into account the signal-intensity-dependent accurate mass error of TOF-MS, hereby restraining 95 % of the measured suspect pharmaceuticals present in surface water. Application on five Belgian river water samples showed the potential of the suspect screening approach, as exemplified by a false-positive rate not higher than 15 % and given that 30 out of 37 restrained suspect compounds were confirmed by the retention time of analytical standards. Subsequently, this paper discusses the validation and applicability of the LVI-UPLC full-spectrum HRMS method for target quantification of the 69 pharmaceuticals in surface water. Analysis of five Belgian river water samples revealed the occurrence of 17 pharmaceuticals in a concentration range of 17 ng L−1 up to 3.1 μg L−1." + }, + { + "abstract": " Figure " + }, + { + "abstract_html": "http://link.springer.com/article/10.1007/s00216-014-7672-4" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2Fs00216-014-7672-4.pdf" + }, + { + "fulltext_html": "http://link.springer.com/article/10.1007/s00216-014-7672-4/fulltext.html" + }, + { + "supplementary_material": "/content/esm/art:10.1007/s00216-014-7672-4/file/MediaObjects/216_2014_7672_MOESM1_ESM.pdf" + }, + { + "figure": "/static-content/images/620/art%253A10.1007%252Fs00216-014-7672-4/MediaObjects/216_2014_7672_Figa_HTML.gif" + }, + { + "216_2014_7672_Figa_HTML.gif": "a3d4d59df9737410ee8541b97eae76dc" + }, + { + "rendered.html": "38f42ec47d5d3b0a4e6e89ce4aff90c0" + } + ], + "http://link.springer.com/article/10.1007/s00216-013-7560-3": [ + { + "publisher": "Springer Berlin Heidelberg" + }, + { + "title": "A fluorescence-based high throughput assay for the determination of small molecule−human serum albumin protein binding" + }, + { + "authors": "Megan M. McCallum" + }, + { + "authors": "Alan J. Pawlak" + }, + { + "authors": "William R. Shadrick" + }, + { + "authors": "Anton Simeonov" + }, + { + "authors": "Ajit Jadhav" + }, + { + "authors": "Adam Yasgar" + }, + { + "authors": "David J. Maloney" + }, + { + "authors": "Leggy A. Arnold" + }, + { + "date": "2014/03/01" + }, + { + "volume": "406" + }, + { + "issue": "7" + }, + { + "firstpage": "1867" + }, + { + "doi": "10.1007/s00216-013-7560-3" + }, + { + "journal": "Analytical and Bioanalytical Chemistry" + }, + { + "description": "Herein, we describe the development of a fluorescence-based high throughput assay to determine the small molecule binding towards human serum albumin (HSA). This innovative competition assay is based " + }, + { + "abstract": "Herein, we describe the development of a fluorescence-based high throughput assay to determine the small molecule binding towards human serum albumin (HSA). This innovative competition assay is based on the use of a novel fluorescent small molecule Red Mega 500 with unique spectroscopic and binding properties. The commercially available probe displays a large fluorescence intensity difference between the protein-bound and protein-unbound state. The competition of small molecules for HSA binding in the presence of probe resulted in low fluorescence intensities. The assay was evaluated with the library of pharmacological active compounds (LOPAC) small molecule library of 1,280 compounds identifying known high protein binders. The small molecule competition of HSA−Red Mega 500 binding was saturable at higher compound concentrations and exhibited IC50 values between 3 and 24 μM. The compound affinity toward HSA was confirmed by isothermal titration calorimetry indicating that the new protein binding assay is a valid high throughput assay to determine plasma protein binding." + }, + { + "abstract": " Figure " + }, + { + "abstract_html": "http://link.springer.com/article/10.1007/s00216-013-7560-3" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2Fs00216-013-7560-3.pdf" + }, + { + "fulltext_html": "http://link.springer.com/article/10.1007/s00216-013-7560-3/fulltext.html" + }, + { + "figure": "/static-content/images/274/art%253A10.1007%252Fs00216-013-7560-3/MediaObjects/216_2013_7560_Figa_HTML.gif" + }, + { + "216_2013_7560_Figa_HTML.gif": "388dde09acd4582efcf02a188e38cc43" + }, + { + "rendered.html": "022b01cfc7320314b92b0d7bf054b764" + } + ], + "http://link.springer.com/article/10.1007/BF01024715": [ + { + "publisher": "Kluwer Academic Publishers" + }, + { + "title": "Continuous cultivation of a yeast strain for biotransformation of L-acetyl phenyl carbinol (L-PAC) from benzaldehyde" + }, + { + "authors": "C. K. M. Tripathi" + }, + { + "authors": "S. K. Basu" + }, + { + "authors": "V. C. Vora" + }, + { + "authors": "J. R. Mason" + }, + { + "authors": "S. J. Pirt" + }, + { + "date": "1988/09/01" + }, + { + "volume": "10" + }, + { + "issue": "9" + }, + { + "firstpage": "635" + }, + { + "doi": "10.1007/BF01024715" + }, + { + "journal": "Biotechnology Letters" + }, + { + "description": "L-PAC production by a yeast strain harvested from glucose limited continuous cultures grown at different dilution rates has been studied. The specific transformation rate is higher for the cells which" + }, + { + "abstract": "L-PAC production by a yeast strain harvested from glucose limited continuous cultures grown at different dilution rates has been studied. The specific transformation rate is higher for the cells which have been grown at higher dilution rates." + }, + { + "abstract_html": "http://link.springer.com/article/10.1007/BF01024715" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2FBF01024715.pdf" + }, + { + "BF01024715": "30adcd173a3f9e496aa0dad49f0ab4fc" + }, + { + "rendered.html": "30adcd173a3f9e496aa0dad49f0ab4fc" + } + ], + "http://link.springer.com/article/10.1007/s40333-014-0028-2": [ + { + "publisher": "Science Press" + }, + { + "title": "Ecophysiological aspects in 105 plants species of saline and arid environments in Tunisia" + }, + { + "authors": "Abdallah Atia" + }, + { + "authors": "Mokded Rabhi" + }, + { + "authors": "Ahmed Debez" + }, + { + "authors": "Chedly Abdelly" + }, + { + "authors": "Houda Gouia" + }, + { + "authors": "Chiraz Chaffei Haouari" + }, + { + "authors": "Abderrazak Smaoui" + }, + { + "date": "2014/12/01" + }, + { + "volume": "6" + }, + { + "issue": "6" + }, + { + "firstpage": "762" + }, + { + "doi": "10.1007/s40333-014-0028-2" + }, + { + "journal": "Journal of Arid Land" + }, + { + "description": "In Tunisian arid regions, plant life forms, ecotypes, physiological types and photosynthetic pathways (C3, C4 or CAM) remain unclear. Understanding the characters of these plant species could be impor" + }, + { + "abstract": "In Tunisian arid regions, plant life forms, ecotypes, physiological types and photosynthetic pathways (C3, C4 or CAM) remain unclear. Understanding the characters of these plant species could be important for land restoration. A literature survey was conducted for 105 species from arid regions of Tunisia. These plant species belong to several ecotypes: halophytes, xerophytes, gypsophytes, psamophytes, xero-halophytes, gypso-halophytes, psamo-halophytes, psamo-xerophytes, xero-gypsophytes and hygro-halophytes. The variation of photosynthetic pathway types in the 105 studied species shows that 56.2% are C3, 41.0% are C4, 1.9% are CAM and 1.0% are C3-CAM. The C3 pathway is more abundant in the halophytes, whereas the C4 one is more common in the xerophytes, gypsophytes, gypso-halophytes and psamo-halophytes. The ratio of C3 to C4 species (C3/C4 ratio) is 0.2 in the psamo-halophytes, 0.8 in the gypso-halophytes, 1.1 in the xerophytes, 1.6 in the xero-halophytes, 1.8 in the hygrohalophytes, 2.0 in the psamophytes and 3.8 in the halophytes. The annuals are mainly C3 plants whereas most of perennials are C4 ones. The C3/C4 ratio is 1.3 in succulent species and 1.4 in non-succulent species. Thus, succulence seems not to affect the distribution of C3 and C4 pathways within the studied plants. This investigation shows high percentages of C4 plants in plants of Tunisian arid regions. However, there are significant differences in their abundance among ecotypes. Based on C3/C4 ratio, the abundance of the C4 pathway is in the following order: psamo-halophytes, gypso-halophytes, xerophytes, xero-halophytes, hygro-halophytes, psamophytes, halophytes. In Tunisian arid regions, C4 species are most abundant in xerophytes and less abundant in halophytes. In the Chenopodiaceae the number of C3 plants is 13 and the number of C4 species is 20 and in the Poaceae the number of C3 was 23 and the number of C4 was 19 species. Thus, the most C4 proportion is in the Chenopodiaceae and Poaceae species. This confirms the fact that the Chenopodiaceae and the Poaceae were the leading families that tolerate salinity and aridity." + }, + { + "abstract_html": "http://link.springer.com/article/10.1007/s40333-014-0028-2" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2Fs40333-014-0028-2.pdf" + }, + { + "rendered.html": "42248e742e8bfc27a820c602aeb64371" + }, + { + "s40333-014-0028-2": "42248e742e8bfc27a820c602aeb64371" + } + ], + "http://link.springer.com/article/10.1007/s40069-014-0084-1": [ + { + "publisher": "Korea Concrete Institute" + }, + { + "title": "Prediction of Concrete Pumping Using Various Rheological Models" + }, + { + "authors": "Myoung Sung Choi" + }, + { + "authors": "Young Jin Kim" + }, + { + "authors": "Jin Keun Kim" + }, + { + "date": "2014/12/01" + }, + { + "volume": "8" + }, + { + "issue": "4" + }, + { + "firstpage": "269" + }, + { + "doi": "10.1007/s40069-014-0084-1" + }, + { + "journal": "International Journal of Concrete Structures and Materials" + }, + { + "description": "When concrete is being transported through a pipe, the lubrication layer is formed at the interface between concrete and the pipe wall and is the major factor facilitating concrete pumping. A possible" + }, + { + "abstract": "When concrete is being transported through a pipe, the lubrication layer is formed at the interface between concrete and the pipe wall and is the major factor facilitating concrete pumping. A possible mechanism that illustrates to the formation of the layer is the shear-induced particle migration and determining the rheological parameters is a paramount factor to simulate the concrete flow in pipe. In this study, numerical simulations considering various rheological models in the shear-induced particle migration were conducted and compared with 170 m full-scale pumping tests. It was found that the multimodal viscosity model representing concrete as a three-phase suspension consisting of cement paste, sand and gravel can accurately simulate the lubrication layer. Moreover, considering the particle shape effects of concrete constituents with increased intrinsic viscosity can more exactly predict the pipe flow of pumped concrete." + }, + { + "abstract_html": "http://link.springer.com/article/10.1007/s40069-014-0084-1" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2Fs40069-014-0084-1.pdf" + }, + { + "fulltext_html": "http://link.springer.com/article/10.1007/s40069-014-0084-1/fulltext.html" + }, + { + "rendered.html": "75b8db48c86c853a8cc2453325de0e0f" + }, + { + "s40069-014-0084-1": "75b8db48c86c853a8cc2453325de0e0f" + } + ], + "http://link.springer.com/article/10.1007/BF02896800": [ + { + "publisher": "Springer-Verlag" + }, + { + "title": "Costruzione di classi filtrali" + }, + { + "authors": "Roberto Magari" + }, + { + "date": "1969/12/01" + }, + { + "volume": "14" + }, + { + "issue": "1" + }, + { + "firstpage": "35" + }, + { + "doi": "10.1007/BF02896800" + }, + { + "journal": "Annali dell’Università di Ferrara" + }, + { + "description": "SiaH una classe filtrale (1) di strutture algebriche di un certo tipo eK una classe di strutture algebriche semplici e a sottoalgebre semplici che siano portate da un funtore dimenticante in strutture" + }, + { + "abstract": "SiaH una classe filtrale (1) di strutture algebriche di un certo tipo eK una classe di strutture algebriche semplici e a sottoalgebre semplici che siano portate da un funtore dimenticante in strutture algebriche diSPH." + }, + { + "abstract": "Dettametafiltrale una classeK nelle predette condizioni si danno condizioni perchè una tal classe sia filtrale e si costruiscono alcune notevoli classi filtrali." + }, + { + "abstract": "A classK of similar algebras is said to be: «filtrale» («semifiltrale» if each congruenceR on each subdirect (direct) product of a family of elements ofK is «associated» with a filterF onI («associated» in the sense of the reduced products theory, i.e.: " + }, + { + "abstract": "A varietyV of algebras is said to be: «sempisimple»: iff each is semisimple, «sotto-semisemplice»: ifV ⊆SPΣ (Σ: class of simple algebras ofV)." + }, + { + "abstract": "An algebra is said to be «regolare» if each congruenceR on each subalgebra of extends to a congruenceS on " + }, + { + "abstract": "In a previous paper ([6]) I proved:" + }, + { + "abstract": "LetK be a class of similar algebras, Σ the class of the simple algebras ofVK \\(\\overline \\Sigma = \\Sigma \\cap HP\\) K. Then:" + }, + { + "abstract": "ifK is «semifiltrale» then \\(\\overline \\Sigma \\) is «semifiltrale». ifK is «filtrale» then:" + }, + { + "abstract": " V K is «sottosemisemplice»." + }, + { + "abstract": "each congruence on each K is associated with a filter." + }, + { + "abstract": "each K is «regolare»." + }, + { + "abstract": "ifK={W} andW is finite thenW is semicategorical (I observe in [6] that this results can be obtained as a simple consequence of Astromoff’s, Foster’s and Pixley’s results)." + }, + { + "abstract": "ifK={W} andW is infinite then there are simple algebras inV K wich are not isomorphic toW and V K ⊆|⊆SP K." + }, + { + "abstract": "Let (a), (b), (c), (d) be the following properties:" + }, + { + "abstract": "Σ is «filtrale»." + }, + { + "abstract": "each algebra ofV K is «regolare»." + }, + { + "abstract": " V K is semisimple." + }, + { + "abstract": " V K=SP K. then the following implications hold " + }, + { + "abstract": "LetK be a class of algebras of a fied type.K is said to be «metafiltrale» iff every is simple and there is a «filtrale» classH of algebras and a forgetful functors δ such that δK=⊆SP H." + }, + { + "abstract": "I find some sufficient conditions for a «metafiltrale» classe to be «filtrale» and I give some noteworthy examples of «filtrali» and «semifiltrali» classes, in particular the varieties of «α-plurireticoli» (cfr. n. 9)." + }, + { + "abstract": "Tipical corollary:every finite systems wich is simple (and has only simple subalgebras) and where ." + }, + { + "abstract_html": "http://link.springer.com/article/10.1007/BF02896800" + }, + { + "language": "it" + }, + { + "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2FBF02896800.pdf" + }, + { + "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f1.jpg" + }, + { + "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f2.jpg" + }, + { + "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f3.jpg" + }, + { + "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f4.jpg" + }, + { + "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f5.jpg" + }, + { + "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f6.jpg" + }, + { + "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f7.jpg" + }, + { + "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f8.jpg" + }, + { + "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f9.jpg" + }, + { + "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f10.jpg" + }, + { + "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f11.jpg" + }, + { + "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f12.jpg" + }, + { + "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f13.jpg" + }, + { + "11565_2008_Article_BF02896800_f3.jpg": "0bbf5af2bcb2347f64231d90e1c812f6" + }, + { + "rendered.html": "3880b5ef1a64dd076881788347e07e8b" + } + ], + "http://link.springer.com/article/10.1007/s10719-014-9555-5": [ + { + "publisher": "Springer US" + }, + { + "title": "Association between serum sulfatide and carotid intima media thickness in patients with familial hypercholesterolemia" + }, + { + "authors": "Gang Li" + }, + { + "authors": "Rui Hu" + }, + { + "firstpage": "1" + }, + { + "doi": "10.1007/s10719-014-9555-5" + }, + { + "journal": "Glycoconjugate Journal" + }, + { + "description": "There is a positive association between sulfatide and atherosclerosis in an animal model for human familial hypercholesterolemia. Carotid intima–media thickness (IMT) is thought to be a marker of athe" + }, + { + "abstract": "There is a positive association between sulfatide and atherosclerosis in an animal model for human familial hypercholesterolemia. Carotid intima–media thickness (IMT) is thought to be a marker of atherosclerosis in humans. We investigated the relationship between sulfatide and carotid IMT in heterozygous familial hypercholesterolemia (FH) patients. Thirty-five genetically-verified heterozygous patients with FH and 34 healthy controls were recruited into our study. We measured serum sulfatide levels, the carotid IMT, and conventional cardiovascular risk factors including obesity parameters, blood pressure, fasting blood glucose, and lipid profiles. Subjects with heterozygous FH had significantly elevated serum sulfatide, elevated total cholesterol, low-density lipoprotein cholesterol, and increased carotid IMT compared with control subjects. In patients with FH, univariate analysis showed that serum sulfatide was significantly correlated with carotid IMT. Multiple linear regression analysis indicated that serum sulfatide was the only independent predictor of carotid IMT in patients with FH. Patients with heterozygous FH had significantly higher carotid IMT and the level of serum sulfatide was independently associated with atherosclerotic progression. (R: 0.720, R2: 0.503, p " + }, + { + "abstract_html": "http://link.springer.com/article/10.1007/s10719-014-9555-5" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2Fs10719-014-9555-5.pdf" + }, + { + "fulltext_html": "http://link.springer.com/article/10.1007/s10719-014-9555-5/fulltext.html" + }, + { + "rendered.html": "4664240a9c97d4f0478b51c0c3ab61dd" + }, + { + "s10719-014-9555-5": "4664240a9c97d4f0478b51c0c3ab61dd" + } + ] +} \ No newline at end of file diff --git a/test/tandf.json b/test/tandf.json new file mode 100644 index 0000000..3cf9c87 --- /dev/null +++ b/test/tandf.json @@ -0,0 +1,357 @@ +{ + "http://www.tandfonline.com/doi/abs/10.1080/02757540.2013.878336": [ + { + "publisher": "Taylor & Francis" + }, + { + "title": "Effect of dye auxiliaries on chemical oxygen demand and colour competitive removal from textile effluents using Posidonia oceanica" + }, + { + "authors": "Sonia Dridi-Dhaouadi" + }, + { + "authors": "Mohamed Farouk Mhenni" + }, + { + "date": "2014-06-12" + }, + { + "pagerange": "pages 579-588" + }, + { + "doi": "10.1080/02757540.2013.878336" + }, + { + "description": "The use of an abundant and widely distributed seagrass species, Posidonia oceanica, as a biosorbent for the direct dye Yellow 44 was successfully shown. The studies were performed on the single dyestuff dissolved in water and in a dyebath containing agents commonly used in the textile industry, i.e. a surfactant (Lavotan TBU), a sequestring agent (Meropan DPE), a softening agent (Eurosoft CI10) and a salt (NaCl). The colour reduction results showed that P. oceanica was found to be more efficient for removal of Yellow 44 from an aqueous solution (162 mg g−1) than from a dyebath solution (135 mg g−1), according to the Langmuir isotherm model. For the single dyestuff sorption, Fourier transform infrared and X-ray photoelectron spectroscopy studies highlighted chemical sorption between the dye alcohol function and the sorbent acid function. The chemical oxygen demand removal percentages were found to be 54.9 and 76.6% for Yellow 44 dissolved in aqueous solution and in dyebath solution, respectively. This conf..." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/02757540.2013.878336" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/02757540.2013.878336" + }, + { + "fulltext_html": "/doi/full/10.1080/02757540.2013.878336" + }, + { + "fulltext_html": "/doi/full/10.1080/02757540.2013.878336" + }, + { + "supplementary_material": "/doi/suppl/10.1080/02757540.2013.878336#tabModule" + }, + { + "supplementary_material": "/doi/suppl/10.1080/02757540.2013.878336#tabModule" + }, + { + "02757540.2013.878336": "e016a9d960a97c5656a75bf37812fe49" + }, + { + "rendered.html": "6c3a26e89007055588c43ac8edfa8287" + } + ], + "http://www.tandfonline.com/doi/abs/10.1080/1747423X.2013.786151": [ + { + "publisher": "Taylor & Francis" + }, + { + "title": "Detecting land-use change from seasonal vegetation dynamics on regional scale with MODIS EVI 250-m time-series imagery" + }, + { + "authors": "Yudi Setiawan" + }, + { + "authors": "Kunihiko Yoshino" + }, + { + "date": "2014-06-05" + }, + { + "pagerange": "pages 304-330" + }, + { + "doi": "10.1080/1747423X.2013.786151" + }, + { + "description": "Simultaneous analysis of land surface attributes and their seasonal changes provides a broader view of land-use and land-cover change. This study attempted to detect the change in inter-annual temporal vegetation dynamics, which reflects a change in land surface attributes. We explored 250-m multi-temporal MODIS EVI 16-day composite data from 2001 to 2007 to characterize a change in vegetation dynamics related to land-use change detection. The MODIS data was filtered in time-frequency space by wavelet function in order to identify and reduce the overall noise so as not to lose useful information from the time series data. The results show that by characterizing temporal vegetation dynamics, it is possible to distinguish actual land-use change based on land-cover dynamics. The result was evaluated using 18,626 reference pixels and showed an overall accuracy of 76.10%. In agricultural land use, such as upland and plantation, the weakest results were caused by mixed pixels from MODIS 250-m grid data as well ..." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/1747423X.2013.786151" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/1747423X.2013.786151" + }, + { + "fulltext_html": "/doi/full/10.1080/1747423X.2013.786151" + }, + { + "fulltext_html": "/doi/full/10.1080/1747423X.2013.786151" + }, + { + "1747423X.2013.786151": "df40110001381ee8c9ff82c14e9b337b" + }, + { + "rendered.html": "7738b7d284697900c670c4237101781c" + } + ], + "http://www.tandfonline.com/doi/abs/10.1080/19376812.2013.838660": [ + { + "publisher": "Routledge" + }, + { + "title": "An Intensity Analysis of land-use and land-cover change in Karatu District, Tanzania: community perceptions and coping strategies" + }, + { + "authors": "Leonia Raphael John" + }, + { + "authors": "Herbert Hambati" + }, + { + "authors": "Frederick Ato Armah" + }, + { + "date": "2014-05-02" + }, + { + "pagerange": "pages 150-173" + }, + { + "doi": "10.1080/19376812.2013.838660" + }, + { + "description": "Land-use and land-cover changes (LULCCs) are the result of complex interactions between the human (cultural, socio-economic and political) and the biophysical environment at different spatial scales. The present study assessed the spatial distribution of LULC (1976–2008) in the high and low altitude zones in the northern highlands of Karatu, Tanzania, using both qualitative (in-depth interviews and focus group discussions) and quantitative techniques (Intensity Analysis). The qualitative approach was used to elicit information on the coping strategies adopted by land users as transitions occurred with time and the Intensity Analysis was used to assess the systematic land losses, gains and persistence of the various land categories with time. The results of the Intensity Analysis show that overall land transformation is decelerating in both agro-ecological zones across the two time intervals. In the low altitude zone, woodland, settlements and bushland are active categories unlike cultivated and grassland,..." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/19376812.2013.838660" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/19376812.2013.838660" + }, + { + "fulltext_html": "/doi/full/10.1080/19376812.2013.838660" + }, + { + "fulltext_html": "/doi/full/10.1080/19376812.2013.838660" + }, + { + "19376812.2013.838660": "ad38dee2f4a2955e64b88f234d5ea8fd" + }, + { + "rendered.html": "9f2cb3dfa837580b736ded0bd98de5ba" + } + ], + "http://www.tandfonline.com/doi/abs/10.1080/13647830.2014.923116": [ + { + "publisher": "Taylor & Francis" + }, + { + "title": "Triple flame: Inherent asymmetries and pentasectional character" + }, + { + "authors": "Albert Jordà Juanós" + }, + { + "authors": "William A. Sirignano" + }, + { + "date": "2014-07-11" + }, + { + "pagerange": "pages 454-473" + }, + { + "doi": "10.1080/13647830.2014.923116" + }, + { + "description": "A two-dimensional triple-flame numerical model of a laminar combustion process reflects flame asymmetric structural features that other analytical models do not generate. It reveals the pentasectional character of the triple flame, composed of the central pure diffusion-flame branch and the fuel-rich and fuel-lean branches, each of which is divided into two sections: a near-stoichiometric section and a previously unreported near-flammability-limits section with combined diffusion and premixed character. Results include propagation velocity, fuel and oxidiser mass fractions, temperature and reaction rates. Realistic stoichiometric ratios and reaction orders match experimental planar flame characteristics. Constant density, a one-step reaction, and a mixture fraction gradient at the inlet as the simulation parameter are imposed. The upstream equivalence ratio or the upstream reactant mass fractions are linear or hyperbolic functions of the transverse coordinate. The use here of experimental kinetics data di..." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/13647830.2014.923116" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/13647830.2014.923116" + }, + { + "fulltext_html": "/doi/full/10.1080/13647830.2014.923116" + }, + { + "fulltext_html": "/doi/full/10.1080/13647830.2014.923116" + }, + { + "13647830.2014.923116": "f1582f18b27ad25acb51ae3c6da0aa2f" + }, + { + "rendered.html": "589eb09898f9adb86f6c917b393a6b92" + } + ], + "http://www.tandfonline.com/doi/abs/10.1080/16841360802338738": [ + { + "publisher": " Routledge " + }, + { + "title": "Double degrees in the context of the Bologna process" + }, + { + "authors": " Anne Klebes‐Pelissier " + }, + { + "date": "2008-12-11" + }, + { + "pagerange": "pages 173-180" + }, + { + "doi": "10.1080/16841360802338738" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/16841360802338738" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/16841360802338738" + }, + { + "fulltext_html": "/doi/full/10.1080/16841360802338738" + }, + { + "fulltext_html": "/doi/full/10.1080/16841360802338738" + }, + { + "16841360802338738": "bcca16511d449aaf5c668fa354914770" + }, + { + "rendered.html": "61d473f6941147703842180e59ba6e8e" + } + ], + "http://www.tandfonline.com/doi/abs/10.1207/S15326926CLP0701_04": [ + { + "publisher": " Lawrence Erlbaum Associates, Inc. " + }, + { + "title": "Litigation Public Relations: The Lawyers' Duty to Balance News Coverage of Their Clients" + }, + { + "authors": " John C. Watson " + }, + { + "date": "2010-01-14" + }, + { + "pagerange": "pages 77-103" + }, + { + "description": "As the 20th century began its final decade, litigation public relations was more rigorously condemned than condoned. By the end of the decade, the proliferation of the practice and the failure of the bar and bench to forbid it had made the criticism virtually moot. This article considers whether there is a basis for making the right to practice litigation public relations an obligation to do so. The article concludes that the right properly belongs to clients and not their attorneys, and finds a basis in contract and malpractice law for requiring attorneys to tend to their clients' interests in the court of public opinion as zealously as they do in courts of law." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "/doi/pdf/10.1207/S15326926CLP0701_04" + }, + { + "fulltext_pdf": "/doi/pdf/10.1207/S15326926CLP0701_04" + }, + { + "rendered.html": "e032e351321d1553f2fafad837a97709" + }, + { + "S15326926CLP0701_04": "a8e25f16f909c51af2c8c77e70adc272" + } + ], + "http://www.tandfonline.com/doi/abs/10.1080/02630672.1992.9689834": [ + { + "publisher": " Taylor & Francis Group " + }, + { + "title": "AUTISM & DRAMATHERAPY" + }, + { + "authors": " Jeremy Carrette " + }, + { + "date": "2011-09-09" + }, + { + "pagerange": "pages 17-20" + }, + { + "doi": "10.1080/02630672.1992.9689834" + }, + { + "description": "The difficulty is to discover the archimedic point at which the technique can be applied effectively. We found that the archimedic point of treatment is the psychological level of an individual on which he is truly spontaneous. J L Moreno (1946, 222)" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/02630672.1992.9689834" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/02630672.1992.9689834" + }, + { + "02630672.1992.9689834": "a90cc82ab7d041c43cc87b1217a86abd" + }, + { + "rendered.html": "82f3ed7f8948007304dfcc6e7674091a" + } + ], + "http://www.tandfonline.com/doi/abs/10.1080/03085147.2012.760347": [ + { + "publisher": "Routledge" + }, + { + "title": "‘Because in Chile [carbon] markets work!’ Exploring an experimental implementation of an emissions trading scheme to deal with industrial air pollution in Santiago" + }, + { + "authors": "Sebastián Ureta" + }, + { + "date": "2014-06-04" + }, + { + "pagerange": "pages 285-306" + }, + { + "doi": "10.1080/03085147.2012.760347" + }, + { + "description": "AbstractEmissions trading schemes have gained an important degree of momentum in recent years, rapidly becoming mainstream solutions to deal with the negative environmental consequences of human activity such as pollution and global warming. However there is still little empirical knowledge about what specific kind of work emissions trading schemes do. Using the analytical tools provided by science and technology studies, especially developments studying markets and economic practices, this paper looks to contribute to filling this void by exploring three kinds of work that emissions trading schemes might do: performing a textbook market of emissions permits, performing a civilized market in which a multitude of heterogeneous actors participate and as exemplars of the validity of certain economic knowledge. In order to explore the usability of this conceptualization the paper will then analyze one of earliest concrete implementations of this device: an emissions trading scheme introduced to deal with indu..." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/03085147.2012.760347" + }, + { + "fulltext_pdf": "/doi/pdf/10.1080/03085147.2012.760347" + }, + { + "fulltext_html": "/doi/full/10.1080/03085147.2012.760347" + }, + { + "fulltext_html": "/doi/full/10.1080/03085147.2012.760347" + }, + { + "03085147.2012.760347": "7c81a6b86b030f843813b273dc63dc6e" + }, + { + "rendered.html": "dc0ad71bc27f5ca9782b5454e66d6605" + } + ] +} \ No newline at end of file diff --git a/test/wiley.json b/test/wiley.json new file mode 100644 index 0000000..6d19150 --- /dev/null +++ b/test/wiley.json @@ -0,0 +1,556 @@ +{ + "http://onlinelibrary.wiley.com/doi/10.1002/anie.201403615/abstract": [ + { + "publisher": "WILEY‐VCH Verlag" + }, + { + "title": "A Supercharged Fluorescent Protein as a Versatile Probe for Homogeneous DNA Detection and Methylation Analysis" + }, + { + "authors": "Lei, Chunyang" + }, + { + "authors": "Huang, Yan" + }, + { + "authors": "Nie, Zhou" + }, + { + "authors": "Hu, Jun" + }, + { + "authors": "Li, Lijun" + }, + { + "authors": "Lu, Guoyan" + }, + { + "authors": "Han, Yitao" + }, + { + "authors": "Yao, Shouzhuo" + }, + { + "date": "2014/08/04" + }, + { + "volume": "53" + }, + { + "issue": "32" + }, + { + "firstpage": "8358" + }, + { + "doi": "10.1002/anie.201403615" + }, + { + "journal": "Angewandte Chemie International Edition" + }, + { + "abstract": "Supercharged proteins are a new class of functional proteins with exceptional stability and potent ability to deliver bio‐macromolecules into cells. As a proof‐of‐principle, a novel application of supercharged proteins as a versatile biosensing platform for nucleic acid detection and epigenetics analysis is presented. Taking supercharged green fluorescent protein (ScGFP) as the signal reporter, a simple turn‐on homogenous method for DNA detection has been developed based on the polyionic nanoscale complex of ScGFP/DNA and toehold strand displacement. This assay shows high sensitivity and potent ability to detect single‐base mismatch. Furthermore, combined with bisulfite conversion, this ScGFP‐based assay was further applied to analyze site‐specific DNA methylation status of genomic DNA extracted from real human colon carcinoma tissue sample with ultrahigh sensitivity (4 amol methylated DNA)." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/anie.201403615/pdf" + }, + { + "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/anie.201403615/full" + }, + { + "supplementary_material": "/doi/10.1002/anie.201403615/suppinfo" + }, + { + "rendered.html": "b3986b19732048c6aad2aba454c1a683" + }, + { + "suppinfo": "3768366620b4ad7feabdf1fd2731096f" + } + ], + "http://onlinelibrary.wiley.com/doi/10.1002/anie.201404164/abstract": [ + { + "publisher": "WILEY‐VCH Verlag" + }, + { + "title": "pH‐Dependent Proton Conducting Behavior in a Metal–Organic Framework Material" + }, + { + "authors": "Phang, Won Ju" + }, + { + "authors": "Lee, Woo Ram" + }, + { + "authors": "Yoo, Kicheon" + }, + { + "authors": "Ryu, Dae Won" + }, + { + "authors": "Kim, BongSoo" + }, + { + "authors": "Hong, Chang Seop" + }, + { + "date": "2014/08/04" + }, + { + "volume": "53" + }, + { + "issue": "32" + }, + { + "firstpage": "8383" + }, + { + "doi": "10.1002/anie.201404164" + }, + { + "journal": "Angewandte Chemie International Edition" + }, + { + "abstract": "A porous metal–organic framework (MOF), [Ni2(dobdc)(H2O)2]⋅6 H2O (Ni2(dobdc) or Ni‐MOF‐74; dobdc4−=2,5‐dioxido‐1,4‐benzenedicarboxylate) with hexagonal channels was synthesized using a microwave‐assisted solvothermal reaction. Soaking Ni2(dobdc) in sulfuric acid solutions at different pH values afforded new proton‐conducting frameworks, H+@Ni2(dobdc). At pH 1.8, the acidified MOF shows proton conductivity of 2.2×10−2 S cm−1 at 80 °C and 95 % relative humidity (RH), approaching the highest values reported for MOFs. Proton conduction occurs via the Grotthuss mechanism with a significantly low activation energy as compared to other proton‐conducting MOFs. Protonated water clusters within the pores of H+@Ni2(dobdc) play an important role in the conduction process." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/anie.201404164/pdf" + }, + { + "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/anie.201404164/full" + }, + { + "supplementary_material": "/doi/10.1002/anie.201404164/suppinfo" + }, + { + "rendered.html": "6d67fe51554fa9c91ea9ffd2dfdf160f" + }, + { + "suppinfo": "1540f0fc2bb23d5da62f9e3be1697443" + } + ], + "http://onlinelibrary.wiley.com/doi/10.1002/anie.200501671/abstract": [ + { + "publisher": "WILEY‐VCH Verlag" + }, + { + "title": "Finding Adiabatically Bound Anions of Guanine through a Combinatorial Computational Approach" + }, + { + "authors": "Harańczyk, Maciej" + }, + { + "authors": "Gutowski, Maciej" + }, + { + "date": "2005/10/14" + }, + { + "volume": "44" + }, + { + "issue": "40" + }, + { + "firstpage": "6585" + }, + { + "doi": "10.1002/anie.200501671" + }, + { + "journal": "Angewandte Chemie International Edition" + }, + { + "abstract": "Enamine–imine transformations of guanine lead to tautomers that support valence anionic states which are adiabatically bound by as much as 8 kcal mol−1 (see scheme). The valence anions might be formed by dissociative electron attachment followed by attachment of a hydrogen atom to a carbon atom. Such tautomers might affect the structure and properties of DNA and RNA exposed to low‐energy electrons." + }, + { + "figure": "http://onlinelibrary.wiley.com/store/10.1002/anie.200501671/asset/image_m/mcontent.gif?v=1&s=a375d92cc9e2ad2c5b874eaae0af7ab08c33ba25" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/anie.200501671/pdf" + }, + { + "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/anie.200501671/full" + }, + { + "supplementary_material": "/doi/10.1002/anie.200501671/suppinfo" + }, + { + "mcontent.gif": "05f920a0b7dd1a6cc70a3d0440edccab" + }, + { + "rendered.html": "89bbb468479dc9891e4319426aa93165" + } + ], + "http://onlinelibrary.wiley.com/doi/10.1002/cbic.201300780/abstract": [ + { + "publisher": "WILEY‐VCH Verlag" + }, + { + "title": "Improving the Stability and Catalyst Lifetime of the Halogenase RebH By Directed Evolution" + }, + { + "authors": "Poor, Catherine B." + }, + { + "authors": "Andorfer, Mary C." + }, + { + "authors": "Lewis, Jared C." + }, + { + "date": "2014/06/16" + }, + { + "volume": "15" + }, + { + "issue": "9" + }, + { + "firstpage": "1286" + }, + { + "doi": "10.1002/cbic.201300780" + }, + { + "journal": "ChemBioChem" + }, + { + "abstract": "We previously reported that the halogenase RebH catalyzes selective halogenation of several heterocycles and carbocycles, but product yields were limited by enzyme instability. Here, we use directed evolution to engineer an RebH variant, 3‐LR, with a Topt over 5 °C higher than that of wild‐type, and 3‐LSR, with a Tm 18 °C higher than that of wild‐type. These enzymes provided significantly improved conversion (up to fourfold) for halogenation of tryptophan and several non‐natural substrates. This initial evolution of RebH not only provides improved enzymes for immediate synthetic applications, but also establishes a robust protocol for further halogenase evolution." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/cbic.201300780/pdf" + }, + { + "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/cbic.201300780/full" + }, + { + "supplementary_material": "/doi/10.1002/cbic.201300780/suppinfo" + }, + { + "pdf": "47a76e20b88a744d6d34754326cb8739" + }, + { + "rendered.html": "cfc05bebad5b51612dadd4a40cb99a86" + } + ], + "http://onlinelibrary.wiley.com/doi/10.1002/open.201300039/abstract": [ + { + "title": "Difluoro‐ and Trifluoromethylation of Electron‐Deficient Alkenes in an Electrochemical Microreactor" + }, + { + "authors": "Arai, Kenta" + }, + { + "authors": "Watts, Kevin" + }, + { + "authors": "Wirth, Thomas" + }, + { + "date": "2014/02/01" + }, + { + "volume": "3" + }, + { + "issue": "1" + }, + { + "firstpage": "23" + }, + { + "doi": "10.1002/open.201300039" + }, + { + "journal": "ChemistryOpen" + }, + { + "abstract": "Electrochemical microreactors, which have electrodes integrated into the flow path, can afford rapid and efficient electrochemical reactions without redox reagents due to the intrinsic properties of short diffusion distances. Taking advantage of electrochemical microreactors, Kolbe electrolysis of di‐ and trifluoroacetic acid in the presence of various electron‐deficient alkenes was performed under constant current at continuous flow at room temperature. As a result, di‐ and trifluoromethylated compounds were effectively produced in either equal or higher yields than identical reactions under batch conditions previously reported by Uneyamas group. The strategy of using electrochemical microreactor technology is useful for an effective fluoromethylation of alkenes based on Kolbe electrolysis in significantly shortened reaction times." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/open.201300039/pdf" + }, + { + "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/open.201300039/full" + }, + { + "supplementary_material": "/doi/10.1002/open.201300039/suppinfo" + }, + { + "pdf": "d2821599b03eaf07bd83f99d8ebb3682" + }, + { + "rendered.html": "454ff6668ce5c4bc987cde329d115759" + } + ], + "http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12175/abstract": [ + { + "title": "Evaluation of 11 single‐locus and seven multilocus DNA barcodes in Lamium L. (Lamiaceae)" + }, + { + "authors": "Krawczyk, K." + }, + { + "authors": "Szczecińska, M." + }, + { + "authors": "Sawicki, J." + }, + { + "date": "2014/03/01" + }, + { + "volume": "14" + }, + { + "issue": "2" + }, + { + "firstpage": "272" + }, + { + "doi": "10.1111/1755-0998.12175" + }, + { + "journal": "Molecular Ecology Resources" + }, + { + "abstract": "The aim of this work was to evaluate the suitability of selected DNA regions in the barcoding of plants, based on the species belonging to the genus Lamium (Lamiaceae). For this purpose, nine chloroplast barcodes, that is, accD, matK, rbcL, rpoA, rpoB, rpoC1, rpoC2, trnH‐psbA, trnL‐trnF, as well as ITS nuclear region, and intron of mitochondrial nad5 gene were tested. Among the single‐locus barcodes, most effective in the identification of Lamium species was the trnH‐psbA spacer and matK gene. The high level of variability and resolving power was also observed in the case of rpoA and rpoC2 genes. Despite the high interspecies variability of ITS region, it turned out to be inapplicable in Lamium identification. An important disadvantage of ITS as a barcode is a limitation of its use in polyploid plants, samples contaminated with fungal material or samples with partially degraded DNA. We have also evaluated five‐two‐locus and two‐three‐locus barcode regions created from a combination of most effective single loci. The best‐performing barcode combinations were matK + trnH‐psbA and matK + rpoA. Both of them had equally high discriminative power to identify Lamium species." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12175/pdf" + }, + { + "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12175/full" + }, + { + "supplementary_material": "/doi/10.1111/1755-0998.12175/suppinfo" + }, + { + "rendered.html": "af1c49bb97a394a132261cf384c19b39" + }, + { + "suppinfo": "c89502626d0a6a1ef837c81c3cc295cd" + } + ], + "http://onlinelibrary.wiley.com/doi/10.1002/j.2161-007X.2012.00017.x/abstract": [ + { + "publisher": "Blackwell Publishing Ltd" + }, + { + "title": "Psychological Care Provided by the Church: Perceptions of Christian Church Members" + }, + { + "authors": "Bornsheuer, Jennifer N." + }, + { + "authors": "Henriksen, Richard C." + }, + { + "authors": "Irby, Beverly J." + }, + { + "date": "2012/10/01" + }, + { + "volume": "57" + }, + { + "issue": "2" + }, + { + "firstpage": "199" + }, + { + "doi": "10.1002/j.2161-007X.2012.00017.x" + }, + { + "journal": "Counseling and Values" + }, + { + "abstract": "Spirituality and religion are integral parts of a person's belief system and support network. Although there are many avenues a person can take when seeking mental health care, conservative Protestant clients have a tendency to seek assistance through their church. There is a paucity of literature about conservative Protestant church members’ perceptions of mental health care. The authors used phenomenology to understand participants’ perceptions of mental health care provided by the church. Themes found within participants’ stories included the importance of the relationship when seeking care, the use of knowledgeable practitioners, and the use of religious practices in counseling." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/j.2161-007X.2012.00017.x/pdf" + }, + { + "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/j.2161-007X.2012.00017.x/full" + }, + { + "full": "35969f79046b93f74113d97aa2da09e6" + }, + { + "rendered.html": "18d9e80ff0fdf4baf7a37a2a6e5dc7e8" + } + ], + "http://onlinelibrary.wiley.com/doi/10.1002/mma.2929/abstract": [ + { + "title": "Error estimates for some quadrature rules with maximal trigonometric degree of exactness" + }, + { + "authors": "Stanić, Marija P." + }, + { + "authors": "Cvetković, Aleksandar S." + }, + { + "authors": "Tomović, Tatjana V." + }, + { + "date": "2014/07/30" + }, + { + "volume": "37" + }, + { + "issue": "11" + }, + { + "firstpage": "1687" + }, + { + "doi": "10.1002/mma.2929" + }, + { + "journal": "Mathematical Methods in the Applied Sciences" + }, + { + "abstract": "In this paper, we give error estimates for quadrature rules with maximal trigonometric degree of exactness with respect to an even weight function on ( − π,π) for integrand analytic in a certain domain of complex plane. Copyright © 2013 John Wiley & Sons, Ltd." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/mma.2929/pdf" + }, + { + "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/mma.2929/full" + }, + { + "pdf": "e2d1cc095d9e28b929f560483f50f608" + }, + { + "rendered.html": "e308edc6c8f86c8e2ead60addc6d0086" + } + ], + "http://onlinelibrary.wiley.com/doi/10.1002/nem.1840/abstract": [ + { + "title": "A semantic context exchange process for the federated management of the future internet" + }, + { + "authors": "Latré, Steven" + }, + { + "authors": "Famaey, Jeroen" + }, + { + "authors": "Turck, Filip De" + }, + { + "date": "2014/01/01" + }, + { + "volume": "24" + }, + { + "issue": "1" + }, + { + "firstpage": "1" + }, + { + "doi": "10.1002/nem.1840" + }, + { + "journal": "International Journal of Network Management" + }, + { + "abstract": "In the Future Internet, federations are set up to cope with the stringent quality requirements of services. While a federated solution offers advantages in terms of scalability, it complicates the exchange of context (e.g. Quality of Service information of services) between federated nodes, as each node requires context to perform management tasks. In this article, we propose a context exchange process that automates the context communication between nodes. A scalable approach is proposed that is able to quickly react to local context updates, while maintaining a high level of expressivity to define relationships between federation partners. We distinguish between the context exchange inside an administrative domain, which focuses on scalability, and the context exchange between federation partners, which emphasizes the trust relationships between partners. In both cases, the process allows defining which context needs to be exchanged when and from where. Inside an administrative domain, a combination of RDF and SPARQL rules are used. This allows modeling the contextual requirements of management algorithms and automatically requesting remote context, only when it is necessary for the management algorithms to proceed. Between domains, an OWL‐based approach is used, which allows describing the complex relationships between federation partners. Triggered by the intra‐domain context exchange process, the contextual capabilities are communicated and refined through policies. Both type of processes are evaluated. The results show that they can infer which context is needed in a timely and scalable manner. As such, it outperforms approaches where context is broadcast both in required bandwidth and end‐to‐end delay. Copyright © 2013 John Wiley & Sons, Ltd." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/nem.1840/pdf" + }, + { + "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/nem.1840/full" + }, + { + "pdf": "d543a5ca15391a60219dd367b6801f85" + }, + { + "rendered.html": "291efd7bc88a419ac70a0eaee2449cdd" + } + ], + "http://onlinelibrary.wiley.com/doi/10.1002/anie.197205681/abstract": [ + { + "publisher": "Hüthig & Wepf Verlag" + }, + { + "title": "Kinetics of Cooperative Conformational Transitions of Linear Biopolymers" + }, + { + "authors": "Schwarz, Gerhard" + }, + { + "authors": "Engel, Jürgen" + }, + { + "date": "1972/07/01" + }, + { + "volume": "11" + }, + { + "issue": "7" + }, + { + "firstpage": "568" + }, + { + "doi": "10.1002/anie.197205681" + }, + { + "journal": "Angewandte Chemie International Edition in English" + }, + { + "abstract": "Cooperative conformational transitions of proteins and nucleic acids are of decisive importance to many processes of molecular biology, and particularly to their regulation. They proceed via numerous interdependent elementary processes, and their kinetics are therefore often complicated. They are frequently also very fast. However, kinetic analyses can be carried out by chemical relaxation methods. The theoretical interpretation is comparatively simple in the case of linear biopolymers. When the linear Ising model extended for kinetics was applied to model peptides and polynucleotides, it provided an insight into the fundamental principles of cooperative transformations." + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/anie.197205681/pdf" + }, + { + "pdf": "ac3c1f65d9ff2cce98946d54bba1b4e5" + }, + { + "rendered.html": "de2a2bebcd8a0ea8b7046dae388c31b2" + } + ] +} \ No newline at end of file From 53700b0498693bba2cd1e3d60da0d5a0d518ff18 Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Tue, 2 Sep 2014 11:08:10 -0400 Subject: [PATCH 078/154] Nature updates & Test --- scrapers/nature.json | 8 ++------ test/nature_test_urls.txt | 9 +++++++++ 2 files changed, 11 insertions(+), 6 deletions(-) create mode 100644 test/nature_test_urls.txt diff --git a/scrapers/nature.json b/scrapers/nature.json index 146155f..eab9c88 100644 --- a/scrapers/nature.json +++ b/scrapers/nature.json @@ -14,11 +14,11 @@ "attribute": "content" }, "date": { - "selector": "//meta[@id='citation_date']", + "selector": "//meta[@name='citation_date']", "attribute": "content" }, "volume": { - "selector": "//meta[@class='citation_volume']", + "selector": "//meta[@name='citation_volume']", "attribute": "content" }, "issue": { @@ -37,10 +37,6 @@ "selector": "//meta[@name='citation_journal_title']", "attribute": "content" }, - "abstract": { - "selector": "//div[@id='abstract']", - "attribute": "text" - }, "language": { "selector": "//meta[@name='DC.language']", "attribute": "content" diff --git a/test/nature_test_urls.txt b/test/nature_test_urls.txt new file mode 100644 index 0000000..9bed3ae --- /dev/null +++ b/test/nature_test_urls.txt @@ -0,0 +1,9 @@ +http://www.nature.com/nature/journal/v512/n7514/full/nature13552.html +http://www.nature.com/nchem/journal/vaop/ncurrent/full/nchem.2041.html +http://www.nature.com/nature/journal/v505/n7481/full/nature12729.html +http://www.nature.com/nature/journal/v459/n7246/full/nature08010.html +http://www.nature.com/nchem/journal/v1/n3/full/nchem.179.html +http://www.nature.com/mp/journal/v6/n1/full/4000812a.html +http://www.nature.com/mp/journal/vaop/ncurrent/full/mp201448a.html +http://www.nature.com/ja/journal/v67/n3/full/ja2013116a.html +http://www.nature.com/scientificamerican/journal/v310/n3/full/scientificamerican0314-23a.html \ No newline at end of file From d99cece8adb272b2f0dc7282c68057cf547c9b48 Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Tue, 2 Sep 2014 11:14:14 -0400 Subject: [PATCH 079/154] Removed Nature, ready for pull --- scrapers/nature.json | 67 --------------------------------------- test/nature_test_urls.txt | 9 ------ 2 files changed, 76 deletions(-) delete mode 100644 scrapers/nature.json delete mode 100644 test/nature_test_urls.txt diff --git a/scrapers/nature.json b/scrapers/nature.json deleted file mode 100644 index eab9c88..0000000 --- a/scrapers/nature.json +++ /dev/null @@ -1,67 +0,0 @@ -{ - 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test/acs.json | 745 -------------------------------- test/acs_test_urls.txt | 7 - test/springer.json | 609 -------------------------- test/springer_test_urls.txt | 8 - test/tandf.json | 357 --------------- test/tandf_test_urls.txt | 8 - test/wiley.json | 556 ------------------------ test/wiley_test_urls.txt | 10 - 15 files changed, 3498 deletions(-) delete mode 100644 scrapers/aaas.json delete mode 100644 scrapers/acs.json delete mode 100644 scrapers/springer.json delete mode 100644 scrapers/tandf.json delete mode 100644 scrapers/wiley.json delete mode 100644 test/aaas.json delete mode 100644 test/aaas_test_urls.txt delete mode 100644 test/acs.json delete mode 100644 test/acs_test_urls.txt delete mode 100644 test/springer.json delete mode 100644 test/springer_test_urls.txt delete mode 100644 test/tandf.json delete mode 100644 test/tandf_test_urls.txt delete mode 100644 test/wiley.json delete mode 100644 test/wiley_test_urls.txt diff --git a/scrapers/aaas.json b/scrapers/aaas.json deleted file mode 100644 index f52090a..0000000 --- a/scrapers/aaas.json +++ /dev/null @@ -1,69 +0,0 @@ -{ - 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}, - "date": { - "selector": "//meta[@name='citation_publication_date']", - "attribute": "content" - }, - "volume": { - "selector": "//meta[@name='citation_volume']", - "attribute": "content" - }, - "issue": { - "selector": "//meta[@name='citation_issue']", - "attribute": "content" - }, - "firstpage": { - "selector": "//meta[@name='citation_firstpage']", - "attribute": "content" - }, - "doi": { - "selector": "//meta[@name='citation_doi']", - "attribute": "content" - }, - "journal": { - "selector": "//meta[@name='citation_journal_title']", - "attribute": "content" - }, - "abstract_html": { - "selector": "//meta[@class='citation_abstract_html_url']", - "attribute": "content", - "download": true - }, - "abstract": { - "selector": "//div[@id='abstract']", - "attribute": "text" - }, - "abstract": { - "selector": "//div[@class='para']", - "attribute": "text" - }, - "figure": { - "selector": "//a[@title='Link to full-size graphical abstract']", - "attribute": "href", - "download": true - }, - "language": { - "selector": "//meta[@name='citation_language']", - "attribute": "content" - }, - "fulltext_pdf": { - "selector": "//meta[@name='citation_pdf_url']", - "attribute": "content", - "download": true - }, - "fulltext_html": { - "selector": "//meta[@name='citation_fulltext_html_url']", - "attribute": "content", - "download": true - }, - "supplementary_material": { - "selector": "//a[@title='Link to supporting information']", - "attribute": "href", - "download": true - } - } -} diff --git a/test/aaas.json b/test/aaas.json deleted file mode 100644 index 012f251..0000000 --- a/test/aaas.json +++ /dev/null @@ -1,834 +0,0 @@ -{ - "http://www.sciencemag.org/content/345/6197/1255215": [ - { - "publisher": "American Association for the Advancement of Science" - }, - { - "title": "Integration of growth and patterning during vascular tissue formation in Arabidopsis" - }, - { - "authors": "Bert De Rybel" - }, - { - "authors": "Milad Adibi" - }, - { - "authors": "Alice S. Breda" - }, - { - "authors": "Jos R. Wendrich" - }, - { - "authors": "Margot E. Smit" - }, - { - "authors": "Ondřej Novák" - }, - { - "authors": "Nobutoshi Yamaguchi" - }, - { - "authors": "Saiko Yoshida" - }, - { - "authors": "Gert Van Isterdael" - }, - { - "authors": "Joakim Palovaara" - }, - { - "authors": "Bart Nijsse" - }, - { - "authors": "Mark V. Boekschoten" - }, - { - "authors": "Guido Hooiveld" - }, - { - "authors": "Tom Beeckman" - }, - { - "authors": "Doris Wagner" - }, - { - "authors": "Karin Ljung" - }, - { - "authors": "Christian Fleck" - }, - { - "authors": "Dolf Weijers" - }, - { - "date": "08/08/2014" - }, - { - "volume": "345" - }, - { - "issue": "6197" - }, - { - "firstpage": "1255215" - }, - { - "doi": "10.1126/science.1255215" - }, - { - "journal": "Science" - }, - { - "abstract": "\n Abstract\n \n Coordination of cell division and pattern formation is central to tissue and organ development, particularly in plants where\n walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these\n hormones converge upon tissue development. We identify a genetic network that reinforces an early embryonic bias in auxin\n distribution to create a local, nonresponding cytokinin source within the root vascular tissue. Experimental and theoretical\n evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions. We further\n demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate\n distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue.\n \n \n " - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://www.sciencemag.org/content/345/6197/1255215.full.pdf" - }, - { - "abstract_html": "http://www.sciencemag.org/content/345/6197/1255215.abstract" - }, - { - "fulltext_html": "http://www.sciencemag.org/content/345/6197/1255215.full" - }, - { - "supplementary_material": "/content/345/6197/1255215/suppl/DC1" - }, - { - "DC1": "5fe7fe941e2881406b05c65f393a22d6" - }, - { - "rendered.html": "c4c922d70fe40f9f0e6866c7d1f69aba" - } - ], - "http://www.sciencemag.org/content/338/6113/1440": [ - { - "publisher": "American Association for the Advancement of Science" - }, - { - "title": "Aggravating Genetic Interactions Allow a Solution to Redundancy in a Bacterial Pathogen" - }, - { - "authors": "Tamara J. O’Connor" - }, - { - "authors": "Dana Boyd" - }, - { - "authors": "Marion S. Dorer" - }, - { - "authors": "Ralph R. Isberg" - }, - { - "date": "12/14/2012" - }, - { - "volume": "338" - }, - { - "issue": "6113" - }, - { - "firstpage": "1440" - }, - { - "doi": "10.1126/science.1229556" - }, - { - "journal": "Science" - }, - { - "abstract": "\n Abstract\n \n Interactions between hosts and pathogens are complex, so understanding the events that govern these interactions requires\n the analysis of molecular mechanisms operating in both organisms. Many pathogens use multiple strategies to target a single\n event in the disease process, confounding the identification of the important determinants of virulence. We developed a genetic\n screening strategy called insertional mutagenesis and depletion (iMAD) that combines bacterial mutagenesis and RNA interference,\n to systematically dissect the interplay between a pathogen and its host. We used this technique to resolve the network of\n proteins secreted by the bacterium Legionella pneumophila to promote intracellular growth, a critical determinant of pathogenicity of this organism. This strategy is broadly applicable,\n allowing the dissection of any interface between two organisms involving numerous interactions.\n \n \n " - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://www.sciencemag.org/content/338/6113/1440.full.pdf" - }, - { - "abstract_html": "http://www.sciencemag.org/content/338/6113/1440.abstract" - }, - { - "fulltext_html": "http://www.sciencemag.org/content/338/6113/1440.full" - }, - { - "supplementary_material": "/content/338/6113/1440/suppl/DC1" - }, - { - "DC1": "6096f22eb0cb20ca7243635aa84967fd" - }, - { - "rendered.html": "ecf22f2fc7b2e6be762b907a96ddbcd6" - } - ], - "http://www.sciencemag.org/content/338/6106/514": [ - { - "publisher": "American Association for the Advancement of Science" - }, - { - "title": "Australopithecus afarensis Scapular Ontogeny, Function, and the Role of Climbing in Human Evolution" - }, - { - "authors": "David J. Green" - }, - { - "authors": "Zeresenay Alemseged" - }, - { - "date": "10/26/2012" - }, - { - "volume": "338" - }, - { - "issue": "6106" - }, - { - "firstpage": "514" - }, - { - "doi": "10.1126/science.1227123" - }, - { - "journal": "Science" - }, - { - "abstract": "\n Abstract\n \n Scapular morphology is predictive of locomotor adaptations among primates, but this skeletal element is scarce in the hominin\n fossil record. Notably, both scapulae of the juvenile Australopithecus afarensis skeleton from Dikika, Ethiopia, have been recovered. These scapulae display several traits characteristic of suspensory apes,\n as do the few known fragmentary adult australopith representatives. Many of these traits change significantly throughout modern\n human ontogeny, but remain stable in apes. Thus, the similarity of juvenile and adult fossil morphologies implies that A. afarensis development was apelike. Additionally, changes in other scapular traits throughout African ape development are associated\n with shifts in locomotor behavior. This affirms the functional relevance of those characteristics, and their presence in australopith\n fossils supports the hypothesis that their locomotor repertoire included a substantial amount of climbing.\n \n \n " - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://www.sciencemag.org/content/338/6106/514.full.pdf" - }, - { - "abstract_html": "http://www.sciencemag.org/content/338/6106/514.abstract" - }, - { - "fulltext_html": "http://www.sciencemag.org/content/338/6106/514.full" - }, - { - "supplementary_material": "/content/338/6106/549.2/suppl/DC1" - }, - { - "supplementary_material": "/content/338/6106/514/suppl/DC1" - }, - { - "supplementary_material": "/content/338/6106/514/suppl/DC2" - }, - { - "DC1": "29be2f1dd06f0f6c6dc84dec8d213102" - }, - { - "rendered.html": "7a753746eeeea3d944ca7191481f7c6e" - } - ], - "http://stke.sciencemag.org/content/7/340/ra82": [ - { - "publisher": "Science Signaling" - }, - { - "title": "Diacylglycerol kinase α establishes T cell polarity by shaping diacylglycerol accumulation at the immunological synapse" - }, - { - "authors": "Anne Chauveau" - }, - { - "authors": "Audrey Le Floc’h" - }, - { - "authors": "Niels S. Bantilan" - }, - { - "authors": "Gary A. Koretzky" - }, - { - "authors": "Morgan Huse" - }, - { - "volume": "7" - }, - { - "issue": "340" - }, - { - "firstpage": "ra82" - }, - { - "doi": "10.1126/scisignal.2005287" - }, - { - "journal": "Science Signaling" - }, - { - "abstract": "Abstract\nPolarization of the T cell microtubule–organizing center (MTOC) to the immunological synapse between the T cell and an antigen-presenting cell (APC) maintains the specificity of T cell effector responses by enabling directional secretion toward the APC. The reorientation of the MTOC is guided by a sharp gradient of the second messenger diacylglycerol (DAG), which is centered at the immunological synapse. We used a single-cell photoactivation approach to demonstrate that diacylglycerol kinase α (DGK-α), which catalyzes the conversion of DAG to phosphatidic acid, determined T cell polarity by limiting the diffusion of DAG. DGK-α–deficient T cells exhibited enlarged accumulations of DAG at the immunological synapse, as well as impaired reorientation of the MTOC. In contrast, T cells lacking the related isoform DGK-ζ did not display polarization defects. We also found that DGK-α localized preferentially to the periphery of the immunological synapse, suggesting that it constrained the area over which DAG accumulated. Phosphoinositide 3-kinase activity was required for the peripheral localization pattern of DGK-α, which suggests a link between DAG and phosphatidylinositol signaling during T cell activation. These results reveal a previously unappreciated function of DGK-α and provide insight into the mechanisms that determine lymphocyte polarity.\n" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://stke.sciencemag.org/content/sigtrans/7/340/ra82.full.pdf" - }, - { - "abstract_html": "http://stke.sciencemag.org/content/7/340/ra82.abstract" - }, - { - "ra82.abstract": "2cce9d016f9aed794f0ace73c4dc9464" - }, - { - "rendered.html": "b8f8b262bec8fd970f2df04ec9aca44a" - } - ], - "http://stm.sciencemag.org/content/6/251/251ra119": [ - { - "publisher": "American Association for the Advancement of Science" - }, - { - "title": "Adult human neural crest–derived cells for articular cartilage repair" - }, - { - "authors": "Karoliina Pelttari" - }, - { - "authors": "Benjamin Pippenger" - }, - { - "authors": "Marcus Mumme" - }, - { - "authors": "Sandra Feliciano" - }, - { - "authors": "Celeste Scotti" - }, - { - "authors": "Pierre Mainil-Varlet" - }, - { - "authors": "Alfredo Procino" - }, - { - "authors": "Brigitte von Rechenberg" - }, - { - "authors": "Thomas Schwamborn" - }, - { - "authors": "Marcel Jakob" - }, - { - "authors": "Clemente Cillo" - }, - { - "authors": "Andrea Barbero" - }, - { - "authors": "Ivan Martin" - }, - { - "date": "08/27/2014" - }, - { - "volume": "6" - }, - { - "issue": "251" - }, - { - "firstpage": "251ra119" - }, - { - "doi": "10.1126/scitranslmed.3009688" - }, - { - "journal": "Science Translational Medicine" - }, - { - "abstract": "\n Abstract\n \n In embryonic models and stem cell systems, mesenchymal cells derived from the neuroectoderm can be distinguished from mesoderm-derived\n cells by their Hox-negative profile—a phenotype associated with enhanced capacity of tissue regeneration. We investigated\n whether developmental origin and Hox negativity correlated with self-renewal and environmental plasticity also in differentiated\n cells from adults. Using hyaline cartilage as a model, we showed that adult human neuroectoderm-derived nasal chondrocytes\n (NCs) can be constitutively distinguished from mesoderm-derived articular chondrocytes (ACs) by lack of expression of specific\n HOX genes, including HOXC4 and HOXD8. In contrast to ACs, serially cloned NCs could be continuously reverted from differentiated to dedifferentiated states, conserving\n the ability to form cartilage tissue in vitro and in vivo. NCs could also be reprogrammed to stably express Hox genes typical of ACs upon implantation into goat articular cartilage defects, directly contributing to cartilage repair.\n Our findings identify previously unrecognized regenerative properties of HOX-negative differentiated neuroectoderm cells in adults, implying a role for NCs in the unmet clinical challenge of articular\n cartilage repair. An ongoing phase 1 clinical trial preliminarily indicated the safety and feasibility of autologous NC–based\n engineered tissues for the treatment of traumatic articular cartilage lesions.\n \n \n " - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://stm.sciencemag.org/content/6/251/251ra119.full.pdf" - }, - { - "abstract_html": "http://stm.sciencemag.org/content/6/251/251ra119.abstract" - }, - { - "fulltext_html": "http://stm.sciencemag.org/content/6/251/251ra119.full" - }, - { - "supplementary_material": "/content/6/232/232fs16/suppl/DC1" - }, - { - "supplementary_material": "/content/5/167/167ra6/suppl/DC1" - }, - { - "supplementary_material": "/content/4/132/132ra55/suppl/DC1" - }, - { - "supplementary_material": "/content/3/101/101ra93/suppl/DC1" - }, - { - "supplementary_material": "/content/6/251/251ra119/suppl/DC1" - }, - { - "251ra119.abstract": "64437cb3e1cb715f20332be915b76772" - }, - { - "rendered.html": "fd0af991de23407282300fea49bc47ed" - } - ], - "http://stm.sciencemag.org/content/1/7/7ra17": [ - { - "publisher": "American Association for the Advancement of Science" - }, - { - "title": "Restoration of Norepinephrine-Modulated Contextual Memory in a Mouse Model of Down Syndrome" - }, - { - "authors": "A. Salehi" - }, - { - "authors": "M. Faizi" - }, - { - "authors": "D. Colas" - }, - { - "authors": "J. Valletta" - }, - { - "authors": "J. Laguna" - }, - { - "authors": "R. Takimoto-Kimura" - }, - { - "authors": "A. Kleschevnikov" - }, - { - "authors": "S. L. Wagner" - }, - { - "authors": "P. Aisen" - }, - { - "authors": "M. Shamloo" - }, - { - "authors": "W. C. Mobley" - }, - { - "date": "11/18/2009" - }, - { - "volume": "1" - }, - { - "issue": "7" - }, - { - "firstpage": "7ra17" - }, - { - "doi": "10.1126/scitranslmed.3000258" - }, - { - "journal": "Science Translational Medicine" - }, - { - "abstract": "\n Abstract\n \n Down syndrome (trisomy 21) is the most common cause of mental retardation in children and leads to marked deficits in contextual\n learning and memory. In rodents, these tasks require the hippocampus and are mediated by several inputs, particularly those\n originating in the locus coeruleus. These afferents mainly use norepinephrine as a transmitter. To explore the basis for contextual\n learning defects in Down syndrome, we examined the Ts65Dn mouse model. These mice, which have three copies of a fragment of\n mouse chromosome 16, exhibited significant deficits in contextual learning together with dysfunction and degeneration of locus\n coeruleus neurons. However, the postsynaptic targets of innervation remained responsive to noradrenergic receptor agonists.\n Indeed, despite advanced locus coeruleus degeneration, we were able to reverse contextual learning failure by using a prodrug\n for norepinephrine called l-threo-3,4-dihydroxyphenylserine, or xamoterol, a β1-adrenergic receptor partial agonist. Moreover, an increased gene dosage of App, in the context of Down syndrome, was necessary for locus coeruleus degeneration. Our findings raise the possibility that\n restoring norepinephrine-mediated neurotransmission could reverse cognitive dysfunction in Down syndrome.\n \n \n " - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://stm.sciencemag.org/content/1/7/7ra17.full.pdf" - }, - { - "abstract_html": "http://stm.sciencemag.org/content/1/7/7ra17.abstract" - }, - { - "fulltext_html": "http://stm.sciencemag.org/content/1/7/7ra17.full" - }, - { - "supplementary_material": "http://www.sciencemag.org/content/343/6174/964/suppl/DC1" - }, - { - "supplementary_material": "/content/5/201/201ra120/suppl/DC1" - }, - { - "supplementary_material": "/content/1/7/7ra17/suppl/DC1" - }, - { - "DC1": "0ad45234188c98efdec1acc4b3033e2b" - }, - { - "rendered.html": "050ac6b02761e37c5e685377391fc791" - } - ], - "http://stke.sciencemag.org/content/1/8/pe11": [ - { - "publisher": "Science Signaling" - }, - { - "title": "A Cytoskeletal Platform for Local Translation in Axons" - }, - { - "authors": "Francisca P. G. Van Horck" - }, - { - "authors": "Christine E. Holt" - }, - { - "volume": "1" - }, - { - "issue": "8" - }, - { - "firstpage": "pe11" - }, - { - "doi": "10.1126/stke.18pe11" - }, - { - "journal": "Science Signaling" - }, - { - "abstract": "Abstract\n Recent data indicate that local translation in growth cones is critical for axon guidance. Evidence from the Drosophila midline axon guidance system suggests that the F-actin-microtubule cross-linker Short stop (Shot) might link the translation machinery to the cytoskeleton in the growth cone. The identification of a complex of translation factors attached to the actin and microtubule networks points to a mechanism by which cytoskeletal dynamics regulate translation in axons and vice versa.\n " - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://stke.sciencemag.org/content/sigtrans/1/8/pe11.full.pdf" - }, - { - "abstract_html": "http://stke.sciencemag.org/content/1/8/pe11.abstract" - }, - { - "pe11.abstract": "4e554ccd229f2d1d25137a18ef8b12b4" - }, - { - "rendered.html": "e0fb49a47083530a38b9076d7df0d03d" - } - ], - "http://www.sciencemag.org/content/298/5601/2157": [ - { - "publisher": "American Association for the Advancement of Science" - }, - { - "title": "The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins" - }, - { - "authors": "Paramvir Dehal" - }, - { - "authors": "Yutaka Satou" - }, - { - "authors": "Robert K. Campbell" - }, - { - "authors": "Jarrod Chapman" - }, - { - "authors": "Bernard Degnan" - }, - { - "authors": "Anthony De Tomaso" - }, - { - "authors": "Brad Davidson" - }, - { - "authors": "Anna Di Gregorio" - }, - { - "authors": "Maarten Gelpke" - }, - { - "authors": "David M. Goodstein" - }, - { - "authors": "Naoe Harafuji" - }, - { - "authors": "Kenneth E. M. Hastings" - }, - { - "authors": "Isaac Ho" - }, - { - "authors": "Kohji Hotta" - }, - { - "authors": "Wayne Huang" - }, - { - "authors": "Takeshi Kawashima" - }, - { - "authors": "Patrick Lemaire" - }, - { - "authors": "Diego Martinez" - }, - { - "authors": "Ian A. Meinertzhagen" - }, - { - "authors": "Simona Necula" - }, - { - "authors": "Masaru Nonaka" - }, - { - "authors": "Nik Putnam" - }, - { - "authors": "Sam Rash" - }, - { - "authors": "Hidetoshi Saiga" - }, - { - "authors": "Masanobu Satake" - }, - { - "authors": "Astrid Terry" - }, - { - "authors": "Lixy Yamada" - }, - { - "authors": "Hong-Gang Wang" - }, - { - "authors": "Satoko Awazu" - }, - { - "authors": "Kaoru Azumi" - }, - { - "authors": "Jeffrey Boore" - }, - { - "authors": "Margherita Branno" - }, - { - "authors": "Stephen Chin-bow" - }, - { - "authors": "Rosaria DeSantis" - }, - { - "authors": "Sharon Doyle" - }, - { - "authors": "Pilar Francino" - }, - { - "authors": "David N. Keys" - }, - { - "authors": "Shinobu Haga" - }, - { - "authors": "Hiroko Hayashi" - }, - { - "authors": "Kyosuke Hino" - }, - { - "authors": "Kaoru S. Imai" - }, - { - "authors": "Kazuo Inaba" - }, - { - "authors": "Shungo Kano" - }, - { - "authors": "Kenji Kobayashi" - }, - { - "authors": "Mari Kobayashi" - }, - { - "authors": "Byung-In Lee" - }, - { - "authors": "Kazuhiro W. Makabe" - }, - { - "authors": "Chitra Manohar" - }, - { - "authors": "Giorgio Matassi" - }, - { - "authors": "Monica Medina" - }, - { - "authors": "Yasuaki Mochizuki" - }, - { - "authors": "Steve Mount" - }, - { - "authors": "Tomomi Morishita" - }, - { - "authors": "Sachiko Miura" - }, - { - "authors": "Akie Nakayama" - }, - { - "authors": "Satoko Nishizaka" - }, - { - "authors": "Hisayo Nomoto" - }, - { - "authors": "Fumiko Ohta" - }, - { - "authors": "Kazuko Oishi" - }, - { - "authors": "Isidore Rigoutsos" - }, - { - "authors": "Masako Sano" - }, - { - "authors": "Akane Sasaki" - }, - { - "authors": "Yasunori Sasakura" - }, - { - "authors": "Eiichi Shoguchi" - }, - { - "authors": "Tadasu Shin-i" - }, - { - "authors": "Antoinetta Spagnuolo" - }, - { - "authors": "Didier Stainier" - }, - { - "authors": "Miho M. Suzuki" - }, - { - "authors": "Olivier Tassy" - }, - { - "authors": "Naohito Takatori" - }, - { - "authors": "Miki Tokuoka" - }, - { - "authors": "Kasumi Yagi" - }, - { - "authors": "Fumiko Yoshizaki" - }, - { - "authors": "Shuichi Wada" - }, - { - "authors": "Cindy Zhang" - }, - { - "authors": "P. Douglas Hyatt" - }, - { - "authors": "Frank Larimer" - }, - { - "authors": "Chris Detter" - }, - { - "authors": "Norman Doggett" - }, - { - "authors": "Tijana Glavina" - }, - { - "authors": "Trevor Hawkins" - }, - { - "authors": "Paul Richardson" - }, - { - "authors": "Susan Lucas" - }, - { - "authors": "Yuji Kohara" - }, - { - "authors": "Michael Levine" - }, - { - "authors": "Nori Satoh" - }, - { - "authors": "Daniel S. Rokhsar" - }, - { - "date": "12/13/2002" - }, - { - "volume": "298" - }, - { - "issue": "5601" - }, - { - "firstpage": "2157" - }, - { - "doi": "10.1126/science.1080049" - }, - { - "journal": "Science" - }, - { - "abstract": "\n Abstract\n The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern\n ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate\n and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. TheCiona genome contains ∼16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates.\n Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The\n ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose\n metabolism that are related to those in bacteria and fungi.\n \n " - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://www.sciencemag.org/content/298/5601/2157.full.pdf" - }, - { - "abstract_html": "http://www.sciencemag.org/content/298/5601/2157.abstract" - }, - { - "fulltext_html": "http://www.sciencemag.org/content/298/5601/2157.full" - }, - { - "supplementary_material": "/content/298/5601/2157/suppl/DC1" - }, - { - "2157.abstract": "45f763e9739badd9fc92e21116168ad9" - }, - { - "rendered.html": "308ecf9932204a34faabbcfa51cc7908" - } - ] -} \ No newline at end of file diff --git a/test/aaas_test_urls.txt b/test/aaas_test_urls.txt deleted file mode 100644 index 392a42c..0000000 --- a/test/aaas_test_urls.txt +++ /dev/null @@ -1,8 +0,0 @@ -http://www.sciencemag.org/content/345/6197/1255215 -http://www.sciencemag.org/content/338/6113/1440 -http://www.sciencemag.org/content/338/6106/514 -http://stke.sciencemag.org/content/7/340/ra82 -http://stm.sciencemag.org/content/6/251/251ra119 -http://stm.sciencemag.org/content/1/7/7ra17 -http://stke.sciencemag.org/content/1/8/pe11 -http://www.sciencemag.org/content/298/5601/2157 \ No newline at end of file diff --git a/test/acs.json b/test/acs.json deleted file mode 100644 index fbec5e7..0000000 --- a/test/acs.json +++ /dev/null @@ -1,745 +0,0 @@ -{ - "http://pubs.acs.org/doi/abs/10.1021/ic50161a007": [ - { - "publisher": " American Chemical Society " - }, - { - "title": "Metal complexes of cyclic triamines. 1. Complexes of 1,4,7-triazacyclononane ([9]aneN3) with nickel(II), copper(II), and zinc(II)" - }, - { - "authors": " Rita. Yang " - }, - { - "authors": " Leverett J. Zompa " - }, - { - "date": "Publication Date: July 1976" - }, - { - "volume": "15" - }, - { - "doi": "10.1021/ic50161a007" - }, - { - "journal": "Inorg. Chem." - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "The Journal of Organic Chemistry" - }, - { - "journal": "The Journal of Organic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "abstract2": "First Page" - }, - { - "language": "EN" - }, - { - "fulltext_html": "/doi/full/10.1021/ic400174r" - }, - { - "fulltext_html": "/doi/full/10.1021/ic101360d" - }, - { - "fulltext_html": "/doi/full/10.1021/ic101210d" - }, - { - "fulltext_html": "/doi/full/10.1021/jo902504d" - }, - { - "fulltext_html": "/doi/full/10.1021/ic8004079" - }, - { - "fulltext_pdf": "/doi/pdf/10.1021/ic50161a007" - }, - { - "rendered.html": "e1ff5b84d8faca6a1227827dd25d0548" - }, - { - "span%3E": "04fa87eedefd1f0728a8c6682379914d" - } - ], - "http://pubs.acs.org/doi/abs/10.1021/ic501196q": [ - { - "publisher": "American Chemical Society" - }, - { - "title": "Ring-Shaped Rhenium(I) Multinuclear Complexes: Improved Synthesis and Photoinduced Multielectron Accumulation" - }, - { - "authors": "Tsuyoshi Asatani" - }, - { - "authors": "Yuki Nakagawa" - }, - { - "authors": "Yusuke Funada" - }, - { - "authors": "Shuhei Sawa" - }, - { - "authors": "Hiroyuki Takeda" - }, - { - "authors": "Tatsuki Morimoto" - }, - { - "authors": "Kazuhide Koike" - }, - { - "authors": "Osamu Ishitani" - }, - { - "date": "Publication Date (Web): July 9, 2014" - }, - { - "volume": "53" - }, - { - "doi": "10.1021/ic501196q" - }, - { - "description": "We successfully developed selective synthesis of strongly emissive ring-shaped Re(I) multinuclear complexes (RnP(x)n+ in Chart 1) with much higher yields compared with the previously reported method. This improved method could also be employed to prepare a novel ring-shaped multinuclear complex composed of structurally different Re(I) units. Each Re unit in RnP(x)n+ could electrochemically accept one electron, and the multielectron reduced states of RnP(x)n+ were stable. In the presence of triethanolamine, the ring-shaped tetranuclear and hexanuclear complexes can be photochemically reduced and accumulate 2.9–3.6 and 4.4 electrons in one molecule, respectively." - }, - { - "description": "In the presence of triethanolamine, ring-shaped Re(I) tetranuclear and hexanuclear complexes can photochemically accumulate four and five electrons in a single molecule, respectively. We succeeded in much improving the synthetic yield for these complexes compared with the previously reported method." - }, - { - "description": "" - }, - { - "journal": "Inorg. Chem." - }, - { - "abstract": "We successfully developed selective synthesis of strongly emissive ring-shaped Re(I) multinuclear complexes (RnP(x)n+ in Chart 1) with much higher yields compared with the previously reported method. This improved method could also be employed to prepare a novel ring-shaped multinuclear complex composed of structurally different Re(I) units. Each Re unit in RnP(x)n+ could electrochemically accept one electron, and the multielectron reduced states of RnP(x)n+ were stable. In the presence of triethanolamine, the ring-shaped tetranuclear and hexanuclear complexes can be photochemically reduced and accumulate 2.9–3.6 and 4.4 electrons in one molecule, respectively." - }, - { - "abstract2": "Abstract" - }, - { - "language": "EN" - }, - { - "fulltext_html": "/doi/full/10.1021/ic501196q" - }, - { - "fulltext_pdf": "/doi/pdf/10.1021/ic501196q" - }, - { - "figure": "/appl/literatum/publisher/achs/journals/content/inocaj/2014/inocaj.2014.53.issue-14/ic501196q/production/images/medium/ic-2014-01196q_0009.gif" - }, - { - "copyright": "Copyright © 2014 American Chemical Society" - }, - { - "rendered.html": "159e464f7294d5bd8fa7a7bb8100a0e9" - }, - { - "span%3E": "61d99547e16199b6bd74628be706a224" - } - ], - "http://pubs.acs.org/doi/abs/10.1021/ic5007007": [ - { - "publisher": "American Chemical Society" - }, - { - "title": "Luminescence Modulations of Rhenium Tricarbonyl Complexes Induced by Structural Variations" - }, - { - "authors": "Hélène C. Bertrand" - }, - { - "authors": "Sylvain Clède" - }, - { - "authors": "Régis Guillot" - }, - { - "authors": "François Lambert" - }, - { - "authors": "Clotilde Policar" - }, - { - "date": "Publication Date (Web): June 6, 2014" - }, - { - "volume": "53" - }, - { - "doi": "10.1021/ic5007007" - }, - { - "description": "Octahedral d6 low-spin Re(I) tricarbonyl complexes are of considerable interest as noninvasive imaging probes and have been deeply studied owing to their biological stability, low toxicity, large Stokes shifts, and long luminescence lifetimes. We reported recently the bimodal IR and luminescence imaging of a Re(I) tricarbonyl complex with a Pyta ligand (4-(2-pyridyl)-1,2,3-triazole) in cells and labeled such metal–carbonyl complexes SCoMPIs for single-core multimodal probes for imaging. Re(I) tricarbonyl complexes have unique photophysical properties allowing for their unequivocal detection in cells but also present some weaknesses such as a very low luminescence quantum yield in aqueous medium. Further optimizations would thus be desirable. We therefore developed new Re(I) tricarbonyl complexes prepared from different ancillary ligands. Complexes with benzothiadiazole–triazole ligands show interesting luminescent quantum yields in acetonitrile and may constitute valuable luminescent metal complexes in or..." - }, - { - "description": "Re(I) tricarbonyl complexes are of considerable interest as bioimaging probes. Single-core multimodal probes for imaging (SCoMPIs) display unique photophysical properties enabling their unequivocal detection in cells. New SCoMPIs were prepared from an ancillary 1-(2-pyridyl)-1,2,3-triazole ligand, denoted Tapy, a regioisomer of the widely used Pyta ligand. When functionalized with long alkyl chains, they show impressive enhancement of their luminescent properties relative to the parent Pyta complex, both in solution and in MDA-MB231 breast cancer cells." - }, - { - "description": "" - }, - { - "journal": "Inorg. Chem." - }, - { - "abstract": "Octahedral d6 low-spin Re(I) tricarbonyl complexes are of considerable interest as noninvasive imaging probes and have been deeply studied owing to their biological stability, low toxicity, large Stokes shifts, and long luminescence lifetimes. We reported recently the bimodal IR and luminescence imaging of a Re(I) tricarbonyl complex with a Pyta ligand (4-(2-pyridyl)-1,2,3-triazole) in cells and labeled such metal–carbonyl complexes SCoMPIs for single-core multimodal probes for imaging. Re(I) tricarbonyl complexes have unique photophysical properties allowing for their unequivocal detection in cells but also present some weaknesses such as a very low luminescence quantum yield in aqueous medium. Further optimizations would thus be desirable. We therefore developed new Re(I) tricarbonyl complexes prepared from different ancillary ligands. Complexes with benzothiadiazole–triazole ligands show interesting luminescent quantum yields in acetonitrile and may constitute valuable luminescent metal complexes in organic media. A series of complexes with bidentate 1-(2-quinolinyl)-1,2,3-triazole (Taquin) and 1-(2-pyridyl)-1,2,3-triazole (Tapy) ligands bearing various 4-substituted alkyl side chains has been designed and synthesized with efficient procedures. Their photophysical properties have been characterized in acetonitrile and in a H2O/DMSO (98/2) mixture and compared with those of the parent Quinta- and Pyta-based complexes. Tapy complexes bearing long alkyl chains show impressive enhancement of their luminescent properties relative to the parent Pyta complex. Theoretical calculations have been performed to further characterize this new class of rhenium tricarbonyl complexes. Preliminary cellular imaging studies in MDA-MB231 breast cancer cells reveal a strong increase in the luminescence signal in cells incubated with the Tapy complex substituted with a C12 alkyl chain. This study points out the interesting potential of the Tapy ligand in coordination chemistry, which has been so far underexploited." - }, - { - "abstract2": "Abstract" - }, - { - "language": "EN" - }, - { - "fulltext_html": "/doi/full/10.1021/ic5007007" - }, - { - "fulltext_pdf": "/doi/pdf/10.1021/ic5007007" - }, - { - "figure": "/appl/literatum/publisher/achs/journals/content/inocaj/2014/inocaj.2014.53.issue-12/ic5007007/production/images/medium/ic-2014-007007_0014.gif" - }, - { - "copyright": "Copyright © 2014 American Chemical Society" - }, - { - "ic-2014-007007_0014.gif": "e67ff4fb6ea512f6ee9cba0aa40b39e1" - }, - { - "rendered.html": "c28639adfb2fb05847d4cdb2dfe92e56" - } - ], - "http://pubs.acs.org/doi/abs/10.1021/ja2105834": [ - { - "publisher": "American Chemical Society" - }, - { - "title": "Mechanisms for CO Production from CO2 Using Reduced Rhenium Tricarbonyl Catalysts" - }, - { - "authors": "Jay Agarwal" - }, - { - "authors": "Etsuko Fujita" - }, - { - "authors": "Henry F. Schaefer, III" - }, - { - "authors": "James T. Muckerman" - }, - { - "date": "Publication Date (Web): February 23, 2012" - }, - { - "volume": "134" - }, - { - "doi": "10.1021/ja2105834" - }, - { - "description": "The chemical conversion of CO2 has been studied by numerous experimental groups. Particularly the use of rhenium tricarbonyl-based molecular catalysts has attracted interest owing to their ability to absorb light, store redox equivalents, and convert CO2 into higher-energy products. The mechanism by which these catalysts mediate reduction, particularly to CO and HCOO–, is poorly understood, and studies aimed at elucidating the reaction pathway have likely been hindered by the large number of species present in solution. Herein the mechanism for carbon monoxide production using rhenium tricarbonyl catalysts has been investigated using density functional theory. The investigation presented proceeds from the experimental work of Meyer’s group (J. Chem. Soc., Chem. Commun.1985, 1414–1416) in DMSO and Fujita’s group (J. Am. Chem. Soc.2003, 125, 11976–11987) in dry DMF. The latter work with a simplified reaction mixture, one that removes the photo-induced reduction step with a sacrificial donor, is used for val..." - }, - { - "description": "" - }, - { - "journal": "J. Am. Chem. Soc." - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "journal": "ACS Catalysis" - }, - { - "journal": "ACS Catalysis" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "The Journal of Physical Chemistry A" - }, - { - "journal": "The Journal of Physical Chemistry A" - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "journal": "Accounts of Chemical Research" - }, - { - "journal": "Accounts of Chemical Research" - }, - { - "abstract": "The chemical conversion of CO2 has been studied by numerous experimental groups. Particularly the use of rhenium tricarbonyl-based molecular catalysts has attracted interest owing to their ability to absorb light, store redox equivalents, and convert CO2 into higher-energy products. The mechanism by which these catalysts mediate reduction, particularly to CO and HCOO–, is poorly understood, and studies aimed at elucidating the reaction pathway have likely been hindered by the large number of species present in solution. Herein the mechanism for carbon monoxide production using rhenium tricarbonyl catalysts has been investigated using density functional theory. The investigation presented proceeds from the experimental work of Meyer’s group (J. Chem. Soc., Chem. Commun.1985, 1414–1416) in DMSO and Fujita’s group (J. Am. Chem. Soc.2003, 125, 11976–11987) in dry DMF. The latter work with a simplified reaction mixture, one that removes the photo-induced reduction step with a sacrificial donor, is used for validation of the proposed mechanism, which involves formation of a rhenium carboxylate dimer, [Re(dmb)(CO)3]2(OCO), where dmb = 4,4′-dimethyl-2,2′-bipyridine. CO2 insertion into this species, and subsequent rearrangement, is proposed to yield CO and the carbonate-bridged [Re(dmb)(CO)3]2(OCO2). Structures and energies for the proposed reaction path are presented and compared to previously published experimental observations." - }, - { - "abstract2": "Abstract" - }, - { - "language": "EN" - }, - { - "fulltext_html": "/doi/full/10.1021/ja2105834" - }, - { - "fulltext_html": "/doi/full/10.1021/ja500403e" - }, - { - "fulltext_html": "/doi/full/10.1021/ic500050q" - }, - { - "fulltext_html": "/doi/full/10.1021/ja409271s" - }, - { - "fulltext_html": "/doi/full/10.1021/cs400332y" - }, - { - "fulltext_html": "/doi/full/10.1021/ic302663c" - }, - { - "fulltext_pdf": "/doi/pdf/10.1021/ja2105834" - }, - { - "figure": "/appl/literatum/publisher/achs/journals/content/jacsat/2012/jacsat.2012.134.issue-11/ja2105834/production/images/medium/ja-2011-105834_0003.gif" - }, - { - "copyright": "Copyright © 2012 American Chemical Society" - }, - { - "ja-2011-105834_0003.gif": "ef696f8cc86dbb4cecd51b1ff8036ec6" - }, - { - "rendered.html": "029bbc92f3e271398b30c340eed51a7e" - } - ], - "http://pubs.acs.org/doi/abs/10.1021/jz1010237": [ - { - "publisher": "American Chemical Society" - }, - { - "title": "New Directions for the Photocatalytic Reduction of CO2: Supramolecular, scCO2 or Biphasic Ionic Liquid−scCO2 Systems" - }, - { - "authors": "David C. Grills" - }, - { - "authors": "Etsuko Fujita" - }, - { - "date": "Publication Date (Web): September 2, 2010" - }, - { - "volume": "1" - }, - { - "doi": "10.1021/jz1010237" - }, - { - "description": "There is an urgent need for the discovery of carbon-neutral sources of energy to avoid the consequences of global warming caused by ever-increasing atmospheric CO2 levels. An attractive possibility is to use CO2 captured from industrial emissions as a feedstock for the production of useful fuels and precursors such as carbon monoxide and methanol. An active field of research to achieve this goal is the development of catalysts capable of harnessing solar energy for use in artificial photosynthetic processes for CO2 reduction. Transition-metal complexes are excellent candidates, and it has already been shown that they can be used to reduce CO2 with high quantum efficiency. However, they generally suffer from poor visible light absorption, short catalyst lifetimes, and poor reaction rates. In this Perspective, the field of photocatalytic CO2 reduction is introduced, and recent developments that seek to improve the efficiency of such catalytic processes are highlighted, especially CO2 reduction with supramol..." - }, - { - "description": "" - }, - { - "journal": "J. Phys. Chem." - }, - { - "journal": "J. Phys. Chem. Lett." - }, - { - "journal": "ACS Catalysis" - }, - { - "journal": "ACS Catalysis" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "The Journal of Physical Chemistry Letters" - }, - { - "journal": "The Journal of Physical Chemistry Letters" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "ACS Catalysis" - }, - { - "journal": "ACS Catalysis" - }, - { - "journal": "Accounts of Chemical Research" - }, - { - "journal": "Accounts of Chemical Research" - }, - { - "journal": "ACS Nano" - }, - { - "journal": "ACS Nano" - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "abstract": "There is an urgent need for the discovery of carbon-neutral sources of energy to avoid the consequences of global warming caused by ever-increasing atmospheric CO2 levels. An attractive possibility is to use CO2 captured from industrial emissions as a feedstock for the production of useful fuels and precursors such as carbon monoxide and methanol. An active field of research to achieve this goal is the development of catalysts capable of harnessing solar energy for use in artificial photosynthetic processes for CO2 reduction. Transition-metal complexes are excellent candidates, and it has already been shown that they can be used to reduce CO2 with high quantum efficiency. However, they generally suffer from poor visible light absorption, short catalyst lifetimes, and poor reaction rates. In this Perspective, the field of photocatalytic CO2 reduction is introduced, and recent developments that seek to improve the efficiency of such catalytic processes are highlighted, especially CO2 reduction with supramolecules and molecular systems in supercritical CO2 (scCO2) or biphasic ionic liquid−scCO2 mixtures." - }, - { - "abstract2": "Abstract" - }, - { - "language": "EN" - }, - { - "fulltext_html": "/doi/full/10.1021/jz1010237" - }, - { - "fulltext_html": "/doi/full/10.1021/cs500730w" - }, - { - "fulltext_html": "/doi/full/10.1021/ic500829p" - }, - { - "fulltext_html": "/doi/full/10.1021/jz500759x" - }, - { - "fulltext_html": "/doi/full/10.1021/ic401031j" - }, - { - "fulltext_html": "/doi/full/10.1021/cs400332y" - }, - { - "fulltext_pdf": "/doi/pdf/10.1021/jz1010237" - }, - { - "figure": "/appl/literatum/publisher/achs/journals/content/jpclcd/2010/jpclcd.2010.1.issue-18/jz1010237/production/images/medium/jz-2010-010237_0004.gif" - }, - { - "copyright": "Copyright © 2010 American Chemical Society" - }, - { - "rendered.html": "58d347ee8062d84c7f90f225d31a9dcc" - }, - { - "span%3E": "5e4c63f805bed5b3336b974c401fccca" - } - ], - "http://pubs.acs.org/doi/abs/10.1021/ar700111a": [ - { - "publisher": " American Chemical Society" - }, - { - "title": "Density Functionals with Broad Applicability in Chemistry" - }, - { - "authors": "Yan Zhao" - }, - { - "authors": "Donald G. Truhlar" - }, - { - "date": "Publication Date (Web): January 11, 2008" - }, - { - "volume": "41" - }, - { - "doi": "10.1021/ar700111a" - }, - { - "description": "Although density functional theory is widely used in the computational chemistry community, the most popular density functional, B3LYP, has some serious shortcomings: (i) it is better for main-group chemistry than for transition metals; (ii) it systematically underestimates reaction barrier heights; (iii) it is inaccurate for interactions dominated by medium-range correlation energy, such as van der Waals attraction, aromatic−aromatic stacking, and alkane isomerization energies. We have developed a variety of databases for testing and designing new density functionals. We used these data to design new density functionals, called M06-class (and, earlier, M05-class) functionals, for which we enforced some fundamental exact constraints such as the uniform-electron-gas limit and the absence of self-correlation energy. Our M06-class functionals depend on spin-up and spin-down electron densities (i.e., spin densities), spin density gradients, spin kinetic energy densities, and, for nonlocal (also called hybrid)..." - }, - { - "journal": "Acc. Chem. Res." - }, - { - "journal": "Environmental Science & Technology" - }, - { - "journal": "Environmental Science & Technology" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "The Journal of Physical Chemistry A" - }, - { - "journal": "The Journal of Physical Chemistry A" - }, - { - "journal": "The Journal of Physical Chemistry B" - }, - { - "journal": "The Journal of Physical Chemistry B" - }, - { - "journal": "The Journal of Physical Chemistry A" - }, - { - "journal": "The Journal of Physical Chemistry A" - }, - { - "journal": "Accounts of Chemical Research" - }, - { - "journal": "Accounts of Chemical Research" - }, - { - "journal": "Nano Letters" - }, - { - "journal": "Nano Letters" - }, - { - "journal": "Nano Letters" - }, - { - "journal": "Nano Letters" - }, - { - "abstract": " Although density functional theory is widely used in the computational chemistry community, the most popular density functional, B3LYP, has some serious shortcomings: (i) it is better for main-group chemistry than for transition metals; (ii) it systematically underestimates reaction barrier heights; (iii) it is inaccurate for interactions dominated by medium-range correlation energy, such as van der Waals attraction, aromatic−aromatic stacking, and alkane isomerization energies. We have developed a variety of databases for testing and designing new density functionals. We used these data to design new density functionals, called M06-class (and, earlier, M05-class) functionals, for which we enforced some fundamental exact constraints such as the uniform-electron-gas limit and the absence of self-correlation energy. Our M06-class functionals depend on spin-up and spin-down electron densities (i.e., spin densities), spin density gradients, spin kinetic energy densities, and, for nonlocal (also called hybrid) functionals, Hartree−Fock exchange. We have developed four new functionals that overcome the above-mentioned difficulties: (a) M06, a hybrid meta functional, is a functional with good accuracy “across-the-board” for transition metals, main group thermochemistry, medium-range correlation energy, and barrier heights; (b) M06-2X, another hybrid meta functional, is not good for transition metals but has excellent performance for main group chemistry, predicts accurate valence and Rydberg electronic excitation energies, and is an excellent functional for aromatic−aromatic stacking interactions; (c) M06-L is not as accurate as M06 for barrier heights but is the most accurate functional for transition metals and is the only local functional (no Hartree−Fock exchange) with better across-the-board average performance than B3LYP; this is very important because only local functionals are affordable for many demanding applications on very large systems; (d) M06-HF has good performance for valence, Rydberg, and charge transfer excited states with minimal sacrifice of ground-state accuracy. In this Account, we compared the performance of the M06-class functionals and one M05-class functional (M05-2X) to that of some popular functionals for diverse databases and their performance on several difficult cases. The tests include barrier heights, conformational energy, and the trend in bond dissociation energies of Grubbsʼ ruthenium catalysts for olefin metathesis. Based on these tests, we recommend (1) the M06-2X, BMK, and M05-2X functionals for main-group thermochemistry and kinetics, (2) M06-2X and M06 for systems where main-group thermochemistry, kinetics, and noncovalent interactions are all important, (3) M06-L and M06 for transition metal thermochemistry, (4) M06 for problems involving multireference rearrangements or reactions where both organic and transition-metal bonds are formed or broken, (5) M06-2X, M05-2X, M06-HF, M06, and M06-L for the study of noncovalent interactions, (6) M06-HF when the use of full Hartree−Fock exchange is important, for example, to avoid the error of self-interaction at long-range, (7) M06-L when a local functional is required, because a local functional has much lower cost for large systems." - }, - { - "abstract2": "Abstract" - }, - { - "language": "EN" - }, - { - "fulltext_html": "/doi/full/10.1021/ar700111a" - }, - { - "fulltext_html": "/doi/full/10.1021/es5026678" - }, - { - "fulltext_html": "/doi/full/10.1021/ic5006659" - }, - { - "fulltext_html": "/doi/full/10.1021/jp5035568" - }, - { - "fulltext_html": "/doi/full/10.1021/jp501408e" - }, - { - "fulltext_html": "/doi/full/10.1021/jp502558p" - }, - { - "fulltext_pdf": "/doi/pdf/10.1021/ar700111a" - }, - { - "copyright": "Copyright © 2008 American Chemical Society" - }, - { - "rendered.html": "c3e74598bb87024ea3ec2d7f2aae2a54" - }, - { - "span%3E": "61d99547e16199b6bd74628be706a224" - } - ], - "http://pubs.acs.org/doi/abs/10.1021/om960044%2B": [ - { - "publisher": " American Chemical Society " - }, - { - "title": "Electrocatalytic Reduction of CO2 Using the Complexes [Re(bpy)(CO)3L]n (n = +1, L = P(OEt)3, CH3CN; n = 0, L = Cl-, Otf-; bpy = 2,2‘-Bipyridine; Otf- = CF3SO3) as Catalyst Precursors:  Infrared Spectroelectrochemical Investigation" - }, - { - "authors": "Frank P. A. Johnson,*,†" - }, - { - "authors": "Michael W. George,†" - }, - { - "authors": "Frantisek Hartl,*,‡ and" - }, - { - "authors": "James J. Turner†" - }, - { - "date": "Publication Date (Web): July 23, 1996" - }, - { - "volume": "15" - }, - { - "doi": "10.1021/om960044+" - }, - { - "description": "This article describes the results of an IR spectroelectrochemical study of the electrocatalytic reduction of carbon dioxide using the complexes [Re(CO)3(bpy)L]n (bpy = 2,2‘-bipyridine; n = 0, L = Cl-, CF3SO3-; n = +1, L = CH3CN, P(OEt)3) as catalyst precursors. The study was performed for the first time with an optically transparent thin-layer electrochemical (OTTLE) cell. The results confirm unambiguously the catalytic activity of the reduced five-coordinate complexes, the radical [Re(CO)3(bpy)]• and the anion [Re(CO)3(bpy)]-. The catalytic behavior of these species could be investigated separately for the first time due to the application of complexes other than those with L = halide, whose catalytic routes may involve simultaneously both radical and anionic catalysis depending on the solvent used. The complex [Re(CO)3(bpy)Cl], so far the most studied catalyst precursor, upon one-electron reduction gives the corresponding radical-anion [Re(CO)3(bpy)Cl]•-, which was previously believed to react directly..." - }, - { - "description": "Electrocatalytic reduction of carbon dioxide has been investigated by IR spectroelectrochemistry using the complexes [Re(CO)3(bpy)L]n (n = 0, L = Cl-, CF3SO3-; n = +1, L = CH3CN, P(OEt)3) as catalyst precursors. Variation of the axial ligand L and the solvent used made it possible to discriminate between the 1e and 2e catalytic routes and, hence, to provide independent spectroscopic evidence for the catalytic activity of the five-coordinate radicals [Re(CO)3(bpy)]• and anions [Re(CO)3(bpy)]-." - }, - { - "description": "" - }, - { - "journal": "Organometallics" - }, - { - "journal": "Organometallics" - }, - { - "journal": "Organometallics" - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Organometallics" - }, - { - "journal": "Organometallics" - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "journal": "Journal of the American Chemical Society" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "journal": "Inorganic Chemistry" - }, - { - "abstract": "This article describes the results of an IR spectroelectrochemical study of the electrocatalytic reduction of carbon dioxide using the complexes [Re(CO)3(bpy)L]n (bpy = 2,2‘-bipyridine; n = 0, L = Cl-, CF3SO3-; n = +1, L = CH3CN, P(OEt)3) as catalyst precursors. The study was performed for the first time with an optically transparent thin-layer electrochemical (OTTLE) cell. The results confirm unambiguously the catalytic activity of the reduced five-coordinate complexes, the radical [Re(CO)3(bpy)]• and the anion [Re(CO)3(bpy)]-. The catalytic behavior of these species could be investigated separately for the first time due to the application of complexes other than those with L = halide, whose catalytic routes may involve simultaneously both radical and anionic catalysis depending on the solvent used. The complex [Re(CO)3(bpy)Cl], so far the most studied catalyst precursor, upon one-electron reduction gives the corresponding radical-anion [Re(CO)3(bpy)Cl]•-, which was previously believed to react directly with CO2. By contrast, this study demonstrates its stability toward attack by CO2, which may only take place after dissociation of the chloride ligand. This conclusion also applies to other six-coordinate radicals [Re(CO)3(bpy)L]• (L = CH3CN (in CH3CN) and P(OEt)3) whose catalytic route requires subsequent one-electron reduction to produce the anionic catalyst [Re(CO)3(bpy)]- (the 2e pathway). The catalytic route of [Re(CO)3(bpy)Cl] in CH3CN therefore deviates from that of the related [Re(CO)3(dmbpy)Cl], the other complex studied by IR (reflectance) spectroelectrochemistry, with the more basic ligand, 4,4‘-dimethyl-2,2‘-bipyridine (dmbpy). The latter complex tends to form the five-coordinate radicals [Re(CO)3(dmbpy)]•, capable of CO2 reduction (the 1e pathway), even in CH3CN, hence eliminating the possibility of the 2e pathway via the anion [Re(CO)3(dmbpy)]-, which operates in the case of the 2,2‘-bipyridine complex. For [Re(CO)3(bpy)L]n (n = 0, L = Cl-, CF3SO3-; n = +1, L = CH3CN), the 1e catalytic route becomes possible in weakly coordinating THF, due to the instability of the radical [Re(CO)3(bpy)(THF)]•. The inherent stability of the radical [Re(CO)3(bpy){P(OEt)3}]• was found convenient for the investigation of the 2e pathway via [Re(CO)3(bpy)]-. The main, spectroscopically observed products of the CO2 reduction are, independent of the 1e and 2e catalytic routes, CO, CO32-, and free CO2H-. The latter product is formed via one-electron reduction of the radical anion [Re(CO)3(bpy)(CO2H)]•-, which is the main byproduct in the catalytic cycle. " - }, - { - "abstract2": "Abstract" - }, - { - "language": "en" - }, - { - "fulltext_html": "/doi/full/10.1021/om960044%2B" - }, - { - "fulltext_html": "/doi/full/10.1021/om500389y" - }, - { - "fulltext_html": "/doi/full/10.1021/ja500403e" - }, - { - "fulltext_html": "/doi/full/10.1021/ic500025k" - }, - { - "fulltext_html": "/doi/full/10.1021/om500044a" - }, - { - "fulltext_html": "/doi/full/10.1021/ja501051s" - }, - { - "fulltext_pdf": "/doi/pdf/10.1021/om960044%2B" - }, - { - "figure": "/appl/literatum/publisher/achs/journals/content/orgnd7/1996/orgnd7.1996.15.issue-15/om960044%2B/production/images/medium/om9600441n00001.gif" - }, - { - "copyright": "Copyright © 1996 American Chemical Society" - }, - { - "om9600441n00001.gif": "d3cd6a0e739ff29fdc972fd8c1360306" - }, - { - "rendered.html": "2b85c69bf2247835acae8dfc33d95ca8" - } - ] -} \ No newline at end of file diff --git a/test/acs_test_urls.txt b/test/acs_test_urls.txt deleted file mode 100644 index 1da039f..0000000 --- a/test/acs_test_urls.txt +++ /dev/null @@ -1,7 +0,0 @@ -http://pubs.acs.org/doi/abs/10.1021/ic50161a007 -http://pubs.acs.org/doi/abs/10.1021/ic501196q -http://pubs.acs.org/doi/abs/10.1021/ic5007007 -http://pubs.acs.org/doi/abs/10.1021/ja2105834 -http://pubs.acs.org/doi/abs/10.1021/jz1010237 -http://pubs.acs.org/doi/abs/10.1021/ar700111a -http://pubs.acs.org/doi/abs/10.1021/om960044%2B \ No newline at end of file diff --git a/test/springer.json b/test/springer.json deleted file mode 100644 index 84b0f3c..0000000 --- a/test/springer.json +++ /dev/null @@ -1,609 +0,0 @@ -{ - "http://link.springer.com/article/10.1007/s00894-014-2429-8": [ - { - "publisher": "Springer Berlin Heidelberg" - }, - { - "title": "Construction and conformational behavior of peptoids with cis-amide bond geometry: design of a peptoid with alternate φ, ψ values of inverse PP-II/PP-II and PP-I structures" - }, - { - "authors": "Fateh Singh Nandel" - }, - { - "authors": "Radhika Rani Jaswal" - }, - { - "authors": "Avneet Saini" - }, - { - "authors": "Vibhuti Nandel" - }, - { - "authors": "Mohd Shafique" - }, - { - "date": "2014/09/01" - }, - { - "volume": "20" - }, - { - "issue": "9" - }, - { - "firstpage": "1" - }, - { - "doi": "10.1007/s00894-014-2429-8" - }, - { - "journal": "Journal of Molecular Modeling" - }, - { - "description": "In peptoids due to the absence of amide protons, the backbone is devoid of hydrogen bond donor, linked by tertiary amide, which can be iso-energetic between cis and trans-amide bond geometry. The pept" - }, - { - "abstract": "In peptoids due to the absence of amide protons, the backbone is devoid of hydrogen bond donor, linked by tertiary amide, which can be iso-energetic between cis and trans-amide bond geometry. The peptoids can be realized with cis amide bond if the side chain of ith residue can engage the carbonyl group of ith-1 residue in CH--O interactions. Simulations studies both in water and DMSO have been carried out. The peptoid Ac-(Ntle)7 -NMe2 can adopt degenerate conformations with alternate φ, ψ values of inverse PP-I and PP-I type structure’s, or vice versa in water. In DMSO, Ac-(Ntle)7-NMe2 also adopts inverse PP-I type structure. Like polyproline, molecule adopting a rigid structure can be used as molecular markers or spacers in biological studies." - }, - { - "abstract": "The peptoid Ac-(Nala-Ntle)3-NMe2 with alternate trans and cis amide bond geometry for Nala and Ntle residue corresponding to inverse PP-II/PP-II type and for Ntle residue of PP-I type." - }, - { - "abstract_html": "http://link.springer.com/article/10.1007/s00894-014-2429-8" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2Fs00894-014-2429-8.pdf" - }, - { - "fulltext_html": "http://link.springer.com/article/10.1007/s00894-014-2429-8/fulltext.html" - }, - { - "supplementary_material": "/content/esm/art:10.1007/s00894-014-2429-8/file/MediaObjects/894_2014_2429_MOESM1_ESM.doc" - }, - { - "894_2014_2429_MOESM1_ESM.doc": "1de5071739e63c48055d35e4d826eecb" - }, - { - "rendered.html": "259cf9345c6fa9e043533b8ac52aa88b" - } - ], - "http://link.springer.com/article/10.1007/s00216-014-7672-4": [ - { - "publisher": "Springer Berlin Heidelberg" - }, - { - "title": "Suspect screening and target quantification of multi-class pharmaceuticals in surface water based on large-volume injection liquid chromatography and time-of-flight mass spectrometry" - }, - { - "authors": "Leendert Vergeynst" - }, - { - "authors": "Herman Van Langenhove" - }, - { - "authors": "Pieter Joos" - }, - { - "authors": "Kristof Demeestere" - }, - { - "date": "2014/04/01" - }, - { - "volume": "406" - }, - { - "issue": "11" - }, - { - "firstpage": "2533" - }, - { - "doi": "10.1007/s00216-014-7672-4" - }, - { - "journal": "Analytical and Bioanalytical Chemistry" - }, - { - "description": "The ever-growing number of emerging micropollutants such as pharmaceuticals requests rapid and sensitive full-spectrum analytical techniques. Time-of-flight high-resolution mass spectrometry (TOF-HRMS" - }, - { - "abstract": "The ever-growing number of emerging micropollutants such as pharmaceuticals requests rapid and sensitive full-spectrum analytical techniques. Time-of-flight high-resolution mass spectrometry (TOF-HRMS) is a promising alternative for the state-of-the-art tandem mass spectrometry instruments because of its ability to simultaneously screen for a virtually unlimited number of suspect analytes and to perform target quantification. The challenge for such suspect screening is to develop a strategy, which minimizes the false-negative rate without restraining numerous false-positives. At the same time, omitting laborious sample enrichment through large-volume injection ultra-performance liquid chromatography (LVI-UPLC) avoids selective preconcentration. A suspect screening strategy was developed using LVI-UPLC-TOF-MS aiming the detection of 69 multi-class pharmaceuticals in surface water without the a priori availability of analytical standards. As a novel approach, the screening takes into account the signal-intensity-dependent accurate mass error of TOF-MS, hereby restraining 95 % of the measured suspect pharmaceuticals present in surface water. Application on five Belgian river water samples showed the potential of the suspect screening approach, as exemplified by a false-positive rate not higher than 15 % and given that 30 out of 37 restrained suspect compounds were confirmed by the retention time of analytical standards. Subsequently, this paper discusses the validation and applicability of the LVI-UPLC full-spectrum HRMS method for target quantification of the 69 pharmaceuticals in surface water. Analysis of five Belgian river water samples revealed the occurrence of 17 pharmaceuticals in a concentration range of 17 ng L−1 up to 3.1 μg L−1." - }, - { - "abstract": " Figure " - }, - { - "abstract_html": "http://link.springer.com/article/10.1007/s00216-014-7672-4" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2Fs00216-014-7672-4.pdf" - }, - { - "fulltext_html": "http://link.springer.com/article/10.1007/s00216-014-7672-4/fulltext.html" - }, - { - "supplementary_material": "/content/esm/art:10.1007/s00216-014-7672-4/file/MediaObjects/216_2014_7672_MOESM1_ESM.pdf" - }, - { - "figure": "/static-content/images/620/art%253A10.1007%252Fs00216-014-7672-4/MediaObjects/216_2014_7672_Figa_HTML.gif" - }, - { - "216_2014_7672_Figa_HTML.gif": "a3d4d59df9737410ee8541b97eae76dc" - }, - { - "rendered.html": "38f42ec47d5d3b0a4e6e89ce4aff90c0" - } - ], - "http://link.springer.com/article/10.1007/s00216-013-7560-3": [ - { - "publisher": "Springer Berlin Heidelberg" - }, - { - "title": "A fluorescence-based high throughput assay for the determination of small molecule−human serum albumin protein binding" - }, - { - "authors": "Megan M. McCallum" - }, - { - "authors": "Alan J. Pawlak" - }, - { - "authors": "William R. Shadrick" - }, - { - "authors": "Anton Simeonov" - }, - { - "authors": "Ajit Jadhav" - }, - { - "authors": "Adam Yasgar" - }, - { - "authors": "David J. Maloney" - }, - { - "authors": "Leggy A. Arnold" - }, - { - "date": "2014/03/01" - }, - { - "volume": "406" - }, - { - "issue": "7" - }, - { - "firstpage": "1867" - }, - { - "doi": "10.1007/s00216-013-7560-3" - }, - { - "journal": "Analytical and Bioanalytical Chemistry" - }, - { - "description": "Herein, we describe the development of a fluorescence-based high throughput assay to determine the small molecule binding towards human serum albumin (HSA). This innovative competition assay is based " - }, - { - "abstract": "Herein, we describe the development of a fluorescence-based high throughput assay to determine the small molecule binding towards human serum albumin (HSA). This innovative competition assay is based on the use of a novel fluorescent small molecule Red Mega 500 with unique spectroscopic and binding properties. The commercially available probe displays a large fluorescence intensity difference between the protein-bound and protein-unbound state. The competition of small molecules for HSA binding in the presence of probe resulted in low fluorescence intensities. The assay was evaluated with the library of pharmacological active compounds (LOPAC) small molecule library of 1,280 compounds identifying known high protein binders. The small molecule competition of HSA−Red Mega 500 binding was saturable at higher compound concentrations and exhibited IC50 values between 3 and 24 μM. The compound affinity toward HSA was confirmed by isothermal titration calorimetry indicating that the new protein binding assay is a valid high throughput assay to determine plasma protein binding." - }, - { - "abstract": " Figure " - }, - { - "abstract_html": "http://link.springer.com/article/10.1007/s00216-013-7560-3" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2Fs00216-013-7560-3.pdf" - }, - { - "fulltext_html": "http://link.springer.com/article/10.1007/s00216-013-7560-3/fulltext.html" - }, - { - "figure": "/static-content/images/274/art%253A10.1007%252Fs00216-013-7560-3/MediaObjects/216_2013_7560_Figa_HTML.gif" - }, - { - "216_2013_7560_Figa_HTML.gif": "388dde09acd4582efcf02a188e38cc43" - }, - { - "rendered.html": "022b01cfc7320314b92b0d7bf054b764" - } - ], - "http://link.springer.com/article/10.1007/BF01024715": [ - { - "publisher": "Kluwer Academic Publishers" - }, - { - "title": "Continuous cultivation of a yeast strain for biotransformation of L-acetyl phenyl carbinol (L-PAC) from benzaldehyde" - }, - { - "authors": "C. K. M. Tripathi" - }, - { - "authors": "S. K. Basu" - }, - { - "authors": "V. C. Vora" - }, - { - "authors": "J. R. Mason" - }, - { - "authors": "S. J. Pirt" - }, - { - "date": "1988/09/01" - }, - { - "volume": "10" - }, - { - "issue": "9" - }, - { - "firstpage": "635" - }, - { - "doi": "10.1007/BF01024715" - }, - { - "journal": "Biotechnology Letters" - }, - { - "description": "L-PAC production by a yeast strain harvested from glucose limited continuous cultures grown at different dilution rates has been studied. The specific transformation rate is higher for the cells which" - }, - { - "abstract": "L-PAC production by a yeast strain harvested from glucose limited continuous cultures grown at different dilution rates has been studied. The specific transformation rate is higher for the cells which have been grown at higher dilution rates." - }, - { - "abstract_html": "http://link.springer.com/article/10.1007/BF01024715" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2FBF01024715.pdf" - }, - { - "BF01024715": "30adcd173a3f9e496aa0dad49f0ab4fc" - }, - { - "rendered.html": "30adcd173a3f9e496aa0dad49f0ab4fc" - } - ], - "http://link.springer.com/article/10.1007/s40333-014-0028-2": [ - { - "publisher": "Science Press" - }, - { - "title": "Ecophysiological aspects in 105 plants species of saline and arid environments in Tunisia" - }, - { - "authors": "Abdallah Atia" - }, - { - "authors": "Mokded Rabhi" - }, - { - "authors": "Ahmed Debez" - }, - { - "authors": "Chedly Abdelly" - }, - { - "authors": "Houda Gouia" - }, - { - "authors": "Chiraz Chaffei Haouari" - }, - { - "authors": "Abderrazak Smaoui" - }, - { - "date": "2014/12/01" - }, - { - "volume": "6" - }, - { - "issue": "6" - }, - { - "firstpage": "762" - }, - { - "doi": "10.1007/s40333-014-0028-2" - }, - { - "journal": "Journal of Arid Land" - }, - { - "description": "In Tunisian arid regions, plant life forms, ecotypes, physiological types and photosynthetic pathways (C3, C4 or CAM) remain unclear. Understanding the characters of these plant species could be impor" - }, - { - "abstract": "In Tunisian arid regions, plant life forms, ecotypes, physiological types and photosynthetic pathways (C3, C4 or CAM) remain unclear. Understanding the characters of these plant species could be important for land restoration. A literature survey was conducted for 105 species from arid regions of Tunisia. These plant species belong to several ecotypes: halophytes, xerophytes, gypsophytes, psamophytes, xero-halophytes, gypso-halophytes, psamo-halophytes, psamo-xerophytes, xero-gypsophytes and hygro-halophytes. The variation of photosynthetic pathway types in the 105 studied species shows that 56.2% are C3, 41.0% are C4, 1.9% are CAM and 1.0% are C3-CAM. The C3 pathway is more abundant in the halophytes, whereas the C4 one is more common in the xerophytes, gypsophytes, gypso-halophytes and psamo-halophytes. The ratio of C3 to C4 species (C3/C4 ratio) is 0.2 in the psamo-halophytes, 0.8 in the gypso-halophytes, 1.1 in the xerophytes, 1.6 in the xero-halophytes, 1.8 in the hygrohalophytes, 2.0 in the psamophytes and 3.8 in the halophytes. The annuals are mainly C3 plants whereas most of perennials are C4 ones. The C3/C4 ratio is 1.3 in succulent species and 1.4 in non-succulent species. Thus, succulence seems not to affect the distribution of C3 and C4 pathways within the studied plants. This investigation shows high percentages of C4 plants in plants of Tunisian arid regions. However, there are significant differences in their abundance among ecotypes. Based on C3/C4 ratio, the abundance of the C4 pathway is in the following order: psamo-halophytes, gypso-halophytes, xerophytes, xero-halophytes, hygro-halophytes, psamophytes, halophytes. In Tunisian arid regions, C4 species are most abundant in xerophytes and less abundant in halophytes. In the Chenopodiaceae the number of C3 plants is 13 and the number of C4 species is 20 and in the Poaceae the number of C3 was 23 and the number of C4 was 19 species. Thus, the most C4 proportion is in the Chenopodiaceae and Poaceae species. This confirms the fact that the Chenopodiaceae and the Poaceae were the leading families that tolerate salinity and aridity." - }, - { - "abstract_html": "http://link.springer.com/article/10.1007/s40333-014-0028-2" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2Fs40333-014-0028-2.pdf" - }, - { - "rendered.html": "42248e742e8bfc27a820c602aeb64371" - }, - { - "s40333-014-0028-2": "42248e742e8bfc27a820c602aeb64371" - } - ], - "http://link.springer.com/article/10.1007/s40069-014-0084-1": [ - { - "publisher": "Korea Concrete Institute" - }, - { - "title": "Prediction of Concrete Pumping Using Various Rheological Models" - }, - { - "authors": "Myoung Sung Choi" - }, - { - "authors": "Young Jin Kim" - }, - { - "authors": "Jin Keun Kim" - }, - { - "date": "2014/12/01" - }, - { - "volume": "8" - }, - { - "issue": "4" - }, - { - "firstpage": "269" - }, - { - "doi": "10.1007/s40069-014-0084-1" - }, - { - "journal": "International Journal of Concrete Structures and Materials" - }, - { - "description": "When concrete is being transported through a pipe, the lubrication layer is formed at the interface between concrete and the pipe wall and is the major factor facilitating concrete pumping. A possible" - }, - { - "abstract": "When concrete is being transported through a pipe, the lubrication layer is formed at the interface between concrete and the pipe wall and is the major factor facilitating concrete pumping. A possible mechanism that illustrates to the formation of the layer is the shear-induced particle migration and determining the rheological parameters is a paramount factor to simulate the concrete flow in pipe. In this study, numerical simulations considering various rheological models in the shear-induced particle migration were conducted and compared with 170 m full-scale pumping tests. It was found that the multimodal viscosity model representing concrete as a three-phase suspension consisting of cement paste, sand and gravel can accurately simulate the lubrication layer. Moreover, considering the particle shape effects of concrete constituents with increased intrinsic viscosity can more exactly predict the pipe flow of pumped concrete." - }, - { - "abstract_html": "http://link.springer.com/article/10.1007/s40069-014-0084-1" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2Fs40069-014-0084-1.pdf" - }, - { - "fulltext_html": "http://link.springer.com/article/10.1007/s40069-014-0084-1/fulltext.html" - }, - { - "rendered.html": "75b8db48c86c853a8cc2453325de0e0f" - }, - { - "s40069-014-0084-1": "75b8db48c86c853a8cc2453325de0e0f" - } - ], - "http://link.springer.com/article/10.1007/BF02896800": [ - { - "publisher": "Springer-Verlag" - }, - { - "title": "Costruzione di classi filtrali" - }, - { - "authors": "Roberto Magari" - }, - { - "date": "1969/12/01" - }, - { - "volume": "14" - }, - { - "issue": "1" - }, - { - "firstpage": "35" - }, - { - "doi": "10.1007/BF02896800" - }, - { - "journal": "Annali dell’Università di Ferrara" - }, - { - "description": "SiaH una classe filtrale (1) di strutture algebriche di un certo tipo eK una classe di strutture algebriche semplici e a sottoalgebre semplici che siano portate da un funtore dimenticante in strutture" - }, - { - "abstract": "SiaH una classe filtrale (1) di strutture algebriche di un certo tipo eK una classe di strutture algebriche semplici e a sottoalgebre semplici che siano portate da un funtore dimenticante in strutture algebriche diSPH." - }, - { - "abstract": "Dettametafiltrale una classeK nelle predette condizioni si danno condizioni perchè una tal classe sia filtrale e si costruiscono alcune notevoli classi filtrali." - }, - { - "abstract": "A classK of similar algebras is said to be: «filtrale» («semifiltrale» if each congruenceR on each subdirect (direct) product of a family of elements ofK is «associated» with a filterF onI («associated» in the sense of the reduced products theory, i.e.: " - }, - { - "abstract": "A varietyV of algebras is said to be: «sempisimple»: iff each is semisimple, «sotto-semisemplice»: ifV ⊆SPΣ (Σ: class of simple algebras ofV)." - }, - { - "abstract": "An algebra is said to be «regolare» if each congruenceR on each subalgebra of extends to a congruenceS on " - }, - { - "abstract": "In a previous paper ([6]) I proved:" - }, - { - "abstract": "LetK be a class of similar algebras, Σ the class of the simple algebras ofVK \\(\\overline \\Sigma = \\Sigma \\cap HP\\) K. Then:" - }, - { - "abstract": "ifK is «semifiltrale» then \\(\\overline \\Sigma \\) is «semifiltrale». ifK is «filtrale» then:" - }, - { - "abstract": " V K is «sottosemisemplice»." - }, - { - "abstract": "each congruence on each K is associated with a filter." - }, - { - "abstract": "each K is «regolare»." - }, - { - "abstract": "ifK={W} andW is finite thenW is semicategorical (I observe in [6] that this results can be obtained as a simple consequence of Astromoff’s, Foster’s and Pixley’s results)." - }, - { - "abstract": "ifK={W} andW is infinite then there are simple algebras inV K wich are not isomorphic toW and V K ⊆|⊆SP K." - }, - { - "abstract": "Let (a), (b), (c), (d) be the following properties:" - }, - { - "abstract": "Σ is «filtrale»." - }, - { - "abstract": "each algebra ofV K is «regolare»." - }, - { - "abstract": " V K is semisimple." - }, - { - "abstract": " V K=SP K. then the following implications hold " - }, - { - "abstract": "LetK be a class of algebras of a fied type.K is said to be «metafiltrale» iff every is simple and there is a «filtrale» classH of algebras and a forgetful functors δ such that δK=⊆SP H." - }, - { - "abstract": "I find some sufficient conditions for a «metafiltrale» classe to be «filtrale» and I give some noteworthy examples of «filtrali» and «semifiltrali» classes, in particular the varieties of «α-plurireticoli» (cfr. n. 9)." - }, - { - "abstract": "Tipical corollary:every finite systems wich is simple (and has only simple subalgebras) and where ." - }, - { - "abstract_html": "http://link.springer.com/article/10.1007/BF02896800" - }, - { - "language": "it" - }, - { - "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2FBF02896800.pdf" - }, - { - "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f1.jpg" - }, - { - "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f2.jpg" - }, - { - "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f3.jpg" - }, - { - "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f4.jpg" - }, - { - "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f5.jpg" - }, - { - "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f6.jpg" - }, - { - "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f7.jpg" - }, - { - "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f8.jpg" - }, - { - "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f9.jpg" - }, - { - "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f10.jpg" - }, - { - "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f11.jpg" - }, - { - "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f12.jpg" - }, - { - "figure": "/static-content/images/25/art%253A10.1007%252FBF02896800/MediaObjects/11565_2008_Article_BF02896800_f13.jpg" - }, - { - "11565_2008_Article_BF02896800_f3.jpg": "0bbf5af2bcb2347f64231d90e1c812f6" - }, - { - "rendered.html": "3880b5ef1a64dd076881788347e07e8b" - } - ], - "http://link.springer.com/article/10.1007/s10719-014-9555-5": [ - { - "publisher": "Springer US" - }, - { - "title": "Association between serum sulfatide and carotid intima media thickness in patients with familial hypercholesterolemia" - }, - { - "authors": "Gang Li" - }, - { - "authors": "Rui Hu" - }, - { - "firstpage": "1" - }, - { - "doi": "10.1007/s10719-014-9555-5" - }, - { - "journal": "Glycoconjugate Journal" - }, - { - "description": "There is a positive association between sulfatide and atherosclerosis in an animal model for human familial hypercholesterolemia. Carotid intima–media thickness (IMT) is thought to be a marker of athe" - }, - { - "abstract": "There is a positive association between sulfatide and atherosclerosis in an animal model for human familial hypercholesterolemia. Carotid intima–media thickness (IMT) is thought to be a marker of atherosclerosis in humans. We investigated the relationship between sulfatide and carotid IMT in heterozygous familial hypercholesterolemia (FH) patients. Thirty-five genetically-verified heterozygous patients with FH and 34 healthy controls were recruited into our study. We measured serum sulfatide levels, the carotid IMT, and conventional cardiovascular risk factors including obesity parameters, blood pressure, fasting blood glucose, and lipid profiles. Subjects with heterozygous FH had significantly elevated serum sulfatide, elevated total cholesterol, low-density lipoprotein cholesterol, and increased carotid IMT compared with control subjects. In patients with FH, univariate analysis showed that serum sulfatide was significantly correlated with carotid IMT. Multiple linear regression analysis indicated that serum sulfatide was the only independent predictor of carotid IMT in patients with FH. Patients with heterozygous FH had significantly higher carotid IMT and the level of serum sulfatide was independently associated with atherosclerotic progression. (R: 0.720, R2: 0.503, p " - }, - { - "abstract_html": "http://link.springer.com/article/10.1007/s10719-014-9555-5" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://link.springer.com/content/pdf/10.1007%2Fs10719-014-9555-5.pdf" - }, - { - "fulltext_html": "http://link.springer.com/article/10.1007/s10719-014-9555-5/fulltext.html" - }, - { - "rendered.html": "4664240a9c97d4f0478b51c0c3ab61dd" - }, - { - "s10719-014-9555-5": "4664240a9c97d4f0478b51c0c3ab61dd" - } - ] -} \ No newline at end of file diff --git a/test/springer_test_urls.txt b/test/springer_test_urls.txt deleted file mode 100644 index 9a1560b..0000000 --- a/test/springer_test_urls.txt +++ /dev/null @@ -1,8 +0,0 @@ -http://link.springer.com/article/10.1007/s00894-014-2429-8 -http://link.springer.com/article/10.1007/s00216-014-7672-4 -http://link.springer.com/article/10.1007/s00216-013-7560-3 -http://link.springer.com/article/10.1007/BF01024715 -http://link.springer.com/article/10.1007/s40333-014-0028-2 -http://link.springer.com/article/10.1007/s40069-014-0084-1 -http://link.springer.com/article/10.1007/BF02896800 -http://link.springer.com/article/10.1007/s10719-014-9555-5 \ No newline at end of file diff --git a/test/tandf.json b/test/tandf.json deleted file mode 100644 index 3cf9c87..0000000 --- a/test/tandf.json +++ /dev/null @@ -1,357 +0,0 @@ -{ - "http://www.tandfonline.com/doi/abs/10.1080/02757540.2013.878336": [ - { - "publisher": "Taylor & Francis" - }, - { - "title": "Effect of dye auxiliaries on chemical oxygen demand and colour competitive removal from textile effluents using Posidonia oceanica" - }, - { - "authors": "Sonia Dridi-Dhaouadi" - }, - { - "authors": "Mohamed Farouk Mhenni" - }, - { - "date": "2014-06-12" - }, - { - "pagerange": "pages 579-588" - }, - { - "doi": "10.1080/02757540.2013.878336" - }, - { - "description": "The use of an abundant and widely distributed seagrass species, Posidonia oceanica, as a biosorbent for the direct dye Yellow 44 was successfully shown. The studies were performed on the single dyestuff dissolved in water and in a dyebath containing agents commonly used in the textile industry, i.e. a surfactant (Lavotan TBU), a sequestring agent (Meropan DPE), a softening agent (Eurosoft CI10) and a salt (NaCl). The colour reduction results showed that P. oceanica was found to be more efficient for removal of Yellow 44 from an aqueous solution (162 mg g−1) than from a dyebath solution (135 mg g−1), according to the Langmuir isotherm model. For the single dyestuff sorption, Fourier transform infrared and X-ray photoelectron spectroscopy studies highlighted chemical sorption between the dye alcohol function and the sorbent acid function. The chemical oxygen demand removal percentages were found to be 54.9 and 76.6% for Yellow 44 dissolved in aqueous solution and in dyebath solution, respectively. This conf..." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/02757540.2013.878336" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/02757540.2013.878336" - }, - { - "fulltext_html": "/doi/full/10.1080/02757540.2013.878336" - }, - { - "fulltext_html": "/doi/full/10.1080/02757540.2013.878336" - }, - { - "supplementary_material": "/doi/suppl/10.1080/02757540.2013.878336#tabModule" - }, - { - "supplementary_material": "/doi/suppl/10.1080/02757540.2013.878336#tabModule" - }, - { - "02757540.2013.878336": "e016a9d960a97c5656a75bf37812fe49" - }, - { - "rendered.html": "6c3a26e89007055588c43ac8edfa8287" - } - ], - "http://www.tandfonline.com/doi/abs/10.1080/1747423X.2013.786151": [ - { - "publisher": "Taylor & Francis" - }, - { - "title": "Detecting land-use change from seasonal vegetation dynamics on regional scale with MODIS EVI 250-m time-series imagery" - }, - { - "authors": "Yudi Setiawan" - }, - { - "authors": "Kunihiko Yoshino" - }, - { - "date": "2014-06-05" - }, - { - "pagerange": "pages 304-330" - }, - { - "doi": "10.1080/1747423X.2013.786151" - }, - { - "description": "Simultaneous analysis of land surface attributes and their seasonal changes provides a broader view of land-use and land-cover change. This study attempted to detect the change in inter-annual temporal vegetation dynamics, which reflects a change in land surface attributes. We explored 250-m multi-temporal MODIS EVI 16-day composite data from 2001 to 2007 to characterize a change in vegetation dynamics related to land-use change detection. The MODIS data was filtered in time-frequency space by wavelet function in order to identify and reduce the overall noise so as not to lose useful information from the time series data. The results show that by characterizing temporal vegetation dynamics, it is possible to distinguish actual land-use change based on land-cover dynamics. The result was evaluated using 18,626 reference pixels and showed an overall accuracy of 76.10%. In agricultural land use, such as upland and plantation, the weakest results were caused by mixed pixels from MODIS 250-m grid data as well ..." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/1747423X.2013.786151" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/1747423X.2013.786151" - }, - { - "fulltext_html": "/doi/full/10.1080/1747423X.2013.786151" - }, - { - "fulltext_html": "/doi/full/10.1080/1747423X.2013.786151" - }, - { - "1747423X.2013.786151": "df40110001381ee8c9ff82c14e9b337b" - }, - { - "rendered.html": "7738b7d284697900c670c4237101781c" - } - ], - "http://www.tandfonline.com/doi/abs/10.1080/19376812.2013.838660": [ - { - "publisher": "Routledge" - }, - { - "title": "An Intensity Analysis of land-use and land-cover change in Karatu District, Tanzania: community perceptions and coping strategies" - }, - { - "authors": "Leonia Raphael John" - }, - { - "authors": "Herbert Hambati" - }, - { - "authors": "Frederick Ato Armah" - }, - { - "date": "2014-05-02" - }, - { - "pagerange": "pages 150-173" - }, - { - "doi": "10.1080/19376812.2013.838660" - }, - { - "description": "Land-use and land-cover changes (LULCCs) are the result of complex interactions between the human (cultural, socio-economic and political) and the biophysical environment at different spatial scales. The present study assessed the spatial distribution of LULC (1976–2008) in the high and low altitude zones in the northern highlands of Karatu, Tanzania, using both qualitative (in-depth interviews and focus group discussions) and quantitative techniques (Intensity Analysis). The qualitative approach was used to elicit information on the coping strategies adopted by land users as transitions occurred with time and the Intensity Analysis was used to assess the systematic land losses, gains and persistence of the various land categories with time. The results of the Intensity Analysis show that overall land transformation is decelerating in both agro-ecological zones across the two time intervals. In the low altitude zone, woodland, settlements and bushland are active categories unlike cultivated and grassland,..." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/19376812.2013.838660" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/19376812.2013.838660" - }, - { - "fulltext_html": "/doi/full/10.1080/19376812.2013.838660" - }, - { - "fulltext_html": "/doi/full/10.1080/19376812.2013.838660" - }, - { - "19376812.2013.838660": "ad38dee2f4a2955e64b88f234d5ea8fd" - }, - { - "rendered.html": "9f2cb3dfa837580b736ded0bd98de5ba" - } - ], - "http://www.tandfonline.com/doi/abs/10.1080/13647830.2014.923116": [ - { - "publisher": "Taylor & Francis" - }, - { - "title": "Triple flame: Inherent asymmetries and pentasectional character" - }, - { - "authors": "Albert Jordà Juanós" - }, - { - "authors": "William A. Sirignano" - }, - { - "date": "2014-07-11" - }, - { - "pagerange": "pages 454-473" - }, - { - "doi": "10.1080/13647830.2014.923116" - }, - { - "description": "A two-dimensional triple-flame numerical model of a laminar combustion process reflects flame asymmetric structural features that other analytical models do not generate. It reveals the pentasectional character of the triple flame, composed of the central pure diffusion-flame branch and the fuel-rich and fuel-lean branches, each of which is divided into two sections: a near-stoichiometric section and a previously unreported near-flammability-limits section with combined diffusion and premixed character. Results include propagation velocity, fuel and oxidiser mass fractions, temperature and reaction rates. Realistic stoichiometric ratios and reaction orders match experimental planar flame characteristics. Constant density, a one-step reaction, and a mixture fraction gradient at the inlet as the simulation parameter are imposed. The upstream equivalence ratio or the upstream reactant mass fractions are linear or hyperbolic functions of the transverse coordinate. The use here of experimental kinetics data di..." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/13647830.2014.923116" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/13647830.2014.923116" - }, - { - "fulltext_html": "/doi/full/10.1080/13647830.2014.923116" - }, - { - "fulltext_html": "/doi/full/10.1080/13647830.2014.923116" - }, - { - "13647830.2014.923116": "f1582f18b27ad25acb51ae3c6da0aa2f" - }, - { - "rendered.html": "589eb09898f9adb86f6c917b393a6b92" - } - ], - "http://www.tandfonline.com/doi/abs/10.1080/16841360802338738": [ - { - "publisher": " Routledge " - }, - { - "title": "Double degrees in the context of the Bologna process" - }, - { - "authors": " Anne Klebes‐Pelissier " - }, - { - "date": "2008-12-11" - }, - { - "pagerange": "pages 173-180" - }, - { - "doi": "10.1080/16841360802338738" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/16841360802338738" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/16841360802338738" - }, - { - "fulltext_html": "/doi/full/10.1080/16841360802338738" - }, - { - "fulltext_html": "/doi/full/10.1080/16841360802338738" - }, - { - "16841360802338738": "bcca16511d449aaf5c668fa354914770" - }, - { - "rendered.html": "61d473f6941147703842180e59ba6e8e" - } - ], - "http://www.tandfonline.com/doi/abs/10.1207/S15326926CLP0701_04": [ - { - "publisher": " Lawrence Erlbaum Associates, Inc. " - }, - { - "title": "Litigation Public Relations: The Lawyers' Duty to Balance News Coverage of Their Clients" - }, - { - "authors": " John C. Watson " - }, - { - "date": "2010-01-14" - }, - { - "pagerange": "pages 77-103" - }, - { - "description": "As the 20th century began its final decade, litigation public relations was more rigorously condemned than condoned. By the end of the decade, the proliferation of the practice and the failure of the bar and bench to forbid it had made the criticism virtually moot. This article considers whether there is a basis for making the right to practice litigation public relations an obligation to do so. The article concludes that the right properly belongs to clients and not their attorneys, and finds a basis in contract and malpractice law for requiring attorneys to tend to their clients' interests in the court of public opinion as zealously as they do in courts of law." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "/doi/pdf/10.1207/S15326926CLP0701_04" - }, - { - "fulltext_pdf": "/doi/pdf/10.1207/S15326926CLP0701_04" - }, - { - "rendered.html": "e032e351321d1553f2fafad837a97709" - }, - { - "S15326926CLP0701_04": "a8e25f16f909c51af2c8c77e70adc272" - } - ], - "http://www.tandfonline.com/doi/abs/10.1080/02630672.1992.9689834": [ - { - "publisher": " Taylor & Francis Group " - }, - { - "title": "AUTISM & DRAMATHERAPY" - }, - { - "authors": " Jeremy Carrette " - }, - { - "date": "2011-09-09" - }, - { - "pagerange": "pages 17-20" - }, - { - "doi": "10.1080/02630672.1992.9689834" - }, - { - "description": "The difficulty is to discover the archimedic point at which the technique can be applied effectively. We found that the archimedic point of treatment is the psychological level of an individual on which he is truly spontaneous. J L Moreno (1946, 222)" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/02630672.1992.9689834" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/02630672.1992.9689834" - }, - { - "02630672.1992.9689834": "a90cc82ab7d041c43cc87b1217a86abd" - }, - { - "rendered.html": "82f3ed7f8948007304dfcc6e7674091a" - } - ], - "http://www.tandfonline.com/doi/abs/10.1080/03085147.2012.760347": [ - { - "publisher": "Routledge" - }, - { - "title": "‘Because in Chile [carbon] markets work!’ Exploring an experimental implementation of an emissions trading scheme to deal with industrial air pollution in Santiago" - }, - { - "authors": "Sebastián Ureta" - }, - { - "date": "2014-06-04" - }, - { - "pagerange": "pages 285-306" - }, - { - "doi": "10.1080/03085147.2012.760347" - }, - { - "description": "AbstractEmissions trading schemes have gained an important degree of momentum in recent years, rapidly becoming mainstream solutions to deal with the negative environmental consequences of human activity such as pollution and global warming. However there is still little empirical knowledge about what specific kind of work emissions trading schemes do. Using the analytical tools provided by science and technology studies, especially developments studying markets and economic practices, this paper looks to contribute to filling this void by exploring three kinds of work that emissions trading schemes might do: performing a textbook market of emissions permits, performing a civilized market in which a multitude of heterogeneous actors participate and as exemplars of the validity of certain economic knowledge. In order to explore the usability of this conceptualization the paper will then analyze one of earliest concrete implementations of this device: an emissions trading scheme introduced to deal with indu..." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/03085147.2012.760347" - }, - { - "fulltext_pdf": "/doi/pdf/10.1080/03085147.2012.760347" - }, - { - "fulltext_html": "/doi/full/10.1080/03085147.2012.760347" - }, - { - "fulltext_html": "/doi/full/10.1080/03085147.2012.760347" - }, - { - "03085147.2012.760347": "7c81a6b86b030f843813b273dc63dc6e" - }, - { - "rendered.html": "dc0ad71bc27f5ca9782b5454e66d6605" - } - ] -} \ No newline at end of file diff --git a/test/tandf_test_urls.txt b/test/tandf_test_urls.txt deleted file mode 100644 index ea5f30b..0000000 --- a/test/tandf_test_urls.txt +++ /dev/null @@ -1,8 +0,0 @@ -http://www.tandfonline.com/doi/abs/10.1080/02757540.2013.878336 -http://www.tandfonline.com/doi/abs/10.1080/1747423X.2013.786151 -http://www.tandfonline.com/doi/abs/10.1080/19376812.2013.838660 -http://www.tandfonline.com/doi/abs/10.1080/13647830.2014.923116 -http://www.tandfonline.com/doi/abs/10.1080/16841360802338738 -http://www.tandfonline.com/doi/abs/10.1207/S15326926CLP0701_04 -http://www.tandfonline.com/doi/abs/10.1080/02630672.1992.9689834 -http://www.tandfonline.com/doi/abs/10.1080/03085147.2012.760347 \ No newline at end of file diff --git a/test/wiley.json b/test/wiley.json deleted file mode 100644 index 6d19150..0000000 --- a/test/wiley.json +++ /dev/null @@ -1,556 +0,0 @@ -{ - "http://onlinelibrary.wiley.com/doi/10.1002/anie.201403615/abstract": [ - { - "publisher": "WILEY‐VCH Verlag" - }, - { - "title": "A Supercharged Fluorescent Protein as a Versatile Probe for Homogeneous DNA Detection and Methylation Analysis" - }, - { - "authors": "Lei, Chunyang" - }, - { - "authors": "Huang, Yan" - }, - { - "authors": "Nie, Zhou" - }, - { - "authors": "Hu, Jun" - }, - { - "authors": "Li, Lijun" - }, - { - "authors": "Lu, Guoyan" - }, - { - "authors": "Han, Yitao" - }, - { - "authors": "Yao, Shouzhuo" - }, - { - "date": "2014/08/04" - }, - { - "volume": "53" - }, - { - "issue": "32" - }, - { - "firstpage": "8358" - }, - { - "doi": "10.1002/anie.201403615" - }, - { - "journal": "Angewandte Chemie International Edition" - }, - { - "abstract": "Supercharged proteins are a new class of functional proteins with exceptional stability and potent ability to deliver bio‐macromolecules into cells. As a proof‐of‐principle, a novel application of supercharged proteins as a versatile biosensing platform for nucleic acid detection and epigenetics analysis is presented. Taking supercharged green fluorescent protein (ScGFP) as the signal reporter, a simple turn‐on homogenous method for DNA detection has been developed based on the polyionic nanoscale complex of ScGFP/DNA and toehold strand displacement. This assay shows high sensitivity and potent ability to detect single‐base mismatch. Furthermore, combined with bisulfite conversion, this ScGFP‐based assay was further applied to analyze site‐specific DNA methylation status of genomic DNA extracted from real human colon carcinoma tissue sample with ultrahigh sensitivity (4 amol methylated DNA)." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/anie.201403615/pdf" - }, - { - "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/anie.201403615/full" - }, - { - "supplementary_material": "/doi/10.1002/anie.201403615/suppinfo" - }, - { - "rendered.html": "b3986b19732048c6aad2aba454c1a683" - }, - { - "suppinfo": "3768366620b4ad7feabdf1fd2731096f" - } - ], - "http://onlinelibrary.wiley.com/doi/10.1002/anie.201404164/abstract": [ - { - "publisher": "WILEY‐VCH Verlag" - }, - { - "title": "pH‐Dependent Proton Conducting Behavior in a Metal–Organic Framework Material" - }, - { - "authors": "Phang, Won Ju" - }, - { - "authors": "Lee, Woo Ram" - }, - { - "authors": "Yoo, Kicheon" - }, - { - "authors": "Ryu, Dae Won" - }, - { - "authors": "Kim, BongSoo" - }, - { - "authors": "Hong, Chang Seop" - }, - { - "date": "2014/08/04" - }, - { - "volume": "53" - }, - { - "issue": "32" - }, - { - "firstpage": "8383" - }, - { - "doi": "10.1002/anie.201404164" - }, - { - "journal": "Angewandte Chemie International Edition" - }, - { - "abstract": "A porous metal–organic framework (MOF), [Ni2(dobdc)(H2O)2]⋅6 H2O (Ni2(dobdc) or Ni‐MOF‐74; dobdc4−=2,5‐dioxido‐1,4‐benzenedicarboxylate) with hexagonal channels was synthesized using a microwave‐assisted solvothermal reaction. Soaking Ni2(dobdc) in sulfuric acid solutions at different pH values afforded new proton‐conducting frameworks, H+@Ni2(dobdc). At pH 1.8, the acidified MOF shows proton conductivity of 2.2×10−2 S cm−1 at 80 °C and 95 % relative humidity (RH), approaching the highest values reported for MOFs. Proton conduction occurs via the Grotthuss mechanism with a significantly low activation energy as compared to other proton‐conducting MOFs. Protonated water clusters within the pores of H+@Ni2(dobdc) play an important role in the conduction process." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/anie.201404164/pdf" - }, - { - "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/anie.201404164/full" - }, - { - "supplementary_material": "/doi/10.1002/anie.201404164/suppinfo" - }, - { - "rendered.html": "6d67fe51554fa9c91ea9ffd2dfdf160f" - }, - { - "suppinfo": "1540f0fc2bb23d5da62f9e3be1697443" - } - ], - "http://onlinelibrary.wiley.com/doi/10.1002/anie.200501671/abstract": [ - { - "publisher": "WILEY‐VCH Verlag" - }, - { - "title": "Finding Adiabatically Bound Anions of Guanine through a Combinatorial Computational Approach" - }, - { - "authors": "Harańczyk, Maciej" - }, - { - "authors": "Gutowski, Maciej" - }, - { - "date": "2005/10/14" - }, - { - "volume": "44" - }, - { - "issue": "40" - }, - { - "firstpage": "6585" - }, - { - "doi": "10.1002/anie.200501671" - }, - { - "journal": "Angewandte Chemie International Edition" - }, - { - "abstract": "Enamine–imine transformations of guanine lead to tautomers that support valence anionic states which are adiabatically bound by as much as 8 kcal mol−1 (see scheme). The valence anions might be formed by dissociative electron attachment followed by attachment of a hydrogen atom to a carbon atom. Such tautomers might affect the structure and properties of DNA and RNA exposed to low‐energy electrons." - }, - { - "figure": "http://onlinelibrary.wiley.com/store/10.1002/anie.200501671/asset/image_m/mcontent.gif?v=1&s=a375d92cc9e2ad2c5b874eaae0af7ab08c33ba25" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/anie.200501671/pdf" - }, - { - "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/anie.200501671/full" - }, - { - "supplementary_material": "/doi/10.1002/anie.200501671/suppinfo" - }, - { - "mcontent.gif": "05f920a0b7dd1a6cc70a3d0440edccab" - }, - { - "rendered.html": "89bbb468479dc9891e4319426aa93165" - } - ], - "http://onlinelibrary.wiley.com/doi/10.1002/cbic.201300780/abstract": [ - { - "publisher": "WILEY‐VCH Verlag" - }, - { - "title": "Improving the Stability and Catalyst Lifetime of the Halogenase RebH By Directed Evolution" - }, - { - "authors": "Poor, Catherine B." - }, - { - "authors": "Andorfer, Mary C." - }, - { - "authors": "Lewis, Jared C." - }, - { - "date": "2014/06/16" - }, - { - "volume": "15" - }, - { - "issue": "9" - }, - { - "firstpage": "1286" - }, - { - "doi": "10.1002/cbic.201300780" - }, - { - "journal": "ChemBioChem" - }, - { - "abstract": "We previously reported that the halogenase RebH catalyzes selective halogenation of several heterocycles and carbocycles, but product yields were limited by enzyme instability. Here, we use directed evolution to engineer an RebH variant, 3‐LR, with a Topt over 5 °C higher than that of wild‐type, and 3‐LSR, with a Tm 18 °C higher than that of wild‐type. These enzymes provided significantly improved conversion (up to fourfold) for halogenation of tryptophan and several non‐natural substrates. This initial evolution of RebH not only provides improved enzymes for immediate synthetic applications, but also establishes a robust protocol for further halogenase evolution." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/cbic.201300780/pdf" - }, - { - "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/cbic.201300780/full" - }, - { - "supplementary_material": "/doi/10.1002/cbic.201300780/suppinfo" - }, - { - "pdf": "47a76e20b88a744d6d34754326cb8739" - }, - { - "rendered.html": "cfc05bebad5b51612dadd4a40cb99a86" - } - ], - "http://onlinelibrary.wiley.com/doi/10.1002/open.201300039/abstract": [ - { - "title": "Difluoro‐ and Trifluoromethylation of Electron‐Deficient Alkenes in an Electrochemical Microreactor" - }, - { - "authors": "Arai, Kenta" - }, - { - "authors": "Watts, Kevin" - }, - { - "authors": "Wirth, Thomas" - }, - { - "date": "2014/02/01" - }, - { - "volume": "3" - }, - { - "issue": "1" - }, - { - "firstpage": "23" - }, - { - "doi": "10.1002/open.201300039" - }, - { - "journal": "ChemistryOpen" - }, - { - "abstract": "Electrochemical microreactors, which have electrodes integrated into the flow path, can afford rapid and efficient electrochemical reactions without redox reagents due to the intrinsic properties of short diffusion distances. Taking advantage of electrochemical microreactors, Kolbe electrolysis of di‐ and trifluoroacetic acid in the presence of various electron‐deficient alkenes was performed under constant current at continuous flow at room temperature. As a result, di‐ and trifluoromethylated compounds were effectively produced in either equal or higher yields than identical reactions under batch conditions previously reported by Uneyamas group. The strategy of using electrochemical microreactor technology is useful for an effective fluoromethylation of alkenes based on Kolbe electrolysis in significantly shortened reaction times." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/open.201300039/pdf" - }, - { - "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/open.201300039/full" - }, - { - "supplementary_material": "/doi/10.1002/open.201300039/suppinfo" - }, - { - "pdf": "d2821599b03eaf07bd83f99d8ebb3682" - }, - { - "rendered.html": "454ff6668ce5c4bc987cde329d115759" - } - ], - "http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12175/abstract": [ - { - "title": "Evaluation of 11 single‐locus and seven multilocus DNA barcodes in Lamium L. (Lamiaceae)" - }, - { - "authors": "Krawczyk, K." - }, - { - "authors": "Szczecińska, M." - }, - { - "authors": "Sawicki, J." - }, - { - "date": "2014/03/01" - }, - { - "volume": "14" - }, - { - "issue": "2" - }, - { - "firstpage": "272" - }, - { - "doi": "10.1111/1755-0998.12175" - }, - { - "journal": "Molecular Ecology Resources" - }, - { - "abstract": "The aim of this work was to evaluate the suitability of selected DNA regions in the barcoding of plants, based on the species belonging to the genus Lamium (Lamiaceae). For this purpose, nine chloroplast barcodes, that is, accD, matK, rbcL, rpoA, rpoB, rpoC1, rpoC2, trnH‐psbA, trnL‐trnF, as well as ITS nuclear region, and intron of mitochondrial nad5 gene were tested. Among the single‐locus barcodes, most effective in the identification of Lamium species was the trnH‐psbA spacer and matK gene. The high level of variability and resolving power was also observed in the case of rpoA and rpoC2 genes. Despite the high interspecies variability of ITS region, it turned out to be inapplicable in Lamium identification. An important disadvantage of ITS as a barcode is a limitation of its use in polyploid plants, samples contaminated with fungal material or samples with partially degraded DNA. We have also evaluated five‐two‐locus and two‐three‐locus barcode regions created from a combination of most effective single loci. The best‐performing barcode combinations were matK + trnH‐psbA and matK + rpoA. Both of them had equally high discriminative power to identify Lamium species." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12175/pdf" - }, - { - "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12175/full" - }, - { - "supplementary_material": "/doi/10.1111/1755-0998.12175/suppinfo" - }, - { - "rendered.html": "af1c49bb97a394a132261cf384c19b39" - }, - { - "suppinfo": "c89502626d0a6a1ef837c81c3cc295cd" - } - ], - "http://onlinelibrary.wiley.com/doi/10.1002/j.2161-007X.2012.00017.x/abstract": [ - { - "publisher": "Blackwell Publishing Ltd" - }, - { - "title": "Psychological Care Provided by the Church: Perceptions of Christian Church Members" - }, - { - "authors": "Bornsheuer, Jennifer N." - }, - { - "authors": "Henriksen, Richard C." - }, - { - "authors": "Irby, Beverly J." - }, - { - "date": "2012/10/01" - }, - { - "volume": "57" - }, - { - "issue": "2" - }, - { - "firstpage": "199" - }, - { - "doi": "10.1002/j.2161-007X.2012.00017.x" - }, - { - "journal": "Counseling and Values" - }, - { - "abstract": "Spirituality and religion are integral parts of a person's belief system and support network. Although there are many avenues a person can take when seeking mental health care, conservative Protestant clients have a tendency to seek assistance through their church. There is a paucity of literature about conservative Protestant church members’ perceptions of mental health care. The authors used phenomenology to understand participants’ perceptions of mental health care provided by the church. Themes found within participants’ stories included the importance of the relationship when seeking care, the use of knowledgeable practitioners, and the use of religious practices in counseling." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/j.2161-007X.2012.00017.x/pdf" - }, - { - "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/j.2161-007X.2012.00017.x/full" - }, - { - "full": "35969f79046b93f74113d97aa2da09e6" - }, - { - "rendered.html": "18d9e80ff0fdf4baf7a37a2a6e5dc7e8" - } - ], - "http://onlinelibrary.wiley.com/doi/10.1002/mma.2929/abstract": [ - { - "title": "Error estimates for some quadrature rules with maximal trigonometric degree of exactness" - }, - { - "authors": "Stanić, Marija P." - }, - { - "authors": "Cvetković, Aleksandar S." - }, - { - "authors": "Tomović, Tatjana V." - }, - { - "date": "2014/07/30" - }, - { - "volume": "37" - }, - { - "issue": "11" - }, - { - "firstpage": "1687" - }, - { - "doi": "10.1002/mma.2929" - }, - { - "journal": "Mathematical Methods in the Applied Sciences" - }, - { - "abstract": "In this paper, we give error estimates for quadrature rules with maximal trigonometric degree of exactness with respect to an even weight function on ( − π,π) for integrand analytic in a certain domain of complex plane. Copyright © 2013 John Wiley & Sons, Ltd." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/mma.2929/pdf" - }, - { - "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/mma.2929/full" - }, - { - "pdf": "e2d1cc095d9e28b929f560483f50f608" - }, - { - "rendered.html": "e308edc6c8f86c8e2ead60addc6d0086" - } - ], - "http://onlinelibrary.wiley.com/doi/10.1002/nem.1840/abstract": [ - { - "title": "A semantic context exchange process for the federated management of the future internet" - }, - { - "authors": "Latré, Steven" - }, - { - "authors": "Famaey, Jeroen" - }, - { - "authors": "Turck, Filip De" - }, - { - "date": "2014/01/01" - }, - { - "volume": "24" - }, - { - "issue": "1" - }, - { - "firstpage": "1" - }, - { - "doi": "10.1002/nem.1840" - }, - { - "journal": "International Journal of Network Management" - }, - { - "abstract": "In the Future Internet, federations are set up to cope with the stringent quality requirements of services. While a federated solution offers advantages in terms of scalability, it complicates the exchange of context (e.g. Quality of Service information of services) between federated nodes, as each node requires context to perform management tasks. In this article, we propose a context exchange process that automates the context communication between nodes. A scalable approach is proposed that is able to quickly react to local context updates, while maintaining a high level of expressivity to define relationships between federation partners. We distinguish between the context exchange inside an administrative domain, which focuses on scalability, and the context exchange between federation partners, which emphasizes the trust relationships between partners. In both cases, the process allows defining which context needs to be exchanged when and from where. Inside an administrative domain, a combination of RDF and SPARQL rules are used. This allows modeling the contextual requirements of management algorithms and automatically requesting remote context, only when it is necessary for the management algorithms to proceed. Between domains, an OWL‐based approach is used, which allows describing the complex relationships between federation partners. Triggered by the intra‐domain context exchange process, the contextual capabilities are communicated and refined through policies. Both type of processes are evaluated. The results show that they can infer which context is needed in a timely and scalable manner. As such, it outperforms approaches where context is broadcast both in required bandwidth and end‐to‐end delay. Copyright © 2013 John Wiley & Sons, Ltd." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/nem.1840/pdf" - }, - { - "fulltext_html": "http://onlinelibrary.wiley.com/doi/10.1002/nem.1840/full" - }, - { - "pdf": "d543a5ca15391a60219dd367b6801f85" - }, - { - "rendered.html": "291efd7bc88a419ac70a0eaee2449cdd" - } - ], - "http://onlinelibrary.wiley.com/doi/10.1002/anie.197205681/abstract": [ - { - "publisher": "Hüthig & Wepf Verlag" - }, - { - "title": "Kinetics of Cooperative Conformational Transitions of Linear Biopolymers" - }, - { - "authors": "Schwarz, Gerhard" - }, - { - "authors": "Engel, Jürgen" - }, - { - "date": "1972/07/01" - }, - { - "volume": "11" - }, - { - "issue": "7" - }, - { - "firstpage": "568" - }, - { - "doi": "10.1002/anie.197205681" - }, - { - "journal": "Angewandte Chemie International Edition in English" - }, - { - "abstract": "Cooperative conformational transitions of proteins and nucleic acids are of decisive importance to many processes of molecular biology, and particularly to their regulation. They proceed via numerous interdependent elementary processes, and their kinetics are therefore often complicated. They are frequently also very fast. However, kinetic analyses can be carried out by chemical relaxation methods. The theoretical interpretation is comparatively simple in the case of linear biopolymers. When the linear Ising model extended for kinetics was applied to model peptides and polynucleotides, it provided an insight into the fundamental principles of cooperative transformations." - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://onlinelibrary.wiley.com/doi/10.1002/anie.197205681/pdf" - }, - { - "pdf": "ac3c1f65d9ff2cce98946d54bba1b4e5" - }, - { - "rendered.html": "de2a2bebcd8a0ea8b7046dae388c31b2" - } - ] -} \ No newline at end of file diff --git a/test/wiley_test_urls.txt b/test/wiley_test_urls.txt deleted file mode 100644 index a8f08b2..0000000 --- a/test/wiley_test_urls.txt +++ /dev/null @@ -1,10 +0,0 @@ -http://onlinelibrary.wiley.com/doi/10.1002/anie.201403615/abstract -http://onlinelibrary.wiley.com/doi/10.1002/anie.201404164/abstract -http://onlinelibrary.wiley.com/doi/10.1002/anie.200501671/abstract -http://onlinelibrary.wiley.com/doi/10.1002/cbic.201300780/abstract -http://onlinelibrary.wiley.com/doi/10.1002/open.201300039/abstract -http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12175/abstract -http://onlinelibrary.wiley.com/doi/10.1002/j.2161-007X.2012.00017.x/abstract -http://onlinelibrary.wiley.com/doi/10.1002/mma.2929/abstract -http://onlinelibrary.wiley.com/doi/10.1002/nem.1840/abstract -http://onlinelibrary.wiley.com/doi/10.1002/anie.197205681/abstract \ No newline at end of file From b6ba671d2f4e666f35095f31207df5701635a6ba Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Tue, 2 Sep 2014 21:24:59 -0400 Subject: [PATCH 081/154] Added PNAS scraper & test --- scrapers/pnas.json | 73 +++++ test/pnas.json | 608 ++++++++++++++++++++++++++++++++++++++++ test/pnas_test_urls.txt | 9 + 3 files changed, 690 insertions(+) create mode 100644 scrapers/pnas.json create mode 100644 test/pnas.json create mode 100644 test/pnas_test_urls.txt diff --git a/scrapers/pnas.json b/scrapers/pnas.json new file mode 100644 index 0000000..1116c6a --- /dev/null +++ b/scrapers/pnas.json @@ -0,0 +1,73 @@ +{ + "url": "pnas\\.org", + "elements": { + "publisher": { + "selector": "//meta[@name='citation_publisher']", + "attribute": "content" + }, + "title": { + "selector": "//meta[@name='citation_title']", + "attribute": "content" + }, + "authors": { + "selector": "//meta[@name='citation_author']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@name='citation_date']", + "attribute": "content" + }, + "volume": { + "selector": "//meta[@name='citation_volume']", + "attribute": "content" + }, + "issue": { + "selector": "//meta[@name='citation_issue']", + "attribute": "content" + }, + "firstpage": { + "selector": "//meta[@name='citation_firstpage']", + "attribute": "content" + }, + "lastpage": { + "selector": "//meta[@name='citation_lastpage']", + "attribute": "content" + }, + "doi": { + "selector": "//meta[@name='citation_doi']", + "attribute": "content" + }, + "journal": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" + }, + "abstract": { + "selector": "//div[@class='section abstract']", + "attribute": "text" + }, + "abstract_html": { + "selector": "//meta[@name='citation_abstract_html_url']", + "attribute": "content", + "download": true + }, + "language": { + "selector": "//meta[@name='DC.Language']", + "attribute": "content" + }, + "fulltext_pdf": { + "selector": "//meta[@name='citation_pdf_url']", + "attribute": "content", + "download": true + }, + "fulltext_html": { + "selector": "//meta[@name='citation_fulltext_html_url']", + "attribute": "content", + "download": true + }, + "supplementary_material": { + "selector": "//a[@rel='supplemental-data']", + "attribute": "href", + "download": true + } + } +} diff --git a/test/pnas.json b/test/pnas.json new file mode 100644 index 0000000..78a4f06 --- /dev/null +++ b/test/pnas.json @@ -0,0 +1,608 @@ +{ + "http://www.pnas.org/content/111/33/12019": [ + { + "publisher": "National Acad Sciences" + }, + { + "title": "Disassembly of mitotic checkpoint complexes by the joint action of the AAA-ATPase TRIP13 and p31comet" + }, + { + "authors": "Esther Eytan" + }, + { + "authors": "Kexi Wang" + }, + { + "authors": "Shirly Miniowitz-Shemtov" + }, + { + "authors": "Danielle Sitry-Shevah" + }, + { + "authors": "Sharon Kaisari" + }, + { + "authors": "Tim J. Yen" + }, + { + "authors": "Song-Tao Liu" + }, + { + "authors": "Avram Hershko" + }, + { + "date": "08/19/2014" + }, + { + "volume": "111" + }, + { + "issue": "33" + }, + { + "firstpage": "12019" + }, + { + "lastpage": "12024" + }, + { + "doi": "10.1073/pnas.1412901111" + }, + { + "journal": "Proceedings of the National Academy of Sciences" + }, + { + "abstract": "\n Abstract\n The mitotic (or spindle assembly) checkpoint system delays anaphase until all chromosomes are correctly attached to the mitotic\n spindle. When the checkpoint is active, a Mitotic Checkpoint Complex (MCC) assembles and inhibits the ubiquitin ligase Anaphase-Promoting\n Complex/Cyclosome (APC/C). MCC is composed of the checkpoint proteins Mad2, BubR1, and Bub3 associated with the APC/C activator\n Cdc20. When the checkpoint signal is turned off, MCC is disassembled and the checkpoint is inactivated. The mechanisms of\n the disassembly of MCC are not sufficiently understood. We have previously observed that ATP hydrolysis is required for the\n action of the Mad2-binding protein p31comet to disassemble MCC. We now show that HeLa cell extracts contain a factor that promotes ATP- and p31comet-dependent disassembly of a Cdc20–Mad2 subcomplex and identify it as Thyroid Receptor Interacting Protein 13 (TRIP13), an\n AAA-ATPase known to interact with p31comet. The joint action of TRIP13 and p31comet also promotes the release of Mad2 from MCC, participates in the complete disassembly of MCC and abrogates checkpoint inhibition\n of APC/C. We propose that TRIP13 plays centrally important roles in the sequence of events leading to MCC disassembly and\n checkpoint inactivation.\n \n " + }, + { + "abstract_html": "http://www.pnas.org/content/111/33/12019.abstract" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://www.pnas.org/content/111/33/12019.full.pdf" + }, + { + "fulltext_html": "http://www.pnas.org/content/111/33/12019.full" + }, + { + "supplementary_material": "/content/111/33/12019/suppl/DCSupplemental" + }, + { + "12019.full": "3e4de6ee23ec43b80929bce80ac814ae" + }, + { + "rendered.html": "c4562ad494ed219d6084f17305827b16" + } + ], + "http://www.pnas.org/content/111/34/12396": [ + { + "publisher": "National Acad Sciences" + }, + { + "title": "Microbial-induced meprin β cleavage in MUC2 mucin and a functional CFTR channel are required to release anchored small intestinal mucus" + }, + { + "authors": "André Schütte" + }, + { + "authors": "Anna Ermund" + }, + { + "authors": "Christoph Becker-Pauly" + }, + { + "authors": "Malin E. V. Johansson" + }, + { + "authors": "Ana M. Rodriguez-Pineiro" + }, + { + "authors": "Fredrik Bäckhed" + }, + { + "authors": "Stefan Müller" + }, + { + "authors": "Daniel Lottaz" + }, + { + "authors": "Judith S. Bond" + }, + { + "authors": "Gunnar C. Hansson" + }, + { + "date": "08/26/2014" + }, + { + "volume": "111" + }, + { + "issue": "34" + }, + { + "firstpage": "12396" + }, + { + "lastpage": "12401" + }, + { + "doi": "10.1073/pnas.1407597111" + }, + { + "journal": "Proceedings of the National Academy of Sciences" + }, + { + "abstract": "\n Abstract\n The mucus that covers and protects the epithelium of the intestine is built around its major structural component, the gel-forming\n MUC2 mucin. The gel-forming mucins have traditionally been assumed to be secreted as nonattached. The colon has a two-layered\n mucus system where the inner mucus is attached to the epithelium, whereas the small intestine normally has a nonattached mucus.\n However, the mucus of the small intestine of meprin β-deficient mice was now found to be attached. Meprin β is an endogenous\n zinc-dependent metalloprotease now shown to cleave the N-terminal region of the MUC2 mucin at two specific sites. When recombinant\n meprin β was added to the attached mucus of meprin β-deficient mice, the mucus was detached from the epithelium. Similar to\n meprin β-deficient mice, germ-free mice have attached mucus as they did not shed the membrane-anchored meprin β into the luminal\n mucus. The ileal mucus of cystic fibrosis (CF) mice with a nonfunctional cystic fibrosis transmembrane conductance regulator\n (CFTR) channel was recently shown to be attached to the epithelium. Addition of recombinant meprin β to CF mucus did not release\n the mucus, but further addition of bicarbonate rendered the CF mucus normal, suggesting that MUC2 unfolding exposed the meprin\n β cleavage sites. Mucus is thus secreted attached to the goblet cells and requires an enzyme, meprin β in the small intestine,\n to be detached and released into the intestinal lumen. This process regulates mucus properties, can be triggered by bacterial\n contact, and is nonfunctional in CF due to poor mucin unfolding.\n \n " + }, + { + "abstract_html": "http://www.pnas.org/content/111/34/12396.abstract" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://www.pnas.org/content/111/34/12396.full.pdf" + }, + { + "fulltext_html": "http://www.pnas.org/content/111/34/12396.full" + }, + { + "supplementary_material": "/content/111/34/12396/suppl/DCSupplemental" + }, + { + "DCSupplemental": "a29c88e1ce8cbabb41fd557d1158ce68" + }, + { + "rendered.html": "e82463b4b3bc6a32c4498503d32144a6" + } + ], + "http://www.pnas.org/content/111/34/12390": [ + { + "publisher": "National Acad Sciences" + }, + { + "title": "Chaperone-enhanced purification of unconventional myosin 15, a molecular motor specialized for stereocilia protein trafficking" + }, + { + "authors": "Jonathan E. Bird" + }, + { + "authors": "Yasuharu Takagi" + }, + { + "authors": "Neil Billington" + }, + { + "authors": "Marie-Paule Strub" + }, + { + "authors": "James R. Sellers" + }, + { + "authors": "Thomas B. Friedman" + }, + { + "date": "08/26/2014" + }, + { + "volume": "111" + }, + { + "issue": "34" + }, + { + "firstpage": "12390" + }, + { + "lastpage": "12395" + }, + { + "doi": "10.1073/pnas.1409459111" + }, + { + "journal": "Proceedings of the National Academy of Sciences" + }, + { + "abstract": "\n Abstract\n Unconventional myosin 15 is a molecular motor expressed in inner ear hair cells that transports protein cargos within developing\n mechanosensory stereocilia. Mutations of myosin 15 cause profound hearing loss in humans and mice; however, the properties\n of this motor and its regulation within the stereocilia organelle are unknown. To address these questions, we expressed a\n subfragment 1-like (S1) truncation of mouse myosin 15, comprising the predicted motor domain plus three light-chain binding\n sites. Following unsuccessful attempts to express functional myosin 15-S1 using the Spodoptera frugiperda (Sf9)-baculovirus system, we discovered that coexpression of the muscle-myosin–specific chaperone UNC45B, in addition to\n the chaperone heat-shock protein 90 (HSP90) significantly increased the yield of functional protein. Surprisingly, myosin\n 15-S1 did not bind calmodulin with high affinity. Instead, the IQ domains bound essential and regulatory light chains that\n are normally associated with class II myosins. We show that myosin 15-S1 is a barbed-end–directed motor that moves actin filaments\n in a gliding assay (∼430 nm·s−1 at 30 °C), using a power stroke of 7.9 nm. The maximum ATPase rate (kcat ∼6 s−1) was similar to the actin-detachment rate (kdet = 6.2 s−1) determined in single molecule optical trapping experiments, indicating that myosin 15-S1 was rate limited by transit through\n strongly actin-bound states, similar to other processive myosin motors. Our data further indicate that in addition to folding\n muscle myosin, UNC45B facilitates maturation of an unconventional myosin. We speculate that chaperone coexpression may be\n a simple method to optimize the purification of other myosin motors from Sf9 insect cells.\n \n " + }, + { + "abstract_html": "http://www.pnas.org/content/111/34/12390.abstract" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://www.pnas.org/content/111/34/12390.full.pdf" + }, + { + "fulltext_html": "http://www.pnas.org/content/111/34/12390.full" + }, + { + "supplementary_material": "/content/111/34/12390/suppl/DCSupplemental" + }, + { + "12390.abstract": "1f36cf2d40f2a295e8b60f3bf8a361fe" + }, + { + "rendered.html": "e4678253091b9ed6a758e328f44764ca" + } + ], + "http://www.pnas.org/content/101/34/12520": [ + { + "publisher": "National Acad Sciences" + }, + { + "title": "Cell mechanosensitivity controls the anisotropy of focal adhesions" + }, + { + "authors": "Alice Nicolas" + }, + { + "authors": "Benjamin Geiger" + }, + { + "authors": "Samuel A. Safran" + }, + { + "date": "08/24/2004" + }, + { + "volume": "101" + }, + { + "issue": "34" + }, + { + "firstpage": "12520" + }, + { + "lastpage": "12525" + }, + { + "doi": "10.1073/pnas.0403539101" + }, + { + "journal": "Proceedings of the National Academy of Sciences of the United States of America" + }, + { + "abstract": "\n \n Abstract\n \n Cellular adhesions are modulated by cytoskeletal forces or external stresses and adapt to the mechanical properties of the\n extracellular matrix. We propose that this mechanosensitivity can be driven at least in part by the elastic, cell-contractility-induced\n deformations of protein molecules that form the adhesion. The model accounts for observations of anisotropic growth and shrinkage\n of focal adhesions in the direction of the force and predicts that focal adhesions only grow within a range of force that\n is determined by the composition and matrix properties. This prediction is consistent with the observations of a force threshold\n for the appearance of elongated focal adhesions and the disruption of adhesions into fibrils on a mobile extracellular matrix.\n The growth dynamics is calculated and the predicted sliding of focal adhesions is consistent with several experiments.\n \n \n " + }, + { + "abstract_html": "http://www.pnas.org/content/101/34/12520.abstract" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://www.pnas.org/content/101/34/12520.full.pdf" + }, + { + "fulltext_html": "http://www.pnas.org/content/101/34/12520.full" + }, + { + "supplementary_material": "/content/101/34/12520/suppl/DC1" + }, + { + "DC1": "0076772b82d2b0c3f1dd442e98a013f9" + }, + { + "rendered.html": "e06f8aa80d9af9e7f4a8c82591b7576c" + } + ], + "http://www.pnas.org/content/71/2/302": [ + { + "publisher": "National Acad Sciences" + }, + { + "title": "Cell-Free Translation of Messenger RNA of Simian Virus 40: Synthesis of the Major Capsid Protein" + }, + { + "authors": "Carol L. Prives" + }, + { + "authors": "Haim Aviv" + }, + { + "authors": "Bruce M. Paterson" + }, + { + "authors": "Bryan E. Roberts" + }, + { + "authors": "Shmuel Rozenblatt" + }, + { + "authors": "Michel Revel" + }, + { + "authors": "Ernest Winocour" + }, + { + "date": "02/01/1974" + }, + { + "volume": "71" + }, + { + "issue": "2" + }, + { + "firstpage": "302" + }, + { + "lastpage": "306" + }, + { + "journal": "Proceedings of the National Academy of Sciences" + }, + { + "abstract": "\n Abstract\n Extracts of wheat germ are capable of synthesizing the major capsid protein of simian virus 40. Poly(A)-containing RNA from\n BS-C-1 cells infected with simian virus 40 directed the synthesis of a novel polypeptide that migrates in polyacrylamide gels\n together with the major capsid polypeptide of simian virus 40, VP-1. The patterns of the major tryptic peptides of purified\n VP-1 and the novel polypeptide synthesized in vitro were identical after two-dimensional paper electrophoresis. The novel polypeptide was not synthesized in response to poly(A)-rich\n RNA from uninfected cells or from virus-infected cells treated with cytosine arabinoside. Messenger RNA from infected cells\n purified by selective hybridization to DNA of simian virus 40 directs the synthesis of a major polypeptide of electrophoretic\n mobility similar to that of VP-1 of simian virus 40. This approach should prove useful in identifying additional products\n specified by DNA tumor viruses.\n \n " + }, + { + "abstract_html": "http://www.pnas.org/content/71/2/302.abstract" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://www.pnas.org/content/71/2/302.full.pdf" + }, + { + "302.abstract": "ca6e67b294a77aac0fa426e85232f1f5" + }, + { + "rendered.html": "ecb901b53714839fdb8a2d996623c138" + } + ], + "http://www.pnas.org/content/109/24/9248": [ + { + "publisher": "National Acad Sciences" + }, + { + "title": "Heart wall myofibers are arranged in minimal surfaces to optimize organ function" + }, + { + "authors": "Peter Savadjiev" + }, + { + "authors": "Gustav J. Strijkers" + }, + { + "authors": "Adrianus J. Bakermans" + }, + { + "authors": "Emmanuel Piuze" + }, + { + "authors": "Steven W. Zucker" + }, + { + "authors": "Kaleem Siddiqi" + }, + { + "date": "06/12/2012" + }, + { + "volume": "109" + }, + { + "issue": "24" + }, + { + "firstpage": "9248" + }, + { + "lastpage": "9253" + }, + { + "doi": "10.1073/pnas.1120785109" + }, + { + "journal": "Proceedings of the National Academy of Sciences" + }, + { + "abstract": "\n Abstract\n Heart wall myofibers wind as helices around the ventricles, strengthening them in a manner analogous to the reinforcement\n of concrete cylindrical columns by spiral steel cables [Richart FE, et al. (1929) Univ of Illinois, Eng Exp Stn Bull 190].\n A multitude of such fibers, arranged smoothly and regularly, contract and relax as an integrated functional unit as the heart\n beats. To orchestrate this motion, fiber tangling must be avoided and pumping should be efficient. Current models of myofiber\n orientation across the heart wall suggest groupings into sheets or bands, but the precise geometry of bundles of myofibers\n is unknown. Here we show that this arrangement takes the form of a special minimal surface, the generalized helicoid [Blair\n DE, Vanstone JR (1978) Minimal Submanifolds and Geodesics 13–16], closing the gap between individual myofibers and their collective wall structure. The model holds across species,\n with a smooth variation in its three curvature parameters within the myocardial wall providing tight fits to diffusion magnetic\n resonance images from the rat, the dog, and the human. Mathematically it explains how myofibers are bundled in the heart wall\n while economizing fiber length and optimizing ventricular ejection volume as they contract. The generalized helicoid provides\n a unique foundation for analyzing the fibrous composite of the heart wall and should therefore find applications in heart\n tissue engineering and in the study of heart muscle diseases.\n \n " + }, + { + "abstract_html": "http://www.pnas.org/content/109/24/9248.abstract" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://www.pnas.org/content/109/24/9248.full.pdf" + }, + { + "fulltext_html": "http://www.pnas.org/content/109/24/9248.full" + }, + { + "supplementary_material": "/content/109/24/9248/suppl/DCSupplemental" + }, + { + "DCSupplemental": "5bf113bd006256852685f7baad425748" + }, + { + "rendered.html": "bbf7da42dcfa67ee9b7072bc470bf967" + } + ], + "http://www.pnas.org/content/111/24/8788": [ + { + "publisher": "National Acad Sciences" + }, + { + "title": "Experimental evidence of massive-scale emotional contagion through social networks" + }, + { + "authors": "Adam D. I. Kramer" + }, + { + "authors": "Jamie E. Guillory" + }, + { + "authors": "Jeffrey T. Hancock" + }, + { + "date": "06/17/2014" + }, + { + "volume": "111" + }, + { + "issue": "24" + }, + { + "firstpage": "8788" + }, + { + "lastpage": "8790" + }, + { + "doi": "10.1073/pnas.1320040111" + }, + { + "journal": "Proceedings of the National Academy of Sciences" + }, + { + "abstract": "\n Abstract\n Emotional states can be transferred to others via emotional contagion, leading people to experience the same emotions without\n their awareness. Emotional contagion is well established in laboratory experiments, with people transferring positive and\n negative emotions to others. Data from a large real-world social network, collected over a 20-y period suggests that longer-lasting\n moods (e.g., depression, happiness) can be transferred through networks [Fowler JH, Christakis NA (2008) BMJ 337:a2338], although the results are controversial. In an experiment with people who use Facebook, we test whether emotional\n contagion occurs outside of in-person interaction between individuals by reducing the amount of emotional content in the News\n Feed. When positive expressions were reduced, people produced fewer positive posts and more negative posts; when negative\n expressions were reduced, the opposite pattern occurred. These results indicate that emotions expressed by others on Facebook\n influence our own emotions, constituting experimental evidence for massive-scale contagion via social networks. This work\n also suggests that, in contrast to prevailing assumptions, in-person interaction and nonverbal cues are not strictly necessary\n for emotional contagion, and that the observation of others’ positive experiences constitutes a positive experience for people.\n \n " + }, + { + "abstract_html": "http://www.pnas.org/content/111/24/8788.abstract" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://www.pnas.org/content/111/24/8788.full.pdf" + }, + { + "fulltext_html": "http://www.pnas.org/content/111/24/8788.full" + }, + { + "8788.full": "6479c6f32c31b9edba389ef3fff7fc93" + }, + { + "rendered.html": "d1a4184cea26192b275792bcb3095b6d" + } + ], + "http://www.pnas.org/content/111/29/10779.1": [ + { + "publisher": "National Acad Sciences" + }, + { + "title": "Editorial Expression of Concern: Experimental evidence of massivescale emotional contagion through social networks" + }, + { + "date": "07/22/2014" + }, + { + "volume": "111" + }, + { + "issue": "29" + }, + { + "firstpage": "10779" + }, + { + "lastpage": "10779" + }, + { + "doi": "10.1073/pnas.1412469111" + }, + { + "journal": "Proceedings of the National Academy of Sciences" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://www.pnas.org/content/111/29/10779.1.full.pdf" + }, + { + "fulltext_html": "http://www.pnas.org/content/111/29/10779.1.full" + }, + { + "10779.1.full.pdf": "f1ff6f1b35c5397c8e7762ffe36fed02" + }, + { + "rendered.html": "553e807bf9b1e31721733c8f49db590e" + } + ], + "http://www.pnas.org/content/111/35/12758": [ + { + "publisher": "National Acad Sciences" + }, + { + "title": "Experimental basis for a new allosteric model for multisubunit proteins" + }, + { + "authors": "Cristiano Viappiani" + }, + { + "authors": "Stefania Abbruzzetti" + }, + { + "authors": "Luca Ronda" + }, + { + "authors": "Stefano Bettati" + }, + { + "authors": "Eric. R. Henry" + }, + { + "authors": "Andrea Mozzarelli" + }, + { + "authors": "William A. Eaton" + }, + { + "date": "09/02/2014" + }, + { + "volume": "111" + }, + { + "issue": "35" + }, + { + "firstpage": "12758" + }, + { + "lastpage": "12763" + }, + { + "doi": "10.1073/pnas.1413566111" + }, + { + "journal": "Proceedings of the National Academy of Sciences" + }, + { + "abstract": "\n Abstract\n Monod, Wyman, and Changeux (MWC) explained allostery in multisubunit proteins with a widely applied theoretical model in which\n binding of small molecules, so-called allosteric effectors, affects reactivity by altering the equilibrium between more reactive\n (R) and less reactive (T) quaternary structures. In their model, each quaternary structure has a single reactivity. Here,\n we use silica gels to trap protein conformations and a new kind of laser photolysis experiment to show that hemoglobin, the\n paradigm of allostery, exhibits two ligand binding phases with the same fast and slow rates in both R and T quaternary structures.\n Allosteric effectors change the fraction of each phase but not the rates. These surprising results are readily explained by\n the simplest possible extension of the MWC model to include a preequilibrium between two tertiary conformations that have\n the same functional properties within each quaternary structure. They also have important implications for the long-standing\n question of a structural explanation for the difference in hemoglobin oxygen affinity of the two quaternary structures.\n \n " + }, + { + "abstract_html": "http://www.pnas.org/content/111/35/12758.abstract" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://www.pnas.org/content/111/35/12758.full.pdf" + }, + { + "fulltext_html": "http://www.pnas.org/content/111/35/12758.full" + }, + { + "supplementary_material": "/content/111/35/12758/suppl/DCSupplemental" + }, + { + "12758.abstract": "886f0f703849b8ce926b57b3581915cb" + }, + { + "rendered.html": "2cd299dcb051059fe566dce2f1168b3d" + } + ] +} \ No newline at end of file diff --git a/test/pnas_test_urls.txt b/test/pnas_test_urls.txt new file mode 100644 index 0000000..d8f922d --- /dev/null +++ b/test/pnas_test_urls.txt @@ -0,0 +1,9 @@ +http://www.pnas.org/content/111/33/12019 +http://www.pnas.org/content/111/34/12396 +http://www.pnas.org/content/111/34/12390 +http://www.pnas.org/content/101/34/12520 +http://www.pnas.org/content/71/2/302 +http://www.pnas.org/content/109/24/9248 +http://www.pnas.org/content/111/24/8788 +http://www.pnas.org/content/111/29/10779.1 +http://www.pnas.org/content/111/35/12758 \ No newline at end of file From 159ec314ef69a24bcf50a48be98e44153c935831 Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Tue, 2 Sep 2014 22:32:18 -0400 Subject: [PATCH 082/154] RSC Scrapers --- scrapers/rsc.json | 77 ++++++ test/rsc.json | 581 +++++++++++++++++++++++++++++++++++++++++ test/rsc_test_urls.txt | 9 + 3 files changed, 667 insertions(+) create mode 100644 scrapers/rsc.json create mode 100644 test/rsc.json create mode 100644 test/rsc_test_urls.txt diff --git a/scrapers/rsc.json b/scrapers/rsc.json new file mode 100644 index 0000000..c9e8ab6 --- /dev/null +++ b/scrapers/rsc.json @@ -0,0 +1,77 @@ +{ + "url": "pubs\\.rsc\\.org", + "elements": { + "publisher": { + "selector": "//meta[@name='DC.publisher']", + "attribute": "content" + }, 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bis(N-(4-ethynylphenyl)carbazole)bipyridine fullerene complexes" + }, + { + "authors": "Sai-Ho Lee" + }, + { + "authors": "Chris Tsz-Leung Chan" + }, + { + "authors": "Keith Man-Chung Wong" + }, + { + "authors": "Wai Han Lam" + }, + { + "authors": "Wai-Ming Kwok" + }, + { + "authors": "Vivian Wing-Wah Yam" + }, + { + "date": "2014-09-02" + }, + { + "volume": "" + }, + { + "issue": "" + }, + { + "firstpage": "" + }, + { + "lastpage": "" + }, + { + "doi": "10.1039/C4DT01397B" + }, + { + "journal": "Dalton Trans." + }, + { + "abstract": "" + }, + { + "abstract_html": "http://pubs.rsc.org/en/content/articlelanding/2014/dt/c4dt01397b" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://pubs.rsc.org/en/content/articlepdf/2014/dt/c4dt01397b" + }, + { + "fulltext_html": "http://pubs.rsc.org/en/content/articlehtml/2014/dt/c4dt01397b" + }, + { + "figure": "http://sod-a.rsc-cdn.org/pubs.rsc.org/content/NewImages/Ajax-GA-Loader.gif" + }, + { + "caption": "Graphical abstract: Synthesis 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Soc." + }, + { + "abstract": "" + }, + { + "abstract_html": "http://pubs.rsc.org/en/content/articlelanding/1877/js/js8773200001" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://pubs.rsc.org/en/content/articlepdf/1877/js/js8773200001" + }, + { + "fulltext_html": "http://pubs.rsc.org/en/content/articlehtml/1877/js/js8773200001" + }, + { + "js8773200001": "07b793d5f63299d1d7093a65bb459e1f" + }, + { + "rendered.html": "b78de4e8e5a1862146b3d9f3ef88d8f2" + } + ], + "http://pubs.rsc.org/en/content/articlelanding/2002/p2/b208395g": [ + { + "publisher": "The Royal Society of Chemistry" + }, + { + "title": "Stereoelectronic substituent effects on intramolecular H-bonding in crowded o-anisic acids" + }, + { + "authors": "Ingeborg I. Schuster" + }, + { + "date": "2002-12-06" + }, + { + "volume": "" + }, + { + "issue": "12" + }, + { + "firstpage": "1961" + }, + { + "lastpage": "1966" + }, + { + "doi": "10.1039/B208395G" + }, + { + "journal": "J. Chem. Soc., Perkin Trans. 2" + }, + { + "abstract": "" + }, + { + "abstract_html": "http://pubs.rsc.org/en/content/articlelanding/2002/p2/b208395g" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://pubs.rsc.org/en/content/articlepdf/2002/p2/b208395g" + }, + { + "fulltext_html": "http://pubs.rsc.org/en/content/articlehtml/2002/p2/b208395g" + }, + { + "figure": "http://sod-a.rsc-cdn.org/pubs.rsc.org/content/NewImages/Ajax-GA-Loader.gif" + }, + { + "caption": "Graphical abstract: Stereoelectronic substituent effects on intramolecular H-bonding in crowded o-anisic acids" + }, + { + "b208395g": "00178173eb233f33a199643034d89dd9" + }, + { + "rendered.html": "13db463737f054c796b5684fc25c4bef" + } + ], + "http://pubs.rsc.org/en/content/articlelanding/2014/ob/c4ob01156b": [ + { + "publisher": "The Royal Society of Chemistry" + }, + { + "title": "Selective transamidation of 3-oxo-N-acyl homoserine lactones by hydrazine derivatives" + }, + { + "authors": "Michael A. Bertucci" + }, + { + "authors": "Stephen J. Lee" + }, + { + "authors": "Michel R. Gagné" + }, + { + "date": "2014-08-27" + }, + { + "volume": "12" + }, + { + "issue": "37" + }, + { + "firstpage": "7197" + }, + { + "lastpage": "7200" + }, + { + "doi": "10.1039/C4OB01156B" + }, + { + "journal": "Org. Biomol. Chem." + }, + { + "abstract": "" + }, + { + "abstract_html": "http://pubs.rsc.org/en/content/articlelanding/2014/ob/c4ob01156b" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://pubs.rsc.org/en/content/articlepdf/2014/ob/c4ob01156b" + }, + { + "fulltext_html": "http://pubs.rsc.org/en/content/articlehtml/2014/ob/c4ob01156b" + }, + { + "figure": "http://sod-a.rsc-cdn.org/pubs.rsc.org/content/NewImages/Ajax-GA-Loader.gif" + }, + { + "caption": "Graphical abstract: Selective transamidation of 3-oxo-N-acyl homoserine lactones by hydrazine derivatives" + }, + { + "Ajax-GA-Loader.gif": "9dc2c7c4f07aa2db72f1b4f2c81dc0b8" + }, + { + "rendered.html": "cb30ee8ed2e1f2038f18c2d7aea131aa" + } + ], + "http://pubs.rsc.org/en/content/articlelanding/2012/jm/c2jm35601e": [ + { + "publisher": "The Royal Society of Chemistry" + }, + { + "title": "Nanonet as a scaffold with targeted functionalities" + }, + { + "authors": "Yanli Zhao" + }, + { + "authors": "George Grüner" + }, + { + "date": "2012-11-20" + }, + { + "volume": "22" + }, + { + "issue": "48" + }, + { + "firstpage": "24983" + }, + { + "lastpage": "24991" + }, + { + "doi": "10.1039/C2JM35601E" + }, + { + "journal": "J. Mater. Chem." + }, + { + "abstract": "" + }, + { + "abstract_html": "http://pubs.rsc.org/en/content/articlelanding/2012/jm/c2jm35601e" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://pubs.rsc.org/en/content/articlepdf/2012/jm/c2jm35601e" + }, + { + "fulltext_html": "http://pubs.rsc.org/en/content/articlehtml/2012/jm/c2jm35601e" + }, + { + "figure": "http://sod-a.rsc-cdn.org/pubs.rsc.org/content/NewImages/Ajax-GA-Loader.gif" + }, + { + "caption": "Graphical abstract: Nanonet as a scaffold with targeted functionalities" + }, + { + "c2jm35601e": "7305ec9e37ef1bda51778bc18024fed5" + }, + { + "rendered.html": "8112e882512605d7aaba845bea9be201" + } + ], + "http://pubs.rsc.org/en/content/articlelanding/2014/ja/c4ja00172a": [ + { + "publisher": "The Royal Society of Chemistry" + }, + { + "title": "Studies of rare earth elements to distinguish nephrite samples from different deposits using direct current glow discharge mass spectrometry" + }, + { + "authors": "Bilige Siqin" + }, + { + "authors": "Rong Qian" + }, + { + "authors": "Shangjun Zhuo" + }, + { + "authors": "Jie Gao" + }, + { + "authors": "Jun Jin" + }, + { + "authors": "Zhaoyin Wen" + }, + { + "date": "2014-08-28" + }, + { + "volume": "" + }, + { + "issue": "" + }, + { + "firstpage": "" + }, + { + "lastpage": "" + }, + { + "doi": "10.1039/C4JA00172A" + }, + { + "journal": "J. Anal. At. Spectrom." + }, + { + "abstract": "" + }, + { + "abstract_html": "http://pubs.rsc.org/en/content/articlelanding/2014/ja/c4ja00172a" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://pubs.rsc.org/en/content/articlepdf/2014/ja/c4ja00172a" + }, + { + "fulltext_html": "http://pubs.rsc.org/en/content/articlehtml/2014/ja/c4ja00172a" + }, + { + "figure": "http://sod-a.rsc-cdn.org/pubs.rsc.org/content/NewImages/Ajax-GA-Loader.gif" + }, + { + "caption": "Graphical abstract: Studies of rare earth elements to distinguish nephrite samples from different deposits using direct current glow discharge mass spectrometry" + }, + { + "Ajax-GA-Loader.gif": "9dc2c7c4f07aa2db72f1b4f2c81dc0b8" + }, + { + "rendered.html": "a0fabb2bf6660702f7d26f330a5a7337" + } + ], + "http://pubs.rsc.org/en/content/articlelanding/2014/ra/c4ra05382f": [ + { + "publisher": "The Royal Society of Chemistry" + }, + { + "title": "A co-precipitated Mg-Ti nano-composite with high capacity and rapid hydrogen absorption kinetics at room temperature" + }, + { + "authors": "Yana Liu" + }, + { + "authors": "Jianxin Zou" + }, + { + "authors": "Xiaoqin Zeng" + }, + { + "authors": "Wenjiang Ding" + }, + { + "date": "2014-09-02" + }, + { + "volume": "" + }, + { + "issue": "" + }, + { + "firstpage": "" + }, + { + "lastpage": "" + }, + { + "doi": "10.1039/C4RA05382F" + }, + { + "journal": "RSC Adv." + }, + { + "abstract": "" + }, + { + "abstract_html": "http://pubs.rsc.org/en/content/articlelanding/2014/ra/c4ra05382f" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://pubs.rsc.org/en/content/articlepdf/2014/ra/c4ra05382f" + }, + { + "fulltext_html": "http://pubs.rsc.org/en/content/articlehtml/2014/ra/c4ra05382f" + }, + { + "c4ra05382f": "b04160f7e5ac23760de63f64473c4f88" + }, + { + "rendered.html": "9655386d25fb364d2a735334f77ba601" + } + ], + "http://pubs.rsc.org/en/content/articlelanding/2014/lc/c4lc00443d": [ + { + "publisher": "The Royal Society of Chemistry" + }, + { + "title": "An integrated CMOS quantitative-polymerase-chain-reaction lab-on-chip for point-of-care diagnostics" + }, + { + "authors": "Haig Norian" + }, + { + "authors": "Ryan M. Field" + }, + { + "authors": "Ioannis Kymissis" + }, + { + "authors": "Kenneth L. Shepard" + }, + { + "date": "2014-09-01" + }, + { + "volume": "" + }, + { + "issue": "" + }, + { + "firstpage": "" + }, + { + "lastpage": "" + }, + { + "doi": "10.1039/C4LC00443D" + }, + { + "journal": "Lab Chip" + }, + { + "abstract": "" + }, + { + "abstract_html": "http://pubs.rsc.org/en/content/articlelanding/2014/lc/c4lc00443d" + }, + { + "language": "en" + }, + { + "fulltext_pdf": "http://pubs.rsc.org/en/content/articlepdf/2014/lc/c4lc00443d" + }, + { + "fulltext_html": "http://pubs.rsc.org/en/content/articlehtml/2014/lc/c4lc00443d" + }, + { + "figure": "http://sod-a.rsc-cdn.org/pubs.rsc.org/content/NewImages/Ajax-GA-Loader.gif" + }, + { + "caption": "Graphical abstract: An integrated CMOS quantitative-polymerase-chain-reaction lab-on-chip for point-of-care diagnostics" + }, + { + "c4lc00443d": "03e46ecf67f34f15eb830ee4f1d5a2d7" + }, + { + "rendered.html": "91c1d8cc884481b34c3755a31cfe4711" + } + ] +} \ No newline at end of file diff --git a/test/rsc_test_urls.txt b/test/rsc_test_urls.txt new file mode 100644 index 0000000..5a73765 --- /dev/null +++ b/test/rsc_test_urls.txt @@ -0,0 +1,9 @@ +http://pubs.rsc.org/en/content/articlelanding/2014/dt/c4dt01397b +http://pubs.rsc.org/en/Content/ArticleLanding/2014/CC/C4CC04440A +http://pubs.rsc.org/en/content/articlelanding/1877/js/js8773200001 +http://pubs.rsc.org/en/content/articlelanding/2002/p2/b208395g +http://pubs.rsc.org/en/content/articlelanding/2014/ob/c4ob01156b +http://pubs.rsc.org/en/content/articlelanding/2012/jm/c2jm35601e +http://pubs.rsc.org/en/content/articlelanding/2014/ja/c4ja00172a +http://pubs.rsc.org/en/content/articlelanding/2014/ra/c4ra05382f +http://pubs.rsc.org/en/content/articlelanding/2014/lc/c4lc00443d \ No newline at end of file From e6c738d6b942be85b02f5758c8aa3e65c9d59800 Mon Sep 17 00:00:00 2001 From: Phil OSx Date: Tue, 2 Sep 2014 23:15:43 -0400 Subject: [PATCH 083/154] JAMA and related sub-journal scraper --- scrapers/jama.json | 64 +++ test/jama.json | 1063 +++++++++++++++++++++++++++++++++++++++ test/jama_test_urls.txt | 13 + 3 files changed, 1140 insertions(+) create mode 100644 scrapers/jama.json create mode 100644 test/jama.json create mode 100644 test/jama_test_urls.txt diff --git a/scrapers/jama.json b/scrapers/jama.json new file mode 100644 index 0000000..cb6d01e --- /dev/null +++ b/scrapers/jama.json @@ -0,0 +1,64 @@ +{ + "url": "jamanetwork\\.com", + "elements": { + "publisher": { + "selector": "//meta[@name='citation_publisher']", + "attribute": "content" + }, + "title": { + "selector": "//meta[@name='citation_title']", + "attribute": "content" + }, + "authors": { + "selector": "//meta[@name='citation_author']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@name='citation_date']", + "attribute": "content" + }, + "volume": { + "selector": "//meta[@name='citation_volume']", + "attribute": "content" + }, + "issue": { + "selector": "//meta[@name='citation_issue']", + "attribute": "content" + }, + "firstpage": { + "selector": "//meta[@name='citation_firstpage']", + "attribute": "content" + }, + "lastpage": { + "selector": "//meta[@name='citation_lastpage']", + "attribute": "content" + }, + "doi": { + "selector": "//meta[@name='citation_doi']", + "attribute": "content" + }, + "journal": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" + }, + "abstract": { + "selector": "//span[@class='Abstract 0']", + "attribute": "text" + }, + "firstpage_preview": { + "selector": "//img[@id='imgFPPPPopup']", + "attriubute": "src", + "download": true + }, + "fulltext_pdf": { + "selector": "//meta[@name='citation_pdf_url']", + "attribute": "content", + "download": true + }, + "supplementary_material": { + "selector": "//a[@class='supplementLink']", + "attribute": "href", + "download": true + } + } +} diff --git a/test/jama.json b/test/jama.json new file mode 100644 index 0000000..dbc0b8d --- /dev/null +++ b/test/jama.json @@ -0,0 +1,1063 @@ +{ + "http://jama.jamanetwork.com/article.aspx?articleid=1456072": [ + { + "publisher": "American Medical Association" + }, + { + "title": "Association of Childhood Pertussis With Receipt of 5 Doses of Pertussis Vaccine by Time Since Last Vaccine Dose, California, 2010" + }, + { + "authors": "Lara K. Misegades" + }, + { + "authors": "Kathleen Winter" + }, + { + "authors": "Kathleen Harriman" + }, + { + "authors": "John Talarico" + }, + { + "authors": "Nancy E. Messonnier" + }, + { + "authors": "Thomas A. Clark" + }, + { + "authors": "Stacey W. Martin" + }, + { + "date": "2012/11/28" + }, + { + "volume": "308" + }, + { + "issue": "20" + }, + { + "firstpage": "2126" + }, + { + "lastpage": "2132" + }, + { + "doi": "10.1001/jama.2012.14939" + }, + { + "journal": "JAMA" + }, + { + "abstract": "Context In 2010, California experienced its largest pertussis epidemic in more than 60 years; a substantial burden of disease was noted in the 7- to 10-year-old age group despite high diphtheria, tetanus, and acellular pertussis vaccine (DTaP) coverage, indicating the possibility of waning protection.Objective To evaluate the association between pertussis and receipt of 5 DTaP doses by time since fifth DTaP dose.Design, Setting, and Participants Case-control evaluation conducted in 15 California counties. Cases (n = 682) were all suspected, probable, and confirmed pertussis cases among children aged 4 to 10 years reported from January through December 14, 2010; controls (n = 2016) were children in the same age group who received care from the clinicians reporting the cases. Three controls were selected per case. Vaccination histories were obtained from medical records and immunization registries.Main Outcome Measures Primary outcomes were (1) odds ratios (ORs) for the association between pertussis and receipt of the 5-dose DTaP series and (2) ORs for the association between pertussis and time since completion (<12, 12-23, 24-35, 36-47, 48-59, or ≥60 months) of the 5-dose DTaP series. Logistic regression was used to calculate ORs, accounting for clustering by county and clinician, and vaccine effectiveness (VE) was estimated as (1 − OR) × 100%.Results Among cases and controls, 53 (7.8%) and 19 (0.9%) had not received any pertussis-containing vaccines, respectively. Compared with controls, children with pertussis had a lower odds of having received all 5 doses of DTaP (OR, 0.11; 95% CI, 0.06-0.21 [estimated VE, 88.7%; 95% CI, 79.4%-93.8%]). When children were categorized by time since completion of the DTaP series, using an unvaccinated reference group, children with pertussis compared with controls were less likely to have received their fifth dose within the prior 12 months (19 [2.8%] vs 354 [17.6%], respectively; OR, 0.02; 95% CI, 0.01-0.04 [estimated VE, 98.1%; 95% CI, 96.1%-99.1%]). This association was evident with longer time since vaccination, with ORs increasing with time since the fifth dose. At 60 months or longer (n = 231 cases [33.9%] and n = 288 controls [14.3%]), the OR was 0.29 (95% CI, 0.15-0.54 [estimated VE, 71.2%; 95% CI, 45.8%-84.8%]). Accordingly, the estimated VE declined each year after receipt of the fifth dose of DTaP.Conclusion Among children in 15 California counties, children with pertussis, compared with controls, had lower odds of having received the 5-dose DTaP series; as time since last DTaP dose increased, the odds increased, which is consistent with a progressive decrease in estimated vaccine effectiveness each year after the final dose of pertussis vaccine." + }, + { + "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/28295/joc120116_2126_2132.pdf" + }, + { + "joc120116_2126_2132.pdf": "360c3126d8eacbbb89686c3ad560884f" + }, + { + "rendered.html": "7c3a59efb7e6416c5e632a8ed1619dd1" + } + ], + "http://jama.jamanetwork.com/article.aspx?articleid=1890398": [ + { + "publisher": "American Medical Association" + }, + { + "title": "Effect of Providing Conditional Economic Compensation on Uptake of Voluntary Medical Male Circumcision in Kenya: A Randomized Clinical Trial" + }, + { + "authors": "Harsha Thirumurthy" + }, + { + "authors": "Samuel H. Masters" + }, + { + "authors": "Samwel Rao" + }, + { + "authors": "Megan A. Bronson" + }, + { + "authors": "Michele Lanham" + }, + { + "authors": "Eunice Omanga" + }, + { + "authors": "Emily Evens" + }, + { + "authors": "Kawango Agot" + }, + { + "date": "2014/08/20" + }, + { + "volume": "312" + }, + { + "issue": "7" + }, + { + "firstpage": "703" + }, + { + "lastpage": "711" + }, + { + "doi": "10.1001/jama.2014.9087" + }, + { + "journal": "JAMA" + }, + { + "abstract": "Importance \n Novel strategies are needed to increase the uptake of voluntary medical male circumcision (VMMC) in sub-Saharan Africa and enhance the effectiveness of male circumcision as an HIV prevention strategy.Objective \n To determine whether small economic incentives could increase circumcision prevalence by addressing reported economic barriers to VMMC and behavioral factors such as present-biased decision making.Design, Setting, and Participants \n Randomized clinical trial conducted between June 22, 2013, and February 4, 2014, among 1504 uncircumcised men aged 25 to 49 years in Nyanza region, Kenya. VMMC services were provided free of charge and participants were randomized to 1 of 3 intervention groups or a control group.Interventions \n Participants in the 3 intervention groups received varying amounts of compensation conditional on undergoing circumcision at 1 of 9 study clinics within 2 months of enrollment. Compensation took the form of food vouchers worth 200 Kenya shillings (≈US $2.50), 700 Kenya shillings (≈US $8.75), or 1200 Kenya shillings (≈US $15.00), which reflected a portion of transportation costs and lost wages associated with getting circumcised. The control group received no compensation.Main Outcomes and Measures \n VMMC uptake within 2 months.Results \n Analysis of data for 1502 participants with complete data showed that VMMC uptake within 2 months was higher in the US $8.75 group (6.6%; 95% CI, 4.3%-9.5% [25 of 381]) and the US $15.00 group (9.0%; 95% CI, 6.3%-12.4% [34 of 377]) than in the US $2.50 group (1.9%; 95% CI, 0.8%-3.8% [7 of 374]) and the control group (1.6%; 95% CI, 0.6%-3.5% [6 of 370]). In logistic regression analysis, the US $8.75 group had significantly higher VMMC uptake than the control group (adjusted odds ratio [AOR] 4.3; 95% CI, 1.7-10.7), as did the US $15.00 group (AOR 6.2; 95% CI, 2.6-15.0). Effect sizes for the US $8.75 and US $15.00 groups did not differ significantly (P = .20).Conclusions and Relevance \n Among uncircumcised men in Kenya, compensation in the form of food vouchers worth approximately US $8.75 or US $15.00, compared with lesser or no compensation, resulted in a modest increase in the prevalence of circumcision after 2 months. The effects of more intense promotion or longer implementation require further investigation.Trial Registration \n clinicaltrials.gov Identifier: NCT01857700" + }, + { + "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/930672/joi140100.pdf" + }, + { + "joi140100.pdf": "5949b7996bea79e8af0b657e8614cd8f" + }, + { + "rendered.html": "da2585e1b351450d05d0c4b144f1c757" + } + ], + "http://jama.jamanetwork.com/article.aspx?articleid=1896983": [ + { + "publisher": "American Medical Association" + }, + { + "title": "Newborn Screening for Severe Combined Immunodeficiency in 11 Screening Programs in the United States" + }, + { + "authors": "Antonia Kwan" + }, + { + "authors": "Roshini S. Abraham" + }, + { + "authors": "Robert Currier" + }, + { + "authors": "Amy Brower" + }, + { + "authors": "Karen Andruszewski" + }, + { + "authors": "Jordan K. Abbott" + }, + { + "authors": "Mei Baker" + }, + { + "authors": "Mark Ballow" + }, + { + "authors": "Louis E. Bartoshesky" + }, + { + "authors": "Francisco A. Bonilla" + }, + { + "authors": "Charles Brokopp" + }, + { + "authors": "Edward Brooks" + }, + { + "authors": "Michele Caggana" + }, + { + "authors": "Jocelyn Celestin" + }, + { + "authors": "Joseph A. Church" + }, + { + "authors": "Anne Marie Comeau" + }, + { + "authors": "James A. Connelly" + }, + { + "authors": "Morton J. Cowan" + }, + { + "authors": "Charlotte Cunningham-Rundles" + }, + { + "authors": "Trivikram Dasu" + }, + { + "authors": "Nina Dave" + }, + { + "authors": "Maria T. De La Morena" + }, + { + "authors": "Ulrich Duffner" + }, + { + "authors": "Chin-To Fong" + }, + { + "authors": "Lisa Forbes" + }, + { + "authors": "Debra Freedenberg" + }, + { + "authors": "Erwin W. Gelfand" + }, + { + "authors": "Jaime E. Hale" + }, + { + "authors": "I. Celine Hanson" + }, + { + "authors": "Beverly N. Hay" + }, + { + "authors": "Diana Hu" + }, + { + "authors": "Anthony Infante" + }, + { + "authors": "Daisy Johnson" + }, + { + "authors": "Neena Kapoor" + }, + { + "authors": "Denise M. Kay" + }, + { + "authors": "Donald B. Kohn" + }, + { + "authors": "Rachel Lee" + }, + { + "authors": "Heather Lehman" + }, + { + "authors": "Zhili Lin" + }, + { + "authors": "Fred Lorey" + }, + { + "authors": "Aly Abdel-Mageed" + }, + { + "authors": "Adrienne Manning" + }, + { + "authors": "Sean McGhee" + }, + { + "authors": "Theodore B. Moore" + }, + { + "authors": "Stanley J. Naides" + }, + { + "authors": "Luigi D. Notarangelo" + }, + { + "authors": "Jordan S. Orange" + }, + { + "authors": "Sung-Yun Pai" + }, + { + "authors": "Matthew Porteus" + }, + { + "authors": "Ray Rodriguez" + }, + { + "authors": "Neil Romberg" + }, + { + "authors": "John Routes" + }, + { + "authors": "Mary Ruehle" + }, + { + "authors": "Arye Rubenstein" + }, + { + "authors": "Carlos A. Saavedra-Matiz" + }, + { + "authors": "Ginger Scott" + }, + { + "authors": "Patricia M. Scott" + }, + { + "authors": "Elizabeth Secord" + }, + { + "authors": "Christine Seroogy" + }, + { + "authors": "William T. Shearer" + }, + { + "authors": "Subhadra Siegel" + }, + { + "authors": "Stacy K. Silvers" + }, + { + "authors": "E. Richard Stiehm" + }, + { + "authors": "Robert W. Sugerman" + }, + { + "authors": "John L. Sullivan" + }, + { + "authors": "Susan Tanksley" + }, + { + "authors": "Millard L. Tierce" + }, + { + "authors": "James Verbsky" + }, + { + "authors": "Beth Vogel" + }, + { + "authors": "Rosalyn Walker" + }, + { + "authors": "Kelly Walkovich" + }, + { + "authors": "Jolan E. Walter" + }, + { + "authors": "Richard L. Wasserman" + }, + { + "authors": "Michael S. Watson" + }, + { + "authors": "Geoffrey A. Weinberg" + }, + { + "authors": "Leonard B. Weiner" + }, + { + "authors": "Heather Wood" + }, + { + "authors": "Anne B. Yates" + }, + { + "authors": "Jennifer M. Puck" + }, + { + "date": "2014/08/20" + }, + { + "volume": "312" + }, + { + "issue": "7" + }, + { + "firstpage": "729" + }, + { + "lastpage": "738" + }, + { + "doi": "10.1001/jama.2014.9132" + }, + { + "journal": "JAMA" + }, + { + "abstract": "Importance \n Newborn screening for severe combined immunodeficiency (SCID) using assays to detect T-cell receptor excision circles (TRECs) began in Wisconsin in 2008, and SCID was added to the national recommended uniform panel for newborn screened disorders in 2010. Currently 23 states, the District of Columbia, and the Navajo Nation conduct population-wide newborn screening for SCID. The incidence of SCID is estimated at 1 in 100 000 births.Objectives \n To present data from a spectrum of SCID newborn screening programs, establish population-based incidence for SCID and other conditions with T-cell lymphopenia, and document early institution of effective treatments.Design \n Epidemiological and retrospective observational study.Setting \n Representatives in states conducting SCID newborn screening were invited to submit their SCID screening algorithms, test performance data, and deidentified clinical and laboratory information regarding infants screened and cases with nonnormal results. Infants born from the start of each participating program from January 2008 through the most recent evaluable date prior to July 2013 were included. Representatives from 10 states plus the Navajo Area Indian Health Service contributed data from 3 030 083 newborns screened with a TREC test.Main Outcomes and Measures \n Infants with SCID and other diagnoses of T-cell lymphopenia were classified. Incidence and, where possible, etiologies were determined. Interventions and survival were tracked.Results \n Screening detected 52 cases of typical SCID, leaky SCID, and Omenn syndrome, affecting 1 in 58 000 infants (95% CI, 1/46 000-1/80 000). Survival of SCID-affected infants through their diagnosis and immune reconstitution was 87% (45/52), 92% (45/49) for infants who received transplantation, enzyme replacement, and/or gene therapy. Additional interventions for SCID and non-SCID T-cell lymphopenia included immunoglobulin infusions, preventive antibiotics, and avoidance of live vaccines. Variations in definitions and follow-up practices influenced the rates of detection of non-SCID T-cell lymphopenia.Conclusions and Relevance \n Newborn screening in 11 programs in the United States identified SCID in 1 in 58 000 infants, with high survival. The usefulness of detection of non-SCID T-cell lymphopenias by the same screening remains to be determined." + }, + { + "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/930672/joi140101.pdf" + }, + { + "joi140101.pdf": "2a774d4c1d2b03c863402ba9eb1d80f8" + }, + { + "rendered.html": "76bd4d703e2bbd945ec4b2eda057f242" + } + ], + "http://jama.jamanetwork.com/article.aspx?articleid=221033": [ + { + "publisher": "American Medical Association" + }, + { + "title": "Association Between Time to Initiation of Adjuvant Chemotherapy and Survival in Colorectal Cancer: A Systematic Review and Meta-analysis" + }, + { + "authors": "James J. Biagi" + }, + { + "authors": "Michael J. Raphael" + }, + { + "authors": "William J. Mackillop" + }, + { + "authors": "Weidong Kong" + }, + { + "authors": "Will D. King" + }, + { + "authors": "Christopher M. Booth" + }, + { + "date": "2011/06/08" + }, + { + "volume": "305" + }, + { + "issue": "22" + }, + { + "firstpage": "2335" + }, + { + "lastpage": "2342" + }, + { + "doi": "10.1001/jama.2011.749" + }, + { + "journal": "JAMA" + }, + { + "abstract": "Context Adjuvant chemotherapy (AC) improves survival among patients with resected colorectal cancer. However, the optimal timing from surgery to initiation of AC is unknown.Objective To determine the relationship between time to AC and survival outcomes via a systematic review and meta-analysis.Data Sources MEDLINE (1975 through January 2011), EMBASE, the Cochrane Database of Systematic Reviews, and the Cochrane Central Register of Controlled Trials were searched to identify studies that described the relationship between time to AC and survival.Study Selection Studies were only included if the relevant prognostic factors were adequately described and either comparative groups were balanced or results adjusted for these prognostic factors.Data Extraction \n Hazard ratios (HRs) for overall survival and disease-free survival from each study were converted to a regression coefficient (β) and standard error corresponding to a continuous representation per 4 weeks of time to AC. The adjusted β from individual studies were combined using a fixed-effects model. Inverse variance (1/SE2) was used to weight individual studies. Publication bias was investigated using the trim and fill approach.\n Results We identified 10 eligible studies involving 15 410 patients (7 published articles, 3 abstracts). Nine of the studies were cohort or population based and 1 was a secondary analysis from a randomized trial of chemotherapy. Six studies reported time to AC as a binary variable and 4 as 3 or more categories. Meta-analysis demonstrated that a 4-week increase in time to AC was associated with a significant decrease in both overall survival (HR, 1.14; 95% confidence interval [CI], 1.10-1.17) and disease-free survival (HR, 1.14; 95% CI, 1.10-1.18). There was no significant heterogeneity among included studies. Results remained significant after adjustment for potential publication bias and when the analysis was repeated to exclude studies of largest weight.Conclusion In a meta-analysis of the available literature on time to AC, longer time to AC was associated with worse survival among patients with resected colorectal cancer." + }, + { + "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/20331/jrv15007_2335_2342.pdf" + }, + { + "supplementary_material": "/data/Journals/JAMA/20331/JWE15064_06_08_2011.pdf" + }, + { + "JWE15064_06_08_2011.pdf": "ee00ef66577d6d30aedb1c1fe7b20c69" + }, + { + "rendered.html": "892832b400e732b714a583074c0fed6a" + } + ], + "http://jama.jamanetwork.com/article.aspx?articleid=397582": [ + { + "publisher": "American Medical Association" + }, + { + "title": "Comparison of Warfarin and External Pneumatic Compression in Prevention of Venous Thrombosis After Total Hip Replacement" + }, + { + "authors": "Charles W. Francis" + }, + { + "authors": "Vincent D. Pellegrini" + }, + { + "authors": "Victor J. Marder" + }, + { + "authors": "Saara Totterman" + }, + { + "authors": "Carl M. Harris" + }, + { + "authors": "K. Ruben Gabriel" + }, + { + "authors": "Michael V. Azodo" + }, + { + "authors": "Kristin M. Leibert" + }, + { + "date": "1992/06/03" + }, + { + "volume": "267" + }, + { + "issue": "21" + }, + { + "firstpage": "2911" + }, + { + "lastpage": "2915" + }, + { + "doi": "10.1001/jama.1992.03480210073035" + }, + { + "journal": "JAMA" + }, + { + "abstract": "Objective. \n —To compare the effectiveness and safety of warfarin and external pneumatic compression (EPC) in prevention of venous thrombosis after total hip replacement.Design. \n —Prospective, randomized trial in consecutive patients, with blinded assessment of the primary end point.Setting. \n —University medical center and large community hospital.Patients. \n —Patients over age 18 years scheduled for elective primary total hip replacement were eligible. Of 254 patients interviewed, 232 were randomized, 220 patients had surgery and received prophylaxis, and 201 had venography.Interventions. \n —Patients were randomly assigned to prophylaxis with a device providing bilateral sequential EPC to both the calf and thigh or to receive warfarin in a low-intensity regimen beginning 10 to 14 days preoperatively. Prophylaxis was continued until venography.Main Outcome Measures. \n —Venous thrombosis was diagnosed by venography between postoperative days 6 and 8. Bleeding was assessed by surgical blood loss, transfusion requirements, changes in hematocrit, and clinically identified bleeding complications.Results. \n —The total incidence of venous thrombosis was virtually the same in the warfarin and EPC groups (31% vs 27%), but the distribution of thrombi was different. Proximal thrombosis occurred in 12% of patients in the EPC group compared with only 3% in the warfarin group (P=.012, 95% confidence interval for difference, 2% to 18%). In contrast, calf vein thrombosis was more frequent in the warfarin group (21%) than in the EPC group (12%) (P=.021,95% confidence interval for difference, 0% to 18%). Most proximal thrombi in EPC-treated patients were located within 15 cm of the femoral head and were not continuous with thrombi in deep calf veins. The high incidence of proximal thrombosis in the EPC group resulted in termination of the study by the safety monitoring committee. Blood loss and bleeding complications were similar in the two groups.Conclusion. \n —Warfarin therapy is significantly more effective than EPC in preventing serious proximal vein thrombosis after total hip replacement. The greater effectiveness of warfarin therapy in preventing proximal vein thrombi and of EPC in preventing thrombosis in the calf suggests that there are differences in the pathogenesis of thrombosis in these two locations.(JAMA. 1992;267:2911-2915)" + }, + { + "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/9595/jama_267_21_035.pdf" + }, + { + "jama_267_21_035.pdf": "470c33ae1ab47eec10a5ef53f43243a4" + }, + { + "rendered.html": "0e58eeed8c635bd69b83c3f1d4ef74b8" + } + ], + "http://jama.jamanetwork.com/article.aspx?articleid=346304": [ + { + "publisher": "American Medical Association" + }, + { + "title": "Skeletal Complications in a Series of Human Renal Allografts" + }, + { + "authors": "Michael C. Hall" + }, + { + "authors": "Stanley M. Elmore" + }, + { + "authors": "Robert W. Bright" + }, + { + "authors": "James C. Pierce" + }, + { + "authors": "David M. Hume" + }, + { + "date": "1969/06/09" + }, + { + "volume": "208" + }, + { + "issue": "10" + }, + { + "firstpage": "1825" + }, + { + "lastpage": "1829" + }, + { + "doi": "10.1001/jama.1969.03160100015004" + }, + { + "journal": "JAMA" + }, + { + "abstract": "Between August 1962 and May 1968, 140 renal transplantations were performed. Of the patients in this series, prior to transplantation, three were found with severe epiphysiolyses of the femoral heads, one with stress fractures of the femoral necks, and three with avascular necrosis of the femoral heads. It is suggested that these deformities should be stabilized as in other children. After transplantation, avascular necrosis of a femoral head or condyle developed in six patients. The cause is unknown but is believed related to the use of prednisone. Three infections of bone or joint have occurred." + }, + { + "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/8452/jama_208_10_004.pdf" + }, + { + "jama_208_10_004.pdf": "afd66c7a906d0b5d9a7d10f397fb4ae5" + }, + { + "rendered.html": "a495d539c00336470afa4d9db272b7c6" + } + ], + "http://jama.jamanetwork.com/article.aspx?articleid=1900512": [ + { + "publisher": "American Medical Association" + }, + { + "title": "Use of and Mortality After Bilateral Mastectomy Compared With Other Surgical Treatments for Breast Cancer in California, 1998-2011" + }, + { + "authors": "Allison W. Kurian" + }, + { + "authors": "Daphne Y. Lichtensztajn" + }, + { + "authors": "Theresa H. M. Keegan" + }, + { + "authors": "David O. Nelson" + }, + { + "authors": "Christina A. Clarke" + }, + { + "authors": "Scarlett L. Gomez" + }, + { + "date": "2014/09/03" + }, + { + "volume": "312" + }, + { + "issue": "9" + }, + { + "firstpage": "902" + }, + { + "lastpage": "914" + }, + { + "doi": "10.1001/jama.2014.10707" + }, + { + "journal": "JAMA" + }, + { + "abstract": "Importance \n Bilateral mastectomy is increasingly used to treat unilateral breast cancer. Because it may have medical and psychosocial complications, a better understanding of its use and outcomes is essential to optimizing cancer care.Objective \n To compare use of and mortality after bilateral mastectomy, breast-conserving therapy with radiation, and unilateral mastectomy.Design, Setting, and Participants \n Observational cohort study within the population-based California Cancer Registry; participants were women diagnosed with stages 0-III unilateral breast cancer in California from 1998 through 2011, with median follow-up of 89.1 months.Main Outcomes and Measures \n Factors associated with surgery use (from polytomous logistic regression); overall and breast cancer–specific mortality (from propensity score weighting and Cox proportional hazards analysis).Results \n Among 189 734 patients, the rate of bilateral mastectomy increased from 2.0% (95% CI, 1.7%-2.2%) in 1998 to 12.3% (95% CI, 11.8%-12.9%) in 2011, an annual increase of 14.3% (95% CI, 13.1%-15.5%); among women younger than 40 years, the rate increased from 3.6% (95% CI, 2.3%-5.0%) in 1998 to 33% (95% CI, 29.8%-36.5%) in 2011. Bilateral mastectomy was more often used by non-Hispanic white women, those with private insurance, and those who received care at a National Cancer Institute (NCI)–designated cancer center (8.6% [95% CI, 8.1%-9.2%] among NCI cancer center patients vs 6.0% [95% CI, 5.9%-6.1%] among non-NCI cancer center patients; odds ratio [OR], 1.13 [95% CI, 1.04-1.22]); in contrast, unilateral mastectomy was more often used by racial/ethnic minorities (Filipina, 52.8% [95% CI, 51.6%-54.0%]; OR, 2.00 [95% CI, 1.90-2.11] and Hispanic, 45.6% [95% CI, 45.0%-46.2%]; OR, 1.16 [95% CI, 1.13-1.20] vs non-Hispanic white, 35.2% [95% CI, 34.9%-35.5%]) and those with public/Medicaid insurance (48.4% [95% CI, 47.8%-48.9%]; OR, 1.08 [95% CI, 1.05-1.11] vs private insurance, 36.6% [95% CI, 36.3%-36.8%]). Compared with breast-conserving surgery with radiation (10-year mortality, 16.8% [95% CI, 16.6%-17.1%]), unilateral mastectomy was associated with higher all-cause mortality (hazard ratio [HR], 1.35 [95% CI, 1.32-1.39]; 10-year mortality, 20.1% [95% CI, 19.9%-20.4%]). There was no significant mortality difference compared with bilateral mastectomy (HR, 1.02 [95% CI, 0.94-1.11]; 10-year mortality, 18.8% [95% CI, 18.6%-19.0%]). Propensity analysis showed similar results.Conclusions and Relevance \n Use of bilateral mastectomy increased significantly throughout California from 1998 through 2011 and was not associated with lower mortality than that achieved with breast-conserving surgery plus radiation. Unilateral mastectomy was associated with higher mortality than were the other 2 surgical options." + }, + { + "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/930710/joi140111.pdf" + }, + { + "supplementary_material": "/data/Journals/JAMA/930710/JOI140111supp1_prod.pdf" + }, + { + "JOI140111supp1_prod.pdf": "9ea1385918727382384248cda7a17f8a" + }, + { + "rendered.html": "c878e816f3cc71b5da1112f9402fe3dd" + } + ], + "http://jama.jamanetwork.com/article.aspx?articleid=1900503": [ + { + "publisher": "American Medical Association" + }, + { + "title": "Regulation and Comparative Effectiveness Research—Reply" + }, + { + "authors": "Richard Platt" + }, + { + "authors": "Nancy E. Kass" + }, + { + "authors": "Deven McGraw" + }, + { + "date": "2014/09/03" + }, + { + "volume": "312" + }, + { + "issue": "9" + }, + { + "firstpage": "964" + }, + { + "lastpage": "964" + }, + { + "doi": "10.1001/jama.2014.7667" + }, + { + "journal": "JAMA" + }, + { + "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/930710/jlr140062.pdf" + }, + { + "jlr140062.pdf": "eea70173d47fcecec5a172608459f0ee" + }, + { + "rendered.html": "572129b8a81299e0b2e60c04a7cef7bf" + } + ], + "http://jama.jamanetwork.com/article.aspx?articleid=1900482": [ + { + "title": "Colchicine for Prevention of Postpericardiotomy Syndrome and Postoperative Atrial Fibrillation: The COPPS-2 Randomized Clinical Trial" + }, + { + "authors": "Massimo Imazio" + }, + { + "authors": "Antonio Brucato" + }, + { + "authors": "Paolo Ferrazzi" + }, + { + "authors": "Alberto Pullara" + }, + { + "authors": "Yehuda Adler" + }, + { + "authors": "Alberto Barosi" + }, + { + "authors": "Alida L. Caforio" + }, + { + "authors": "Roberto Cemin" + }, + { + "authors": "Fabio Chirillo" + }, + { + "authors": "Chiara Comoglio" + }, + { + "authors": "Diego Cugola" + }, + { + "authors": "Davide Cumetti" + }, + { + "authors": "Oleksandr Dyrda" + }, + { + "authors": "Stefania Ferrua" + }, + { + "authors": "Yaron Finkelstein" + }, + { + "authors": "Roberto Flocco" + }, + { + "authors": "Anna Gandino" + }, + { + "authors": "Brian Hoit" + }, + { + "authors": "Francesco Innocente" + }, + { + "authors": "Silvia Maestroni" + }, + { + "authors": "Francesco Musumeci" + }, + { + "authors": "Jae Oh" + }, + { + "authors": "Amedeo Pergolini" + }, + { + "authors": "Vincenzo Polizzi" + }, + { + "authors": "Arsen Ristić" + }, + { + "authors": "Caterina Simon" + }, + { + "authors": "David H Spodick" + }, + { + "authors": "Vincenzo Tarzia" + }, + { + "authors": "Stefania Trimboli" + }, + { + "authors": "Anna Valenti" + }, + { + "authors": "Riccardo Belli" + }, + { + "authors": "Fiorenzo Gaita" + }, + { + "authors": " " + }, + { + "firstpage": "" + }, + { + "lastpage": "" + }, + { + "doi": "10.1001/jama.2014.11026" + }, + { + "journal": "JAMA" + }, + { + "abstract": "Importance \n Postpericardiotomy syndrome, postoperative atrial fibrillation (AF), and postoperative effusions may be responsible for increased morbidity and health care costs after cardiac surgery. Postoperative use of colchicine prevented these complications in a single trial.Objective \n To determine the efficacy and safety of perioperative use of oral colchicine in reducing postpericardiotomy syndrome, postoperative AF, and postoperative pericardial or pleural effusions.Design, Setting, and Participants \n Investigator-initiated, double-blind, placebo-controlled, randomized clinical trial among 360 consecutive candidates for cardiac surgery enrolled in 11 Italian centers between March 2012 and March 2014. At enrollment, mean age of the trial participants was 67.5 years (SD, 10.6 years), 69% were men, and 36% had planned valvular surgery. Main exclusion criteria were absence of sinus rhythm at enrollment, cardiac transplantation, and contraindications to colchicine.Interventions \n Patients were randomized to receive placebo (n=180) or colchicine (0.5 mg twice daily in patients ≥70 kg or 0.5 mg once daily in patients <70 kg; n=180) starting between 48 and 72 hours before surgery and continued for 1 month after surgery.Main Outcomes and Measures \n Occurrence of postpericardiotomy syndrome within 3 months; main secondary study end points were postoperative AF and pericardial or pleural effusion.Results \n The primary end point of postpericardiotomy syndrome occurred in 35 patients (19.4%) assigned to colchicine and in 53 (29.4%) assigned to placebo (absolute difference, 10.0%; 95% CI, 1.1%-18.7%; number needed to treat = 10). There were no significant differences between the colchicine and placebo groups for the secondary end points of postoperative AF (colchicine, 61 patients [33.9%]; placebo, 75 patients [41.7%]; absolute difference, 7.8%; 95% CI, −2.2% to 17.6%) or postoperative pericardial/pleural effusion (colchicine, 103 patients [57.2%]; placebo, 106 patients [58.9%]; absolute difference, 1.7%; 95% CI, −8.5% to 11.7%), although there was a reduction in postoperative AF in the prespecified on-treatment analysis (placebo, 61/148 patients [41.2%]; colchicine, 38/141 patients [27.0%]; absolute difference, 14.2%; 95% CI, 3.3%-24.7%). Adverse events occurred in 21 patients (11.7%) in the placebo group vs 36 (20.0%) in the colchicine group (absolute difference, 8.3%; 95% CI; 0.76%-15.9%; number needed to harm = 12), but discontinuation rates were similar. No serious adverse events were observed.Conclusions and Relevance \n Among patients undergoing cardiac surgery, perioperative use of colchicine compared with placebo reduced the incidence of postpericardiotomy syndrome but not of postoperative AF or postoperative pericardial/pleural effusion. The increased risk of gastrointestinal adverse effects reduced the potential benefits of colchicine in this setting.Trial Registration \n clinicaltrials.gov Identifier: NCT01552187" + }, + { + "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/0/joi140113.pdf" + }, + { + "supplementary_material": "/data/Journals/JAMA/0/JOI140113supp1_prod.pdf" + }, + { + "supplementary_material": "/data/Journals/JAMA/0/JOI140113supp2_prod.pdf" + }, + { + "JOI140113supp2_prod.pdf": "4fc349d4f4b363dabb9578e8f5016a39" + }, + { + "rendered.html": "471ffa98e8b61da776545161240a1929" + } + ], + "http://archneur.jamanetwork.com/article.aspx?articleid=1875833": [ + { + "publisher": "American Medical Association" + }, + { + "title": "Effect of 1 Night of Total Sleep Deprivation on Cerebrospinal Fluid β-Amyloid 42 in Healthy Middle-Aged Men: A Randomized Clinical Trial" + }, + { + "authors": "Sharon Ooms" + }, + { + "authors": "Sebastiaan Overeem" + }, + { + "authors": "Kees Besse" + }, + { + "authors": "Marcel Olde Rikkert" + }, + { + "authors": "Marcel Verbeek" + }, + { + "authors": "Jurgen A. H. R. Claassen" + }, + { + "date": "2014/08/01" + }, + { + "volume": "71" + }, + { + "issue": "8" + }, + { + "firstpage": "971" + }, + { + "lastpage": "977" + }, + { + "doi": "10.1001/jamaneurol.2014.1173" + }, + { + "journal": "JAMA Neurology" + }, + { + "abstract": "Importance \n Increasing evidence suggests a relationship between poor sleep and the risk of developing Alzheimer disease. A previous study found an effect of sleep on β-amyloid (Aβ), which is a key protein in Alzheimer disease pathology.Objective \n To determine the effect of 1 night of total sleep deprivation on cerebrospinal fluid Aβ42 protein levels in healthy middle-aged men.Design, Setting, and Participants \n The Alzheimer, Wakefulness, and Amyloid Kinetics (AWAKE) study at the Radboud Alzheimer Center, a randomized clinical trial that took place between June 1, 2012, and October 1, 2012. Participants were cognitively normal middle-aged men (40-60 years of age) with normal sleep (n = 26) recruited from the local population.Interventions \n Participants were randomized to 1 night with unrestricted sleep (n = 13) or 1 night of total sleep deprivation (24 hours of wakefulness) (n = 13).Main Outcomes and Measures \n Sleep was monitored using continuous polysomnographic recording from 3 pm until 10 am. Cerebrospinal fluid samples were collected using an intrathecal catheter at defined times to compare cerebral Aβ42 concentrations between evening and morning.Results \n A night of unrestricted sleep led to a 6% decrease in Aβ42 levels of 25.3 pg/mL (95% CI [0.94, 49.6], P = .04), whereas sleep deprivation counteracted this decrease. When accounting for the individual trajectories of Aβ42 over time, a difference of 75.8 pg/mL of Aβ42 was shown between the unrestricted sleep and sleep deprivation group (95% CI [3.4, 148.4], P = .04). The individual trajectories of evening and morning Aβ42 concentrations differed between the unrestricted sleep and sleep deprivation groups (P = .04) in contrast to stable Aβ40, tau, and total protein levels.Conclusions and Relevance \n Sleep deprivation, or prolonged wakefulness, interferes with a physiological morning decrease in Aβ42. We hypothesize that chronic sleep deprivation increases cerebral Aβ42 levels, which elevates the risk of Alzheimer disease.Trial Registration \n clinicaltrials.gov Identifier: NCT01194713" + }, + { + "fulltext_pdf": "http://archneur.jamanetwork.com/data/Journals/NEUR/930612/noi140040.pdf" + }, + { + "noi140040.pdf": "bdcb16f6f241a62ed954d7947ba628a1" + }, + { + "rendered.html": "e0fdc7f214ce57a8a710d4da425cf135" + } + ], + "http://archsurg.jamanetwork.com/article.aspx?articleid=1899998": [ + { + "title": "Mandated Self-reporting of Ventilator-Associated Pneumonia Bundle and Catheter-Related Bloodstream Infection Bundle Compliance and Infection Rates" + }, + { + "authors": "Ryan A. Helmick" + }, + { + "authors": "Meredith L. Knofsky" + }, + { + "authors": "Carla C. Braxton" + }, + { + "authors": "Anuradha Subramanian" + }, + { + "authors": "Patricia Byers" + }, + { + "authors": "Charlie K. W. Lan" + }, + { + "authors": "Samir S. Awad" + }, + { + "firstpage": "" + }, + { + "lastpage": "" + }, + { + "doi": "10.1001/jamasurg.2014.1627" + }, + { + "journal": "JAMA Surgery" + }, + { + "abstract": "Importance \n As quality measures increasingly become tied to payment, evaluating the most effective ways to provide high-quality care becomes more important.Objectives \n To determine whether mandated reporting for ventilator and catheter bundle compliance is correlated with decreased infection rates, and to determine whether labor-intensive audits are correlated with compliance.Design, Setting, and Participants \n Multiyear retrospective review of aggregated data from all patients admitted to 15 intensive care units in a Veterans Affairs hospital setting (the Veterans Integrated Service Network 16) from 2009 to 2011.Exposures \n Ventilator-associated pneumonia and catheter-related bloodstream infections.Main Outcomes and Measures \n Mean rates of ventilator-associated pneumonia and catheter-related bloodstream infection were analyzed by year. Relationships between infection rates, self-reported compliance, and audits were analyzed by Pearson correlation.Results \n During the study period, ventilator-associated pneumonia decreased from 2.50 to 1.60 infections per 1000 ventilator days (P = .07). The rate of pneumonia was not correlated with self-reported compliance overall (R = 0.19) or by individual year (2009, R = 0.30; 2010, R = 0.24; 2011, R = 0.46); there was a correlation in cardiac intensive care units (R = −0.70) but not other types of intensive care units (mixed, R = −0.18; medical, R = 0.42; surgical, R = 0.34). Catheter-related bloodstream infections decreased from 2.38 to 0.73 infections per 1000 catheter days (P = .04). The rate of catheter infection was not correlated with self-reported compliance overall (R = −0.18), by individual year (2009, R = −0.39; 2010, R = −0.42; 2011, R = 0.37), or by intensive care unit type (mixed, R = −0.19; cardiac, R = 0.55; medical, R = 0.17; surgical, R = −0.44).Conclusions and Relevance \n Current mandated self-reported compliance and audit measures are poorly correlated with decreased ventilator-associated pneumonia or catheter-related bloodstream infection." + }, + { + "fulltext_pdf": "http://archsurg.jamanetwork.com/data/Journals/SURG/0/soi140073.pdf" + }, + { + "rendered.html": "014dc2d0425809f290ac1f2acec8079d" + }, + { + "soi140073.pdf": "bc0e2a5d35a1fe64be6c69d3e641a521" + } + ], + "http://archinte.jamanetwork.com/article.aspx?articleid=1899761": [ + { + "title": "Association of Treatment With Carvedilol vs Metoprolol Succinate and Mortality in Patients With Heart Failure" + }, + { + "authors": "Björn Pasternak" + }, + { + "authors": "Henrik Svanström" + }, + { + "authors": "Mads Melbye" + }, + { + "authors": "Anders Hviid" + }, + { + "firstpage": "" + }, + { + "lastpage": "" + }, + { + "doi": "10.1001/jamainternmed.2014.3258" + }, + { + "journal": "JAMA Internal Medicine" + }, + { + "abstract": "Importance \n The β-blockers carvedilol and metoprolol succinate both reduce mortality in patients with heart failure (HF), but the comparative clinical effectiveness of these drugs is unknown.Objective \n To investigate whether carvedilol is associated with improved survival compared with metoprolol succinate.Design, Setting, and Participants \n Cohort study of patients with incident HF with reduced left ventricular ejection fraction (LVEF) (≤40%) who received carvedilol (n = 6026) or metoprolol succinate (n = 5638) using data from a Danish national HF registry linked with health care and administrative databases. Main Outcomes and Measures \n All-cause mortality (primary outcome) and cardiovascular mortality (secondary outcome) were analyzed using Cox regression with adjustment for a propensity score, derived from a range of clinical, socioeconomic, and demographic characteristics.Results \n The mean (SD) age of the patients was 69.3 (9.1) years, 71% were men, and 51% were hospitalized at index HF diagnosis. During a median (interquartile range) 2.4 (1.0-3.0) years of follow-up, 875 carvedilol users and 754 metoprolol users died; the cumulative incidence of mortality was 18.3% and 18.8%, respectively. The adjusted hazard ratio for carvedilol users vs metoprolol users was 0.99 (95% CI, 0.88 to 1.11), corresponding to an absolute risk difference of –0.07 (95% CI, –0.84 to 0.77) deaths per 100 person-years. Estimates were consistent across subgroup analyses by sex, age, levels of LVEF, New York Heart Association classification, and history of ischemic heart disease. A higher proportion of carvedilol users achieved the recommended daily target dose (50 mg; 3124 [52%]) than did metoprolol users (200 mg; 689 [12%]); among patients who reached the target dose, the adjusted hazard ratio was 0.97 (95% CI, 0.72-1.30). A robustness analysis with 1:1 propensity score matching confirmed the primary findings (hazard ratio, 0.97 [95% CI, 0.84-1.13]). The adjusted hazard ratio for cardiovascular mortality was 1.05 (95% CI, 0.88-1.26).Conclusions and Relevance \n These findings from real-world clinical practice indicate that the effectiveness of carvedilol and metoprolol succinate in patients with HF is similar." + }, + { + "fulltext_pdf": "http://archinte.jamanetwork.com/data/Journals/INTEMED/0/ioi140062.pdf" + }, + { + "ioi140062.pdf": "c15954aa524d174e32fcf4b7f2ebbd44" + }, + { + "rendered.html": "ebd00d779c609998c3c63a80889ec3bb" + } + ], + "http://archneurpsyc.jamanetwork.com/article.aspx?articleid=652906": [ + { + "publisher": "American Medical Association" + }, + { + "title": "Penicillin Treatment of General Paresis (Dementia Paralytica): Results of Treatment in 1,086 Patients the Majority of Whom Were Followed for More Than Five Years" + }, + { + "authors": "RICHARD D. HAHN" + }, + { + "authors": "BRUCE WEBSTER" + }, + { + "authors": "GEORGE WEICKHARDT" + }, + { + "authors": "EVAN THOMAS" + }, + { + "authors": "WILLIAM TIMBERLAKE" + }, + { + "authors": "HARRY SOLOMON" + }, + { + "authors": "JOHN H. STOKES" + }, + { + "authors": "JOSEPH EARLE MOORE" + }, + { + "authors": "ALBERT HEYMAN" + }, + { + "authors": "GEORGE GAMMON" + }, + { + "authors": "GERALDINE A. GLEESON" + }, + { + "authors": "ARTHUR C. CURTIS" + }, + { + "authors": "JOHN C. CUTLER" + }, + { + "date": "1959/05/01" + }, + { + "volume": "81" + }, + { + "issue": "5" + }, + { + "firstpage": "557" + }, + { + "lastpage": "590" + }, + { + "doi": "10.1001/archneurpsyc.1959.02340170023003" + }, + { + "journal": "A.M.A. Archives of Neurology & Psychiatry" + }, + { + "abstract": "Introduction \n This paper is a cooperative report of the clinical, spinal fluid, and serologic findings in a group of 1,086 patients with general paresis (dementia paralytica) treated with penicillin with or without fever therapy at eight different hospitals. A detailed account of the formation and function of this cooperative clinical study has been given previously as an introduction to the presentation of the group experience in treatment of asymptomatic central nervous system syphilis.1Shortly after the effectiveness of penicillin in the treatment of early syphilis was reported, various investigators began to study the efficacy of this new antibiotic in the treatment of central nervous system syphilis. These investigations were supported in part by grants from the Office of Scientific Research and Development, the National Institutes of Health, and the Division of Venereal Disease, U. S. Public Health Service. The findings of the individual investigators have provided much of the" + }, + { + "fulltext_pdf": "http://archneurpsyc.jamanetwork.com/data/Journals/NEURPSYCH/18617/archneurpsyc_81_5_003.pdf" + }, + { + "archneurpsyc_81_5_003.pdf": "1277c698578bda37fe5664516b975c20" + }, + { + "rendered.html": "9cb6a3cbcad113ea0f4b68428e2f9c9d" + } + ] +} \ No newline at end of file diff --git a/test/jama_test_urls.txt b/test/jama_test_urls.txt new file mode 100644 index 0000000..600d09b --- /dev/null +++ b/test/jama_test_urls.txt @@ -0,0 +1,13 @@ +http://jama.jamanetwork.com/article.aspx?articleid=1456072 +http://jama.jamanetwork.com/article.aspx?articleid=1890398 +http://jama.jamanetwork.com/article.aspx?articleid=1896983 +http://jama.jamanetwork.com/article.aspx?articleid=221033 +http://jama.jamanetwork.com/article.aspx?articleid=397582 +http://jama.jamanetwork.com/article.aspx?articleid=346304 +http://jama.jamanetwork.com/article.aspx?articleid=1900512 +http://jama.jamanetwork.com/article.aspx?articleid=1900503 +http://jama.jamanetwork.com/article.aspx?articleid=1900482 +http://archneur.jamanetwork.com/article.aspx?articleid=1875833 +http://archsurg.jamanetwork.com/article.aspx?articleid=1899998 +http://archinte.jamanetwork.com/article.aspx?articleid=1899761 +http://archneurpsyc.jamanetwork.com/article.aspx?articleid=652906 \ No newline at end of file From 062c4198747dbdcd178d98ef74a543ab7e406a7f Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Thu, 2 Oct 2014 19:56:06 +0100 Subject: [PATCH 084/154] acs must be headless --- scrapers/acs.json | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/scrapers/acs.json b/scrapers/acs.json index b32dca3..2fe2a6f 100644 --- a/scrapers/acs.json +++ b/scrapers/acs.json @@ -1,5 +1,6 @@ { "url": "pubs\\.acs\\.org", + "headless": true, "elements": { "publisher": { "selector": "//meta[@name='dc.Publisher']", @@ -49,12 +50,16 @@ "fulltext_html": { "selector": "//a[@title='View the Full Text HTML']", "attribute": "href", - "download": true + "download": { + "rename": "fulltext.html" + } }, "fulltext_pdf": { "selector": "//a[@title='Download the PDF Full Text']", "attribute": "href", - "download": true + "download": { + "rename": "fulltext.pdf" + } }, "supplementary_material": { "selector": "//a[title='View Supporting Information']", @@ -72,4 +77,3 @@ } } } - From 38d63e03b9d81f6d68107b47747580b9f9512ce8 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Thu, 2 Oct 2014 23:00:58 +0100 Subject: [PATCH 085/154] temporarily remove broken jama scraper --- scrapers/jama.json | 64 --- test/jama.json | 1063 --------------------------------------- test/jama_test_urls.txt | 13 - 3 files changed, 1140 deletions(-) delete mode 100644 scrapers/jama.json delete mode 100644 test/jama.json delete mode 100644 test/jama_test_urls.txt diff --git a/scrapers/jama.json b/scrapers/jama.json deleted file mode 100644 index cb6d01e..0000000 --- a/scrapers/jama.json +++ /dev/null @@ -1,64 +0,0 @@ -{ - "url": "jamanetwork\\.com", - "elements": { - "publisher": { - "selector": "//meta[@name='citation_publisher']", - "attribute": "content" - }, - "title": { - "selector": "//meta[@name='citation_title']", - "attribute": "content" - }, - "authors": { - "selector": "//meta[@name='citation_author']", - "attribute": "content" - }, - "date": { - "selector": "//meta[@name='citation_date']", - "attribute": "content" - }, - "volume": { - "selector": "//meta[@name='citation_volume']", - "attribute": "content" - }, - "issue": { - "selector": "//meta[@name='citation_issue']", - "attribute": "content" - }, - "firstpage": { - "selector": "//meta[@name='citation_firstpage']", - "attribute": "content" - }, - "lastpage": { - "selector": "//meta[@name='citation_lastpage']", - "attribute": "content" - }, - "doi": { - "selector": "//meta[@name='citation_doi']", - "attribute": "content" - }, - "journal": { - "selector": "//meta[@name='citation_journal_title']", - "attribute": "content" - }, - "abstract": { - "selector": "//span[@class='Abstract 0']", - "attribute": "text" - }, - "firstpage_preview": { - "selector": "//img[@id='imgFPPPPopup']", - "attriubute": "src", - "download": true - }, - "fulltext_pdf": { - "selector": "//meta[@name='citation_pdf_url']", - "attribute": "content", - "download": true - }, - "supplementary_material": { - "selector": "//a[@class='supplementLink']", - "attribute": "href", - "download": true - } - } -} diff --git a/test/jama.json b/test/jama.json deleted file mode 100644 index dbc0b8d..0000000 --- a/test/jama.json +++ /dev/null @@ -1,1063 +0,0 @@ -{ - "http://jama.jamanetwork.com/article.aspx?articleid=1456072": [ - { - "publisher": "American Medical Association" - }, - { - "title": "Association of Childhood Pertussis With Receipt of 5 Doses of Pertussis Vaccine by Time Since Last Vaccine Dose, California, 2010" - }, - { - "authors": "Lara K. Misegades" - }, - { - "authors": "Kathleen Winter" - }, - { - "authors": "Kathleen Harriman" - }, - { - "authors": "John Talarico" - }, - { - "authors": "Nancy E. Messonnier" - }, - { - "authors": "Thomas A. Clark" - }, - { - "authors": "Stacey W. Martin" - }, - { - "date": "2012/11/28" - }, - { - "volume": "308" - }, - { - "issue": "20" - }, - { - "firstpage": "2126" - }, - { - "lastpage": "2132" - }, - { - "doi": "10.1001/jama.2012.14939" - }, - { - "journal": "JAMA" - }, - { - "abstract": "Context In 2010, California experienced its largest pertussis epidemic in more than 60 years; a substantial burden of disease was noted in the 7- to 10-year-old age group despite high diphtheria, tetanus, and acellular pertussis vaccine (DTaP) coverage, indicating the possibility of waning protection.Objective To evaluate the association between pertussis and receipt of 5 DTaP doses by time since fifth DTaP dose.Design, Setting, and Participants Case-control evaluation conducted in 15 California counties. Cases (n = 682) were all suspected, probable, and confirmed pertussis cases among children aged 4 to 10 years reported from January through December 14, 2010; controls (n = 2016) were children in the same age group who received care from the clinicians reporting the cases. Three controls were selected per case. Vaccination histories were obtained from medical records and immunization registries.Main Outcome Measures Primary outcomes were (1) odds ratios (ORs) for the association between pertussis and receipt of the 5-dose DTaP series and (2) ORs for the association between pertussis and time since completion (<12, 12-23, 24-35, 36-47, 48-59, or ≥60 months) of the 5-dose DTaP series. Logistic regression was used to calculate ORs, accounting for clustering by county and clinician, and vaccine effectiveness (VE) was estimated as (1 − OR) × 100%.Results Among cases and controls, 53 (7.8%) and 19 (0.9%) had not received any pertussis-containing vaccines, respectively. Compared with controls, children with pertussis had a lower odds of having received all 5 doses of DTaP (OR, 0.11; 95% CI, 0.06-0.21 [estimated VE, 88.7%; 95% CI, 79.4%-93.8%]). When children were categorized by time since completion of the DTaP series, using an unvaccinated reference group, children with pertussis compared with controls were less likely to have received their fifth dose within the prior 12 months (19 [2.8%] vs 354 [17.6%], respectively; OR, 0.02; 95% CI, 0.01-0.04 [estimated VE, 98.1%; 95% CI, 96.1%-99.1%]). This association was evident with longer time since vaccination, with ORs increasing with time since the fifth dose. At 60 months or longer (n = 231 cases [33.9%] and n = 288 controls [14.3%]), the OR was 0.29 (95% CI, 0.15-0.54 [estimated VE, 71.2%; 95% CI, 45.8%-84.8%]). Accordingly, the estimated VE declined each year after receipt of the fifth dose of DTaP.Conclusion Among children in 15 California counties, children with pertussis, compared with controls, had lower odds of having received the 5-dose DTaP series; as time since last DTaP dose increased, the odds increased, which is consistent with a progressive decrease in estimated vaccine effectiveness each year after the final dose of pertussis vaccine." - }, - { - "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/28295/joc120116_2126_2132.pdf" - }, - { - "joc120116_2126_2132.pdf": "360c3126d8eacbbb89686c3ad560884f" - }, - { - "rendered.html": "7c3a59efb7e6416c5e632a8ed1619dd1" - } - ], - "http://jama.jamanetwork.com/article.aspx?articleid=1890398": [ - { - "publisher": "American Medical Association" - }, - { - "title": "Effect of Providing Conditional Economic Compensation on Uptake of Voluntary Medical Male Circumcision in Kenya: A Randomized Clinical Trial" - }, - { - "authors": "Harsha Thirumurthy" - }, - { - "authors": "Samuel H. Masters" - }, - { - "authors": "Samwel Rao" - }, - { - "authors": "Megan A. Bronson" - }, - { - "authors": "Michele Lanham" - }, - { - "authors": "Eunice Omanga" - }, - { - "authors": "Emily Evens" - }, - { - "authors": "Kawango Agot" - }, - { - "date": "2014/08/20" - }, - { - "volume": "312" - }, - { - "issue": "7" - }, - { - "firstpage": "703" - }, - { - "lastpage": "711" - }, - { - "doi": "10.1001/jama.2014.9087" - }, - { - "journal": "JAMA" - }, - { - "abstract": "Importance \n Novel strategies are needed to increase the uptake of voluntary medical male circumcision (VMMC) in sub-Saharan Africa and enhance the effectiveness of male circumcision as an HIV prevention strategy.Objective \n To determine whether small economic incentives could increase circumcision prevalence by addressing reported economic barriers to VMMC and behavioral factors such as present-biased decision making.Design, Setting, and Participants \n Randomized clinical trial conducted between June 22, 2013, and February 4, 2014, among 1504 uncircumcised men aged 25 to 49 years in Nyanza region, Kenya. VMMC services were provided free of charge and participants were randomized to 1 of 3 intervention groups or a control group.Interventions \n Participants in the 3 intervention groups received varying amounts of compensation conditional on undergoing circumcision at 1 of 9 study clinics within 2 months of enrollment. Compensation took the form of food vouchers worth 200 Kenya shillings (≈US $2.50), 700 Kenya shillings (≈US $8.75), or 1200 Kenya shillings (≈US $15.00), which reflected a portion of transportation costs and lost wages associated with getting circumcised. The control group received no compensation.Main Outcomes and Measures \n VMMC uptake within 2 months.Results \n Analysis of data for 1502 participants with complete data showed that VMMC uptake within 2 months was higher in the US $8.75 group (6.6%; 95% CI, 4.3%-9.5% [25 of 381]) and the US $15.00 group (9.0%; 95% CI, 6.3%-12.4% [34 of 377]) than in the US $2.50 group (1.9%; 95% CI, 0.8%-3.8% [7 of 374]) and the control group (1.6%; 95% CI, 0.6%-3.5% [6 of 370]). In logistic regression analysis, the US $8.75 group had significantly higher VMMC uptake than the control group (adjusted odds ratio [AOR] 4.3; 95% CI, 1.7-10.7), as did the US $15.00 group (AOR 6.2; 95% CI, 2.6-15.0). Effect sizes for the US $8.75 and US $15.00 groups did not differ significantly (P = .20).Conclusions and Relevance \n Among uncircumcised men in Kenya, compensation in the form of food vouchers worth approximately US $8.75 or US $15.00, compared with lesser or no compensation, resulted in a modest increase in the prevalence of circumcision after 2 months. The effects of more intense promotion or longer implementation require further investigation.Trial Registration \n clinicaltrials.gov Identifier: NCT01857700" - }, - { - "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/930672/joi140100.pdf" - }, - { - "joi140100.pdf": "5949b7996bea79e8af0b657e8614cd8f" - }, - { - "rendered.html": "da2585e1b351450d05d0c4b144f1c757" - } - ], - "http://jama.jamanetwork.com/article.aspx?articleid=1896983": [ - { - "publisher": "American Medical Association" - }, - { - "title": "Newborn Screening for Severe Combined Immunodeficiency in 11 Screening Programs in the United States" - }, - { - "authors": "Antonia Kwan" - }, - { - "authors": "Roshini S. Abraham" - }, - { - "authors": "Robert Currier" - }, - { - "authors": "Amy Brower" - }, - { - "authors": "Karen Andruszewski" - }, - { - "authors": "Jordan K. Abbott" - }, - { - "authors": "Mei Baker" - }, - { - "authors": "Mark Ballow" - }, - { - "authors": "Louis E. Bartoshesky" - }, - { - "authors": "Francisco A. Bonilla" - }, - { - "authors": "Charles Brokopp" - }, - { - "authors": "Edward Brooks" - }, - { - "authors": "Michele Caggana" - }, - { - "authors": "Jocelyn Celestin" - }, - { - "authors": "Joseph A. Church" - }, - { - "authors": "Anne Marie Comeau" - }, - { - "authors": "James A. Connelly" - }, - { - "authors": "Morton J. Cowan" - }, - { - "authors": "Charlotte Cunningham-Rundles" - }, - { - "authors": "Trivikram Dasu" - }, - { - "authors": "Nina Dave" - }, - { - "authors": "Maria T. De La Morena" - }, - { - "authors": "Ulrich Duffner" - }, - { - "authors": "Chin-To Fong" - }, - { - "authors": "Lisa Forbes" - }, - { - "authors": "Debra Freedenberg" - }, - { - "authors": "Erwin W. Gelfand" - }, - { - "authors": "Jaime E. Hale" - }, - { - "authors": "I. Celine Hanson" - }, - { - "authors": "Beverly N. Hay" - }, - { - "authors": "Diana Hu" - }, - { - "authors": "Anthony Infante" - }, - { - "authors": "Daisy Johnson" - }, - { - "authors": "Neena Kapoor" - }, - { - "authors": "Denise M. Kay" - }, - { - "authors": "Donald B. Kohn" - }, - { - "authors": "Rachel Lee" - }, - { - "authors": "Heather Lehman" - }, - { - "authors": "Zhili Lin" - }, - { - "authors": "Fred Lorey" - }, - { - "authors": "Aly Abdel-Mageed" - }, - { - "authors": "Adrienne Manning" - }, - { - "authors": "Sean McGhee" - }, - { - "authors": "Theodore B. Moore" - }, - { - "authors": "Stanley J. Naides" - }, - { - "authors": "Luigi D. Notarangelo" - }, - { - "authors": "Jordan S. Orange" - }, - { - "authors": "Sung-Yun Pai" - }, - { - "authors": "Matthew Porteus" - }, - { - "authors": "Ray Rodriguez" - }, - { - "authors": "Neil Romberg" - }, - { - "authors": "John Routes" - }, - { - "authors": "Mary Ruehle" - }, - { - "authors": "Arye Rubenstein" - }, - { - "authors": "Carlos A. Saavedra-Matiz" - }, - { - "authors": "Ginger Scott" - }, - { - "authors": "Patricia M. Scott" - }, - { - "authors": "Elizabeth Secord" - }, - { - "authors": "Christine Seroogy" - }, - { - "authors": "William T. Shearer" - }, - { - "authors": "Subhadra Siegel" - }, - { - "authors": "Stacy K. Silvers" - }, - { - "authors": "E. Richard Stiehm" - }, - { - "authors": "Robert W. Sugerman" - }, - { - "authors": "John L. Sullivan" - }, - { - "authors": "Susan Tanksley" - }, - { - "authors": "Millard L. Tierce" - }, - { - "authors": "James Verbsky" - }, - { - "authors": "Beth Vogel" - }, - { - "authors": "Rosalyn Walker" - }, - { - "authors": "Kelly Walkovich" - }, - { - "authors": "Jolan E. Walter" - }, - { - "authors": "Richard L. Wasserman" - }, - { - "authors": "Michael S. Watson" - }, - { - "authors": "Geoffrey A. Weinberg" - }, - { - "authors": "Leonard B. Weiner" - }, - { - "authors": "Heather Wood" - }, - { - "authors": "Anne B. Yates" - }, - { - "authors": "Jennifer M. Puck" - }, - { - "date": "2014/08/20" - }, - { - "volume": "312" - }, - { - "issue": "7" - }, - { - "firstpage": "729" - }, - { - "lastpage": "738" - }, - { - "doi": "10.1001/jama.2014.9132" - }, - { - "journal": "JAMA" - }, - { - "abstract": "Importance \n Newborn screening for severe combined immunodeficiency (SCID) using assays to detect T-cell receptor excision circles (TRECs) began in Wisconsin in 2008, and SCID was added to the national recommended uniform panel for newborn screened disorders in 2010. Currently 23 states, the District of Columbia, and the Navajo Nation conduct population-wide newborn screening for SCID. The incidence of SCID is estimated at 1 in 100 000 births.Objectives \n To present data from a spectrum of SCID newborn screening programs, establish population-based incidence for SCID and other conditions with T-cell lymphopenia, and document early institution of effective treatments.Design \n Epidemiological and retrospective observational study.Setting \n Representatives in states conducting SCID newborn screening were invited to submit their SCID screening algorithms, test performance data, and deidentified clinical and laboratory information regarding infants screened and cases with nonnormal results. Infants born from the start of each participating program from January 2008 through the most recent evaluable date prior to July 2013 were included. Representatives from 10 states plus the Navajo Area Indian Health Service contributed data from 3 030 083 newborns screened with a TREC test.Main Outcomes and Measures \n Infants with SCID and other diagnoses of T-cell lymphopenia were classified. Incidence and, where possible, etiologies were determined. Interventions and survival were tracked.Results \n Screening detected 52 cases of typical SCID, leaky SCID, and Omenn syndrome, affecting 1 in 58 000 infants (95% CI, 1/46 000-1/80 000). Survival of SCID-affected infants through their diagnosis and immune reconstitution was 87% (45/52), 92% (45/49) for infants who received transplantation, enzyme replacement, and/or gene therapy. Additional interventions for SCID and non-SCID T-cell lymphopenia included immunoglobulin infusions, preventive antibiotics, and avoidance of live vaccines. Variations in definitions and follow-up practices influenced the rates of detection of non-SCID T-cell lymphopenia.Conclusions and Relevance \n Newborn screening in 11 programs in the United States identified SCID in 1 in 58 000 infants, with high survival. The usefulness of detection of non-SCID T-cell lymphopenias by the same screening remains to be determined." - }, - { - "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/930672/joi140101.pdf" - }, - { - "joi140101.pdf": "2a774d4c1d2b03c863402ba9eb1d80f8" - }, - { - "rendered.html": "76bd4d703e2bbd945ec4b2eda057f242" - } - ], - "http://jama.jamanetwork.com/article.aspx?articleid=221033": [ - { - "publisher": "American Medical Association" - }, - { - "title": "Association Between Time to Initiation of Adjuvant Chemotherapy and Survival in Colorectal Cancer: A Systematic Review and Meta-analysis" - }, - { - "authors": "James J. Biagi" - }, - { - "authors": "Michael J. Raphael" - }, - { - "authors": "William J. Mackillop" - }, - { - "authors": "Weidong Kong" - }, - { - "authors": "Will D. King" - }, - { - "authors": "Christopher M. Booth" - }, - { - "date": "2011/06/08" - }, - { - "volume": "305" - }, - { - "issue": "22" - }, - { - "firstpage": "2335" - }, - { - "lastpage": "2342" - }, - { - "doi": "10.1001/jama.2011.749" - }, - { - "journal": "JAMA" - }, - { - "abstract": "Context Adjuvant chemotherapy (AC) improves survival among patients with resected colorectal cancer. However, the optimal timing from surgery to initiation of AC is unknown.Objective To determine the relationship between time to AC and survival outcomes via a systematic review and meta-analysis.Data Sources MEDLINE (1975 through January 2011), EMBASE, the Cochrane Database of Systematic Reviews, and the Cochrane Central Register of Controlled Trials were searched to identify studies that described the relationship between time to AC and survival.Study Selection Studies were only included if the relevant prognostic factors were adequately described and either comparative groups were balanced or results adjusted for these prognostic factors.Data Extraction \n Hazard ratios (HRs) for overall survival and disease-free survival from each study were converted to a regression coefficient (β) and standard error corresponding to a continuous representation per 4 weeks of time to AC. The adjusted β from individual studies were combined using a fixed-effects model. Inverse variance (1/SE2) was used to weight individual studies. Publication bias was investigated using the trim and fill approach.\n Results We identified 10 eligible studies involving 15 410 patients (7 published articles, 3 abstracts). Nine of the studies were cohort or population based and 1 was a secondary analysis from a randomized trial of chemotherapy. Six studies reported time to AC as a binary variable and 4 as 3 or more categories. Meta-analysis demonstrated that a 4-week increase in time to AC was associated with a significant decrease in both overall survival (HR, 1.14; 95% confidence interval [CI], 1.10-1.17) and disease-free survival (HR, 1.14; 95% CI, 1.10-1.18). There was no significant heterogeneity among included studies. Results remained significant after adjustment for potential publication bias and when the analysis was repeated to exclude studies of largest weight.Conclusion In a meta-analysis of the available literature on time to AC, longer time to AC was associated with worse survival among patients with resected colorectal cancer." - }, - { - "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/20331/jrv15007_2335_2342.pdf" - }, - { - "supplementary_material": "/data/Journals/JAMA/20331/JWE15064_06_08_2011.pdf" - }, - { - "JWE15064_06_08_2011.pdf": "ee00ef66577d6d30aedb1c1fe7b20c69" - }, - { - "rendered.html": "892832b400e732b714a583074c0fed6a" - } - ], - "http://jama.jamanetwork.com/article.aspx?articleid=397582": [ - { - "publisher": "American Medical Association" - }, - { - "title": "Comparison of Warfarin and External Pneumatic Compression in Prevention of Venous Thrombosis After Total Hip Replacement" - }, - { - "authors": "Charles W. Francis" - }, - { - "authors": "Vincent D. Pellegrini" - }, - { - "authors": "Victor J. Marder" - }, - { - "authors": "Saara Totterman" - }, - { - "authors": "Carl M. Harris" - }, - { - "authors": "K. Ruben Gabriel" - }, - { - "authors": "Michael V. Azodo" - }, - { - "authors": "Kristin M. Leibert" - }, - { - "date": "1992/06/03" - }, - { - "volume": "267" - }, - { - "issue": "21" - }, - { - "firstpage": "2911" - }, - { - "lastpage": "2915" - }, - { - "doi": "10.1001/jama.1992.03480210073035" - }, - { - "journal": "JAMA" - }, - { - "abstract": "Objective. \n —To compare the effectiveness and safety of warfarin and external pneumatic compression (EPC) in prevention of venous thrombosis after total hip replacement.Design. \n —Prospective, randomized trial in consecutive patients, with blinded assessment of the primary end point.Setting. \n —University medical center and large community hospital.Patients. \n —Patients over age 18 years scheduled for elective primary total hip replacement were eligible. Of 254 patients interviewed, 232 were randomized, 220 patients had surgery and received prophylaxis, and 201 had venography.Interventions. \n —Patients were randomly assigned to prophylaxis with a device providing bilateral sequential EPC to both the calf and thigh or to receive warfarin in a low-intensity regimen beginning 10 to 14 days preoperatively. Prophylaxis was continued until venography.Main Outcome Measures. \n —Venous thrombosis was diagnosed by venography between postoperative days 6 and 8. Bleeding was assessed by surgical blood loss, transfusion requirements, changes in hematocrit, and clinically identified bleeding complications.Results. \n —The total incidence of venous thrombosis was virtually the same in the warfarin and EPC groups (31% vs 27%), but the distribution of thrombi was different. Proximal thrombosis occurred in 12% of patients in the EPC group compared with only 3% in the warfarin group (P=.012, 95% confidence interval for difference, 2% to 18%). In contrast, calf vein thrombosis was more frequent in the warfarin group (21%) than in the EPC group (12%) (P=.021,95% confidence interval for difference, 0% to 18%). Most proximal thrombi in EPC-treated patients were located within 15 cm of the femoral head and were not continuous with thrombi in deep calf veins. The high incidence of proximal thrombosis in the EPC group resulted in termination of the study by the safety monitoring committee. Blood loss and bleeding complications were similar in the two groups.Conclusion. \n —Warfarin therapy is significantly more effective than EPC in preventing serious proximal vein thrombosis after total hip replacement. The greater effectiveness of warfarin therapy in preventing proximal vein thrombi and of EPC in preventing thrombosis in the calf suggests that there are differences in the pathogenesis of thrombosis in these two locations.(JAMA. 1992;267:2911-2915)" - }, - { - "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/9595/jama_267_21_035.pdf" - }, - { - "jama_267_21_035.pdf": "470c33ae1ab47eec10a5ef53f43243a4" - }, - { - "rendered.html": "0e58eeed8c635bd69b83c3f1d4ef74b8" - } - ], - "http://jama.jamanetwork.com/article.aspx?articleid=346304": [ - { - "publisher": "American Medical Association" - }, - { - "title": "Skeletal Complications in a Series of Human Renal Allografts" - }, - { - "authors": "Michael C. Hall" - }, - { - "authors": "Stanley M. Elmore" - }, - { - "authors": "Robert W. Bright" - }, - { - "authors": "James C. Pierce" - }, - { - "authors": "David M. Hume" - }, - { - "date": "1969/06/09" - }, - { - "volume": "208" - }, - { - "issue": "10" - }, - { - "firstpage": "1825" - }, - { - "lastpage": "1829" - }, - { - "doi": "10.1001/jama.1969.03160100015004" - }, - { - "journal": "JAMA" - }, - { - "abstract": "Between August 1962 and May 1968, 140 renal transplantations were performed. Of the patients in this series, prior to transplantation, three were found with severe epiphysiolyses of the femoral heads, one with stress fractures of the femoral necks, and three with avascular necrosis of the femoral heads. It is suggested that these deformities should be stabilized as in other children. After transplantation, avascular necrosis of a femoral head or condyle developed in six patients. The cause is unknown but is believed related to the use of prednisone. Three infections of bone or joint have occurred." - }, - { - "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/8452/jama_208_10_004.pdf" - }, - { - "jama_208_10_004.pdf": "afd66c7a906d0b5d9a7d10f397fb4ae5" - }, - { - "rendered.html": "a495d539c00336470afa4d9db272b7c6" - } - ], - "http://jama.jamanetwork.com/article.aspx?articleid=1900512": [ - { - "publisher": "American Medical Association" - }, - { - "title": "Use of and Mortality After Bilateral Mastectomy Compared With Other Surgical Treatments for Breast Cancer in California, 1998-2011" - }, - { - "authors": "Allison W. Kurian" - }, - { - "authors": "Daphne Y. Lichtensztajn" - }, - { - "authors": "Theresa H. M. Keegan" - }, - { - "authors": "David O. Nelson" - }, - { - "authors": "Christina A. Clarke" - }, - { - "authors": "Scarlett L. Gomez" - }, - { - "date": "2014/09/03" - }, - { - "volume": "312" - }, - { - "issue": "9" - }, - { - "firstpage": "902" - }, - { - "lastpage": "914" - }, - { - "doi": "10.1001/jama.2014.10707" - }, - { - "journal": "JAMA" - }, - { - "abstract": "Importance \n Bilateral mastectomy is increasingly used to treat unilateral breast cancer. Because it may have medical and psychosocial complications, a better understanding of its use and outcomes is essential to optimizing cancer care.Objective \n To compare use of and mortality after bilateral mastectomy, breast-conserving therapy with radiation, and unilateral mastectomy.Design, Setting, and Participants \n Observational cohort study within the population-based California Cancer Registry; participants were women diagnosed with stages 0-III unilateral breast cancer in California from 1998 through 2011, with median follow-up of 89.1 months.Main Outcomes and Measures \n Factors associated with surgery use (from polytomous logistic regression); overall and breast cancer–specific mortality (from propensity score weighting and Cox proportional hazards analysis).Results \n Among 189 734 patients, the rate of bilateral mastectomy increased from 2.0% (95% CI, 1.7%-2.2%) in 1998 to 12.3% (95% CI, 11.8%-12.9%) in 2011, an annual increase of 14.3% (95% CI, 13.1%-15.5%); among women younger than 40 years, the rate increased from 3.6% (95% CI, 2.3%-5.0%) in 1998 to 33% (95% CI, 29.8%-36.5%) in 2011. Bilateral mastectomy was more often used by non-Hispanic white women, those with private insurance, and those who received care at a National Cancer Institute (NCI)–designated cancer center (8.6% [95% CI, 8.1%-9.2%] among NCI cancer center patients vs 6.0% [95% CI, 5.9%-6.1%] among non-NCI cancer center patients; odds ratio [OR], 1.13 [95% CI, 1.04-1.22]); in contrast, unilateral mastectomy was more often used by racial/ethnic minorities (Filipina, 52.8% [95% CI, 51.6%-54.0%]; OR, 2.00 [95% CI, 1.90-2.11] and Hispanic, 45.6% [95% CI, 45.0%-46.2%]; OR, 1.16 [95% CI, 1.13-1.20] vs non-Hispanic white, 35.2% [95% CI, 34.9%-35.5%]) and those with public/Medicaid insurance (48.4% [95% CI, 47.8%-48.9%]; OR, 1.08 [95% CI, 1.05-1.11] vs private insurance, 36.6% [95% CI, 36.3%-36.8%]). Compared with breast-conserving surgery with radiation (10-year mortality, 16.8% [95% CI, 16.6%-17.1%]), unilateral mastectomy was associated with higher all-cause mortality (hazard ratio [HR], 1.35 [95% CI, 1.32-1.39]; 10-year mortality, 20.1% [95% CI, 19.9%-20.4%]). There was no significant mortality difference compared with bilateral mastectomy (HR, 1.02 [95% CI, 0.94-1.11]; 10-year mortality, 18.8% [95% CI, 18.6%-19.0%]). Propensity analysis showed similar results.Conclusions and Relevance \n Use of bilateral mastectomy increased significantly throughout California from 1998 through 2011 and was not associated with lower mortality than that achieved with breast-conserving surgery plus radiation. Unilateral mastectomy was associated with higher mortality than were the other 2 surgical options." - }, - { - "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/930710/joi140111.pdf" - }, - { - "supplementary_material": "/data/Journals/JAMA/930710/JOI140111supp1_prod.pdf" - }, - { - "JOI140111supp1_prod.pdf": "9ea1385918727382384248cda7a17f8a" - }, - { - "rendered.html": "c878e816f3cc71b5da1112f9402fe3dd" - } - ], - "http://jama.jamanetwork.com/article.aspx?articleid=1900503": [ - { - "publisher": "American Medical Association" - }, - { - "title": "Regulation and Comparative Effectiveness Research—Reply" - }, - { - "authors": "Richard Platt" - }, - { - "authors": "Nancy E. Kass" - }, - { - "authors": "Deven McGraw" - }, - { - "date": "2014/09/03" - }, - { - "volume": "312" - }, - { - "issue": "9" - }, - { - "firstpage": "964" - }, - { - "lastpage": "964" - }, - { - "doi": "10.1001/jama.2014.7667" - }, - { - "journal": "JAMA" - }, - { - "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/930710/jlr140062.pdf" - }, - { - "jlr140062.pdf": "eea70173d47fcecec5a172608459f0ee" - }, - { - "rendered.html": "572129b8a81299e0b2e60c04a7cef7bf" - } - ], - "http://jama.jamanetwork.com/article.aspx?articleid=1900482": [ - { - "title": "Colchicine for Prevention of Postpericardiotomy Syndrome and Postoperative Atrial Fibrillation: The COPPS-2 Randomized Clinical Trial" - }, - { - "authors": "Massimo Imazio" - }, - { - "authors": "Antonio Brucato" - }, - { - "authors": "Paolo Ferrazzi" - }, - { - "authors": "Alberto Pullara" - }, - { - "authors": "Yehuda Adler" - }, - { - "authors": "Alberto Barosi" - }, - { - "authors": "Alida L. Caforio" - }, - { - "authors": "Roberto Cemin" - }, - { - "authors": "Fabio Chirillo" - }, - { - "authors": "Chiara Comoglio" - }, - { - "authors": "Diego Cugola" - }, - { - "authors": "Davide Cumetti" - }, - { - "authors": "Oleksandr Dyrda" - }, - { - "authors": "Stefania Ferrua" - }, - { - "authors": "Yaron Finkelstein" - }, - { - "authors": "Roberto Flocco" - }, - { - "authors": "Anna Gandino" - }, - { - "authors": "Brian Hoit" - }, - { - "authors": "Francesco Innocente" - }, - { - "authors": "Silvia Maestroni" - }, - { - "authors": "Francesco Musumeci" - }, - { - "authors": "Jae Oh" - }, - { - "authors": "Amedeo Pergolini" - }, - { - "authors": "Vincenzo Polizzi" - }, - { - "authors": "Arsen Ristić" - }, - { - "authors": "Caterina Simon" - }, - { - "authors": "David H Spodick" - }, - { - "authors": "Vincenzo Tarzia" - }, - { - "authors": "Stefania Trimboli" - }, - { - "authors": "Anna Valenti" - }, - { - "authors": "Riccardo Belli" - }, - { - "authors": "Fiorenzo Gaita" - }, - { - "authors": " " - }, - { - "firstpage": "" - }, - { - "lastpage": "" - }, - { - "doi": "10.1001/jama.2014.11026" - }, - { - "journal": "JAMA" - }, - { - "abstract": "Importance \n Postpericardiotomy syndrome, postoperative atrial fibrillation (AF), and postoperative effusions may be responsible for increased morbidity and health care costs after cardiac surgery. Postoperative use of colchicine prevented these complications in a single trial.Objective \n To determine the efficacy and safety of perioperative use of oral colchicine in reducing postpericardiotomy syndrome, postoperative AF, and postoperative pericardial or pleural effusions.Design, Setting, and Participants \n Investigator-initiated, double-blind, placebo-controlled, randomized clinical trial among 360 consecutive candidates for cardiac surgery enrolled in 11 Italian centers between March 2012 and March 2014. At enrollment, mean age of the trial participants was 67.5 years (SD, 10.6 years), 69% were men, and 36% had planned valvular surgery. Main exclusion criteria were absence of sinus rhythm at enrollment, cardiac transplantation, and contraindications to colchicine.Interventions \n Patients were randomized to receive placebo (n=180) or colchicine (0.5 mg twice daily in patients ≥70 kg or 0.5 mg once daily in patients <70 kg; n=180) starting between 48 and 72 hours before surgery and continued for 1 month after surgery.Main Outcomes and Measures \n Occurrence of postpericardiotomy syndrome within 3 months; main secondary study end points were postoperative AF and pericardial or pleural effusion.Results \n The primary end point of postpericardiotomy syndrome occurred in 35 patients (19.4%) assigned to colchicine and in 53 (29.4%) assigned to placebo (absolute difference, 10.0%; 95% CI, 1.1%-18.7%; number needed to treat = 10). There were no significant differences between the colchicine and placebo groups for the secondary end points of postoperative AF (colchicine, 61 patients [33.9%]; placebo, 75 patients [41.7%]; absolute difference, 7.8%; 95% CI, −2.2% to 17.6%) or postoperative pericardial/pleural effusion (colchicine, 103 patients [57.2%]; placebo, 106 patients [58.9%]; absolute difference, 1.7%; 95% CI, −8.5% to 11.7%), although there was a reduction in postoperative AF in the prespecified on-treatment analysis (placebo, 61/148 patients [41.2%]; colchicine, 38/141 patients [27.0%]; absolute difference, 14.2%; 95% CI, 3.3%-24.7%). Adverse events occurred in 21 patients (11.7%) in the placebo group vs 36 (20.0%) in the colchicine group (absolute difference, 8.3%; 95% CI; 0.76%-15.9%; number needed to harm = 12), but discontinuation rates were similar. No serious adverse events were observed.Conclusions and Relevance \n Among patients undergoing cardiac surgery, perioperative use of colchicine compared with placebo reduced the incidence of postpericardiotomy syndrome but not of postoperative AF or postoperative pericardial/pleural effusion. The increased risk of gastrointestinal adverse effects reduced the potential benefits of colchicine in this setting.Trial Registration \n clinicaltrials.gov Identifier: NCT01552187" - }, - { - "fulltext_pdf": "http://jama.jamanetwork.com/data/Journals/JAMA/0/joi140113.pdf" - }, - { - "supplementary_material": "/data/Journals/JAMA/0/JOI140113supp1_prod.pdf" - }, - { - "supplementary_material": "/data/Journals/JAMA/0/JOI140113supp2_prod.pdf" - }, - { - "JOI140113supp2_prod.pdf": "4fc349d4f4b363dabb9578e8f5016a39" - }, - { - "rendered.html": "471ffa98e8b61da776545161240a1929" - } - ], - "http://archneur.jamanetwork.com/article.aspx?articleid=1875833": [ - { - "publisher": "American Medical Association" - }, - { - "title": "Effect of 1 Night of Total Sleep Deprivation on Cerebrospinal Fluid β-Amyloid 42 in Healthy Middle-Aged Men: A Randomized Clinical Trial" - }, - { - "authors": "Sharon Ooms" - }, - { - "authors": "Sebastiaan Overeem" - }, - { - "authors": "Kees Besse" - }, - { - "authors": "Marcel Olde Rikkert" - }, - { - "authors": "Marcel Verbeek" - }, - { - "authors": "Jurgen A. H. R. Claassen" - }, - { - "date": "2014/08/01" - }, - { - "volume": "71" - }, - { - "issue": "8" - }, - { - "firstpage": "971" - }, - { - "lastpage": "977" - }, - { - "doi": "10.1001/jamaneurol.2014.1173" - }, - { - "journal": "JAMA Neurology" - }, - { - "abstract": "Importance \n Increasing evidence suggests a relationship between poor sleep and the risk of developing Alzheimer disease. A previous study found an effect of sleep on β-amyloid (Aβ), which is a key protein in Alzheimer disease pathology.Objective \n To determine the effect of 1 night of total sleep deprivation on cerebrospinal fluid Aβ42 protein levels in healthy middle-aged men.Design, Setting, and Participants \n The Alzheimer, Wakefulness, and Amyloid Kinetics (AWAKE) study at the Radboud Alzheimer Center, a randomized clinical trial that took place between June 1, 2012, and October 1, 2012. Participants were cognitively normal middle-aged men (40-60 years of age) with normal sleep (n = 26) recruited from the local population.Interventions \n Participants were randomized to 1 night with unrestricted sleep (n = 13) or 1 night of total sleep deprivation (24 hours of wakefulness) (n = 13).Main Outcomes and Measures \n Sleep was monitored using continuous polysomnographic recording from 3 pm until 10 am. Cerebrospinal fluid samples were collected using an intrathecal catheter at defined times to compare cerebral Aβ42 concentrations between evening and morning.Results \n A night of unrestricted sleep led to a 6% decrease in Aβ42 levels of 25.3 pg/mL (95% CI [0.94, 49.6], P = .04), whereas sleep deprivation counteracted this decrease. When accounting for the individual trajectories of Aβ42 over time, a difference of 75.8 pg/mL of Aβ42 was shown between the unrestricted sleep and sleep deprivation group (95% CI [3.4, 148.4], P = .04). The individual trajectories of evening and morning Aβ42 concentrations differed between the unrestricted sleep and sleep deprivation groups (P = .04) in contrast to stable Aβ40, tau, and total protein levels.Conclusions and Relevance \n Sleep deprivation, or prolonged wakefulness, interferes with a physiological morning decrease in Aβ42. We hypothesize that chronic sleep deprivation increases cerebral Aβ42 levels, which elevates the risk of Alzheimer disease.Trial Registration \n clinicaltrials.gov Identifier: NCT01194713" - }, - { - "fulltext_pdf": "http://archneur.jamanetwork.com/data/Journals/NEUR/930612/noi140040.pdf" - }, - { - "noi140040.pdf": "bdcb16f6f241a62ed954d7947ba628a1" - }, - { - "rendered.html": "e0fdc7f214ce57a8a710d4da425cf135" - } - ], - "http://archsurg.jamanetwork.com/article.aspx?articleid=1899998": [ - { - "title": "Mandated Self-reporting of Ventilator-Associated Pneumonia Bundle and Catheter-Related Bloodstream Infection Bundle Compliance and Infection Rates" - }, - { - "authors": "Ryan A. Helmick" - }, - { - "authors": "Meredith L. Knofsky" - }, - { - "authors": "Carla C. Braxton" - }, - { - "authors": "Anuradha Subramanian" - }, - { - "authors": "Patricia Byers" - }, - { - "authors": "Charlie K. W. Lan" - }, - { - "authors": "Samir S. Awad" - }, - { - "firstpage": "" - }, - { - "lastpage": "" - }, - { - "doi": "10.1001/jamasurg.2014.1627" - }, - { - "journal": "JAMA Surgery" - }, - { - "abstract": "Importance \n As quality measures increasingly become tied to payment, evaluating the most effective ways to provide high-quality care becomes more important.Objectives \n To determine whether mandated reporting for ventilator and catheter bundle compliance is correlated with decreased infection rates, and to determine whether labor-intensive audits are correlated with compliance.Design, Setting, and Participants \n Multiyear retrospective review of aggregated data from all patients admitted to 15 intensive care units in a Veterans Affairs hospital setting (the Veterans Integrated Service Network 16) from 2009 to 2011.Exposures \n Ventilator-associated pneumonia and catheter-related bloodstream infections.Main Outcomes and Measures \n Mean rates of ventilator-associated pneumonia and catheter-related bloodstream infection were analyzed by year. Relationships between infection rates, self-reported compliance, and audits were analyzed by Pearson correlation.Results \n During the study period, ventilator-associated pneumonia decreased from 2.50 to 1.60 infections per 1000 ventilator days (P = .07). The rate of pneumonia was not correlated with self-reported compliance overall (R = 0.19) or by individual year (2009, R = 0.30; 2010, R = 0.24; 2011, R = 0.46); there was a correlation in cardiac intensive care units (R = −0.70) but not other types of intensive care units (mixed, R = −0.18; medical, R = 0.42; surgical, R = 0.34). Catheter-related bloodstream infections decreased from 2.38 to 0.73 infections per 1000 catheter days (P = .04). The rate of catheter infection was not correlated with self-reported compliance overall (R = −0.18), by individual year (2009, R = −0.39; 2010, R = −0.42; 2011, R = 0.37), or by intensive care unit type (mixed, R = −0.19; cardiac, R = 0.55; medical, R = 0.17; surgical, R = −0.44).Conclusions and Relevance \n Current mandated self-reported compliance and audit measures are poorly correlated with decreased ventilator-associated pneumonia or catheter-related bloodstream infection." - }, - { - "fulltext_pdf": "http://archsurg.jamanetwork.com/data/Journals/SURG/0/soi140073.pdf" - }, - { - "rendered.html": "014dc2d0425809f290ac1f2acec8079d" - }, - { - "soi140073.pdf": "bc0e2a5d35a1fe64be6c69d3e641a521" - } - ], - "http://archinte.jamanetwork.com/article.aspx?articleid=1899761": [ - { - "title": "Association of Treatment With Carvedilol vs Metoprolol Succinate and Mortality in Patients With Heart Failure" - }, - { - "authors": "Björn Pasternak" - }, - { - "authors": "Henrik Svanström" - }, - { - "authors": "Mads Melbye" - }, - { - "authors": "Anders Hviid" - }, - { - "firstpage": "" - }, - { - "lastpage": "" - }, - { - "doi": "10.1001/jamainternmed.2014.3258" - }, - { - "journal": "JAMA Internal Medicine" - }, - { - "abstract": "Importance \n The β-blockers carvedilol and metoprolol succinate both reduce mortality in patients with heart failure (HF), but the comparative clinical effectiveness of these drugs is unknown.Objective \n To investigate whether carvedilol is associated with improved survival compared with metoprolol succinate.Design, Setting, and Participants \n Cohort study of patients with incident HF with reduced left ventricular ejection fraction (LVEF) (≤40%) who received carvedilol (n = 6026) or metoprolol succinate (n = 5638) using data from a Danish national HF registry linked with health care and administrative databases. Main Outcomes and Measures \n All-cause mortality (primary outcome) and cardiovascular mortality (secondary outcome) were analyzed using Cox regression with adjustment for a propensity score, derived from a range of clinical, socioeconomic, and demographic characteristics.Results \n The mean (SD) age of the patients was 69.3 (9.1) years, 71% were men, and 51% were hospitalized at index HF diagnosis. During a median (interquartile range) 2.4 (1.0-3.0) years of follow-up, 875 carvedilol users and 754 metoprolol users died; the cumulative incidence of mortality was 18.3% and 18.8%, respectively. The adjusted hazard ratio for carvedilol users vs metoprolol users was 0.99 (95% CI, 0.88 to 1.11), corresponding to an absolute risk difference of –0.07 (95% CI, –0.84 to 0.77) deaths per 100 person-years. Estimates were consistent across subgroup analyses by sex, age, levels of LVEF, New York Heart Association classification, and history of ischemic heart disease. A higher proportion of carvedilol users achieved the recommended daily target dose (50 mg; 3124 [52%]) than did metoprolol users (200 mg; 689 [12%]); among patients who reached the target dose, the adjusted hazard ratio was 0.97 (95% CI, 0.72-1.30). A robustness analysis with 1:1 propensity score matching confirmed the primary findings (hazard ratio, 0.97 [95% CI, 0.84-1.13]). The adjusted hazard ratio for cardiovascular mortality was 1.05 (95% CI, 0.88-1.26).Conclusions and Relevance \n These findings from real-world clinical practice indicate that the effectiveness of carvedilol and metoprolol succinate in patients with HF is similar." - }, - { - "fulltext_pdf": "http://archinte.jamanetwork.com/data/Journals/INTEMED/0/ioi140062.pdf" - }, - { - "ioi140062.pdf": "c15954aa524d174e32fcf4b7f2ebbd44" - }, - { - "rendered.html": "ebd00d779c609998c3c63a80889ec3bb" - } - ], - "http://archneurpsyc.jamanetwork.com/article.aspx?articleid=652906": [ - { - "publisher": "American Medical Association" - }, - { - "title": "Penicillin Treatment of General Paresis (Dementia Paralytica): Results of Treatment in 1,086 Patients the Majority of Whom Were Followed for More Than Five Years" - }, - { - "authors": "RICHARD D. HAHN" - }, - { - "authors": "BRUCE WEBSTER" - }, - { - "authors": "GEORGE WEICKHARDT" - }, - { - "authors": "EVAN THOMAS" - }, - { - "authors": "WILLIAM TIMBERLAKE" - }, - { - "authors": "HARRY SOLOMON" - }, - { - "authors": "JOHN H. STOKES" - }, - { - "authors": "JOSEPH EARLE MOORE" - }, - { - "authors": "ALBERT HEYMAN" - }, - { - "authors": "GEORGE GAMMON" - }, - { - "authors": "GERALDINE A. GLEESON" - }, - { - "authors": "ARTHUR C. CURTIS" - }, - { - "authors": "JOHN C. CUTLER" - }, - { - "date": "1959/05/01" - }, - { - "volume": "81" - }, - { - "issue": "5" - }, - { - "firstpage": "557" - }, - { - "lastpage": "590" - }, - { - "doi": "10.1001/archneurpsyc.1959.02340170023003" - }, - { - "journal": "A.M.A. Archives of Neurology & Psychiatry" - }, - { - "abstract": "Introduction \n This paper is a cooperative report of the clinical, spinal fluid, and serologic findings in a group of 1,086 patients with general paresis (dementia paralytica) treated with penicillin with or without fever therapy at eight different hospitals. A detailed account of the formation and function of this cooperative clinical study has been given previously as an introduction to the presentation of the group experience in treatment of asymptomatic central nervous system syphilis.1Shortly after the effectiveness of penicillin in the treatment of early syphilis was reported, various investigators began to study the efficacy of this new antibiotic in the treatment of central nervous system syphilis. These investigations were supported in part by grants from the Office of Scientific Research and Development, the National Institutes of Health, and the Division of Venereal Disease, U. S. Public Health Service. The findings of the individual investigators have provided much of the" - }, - { - "fulltext_pdf": "http://archneurpsyc.jamanetwork.com/data/Journals/NEURPSYCH/18617/archneurpsyc_81_5_003.pdf" - }, - { - "archneurpsyc_81_5_003.pdf": "1277c698578bda37fe5664516b975c20" - }, - { - "rendered.html": "9cb6a3cbcad113ea0f4b68428e2f9c9d" - } - ] -} \ No newline at end of file diff --git a/test/jama_test_urls.txt b/test/jama_test_urls.txt deleted file mode 100644 index 600d09b..0000000 --- a/test/jama_test_urls.txt +++ /dev/null @@ -1,13 +0,0 @@ -http://jama.jamanetwork.com/article.aspx?articleid=1456072 -http://jama.jamanetwork.com/article.aspx?articleid=1890398 -http://jama.jamanetwork.com/article.aspx?articleid=1896983 -http://jama.jamanetwork.com/article.aspx?articleid=221033 -http://jama.jamanetwork.com/article.aspx?articleid=397582 -http://jama.jamanetwork.com/article.aspx?articleid=346304 -http://jama.jamanetwork.com/article.aspx?articleid=1900512 -http://jama.jamanetwork.com/article.aspx?articleid=1900503 -http://jama.jamanetwork.com/article.aspx?articleid=1900482 -http://archneur.jamanetwork.com/article.aspx?articleid=1875833 -http://archsurg.jamanetwork.com/article.aspx?articleid=1899998 -http://archinte.jamanetwork.com/article.aspx?articleid=1899761 -http://archneurpsyc.jamanetwork.com/article.aspx?articleid=652906 \ No newline at end of file From 15bd2075f85b6b42e942d5751f1a59513df2ae89 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Thu, 2 Oct 2014 23:03:34 +0100 Subject: [PATCH 086/154] remove broken science direct scraper --- scrapers/science_direct.json | 43 ------ test/science_direct.json | 233 ------------------------------ test/science_direct_test_urls.txt | 6 - 3 files changed, 282 deletions(-) delete mode 100644 scrapers/science_direct.json delete mode 100644 test/science_direct.json delete mode 100644 test/science_direct_test_urls.txt diff --git a/scrapers/science_direct.json b/scrapers/science_direct.json deleted file mode 100644 index 30659aa..0000000 --- a/scrapers/science_direct.json +++ /dev/null @@ -1,43 +0,0 @@ -{ - "url": "sciencedirect.com", - "elements": { - "fulltext_pdf": { - "selector": "//a[@id='pdfLink']", - "attribute": "href", - "download": true - }, - "fulltext_html": { - "selector": "//meta[@name='citation_fulltext_html_url']", - "attribute": "content", - "download": true - }, - "title": { - "selector": "//h1[@class='svTitle']" - }, - "author": { - "selector": "//a[@class='authorName']" - }, - "date": { - "selector": "//meta[@name='citation_date']", - "attribute": "content" - }, - "doi": { - "selector": "//dd[@class='doiLink']/dd[@class='doi']/span" - }, - "volume": { - "selector": "//p[@class='volIssue']/a", - "patternProperties": "/Volume: ([0-9]+)/g" - }, - "issue": { - "selector": "//meta[@name='citation_issue']", - "attribute": "content" - }, - "firstpage": { - "selector": "//meta[@name='citation_firstpage']", - "attribute": "content" - }, - "abstract": { - "selector": "//div[@class='abstract svAbstract ']/p" - } - } -} diff --git a/test/science_direct.json b/test/science_direct.json deleted file mode 100644 index c86b7ec..0000000 --- a/test/science_direct.json +++ /dev/null @@ -1,233 +0,0 @@ -{ - "http://www.sciencedirect.com/science/article/pii/S2211124714004343": [ - { - "fulltext_pdf": "http://www.sciencedirect.com/science/article/pii/S2211124714004343/pdfft?md5=82ec6328cc3285896d7ac5e5cebe8648&pid=1-s2.0-S2211124714004343-main.pdf" - }, - { - "title": "Diet-Induced Alterations in Gut Microflora Contribute to Lethal Pulmonary Damage in TLR2/TLR4-Deficient Mice " - }, - { - "author": "Yewei Ji" - }, - { - "author": "Shengyi Sun" - }, - { - "author": "Julia K. Goodrich" - }, - { - "author": "Hana Kim" - }, - { - "author": "Angela C. Poole" - }, - { - "author": "Gerald E. Duhamel" - }, - { - "author": "Ruth E. Ley" - }, - { - "author": "Ling Qi" - }, - { - "doi": " DOI: 10.1016/j.celrep.2014.05.040" - }, - { - "abstract": "Chronic intake of Western diet has driven an epidemic of obesity and metabolic syndrome, but how it induces mortality remains unclear. Here, we show that chronic intake of a high-fat diet (HFD), not a low-fat diet, leads to severe pulmonary damage and mortality in mice deficient in Toll-like receptors 2 and 4 (DKO). Diet-induced pulmonary lesions are blocked by antibiotic treatment and are transmissible to wild-type mice upon either cohousing or fecal transplantation, pointing to the existence of bacterial pathogens. Indeed, diet and innate deficiency exert significant impact on gut microbiota composition. 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Mueller" - }, - { - "author": "Pascal Crépey" - }, - { - "author": "Avner Bar-Hen" - }, - { - "doi": " DOI: 10.1016/j.epidem.2014.05.001" - }, - { - "volume": "Volume 8" - }, - { - "abstract": "Drug sales data have increasingly been used for disease surveillance during recent years. Our objective was to assess the value of drug sales data as an operational early detection tool for gastroenteritis epidemics at national and regional level in France. For the period 2008–2013, we compared temporal trends of drug sales for the treatment of gastroenteritis with trends of cases reported by a Sentinel Network of general practitioners. We benchmarked detection models to select the one with the best sensitivity, false alert proportion and timeliness, and developed a prospective framework to assess the operational performance of the system. Drug sales data allowed the detection of seasonal gastrointestinal epidemics occurring in winter with a distinction between prescribed and non-prescribed drugs. Sales of non-prescribed drugs allowed epidemic detection on average 2.25 weeks earlier than Sentinel data. These results confirm the value of drug sales data for real-time monitoring of gastroenteritis epidemic activity." - } - ], - "http://www.sciencedirect.com/science/article/pii/S1755436514000206": [ - { - "fulltext_pdf": "http://www.sciencedirect.com/science/article/pii/S1755436514000206/pdfft?md5=1474e634a576549b859cea84bd8a18b2&pid=1-s2.0-S1755436514000206-main.pdf" - }, - { - "title": "OutbreakTools: A new platform for disease outbreak analysis using the R software" - }, - { - "author": "Thibaut Jombart" - }, - { - "author": "David M. Aanensen" - }, - { - "author": "Marc Baguelin" - }, - { - "author": "Paul Birrell" - }, - { - "author": "Simon Cauchemez" - }, - { - "author": "Anton Camacho" - }, - { - "author": "Caroline Colijn" - }, - { - "author": "Caitlin Collins" - }, - { - "author": "Anne Cori" - }, - { - "author": "Xavier Didelot" - }, - { - "author": "Christophe Fraser" - }, - { - "author": "Simon Frost" - }, - { - "author": "Niel Hens" - }, - { - "author": "Joseph Hugues" - }, - { - "author": "Michael Höhle" - }, - { - "author": "Lulla Opatowski" - }, - { - "author": "Andrew Rambaut" - }, - { - "author": "Oliver Ratmann" - }, - { - "author": "Samuel Soubeyrand" - }, - { - "author": "Marc A. Suchard" - }, - { - "author": "Jacco Wallinga" - }, - { - "author": "Rolf Ypma" - }, - { - "author": "Neil Ferguson" - }, - { - "doi": " DOI: 10.1016/j.epidem.2014.04.003" - }, - { - "volume": "Volume 7" - }, - { - "abstract": "The investigation of infectious disease outbreaks relies on the analysis of increasingly complex and diverse data, which offer new prospects for gaining insights into disease transmission processes and informing public health policies. However, the potential of such data can only be harnessed using a number of different, complementary approaches and tools, and a unified platform for the analysis of disease outbreaks is still lacking. In this paper, we present the new R package OutbreakTools, which aims to provide a basis for outbreak data management and analysis in R. OutbreakTools is developed by a community of epidemiologists, statisticians, modellers and bioinformaticians, and implements classes and methods for storing, handling and visualizing outbreak data. It includes real and simulated outbreak datasets. 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Teasdale" - }, - { - "author": "David Liebl" - }, - { - "doi": " DOI: 10.1016/j.mex.2014.05.002" - }, - { - "volume": "Volume 1" - }, - { - "abstract": "In contrast to phagocytosis, macropinocytosis is not directly initiated by interactions between cell surface receptors and cargo ligands, but is a result of constitutive membrane ruffling driven by dynamic remodelling of cortical actin cytoskeleton in response to stimulation of growth factor receptors. Wang et al. (2010) [13] developed a reliable assay that allows quantitative assessment of the efficiency and kinetics of macropinosome biogenesis and/or maturation in cells where the function of a targeted protein has been perturbed by pharmacological inhibitors or by knock-down or knock-out approaches. In this manuscript we describe a modified quantitative protocol to measure the rate and volume of fluid phase uptake in adherent cells. This assay:" - }, - { - "abstract": "" - }, - { - "rendered.html": "17e602d25e2a307fad746536bb2385c8" - } - ], - "http://www.sciencedirect.com/science/article/pii/S221501611400003X": [ - { - "fulltext_pdf": "http://www.sciencedirect.com/science/article/pii/S221501611400003X/pdfft?md5=7e5614118d66b8be106028e92f479c86&pid=1-s2.0-S221501611400003X-main.pdf" - }, - { - "title": "The Nav channel bench series: Plasmid preparation" - }, - { - "author": "Daniel H. Feldman" - }, - { - "author": "Christoph Lossin" - }, - { - "doi": " DOI: 10.1016/j.mex.2014.01.002" - }, - { - "volume": "Volume 1" - }, - { - "abstract": "Research involving recombinant voltage-gated sodium (Nav) channels has unique challenges. Multiple factors contribute, but undoubtedly at the top of the list is these channels’ DNA instability. Once introduced into bacterial hosts, Nav channel plasmid DNA will almost invariably emerge mutagenized and unusable, unless special conditions are adopted. This is particularly true for Nav1.1 (gene name SCN1A), Nav1.2 (SCN2A), and Nav1.6 (SCN8A), but less so for Nav1.4 (SCN4A) and Nav1.5 (SCN5A) while other Nav channel isoforms such as Nav1.7 (SCN9A) lie in between. The following recommendations for Nav plasmid DNA amplification and preparation address this problem. Three points are essential:" - }, - { - "abstract": "" - }, - { - "rendered.html": "27c831f847713528e12467b14b81eea2" - } - ] -} \ No newline at end of file diff --git a/test/science_direct_test_urls.txt b/test/science_direct_test_urls.txt deleted file mode 100644 index 46ca188..0000000 --- a/test/science_direct_test_urls.txt +++ /dev/null @@ -1,6 +0,0 @@ -http://www.sciencedirect.com/science/article/pii/S2211124714004343 -http://www.sciencedirect.com/science/article/pii/S1755436514000218 -http://www.sciencedirect.com/science/article/pii/S1755436514000206 -http://www.sciencedirect.com/science/article/pii/S2211124714004355 -http://www.sciencedirect.com/science/article/pii/S2215016114200112 -http://www.sciencedirect.com/science/article/pii/S221501611400003X From 03dfee12751d6aeaf93d063bec22767554728bbf Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Thu, 2 Oct 2014 23:04:59 +0100 Subject: [PATCH 087/154] update tests for latest quickscrape --- scripts/make_tests.rb | 9 +- test/elife.json | 1000 +++++++++++++++------------ test/mdpi.json | 1370 ++++++++++++++++++++++--------------- test/peerj.json | 1244 +++++++++++++++++++--------------- test/plos.json | 802 ++++++++++++---------- test/pnas.json | 1497 ++++++++++++++++++++++++----------------- test/rsc.json | 1453 +++++++++++++++++++++++---------------- test/test_all.rb | 5 +- 8 files changed, 4351 insertions(+), 3029 deletions(-) diff --git a/scripts/make_tests.rb b/scripts/make_tests.rb index ed15cc7..13d988b 100755 --- a/scripts/make_tests.rb +++ b/scripts/make_tests.rb @@ -68,12 +68,15 @@ results = JSON.load(File.open 'results.json') files = Dir['*'] files = files.keep_if { |f| f != 'results.json' } + file_hashes = [] files.each do |f| - results << { f => Digest::MD5.file(f).hexdigest } + file_hashes << { f => Digest::MD5.file(f).hexdigest } end + results['file_hashes'] = file_hashes + end if (index + 1) < urls.length - puts "waiting 15 seconds before next scrape" - sleep(15) + puts "waiting 5 seconds before next scrape" + sleep(5) end end # store results for this URL diff --git a/test/elife.json b/test/elife.json index 0c53d39..ba17aaf 100644 --- a/test/elife.json +++ b/test/elife.json @@ -1,417 +1,587 @@ { - "http://elifesciences.org/content/3/e03080": [ - { - "publisher": "eLife Sciences Publications Limited" - }, - { - "journal": "eLife" - }, - { - "title": "Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine" - }, - { - "authors": "Wilson Wong" - }, - { - "authors": "Xiao-chen Bai" - }, - { - "authors": "Alan Brown" - }, - { - "authors": "Israel S Fernandez" - }, - { - "authors": "Eric Hanssen" - }, - { - "authors": "Melanie Condron" - }, - { - "authors": "Yan Hong Tan" - 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}, - { - "journal": "Molecules" - }, - { - "title": "Development of Simple Sequence Repeat (SSR) Markers of Sesame (Sesamum indicum) from a Genome Survey" - }, - { - "date": "2014-04-22" - }, - { - "doi": "10.3390/molecules19045150" - }, - { - "volume": "19" - }, - { - "issue": "4" - }, - { - "firstpage": "5150" - }, - { - "description": "Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world’s population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding." - }, - { - "abstract": "Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world’s population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding." - }, - { - "fulltext_html": "http://www.mdpi.com/1420-3049/19/4/5150/htm" - }, - { - "fulltext_pdf": "http://www.mdpi.com/1420-3049/19/4/5150/pdf" - }, - { - "figure": "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g001-1024.png" - }, - { - "figure": "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g002-1024.png" - }, - { - "figure": "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g003-1024.png" - }, - { - "figure": "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g004-1024.png" - }, - { - "figure": "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g005-1024.png" - }, - { - "figure_caption": "\n Figure 1.\n Distribution of various classes of simple repeat motifs with different numbers of repeats in the sesame genome.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 2.\n (a) Percentage of different dinucleotide repeat motifs in the sesame genome. and (b) Percentage of different motifs in trinucleotide repeat motifs in the sesame genome.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 3.\n Population structure of sesame accessions. STRUCTURE was constructed by all loci. K = 2. Clusters are indicated by different colours. Samples included in all clusters are listed in Table S3.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 4.\n Phylogenetic tree of 31 sesame accessions derived from NJ analysis based on 218 SSR markers. Bootstrap values >50 are shown.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 5.\n Dendrogram of 23 sesame varieties based on 20 high polymorphism markers. Samples are listed in Table S4.\n \n Click here to enlarge figure\n \n " - }, - { - "molecules-19-05150-g004-1024.png": "f8a819eeb997cb72ac2651f6a37c1f78" - }, - { - "molecules-19-05150-g005-1024.png": "62eb6d8e24dd966f32a6124e61a0de69" - }, - { - "htm": "9c6c990abc3132b88e83d0bd78f7f95b" - }, - { - "molecules-19-05150-g002-1024.png": "94703bfe8b0b62cf8548e84f0298dd32" - }, - { - "pdf": "36fcc2bbb7d479c5542b09f6249cd262" - }, - { - "molecules-19-05150-g003-1024.png": "1e4034516b7343ad496f6b7105c512ec" - }, - { - "molecules-19-05150-g001-1024.png": "a3c4dc0eb2508db7a66a9eacb4fb387c" - }, - { - "rendered.html": "fdda905ed712b6c4698bb3a986e7cdb3" - } - ], - "http://www.mdpi.com/1420-3049/19/7/9502": [ - { - "publisher": "Multidisciplinary Digital Publishing Institute" - }, - { - "journal": "Molecules" - }, - { - "title": "Effects of Icariin on Reproductive Functions in Male Rats" - }, - { - "date": "2014-07-03" - }, - { - "doi": "10.3390/molecules19079502" - }, - { - "volume": "19" - }, - { - "issue": "7" - }, - { - "firstpage": "9502" - }, - { - "description": "The present study investigated the effects and potential mechanism(s) of action of icariin on the reproductive functions of male rats. Adult rats were treated orally with icariin at doses of 0 (control), 50, 100, or 200 mg/kg body weight for 35 consecutive days. The results show that icariin had virtually no effect on the body weight or organ coefficients of the testes or epididymides. However, 100 mg/kg icariin significantly increased epididymal sperm counts. In addition, 50 and 100 mg/kg icariin significantly increased testosterone levels. Real-time PCR suggests icariin may be involved in testosterone production via mRNA expression regulation of genes such as peripheral type benzodiazepine receptor (PBR) and steroidogenic acute regulatory protein (StAR). Furthermore, 100 mg/kg icariin treatment also affected follicle stimulating hormone receptor (FSHR) and claudin-11 mRNA expression in Sertoli cells. Superoxide dismutase (SOD) activity and malondialdehyde (MDA) levels were measured in the testes; 50 and 100 mg/kg icariin treatment improved antioxidative capacity, while 200 mg/kg icariin treatment upregulated oxidative stress. These results collectively suggest that icariin within a certain dose range is beneficial to male reproductive functions; meanwhile, higher doses of icariin may damage reproductive functions by increasing oxidative stress in the testes." - }, - { - "abstract": "The present study investigated the effects and potential mechanism(s) of action of icariin on the reproductive functions of male rats. Adult rats were treated orally with icariin at doses of 0 (control), 50, 100, or 200 mg/kg body weight for 35 consecutive days. The results show that icariin had virtually no effect on the body weight or organ coefficients of the testes or epididymides. However, 100 mg/kg icariin significantly increased epididymal sperm counts. In addition, 50 and 100 mg/kg icariin significantly increased testosterone levels. Real-time PCR suggests icariin may be involved in testosterone production via mRNA expression regulation of genes such as peripheral type benzodiazepine receptor (PBR) and steroidogenic acute regulatory protein (StAR). Furthermore, 100 mg/kg icariin treatment also affected follicle stimulating hormone receptor (FSHR) and claudin-11 mRNA expression in Sertoli cells. Superoxide dismutase (SOD) activity and malondialdehyde (MDA) levels were measured in the testes; 50 and 100 mg/kg icariin treatment improved antioxidative capacity, while 200 mg/kg icariin treatment upregulated oxidative stress. These results collectively suggest that icariin within a certain dose range is beneficial to male reproductive functions; meanwhile, higher doses of icariin may damage reproductive functions by increasing oxidative stress in the testes." - }, - { - "fulltext_pdf": "http://www.mdpi.com/1420-3049/19/7/9502/pdf" - }, - { - "pdf": "04bad9a75a92c8fd28a47c83dfbd9caa" - }, - { - "rendered.html": "026c9b22b4fa5f6dbe22c31a3435644a" - } - ], - "http://www.mdpi.com/1420-3049/12/3/290": [ - { - "publisher": "Molecular Diversity Preservation International" - }, - { - "journal": "Molecules" - }, - { - "title": "Modelingof Acetylene Pyrolysis under Steel Vacuum Carburizing Conditions in a Tubular Flow Reactor" - }, - { - "date": "2007-03-02" - }, - { - "doi": "10.3390/12030290" - }, - { - "volume": "12" - }, - { - "issue": "3" - }, - { - "firstpage": "290" - }, - { - "description": "In the present work, the pyrolysis of acetylene was studied under steel vacuumcarburizing conditions in a tubular flow reactor. The pyrolysis temperature ranged from650 °C to 1050 °C. The partial pressure of acetylene in the feed mixture was 10 and 20mbar, respectively, while the rest of the mixture consisted of nitrogen. The total pressureof the mixture was 1.6 bar. A kinetic mechanism which consists of seven species andnine reactions has been used in the commercial computational fluid dynamics (CFD)software Fluent. The species transport and reaction model of Fluent was used in thesimulations. A comparison of simulated and experimental results is presented in thispaper." - }, - { - "abstract": "In the present work, the pyrolysis of acetylene was studied under steel vacuumcarburizing conditions in a tubular flow reactor. The pyrolysis temperature ranged from650 °C to 1050 °C. The partial pressure of acetylene in the feed mixture was 10 and 20mbar, respectively, while the rest of the mixture consisted of nitrogen. The total pressureof the mixture was 1.6 bar. A kinetic mechanism which consists of seven species andnine reactions has been used in the commercial computational fluid dynamics (CFD)software Fluent. The species transport and reaction model of Fluent was used in thesimulations. A comparison of simulated and experimental results is presented in thispaper." - }, - { - "fulltext_pdf": "http://www.mdpi.com/1420-3049/12/3/290/pdf" - }, - { - "pdf": "f81f429b42f2cd8a752b50892d713ca0" - }, - { - "rendered.html": "0a598a2fd773a3873fe0667805a9d2a1" - } - ], - "http://www.mdpi.com/2077-0472/4/2/199/htm": [ - { - "publisher": "Multidisciplinary Digital Publishing Institute" - }, - { - "journal": "Agriculture" - }, - { - "title": "Rapid Development of Microsatellite Markers for Plantago ovata Forsk.: Using Next Generation Sequencing and Their Cross-Species Transferability" - }, - { - "date": "2014-06-20" - }, - { - "doi": "10.3390/agriculture4020199" - }, - { - "volume": "4" - }, - { - "issue": "2" - }, - { - "firstpage": "199" - }, - { - "description": "Isabgol (Plantago ovata Forsk.) is an important medicinal plant having high pharmacological activity in its seed husk, which is substantially used in the food, beverages and packaging industries. Nevertheless, isabgol lags behind in research, particularly for genomic resources, like molecular markers, genetic maps, etc. Presently, molecular markers can be easily developed through next generation sequencing technologies, more efficiently, cost effectively and in less time than ever before. This study was framed keeping in view the need to develop molecular markers for this economically important crop by employing a microsatellite enrichment protocol using a next generation sequencing platform (ion torrent PGM™) to obtain simple sequence repeats (SSRs) for Plantago ovata for the very first time. A total of 3447 contigs were assembled, which contained 249 SSRs. Thirty seven loci were randomly selected for primer development; of which, 30 loci were successfully amplified. The developed microsatellite markers showed the amplification of the expected size and cross-amplification in another six species of Plantago. The SSR markers were unable to show polymorphism within P. ovata, suggesting that low variability exists within genotypes of P. ovata. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing SSR markers for non-model species, and the markers so-observed could be useful in the molecular breeding of P. ovata." - }, - { - "abstract": "Isabgol (Plantago ovata Forsk.) is an important medicinal plant having high pharmacological activity in its seed husk, which is substantially used in the food, beverages and packaging industries. Nevertheless, isabgol lags behind in research, particularly for genomic resources, like molecular markers, genetic maps, etc. Presently, molecular markers can be easily developed through next generation sequencing technologies, more efficiently, cost effectively and in less time than ever before. This study was framed keeping in view the need to develop molecular markers for this economically important crop by employing a microsatellite enrichment protocol using a next generation sequencing platform (ion torrent PGM™) to obtain simple sequence repeats (SSRs) for Plantago ovata for the very first time. A total of 3447 contigs were assembled, which contained 249 SSRs. Thirty seven loci were randomly selected for primer development; of which, 30 loci were successfully amplified. The developed microsatellite markers showed the amplification of the expected size and cross-amplification in another six species of Plantago. The SSR markers were unable to show polymorphism within P. ovata, suggesting that low variability exists within genotypes of P. ovata. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing SSR markers for non-model species, and the markers so-observed could be useful in the molecular breeding of P. ovata." - }, - { - "fulltext_html": "http://www.mdpi.com/2077-0472/4/2/199/htm" - }, - { - "fulltext_pdf": "http://www.mdpi.com/2077-0472/4/2/199/pdf" - }, - { - "figure": "/agriculture/agriculture-04-00199/article_deploy/html/images/agriculture-04-00199-g001-1024.png" - }, - { - "figure": "/agriculture/agriculture-04-00199/article_deploy/html/images/agriculture-04-00199-g002-1024.png" - }, - { - "figure": "/agriculture/agriculture-04-00199/article_deploy/html/images/agriculture-04-00199-g003-1024.png" - }, - { - "figure_caption": "\n Figure 1.\n Frequency distribution of microsatellites in P. ovata based on the di-repeat and tri-repeat motif sequence types.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 2.\n Agarose gel image showing amplification patterns of SSR markers, APOM 23 and APOM 25, among six genotypes of P. ovata and allied species. M, 100 bp plus ladder (Thermo Scientific); 1, GI-3; 2: GI-2; 3, RI-89; 4, DPO13; 5, DPO13; 6, EC124345; 7, Plantago arneria; 8, Plantago coronopus; 9, Plantago psyllium; 10, Plantago indica; 11, Plantago serraria, 12, Plantago lanceolata.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 3.\n Dendrogram based on UPGMA clustering of 12 genotypes of isabgol using SSR markers.\n \n Click here to enlarge figure\n \n " - }, - { - "agriculture-04-00199-g003-1024.png": "3979c2a3fc22c8f8a04a4bd15ae55e05" - }, - { - "agriculture-04-00199-g002-1024.png": "3dee15bacd3d66f75d41d167cd833e85" - }, - { - "htm": "a37d92f2487441423d11442febf28340" - }, - { - "pdf": "3764be3556ed014d2221707bc860dba9" - }, - { - "rendered.html": "f3fd0cb07325a2e626a82e931b6d4710" - }, - { - "agriculture-04-00199-g001-1024.png": "7be1acb663571046fae8d49eeda6eeba" - } - ], - "http://www.mdpi.com/1999-4893/7/3/363": [ - { - "publisher": "Multidisciplinary Digital Publishing Institute" - }, - { - "journal": "Algorithms" - }, - { - "title": "Pressure Model of Control Valve Based on LS-SVM with the Fruit Fly Algorithm" - }, - { - "date": "2014-07-11" - }, - { - "doi": "10.3390/a7030363" - }, - { - "volume": "7" - }, - { - "issue": "3" - }, - { - "firstpage": "363" - }, - { - "description": "Control valve is a kind of essential terminal control component which is hard to model by traditional methodologies because of its complexity and nonlinearity. This paper proposes a new modeling method for the upstream pressure of control valve using the least squares support vector machine (LS-SVM), which has been successfully used to identify nonlinear system. In order to improve the modeling performance, the fruit fly optimization algorithm (FOA) is used to optimize two critical parameters of LS-SVM. As an example, a set of actual production data from a controlling system of chlorine in a salt chemistry industry is applied. The validity of LS-SVM modeling method using FOA is verified by comparing the predicted results with the actual data with a value of MSE 2.474 × 10−3. Moreover, it is demonstrated that the initial position of FOA does not affect its optimal ability. By comparison, simulation experiments based on PSO algorithm and the grid search method are also carried out. The results show that LS-SVM based on FOA has equal performance in prediction accuracy. However, from the respect of calculation time, FOA has a significant advantage and is more suitable for the online prediction." - }, - { - "abstract": "Control valve is a kind of essential terminal control component which is hard to model by traditional methodologies because of its complexity and nonlinearity. This paper proposes a new modeling method for the upstream pressure of control valve using the least squares support vector machine (LS-SVM), which has been successfully used to identify nonlinear system. In order to improve the modeling performance, the fruit fly optimization algorithm (FOA) is used to optimize two critical parameters of LS-SVM. As an example, a set of actual production data from a controlling system of chlorine in a salt chemistry industry is applied. The validity of LS-SVM modeling method using FOA is verified by comparing the predicted results with the actual data with a value of MSE 2.474 × 10−3. Moreover, it is demonstrated that the initial position of FOA does not affect its optimal ability. By comparison, simulation experiments based on PSO algorithm and the grid search method are also carried out. The results show that LS-SVM based on FOA has equal performance in prediction accuracy. However, from the respect of calculation time, FOA has a significant advantage and is more suitable for the online prediction." - }, - { - "fulltext_pdf": "http://www.mdpi.com/1999-4893/7/3/363/pdf" - }, - { - "pdf": "c24f1907c6da67ae8ed8ab4d214965cb" - }, - { - "rendered.html": "433e8866f2f35de4ff10aee12cbac396" - } - ], - "http://www.mdpi.com/2076-3425/2/3/347/htm": [ - { - "publisher": "Molecular Diversity Preservation International" - }, - { - "journal": "Brain Sciences" - }, - { - "title": "Internet and Gaming Addiction: A Systematic Literature Review of Neuroimaging Studies" - }, - { - "date": "2012-09-05" - }, - { - "doi": "10.3390/brainsci2030347" - }, - { - "volume": "2" - }, - { - "issue": "3" - }, - { - "firstpage": "347" - }, - { - "description": "In the past decade, research has accumulated suggesting that excessive Internet use can lead to the development of a behavioral addiction. Internet addiction has been considered as a serious threat to mental health and the excessive use of the Internet has been linked to a variety of negative psychosocial consequences. The aim of this review is to identify all empirical studies to date that used neuroimaging techniques to shed light upon the emerging mental health problem of Internet and gaming addiction from a neuroscientific perspective. Neuroimaging studies offer an advantage over traditional survey and behavioral research because with this method, it is possible to distinguish particular brain areas that are involved in the development and maintenance of addiction. A systematic literature search was conducted, identifying 18 studies. These studies provide compelling evidence for the similarities between different types of addictions, notably substance-related addictions and Internet and gaming addiction, on a variety of levels. On the molecular level, Internet addiction is characterized by an overall reward deficiency that entails decreased dopaminergic activity. On the level of neural circuitry, Internet and gaming addiction led to neuroadaptation and structural changes that occur as a consequence of prolonged increased activity in brain areas associated with addiction. On a behavioral level, Internet and gaming addicts appear to be constricted with regards to their cognitive functioning in various domains. The paper shows that understanding the neuronal correlates associated with the development of Internet and gaming addiction will promote future research and will pave the way for the development of addiction treatment approaches." - }, - { - "abstract": "In the past decade, research has accumulated suggesting that excessive Internet use can lead to the development of a behavioral addiction. Internet addiction has been considered as a serious threat to mental health and the excessive use of the Internet has been linked to a variety of negative psychosocial consequences. The aim of this review is to identify all empirical studies to date that used neuroimaging techniques to shed light upon the emerging mental health problem of Internet and gaming addiction from a neuroscientific perspective. Neuroimaging studies offer an advantage over traditional survey and behavioral research because with this method, it is possible to distinguish particular brain areas that are involved in the development and maintenance of addiction. A systematic literature search was conducted, identifying 18 studies. These studies provide compelling evidence for the similarities between different types of addictions, notably substance-related addictions and Internet and gaming addiction, on a variety of levels. On the molecular level, Internet addiction is characterized by an overall reward deficiency that entails decreased dopaminergic activity. On the level of neural circuitry, Internet and gaming addiction led to neuroadaptation and structural changes that occur as a consequence of prolonged increased activity in brain areas associated with addiction. On a behavioral level, Internet and gaming addicts appear to be constricted with regards to their cognitive functioning in various domains. The paper shows that understanding the neuronal correlates associated with the development of Internet and gaming addiction will promote future research and will pave the way for the development of addiction treatment approaches." - }, - { - "fulltext_html": "http://www.mdpi.com/2076-3425/2/3/347/htm" - }, - { - "fulltext_pdf": "http://www.mdpi.com/2076-3425/2/3/347/pdf" - }, - { - "htm": "46820ea8dbad57c010a030db1fb8d257" - }, - { - "pdf": "f26da200c65aee82debda1b3f00dfb45" - }, - { - "rendered.html": "022bd9be411f343674d8382633657a08" - } - ], - "http://www.mdpi.com/2073-431X/2/4/152/htm": [ - { - "publisher": "Multidisciplinary Digital Publishing Institute" - }, - { - "journal": "Computers" - }, - { - "title": "Static Three-Dimensional Fuzzy Routing Based on the Receiving Probability in Wireless Sensor Networks" - }, - { - "date": "2013-11-12" - }, - { - "doi": "10.3390/computers2040152" - }, - { - "volume": "2" - }, - { - "issue": "4" - }, - { - "firstpage": "152" - }, - { - "description": "A Wireless Sensor Network (WSN) is a collection of low-cost, low-power and large-scale wireless sensor nodes. Routing protocols are an important topic in WSN. Every sensor node should use a proper mechanism to transmit the generated packets to its destination, usually a base station. In previous works, routing protocols use the global information of the network that causes the redundant packets to be increased. Moreover, it leads to an increase in the network traffic, to a decrease in the delivery ratio of data packets, and to a reduction in network life. In this paper, we propose a new inferential routing protocol called SFRRP (Static Three-Dimensional Fuzzy Routing based on the Receiving Probability). The proposed protocol solves the above mentioned problems considerably. The data packets are transmitted by hop-to-hop delivery to the base station. It uses a fuzzy procedure to transmit the sensed data or the buffered data packets to one of the neighbors called selected node. In the proposed fuzzy system, the distance and number of neighbors are input variables, while the receiving probability is the output variable. SFRRP just uses the local neighborhood information to forward the packets and is not needed by any redundant packet for route discovery. The proposed protocol has some advantages such as a high delivery ratio, less delay time, high network life, and less network traffic. The performance of the proposed protocol surpasses the performance of the Flooding routing protocol in terms of delivery ratio, delay time and network lifetime." - }, - { - "abstract": "A Wireless Sensor Network (WSN) is a collection of low-cost, low-power and large-scale wireless sensor nodes. Routing protocols are an important topic in WSN. Every sensor node should use a proper mechanism to transmit the generated packets to its destination, usually a base station. In previous works, routing protocols use the global information of the network that causes the redundant packets to be increased. Moreover, it leads to an increase in the network traffic, to a decrease in the delivery ratio of data packets, and to a reduction in network life. In this paper, we propose a new inferential routing protocol called SFRRP (Static Three-Dimensional Fuzzy Routing based on the Receiving Probability). The proposed protocol solves the above mentioned problems considerably. The data packets are transmitted by hop-to-hop delivery to the base station. It uses a fuzzy procedure to transmit the sensed data or the buffered data packets to one of the neighbors called selected node. In the proposed fuzzy system, the distance and number of neighbors are input variables, while the receiving probability is the output variable. SFRRP just uses the local neighborhood information to forward the packets and is not needed by any redundant packet for route discovery. The proposed protocol has some advantages such as a high delivery ratio, less delay time, high network life, and less network traffic. The performance of the proposed protocol surpasses the performance of the Flooding routing protocol in terms of delivery ratio, delay time and network lifetime." - }, - { - "fulltext_html": "http://www.mdpi.com/2073-431X/2/4/152/htm" - }, - { - "fulltext_pdf": "http://www.mdpi.com/2073-431X/2/4/152/pdf" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g001-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g002-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g003-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g004-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g005-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g006-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g007-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g008-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g009-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g010-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g011-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g012-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g013-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g014-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g015-1024.png" - }, - { - "figure": "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g016-1024.png" - }, - { - "figure_caption": "\n Figure 1.\n The fuzzy value for a room temperature.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 2.\n A fuzzy logic system.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 3.\n A network model to route the data packets by Static Three-Dimensional Fuzzy Routing Based on the Receiving Probability (SFRRP) in a typical Wireless Sensor Network (WSN).\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 4.\n Memberships of the input variable distance.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 5.\n Memberships of the input variable number of neighbors.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 6.\n Memberships of the output variable receiving probability.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 7.\n Schematic of the fuzzy rules, (a) rules based on receiving probability and distance; and (b) rules based on receiving probability and number of neighbors.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 8.\n Scheme of the SFRRP functionality to choose the selected node.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 9.\n Work flow of SFRRP.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 10.\n Impact of data generation rate, (a) average delivery rate; (b) average delay; and (c) network life.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 11.\n Impact of buffer size, (a) average delivery rate; (b) average delay; and (c) network life.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 12.\n Impact of node initial energy, (a) average delivery rate; (b) average delay; and (c) network life.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 13.\n Total energy consumption of the nodes.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 14.\n The residual energy of the nodes in the proposed protocol.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 15.\n Number of live nodes.\n \n Click here to enlarge figure\n \n " - }, - { - "figure_caption": "\n Figure 16.\n Percent of filled node buffer.\n \n Click here to enlarge figure\n \n " - }, - { - "computers-02-00152-g014-1024.png": "5b0efd717600f47404abf05be4a64965" - }, - { - "computers-02-00152-g012-1024.png": "4c856d5686ffd51727c0dd8e08610f6c" - }, - { - "computers-02-00152-g016-1024.png": "a2ce86f98e0566497eef554a7629ff77" - }, - { - "computers-02-00152-g015-1024.png": "7e5a61c578e226758c2c5b3ad7e9689e" - }, - { - "computers-02-00152-g001-1024.png": "2ae71a48f49dee23127205d8c52628e7" - }, - { - "htm": "f81fd6fb069ea7a2308235b67665fb29" - }, - { - "computers-02-00152-g005-1024.png": "7c90363213d7fd98f5e7a20b08a19c80" - }, - { - "pdf": "639d60f2edf4a21b5eb4760f08c2ef18" - }, - { - "computers-02-00152-g010-1024.png": "9819440057f17feefe12b8763c3f97f7" - }, - { - "computers-02-00152-g011-1024.png": "3705c3ea855bb92556bff9587730ec98" - }, - { - "rendered.html": "c3304d0e156f1219d53a49c6f3bec52f" - }, - { - "computers-02-00152-g013-1024.png": "00bf36ffe2dcb774498fadc260ca8f7e" - }, - { - "computers-02-00152-g006-1024.png": "a30a231c7a2976768d0a5fc58f832c3b" - }, - { - "computers-02-00152-g004-1024.png": "14aade47890186768c9fa855a00cb7a6" - }, - { - "computers-02-00152-g008-1024.png": "c3bee75cde33eb4fe72b05a63510fd1a" - }, - { - "computers-02-00152-g009-1024.png": "8f41e4c7fcb10243ab992d7667f4da2a" - }, - { - "computers-02-00152-g003-1024.png": "e5814b3183dde01975554174095387c9" - }, - { - "computers-02-00152-g002-1024.png": "ef45f1466a733db20859a2d81d8adbbe" - }, - { - "computers-02-00152-g007-1024.png": "4caf09516a4b4497b31ada9ee92761ac" - } - ] + "http://www.mdpi.com/1420-3049/19/4/5150/htm": { + "publisher": { + "value": [ + "Multidisciplinary Digital Publishing Institute" + ] + }, + "journal": { + "value": [ + "Molecules" + ] + }, + "title": { + "value": [ + "Development of Simple Sequence Repeat (SSR) Markers of Sesame (Sesamum indicum) from a Genome Survey" + ] + }, + "authors": { + "value": [ + + ] + }, + "date": { + "value": [ + "2014-04-22" + ] + }, + "doi": { + "value": [ + "10.3390/molecules19045150" + ] + }, + "volume": { + "value": [ + "19" + ] + }, + "issue": { + "value": [ + "4" + ] + }, + "firstpage": { + "value": [ + "5150" + ] + }, + "description": { + "value": [ + "Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world’s population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding." + ] + }, + "abstract": { + "value": [ + "Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world’s population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding." + ] + }, + "fulltext_html": { + "value": [ + "http://www.mdpi.com/1420-3049/19/4/5150/htm" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.mdpi.com/1420-3049/19/4/5150/pdf" + ] + }, + "fulltext_xml": { + "value": [ + + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "figure": { + "value": [ + "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g001-1024.png", + "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g002-1024.png", + "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g003-1024.png", + "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g004-1024.png", + "/molecules/molecules-19-05150/article_deploy/html/images/molecules-19-05150-g005-1024.png" + ] + }, + "figure_caption": { + "value": [ + "\n Figure 1.\n Distribution of various classes of simple repeat motifs with different numbers of repeats in the sesame genome.\n \n Click here to enlarge figure\n \n ", + "\n Figure 2.\n (a) Percentage of different dinucleotide repeat motifs in the sesame genome. and (b) Percentage of different motifs in trinucleotide repeat motifs in the sesame genome.\n \n Click here to enlarge figure\n \n ", + "\n Figure 3.\n Population structure of sesame accessions. STRUCTURE was constructed by all loci. K = 2. Clusters are indicated by different colours. Samples included in all clusters are listed in Table S3.\n \n Click here to enlarge figure\n \n ", + "\n Figure 4.\n Phylogenetic tree of 31 sesame accessions derived from NJ analysis based on 218 SSR markers. Bootstrap values >50 are shown.\n \n Click here to enlarge figure\n \n ", + "\n Figure 5.\n Dendrogram of 23 sesame varieties based on 20 high polymorphism markers. Samples are listed in Table S4.\n \n Click here to enlarge figure\n \n " + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_hashes": [ + { + "fulltext.html": "c9b9618f32515dae9c9ca37ea7a57758" + }, + { + "fulltext.pdf": "36fcc2bbb7d479c5542b09f6249cd262" + }, + { + "molecules-19-05150-g001-1024.png": "a3c4dc0eb2508db7a66a9eacb4fb387c" + }, + { + "molecules-19-05150-g002-1024.png": "94703bfe8b0b62cf8548e84f0298dd32" + }, + { + "molecules-19-05150-g003-1024.png": "1e4034516b7343ad496f6b7105c512ec" + }, + { + "molecules-19-05150-g004-1024.png": "f8a819eeb997cb72ac2651f6a37c1f78" + }, + { + "molecules-19-05150-g005-1024.png": "62eb6d8e24dd966f32a6124e61a0de69" + } + ] + }, + "http://www.mdpi.com/1420-3049/19/7/9502": { + "publisher": { + "value": [ + "Multidisciplinary Digital Publishing Institute" + ] + }, + "journal": { + "value": [ + "Molecules" + ] + }, + "title": { + "value": [ + "Effects of Icariin on Reproductive Functions in Male Rats" + ] + }, + "authors": { + "value": [ + + ] + }, + "date": { + "value": [ + "2014-07-03" + ] + }, + "doi": { + "value": [ + "10.3390/molecules19079502" + ] + }, + "volume": { + "value": [ + "19" + ] + }, + "issue": { + "value": [ + "7" + ] + }, + "firstpage": { + "value": [ + "9502" + ] + }, + "description": { + "value": [ + "The present study investigated the effects and potential mechanism(s) of action of icariin on the reproductive functions of male rats. Adult rats were treated orally with icariin at doses of 0 (control), 50, 100, or 200 mg/kg body weight for 35 consecutive days. The results show that icariin had virtually no effect on the body weight or organ coefficients of the testes or epididymides. However, 100 mg/kg icariin significantly increased epididymal sperm counts. In addition, 50 and 100 mg/kg icariin significantly increased testosterone levels. Real-time PCR suggests icariin may be involved in testosterone production via mRNA expression regulation of genes such as peripheral type benzodiazepine receptor (PBR) and steroidogenic acute regulatory protein (StAR). Furthermore, 100 mg/kg icariin treatment also affected follicle stimulating hormone receptor (FSHR) and claudin-11 mRNA expression in Sertoli cells. Superoxide dismutase (SOD) activity and malondialdehyde (MDA) levels were measured in the testes; 50 and 100 mg/kg icariin treatment improved antioxidative capacity, while 200 mg/kg icariin treatment upregulated oxidative stress. These results collectively suggest that icariin within a certain dose range is beneficial to male reproductive functions; meanwhile, higher doses of icariin may damage reproductive functions by increasing oxidative stress in the testes." + ] + }, + "abstract": { + "value": [ + "The present study investigated the effects and potential mechanism(s) of action of icariin on the reproductive functions of male rats. Adult rats were treated orally with icariin at doses of 0 (control), 50, 100, or 200 mg/kg body weight for 35 consecutive days. The results show that icariin had virtually no effect on the body weight or organ coefficients of the testes or epididymides. However, 100 mg/kg icariin significantly increased epididymal sperm counts. In addition, 50 and 100 mg/kg icariin significantly increased testosterone levels. Real-time PCR suggests icariin may be involved in testosterone production via mRNA expression regulation of genes such as peripheral type benzodiazepine receptor (PBR) and steroidogenic acute regulatory protein (StAR). Furthermore, 100 mg/kg icariin treatment also affected follicle stimulating hormone receptor (FSHR) and claudin-11 mRNA expression in Sertoli cells. Superoxide dismutase (SOD) activity and malondialdehyde (MDA) levels were measured in the testes; 50 and 100 mg/kg icariin treatment improved antioxidative capacity, while 200 mg/kg icariin treatment upregulated oxidative stress. These results collectively suggest that icariin within a certain dose range is beneficial to male reproductive functions; meanwhile, higher doses of icariin may damage reproductive functions by increasing oxidative stress in the testes." + ] + }, + "fulltext_html": { + "value": [ + "http://www.mdpi.com/1420-3049/19/7/9502/htm" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.mdpi.com/1420-3049/19/7/9502/pdf" + ] + }, + "fulltext_xml": { + "value": [ + + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "figure": { + "value": [ + + ] + }, + "figure_caption": { + "value": [ + + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_hashes": [ + { + "fulltext.html": "4a583800f094eed26aeb3f929e8679cd" + }, + { + "fulltext.pdf": "04bad9a75a92c8fd28a47c83dfbd9caa" + } + ] + }, + "http://www.mdpi.com/1420-3049/12/3/290": { + "publisher": { + "value": [ + "Molecular Diversity Preservation International" + ] + }, + "journal": { + "value": [ + "Molecules" + ] + }, + "title": { + "value": [ + "Modelingof Acetylene Pyrolysis under Steel Vacuum Carburizing Conditions in a Tubular Flow Reactor" + ] + }, + "authors": { + "value": [ + + ] + }, + "date": { + "value": [ + "2007-03-02" + ] + }, + "doi": { + "value": [ + "10.3390/12030290" + ] + }, + "volume": { + "value": [ + "12" + ] + }, + "issue": { + "value": [ + "3" + ] + }, + "firstpage": { + "value": [ + "290" + ] + }, + "description": { + "value": [ + "In the present work, the pyrolysis of acetylene was studied under steel vacuumcarburizing conditions in a tubular flow reactor. The pyrolysis temperature ranged from650 °C to 1050 °C. The partial pressure of acetylene in the feed mixture was 10 and 20mbar, respectively, while the rest of the mixture consisted of nitrogen. The total pressureof the mixture was 1.6 bar. A kinetic mechanism which consists of seven species andnine reactions has been used in the commercial computational fluid dynamics (CFD)software Fluent. The species transport and reaction model of Fluent was used in thesimulations. A comparison of simulated and experimental results is presented in thispaper." + ] + }, + "abstract": { + "value": [ + "In the present work, the pyrolysis of acetylene was studied under steel vacuumcarburizing conditions in a tubular flow reactor. The pyrolysis temperature ranged from650 °C to 1050 °C. The partial pressure of acetylene in the feed mixture was 10 and 20mbar, respectively, while the rest of the mixture consisted of nitrogen. The total pressureof the mixture was 1.6 bar. A kinetic mechanism which consists of seven species andnine reactions has been used in the commercial computational fluid dynamics (CFD)software Fluent. The species transport and reaction model of Fluent was used in thesimulations. A comparison of simulated and experimental results is presented in thispaper." + ] + }, + "fulltext_html": { + "value": [ + + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.mdpi.com/1420-3049/12/3/290/pdf" + ] + }, + "fulltext_xml": { + "value": [ + + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "figure": { + "value": [ + + ] + }, + "figure_caption": { + "value": [ + + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_hashes": [ + { + "fulltext.pdf": "f81f429b42f2cd8a752b50892d713ca0" + } + ] + }, + "http://www.mdpi.com/2077-0472/4/2/199/htm": { + "publisher": { + "value": [ + "Multidisciplinary Digital Publishing Institute" + ] + }, + "journal": { + "value": [ + "Agriculture" + ] + }, + "title": { + "value": [ + "Rapid Development of Microsatellite Markers for Plantago ovata Forsk.: Using Next Generation Sequencing and Their Cross-Species Transferability" + ] + }, + "authors": { + "value": [ + + ] + }, + "date": { + "value": [ + "2014-06-20" + ] + }, + "doi": { + "value": [ + "10.3390/agriculture4020199" + ] + }, + "volume": { + "value": [ + "4" + ] + }, + "issue": { + "value": [ + "2" + ] + }, + "firstpage": { + "value": [ + "199" + ] + }, + "description": { + "value": [ + "Isabgol (Plantago ovata Forsk.) is an important medicinal plant having high pharmacological activity in its seed husk, which is substantially used in the food, beverages and packaging industries. Nevertheless, isabgol lags behind in research, particularly for genomic resources, like molecular markers, genetic maps, etc. Presently, molecular markers can be easily developed through next generation sequencing technologies, more efficiently, cost effectively and in less time than ever before. This study was framed keeping in view the need to develop molecular markers for this economically important crop by employing a microsatellite enrichment protocol using a next generation sequencing platform (ion torrent PGM™) to obtain simple sequence repeats (SSRs) for Plantago ovata for the very first time. A total of 3447 contigs were assembled, which contained 249 SSRs. Thirty seven loci were randomly selected for primer development; of which, 30 loci were successfully amplified. The developed microsatellite markers showed the amplification of the expected size and cross-amplification in another six species of Plantago. The SSR markers were unable to show polymorphism within P. ovata, suggesting that low variability exists within genotypes of P. ovata. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing SSR markers for non-model species, and the markers so-observed could be useful in the molecular breeding of P. ovata." + ] + }, + "abstract": { + "value": [ + "Isabgol (Plantago ovata Forsk.) is an important medicinal plant having high pharmacological activity in its seed husk, which is substantially used in the food, beverages and packaging industries. Nevertheless, isabgol lags behind in research, particularly for genomic resources, like molecular markers, genetic maps, etc. Presently, molecular markers can be easily developed through next generation sequencing technologies, more efficiently, cost effectively and in less time than ever before. This study was framed keeping in view the need to develop molecular markers for this economically important crop by employing a microsatellite enrichment protocol using a next generation sequencing platform (ion torrent PGM™) to obtain simple sequence repeats (SSRs) for Plantago ovata for the very first time. A total of 3447 contigs were assembled, which contained 249 SSRs. Thirty seven loci were randomly selected for primer development; of which, 30 loci were successfully amplified. The developed microsatellite markers showed the amplification of the expected size and cross-amplification in another six species of Plantago. The SSR markers were unable to show polymorphism within P. ovata, suggesting that low variability exists within genotypes of P. ovata. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing SSR markers for non-model species, and the markers so-observed could be useful in the molecular breeding of P. ovata." + ] + }, + "fulltext_html": { + "value": [ + "http://www.mdpi.com/2077-0472/4/2/199/htm" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.mdpi.com/2077-0472/4/2/199/pdf" + ] + }, + "fulltext_xml": { + "value": [ + + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "figure": { + "value": [ + "/agriculture/agriculture-04-00199/article_deploy/html/images/agriculture-04-00199-g001-1024.png", + "/agriculture/agriculture-04-00199/article_deploy/html/images/agriculture-04-00199-g002-1024.png", + "/agriculture/agriculture-04-00199/article_deploy/html/images/agriculture-04-00199-g003-1024.png" + ] + }, + "figure_caption": { + "value": [ + "\n Figure 1.\n Frequency distribution of microsatellites in P. ovata based on the di-repeat and tri-repeat motif sequence types.\n \n Click here to enlarge figure\n \n ", + "\n Figure 2.\n Agarose gel image showing amplification patterns of SSR markers, APOM 23 and APOM 25, among six genotypes of P. ovata and allied species. M, 100 bp plus ladder (Thermo Scientific); 1, GI-3; 2: GI-2; 3, RI-89; 4, DPO13; 5, DPO13; 6, EC124345; 7, Plantago arneria; 8, Plantago coronopus; 9, Plantago psyllium; 10, Plantago indica; 11, Plantago serraria, 12, Plantago lanceolata.\n \n Click here to enlarge figure\n \n ", + "\n Figure 3.\n Dendrogram based on UPGMA clustering of 12 genotypes of isabgol using SSR markers.\n \n Click here to enlarge figure\n \n " + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_hashes": [ + { + "agriculture-04-00199-g001-1024.png": "7be1acb663571046fae8d49eeda6eeba" + }, + { + "agriculture-04-00199-g002-1024.png": "3dee15bacd3d66f75d41d167cd833e85" + }, + { + "agriculture-04-00199-g003-1024.png": "3979c2a3fc22c8f8a04a4bd15ae55e05" + }, + { + "fulltext.html": "be81dea88e6558d2ae16500c3133817c" + }, + { + "fulltext.pdf": "3764be3556ed014d2221707bc860dba9" + } + ] + }, + "http://www.mdpi.com/1999-4893/7/3/363": { + "publisher": { + "value": [ + "Multidisciplinary Digital Publishing Institute" + ] + }, + "journal": { + "value": [ + "Algorithms" + ] + }, + "title": { + "value": [ + "Pressure Model of Control Valve Based on LS-SVM with the Fruit Fly Algorithm" + ] + }, + "authors": { + "value": [ + + ] + }, + "date": { + "value": [ + "2014-07-11" + ] + }, + "doi": { + "value": [ + "10.3390/a7030363" + ] + }, + "volume": { + "value": [ + "7" + ] + }, + "issue": { + "value": [ + "3" + ] + }, + "firstpage": { + "value": [ + "363" + ] + }, + "description": { + "value": [ + "Control valve is a kind of essential terminal control component which is hard to model by traditional methodologies because of its complexity and nonlinearity. This paper proposes a new modeling method for the upstream pressure of control valve using the least squares support vector machine (LS-SVM), which has been successfully used to identify nonlinear system. In order to improve the modeling performance, the fruit fly optimization algorithm (FOA) is used to optimize two critical parameters of LS-SVM. As an example, a set of actual production data from a controlling system of chlorine in a salt chemistry industry is applied. The validity of LS-SVM modeling method using FOA is verified by comparing the predicted results with the actual data with a value of MSE 2.474 × 10−3. Moreover, it is demonstrated that the initial position of FOA does not affect its optimal ability. By comparison, simulation experiments based on PSO algorithm and the grid search method are also carried out. The results show that LS-SVM based on FOA has equal performance in prediction accuracy. However, from the respect of calculation time, FOA has a significant advantage and is more suitable for the online prediction." + ] + }, + "abstract": { + "value": [ + "Control valve is a kind of essential terminal control component which is hard to model by traditional methodologies because of its complexity and nonlinearity. This paper proposes a new modeling method for the upstream pressure of control valve using the least squares support vector machine (LS-SVM), which has been successfully used to identify nonlinear system. In order to improve the modeling performance, the fruit fly optimization algorithm (FOA) is used to optimize two critical parameters of LS-SVM. As an example, a set of actual production data from a controlling system of chlorine in a salt chemistry industry is applied. The validity of LS-SVM modeling method using FOA is verified by comparing the predicted results with the actual data with a value of MSE 2.474 × 10−3. Moreover, it is demonstrated that the initial position of FOA does not affect its optimal ability. By comparison, simulation experiments based on PSO algorithm and the grid search method are also carried out. The results show that LS-SVM based on FOA has equal performance in prediction accuracy. However, from the respect of calculation time, FOA has a significant advantage and is more suitable for the online prediction." + ] + }, + "fulltext_html": { + "value": [ + + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.mdpi.com/1999-4893/7/3/363/pdf" + ] + }, + "fulltext_xml": { + "value": [ + + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "figure": { + "value": [ + + ] + }, + "figure_caption": { + "value": [ + + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_hashes": [ + { + "fulltext.pdf": "c24f1907c6da67ae8ed8ab4d214965cb" + } + ] + }, + "http://www.mdpi.com/2076-3425/2/3/347/htm": { + "publisher": { + "value": [ + "Molecular Diversity Preservation International" + ] + }, + "journal": { + "value": [ + "Brain Sciences" + ] + }, + "title": { + "value": [ + "Internet and Gaming Addiction: A Systematic Literature Review of Neuroimaging Studies" + ] + }, + "authors": { + "value": [ + + ] + }, + "date": { + "value": [ + "2012-09-05" + ] + }, + "doi": { + "value": [ + "10.3390/brainsci2030347" + ] + }, + "volume": { + "value": [ + "2" + ] + }, + "issue": { + "value": [ + "3" + ] + }, + "firstpage": { + "value": [ + "347" + ] + }, + "description": { + "value": [ + "In the past decade, research has accumulated suggesting that excessive Internet use can lead to the development of a behavioral addiction. Internet addiction has been considered as a serious threat to mental health and the excessive use of the Internet has been linked to a variety of negative psychosocial consequences. The aim of this review is to identify all empirical studies to date that used neuroimaging techniques to shed light upon the emerging mental health problem of Internet and gaming addiction from a neuroscientific perspective. Neuroimaging studies offer an advantage over traditional survey and behavioral research because with this method, it is possible to distinguish particular brain areas that are involved in the development and maintenance of addiction. A systematic literature search was conducted, identifying 18 studies. These studies provide compelling evidence for the similarities between different types of addictions, notably substance-related addictions and Internet and gaming addiction, on a variety of levels. On the molecular level, Internet addiction is characterized by an overall reward deficiency that entails decreased dopaminergic activity. On the level of neural circuitry, Internet and gaming addiction led to neuroadaptation and structural changes that occur as a consequence of prolonged increased activity in brain areas associated with addiction. On a behavioral level, Internet and gaming addicts appear to be constricted with regards to their cognitive functioning in various domains. The paper shows that understanding the neuronal correlates associated with the development of Internet and gaming addiction will promote future research and will pave the way for the development of addiction treatment approaches." + ] + }, + "abstract": { + "value": [ + "In the past decade, research has accumulated suggesting that excessive Internet use can lead to the development of a behavioral addiction. Internet addiction has been considered as a serious threat to mental health and the excessive use of the Internet has been linked to a variety of negative psychosocial consequences. The aim of this review is to identify all empirical studies to date that used neuroimaging techniques to shed light upon the emerging mental health problem of Internet and gaming addiction from a neuroscientific perspective. Neuroimaging studies offer an advantage over traditional survey and behavioral research because with this method, it is possible to distinguish particular brain areas that are involved in the development and maintenance of addiction. A systematic literature search was conducted, identifying 18 studies. These studies provide compelling evidence for the similarities between different types of addictions, notably substance-related addictions and Internet and gaming addiction, on a variety of levels. On the molecular level, Internet addiction is characterized by an overall reward deficiency that entails decreased dopaminergic activity. On the level of neural circuitry, Internet and gaming addiction led to neuroadaptation and structural changes that occur as a consequence of prolonged increased activity in brain areas associated with addiction. On a behavioral level, Internet and gaming addicts appear to be constricted with regards to their cognitive functioning in various domains. The paper shows that understanding the neuronal correlates associated with the development of Internet and gaming addiction will promote future research and will pave the way for the development of addiction treatment approaches." + ] + }, + "fulltext_html": { + "value": [ + "http://www.mdpi.com/2076-3425/2/3/347/htm" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.mdpi.com/2076-3425/2/3/347/pdf" + ] + }, + "fulltext_xml": { + "value": [ + + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "figure": { + "value": [ + + ] + }, + "figure_caption": { + "value": [ + + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_hashes": [ + { + "fulltext.html": "5f160c82e09bf6ad566db56ed4737e55" + }, + { + "fulltext.pdf": "f26da200c65aee82debda1b3f00dfb45" + } + ] + }, + "http://www.mdpi.com/2073-431X/2/4/152/htm": { + "publisher": { + "value": [ + "Multidisciplinary Digital Publishing Institute" + ] + }, + "journal": { + "value": [ + "Computers" + ] + }, + "title": { + "value": [ + "Static Three-Dimensional Fuzzy Routing Based on the Receiving Probability in Wireless Sensor Networks" + ] + }, + "authors": { + "value": [ + + ] + }, + "date": { + "value": [ + "2013-11-12" + ] + }, + "doi": { + "value": [ + "10.3390/computers2040152" + ] + }, + "volume": { + "value": [ + "2" + ] + }, + "issue": { + "value": [ + "4" + ] + }, + "firstpage": { + "value": [ + "152" + ] + }, + "description": { + "value": [ + "A Wireless Sensor Network (WSN) is a collection of low-cost, low-power and large-scale wireless sensor nodes. Routing protocols are an important topic in WSN. Every sensor node should use a proper mechanism to transmit the generated packets to its destination, usually a base station. In previous works, routing protocols use the global information of the network that causes the redundant packets to be increased. Moreover, it leads to an increase in the network traffic, to a decrease in the delivery ratio of data packets, and to a reduction in network life. In this paper, we propose a new inferential routing protocol called SFRRP (Static Three-Dimensional Fuzzy Routing based on the Receiving Probability). The proposed protocol solves the above mentioned problems considerably. The data packets are transmitted by hop-to-hop delivery to the base station. It uses a fuzzy procedure to transmit the sensed data or the buffered data packets to one of the neighbors called selected node. In the proposed fuzzy system, the distance and number of neighbors are input variables, while the receiving probability is the output variable. SFRRP just uses the local neighborhood information to forward the packets and is not needed by any redundant packet for route discovery. The proposed protocol has some advantages such as a high delivery ratio, less delay time, high network life, and less network traffic. The performance of the proposed protocol surpasses the performance of the Flooding routing protocol in terms of delivery ratio, delay time and network lifetime." + ] + }, + "abstract": { + "value": [ + "A Wireless Sensor Network (WSN) is a collection of low-cost, low-power and large-scale wireless sensor nodes. Routing protocols are an important topic in WSN. Every sensor node should use a proper mechanism to transmit the generated packets to its destination, usually a base station. In previous works, routing protocols use the global information of the network that causes the redundant packets to be increased. Moreover, it leads to an increase in the network traffic, to a decrease in the delivery ratio of data packets, and to a reduction in network life. In this paper, we propose a new inferential routing protocol called SFRRP (Static Three-Dimensional Fuzzy Routing based on the Receiving Probability). The proposed protocol solves the above mentioned problems considerably. The data packets are transmitted by hop-to-hop delivery to the base station. It uses a fuzzy procedure to transmit the sensed data or the buffered data packets to one of the neighbors called selected node. In the proposed fuzzy system, the distance and number of neighbors are input variables, while the receiving probability is the output variable. SFRRP just uses the local neighborhood information to forward the packets and is not needed by any redundant packet for route discovery. The proposed protocol has some advantages such as a high delivery ratio, less delay time, high network life, and less network traffic. The performance of the proposed protocol surpasses the performance of the Flooding routing protocol in terms of delivery ratio, delay time and network lifetime." + ] + }, + "fulltext_html": { + "value": [ + "http://www.mdpi.com/2073-431X/2/4/152/htm" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.mdpi.com/2073-431X/2/4/152/pdf" + ] + }, + "fulltext_xml": { + "value": [ + + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "figure": { + "value": [ + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g001.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g002.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g003.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g004.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g005.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g006.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g007.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g008.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g009.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g010.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g011.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g012.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g013.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g014.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g015.png", + "/computers/computers-02-00152/article_deploy/html/images/computers-02-00152-g016.png" + ] + }, + "figure_caption": { + "value": [ + "\n Figure 1.\n The fuzzy value for a room temperature.\n \n Click here to enlarge figure\n \n ", + "\n Figure 2.\n A fuzzy logic system.\n \n Click here to enlarge figure\n \n ", + "\n Figure 3.\n A network model to route the data packets by Static Three-Dimensional Fuzzy Routing Based on the Receiving Probability (SFRRP) in a typical Wireless Sensor Network (WSN).\n \n Click here to enlarge figure\n \n ", + "\n Figure 4.\n Memberships of the input variable distance.\n \n Click here to enlarge figure\n \n ", + "\n Figure 5.\n Memberships of the input variable number of neighbors.\n \n Click here to enlarge figure\n \n ", + "\n Figure 6.\n Memberships of the output variable receiving probability.\n \n Click here to enlarge figure\n \n ", + "\n Figure 7.\n Schematic of the fuzzy rules, (a) rules based on receiving probability and distance; and (b) rules based on receiving probability and number of neighbors.\n \n Click here to enlarge figure\n \n ", + "\n Figure 8.\n Scheme of the SFRRP functionality to choose the selected node.\n \n Click here to enlarge figure\n \n ", + "\n Figure 9.\n Work flow of SFRRP.\n \n Click here to enlarge figure\n \n ", + "\n Figure 10.\n Impact of data generation rate, (a) average delivery rate; (b) average delay; and (c) network life.\n \n Click here to enlarge figure\n \n ", + "\n Figure 11.\n Impact of buffer size, (a) average delivery rate; (b) average delay; and (c) network life.\n \n Click here to enlarge figure\n \n ", + "\n Figure 12.\n Impact of node initial energy, (a) average delivery rate; (b) average delay; and (c) network life.\n \n Click here to enlarge figure\n \n ", + "\n Figure 13.\n Total energy consumption of the nodes.\n \n Click here to enlarge figure\n \n ", + "\n Figure 14.\n The residual energy of the nodes in the proposed protocol.\n \n Click here to enlarge figure\n \n ", + "\n Figure 15.\n Number of live nodes.\n \n Click here to enlarge figure\n \n ", + "\n Figure 16.\n Percent of filled node buffer.\n \n Click here to enlarge figure\n \n " + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_hashes": [ + { + "computers-02-00152-g001.png": "cef36a0b6e5fb999617c61d9187c6391" + }, + { + "computers-02-00152-g002.png": "7db8b717396c30251ffc2d3ba7cdf661" + }, + { + "computers-02-00152-g003.png": "d62941ff17d4a4aadeba3c39e403d91b" + }, + { + "computers-02-00152-g004.png": "bb5d0f266dc5be4c9033f6da2f26f47e" + }, + { + "computers-02-00152-g005.png": "aa050273c449ed92bd24fcf10d99900c" + }, + { + "computers-02-00152-g006.png": "cf8a695427ae150fd458340d6940ecad" + }, + { + "computers-02-00152-g007.png": "2a5da3300799c1eb563231d32ce6cc60" + }, + { + "computers-02-00152-g008.png": "16181ed722daa58fc8971a590119f3ac" + }, + { + "computers-02-00152-g009.png": "3623e28cb28f87201548b24e0a9e36cd" + }, + { + "computers-02-00152-g010.png": "bdf676a1bfd9a8ca5ec84d342657fc34" + }, + { + "computers-02-00152-g011.png": "80f44930263eee375f60c1b5ef3fe417" + }, + { + "computers-02-00152-g012.png": "f65149570b02739a481423ba4921ae48" + }, + { + "computers-02-00152-g013.png": "fe07b361b85f149ba0bcdbfac5e8f07a" + }, + { + "computers-02-00152-g014.png": "13df108c772b82c2ef1eaa3404f6bc72" + }, + { + "computers-02-00152-g015.png": "7005bd9a74a1fb18f3178979d2e97743" + }, + { + "computers-02-00152-g016.png": "4cb244815df8fb4f3a7dcd8c1e1158f3" + }, + { + "fulltext.html": "fec85a9bdabfd66e89cf607b94ffd4a4" + }, + { + "fulltext.pdf": "639d60f2edf4a21b5eb4760f08c2ef18" + } + ] + } } \ No newline at end of file diff --git a/test/peerj.json b/test/peerj.json index c62dfed..4db4923 100644 --- a/test/peerj.json +++ b/test/peerj.json @@ -1,558 +1,690 @@ { - "https://peerj.com/articles/102/": [ - { - "publisher": "PeerJ Inc." - }, - { - "journal": "PeerJ" - }, - { - "title": "Affect-focused psychodynamic psychotherapy for depression and anxiety through the Internet: a randomized controlled trial" - }, - { - "authors": "Robert Johansson" - }, - { - "authors": "Martin Björklund" - }, - { - "authors": "Christoffer Hornborg" - }, - { - "authors": "Stina Karlsson" - }, - { - "authors": "Hugo Hesser" - }, - { - "authors": "Brjánn Ljótsson" - }, - { - "authors": "Andréas Rousseau" - }, - { - "authors": "Ronald J. Frederick" - }, - { - "authors": "Gerhard Andersson" - }, - { - "date": "2013-07-09" - }, - { - "doi": "10.7717/peerj.102" - }, - { - "volume": "1" - }, - { - "firstpage": "e102" - }, - { - "description": "Background. Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base. Research has indicated an association between therapist-facilitated affective experience and outcome in psychodynamic therapy. Affect-phobia therapy (APT), as outlined by McCullough et al., is a psychodynamic treatment that emphasizes a strong focus on expression and experience of affect. This model has neither been evaluated for depression nor anxiety disorders in a randomized controlled trial. While Internet-delivered psychodynamic treatments for depression and generalized anxiety disorder exist, they have not been based on APT. The aim of this randomized controlled trial was to investigate the efficacy of an Internet-based, psychodynamic, guided self-help treatment based on APT for depression and anxiety disorders.Methods. One hundred participants with diagnoses of mood and anxiety disorders participated in a randomized (1:1 ratio) controlled trial of an active group versus a control condition. The treatment group received a 10-week, psychodynamic, guided self-help treatment based on APT that was delivered through the Internet. The treatment consisted of eight text-based treatment modules and included therapist contact (9.5 min per client and week, on average) in a secure online environment. Participants in the control group also received online therapist support and clinical monitoring of symptoms, but received no treatment modules. Outcome measures were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). Process measures were also included. All measures were administered weekly during the treatment period and at a 7-month follow-up.Results. Mixed models analyses using the full intention-to-treat sample revealed significant interaction effects of group and time on all outcome measures, when comparing treatment to the control group. A large between-group effect size of Cohen’s d = 0.77 (95% CI: 0.37–1.18) was found on the PHQ-9 and a moderately large between-group effect size d = 0.48 (95% CI: 0.08–0.87) was found on the GAD-7. The number of patients who recovered (had no diagnoses of depression and anxiety, and had less than 10 on both the PHQ-9 and the GAD-7) were at post-treatment 52% in the treatment group and 24% in the control group. This difference was significant, χ2(N = 100, d f = 1) = 8.3, p < .01. From post-treatment to follow-up, treatment gains were maintained on the PHQ-9, and significant improvements were seen on the GAD-7.Conclusion. This study provides initial support for the efficacy of Internet-delivered psychodynamic therapy based on the affect-phobia model in the treatment of depression and anxiety disorders. The results support the conclusion that psychodynamic treatment approaches may be transferred to the guided self-help format and delivered via the Internet." - }, - { - "abstract": "Background. Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base. Research has indicated an association between therapist-facilitated affective experience and outcome in psychodynamic therapy. Affect-phobia therapy (APT), as outlined by McCullough et al., is a psychodynamic treatment that emphasizes a strong focus on expression and experience of affect. This model has neither been evaluated for depression nor anxiety disorders in a randomized controlled trial. While Internet-delivered psychodynamic treatments for depression and generalized anxiety disorder exist, they have not been based on APT. The aim of this randomized controlled trial was to investigate the efficacy of an Internet-based, psychodynamic, guided self-help treatment based on APT for depression and anxiety disorders.Methods. One hundred participants with diagnoses of mood and anxiety disorders participated in a randomized (1:1 ratio) controlled trial of an active group versus a control condition. The treatment group received a 10-week, psychodynamic, guided self-help treatment based on APT that was delivered through the Internet. The treatment consisted of eight text-based treatment modules and included therapist contact (9.5 min per client and week, on average) in a secure online environment. Participants in the control group also received online therapist support and clinical monitoring of symptoms, but received no treatment modules. Outcome measures were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). Process measures were also included. All measures were administered weekly during the treatment period and at a 7-month follow-up.Results. Mixed models analyses using the full intention-to-treat sample revealed significant interaction effects of group and time on all outcome measures, when comparing treatment to the control group. A large between-group effect size of Cohen’s d = 0.77 (95% CI: 0.37–1.18) was found on the PHQ-9 and a moderately large between-group effect size d = 0.48 (95% CI: 0.08–0.87) was found on the GAD-7. The number of patients who recovered (had no diagnoses of depression and anxiety, and had less than 10 on both the PHQ-9 and the GAD-7) were at post-treatment 52% in the treatment group and 24% in the control group. This difference was significant, χ2(N = 100, d f = 1) = 8.3, p < .01. From post-treatment to follow-up, treatment gains were maintained on the PHQ-9, and significant improvements were seen on the GAD-7.Conclusion. This study provides initial support for the efficacy of Internet-delivered psychodynamic therapy based on the affect-phobia model in the treatment of depression and anxiety disorders. The results support the conclusion that psychodynamic treatment approaches may be transferred to the guided self-help format and delivered via the Internet." - }, - { - "fulltext_html": "https://peerj.com/articles/102" - }, - { - "fulltext_pdf": "https://peerj.com/articles/102.pdf" - }, - { - "supplementary_material": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/S1_CONSORT_checklist.pdf" - }, - { - "supplementary_material": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/S2_trial_protocol.pdf" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/fig-1-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/fig-2-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/fig-3-full.png" - }, - { - "figure_caption": "\nFigure 1: CONSORT flowchart.\n\n  Download full-size image\nDOI: 10.7717/peerj.102/fig-1\n\n" - }, - { - "figure_caption": "\nFigure 2: Malan’s two triangles - the triangle of conflict and the triangle of person.\nThe two triangles (Malan, 1995) represent what David Malan called “the universal principle of psychodynamic psychotherapy”. That is, defenses (D) and anxieties (A) can block the expression of true feelings (F). These patterns began with past persons (P), are maintained with current persons (C), and are often enacted with the therapist (T).\n  Download full-size image\nDOI: 10.7717/peerj.102/fig-2\n\n" - }, - { - "figure_caption": "\nFigure 3: Weekly PHQ-9 and GAD-7 scores.\nWeekly scores on the PHQ-9 and the GAD-7 for both groups. Vertical bars denote 95% confidence intervals (CI). PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.\n  Download full-size image\nDOI: 10.7717/peerj.102/fig-3\n\n" - }, - { - "fig-3-full.png": "0146a2e575c584b50ab4832654e97a96" - }, - { - "fig-1-full.png": "c72e8d96d4bda0fef5f986543c7a5970" - }, - { - "rendered.html": "4461035334376c3cc6b33d56467df660" - }, - { - "102.pdf": "8e2c1cb94b99943cc618c437f8fd1618" - }, - { - "102": "460e830d7dd7a3f929828342b9b6f12b" - }, - { - "S2_trial_protocol.pdf": "26787550a80a05fc451d245fb7107183" - }, - { - "S1_CONSORT_checklist.pdf": "eef414787965a937fc479d31f86a9541" - }, - { - "fig-2-full.png": "9072aa50632170a8558ee1bd2d086e38" - } - ], - "https://peerj.com/articles/234/": [ - { - "publisher": "PeerJ Inc." - }, - { - "journal": "PeerJ" - }, - { - "title": "A new specimen of the Early Cretaceous bird Hongshanornis longicresta: insights into the aerodynamics and diet of a basal ornithuromorph" - }, - { - "authors": "Luis M. Chiappe" - }, - { - "authors": "Bo Zhao" - }, - { - "authors": "Jingmai K. O’Connor" - }, - { - "authors": "Gao Chunling" - }, - { - "authors": "Xuri Wang" - }, - { - "authors": "Michael Habib" - }, - { - "authors": "Jesus Marugan-Lobon" - }, - { - "authors": "Qingjin Meng" - }, - { - "authors": "Xiaodong Cheng" - }, - { - "date": "2014-01-02" - }, - { - "doi": "10.7717/peerj.234" - }, - { - "volume": "2" - }, - { - "firstpage": "e234" - }, - { - "description": "The discovery of Hongshanornis longicresta, a small ornithuromorph bird with unusually long hindlimb proportions, was followed by the discovery of two closely related species, Longicrusavis houi and Parahongshanornis chaoyangensis. Together forming the Hongshanornithidae, these species reveal important information about the early diversity and morphological specialization of ornithuromorphs, the clade that contains all living birds. Here we report on a new specimen (DNHM D2945/6) referable to Hongshanornis longicresta that contributes significant information to better understand the morphology, trophic ecology, and aerodynamics of this species, as well as the taxonomy of the Hongshanornithidae. Most notable are the well-preserved wings and feathered tail of DNHM D2945/6, which afford an accurate reconstruction of aerodynamic parameters indicating that as early as 125 million years ago, basal ornithuromorphs had evolved aerodynamic surfaces comparable in size and design to those of many modern birds, and flight modes alike to those of some small living birds." - }, - { - "abstract": "The discovery of Hongshanornis longicresta, a small ornithuromorph bird with unusually long hindlimb proportions, was followed by the discovery of two closely related species, Longicrusavis houi and Parahongshanornis chaoyangensis. Together forming the Hongshanornithidae, these species reveal important information about the early diversity and morphological specialization of ornithuromorphs, the clade that contains all living birds. Here we report on a new specimen (DNHM D2945/6) referable to Hongshanornis longicresta that contributes significant information to better understand the morphology, trophic ecology, and aerodynamics of this species, as well as the taxonomy of the Hongshanornithidae. Most notable are the well-preserved wings and feathered tail of DNHM D2945/6, which afford an accurate reconstruction of aerodynamic parameters indicating that as early as 125 million years ago, basal ornithuromorphs had evolved aerodynamic surfaces comparable in size and design to those of many modern birds, and flight modes alike to those of some small living birds." - }, - { - "fulltext_html": "https://peerj.com/articles/234" - }, - { - "fulltext_pdf": "https://peerj.com/articles/234.pdf" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-1-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-2-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-3-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-4-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-5-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-6-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-7-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-8-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-9-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-10-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-11-full.png" - }, - { - "figure_caption": "\nFigure 1: Photograph of DNHM D2945.\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-1\n\n" - }, - { - "figure_caption": "\nFigure 2: Interpretive drawing of DNHM D2945.\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pt, proximal tarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-2\n\n" - }, - { - "figure_caption": "\nFigure 3: Photograph of DNHM D2946.\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-3\n\n" - }, - { - "figure_caption": "\nFigure 4: Interpretive drawing of DNHM D2946.\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; st, sternum; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-4\n\n" - }, - { - "figure_caption": "\nFigure 5: Close up photograph of the skull of DNHM D2945 in right lateral view and detail (inset) of the central portion of its maxilla.\nAbbreviations: al, alveoli.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-5\n\n" - }, - { - "figure_caption": "\nFigure 6: Photograph (A) and interpretive drawing (B) of the thoracic girdle and vertebral series, rib cage, and humeri of DNHM D2946.\nAbbreviations: co, coracoid; fu, furcula; hu, humerus; lt, lateral trabecular; ra, radius; rb, ribs; sc, scapula; sp, supracondylar process; st, sternum; up, uncinate process.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-6\n\n" - }, - { - "figure_caption": "\nFigure 7: Photograph of the left manus of DNHM D2945/6 in ventral (A; DNHM D2945) and dorsal (B; DNHM D2946) views.\nAbbreviations: mc I-III, metacarpals I-III; p1-I, phalanx 1 (proximal) of digit I (alular digit); p2-I, phalanx 2 (ungual) of digit I (alular digit); p1-II, phalanx 1 (proximal) of digit II (major digit); p2-II, phalanx 2 (intermediate) of digit II (major digit); p3-II, phalanx 3 (ungual) of digit II (major digit); p1-III, phalanx 1 (proximal) of digit III (minor digit); p2-III, phalanx 2 of digit III (minor digit); ra, radius; sl, semilunate carpal; ul, ulna.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-7\n\n" - }, - { - "figure_caption": "\nFigure 8: Close up photograph of the right knee (medial view) and pubic symphysis (left laterocaudal view) of DNHM D2946.\nNote the detail of the gastroliths. Abbreviations: fe, femur; fi, fibula; gl, gastroliths, pu, pubis; ti, tibia. (l) and (r) refer to the left and right pubis, respectively.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-8\n\n" - }, - { - "figure_caption": "\nFigure 9: Close up photograph of the left knee (lateral view) of DNHM D2946.\nAbbreviations: cn, cnemial crest; fc, fibular condyle; fe, femur; fi, fibula; ld, lateral articular facet of tibia; md, medial articular facet of tibia; ti, tibia.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-9\n\n" - }, - { - "figure_caption": "\nFigure 10: Close up photograph of the feet and rectrices of DNHM D2945.\nAbbreviations: mt, metatarsals; re, rectrices; I-IV, digits I-IV.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-10\n\n" - }, - { - "figure_caption": "\nFigure 11: Interpretive drawing of the outline of the wings and feathered tail of DNHM D2945/6 (see Figs. 1 and 3 for the maximum extent of the primaries and secondaries).\nThe aerodynamic parameters used in this study were derived from this reconstruction (see Materials and Methods).\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-11\n\n" - }, - { - "fig-4-full.png": "9e43600b181b87de53f52d1ee145aec8" - }, - { - "fig-3-full.png": "165114a6bd917393af1c628e4f15cc23" - }, - { - "fig-7-full.png": "7040496f9de9004852cf2bae90034fe7" - }, - { - "fig-9-full.png": "3d3868736ac56e4f2e8e6395d05df051" - }, - { - "fig-10-full.png": "d3d1eadb360073c696eef317130004e8" - }, - { - "234": "9be160e6461eae366392ccc3945e7070" - }, - { - "fig-1-full.png": "5870a310df205fb7216bd358568a11d9" - }, - { - "fig-6-full.png": "28860f72dcafe1bae43e29c49374e644" - }, - { - "rendered.html": "9baf1d55e8d7429ee2d6349afd8ab221" - }, - { - "fig-11-full.png": "0ce3c5edbe7822a1c6b5ea26f6cfd1c4" - }, - { - "234.pdf": "3aa12392730333dd193322c7fb7ac72c" - }, - { - "fig-8-full.png": "73da14b5d45b36d95a9fa8a206651336" - }, - { - "fig-5-full.png": "95ed20e2b3abffa642caccf50c73941d" - }, - { - "fig-2-full.png": "af0dbb6dbbdd9dc38ba8fdb5a4409d26" - } - ], - "https://peerj.com/articles/275/": [ - { - "publisher": "PeerJ Inc." - }, - { - "journal": "PeerJ" - }, - { - "title": "Spectral characteristics of the mutant form GGBP/H152C of D-glucose/D-galactose-binding protein labeled with fluorescent dye BADAN: influence of external factors" - }, - { - "authors": "Alexander V. Fonin" - }, - { - "authors": "Olga V. Stepanenko" - }, - { - "authors": "Olga I. Povarova" - }, - { - "authors": "Catherine A. Volova" - }, - { - "authors": "Elizaveta M. Philippova" - }, - { - "authors": "Grigory S. Bublikov" - }, - { - "authors": "Irina M. Kuznetsova" - }, - { - "authors": "Alexander P. Demchenko" - }, - { - "authors": "Konstantin K. Turoverov" - }, - { - "date": "2014-03-18" - }, - { - "doi": "10.7717/peerj.275" - }, - { - "volume": "2" - }, - { - "firstpage": "e275" - }, - { - "description": "The mutant form GGBP/H152C of the D-glucose/D-galactose-binding protein with the solvatochromic dye BADAN linked to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various external factors on the physical-chemical properties of GGBP/H152C-BADAN and its complex with glucose. The high affinity (Kd = 8.5 µM) and high binding rate of glucose make GGBP/H152C-BADAN a good candidate to determine the sugar content in biological fluids extracted using transdermal techniques. It was shown that changes in the ionic strength and pH of solution within the physiological range did not have a significant influence on the fluorescent characteristics of GGBP/H152C-BADAN. The mutant form GGBP/H152C has relatively low resistance to denaturation action of GdnHCl and urea. This result emphasizes the need to find more stable proteins for the creation of a sensitive element for a glucose biosensor system." - }, - { - "abstract": "The mutant form GGBP/H152C of the D-glucose/D-galactose-binding protein with the solvatochromic dye BADAN linked to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various external factors on the physical-chemical properties of GGBP/H152C-BADAN and its complex with glucose. The high affinity (Kd = 8.5 µM) and high binding rate of glucose make GGBP/H152C-BADAN a good candidate to determine the sugar content in biological fluids extracted using transdermal techniques. It was shown that changes in the ionic strength and pH of solution within the physiological range did not have a significant influence on the fluorescent characteristics of GGBP/H152C-BADAN. The mutant form GGBP/H152C has relatively low resistance to denaturation action of GdnHCl and urea. This result emphasizes the need to find more stable proteins for the creation of a sensitive element for a glucose biosensor system." - }, - { - "fulltext_html": "https://peerj.com/articles/275" - }, - { - "fulltext_pdf": "https://peerj.com/articles/275.pdf" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-1-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-2-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-3-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-4-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-5-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-6-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-7-full.png" - }, - { - "figure_caption": "\nFigure 1: Determination of the dissociation constant (Kd) of the complex of GGBP/H152C-BADAN with glucose (Glc).\nThe excitation wavelength was 387 nm, the emission wavelength was 545 nm.\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-1\n\n" - }, - { - "figure_caption": "\nFigure 2: The kinetics of Glc binding to GGBP/H152C-BADAN in solutions with different viscosities.\nGlc concentration was 20 mM. The excitation wavelength was 405 nm. Curve 1, 2 and 3 represents the control, Glc binding to GGBP/H152C-BADAN in a PBS solution, and in PBS-glycerol solution with viscosity equal to 4.0 cP. Inset: The kinetic curves 1 and 2 in interval from 0.01 to 0.08 s are given.\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-2\n\n" - }, - { - "figure_caption": "\nFigure 3: The effect of solvent viscosity and temperature on the fluorescence quantum yield of the GGBP/H152C-BADAN in the open (circles) and closed (triangles) forms.\nThe excitation wavelength was 387 nm.\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-3\n\n" - }, - { - "figure_caption": "\nFigure 4: GdnHCl-induced (A, B) and urea-induced (C, D) conformational changing of GGBP/H152C-BADAN structure in open (circles) and closed forms (triangles).\n(A) and (C) represents the dependence of the fluorescence intensity (the excitation wavelength was 387 nm, the emission wavelength was 545 nm) on the denaturants concentration. (B) and (D) represents the dependence of the parameter A = I320/I365 (I320 and I365 fluorescence intensities recorded at 320 and 365 nm, respectively) on the denaturants concentration (the excitation wavelength was 297 nm).\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-4\n\n" - }, - { - "figure_caption": "\nFigure 5: Changes of ellipticity at 222 nm of GGBP/H152C-BADAN and GGBP/H152C-BADAN–Glc on the GdnHCl concentration.\n\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-5\n\n" - }, - { - "figure_caption": "\nFigure 6: The effect of the pH solution on the fluorescent characteristics of GGBP/H152C-BADAN in the open (the solid curves) and closed (the dashed curves) forms.\n(A) The excitation wavelength was 297 nm. (B) The excitation wavelength was 387 nm. The pH values of the solution were 2.8 (black curves), 4.2 (red curves), 6.4 (blue curves), 7.4 (dark green curves) and 9.6 (dark red curves).\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-6\n\n" - }, - { - "figure_caption": "\nFigure 7: The effect of NaCl and MgCl2 on the fluorescent characteristics of GGBP/H152C-BADAN in open (solid curves) and closed (dashed curves) forms.\n(A) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.8 M NaCl (red curve) and 2.5 M NaCl (blue curve). (B) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.1 M MgCl2 (red curve) and 0.5 M MgCl2 (blue curve). The fluorescence spectra of GGBP/H152C-BADAN in PBS solution appear in black. (The excitation wavelength was 387 nm.)\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-7\n\n" - }, - { - "fig-4-full.png": "e3ea581b9d3ae478cc5c7e3c630576e8" - }, - { - "fig-3-full.png": "c41e4a8c837cfe6aeabff81982844a98" - }, - { - "fig-7-full.png": "b76d31a596a07e5ef4fe238d687c5729" - }, - { - "275.pdf": "6b554c704f1ed7a8129863a2869036eb" - }, - { - "fig-1-full.png": "3698cf17a11ba9ef9183634bd3801b49" - }, - { - "fig-6-full.png": "fff6b0de359e83441f6b5838d862fd93" - }, - { - "rendered.html": "30d93308f1f8fa6d21f202254c6fa516" - }, - { - "275": "c067c205f735cbb13d14a7771502cc30" - }, - { - "fig-5-full.png": "97904c56a6215db7065fd1830624f708" - }, - { - "fig-2-full.png": "90442c7e0490029e4d59193979537f6a" - } - ], - "https://peerj.com/articles/311/": [ - { - "publisher": "PeerJ Inc." - }, - { - "journal": "PeerJ" - }, - { - "title": "Religious attendance after elevated depressive symptoms: is selection bias at work?" - }, - { - "authors": "Lloyd Balbuena" - }, - { - "authors": "Marilyn Baetz" - }, - { - "authors": "Rudy Bowen" - }, - { - "date": "2014-03-13" - }, - { - "doi": "10.7717/peerj.311" - }, - { - "volume": "2" - }, - { - "firstpage": "e311" - }, - { - "description": "In an attempt to determine if selection bias could be a reason that religious attendance and depression are related, the predictive value of elevated depressive symptoms for a decrease in future attendance at religious services was examined in a longitudinal panel of 1,673 Dutch adults. Religious attendance was assessed yearly over five years using the single question, “how often do you attend religious gatherings nowadays?” Depressive symptoms were assessed four times within the first year using the Depression subscale of the Brief Symptom Inventory. Logistic regression models of change in attendance were created, stratifying by baseline attendance status. Attenders who developed elevated symptoms were less likely to subsequently decrease their attendance (relative risk ratio: 0.55, 95% CI [0.38–0.79]) relative to baseline as compared to those without elevated symptoms. This inverse association remained significant after controlling for health and demographic covariates, and when using multiply imputed data to account for attrition. Non-attenders were unlikely to start attending after elevated depressive symptoms. This study provides counter evidence against previous findings that church attenders are a self-selected healthier group." - }, - { - "abstract": "In an attempt to determine if selection bias could be a reason that religious attendance and depression are related, the predictive value of elevated depressive symptoms for a decrease in future attendance at religious services was examined in a longitudinal panel of 1,673 Dutch adults. Religious attendance was assessed yearly over five years using the single question, “how often do you attend religious gatherings nowadays?” Depressive symptoms were assessed four times within the first year using the Depression subscale of the Brief Symptom Inventory. Logistic regression models of change in attendance were created, stratifying by baseline attendance status. Attenders who developed elevated symptoms were less likely to subsequently decrease their attendance (relative risk ratio: 0.55, 95% CI [0.38–0.79]) relative to baseline as compared to those without elevated symptoms. This inverse association remained significant after controlling for health and demographic covariates, and when using multiply imputed data to account for attrition. Non-attenders were unlikely to start attending after elevated depressive symptoms. This study provides counter evidence against previous findings that church attenders are a self-selected healthier group." - }, - { - "fulltext_html": "https://peerj.com/articles/311" - }, - { - "fulltext_pdf": "https://peerj.com/articles/311.pdf" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/311/1/fig-1-full.png" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/311/1/fig-2-full.png" - }, - { - "figure_caption": "\nFigure 1: Subjects.\n(A) LISS datasets used and participant flowchart; (B) schedule of religion and depression assessments.\n  Download full-size image\nDOI: 10.7717/peerj.311/fig-1\n\n" - }, - { - "figure_caption": "\nFigure 2: Probabilities.\nPredicted probabilities of a decrease, same, and increase in religious attendance (95% CI).\n  Download full-size image\nDOI: 10.7717/peerj.311/fig-2\n\n" - }, - { - "311.pdf": "8aa4a538c24c0f3bfcc8b9fa5cd63d7c" - }, - { - "fig-1-full.png": "3ff19ca931ac3850d2e6d045efb5d213" - }, - { - "311": "7c457cc73a24cb05df634e0d01dbe561" - }, - { - "rendered.html": "9d3054adc95559f5e507e87f2c2f2ae0" - }, - { - "fig-2-full.png": "b6a99fff0a72af9fde1e550f80d43799" - } - ], - "https://peerj.com/articles/384/": [ - { - "publisher": "PeerJ Inc." - }, - { - "journal": "PeerJ" - }, - { - "title": "Mutation analysis of the SLC26A4, FOXI1 and KCNJ10 genes in individuals with congenital hearing loss" - }, - { - "authors": "Lynn M. Pique" - }, - { - "authors": "Marie-Luise Brennan" - }, - { - "authors": "Colin J. Davidson" - }, - { - "authors": "Frederick Schaefer" - }, - { - "authors": "John Greinwald Jr" - }, - { - "authors": "Iris Schrijver" - }, - { - "date": "2014-05-08" - }, - { - "doi": "10.7717/peerj.384" - }, - { - "volume": "2" - }, - { - "firstpage": "e384" - }, - { - "description": "Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype." - }, - { - "abstract": "Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype." - }, - { - "fulltext_html": "https://peerj.com/articles/384" - }, - { - "fulltext_pdf": "https://peerj.com/articles/384.pdf" - }, - { - "figure": "https://dfzljdn9uc3pi.cloudfront.net/2014/384/1/fig-1-full.png" - }, - { - "figure_caption": "\nFigure 1: Identification of the heterozygous SLC26A4 deletion g.8091T-22145Cdel in subject PDS41.\n(A) The SLC26A4 MLPA probe mix includes probes for the 21 SLC26A4 exons, 14 reference probes and three probes specific for the point mutations c.1001+1G>A (IV S8+1G>A), c.707T>C (p.Leu236Pro) and c.1246A>C (p.Thr416Pro). Subject PDS41 is heterozygous for a deletion (g.8091T-22145Cdel) spanning exons 4–6 in SLC26A4, as evidenced by the reproducible reduction in peak height for these three exon probes (peaks labeled 4, 5, 6) relative to the control. PDS41 also has a heterozygous c.1246A>C (p.Thr416Pro) mutation that was previously identified by sequencing and confirmed by these MLPA results (peak labeled p.T416P). (B) Sequencing chromatogram of the deletion breakpoints in SLC26A4 IVS3 and IVS6. The deletion removes a total of 14,053 bp. IVS, intervening sequence.\n  Download full-size image\nDOI: 10.7717/peerj.384/fig-1\n\n" - }, - { - "fig-1-full.png": "6ee6bf8676df1087e9d724bfdc9178e8" - }, - { - "rendered.html": "96b5f65a07b9df06ab331f682f347d53" - }, - { - "384.pdf": "b2020a8f8037228e6face4a220751932" - }, - { - "384": "003b6f777ee95fffaf497181c427420b" - } - ] + "https://peerj.com/articles/102/": { + "publisher": { + "value": [ + "PeerJ Inc." + ] + }, + "journal": { + "value": [ + "PeerJ" + ] + }, + "title": { + "value": [ + "Affect-focused psychodynamic psychotherapy for depression and anxiety through the Internet: a randomized controlled trial" + ] + }, + "authors": { + "value": [ + "Robert Johansson", + "Martin Björklund", + "Christoffer Hornborg", + "Stina Karlsson", + "Hugo Hesser", + "Brjánn Ljótsson", + "Andréas Rousseau", + "Ronald J. Frederick", + "Gerhard Andersson" + ] + }, + "date": { + "value": [ + "2013-07-09" + ] + }, + "doi": { + "value": [ + "10.7717/peerj.102" + ] + }, + "volume": { + "value": [ + "1" + ] + }, + "issue": { + "value": [ + + ] + }, + "firstpage": { + "value": [ + "e102" + ] + }, + "description": { + "value": [ + "Background. Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base. Research has indicated an association between therapist-facilitated affective experience and outcome in psychodynamic therapy. Affect-phobia therapy (APT), as outlined by McCullough et al., is a psychodynamic treatment that emphasizes a strong focus on expression and experience of affect. This model has neither been evaluated for depression nor anxiety disorders in a randomized controlled trial. While Internet-delivered psychodynamic treatments for depression and generalized anxiety disorder exist, they have not been based on APT. The aim of this randomized controlled trial was to investigate the efficacy of an Internet-based, psychodynamic, guided self-help treatment based on APT for depression and anxiety disorders.Methods. One hundred participants with diagnoses of mood and anxiety disorders participated in a randomized (1:1 ratio) controlled trial of an active group versus a control condition. The treatment group received a 10-week, psychodynamic, guided self-help treatment based on APT that was delivered through the Internet. The treatment consisted of eight text-based treatment modules and included therapist contact (9.5 min per client and week, on average) in a secure online environment. Participants in the control group also received online therapist support and clinical monitoring of symptoms, but received no treatment modules. Outcome measures were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). Process measures were also included. All measures were administered weekly during the treatment period and at a 7-month follow-up.Results. Mixed models analyses using the full intention-to-treat sample revealed significant interaction effects of group and time on all outcome measures, when comparing treatment to the control group. A large between-group effect size of Cohen’s d = 0.77 (95% CI: 0.37–1.18) was found on the PHQ-9 and a moderately large between-group effect size d = 0.48 (95% CI: 0.08–0.87) was found on the GAD-7. The number of patients who recovered (had no diagnoses of depression and anxiety, and had less than 10 on both the PHQ-9 and the GAD-7) were at post-treatment 52% in the treatment group and 24% in the control group. This difference was significant, χ2(N = 100, d f = 1) = 8.3, p < .01. From post-treatment to follow-up, treatment gains were maintained on the PHQ-9, and significant improvements were seen on the GAD-7.Conclusion. This study provides initial support for the efficacy of Internet-delivered psychodynamic therapy based on the affect-phobia model in the treatment of depression and anxiety disorders. The results support the conclusion that psychodynamic treatment approaches may be transferred to the guided self-help format and delivered via the Internet." + ] + }, + "abstract": { + "value": [ + "Background. Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base. Research has indicated an association between therapist-facilitated affective experience and outcome in psychodynamic therapy. Affect-phobia therapy (APT), as outlined by McCullough et al., is a psychodynamic treatment that emphasizes a strong focus on expression and experience of affect. This model has neither been evaluated for depression nor anxiety disorders in a randomized controlled trial. While Internet-delivered psychodynamic treatments for depression and generalized anxiety disorder exist, they have not been based on APT. The aim of this randomized controlled trial was to investigate the efficacy of an Internet-based, psychodynamic, guided self-help treatment based on APT for depression and anxiety disorders.Methods. One hundred participants with diagnoses of mood and anxiety disorders participated in a randomized (1:1 ratio) controlled trial of an active group versus a control condition. The treatment group received a 10-week, psychodynamic, guided self-help treatment based on APT that was delivered through the Internet. The treatment consisted of eight text-based treatment modules and included therapist contact (9.5 min per client and week, on average) in a secure online environment. Participants in the control group also received online therapist support and clinical monitoring of symptoms, but received no treatment modules. Outcome measures were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). Process measures were also included. All measures were administered weekly during the treatment period and at a 7-month follow-up.Results. Mixed models analyses using the full intention-to-treat sample revealed significant interaction effects of group and time on all outcome measures, when comparing treatment to the control group. A large between-group effect size of Cohen’s d = 0.77 (95% CI: 0.37–1.18) was found on the PHQ-9 and a moderately large between-group effect size d = 0.48 (95% CI: 0.08–0.87) was found on the GAD-7. The number of patients who recovered (had no diagnoses of depression and anxiety, and had less than 10 on both the PHQ-9 and the GAD-7) were at post-treatment 52% in the treatment group and 24% in the control group. This difference was significant, χ2(N = 100, d f = 1) = 8.3, p < .01. From post-treatment to follow-up, treatment gains were maintained on the PHQ-9, and significant improvements were seen on the GAD-7.Conclusion. This study provides initial support for the efficacy of Internet-delivered psychodynamic therapy based on the affect-phobia model in the treatment of depression and anxiety disorders. The results support the conclusion that psychodynamic treatment approaches may be transferred to the guided self-help format and delivered via the Internet." + ] + }, + "fulltext_html": { + "value": [ + "https://peerj.com/articles/102" + ] + }, + "fulltext_pdf": { + "value": [ + "https://peerj.com/articles/102.pdf" + ] + }, + "fulltext_xml": { + "value": [ + "/articles/102.xml" + ] + }, + "supplementary_material": { + "value": [ + "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/S1_CONSORT_checklist.pdf", + "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/S2_trial_protocol.pdf" + ] + }, + "figure": { + "value": [ + "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/fig-1-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/fig-2-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/fig-3-full.png" + ] + }, + "figure_caption": { + "value": [ + "\nFigure 1: CONSORT flowchart.\n\n  Download full-size image\nDOI: 10.7717/peerj.102/fig-1\n\n", + "\nFigure 2: Malan’s two triangles - the triangle of conflict and the triangle of person.\nThe two triangles (Malan, 1995) represent what David Malan called “the universal principle of psychodynamic psychotherapy”. That is, defenses (D) and anxieties (A) can block the expression of true feelings (F). These patterns began with past persons (P), are maintained with current persons (C), and are often enacted with the therapist (T).\n  Download full-size image\nDOI: 10.7717/peerj.102/fig-2\n\n", + "\nFigure 3: Weekly PHQ-9 and GAD-7 scores.\nWeekly scores on the PHQ-9 and the GAD-7 for both groups. Vertical bars denote 95% confidence intervals (CI). PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.\n  Download full-size image\nDOI: 10.7717/peerj.102/fig-3\n\n" + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_hashes": [ + { + "fig-1-full.png": "c72e8d96d4bda0fef5f986543c7a5970" + }, + { + "fig-2-full.png": "9072aa50632170a8558ee1bd2d086e38" + }, + { + "fig-3-full.png": "0146a2e575c584b50ab4832654e97a96" + }, + { + "fulltext.html": "63379447ccbb411a3b65c2c28efba3f9" + }, + { + "fulltext.pdf": "8e2c1cb94b99943cc618c437f8fd1618" + }, + { + "fulltext.xml": "19e85ee275fb13e0d50a9fbd8c6e5b56" + }, + { + "S1_CONSORT_checklist.pdf": "eef414787965a937fc479d31f86a9541" + }, + { + "S2_trial_protocol.pdf": "26787550a80a05fc451d245fb7107183" + } + ] + }, + "https://peerj.com/articles/234/": { + "publisher": { + "value": [ + "PeerJ Inc." + ] + }, + "journal": { + "value": [ + "PeerJ" + ] + }, + "title": { + "value": [ + "A new specimen of the Early Cretaceous bird Hongshanornis longicresta: insights into the aerodynamics and diet of a basal ornithuromorph" + ] + }, + "authors": { + "value": [ + "Luis M. Chiappe", + "Bo Zhao", + "Jingmai K. O’Connor", + "Gao Chunling", + "Xuri Wang", + "Michael Habib", + "Jesus Marugan-Lobon", + "Qingjin Meng", + "Xiaodong Cheng" + ] + }, + "date": { + "value": [ + "2014-01-02" + ] + }, + "doi": { + "value": [ + "10.7717/peerj.234" + ] + }, + "volume": { + "value": [ + "2" + ] + }, + "issue": { + "value": [ + + ] + }, + "firstpage": { + "value": [ + "e234" + ] + }, + "description": { + "value": [ + "The discovery of Hongshanornis longicresta, a small ornithuromorph bird with unusually long hindlimb proportions, was followed by the discovery of two closely related species, Longicrusavis houi and Parahongshanornis chaoyangensis. Together forming the Hongshanornithidae, these species reveal important information about the early diversity and morphological specialization of ornithuromorphs, the clade that contains all living birds. Here we report on a new specimen (DNHM D2945/6) referable to Hongshanornis longicresta that contributes significant information to better understand the morphology, trophic ecology, and aerodynamics of this species, as well as the taxonomy of the Hongshanornithidae. Most notable are the well-preserved wings and feathered tail of DNHM D2945/6, which afford an accurate reconstruction of aerodynamic parameters indicating that as early as 125 million years ago, basal ornithuromorphs had evolved aerodynamic surfaces comparable in size and design to those of many modern birds, and flight modes alike to those of some small living birds." + ] + }, + "abstract": { + "value": [ + "The discovery of Hongshanornis longicresta, a small ornithuromorph bird with unusually long hindlimb proportions, was followed by the discovery of two closely related species, Longicrusavis houi and Parahongshanornis chaoyangensis. Together forming the Hongshanornithidae, these species reveal important information about the early diversity and morphological specialization of ornithuromorphs, the clade that contains all living birds. Here we report on a new specimen (DNHM D2945/6) referable to Hongshanornis longicresta that contributes significant information to better understand the morphology, trophic ecology, and aerodynamics of this species, as well as the taxonomy of the Hongshanornithidae. Most notable are the well-preserved wings and feathered tail of DNHM D2945/6, which afford an accurate reconstruction of aerodynamic parameters indicating that as early as 125 million years ago, basal ornithuromorphs had evolved aerodynamic surfaces comparable in size and design to those of many modern birds, and flight modes alike to those of some small living birds." + ] + }, + "fulltext_html": { + "value": [ + "https://peerj.com/articles/234" + ] + }, + "fulltext_pdf": { + "value": [ + "https://peerj.com/articles/234.pdf" + ] + }, + "fulltext_xml": { + "value": [ + "/articles/234.xml" + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "figure": { + "value": [ + "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-1-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-2-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-3-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-4-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-5-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-6-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-7-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-8-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-9-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-10-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-11-full.png" + ] + }, + "figure_caption": { + "value": [ + "\nFigure 1: Photograph of DNHM D2945.\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-1\n\n", + "\nFigure 2: Interpretive drawing of DNHM D2945.\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pt, proximal tarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-2\n\n", + "\nFigure 3: Photograph of DNHM D2946.\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-3\n\n", + "\nFigure 4: Interpretive drawing of DNHM D2946.\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; st, sternum; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-4\n\n", + "\nFigure 5: Close up photograph of the skull of DNHM D2945 in right lateral view and detail (inset) of the central portion of its maxilla.\nAbbreviations: al, alveoli.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-5\n\n", + "\nFigure 6: Photograph (A) and interpretive drawing (B) of the thoracic girdle and vertebral series, rib cage, and humeri of DNHM D2946.\nAbbreviations: co, coracoid; fu, furcula; hu, humerus; lt, lateral trabecular; ra, radius; rb, ribs; sc, scapula; sp, supracondylar process; st, sternum; up, uncinate process.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-6\n\n", + "\nFigure 7: Photograph of the left manus of DNHM D2945/6 in ventral (A; DNHM D2945) and dorsal (B; DNHM D2946) views.\nAbbreviations: mc I-III, metacarpals I-III; p1-I, phalanx 1 (proximal) of digit I (alular digit); p2-I, phalanx 2 (ungual) of digit I (alular digit); p1-II, phalanx 1 (proximal) of digit II (major digit); p2-II, phalanx 2 (intermediate) of digit II (major digit); p3-II, phalanx 3 (ungual) of digit II (major digit); p1-III, phalanx 1 (proximal) of digit III (minor digit); p2-III, phalanx 2 of digit III (minor digit); ra, radius; sl, semilunate carpal; ul, ulna.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-7\n\n", + "\nFigure 8: Close up photograph of the right knee (medial view) and pubic symphysis (left laterocaudal view) of DNHM D2946.\nNote the detail of the gastroliths. Abbreviations: fe, femur; fi, fibula; gl, gastroliths, pu, pubis; ti, tibia. (l) and (r) refer to the left and right pubis, respectively.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-8\n\n", + "\nFigure 9: Close up photograph of the left knee (lateral view) of DNHM D2946.\nAbbreviations: cn, cnemial crest; fc, fibular condyle; fe, femur; fi, fibula; ld, lateral articular facet of tibia; md, medial articular facet of tibia; ti, tibia.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-9\n\n", + "\nFigure 10: Close up photograph of the feet and rectrices of DNHM D2945.\nAbbreviations: mt, metatarsals; re, rectrices; I-IV, digits I-IV.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-10\n\n", + "\nFigure 11: Interpretive drawing of the outline of the wings and feathered tail of DNHM D2945/6 (see Figs. 1 and 3 for the maximum extent of the primaries and secondaries).\nThe aerodynamic parameters used in this study were derived from this reconstruction (see Materials and Methods).\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-11\n\n" + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_hashes": [ + { + "fig-1-full.png": "5870a310df205fb7216bd358568a11d9" + }, + { + "fig-10-full.png": "d3d1eadb360073c696eef317130004e8" + }, + { + "fig-11-full.png": "0ce3c5edbe7822a1c6b5ea26f6cfd1c4" + }, + { + "fig-2-full.png": "af0dbb6dbbdd9dc38ba8fdb5a4409d26" + }, + { + "fig-3-full.png": "165114a6bd917393af1c628e4f15cc23" + }, + { + "fig-4-full.png": "9e43600b181b87de53f52d1ee145aec8" + }, + { + "fig-5-full.png": "95ed20e2b3abffa642caccf50c73941d" + }, + { + "fig-6-full.png": "28860f72dcafe1bae43e29c49374e644" + }, + { + "fig-7-full.png": "7040496f9de9004852cf2bae90034fe7" + }, + { + "fig-8-full.png": "73da14b5d45b36d95a9fa8a206651336" + }, + { + "fig-9-full.png": "3d3868736ac56e4f2e8e6395d05df051" + }, + { + "fulltext.html": "b4033b0dd05addef2c0d237438ddaca2" + }, + { + "fulltext.pdf": "3aa12392730333dd193322c7fb7ac72c" + }, + { + "fulltext.xml": "a322b65a64bb8bcb3c5756b49eeb0ad6" + } + ] + }, + "https://peerj.com/articles/275/": { + "publisher": { + "value": [ + "PeerJ Inc." + ] + }, + "journal": { + "value": [ + "PeerJ" + ] + }, + "title": { + "value": [ + "Spectral characteristics of the mutant form GGBP/H152C of D-glucose/D-galactose-binding protein labeled with fluorescent dye BADAN: influence of external factors" + ] + }, + "authors": { + "value": [ + "Alexander V. Fonin", + "Olga V. Stepanenko", + "Olga I. Povarova", + "Catherine A. Volova", + "Elizaveta M. Philippova", + "Grigory S. Bublikov", + "Irina M. Kuznetsova", + "Alexander P. Demchenko", + "Konstantin K. Turoverov" + ] + }, + "date": { + "value": [ + "2014-03-18" + ] + }, + "doi": { + "value": [ + "10.7717/peerj.275" + ] + }, + "volume": { + "value": [ + "2" + ] + }, + "issue": { + "value": [ + + ] + }, + "firstpage": { + "value": [ + "e275" + ] + }, + "description": { + "value": [ + "The mutant form GGBP/H152C of the D-glucose/D-galactose-binding protein with the solvatochromic dye BADAN linked to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various external factors on the physical-chemical properties of GGBP/H152C-BADAN and its complex with glucose. The high affinity (Kd = 8.5 µM) and high binding rate of glucose make GGBP/H152C-BADAN a good candidate to determine the sugar content in biological fluids extracted using transdermal techniques. It was shown that changes in the ionic strength and pH of solution within the physiological range did not have a significant influence on the fluorescent characteristics of GGBP/H152C-BADAN. The mutant form GGBP/H152C has relatively low resistance to denaturation action of GdnHCl and urea. This result emphasizes the need to find more stable proteins for the creation of a sensitive element for a glucose biosensor system." + ] + }, + "abstract": { + "value": [ + "The mutant form GGBP/H152C of the D-glucose/D-galactose-binding protein with the solvatochromic dye BADAN linked to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various external factors on the physical-chemical properties of GGBP/H152C-BADAN and its complex with glucose. The high affinity (Kd = 8.5 µM) and high binding rate of glucose make GGBP/H152C-BADAN a good candidate to determine the sugar content in biological fluids extracted using transdermal techniques. It was shown that changes in the ionic strength and pH of solution within the physiological range did not have a significant influence on the fluorescent characteristics of GGBP/H152C-BADAN. The mutant form GGBP/H152C has relatively low resistance to denaturation action of GdnHCl and urea. This result emphasizes the need to find more stable proteins for the creation of a sensitive element for a glucose biosensor system." + ] + }, + "fulltext_html": { + "value": [ + "https://peerj.com/articles/275" + ] + }, + "fulltext_pdf": { + "value": [ + "https://peerj.com/articles/275.pdf" + ] + }, + "fulltext_xml": { + "value": [ + "/articles/275.xml" + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "figure": { + "value": [ + "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-1-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-2-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-3-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-4-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-5-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-6-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-7-full.png" + ] + }, + "figure_caption": { + "value": [ + "\nFigure 1: Determination of the dissociation constant (Kd) of the complex of GGBP/H152C-BADAN with glucose (Glc).\nThe excitation wavelength was 387 nm, the emission wavelength was 545 nm.\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-1\n\n", + "\nFigure 2: The kinetics of Glc binding to GGBP/H152C-BADAN in solutions with different viscosities.\nGlc concentration was 20 mM. The excitation wavelength was 405 nm. Curve 1, 2 and 3 represents the control, Glc binding to GGBP/H152C-BADAN in a PBS solution, and in PBS-glycerol solution with viscosity equal to 4.0 cP. Inset: The kinetic curves 1 and 2 in interval from 0.01 to 0.08 s are given.\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-2\n\n", + "\nFigure 3: The effect of solvent viscosity and temperature on the fluorescence quantum yield of the GGBP/H152C-BADAN in the open (circles) and closed (triangles) forms.\nThe excitation wavelength was 387 nm.\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-3\n\n", + "\nFigure 4: GdnHCl-induced (A, B) and urea-induced (C, D) conformational changing of GGBP/H152C-BADAN structure in open (circles) and closed forms (triangles).\n(A) and (C) represents the dependence of the fluorescence intensity (the excitation wavelength was 387 nm, the emission wavelength was 545 nm) on the denaturants concentration. (B) and (D) represents the dependence of the parameter A = I320/I365 (I320 and I365 fluorescence intensities recorded at 320 and 365 nm, respectively) on the denaturants concentration (the excitation wavelength was 297 nm).\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-4\n\n", + "\nFigure 5: Changes of ellipticity at 222 nm of GGBP/H152C-BADAN and GGBP/H152C-BADAN–Glc on the GdnHCl concentration.\n\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-5\n\n", + "\nFigure 6: The effect of the pH solution on the fluorescent characteristics of GGBP/H152C-BADAN in the open (the solid curves) and closed (the dashed curves) forms.\n(A) The excitation wavelength was 297 nm. (B) The excitation wavelength was 387 nm. The pH values of the solution were 2.8 (black curves), 4.2 (red curves), 6.4 (blue curves), 7.4 (dark green curves) and 9.6 (dark red curves).\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-6\n\n", + "\nFigure 7: The effect of NaCl and MgCl2 on the fluorescent characteristics of GGBP/H152C-BADAN in open (solid curves) and closed (dashed curves) forms.\n(A) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.8 M NaCl (red curve) and 2.5 M NaCl (blue curve). (B) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.1 M MgCl2 (red curve) and 0.5 M MgCl2 (blue curve). The fluorescence spectra of GGBP/H152C-BADAN in PBS solution appear in black. (The excitation wavelength was 387 nm.)\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-7\n\n" + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_hashes": [ + { + "fig-1-full.png": "3698cf17a11ba9ef9183634bd3801b49" + }, + { + "fig-2-full.png": "90442c7e0490029e4d59193979537f6a" + }, + { + "fig-3-full.png": "c41e4a8c837cfe6aeabff81982844a98" + }, + { + "fig-4-full.png": "e3ea581b9d3ae478cc5c7e3c630576e8" + }, + { + "fig-5-full.png": "97904c56a6215db7065fd1830624f708" + }, + { + "fig-6-full.png": "fff6b0de359e83441f6b5838d862fd93" + }, + { + "fig-7-full.png": "b76d31a596a07e5ef4fe238d687c5729" + }, + { + "fulltext.html": "6e5fc1f3587b4c0eb4810a455b290a23" + }, + { + "fulltext.pdf": "6b554c704f1ed7a8129863a2869036eb" + }, + { + "fulltext.xml": "033fb090781f7a84c4e7b5ac43dec2b6" + } + ] + }, + "https://peerj.com/articles/311/": { + "publisher": { + "value": [ + "PeerJ Inc." + ] + }, + "journal": { + "value": [ + "PeerJ" + ] + }, + "title": { + "value": [ + "Religious attendance after elevated depressive symptoms: is selection bias at work?" + ] + }, + "authors": { + "value": [ + "Lloyd Balbuena", + "Marilyn Baetz", + "Rudy Bowen" + ] + }, + "date": { + "value": [ + "2014-03-13" + ] + }, + "doi": { + "value": [ + "10.7717/peerj.311" + ] + }, + "volume": { + "value": [ + "2" + ] + }, + "issue": { + "value": [ + + ] + }, + "firstpage": { + "value": [ + "e311" + ] + }, + "description": { + "value": [ + "In an attempt to determine if selection bias could be a reason that religious attendance and depression are related, the predictive value of elevated depressive symptoms for a decrease in future attendance at religious services was examined in a longitudinal panel of 1,673 Dutch adults. Religious attendance was assessed yearly over five years using the single question, “how often do you attend religious gatherings nowadays?” Depressive symptoms were assessed four times within the first year using the Depression subscale of the Brief Symptom Inventory. Logistic regression models of change in attendance were created, stratifying by baseline attendance status. Attenders who developed elevated symptoms were less likely to subsequently decrease their attendance (relative risk ratio: 0.55, 95% CI [0.38–0.79]) relative to baseline as compared to those without elevated symptoms. This inverse association remained significant after controlling for health and demographic covariates, and when using multiply imputed data to account for attrition. Non-attenders were unlikely to start attending after elevated depressive symptoms. This study provides counter evidence against previous findings that church attenders are a self-selected healthier group." + ] + }, + "abstract": { + "value": [ + "In an attempt to determine if selection bias could be a reason that religious attendance and depression are related, the predictive value of elevated depressive symptoms for a decrease in future attendance at religious services was examined in a longitudinal panel of 1,673 Dutch adults. Religious attendance was assessed yearly over five years using the single question, “how often do you attend religious gatherings nowadays?” Depressive symptoms were assessed four times within the first year using the Depression subscale of the Brief Symptom Inventory. Logistic regression models of change in attendance were created, stratifying by baseline attendance status. Attenders who developed elevated symptoms were less likely to subsequently decrease their attendance (relative risk ratio: 0.55, 95% CI [0.38–0.79]) relative to baseline as compared to those without elevated symptoms. This inverse association remained significant after controlling for health and demographic covariates, and when using multiply imputed data to account for attrition. Non-attenders were unlikely to start attending after elevated depressive symptoms. This study provides counter evidence against previous findings that church attenders are a self-selected healthier group." + ] + }, + "fulltext_html": { + "value": [ + "https://peerj.com/articles/311" + ] + }, + "fulltext_pdf": { + "value": [ + "https://peerj.com/articles/311.pdf" + ] + }, + "fulltext_xml": { + "value": [ + "/articles/311.xml" + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "figure": { + "value": [ + "https://dfzljdn9uc3pi.cloudfront.net/2014/311/1/fig-1-full.png", + "https://dfzljdn9uc3pi.cloudfront.net/2014/311/1/fig-2-full.png" + ] + }, + "figure_caption": { + "value": [ + "\nFigure 1: Subjects.\n(A) LISS datasets used and participant flowchart; (B) schedule of religion and depression assessments.\n  Download full-size image\nDOI: 10.7717/peerj.311/fig-1\n\n", + "\nFigure 2: Probabilities.\nPredicted probabilities of a decrease, same, and increase in religious attendance (95% CI).\n  Download full-size image\nDOI: 10.7717/peerj.311/fig-2\n\n" + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_hashes": [ + { + "fig-1-full.png": "3ff19ca931ac3850d2e6d045efb5d213" + }, + { + "fig-2-full.png": "b6a99fff0a72af9fde1e550f80d43799" + }, + { + "fulltext.html": "f295d3b2bedfd76a24ce69bfb9d40b79" + }, + { + "fulltext.pdf": "8aa4a538c24c0f3bfcc8b9fa5cd63d7c" + }, + { + "fulltext.xml": "c7b28594cefc8f9bd2fd61bc226056a9" + } + ] + }, + "https://peerj.com/articles/384/": { + "publisher": { + "value": [ + "PeerJ Inc." + ] + }, + "journal": { + "value": [ + "PeerJ" + ] + }, + "title": { + "value": [ + "Mutation analysis of the SLC26A4, FOXI1 and KCNJ10 genes in individuals with congenital hearing loss" + ] + }, + "authors": { + "value": [ + "Lynn M. Pique", + "Marie-Luise Brennan", + "Colin J. Davidson", + "Frederick Schaefer", + "John Greinwald Jr", + "Iris Schrijver" + ] + }, + "date": { + "value": [ + "2014-05-08" + ] + }, + "doi": { + "value": [ + "10.7717/peerj.384" + ] + }, + "volume": { + "value": [ + "2" + ] + }, + "issue": { + "value": [ + + ] + }, + "firstpage": { + "value": [ + "e384" + ] + }, + "description": { + "value": [ + "Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype." + ] + }, + "abstract": { + "value": [ + "Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype." + ] + }, + "fulltext_html": { + "value": [ + "https://peerj.com/articles/384" + ] + }, + "fulltext_pdf": { + "value": [ + "https://peerj.com/articles/384.pdf" + ] + }, + "fulltext_xml": { + "value": [ + "/articles/384.xml" + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "figure": { + "value": [ + "https://dfzljdn9uc3pi.cloudfront.net/2014/384/1/fig-1-full.png" + ] + }, + "figure_caption": { + "value": [ + "\nFigure 1: Identification of the heterozygous SLC26A4 deletion g.8091T-22145Cdel in subject PDS41.\n(A) The SLC26A4 MLPA probe mix includes probes for the 21 SLC26A4 exons, 14 reference probes and three probes specific for the point mutations c.1001+1G>A (IV S8+1G>A), c.707T>C (p.Leu236Pro) and c.1246A>C (p.Thr416Pro). Subject PDS41 is heterozygous for a deletion (g.8091T-22145Cdel) spanning exons 4–6 in SLC26A4, as evidenced by the reproducible reduction in peak height for these three exon probes (peaks labeled 4, 5, 6) relative to the control. PDS41 also has a heterozygous c.1246A>C (p.Thr416Pro) mutation that was previously identified by sequencing and confirmed by these MLPA results (peak labeled p.T416P). (B) Sequencing chromatogram of the deletion breakpoints in SLC26A4 IVS3 and IVS6. The deletion removes a total of 14,053 bp. IVS, intervening sequence.\n  Download full-size image\nDOI: 10.7717/peerj.384/fig-1\n\n" + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_hashes": [ + { + "fig-1-full.png": "6ee6bf8676df1087e9d724bfdc9178e8" + }, + { + "fulltext.html": "b7306f1715e3bdba6bbbc4d788579fde" + }, + { + "fulltext.pdf": "b2020a8f8037228e6face4a220751932" + }, + { + "fulltext.xml": "03352087dcff14b9fba0271c47574759" + } + ] + } } \ No newline at end of file diff --git a/test/plos.json b/test/plos.json index f6337e5..bec8ed0 100644 --- a/test/plos.json +++ b/test/plos.json @@ -1,344 +1,462 @@ { - "http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001874": [ - { - "fulltext_pdf": "http://dx.plos.org/10.1371/journal.pbio.1001874.pdf" - }, - { - "title": "Extracellular Vesicle-Mediated Transfer of Genetic Information between the Hematopoietic System and the Brain in Response to Inflammation" - }, - { - "author": "Kirsten Ridder" - }, - { - "author": "Sascha Keller" - }, - { - "author": "Maria Dams" - }, - { - "author": "Anne-Kathleen Rupp" - }, - { - "author": "Jessica Schlaudraff" - }, - { - "author": "Domenico Del Turco" - }, - { - "author": "Julia Starmann" - }, - { - "author": "Jadranka Macas" - }, - { - "author": "Darja Karpova" - }, - { - "author": "Kavi Devraj" - }, - { - "author": "Candan Depboylu" - }, - { - "author": "Britta Landfried" - }, - { - "author": "Bernd Arnold" - }, - { - "author": "Karl H. Plate" - }, - { - "author": "Günter Höglinger" - }, - { - "author": "Holger Sültmann" - }, - { - "author": "Peter Altevogt" - }, - { - "author": "Stefan Momma" - }, - { - "date": "2014/6/3" - }, - { - "doi": "10.1371/journal.pbio.1001874" - }, - { - "volume": "12" - }, - { - "issue": "6" - }, - { - "firstpage": "e1001874" - }, - { - "description": "PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines." - }, - { - "abstract": "AbstractMechanisms behind how the immune system signals to the brain in response to systemic inflammation are not fully understood. Transgenic mice expressing Cre recombinase specifically in the hematopoietic lineage in a Cre reporter background display recombination and marker gene expression in Purkinje neurons. Here we show that reportergene expression in neurons is caused by intercellular transfer of functional Cre recombinase messenger RNA from immune cells into neurons in the absence of cell fusion. In vitro purified secreted extracellular vesicles (EVs) from blood cells contain Cre mRNA, which induces recombination in neurons when injected into the brain. Although Cre-mediated recombination events in the brain occur very rarely in healthy animals, their number increases considerably in different injury models, particularly under inflammatory conditions, and extend beyond Purkinje neurons to other neuronal populations in cortex, hippocampus, and substantia nigra. Recombined Purkinje neurons differ in their miRNA profile from their nonrecombined counterparts, indicating physiological significance. These observations reveal the existence of a previously unrecognized mechanism to communicate RNA-based signals between the hematopoietic system and various organs, including the brain, in response to inflammation.\n" - }, - { - "abstract": "\nAuthor Summary\nPeripheral infections leading to an inflammatory response can initiate signaling from the hematopoietic system to various organs including the brain. The traditional view of this communication between blood and brain is that individual factors are released by immune cells that in turn bind to neuronal or nonneuronal target cells in the brain where they exert their effects. By using a genetic tracing system, we now show that extracellular vesicles, small membrane structures that can contain a multitude of different molecules, can transfer functional RNA directly from blood cells to neurons. Although this type of signaling is highly restricted in the healthy animal, inflammatory injuries increase both the frequency of transfer and the range of the neuronal target populations in the brain. By showing altered miRNA profiles in neurons receiving extracellular vesicle cargo, we predict a complex regulation of gene expression in neural cells in response to peripheral inflammation.\n" - }, - { - "journal.pbio.1001874.pdf": "c730b7b2434f950ea409d74a78c30316" - }, - { - "rendered.html": "264e78eb7494e3c8cffe3da98b88806b" - } - ], - "http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001882": [ - { - "fulltext_pdf": "http://dx.plos.org/10.1371/journal.pbio.1001882.pdf" - }, - { - "title": "The Billion Cell Construct: Will Three-Dimensional Printing Get Us There?" - }, - { - "author": "Jordan S. Miller" - }, - { - "date": "2014/6/17" - }, - { - "doi": "10.1371/journal.pbio.1001882" - }, - { - "volume": "12" - }, - { - "issue": "6" - }, - { - "firstpage": "e1001882" - }, - { - "description": "PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines." - }, - { - "abstract": "AbstractHow structure relates to function—across spatial scales, from the single molecule to the whole organism—is a central theme in biology. Bioengineers, however, wrestle with the converse question: will function follow form? That is, we struggle to approximate the architecture of living tissues experimentally, hoping that the structure we create will lead to the function we desire. A new means to explore the relationship between form and function in living tissue has arrived with three-dimensional printing, but the technology is not without limitations.\n" - }, - { - "journal.pbio.1001882.pdf": "b1a6bb4e193cb39cc6aef1b1866dcb3b" - }, - { - "rendered.html": "3842a2f207852e476a6c31c7baeed87b" - } - ], - "http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004441": [ - { - "fulltext_pdf": "http://dx.plos.org/10.1371/journal.pgen.1004441.pdf" - }, - { - "title": "An Operon of Three Transcriptional Regulators Controls Horizontal Gene Transfer of the Integrative and Conjugative Element ICEclc in Pseudomonas knackmussii B13" - }, - { - "author": "Nicolas Pradervand" - }, - { - "author": "Sandra Sulser" - }, - { - "author": "François Delavat" - }, - { - "author": "Ryo Miyazaki" - }, - { - "author": "Iker Lamas" - }, - { - "author": "Jan Roelof van der Meer" - }, - { - "date": "2014/6/19" - }, - { - "doi": "10.1371/journal.pgen.1004441" - }, - { - "volume": "10" - }, - { - "issue": "6" - }, - { - "firstpage": "e1004441" - }, - { - "description": "PLOS Genetics is an open-access" - }, - { - "abstract": "AbstractThe integrative and conjugative element ICEclc is a mobile genetic element in Pseudomonas knackmussii B13, and an experimental model for a widely distributed group of elements in Proteobacteria. ICEclc is transferred from specialized transfer competent cells, which arise at a frequency of 3-5% in a population at stationary phase. Very little is known about the different factors that control the transfer frequency of this ICE family. Here we report the discovery of a three-gene operon encoded by ICEclc, which exerts global control on transfer initiation. The operon consists of three consecutive regulatory genes, encoding a TetR-type repressor MfsR, a MarR-type regulator and a LysR-type activator TciR. We show that MfsR autoregulates expression of the operon, whereas TciR is a global activator of ICEclc gene expression, but no clear role was yet found for MarR. Deletion of mfsR increases expression of tciR and marR, causing the proportion of transfer competent cells to reach almost 100% and transfer frequencies to approach 1 per donor. mfsR deletion also caused a two orders of magnitude loss in population viability, individual cell growth arrest and loss of ICEclc. This indicates that autoregulation is an important feature maintaining ICE transfer but avoiding fitness loss. Bioinformatic analysis showed that the mfsR-marR-tciR operon is unique for ICEclc and a few highly related ICE, whereas tciR orthologues occur more widely in a large variety of suspected ICE among Proteobacteria.\n" - }, - { - "abstract": "\nAuthor Summary\nIntegrative and conjugative elements (ICEs) are a relatively newly recognized class of mobile elements in bacteria, which integrate at one or more positions in a host chromosome, can be excised, circularized, and transfer by conjugation to a new recipient cell. Genome sequencing indicated that ICEs often carry genes with potential adaptive functions for the host. Various ICE-types have been described and ICEclc is a useful model for a wide class of elements found in Beta- and Gammaproteobacteria. Because ICEs normally remain “silent” in the host chromosome and often lack selectable markers, their lifestyle is difficult to study. One of the characteristics of ICEclc is that transfer is initiated in only 3-5% of donor cells in a population during stationary phase. Here, we describe an operon of three regulatory genes, two of which control the transfer initiation of ICEclc. Our findings suggest that the low transfer rate results from the repression of an activator and that this is essential to minimize the deleterious effect of hyper-activation of transfer initiation. While the individual regulatory genes are quite common on ICEs, they rarely occur in this configuration.\n" - }, - { - "journal.pgen.1004441.pdf": "037d0a292bcca909943daf27a1e51f77" - }, - { - "rendered.html": "7f62500dce027f9e941b755ba2b8eef3" - } - ], - "http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004433": [ - { - "fulltext_pdf": "http://dx.plos.org/10.1371/journal.pgen.1004433.pdf" - }, - { - "title": "A Novel Peptidoglycan Binding Protein Crucial for PBP1A-Mediated Cell Wall Biogenesis in Vibrio cholerae" - }, - { - "author": "Tobias Dörr" - }, - { - "author": "Hubert Lam" - }, - { - "author": "Laura Alvarez" - }, - { - "author": "Felipe Cava" - }, - { - "author": "Brigid M. Davis" - }, - { - "author": "Matthew K. Waldor" - }, - { - "date": "2014/6/19" - }, - { - "doi": "10.1371/journal.pgen.1004433" - }, - { - "volume": "10" - }, - { - "issue": "6" - }, - { - "firstpage": "e1004433" - }, - { - "description": "PLOS Genetics is an open-access" - }, - { - "abstract": "AbstractThe bacterial cell wall, which is comprised of a mesh of polysaccharide strands crosslinked via peptide bridges (peptidoglycan, PG), is critical for maintenance of cell shape and survival. PG assembly is mediated by a variety of Penicillin Binding Proteins (PBP) whose fundamental activities have been characterized in great detail; however, there is limited knowledge of the factors that modulate their activities in different environments or growth phases. In Vibrio cholerae, the cause of cholera, PG synthesis during the transition into stationary phase is primarily mediated by the bifunctional enzyme PBP1A. Here, we screened an ordered V. cholerae transposon library for mutants that are sensitive to growth inhibition by non-canonical D-amino acids (DAA), which prevent growth and maintenance of cell shape in PBP1A-deficient V. cholerae. In addition to PBP1A and its lipoprotein activator LpoA, we found that CsiV, a small periplasmic protein with no previously described function, is essential for growth in the presence of DAA. Deletion of csiV, like deletion of lpoA or the PBP1A–encoding gene mrcA, causes cells to lose their rod shape in the presence of DAA or the beta-lactam antibiotic cefsulodin, and all three mutations are synthetically lethal with deletion of mrcB, which encodes PBP1B, V. cholerae's second key bifunctional PBP. CsiV interacts with LpoA and PG but apparently not with PBP1A, supporting the hypothesis that CsiV promotes LpoA's role as an activator of PBP1A, and thereby modulates V. cholerae PG biogenesis. Finally, the requirement for CsiV in PBP1A-mediated growth of V. cholerae can be overcome either by augmenting PG synthesis or by reducing PG degradation, thereby highlighting the importance of balancing these two processes for bacterial survival.\n" - }, - { - "abstract": "\nAuthor Summary\nBacteria surround themselves with a mesh-like peptidoglycan (PG) cell wall, which is essential for maintenance of cell shape and survival. While the enzymes that catalyze the assembly of the cell wall (aka penicillin-binding proteins (PBPs)) have been extensively characterized, our understanding of the factors that modulate the activities of these enzymes is less developed. Here, using a genetic screen, we identified a gene of unknown function that plays a crucial role in PBP1A-mediated cell wall synthesis in Vibrio cholerae, the bacterium causing cholera. V. cholerae mutants lacking this gene, whose protein product was re-named CsiV (for Cell shape integrity Vibrio), share many phenotypes with PBP1A mutants, including becoming spherical during stationary phase. We show that CsiV interacts with LpoA, a lipoprotein activator of PBP1A, as well as with PG. CsiV, LpoA, or PBP1A are all required for survival of V. cholerae lacking PBP1B, and mutants lacking any of these factors show marked changes in PG content in stationary phase. Collectively, our data suggest that CsiV acts through LpoA to promote PG biogenesis in V. cholerae and other vibrio species as well as in the other genera where this protein is found.\n" - }, - { - "journal.pgen.1004433.pdf": "890d664254554ae5142d7a8e0d10633e" - }, - { - "rendered.html": "1f0c36ede91377b79f56d7c81ced323f" - } - ], - "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0098781": [ - { - "fulltext_pdf": "http://dx.plos.org/10.1371/journal.pone.0098781.pdf" - }, - { - "title": "Foldscope: Origami-Based Paper Microscope" - }, - { - "author": "James S. Cybulski" - }, - { - "author": "James Clements" - }, - { - "author": "Manu Prakash" - }, - { - "date": "2014/6/18" - }, - { - "doi": "10.1371/journal.pone.0098781" - }, - { - "volume": "9" - }, - { - "issue": "6" - }, - { - "firstpage": "e98781" - }, - { - "description": "PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world." - }, - { - "abstract": "AbstractHere we describe an ultra-low-cost origami-based approach for large-scale manufacturing of microscopes, specifically demonstrating brightfield, darkfield, and fluorescence microscopes. Merging principles of optical design with origami enables high-volume fabrication of microscopes from 2D media. Flexure mechanisms created via folding enable a flat compact design. Structural loops in folded paper provide kinematic constraints as a means for passive self-alignment. This light, rugged instrument can survive harsh field conditions while providing a diversity of imaging capabilities, thus serving wide-ranging applications for cost-effective, portable microscopes in science and education.\n" - }, - { - "journal.pone.0098781.pdf": "5dfa35bcba2f631b40673c498c62f64b" - }, - { - "rendered.html": "7f91873f6353563e6ed11951ff5530c2" - } - ], - "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099348": [ - { - "fulltext_pdf": "https://peerj.com/articles/384.pdf" - }, - { - "fulltext_html": "https://peerj.com/articles/384" - }, - { - "title": "Mutation analysis of the SLC26A4, FOXI1 and KCNJ10 genes in individuals with congenital hearing loss" - }, - { - "author": "Lynn M. Pique" - }, - { - "author": "Marie-Luise Brennan" - }, - { - "author": "Colin J. Davidson" - }, - { - "author": "Frederick Schaefer" - }, - { - "author": "John Greinwald Jr" - }, - { - "author": "Iris Schrijver" - }, - { - "date": "2014-05-08" - }, - { - "doi": "10.7717/peerj.384" - }, - { - "volume": "2" - }, - { - "firstpage": "e384" - }, - { - "description": "Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype." - }, - { - "abstract": "Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype." - }, - { - "384": "72292ac92c4e073b47f2c50fb54dda67" - }, - { - "384.pdf": "b2020a8f8037228e6face4a220751932" - }, - { - "rendered.html": "8ef2fb18332a90a7fbbe6d533affb0ac" - } - ] + "http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001874": { + "fulltext_pdf": { + "value": [ + "http://dx.plos.org/10.1371/journal.pbio.1001874.pdf" + ] + }, + "fulltext_html": { + "value": [ + + ] + }, + "fulltext_xml": { + "value": [ + "/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pbio.1001874&representation=XML" + ] + }, + "title": { + "value": [ + "Extracellular Vesicle-Mediated Transfer of Genetic Information between the Hematopoietic System and the Brain in Response to Inflammation" + ] + }, + "author": { + "value": [ + "Kirsten Ridder", + "Sascha Keller", + "Maria Dams", + "Anne-Kathleen Rupp", + "Jessica Schlaudraff", + "Domenico Del Turco", + "Julia Starmann", + "Jadranka Macas", + "Darja Karpova", + "Kavi Devraj", + "Candan Depboylu", + "Britta Landfried", + "Bernd Arnold", + "Karl H. Plate", + "Günter Höglinger", + "Holger Sültmann", + "Peter Altevogt", + "Stefan Momma" + ] + }, + "date": { + "value": [ + "2014/6/3" + ] + }, + "doi": { + "value": [ + "10.1371/journal.pbio.1001874" + ] + }, + "volume": { + "value": [ + "12" + ] + }, + "issue": { + "value": [ + "6" + ] + }, + "firstpage": { + "value": [ + "e1001874" + ] + }, + "description": { + "value": [ + "PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines." + ] + }, + "abstract": { + "value": [ + "AbstractMechanisms behind how the immune system signals to the brain in response to systemic inflammation are not fully understood. Transgenic mice expressing Cre recombinase specifically in the hematopoietic lineage in a Cre reporter background display recombination and marker gene expression in Purkinje neurons. Here we show that reportergene expression in neurons is caused by intercellular transfer of functional Cre recombinase messenger RNA from immune cells into neurons in the absence of cell fusion. In vitro purified secreted extracellular vesicles (EVs) from blood cells contain Cre mRNA, which induces recombination in neurons when injected into the brain. Although Cre-mediated recombination events in the brain occur very rarely in healthy animals, their number increases considerably in different injury models, particularly under inflammatory conditions, and extend beyond Purkinje neurons to other neuronal populations in cortex, hippocampus, and substantia nigra. Recombined Purkinje neurons differ in their miRNA profile from their nonrecombined counterparts, indicating physiological significance. These observations reveal the existence of a previously unrecognized mechanism to communicate RNA-based signals between the hematopoietic system and various organs, including the brain, in response to inflammation.\n", + "\nAuthor Summary\nPeripheral infections leading to an inflammatory response can initiate signaling from the hematopoietic system to various organs including the brain. The traditional view of this communication between blood and brain is that individual factors are released by immune cells that in turn bind to neuronal or nonneuronal target cells in the brain where they exert their effects. By using a genetic tracing system, we now show that extracellular vesicles, small membrane structures that can contain a multitude of different molecules, can transfer functional RNA directly from blood cells to neurons. Although this type of signaling is highly restricted in the healthy animal, inflammatory injuries increase both the frequency of transfer and the range of the neuronal target populations in the brain. By showing altered miRNA profiles in neurons receiving extracellular vesicle cargo, we predict a complex regulation of gene expression in neural cells in response to peripheral inflammation.\n" + ] + }, + "file_hashes": [ + { + "fulltext.pdf": "c730b7b2434f950ea409d74a78c30316" + }, + { + "fulltext.xml": "40397e5bedf709fd1e98d19dc8a8a8fb" + } + ] + }, + "http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001882": { + "fulltext_pdf": { + "value": [ + "http://dx.plos.org/10.1371/journal.pbio.1001882.pdf" + ] + }, + "fulltext_html": { + "value": [ + + ] + }, + "fulltext_xml": { + "value": [ + "/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pbio.1001882&representation=XML" + ] + }, + "title": { + "value": [ + "The Billion Cell Construct: Will Three-Dimensional Printing Get Us There?" + ] + }, + "author": { + "value": [ + "Jordan S. Miller" + ] + }, + "date": { + "value": [ + "2014/6/17" + ] + }, + "doi": { + "value": [ + "10.1371/journal.pbio.1001882" + ] + }, + "volume": { + "value": [ + "12" + ] + }, + "issue": { + "value": [ + "6" + ] + }, + "firstpage": { + "value": [ + "e1001882" + ] + }, + "description": { + "value": [ + "PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines." + ] + }, + "abstract": { + "value": [ + "AbstractHow structure relates to function—across spatial scales, from the single molecule to the whole organism—is a central theme in biology. Bioengineers, however, wrestle with the converse question: will function follow form? That is, we struggle to approximate the architecture of living tissues experimentally, hoping that the structure we create will lead to the function we desire. A new means to explore the relationship between form and function in living tissue has arrived with three-dimensional printing, but the technology is not without limitations.\n" + ] + }, + "file_hashes": [ + { + "fulltext.pdf": "b1a6bb4e193cb39cc6aef1b1866dcb3b" + }, + { + "fulltext.xml": "cc5a11cbce83bca1b9f4718f0ff90f56" + } + ] + }, + "http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004441": { + "fulltext_pdf": { + "value": [ + "http://dx.plos.org/10.1371/journal.pgen.1004441.pdf" + ] + }, + "fulltext_html": { + "value": [ + + ] + }, + "fulltext_xml": { + "value": [ + "/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pgen.1004441&representation=XML" + ] + }, + "title": { + "value": [ + "An Operon of Three Transcriptional Regulators Controls Horizontal Gene Transfer of the Integrative and Conjugative Element ICEclc in Pseudomonas knackmussii B13" + ] + }, + "author": { + "value": [ + "Nicolas Pradervand", + "Sandra Sulser", + "François Delavat", + "Ryo Miyazaki", + "Iker Lamas", + "Jan Roelof van der Meer" + ] + }, + "date": { + "value": [ + "2014/6/19" + ] + }, + "doi": { + "value": [ + "10.1371/journal.pgen.1004441" + ] + }, + "volume": { + "value": [ + "10" + ] + }, + "issue": { + "value": [ + "6" + ] + }, + "firstpage": { + "value": [ + "e1004441" + ] + }, + "description": { + "value": [ + "PLOS Genetics is an open-access" + ] + }, + "abstract": { + "value": [ + "AbstractThe integrative and conjugative element ICEclc is a mobile genetic element in Pseudomonas knackmussii B13, and an experimental model for a widely distributed group of elements in Proteobacteria. ICEclc is transferred from specialized transfer competent cells, which arise at a frequency of 3-5% in a population at stationary phase. Very little is known about the different factors that control the transfer frequency of this ICE family. Here we report the discovery of a three-gene operon encoded by ICEclc, which exerts global control on transfer initiation. The operon consists of three consecutive regulatory genes, encoding a TetR-type repressor MfsR, a MarR-type regulator and a LysR-type activator TciR. We show that MfsR autoregulates expression of the operon, whereas TciR is a global activator of ICEclc gene expression, but no clear role was yet found for MarR. Deletion of mfsR increases expression of tciR and marR, causing the proportion of transfer competent cells to reach almost 100% and transfer frequencies to approach 1 per donor. mfsR deletion also caused a two orders of magnitude loss in population viability, individual cell growth arrest and loss of ICEclc. This indicates that autoregulation is an important feature maintaining ICE transfer but avoiding fitness loss. Bioinformatic analysis showed that the mfsR-marR-tciR operon is unique for ICEclc and a few highly related ICE, whereas tciR orthologues occur more widely in a large variety of suspected ICE among Proteobacteria.\n", + "\nAuthor Summary\nIntegrative and conjugative elements (ICEs) are a relatively newly recognized class of mobile elements in bacteria, which integrate at one or more positions in a host chromosome, can be excised, circularized, and transfer by conjugation to a new recipient cell. Genome sequencing indicated that ICEs often carry genes with potential adaptive functions for the host. Various ICE-types have been described and ICEclc is a useful model for a wide class of elements found in Beta- and Gammaproteobacteria. Because ICEs normally remain “silent” in the host chromosome and often lack selectable markers, their lifestyle is difficult to study. One of the characteristics of ICEclc is that transfer is initiated in only 3-5% of donor cells in a population during stationary phase. Here, we describe an operon of three regulatory genes, two of which control the transfer initiation of ICEclc. Our findings suggest that the low transfer rate results from the repression of an activator and that this is essential to minimize the deleterious effect of hyper-activation of transfer initiation. While the individual regulatory genes are quite common on ICEs, they rarely occur in this configuration.\n" + ] + }, + "file_hashes": [ + { + "fulltext.pdf": "037d0a292bcca909943daf27a1e51f77" + }, + { + "fulltext.xml": "09305c9e8d09f37ba7107df1fd0c7cd0" + } + ] + }, + "http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004433": { + "fulltext_pdf": { + "value": [ + "http://dx.plos.org/10.1371/journal.pgen.1004433.pdf" + ] + }, + "fulltext_html": { + "value": [ + + ] + }, + "fulltext_xml": { + "value": [ + "/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pgen.1004433&representation=XML" + ] + }, + "title": { + "value": [ + "A Novel Peptidoglycan Binding Protein Crucial for PBP1A-Mediated Cell Wall Biogenesis in Vibrio cholerae" + ] + }, + "author": { + "value": [ + "Tobias Dörr", + "Hubert Lam", + "Laura Alvarez", + "Felipe Cava", + "Brigid M. Davis", + "Matthew K. Waldor" + ] + }, + "date": { + "value": [ + "2014/6/19" + ] + }, + "doi": { + "value": [ + "10.1371/journal.pgen.1004433" + ] + }, + "volume": { + "value": [ + "10" + ] + }, + "issue": { + "value": [ + "6" + ] + }, + "firstpage": { + "value": [ + "e1004433" + ] + }, + "description": { + "value": [ + "PLOS Genetics is an open-access" + ] + }, + "abstract": { + "value": [ + "AbstractThe bacterial cell wall, which is comprised of a mesh of polysaccharide strands crosslinked via peptide bridges (peptidoglycan, PG), is critical for maintenance of cell shape and survival. PG assembly is mediated by a variety of Penicillin Binding Proteins (PBP) whose fundamental activities have been characterized in great detail; however, there is limited knowledge of the factors that modulate their activities in different environments or growth phases. In Vibrio cholerae, the cause of cholera, PG synthesis during the transition into stationary phase is primarily mediated by the bifunctional enzyme PBP1A. Here, we screened an ordered V. cholerae transposon library for mutants that are sensitive to growth inhibition by non-canonical D-amino acids (DAA), which prevent growth and maintenance of cell shape in PBP1A-deficient V. cholerae. In addition to PBP1A and its lipoprotein activator LpoA, we found that CsiV, a small periplasmic protein with no previously described function, is essential for growth in the presence of DAA. Deletion of csiV, like deletion of lpoA or the PBP1A–encoding gene mrcA, causes cells to lose their rod shape in the presence of DAA or the beta-lactam antibiotic cefsulodin, and all three mutations are synthetically lethal with deletion of mrcB, which encodes PBP1B, V. cholerae's second key bifunctional PBP. CsiV interacts with LpoA and PG but apparently not with PBP1A, supporting the hypothesis that CsiV promotes LpoA's role as an activator of PBP1A, and thereby modulates V. cholerae PG biogenesis. Finally, the requirement for CsiV in PBP1A-mediated growth of V. cholerae can be overcome either by augmenting PG synthesis or by reducing PG degradation, thereby highlighting the importance of balancing these two processes for bacterial survival.\n", + "\nAuthor Summary\nBacteria surround themselves with a mesh-like peptidoglycan (PG) cell wall, which is essential for maintenance of cell shape and survival. While the enzymes that catalyze the assembly of the cell wall (aka penicillin-binding proteins (PBPs)) have been extensively characterized, our understanding of the factors that modulate the activities of these enzymes is less developed. Here, using a genetic screen, we identified a gene of unknown function that plays a crucial role in PBP1A-mediated cell wall synthesis in Vibrio cholerae, the bacterium causing cholera. V. cholerae mutants lacking this gene, whose protein product was re-named CsiV (for Cell shape integrity Vibrio), share many phenotypes with PBP1A mutants, including becoming spherical during stationary phase. We show that CsiV interacts with LpoA, a lipoprotein activator of PBP1A, as well as with PG. CsiV, LpoA, or PBP1A are all required for survival of V. cholerae lacking PBP1B, and mutants lacking any of these factors show marked changes in PG content in stationary phase. Collectively, our data suggest that CsiV acts through LpoA to promote PG biogenesis in V. cholerae and other vibrio species as well as in the other genera where this protein is found.\n" + ] + }, + "file_hashes": [ + { + "fulltext.pdf": "890d664254554ae5142d7a8e0d10633e" + }, + { + "fulltext.xml": "078a5543dd025d13f966e683187b85fd" + } + ] + }, + "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0098781": { + "fulltext_pdf": { + "value": [ + "http://dx.plos.org/10.1371/journal.pone.0098781.pdf" + ] + }, + "fulltext_html": { + "value": [ + + ] + }, + "fulltext_xml": { + "value": [ + "/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0098781&representation=XML" + ] + }, + "title": { + "value": [ + "Foldscope: Origami-Based Paper Microscope" + ] + }, + "author": { + "value": [ + "James S. Cybulski", + "James Clements", + "Manu Prakash" + ] + }, + "date": { + "value": [ + "2014/6/18" + ] + }, + "doi": { + "value": [ + "10.1371/journal.pone.0098781" + ] + }, + "volume": { + "value": [ + "9" + ] + }, + "issue": { + "value": [ + "6" + ] + }, + "firstpage": { + "value": [ + "e98781" + ] + }, + "description": { + "value": [ + "PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world." + ] + }, + "abstract": { + "value": [ + "AbstractHere we describe an ultra-low-cost origami-based approach for large-scale manufacturing of microscopes, specifically demonstrating brightfield, darkfield, and fluorescence microscopes. Merging principles of optical design with origami enables high-volume fabrication of microscopes from 2D media. Flexure mechanisms created via folding enable a flat compact design. Structural loops in folded paper provide kinematic constraints as a means for passive self-alignment. This light, rugged instrument can survive harsh field conditions while providing a diversity of imaging capabilities, thus serving wide-ranging applications for cost-effective, portable microscopes in science and education.\n" + ] + }, + "file_hashes": [ + { + "fulltext.pdf": "5dfa35bcba2f631b40673c498c62f64b" + }, + { + "fulltext.xml": "49e918d4fee77f96ff9f1d49615f3785" + } + ] + }, + "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099348": { + "fulltext_pdf": { + "value": [ + "http://dx.plos.org/10.1371/journal.pone.0099348.pdf" + ] + }, + "fulltext_html": { + "value": [ + + ] + }, + "fulltext_xml": { + "value": [ + "/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0099348&representation=XML" + ] + }, + "title": { + "value": [ + "Co-Infection of Blacklegged Ticks with Babesia microti and Borrelia burgdorferi Is Higher than Expected and Acquired from Small Mammal Hosts" + ] + }, + "author": { + "value": [ + "Michelle H. Hersh", + "Richard S. Ostfeld", + "Diana J. McHenry", + "Michael Tibbetts", + "Jesse L. Brunner", + "Mary E. Killilea", + "Kathleen LoGiudice", + "Kenneth A. Schmidt", + "Felicia Keesing" + ] + }, + "date": { + "value": [ + "2014/6/18" + ] + }, + "doi": { + "value": [ + "10.1371/journal.pone.0099348" + ] + }, + "volume": { + "value": [ + "9" + ] + }, + "issue": { + "value": [ + "6" + ] + }, + "firstpage": { + "value": [ + "e99348" + ] + }, + "description": { + "value": [ + "PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world." + ] + }, + "abstract": { + "value": [ + "AbstractHumans in the northeastern and midwestern United States are at increasing risk of acquiring tickborne diseases – not only Lyme disease, but also two emerging diseases, human granulocytic anaplasmosis and human babesiosis. Co-infection with two or more of these pathogens can increase the severity of health impacts. The risk of co-infection is intensified by the ecology of these three diseases because all three pathogens (Borrelia burgdorferi, Anaplasma phagocytophilum, and Babesia microti) are transmitted by the same vector, blacklegged ticks (Ixodes scapularis), and are carried by many of the same reservoir hosts. The risk of exposure to multiple pathogens from a single tick bite and the sources of co-infected ticks are not well understood. In this study, we quantify the risk of co-infection by measuring infection prevalence in 4,368 questing nymphs throughout an endemic region for all three diseases (Dutchess County, NY) to determine if co-infections occur at frequencies other than predicted by independent assortment of pathogens. Further, we identify sources of co-infection by quantifying rates of co-infection on 3,275 larval ticks fed on known hosts. We find significant deviations of levels of co-infection in questing nymphs, most notably 83% more co-infection with Babesia microti and Borrelia burgdorferi than predicted by chance alone. Further, this pattern of increased co-infection was observed in larval ticks that fed on small mammal hosts, but not on meso-mammal, sciurid, or avian hosts. Co-infections involving A. phagocytophilum were less common, and fewer co-infections of A. phagocytophilum and B. microti than predicted by chance were observed in both questing nymphs and larvae fed on small mammals. Medical practitioners should be aware of the elevated risk of B. microti/B. burgdorferi co-infection.\n" + ] + }, + "file_hashes": [ + { + "fulltext.pdf": "71ff4b0cd5933789dbb0a38d756c6193" + }, + { + "fulltext.xml": "b8506c6bdd446151410a270ea4fde031" + } + ] + } } \ No newline at end of file diff --git a/test/pnas.json b/test/pnas.json index 78a4f06..95efcab 100644 --- a/test/pnas.json +++ b/test/pnas.json @@ -1,608 +1,893 @@ { - "http://www.pnas.org/content/111/33/12019": [ - { - "publisher": "National Acad Sciences" - }, - { - "title": "Disassembly of mitotic checkpoint complexes by the joint action of the AAA-ATPase TRIP13 and p31comet" - }, - { - "authors": "Esther Eytan" - }, - { - "authors": "Kexi Wang" - }, - { - "authors": "Shirly Miniowitz-Shemtov" - }, - { - "authors": "Danielle Sitry-Shevah" - }, - { - "authors": "Sharon Kaisari" - }, - { - "authors": "Tim J. Yen" - }, - { - "authors": "Song-Tao Liu" - }, - { - "authors": "Avram Hershko" - }, - { - "date": "08/19/2014" - }, - { - "volume": "111" - }, - { - "issue": "33" - }, - { - "firstpage": "12019" - }, - { - "lastpage": "12024" - }, - { - "doi": "10.1073/pnas.1412901111" - }, - { - "journal": "Proceedings of the National Academy of Sciences" - }, - { - "abstract": "\n Abstract\n The mitotic (or spindle assembly) checkpoint system delays anaphase until all chromosomes are correctly attached to the mitotic\n spindle. When the checkpoint is active, a Mitotic Checkpoint Complex (MCC) assembles and inhibits the ubiquitin ligase Anaphase-Promoting\n Complex/Cyclosome (APC/C). MCC is composed of the checkpoint proteins Mad2, BubR1, and Bub3 associated with the APC/C activator\n Cdc20. When the checkpoint signal is turned off, MCC is disassembled and the checkpoint is inactivated. The mechanisms of\n the disassembly of MCC are not sufficiently understood. We have previously observed that ATP hydrolysis is required for the\n action of the Mad2-binding protein p31comet to disassemble MCC. We now show that HeLa cell extracts contain a factor that promotes ATP- and p31comet-dependent disassembly of a Cdc20–Mad2 subcomplex and identify it as Thyroid Receptor Interacting Protein 13 (TRIP13), an\n AAA-ATPase known to interact with p31comet. The joint action of TRIP13 and p31comet also promotes the release of Mad2 from MCC, participates in the complete disassembly of MCC and abrogates checkpoint inhibition\n of APC/C. We propose that TRIP13 plays centrally important roles in the sequence of events leading to MCC disassembly and\n checkpoint inactivation.\n \n " - }, - { - "abstract_html": "http://www.pnas.org/content/111/33/12019.abstract" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://www.pnas.org/content/111/33/12019.full.pdf" - }, - { - "fulltext_html": "http://www.pnas.org/content/111/33/12019.full" - }, - { - "supplementary_material": "/content/111/33/12019/suppl/DCSupplemental" - }, - { - "12019.full": "3e4de6ee23ec43b80929bce80ac814ae" - }, - { - "rendered.html": "c4562ad494ed219d6084f17305827b16" - } - ], - "http://www.pnas.org/content/111/34/12396": [ - { - "publisher": "National Acad Sciences" - }, - { - "title": "Microbial-induced meprin β cleavage in MUC2 mucin and a functional CFTR channel are required to release anchored small intestinal mucus" - }, - { - "authors": "André Schütte" - }, - { - "authors": "Anna Ermund" - }, - { - "authors": "Christoph Becker-Pauly" - }, - { - "authors": "Malin E. V. Johansson" - }, - { - "authors": "Ana M. Rodriguez-Pineiro" - }, - { - "authors": "Fredrik Bäckhed" - }, - { - "authors": "Stefan Müller" - }, - { - "authors": "Daniel Lottaz" - }, - { - "authors": "Judith S. Bond" - }, - { - "authors": "Gunnar C. Hansson" - }, - { - "date": "08/26/2014" - }, - { - "volume": "111" - }, - { - "issue": "34" - }, - { - "firstpage": "12396" - }, - { - "lastpage": "12401" - }, - { - "doi": "10.1073/pnas.1407597111" - }, - { - "journal": "Proceedings of the National Academy of Sciences" - }, - { - "abstract": "\n Abstract\n The mucus that covers and protects the epithelium of the intestine is built around its major structural component, the gel-forming\n MUC2 mucin. The gel-forming mucins have traditionally been assumed to be secreted as nonattached. The colon has a two-layered\n mucus system where the inner mucus is attached to the epithelium, whereas the small intestine normally has a nonattached mucus.\n However, the mucus of the small intestine of meprin β-deficient mice was now found to be attached. Meprin β is an endogenous\n zinc-dependent metalloprotease now shown to cleave the N-terminal region of the MUC2 mucin at two specific sites. When recombinant\n meprin β was added to the attached mucus of meprin β-deficient mice, the mucus was detached from the epithelium. Similar to\n meprin β-deficient mice, germ-free mice have attached mucus as they did not shed the membrane-anchored meprin β into the luminal\n mucus. The ileal mucus of cystic fibrosis (CF) mice with a nonfunctional cystic fibrosis transmembrane conductance regulator\n (CFTR) channel was recently shown to be attached to the epithelium. Addition of recombinant meprin β to CF mucus did not release\n the mucus, but further addition of bicarbonate rendered the CF mucus normal, suggesting that MUC2 unfolding exposed the meprin\n β cleavage sites. Mucus is thus secreted attached to the goblet cells and requires an enzyme, meprin β in the small intestine,\n to be detached and released into the intestinal lumen. This process regulates mucus properties, can be triggered by bacterial\n contact, and is nonfunctional in CF due to poor mucin unfolding.\n \n " - }, - { - "abstract_html": "http://www.pnas.org/content/111/34/12396.abstract" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://www.pnas.org/content/111/34/12396.full.pdf" - }, - { - "fulltext_html": "http://www.pnas.org/content/111/34/12396.full" - }, - { - "supplementary_material": "/content/111/34/12396/suppl/DCSupplemental" - }, - { - "DCSupplemental": "a29c88e1ce8cbabb41fd557d1158ce68" - }, - { - "rendered.html": "e82463b4b3bc6a32c4498503d32144a6" - } - ], - "http://www.pnas.org/content/111/34/12390": [ - { - "publisher": "National Acad Sciences" - }, - { - "title": "Chaperone-enhanced purification of unconventional myosin 15, a molecular motor specialized for stereocilia protein trafficking" - }, - { - "authors": "Jonathan E. Bird" - }, - { - "authors": "Yasuharu Takagi" - }, - { - "authors": "Neil Billington" - }, - { - "authors": "Marie-Paule Strub" - }, - { - "authors": "James R. Sellers" - }, - { - "authors": "Thomas B. Friedman" - }, - { - "date": "08/26/2014" - }, - { - "volume": "111" - }, - { - "issue": "34" - }, - { - "firstpage": "12390" - }, - { - "lastpage": "12395" - }, - { - "doi": "10.1073/pnas.1409459111" - }, - { - "journal": "Proceedings of the National Academy of Sciences" - }, - { - "abstract": "\n Abstract\n Unconventional myosin 15 is a molecular motor expressed in inner ear hair cells that transports protein cargos within developing\n mechanosensory stereocilia. Mutations of myosin 15 cause profound hearing loss in humans and mice; however, the properties\n of this motor and its regulation within the stereocilia organelle are unknown. To address these questions, we expressed a\n subfragment 1-like (S1) truncation of mouse myosin 15, comprising the predicted motor domain plus three light-chain binding\n sites. Following unsuccessful attempts to express functional myosin 15-S1 using the Spodoptera frugiperda (Sf9)-baculovirus system, we discovered that coexpression of the muscle-myosin–specific chaperone UNC45B, in addition to\n the chaperone heat-shock protein 90 (HSP90) significantly increased the yield of functional protein. Surprisingly, myosin\n 15-S1 did not bind calmodulin with high affinity. Instead, the IQ domains bound essential and regulatory light chains that\n are normally associated with class II myosins. We show that myosin 15-S1 is a barbed-end–directed motor that moves actin filaments\n in a gliding assay (∼430 nm·s−1 at 30 °C), using a power stroke of 7.9 nm. The maximum ATPase rate (kcat ∼6 s−1) was similar to the actin-detachment rate (kdet = 6.2 s−1) determined in single molecule optical trapping experiments, indicating that myosin 15-S1 was rate limited by transit through\n strongly actin-bound states, similar to other processive myosin motors. Our data further indicate that in addition to folding\n muscle myosin, UNC45B facilitates maturation of an unconventional myosin. We speculate that chaperone coexpression may be\n a simple method to optimize the purification of other myosin motors from Sf9 insect cells.\n \n " - }, - { - "abstract_html": "http://www.pnas.org/content/111/34/12390.abstract" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://www.pnas.org/content/111/34/12390.full.pdf" - }, - { - "fulltext_html": "http://www.pnas.org/content/111/34/12390.full" - }, - { - "supplementary_material": "/content/111/34/12390/suppl/DCSupplemental" - }, - { - "12390.abstract": "1f36cf2d40f2a295e8b60f3bf8a361fe" - }, - { - "rendered.html": "e4678253091b9ed6a758e328f44764ca" - } - ], - "http://www.pnas.org/content/101/34/12520": [ - { - "publisher": "National Acad Sciences" - }, - { - "title": "Cell mechanosensitivity controls the anisotropy of focal adhesions" - }, - { - "authors": "Alice Nicolas" - }, - { - "authors": "Benjamin Geiger" - }, - { - "authors": "Samuel A. Safran" - }, - { - "date": "08/24/2004" - }, - { - "volume": "101" - }, - { - "issue": "34" - }, - { - "firstpage": "12520" - }, - { - "lastpage": "12525" - }, - { - "doi": "10.1073/pnas.0403539101" - }, - { - "journal": "Proceedings of the National Academy of Sciences of the United States of America" - }, - { - "abstract": "\n \n Abstract\n \n Cellular adhesions are modulated by cytoskeletal forces or external stresses and adapt to the mechanical properties of the\n extracellular matrix. We propose that this mechanosensitivity can be driven at least in part by the elastic, cell-contractility-induced\n deformations of protein molecules that form the adhesion. The model accounts for observations of anisotropic growth and shrinkage\n of focal adhesions in the direction of the force and predicts that focal adhesions only grow within a range of force that\n is determined by the composition and matrix properties. This prediction is consistent with the observations of a force threshold\n for the appearance of elongated focal adhesions and the disruption of adhesions into fibrils on a mobile extracellular matrix.\n The growth dynamics is calculated and the predicted sliding of focal adhesions is consistent with several experiments.\n \n \n " - }, - { - "abstract_html": "http://www.pnas.org/content/101/34/12520.abstract" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://www.pnas.org/content/101/34/12520.full.pdf" - }, - { - "fulltext_html": "http://www.pnas.org/content/101/34/12520.full" - }, - { - "supplementary_material": "/content/101/34/12520/suppl/DC1" - }, - { - "DC1": "0076772b82d2b0c3f1dd442e98a013f9" - }, - { - "rendered.html": "e06f8aa80d9af9e7f4a8c82591b7576c" - } - ], - "http://www.pnas.org/content/71/2/302": [ - { - "publisher": "National Acad Sciences" - }, - { - "title": "Cell-Free Translation of Messenger RNA of Simian Virus 40: Synthesis of the Major Capsid Protein" - }, - { - "authors": "Carol L. Prives" - }, - { - "authors": "Haim Aviv" - }, - { - "authors": "Bruce M. Paterson" - }, - { - "authors": "Bryan E. Roberts" - }, - { - "authors": "Shmuel Rozenblatt" - }, - { - "authors": "Michel Revel" - }, - { - "authors": "Ernest Winocour" - }, - { - "date": "02/01/1974" - }, - { - "volume": "71" - }, - { - "issue": "2" - }, - { - "firstpage": "302" - }, - { - "lastpage": "306" - }, - { - "journal": "Proceedings of the National Academy of Sciences" - }, - { - "abstract": "\n Abstract\n Extracts of wheat germ are capable of synthesizing the major capsid protein of simian virus 40. Poly(A)-containing RNA from\n BS-C-1 cells infected with simian virus 40 directed the synthesis of a novel polypeptide that migrates in polyacrylamide gels\n together with the major capsid polypeptide of simian virus 40, VP-1. The patterns of the major tryptic peptides of purified\n VP-1 and the novel polypeptide synthesized in vitro were identical after two-dimensional paper electrophoresis. The novel polypeptide was not synthesized in response to poly(A)-rich\n RNA from uninfected cells or from virus-infected cells treated with cytosine arabinoside. Messenger RNA from infected cells\n purified by selective hybridization to DNA of simian virus 40 directs the synthesis of a major polypeptide of electrophoretic\n mobility similar to that of VP-1 of simian virus 40. This approach should prove useful in identifying additional products\n specified by DNA tumor viruses.\n \n " - }, - { - "abstract_html": "http://www.pnas.org/content/71/2/302.abstract" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://www.pnas.org/content/71/2/302.full.pdf" - }, - { - "302.abstract": "ca6e67b294a77aac0fa426e85232f1f5" - }, - { - "rendered.html": "ecb901b53714839fdb8a2d996623c138" - } - ], - "http://www.pnas.org/content/109/24/9248": [ - { - "publisher": "National Acad Sciences" - }, - { - "title": "Heart wall myofibers are arranged in minimal surfaces to optimize organ function" - }, - { - "authors": "Peter Savadjiev" - }, - { - "authors": "Gustav J. Strijkers" - }, - { - "authors": "Adrianus J. Bakermans" - }, - { - "authors": "Emmanuel Piuze" - }, - { - "authors": "Steven W. Zucker" - }, - { - "authors": "Kaleem Siddiqi" - }, - { - "date": "06/12/2012" - }, - { - "volume": "109" - }, - { - "issue": "24" - }, - { - "firstpage": "9248" - }, - { - "lastpage": "9253" - }, - { - "doi": "10.1073/pnas.1120785109" - }, - { - "journal": "Proceedings of the National Academy of Sciences" - }, - { - "abstract": "\n Abstract\n Heart wall myofibers wind as helices around the ventricles, strengthening them in a manner analogous to the reinforcement\n of concrete cylindrical columns by spiral steel cables [Richart FE, et al. (1929) Univ of Illinois, Eng Exp Stn Bull 190].\n A multitude of such fibers, arranged smoothly and regularly, contract and relax as an integrated functional unit as the heart\n beats. To orchestrate this motion, fiber tangling must be avoided and pumping should be efficient. Current models of myofiber\n orientation across the heart wall suggest groupings into sheets or bands, but the precise geometry of bundles of myofibers\n is unknown. Here we show that this arrangement takes the form of a special minimal surface, the generalized helicoid [Blair\n DE, Vanstone JR (1978) Minimal Submanifolds and Geodesics 13–16], closing the gap between individual myofibers and their collective wall structure. The model holds across species,\n with a smooth variation in its three curvature parameters within the myocardial wall providing tight fits to diffusion magnetic\n resonance images from the rat, the dog, and the human. Mathematically it explains how myofibers are bundled in the heart wall\n while economizing fiber length and optimizing ventricular ejection volume as they contract. The generalized helicoid provides\n a unique foundation for analyzing the fibrous composite of the heart wall and should therefore find applications in heart\n tissue engineering and in the study of heart muscle diseases.\n \n " - }, - { - "abstract_html": "http://www.pnas.org/content/109/24/9248.abstract" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://www.pnas.org/content/109/24/9248.full.pdf" - }, - { - "fulltext_html": "http://www.pnas.org/content/109/24/9248.full" - }, - { - "supplementary_material": "/content/109/24/9248/suppl/DCSupplemental" - }, - { - "DCSupplemental": "5bf113bd006256852685f7baad425748" - }, - { - "rendered.html": "bbf7da42dcfa67ee9b7072bc470bf967" - } - ], - "http://www.pnas.org/content/111/24/8788": [ - { - "publisher": "National Acad Sciences" - }, - { - "title": "Experimental evidence of massive-scale emotional contagion through social networks" - }, - { - "authors": "Adam D. I. Kramer" - }, - { - "authors": "Jamie E. Guillory" - }, - { - "authors": "Jeffrey T. Hancock" - }, - { - "date": "06/17/2014" - }, - { - "volume": "111" - }, - { - "issue": "24" - }, - { - "firstpage": "8788" - }, - { - "lastpage": "8790" - }, - { - "doi": "10.1073/pnas.1320040111" - }, - { - "journal": "Proceedings of the National Academy of Sciences" - }, - { - "abstract": "\n Abstract\n Emotional states can be transferred to others via emotional contagion, leading people to experience the same emotions without\n their awareness. Emotional contagion is well established in laboratory experiments, with people transferring positive and\n negative emotions to others. Data from a large real-world social network, collected over a 20-y period suggests that longer-lasting\n moods (e.g., depression, happiness) can be transferred through networks [Fowler JH, Christakis NA (2008) BMJ 337:a2338], although the results are controversial. In an experiment with people who use Facebook, we test whether emotional\n contagion occurs outside of in-person interaction between individuals by reducing the amount of emotional content in the News\n Feed. When positive expressions were reduced, people produced fewer positive posts and more negative posts; when negative\n expressions were reduced, the opposite pattern occurred. These results indicate that emotions expressed by others on Facebook\n influence our own emotions, constituting experimental evidence for massive-scale contagion via social networks. This work\n also suggests that, in contrast to prevailing assumptions, in-person interaction and nonverbal cues are not strictly necessary\n for emotional contagion, and that the observation of others’ positive experiences constitutes a positive experience for people.\n \n " - }, - { - "abstract_html": "http://www.pnas.org/content/111/24/8788.abstract" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://www.pnas.org/content/111/24/8788.full.pdf" - }, - { - "fulltext_html": "http://www.pnas.org/content/111/24/8788.full" - }, - { - "8788.full": "6479c6f32c31b9edba389ef3fff7fc93" - }, - { - "rendered.html": "d1a4184cea26192b275792bcb3095b6d" - } - ], - "http://www.pnas.org/content/111/29/10779.1": [ - { - "publisher": "National Acad Sciences" - }, - { - "title": "Editorial Expression of Concern: Experimental evidence of massivescale emotional contagion through social networks" - }, - { - "date": "07/22/2014" - }, - { - "volume": "111" - }, - { - "issue": "29" - }, - { - "firstpage": "10779" - }, - { - "lastpage": "10779" - }, - { - "doi": "10.1073/pnas.1412469111" - }, - { - "journal": "Proceedings of the National Academy of Sciences" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://www.pnas.org/content/111/29/10779.1.full.pdf" - }, - { - "fulltext_html": "http://www.pnas.org/content/111/29/10779.1.full" - }, - { - "10779.1.full.pdf": "f1ff6f1b35c5397c8e7762ffe36fed02" - }, - { - "rendered.html": "553e807bf9b1e31721733c8f49db590e" - } - ], - "http://www.pnas.org/content/111/35/12758": [ - { - "publisher": "National Acad Sciences" - }, - { - "title": "Experimental basis for a new allosteric model for multisubunit proteins" - }, - { - "authors": "Cristiano Viappiani" - }, - { - "authors": "Stefania Abbruzzetti" - }, - { - "authors": "Luca Ronda" - }, - { - "authors": "Stefano Bettati" - }, - { - "authors": "Eric. R. Henry" - }, - { - "authors": "Andrea Mozzarelli" - }, - { - "authors": "William A. Eaton" - }, - { - "date": "09/02/2014" - }, - { - "volume": "111" - }, - { - "issue": "35" - }, - { - "firstpage": "12758" - }, - { - "lastpage": "12763" - }, - { - "doi": "10.1073/pnas.1413566111" - }, - { - "journal": "Proceedings of the National Academy of Sciences" - }, - { - "abstract": "\n Abstract\n Monod, Wyman, and Changeux (MWC) explained allostery in multisubunit proteins with a widely applied theoretical model in which\n binding of small molecules, so-called allosteric effectors, affects reactivity by altering the equilibrium between more reactive\n (R) and less reactive (T) quaternary structures. In their model, each quaternary structure has a single reactivity. Here,\n we use silica gels to trap protein conformations and a new kind of laser photolysis experiment to show that hemoglobin, the\n paradigm of allostery, exhibits two ligand binding phases with the same fast and slow rates in both R and T quaternary structures.\n Allosteric effectors change the fraction of each phase but not the rates. These surprising results are readily explained by\n the simplest possible extension of the MWC model to include a preequilibrium between two tertiary conformations that have\n the same functional properties within each quaternary structure. They also have important implications for the long-standing\n question of a structural explanation for the difference in hemoglobin oxygen affinity of the two quaternary structures.\n \n " - }, - { - "abstract_html": "http://www.pnas.org/content/111/35/12758.abstract" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://www.pnas.org/content/111/35/12758.full.pdf" - }, - { - "fulltext_html": "http://www.pnas.org/content/111/35/12758.full" - }, - { - "supplementary_material": "/content/111/35/12758/suppl/DCSupplemental" - }, - { - "12758.abstract": "886f0f703849b8ce926b57b3581915cb" - }, - { - "rendered.html": "2cd299dcb051059fe566dce2f1168b3d" - } - ] + "http://www.pnas.org/content/111/33/12019": { + "publisher": { + "value": [ + "National Acad Sciences" + ] + }, + "title": { + "value": [ + "Disassembly of mitotic checkpoint complexes by the joint action of the AAA-ATPase TRIP13 and p31comet" + ] + }, + "authors": { + "value": [ + "Esther Eytan", + "Kexi Wang", + "Shirly Miniowitz-Shemtov", + "Danielle Sitry-Shevah", + "Sharon Kaisari", + "Tim J. Yen", + "Song-Tao Liu", + "Avram Hershko" + ] + }, + "date": { + "value": [ + "08/19/2014" + ] + }, + "volume": { + "value": [ + "111" + ] + }, + "issue": { + "value": [ + "33" + ] + }, + "firstpage": { + "value": [ + "12019" + ] + }, + "lastpage": { + "value": [ + "12024" + ] + }, + "doi": { + "value": [ + "10.1073/pnas.1412901111" + ] + }, + "journal": { + "value": [ + "Proceedings of the National Academy of Sciences" + ] + }, + "abstract": { + "value": [ + "\n Abstract\n The mitotic (or spindle assembly) checkpoint system delays anaphase until all chromosomes are correctly attached to the mitotic\n spindle. When the checkpoint is active, a Mitotic Checkpoint Complex (MCC) assembles and inhibits the ubiquitin ligase Anaphase-Promoting\n Complex/Cyclosome (APC/C). MCC is composed of the checkpoint proteins Mad2, BubR1, and Bub3 associated with the APC/C activator\n Cdc20. When the checkpoint signal is turned off, MCC is disassembled and the checkpoint is inactivated. The mechanisms of\n the disassembly of MCC are not sufficiently understood. We have previously observed that ATP hydrolysis is required for the\n action of the Mad2-binding protein p31comet to disassemble MCC. We now show that HeLa cell extracts contain a factor that promotes ATP- and p31comet-dependent disassembly of a Cdc20–Mad2 subcomplex and identify it as Thyroid Receptor Interacting Protein 13 (TRIP13), an\n AAA-ATPase known to interact with p31comet. The joint action of TRIP13 and p31comet also promotes the release of Mad2 from MCC, participates in the complete disassembly of MCC and abrogates checkpoint inhibition\n of APC/C. We propose that TRIP13 plays centrally important roles in the sequence of events leading to MCC disassembly and\n checkpoint inactivation.\n \n " + ] + }, + "abstract_html": { + "value": [ + "http://www.pnas.org/content/111/33/12019.abstract" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.pnas.org/content/111/33/12019.full.pdf" + ] + }, + "fulltext_html": { + "value": [ + "http://www.pnas.org/content/111/33/12019.full" + ] + }, + "supplementary_material": { + "value": [ + "/content/111/33/12019/suppl/DCSupplemental" + ] + }, + "file_hashes": [ + { + "12019.abstract": "4e869f429e6c09261677a36f131652e2" + }, + { + "12019.full": "7332368f057b0639f6665dabe7cd2ae2" + }, + { + "12019.full.pdf": "2b89720e492289665f2c6c4bf7cc38dd" + }, + { + "DCSupplemental": "6f962f450a3df0b85a264f9f988ade58" + } + ] + }, + "http://www.pnas.org/content/111/34/12396": { + "publisher": { + "value": [ + "National Acad Sciences" + ] + }, + "title": { + "value": [ + "Microbial-induced meprin β cleavage in MUC2 mucin and a functional CFTR channel are required to release anchored small intestinal mucus" + ] + }, + "authors": { + "value": [ + "André Schütte", + "Anna Ermund", + "Christoph Becker-Pauly", + "Malin E. V. Johansson", + "Ana M. Rodriguez-Pineiro", + "Fredrik Bäckhed", + "Stefan Müller", + "Daniel Lottaz", + "Judith S. Bond", + "Gunnar C. Hansson" + ] + }, + "date": { + "value": [ + "08/26/2014" + ] + }, + "volume": { + "value": [ + "111" + ] + }, + "issue": { + "value": [ + "34" + ] + }, + "firstpage": { + "value": [ + "12396" + ] + }, + "lastpage": { + "value": [ + "12401" + ] + }, + "doi": { + "value": [ + "10.1073/pnas.1407597111" + ] + }, + "journal": { + "value": [ + "Proceedings of the National Academy of Sciences" + ] + }, + "abstract": { + "value": [ + "\n Abstract\n The mucus that covers and protects the epithelium of the intestine is built around its major structural component, the gel-forming\n MUC2 mucin. The gel-forming mucins have traditionally been assumed to be secreted as nonattached. The colon has a two-layered\n mucus system where the inner mucus is attached to the epithelium, whereas the small intestine normally has a nonattached mucus.\n However, the mucus of the small intestine of meprin β-deficient mice was now found to be attached. Meprin β is an endogenous\n zinc-dependent metalloprotease now shown to cleave the N-terminal region of the MUC2 mucin at two specific sites. When recombinant\n meprin β was added to the attached mucus of meprin β-deficient mice, the mucus was detached from the epithelium. Similar to\n meprin β-deficient mice, germ-free mice have attached mucus as they did not shed the membrane-anchored meprin β into the luminal\n mucus. The ileal mucus of cystic fibrosis (CF) mice with a nonfunctional cystic fibrosis transmembrane conductance regulator\n (CFTR) channel was recently shown to be attached to the epithelium. Addition of recombinant meprin β to CF mucus did not release\n the mucus, but further addition of bicarbonate rendered the CF mucus normal, suggesting that MUC2 unfolding exposed the meprin\n β cleavage sites. Mucus is thus secreted attached to the goblet cells and requires an enzyme, meprin β in the small intestine,\n to be detached and released into the intestinal lumen. This process regulates mucus properties, can be triggered by bacterial\n contact, and is nonfunctional in CF due to poor mucin unfolding.\n \n " + ] + }, + "abstract_html": { + "value": [ + "http://www.pnas.org/content/111/34/12396.abstract" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.pnas.org/content/111/34/12396.full.pdf" + ] + }, + "fulltext_html": { + "value": [ + "http://www.pnas.org/content/111/34/12396.full" + ] + }, + "supplementary_material": { + "value": [ + "/content/111/34/12396/suppl/DCSupplemental" + ] + }, + "file_hashes": [ + { + "12396.abstract": "ca082186a4c61359f66319b740757716" + }, + { + "12396.full": "259838128b20185244d84dc2a3c9a068" + }, + { + "12396.full.pdf": "662864d14aad055c3a013c0d21907d11" + }, + { + "DCSupplemental": "1afdc9c14911b0b883b471a223525a87" + } + ] + }, + "http://www.pnas.org/content/111/34/12390": { + "publisher": { + "value": [ + "National Acad Sciences" + ] + }, + "title": { + "value": [ + "Chaperone-enhanced purification of unconventional myosin 15, a molecular motor specialized for stereocilia protein trafficking" + ] + }, + "authors": { + "value": [ + "Jonathan E. Bird", + "Yasuharu Takagi", + "Neil Billington", + "Marie-Paule Strub", + "James R. Sellers", + "Thomas B. Friedman" + ] + }, + "date": { + "value": [ + "08/26/2014" + ] + }, + "volume": { + "value": [ + "111" + ] + }, + "issue": { + "value": [ + "34" + ] + }, + "firstpage": { + "value": [ + "12390" + ] + }, + "lastpage": { + "value": [ + "12395" + ] + }, + "doi": { + "value": [ + "10.1073/pnas.1409459111" + ] + }, + "journal": { + "value": [ + "Proceedings of the National Academy of Sciences" + ] + }, + "abstract": { + "value": [ + "\n Abstract\n Unconventional myosin 15 is a molecular motor expressed in inner ear hair cells that transports protein cargos within developing\n mechanosensory stereocilia. Mutations of myosin 15 cause profound hearing loss in humans and mice; however, the properties\n of this motor and its regulation within the stereocilia organelle are unknown. To address these questions, we expressed a\n subfragment 1-like (S1) truncation of mouse myosin 15, comprising the predicted motor domain plus three light-chain binding\n sites. Following unsuccessful attempts to express functional myosin 15-S1 using the Spodoptera frugiperda (Sf9)-baculovirus system, we discovered that coexpression of the muscle-myosin–specific chaperone UNC45B, in addition to\n the chaperone heat-shock protein 90 (HSP90) significantly increased the yield of functional protein. Surprisingly, myosin\n 15-S1 did not bind calmodulin with high affinity. Instead, the IQ domains bound essential and regulatory light chains that\n are normally associated with class II myosins. We show that myosin 15-S1 is a barbed-end–directed motor that moves actin filaments\n in a gliding assay (∼430 nm·s−1 at 30 °C), using a power stroke of 7.9 nm. The maximum ATPase rate (kcat ∼6 s−1) was similar to the actin-detachment rate (kdet = 6.2 s−1) determined in single molecule optical trapping experiments, indicating that myosin 15-S1 was rate limited by transit through\n strongly actin-bound states, similar to other processive myosin motors. Our data further indicate that in addition to folding\n muscle myosin, UNC45B facilitates maturation of an unconventional myosin. We speculate that chaperone coexpression may be\n a simple method to optimize the purification of other myosin motors from Sf9 insect cells.\n \n " + ] + }, + "abstract_html": { + "value": [ + "http://www.pnas.org/content/111/34/12390.abstract" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.pnas.org/content/111/34/12390.full.pdf" + ] + }, + "fulltext_html": { + "value": [ + "http://www.pnas.org/content/111/34/12390.full" + ] + }, + "supplementary_material": { + "value": [ + "/content/111/34/12390/suppl/DCSupplemental" + ] + }, + "file_hashes": [ + { + "12390.abstract": "18700f2015ae1db03ea524c2a79a2307" + }, + { + "12390.full": "d5508b221f76a3c6512d9ee26a6c412c" + }, + { + "12390.full.pdf": "ff979154097a61a629c318ac3a99bda2" + }, + { + "DCSupplemental": "ea92c258a30ae255981b460fd8639ea6" + } + ] + }, + "http://www.pnas.org/content/101/34/12520": { + "publisher": { + "value": [ + "National Acad Sciences" + ] + }, + "title": { + "value": [ + "Cell mechanosensitivity controls the anisotropy of focal adhesions" + ] + }, + "authors": { + "value": [ + "Alice Nicolas", + "Benjamin Geiger", + "Samuel A. Safran" + ] + }, + "date": { + "value": [ + "08/24/2004" + ] + }, + "volume": { + "value": [ + "101" + ] + }, + "issue": { + "value": [ + "34" + ] + }, + "firstpage": { + "value": [ + "12520" + ] + }, + "lastpage": { + "value": [ + "12525" + ] + }, + "doi": { + "value": [ + "10.1073/pnas.0403539101" + ] + }, + "journal": { + "value": [ + "Proceedings of the National Academy of Sciences of the United States of America" + ] + }, + "abstract": { + "value": [ + "\n \n Abstract\n \n Cellular adhesions are modulated by cytoskeletal forces or external stresses and adapt to the mechanical properties of the\n extracellular matrix. We propose that this mechanosensitivity can be driven at least in part by the elastic, cell-contractility-induced\n deformations of protein molecules that form the adhesion. The model accounts for observations of anisotropic growth and shrinkage\n of focal adhesions in the direction of the force and predicts that focal adhesions only grow within a range of force that\n is determined by the composition and matrix properties. This prediction is consistent with the observations of a force threshold\n for the appearance of elongated focal adhesions and the disruption of adhesions into fibrils on a mobile extracellular matrix.\n The growth dynamics is calculated and the predicted sliding of focal adhesions is consistent with several experiments.\n \n \n " + ] + }, + "abstract_html": { + "value": [ + "http://www.pnas.org/content/101/34/12520.abstract" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.pnas.org/content/101/34/12520.full.pdf" + ] + }, + "fulltext_html": { + "value": [ + "http://www.pnas.org/content/101/34/12520.full" + ] + }, + "supplementary_material": { + "value": [ + "/content/101/34/12520/suppl/DC1" + ] + }, + "file_hashes": [ + { + "12520.abstract": "be9e776a2627b77c4b6b8dff6b9a0981" + }, + { + "12520.full": "834f11821ed9e2ef989c862920e0f7fa" + }, + { + "12520.full.pdf": "097a6ef0b44f4cd99edba11588fc3a76" + }, + { + "DC1": "98f9f3ea4bdbfc91c0abec479fd2cf58" + } + ] + }, + "http://www.pnas.org/content/71/2/302": { + "publisher": { + "value": [ + "National Acad Sciences" + ] + }, + "title": { + "value": [ + "Cell-Free Translation of Messenger RNA of Simian Virus 40: Synthesis of the Major Capsid Protein" + ] + }, + "authors": { + "value": [ + "Carol L. Prives", + "Haim Aviv", + "Bruce M. Paterson", + "Bryan E. Roberts", + "Shmuel Rozenblatt", + "Michel Revel", + "Ernest Winocour" + ] + }, + "date": { + "value": [ + "02/01/1974" + ] + }, + "volume": { + "value": [ + "71" + ] + }, + "issue": { + "value": [ + "2" + ] + }, + "firstpage": { + "value": [ + "302" + ] + }, + "lastpage": { + "value": [ + "306" + ] + }, + "doi": { + "value": [ + + ] + }, + "journal": { + "value": [ + "Proceedings of the National Academy of Sciences" + ] + }, + "abstract": { + "value": [ + "\n Abstract\n Extracts of wheat germ are capable of synthesizing the major capsid protein of simian virus 40. Poly(A)-containing RNA from\n BS-C-1 cells infected with simian virus 40 directed the synthesis of a novel polypeptide that migrates in polyacrylamide gels\n together with the major capsid polypeptide of simian virus 40, VP-1. The patterns of the major tryptic peptides of purified\n VP-1 and the novel polypeptide synthesized in vitro were identical after two-dimensional paper electrophoresis. The novel polypeptide was not synthesized in response to poly(A)-rich\n RNA from uninfected cells or from virus-infected cells treated with cytosine arabinoside. Messenger RNA from infected cells\n purified by selective hybridization to DNA of simian virus 40 directs the synthesis of a major polypeptide of electrophoretic\n mobility similar to that of VP-1 of simian virus 40. This approach should prove useful in identifying additional products\n specified by DNA tumor viruses.\n \n " + ] + }, + "abstract_html": { + "value": [ + "http://www.pnas.org/content/71/2/302.abstract" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.pnas.org/content/71/2/302.full.pdf" + ] + }, + "fulltext_html": { + "value": [ + + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "file_hashes": [ + { + "302.abstract": "fe44cb6682d599bcc8957462a285f842" + }, + { + "302.full.pdf": "6758e842f8fb46351debdc09771e54b3" + } + ] + }, + "http://www.pnas.org/content/109/24/9248": { + "publisher": { + "value": [ + "National Acad Sciences" + ] + }, + "title": { + "value": [ + "Heart wall myofibers are arranged in minimal surfaces to optimize organ function" + ] + }, + "authors": { + "value": [ + "Peter Savadjiev", + "Gustav J. Strijkers", + "Adrianus J. Bakermans", + "Emmanuel Piuze", + "Steven W. Zucker", + "Kaleem Siddiqi" + ] + }, + "date": { + "value": [ + "06/12/2012" + ] + }, + "volume": { + "value": [ + "109" + ] + }, + "issue": { + "value": [ + "24" + ] + }, + "firstpage": { + "value": [ + "9248" + ] + }, + "lastpage": { + "value": [ + "9253" + ] + }, + "doi": { + "value": [ + "10.1073/pnas.1120785109" + ] + }, + "journal": { + "value": [ + "Proceedings of the National Academy of Sciences" + ] + }, + "abstract": { + "value": [ + "\n Abstract\n Heart wall myofibers wind as helices around the ventricles, strengthening them in a manner analogous to the reinforcement\n of concrete cylindrical columns by spiral steel cables [Richart FE, et al. (1929) Univ of Illinois, Eng Exp Stn Bull 190].\n A multitude of such fibers, arranged smoothly and regularly, contract and relax as an integrated functional unit as the heart\n beats. To orchestrate this motion, fiber tangling must be avoided and pumping should be efficient. Current models of myofiber\n orientation across the heart wall suggest groupings into sheets or bands, but the precise geometry of bundles of myofibers\n is unknown. Here we show that this arrangement takes the form of a special minimal surface, the generalized helicoid [Blair\n DE, Vanstone JR (1978) Minimal Submanifolds and Geodesics 13–16], closing the gap between individual myofibers and their collective wall structure. The model holds across species,\n with a smooth variation in its three curvature parameters within the myocardial wall providing tight fits to diffusion magnetic\n resonance images from the rat, the dog, and the human. Mathematically it explains how myofibers are bundled in the heart wall\n while economizing fiber length and optimizing ventricular ejection volume as they contract. The generalized helicoid provides\n a unique foundation for analyzing the fibrous composite of the heart wall and should therefore find applications in heart\n tissue engineering and in the study of heart muscle diseases.\n \n " + ] + }, + "abstract_html": { + "value": [ + "http://www.pnas.org/content/109/24/9248.abstract" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.pnas.org/content/109/24/9248.full.pdf" + ] + }, + "fulltext_html": { + "value": [ + "http://www.pnas.org/content/109/24/9248.full" + ] + }, + "supplementary_material": { + "value": [ + "/content/109/24/9248/suppl/DCSupplemental" + ] + }, + "file_hashes": [ + { + "9248.abstract": "e0462616d7f1f2132571effd2331416b" + }, + { + "9248.full": "98fca17a7e73a9b449a582bfa30ad32c" + }, + { + "9248.full.pdf": "b73199c77ccf2955c3c78981d3320670" + }, + { + "DCSupplemental": "d6c4e4e465b3932acfedb2f3cf914d9d" + } + ] + }, + "http://www.pnas.org/content/111/24/8788": { + "publisher": { + "value": [ + "National Acad Sciences" + ] + }, + "title": { + "value": [ + "Experimental evidence of massive-scale emotional contagion through social networks" + ] + }, + "authors": { + "value": [ + "Adam D. I. Kramer", + "Jamie E. Guillory", + "Jeffrey T. Hancock" + ] + }, + "date": { + "value": [ + "06/17/2014" + ] + }, + "volume": { + "value": [ + "111" + ] + }, + "issue": { + "value": [ + "24" + ] + }, + "firstpage": { + "value": [ + "8788" + ] + }, + "lastpage": { + "value": [ + "8790" + ] + }, + "doi": { + "value": [ + "10.1073/pnas.1320040111" + ] + }, + "journal": { + "value": [ + "Proceedings of the National Academy of Sciences" + ] + }, + "abstract": { + "value": [ + "\n Abstract\n Emotional states can be transferred to others via emotional contagion, leading people to experience the same emotions without\n their awareness. Emotional contagion is well established in laboratory experiments, with people transferring positive and\n negative emotions to others. Data from a large real-world social network, collected over a 20-y period suggests that longer-lasting\n moods (e.g., depression, happiness) can be transferred through networks [Fowler JH, Christakis NA (2008) BMJ 337:a2338], although the results are controversial. In an experiment with people who use Facebook, we test whether emotional\n contagion occurs outside of in-person interaction between individuals by reducing the amount of emotional content in the News\n Feed. When positive expressions were reduced, people produced fewer positive posts and more negative posts; when negative\n expressions were reduced, the opposite pattern occurred. These results indicate that emotions expressed by others on Facebook\n influence our own emotions, constituting experimental evidence for massive-scale contagion via social networks. This work\n also suggests that, in contrast to prevailing assumptions, in-person interaction and nonverbal cues are not strictly necessary\n for emotional contagion, and that the observation of others’ positive experiences constitutes a positive experience for people.\n \n " + ] + }, + "abstract_html": { + "value": [ + "http://www.pnas.org/content/111/24/8788.abstract" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.pnas.org/content/111/24/8788.full.pdf" + ] + }, + "fulltext_html": { + "value": [ + "http://www.pnas.org/content/111/24/8788.full" + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "file_hashes": [ + { + "8788.abstract": "a8ceb8815c015c460ee9200b69bddd2c" + }, + { + "8788.full": "5571078dbc9c89db63169e9bbac2e532" + }, + { + "8788.full.pdf": "42a734fa406ae79624cefe2dd88e707f" + } + ] + }, + "http://www.pnas.org/content/111/29/10779.1": { + "publisher": { + "value": [ + "National Acad Sciences" + ] + }, + "title": { + "value": [ + "Editorial Expression of Concern: Experimental evidence of massivescale emotional contagion through social networks" + ] + }, + "authors": { + "value": [ + + ] + }, + "date": { + "value": [ + "07/22/2014" + ] + }, + "volume": { + "value": [ + "111" + ] + }, + "issue": { + "value": [ + "29" + ] + }, + "firstpage": { + "value": [ + "10779" + ] + }, + "lastpage": { + "value": [ + "10779" + ] + }, + "doi": { + "value": [ + "10.1073/pnas.1412469111" + ] + }, + "journal": { + "value": [ + "Proceedings of the National Academy of Sciences" + ] + }, + "abstract": { + "value": [ + + ] + }, + "abstract_html": { + "value": [ + + ] + }, + "language": { + "value": [ + "en" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.pnas.org/content/111/29/10779.1.full.pdf" + ] + }, + "fulltext_html": { + "value": [ + "http://www.pnas.org/content/111/29/10779.1.full" + ] + }, + "supplementary_material": { + "value": [ + + ] + }, + "file_hashes": [ + { + "10779.1.full": "c010b1e0c1aae60bf8306c448c182c3a" + }, + { + "10779.1.full.pdf": "74ab5eacd108d03d913a503223f5ffa3" + } + ] + }, + "http://www.pnas.org/content/111/35/12758": { + "publisher": { + "value": [ + "National Acad Sciences" + ] + }, + "title": { + "value": [ + "Experimental basis for a new allosteric model for multisubunit proteins" + ] + }, + "authors": { + "value": [ + "Cristiano Viappiani", + "Stefania Abbruzzetti", + "Luca Ronda", + "Stefano Bettati", + "Eric. R. Henry", + "Andrea Mozzarelli", + "William A. Eaton" + ] + }, + "date": { + "value": [ + "09/02/2014" + ] + }, + "volume": { + "value": [ + "111" + ] + }, + "issue": { + "value": [ + "35" + ] + }, + "firstpage": { + "value": [ + "12758" + ] + }, + "lastpage": { + "value": [ + "12763" + ] + }, + "doi": { + "value": [ + "10.1073/pnas.1413566111" + ] + }, + "journal": { + "value": [ + "Proceedings of the National Academy of Sciences" + ] + }, + "abstract": { + "value": [ + "\n Abstract\n Monod, Wyman, and Changeux (MWC) explained allostery in multisubunit proteins with a widely applied theoretical model in which\n binding of small molecules, so-called allosteric effectors, affects reactivity by altering the equilibrium between more reactive\n (R) and less reactive (T) quaternary structures. In their model, each quaternary structure has a single reactivity. Here,\n we use silica gels to trap protein conformations and a new kind of laser photolysis experiment to show that hemoglobin, the\n paradigm of allostery, exhibits two ligand binding phases with the same fast and slow rates in both R and T quaternary structures.\n Allosteric effectors change the fraction of each phase but not the rates. These surprising results are readily explained by\n the simplest possible extension of the MWC model to include a preequilibrium between two tertiary conformations that have\n the same functional properties within each quaternary structure. They also have important implications for the long-standing\n question of a structural explanation for the difference in hemoglobin oxygen affinity of the two quaternary structures.\n \n " + ] + }, + "abstract_html": { + "value": [ + "http://www.pnas.org/content/111/35/12758.abstract" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.pnas.org/content/111/35/12758.full.pdf" + ] + }, + "fulltext_html": { + "value": [ + "http://www.pnas.org/content/111/35/12758.full" + ] + }, + "supplementary_material": { + "value": [ + "/content/111/35/12758/suppl/DCSupplemental" + ] + }, + "file_hashes": [ + { + "12758.abstract": "480761a5cf78bb983533f453f8ad2e67" + }, + { + "12758.full": "ea072586b40f13a211dd582482449afe" + }, + { + "12758.full.pdf": "7f63385f9b57ecbbb08326ff106b3c5b" + }, + { + "DCSupplemental": "5de0aeaa14535b0a5c8ad7b9fc7a67b2" + } + ] + } } \ No newline at end of file diff --git a/test/rsc.json b/test/rsc.json index 67e840e..0bf1ff0 100644 --- a/test/rsc.json +++ b/test/rsc.json @@ -1,581 +1,876 @@ { - "http://pubs.rsc.org/en/content/articlelanding/2014/dt/c4dt01397b": [ - { - "publisher": "The Royal Society of Chemistry" - }, - { - "title": "Synthesis and photoinduced electron transfer in platinum(II) bis(N-(4-ethynylphenyl)carbazole)bipyridine fullerene complexes" - }, - { - "authors": "Sai-Ho Lee" - }, - { - "authors": "Chris Tsz-Leung Chan" - }, - { - "authors": "Keith Man-Chung Wong" - }, - { - "authors": "Wai Han Lam" - }, - { - "authors": "Wai-Ming Kwok" - }, - { - "authors": "Vivian Wing-Wah Yam" - }, - { - "date": "2014-09-02" - }, - { - "volume": "" - }, - { - "issue": "" - }, - { - "firstpage": "" - }, - { - "lastpage": "" - }, - { - "doi": "10.1039/C4DT01397B" - }, - { - "journal": "Dalton Trans." - }, - { - "abstract": "" - }, - { - "abstract_html": "http://pubs.rsc.org/en/content/articlelanding/2014/dt/c4dt01397b" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://pubs.rsc.org/en/content/articlepdf/2014/dt/c4dt01397b" - }, - { - "fulltext_html": "http://pubs.rsc.org/en/content/articlehtml/2014/dt/c4dt01397b" - }, - { - "figure": "http://sod-a.rsc-cdn.org/pubs.rsc.org/content/NewImages/Ajax-GA-Loader.gif" - }, - { - "caption": "Graphical abstract: Synthesis and photoinduced electron transfer in platinum(ii) bis(N-(4-ethynylphenyl)carbazole)bipyridine fullerene complexes" - }, - { - "Ajax-GA-Loader.gif": "9dc2c7c4f07aa2db72f1b4f2c81dc0b8" - }, - { - "rendered.html": "b1475d5207cbd4804e690a89207ddbef" - } - ], - "http://pubs.rsc.org/en/Content/ArticleLanding/2014/CC/C4CC04440A": [ - { - "publisher": "The Royal Society of Chemistry" - }, - { - "title": "Facile Assembly of Light-Driven Molecular Motors onto a Solid Surface" - }, - { - "authors": "Jiawen Chen" - }, - { - "authors": "Kuang-Yen Chen" - }, - { - "authors": "Gregory T Carroll" - }, - { - "authors": "Ben L Feringa" - }, - { - "date": "2014-09-02" - }, - { - "volume": "" - }, - { - "issue": "" - }, - { - "firstpage": "" - }, - { - "lastpage": "" - }, - { - "doi": "10.1039/C4CC04440A" - }, - { - "journal": "Chem. Commun." - }, - { - "abstract": "" - }, - { - "abstract_html": "http://pubs.rsc.org/en/content/articlelanding/2014/cc/c4cc04440a" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://pubs.rsc.org/en/content/articlepdf/2014/cc/c4cc04440a" - }, - { - "fulltext_html": "http://pubs.rsc.org/en/content/articlehtml/2014/cc/c4cc04440a" - }, - { - "c4cc04440a": "80e5b009cfc792b9803f5f7d780d19d8" - }, - { - "rendered.html": "d18b562038d1b44858a4b59c19d993d9" - } - ], - "http://pubs.rsc.org/en/content/articlelanding/1877/js/js8773200001": [ - { - "publisher": "The Royal Society of Chemistry" - }, - { - "title": "I.—On the estimation of manganese in spiegeleisen, and of manganese and iron in manganiferous iron ores" - }, - { - "authors": "Edward Riley" - }, - { - "date": "1877-01-01" - }, - { - "volume": "32" - }, - { - "issue": "0" - }, - { - "firstpage": "1" - }, - { - "lastpage": "28" - }, - { - "doi": "10.1039/JS8773200001" - }, - { - "journal": "J. Chem. Soc." - }, - { - "abstract": "" - }, - { - "abstract_html": "http://pubs.rsc.org/en/content/articlelanding/1877/js/js8773200001" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://pubs.rsc.org/en/content/articlepdf/1877/js/js8773200001" - }, - { - "fulltext_html": "http://pubs.rsc.org/en/content/articlehtml/1877/js/js8773200001" - }, - { - "js8773200001": "07b793d5f63299d1d7093a65bb459e1f" - }, - { - "rendered.html": "b78de4e8e5a1862146b3d9f3ef88d8f2" - } - ], - "http://pubs.rsc.org/en/content/articlelanding/2002/p2/b208395g": [ - { - "publisher": "The Royal Society of Chemistry" - }, - { - "title": "Stereoelectronic substituent effects on intramolecular H-bonding in crowded o-anisic acids" - }, - { - "authors": "Ingeborg I. Schuster" - }, - { - "date": "2002-12-06" - }, - { - "volume": "" - }, - { - "issue": "12" - }, - { - "firstpage": "1961" - }, - { - "lastpage": "1966" - }, - { - "doi": "10.1039/B208395G" - }, - { - "journal": "J. Chem. Soc., Perkin Trans. 2" - }, - { - "abstract": "" - }, - { - "abstract_html": "http://pubs.rsc.org/en/content/articlelanding/2002/p2/b208395g" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://pubs.rsc.org/en/content/articlepdf/2002/p2/b208395g" - }, - { - "fulltext_html": "http://pubs.rsc.org/en/content/articlehtml/2002/p2/b208395g" - }, - { - "figure": "http://sod-a.rsc-cdn.org/pubs.rsc.org/content/NewImages/Ajax-GA-Loader.gif" - }, - { - "caption": "Graphical abstract: Stereoelectronic substituent effects on intramolecular H-bonding in crowded o-anisic acids" - }, - { - "b208395g": "00178173eb233f33a199643034d89dd9" - }, - { - "rendered.html": "13db463737f054c796b5684fc25c4bef" - } - ], - "http://pubs.rsc.org/en/content/articlelanding/2014/ob/c4ob01156b": [ - { - "publisher": "The Royal Society of Chemistry" - }, - { - "title": "Selective transamidation of 3-oxo-N-acyl homoserine lactones by hydrazine derivatives" - }, - { - "authors": "Michael A. Bertucci" - }, - { - "authors": "Stephen J. Lee" - }, - { - "authors": "Michel R. Gagné" - }, - { - "date": "2014-08-27" - }, - { - "volume": "12" - }, - { - "issue": "37" - }, - { - "firstpage": "7197" - }, - { - "lastpage": "7200" - }, - { - "doi": "10.1039/C4OB01156B" - }, - { - "journal": "Org. Biomol. Chem." - }, - { - "abstract": "" - }, - { - "abstract_html": "http://pubs.rsc.org/en/content/articlelanding/2014/ob/c4ob01156b" - }, - { - "language": "en" - }, - { - "fulltext_pdf": "http://pubs.rsc.org/en/content/articlepdf/2014/ob/c4ob01156b" - }, - { - "fulltext_html": "http://pubs.rsc.org/en/content/articlehtml/2014/ob/c4ob01156b" - }, - { - "figure": "http://sod-a.rsc-cdn.org/pubs.rsc.org/content/NewImages/Ajax-GA-Loader.gif" - }, - { - "caption": "Graphical abstract: Selective transamidation of 3-oxo-N-acyl homoserine lactones by hydrazine derivatives" - }, - { - "Ajax-GA-Loader.gif": "9dc2c7c4f07aa2db72f1b4f2c81dc0b8" - }, - { - "rendered.html": "cb30ee8ed2e1f2038f18c2d7aea131aa" - } - ], - "http://pubs.rsc.org/en/content/articlelanding/2012/jm/c2jm35601e": [ - { - "publisher": "The Royal Society of Chemistry" - }, - { - "title": "Nanonet as a scaffold with targeted functionalities" - }, - { - "authors": "Yanli Zhao" - }, - { - "authors": "George Grüner" - }, - { - "date": "2012-11-20" - }, - { - "volume": "22" - }, - { - "issue": "48" - }, - { - "firstpage": "24983" - }, - { - "lastpage": "24991" - }, - { - "doi": "10.1039/C2JM35601E" - }, - { - "journal": "J. Mater. 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Shepard" + ] + }, + "date": { + "value": [ + "2014-09-16" + ] + }, + "volume": { + "value": [ + "14" + ] + }, + "issue": { + "value": [ + "20" + ] + }, + "firstpage": { + "value": [ + "4076" + ] + }, + "lastpage": { + "value": [ + "4084" + ] + }, + "doi": { + "value": [ + "10.1039/C4LC00443D" + ] + }, + "journal": { + "value": [ + "Lab Chip" + ] + }, + "abstract": { + "value": [ + "" + ] + }, + "abstract_html": { + "value": [ + "http://pubs.rsc.org/en/content/articlelanding/2014/lc/c4lc00443d" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "fulltext_pdf": { + "value": [ + "http://pubs.rsc.org/en/content/articlepdf/2014/lc/c4lc00443d" + ] + }, + "fulltext_html": { + "value": [ + "http://pubs.rsc.org/en/content/articlehtml/2014/lc/c4lc00443d" + ] + }, + "figure": { + "value": [ + "http://sod-a.rsc-cdn.org/pubs.rsc.org/content/NewImages/Ajax-GA-Loader.gif" + ] + }, + "caption": { + "value": [ + "Graphical abstract: An integrated CMOS quantitative-polymerase-chain-reaction lab-on-chip for point-of-care diagnostics" + ] + }, + "file_hashes": [ + { + "Ajax-GA-Loader.gif": "6b5bab0837b7f4bc2ec893f1d7e3a861" + }, + { + "c4lc00443d": "1a53773fb4ee6c706817958beb7b7d8c" + } + ] + } } \ No newline at end of file diff --git a/test/test_all.rb b/test/test_all.rb index 75635b6..d3f8891 100755 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -67,14 +67,17 @@ def coverage(scraperjsonpath, results) results = JSON.load(File.open 'results.json') files = Dir['*'] files = files.keep_if { |f| f != 'results.json' }.map{ |f| f.strip } + file_hashes = [] files.each do |f| - results << { f => Digest::MD5.file(f).hexdigest } + file_hashes << { f => Digest::MD5.file(f).hexdigest } end + results['file_hashes'] = file_hashes end coverage_files << coverage(scraper, results) # compare results to expected expected.each do |hash| key = hash.keys.first + next if key == 'file_hashes' exp_val = hash[key] exist = results.detect { |result| result.key? key } match = results.detect { |result| result[key] == exp_val } From fbfc8c5dd82362822c765f1c5461b4f8203a1d44 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Thu, 2 Oct 2014 23:09:49 +0100 Subject: [PATCH 088/154] specify quickscrape version --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 5b60593..b68a6bd 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,6 +9,6 @@ before_install: - sudo apt-get install -y python g++ make nodejs libfontconfig1 - curl --insecure https://www.npmjs.org/install.sh | bash install: - - sudo -H npm install --global quickscrape + - sudo -H npm install --global quickscrape@0.3.0 script: - ruby test/test_all.rb From f0f8c10f487b1546130c4478e73ee294be610274 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Mon, 6 Oct 2014 22:26:29 +0100 Subject: [PATCH 089/154] bump quickscrape dependency --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index b68a6bd..ea9ed0b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,6 +9,6 @@ before_install: - sudo apt-get install -y python g++ make nodejs libfontconfig1 - curl --insecure https://www.npmjs.org/install.sh | bash install: - - sudo -H npm install --global quickscrape@0.3.0 + - sudo -H npm install --global quickscrape@0.3.2 script: - ruby test/test_all.rb From 28c741541398803ed6dceb58c023667f1015c202 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Mon, 6 Oct 2014 22:38:29 +0100 Subject: [PATCH 090/154] don't include file hash results in coverage --- test/test_all.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/test_all.rb b/test/test_all.rb index d3f8891..bc7c2f9 100755 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -19,7 +19,7 @@ def coverage(scraperjsonpath, results) # calculate coverage elements.each do |element| # calculate coverage for this line - if results.detect { |result| result.key? element } + if results.detect { |result| result.is_a? Hash && result.key? element } coverage << 1 else coverage << 0 From 83d7ee0853d92a49b7f13efdb9c16017a54f9621 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Tue, 7 Oct 2014 09:40:54 +0100 Subject: [PATCH 091/154] migrate to nvm --- .travis.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.travis.yml b/.travis.yml index ea9ed0b..ac86dfc 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,12 +3,12 @@ rvm: - 2.1.0 before_install: - sudo apt-get update -qq - - sudo apt-get install -y software-properties-common python-software-properties - - sudo add-apt-repository -y ppa:chris-lea/node.js - - sudo apt-get update - - sudo apt-get install -y python g++ make nodejs libfontconfig1 - - curl --insecure https://www.npmjs.org/install.sh | bash + - sudo apt-get install -y software-properties-common + - sudo apt-get install -y build-essential libfontconfig1 + - curl https://raw.githubusercontent.com/creationix/nvm/v0.17.2/install.sh | bash + - nvm install 0.10 + - nvm use 0.10 install: - - sudo -H npm install --global quickscrape@0.3.2 + - npm install --global quickscrape@0.3.2 script: - ruby test/test_all.rb From a59d3f3a36b03c4f0f5ac4a76f7eec573975addc Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Tue, 7 Oct 2014 09:42:03 +0100 Subject: [PATCH 092/154] restart bash after nvm install --- .travis.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index ac86dfc..d331a52 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,8 +4,9 @@ rvm: before_install: - sudo apt-get update -qq - sudo apt-get install -y software-properties-common - - sudo apt-get install -y build-essential libfontconfig1 + - sudo apt-get install -y build-essential libfontconfig - curl https://raw.githubusercontent.com/creationix/nvm/v0.17.2/install.sh | bash + - bash && . ~/.profile - nvm install 0.10 - nvm use 0.10 install: From d0bf3f1bc9ceae5a6025b6921be85cf6f615c071 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Tue, 7 Oct 2014 09:45:37 +0100 Subject: [PATCH 093/154] travis comes with nvm! --- .travis.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index d331a52..258451f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -5,8 +5,6 @@ before_install: - sudo apt-get update -qq - sudo apt-get install -y software-properties-common - sudo apt-get install -y build-essential libfontconfig - - curl https://raw.githubusercontent.com/creationix/nvm/v0.17.2/install.sh | bash - - bash && . ~/.profile - nvm install 0.10 - nvm use 0.10 install: From 5a0ede793c0821093356dbda994aaf44b72437f7 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Tue, 7 Oct 2014 10:05:38 +0100 Subject: [PATCH 094/154] need latest 0.10.32 --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 258451f..aaa6b25 100644 --- a/.travis.yml +++ b/.travis.yml @@ -5,8 +5,8 @@ before_install: - sudo apt-get update -qq - sudo apt-get install -y software-properties-common - sudo apt-get install -y build-essential libfontconfig - - nvm install 0.10 - - nvm use 0.10 + - nvm install 0.10.32 + - nvm use 0.10.32 install: - npm install --global quickscrape@0.3.2 script: From e32730ba6c282e572f8c74441d9ea10d2c4df3a6 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Tue, 7 Oct 2014 10:24:23 +0100 Subject: [PATCH 095/154] use latest npm --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index aaa6b25..c907d8f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,6 +7,7 @@ before_install: - sudo apt-get install -y build-essential libfontconfig - nvm install 0.10.32 - nvm use 0.10.32 + - npm update npm -g install: - npm install --global quickscrape@0.3.2 script: From 15e7f35fd6674cb5d62c21e51b47bcf4d2e24006 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 11 Jan 2015 10:43:51 +0000 Subject: [PATCH 096/154] peerj scraper is complete - showcase of latest scraperJSON --- scrapers/peerj.json | 88 ++++- test/peerj.json | 849 +++++++++++++++++++++++++++++++++++++++----- 2 files changed, 829 insertions(+), 108 deletions(-) diff --git a/scrapers/peerj.json b/scrapers/peerj.json index 6d9b3ac..55a1fb7 100644 --- a/scrapers/peerj.json +++ b/scrapers/peerj.json @@ -5,22 +5,46 @@ "selector": "//meta[@name='citation_publisher']", "attribute": "content" }, - "journal": { + "journal_name": { "selector": "//meta[@name='citation_journal_title']", "attribute": "content" }, + "journal_issn": { + "selector": "//meta[@name='citation_issn']", + "attribute": "content" + }, "title": { "selector": "//meta[@name='citation_title']", "attribute": "content" }, - "authors": { + "keywords": { + "selector": "//meta[@name='citation_keywords']", + "attribute": "content" + }, + "author_name": { "selector": "//meta[@name='citation_author']", "attribute": "content" }, - "date": { + "author_institution": { + "selector": "//meta[@name='citation_author_institution']", + "attribute": "content" + }, + "editor_name": { + "selector": "//dd[@itemprop='editor']", + "attribute": "text" + }, + "date_published": { "selector": "//meta[@name='citation_date']", "attribute": "content" }, + "date_accepted": { + "selector": "//time[@itemprop='dateAccepted']", + "attribute": "text" + }, + "date_submitted": { + "selector": "//time[@itemprop='dateCreated']", + "attribute": "text" + }, "doi": { "selector": "//meta[@name='citation_doi']", "attribute": "content" @@ -37,14 +61,54 @@ "selector": "//meta[@name='citation_firstpage']", "attribute": "content" }, - "description": { - "selector": "//meta[@name='description']", - "attribute": "content" - }, "abstract": { "selector": "//meta[@name='description']", "attribute": "content" }, + "abstract_html": { + "selector": "//div[contains(@class, 'abstract')]", + "attribute": "html" + }, + "introduction_html": { + "selector": "//section[@id='intro']", + "attribute": "html" + }, + "methods_html": { + "selector": "//section[@id='materials|methods']", + "attribute": "html" + }, + "results_html": { + "selector": "//section[@id='results']", + "attribute": "html" + }, + "discussion_html": { + "selector": "//section[@id='discussion']", + "attribute": "html" + }, + "conclusion_html": { + "selector": "//section[@id='conclusion']", + "attribute": "html" + }, + "author_contrib_html": { + "selector": "//section[@id='author-contributions']", + "attribute": "html" + }, + "competing_interests_html": { + "selector": "//section[@id='competing-interests']", + "attribute": "html" + }, + "references_html": { + "selector": "//div[@itemprop='citation']", + "attribute": "html" + }, + "figures_html": { + "selector": "//figure[@id[starts-with(.,'fig-')]]", + "attribute": "html" + }, + "tables_html": { + "selector": "//figure[@id[starts-with(.,'table-')]]", + "attribute": "html" + }, "fulltext_html": { "selector": "//meta[@name='citation_fulltext_html_url']", "attribute": "content", @@ -66,26 +130,22 @@ "rename": "fulltext.xml" } }, - "supplementary_material": { + "supplementary_file": { "selector": "//a[contains(concat(' ', normalize-space(@class), ' '), ' article-supporting-download ')]", "attribute": "href", "download": true }, - "figure": { + "figures_image": { "selector": "//div[contains(concat(' ', normalize-space(@class), ' '), ' article-image-download ')]/a", "attribute": "href", "download": true }, - "figure_caption": { - "selector": "//figcaption", - "attribute": "text" - }, "license": { "selector": "//div[contains(concat(' ', normalize-space(@class), ' '), ' license-p ')]", "attribute": "text" }, "copyright": { - "selector": "//div[contains(@class, 'copyright')]", + "selector": "//span[starts-with(@itemprop, 'copyright')]", "attribute": "text" } } diff --git a/test/peerj.json b/test/peerj.json index 4db4923..9ebbac3 100644 --- a/test/peerj.json +++ b/test/peerj.json @@ -5,17 +5,27 @@ "PeerJ Inc." ] }, - "journal": { + "journal_name": { "value": [ "PeerJ" ] }, + "journal_issn": { + "value": [ + "2167-8359" + ] + }, "title": { "value": [ "Affect-focused psychodynamic psychotherapy for depression and anxiety through the Internet: a randomized controlled trial" ] }, - "authors": { + "keywords": { + "value": [ + "Depression; Anxiety; Psychotherapy; Psychodynamic therapy; Internet; Affect; Emotion; Internet-delivered treatments; e-health" + ] + }, + "author_name": { "value": [ "Robert Johansson", "Martin Björklund", @@ -28,11 +38,41 @@ "Gerhard Andersson" ] }, - "date": { + "author_institution": { + "value": [ + "Department of Behavioural Sciences and Learning, Linköping University, Linköping, Sweden", + "Department of Behavioural Sciences and Learning, Linköping University, Linköping, Sweden", + "Department of Behavioural Sciences and Learning, Linköping University, Linköping, Sweden", + "Department of Behavioural Sciences and Learning, Linköping University, Linköping, Sweden", + "Department of Behavioural Sciences and Learning, Linköping University, Linköping, Sweden", + "Department of Clinical Neuroscience, Division of Psychology, Karolinska Institutet, Sweden", + "Psychiatric Clinic, University Hospital of Linköping, Linköping, Sweden", + "Center for Courageous Living, California, United States", + "Department of Behavioural Sciences and Learning, Linköping University, Linköping, Sweden", + "Department of Clinical Neuroscience, Psychiatry Section, Karolinska Institutet, Stockholm, Sweden", + "Swedish Institute for Disability Research, Linköping University, Linköping, Sweden" + ] + }, + "editor_name": { + "value": [ + "Gary Collins" + ] + }, + "date_published": { "value": [ "2013-07-09" ] }, + "date_accepted": { + "value": [ + "2013-06-21" + ] + }, + "date_submitted": { + "value": [ + "2013-05-26" + ] + }, "doi": { "value": [ "10.7717/peerj.102" @@ -53,14 +93,124 @@ "e102" ] }, - "description": { + "abstract": { "value": [ "Background. Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base. Research has indicated an association between therapist-facilitated affective experience and outcome in psychodynamic therapy. Affect-phobia therapy (APT), as outlined by McCullough et al., is a psychodynamic treatment that emphasizes a strong focus on expression and experience of affect. This model has neither been evaluated for depression nor anxiety disorders in a randomized controlled trial. While Internet-delivered psychodynamic treatments for depression and generalized anxiety disorder exist, they have not been based on APT. The aim of this randomized controlled trial was to investigate the efficacy of an Internet-based, psychodynamic, guided self-help treatment based on APT for depression and anxiety disorders.Methods. One hundred participants with diagnoses of mood and anxiety disorders participated in a randomized (1:1 ratio) controlled trial of an active group versus a control condition. The treatment group received a 10-week, psychodynamic, guided self-help treatment based on APT that was delivered through the Internet. The treatment consisted of eight text-based treatment modules and included therapist contact (9.5 min per client and week, on average) in a secure online environment. Participants in the control group also received online therapist support and clinical monitoring of symptoms, but received no treatment modules. Outcome measures were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). Process measures were also included. All measures were administered weekly during the treatment period and at a 7-month follow-up.Results. Mixed models analyses using the full intention-to-treat sample revealed significant interaction effects of group and time on all outcome measures, when comparing treatment to the control group. A large between-group effect size of Cohen’s d = 0.77 (95% CI: 0.37–1.18) was found on the PHQ-9 and a moderately large between-group effect size d = 0.48 (95% CI: 0.08–0.87) was found on the GAD-7. The number of patients who recovered (had no diagnoses of depression and anxiety, and had less than 10 on both the PHQ-9 and the GAD-7) were at post-treatment 52% in the treatment group and 24% in the control group. This difference was significant, χ2(N = 100, d f = 1) = 8.3, p < .01. From post-treatment to follow-up, treatment gains were maintained on the PHQ-9, and significant improvements were seen on the GAD-7.Conclusion. This study provides initial support for the efficacy of Internet-delivered psychodynamic therapy based on the affect-phobia model in the treatment of depression and anxiety disorders. The results support the conclusion that psychodynamic treatment approaches may be transferred to the guided self-help format and delivered via the Internet." ] }, - "abstract": { + "abstract_html": { "value": [ - "Background. Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base. Research has indicated an association between therapist-facilitated affective experience and outcome in psychodynamic therapy. Affect-phobia therapy (APT), as outlined by McCullough et al., is a psychodynamic treatment that emphasizes a strong focus on expression and experience of affect. This model has neither been evaluated for depression nor anxiety disorders in a randomized controlled trial. While Internet-delivered psychodynamic treatments for depression and generalized anxiety disorder exist, they have not been based on APT. The aim of this randomized controlled trial was to investigate the efficacy of an Internet-based, psychodynamic, guided self-help treatment based on APT for depression and anxiety disorders.Methods. One hundred participants with diagnoses of mood and anxiety disorders participated in a randomized (1:1 ratio) controlled trial of an active group versus a control condition. The treatment group received a 10-week, psychodynamic, guided self-help treatment based on APT that was delivered through the Internet. The treatment consisted of eight text-based treatment modules and included therapist contact (9.5 min per client and week, on average) in a secure online environment. Participants in the control group also received online therapist support and clinical monitoring of symptoms, but received no treatment modules. Outcome measures were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). Process measures were also included. All measures were administered weekly during the treatment period and at a 7-month follow-up.Results. Mixed models analyses using the full intention-to-treat sample revealed significant interaction effects of group and time on all outcome measures, when comparing treatment to the control group. A large between-group effect size of Cohen’s d = 0.77 (95% CI: 0.37–1.18) was found on the PHQ-9 and a moderately large between-group effect size d = 0.48 (95% CI: 0.08–0.87) was found on the GAD-7. The number of patients who recovered (had no diagnoses of depression and anxiety, and had less than 10 on both the PHQ-9 and the GAD-7) were at post-treatment 52% in the treatment group and 24% in the control group. This difference was significant, χ2(N = 100, d f = 1) = 8.3, p < .01. From post-treatment to follow-up, treatment gains were maintained on the PHQ-9, and significant improvements were seen on the GAD-7.Conclusion. This study provides initial support for the efficacy of Internet-delivered psychodynamic therapy based on the affect-phobia model in the treatment of depression and anxiety disorders. The results support the conclusion that psychodynamic treatment approaches may be transferred to the guided self-help format and delivered via the Internet." + "\n

Background. Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base. Research has indicated an association between therapist-facilitated affective experience and outcome in psychodynamic therapy. Affect-phobia therapy (APT), as outlined by McCullough et al., is a psychodynamic treatment that emphasizes a strong focus on expression and experience of affect. This model has neither been evaluated for depression nor anxiety disorders in a randomized controlled trial. While Internet-delivered psychodynamic treatments for depression and generalized anxiety disorder exist, they have not been based on APT. The aim of this randomized controlled trial was to investigate the efficacy of an Internet-based, psychodynamic, guided self-help treatment based on APT for depression and anxiety disorders.

\n

Methods. One hundred participants with diagnoses of mood and anxiety disorders participated in a randomized (1:1 ratio) controlled trial of an active group versus a control condition. The treatment group received a 10-week, psychodynamic, guided self-help treatment based on APT that was delivered through the Internet. The treatment consisted of eight text-based treatment modules and included therapist contact (9.5 min per client and week, on average) in a secure online environment. Participants in the control group also received online therapist support and clinical monitoring of symptoms, but received no treatment modules. Outcome measures were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). Process measures were also included. All measures were administered weekly during the treatment period and at a 7-month follow-up.

\n

Results. Mixed models analyses using the full intention-to-treat sample revealed significant interaction effects of group and time on all outcome measures, when comparing treatment to the control group. A large between-group effect size of Cohen’s d = 0.77 (95% CI: 0.37–1.18) was found on the PHQ-9 and a moderately large between-group effect size d = 0.48 (95% CI: 0.08–0.87) was found on the GAD-7. The number of patients who recovered (had no diagnoses of depression and anxiety, and had less than 10 on both the PHQ-9 and the GAD-7) were at post-treatment 52% in the treatment group and 24% in the control group. This difference was significant, χ2(N = 100, d f = 1) = 8.3, p < .01. From post-treatment to follow-up, treatment gains were maintained on the PHQ-9, and significant improvements were seen on the GAD-7.

\n

Conclusion. This study provides initial support for the efficacy of Internet-delivered psychodynamic therapy based on the affect-phobia model in the treatment of depression and anxiety disorders. The results support the conclusion that psychodynamic treatment approaches may be transferred to the guided self-help format and delivered via the Internet.

\n" + ] + }, + "introduction_html": { + "value": [ + "

Introduction

\n

The aim of this randomized controlled trial was to investigate the efficacy of an Internet-delivered psychodynamic guided self-help treatment for depression and anxiety disorders that was based on the affect-phobia model of psychopathology (McCullough et al., 2003). The project extends previous research on Internet-delivered psychological treatments in general, and that of Internet-delivered psychodynamic psychotherapy in particular (Andersson et al., 2012; Johansson et al., 2012). An overview of the trial can be seen in Fig. 1.

\n
\"CONSORT
\n

\nFigure 1: CONSORT flowchart.

\n

Depression and anxiety disorders are major world-wide health problems which lower the quality of life for the individual and generate large costs for society (Ebmeier, Donaghey & Steele, 2006; Smit et al., 2006). Lifetime prevalence for mood disorders and anxiety disorders in the US have been estimated to be 20.8% and 28.8%, respectively (Kessler et al., 2005).

\n

Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base (Town et al., 2012), with research support for e.g., depression (Driessen et al., 2010), social anxiety disorder (Leichsenring et al., 2013), panic disorder (Milrod et al., 2007), and generalized anxiety disorder (Leichsenring et al., 2009). There is a variation among the psychodynamic therapies in the degree to which they focus on expression and experience of affect. Diener, Hilsenroth & Weinberger (2007) conducted a meta-analysis of high-quality studies that had examined the role of therapist focus on affect in psychodynamic psychotherapy. The results indicated that the more therapists facilitated the affective experience/expression in psychodynamic therapy, the more patients improved (Diener, Hilsenroth & Weinberger, 2007). Thus, keeping a focus on affect may be one way of enhancing psychodynamic psychotherapies.

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One psychodynamic treatment that has a strong focus on expression and experience of affect is affect-phobia therapy (APT), developed by McCullough et al. (2003). APT follows a treatment model which adheres to the fundamental structure of psychodynamic psychotherapy as outlined by Malan’s triangle of conflict (i.e., the experience/expression of feelings (F) is blocked by defenses (D) and anxieties (A)) and triangle of person (i.e., conflicted patterns began with past persons (P), are maintained with current persons (C), and can be enacted with a therapist (T)), as illustrated in Fig. 2 (Malan, 1995). Typically in APT, the therapist clarifies a client’s defenses, helps the client to observe and experience the underlying affects, and helps the client to regulate associated anxiety (McCullough et al., 2003). Formally, the treatment includes three main treatment objectives: defense restructuring (recognizing and relinquishing maladaptive defenses), affect restructuring (desensitization of affects through exposure to conflicted feeling), and self/other restructuring (improvement in sense of self and relationship with others). The main goal of psychodynamic psychotherapy based on the APT model is to help clients experience and to adaptively express previously avoided feelings (McCullough et al., 2003). That goal is shared with an entire set of psychodynamic psychotherapies that are grouped under the umbrella term experiential dynamic therapies (Osimo & Stein, 2012), which in addition to APT includes, for example, Intensive Short-Term Dynamic Psychotherapy (Abbass, Town & Driessen, 2012; Davanloo, 2000), and Accelerated Experiential Dynamic Psychotherapy (Fosha, 2000). Two randomized trials, investigating the efficacy of APT in the treatment of personality disorders, found that APT can be effective in reducing general psychiatric symptoms (Svartberg, Stiles & Seltzer, 2004; Winston et al., 1994). However, except for case-series and some small uncontrolled studies (e.g., Dornelas et al., 2010), to date no trial has investigated the efficacy of APT for patients with a principal Axis I disorder.

\n
\"Malan’s
\n

\nFigure 2: Malan’s two triangles - the triangle of conflict and the triangle of person.

\nThe two triangles (Malan, 1995) represent what David Malan called “the universal principle of psychodynamic psychotherapy”. That is, defenses (D) and anxieties (A) can block the expression of true feelings (F). These patterns began with past persons (P), are maintained with current persons (C), and are often enacted with the therapist (T).

During the last decade, numerous trials on guided self-help and Internet-delivered cognitive behavior therapy (CBT) for various psychiatric disorders have been conducted (Andersson, 2009; Hedman, Ljótsson & Lindefors, 2012; Johansson & Andersson, 2012). For mild to moderate depression and anxiety disorders, it seems safe to conclude that these treatments are as effective as face-to-face treatments (Cuijpers et al., 2010). While most research regarding Internet-based psychological treatments have concerned CBT, there are exceptions. Results from two recent randomized controlled trials focusing on the treatment of depression and generalized anxiety disorder indicate that psychodynamic treatments can also be delivered via the Internet (Andersson et al., 2012; Johansson et al., 2012).

\n

This randomized controlled trial aimed to examine the effects of an Internet-delivered psychodynamic treatment based on the affect-phobia model of psychopathology. Participants had depression and anxiety disorders. The treatment was given as self-help with additional therapist support via the Internet, and compared to a control group who also received online support. As compared with the control condition, a significant effect of treatment was expected both on measures of depression and anxiety for the full sample. In addition, a larger effect was expected on measures of depression for participants with depression as their main presenting problem as compared with those who did not have this as the main problem. Similar, a larger effect on anxiety measures was expected for participants with a principal anxiety diagnosis as compared with those who did not have such a diagnosis. We also investigated the uncontrolled effects of the treatment 7 months following the completion of the treatment.

" + ] + }, + "methods_html": { + "value": [ + + ] + }, + "results_html": { + "value": [ + "

Results

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Enrollment and baseline characteristics

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One hundred individuals with depression and/or anxiety disorders were enrolled in the study. There were no significant pre-treatment mean differences between the treatment group and the control group on any outcome measures (all t’s < 0.97, all p’s > .33). Additionally, there were no significant differences between the groups on any demographic data or current/past treatment with medication and/or psychological treatment. A complete description of demographic data of included participants is available in Table 1.

\n
\nTable 1:
Demographic description of the participants.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Treatment groupControl groupTotal
GenderMale8 (16%)10 (20%)18 (18%)
Female42 (84%)40 (80%)82 (82%)
AgeMean (SD)43.1 (13.9)46.6 (12.1)44.9 (13.1)
Min-Max19–7223–7719–77
Marital statusMarried or co-habiting31 (62%)36 (72%)67 (67%)
Other19 (38%)14 (28%)33 (33%)
Educational levelCollege or university, at least 3 years27 (54%)29 (58%)56 (56%)
Other23 (46%)21 (42%)44 (44%)
Employment statusEmployed or student41 (82%)33 (66%)74 (74%)
Other9 (18%)17 (34%)26 (26%)
Psychological treatmentNo experience15 (30%)16 (32%)31 (31%)
Prior experience35 (70%)31 (62%)66 (66%)
Ongoing0 (0%)3 (6%)3 (3%)
Pharmacological treatmentNo experience27 (54%)22 (44%)49 (49%)
Prior experience14 (28%)12 (24%)26 (26%)
Ongoing9 (18%)16 (32%)25 (25%)
\n

Regarding subgroups of principal depression and anxiety, there was a difference between subgroups in the number of participants in an acute episode of depression, χ2(N = 100, d f = 1) = 39.4, p < .001, with 55/57 (96.5%; two participants had depression not otherwise specified) compared to 17/43 (39.5%) for subgroups of depression and anxiety, respectively. Similarly, there were significantly more participants with a principal anxiety disorder that had GAD (67.4%) compared to 35.1% from the depression subgroup, χ2(N = 100, d f = 1) = 10.3, p < .001. There were no differences between subgroups regarding diagnoses of panic disorder and social phobia. Also, there were no differences in any demographics. However, there was a significant difference between subgroups in depression severity as measured by the PHQ-9 at baseline, t(98) = 3.70, p < .001. However, no significant baseline difference on the GAD-7 was found t(98) = 1.23, p = .22.

Attrition and adherence

\n

At post-treatment, 100% of the data was collected. At the 7-month follow-up, 47/50 (94%) of the self-report measures and 40/50 (80%) of the data from the follow-up interviews (i.e., diagnostic data and estimates of global improvement) were collected. Adherence to treatment was defined as the number of modules completed. A module was only considered completed if the homework assignment had been sent to the therapist. Out of the 50 participants receiving treatment, 42 (84%) completed all modules. Only 4 participants (8%) completed less than half of the program.

Outcome and process measures

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Means, standard deviations and effect sizes within and between groups for the self-report measures are presented in Tables 2 and 3. Both the treatment group and the control group had substantial within-group effects after the 10-week period. Mixed models analyses revealed significant interaction effects of treatment group and time on the PHQ-9, F(1, 102.1) = 19.94, p < .001, and the GAD-7, F(1, 105.1) = 7.86, p < .01. Both interaction effects were significant at the Bonferroni-corrected alpha level of p < .0125. Estimates of fixed effects for the PHQ-9 and the GAD-7 were as follows. Intercept: 12.37 and 10.71 (p’s < .001); Group: 0.11 and 0.14 (p’s > .85); Time: −0.64 and −0.49 (p’s < .001); Group × Time: 0.40 and 0.23 (p’s < .01). Random effects for the PHQ-9 and the GAD-7 were estimated as follows. Intercept: 14.33 and 12.78 (p’s < .001); Time: 0.15 and 0.12 (p’s < .001). Between-group effect sizes at post-treatment was large (d = 0.77) for depression and moderate (d = 0.48) for anxiety, favoring treatment over control. The continuous within-group changes on the PHQ-9 and the GAD-7 are illustrated in Fig. 3. At the 7-month follow-up, the treatment effect was stable. Paired t-tests conducted post hoc showed that there were significant post-treatment versus follow-up decrease on the GAD-7, t(46) = 2.03, p < .05, and a trend towards a significant decrease on the PHQ-9, t(46) = 1.42, p = .16. For the EPS-25 and the FFMQ, there were also significant interaction effects of treatment group and time (F(1, 104.5) = 26.5 and F(1, 101.2) = 29.9, respectively; Both p’s < .001). Both these interaction effects were significant at the Bonferroni-corrected alpha level of p < .0125. Fixed effects for the EPS-25 and the FFMQ were estimated as follows. Intercept: 4.70 and 72.76 (p’s < .001); Group: −0.16 and 3.67 (p’s > .15); Time: −0.18 and 1.39 (p’s < .001); Group × Time: 0.13 and −1.17 (p’s < .001). Estimates of random effects for the EPS-25 and the FFMQ were as follows. Intercept: 1.25 and 156.37 (p’s < .001); Time: 0.013 and 0.98 (p’s < .001). The between-group effect at post-treatment was large for the EPS-25 (d = 0.82) and moderate to large (d = 0.65) for the FFMQ.

\n
\nTable 2:
Means, SDs and effect sizes (Cohen’s d) for measures of depression and anxiety.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Mean (SD)Effect size Cohen’s d (95% CI)Linear mixed models
Measure and groupPre-treatmentPost-treatment7-month
follow-up
Between-group,
post-treatment
Within-group
pre-post-treatment
Within-group
pre-7-month follow-up
Effect\n p\n
\n PHQ-9\n
Treatment group
(n = 50)
13.90 (3.6)6.32 (4.2)5.55 (3.5)0.77 (0.37–1.18)1.93 (1.31–2.55)2.43 (1.72–3.14)Group.89
Depression subgroup
(n = 28)
15.32 (3.3)5.89 (2.8)5.96 (3.5)0.95 (0.40–1.50)3.10 (1.87–4.32)2.82 (1.78–3.87)Time < .001
Anxiety subgroup
(n = 22)
12.09 (3.3)6.86 (5.5)5.00 (3.4)0.55 (−0.06–1.16)1.12 (0.49–1.75)2.17 (1.11–3.24)G × T < .001
Control group
(n = 50)
13.96 (4.7)10.26 (5.9)0.69 (0.40–0.97)
Depression subgroup
(n = 29)
15.07 (4.4)10.59 (6.4)0.79 (0.37–1.22)
Anxiety subgroup
(n = 21)
12.43 (4.7)9.81 (5.2)0.53 (0.20–0.85)
\n GAD-7\n
Treatment group
(n = 50)
11.46 (4.0)6.12 (4.5)5.34 (4.1)0.48 (0.08–0.87)1.25 (0.79–1.71)1.51 (0.97–2.06)Group.85
Depression subgroup
(n = 28)
10.86 (4.1)5.46 (3.9)5.19 (4.1)0.56 (0.03–1.09)1.35 (0.75–1.95)1.43 (0.73–2.10)Time < .001
Anxiety subgroup
(n = 22)
12.23 (3.8)6.95 (5.3)5.55 (4.2)0.39 (−0.21–0.99)1.15 (0.44–1.86)1.62 (0.72–2.52)G × T < .01
Control group
(n = 50)
12.26 (4.2)8.40 (5.0)0.82 (0.51–1.13)
Depression subgroup
(n = 29)
11.97 (5.0)8.03 (5.3)0.76 (0.39–1.13)
Anxiety subgroup
(n = 21)
12.67 (2.8)8.90 (4.7)0.93 (0.36–1.50)
\n\n
\n

Notes:

\n

The confidence intervals were calculated using the standard error and an alpha level of 0.05. A confidence interval that do not overlap zero indicates a significance of p < .05. p values are given for linear mixed models using data from pre-treatment and post-treatment and all individuals (N = 100). The p value associated with the main effect of group denotes significance of average difference between groups at the pre-treatment assessment. The p value associated with the effect of time denotes the significance of average change over all assessment periods across treatment. The p value associated with the effect of G × T (group × time) denotes significance of difference between the treatment group and the control group in change over all assessment periods. Effect sizes are calculated as standardized mean differences. PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.

\n
\nTable 3:
Means, SDs and effect sizes (Cohen’s d) for measures of emotional processing and mindfulness skills.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Mean (SD)Effect size Cohen’s d (95% CI)Linear mixed models
Measure and groupPre-treatmentPost-treatment7-month
follow-up
Between-group,
post-treatment
Within-group
pre-post-treatment
Within-group
pre-7-month follow-up
Effect\n p\n
\n EPS-25\n Group.50
Treatment group
(n = 50)
5.00 (1.03)2.86 (1.48)2.84 (1.65)0.82 (0.41–1.23)1.67 (1.13–2.21)1.51 (1.00–2.01)Time < .001
Control group
(n = 50)
4.93 (1.01)4.17 (1.73)0.50 (0.22–0.77)G × T < .001
\n FFMQ\n Group.15
Treatment group
(n = 50)
76.70 (10.9)88.00 (12.0)88.98 (13.3)0.65 (0.25–1.05)0.98 (0.65–1.31)0.99 (0.59–1.39)Time < .001
Control group
(n = 50)
77.18 (14.1)78.44 (17.1)0.08 (−0.11–0.27)G × T < .001
\n\n
\n

Notes:

\n

The confidence intervals were calculated using the standard error and an alpha level of 0.05. A confidence interval that do not overlap zero indicates a significance of p < .05. p values are given for linear mixed models using data from pre-treatment and post-treatment and all individuals (N = 100). The p value associated with the main effect of group denotes significance of average difference between groups at the pre-treatment assessment. The p value associated with the effect of time denotes the significance of average change over all assessment periods across treatment. The p value associated with the effect of G × T (group × time) denotes significance of difference between the treatment group and the control group in change over all assessment periods. Effect sizes are calculated as standardized mean differences. EPS-25: Emotional Processing Scale; FFMQ: Five Facets of Mindfulness Questionnaire.

\n
\"Weekly
\n

\nFigure 3: Weekly PHQ-9 and GAD-7 scores.

\nWeekly scores on the PHQ-9 and the GAD-7 for both groups. Vertical bars denote 95% confidence intervals (CI). PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.

Diagnoses

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The number of diagnoses among participants at pre-treatment, post-treatment and at the 7-month follow-up are illustrated in Table 4. At post-treatment, there were significantly fewer participants with a diagnosis of major depression in the treatment group (10%) than in the control group (32%). The difference was significant (χ2(N = 100, d f = 1) = 7.3, p < .01). Reductions in the number of diagnoses of GAD, SP or PD were not significantly different between groups at post-treatment.

\n
\nTable 4:
Frequency data of DSM-IV diagnoses.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Treatment groupControl group
DiagnosisPre-treatmentPost-treatment7-month follow-upPre-treatmentPost-treatment
DEP35 (70%)5 (10%)6 (12%)37 (74%)16 (32%)
GAD23 (46%)13 (26%)10 (20%)26 (52%)18 (36%)
SP19 (38%)10 (20%)9 (18%)17 (34%)13 (26%)
PD11 (22%)5 (10%)6 (12%)9 (18%)5 (10%)
\n Number of diagnoses\n
04 (8%)28 (56%)31 (62%)0 (0%)18 (36%)
116 (32%)13 (26%)8 (16%)23 (46%)18 (36%)
219 (38%)7 (14%)10 (20%)16 (32%)9 (18%)
310 (20%)2 (4%)1 (2%)10 (20%)4 (8%)
41 (2%)0 (0%)0 (0%)1 (2%)1 (2%)
Total number of diagnoses8833318949
\n\n
\n

Notes:

\n

The four participants with zero diagnoses listed at pre-treatment fulfilled DSM-IV criteria for depression and anxiety, not otherwise specified. DEP, GAD, SP, PD: Diagnoses of major depression, generalized anxiety disorder, social phobia and panic disorder.

\n

Recovery after treatment and clinical global improvement

\n

Categorical rates of recovery after treatment (i.e., a participant who did not fulfill criteria for any DSM-IV diagnosis and reached a score less than 10 on both the PHQ-9 and the GAD-7) were significantly different at post-treatment between the treatment group (n = 26; 52.0%) and the control group (n = 12; 24.0%), χ2(N = 100, d f = 1) = 8.3, p < .01. At follow-up there were 25 participants (50.0%) from the treatment group who met the criteria for recovery.

\n

Post-treatment interviews resulted in estimates of clinical global improvement according to the CGI-I (Guy, 1976). In the treatment group, 28 participants (56.0%) were much or very much improved while this was only true for 11 (22.0%) in the control group. This difference was significant, χ2(N = 100, d f = 1) = 12.1, p < .001. At follow-up, this figure was 52% (n = 26) in the treatment group.

Subgroups of principal depression and anxiety

\n

There were no significant interaction effect of group, subgroup and time on neither the PHQ-9 nor the GAD-7. This was despite the fact that the treatment had a very large within-group group effect (d = 3.10) on the PHQ-9 in the depression subgroup, compared to for those in the anxiety subgroup (d = 1.12). Thus, there were no indications that the treatment was more effective in reducing symptoms of depression among participants with a principal diagnosis of depression, or analogously for anxiety symptoms.

Therapist time

\n

In the treatment group, the average therapist time per client and week was 9.5 min (S D = 4.0). While there was a significant difference in average therapist time per week between therapists (F(2, 47) = 7.73, p < .001), there were no correlations between therapist time and change scores on any of the outcome measures (all r’s < .19, all p’s > .18). The average therapist time per client and week was 2.3 min (S D = 0.86) in the control group. As expected, therapist time was significantly less in the control group than in the treatment group, t(98) = 12.4, p < .001.

Participants’ evaluation of the treatment

\n

Most participants were satisfied (46%) or very satisfied (36%) with the overall treatment they had received. Nine (18%) were indifferent or mildly dissatisfied, and no one was clearly dissatisfied. An absolute majority (82%) thought that the amount of text was appropriate. A similar amount of participants considered the text interesting and relevant, all the time (46%) or most of the time (40%). Most participants considered the treatment to be very demanding (28%), demanding (42%) or somewhat demanding (26%). Importantly though, a majority considered the treatment very much worth the effort (52%) or worth the effort (38%).

" + ] + }, + "discussion_html": { + "value": [ + "

Discussion

\n

This randomized controlled trial aimed to evaluate the effects of affect-phobia therapy in the format of guided self-help through the Internet in a sample of participants with depression and anxiety disorders. The results indicated that the treatment was effective in reducing symptoms of depression and anxiety, and also in facilitating emotional processing and mindfulness skills. Subgroup analyses gave no indications of differential efficacy between participants with a principal diagnosis of depression and those with principal anxiety. Treatment gains were maintained in the 7-month follow-up.

\n

The treatment manual used in this study aimed to implement a psychodynamic treatment based on the affect-phobia model in self-help format. This approach calls for a discussion on similarities and differences to the original APT manual. An assumption of this implementation was that the core principles of affect-phobia treatment manual could be retained. This included the general model of psychopathology (i.e., as illustrated by the triangle of conflict in Fig. 2) and the overall structure of the therapy. While the treatment emphasized how affect-phobic patterns in a person’s current life (C) began with past persons (P), as illustrated in Malan’s triangle of person, the treatment did not address how these patterns could potentially be enacted with the therapist (T). Importantly, these patterns were not regarded as non-existing, but rather the treatment material did not address them nor was it part of the role of the therapists to address these patterns. While the therapist role might overlap between guided self-help and face-to-face therapy in several aspects (Paxling et al., 2013), there is a difference in the present study in how the treatment material taught “emotional mindfulness” as a way of conducting exposure to one’s feelings without the therapist being present. Some authors have suggested that exposure with response prevention may result in better effects of treatment when patients conduct the exposure by themselves, in their natural environment (Röper & Rachman, 1976; Salkovskis, 1985). If this is also the case in affect-phobia therapy and how that would affect outcome is a question for further research, but it is possible that self-exposure to feelings is at least as effective as exposure with a therapist present. Importantly, as exposure with response prevention is assumed to be an active mechanism in the treatment tested in this study, this would imply similarities in working mechanisms in affect-focused psychodynamic treatment and cognitive behavioral therapy based on principles of exposure. Similarly, several contemporary CBT treatments have components of emotion regulation techniques (e.g., Berking et al., 2013; Bryant et al., 2013), that seem overlapping to affect-phobia treatment. Future research should investigate further similarities and differences between affect-focused psychodynamic therapy and various CBT models. Summing up, despite the aforementioned differences to the original APT manual, we believe that the manual used in the current study is indeed a valid implementation of a psychodynamic therapy based on the affect-phobia model.

\n

In affect-phobia therapy, the model of psychopathology is the same across disorders, i.e., the triangle of conflict is assumed to explain both etiology and maintenance of for example depression and anxiety disorders (McCullough et al., 2003). This aim is similar to transdiagnostic and unified protocols where the treatment material has been arranged to fit a broader range of patients (Barlow, Allen & Choate, 2004; Craske, 2012). Hence, affect-phobia therapy could be described as a transdiagnostic treatment. While there are several studies on the efficacy of cognitive behavioral transdiagnostic treatments for anxiety disorders (Farchione et al., 2012; McEvoy, Nathan & Norton, 2009), few exist that explicitly target both depression and anxiety. However, one uncontrolled trial testing the effectiveness of a group-based intervention (McEvoy & Nathan, 2007) resulted in promising outcomes and showed comparable efficacy to several disorder-specific treatments. More recently, Titov et al. (2011) provided evidence of the efficacy of an Internet-delivered transdiagnostic program that targeted both anxiety and depression, when compared to a waiting-list. Both these treatments yielded within-group effect sizes of Cohen’s d around 1.0 for measures of depression and anxiety. Hence, the affect-phobia treatment tested in this study, seems to stand well when compared to other transdiagnostic treatments tested.

\n

There are methodological limitations that need to be considered. First, as we recruited participants from the community and not from, for example, a treatment clinic, the external validity of the findings are challenging to interpret. While there are studies on ICBT that suggests generalizability to clinical settings (e.g., Bergström et al., 2010; Hedman et al., 2013), this has yet to be proven for Internet-delivered psychodynamic therapy. Moreover, more than half of the participants in the present study had three years or more of university education. While this factor might have biased the results, the average severity of depression and anxiety symptoms was moderate to moderately severe (Kroenke et al., 2010), and more than half of the participants had comorbid disorders, suggesting clinical representativity (Kessler, Merikangas & Wang, 2007). A second methodological limitation concerns the substantial within-group effects in the control group that make the results harder to interpret. These effects are probably due to the weekly clinical monitoring and supportive contact with the therapists in addition to the extensive test procedures such as telephone interviews before and after the treatment period. While these aspects might have biased the results, it also highlights the need for research regarding specific factors in guided self-help treatments. A third limitation concerns how missing data were handled at the 7-month follow-up for the categorical measure of recovery. For that measure, missing data at follow-up were replaced by that from post-treatment. When using that approach in longitudinal analysis, there is a known risk for estimation bias (Gueorguieva & Krystal, 2004). While we did not compare the recovery rates over time (i.e., did not include this measure in any longitudinal analysis) we still acknowledge that some method of multiple imputation could have been used to account for the missing data (Graham, 2009). Another limitation concerns the subgroup analyses. As the total sample size was appropriate for the comparison between treatment and control, it seemed not to have been adequate for the analyses regarding subgroups of principal depression and anxiety. This implies that a larger sample size would be needed in future research if investigating the effect of a transdiagnostic treatment on specific diagnoses in a sample with multiple disorders. A related limitation concerns the definition of the subgroups in this study. The group with principal anxiety disorders is a heterogeneous group, e.g., in the sense that it includes both fear disorders (e.g., panic disorder) and worry disorders (GAD). This may have confounded the subgroup analyses. A final limitation that needs to be addressed concerns the therapists in the study, all of whom were psychologists in training, albeit during the last semester of training in a five year program and under regular supervision. It is possible that more experienced therapists would have enabled even larger treatment effects. A related concern is that psychologists in training conducted all diagnostic interviews. While the psychologists were explicitly trained in the diagnostic procedures and received supervision, there is a possibility that their level of experience may have affected how the diagnostic categories were defined. Importantly though, the MINI interview has been designed to be administered by non-experts.

" + ] + }, + "conclusion_html": { + "value": [ + + ] + }, + "author_contrib_html": { + "value": [ + + ] + }, + "competing_interests_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\nAbbass A, Town J, Driessen E. 2012. Intensive short-term dynamic psychotherapy: a systematic review and meta-analysis of outcome research. Harvard Review of Psychiatry 20:97-108 \n", + "\nAndersson G. 2009. Using the Internet to provide cognitive behaviour therapy. Behaviour Research and Therapy 47:175-180 \n", + "\nAndersson G, Paxling B, Roch-Norlund P, Östman G, Norgren A, Almlöv J, Georén L, Breitholtz E, Dahlin M, Cuijpers P, Carlbring P, Silverberg F. 2012. Internet-based psychodynamic vs. cognitive behavioural guided self-help for generalized anxiety disorder: a randomised controlled trial. Psychotherapy and Psychosomatics 81:344-355 \n", + "\nBaer RA, Smith GT, Hopkins J, Krietemeyer J, Toney L. 2006. Using self-report assessment methods to explore facets of mindfulness. Assessment 13:27-45 \n", + "\nBaker R, Thomas S, Thomas PW, Gower P, Santonastaso M, Whittlesea A. 2010. The emotional processing scale: scale refinement and abridgement (EPS-25) Journal of Psychosomatic Research 68:83-88 \n", + "\nBarlow DH, Allen LB, Choate ML. 2004. Toward a unified treatment for emotional disorders. Behavior Therapy 35:205-230 \n", + "\nBergström J, Andersson G, Ljótsson B, Rück C, Andréewitch S, Karlsson A, Carlbring P, Andersson E, Lindefors N. 2010. Internet-versus group-administered cognitive behaviour therapy for panic disorder in a psychiatric setting: a randomised trial. BMC Psychiatry 10:54 \n", + "\nBerking M, Ebert D, Cuijpers P, Hofmann SG. 2013. Emotion regulation skills training enhances the efficacy of inpatient cognitive behavioral therapy for major depressive disorder: a randomized controlled trial. Psychotherapy and Psychosomatics 82:234-245 \n", + "\nBorenstein M, Hedges LV, Higgins JPT, Rothstein HR. 2009. Introduction to meta-analysis. Chichester: John Wiley & Sons. \n", + "\nBryant RA, Mastrodomenico J, Hopwood S, Kenny L, Cahill C, Kandris E, Taylor K. 2013. Augmenting cognitive behaviour therapy for post-traumatic stress disorder with emotion tolerance training: a randomized controlled trial. Psychological Medicine 1-8 \n", + "\nCohen J. 1988. Statistical power analysis for the behavioral sciences (2nd ed). Hillsdale: Lawrence Erlbaum Associates. \n", + "\nCraske MG. 2012. Transdiagnostic treatment for anxiety and depression. Depression and Anxiety 29:749-753 \n", + "\nCuijpers P, Donker T, Van Straten A, Li J, Andersson G. 2010. Is guided self-help as effective as face-to-face psychotherapy for depression and anxiety disorders? A systematic review and meta-analysis of comparative outcome studies. Psychological Medicine 40:1943-1957 \n", + "\nDavanloo H. 2000. Intensive short-term dynamic psychotherapy: selected papers of Habib Davanloo. Chichester: Wiley. \n", + "\nDiener MJ, Hilsenroth MJ, Weinberger J. 2007. Therapist affect focus and patient outcomes in psychodynamic psychotherapy: a meta-analysis. The American Journal of Psychiatry 164:936-941 \n", + "\nDornelas E, Ferrand J, Stepnowski R, Barbagallo J, McCullough L. 2010. A pilot study of affect-focused psychotherapy for antepartum depression. Journal of Psychotherapy Integration 20:364-382 \n", + "\nDriessen E, Cuijpers P, De Maat SCM, Abbass A, De Jonghe F, Dekker JJM. 2010. The efficacy of short-term psychodynamic psychotherapy for depression: a meta-analysis. Clinical Psychology Review 30:25-36 \n", + "\nEbmeier KP, Donaghey C, Steele JD. 2006. Recent developments and current controversies in depression. Lancet 367:153-167 \n", + "\nFann JR, Berry DL, Wolpin S, Austin-Seymour M, Bush N, Halpenny B, Lober WB, McCorkle R. 2009. Depression screening using the Patient Health Questionnaire-9 administered on a touch screen computer. Psycho-oncology 18:14-22 \n", + "\nFarchione TJ, Fairholme CP, Ellard KK, Boisseau CL, Thompson-Hollands J, Carl JR, Gallagher MW, Barlow DH. 2012. Unified protocol for transdiagnostic treatment of emotional disorders: a randomized controlled trial. Behavior Therapy 43:666-678 \n", + "\nFosha D. 2000. The transforming power of affect: a model for accelerated change. New York: BasicBooks. \n", + "\nFrederick RJ. 2009. Living like you mean it: use the wisdom and power of your emotions to get the life you really want. San Francisco: Jossey-Bass. \n", + "\nGraham JW. 2009. Missing data analysis: making it work in the real world. Annual Review of Psychology 60:549-576 \n", + "\nGueorguieva R, Krystal JH. 2004. Move over ANOVA: progress in analyzing repeated-measures data and its reflection in papers published in the Archives of General Psychiatry. Archives of General Psychiatry 61:310-317 \n", + "\nGuy W. 1976. Clinical global impressions. ECDEU assessment manual for psychopharmacology. Rockville: NIMH. \n", + "\nHedman E, Ljótsson B, Lindefors N. 2012. Cognitive behavior therapy via the Internet: a systematic review of applications, clinical efficacy and cost-effectiveness. Expert Review of Pharmacoeconomics & Outcomes Research 12:745-764 \n", + "\nHedman E, Ljótsson B, Rück C, Bergström J, Andersson G, Kaldo V, Jansson L, Andersson E, Blom K, El Alaoui S, Falk L, Ivarsson J, Nasri B, Rydh S, Lindefors N. 2013. Effectiveness of Internet-based cognitive behaviour therapy for panic disorder in routine psychiatric care. Acta Psychiatrica Scandinavica Epub ahead of print Feb 14 2013\n", + "\nJohansson R, Andersson G. 2012. Internet-based psychological treatments for depression. Expert Review of Neurotherapeutics 12:861-870 \n", + "\nJohansson R, Ekbladh S, Hebert A, Lindström M, Möller S, Petitt E, Poysti S, Larsson MH, Rousseau A, Carlbring P, Cuijpers P, Andersson G. 2012. Psychodynamic guided self-help for adult depression through the internet: a randomised controlled trial. PLoS ONE 7:e38021 \n", + "\nKessler RC, Berglund P, Demler O, Jin R, Merikangas KR, Walters EE. 2005. Lifetime prevalence and age-of-onset distributions of DSM-IV disorders in the National Comorbidity Survey Replication. Archives of General Psychiatry 62:593-602 \n", + "\nKessler RC, Merikangas KR, Wang PS. 2007. Prevalence, comorbidity, and service utilization for mood disorders in the United States at the beginning of the twenty-first century. Annual Review of Clinical Psychology 3:137-158 \n", + "\nKroenke K, Spitzer RL, Williams JB. 2001. The PHQ-9: validity of a brief depression severity measure. Journal of General Internal Medicine 16:606-613 \n", + "\nKroenke K, Spitzer RL, Williams JBW, Löwe B. 2010. The patient health questionnaire somatic, anxiety, and depressive symptom scales: a systematic review. General Hospital Psychiatry 32:345-359 \n", + "\nLeichsenring F, Salzer S, Beutel ME, Herpertz S, Hiller W, Hoyer J, Huesing J, Joraschky P, Nolting B, Poehlmann K, Ritter V, Stangier U, Strauss B, Stuhldreher N, Tefikow S, Teismann T, Willutzki U, Wiltink J, Leibing E. 2013. Psychodynamic therapy and cognitive-behavioral therapy in social anxiety disorder: a multicenter randomized controlled trial. The American Journal of Psychiatry Epub ahead of print May 17 2013\n", + "\nLeichsenring F, Salzer S, Jaeger U, Kächele H, Kreische R, Leweke F, Rüger U, Winkelbach C, Leibing E. 2009. Short-term psychodynamic psychotherapy and cognitive-behavioral therapy in generalized anxiety disorder: a randomized, controlled trial. The American Journal of Psychiatry 166:875-881 \n", + "\nLilja JL, Frodi-Lundgren A, Hanse JJ, Josefsson T, Lundh L-G, Sköld C, Hansen E, Broberg AG. 2011. Five Facets Mindfulness Questionnaire - reliability and factor structure: a Swedish version. Cognitive Behaviour Therapy 40:291-303 \n", + "\nMalan D. 1995. Individual psychotherapy and the science of psychodynamics (2nd ed). Oxford: Butterworth-Heinemann. \n", + "\nMallinckrodt CH, Clark WS, David SR. 2001. Accounting for dropout bias using mixed-effects models. Journal of Biopharmaceutical Statistics 11:9-21 \n", + "\nMcCullough L, Kuhn N, Andrews S, Kaplan A, Wolf J, Hurley CL. 2003. Treating affect phobia: a manual for short-term dynamic psychotherapy. New York: Guilford Press. \n", + "\nMcEvoy P, Nathan P. 2007. Effectiveness of cognitive behavior therapy for diagnostically heterogeneous groups: a benchmarking study. Journal of Consulting and Clinical Psychology 75:344-350 \n", + "\nMcEvoy P, Nathan P, Norton P. 2009. Efficacy of transdiagnostic treatments: a review of published outcome studies and future research directions. Journal of Cognitive Psychotherapy: An International Quarterly 23:20-33 \n", + "\nMilrod B, Leon AC, Busch F, Rudden M, Schwalberg M, Clarkin J, Aronson A, Singer M, Turchin W, Klass ET, Graf E, Teres JJ, Shear MK. 2007. A randomized controlled clinical trial of psychoanalytic psychotherapy for panic disorder. The American Journal of Psychiatry 164:265-272 \n", + "\nOsimo F, Stein MJ. 2012. Theory and practice of experiential dynamic psychotherapy. London: Karnac. \n", + "\nPaxling B, Lundgren S, Norman A, Almlöv J, Carlbring P, Cuijpers P, Andersson G. 2013. Therapist behaviours in internet-delivered cognitive behaviour therapy: analyses of e-mail correspondence in the treatment of generalized anxiety disorder. Behavioural and Cognitive Psychotherapy 41:280-289 \n", + "\nRöper G, Rachman S. 1976. Obsessional-compulsive checking: experimental replication and development. Behaviour Research and Therapy 14:25-32 \n", + "\nSalkovskis PM. 1985. Obsessional-compulsive problems: a cognitive-behavioural analysis. Behaviour Research and Therapy 23:571-583 \n", + "\nSchulz KF, Altman DG, Moher D. 2010. CONSORT 2010 statement: updated guidelines for reporting parallel group randomised trials. PLoS Medicine 7:e1000251 \n", + "\nShapiro S, Wilk M. 1965. An analysis of variance test for normality (complete samples) Biometrika 52:591-611 \n", + "\nSheehan DV, Lecrubier Y, Sheehan KH, Amorim P, Janavs J, Weiller E, Hergueta T, Baker R, Dunbar GC. 1998. The Mini-International Neuropsychiatric Interview (M.I.N.I.): the development and validation of a structured diagnostic psychiatric interview for DSM-IV and ICD-10. The Journal of Clinical Psychiatry 59(Suppl 2):22-33 Quiz 34–57\n", + "\nSmit F, Cuijpers P, Oostenbrink J, Batelaan N, De Graaf R, Beekman A. 2006. Costs of nine common mental disorders: implications for curative and preventive psychiatry. The Journal of Mental Health Policy and Economics 9:193-200 \n", + "\nSpitzer RL, Kroenke K, Williams JBW, Löwe B. 2006. A brief measure for assessing generalized anxiety disorder: the GAD-7. Archives of Internal Medicine 166:1092-1097 \n", + "\nSvartberg M, Stiles TC, Seltzer MH. 2004. Randomized, controlled trial of the effectiveness of short-term dynamic psychotherapy and cognitive therapy for cluster C personality disorders. The American Journal of Psychiatry 161:810-817 \n", + "\nTitov N, Dear BF, Schwencke G, Andrews G, Johnston L, Craske MG, McEvoy P. 2011. Transdiagnostic internet treatment for anxiety and depression: a randomised controlled trial. Behaviour Research and Therapy 49:441-452 \n", + "\nTown JM, Diener MJ, Abbass A, Leichsenring F, Driessen E, Rabung S. 2012. A meta-analysis of psychodynamic psychotherapy outcomes: evaluating the effects of research-specific procedures. Psychotherapy (Chicago, Ill.) 49:276-290 \n", + "\nVerbeke G, Molenberghs G. 2000. Linear mixed models for longitudinal data. New York: Springer. \n", + "\nWinston A, Laikin M, Pollack J, Samstag LW, McCullough L, Muran JC. 1994. Short-term psychotherapy of personality disorders. The American Journal of Psychiatry 151:190-194 \n" + ] + }, + "figures_html": { + "value": [ + "
\"CONSORT
\n

\nFigure 1: CONSORT flowchart.

\n
", + "
\"Malan’s
\n

\nFigure 2: Malan’s two triangles - the triangle of conflict and the triangle of person.

\nThe two triangles (Malan, 1995) represent what David Malan called “the universal principle of psychodynamic psychotherapy”. That is, defenses (D) and anxieties (A) can block the expression of true feelings (F). These patterns began with past persons (P), are maintained with current persons (C), and are often enacted with the therapist (T).
", + "
\"Weekly
\n

\nFigure 3: Weekly PHQ-9 and GAD-7 scores.

\nWeekly scores on the PHQ-9 and the GAD-7 for both groups. Vertical bars denote 95% confidence intervals (CI). PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.
" + ] + }, + "tables_html": { + "value": [ + "
\nTable 1:
Demographic description of the participants.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Treatment groupControl groupTotal
GenderMale8 (16%)10 (20%)18 (18%)
Female42 (84%)40 (80%)82 (82%)
AgeMean (SD)43.1 (13.9)46.6 (12.1)44.9 (13.1)
Min-Max19–7223–7719–77
Marital statusMarried or co-habiting31 (62%)36 (72%)67 (67%)
Other19 (38%)14 (28%)33 (33%)
Educational levelCollege or university, at least 3 years27 (54%)29 (58%)56 (56%)
Other23 (46%)21 (42%)44 (44%)
Employment statusEmployed or student41 (82%)33 (66%)74 (74%)
Other9 (18%)17 (34%)26 (26%)
Psychological treatmentNo experience15 (30%)16 (32%)31 (31%)
Prior experience35 (70%)31 (62%)66 (66%)
Ongoing0 (0%)3 (6%)3 (3%)
Pharmacological treatmentNo experience27 (54%)22 (44%)49 (49%)
Prior experience14 (28%)12 (24%)26 (26%)
Ongoing9 (18%)16 (32%)25 (25%)
\n", + "
\nTable 2:
Means, SDs and effect sizes (Cohen’s d) for measures of depression and anxiety.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Mean (SD)Effect size Cohen’s d (95% CI)Linear mixed models
Measure and groupPre-treatmentPost-treatment7-month
follow-up
Between-group,
post-treatment
Within-group
pre-post-treatment
Within-group
pre-7-month follow-up
Effect\n p\n
\n PHQ-9\n
Treatment group
(n = 50)
13.90 (3.6)6.32 (4.2)5.55 (3.5)0.77 (0.37–1.18)1.93 (1.31–2.55)2.43 (1.72–3.14)Group.89
Depression subgroup
(n = 28)
15.32 (3.3)5.89 (2.8)5.96 (3.5)0.95 (0.40–1.50)3.10 (1.87–4.32)2.82 (1.78–3.87)Time < .001
Anxiety subgroup
(n = 22)
12.09 (3.3)6.86 (5.5)5.00 (3.4)0.55 (−0.06–1.16)1.12 (0.49–1.75)2.17 (1.11–3.24)G × T < .001
Control group
(n = 50)
13.96 (4.7)10.26 (5.9)0.69 (0.40–0.97)
Depression subgroup
(n = 29)
15.07 (4.4)10.59 (6.4)0.79 (0.37–1.22)
Anxiety subgroup
(n = 21)
12.43 (4.7)9.81 (5.2)0.53 (0.20–0.85)
\n GAD-7\n
Treatment group
(n = 50)
11.46 (4.0)6.12 (4.5)5.34 (4.1)0.48 (0.08–0.87)1.25 (0.79–1.71)1.51 (0.97–2.06)Group.85
Depression subgroup
(n = 28)
10.86 (4.1)5.46 (3.9)5.19 (4.1)0.56 (0.03–1.09)1.35 (0.75–1.95)1.43 (0.73–2.10)Time < .001
Anxiety subgroup
(n = 22)
12.23 (3.8)6.95 (5.3)5.55 (4.2)0.39 (−0.21–0.99)1.15 (0.44–1.86)1.62 (0.72–2.52)G × T < .01
Control group
(n = 50)
12.26 (4.2)8.40 (5.0)0.82 (0.51–1.13)
Depression subgroup
(n = 29)
11.97 (5.0)8.03 (5.3)0.76 (0.39–1.13)
Anxiety subgroup
(n = 21)
12.67 (2.8)8.90 (4.7)0.93 (0.36–1.50)
\n\n
\n

Notes:

\n

The confidence intervals were calculated using the standard error and an alpha level of 0.05. A confidence interval that do not overlap zero indicates a significance of p < .05. p values are given for linear mixed models using data from pre-treatment and post-treatment and all individuals (N = 100). The p value associated with the main effect of group denotes significance of average difference between groups at the pre-treatment assessment. The p value associated with the effect of time denotes the significance of average change over all assessment periods across treatment. The p value associated with the effect of G × T (group × time) denotes significance of difference between the treatment group and the control group in change over all assessment periods. Effect sizes are calculated as standardized mean differences. PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.

\n
", + "
\nTable 3:
Means, SDs and effect sizes (Cohen’s d) for measures of emotional processing and mindfulness skills.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Mean (SD)Effect size Cohen’s d (95% CI)Linear mixed models
Measure and groupPre-treatmentPost-treatment7-month
follow-up
Between-group,
post-treatment
Within-group
pre-post-treatment
Within-group
pre-7-month follow-up
Effect\n p\n
\n EPS-25\n Group.50
Treatment group
(n = 50)
5.00 (1.03)2.86 (1.48)2.84 (1.65)0.82 (0.41–1.23)1.67 (1.13–2.21)1.51 (1.00–2.01)Time < .001
Control group
(n = 50)
4.93 (1.01)4.17 (1.73)0.50 (0.22–0.77)G × T < .001
\n FFMQ\n Group.15
Treatment group
(n = 50)
76.70 (10.9)88.00 (12.0)88.98 (13.3)0.65 (0.25–1.05)0.98 (0.65–1.31)0.99 (0.59–1.39)Time < .001
Control group
(n = 50)
77.18 (14.1)78.44 (17.1)0.08 (−0.11–0.27)G × T < .001
\n\n
\n

Notes:

\n

The confidence intervals were calculated using the standard error and an alpha level of 0.05. A confidence interval that do not overlap zero indicates a significance of p < .05. p values are given for linear mixed models using data from pre-treatment and post-treatment and all individuals (N = 100). The p value associated with the main effect of group denotes significance of average difference between groups at the pre-treatment assessment. The p value associated with the effect of time denotes the significance of average change over all assessment periods across treatment. The p value associated with the effect of G × T (group × time) denotes significance of difference between the treatment group and the control group in change over all assessment periods. Effect sizes are calculated as standardized mean differences. EPS-25: Emotional Processing Scale; FFMQ: Five Facets of Mindfulness Questionnaire.

\n
", + "
\nTable 4:
Frequency data of DSM-IV diagnoses.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Treatment groupControl group
DiagnosisPre-treatmentPost-treatment7-month follow-upPre-treatmentPost-treatment
DEP35 (70%)5 (10%)6 (12%)37 (74%)16 (32%)
GAD23 (46%)13 (26%)10 (20%)26 (52%)18 (36%)
SP19 (38%)10 (20%)9 (18%)17 (34%)13 (26%)
PD11 (22%)5 (10%)6 (12%)9 (18%)5 (10%)
\n Number of diagnoses\n
04 (8%)28 (56%)31 (62%)0 (0%)18 (36%)
116 (32%)13 (26%)8 (16%)23 (46%)18 (36%)
219 (38%)7 (14%)10 (20%)16 (32%)9 (18%)
310 (20%)2 (4%)1 (2%)10 (20%)4 (8%)
41 (2%)0 (0%)0 (0%)1 (2%)1 (2%)
Total number of diagnoses8833318949
\n\n
\n

Notes:

\n

The four participants with zero diagnoses listed at pre-treatment fulfilled DSM-IV criteria for depression and anxiety, not otherwise specified. DEP, GAD, SP, PD: Diagnoses of major depression, generalized anxiety disorder, social phobia and panic disorder.

\n
" ] }, "fulltext_html": { @@ -78,26 +228,19 @@ "/articles/102.xml" ] }, - "supplementary_material": { + "supplementary_file": { "value": [ "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/S1_CONSORT_checklist.pdf", "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/S2_trial_protocol.pdf" ] }, - "figure": { + "figures_image": { "value": [ "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/fig-1-full.png", "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/fig-2-full.png", "https://dfzljdn9uc3pi.cloudfront.net/2013/102/1/fig-3-full.png" ] }, - "figure_caption": { - "value": [ - "\nFigure 1: CONSORT flowchart.\n\n  Download full-size image\nDOI: 10.7717/peerj.102/fig-1\n\n", - "\nFigure 2: Malan’s two triangles - the triangle of conflict and the triangle of person.\nThe two triangles (Malan, 1995) represent what David Malan called “the universal principle of psychodynamic psychotherapy”. That is, defenses (D) and anxieties (A) can block the expression of true feelings (F). These patterns began with past persons (P), are maintained with current persons (C), and are often enacted with the therapist (T).\n  Download full-size image\nDOI: 10.7717/peerj.102/fig-2\n\n", - "\nFigure 3: Weekly PHQ-9 and GAD-7 scores.\nWeekly scores on the PHQ-9 and the GAD-7 for both groups. Vertical bars denote 95% confidence intervals (CI). PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.\n  Download full-size image\nDOI: 10.7717/peerj.102/fig-3\n\n" - ] - }, "license": { "value": [ @@ -105,7 +248,8 @@ }, "copyright": { "value": [ - + "2013", + "Johansson et al." ] }, "file_hashes": [ @@ -119,7 +263,7 @@ "fig-3-full.png": "0146a2e575c584b50ab4832654e97a96" }, { - "fulltext.html": "63379447ccbb411a3b65c2c28efba3f9" + "fulltext.html": "85a83823a2dca2801273de54f310ea7b" }, { "fulltext.pdf": "8e2c1cb94b99943cc618c437f8fd1618" @@ -141,17 +285,27 @@ "PeerJ Inc." ] }, - "journal": { + "journal_name": { "value": [ "PeerJ" ] }, + "journal_issn": { + "value": [ + "2167-8359" + ] + }, "title": { "value": [ "A new specimen of the Early Cretaceous bird Hongshanornis longicresta: insights into the aerodynamics and diet of a basal ornithuromorph" ] }, - "authors": { + "keywords": { + "value": [ + "Cretaceous; Birds; Aerodynamics; Morphology; China" + ] + }, + "author_name": { "value": [ "Luis M. Chiappe", "Bo Zhao", @@ -164,11 +318,40 @@ "Xiaodong Cheng" ] }, - "date": { + "author_institution": { + "value": [ + "Dinosaur Institute, Natural History Museum of Los Angeles County, Los Angeles, CA, USA", + "Dalian Natural History Museum, District Dalian, PR China", + "Institute of Vertebrate Paleontology and Paleoanthroplogy, Beijing, PR China", + "Dalian Natural History Museum, District Dalian, PR China", + "Dalian Natural History Museum, District Dalian, PR China", + "Institute of Geology, Chinese Academy of Geological Sciences, Beijing, PR China", + "University of Southern California, Health Sciences Campus, Los Angeles, CA, USA", + "Unidad de Paleontología, Dpto. Biología, Universidad Autónoma de Madrid, Cantoblanco, Spain", + "Beijing Natural History Museum, Beijing, PR China", + "Dalian Natural History Museum, District Dalian, PR China" + ] + }, + "editor_name": { + "value": [ + "J Thewissen" + ] + }, + "date_published": { "value": [ "2014-01-02" ] }, + "date_accepted": { + "value": [ + "2013-12-11" + ] + }, + "date_submitted": { + "value": [ + "2013-08-30" + ] + }, "doi": { "value": [ "10.7717/peerj.234" @@ -189,14 +372,140 @@ "e234" ] }, - "description": { + "abstract": { "value": [ "The discovery of Hongshanornis longicresta, a small ornithuromorph bird with unusually long hindlimb proportions, was followed by the discovery of two closely related species, Longicrusavis houi and Parahongshanornis chaoyangensis. Together forming the Hongshanornithidae, these species reveal important information about the early diversity and morphological specialization of ornithuromorphs, the clade that contains all living birds. Here we report on a new specimen (DNHM D2945/6) referable to Hongshanornis longicresta that contributes significant information to better understand the morphology, trophic ecology, and aerodynamics of this species, as well as the taxonomy of the Hongshanornithidae. Most notable are the well-preserved wings and feathered tail of DNHM D2945/6, which afford an accurate reconstruction of aerodynamic parameters indicating that as early as 125 million years ago, basal ornithuromorphs had evolved aerodynamic surfaces comparable in size and design to those of many modern birds, and flight modes alike to those of some small living birds." ] }, - "abstract": { + "abstract_html": { "value": [ - "The discovery of Hongshanornis longicresta, a small ornithuromorph bird with unusually long hindlimb proportions, was followed by the discovery of two closely related species, Longicrusavis houi and Parahongshanornis chaoyangensis. Together forming the Hongshanornithidae, these species reveal important information about the early diversity and morphological specialization of ornithuromorphs, the clade that contains all living birds. Here we report on a new specimen (DNHM D2945/6) referable to Hongshanornis longicresta that contributes significant information to better understand the morphology, trophic ecology, and aerodynamics of this species, as well as the taxonomy of the Hongshanornithidae. Most notable are the well-preserved wings and feathered tail of DNHM D2945/6, which afford an accurate reconstruction of aerodynamic parameters indicating that as early as 125 million years ago, basal ornithuromorphs had evolved aerodynamic surfaces comparable in size and design to those of many modern birds, and flight modes alike to those of some small living birds." + "

The discovery of Hongshanornis longicresta, a small ornithuromorph bird with unusually long hindlimb proportions, was followed by the discovery of two closely related species, Longicrusavis houi and Parahongshanornis chaoyangensis. Together forming the Hongshanornithidae, these species reveal important information about the early diversity and morphological specialization of ornithuromorphs, the clade that contains all living birds. Here we report on a new specimen (DNHM D2945/6) referable to Hongshanornis longicresta that contributes significant information to better understand the morphology, trophic ecology, and aerodynamics of this species, as well as the taxonomy of the Hongshanornithidae. Most notable are the well-preserved wings and feathered tail of DNHM D2945/6, which afford an accurate reconstruction of aerodynamic parameters indicating that as early as 125 million years ago, basal ornithuromorphs had evolved aerodynamic surfaces comparable in size and design to those of many modern birds, and flight modes alike to those of some small living birds.

" + ] + }, + "introduction_html": { + "value": [ + "

Introduction

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Until the recent discoveries from the Jehol Group (Zhou & Zhang, 2007; Chiappe, 2007; O’Connor, Chiappe & Bell, 2011; Zhou, Zhou & O’Connor, 2012) and other Early Cretaceous sites (You et al., 2006) in northern China, the morphological and taxonomical diversity of the basal Ornithuromorpha—which advanced members include all living birds—remained one of the most poorly understood chapters of avian evolutionary history. The global record of these Cretaceous birds was sparse and limited to either incompletely known taxa such as Ambiortus dementjevi (Kurochkin, 1982), Vorona berivotrensis (Forster et al., 1996), or Ichthyornis dispar (Marsh, 1880; Clarke, 2004), or highly specialized forms such as the flightless Patagopteryx deferrariisi (Alvarenga & Bonaparte, 1992; Chiappe, 2002) and the foot-propelled diving hesperornithiforms (Marsh, 1880; Martin & Tate, 1976). The abundant discoveries from the Early Cretaceous Jehol Group of northern China have resulted in the recognition of a diversity of basal ornithuromorph taxa (e.g., Yanornis martini, Yixianornis grabaui, Gansus yumenensis, Hongshanornis longicresta, Archaeorhynchus spathula, Longicrusavis houi, Parahongshanornis chaoyangensis, Jianchangornis microdonta, Schizooura lii, Piscivoravis lii) (Zhou & Zhang, 2001; Zhou & Zhang, 2005; Zhou & Zhang, 2006; Clarke, Zhou & Zhang, 2006; You et al., 2006; Zhou, Zhang & Li, 2009; O’Connor, Gao & Chiappe, 2010; Li et al., 2010; Zhou, Zhou & O’Connor, 2012; Zhou, Zhou & O’Connor, 2013a), which are known by nearly complete specimens (albeit for the most part preserved bi-dimensionally) and in some instances by multiple specimens (e.g., Yanornis martini, Gansus yumenensis, Archaeorhynchus spathula). These specimens have significantly helped to refine our understanding of basal ornithuromorph morphology but despite these recent advances, specimens of these birds remain relatively rare, the vast majority of the Chinese Early Cretaceous birds belong to more primitive groups such as Enantiornithes and basal pygostylians (e.g., Confuciusornithidae, Sapeornithidae).

\n

Among the newly unearthed avifauna of Chinese basal ornithuromorphs are the hongshanornithids, which are particularly noticeable because of their small size (Table 1) and because they are the only lineage of basal ornithuromorphs known from both the Yixian and Jiufotang formations of the Jehol Group. Originally recognized by the discovery of the holotype of Hongshanornis longicresta (Zhou & Zhang, 2005), subsequent discoveries have added the closely related species Longicrusavis houi (O’Connor, Gao & Chiappe, 2010) and Parahongshanornis chaoyangensis (Li, Zhou & Clarke, 2011). To date, while two additional specimens of Hongshanornis longicresta have been recognized in the literature (Li, Zhou & Clarke, 2011; Zheng et al., 2011), the published anatomical information on this taxon is still limited to the preliminary description of the holotype, which skeleton is entirely preserved as voids on two slabs (Zhou & Zhang, 2005). Here we provide a detailed description of the anatomy of another specimen of Hongshanornis longicresta, DNHM D2945/6 (Figs. 14), which preservation provides critical evidence for understanding better the morphology and function of these birds. Furthermore, despite the new discoveries of basal ornithuromorphs, the integument of these birds has remained poorly known in comparison to other basal avians from the Jehol Biota, in particular what refers to the rectricial morphology (Zhou, Zhou & O’Connor, 2012). The complete wing and tail surfaces of DNHM D2945/6, which arguably boasts one of the best-preserved fan-shaped tails from the Mesozoic, reveals important new information about the integumentary evolution and flight capabilities of basal ornithuromorphs.

\n
\nTable 1:
Comparisons of selective measurements in hongshanornithids.
\nThe values highlight the similar sizes and proportions of the three named species of hongshanornithids: Hongshanornis longicresta (DNHM D2945/6 and IVPP V14533), Parahongshanornis chaoyangensis (PMOL-AB00161), and Longicrusavis houi (PKUP 1069).\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
ElementDNHM D2945/6IVPP V14533PMOL-AB00161PKUP 1069
Skull30.530.7
Humerus24.626.029.026.0
Ulna24.524.027.025.0
Carpometacarpus13.013.012.313.1
Manual digit II18.117.7
Femur22.022.024.024.3
Tibiotarsus35.538.038.037.6
Tarsometatarsus20.622.022.021.5
Pedal digit III20.0
\n
\"Photograph
\n

\nFigure 1: Photograph of DNHM D2945.

\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.
\"Interpretive
\n

\nFigure 2: Interpretive drawing of DNHM D2945.

\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pt, proximal tarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.
\"Photograph
\n

\nFigure 3: Photograph of DNHM D2946.

\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.
\"Interpretive
\n

\nFigure 4: Interpretive drawing of DNHM D2946.

\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; st, sternum; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.
" + ] + }, + "methods_html": { + "value": [ + + ] + }, + "results_html": { + "value": [ + "

Results

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Description

\n

In this description we primarily highlight morphological information from the new specimen (DNHM D2945/6) that either supplements or contradicts the description of the holotype (Zhou & Zhang, 2005). Anatomical nomenclature mainly follows Baumel & Witmer (1993); certain structures not cited therein follow Howard (1929). While the Latin terminology used by Baumel & Witmer (1993) is retained for muscles and ligaments, osteological structures are described using the English equivalents of the Latin terms.

\n

The entire skeleton of DNHM D2945/6 is preserved and visible in two slabs; the bones are broken between the two, leaving clear voids. DNHM D2945 preserves the bones of the skull, most of the axial skeleton, right radius, major digit and tibiotarsus, and both feet (Figs. 1 and 2). DNHM D2946 preserves most of the bones of the wings and thoracic girdle, both femora, the left tibiotarsus, and the distal ends of the pubes (Figs. 3 and 4).

\n

Skull

\n

The skull is rather poorly preserved, embedded in a well-indurated rusty concretion; the shape of the skull is well preserved, but few anatomical details can be discerned (Fig. 5). As in the holotype, the skull constricts abruptly into a low and pointed rostrum, different from the more robust rostrum of Longicrusavis houi (O’Connor, Gao & Chiappe, 2010). Impressions of five teeth can be clearly identified in the maxilla (Fig. 5), contradicting the previous description of Hongshanornis longicresta as edentulous (Zhou & Zhang, 2005; Zheng et al., 2011). Teeth were suggested for hongshanornithids on the basis of structures that appeared to be alveoli preserved in the upper jaw of Longicrusavis houi (O’Connor, Gao & Chiappe, 2010). The presence of teeth in the premaxilla, however, cannot be determined in DNHM D2945. There are no obvious pits or scaring on the maxilla or premaxilla to indicate that a beak was present, as in the edentulous Archaeorhynchus spathula (Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2013b).

\n
\"Close
\n
\nFigure 5: Close up photograph of the skull of DNHM D2945 in right lateral view and detail (inset) of the central portion of its maxilla.
\nAbbreviations: al, alveoli.

The mandibular symphysial ossification (predentary bone of Zhou & Martin, 2011) is visible as a void in DNHM D2945. The fragmentary remains of two to four teeth are preserved set in the dentary. This confirms the presence of teeth in the dentary of hongshanornithids, which was hypothesized by O’Connor, Gao & Chiappe (2010). Crowns cannot be discerned, but the dentary teeth appear to be smaller than those preserved in the maxilla. The dentary is caudally unforked and unfused to the surangular, as in other basal ornithuromorphs.

Axial skeleton

\n

The cervical vertebrae are poorly preserved, revealing little more than the remnants of low neural spines. The anterior dorsal vertebrae (visible in ventral view in DNHM D2945) bear compressed centra lacking ventral processes; the posterior dorsals have thicker centra. The articulations are amphyplatan or amphicoelic and the elements are not fused in a notarium. The lateral surfaces of the dorsal vertebrae are excavated by a broad fossa, as in other basal ornithuromorphs (e.g., Yanornis martini, Longicrusavis houi).

\n

The synsacrum is incomplete and broken between the two slabs (dorsally exposed in DNHM D2946 and ventrally exposed in DNHM D2945) (Figs. 14). A number of well-differentiated costal processes project from the side of the synsacrum—these processes have expanded distal ends for their attachment to the ilium. Judging by the number of costal processes articulated to the ilium, the synsacrum was composed of no less than nine vertebrae (the synsacral count cannot be determined in either the holotype of Hongshanornis longicresta or Longicrusavis houi), which is comparable to other basal ornithuromorphs and more than is typical of the more primitive enantiornithines (Chiappe, 1996). The ventral surface of the synsacrum (anterior half preserved in DNHM D2945) is smooth, lacking a distinct groove (e.g., Archaeorhynchus spathula, Patagopteryx deferrariisi). Dorsally, the portion of synsacrum preserved in slab DNHM D2946—corresponding largely to the postacetabular portion—is longitudinally scarred by a pair of shallow grooves.

\n

At least four uncinate processes can be discerned, including one that is completely preserved (DNHM D2946). These ossifications are long (extending across two ribs) with broad bases and tapered outlines (Fig. 6). The uncinate processes appear not to be fused to the ribs, as in the holotype. Several ventral ribs are preserved in articulation with the sternum (DNHM D2946). The proximal ends of the thoracic ribs are very robust, the expanded proximal portion abruptly narrows towards the much thinner shaft (Fig. 6).

\n
\"Photograph
\n
\nFigure 6: Photograph (A) and interpretive drawing (B) of the thoracic girdle and vertebral series, rib cage, and humeri of DNHM D2946.
\nAbbreviations: co, coracoid; fu, furcula; hu, humerus; lt, lateral trabecular; ra, radius; rb, ribs; sc, scapula; sp, supracondylar process; st, sternum; up, uncinate process.

Appendicular skeleton

\n

The furcula is delicate and U-shaped as in many other basal ornithuromorpha (e.g., Clarke, Zhou & Zhang, 2006; You et al., 2006; Zhou, Zhang & Li, 2009; Zhou, Zhou & O’Connor, 2013b). The interclavicular angle is estimated to be approximately 45°(Fig. 6). The rami are transversely compressed proximally, becoming more dorsoventrally compressed and wider towards the symphysis. The caudal surface of the bone exhibits a distinct trough running along the distal half of the rami and converging towards the symphysial region. The proximal compression and caudal groove of the furcula of DNHM D2946 are comparable to that reported by Li, Wang & Hou (2011) as diagnostic characters of Parahongshanornis chaoyangensis. The presence of these conditions in DNHM D2946 indicates that such characters are unlikely to be diagnostic of the latter taxon. A cross section of the furcula in slab DNHM D2945 indicates the bone may have been hollow. No long hypocleidium like that reported in the holotype of Hongshanornis longicresta (IVPP V14533) is visible but the symphysial region of DNHM D2945/46 is covered by the distal portion of the left coracoid, thus making it unclear if a hypocleidium was present or not. The similarity between the furcula of DNHM D2945/46 and that of Longicrusavis houi and Parahongshanornis chaoyangensis, taxa lacking a long hypocleidium and possessing only a small tubercle at the symphysis (O’Connor, Gao & Chiappe, 2010; Li, Wang & Hou, 2011), suggests that the furcula of hongshanornithids possibly lacked a well-developed hypocleidium.

\n

The sternum, primarily preserved in DNHM D2946 in dorsal view, has a slightly rounded cranial margin (Fig. 6). Distally on the left side of the sternum, a bony bar with a terminal expansion is preserved. Damage makes it difficult to interpret this region of the sternum. One alternative is that this bar corresponds to a slightly displaced, lateral trabecula with an expanded distal end; the lateral trabecula of the sternum of various basal ornithuromorphs (e.g., Archaeorhynchus spathula, Jianchangornis microdonta, Yixianornis grabaui, Yanornis martini) is distally expanded in varying degrees (Zhou, Zhou & O’Connor, 2013b). Alternatively, it may represent the lateral margin of a sternal fenestra, such as those present in the basal ornithuromorphs Songlingornis linghensis, Yixianornis grabaui, and Yanornis martini (Clarke, Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2013b), a feature apparently absent in the sternum of the holotype of Hongshanornis longicresta. Zhou & Zhang (2005) described the sternum of the latter with lateral processes lacking a distal expansion; however the sternum of this specimen is too poorly preserved to confidently support the absence of such expansion.

\n

The strut-like coracoids articulate adjacent to each other on the cranial margin of the sternum, nearly touching each other if not slightly overlapping (Fig. 6). There is a depression (possibly corresponding to the impression of the m. sternocoracoidei of modern birds) on the dorsal surface of the sternal half of these bones (also present in Jehol ornithuromorphs such Jianchangornis microdonta and Yixianornis grabaui). This feature in ornithuromorphs is not as pronounced as the dorsal fossa that excavates the coracoids of many Late Cretaceous enantiornithines (Chiappe & Walker, 2002). The proximal ends of the coracoids are poorly preserved so that a procoracoid process cannot be identified—the presence of this process in Hongshanornis longicresta is not as clear as was suggested by Zhou & Zhang (2005) and remains equivocal in this taxon. However, a procoracoid process is known in almost every other Early Cretaceous ornithuromorph (e.g., Jianchangornis microdonta, Yixianornis grabaui, Yanornis martini, Gansus yumenensis) (Zhou & Zhang, 2001; Clarke, Zhou & Zhang, 2006; You et al., 2006; Zhou, Zhou & O’Connor, 2012). The body of the coracoid exhibits no evidence of either a supracoracoid nerve foramen or medial notch (incisura n. supracoracoidei). Both the lateral and medial borders of this bone are clearly concave, indicating that the convex lateral margin described by Zhou & Zhang (2005) for the poorly preserved holotype is incorrect. A lateral process is present; its squared off morphology is consistent with that of other Early Cretaceous ornithuromorphs (e.g., Ambiortus dementjevi, Yixianornis grabaui, Gansus yumenensis) (Clarke, Zhou & Zhang, 2006; Kurochkin, 1982; You et al., 2006).

\n

Both humeri are exposed in caudal view in DNHM D2946 (Fig. 6). The head is prominent—largely projected caudally—and proximally flat. Such design is more reminiscent to that of the humeral head of Patagopteryx deferrariisi and other basal ornithuromorphs (i.e., Archaeorhynchus spathula, Jianchangornis microdonta) and it differs from the domed-head of modern birds (Chiappe, 2002). The proximal third of the humerus appears to be very broad, expanded as in the holotype of Hongshanornis longicresta, Ichthyornis dispar and Ambiortus dementjevi (Kurochkin, 1985; Clarke, 2004) (Fig. 6). The caudal surface is not perforated by a pneumotricipital foramen and the pneumotricipital fossa is minimally developed. A distinct furrow—presumably the capital incisure—separates the ventral margin of the head from the ventral tubercle. Ventral to the latter, on the ventroproximal corner (and the bicipital area) of the bone, there is a shallow circular depression also present in Ichthyornis dispar, possibly corresponding to the attachment site of the m. pectoralis superficialis (Clarke, 2004). The deltopectoral crest is large—extending longitudinally for more than 1/3 the length of the bone (Fig. 6)—and rounded, lacking the cranial deflection of more advanced ornithuromorphs (neornithines). Distally, the margin of the crest gradually diminishes along the dorsal border of the shaft, typical of Cretaceous ornithuromorphs (e.g., Jianchangornis microdonta, Yixianornis grabaui, Archaeorhynchus spathula), as opposed to the rapid step-like constriction of this crest in most basal birds (e.g., Confuciusornis sanctus, Sapeornis chaoyangensis, Rapaxavis pani) and some basal ornithuromorphs (e.g., Schizooura lii, Zhongjianornis yangi).

\n

In caudal view (DNHM D2946) the distal humeri bear no evidence of humerotriciptial or scapulotricipital grooves (Fig. 6). The olecranon fossa is present but poorly developed. A well-developed dorsal supracondylar process is present, clearest on the right humerus (DNHM D2946) as in Longicrusavis houi (O’Connor, Gao & Chiappe, 2010) and Ichthyornis dispar (Clarke, 2004). The flexor process is small and poorly developed; the transversal distal margin is roughly perpendicular from the longitudinal axis of the shaft as in other ornithuromorphs, not angled as in many enantiornithines (Chiappe & Walker, 2002). The cranial surfaces of the humeri are not visible, planted in the matrix.

\n

The radius is straight and roughly half the width of the ulna. The ulna, comparable in length to that of the humerus (Table 1), is exposed in caudal-dorsal view. Remige papillae are absent. The olecranon process is weakly developed. Distally, the ulna’s dorsal condyle is rounded in caudal view. Near its articulation with the radius, it exhibits a small circular depression that may correspond to the radial depression of living birds (Baumel & Witmer, 1993).

\n

The radius and ulna are in articulation with the proximal carpals and the carpometacarpus (Fig. 7). The radiale is in articulation with the radius. The left carpometacarpus, exposed dorsally in DNHM D2946, is completely fused, proximally and distally. Close to the contact between the major (II) and alular (I) metacarpals there is a raised area. Both the major (II) and minor (III) metacarpals are straight (Fig. 7). Proximally, there is a small depression on the minor metacarpal. The proximal end of the intermetacarpal space extends proximal to the level of the distal end of the alular metacarpal (Fig. 7). The alular (I) metacarpal is subrectangular. An extensor process is not absent, only minimally developed in such a way that the proximal end of the alular metacarpal is slightly more expanded than its distal end (Fig. 7), as in some other Cretaceous ornithurmorphs (e.g., Jianchangornis microdonta, Gansus yumenensis, Yixianornis grabaui).

\n
\"Photograph
\n
\nFigure 7: Photograph of the left manus of DNHM D2945/6 in ventral (A; DNHM D2945) and dorsal (B; DNHM D2946) views.
\nAbbreviations: mc I-III, metacarpals I-III; p1-I, phalanx 1 (proximal) of digit I (alular digit); p2-I, phalanx 2 (ungual) of digit I (alular digit); p1-II, phalanx 1 (proximal) of digit II (major digit); p2-II, phalanx 2 (intermediate) of digit II (major digit); p3-II, phalanx 3 (ungual) of digit II (major digit); p1-III, phalanx 1 (proximal) of digit III (minor digit); p2-III, phalanx 2 of digit III (minor digit); ra, radius; sl, semilunate carpal; ul, ulna.

The alular digit bears two phalanges. The second phalanx, a claw, extends slightly past the distal end of the major metacarpal, as described by Zhou & Zhang (2005) for the holotype. The major digit has three phalanges; the proximal phalanx is broad bearing a well-developed, sinusoidal lateral flange (Fig. 7). As in the holotype, the intermediate phalanx is S-shaped (Zhou & Zhang, 2005). The claw of the major digit is much smaller than that of the alular digit. The minor digit bears a single, wedge-shaped phalanx that tapers distally; Longicrusavis houi and the Hongshanornis longicresta holotype bear two phalanges on this digit, the second being extremely reduced (and not an ungual) suggesting that this small phalanx is simply not preserved in DNHM D2945/6.

\n

The ilia are poorly preserved and broken between the two slabs; the left is visible in medial view in DNHM D2945, while portions of the right are preserved in DNHM D2946 in dorsal view. The preacetabular wing has a straight dorsal margin that tapers cranially. The caudal half of the ventral margin of the preacetabular wing defines a broad notch, a condition observed in other Jehol ornithuromorphs (e.g., Archaeorhynchus spathula, Schizooura lii) (Zhou, Zhou & O’Connor, 2012; Zhou, Zhou & O’Connor, 2013b).

\n

A fragment of the pubis is preserved near the midshaft of the right tibiotarsus in DNHM D2946 (Figs. 14 and 8). The distal ends of both pubes are in contact and only slightly disarticulated. They are not fused but their flat medial surfaces form a short, expanded symphysis, although a distinct ‘boot’, with a prominent caudal projection, like that of some enantiornithines is absent (Chiappe & Walker, 2002) (Fig. 8). The presence of this distal pubic expansion, identical to that present in Parahongshanornis chaoyangensis, indicates that unlike what was claimed by Li, Wang & Hou (2011), this feature is not diagnostic of the latter species. The cross-section of the shaft of the distal portion of the pubis is oval, with the main axis oriented craniocaudally. No pygostyle or caudal vertebrae are preserved in DNHM D2945/6.

\n
\"Close
\n
\nFigure 8: Close up photograph of the right knee (medial view) and pubic symphysis (left laterocaudal view) of DNHM D2946.
\nNote the detail of the gastroliths. Abbreviations: fe, femur; fi, fibula; gl, gastroliths, pu, pubis; ti, tibia. (l) and (r) refer to the left and right pubis, respectively.

The elongate hindlimbs are completely preserved in both slabs as partly bone and partly void (Figs. 14). The left femur is preserved in articulation with the left ilium in DNHM D2945—its rounded head is visible through the acetabulum, which is exposed medially. The femoral shaft is only slightly bowed craniocaudally. Its laterodistal end is exposed in DNHM D2946; similar to other Jehol ornithuromorphs (e.g., Yixianornis grabaui), there is minimal development of the fibular trochlea and tibiofibular crest, which are developed in Patagopteryx deferrariisi and ornithurines (Chiappe, 2002; Clarke, 2004).

\n

The tibiotarsus is more than 150% the length of the femur (tibiotarsus: femur = 1.6) (Table 1). The right element is in articulation with the fibula, which is exposed caudally in DNHM D2946. Proximally, the tibiotarsus exhibits a large, well-developed cnemial crest (Fig. 9). This crest, exposed laterally in DNHM D2946, is limited proximally, and projects proximally beyond the proximal articular surface of the tibiotarsus. Its cranial edge develops into an inflated quadrangular prominence that projects laterally (Fig. 9). The morphology of this crest is comparable to that of other Early Cretaceous ornithuromorphs (e.g., Schizooura lii, Yixianornis grabaui) (Clarke, Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2012). This cranial prominence is separated by a lateral trough from the proximal articular surface of the tibiotarsus. It is not possible to determine whether the tibiotarsus had one or two cnemial crests; if a cranial cnemial crest were present, it would be embedded in sediment and obstructed by the lateral cnemial crest. In caudal view, the proximal fourth of the tibiotarsus is marked by a robust ridge that slants towards the proximomedial corner of the bone—this feature is not present in Longicrusavis houi, further distinguishing this taxon from Hongshanornis longicresta.

\n
\"Close
\n
\nFigure 9: Close up photograph of the left knee (lateral view) of DNHM D2946.
\nAbbreviations: cn, cnemial crest; fc, fibular condyle; fe, femur; fi, fibula; ld, lateral articular facet of tibia; md, medial articular facet of tibia; ti, tibia.

Distally, the tibia is largely fused to the distal tarsals, however the suture of an ample ascending process of the astragalus remains visible on both the left (DNHM D2946) and right (DNHM D2945) tibiotarsi. The distal condyles are preserved in cranial view in DNHM D2945. The lateral condyle is larger than the medial condyle, as in other basal ornithuromorphs (Chiappe, 1996; Zhou & Zhang, 2006), and separated by a wide intercondylar groove (incisura intercondylaris). The cranial surface of the distal end is scarred by a deep extensor sulcus, which ends near a raised area just proximal to the intercondylar groove—a supratendinal bridge like that of more advanced ornithurines is not developed. The lateral epicondyle is minimally developed and there is only a slightly developed, crescent-like lateral epicondylar depression. Caudally, neither the lateral nor medial crests of the cartilaginous trochlea of the tibia (trochlea cartilaginous tibialis) are developed. These crests are slightly developed in Yixianornis grabaui and well developed in Apsaravis ukhaana (Norell & Clark, 2001; Clarke, Zhou & Zhang, 2006). The fibula is very slender (Figs. 8 and 9)—its distal end does not seem to extend beyond the midpoint of the tibiotarsus.

\n

Both tarsometatarsi are well-exposed in cranial view in DNHM D2945. As reported in the holotype of Hongshanornis longicresta (Zhou & Zhang, 2005), metatarsals II–IV are completely fused to one another. The intercotylar prominence is at best minimally developed. The proximal cotyla are slightly concave—the lateral one is slightly more distally placed than the medial one. Metatarsal III is plantarly displaced so that proximally, metatarsal II and metatarsal IV form ridges defining a recess excavating the central portion of the tarsometatarsus. Such morphology is consistent with that of other basal ornithuromorphs (e.g., Yanornis martini, Yixianornis grabaui, Gansus yumenensis, Ichthyornis dispar). Inside this proximocentral recess there is a foramen located between metatarsals III and IV, and medial to it, a tubercle on metatarsal II (possibly corresponding to the m. tibialis cranialis tuberosity of modern birds). Metatarsal III is the longest; metatarsal IV is slightly shorter, followed by the even shorter metatarsal II (Fig. 10). Metatarsal I is robust and fairly straight, with a concave medial margin. A distal vascular foramen is located between metatarsals III and IV as in Longicrusavis houi; the distal margin of the foramen is raised. The foramen seems to penetrate the bone at an oblique angle—from cranial to plantar surfaces. All trochleae appear to be ginglymous.

\n
\"Close
\n
\nFigure 10: Close up photograph of the feet and rectrices of DNHM D2945.
\nAbbreviations: mt, metatarsals; re, rectrices; I-IV, digits I-IV.

Digit III is the longest (Table 1); digit II is substantially shorter than IV (Fig. 10). Digit I is short and slender. All the pedal phalanges are long and slender and decrease in length distally. The phalanges of the second and third digits are approximately 2/3 the length of the preceding phalanx. The phalanges of digit IV are subequal, but still slightly decrease in length distally. The ungual phalanges bear distinct flexor tubercles. The morphology of the distal tarsometatarsus and the proportions of the pedal phalanges are consistent with cursorial function (Hopson, 2001), as in other Early Cretaceous ornithuromorphs.

Plumage

\n

DNHM D2945/6 preserves significant portions of the plumage of the wing, tail, and around the skull and neck. The feathers preserved over the skull question the assumption that this species was characterized by the presence of a feathery crest projecting from the head (Zhou & Zhang, 2005). DNHM D2945/6 shows nothing of that sort. The relatively short feathers of the head become gradually shorter until the plumage ends at the junction of the rostrum and the orbit, thus indicating that the culmen was devoid of feathers (whether it was covered by skin or a corneous beak is unknown). Furthermore, contrary to what was suggested by Zheng et al. (2011) for another specimen putatively identified as Hongshanornis longicresta (STM 35-3), DNHM D2945/6 indicates that these birds had relatively broad, but long and tapered, wings (Figs. 14 and 11).

\n
\"Interpretive
\n
\nFigure 11: Interpretive drawing of the outline of the wings and feathered tail of DNHM D2945/6 (see Figs. 1 and 3 for the maximum extent of the primaries and secondaries).
\nThe aerodynamic parameters used in this study were derived from this reconstruction (see Materials and Methods).

The most distal primaries are clearly much shorter than the remaining primaries. Based on the well-preserved outline of the wing, our estimation of the wingspan of DNHM D2945/6 is approximately 0.32 m and the wing area is 0.016 m2 (Fig. 11). There is exquisite evidence of rectrices forming a fan-like tail preserved in natural orientation, about the extended feet. Although visualization of individual feathers is difficult due to overlap, the tail appears to be composed of at least 10 vaned rectrices. The precise degree of asymmetry of these feathers cannot be ascertained but it is clear that none of them were strongly asymmetric (Fig. 10). The caudal margin of the feathered tail is rounded and the pair of central rectrices projects distally more than the feathers on either side, thus suggesting a gently graded tail (comparable to the one described for Piscivoravis lii; see Zhou, Zhou & O’Connor, 2013a). The holotype of Hongshanornis longicresta also shows evidence of an extensive feathered tail as a series of partially preserved vaned feathers between the feet (IVPP V14533A); these are very faint and were not described in the original description (see O’Connor, Gao & Chiappe, 2010). In the holotype of Hongshanornis longicresta, the tail is clearly incomplete and only four feathers can be discerned; the tail in DNHM D2945/6 appears complete. The number of preserved feathers is thus greater than the one described in the younger ornithuromorphs Yixianornis grabaui (minimum of eight described) and Piscivoravis lii (at least six described) from the Jiufotang Formation (Clarke, Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2013a).

Gastroliths

\n

At least 11 small geo-gastroliths are clustered in the visceral and pelvic region of DNHM D2945/6. Some of these ‘stomach stones’ are still in place while others are represented by the voids left on the slabs (Figs. 14 and 8). The smallest of the stones is nearly half the size the largest (1.71 mm to 3.08 mm) with the mean being 2.2 mm (Table 2). They range in shape from subspherical to oblong. It is unclear whether gastroliths were preserved with the holotype (IVPP V14533A), although more than 50 small (∼1 mm) geo-gastroliths were reported in the poorly preserved STM 35-3, a specimen identified as of Hongshanornis longicresta by Zheng et al. (2011). Despite the fact that Zheng et al. (2011) did not provide any anatomical evidence supporting the identification of STM 35-5 as Hongshanornis longicresta, the discovery of DNHM D2945/6 provides unquestionable evidence of the behavior of ingesting grit by this basal ornithuromorph species.

\n
\nTable 2:
Measurements (mm) of the gastroliths of DNHM D2945/6.
\nLeft column numbers correspond to numbers on Figs. 2 and 4.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
D2945D2946Mean value
12.212.272.24
23.063.093.08
32.312.072.19
42.052.152.10
52.152.112.13
62.902.592.75
71.841.761.80
81.761.791.78
91.742.081.91
101.841.561.70
112.513.132.82
\n
" + ] + }, + "discussion_html": { + "value": [ + "

Discussion

\n

The specimen described here, DNHM D2945/6, is indistinguishable from the holotype of Hongshanornis longicresta and is thus referred to this taxon. DNHM D2945/6 is from the same locality and formation (Yixian) that yielded the closely related Longicrusavis houi (PKVP 1069; O’Connor, Gao & Chiappe, 2010). The coexistence of these two closely related taxa in a single fauna suggests that Hongshanornithidae was a diverse component of the avifauna of the Yixian Formation.

\n

DNHM D2945/6 reveals important new information regarding the morphology, diet, and ecology of Hongshanornis longicresta and other Early Cretaceous ornithuromorphs. The new specimen of Hongshanornis longicresta preserves actual fossilized bone rather than voids of bone, as in the holotype (IVPP V 14533), and as such this new specimen helps clarify the osteology of the taxon. DNHM D2945/6 documents the presence of two different skull morphologies within Hongshanornithidae. It also confirms that the upper and lower jaws of these birds were toothed, a conclusion previously suggested by morphologies preserved in the holotype of Longicrusavis houi (O’Connor, Gao & Chiappe, 2010). Additionally, DNHM D2945/6 shows that the lateral margin of the coracoid of hongshanornithids was concave, as is typical of other basal ornithuromorphs, and not convex as reported by Zhou & Zhang (2005). DNHM D2945/6 also preserves a dorsal supracondylar process, a feature present in Longicrusavis houi and many extant shorebirds.

\n

The presence of a hypocleidium in Hongshanornis longicresta is still controversial. This process does not appear present in DNHM D2945/6, however preservation prevents us from making an unequivocal statement. While most known Early Cretaceous ornithuromorphs do not possess even the smallest hypocleidium, basal ornithuromorphs with furculae bearing a distinct hypocleidium have been recently reported (Zhou, Zhou & O’Connor, 2012). Such discoveries lend credibility to Zhou and Zhang’s (2005) claim that the furcula of Hongshanornis longicresta possessed a hypocleidium, although well-preserved specimens are necessary to corroborate such a claim.

\n

Furthermore, the anatomy of DNHM D2945/6 partially undermines the anatomical basis used by Li, Wang & Hou (2011) to diagnose the hongshanornithid Parahongshanornis chaoyangensis. The compression of the proximal portion of the furcula and caudal groove of this bone in DNHM D2945/6 indicate that these characters cannot be considered as diagnostic of Parahongshanornis chaoyangensis. This is the same for the distal expansion of the pubes, a condition that is identical in DNHM D2945/6 and the holotype of Parahongshanornis chaoyangensis.

\n

Diet

\n

The presence of teeth on both the maxilla and the dentary, and the reinterpretation of the hongshanornithids as toothed birds, impact earlier ecological inferences for the clade, suggesting they were less specialized trophically than previously imagined. The presence of at least two distinct skull morphologies within Hongshanornithidae indicates intraclade trophic diversity, and niche partitioning within the specialized wading ecology inferred to have been occupied by this clade.

\n

The geo-gastroliths preserved associated with the visceral region of DNHM D2945/6 offer a glimpse into the digestive system and dietary preferences of hongshanornithids. A variety of aquatic and terrestrial organisms regularly ingest sand, fine gravel, or coarse sand. These ‘stomach stones’ or grit are assumed to perform a variety of functions ranging from acting like ballast in aquatic animals to parasite control and hunger placation (Wings, 2007). Most typically, however, geo-gastroliths are interpreted as grinding devices assisting the digestion of hard food items. Geo-gastroliths are not only common among living crocodiles (Taylor, 1993; Henderson, 2003) and birds (Gionfriddo & Best, 1999) but they also have been documented in a variety of extinct archosaurian clades, including pterosaurs (Codorniú, Chiappe & Cid, 2013) and every major group of dinosaurs (Osborn, 1924; Ji et al., 1998; Weems, Culp & Wings, 2007; Wings & Sander, 2007). Geo-gastroliths have also been discovered in association with the skeletons of a number of Early Cretaceous ornithuromorphs from China (e.g., Yanornis martini, Gansus yumenensis, Archaeorhynchus spathula) (Zhou et al., 2004; You et al., 2006; Zhou, Zhou & O’Connor, 2013b). The presence of geo-gastroliths in fossil dinosaurs (including birds) is generally regarded as indicative of herbivory (Ji et al., 1998; Gionfriddo & Best, 1999; Kobayashi et al., 1999; Wings, 2007; Xu et al., 2009; Zanno & Makovicky, 2011; Brusatte, 2012), however such a correlation is not as consistent as often assumed. In the case of DNHM D2945/6, the closely associated cluster of fairly evenly sized stones located in the abdominal cavity distal to the sternum but proximal to the pelvic girdle, is consistent with the interpretation of these geo-gastroliths as gizzard stones. Furthermore, the report by Zheng et al. (2011) of a specimen (STM 35-3, identified as of Hongshanornis longicresta) containing seeds in a crop provides evidence that these birds were granivorous. Such evidence is consistent with both the preservation of geo-gastroliths in DNHM D2945/6 and STM 35-3, and the functional interpretation that highlights the role these stones play in processing hard foods.

Caudal plumage

\n

Very little is known about the rectrices of basal ornithuromorphs and DNHM D2945/6 represents what is possibly the most informative example for understanding the morphology of the tail of these birds. Only two types of feathered tails—fan-shaped and forked—have been reported for basal ornithuromorphs (Zhou & Zhang, 2001; Clarke, Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2012; Zhou, Zhou & O’Connor, 2013a). Such limited diversity contrasts with what is known for their sister-group, the Enantiornithes, in which a larger number of tail morphologies (including one inferred to be aerodynamic; O’Connor et al., 2009) are known (Zhang & Zhou, 2000; Zheng, Zhang & Hou, 2007; O’Connor, Gao & Chiappe, 2010; O’Connor et al., 2012).

\n

DNHM D2945/6 provides evidence that as early as 125 million year ago, basal ornithuromorphs had evolved a feathered tail comparable in size and design to those of many modern birds. Such tail had rectrices suitable of fanning and capable of generating aerodynamic forces much greater than those of more basal birds (Gatesy & Dial, 1996).

\n

In living birds, all but the central pair of rectrices of a fan-shaped tail anchor on a musculo-adipose organ, the rectricial bulb, which controls the fanning of the feathers and as such, plays a critical role in flight (Gatesy & Dial, 1996). The rectricial bulb is in turn supported by, and intimately connected to, the pygostyle. Nonetheless, because no direct evidence of a rectricial bulb has ever been found in any Mesozoic bird, whether the pygostyle is a reliable osteological correlate of the rectricial bulb has been questioned (Clarke, Zhou & Zhang, 2006). The morphology of the pygostyle of basal ornithuromorphs (and of their living relatives) differs from that typical of more basal birds, which commonly possess a long, robust, and club-shaped pygostyle (e.g., Confuciusornithidae, Enantiornithes). In contrast, the pygostyle of ornithuromorphs is relatively small, more delicate, and plough-shaped—even if the pygostyle of hongshanornithids is poorly known (and missing in DNHM 2945/6), its morphology seems to agree with that of other basal ornithuromorphs (Zhou & Zhang, 2005). The morphological difference between the pygostyle of ornithuromorphs and that of more basal birds led Clarke, Zhou & Zhang (2006) to hypothesize that the rectricial bulb evolved in concert with both the modern avian pygostyle (plough-shaped) and aerodynamic tail morphologies such as those known for basal ornithuromorph taxa. This hypothesis, however, has been somewhat challenged by the recent report of a tail formed by long, shafted rectrices in the enantiornithine Shanweiniao cooperorum (O’Connor et al., 2009). In the holotype and only known specimen of this taxon, the impressions of four vaned feathers can be seen projecting from the end of the caudal vertebral series. Such evidence suggests that the presence of a large and club-shaped pygostyle, like the one characteristic of enantiornithines, might not have excluded the development of a fan-shaped feather tail among non-ornithuromorph birds from such tail feather morphologies (O’Connor et al., 2009), and therefore that a rectricial bulb might have evolved either prior to the origin of the Ornithuromorpha or independently in more than one clade of birds (e.g., Ornithuromorpha and Enantiornithes). The derived phylogenetic position of Shanweiniao cooperorum, nested among advanced enantiornithines (O’Connor & Zhou, 2012), and the widespread presence of pintail morphologies lacking vaned rectrices capable of fanning among other enantiornithines (O’Connor et al., 2012) favor interpretations of the aerodynamic tail of Shanweiniao (and presumably the rectricial bulb that operated the fanning of its rectrices) as an independent evolutionary event. Likewise, the presence of fan-shaped feathered tails and modern-like pygostyles in a variety of basal ornithuromorphs (e.g., Hongshanornis longicresta, Yixianornis grabaui, Yanornis martini, Piscivoravis lii) supports the argument that such morphologies are ancestral for Ornithuromorpha (Clarke, Zhou & Zhang, 2006).

Aerodynamics

\n

DNHM D2945/6 possesses relatively broad, but tapered wings. Compared to a general regression of mass against wing area for birds (data taken from Greenewalt, 1962), the relative wing area for DNHM D2945/6 is somewhat larger than average, when using the mean body mass estimate (42 g; residual of −0.37) (see Materials and Methods). However, using the heaviest mass estimate for DNHM D2945/6 (65 g) (see Materials and Methods) yields an average wing area, and therefore a typical wing loading compared to a modern bird of similar size (residual of −0.04).

\n

The overall size of DNHM D2945/6, along with its wing shape, is qualitatively similar to that of some living passerines with flexible diets (e.g., Monticola solitarius, Sturnus vulgaris, Turdus naumanni). These same living birds also tend to have somewhat tapering wings without extensive wing tip slotting. As a result, we tentatively suggest that DNHM D2945/6 may have lacked extensive wingtip slotting, even if direct evidence of this is not available in the specimen. Additional specimens will be required to confirm this prediction. Tip slots are most effective at slow speeds, where they can increase effective aspect ratio in wings with low geometric aspect ratio (Tucker, 1993). As a result, it is generally expected that birds without tip slots tend to either have high geometric aspect ratio (which is not relevant to DNHM D2945/6), or else tend to fly at relatively high speeds. Based on its intermediate size and moderate aspect ratio, DNHM D2945/6 would be expected to flap continuously at low speeds, but may have switched to flap-bounding (a cycle of flapping and bounding with the wings flexed) at higher rates of travel, since this type of gait transition is seen among modern birds with similar wing shape and body size to DNHM D2945/6. We note that such gait transitions are related to flight speed and cost of transport, both of which relate to total body size and wing loading (Tobalske, Peacock & Dial, 1999; Tobalske, 2001). Since we have reliable measurements of the specimen dimensions, conservative predictions of gait are possible for DNHM D2945/6, even though the wings of the specimen lack feather details. For the same reasons, we do not expect that these gait transitions would be particularly sensitive to specifics of osteology (i.e., differences in skeletal structure between basal ornithuromorphs and modern birds). So long as DNHM D2945/6 was able to fly continuously for significant distances, the same basic patterns of cost of transport relative to size and flight speed should apply to both living neornithines and DNHM D2945/6.

\n

Tail positioning and effective functional area are more difficult to estimate in fossil taxa than the same variables for the wings, because avian tails can be used at extremely fanned or collapsed states (or any number of positions in between). While the degree of asymmetry of the rectrices is unclear, the lateral feathers of the tail in DNHM D2945/6 appear to be less asymmetrical than it would expected if these feathers were regularly oriented with their long axis fully transverse to the air flow (as would be the case for primary feathers on the wings or the lateral rectrices in a fully fanned tail). This suggests that the tail was typically deployed as a partially fanned “wedge”, rather than a full fan. This is not uncommon among modern birds with long tails, such as flycatchers, accipiters, and sunbitterns (M Habib, pers. observation).

\n

The preserved plumage of DNHM D2945/6 indicates that hongshanornithids had wing and tail surfaces comparable to those of living birds of similar sizes. In general, the morphology of the wing and feathered tail of DNHM D2945/6, combined with estimates of its weight, is indicative of a flight mode comparable to the intermittent flight of many medium-sized passerines and congruent with the conclusions reached by Close & Rayfield (2012), whose geometric morphometric analysis of furculae interpreted Hongshanornis longicresta as a continuous flapper.

" + ] + }, + "conclusion_html": { + "value": [ + + ] + }, + "author_contrib_html": { + "value": [ + + ] + }, + "competing_interests_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\nAlexander RMcN. 1983. Allometry of the leg bones of moas (Dinornithes) and other birds. Journal of Zoology 200:215-223 \n", + "\nAlvarenga HM, Bonaparte JF. 1992. A new flightless land bird from the Cretaceous of Patagonia. In: Campbell KC, ed. Papers in avian paleontology honoring pierce brodkorb. Los Angeles: Natural History Museum of Los Angeles County. 51-64 \n", + "\nBaumel JJ, Witmer LM. 1993. Osteologia. In: Baumel JJ, King AS, Breazile JE, Evans HE, Vanden Berge JC, eds. Handbook of avian anatomy: nomina anatomica avium (Second Edition). Cambridge: Nuttall Ornithological Club. 45-132 \n", + "\nBrusatte SL. 2012. Dinosaur paleobiology. Chichester: Wiley-Blackwell. 322 \n", + "\nChang S, Zhang H, Renne PR, Fang Y. 2009. High-precision 40Ar/39Ar age for the Jehol Biota. 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Morphology, phylogenetic taxonomy, and systematics of Ichthyornis and Apatornis (Avialae: Ornithurae) Bulletin of the American Museum of Natural History 286:1-179 \n", + "\nClarke JA, Zhou Z, Zhang F. 2006. Insight into the evolution of avian flight from a new clade of Early Cretaceous ornithurines from China and the morphology of Yixianornis grabaui. Journal of Anatomy 208:287-308 \n", + "\nClose RA, Rayfield EJ. 2012. Functional morphometric analysis of the furcula in Mesozoic birds. PLoS ONE 7(5):e36664 \n", + "\nCodorniú L, Chiappe LM, Cid FD. 2013. First occurrence of stomach stones in pterosaurs. Journal of Vertebrate Paleontology 33:647-654 \n", + "\nDunning JB. 2008. CRC handbook of avian body masses (Second Edition). Boca Raton: CRC Press. 655 \n", + "\nForster CA, Chiappe LM, Krause DW, Sampson SD. 1996. The first Cretaceous bird from Madagascar. Nature 382:532-534 \n", + "\nGatesy SM, Dial KP. 1996. From frond to fan: Archaeopteryx and the evolution of short tailed birds. Evolution 50:2037-2048 \n", + "\nGionfriddo JP, Best LB. 1999. Grit use by birds: a review. Current Ornithology 15:89-148 \n", + "\nGreenewalt CH. 1962. Dimensional relationships for flying animals. Smithsonian Miscellaneous Collections 144(2):1-46 \n", + "\nHenderson DM. 2003. Effects of stomach stones on the buoyancy and equilibrium of a floating crocodilian: a computational analysis. Canadian Journal of Zoology 81:1346-1357 \n", + "\nHone DW, Dyke GJ, Haden M, Benton MJ. 2008. Body size evolution in Mesozoic birds. Journal of Evolutionary Biology 21:618-624 \n", + "\nHopson JA. 2001. Ecomorpology of avian and nonavian theropod phalangeal proportions: implications for the arboreal versus terrestrial origin of bird flight. In: Gauthier J, Gall LF, eds. New perspectives on the origins and early evolution of birds. New Haven: Peabody Museum of Natural History. 211-235 \n", + "\nHoward H. 1929. The avifauna of Emeryville shellmound. University of California Publications in Zoology 32(2):301-394 \n", + "\nJi Q, Currie PJ, Norell MA, Ji SA. 1998. Two feathered dinosaurs from northeastern China. Nature 393:753-761 \n", + "\nKobayashi Y, Lu JC, Dong ZM, Barsbold R, Azuma Y. 1999. Herbivorous diet in an ornithomimid dinosaur. Nature 402:480-481 \n", + "\nKurochkin EN. 1982. New order of birds from the Lower Cretaceous in Mongolia. Paleontological Journal 1982:215-218 \n", + "\nKurochkin EN. 1985. A true carinate bird from Lower Cretaceous deposits in Mongolia and other evidence of early Cretaceous birds in Asia. Cretaceous Research 6:271-278 \n", + "\nLi DS, Sullivan C, Zhou AH, Zhang FC. 2010. Basal birds from China: a brief review. Chinese Birds 1:83-96 \n", + "\nLi L, Wang J, Hou S. 2011. A new ornithurine bird (Hongshanornithidae) from the Jiufotang Formation of Chaoyang, Liaoning, China. Vertebrata PalAsiatica 49(2):195-200 \n", + "\nLi Z, Zhou Z, Clarke JA. 2011. A reevaluation of the relationships among basal ornithurine birds from China and new information on the anatomy of Hongshanornis longicresta. In: 71st annual meeting, society of vertebrate paleontology (November 2011), Supplement to the online Journal of Vertebrate Paleontology. 144 \n", + "\nMaloiy GMO, Alexander RM, Njau R, Jayes AS. 1979. Allometry of the legs of running birds. Journal of Zoology 187:161-167 \n", + "\nMarsh OC. 1880. Odontornithes: a monograph on the extinct birds of North America. Washington: Government Printing Office. 312 \n", + "\nMartin LD, Tate J. 1976. The skeleton of Baptornis advenus (Aves: Hesperornithiformes) Smithsonian Contributions to Paleobiology 27:35-66 \n", + "\nNorell MA, Clark JA. 2001. Fossil that fills a critical gap in avian evolution. Nature 409:181-182 \n", + "\nO’Connor JK, Chiappe LM, Bell A. 2011. Pre-modern birds: avian divergences in the Mesozoic. In: Dyke GD, Kaiser G, eds. Living dinosaurs: the evolutionary history of birds. New Jersey: J. Wiley & Sons. 39-114 \n", + "\nO’Connor JK, Chiappe LM, Chuong CM, Bottjer D, You H. 2012. Homology and potential cellular and molecular mechanisms for the development of unique feather morphologies in early birds. Geosciences 2(3):157-177 \n", + "\nO’Connor JK, Gao KQ, Chiappe LM. 2010. A new ornithuromorph (Aves: Ornithothoraces) bird from the Jehol Group indicative of higher-level diversity. Journal of Vertebrate Paleontology 30:311-321 \n", + "\nO’Connor JK, Wang XR, Chiappe LM, Gao CH, Meng QJ, Cheng XD, Liu JY. 2009. Phylogenetic support for a specialized clade of Cretaceous enantiornithine birds with information from a new species. Journal of Vertebrate Paleontology 29:188-204 \n", + "\nO’Connor JK, Zhou Z. 2012. A redescription of Chaoyangia beishanensis (Aves) and a comprehensive phylogeny of Mesozoic birds. Journal of Systematic Palaeontology 2(7):889-906 \n", + "\nOsborn HF. 1924. 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American Zoology 41:177-187 \n", + "\nTobalske BW, Peacock W, Dial KP. 1999. Kinematics of flap-bounding flight in the zebra finch over a wide range of speeds. Journal of Experimental Biology 202:1725-1739 \n", + "\nTucker VA. 1993. Gliding birds: reduction of induced drag by wing tip slots between primary feathers. Journal of Experimental Biology 180:285-310 \n", + "\nWeems RE, Culp MJ, Wings O. 2007. Evidence for prosauropod dinosaur gastroliths in the Bull Run Formation (Upper Triassic, Norian) of Virginia. Ichnos 14:271-295 \n", + "\nWings O. 2007. A review of gastrolith function with implications for fossil vertebrates and a revised classification. Acta Palaeontologica Polonica 52:1-16 \n", + "\nWings O, Sander PM. 2007. No gastric mill in sauropod dinosaurs: new evidence from analysis of gastrolith mass and function in ostriches. Proceedings of the Royal Society B: Biological Sciences 274:635-640 \n", + "\nXu X, Clark JM, Mo J, Choiniere J, Forster CA, Erickson GM, Hone DWE, Sullivan C, Eberth DA, Nesbitt S, Zhao Q, Hernandez R, Jia CK, Han FL, Guo Y. 2009. A Jurassic ceratosaur from China helps clarify avian digital homologies. Nature 459:940-944 \n", + "\nYang W, Li S, Jiang B. 2007. New evidence for Cretaceous age of the feathered dinosaurs of Liaoning: zircon U-Pb SHRIMP dating of the Yixian Formation in Sihetun, Northeast China. Cretaceous Research 28:177-182 \n", + "\nYou HL, Lamanna MC, Harris JD, Chiappe LM, O’Connor JK, Ji SA, Lu JC, Yuan CX, Li DQ, Zhang X, Lacovara KJ, Dodson P, Ji Q. 2006. A nearly modern amphibious bird from the Early Cretaceous of northwestern China. Science 312:1640-1643 \n", + "\nZanno L, Makovicky P. 2011. Herbivorous ecomorphology and specialization patterns in theropod dinosaur evolution. Proceedings of the National Academy of Sciences 108:232-237 \n", + "\nZhang F, Zhou Z. 2000. A primitive enantiornithine bird and the origin of feathers. Science 290:1955-1960 \n", + "\nZheng X, Zhang Z, Hou L. 2007. A new enantiornitine bird with four long rectrices from the Early Cretaceous of northern Hebei, China. Acta Geologica Sinica 81:703-708 \n", + "\nZheng XT, Martin LD, Zhou ZH, Burnham DA, Zhang FC, Miao D. 2011. Fossil evidence of avian crops from the Early Cretaceous of China. Proceedings of the National Academy of Sciences of the United States of America 108:15904-15907 \n", + "\nZhou ZH, Clarke J, Zhang F, Wings O. 2004. Gastroliths in Yanornis: an indication of the earliest radical diet-switching and gizzard plasticity in the lineage leading to living birds. Naturwissenschaften 91:571-574 \n", + "\nZhou ZH, Martin LD. 2011. Distribution of the predentary bone in Mesozoic ornithurine birds. Journal of Systematic Palaeontology 9:25-31 \n", + "\nZhou ZH, Zhang F. 2001. Two new ornithurine birds from the Early Cretaceous of western Liaoning, China. Kexue Tongbao 46:371-377 \n", + "\nZhou ZH, Zhang F. 2005. Discovery of an ornithurine bird and its implication for Early Cretaceous avian radiation. Proceedings of the National Academy of Sciences 102:18998-19002 \n", + "\nZhou ZH, Zhang FC. 2006. A beaked basal ornithurine bird (Aves, Ornithurae) from the Lower Cretaceous of China. Zoologica Scripta 35:363-373 \n", + "\nZhou ZH, Zhang FC. 2007. Mesozoic birds of China – a synoptic review. Frontiers of Biology in China 2(1):1-14 \n", + "\nZhou ZH, Zhang FC, Li ZH. 2009. A New Basal Ornithurine Bird (Jianchangornis microdonta gen. et sp. nov.) from the Lower Cretaceous of China. Vertebrata PalAsiatica 47(4):299-310 \n", + "\nZhou S, Zhou ZH, O’Connor JK. 2012. A new toothless ornithurine bird (Schizooura lii gen. et sp. nov.) from the Lower Cretaceous of China. Vertebrata Palasiatica 50(1):9-24 \n", + "\nZhou S, Zhou ZH, O’Connor JK. 2013a. A new piscivorous ornithuromorph from the Jehol Biota. Historical Biology: An International Journal of Paleobiology \n", + "\nZhou S, Zhou ZH, O’Connor JK. 2013b. Anatomy of the Basal Ornithuromorph Bird Archaeorhynchus spathula from the Early Cretaceous of Liaoning, China. Journal of Vertebrate Paleontology 33(1):141-152 \n" + ] + }, + "figures_html": { + "value": [ + "
\"Photograph
\n

\nFigure 1: Photograph of DNHM D2945.

\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.
", + "
\"Interpretive
\n

\nFigure 2: Interpretive drawing of DNHM D2945.

\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pt, proximal tarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.
", + "
\"Photograph
\n

\nFigure 3: Photograph of DNHM D2946.

\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.
", + "
\"Interpretive
\n

\nFigure 4: Interpretive drawing of DNHM D2946.

\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; st, sternum; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.
", + "
\"Close
\n
\nFigure 5: Close up photograph of the skull of DNHM D2945 in right lateral view and detail (inset) of the central portion of its maxilla.
\nAbbreviations: al, alveoli.
", + "
\"Photograph
\n
\nFigure 6: Photograph (A) and interpretive drawing (B) of the thoracic girdle and vertebral series, rib cage, and humeri of DNHM D2946.
\nAbbreviations: co, coracoid; fu, furcula; hu, humerus; lt, lateral trabecular; ra, radius; rb, ribs; sc, scapula; sp, supracondylar process; st, sternum; up, uncinate process.
", + "
\"Photograph
\n
\nFigure 7: Photograph of the left manus of DNHM D2945/6 in ventral (A; DNHM D2945) and dorsal (B; DNHM D2946) views.
\nAbbreviations: mc I-III, metacarpals I-III; p1-I, phalanx 1 (proximal) of digit I (alular digit); p2-I, phalanx 2 (ungual) of digit I (alular digit); p1-II, phalanx 1 (proximal) of digit II (major digit); p2-II, phalanx 2 (intermediate) of digit II (major digit); p3-II, phalanx 3 (ungual) of digit II (major digit); p1-III, phalanx 1 (proximal) of digit III (minor digit); p2-III, phalanx 2 of digit III (minor digit); ra, radius; sl, semilunate carpal; ul, ulna.
", + "
\"Close
\n
\nFigure 8: Close up photograph of the right knee (medial view) and pubic symphysis (left laterocaudal view) of DNHM D2946.
\nNote the detail of the gastroliths. Abbreviations: fe, femur; fi, fibula; gl, gastroliths, pu, pubis; ti, tibia. (l) and (r) refer to the left and right pubis, respectively.
", + "
\"Close
\n
\nFigure 9: Close up photograph of the left knee (lateral view) of DNHM D2946.
\nAbbreviations: cn, cnemial crest; fc, fibular condyle; fe, femur; fi, fibula; ld, lateral articular facet of tibia; md, medial articular facet of tibia; ti, tibia.
", + "
\"Close
\n
\nFigure 10: Close up photograph of the feet and rectrices of DNHM D2945.
\nAbbreviations: mt, metatarsals; re, rectrices; I-IV, digits I-IV.
", + "
\"Interpretive
\n
\nFigure 11: Interpretive drawing of the outline of the wings and feathered tail of DNHM D2945/6 (see Figs. 1 and 3 for the maximum extent of the primaries and secondaries).
\nThe aerodynamic parameters used in this study were derived from this reconstruction (see Materials and Methods).
" + ] + }, + "tables_html": { + "value": [ + "
\nTable 1:
Comparisons of selective measurements in hongshanornithids.
\nThe values highlight the similar sizes and proportions of the three named species of hongshanornithids: Hongshanornis longicresta (DNHM D2945/6 and IVPP V14533), Parahongshanornis chaoyangensis (PMOL-AB00161), and Longicrusavis houi (PKUP 1069).\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
ElementDNHM D2945/6IVPP V14533PMOL-AB00161PKUP 1069
Skull30.530.7
Humerus24.626.029.026.0
Ulna24.524.027.025.0
Carpometacarpus13.013.012.313.1
Manual digit II18.117.7
Femur22.022.024.024.3
Tibiotarsus35.538.038.037.6
Tarsometatarsus20.622.022.021.5
Pedal digit III20.0
\n", + "
\nTable 2:
Measurements (mm) of the gastroliths of DNHM D2945/6.
\nLeft column numbers correspond to numbers on Figs. 2 and 4.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
D2945D2946Mean value
12.212.272.24
23.063.093.08
32.312.072.19
42.052.152.10
52.152.112.13
62.902.592.75
71.841.761.80
81.761.791.78
91.742.081.91
101.841.561.70
112.513.132.82
\n" ] }, "fulltext_html": { @@ -214,12 +523,12 @@ "/articles/234.xml" ] }, - "supplementary_material": { + "supplementary_file": { "value": [ ] }, - "figure": { + "figures_image": { "value": [ "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-1-full.png", "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-2-full.png", @@ -234,21 +543,6 @@ "https://dfzljdn9uc3pi.cloudfront.net/2014/234/1/fig-11-full.png" ] }, - "figure_caption": { - "value": [ - "\nFigure 1: Photograph of DNHM D2945.\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-1\n\n", - "\nFigure 2: Interpretive drawing of DNHM D2945.\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pt, proximal tarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-2\n\n", - "\nFigure 3: Photograph of DNHM D2946.\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-3\n\n", - "\nFigure 4: Interpretive drawing of DNHM D2946.\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; st, sternum; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-4\n\n", - "\nFigure 5: Close up photograph of the skull of DNHM D2945 in right lateral view and detail (inset) of the central portion of its maxilla.\nAbbreviations: al, alveoli.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-5\n\n", - "\nFigure 6: Photograph (A) and interpretive drawing (B) of the thoracic girdle and vertebral series, rib cage, and humeri of DNHM D2946.\nAbbreviations: co, coracoid; fu, furcula; hu, humerus; lt, lateral trabecular; ra, radius; rb, ribs; sc, scapula; sp, supracondylar process; st, sternum; up, uncinate process.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-6\n\n", - "\nFigure 7: Photograph of the left manus of DNHM D2945/6 in ventral (A; DNHM D2945) and dorsal (B; DNHM D2946) views.\nAbbreviations: mc I-III, metacarpals I-III; p1-I, phalanx 1 (proximal) of digit I (alular digit); p2-I, phalanx 2 (ungual) of digit I (alular digit); p1-II, phalanx 1 (proximal) of digit II (major digit); p2-II, phalanx 2 (intermediate) of digit II (major digit); p3-II, phalanx 3 (ungual) of digit II (major digit); p1-III, phalanx 1 (proximal) of digit III (minor digit); p2-III, phalanx 2 of digit III (minor digit); ra, radius; sl, semilunate carpal; ul, ulna.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-7\n\n", - "\nFigure 8: Close up photograph of the right knee (medial view) and pubic symphysis (left laterocaudal view) of DNHM D2946.\nNote the detail of the gastroliths. Abbreviations: fe, femur; fi, fibula; gl, gastroliths, pu, pubis; ti, tibia. (l) and (r) refer to the left and right pubis, respectively.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-8\n\n", - "\nFigure 9: Close up photograph of the left knee (lateral view) of DNHM D2946.\nAbbreviations: cn, cnemial crest; fc, fibular condyle; fe, femur; fi, fibula; ld, lateral articular facet of tibia; md, medial articular facet of tibia; ti, tibia.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-9\n\n", - "\nFigure 10: Close up photograph of the feet and rectrices of DNHM D2945.\nAbbreviations: mt, metatarsals; re, rectrices; I-IV, digits I-IV.\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-10\n\n", - "\nFigure 11: Interpretive drawing of the outline of the wings and feathered tail of DNHM D2945/6 (see Figs. 1 and 3 for the maximum extent of the primaries and secondaries).\nThe aerodynamic parameters used in this study were derived from this reconstruction (see Materials and Methods).\n  Download full-size image\nDOI: 10.7717/peerj.234/fig-11\n\n" - ] - }, "license": { "value": [ @@ -256,7 +550,8 @@ }, "copyright": { "value": [ - + "2014", + "Chiappe et al." ] }, "file_hashes": [ @@ -294,7 +589,7 @@ "fig-9-full.png": "3d3868736ac56e4f2e8e6395d05df051" }, { - "fulltext.html": "b4033b0dd05addef2c0d237438ddaca2" + "fulltext.html": "2727dc9caa1a8337b6ea911d56d706c7" }, { "fulltext.pdf": "3aa12392730333dd193322c7fb7ac72c" @@ -310,17 +605,27 @@ "PeerJ Inc." ] }, - "journal": { + "journal_name": { "value": [ "PeerJ" ] }, + "journal_issn": { + "value": [ + "2167-8359" + ] + }, "title": { "value": [ "Spectral characteristics of the mutant form GGBP/H152C of D-glucose/D-galactose-binding protein labeled with fluorescent dye BADAN: influence of external factors" ] }, - "authors": { + "keywords": { + "value": [ + "D-glucose/D-galactose-binding protein; Fluorescent dye BADAN; Protein stability; Biosensors; Glucose binding constant" + ] + }, + "author_name": { "value": [ "Alexander V. Fonin", "Olga V. Stepanenko", @@ -333,11 +638,43 @@ "Konstantin K. Turoverov" ] }, - "date": { + "author_institution": { + "value": [ + "Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russia", + "Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russia", + "Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russia", + "Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russia", + "Department of Biology, St. Petersburg State University, St. Petersburg, Russia", + "Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russia", + "Department of Physical Electronics, St. Petersburg State Polytechnical University, St. Petersburg, Russia", + "Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russia", + "Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russia", + "Department of Biophysics, St. Petersburg State Polytechnical University, St. Petersburg, Russia", + "Laboratory of Nanobiotechnologies, Palladin Institute of Biochemistry of the National Academy of Sciences of Ukraine, Kiev, Ukraine", + "Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russia", + "Department of Biophysics, St. Petersburg State Polytechnical University, St. Petersburg, Russia" + ] + }, + "editor_name": { + "value": [ + "Vladimir Uversky" + ] + }, + "date_published": { "value": [ "2014-03-18" ] }, + "date_accepted": { + "value": [ + "2014-01-26" + ] + }, + "date_submitted": { + "value": [ + "2013-11-15" + ] + }, "doi": { "value": [ "10.7717/peerj.275" @@ -358,14 +695,105 @@ "e275" ] }, - "description": { + "abstract": { "value": [ "The mutant form GGBP/H152C of the D-glucose/D-galactose-binding protein with the solvatochromic dye BADAN linked to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various external factors on the physical-chemical properties of GGBP/H152C-BADAN and its complex with glucose. The high affinity (Kd = 8.5 µM) and high binding rate of glucose make GGBP/H152C-BADAN a good candidate to determine the sugar content in biological fluids extracted using transdermal techniques. It was shown that changes in the ionic strength and pH of solution within the physiological range did not have a significant influence on the fluorescent characteristics of GGBP/H152C-BADAN. The mutant form GGBP/H152C has relatively low resistance to denaturation action of GdnHCl and urea. This result emphasizes the need to find more stable proteins for the creation of a sensitive element for a glucose biosensor system." ] }, - "abstract": { + "abstract_html": { "value": [ - "The mutant form GGBP/H152C of the D-glucose/D-galactose-binding protein with the solvatochromic dye BADAN linked to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various external factors on the physical-chemical properties of GGBP/H152C-BADAN and its complex with glucose. The high affinity (Kd = 8.5 µM) and high binding rate of glucose make GGBP/H152C-BADAN a good candidate to determine the sugar content in biological fluids extracted using transdermal techniques. It was shown that changes in the ionic strength and pH of solution within the physiological range did not have a significant influence on the fluorescent characteristics of GGBP/H152C-BADAN. The mutant form GGBP/H152C has relatively low resistance to denaturation action of GdnHCl and urea. This result emphasizes the need to find more stable proteins for the creation of a sensitive element for a glucose biosensor system." + "

The mutant form GGBP/H152C of the D-glucose/D-galactose-binding protein with the solvatochromic dye BADAN linked to cysteine residue Cys 152 can be used as a potential base for a sensitive element of glucose biosensor system. We investigated the influence of various external factors on the physical-chemical properties of GGBP/H152C-BADAN and its complex with glucose. The high affinity (Kd = 8.5 µM) and high binding rate of glucose make GGBP/H152C-BADAN a good candidate to determine the sugar content in biological fluids extracted using transdermal techniques. It was shown that changes in the ionic strength and pH of solution within the physiological range did not have a significant influence on the fluorescent characteristics of GGBP/H152C-BADAN. The mutant form GGBP/H152C has relatively low resistance to denaturation action of GdnHCl and urea. This result emphasizes the need to find more stable proteins for the creation of a sensitive element for a glucose biosensor system.

" + ] + }, + "introduction_html": { + "value": [ + "

Introduction

\n

Operation of most of the glucose biosensors for continuous, non-invasive glucose monitoring in biological fluids is based on specific enzymatic glucose oxidation by glucose oxidase (Tang et al., 2004) or phosphorylation by glucokinase (Katsube et al., 1990). The main drawback of such sensors is that its sensitive element is consumable due to the irreversible nature of the reaction of sensitive elements with analyte. A more promising direction for non-invasive glucometer design is the development of a biosensor system with a protein-sensitive element those reaction with glucose is reversible. Such proteins are concanavalin A and the D-glucose/D-galactose-binding protein (GGBP). The application of GGBP is promising because the protein–glucose binding promotes a significant change in the tertiary structure of GGBP (Amiss et al., 2007; Sakaguchi-Mikami et al., 2008; Saxl et al., 2009; Yesylevskyy, Kharkyanen & Demchenko, 2006). One of the most common methods for detecting conformational changes in proteins is fluorescence. Despite the significant structural changes of GGBP that occur when it interacts with glucose the intrinsic UV fluorescence characteristics remains practically unchanged (Stepanenko et al., 2011a; Stepanenko et al., 2011b). Thus, the fluorescent response to glucose binding to GGBP could be obtained using fluorescence of dye linked to protein (Amiss et al., 2007; Khan, Gnudi & Pickup, 2008; Khan, Saxl & Pickup, 2010; Sakaguchi-Mikami et al., 2008; Saxl et al., 2011; Saxl et al., 2009) or the changes of FRET signal of chimeric constructs based on GGBP and fluorescent proteins (Ge, Tolosa & Rao, 2004; Ye & Schultz, 2003).

\n

One of the promising candidates for the role of a glucose biosensor system sensitive element is the GGBP/H152C mutant form of GGBP in which the histidine at position 152 has been replaced with a cysteine and fluorescent dye BADAN linked to the Cys 152 (Khan, Gnudi & Pickup, 2008). It was shown that the fluorescence intensity of the dye linked to the protein increased three-fold in response to binding of GGBP/H152C with glucose (the transition of GGBP/H152C from its open to closed forms) (Khan, Gnudi & Pickup, 2008; Khan, Saxl & Pickup, 2010). The replacement of histidine 152 with cysteine was used for labeling with the fluorescent dye of series of GGBP mutant forms for glucose monitoring (Khan, Saxl & Pickup, 2010; Saxl et al., 2011). Continuous glucose concentration measurements in analyzable mediums could be achieved using a protein-sensitive element having as much as possible, a high stability, and which properties do not significantly change on the possible composition variations of the biological fluids, in which to determine glucose.

\n

In this connection aim of this work was to study the effect of different external factors (i.e., changing the pH, viscosity, ionic strength of solution) on the fluorescence characteristics of the GGBP/H152C mutant in its open and closed forms and on the response time of the recorded signal to glucose change in the assay medium. One way to assess the stability of proteins is to study their unfolding under the action of chemical denaturants. Thus we also investigated denaturation GGBP/H152C under the GdnHCl and urea action.

" + ] + }, + "methods_html": { + "value": [ + "

Materials and Methods

\n

Materials

\n

D-glucose, acetonitrile (Sigma, USA), NaCl (Vekton, Russia), fluorescent dyes BADAN and quinine sulfate (AnaSpec, USA), guanidine hydrochloride (Nacalai Tesque, Japan), and glycerol (Merck, Germany) were used without further purification. The mutant form of the D-glucose/D-galactose–binding protein GGBP/H152C was obtained, separated and purified as described previously (Stepanenko et al., 2011a). The labeling of GGBP/H152C with the fluorescent dye BADAN was performed as described by Khan, Saxl & Pickup (2010). The experiments were performed in solutions with protein concentrations ranging from 0.2 to 0.8 mg/ml. For the formation of the protein-ligand complex, 5 µM–20 mM of D-glucose was added to the protein solution. The measurements were made in buffer solutions containing citric acid and Na2HPO4 (pH 2.8, 4.2, 6.0, 7.1), PBS (pH 7.4) and TrisHCl (pH 7.2, 9.6).

Fluorescence measurements

\n

The fluorescence experiments were carried out using Cary Eclipse (Agilent, Australia) and homemade (Turoverov et al., 1998) spectrofluorimeters. The kinetics of GGBP/H152C-BADAN binding with glucose was measured using a stopped flow apparatus MOS 450 (Bio-Logic, France). The excitation wavelengths for the intrinsic protein fluorescence spectra were 297 or 280 nm. The dye fluorescence was excited at 387 or 405 nm. The position and form of the fluorescence spectra were characterized by the parameter A = I320/I365, where I320 and I365 are the fluorescence intensities measured at emission wavelengths of 320 and 365 nm, respectively (Kuznetsova, Yakusheva & Turoverov, 1999; Turoverov & Kuznetsova, 2003). The values of parameter A and the fluorescence spectra were corrected using the instrument’s spectral sensitivity. The quantum yield of BADAN fluorescence was determined according to the procedure described previously (Kuznetsova et al., 2012b). Quinine sulfate in 0.1 M H2SO4 was used as a reference solution. The measurements were made at 23°C with micro-cells (10 × 10 × 4 mm; Starna, Great Britain).

Determination of protein-ligand dissociation constant

\n

The fluorescence intensity of protein solution in the ligand presence can be determined by equation (1)IC0=αFC0IF+αBC0IB\n where IF and IB are the fluorescence intensity of protein in free state and bounded with ligand, respectively, and αF(C0) and αB(C0) are the relative fraction of this protein states in the solution at concentration of added ligand C0, αF(C0) + αB(C0) = 1. Thus, the fraction of bounded protein is determined as: (2)αB=IC0IFIBIF=CbCp\n where Cp is the total protein concentration and Cb is the concentration of protein bounded with ligand. The dissociation constant, Kd can be expressed as follows (Kuznetsova et al., 2012a): (3)Kd=receptor×ligandcomplex=CpCb×CfCb\n where Cf is concentration of free ligand, which can be calculated from the equation: (4)Cb=C0Cf\n here C0 is concentration of added ligand. Eliminating Cf from the Eq. (3), we can obtain the next equation for Cb: (5)Cb=Kd+Cp+C0Kd+Cp+C024Cp×C02.\n Combining the Eqs. (2) and (5), we have the equation for definition of Kd, using the difference of fluorescence intensity of mutant proteins in the presence and in the absence of glucose: (6)IC0=IF+IBIF×Kd+Cp+C0Kd+Cp+C024Cp×C02Cp.\n The wavelength of registration was chosen as that of the maximal difference in the fluorescence intensity of the ligand-free and bound states of the studied protein. Approximation of experimental data was performed via the nonlinear regression method using Sigma Plot program.

" + ] + }, + "results_html": { + "value": [ + + ] + }, + "discussion_html": { + "value": [ + + ] + }, + "conclusion_html": { + "value": [ + + ] + }, + "author_contrib_html": { + "value": [ + + ] + }, + "competing_interests_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\nAmiss TJ, Sherman DB, Nycz CM, Andaluz SA, Pitner JB. 2007. Engineering and rapid selection of a low-affinity glucose/galactose-binding protein for a glucose biosensor. Protein Science 16:2350-2359 \n", + "\nBongrand P. 1999. Ligand–receptor interactions. Reports on Progress in Physics 62:921-968 \n", + "\nBorrok MJ, Kiessling LL, Forest KT. 2007. Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures. Protein Science 16:1032-1041 \n", + "\nDintenfass L. 1985. Blood viscosity, hyperviscosity, and hyperviscosaemia. Netherlands: Kluwer Academic Publishers Group. \n", + "\nGe X, Rao G, Tolosa L. 2008. On the possibility of real-time monitoring of glucose in cell culture by microdialysis using a fluorescent glucose binding protein sensor. Biotechnology Progress 24:691-697 \n", + "\nGe X, Tolosa L, Rao G. 2004. Dual-labeled glucose binding protein for ratiometric measurements of glucose. Analytical Chemistry 76:1403-1410 \n", + "\nHeinemann L. 2003. Continuous glucose monitoring by means of the microdialysis technique: underlying fundamental aspects. Diabetes Technology & Therapeutics 5:545-561 \n", + "\nKatsube T, Katoh M, Maekawa H, Hara M, Yamaguchi S, Uchida N, Shimomura T. 1990. Stabilization of an FET glucose sensor with the thermophilic enzyme glucokinase. Sensors and Actuators B: Chemical 1:504-507 \n", + "\nKhan F, Gnudi L, Pickup JC. 2008. Fluorescence-based sensing of glucose using engineered glucose/galactose-binding protein: a comparison of fluorescence resonance energy transfer and environmentally sensitive dye labelling strategies. Biochemical and Biophysical Research Communications 365:102-106 \n", + "\nKhan F, Saxl TE, Pickup JC. 2010. Fluorescence intensity- and lifetime-based glucose sensing using an engineered high-Kd mutant of glucose/galactose-binding protein. Analytical Biochemistry 399:39-43 \n", + "\nKoehorst RB, Spruijt RB, Hemminga MA. 2008. Site-directed fluorescence labeling of a membrane protein with BADAN: probing protein topology and local environment. Biophysical Journal 94:3945-3955 \n", + "\nKost J, Mitragotri S, Gabbay RA, Pishko M, Langer R. 2000. Transdermal monitoring of glucose and other analytes using ultrasound. Nature Medicine 6:347-350 \n", + "\nKuznetsova IM, Stepanenko Olga V, Turoverov KK, Zhu L, Zhou JM, Fink AL, Uversky VN. 2002. Unraveling multistate unfolding of rabbit muscle creatine kinase. Biochimica et Biophysica Acta/Protein Structure and Molecular Enzimology 1596:138-155 \n", + "\nKuznetsova IM, Sulatskaya AI, Povarova OI, Turoverov KK. 2012a. Reevaluation of ANS binding to human and bovine serum albumins: key role of equilibrium microdialysis in ligand-receptor binding characterization. PLoS ONE 7:e40845 \n", + "\nKuznetsova IM, Sulatskaya AI, Uversky VN, Turoverov KK. 2012b. A new trend in the experimental methodology for the analysis of the thioflavin T binding to amyloid fibrils. Molecular Neurobiology 45:488-498 \n", + "\nKuznetsova IM, Yakusheva TA, Turoverov KK. 1999. Contribution of separate tryptophan residues to intrinsic fluorescence of actin. Analysis of 3D structure. FEBS Letters 452:205-210 \n", + "\nLoutfy RO, Arnold BA. 1982. Effect of viscosity and temperature on torsional relaxation of molecular rotors. The Journal of Physical Chemistry 86:4205-4211 \n", + "\nOliver NS, Toumazou C, Cass AE, Johnston DG. 2009. Glucose sensors: a review of current and emerging technology. Diabetic Medicine 26:197-210 \n", + "\nOwenius R, Osterlund M, Lindgren M, Svensson M, Olsen OH, Persson E, Freskgard PO, Carlsson U. 1999. Properties of spin and fluorescent labels at a receptor–ligand interface. Biophysical Journal 77:2237-2250 \n", + "\nPovarova OI, Kuznetsova IM, Turoverov KK. 2010. Differences in the pathways of proteins unfolding induced by urea and guanidine hydrochloride: molten globule state and aggregates. PLoS ONE 5:e15035 \n", + "\nRenard E. 2005. Monitoring glycemic control: the importance of self-monitoring of blood glucose. American Journal of Medicine 118:12S-19S \n", + "\nRhee SY, Chon S, Koh G, Paeng JR, Oh S, Woo JT, Kim SW, Kim JW, Kim YS. 2007. Clinical experience of an iontophoresis based glucose measuring system. Journal of Korean Medical Science 22:70-73 \n", + "\nSakaguchi-Mikami A, Taneoka A, Yamoto R, Ferri S, Sode K. 2008. Engineering of ligand specificity of periplasmic binding protein for glucose sensing. Biotechnology Letters 30:1453-1460 \n", + "\nSaxl T, Khan F, Ferla M, Birch D, Pickup J. 2011. A fluorescence lifetime-based fibre-optic glucose sensor using glucose/galactose-binding protein. Analyst 136:968-972 \n", + "\nSaxl T, Khan F, Matthews DR, Zhi ZL, Rolinski O, Ameer-Beg S, Pickup J. 2009. Fluorescence lifetime spectroscopy and imaging of nano-engineered glucose sensor microcapsules based on glucose/galactose-binding protein. Biosensors and Bioelectronics 24:3229-3234 \n", + "\nStepanenko Olga V, Fonin AV, Morozova KS, Verkhusha VV, Kuznetsova IM, Turoverov KK, Staiano M, D’Auria S. 2011a. New insight in protein-ligand interactions. 2. Stability and properties of two mutant forms of the D-galactose/D-glucose-binding protein from E. coli. The Journal of Physical Chemistry B 115:9022-9032 \n", + "\nStepanenko Olga V, Povarova OI, Fonin AV, Kuznetsova IM, Turoverov KK, Staiano M, Varriale A, D’Auria S. 2011b. New insight into protein-ligand interactions. The case of the D-galactose/D-glucose-binding protein from Escherichia coli. The Journal of Physical Chemistry B 115:2765-2773 \n", + "\nStepanenko Olesya V, Verkhusha VV, Kazakov VI, Shavlovsky MM, Kuznetsova IM, Uversky VN, Turoverov KK. 2004. Comparative studies on the structure and stability of fluorescent proteins EGFP, zFP506, mRFP1, “dimer2”, and DsRed1. Biochemistry 43:14913-14923 \n", + "\nTang H, Chen J, Yao S, Nie L, Deng G, Kuang Y. 2004. Amperometric glucose biosensor based on adsorption of glucose oxidase at platinum nanoparticle-modified carbon nanotube electrode. Analytical Biochemistry 331:89-97 \n", + "\nTolosa L, Gryczynski I, Eichhorn LR, Dattelbaum JD, Castellano FN, Rao G, Lakowicz JR. 1999. Glucose sensor for low-cost lifetime-based sensing using a genetically engineered protein. Analytical Biochemistry 267:114-120 \n", + "\nTuroverov KK, Biktashev AG, Dorofeiuk AV, Kuznetsova IM. 1998. A complex of apparatus and programs for the measurement of spectral, polarization and kinetic characteristics of fluorescence in solution. Tsitologiia 40:806-817 \n", + "\nTuroverov KK, Kuznetsova IM. 2003. Intrinsic fluorescence of actin. Journal of Fluorescence 13:41-57 \n", + "\nVerkhusha VV, Kuznetsova IM, Stepanenko Olesya V, Zaraisky AG, Shavlovsky MM, Turoverov KK, Uversky VN. 2003. High stability of Discosoma DsRed as compared to Aequorea EGFP. Biochemistry 42:7879-7884 \n", + "\nVyas NK, Vyas MN, Quiocho FA. 1988. Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. Science 242:1290-1295 \n", + "\nYe K, Schultz JS. 2003. Genetic engineering of an allosterically based glucose indicator protein for continuous glucose monitoring by fluorescence resonance energy transfer. Analytical Chemistry 75:3451-3459 \n", + "\nYesylevskyy SO, Kharkyanen VN, Demchenko AP. 2006. The change of protein intradomain mobility on ligand binding: is it a commonly observed phenomenon? Biophysical Journal 91:3002-3013 \n" + ] + }, + "figures_html": { + "value": [ + "
\"Determination
\n

\nFigure 1: Determination of the dissociation constant (Kd) of the complex of GGBP/H152C-BADAN with glucose (Glc).

\nThe excitation wavelength was 387 nm, the emission wavelength was 545 nm.
", + "
\"The
\n

\nFigure 2: The kinetics of Glc binding to GGBP/H152C-BADAN in solutions with different viscosities.

\nGlc concentration was 20 mM. The excitation wavelength was 405 nm. Curve 1, 2 and 3 represents the control, Glc binding to GGBP/H152C-BADAN in a PBS solution, and in PBS-glycerol solution with viscosity equal to 4.0 cP. Inset: The kinetic curves 1 and 2 in interval from 0.01 to 0.08 s are given.
", + "
\"The
\n

\nFigure 3: The effect of solvent viscosity and temperature on the fluorescence quantum yield of the GGBP/H152C-BADAN in the open (circles) and closed (triangles) forms.

\nThe excitation wavelength was 387 nm.
", + "
\"GdnHCl-induced
\n

\nFigure 4: GdnHCl-induced (A, B) and urea-induced (C, D) conformational changing of GGBP/H152C-BADAN structure in open (circles) and closed forms (triangles).

\n(A) and (C) represents the dependence of the fluorescence intensity (the excitation wavelength was 387 nm, the emission wavelength was 545 nm) on the denaturants concentration. (B) and (D) represents the dependence of the parameter A = I320/I365 (I320 and I365 fluorescence intensities recorded at 320 and 365 nm, respectively) on the denaturants concentration (the excitation wavelength was 297 nm).
", + "
\"Changes
\n

\nFigure 5: Changes of ellipticity at 222 nm of GGBP/H152C-BADAN and GGBP/H152C-BADAN–Glc on the GdnHCl concentration.

\n
", + "
\"The
\n

\nFigure 6: The effect of the pH solution on the fluorescent characteristics of GGBP/H152C-BADAN in the open (the solid curves) and closed (the dashed curves) forms.

\n(A) The excitation wavelength was 297 nm. (B) The excitation wavelength was 387 nm. The pH values of the solution were 2.8 (black curves), 4.2 (red curves), 6.4 (blue curves), 7.4 (dark green curves) and 9.6 (dark red curves).
", + "
\"The
\n

\nFigure 7: The effect of NaCl and MgCl2 on the fluorescent characteristics of GGBP/H152C-BADAN in open (solid curves) and closed (dashed curves) forms.

\n(A) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.8 M NaCl (red curve) and 2.5 M NaCl (blue curve). (B) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.1 M MgCl2 (red curve) and 0.5 M MgCl2 (blue curve). The fluorescence spectra of GGBP/H152C-BADAN in PBS solution appear in black. (The excitation wavelength was 387 nm.)
" + ] + }, + "tables_html": { + "value": [ + ] }, "fulltext_html": { @@ -383,12 +811,12 @@ "/articles/275.xml" ] }, - "supplementary_material": { + "supplementary_file": { "value": [ ] }, - "figure": { + "figures_image": { "value": [ "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-1-full.png", "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-2-full.png", @@ -399,17 +827,6 @@ "https://dfzljdn9uc3pi.cloudfront.net/2014/275/1/fig-7-full.png" ] }, - "figure_caption": { - "value": [ - "\nFigure 1: Determination of the dissociation constant (Kd) of the complex of GGBP/H152C-BADAN with glucose (Glc).\nThe excitation wavelength was 387 nm, the emission wavelength was 545 nm.\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-1\n\n", - "\nFigure 2: The kinetics of Glc binding to GGBP/H152C-BADAN in solutions with different viscosities.\nGlc concentration was 20 mM. The excitation wavelength was 405 nm. Curve 1, 2 and 3 represents the control, Glc binding to GGBP/H152C-BADAN in a PBS solution, and in PBS-glycerol solution with viscosity equal to 4.0 cP. Inset: The kinetic curves 1 and 2 in interval from 0.01 to 0.08 s are given.\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-2\n\n", - "\nFigure 3: The effect of solvent viscosity and temperature on the fluorescence quantum yield of the GGBP/H152C-BADAN in the open (circles) and closed (triangles) forms.\nThe excitation wavelength was 387 nm.\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-3\n\n", - "\nFigure 4: GdnHCl-induced (A, B) and urea-induced (C, D) conformational changing of GGBP/H152C-BADAN structure in open (circles) and closed forms (triangles).\n(A) and (C) represents the dependence of the fluorescence intensity (the excitation wavelength was 387 nm, the emission wavelength was 545 nm) on the denaturants concentration. (B) and (D) represents the dependence of the parameter A = I320/I365 (I320 and I365 fluorescence intensities recorded at 320 and 365 nm, respectively) on the denaturants concentration (the excitation wavelength was 297 nm).\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-4\n\n", - "\nFigure 5: Changes of ellipticity at 222 nm of GGBP/H152C-BADAN and GGBP/H152C-BADAN–Glc on the GdnHCl concentration.\n\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-5\n\n", - "\nFigure 6: The effect of the pH solution on the fluorescent characteristics of GGBP/H152C-BADAN in the open (the solid curves) and closed (the dashed curves) forms.\n(A) The excitation wavelength was 297 nm. (B) The excitation wavelength was 387 nm. The pH values of the solution were 2.8 (black curves), 4.2 (red curves), 6.4 (blue curves), 7.4 (dark green curves) and 9.6 (dark red curves).\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-6\n\n", - "\nFigure 7: The effect of NaCl and MgCl2 on the fluorescent characteristics of GGBP/H152C-BADAN in open (solid curves) and closed (dashed curves) forms.\n(A) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.8 M NaCl (red curve) and 2.5 M NaCl (blue curve). (B) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.1 M MgCl2 (red curve) and 0.5 M MgCl2 (blue curve). The fluorescence spectra of GGBP/H152C-BADAN in PBS solution appear in black. (The excitation wavelength was 387 nm.)\n  Download full-size image\nDOI: 10.7717/peerj.275/fig-7\n\n" - ] - }, "license": { "value": [ @@ -417,7 +834,8 @@ }, "copyright": { "value": [ - + "2014", + "Fonin et al." ] }, "file_hashes": [ @@ -443,7 +861,7 @@ "fig-7-full.png": "b76d31a596a07e5ef4fe238d687c5729" }, { - "fulltext.html": "6e5fc1f3587b4c0eb4810a455b290a23" + "fulltext.html": "cc1c3413ec3e0b9e1702e1ceda56c309" }, { "fulltext.pdf": "6b554c704f1ed7a8129863a2869036eb" @@ -459,28 +877,60 @@ "PeerJ Inc." ] }, - "journal": { + "journal_name": { "value": [ "PeerJ" ] }, + "journal_issn": { + "value": [ + "2167-8359" + ] + }, "title": { "value": [ "Religious attendance after elevated depressive symptoms: is selection bias at work?" ] }, - "authors": { + "keywords": { + "value": [ + "Selection bias; Religious attendance; Mental health" + ] + }, + "author_name": { "value": [ "Lloyd Balbuena", "Marilyn Baetz", "Rudy Bowen" ] }, - "date": { + "author_institution": { + "value": [ + "Department of Psychiatry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada", + "Department of Psychiatry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada", + "Department of Psychiatry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada" + ] + }, + "editor_name": { + "value": [ + "Timothy Moss" + ] + }, + "date_published": { "value": [ "2014-03-13" ] }, + "date_accepted": { + "value": [ + "2014-02-26" + ] + }, + "date_submitted": { + "value": [ + "2013-12-16" + ] + }, "doi": { "value": [ "10.7717/peerj.311" @@ -501,14 +951,106 @@ "e311" ] }, - "description": { + "abstract": { "value": [ "In an attempt to determine if selection bias could be a reason that religious attendance and depression are related, the predictive value of elevated depressive symptoms for a decrease in future attendance at religious services was examined in a longitudinal panel of 1,673 Dutch adults. Religious attendance was assessed yearly over five years using the single question, “how often do you attend religious gatherings nowadays?” Depressive symptoms were assessed four times within the first year using the Depression subscale of the Brief Symptom Inventory. Logistic regression models of change in attendance were created, stratifying by baseline attendance status. Attenders who developed elevated symptoms were less likely to subsequently decrease their attendance (relative risk ratio: 0.55, 95% CI [0.38–0.79]) relative to baseline as compared to those without elevated symptoms. This inverse association remained significant after controlling for health and demographic covariates, and when using multiply imputed data to account for attrition. Non-attenders were unlikely to start attending after elevated depressive symptoms. This study provides counter evidence against previous findings that church attenders are a self-selected healthier group." ] }, - "abstract": { + "abstract_html": { "value": [ - "In an attempt to determine if selection bias could be a reason that religious attendance and depression are related, the predictive value of elevated depressive symptoms for a decrease in future attendance at religious services was examined in a longitudinal panel of 1,673 Dutch adults. Religious attendance was assessed yearly over five years using the single question, “how often do you attend religious gatherings nowadays?” Depressive symptoms were assessed four times within the first year using the Depression subscale of the Brief Symptom Inventory. Logistic regression models of change in attendance were created, stratifying by baseline attendance status. Attenders who developed elevated symptoms were less likely to subsequently decrease their attendance (relative risk ratio: 0.55, 95% CI [0.38–0.79]) relative to baseline as compared to those without elevated symptoms. This inverse association remained significant after controlling for health and demographic covariates, and when using multiply imputed data to account for attrition. Non-attenders were unlikely to start attending after elevated depressive symptoms. This study provides counter evidence against previous findings that church attenders are a self-selected healthier group." + "

In an attempt to determine if selection bias could be a reason that religious attendance and depression are related, the predictive value of elevated depressive symptoms for a decrease in future attendance at religious services was examined in a longitudinal panel of 1,673 Dutch adults. Religious attendance was assessed yearly over five years using the single question, “how often do you attend religious gatherings nowadays?” Depressive symptoms were assessed four times within the first year using the Depression subscale of the Brief Symptom Inventory. Logistic regression models of change in attendance were created, stratifying by baseline attendance status. Attenders who developed elevated symptoms were less likely to subsequently decrease their attendance (relative risk ratio: 0.55, 95% CI [0.38–0.79]) relative to baseline as compared to those without elevated symptoms. This inverse association remained significant after controlling for health and demographic covariates, and when using multiply imputed data to account for attrition. Non-attenders were unlikely to start attending after elevated depressive symptoms. This study provides counter evidence against previous findings that church attenders are a self-selected healthier group.

" + ] + }, + "introduction_html": { + "value": [ + "

Introduction

\n

Attendance at religious services is usually reported to be inversely related to depression (Baetz et al., 2004; Balbuena, Baetz & Bowen, 2013; Hayward et al., 2012; Maselko, Gilman & Buka, 2009). However, as with many findings in the literature on religion and depression, the results have not been consistent, with other studies reporting a null (Ellison & Flannelly, 2009; Miller et al., 2012; Schnittker, 2001) or curvilinear relationship of attendance and depression (Taylor, Chatters & Nguyen, 2013). This inconsistency has been due in part to the predominance of cross-sectional designs, which cannot establish causation. We are aware of only three longitudinal studies examining the relation of depression to subsequent religious attendance. Recently, it was reported (Maselko et al., 2012) that women having an onset of depression prior to age 18 were more likely to stop attending religious services as adults compared to those with adult-onset MDE and those with no lifetime MDE. Similarly, a longitudinal study (Horowitz & Garber, 2003) reported that depressive episodes in grades 7–11 predicted lower levels of religious attendance in grade 12. The latter result is ambiguous because religious attendance in grade 6 also predicted lower odds of depression in grades 7–12, although the effect was just shy of statistical significance. Miller and colleagues (2002) followed a cohort of 146 individuals who had an MDE in childhood together with a control group of 123 who had no psychiatric disorder over 11 years. At follow-up, the rates of religious attendance between groups did not differ by childhood depression status. It is noteworthy that these studies covered the adolescence-to-adult transition period. Late adolescence is generally a time of profound change. The quest to establish one’s identity and career (Arnett, 2000) and experimentation with cohabitation, drugs, and alcohol (Benda & Corwyn, 1997; Thornton, Axinn & Hill, 1992; Uecker, Regnerus & Vaaler, 2007) could precipitate internal conflicts with religious doctrine, leading to declines in religious attendance. In short, the developmental processes occurring during adolescence confounds the relation of depression with religious attendance, in either causal direction.

\n

Selection effects might work in two ways to confound the relation of depression with subsequent religious attendance. First, depressed individuals may withdraw from public worship as part of the overall social disengagement that occurs in depression (Maselko et al., 2012). Secondly, churchgoers might be less susceptible to depression. A meta-analysis of 94 studies reported a positive correlation of agreeableness, conscientiousness, and sociability with religious social investment (Lodi-Smith & Roberts, 2007). In summary, theory suggests that depressed individuals select themselves out of the churchgoing demographic while healthy ones select themselves into it. These selection effects, if operative, would likely overestimate the protective value of religion for mental health.

\n

The protective value of religiosity does have empirical support. Coping with adversity through religion is well-documented in the literature (Pargament, 1997). “Turning to God or religion” as a coping strategy has been reported in cancer patients (Bussing, Ostermann & Koenig, 2007), newly bereaved individuals (Brown et al., 2004), and new immigrants (Connor, 2009). A study comparing religiosity and spirituality before and after HIV patients were informed of the diagnosis (Ironson, Stuetzle & Fletcher, 2006) reported that religiosity (including attendance) increased after the diagnosis became known. Furthermore, increased religiosity was associated with greater CD4 helper cells in the blood, indicating slower HIV progression (Ironson, Stuetzle & Fletcher, 2006). A US longitudinal study reported that depressed individuals were more likely to seek religious consolation—defined as searching for meaning in problems and difficulties (Ferraro & Kelley-Moore, 2000). Importantly, even those with no initial religious affiliation sought religious consolation after depression. This finding seems to support the “no atheists in foxholes” aphorism. However, adversity or trauma can also cause individuals to turn away from God or religion (Chen & Koenig, 2006; Fontana & Rosenheck, 2004). We are not aware of longitudinal studies reporting changes to religious attendance per se (vis-a-vis religiosity broadly speaking) after a depressive episode aside from the three studies in adolescence (Horowitz & Garber, 2003; Maselko et al., 2012; Miller et al., 2002) already mentioned.

\n

In this paper, our main objective was to study whether elevated depressive symptoms introduce selection bias in a longitudinal follow-up of religious attendance. Our research questions were as follows. First, do religious attenders who develop elevated depressive symptoms subsequently decrease their attendance level? Second, do non-attenders who develop elevated symptoms begin to attend services?

" + ] + }, + "methods_html": { + "value": [ + "

Materials and Methods

\n

Sample

\n

The data is from the Longitudinal Internet Studies for the Social Sciences (LISS) panel, a random sample of adults living in the Netherlands (Scherpenzeel, 2011). The panel of almost 8,000 individuals was drawn from the Dutch-speaking population based on a list of addresses provided by Statistics Netherlands. The recruitment strategy is described in more detail elsewhere (Scherpenzeel, 2011). LISS is a continuing study in which participants complete online questionnaires monthly on topics including family, economic situation, health, and religion. Each LISS participant has a unique member ID, so it is possible to combine their responses across different survey modules and from one wave to another. For the purpose of our study, we merged the religion (n = 7, 418) and mental health (n = 1, 804) modules, narrowing our sample to those who responded to both surveys (n = 1, 718) (see Fig. 1A). Waves of religion and depression assessments were not simultaneous, so hereafter, use the notations Ri and Di to refer to religion and depression waves, respectively (see Fig. 1B). Our research question requires the following temporal sequence: R1 → D2 to D4 → R2. By comparing attendance level at R2 with R1, we can test whether depression predicts a relative decrease at R2. This design requirement forced us to exclude those individuals (n = 41) who had a different sequence of assessments:

\n

D1 → D2 → R1 → D2 to D4 since for these individuals, one cannot compare attendance levels before and after depression. Our effective sample size was 1,673.

\n
\"Subjects.\"
\n

\nFigure 1: Subjects.

\n(A) LISS datasets used and participant flowchart; (B) schedule of religion and depression assessments.

In the sample, 887 individuals did not attend services and 786 attended services at R1. (Explained in Measures section below.) The characteristics of these groups are described in Table 1. After baseline assessment, D1, depression was assessed during a seven-month span from March to September 2008 while attendance was assessed another four times in addition to R1, and these assessments occurred on each January from 2009 to 2012. Our main analytic strategy was to compare the proportion of individuals that changed their attendance level, stratified by baseline attendance. The change in attendance level was indexed to R1 attendance since there were no further depression assessments after September 2008.

\n
\nTable 1:
Comparison of attenders and non-attenders.
\nCharacteristics of Dutch individuals who responded to mental health (Wave 1) and religious attendance (Wave 1–Jan 2008) of the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands (n = 1, 673).\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Service attenders at R1Non-attenders of service at R1\np of the difference
\n n\n 786887
Mean age (sd)49.60 (18.22)45.90 (17.21)<.001
Civil status
\n Unmarried\n 323 (41)443 (50)<.001
\n Married\n 463 (59)444 (50)
Monthly income
\n Low income (0–500 € per month)\n 77 (10)65 (7).07
\n Not low income (>500 € per month)\n 709 (90)822 (93)
Mean self-rated health (sd)*\n3.12 (0.76)3.13 (0.76).68
With a chronic condition
\n Yes\n 232 (32)227 (27)
\n No\n 497 (68)600 (73).06
Baseline distribution of BSI depression normative scores
\n Very low\n 0 (0)0 (0).38
\n Low\n 0 (0)0 (0)
\n Below average\n 113 (14)145 (16)
\n Average\n 196 (25)234 (26)
\n Above average\n 284 (36)324 (37)
\n High\n 168 (21)162 (18)
\n Very high\n 25 (3)22 (2)
\n\n
\n

Notes:

\n

Figures in this table are n (%) except for age and self-rated health which are mean (sd).

\n
\n*Rated on a scale of 1–5, with higher scores indicating better health.\n
\n

Measures

\n

Religious attendance was assessed with the single question, “Aside from special occasions such as weddings and funerals, how often do you attend religious gatherings nowadays?” This was answered on a 7-point Likert scale coded as 1 = everyday, 2 = more than once a week, 3 = once a week, 4 = at least once a month, 5 = only on special religious days, 6 = less often, and 7 = never. We reverse coded the scale for ease of interpretation—i.e., larger number indicated higher attendance. Among attenders, we used a dichotomous attendance variable for decreased (coded 0) and same/increased (coded 1) and a categorical version: decreased, unchanged, and increased attendance. These categories were formed by subtracting the R1 attendance level from a given follow-up assessment. For non-attenders in R1, a dichotomous variable with unchanged (coded 0) and increased (coded 1) was used.

\n

Our substantive predictor was assessed using the Depression subscale of the Brief Symptom Inventory (Derogatis, 1975). The subscale consists of 6 items rated on a 5-point scale from “Not at all” to “Extremely”. The BSI is itself a short version of the SCL-90 (Derogatis & Melisaratos, 1983). BSI Depression had an internal reliability ranging from 0.70 to 0.92 in four different studies (Boulet & Boss, 1991; Derogatis & Melisaratos, 1983; Johnson et al., 2008; Kellett et al., 2003) and correlated with the Beck Depression Inventory, r = .71 and r = .77, in two other studies (Stukenberg, Dura & Kiecolt-Glaser, 1990; Prinz et al., 2013). Two studies validated BSI Depression against either DSM-III or DSM-IV-TR major depression (Stukenberg, Dura & Kiecolt-Glaser, 1990; Johnson et al., 2008). ROC analyses reported area under the curve as 0.83 in community dwelling older adults, but a more modest 0.65 among psychiatric inpatients.

\n

For copyright reasons, the LISS dataset only provided the normative category of each respondent and not the responses to individual questions. These normative categories of BSI depression were: 1 = very low, 2 = low, 3 = below average, 4 = average, and 5 = above average, 6 = high, 7 = very high. We dichotomized them into low (very low to above average) and elevated (high to very high). The cut-off was chosen because it resulted in a better approximation of the prevalence of depression in the Netherlands (Bijl, Ravelli & van Zessen, 1998) compared to alternative cut-offs.

Covariates

\n

We controlled for possible confounders including chronic health conditions, income, marital status, age, and gender. Chronic conditions were assessed with the single question, “Do you suffer from any kind of long-standing disease, affliction or handicap, or do you suffer from the consequences of an accident?” Income was assessed using a monthly personal gross income with five categories: 0–500, 501–1500, 1501–2500, 2501–3500, and 3501 and higher Euros per month. Marital status was used as an index of social support and was categorized into 1 = Married; 2 = Separated/Divorced/Widowed; 3 = Not Married. All covariates were measured between December 2007 and January 2008.

Statistical analysis

\n

We first compared demographic characteristics of attenders and non-attenders at baseline. To examine whether elevated depressive symptoms predicted subsequent decreased attendance, we crosstabulated dichotomized attendance with level of symptoms among attenders, for each religion follow-up year. Chi-square tests of association were performed. To examine change longitudinally and control for confounders, we created a multinomial logistic regression model among attenders. Relative risk ratios of decreasing or increasing attendance over maintaining attendance were calculated.

\n

To examine if non-attenders start attending services after elevated depression, a binary logistic regression model was created with change in attendance (0 = no change; 1 = attended) as dependent variable. We entered the covariates in all regression models to control for confounding and robust standard errors were calculated to account for correlated errors in repeated observations.

Missing data

\n

Missing values for the covariates at baseline did not differ between attenders and non-attenders. To examine whether our results would be biased by differential attrition between attenders and non-attenders, we performed multiple imputation on our dependent and predictor variables using a set of 15 socio-demographic and psychological variables assessed at baseline. (These variables are available from the authors upon request.) The imputation procedure was implemented using REALCOM-IMPUTE (Carpenter, Goldstein & Kenward, 2011) software and 10 imputed datasets were generated, which were then analyzed using Stata 12.1. Our regression models were then repeated using the multiply imputed data.

" + ] + }, + "results_html": { + "value": [ + "

Results

\n

Religious attenders were more likely to be female, older, and married as compared to non-attenders. Attenders and non-attenders were similar in self-rated health, in the proportion having chronic conditions, and in the distribution of BSI Depression normative scores. From March to September 2008, 491 individuals developed elevated depression. The chi-square tests in each of the four follow-up waves showed no association between depression status and subsequent decrease in attendance with one exception. In 2012, those with elevated BSI Depression among baseline attenders were more likely to keep or increase their 2008 attendance levels. In post-hoc analysis, we repeated the change in attendance analysis by depression category stratified first by gender and then by age category. In gender-stratified analysis, no associations were found in each attendance follow-up. In age-stratified analysis, no associations were found in the first two years after depression assessments took place. In both R3 and R4, those 48 years old and above and with elevated depression were more likely to maintain or increase attendance levels (both p’s < .05). (See Table 2. The tables stratified by gender or age category are available from the authors by request.)

\n
\nTable 2:
Change in attendance by depression status.
\nBSI depression vs changes in attendance in the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Service attenders at R1Non-attenders of service at R1
\n 2009 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2009 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase371 (73)184 (78)2.31.13Same394 (67)177 (69).47.49
Decrease139 (27)52 (22)Increase194 (33)78 (31)
\n 2010 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2010 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase392 (77)191 (81)1.56.21Same348 (59)154 (60).11.74
Decrease118 (23)45 (19)Increase240 (41)101 (40)
\n 2011 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2011 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase390 (76)189 (80)1.22.27Same315 (54)142 (56).32.57
Decrease120 (24)47 (20)Increase273 (46)113 (44)
\n 2012 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2012 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase367 (72)189 (80)5.61\n .02\n Same291 (49)136 (53)1.05.31
Decrease143 (28)47 (20)Increase297 (50)119 (47)
\n\n
\n

Notes:

\n

If the individual had a norm-referenced score of “high” or “very high” in any of the three assessments in 2008, the individual was assigned to elevated and otherwise to unelevated.

\n

\n

\n
BSI
\n

Brief Symptom Inventory

\n
\n

\n

In multinomial logistic regression modeling, elevated symptoms predicted lower probability of a decrease in attendance (relative risk ratio = 0.55, 95% CI [0.38–0.79]) relative to baseline attendance levels among attenders (see Table 3 and Fig. 2). Among non-attenders, elevated symptoms were unrelated to a subsequent increase in attendance with one exception. The estimates were not materially different when the models were run using multiply imputed data.

\n
\nTable 3:
Regression models.
\nLogistic models of change in religious attendance levels over 5 years from the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Religious attenders at baselineNon-attenders at baseline
Model 1a:
complete cases
Model 1Aa:
multiply imputed data
(10 imputations)
Model 2a:
complete cases
Model 2Aa:
multiply imputed data
(10 imputations)
Relative risk ratio
(95% CI)
Relative risk ratio
(95% CI)
Odds ratio
(95% CI)
Odds ratio
(95% CI)
\n Outcome: decreased attendance\n
Predictor: elevated depression\n 0.55 (0.38–0.79)\n \n **\n \n \n 0.58 (0.41–0.83)\n \n **\n \n N/AN/A
\n Outcome: same attendance\n \n (Reference category)\n \n (Reference category)\n
\n Outcome: increased attendance\n
Predictor: elevated depression0.90 (0.68–1.19)1.27 (0.78–2.07)0.93 (0.73–1.18)1.10 (0.55–2.21)
\n\n
\n

Notes:

\n
\naIn these models, the following covariates have been controlled: existing chronic condition, gender, marital status, income, and age.\n
\n
\n**p values: .01.\n
\n
\"Probabilities.\"
\n

\nFigure 2: Probabilities.

\nPredicted probabilities of a decrease, same, and increase in religious attendance (95% CI).
" + ] + }, + "discussion_html": { + "value": [ + "

Discussion

\n

The main finding in this study is that elevated BSI depression does not cause a subsequent decrease in attendance. On the contrary, elevated BSI depression predicts same or increased levels of attendance as compared with prior to elevated BSI depression. None of our results across three analytical strategies showed a decrease in attendance. Although unstratified analyses did not yield a significant association, gender and age-stratified results indicated an association of continued or increased attendance with elevated symptoms. We do not interpret this association because other variables could possibly explain the association. The multinomial logistic model among attenders, with covariates controlled for, indicated that elevated symptoms predicted same or increased attendance. As a secondary finding, non-attenders were not likely to seek recourse in religion by starting to attend services.

\n

Our main finding addresses the issue of selection bias in studies of religious attendance and mental health. To recap, when depressed individuals stop attending services, the apparent protection afforded by attendance would be inflated. This selection bias would be most pronounced in cross-sectional studies. In longitudinal epidemiologic studies, bias remains an issue because there might be differential attrition in attendance by depression status. Since we found that attenders who develop elevated symptoms become less likely to drop out of worship, then they might in effect be overrepresented among churchgoers. Therefore, the protective effect of religious attendance might in fact be underestimated, contrary to the reverse causation argument.

\n

Religious individuals turn to their faith in times of distress as a means of coping (Brown et al., 2004; Bussing, Ostermann & Koenig, 2007; Ironson, Stuetzle & Fletcher, 2006). Religious worship is a source of social support and allows individuals to cope with life-threatening conditions by providing “medicine for the spirit” (Cummings & Pargament, 2010). A longitudinal study (Li & Ferraro, 2005) on depression and volunteering among older adults reported that elevated depression at wave 2 predicted seeking out volunteering opportunities at wave 3. This was explained as a compensatory mechanism to alleviate negative affect, via social integration. These older adults had physical health problems in addition to depression and the physical health problems were the operative barriers. Consistent with this finding, Chen & Koenig (2006) reported that in elderly, medically ill individuals, an increased severity of physical illness predicted a decrease in organizational religiousness. Importantly, the association was completely mediated by physical activity limitations. Together with our own results, these suggest that it is not depression per se that causes a disengagement from participation in religious service. In effect, reverse causation and non-random attrition might be more relevant to studies examining religious attendance and physical health.

\n

The null association of elevated depression with subsequent attendance among non-attenders indicates that non-attenders do not start attending in the face of adversity. By contrast, Ferraro & Kelley-Moore (2000) reported that depression, cancer, and chronic conditions lead to consolation-seeking even among those with no religious affiliation. The two points of view can be reconciled because attendance is not necessary for consolation-seeking. The need to find meaning in illness is shared by believers and non-believers who may turn to nature, arts, music, and relationships (Burnard, 1988).

\n

An intriguing study (Farias et al., 2013) reported that rowers about to enter a competition reported greater belief in science as compared with those in a training session. The authors concluded that affirming one’s secular worldview serves a similar function as religious faith in moments of stress or existential anxiety. Hence, affiliated individuals cope by means of religion while non-attending ones seek support and meaning elsewhere. It appears that depressive symptoms are not a strong driver of entry into or exit from the churchgoing demographic. More empirical research is needed to validate this interpretation.

\n

Our study has several important limitations. First, we relied on the depression subscale of the BSI to assess depressive symptoms. It has been argued that although the global BSI scale is a valid measure of distress, it is not intended to screen for particular psychiatric disorders (Asner-Self, Schreiber & Marotta, 2006). We set the BSI cut-off for depression at “high” or “very high” but there is no way to tell whether this is in concordance with clinically diagnosed depression. We therefore allow for the possibility that the depressed group that we studied might differ from a group with formally diagnosed major depression (Sareen et al., 2013). Secondly, there were no assessments of depression from 2009 to 2012—the period during which religious attendance was compared to initial attendance. As such, all religious attendance changes were indexed to depression levels in 2008 only. We cannot rule out the possibility that attendance levels after 2008 were related to unmeasured elevated symptoms after 2008. Third, the sample that we worked with was restricted to LISS participants who responded to both religion and mental health modules and might not be representative of the Dutch national population. Fourth, while we have ruled out sampling bias in terms of attrition in attendance, we could not address whether personality traits such as greater resilience to depression characterized attenders in the first place. Finally, other health-related reasons, including physical disability, might be correlated with depression and could cause selection bias. This is beyond the scope of our study. The major strength of this study was that depression assessments were proximal to those of religion. Our sample also consisted of a small fraction (5%) of late adolescents and is less affected by the well-reported decline in religious attendance in adolescence.

\n

Within the limitations of our study, we conclude that elevated depressive symptoms do not cause religiously affiliated individuals to subsequently decrease attendance at religious services.

" + ] + }, + "conclusion_html": { + "value": [ + + ] + }, + "author_contrib_html": { + "value": [ + + ] + }, + "competing_interests_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\nArnett JJ. 2000. Emerging adulthood—a theory of development from the late teens through the twenties. American Psychologist 55:469-480 \n", + "\nAsner-Self KK, Schreiber JB, Marotta SA. 2006. A cross-cultural analysis of the Brief Symptom Inventory-18. Cultural Diversity & Ethnic Minority Psychology 12:367-375 \n", + "\nBaetz M, Griffin R, Bowen R, Koenig HG, Marcoux E. 2004. The association between spiritual and religious involvement and depressive symptoms in a Canadian population. Journal of Nervous and Mental Disease 192:818-822 \n", + "\nBalbuena L, Baetz M, Bowen R. 2013. Religious attendance, spirituality, and major depression in Canada: a 14-year follow-up study. Canadian Journal of Psychiatry 58:225-232 \n", + "\nBenda BB, Corwyn RF. 1997. A test of a model with reciprocal effects between religiosity and various forms of delinquency using 2-stage least squares regression. Journal of Social Service Research 22:27-52 \n", + "\nBijl RV, Ravelli A, van Zessen G. 1998. Prevalence of psychiatric disorder in the general population: results of the Netherlands Mental Health Survey and Incidence Study (NEMESIS) Social Psychiatry and Psychiatric Epidemiology 33:587-595 \n", + "\nBoulet J, Boss M. 1991. Reliability and validity of the Brief Symptom Inventory. Psychological Assessment: A Journal of Consulting & Clinical Psychology 3:433-437 \n", + "\nBrown SL, Nesse RM, House JS, Utz RL. 2004. Religion and emotional compensation: results from a prospective study of widowhood. Personality and Social Psychology Bulletin 30:1165-1174 \n", + "\nBurnard P. 1988. The spiritual needs of atheists and agnostics. Professional Nurse 4:130-132 \n", + "\nBussing A, Ostermann T, Koenig HG. 2007. Relevance of religion and spirituality in German patients with chronic diseases. International Journal of Psychiatry in Medicine 37:39-57 \n", + "\nCarpenter JR, Goldstein H, Kenward MG. 2011. REALCOM-IMPUTE software for multilevel multiple imputation with mixed response types. Journal of Statistical Software 45:1-14 \n", + "\nChen YY, Koenig HG. 2006. Do people turn to religion in times of stress?: an examination of change in religiousness among elderly, medically ill patients. Journal of Nervous and Mental Disease 194:114-120 \n", + "\nConnor P. 2009. Immigrant religiosity in Canada: multiple trajectories. International Migration & Integration 10:159-175 \n", + "\nCummings JP, Pargament KI. 2010. Medicine for the spirit: religious coping in individuals with medical conditions. Religions 1:28-53 \n", + "\nDerogatis LR. 1975. Brief Symptom Inventory. Baltimore: Clinical Psychometric Research. \n", + "\nDerogatis LR, Melisaratos N. 1983. The Brief Symptom Inventory—an introductory report. Psychological Medicine 13:595-605 \n", + "\nEllison CG, Flannelly KJ. 2009. Religious involvement and risk of major depression in a prospective nationwide study of African American adults. Journal of Nervous and Mental Disease 197:568-573 \n", + "\nFarias M, Newheiser AK, Kahane G, de Toledo Z. 2013. Scientific faith: belief in science increases in the face of stress and existential anxiety. Journal of Experimental Social Psychology 49:1210-1213 \n", + "\nFerraro KF, Kelley-Moore JA. 2000. Religious consolation among men and women: do health problems spur seeking? Journal for the Scientific Study of Religion 39:220-234 \n", + "\nFontana A, Rosenheck R. 2004. Trauma, change in strength of religious faith, and mental health service use among veterans treated for PTSD. Journal of Nervous and Mental Disease 192:579-584 \n", + "\nHayward RD, Owen AD, Koenig HG, Steffens DC, Payne ME. 2012. Religion and the presence and severity of depression in older adults. American Journal of Geriatric Psychiatry 20:188-192 \n", + "\nHorowitz JL, Garber J. 2003. Relation of intelligence and religiosity to depressive disorders in offspring of depressed and nondepressed mothers. Journal of the American Academy of Child and Adolescent Psychiatry 42:578-586 \n", + "\nIronson G, Stuetzle R, Fletcher MA. 2006. An increase in religiousness/spirituality occurs after HIV diagnosis and predicts slower disease progression over 4 years in people with HIV. Journal of General Internal Medicine 21(Suppl 5):S62-S68 \n", + "\nJohnson ME, Chipp CL, Brems C, Neal DB. 2008. Receiver operating characteristics for the brief symptom inventory depression, paranoid ideation, and psychoticism scales in a large sample of clinical inpatients. Psychological Reports 102:695-705 \n", + "\nKellett S, Beail N, Newman DW, Frankish P. 2003. Utility of the brief symptom inventory in the assessment of psychological distress. Journal of Applied Research in Intellectual Disabilities 16:127-134 \n", + "\nLi YQ, Ferraro KF. 2005. Volunteering and depression in later life: social benefit or selection processes? Journal of Health and Social Behavior 46:68-84 \n", + "\nLodi-Smith J, Roberts BW. 2007. Social investment and personality: a meta-analysis of the relationship of personality traits to investment in work, family, religion, and volunteerism. Personality and Social Psychology Review 11:68-86 \n", + "\nMaselko J, Gilman SE, Buka S. 2009. Religious service attendance and spiritual well-being are differentially associated with risk of major depression. Psychological Medicine 39:1009-1017 \n", + "\nMaselko J, Hayward RD, Hanlon A, Buka S, Meador K. 2012. Religious service attendance and major depression: a case of reverse causality? American Journal of Epidemiology 175:576-583 \n", + "\nMiller L, Weissman M, Gur M, Greenwald S. 2002. Adult religiousness and history of childhood depression: eleven-year follow-up study. Journal of Nervous and Mental Disease 190:86-93 \n", + "\nMiller L, Wickramaratne P, Gameroff MJ, Sage M, Tenke CE, Weissman MM. 2012. Religiosity and major depression in adults at high risk: a ten-year prospective study. American Journal of Psychiatry 169:89-94 \n", + "\nPargament KI. 1997. The psychology of religion and coping: theory, research, practice. New York, London: Guilford Press. \n", + "\nPrinz U, Nutzinger DO, Schulz H, Petermann F, Braukhaus C, Andreas S. 2013. Comparative psychometric analyses of the SCL-90-R and its short versions in patients with affective disorders. BMC Psychiatry 13:104 \n", + "\nSareen J, Henriksen CA, Stein MB, Afifi TO, Lix LM, Enns MW. 2013. Common mental disorder diagnosis and need for treatment are not the same: findings from a population-based longitudinal survey. Psychological Medicine 43:1941-1951 \n", + "\nScherpenzeel A. 2011. Data collection in a probability-based internet panel: how the LISS panel was built and how it can be used. Bulletin of Sociological Methodology 109:56-61 \n", + "\nSchnittker J. 2001. When is faith enough? The effects of religious involvement on depression. Journal for the Scientific Study of Religion 40:393-411 \n", + "\nStukenberg KW, Dura JR, Kiecolt-Glaser JK. 1990. Depression screening scale validation in an elderly, community-dwelling population. Psychological Assessment: A Journal of Consulting & Clinical Psychology 2:134-138 \n", + "\nTaylor RJ, Chatters LM, Nguyen AW. 2013. Religious participation and DSM IV major depressive disorder among Black Caribbeans in the United States. Journal of Immigrant and Minority Health 15:903-909 \n", + "\nThornton A, Axinn WG, Hill DH. 1992. Reciprocal effects of religiosity, cohabitation, and marriage. American Journal of Sociology 98:628-651 \n", + "\nUecker JE, Regnerus MD, Vaaler ML. 2007. Losing my religion: the social sources of religious decline in early adulthood. Social Forces 85:1667-1692 \n" + ] + }, + "figures_html": { + "value": [ + "
\"Subjects.\"
\n

\nFigure 1: Subjects.

\n(A) LISS datasets used and participant flowchart; (B) schedule of religion and depression assessments.
", + "
\"Probabilities.\"
\n

\nFigure 2: Probabilities.

\nPredicted probabilities of a decrease, same, and increase in religious attendance (95% CI).
" + ] + }, + "tables_html": { + "value": [ + "
\nTable 1:
Comparison of attenders and non-attenders.
\nCharacteristics of Dutch individuals who responded to mental health (Wave 1) and religious attendance (Wave 1–Jan 2008) of the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands (n = 1, 673).\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Service attenders at R1Non-attenders of service at R1\np of the difference
\n n\n 786887
Mean age (sd)49.60 (18.22)45.90 (17.21)<.001
Civil status
\n Unmarried\n 323 (41)443 (50)<.001
\n Married\n 463 (59)444 (50)
Monthly income
\n Low income (0–500 € per month)\n 77 (10)65 (7).07
\n Not low income (>500 € per month)\n 709 (90)822 (93)
Mean self-rated health (sd)*\n3.12 (0.76)3.13 (0.76).68
With a chronic condition
\n Yes\n 232 (32)227 (27)
\n No\n 497 (68)600 (73).06
Baseline distribution of BSI depression normative scores
\n Very low\n 0 (0)0 (0).38
\n Low\n 0 (0)0 (0)
\n Below average\n 113 (14)145 (16)
\n Average\n 196 (25)234 (26)
\n Above average\n 284 (36)324 (37)
\n High\n 168 (21)162 (18)
\n Very high\n 25 (3)22 (2)
\n\n
\n

Notes:

\n

Figures in this table are n (%) except for age and self-rated health which are mean (sd).

\n
\n*Rated on a scale of 1–5, with higher scores indicating better health.\n
\n
", + "
\nTable 2:
Change in attendance by depression status.
\nBSI depression vs changes in attendance in the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Service attenders at R1Non-attenders of service at R1
\n 2009 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2009 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase371 (73)184 (78)2.31.13Same394 (67)177 (69).47.49
Decrease139 (27)52 (22)Increase194 (33)78 (31)
\n 2010 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2010 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase392 (77)191 (81)1.56.21Same348 (59)154 (60).11.74
Decrease118 (23)45 (19)Increase240 (41)101 (40)
\n 2011 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2011 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase390 (76)189 (80)1.22.27Same315 (54)142 (56).32.57
Decrease120 (24)47 (20)Increase273 (46)113 (44)
\n 2012 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2012 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase367 (72)189 (80)5.61\n .02\n Same291 (49)136 (53)1.05.31
Decrease143 (28)47 (20)Increase297 (50)119 (47)
\n\n
\n

Notes:

\n

If the individual had a norm-referenced score of “high” or “very high” in any of the three assessments in 2008, the individual was assigned to elevated and otherwise to unelevated.

\n

\n

\n
BSI
\n

Brief Symptom Inventory

\n
\n

\n
", + "
\nTable 3:
Regression models.
\nLogistic models of change in religious attendance levels over 5 years from the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Religious attenders at baselineNon-attenders at baseline
Model 1a:
complete cases
Model 1Aa:
multiply imputed data
(10 imputations)
Model 2a:
complete cases
Model 2Aa:
multiply imputed data
(10 imputations)
Relative risk ratio
(95% CI)
Relative risk ratio
(95% CI)
Odds ratio
(95% CI)
Odds ratio
(95% CI)
\n Outcome: decreased attendance\n
Predictor: elevated depression\n 0.55 (0.38–0.79)\n \n **\n \n \n 0.58 (0.41–0.83)\n \n **\n \n N/AN/A
\n Outcome: same attendance\n \n (Reference category)\n \n (Reference category)\n
\n Outcome: increased attendance\n
Predictor: elevated depression0.90 (0.68–1.19)1.27 (0.78–2.07)0.93 (0.73–1.18)1.10 (0.55–2.21)
\n\n
\n

Notes:

\n
\naIn these models, the following covariates have been controlled: existing chronic condition, gender, marital status, income, and age.\n
\n
\n**p values: .01.\n
\n
" ] }, "fulltext_html": { @@ -526,23 +1068,17 @@ "/articles/311.xml" ] }, - "supplementary_material": { + "supplementary_file": { "value": [ ] }, - "figure": { + "figures_image": { "value": [ "https://dfzljdn9uc3pi.cloudfront.net/2014/311/1/fig-1-full.png", "https://dfzljdn9uc3pi.cloudfront.net/2014/311/1/fig-2-full.png" ] }, - "figure_caption": { - "value": [ - "\nFigure 1: Subjects.\n(A) LISS datasets used and participant flowchart; (B) schedule of religion and depression assessments.\n  Download full-size image\nDOI: 10.7717/peerj.311/fig-1\n\n", - "\nFigure 2: Probabilities.\nPredicted probabilities of a decrease, same, and increase in religious attendance (95% CI).\n  Download full-size image\nDOI: 10.7717/peerj.311/fig-2\n\n" - ] - }, "license": { "value": [ @@ -550,7 +1086,8 @@ }, "copyright": { "value": [ - + "2014", + "Balbuena et al." ] }, "file_hashes": [ @@ -561,7 +1098,7 @@ "fig-2-full.png": "b6a99fff0a72af9fde1e550f80d43799" }, { - "fulltext.html": "f295d3b2bedfd76a24ce69bfb9d40b79" + "fulltext.html": "f11beaa73560a0396f103442fe9132eb" }, { "fulltext.pdf": "8aa4a538c24c0f3bfcc8b9fa5cd63d7c" @@ -577,17 +1114,27 @@ "PeerJ Inc." ] }, - "journal": { + "journal_name": { "value": [ "PeerJ" ] }, + "journal_issn": { + "value": [ + "2167-8359" + ] + }, "title": { "value": [ "Mutation analysis of the SLC26A4, FOXI1 and KCNJ10 genes in individuals with congenital hearing loss" ] }, - "authors": { + "keywords": { + "value": [ + "Pendred; MLPA; DFNB4; \n SLC26A4\n ; FOXI1 and KCNJ10; Genotyping; Genetics; SNHL" + ] + }, + "author_name": { "value": [ "Lynn M. Pique", "Marie-Luise Brennan", @@ -597,11 +1144,37 @@ "Iris Schrijver" ] }, - "date": { + "author_institution": { + "value": [ + "Department of Pathology, Stanford University Medical Center, Stanford, CA, USA", + "Department of Pediatrics, Stanford University Medical Center, Stanford, CA, USA", + "Life Technologies, South San Francisco, CA, USA", + "Molecular Genetics, Center for Genetic Testing at Saint Francis Hospital, Tulsa, OK, USA", + "Divisions of Human Genetics and Otolaryngology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA", + "Department of Pathology, Stanford University Medical Center, Stanford, CA, USA", + "Department of Pediatrics, Stanford University Medical Center, Stanford, CA, USA" + ] + }, + "editor_name": { + "value": [ + "Paula Soares" + ] + }, + "date_published": { "value": [ "2014-05-08" ] }, + "date_accepted": { + "value": [ + "2014-04-25" + ] + }, + "date_submitted": { + "value": [ + "2013-10-09" + ] + }, "doi": { "value": [ "10.7717/peerj.384" @@ -622,14 +1195,106 @@ "e384" ] }, - "description": { + "abstract": { "value": [ "Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype." ] }, - "abstract": { + "abstract_html": { "value": [ - "Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype." + "

Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4–6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype.

" + ] + }, + "introduction_html": { + "value": [ + "

Introduction

\n

Hearing loss is a common congenital defect. The estimated incidence of permanent hearing loss at birth, defined as a sensorineural loss of 35 dB or more in the U.S., is one in 500 newborns (Morton & Nance, 2006). The origins of hearing loss may be genetic, environmental or multifactorial, with at least 50% of prelingual hearing loss in industrialized countries attributable to genetic abnormalities (Vele & Schrijver, 2008). Approximately 70% of prelingual hearing loss is non-syndromic; the remaining 30% is accompanied by additional clinical findings and is considered syndromic (Hilgert, Smith & Van Camp, 2009). Inheritance of hearing loss can be recessive, dominant, X-linked or mitochondrial, with autosomal recessive inheritance constituting roughly 80% of non-syndromic sensorineural hearing loss (SNHL). Mutations of a single gene, GJB2 (OMIM *121011), which encodes the connexin 26 protein, account for the majority of autosomal recessive non-syndromic SNHL (Kenneson, Van Naarden Braun & Boyle, 2002). Mutations of the SLC26A4 gene (OMIM *605646) are the second most frequent cause of autosomal recessive non-syndromic SNHL (Hilgert, Smith & Van Camp, 2009) and produce a phenotypic spectrum of hearing loss disorders encompassing both Pendred syndrome (PDS; OMIM #274600) and DFNB4 (OMIM #600791) (Everett et al., 1997; Li et al., 1998). SLC26A4 is composed of 21 exons and encodes the 780 amino acid transmembrane anion transporter protein pendrin (Everett et al., 1997; Everett et al., 1999; Royaux et al., 2000; Royaux et al., 2001), which plays a key role in maintaining the endocochlear potential (Everett et al., 1999; Royaux et al., 2003).

\n

PDS and DFNB4 are typically characterized by congenital, bilateral sensorineural hearing loss which can be progressive and is usually severe to profound. There is considerable variability of symptoms. Vestibular dysfunction as well as non-pathognomonic temporal bone abnormalities, in particular enlargement of the vestibular aqueduct (EVA), can also be present in these conditions. DFNB4, also known as non-syndromic enlarged vestibular aqueduct (NS-EVA), is not associated with other clinical findings. PDS, in contrast, classically manifests additional symptoms such as the development of an incompletely penetrant euthyroid goiter, which can be present at birth but is more likely to develop in late childhood to early adulthood. PDS is also typically accompanied by Mondini dysplasia, a reduction of the number of turns of the cochlea combined with the characteristic bilateral EVA (Schrijver & Gardner, 2006). Although the Mondini malformation can be used as a criterion for diagnosis, it is thought to be clinically heterogeneous and it remains uncertain what proportion of Mondini malformations are linked to Pendred syndrome (Reardon et al., 1997). Other, less well defined, temporal bone abnormalities can (and typically are) seen in those individuals lacking Mondini dysplasia.

\n

PDS was originally estimated to be responsible for 7.5% of hereditary hearing loss cases (Fraser, 1965) but the actual incidence has not been determined due to difficulties inherent in diagnosing PDS, the degree of phenotypic variability (i.e., isolated hearing loss versus multisystem involvement), the frequently late onset and reduced penetrance of the goiter, and the lack of pathognomonic findings (Blons et al., 2004). Nevertheless, PDS is thought to be one of the most common forms of syndromic deafness and mutations of SLC26A4 were reported to be the second most frequent cause of autosomal recessive non-syndromic sensorineural hearing loss worldwide (Hilgert, Smith & Van Camp, 2009).

\n

More than 260 mutations in the SLC26A4 gene have been identified to date (http://www.hgmd.cf.ac.uk/ac/gene.php?gene=SLC26A4), including deletions spanning multiple exons (Park et al., 2003; Hu et al., 2007; Pera et al., 2008a; Anwar et al., 2009; Siem et al., 2010). Until recently, however, individuals with SNHL and possible PDS or DFNB4 were not systematically analyzed for the presence of multiexon deletions and duplications. Multiplex Ligation-dependent Probe Amplification (MLPA) analysis of 37 probands in a Scandinavian cohort of 109 patients suspected to have PDS/DFNB4 identified a homozygous SLC26A4 deletion of exons 4–6 in one individual, indicating that intragenic deletions and duplications may contribute to the phenotype (Rendtorff et al., 2013). Mutations of the FOXI1 and the KCNJ10 genes have also been associated with PDS/DFNB4 and were reported to be digenically inherited with heterozygous mutations in SLC26A4 (Yang et al., 2007; Yang et al., 2009). FOXI1 encodes a transcription factor that binds to the promoter region of SLC26A4 and is responsible for upstream regulation of the gene. KCNJ10 encodes an inwardly rectifying potassium (K+) channel that is involved in generating and maintaining the endocochlear potential (Marcus et al., 2002). Intragenic deletions of SLC26A4 as well as digenic mutations with either FOXI1 or KCNJ10 have all been implicated in PDS/DFNB4 pathogenesis but the extent of their involvement as well as their clinical relevance for SNHL remains unclear.

\n

We investigated the contribution of intragenic SLC26A4 copy number changes by performing MLPA analysis on DNA samples from 107 probands with congenital SNHL who had only one identified SLC26A4 mutation. Although it has been recommended to consider SLC26A4 mutation analysis if there is progressive hearing loss, goiter, Mondini dysplasia, or EVA (Hilgert, Smith & Van Camp, 2009), the clinical testing strategy often adheres to the following algorithm: For individuals with congenital hearing loss that is consistent with autosomal recessive inheritance and that appears non-syndromic, diagnostic testing typically starts with GJB2 sequence analysis. If clinical testing does not identify two pathogenic mutations, then inner ear imaging studies by MRI or CT for temporal bone anomalies may be performed. However, clinical testing of SLC26A4 without MRI or CT is also considered acceptable because mutations in this gene are thought to be a frequent cause of SNHL (Alasti, Van Camp & Smith, 1998, updated 2012). This approach to the clinical work-up is quite common in the U.S., in part because the same DNA specimen can be used for both molecular tests sequentially and in part because imaging studies in the pediatric population can be challenging. As a result, our patients were selected based on the presence of congenital SNHL compatible with autosomal recessive inheritance, absence of two hearing loss-associated GJB2 mutations, and the presence of only one known mutation in SLC26A4. In these individuals, we performed MLPA of SLC26A4 and in a subset we also sequenced the coding regions and splice sites of FOXI1 and KCNJ10 to evaluate alternative etiologies.

" + ] + }, + "methods_html": { + "value": [ + "

Materials and Methods

\n

Study subjects

\n

A total of 107 individuals participated in this study. Participants provided written informed consent as appropriate. All were enrolled with IRB approval from the Stanford University Administrative Panels for the Protection of Human Subjects (IRB Approval Numbers IRB-14011 and IRB-8353). Participants included individuals from Stanford University Medical Center (n = 60, Stanford, CA), the Center for Genetic Testing at Saint Francis Hospital (n = 30, Tulsa, OK) and Cincinnati Children’s Hospital Medical Center (n = 17, Cincinnati, OH). All participants were probands presenting with congenital SNHL who prior to enrollment, had all received GJB2 testing and been sequenced for mutations in the exons, splice sites and promoter region of the SLC26A4 gene (GenBank: NC_000007.13) as part of routine clinical care. Patients who did not have two pathogenic GJB2 mutations and who had only one identified SLC26A4 mutation were then eligible for additional genetic testing by MLPA in an effort to identify a second disease-causing mutation. FOXI1 (GenBank: NG_012068.1) and KCNJ10 (GenBank: NG_016411.1) were also sequenced in a subset of the Stanford patient group (n = 29/60) for whom sample was available.

\n

Because imaging analysis is not routinely ordered on children with phenotypically non-syndromic SNHL prior to SLC26A4 sequencing, imaging analysis results were available for only a portion of the subjects (n = 46/107; 43%) and indicated the presence of EVA in 56% (n = 26/46) and Mondini malformation in none of the probands. Vestibular dysfunction complaints were noted in only one of 54 participants for whom this information was reported. Thyroid manifestations were reported in none of the Stanford probands for whom this information was available (n = 0/37), including five individuals older than 13 years of age.

Detection and characterization of intragenic rearrangements

\n

Genomic DNA samples extracted from peripheral blood by standard methods were analyzed for copy number mutations by MLPA, using the SALSA MLPA kit P280 Pendred-SLC26A4 (MRC-Holland, Amsterdam, the Netherlands) according to the manufacturer’s protocol. Capillary electrophoresis of PCR products was performed using either an ABI 310 or an ABI 3500 Genetic Analyzer (Life Technologies, Grand Island, NY, USA) and the resulting data were analyzed using GeneMarker 1.51 software (SoftGenetics, LLC., State College, PA, USA).

\n

For breakpoint analysis in the single proband with an identified SLC26A4 deletion, PCR products were electrophoresed on an agarose gel and the 494 base pair (bp) fragment corresponding to the deletion was excised and purified using the QIAquick Gel Extraction Kit (Qiagen, Germantown, MD). The amplicon was then sequenced on an ABI 3730xl Genetic Analyzer (Life Technologies, Grand Island, NY, USA) to confirm the breakpoints of the deletion.

\nFOXI1 and KCNJ10 sequencing

\n

Almost half (n = 29/60) of the Stanford University proband samples had direct DNA sequencing of the coding exons, including intron/exon boundaries ±20 bp into the introns, of FOXI1 and KCNJ10. Primers were designed to amplify and sequence exons 1 and 2 of FOXI1 and exon 2 of KCNJ10 (Table 1). Amplicons were purified using the QIAquick PCR Purification Kit (Qiagen, Germantown, MD) and then sequenced on an ABI 3730xl Genetic Analyzer (Life Technologies, Grand Island, NY, USA). Sequences were compared against either the FOXI1 (GenBank: NG_012068.1) or the KCNJ10 (GenBank: NG_016411.1) reference sequence using Mutation Surveyor 2.51 software (SoftGenetics, LLC., State College, PA, USA). Nonsynonymous sequence variants detected in the coding regions of the FOXI1 and KCNJ10 genes were further analyzed using the mutation interpretation tools SIFT (Sorting Intolerant From Tolerant, http://sift.jcvi.org/) and PolyPhen-2 (Polymorphism Phenotyping v2, http://genetics.bwh.harvard.edu/pph2/), which predict the effect of an amino acid substitution on protein function.

\n
\nTable 1:
Primers used for the amplification of FOXI1 and KCNJ10.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GeneExonPrimer namePrimer sequence (5′ to 3′)\n T\n \n a\n \n
\n FOXI1\n 1FOXI1-1FTGAGCACCTGTCAGGGGCAG61
\n FOXI1\n 1FOXI1-1RGAACTTTCTAGAATGGGGTCTTG61
\n FOXI1\n 1FOXI1-1RintCCCTGTGGGTGGAAGAAGT55
\n FOXI1\n 2FOXI1-2FGACAATAAGGAGGAACAGAAG55
\n FOXI1\n 2FOXI1-2RGCATGGAGGACCTCTACTG55
\n KCNJ10\n 2KCNJ10-2aFGTTAATTCCTCCCTCCCATGG59
\n KCNJ10\n 2KCNJ10-2aRGTTCTCCCCTTCCTTGGTTTG59
\n KCNJ10\n 2KCNJ10-2bFGAGACCATTCGTTTCAGCCAG59
\n KCNJ10\n 2KCNJ10-2bRAAGAAGAGGGAGTGGAGGATG59
\n
" + ] + }, + "results_html": { + "value": [ + "

Results

\n

In order to assess the potential diagnostic benefits of deletion/duplication analysis of the SLC26A4 gene, we performed MLPA on genomic DNA samples from 107 patients with congenital hearing loss in whom only one SLC26A4 mutation had been found by sequencing. Only one individual, PDS41, (1/107 unknown alleles; 0.93%) had MLPA results indicative of such a copy number variation—a putative heterozygous deletion spanning exons 4–6 of the gene (Fig. 1). Because deletions of these same SLC26A4 exons were previously described in a Spanish patient (Pera et al., 2008a) and in two Norwegian patients of Lebanese descent (Siem et al., 2010; Rendtorff et al., 2013), we investigated the possibility that our MLPA assay had detected a known rearrangement in our proband. Flanking PCR primers were designed to analyze the breakpoints of the deletion (PDS IVS3 Forward: 5′-ACAATGTCCATGCCACAACC-3′ and PDS IVS6 Reverse: 5′-ACAGAGACCATTACATACATAC-3′). A duplex reaction including both the breakpoint primers and a set of control primers for the amplification of exon 4 (PDS Ex4 Forward: 5′-AGGCAAAGTCATAAGTGGAAC-3′ and PDS Ex4 Reverse: 5′-ACCTAATAGAGGTATAATGCAC-3′) resulted in two products: a 494 bp fragment corresponding to the deletion and a 289 bp fragment amplified from the control primers (data not shown). The presence of the 289 bp amplicon indicated that the deletion was indeed heterozygous. Subsequent sequencing of the 494 bp amplicon confirmed the presence of g.8091T-22145Cdel (Fig. 1). This deletion removes 14,053 bp from the SLC26A4 gene, disrupting the open reading frame and truncating the protein at amino acid residue 105 in the first transmembrane domain.

\n
\"Identification
\n

\nFigure 1: Identification of the heterozygous SLC26A4 deletion g.8091T-22145Cdel in subject PDS41.

\n(A) The SLC26A4 MLPA probe mix includes probes for the 21 SLC26A4 exons, 14 reference probes and three probes specific for the point mutations c.1001+1G>A (IV S8+1G>A), c.707T>C (p.Leu236Pro) and c.1246A>C (p.Thr416Pro). Subject PDS41 is heterozygous for a deletion (g.8091T-22145Cdel) spanning exons 4–6 in SLC26A4, as evidenced by the reproducible reduction in peak height for these three exon probes (peaks labeled 4, 5, 6) relative to the control. PDS41 also has a heterozygous c.1246A>C (p.Thr416Pro) mutation that was previously identified by sequencing and confirmed by these MLPA results (peak labeled p.T416P). (B) Sequencing chromatogram of the deletion breakpoints in SLC26A4 IVS3 and IVS6. The deletion removes a total of 14,053 bp. IVS, intervening sequence.

In addition to performing MLPA analysis on samples from our patient cohort, we investigated other genes potentially contributing to their SNHL by sequencing 29 probands for variants in the coding regions of the FOXI1 and KCNJ10 genes. We identified a heterozygous variant of FOXI1, c.677C>T (p.Thr226Ile), in one patient, PDS29 (1/29 unknown alleles; 3.4%). This FOXI1 substitution has not been previously described in SNHL. It represents a rare variant (dbSNP:rs115399307; minor allele frequency of 0.3%, http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=115399307) of unknown clinical significance. The SIFT and PolyPhen-2 programs predicted the substitution to be “tolerated” and “benign”, respectively. Two heterozygous variants of KCNJ10 were also detected in this group (2/29 unknown alleles; 6.9%), each in a separate proband. The substitution c.812G> A(p.Arg271His) in PDS21 was predicted by SIFT and PolyPhen-2 to be “tolerated” and “benign”, respectively. This substitution is also a rare sequence variant (dbSNP: rs3795339; minor allele frequency of 0.6%, http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3795339) of uncertain clinical significance that has been reported previously in a single heterozygous Chinese proband with non-syndromic EVA and zero mutations of SLC26A4 (Chai et al., 2013). In that same study, however, the c.812G>A (p.Arg271His) variant was found in 10/200 or 5% of normal hearing controls, suggesting that this substitution may be a polymorphism in the Chinese population. The other KCNJ10 variant, c.811C>T (p.Arg271Cys), was discovered in patient PDS23 and it also affects amino acid residue 271. Although this substitution is predicted to “affect protein function” by SIFT and to be “possibly damaging” by PolyPhen-2, it is a reported polymorphism of unknown clinical significance (dbSNP: rs1130183) with a minor allele frequency of 2.3% (dbSNP: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type= rs&rs=1130183). This substitution has been previously reported in three Italian individuals affected with SNHL, who also had bilateral inner ear malformations (Cirello et al., 2012) and has been associated with seizure susceptibility (Buono et al., 2004; Lenzen et al., 2005).

" + ] + }, + "discussion_html": { + "value": [ + "

Discussion

\n

The autosomal recessive inheritance of PDS and DFNB4 is well established and yet, for many affected individuals, analysis of the coding sequences and splice sites of the SLC26A4 gene has failed to identify one or both of the mutations required to cause these disorders (Campbell et al., 2001; Tsukamoto et al., 2003; Pryor et al., 2005; Albert et al., 2006; Yang et al., 2007; Wu et al., 2010). In fact, an analysis of six studies with a total enrollment of 769 hearing impaired probands with EVA, a non-pathognomonic clinical finding that is a hallmark of PDS and DFNB4, reveals that only 25% have biallelic SLC26A4 mutations (Table 2). Of these same probands, 45% have at least one SLC26A4 mutation, a percentage slightly lower than the 50% reported by GeneReviews as the proportion of PDS/DFNB4 accounted for by mutations in SLC26A4 (http://www.ncbi.nlm.nih.gov/books/NBK1467/). Among the six included studies, there are considerable differences in the reported percentages of individuals segregating monoallelic or biallelic SLC26A4 mutations. The proportion of probands for whom at least one SLC26A4 mutation is detected ranges from as low as 30–40% (Campbell et al., 2001; Albert et al., 2006; Yang et al., 2007) to as high as 80–90% (Tsukamoto et al., 2003; Wu et al., 2010). The percentage of probands in whom biallelic mutations are found varies accordingly, from a low of 13% (Yang et al., 2007) to a high of 62% (Wu et al., 2010). This variation may be attributed to differences in the selection criteria of each study and/or to the patient population being tested; however, in all cases, there is a substantial proportion of individuals for whom the genotype is either incomplete or for whom no mutations in SLC26A4 were identified at all. This has implications for genetic counseling regarding recurrence risk, whether to pursue imaging, and, more broadly, understanding of disease pathogenesis. The inability to identify both mutations in individuals suspected of having a PDS/DFNB4 hearing loss etiology suggests the possible involvement of (1) mutations in unexamined regions of SLC26A4; (2) mutations in other, as yet to be implicated genes; or (3) other factors, such as those that may regulate gene expression.

\n
\nTable 2:
Percentages of PDS/DFNB4 probands with SLC26A4 mutations.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
ReferenceProbands2 Mutations1 Mutation0 MutationsStudy selection criteria
\n Campbell et al., 2001\n 589 (16%)14 (24%)35 (60%)Recessive HL with DVA or Mondini dysplasia
\n Tsukamoto et al., 2003\n 4224 (57%)10 (24%)8 (19%)Pendred (goiter) or bilateral HL with EVA
\n Pryor et al., 2005\n 3914 (36%)14 (36%)11 (28%)EVA in at least one ear
\n Albert et al., 2006\n 10024 (24%)16 (16%)60 (60%)Bilateral, recessive HL; EVA; no GJB2 mutations
\n Yang et al., 2007\n 42957 (13%)75 (17%)297 (69%)HL with EVA
\n Wu et al., 2010\n 10163 (62%)24 (24%)14 (14%)Bilateral EVA
\n Total\n 769191 (25%)153 (20%)425 (55%)
\n\n
\n

Notes:

\n

\n

\n
HL
\n

hearing loss

\n
DVA
\n

dilated vestibular aqueduct

\n
EVA
\n

enlarged vestibular aqueduct

\n
\n

\n

The selection of study subjects is an important factor that is not consistent between studies. Our patient selection was based primarily on the genetic testing of GJB2 and SLC26A4 as is common in the clinical work-up for children with SNHL in the U.S., with imaging studies performed on only a subset of patients. Even in this relatively general SNHL patient population, however, we saw a considerable enrichment for probands with single SLC26A4 mutations, compared to unaffected individuals. In the experience of the Stanford Molecular Pathology Laboratory, the frequency of heterozygous SLC26A4 mutations in probands tested with a GJB2 and SLC26A4 algorithm and in whom two pathogenic mutations are not identified is 12.3%, which is significantly higher (p < 0.001) than the expected carrier frequency. Using a frequency of 1/500 for congenital bilateral hearing loss of ≥40 dB (Hilgert, Smith & Van Camp, 2009), and the estimate that SLC26A4 related SNHL would account for up to 7.5%, then the frequency of such hearing loss could approximate one in 7,000. Assuming Hardy–Weinberg equilibrium, the carrier frequency would be about 1:50 (2%). This is congruent with a study in which pathogenic or possibly pathogenic mutations were identified in 1.9% of normal-hearing controls (8/428 controls; p.E29Q, p.F354S, p.F667C, p.D724G, p.G740S) (Pera et al., 2008b). An “excess” of heterozygous mutations in individuals with SNHL compared to controls has also been observed for GJB2 (Putcha et al., 2007), a gene for which neighboring deletions can affect gene expression (Rodriguez-Paris & Schrijver, 2009).

\n

Given that SLC26A4 related SNHL is autosomal recessive, we postulated that these ‘missing’ SLC26A4 mutations may be the result of intragenic deletions or duplications of one or more exons for which patients are not routinely tested. We selected 107 individuals with SNHL and monoallelic mutations of SLC26A4 for MLPA analysis of the SLC26A4 gene to explore this further. A handful of multiexon SLC26A4 deletions have been described in the literature (Park et al., 2003; Hu et al., 2007; Pera et al., 2008a; Anwar et al., 2009; Siem et al., 2010) but it is unclear how many of the probands in these cohorts were tested for intragenic deletions and duplications. Recently, however, in a study of 109 Scandinavian probands with suspected PDS/DFNB4, 37 individuals with only one or zero mutations of SLC26A4 were systematically screened for copy number variants by MLPA (Rendtorff et al., 2013). Only one harbored a homozygous deletion, of exons 4–6 (n = 2/63 unknown alleles; 3.2%). In our study of hearing impaired individuals with one previously identified SLC26A4 mutation, we found an intragenic deletion in a single individual only (n = 1/107 unknown alleles; 0.93%). This deletion also spanned exons 4–6 of the SLC26A4 gene and was previously detected in a patient of Spanish descent (Pera et al., 2008a). An analysis of the deletion breakpoints confirmed that our subject carried a heterozygous copy of g.8091T-22145Cdel (Fig. 1). To date, deletions and duplications seem to represent approximately 1.8% of missing SLC26A4 mutations overall (n = 3/170 unknown alleles) (Rendtorff et al., 2013; this study). Despite accounting for a low percentage of the ‘missing’ mutations, clinical testing for multiexon deletions and duplications of additional patients with potential PDS/DFNB4 etiology may remain warranted in order to more firmly establish frequencies and elucidate their relative contribution to the phenotype.

\n

Alternatively, unrecognized mutations in unexamined, noncoding regions of the gene may be responsible for the ‘missing’ SLC26A4 mutations and contribute to the PDS/DFNB4 phenotype. For example, intronic mutations may create cryptic splice sites and mutations in the promoter region may disrupt the binding of regulatory elements. Indeed, a cis-regulatory element that binds transcription factor FOXI1 has been described in the SLC26A4 promoter region (Yang et al., 2007). The regulatory element consists of two head-to-head binding sites, FBS1 and FBS2, and a mutation within this cis-element, c.-103T>C, has been shown to disrupt transcriptional activation of the gene by FOXI1. However, none of the probands included in this study carried mutations in the promoter region.

\n

Mutations of the FOXI1 gene itself have also been implicated in PDS and DFNB4. Monoallelic variants of FOXI1 were documented in six patients with either PDS or non-syndromic EVA and were shown to compromise the ability of FOXI1 to transcriptionally activate SLC26A4 (Yang et al., 2007). One of these six probands segregated the DFNB4 phenotype with one heterozygous mutation each of FOXI1 and SLC26A4. This finding was consistent with the EVA phenotype observed in the Slc26a4+/−; Foxi1+/− double-heterozygous mouse model and suggests that the transcriptional regulatory machinery of SLC26A4 plays a role in PDS/DFNB4 pathogenesis. Mutations of KCNJ10, a gene that encodes a K+ channel protein, have also been associated with PDS/DFNB4 (Marcus et al., 2002). Protein expression studies in SLC26A4 knockout mice have indicated that the absence of pendrin expression reduces KCNJ10 protein levels, supporting the hypothesis that deafness in the mouse model is secondary to loss of KCNJ10 function (Wangemann et al., 2004). A similar reduction of KCNJ10 expression was observed in the stria vascularis of the inner ear in the haploinsufficient Slc26a4+/− mouse mutant (Yang et al., 2009). In that same study, two individuals with the PDS/DFNB4 phenotype were reported to be double heterozygous for mutations of the SLC26A4 and KCNJ10 genes, further supporting a digenic model of inheritance.

\n

We examined to what extent digenic inheritance may contribute to the PDS/DFNB4 phenotype by sequencing the coding regions and splice sites of FOXI1 and KCNJ10 in about half (n = 29/60) of the Stanford University probands enrolled in the study for whom enough sample was available for the additional analysis. Our initial sequencing of FOXI1 and KCNJ10 in these subjects resulted in three nonsynonymous variants overall; all three of these heterozygous substitutions are listed in the dbSNP database as having unknown clinical significance. Nonetheless, functional studies must be conducted to investigate the effects of the FOXI1 variant on SLC26A4 transcriptional activation and the impact of the two KCNJ10 variants on K+ channel conductance before a determination of the pathogenicity of these three variants and their effect on SNHL phenotypes can be more definitively made.

\n

Although unlikely, if the FOXI1 variant and the two KCNJ10 variants detected in our probands are indeed digenic mutations acting in conjunction with mutations of SLC26A4, then 3.4% and 6.9% of the missing mutant alleles in our SNHL patients would be attributable to variants in FOXI1 and KCNJ10, respectively. However, the number of patients tested for FOXI1 and KCNJ10 variants (n = 29/107 total probands) is too small a sample size to merit this conclusion. Consequently, a meta-analysis of published studies in which FOXI1 and KCNJ10 were sequenced in SNHL patients with inner ear malformations was conducted. The meta-analysis does not support the frequencies observed in our patients (Table 3) and shows instead that, overall, 1.3% and 3.1% of suspected PDS/DFNB4 patients have variants in FOXI1 and KCNJ10, respectively. In fact, considering that the KCNJ10 variant c.812G>A (p.Arg271His) may be a polymorphism in the Chinese population and the KCNJ10 variant c.811C>T (p.Arg271Cys) is a reported polymorphism in the dbSNP database, the frequency of KCNJ10 variants in PDS/DFNB4 patients may be inflated by the inclusion of the Chinese and Italian probands carrying these substitutions and may actually be lower. The great majority of reported FOXI1 and KCNJ10 variants are from the initial studies that implicated the genes in the digenic inheritance of PDS/DFNB4 (Yang et al., 2007; Yang et al., 2009). However, the actual contribution of FOXI1 and KCNJ10 mutations to SNHL may be more limited, as illustrated by several subsequent studies in which either no FOXI1 variants (Wu et al., 2010; Mercer, Mutton & Dahl, 2011; Lai et al., 2012; Chen et al., 2012; Chai et al., 2013), or no KCNJ10 variants (Mercer, Mutton & Dahl, 2011; Chen et al., 2012) were identified.

\n
\nTable 3:
Meta-analysis of the frequency of FOXI1 and KCNJ10 variants in PDS/DFNB4 probands.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GenePopulation
origin
ReferenceControls1\nInclusion criteria for SLC26A4 sequencingSelection criteria for
FOXI1 sequencing
Subjects with nonsynonymous variants
\n FOXI1\n US/Sweden\n Yang et al., 2007\n 250EVA with or without Mondini dysplasia0 or 1 SLC26A4 mutations6/372 (1.6%)2\n
\n FOXI1\n Taiwan\n Wu et al., 2010\n 100Bilateral EVA with or without other IEMs0 or 1 SLC26A4 mutations0/38 (0.0%)
\n FOXI1\n Australia\n Mercer, Mutton & Dahl, 2011\n 96EVAPhenotype only0/44 (0.0%)
\n FOXI1\n Italy\n Cirello et al., 2012\n 80Bilateral IEMs/family history of PS/goiter0 or 1 SLC26A4 mutations1/14 (7.1%)3\n
\n FOXI1\n China\n Lai et al., 2012\n 100EVA0 or 1 SLC26A4 mutations0/8 (0.0%)
\n FOXI1\n China\n Chen et al., 2012\n IEM’s0 or 1 SLC26A4 mutations0/15 (0.0%)
\n FOXI1\n China\n Chai et al., 2013\n 200Nonsyndromic EVA0 or 1 SLC26A4 mutations0/33 (0.0%)
\nReported FOXI1 frequency= 7/524 (1.3%)\n
\n FOXI1\n USThis studySensorineural hearing loss1 SLC26A4 mutation1/29 (3.4%)
\nTotal combined FOXI1 frequency= 8/553 (1.4%)\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GenePopulation
origin
ReferenceControls1\nInclusion criteria for
SLC26A4 sequencing
Selection criteria for
KCNJ10 sequencing
Subjects with nonsynonymous variants
\n KCNJ10\n China/US/
Canada
\n Yang et al., 2009\n 400EVA with or without Mondini dysplasia1 SLC26A4 mutation2/89 (2.2%)4\n
\n KCNJ10\n Australia\n Mercer, Mutton & Dahl, 2011\n 96EVAPhenotype only0/44 (0.0%)
\n KCNJ10\n Italy\n Cirello et al., 2012\n 80Bilateral IEMs/family history of PS/goiter0 or 1 SLC26A4 mutations3/14 (21.4%)5\n
\n KCNJ10\n China\n Chen et al., 2012\n IEM’s0 or 1 SLC26A4 mutations0/15 (0.0%)
\n KCNJ10\n China\n Chai et al., 2013\n 200Nonsyndromic EVA0 or 1 SLC26A4 mutations1/33 (3.0%)6\n
\nReported KCNJ10 frequency = 6/195 (3.1%)\n
\n KCNJ10\n USThis studySensorineural hearing loss1 SLC26A4 mutation2/29 (6.9%)
\nTotal combined KCNJ10 frequency= 8/224 (3.6%)\n
\n
\n\n
\n

Notes:

\n
\n1All controls had normal hearing and, unless otherwise noted, none harbored any of the novel variants.\n
\n
\n2Five variants (p.G258E, p.N161del, p.G258R, p.R267Q and p.G335V) were detected in six probands and were shown to compromise SLC26A4 transcriptional activation.\n
\n
\n3Functional analysis of the identified novel variant (p.P239L) showed no impairment of SLC26A4 transcriptional activation.\n
\n
\n4Two identified missense mutations (p.P194H and p.R348C) were shown to impair K+ channel conductance.\n
\n
\n5One previously reported variant (p.R271C) was identified in 3 probands.\n
\n
\n6One heterozygous variant (p.R271H) was detected in a single proband; this variant was also found in 10/200 normal hearing controls.\n
\n

\n

\n
EVA
\n

Enlarged vestibular aqueduct

\n
IEM
\n

Inner ear malformation

\n
PS
\n

Pendred syndrome

\n
\n

\n

The genetic basis of hearing loss is diagnostically challenging with over 100 genes implicated (http://hereditaryhearingloss.org). The phenotypic variability observed within the PDS/DFNB4 spectrum also complicates diagnosis with changes in the same gene, SLC26A4, responsible for syndromic as well as non-syndromic hearing loss. Most clinical centers have historically utilized tiered testing in the assessment of hearing loss genetic etiology. However, with the advent of large-scale massively parallel sequencing (MPS), future approaches will likely employ testing platforms that are more comprehensive, cost effective and efficient (Shearer & Smith, 2012). Additional sources of genetic mutation, such as deletions and duplications, will need to be included in these new testing approaches.

" + ] + }, + "conclusion_html": { + "value": [ + + ] + }, + "author_contrib_html": { + "value": [ + + ] + }, + "competing_interests_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\nAlasti F, Van Camp G, Smith RJH. 1998 (Updated 2012). Pendred Syndrome/DFNB4. In: Pagon RA, Adam MP, Ardinger HH, et al. eds. Seattle, WA: University of Washington. Available at http://www.ncbi.nlm.nih.gov/books/NBK1467/\n", + "\nAlbert S, Blons H, Jonard L, Feldmann D, Chauvin P, Loundon N, Sergent-Allaoui A, Houang M, Joannard A, Schmerber S, Delobel B, Leman J, Journel H, Catros H, Dollfus H, Eliot MM, David A, Calais C, Drouin-Garraud V, Obstoy MF, Tran Ba Huy P, Lacombe D, Duriez F, Francannet C, Bitoun P, Petit C, Garabédian EN, Couderc R, Marlin S, Denoyelle F. 2006. SLC26A4 gene is frequently involved in nonsyndromic hearing impairment with enlarged vestibular aqueduct in Caucasian populations. European Journal of Human Genetics 14:773-779 \n", + "\nAnwar S, Riazuddin S, Ahmed ZM, Tasneem S, Ateeq-ul-Jaleel Khan SY, Griffith AJ, Friedman TB, Riazuddin S. 2009. SLC26A4 mutation spectrum associated with DFNB4 deafness and Pendred’s syndrome in Pakistanis. Journal of Human Genetics 54:266-270 \n", + "\nBlons H, Feldmann D, Duval V, Messaz O, Denoyelle F, Loundon N, Sergout-Allaoui A, Houang M, Duriez F, Lacombe D, Delobel B, Leman J, Catros H, Journel H, Drouin-Garraud V, Obstoy MF, Toutain A, Oden S, Toublanc JE, Couderc R, Petit C, Garabédian EN, Marlin S. 2004. Screening of SLC26A4 (PDS) gene in Pendred’s syndrome: a large spectrum of mutations in France and phenotypic heterogeneity. Clinical Genetics 66:333-340 \n", + "\nBuono RJ, Lohoff FW, Sander T, Sperling MR, O’Connor MJ, Dlugos DJ, Ryan SG, Golden GT, Zhao H, Scattergood TM, Berrettini WH, Ferraro TN. 2004. Association between variation in the human KCNJ10 potassium ion channel gene and seizure susceptibility. Epilepsy Research 58:175-183 \n", + "\nCampbell C, Cucci RA, Prasad S, Green GE, Edeal JB, Galer CE, Karniski LP, Sheffield VC, Smith RJ. 2001. Pendred syndrome, DFNB4, and PDS/SLC26A4 identification of eight novel mutations and possible genotype-phenotype correlations. Human Mutation 17:403-411 \n", + "\nChai Y, Huang Z, Tao Z, Li X, Li L, Li Y, Wu H, Yang T. 2013. Molecular etiology of hearing impairment associated with nonsyndromic enlarged vestibular aqueduct in East China. American Journal of Medical Genetics Part A 161:2226-2233 \n", + "\nChen K, Wang X, Sun L, Jiang H. 2012. Screening of SLC26A4, FOXI1, KCNJ10, and GJB2 in bilateral deafness patients with inner ear malformation. Otolaryngology Head and Neck Surgery 146:972-978 \n", + "\nCirello V, Bazzini C, Vezzoli V, Muzza M, Rodighiero S, Castorina P, Maffini A, Bottà G, Persani L, Beck-Peccoz P, Meyer G, Fugazzola L. 2012. Molecular and functional studies of 4 candidate loci in Pendred syndrome and nonsyndromic hearing loss. Molecular and Cellular Endocrinology 351:342-350 \n", + "\nEverett LA, Glaser B, Beck JC, Idol JR, Buchs A, Heyman M, Adawi F, Hazani E, Nassir E, Baxevanis AD, Sheffield VC, Green ED. 1997. Pendred syndrome is caused by mutations in a putative sulphate transporter gene (PDS) Nature Genetics 17:411-422 \n", + "\nEverett LA, Morsli H, Wu DK, Green ED. 1999. Expression pattern of the mouse ortholog of the Pendred’s syndrome gene (Pds) suggests a key role for pendrin in the inner ear. Proceedings of the National Academy of Sciences of the United States of America 96:9727-9732 \n", + "\nFraser GR. 1965. Association of congenital deafness with goitre (Pendred’s syndrome), a study of 207 families. Annals of Human Genetics 28:201-249 \n", + "\nHilgert N, Smith RJ, Van Camp G. 2009. Forty-six genes causing nonsyndromic hearing impairment: which ones should be analyzed in DNA diagnostics? Mutation Research 681:189-196 \n", + "\nHu H, Wu L, Feng Y, Pan Q, Long Z, Li J, Dai H, Xia K, Liang D, Niikawa N, Xia J. 2007. Molecular analysis of hearing loss associated with enlarged vestibular aqueduct in the mainland Chinese: a unique SLC26A4 mutation spectrum. Journal of Human Genetics 52:492-497 \n", + "\nKenneson A, Van Naarden Braun K, Boyle C. 2002. GJB2 (connexin 26) variants and nonsyndromic sensorineural hearing loss: a HuGE review. Genetics in Medicine 4:258-274 \n", + "\nLai R, Hu P, Zhu F, Zhu G, Vivero R, Peng A, Wu W, Xiao Z, Liu X, Xie D. 2012. Genetic diagnosis and cochlear implantation for patients with nonsyndromic hearing loss and enlarged vestibular aqueduct. The Journal of Laryngology & Otology 126:349-355 \n", + "\nLenzen KP, Heils A, Lorenz S, Hempelmann A, Höfels S, Lohoff FW, Schmitz B, Sander T. 2005. Supportive evidence for an allelic association of the human KCNJ10 potassium channel gene with idiopathic generalized epilepsy. Epilepsy Research 63:113-118 \n", + "\nLi XC, Everett LA, Lalwani AK, Desmukh D, Friedman TB, Green ED, Wilcox ER. 1998. A mutation in PDS causes non-syndromic recessive deafness. Nature Genetics 18:215-217 \n", + "\nMarcus DC, Wu T, Wangemann P, Kofuji P. 2002. KCNJ10 (Kir4.1) potassium channel knockout abolishes endocochlear potential. American Journal of Physiology Cell Physiology 282:C403-C407 \n", + "\nMercer S, Mutton P, Dahl HH. 2011. Identification of SLC26A4 mutations in patients with hearing loss and enlarged vestibular aqueduct using high-resolution melting curve analysis. Genetic Testing and Molecular Biomarkers 15:365-368 \n", + "\nMorton CC, Nance WE. 2006. Newborn hearing screening—a silent revolution. New England Journal of Medicine 354:2151-2164 \n", + "\nPark HJ, Shaukat S, Liu XZ, Hahn SH, Naz S, Ghosh M, Kim HN, Moon SK, Abe S, Tukamoto K, Riazuddin S, Kabra M, Erdenetungalag R, Radnaabazar J, Khan S, Pandya A, Usami SI, Nance WE, Wilcox ER, Riazuddin S, Griffith AJ. 2003. Origins and frequencies of SLC26A4 (PDS) mutations in east and south Asians: global implications for the epidemiology of deafness. Journal of Medical Genetics 40:242-248 \n", + "\nPera A, Villamar M, Viñuela A, Gandía M, Medà C, Moreno F, Hernández-Chico C. 2008a. A mutational analysis of the SLC26A4 gene in Spanish hearing-impaired families provides new insights into the genetic causes of Pendred syndrome and DFNB4 hearing loss. European Journal of Human Genetics 16:888-896 \n", + "\nPera A, Dossena S, Rodighiero S, Gandía M, Bottà G, Meyer G, Moreno F, Nofziger C, Hernández-Chico C, Paulmichl M. 2008b. Functional assessment of allelic variants in the SLC26A4 gene involved in Pendred syndrome and nonsyndromic EVA. Proceedings of the National Academy of Sciences of the United States of America 105:18608-18613 \n", + "\nPryor SP, Madeo AC, Reynolds JC, Sarlis NJ, Arnos KS, Nance WE, Yang Y, Zalewski CK, Brewer CC, Butman JA, Griffith AJ. 2005. SLC26A4/PDS genotype–phenotype correlation in hearing loss with enlargement of the vestibular aqueduct (EVA): evidence that Pendred syndrome and non-syndromic EVA are distinct clinical and genetic entities. Journal of Medical Genetics 42:159-165 \n", + "\nPutcha GV, Bejjani BA, Bleoo S, Booker JK, Carey JC, Carson N, Das S, Dempsey MA, Gastier-Foster JM, Greinwald JH, Hoffmann ML, Jeng LJ, Kenna MA, Khababa I, Lilley M, Mao R, Muralidharan K, Otani IM, Rehm HL, Schaefer F, Seltzer WK, Spector EB, Springer MA, Weck KE, Wenstrup RJ, Withrow S, Wu BL, Zariwala MA, Schrijver I. 2007. A multicenter study of the frequency and distribution of GJB2 and GJB6 mutations in a large North American cohort. Genetics in Medicine 9:413-426 \n", + "\nReardon W, Coffey R, Phelps PD, Luxon LM, Stephens D, Kendall-Taylor P, Britton KE, Grossman A, Trembath R. 1997. Pendred syndrome—100 years of underascertainment? QJM 90:443-447 \n", + "\nRendtorff N, Schrijver I, Lodahl M, Rodriguez-Paris J, Johnsen T, Hansén E, Nickelsen L, Tümer Z, Fagerheim T, Wetke R, Tranebjaerg L. 2013. SLC26A4 mutation frequency and spectrum in 109 Danish Pendred syndrome/DFNB4 probands and a report of nine novel mutations. Clinical Genetics 84(4):388-391 \n", + "\nRodriguez-Paris J, Schrijver I. 2009. The digenic hypothesis unraveled: the GJB6 del(GJB6-D13S1830) mutation causes allele-specific loss of GJB2 expression in cis. Biochemical and Biophysical Research Communications 389:354-359 \n", + "\nRoyaux IE, Suzuki K, Mori A, Katoh R, Everett LA, Kohn LD, Green ED. 2000. Pendrin, the protein encoded by the Pendred syndrome gene (PDS), is an apical porter of iodide in the thyroid and is regulated by thyroglobulin in FRTL-5 cells. Endocrinology 141:839-845 \n", + "\nRoyaux IE, Wall SM, Karniski LP, Everett LA, Suzuki K, Knepper MA, Green ED. 2001. Pendrin, encoded by the Pendred syndrome gene, resides in the apical region of renal intercalated cells and mediates bicarbonate secretion. Proceedings of the National Academy of Sciences of the United States of America 98:4221-4226 \n", + "\nRoyaux IE, Belyantseva IA, Wu T, Kachar B, Everett LA, Marcus DC, Green ED. 2003. Localization and functional studies of pendrin in the mouse inner ear provide insight about the etiology of deafness in pendred syndrome. Journal of the Association for Research in Otolaryngology 4:394-404 \n", + "\nSchrijver I, Gardner P. 2006. Hereditary sensorineural hearing loss: advances in molecular genetics and mutation analysis. Expert Review of Molecular Diagnostics 6:375-386 \n", + "\nShearer AE, Smith RJ. 2012. Genetics: advances in genetic testing for deafness. Current Opinion in Pediatrics 24:679-686 \n", + "\nSiem G, Fagerheim T, Jonsrud C, Laurent C, Teig E, Harris S, Leren TP, Früh A, Heimdal K. 2010. Causes of hearing impairment in the Norwegian paediatric cochlear implant program. International Journal of Audiology 49:596-605 \n", + "\nTsukamoto K, Suzuki H, Harada D, Namba A, Abe S, Usami S. 2003. Distribution and frequencies of PDS (SLC26A4) mutations in Pendred syndrome and nonsyndromic hearing loss associated with enlarged vestibular aqueduct: a unique spectrum of mutations in Japanese. European Journal of Human Genetics 11:916-922 \n", + "\nVele O, Schrijver I. 2008. Inherited hearing loss: molecular genetics and diagnostic testing. Expert Opinion on Medical Diagnostics 2:231-248 \n", + "\nWangemann P, Itza EM, Albrecht B, Wu T, Jabba SV, Maganti RJ, Lee JH, Everett LA, Wall SM, Royaux IE, Green ED, Marcus DC. 2004. Loss of KCNJ10 protein expression abolishes endocochlear potential and causes deafness in Pendred syndrome mouse model. BMC Medicine 2:30 \n", + "\nWu CC, Lu YC, Chen PJ, Yeh PL, Su YN, Hwu WL, Hsu CJ. 2010. Phenotypic analyses and mutation screening of the SLC26A4 and FOXI1 genes in 101 Taiwanese families with bilateral nonsyndromic enlarged vestibular aqueduct (DFNB4) or Pendred syndrome. Audiology & Neurotology 15:57-66 \n", + "\nYang T, Vidarsson H, Rodrigo-Blomqvist S, Rosengren SS, Enerback S, Smith RJ. 2007. Transcriptional control of SLC26A4 is involved in Pendred syndrome and nonsyndromic enlargement of vestibular aqueduct (DFNB4) The American Journal of Human Genetics 80:1055-1063 \n", + "\nYang T, Gurrola JG, Wu H, Chiu SM, Wangemann P, Snyder PM, Smith RJ. 2009. Mutations of KCNJ10 together with mutations of SLC26A4 cause digenic nonsyndromic hearing loss associated with enlarged vestibular aqueduct syndrome. The American Journal of Human Genetics 84:651-657 \n" + ] + }, + "figures_html": { + "value": [ + "
\"Identification
\n

\nFigure 1: Identification of the heterozygous SLC26A4 deletion g.8091T-22145Cdel in subject PDS41.

\n(A) The SLC26A4 MLPA probe mix includes probes for the 21 SLC26A4 exons, 14 reference probes and three probes specific for the point mutations c.1001+1G>A (IV S8+1G>A), c.707T>C (p.Leu236Pro) and c.1246A>C (p.Thr416Pro). Subject PDS41 is heterozygous for a deletion (g.8091T-22145Cdel) spanning exons 4–6 in SLC26A4, as evidenced by the reproducible reduction in peak height for these three exon probes (peaks labeled 4, 5, 6) relative to the control. PDS41 also has a heterozygous c.1246A>C (p.Thr416Pro) mutation that was previously identified by sequencing and confirmed by these MLPA results (peak labeled p.T416P). (B) Sequencing chromatogram of the deletion breakpoints in SLC26A4 IVS3 and IVS6. The deletion removes a total of 14,053 bp. IVS, intervening sequence.
" + ] + }, + "tables_html": { + "value": [ + "
\nTable 1:
Primers used for the amplification of FOXI1 and KCNJ10.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GeneExonPrimer namePrimer sequence (5′ to 3′)\n T\n \n a\n \n
\n FOXI1\n 1FOXI1-1FTGAGCACCTGTCAGGGGCAG61
\n FOXI1\n 1FOXI1-1RGAACTTTCTAGAATGGGGTCTTG61
\n FOXI1\n 1FOXI1-1RintCCCTGTGGGTGGAAGAAGT55
\n FOXI1\n 2FOXI1-2FGACAATAAGGAGGAACAGAAG55
\n FOXI1\n 2FOXI1-2RGCATGGAGGACCTCTACTG55
\n KCNJ10\n 2KCNJ10-2aFGTTAATTCCTCCCTCCCATGG59
\n KCNJ10\n 2KCNJ10-2aRGTTCTCCCCTTCCTTGGTTTG59
\n KCNJ10\n 2KCNJ10-2bFGAGACCATTCGTTTCAGCCAG59
\n KCNJ10\n 2KCNJ10-2bRAAGAAGAGGGAGTGGAGGATG59
\n", + "
\nTable 2:
Percentages of PDS/DFNB4 probands with SLC26A4 mutations.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
ReferenceProbands2 Mutations1 Mutation0 MutationsStudy selection criteria
\n Campbell et al., 2001\n 589 (16%)14 (24%)35 (60%)Recessive HL with DVA or Mondini dysplasia
\n Tsukamoto et al., 2003\n 4224 (57%)10 (24%)8 (19%)Pendred (goiter) or bilateral HL with EVA
\n Pryor et al., 2005\n 3914 (36%)14 (36%)11 (28%)EVA in at least one ear
\n Albert et al., 2006\n 10024 (24%)16 (16%)60 (60%)Bilateral, recessive HL; EVA; no GJB2 mutations
\n Yang et al., 2007\n 42957 (13%)75 (17%)297 (69%)HL with EVA
\n Wu et al., 2010\n 10163 (62%)24 (24%)14 (14%)Bilateral EVA
\n Total\n 769191 (25%)153 (20%)425 (55%)
\n\n
\n

Notes:

\n

\n

\n
HL
\n

hearing loss

\n
DVA
\n

dilated vestibular aqueduct

\n
EVA
\n

enlarged vestibular aqueduct

\n
\n

\n
", + "
\nTable 3:
Meta-analysis of the frequency of FOXI1 and KCNJ10 variants in PDS/DFNB4 probands.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GenePopulation
origin
ReferenceControls1\nInclusion criteria for SLC26A4 sequencingSelection criteria for
FOXI1 sequencing
Subjects with nonsynonymous variants
\n FOXI1\n US/Sweden\n Yang et al., 2007\n 250EVA with or without Mondini dysplasia0 or 1 SLC26A4 mutations6/372 (1.6%)2\n
\n FOXI1\n Taiwan\n Wu et al., 2010\n 100Bilateral EVA with or without other IEMs0 or 1 SLC26A4 mutations0/38 (0.0%)
\n FOXI1\n Australia\n Mercer, Mutton & Dahl, 2011\n 96EVAPhenotype only0/44 (0.0%)
\n FOXI1\n Italy\n Cirello et al., 2012\n 80Bilateral IEMs/family history of PS/goiter0 or 1 SLC26A4 mutations1/14 (7.1%)3\n
\n FOXI1\n China\n Lai et al., 2012\n 100EVA0 or 1 SLC26A4 mutations0/8 (0.0%)
\n FOXI1\n China\n Chen et al., 2012\n IEM’s0 or 1 SLC26A4 mutations0/15 (0.0%)
\n FOXI1\n China\n Chai et al., 2013\n 200Nonsyndromic EVA0 or 1 SLC26A4 mutations0/33 (0.0%)
\nReported FOXI1 frequency= 7/524 (1.3%)\n
\n FOXI1\n USThis studySensorineural hearing loss1 SLC26A4 mutation1/29 (3.4%)
\nTotal combined FOXI1 frequency= 8/553 (1.4%)\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GenePopulation
origin
ReferenceControls1\nInclusion criteria for
SLC26A4 sequencing
Selection criteria for
KCNJ10 sequencing
Subjects with nonsynonymous variants
\n KCNJ10\n China/US/
Canada
\n Yang et al., 2009\n 400EVA with or without Mondini dysplasia1 SLC26A4 mutation2/89 (2.2%)4\n
\n KCNJ10\n Australia\n Mercer, Mutton & Dahl, 2011\n 96EVAPhenotype only0/44 (0.0%)
\n KCNJ10\n Italy\n Cirello et al., 2012\n 80Bilateral IEMs/family history of PS/goiter0 or 1 SLC26A4 mutations3/14 (21.4%)5\n
\n KCNJ10\n China\n Chen et al., 2012\n IEM’s0 or 1 SLC26A4 mutations0/15 (0.0%)
\n KCNJ10\n China\n Chai et al., 2013\n 200Nonsyndromic EVA0 or 1 SLC26A4 mutations1/33 (3.0%)6\n
\nReported KCNJ10 frequency = 6/195 (3.1%)\n
\n KCNJ10\n USThis studySensorineural hearing loss1 SLC26A4 mutation2/29 (6.9%)
\nTotal combined KCNJ10 frequency= 8/224 (3.6%)\n
\n
\n\n
\n

Notes:

\n
\n1All controls had normal hearing and, unless otherwise noted, none harbored any of the novel variants.\n
\n
\n2Five variants (p.G258E, p.N161del, p.G258R, p.R267Q and p.G335V) were detected in six probands and were shown to compromise SLC26A4 transcriptional activation.\n
\n
\n3Functional analysis of the identified novel variant (p.P239L) showed no impairment of SLC26A4 transcriptional activation.\n
\n
\n4Two identified missense mutations (p.P194H and p.R348C) were shown to impair K+ channel conductance.\n
\n
\n5One previously reported variant (p.R271C) was identified in 3 probands.\n
\n
\n6One heterozygous variant (p.R271H) was detected in a single proband; this variant was also found in 10/200 normal hearing controls.\n
\n

\n

\n
EVA
\n

Enlarged vestibular aqueduct

\n
IEM
\n

Inner ear malformation

\n
PS
\n

Pendred syndrome

\n
\n

\n
" ] }, "fulltext_html": { @@ -647,21 +1312,16 @@ "/articles/384.xml" ] }, - "supplementary_material": { + "supplementary_file": { "value": [ ] }, - "figure": { + "figures_image": { "value": [ "https://dfzljdn9uc3pi.cloudfront.net/2014/384/1/fig-1-full.png" ] }, - "figure_caption": { - "value": [ - "\nFigure 1: Identification of the heterozygous SLC26A4 deletion g.8091T-22145Cdel in subject PDS41.\n(A) The SLC26A4 MLPA probe mix includes probes for the 21 SLC26A4 exons, 14 reference probes and three probes specific for the point mutations c.1001+1G>A (IV S8+1G>A), c.707T>C (p.Leu236Pro) and c.1246A>C (p.Thr416Pro). Subject PDS41 is heterozygous for a deletion (g.8091T-22145Cdel) spanning exons 4–6 in SLC26A4, as evidenced by the reproducible reduction in peak height for these three exon probes (peaks labeled 4, 5, 6) relative to the control. PDS41 also has a heterozygous c.1246A>C (p.Thr416Pro) mutation that was previously identified by sequencing and confirmed by these MLPA results (peak labeled p.T416P). (B) Sequencing chromatogram of the deletion breakpoints in SLC26A4 IVS3 and IVS6. The deletion removes a total of 14,053 bp. IVS, intervening sequence.\n  Download full-size image\nDOI: 10.7717/peerj.384/fig-1\n\n" - ] - }, "license": { "value": [ @@ -669,7 +1329,8 @@ }, "copyright": { "value": [ - + "2014", + "Pique et al." ] }, "file_hashes": [ @@ -677,7 +1338,7 @@ "fig-1-full.png": "6ee6bf8676df1087e9d724bfdc9178e8" }, { - "fulltext.html": "b7306f1715e3bdba6bbbc4d788579fde" + "fulltext.html": "af847e85d95db9610fc61891d0cbda89" }, { "fulltext.pdf": "b2020a8f8037228e6face4a220751932" From 6dba2410e04267929d755816708471a979652ab0 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 11 Jan 2015 10:44:54 +0000 Subject: [PATCH 097/154] bump quickscrape dependency version --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index c907d8f..2009726 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,6 +9,6 @@ before_install: - nvm use 0.10.32 - npm update npm -g install: - - npm install --global quickscrape@0.3.2 + - npm install --global quickscrape@0.3.3 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+0000 Subject: [PATCH 099/154] tests for license and copyright improvements --- test/peerj.json | 35 +++++++++++++++-------------------- 1 file changed, 15 insertions(+), 20 deletions(-) diff --git a/test/peerj.json b/test/peerj.json index 9ebbac3..74ed8e8 100644 --- a/test/peerj.json +++ b/test/peerj.json @@ -243,13 +243,12 @@ }, "license": { "value": [ - + "This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited." ] }, "copyright": { "value": [ - "2013", - "Johansson et al." + "© 2013 Johansson et al.\n" ] }, "file_hashes": [ @@ -263,7 +262,7 @@ "fig-3-full.png": "0146a2e575c584b50ab4832654e97a96" }, { - "fulltext.html": "85a83823a2dca2801273de54f310ea7b" + "fulltext.html": "6db09548710a57d431f59ed99222e041" }, { "fulltext.pdf": "8e2c1cb94b99943cc618c437f8fd1618" @@ -545,13 +544,12 @@ }, "license": { "value": [ - + "This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited." ] }, "copyright": { "value": [ - "2014", - "Chiappe et al." + "© 2014 Chiappe et al.\n" ] }, "file_hashes": [ @@ -589,7 +587,7 @@ "fig-9-full.png": "3d3868736ac56e4f2e8e6395d05df051" }, { - "fulltext.html": "2727dc9caa1a8337b6ea911d56d706c7" + "fulltext.html": "d9f257ed6908df4c56ae1be06e501e89" }, { "fulltext.pdf": "3aa12392730333dd193322c7fb7ac72c" @@ -829,13 +827,12 @@ }, "license": { "value": [ - + "This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited." ] }, "copyright": { "value": [ - "2014", - "Fonin et al." + "© 2014 Fonin et al.\n" ] }, "file_hashes": [ @@ -861,7 +858,7 @@ "fig-7-full.png": "b76d31a596a07e5ef4fe238d687c5729" }, { - "fulltext.html": "cc1c3413ec3e0b9e1702e1ceda56c309" + "fulltext.html": "bda96b3c9b38dda43393d8f36acf393c" }, { "fulltext.pdf": "6b554c704f1ed7a8129863a2869036eb" @@ -1081,13 +1078,12 @@ }, "license": { "value": [ - + "This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited." ] }, "copyright": { "value": [ - "2014", - "Balbuena et al." + "© 2014 Balbuena et al.\n" ] }, "file_hashes": [ @@ -1098,7 +1094,7 @@ "fig-2-full.png": "b6a99fff0a72af9fde1e550f80d43799" }, { - "fulltext.html": "f11beaa73560a0396f103442fe9132eb" + "fulltext.html": "b1926638ed43aa476351c64095ce6b54" }, { "fulltext.pdf": "8aa4a538c24c0f3bfcc8b9fa5cd63d7c" @@ -1324,13 +1320,12 @@ }, "license": { "value": [ - + "This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited." ] }, "copyright": { "value": [ - "2014", - "Pique et al." + "© 2014 Pique et al.\n" ] }, "file_hashes": [ @@ -1338,7 +1333,7 @@ "fig-1-full.png": "6ee6bf8676df1087e9d724bfdc9178e8" }, { - "fulltext.html": "af847e85d95db9610fc61891d0cbda89" + "fulltext.html": "022bdb4b899eaedf165ad2693e1aa401" }, { "fulltext.pdf": "b2020a8f8037228e6face4a220751932" From 23cbdd46358e557ae3b2f5dc98eb84d07405851e Mon Sep 17 00:00:00 2001 From: Peter Murray-Rust Date: Mon, 12 Jan 2015 16:06:50 +0000 Subject: [PATCH 100/154] added bmc and trialsjournal scrapers --- scrapers/bmc.json | 90 +++++++++++++++++++++++++++++++++++++ scrapers/trialsjournal.json | 90 +++++++++++++++++++++++++++++++++++++ 2 files changed, 180 insertions(+) create mode 100644 scrapers/bmc.json create mode 100644 scrapers/trialsjournal.json diff --git a/scrapers/bmc.json b/scrapers/bmc.json new file mode 100644 index 0000000..9d947b2 --- /dev/null +++ b/scrapers/bmc.json @@ -0,0 +1,90 @@ +{ +"url": "www\\.biomedcentral\\.com", +"elements": { +"publisher": { +"selector": "//meta[@name='citation_publisher']", +"attribute": "content" +}, +"journal": { +"selector": "//meta[@name='citation_journal_title']", +"attribute": "content" +}, +"title": { +"selector": "//meta[@name='citation_title']", +"attribute": "content" +}, +"authors": { +"selector": "//meta[@name='citation_author']", +"attribute": "content" +}, +"date": { +"selector": "//meta[@name='citation_date']", +"attribute": "content" +}, +"doi": { +"selector": "//meta[@name='citation_doi']", +"attribute": "content" +}, +"volume": { +"selector": "//meta[@name='citation_volume']", +"attribute": "content" +}, +"issue": { +"selector": "//meta[@name='citation_issue']", +"attribute": "content" +}, +"firstpage": { +"selector": "//meta[@name='citation_firstpage']", +"attribute": "content" +}, +"description": { +"selector": "//meta[@name='description']", +"attribute": "content" +}, +"abstract": { +"selector": "//meta[@name='description']", +"attribute": "content" +}, +"fulltext_html": { +"selector": "//meta[@name='citation_fulltext_html_url']", +"attribute": "content", +"download": { +"rename": "fulltext.html" +} +}, +"fulltext_pdf": { +"selector": "//meta[@name='citation_pdf_url']", +"attribute": "content", +"download": { +"rename": "fulltext.pdf" +} +}, +"fulltext_xml": { +"selector": "//a[.='Download XML']", +"attribute": "href", +"download": { +"rename": "fulltext.xml" +} +}, +"supplementary_material": { +"selector": "//link[starts-with(@title,'Additional file')]", +"attribute": "href", +"download": true +}, +"figure": { +"selector": "//div[@class='fig']/p/a/img", +"attribute": "src", +"download": true +}, +"figure_caption": { +"selector": "//div[@class='fig']//strong" +}, +"license": { +"selector": "//p[a/@href='http://creativecommons.org/licenses/by/4.0']" +}, +"copyright": { +"selector": "//p[contains(.,'licensee')]" +} +} +} + diff --git a/scrapers/trialsjournal.json b/scrapers/trialsjournal.json new file mode 100644 index 0000000..6ebd87e --- /dev/null +++ b/scrapers/trialsjournal.json @@ -0,0 +1,90 @@ +{ +"url": "www\\.trialsjournal\\.com", +"elements": { +"publisher": { +"selector": "//meta[@name='citation_publisher']", +"attribute": "content" +}, +"journal": { +"selector": "//meta[@name='citation_journal_title']", +"attribute": "content" +}, +"title": { +"selector": "//meta[@name='citation_title']", +"attribute": "content" +}, +"authors": { +"selector": "//meta[@name='citation_author']", +"attribute": "content" +}, +"date": { +"selector": "//meta[@name='citation_date']", +"attribute": "content" +}, +"doi": { +"selector": "//meta[@name='citation_doi']", +"attribute": "content" +}, +"volume": { +"selector": "//meta[@name='citation_volume']", +"attribute": "content" +}, +"issue": { +"selector": "//meta[@name='citation_issue']", +"attribute": "content" +}, +"firstpage": { +"selector": "//meta[@name='citation_firstpage']", +"attribute": "content" +}, +"description": { +"selector": "//meta[@name='description']", +"attribute": "content" +}, +"abstract": { +"selector": "//meta[@name='description']", +"attribute": "content" +}, +"fulltext_html": { +"selector": "//meta[@name='citation_fulltext_html_url']", +"attribute": "content", +"download": { +"rename": "fulltext.html" +} +}, +"fulltext_pdf": { +"selector": "//meta[@name='citation_pdf_url']", +"attribute": "content", +"download": { +"rename": "fulltext.pdf" +} +}, +"fulltext_xml": { +"selector": "//a[.='Download XML']", +"attribute": "href", +"download": { +"rename": "fulltext.xml" +} +}, +"supplementary_material": { +"selector": "//link[starts-with(@title,'Additional file')]", +"attribute": "href", +"download": true +}, +"figure": { +"selector": "//div[@class='fig']/p/a/img", +"attribute": "src", +"download": true +}, +"figure_caption": { +"selector": "//div[@class='fig']//strong" +}, +"license": { +"selector": "//p[a/@href='http://creativecommons.org/licenses/by/4.0']" +}, +"copyright": { +"selector": "//p[contains(.,'licensee')]" +} +} +} + From 6ed03c4c5a0eb293d945bffb376dad2bc520b76e Mon Sep 17 00:00:00 2001 From: Saulius Grazulis Date: Fri, 23 Jan 2015 15:43:28 +0200 Subject: [PATCH 101/154] Adding the first version of my Acta Cryst. E scrapers. Four scrapers are designed for four different URLs that deliver slightly different contents. --- scrapers/acta-e-body.json | 24 ++++++++++++++++++++++++ scrapers/acta-e-doi.json | 23 +++++++++++++++++++++++ scrapers/acta-e-index.json | 35 +++++++++++++++++++++++++++++++++++ scrapers/acta-e-scripts.json | 31 +++++++++++++++++++++++++++++++ 4 files changed, 113 insertions(+) create mode 100644 scrapers/acta-e-body.json create mode 100644 scrapers/acta-e-doi.json create mode 100644 scrapers/acta-e-index.json create mode 100644 scrapers/acta-e-scripts.json diff --git a/scrapers/acta-e-body.json b/scrapers/acta-e-body.json new file mode 100644 index 0000000..a6e196e --- /dev/null +++ b/scrapers/acta-e-body.json @@ -0,0 +1,24 @@ +{ + "url": "journals\\.iucr\\.org/.*bdy\\.html", + "elements" : { + "authors": { + "selector": "//div[@class='AU']//span[@class='au']", + "attribute": "class" + }, + "authorUrl": { + "selector": "//div[@class='AU']", + "attribute": "class" + }, + "doi": { + "selector": "//meta[@name='DC.identifier']", + "attribute": "content" + }, + "fulltext_pdf": { + "selector": "//meta[@name='citation_pdf_url']", + "attribute": "content", + "download": { + "rename": "fulltext.pdf" + } + } + } +} diff --git a/scrapers/acta-e-doi.json b/scrapers/acta-e-doi.json new file mode 100644 index 0000000..05dd218 --- /dev/null +++ b/scrapers/acta-e-doi.json @@ -0,0 +1,23 @@ +{ + "url": "dx\\.doi\\.org/10.1107/", + "elements": { + "doi": { + "selector": "//meta[@name='DC.identifier']", + "attribute": "content" + }, + "fulltext_pdf": { + "selector": "//a[img[@alt='pdf version']]", + "attribute": "href", + "download": { + "rename": "fulltext.pdf" + } + }, + "fulltext_html": { + "selector": "//a[img[@alt='HTML version']]", + "attribute": "href", + "download": { + "rename": "fulltext.html" + } + } + } +} diff --git a/scrapers/acta-e-index.json b/scrapers/acta-e-index.json new file mode 100644 index 0000000..5798b87 --- /dev/null +++ b/scrapers/acta-e-index.json @@ -0,0 +1,35 @@ +{ + "url": "journals\\.iucr\\.org.*/index\\.html", + "elements" : { + "authors": { + "selector": "//meta[@name='citation_author']", + "attribute": "content" + }, + "title": { + "selector": "//meta[@name='citation_title']", + "attribute": "content" + }, + "html_title": { + "selector": "//title", + "attribute": "text" + }, + "doi": { + "selector": "//meta[@name='DC.identifier']", + "attribute": "content" + }, + "fulltext_pdf": { + "selector": "//meta[@name='citation_pdf_url']", + "attribute": "content", + "download": { + "rename": "fulltext.pdf" + } + }, + "fulltext_html": { + "selector": "//frame[@name='iucr_body']", + "attribute": "src", + "download": { + "rename": "fulltext.html" + } + } + } +} diff --git a/scrapers/acta-e-scripts.json b/scrapers/acta-e-scripts.json new file mode 100644 index 0000000..067ccdc --- /dev/null +++ b/scrapers/acta-e-scripts.json @@ -0,0 +1,31 @@ +{ + "url": "scripts\\.iucr\\.org", + "elements" : { + "authors": { + "selector": "//div[@class='AU']//span[@class='au']", + "attribute": "class" + }, + "authorUrl": { + "selector": "//div[@class='AU']", + "attribute": "class" + }, + "doi": { + "selector": "//meta[@name='DC.identifier']", + "attribute": "content" + }, + "fulltext_pdf": { + "selector": "//a[img[@alt='pdf version']]", + "attribute": "href", + "download": { + "rename": "fulltext.pdf" + } + }, + "fulltext_html": { + "selector": "//frame[@name='iucr_body']", + "attribute": "src", + "download": { + "rename": "fulltext.html" + } + } + } +} From 20e4c776f0ca1a3d6e7fffbac38c1fd9be84f243 Mon Sep 17 00:00:00 2001 From: Saulius Grazulis Date: Fri, 23 Jan 2015 15:44:55 +0200 Subject: [PATCH 102/154] Adding 5 test URLs from Acta Cryst. E to test scrapers for the DOI-based IUCr paper landing pages. --- test/acta-e_test_urls.txt | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 test/acta-e_test_urls.txt diff --git a/test/acta-e_test_urls.txt b/test/acta-e_test_urls.txt new file mode 100644 index 0000000..6440352 --- /dev/null +++ b/test/acta-e_test_urls.txt @@ -0,0 +1,5 @@ +http://dx.doi.org/10.1107/S1600536812006691 +http://dx.doi.org/10.1107/S1600536812007611 +http://dx.doi.org/10.1107/S160053681200801X +http://dx.doi.org/10.1107/S1600536812001924 +http://dx.doi.org/10.1107/S1600536812003224 From 65438441c6bde175ff03107e10e96fb48a55a4f2 Mon Sep 17 00:00:00 2001 From: Saulius Grazulis Date: Fri, 23 Jan 2015 15:49:09 +0200 Subject: [PATCH 103/154] Adding 5 more test URLs for IUCr Acta Cryst. E papers (this time scraping their ".../index.html" pages). --- test/acta-e_test_urls.txt | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/test/acta-e_test_urls.txt b/test/acta-e_test_urls.txt index 6440352..b966d79 100644 --- a/test/acta-e_test_urls.txt +++ b/test/acta-e_test_urls.txt @@ -3,3 +3,8 @@ http://dx.doi.org/10.1107/S1600536812007611 http://dx.doi.org/10.1107/S160053681200801X http://dx.doi.org/10.1107/S1600536812001924 http://dx.doi.org/10.1107/S1600536812003224 +http://journals.iucr.org/e/issues/2012/03/00/wm2588/index.html +http://journals.iucr.org/e/issues/2012/03/00/vn2032/index.html +http://journals.iucr.org/e/issues/2012/03/00/ru2029/index.html +http://journals.iucr.org/e/issues/2012/03/00/hy2496/index.html +http://journals.iucr.org/e/issues/2012/03/00/br2188/index.html From 1d189b841c43391ccb00d32d14bcc851842d3455 Mon Sep 17 00:00:00 2001 From: Saulius Grazulis Date: Fri, 23 Jan 2015 16:20:27 +0200 Subject: [PATCH 104/154] Updating the Acta Cryst. E body scraper (it now correctly picks out full author names and author IUCr URLs), generating 5 URLs to check this scraper. --- scrapers/acta-e-body.json | 6 +++--- test/acta-e_test_urls.txt | 5 +++++ 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/scrapers/acta-e-body.json b/scrapers/acta-e-body.json index a6e196e..056d777 100644 --- a/scrapers/acta-e-body.json +++ b/scrapers/acta-e-body.json @@ -3,11 +3,11 @@ "elements" : { "authors": { "selector": "//div[@class='AU']//span[@class='au']", - "attribute": "class" + "attribute": "text" }, "authorUrl": { - "selector": "//div[@class='AU']", - "attribute": "class" + "selector": "//div[@class='AU']//a[contains(@href, '/citedin')]", + "attribute": "href" }, "doi": { "selector": "//meta[@name='DC.identifier']", diff --git a/test/acta-e_test_urls.txt b/test/acta-e_test_urls.txt index b966d79..bd19d10 100644 --- a/test/acta-e_test_urls.txt +++ b/test/acta-e_test_urls.txt @@ -8,3 +8,8 @@ http://journals.iucr.org/e/issues/2012/03/00/vn2032/index.html http://journals.iucr.org/e/issues/2012/03/00/ru2029/index.html http://journals.iucr.org/e/issues/2012/03/00/hy2496/index.html http://journals.iucr.org/e/issues/2012/03/00/br2188/index.html +http://journals.iucr.org/e/issues/2012/03/00/wm2588/wm2588bdy.html +http://journals.iucr.org/e/issues/2012/03/00/vn2032/vn2032bdy.html +http://journals.iucr.org/e/issues/2012/03/00/ru2029/ru2029bdy.html +http://journals.iucr.org/e/issues/2012/03/00/hy2496/hy2496bdy.html +http://journals.iucr.org/e/issues/2012/03/00/br2188/br2188bdy.html From 1c8db30db098c522cd08cf0cb09787f633fa4a6c Mon Sep 17 00:00:00 2001 From: Saulius Grazulis Date: Fri, 23 Jan 2015 16:35:06 +0200 Subject: [PATCH 105/154] Fixing the last IUCr Acta Cryst. E scraper, acta-e-scripts.json, which is for extracting (meta)data from the http://scripts.iucr.org/cgi-bin/paper?... based URIs. Adding five example URLs for testing. --- scrapers/acta-e-scripts.json | 15 ++++----------- test/acta-e_test_urls.txt | 5 +++++ 2 files changed, 9 insertions(+), 11 deletions(-) diff --git a/scrapers/acta-e-scripts.json b/scrapers/acta-e-scripts.json index 067ccdc..1530614 100644 --- a/scrapers/acta-e-scripts.json +++ b/scrapers/acta-e-scripts.json @@ -2,12 +2,12 @@ "url": "scripts\\.iucr\\.org", "elements" : { "authors": { - "selector": "//div[@class='AU']//span[@class='au']", - "attribute": "class" + "selector": "//a[contains(@href, 'author_name=')]", + "attribute": "text" }, "authorUrl": { - "selector": "//div[@class='AU']", - "attribute": "class" + "selector": "//a[contains(@href, 'author_name=')]", + "attribute": "href" }, "doi": { "selector": "//meta[@name='DC.identifier']", @@ -19,13 +19,6 @@ "download": { "rename": "fulltext.pdf" } - }, - "fulltext_html": { - "selector": "//frame[@name='iucr_body']", - "attribute": "src", - "download": { - "rename": "fulltext.html" - } } } } diff --git a/test/acta-e_test_urls.txt b/test/acta-e_test_urls.txt index bd19d10..0725020 100644 --- a/test/acta-e_test_urls.txt +++ b/test/acta-e_test_urls.txt @@ -13,3 +13,8 @@ http://journals.iucr.org/e/issues/2012/03/00/vn2032/vn2032bdy.html http://journals.iucr.org/e/issues/2012/03/00/ru2029/ru2029bdy.html http://journals.iucr.org/e/issues/2012/03/00/hy2496/hy2496bdy.html http://journals.iucr.org/e/issues/2012/03/00/br2188/br2188bdy.html +http://scripts.iucr.org/cgi-bin/paper?S1600536812006691 +http://scripts.iucr.org/cgi-bin/paper?S1600536812007611 +http://scripts.iucr.org/cgi-bin/paper?S160053681200801X +http://scripts.iucr.org/cgi-bin/paper?S1600536812001924 +http://scripts.iucr.org/cgi-bin/paper?S1600536812003224 From 520f5184ca91dc66b9e53b51750505fa55fc724c Mon Sep 17 00:00:00 2001 From: Saulius Grazulis Date: Sat, 24 Jan 2015 13:34:41 +0200 Subject: [PATCH 106/154] Adding most of the metadata extraction "rules" to the "scrapers/acta-e-body.json" scraper. --- scrapers/acta-e-body.json | 111 ++++++++++++++++++++++++++++++++++++-- 1 file changed, 108 insertions(+), 3 deletions(-) diff --git a/scrapers/acta-e-body.json b/scrapers/acta-e-body.json index 056d777..6e3a84b 100644 --- a/scrapers/acta-e-body.json +++ b/scrapers/acta-e-body.json @@ -1,18 +1,123 @@ { "url": "journals\\.iucr\\.org/.*bdy\\.html", + "comment": "A scraper for the IUCr Acta Cryst. E journal (S.G.)", + "comment": "The full text HTML is not downloaded in this file since the page only gives a frame set, not the text itself.", "elements" : { - "authors": { + "htmlBodyAuthors": { "selector": "//div[@class='AU']//span[@class='au']", "attribute": "text" }, - "authorUrl": { + "htmlBodyAuthorUrls": { "selector": "//div[@class='AU']//a[contains(@href, '/citedin')]", "attribute": "href" }, + + "publisher": { + "selector": "//meta[@name='DC.publisher']", + "attribute": "content" + }, + "creators": { + "selector": "//meta[@name='DC.creator']", + "attribute": "content" + }, + "contributors": { + "selector": "//meta[@name='DC.contributor']", + "attribute": "content" + }, + "source": { + "selector": "//meta[@name='DC.source']", + "attribute": "content" + }, + "license": { + "selector": "//meta[@name='DC.rights']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@name='DC.date']", + "attribute": "content" + }, + "language": { + "selector": "//meta[@name='DC.language']", + "attribute": "content" + }, + "description": { + "selector": "//meta[@name='DC.description']", + "attribute": "content" + }, + + "title": { + "selector": "//meta[@name='citation_title']", + "attribute": "content" + }, + "authors": { + "selector": "//meta[@name='citation_author']", + "attribute": "content" + }, + "author_institutions": { + "selector": "//meta[@name='citation_author_institution']", + "attribute": "content" + }, + "author_emails": { + "selector": "//meta[@name='citation_author_email']", + "attribute": "content" + }, + "citationDate": { + "selector": "//meta[@name='citation_date']", + "attribute": "content" + }, + "onlineDate": { + "selector": "//meta[@name='citation_online_date']", + "attribute": "content" + }, + "volume": { + "selector": "//meta[@name='citation_volume']", + "attribute": "content" + }, + "issue": { + "selector": "//meta[@name='citation_issue']", + "attribute": "content" + }, + "firstpage": { + "selector": "//meta[@name='citation_firstpage']", + "attribute": "content" + }, + "lastpage": { + "selector": "//meta[@name='citation_lastpage']", + "attribute": "content" + }, "doi": { - "selector": "//meta[@name='DC.identifier']", + "selector": "//meta[@name='citation_doi']", + "attribute": "content" + }, + "journal": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" + }, + "issn": { + "selector": "//meta[@name='citation_issn']", "attribute": "content" }, + "abstract": { + "selector": "//meta[@name='citation_abstract']", + "attribute": "text" + }, + "abstract_html": { + "selector": "//meta[@name='citation_abstract_html_url']", + "attribute": "content", + "download": { + "rename": "abstract.html" + } + }, + "references": { + "selector": "//meta[@name='citation_reference']", + "attribute": "content" + }, + + "fulltext_html_frameset": { + "selector": "//meta[@name='citation_fulltext_url']", + "attribute": "content", + "download": false + }, "fulltext_pdf": { "selector": "//meta[@name='citation_pdf_url']", "attribute": "content", From 5d861c1ed15f4dc615f8453e7853e1be9c42231c Mon Sep 17 00:00:00 2001 From: Saulius Grazulis Date: Sat, 24 Jan 2015 14:24:40 +0200 Subject: [PATCH 107/154] Changing "author_emails" to "corresponding_author_email" in 'scrapers/acta-e-body.json'. --- scrapers/acta-e-body.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scrapers/acta-e-body.json b/scrapers/acta-e-body.json index 6e3a84b..b8cf0f3 100644 --- a/scrapers/acta-e-body.json +++ b/scrapers/acta-e-body.json @@ -57,7 +57,7 @@ "selector": "//meta[@name='citation_author_institution']", "attribute": "content" }, - "author_emails": { + "corresponding_author_email": { "selector": "//meta[@name='citation_author_email']", "attribute": "content" }, From 2b3967dc888b2697695bfac14f66233bcb524115 Mon Sep 17 00:00:00 2001 From: Saulius Grazulis Date: Sat, 24 Jan 2015 15:08:53 +0200 Subject: [PATCH 108/154] Adding a rule to extract HTML text with citations from the Acta Cryst. E paper. --- scrapers/acta-e-body.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/scrapers/acta-e-body.json b/scrapers/acta-e-body.json index b8cf0f3..9f8fe3a 100644 --- a/scrapers/acta-e-body.json +++ b/scrapers/acta-e-body.json @@ -112,6 +112,10 @@ "selector": "//meta[@name='citation_reference']", "attribute": "content" }, + "htmlCitations": { + "selector": "//div[@class='BIBL']", + "attribute": "html" + }, "fulltext_html_frameset": { "selector": "//meta[@name='citation_fulltext_url']", From d98f6dd85b33e053f2372cde7a854c940cf4b339 Mon Sep 17 00:00:00 2001 From: Saulius Grazulis Date: Sat, 24 Jan 2015 15:13:35 +0200 Subject: [PATCH 109/154] Adding rule to downoad figures (aka schemes) from Acta Cryst. E papers to scrapers/acta-e-body.json. --- scrapers/acta-e-body.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/scrapers/acta-e-body.json b/scrapers/acta-e-body.json index 9f8fe3a..9a64de6 100644 --- a/scrapers/acta-e-body.json +++ b/scrapers/acta-e-body.json @@ -117,6 +117,12 @@ "attribute": "html" }, + "figure": { + "selector": "//div[@class='scheme']//img", + "attribute": "src", + "download": true + }, + "fulltext_html_frameset": { "selector": "//meta[@name='citation_fulltext_url']", "attribute": "content", From b2239d358f15de0dd2e532168b4f5134d05764d3 Mon Sep 17 00:00:00 2001 From: Saulius Grazulis Date: Sat, 24 Jan 2015 15:19:28 +0200 Subject: [PATCH 110/154] Now longer downloading the frameset HTML in "scrapers/acta-e-doi.json", and commenting the choice. --- scrapers/acta-e-doi.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scrapers/acta-e-doi.json b/scrapers/acta-e-doi.json index 05dd218..9d4a359 100644 --- a/scrapers/acta-e-doi.json +++ b/scrapers/acta-e-doi.json @@ -1,5 +1,7 @@ { "url": "dx\\.doi\\.org/10.1107/", + "comment": "A scraper for the IUCr Acta Cryst. E journal (S.G.)", + "comment": "The full text HTML is not downloaded in this file since the page only gives a frame set, not the text itself.", "elements": { "doi": { "selector": "//meta[@name='DC.identifier']", @@ -15,9 +17,7 @@ "fulltext_html": { "selector": "//a[img[@alt='HTML version']]", "attribute": "href", - "download": { - "rename": "fulltext.html" - } + "download": false } } } From db3f043bca1605d1f7fb718612a0c3cba468c3ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Saulius=20Gra=C5=BEulis?= Date: Sat, 24 Jan 2015 15:22:30 +0200 Subject: [PATCH 111/154] Reformatting the "scrapers/acta-e-doi.json" code using Emacs. --- scrapers/acta-e-doi.json | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/scrapers/acta-e-doi.json b/scrapers/acta-e-doi.json index 9d4a359..e26e8c3 100644 --- a/scrapers/acta-e-doi.json +++ b/scrapers/acta-e-doi.json @@ -1,23 +1,23 @@ { - "url": "dx\\.doi\\.org/10.1107/", - "comment": "A scraper for the IUCr Acta Cryst. E journal (S.G.)", - "comment": "The full text HTML is not downloaded in this file since the page only gives a frame set, not the text itself.", - "elements": { - "doi": { - "selector": "//meta[@name='DC.identifier']", - "attribute": "content" - }, - "fulltext_pdf": { - "selector": "//a[img[@alt='pdf version']]", - "attribute": "href", + "url": "dx\\.doi\\.org/10.1107/", + "comment": "A scraper for the IUCr Acta Cryst. E journal (S.G.)", + "comment": "The full text HTML is not downloaded in this file since the page only gives a frame set, not the text itself.", + "elements": { + "doi": { + "selector": "//meta[@name='DC.identifier']", + "attribute": "content" + }, + "fulltext_pdf": { + "selector": "//a[img[@alt='pdf version']]", + "attribute": "href", "download": { "rename": "fulltext.pdf" } - }, - "fulltext_html": { - "selector": "//a[img[@alt='HTML version']]", - "attribute": "href", - "download": false - } - } + }, + "fulltext_html": { + "selector": "//a[img[@alt='HTML version']]", + "attribute": "href", + "download": false + } + } } From 4154c9ae02ef58c6adc01f9d750aef780e39ee09 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Saulius=20Gra=C5=BEulis?= Date: Sat, 24 Jan 2015 15:29:56 +0200 Subject: [PATCH 112/154] Transfering all DC based metadata tag extraction from "scrapers/acta-e-body.json" to "scrapers/acta-e-doi.json". --- scrapers/acta-e-doi.json | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/scrapers/acta-e-doi.json b/scrapers/acta-e-doi.json index e26e8c3..800d1db 100644 --- a/scrapers/acta-e-doi.json +++ b/scrapers/acta-e-doi.json @@ -7,6 +7,39 @@ "selector": "//meta[@name='DC.identifier']", "attribute": "content" }, + "publisher": { + "selector": "//meta[@name='DC.publisher']", + "attribute": "content" + }, + "creators": { + "selector": "//meta[@name='DC.creator']", + "attribute": "content" + }, + "contributors": { + "selector": "//meta[@name='DC.contributor']", + "attribute": "content" + }, + "source": { + "selector": "//meta[@name='DC.source']", + "attribute": "content" + }, + "license": { + "selector": "//meta[@name='DC.rights']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@name='DC.date']", + "attribute": "content" + }, + "language": { + "selector": "//meta[@name='DC.language']", + "attribute": "content" + }, + "description": { + "selector": "//meta[@name='DC.description']", + "attribute": "content" + }, + "fulltext_pdf": { "selector": "//a[img[@alt='pdf version']]", "attribute": "href", From 52e0dde7b5dcf348ec68c8d0ca5b2c2f17730a1d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Saulius=20Gra=C5=BEulis?= Date: Sat, 24 Jan 2015 15:44:53 +0200 Subject: [PATCH 113/154] Completing "scrapers/acta-e-index.json" to extract DC.* and citation_* metas. Renaming DC.identifier key from "doi" to "identifier" in all Acta Cryst. E scaper JSONs completed so far. --- scrapers/acta-e-body.json | 4 ++ scrapers/acta-e-doi.json | 2 +- scrapers/acta-e-index.json | 117 +++++++++++++++++++++++++++++++++++-- 3 files changed, 117 insertions(+), 6 deletions(-) diff --git a/scrapers/acta-e-body.json b/scrapers/acta-e-body.json index 9a64de6..406cb18 100644 --- a/scrapers/acta-e-body.json +++ b/scrapers/acta-e-body.json @@ -12,6 +12,10 @@ "attribute": "href" }, + "identifier": { + "selector": "//meta[@name='DC.identifier']", + "attribute": "content" + }, "publisher": { "selector": "//meta[@name='DC.publisher']", "attribute": "content" diff --git a/scrapers/acta-e-doi.json b/scrapers/acta-e-doi.json index 800d1db..1af0e8c 100644 --- a/scrapers/acta-e-doi.json +++ b/scrapers/acta-e-doi.json @@ -3,7 +3,7 @@ "comment": "A scraper for the IUCr Acta Cryst. E journal (S.G.)", "comment": "The full text HTML is not downloaded in this file since the page only gives a frame set, not the text itself.", "elements": { - "doi": { + "identifier": { "selector": "//meta[@name='DC.identifier']", "attribute": "content" }, diff --git a/scrapers/acta-e-index.json b/scrapers/acta-e-index.json index 5798b87..717aea8 100644 --- a/scrapers/acta-e-index.json +++ b/scrapers/acta-e-index.json @@ -1,6 +1,116 @@ { - "url": "journals\\.iucr\\.org.*/index\\.html", + "url": "journals\\.iucr\\.org.*/index\\.html", + "comment": "A scraper for the IUCr Acta Cryst. E journal (S.G.)", + "comment": "This scraper correctly downloads the HTML body of the paper.", "elements" : { + "identifier": { + "selector": "//meta[@name='DC.identifier']", + "attribute": "content" + }, + "publisher": { + "selector": "//meta[@name='DC.publisher']", + "attribute": "content" + }, + "creators": { + "selector": "//meta[@name='DC.creator']", + "attribute": "content" + }, + "contributors": { + "selector": "//meta[@name='DC.contributor']", + "attribute": "content" + }, + "source": { + "selector": "//meta[@name='DC.source']", + "attribute": "content" + }, + "license": { + "selector": "//meta[@name='DC.rights']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@name='DC.date']", + "attribute": "content" + }, + "language": { + "selector": "//meta[@name='DC.language']", + "attribute": "content" + }, + "description": { + "selector": "//meta[@name='DC.description']", + "attribute": "content" + }, + + "title": { + "selector": "//meta[@name='citation_title']", + "attribute": "content" + }, + "authors": { + "selector": "//meta[@name='citation_author']", + "attribute": "content" + }, + "author_institutions": { + "selector": "//meta[@name='citation_author_institution']", + "attribute": "content" + }, + "corresponding_author_email": { + "selector": "//meta[@name='citation_author_email']", + "attribute": "content" + }, + "citationDate": { + "selector": "//meta[@name='citation_date']", + "attribute": "content" + }, + "onlineDate": { + "selector": "//meta[@name='citation_online_date']", + "attribute": "content" + }, + "volume": { + "selector": "//meta[@name='citation_volume']", + "attribute": "content" + }, + "issue": { + "selector": "//meta[@name='citation_issue']", + "attribute": "content" + }, + "firstpage": { + "selector": "//meta[@name='citation_firstpage']", + "attribute": "content" + }, + "lastpage": { + "selector": "//meta[@name='citation_lastpage']", + "attribute": "content" + }, + "doi": { + "selector": "//meta[@name='citation_doi']", + "attribute": "content" + }, + "journal": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" + }, + "issn": { + "selector": "//meta[@name='citation_issn']", + "attribute": "content" + }, + "abstract": { + "selector": "//meta[@name='citation_abstract']", + "attribute": "text" + }, + "abstract_html": { + "selector": "//meta[@name='citation_abstract_html_url']", + "attribute": "content", + "download": { + "rename": "abstract.html" + } + }, + "references": { + "selector": "//meta[@name='citation_reference']", + "attribute": "content" + }, + "htmlCitations": { + "selector": "//div[@class='BIBL']", + "attribute": "html" + }, "authors": { "selector": "//meta[@name='citation_author']", "attribute": "content" @@ -13,10 +123,7 @@ "selector": "//title", "attribute": "text" }, - "doi": { - "selector": "//meta[@name='DC.identifier']", - "attribute": "content" - }, + "fulltext_pdf": { "selector": "//meta[@name='citation_pdf_url']", "attribute": "content", From 62774eee826e9beaba512981fd01b05481c5d1e6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Saulius=20Gra=C5=BEulis?= Date: Sat, 24 Jan 2015 15:59:03 +0200 Subject: [PATCH 114/154] Adding all DC.* extraction rules to "scrapers/acta-e-scripts.json". --- scrapers/acta-e-scripts.json | 46 ++++++++++++++++++++++++++++++++---- 1 file changed, 42 insertions(+), 4 deletions(-) diff --git a/scrapers/acta-e-scripts.json b/scrapers/acta-e-scripts.json index 1530614..1652b4b 100644 --- a/scrapers/acta-e-scripts.json +++ b/scrapers/acta-e-scripts.json @@ -1,18 +1,56 @@ { - "url": "scripts\\.iucr\\.org", + "url": "scripts\\.iucr\\.org", + "comment": "A scraper for the IUCr Acta Cryst. E journal (S.G.)", + "comment": "The full text HTML is not downloaded in this file since the page only gives a frame set, not the text itself.", "elements" : { - "authors": { + "htmlBodyAuthors": { "selector": "//a[contains(@href, 'author_name=')]", "attribute": "text" }, - "authorUrl": { + "htmlBodyAuthorUrls": { "selector": "//a[contains(@href, 'author_name=')]", "attribute": "href" }, - "doi": { + + + "identifier": { "selector": "//meta[@name='DC.identifier']", "attribute": "content" }, + + "publisher": { + "selector": "//meta[@name='DC.publisher']", + "attribute": "content" + }, + "creators": { + "selector": "//meta[@name='DC.creator']", + "attribute": "content" + }, + "contributors": { + "selector": "//meta[@name='DC.contributor']", + "attribute": "content" + }, + "source": { + "selector": "//meta[@name='DC.source']", + "attribute": "content" + }, + "license": { + "selector": "//meta[@name='DC.rights']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@name='DC.date']", + "attribute": "content" + }, + "language": { + "selector": "//meta[@name='DC.language']", + "attribute": "content" + }, + "description": { + "selector": "//meta[@name='DC.description']", + "attribute": "content" + }, + "fulltext_pdf": { "selector": "//a[img[@alt='pdf version']]", "attribute": "href", From 90e99f8673f6711782af2e9c11410eaaed471ca8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Saulius=20Gra=C5=BEulis?= Date: Sat, 24 Jan 2015 16:00:28 +0200 Subject: [PATCH 115/154] Adidng comment on the "scrapers/acta-e-scripts.json" scraper input. --- scrapers/acta-e-scripts.json | 1 + 1 file changed, 1 insertion(+) diff --git a/scrapers/acta-e-scripts.json b/scrapers/acta-e-scripts.json index 1652b4b..aba6f66 100644 --- a/scrapers/acta-e-scripts.json +++ b/scrapers/acta-e-scripts.json @@ -2,6 +2,7 @@ "url": "scripts\\.iucr\\.org", "comment": "A scraper for the IUCr Acta Cryst. E journal (S.G.)", "comment": "The full text HTML is not downloaded in this file since the page only gives a frame set, not the text itself.", + "comment": "This scraper probably gets the same input HTML as the 'acta-e-doi.json' scraper. (S.G.)", "elements" : { "htmlBodyAuthors": { "selector": "//a[contains(@href, 'author_name=')]", From 6919497da6dc66bf37e5bcae927034fd7bf773e2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Saulius=20Gra=C5=BEulis?= Date: Sat, 24 Jan 2015 16:07:47 +0200 Subject: [PATCH 116/154] Adding test URLs from other (non-open-access) Acta Cryst. journals. --- test/acta-cryst_test_urls.txt | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 test/acta-cryst_test_urls.txt diff --git a/test/acta-cryst_test_urls.txt b/test/acta-cryst_test_urls.txt new file mode 100644 index 0000000..d3f6b8e --- /dev/null +++ b/test/acta-cryst_test_urls.txt @@ -0,0 +1,12 @@ +http://dx.doi.org/10.1107/S0108270112000455 +http://dx.doi.org/10.1107/S0108270112001011 +http://dx.doi.org/10.1107/S0108270112006014 +http://scripts.iucr.org/cgi-bin/paper?S0108270112000455 +http://scripts.iucr.org/cgi-bin/paper?S0108270112001011 +http://scripts.iucr.org/cgi-bin/paper?S0108270112006014 +http://dx.doi.org/10.1107/S0108768112017466 +http://dx.doi.org/10.1107/S010876811201419X +http://dx.doi.org/10.1107/S0108768112008038 +http://scripts.iucr.org/cgi-bin/paper?S0108768112017466 +http://scripts.iucr.org/cgi-bin/paper?S010876811201419X +http://scripts.iucr.org/cgi-bin/paper?S0108768112008038 From 19935c844e0b803dd14de44f1b16b6ce2d025ba0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Saulius=20Gra=C5=BEulis?= Date: Sat, 24 Jan 2015 16:09:06 +0200 Subject: [PATCH 117/154] Deleting the test file with non-OA IUCr journal URLs, since tests on these journals will fail on machines that do not have library subscrition to IUCr journals :(. --- test/acta-cryst_test_urls.txt | 12 ------------ 1 file changed, 12 deletions(-) delete mode 100644 test/acta-cryst_test_urls.txt diff --git a/test/acta-cryst_test_urls.txt b/test/acta-cryst_test_urls.txt deleted file mode 100644 index d3f6b8e..0000000 --- a/test/acta-cryst_test_urls.txt +++ /dev/null @@ -1,12 +0,0 @@ -http://dx.doi.org/10.1107/S0108270112000455 -http://dx.doi.org/10.1107/S0108270112001011 -http://dx.doi.org/10.1107/S0108270112006014 -http://scripts.iucr.org/cgi-bin/paper?S0108270112000455 -http://scripts.iucr.org/cgi-bin/paper?S0108270112001011 -http://scripts.iucr.org/cgi-bin/paper?S0108270112006014 -http://dx.doi.org/10.1107/S0108768112017466 -http://dx.doi.org/10.1107/S010876811201419X -http://dx.doi.org/10.1107/S0108768112008038 -http://scripts.iucr.org/cgi-bin/paper?S0108768112017466 -http://scripts.iucr.org/cgi-bin/paper?S010876811201419X -http://scripts.iucr.org/cgi-bin/paper?S0108768112008038 From 62cc846eec71736e5906f4922d9d5ca6b20e61d7 Mon Sep 17 00:00:00 2001 From: sauliusg Date: Mon, 26 Jan 2015 14:47:30 +0200 Subject: [PATCH 118/154] trunk/ (saulius@koala.ibt.lt) Setting up the svn:ignore property on trunk/ to ignore the outputs/ directory created by 'quickscrape' and the downloaded sample *.html files. From 1f519fae08ce36d553a629014250a45aeadfdcdc Mon Sep 17 00:00:00 2001 From: sauliusg Date: Mon, 26 Jan 2015 14:48:20 +0200 Subject: [PATCH 119/154] trunk/ (saulius@koala.ibt.lt) Updating the svn:ignore property to correctly ignore the 'outputs/' directory. From 16275a038cf1a84330225c2fb5640e87c0512268 Mon Sep 17 00:00:00 2001 From: sauliusg Date: Mon, 26 Jan 2015 14:52:00 +0200 Subject: [PATCH 120/154] trunk/ (saulius@koala.ibt.lt) Adding rules to download the supplementary CIF and the structure factor file from the Acta Cryst. E papers to the 'scrapers/acta-e-doi.json' scraper. --- scrapers/acta-e-doi.json | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/scrapers/acta-e-doi.json b/scrapers/acta-e-doi.json index 1af0e8c..9f5dc77 100644 --- a/scrapers/acta-e-doi.json +++ b/scrapers/acta-e-doi.json @@ -51,6 +51,22 @@ "selector": "//a[img[@alt='HTML version']]", "attribute": "href", "download": false + }, + + "coordinates_cif": { + "selector": "//a[img[@alt='cif file']]", + "attribute": "href", + "download": { + "rename": "coordinates.cif" + } + }, + + "structure_factors_cif": { + "selector": "//a[img[@alt='structure factors']]", + "attribute": "href", + "download": { + "rename": "sf.hkl" + } } } } From bd636a57fe2f91851f6968147deb161322100239 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Wed, 4 Feb 2015 02:09:34 +0000 Subject: [PATCH 121/154] updated plos scraper --- scrapers/plos.json | 144 +++++++++++++++++++++++++++++++++++++-------- 1 file changed, 120 insertions(+), 24 deletions(-) diff --git a/scrapers/plos.json b/scrapers/plos.json index f6bba67..99b2804 100644 --- a/scrapers/plos.json +++ b/scrapers/plos.json @@ -1,39 +1,62 @@ { "url": "plos.*\\.org", "elements": { - "fulltext_pdf": { - "selector": "//meta[@name='citation_pdf_url']", - "attribute": "content", - "download": { - "rename": "fulltext.pdf" - } + "publisher": { + "selector": "//meta[@name='citation_publisher']", + "attribute": "content" }, - "fulltext_html": { - "selector": "//meta[@name='citation_fulltext_html_url']", - "attribute": "content", - "download": { - "rename": "fulltext.html" - } + "journal_name": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" }, - "fulltext_xml": { - "selector": "//a[@title='Download article XML']", - "attribute": "href", - "download": { - "rename": "fulltext.xml" - } + "journal_issn": { + "selector": "//meta[@name='citation_issn']", + "attribute": "content" }, "title": { "selector": "//meta[@name='citation_title']", "attribute": "content" }, - "author": { - "selector": "//meta[@name='citation_author']", + "keywords": { + "selector": "//meta[@name='citation_keywords']", "attribute": "content" }, - "date": { - "selector": "//meta[@name='citation_date']", + "author_name": { + "selector": "//meta[@name='citation_author']", "attribute": "content" }, + "author_institution": { + "selector": "//ul[contains(@class, 'authors')]//p[text()[contains(., 'Affiliations:')]]", + "attribute": "text", + "regex": { + "source": "Affiliations:\\s+(.+)" + } + }, + "editor_name": { + "selector": "//dd[@itemprop='editor']", + "attribute": "text" + }, + "date_published": { + "selector": "//div[@class='articleinfo']//p[node()[contains(., 'Published')]]", + "attribute": "text", + "regex": { + "source": "Published:\\s(.+)" + } + }, + "date_accepted": { + "selector": "//div[@class='articleinfo']//p[node()[contains(., 'Accepted')]]", + "attribute": "text", + "regex": { + "source": "Accepted:\\s([^;]+)" + } + }, + "date_submitted": { + "selector": "//div[@class='articleinfo']//p[node()[contains(., 'Received')]]", + "attribute": "text", + "regex": { + "source": "Received:\\s([^;]+)" + } + }, "doi": { "selector": "//meta[@name='citation_doi']", "attribute": "content" @@ -50,12 +73,85 @@ "selector": "//meta[@name='citation_firstpage']", "attribute": "content" }, - "description": { + "abstract": { "selector": "//meta[@name='description']", "attribute": "content" }, - "abstract":{ + "abstract_html": { "selector": "//div[contains(@class, 'abstract')]", + "attribute": "html" + }, + "abstract_text": { + "selector": "//meta[@name='twitter:description']", + "attribute": "content" + }, + "introduction_html": { + "selector": "//h3[text()='Introduction']/..", + "attribute": "html" + }, + "methods_html": { + "selector": "//h3[text()='Materials and Methods']/..", + "attribute": "html" + }, + "results_html": { + "selector": "//h3[text()='Results']/..", + "attribute": "html" + }, + "discussion_html": { + "selector": "//h3[text()='Discussion']/..", + "attribute": "html" + }, + "author_contrib_html": { + "selector": "//div[contains(@class, 'contributions')]//p", + "attribute": "html" + }, + "references_html": { + "selector": "//ol[contains(@class, 'references')]/li", + "attribute": "html" + }, + "figures_html": { + "selector": "//div[contains(@class, 'figure')]", + "attribute": "html" + }, + "tables_html": { + "selector": "//div[contains(@class, 'figure')]", + "attribute": "html" + }, + "fulltext_html": { + "selector": "//link[@rel='canonical']", + "attribute": "href", + "download": { + "rename": "fulltext.html" + } + }, + "fulltext_pdf": { + "selector": "//a[@id='downloadPdf']", + "attribute": "href", + "download": { + "rename": "fulltext.pdf" + } + }, + "fulltext_xml": { + "selector": "//a[@id='downloadXml']", + "attribute": "href", + "download": { + "rename": "fulltext.xml" + } + }, + "supplementary_file": { + "selector": "//h3[text()='Supporting Information']/..//a/@href", + "download": true + }, + "figures_image": { + "selector": "//div[contains(@class, 'figure-inline-download')]//a[text()[contains(., 'larger')]]", + "attribute": "href" + }, + "license": { + "selector": "//span[contains(concat(' ', normalize-space(@class), ' '), ' license-p ')]", + "attribute": "text" + }, + "copyright": { + "selector": "//span[starts-with(@itemprop, 'copyright')]/..", "attribute": "text" } } From 2081cb6cf581942d5dedc173b7da418466f3faf0 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sat, 11 Apr 2015 14:46:43 +0100 Subject: [PATCH 122/154] Update PLoS scraper to fix fulltext xml capture --- scrapers/plos.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/scrapers/plos.json b/scrapers/plos.json index 99b2804..63e14c2 100644 --- a/scrapers/plos.json +++ b/scrapers/plos.json @@ -6,8 +6,8 @@ "attribute": "content" }, "journal_name": { - "selector": "//meta[@name='citation_journal_title']", - "attribute": "content" + "selector": "//li[contains(@class, 'home-link')]//a", + "attribute": "text" }, "journal_issn": { "selector": "//meta[@name='citation_issn']", @@ -26,7 +26,7 @@ "attribute": "content" }, "author_institution": { - "selector": "//ul[contains(@class, 'authors')]//p[text()[contains(., 'Affiliations:')]]", + "selector": "//dl[contains(@class, 'authors')]//dd", "attribute": "text", "regex": { "source": "Affiliations:\\s+(.+)" @@ -132,7 +132,7 @@ } }, "fulltext_xml": { - "selector": "//a[@id='downloadXml']", + "selector": "//a[text()='XML']", "attribute": "href", "download": { "rename": "fulltext.xml" From f2d4d6fa805d22c34ea63fa37f15397c64d1db53 Mon Sep 17 00:00:00 2001 From: Robin Wilson Date: Sat, 18 Apr 2015 15:44:16 +0100 Subject: [PATCH 123/154] Fixed typo in MDPI scraper The typo meant that the fulltext XML was not extracted, as it was spelled "fulltest". --- scrapers/mdpi.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scrapers/mdpi.json b/scrapers/mdpi.json index 436cdf5..1b28cbb 100644 --- a/scrapers/mdpi.json +++ b/scrapers/mdpi.json @@ -60,7 +60,7 @@ } }, "fulltext_xml": { - "selector": "//meta[@name='fulltest_xml']", + "selector": "//meta[@name='fulltext_xml']", "attribute": "content", "download": { "rename": "fulltext.xml" From a21a5d3133e18e61950aa3f9a6512929e3d4982c Mon Sep 17 00:00:00 2001 From: Andrius Merkys Date: Sat, 20 Jun 2015 16:27:01 +0100 Subject: [PATCH 124/154] Adding a template for new IUCr journal layout (http://journals.new.iucr.org). --- scrapers/acta-e-new-body.json | 51 +++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 scrapers/acta-e-new-body.json diff --git a/scrapers/acta-e-new-body.json b/scrapers/acta-e-new-body.json new file mode 100644 index 0000000..b11d433 --- /dev/null +++ b/scrapers/acta-e-new-body.json @@ -0,0 +1,51 @@ +{ + "url": "\\w+\\.\\w+", + "elements": { + "fulltext_pdf": { + "selector": "//meta[@name='citation_pdf_url']", + "attribute": "content", + "download": { + "rename": "fulltext.pdf" + } + }, + "fulltext_html": { + "selector": "//meta[@name='citation_fulltext_html_url']", + "attribute": "content", + "download": { + "rename": "fulltext.html" + } + }, + "title": { + "selector": "//meta[@name='citation_title']", + "attribute": "content" + }, + "author": { + "selector": "//meta[@name='citation_author']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@name='citation_date']", + "attribute": "content" + }, + "doi": { + "selector": "//meta[@name='citation_doi']", + "attribute": "content" + }, + "volume": { + "selector": "//meta[@name='citation_volume']", + "attribute": "content" + }, + "issue": { + "selector": "//meta[@name='citation_issue']", + "attribute": "content" + }, + "firstpage": { + "selector": "//meta[@name='citation_firstpage']", + "attribute": "content" + }, + "description": { + "selector": "//meta[@name='description']", + "attribute": "content" + } + } +} From bceca756d8c0c278c7439c6bdd9f48db31d5f141 Mon Sep 17 00:00:00 2001 From: Andrius Merkys Date: Sat, 20 Jun 2015 17:03:16 +0100 Subject: [PATCH 125/154] Implementing the extraction of abstract for new IUCr layout. --- scrapers/acta-e-new-body.json | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/scrapers/acta-e-new-body.json b/scrapers/acta-e-new-body.json index b11d433..4a0acac 100644 --- a/scrapers/acta-e-new-body.json +++ b/scrapers/acta-e-new-body.json @@ -1,5 +1,6 @@ { - "url": "\\w+\\.\\w+", + "url": "journals\\.new\\.iucr\\.org/.*.html", + "comment": "A scraper for the new layout IUCr Acta Cryst. E journal", "elements": { "fulltext_pdf": { "selector": "//meta[@name='citation_pdf_url']", @@ -46,6 +47,10 @@ "description": { "selector": "//meta[@name='description']", "attribute": "content" + }, + "abstract": { + "selector": "//div[@id='abs']", + "attribute": "html" } } } From 91f3782e82e59bac0f7883db33e0e0d7b383daf2 Mon Sep 17 00:00:00 2001 From: Andrius Merkys Date: Sun, 21 Jun 2015 08:05:58 +0100 Subject: [PATCH 126/154] Extracting references. --- scrapers/acta-e-new-body.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/scrapers/acta-e-new-body.json b/scrapers/acta-e-new-body.json index 4a0acac..f974e55 100644 --- a/scrapers/acta-e-new-body.json +++ b/scrapers/acta-e-new-body.json @@ -51,6 +51,10 @@ "abstract": { "selector": "//div[@id='abs']", "attribute": "html" + }, + "references": { + "selector": "//meta[@name='citation_reference']", + "attribute": "content" } } } From 55029815310b550744430c158dca34e855dcf9b7 Mon Sep 17 00:00:00 2001 From: Andrius Merkys Date: Sun, 21 Jun 2015 09:43:24 +0100 Subject: [PATCH 127/154] Fixing 'fulltext_html' and 'description' fields, adding 'abstract_html'. --- scrapers/acta-e-new-body.json | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/scrapers/acta-e-new-body.json b/scrapers/acta-e-new-body.json index f974e55..99b2fbb 100644 --- a/scrapers/acta-e-new-body.json +++ b/scrapers/acta-e-new-body.json @@ -10,7 +10,7 @@ } }, "fulltext_html": { - "selector": "//meta[@name='citation_fulltext_html_url']", + "selector": "//meta[@name='citation_fulltext_url']", "attribute": "content", "download": { "rename": "fulltext.html" @@ -45,13 +45,20 @@ "attribute": "content" }, "description": { - "selector": "//meta[@name='description']", + "selector": "//meta[@name='DC.description']", "attribute": "content" }, "abstract": { "selector": "//div[@id='abs']", "attribute": "html" }, + "abstract_html": { + "selector": "//meta[@name='citation_abstract_html_url']", + "attribute": "content", + "download": { + "rename": "abstract.html" + } + }, "references": { "selector": "//meta[@name='citation_reference']", "attribute": "content" From 6d44bb8e1d1a62f4a82863137232d0b57d6ee2f2 Mon Sep 17 00:00:00 2001 From: Andrius Merkys Date: Sun, 21 Jun 2015 10:02:39 +0100 Subject: [PATCH 128/154] Bringing back some of the elements from acta-e-body.json. --- scrapers/acta-e-new-body.json | 80 +++++++++++++++++++++++++++++++++-- 1 file changed, 77 insertions(+), 3 deletions(-) diff --git a/scrapers/acta-e-new-body.json b/scrapers/acta-e-new-body.json index 99b2fbb..eeddf7a 100644 --- a/scrapers/acta-e-new-body.json +++ b/scrapers/acta-e-new-body.json @@ -2,6 +2,47 @@ "url": "journals\\.new\\.iucr\\.org/.*.html", "comment": "A scraper for the new layout IUCr Acta Cryst. E journal", "elements": { + "identifier": { + "selector": "//meta[@name='DC.identifier']", + "attribute": "content" + }, + "publisher": { + "selector": "//meta[@name='DC.publisher']", + "attribute": "content" + }, + "creators": { + "selector": "//meta[@name='DC.creator']", + "attribute": "content" + }, + "contributors": { + "selector": "//meta[@name='DC.contributor']", + "attribute": "content" + }, + "source": { + "selector": "//meta[@name='DC.source']", + "attribute": "content" + }, + "license": { + "selector": "//meta[@name='DC.rights']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@name='DC.date']", + "attribute": "content" + }, + "language": { + "selector": "//meta[@name='DC.language']", + "attribute": "content" + }, + "description": { + "selector": "//meta[@name='DC.description']", + "attribute": "content" + }, + "fulltext_html_frameset": { + "selector": "//meta[@name='citation_fulltext_url']", + "attribute": "content", + "download": false + }, "fulltext_pdf": { "selector": "//meta[@name='citation_pdf_url']", "attribute": "content", @@ -24,6 +65,22 @@ "selector": "//meta[@name='citation_author']", "attribute": "content" }, + "author_institutions": { + "selector": "//meta[@name='citation_author_institution']", + "attribute": "content" + }, + "corresponding_author_email": { + "selector": "//meta[@name='citation_author_email']", + "attribute": "content" + }, + "citationDate": { + "selector": "//meta[@name='citation_date']", + "attribute": "content" + }, + "onlineDate": { + "selector": "//meta[@name='citation_online_date']", + "attribute": "content" + }, "date": { "selector": "//meta[@name='citation_date']", "attribute": "content" @@ -44,9 +101,21 @@ "selector": "//meta[@name='citation_firstpage']", "attribute": "content" }, - "description": { - "selector": "//meta[@name='DC.description']", - "attribute": "content" + "lastpage": { + "selector": "//meta[@name='citation_lastpage']", + "attribute": "content" + }, + "doi": { + "selector": "//meta[@name='citation_doi']", + "attribute": "content" + }, + "journal": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" + }, + "issn": { + "selector": "//meta[@name='citation_issn']", + "attribute": "content" }, "abstract": { "selector": "//div[@id='abs']", @@ -59,6 +128,11 @@ "rename": "abstract.html" } }, + "figure": { + "selector": "//div[@class='scheme']//img", + "attribute": "src", + "download": true + }, "references": { "selector": "//meta[@name='citation_reference']", "attribute": "content" From e8cbafe292790d07ba01a994e43d099e82785815 Mon Sep 17 00:00:00 2001 From: Andrius Merkys Date: Sun, 21 Jun 2015 10:13:03 +0100 Subject: [PATCH 129/154] Adding 'htmlBodyAuthors' and 'htmlBodyAuthorUrls'. --- scrapers/acta-e-new-body.json | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/scrapers/acta-e-new-body.json b/scrapers/acta-e-new-body.json index eeddf7a..5e2fc10 100644 --- a/scrapers/acta-e-new-body.json +++ b/scrapers/acta-e-new-body.json @@ -2,6 +2,14 @@ "url": "journals\\.new\\.iucr\\.org/.*.html", "comment": "A scraper for the new layout IUCr Acta Cryst. E journal", "elements": { + "htmlBodyAuthors": { + "selector": "//div[@class='au']//span[@class='au']", + "attribute": "text" + }, + "htmlBodyAuthorUrls": { + "selector": "//div[@class='au']//a[contains(@href, '/citedin')]", + "attribute": "href" + }, "identifier": { "selector": "//meta[@name='DC.identifier']", "attribute": "content" From 03a18988922fbeebfce2fdf2186dca11b275cf48 Mon Sep 17 00:00:00 2001 From: Andrius Merkys Date: Sun, 21 Jun 2015 10:24:55 +0100 Subject: [PATCH 130/154] Ceasing to download fulltext HTML, since the download link points to HTML frameset. --- scrapers/acta-e-new-body.json | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/scrapers/acta-e-new-body.json b/scrapers/acta-e-new-body.json index 5e2fc10..5d4ec2c 100644 --- a/scrapers/acta-e-new-body.json +++ b/scrapers/acta-e-new-body.json @@ -1,6 +1,7 @@ { "url": "journals\\.new\\.iucr\\.org/.*.html", "comment": "A scraper for the new layout IUCr Acta Cryst. E journal", + "comment": "The full text HTML is not downloaded in this file since the page only gives a frame set, not the text itself.", "elements": { "htmlBodyAuthors": { "selector": "//div[@class='au']//span[@class='au']", @@ -61,9 +62,7 @@ "fulltext_html": { "selector": "//meta[@name='citation_fulltext_url']", "attribute": "content", - "download": { - "rename": "fulltext.html" - } + "download": false }, "title": { "selector": "//meta[@name='citation_title']", From ccaad3cfaa1358651167c4b831edbcaa3c99b066 Mon Sep 17 00:00:00 2001 From: Andrius Merkys Date: Sun, 21 Jun 2015 10:28:06 +0100 Subject: [PATCH 131/154] Downloading supplementary CIF files. --- scrapers/acta-e-new-body.json | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/scrapers/acta-e-new-body.json b/scrapers/acta-e-new-body.json index 5d4ec2c..503564f 100644 --- a/scrapers/acta-e-new-body.json +++ b/scrapers/acta-e-new-body.json @@ -135,6 +135,13 @@ "rename": "abstract.html" } }, + "cif": { + "selector": "//a[@title='CIF']", + "attribute": "href", + "download": { + "rename": "supplement.cif" + } + }, "figure": { "selector": "//div[@class='scheme']//img", "attribute": "src", From 4369f166947b16e0070272b795483bd2d81c727e Mon Sep 17 00:00:00 2001 From: Andrius Merkys Date: Sun, 21 Jun 2015 10:41:46 +0100 Subject: [PATCH 132/154] Adjusting name of the downloaded CIF file to one used in acta-e-doi.json. --- scrapers/acta-e-new-body.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scrapers/acta-e-new-body.json b/scrapers/acta-e-new-body.json index 503564f..21e1df6 100644 --- a/scrapers/acta-e-new-body.json +++ b/scrapers/acta-e-new-body.json @@ -135,11 +135,11 @@ "rename": "abstract.html" } }, - "cif": { + "coordinates_cif": { "selector": "//a[@title='CIF']", "attribute": "href", "download": { - "rename": "supplement.cif" + "rename": "coordinates.cif" } }, "figure": { From de25fd2d96f4e4666320afbeed9e09866c914821 Mon Sep 17 00:00:00 2001 From: Charles Ravarani Date: Sun, 21 Jun 2015 14:31:29 +0100 Subject: [PATCH 133/154] first pass at Nature scraper --- scrapers/nature.json | 125 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 125 insertions(+) create mode 100644 scrapers/nature.json diff --git a/scrapers/nature.json b/scrapers/nature.json new file mode 100644 index 0000000..70bc405 --- /dev/null +++ b/scrapers/nature.json @@ -0,0 +1,125 @@ +{ + "url": "www\\.nature\\.com/.+/journal/.+/.+/abs/*", + "elements": { + "title": { + "selector": "//meta[@name='DC.title']", + "attribute": "content" + }, + "authors": { + "selector": "//meta[@name='DC.creator']", + "attribute": "content" + }, + "date": { + "selector": "//meta[@name='prism.publicationDate']", + "attribute": "content" + }, + "volume": { + "selector": "//meta[@name='prism.volume']", + "attribute": "content" + }, + "issue": { + "selector": "//meta[@name='prism.issue']", + "attribute": "content" + }, + "section": { + "selector": "//meta[@name='prism.section']", + "attribute": "content" + }, + "doi": { + "selector": "//meta[@name='DC.identifier']", + "attribute": "content" + }, + "fulltext_html": { + "selector": "//p[@class='full-text-link right-arrow']/a", + "attribute": "href", + "download": { + "rename": "fulltext.html" + } + }, + "fulltext_pdf": { + "selector": "//li[@class='download-option articlepdf']/a", + "attribute": "href", + "download": { + "rename": "fulltext.pdf" + } + }, + "keywords": { + "selector": "//div[@class='article-keywords inline-list cleared']//a" + }, + "supplementary_material_movie": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.mov')]", + "attribute": "href", + "download": true + }, + "supplementary_material_pdf": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.pdf')]", + "attribute": "href", + "download": true + }, + "supplementary_material_ms-excel": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.xls')]", + "attribute": "href", + "download": true + }, + "supplementary_material_ms-word": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.doc')]", + "attribute": "href", + "download": true + }, + "supplementary_material_ascii": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.txt')]", + "attribute": "href", + "download": true + }, + "supplementary_material_richtext": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.rtf')]", + "attribute": "href", + "download": true + }, + "supplementary_material_wordperfect": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.wpd')]", + "attribute": "href", + "download": true + }, + "supplementary_material_postscript": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.ps')]", + "attribute": "href", + "download": true + }, + "supplementary_material_encapsulated-postscript": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.eps')]", + "attribute": "href", + "download": true + }, + "supplementary_material_html": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.htm')]", + "attribute": "href", + "download": true + }, + "supplementary_material_audio": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.wav')]", + "attribute": "href", + "download": true + }, + "supplementary_material_mpg": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.mp')]", + "attribute": "href", + "download": true + }, + "supplementary_material_sbml": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.sbml')]", + "attribute": "href", + "download": true + }, + "supplementary_material_xml": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.xml')]", + "attribute": "href", + "download": true + }, + "supplementary_material_owl": { + "selector": "//div[@class='box supp-info']//a[contains(@href, '.owl')]", + "attribute": "href", + "download": true + } + } +} From 4782e3d761160d50a3a5cc5261536accb0add6e0 Mon Sep 17 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Abstract

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How do increasing temporal and spatial distance affect the emotions people feel and express in response to tragic events?\n Standard views suggest that emotional intensity should decrease but are silent on changes in emotional quality. Using a large\n Twitter data set, we identified temporal and spatial patterns in use of emotional and cognitive words in tweets about the\n Sandy Hook Elementary School shooting. Although use of sadness words decreased with time and spatial distance, use of anxiety\n words showed the opposite pattern and was associated with concurrent increases in language reflecting causal thinking. In\n a follow-up experiment, we found that thinking about abstract causes (as opposed to concrete details) of this event similarly\n evoked decreased sadness but increased anxiety, which was associated with perceptions that a similar event might occur in\n the future. These data challenge current theories of emotional reactivity and identify time, space, and abstract causal thinking\n as factors that elicit categorical shifts in emotional responses to tragedy.\n

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Study 1: Using Twitter to Track Responses to the Newtown Shooting Over Time and Space

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We gathered tweets (brief public messages posted to twitter.com) containing the keywords “Newtown” or “Sandy Hook” for nearly 6 months following the tragedy, sampling over three discrete\n time periods: December 14 through December 21, 2012; January 27 through March 3, 2013; and April 26 through May 30, 2013 (see\n Fig. 1a). Tweets were accessed via calls to the Twitter Streaming Application Programming Interface (API; Twitter, 2013). All study procedures were approved by the Columbia University Institutional Review Board.\n

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Fig. 1. \n \n

Distribution of the final sample of tweets containing the keywords “Newtown” or “Sandy Hook” across (a) time and (b) space.\n This sample excluded all instances of retweeted content, tweets in which less than 60% of the words were in the English dictionary,\n multiple tweets from a single user, tweets from different users that contained identical content, and tweets from users whose\n geographic location was not available in their profiles.\n

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Data cleaning

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All tweets were downloaded in real time as they were published to the Streaming API (for details, see the Supplemental Material\n available online). Inspection of the resulting data set revealed that some of the tweets we had sampled were duplicates, were\n spam, or had non-English content. We attempted to filter this content in order to focus our analyses on tweets with original,\n English-language content from individual users. We excluded all instances of retweeted content, tweets in which less than\n 60% of the words were in the English dictionary, multiple tweets from a single user, and tweets from different users that\n contained identical content (see the Supplemental Material for more details on these exclusions).\n

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In order to estimate the proportion of tweets in the cleaned data set that were issued by personal rather than news media\n accounts, we had four raters code a random sample of 1,000 tweets as having been posted by an individual person or by a news\n media organization (an “unclear/other” option was also available), on the basis of the name of the account and the content\n of the tweet. Tweets were coded in groups of 200 at a time, and each tweet was coded by two raters. These judgments showed\n good levels of average absolute agreement (93%; Krippendorff’s α = .66). They indicated that the majority of tweets in the\n cleaned data set had been posted by individuals (82%) and a minority had been posted by news media organizations (5%; see\n Table S1 in the Supplemental Material for further description of this sample of tweets).\n

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Variables of interest

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Predictor variables

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Each message from Twitter was time-stamped, which allowed us to quantify temporal distance from the tragedy (in seconds).\n To quantify spatial distance, we constrained our analyses to users whose location field in their Twitter profile made it possible\n to locate them to a U.S. city or state (e.g., “New York City,” “Arcata, California,” “Colorado,” or “Florida panhandle”).\n This left us with a data set of 43,548 tweets (see Fig. 1b for their geographic distribution). We used an open-source geocoding database to convert this location information to approximate\n latitude and longitude coordinates (OpenStreetMap Contributors, 2013) and conducted subsequent manual checks to flag and correct or remove geocoding errors and ambiguities (see the Supplemental\n Material). To validate these geocoded coordinates, we compared them against captured GPS location data, which were available\n for approximately 0.6% of our sample, and found that the two types of location data agreed within 200 miles for 92% of tweets\n with both types of data available. Finally, for each tweet, we calculated the geometric distance from Sandy Hook, Connecticut,\n using the Haversine formula (Sinnott, 1984). We used this measure in our analyses of spatial distance.\n

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Outcome variables

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We derived several outcome variables of psychological relevance on a tweet-by-tweet basis. For an index of the societal-level\n expression of thoughts related to this tragedy across time and space, we estimated tragedy-related tweet volume for each tweet\n in our data set. Specifically, we determined the per-second rate of publication of tragedy-related tweets at the moment the\n tweet was published. We refer to this variable as the tweet-per-second rate. We next quantified the emotional and cognitive content of the tweets using Linguistic Inquiry and Word Count (LIWC), a prominent\n lexicon and software package that computes frequencies of words reflective of particular psychological states (Pennebaker, Chung, Ireland, Gonzales, & Booth, 2007). The LIWC dictionary includes multiple word categories that have been validated against human judgments of texts’ psychological\n content. We focused on three broad classes of content. First, we considered present-tense verbs and first-person pronouns,\n which indicate attention to one’s self and one’s present temporal context and thus reflect a sense of psychological immediacy\n (Tausczik & Pennebaker, 2010). Second, we considered affect words, which are reflective of experience and expression of emotional states in general (Kahn, Tobin, Massey, & Anderson, 2007), as well as sadness words, anxiety words, and anger words, categories that reflect particular kinds of negative emotion\n (Tausczik & Pennebaker, 2010; Tov, Ng, Lin, & Qiu, 2013). Third, we looked at words that reflect attention to causal processes, which in the context of traumatic events are known\n to mark a relatively complex and abstract style of thought focused on creating causal explanations (Boals & Klein, 2005; Tausczik & Pennebaker, 2010).\n

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Analyses

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We used regression models to quantify independent effects of time (rescaled for interpretation as number of months) and approximate\n distance (rescaled for interpretation as thousands of miles) on tweet features; rescalings were conducted via multiplication\n by a conversion factor. We simultaneously included covariates of no interest to model effects of total tweet word count, county-level\n population density (U.S. Census Bureau, 2013), local politics (i.e., percentage of the popular vote Mitt Romney received in the 2012 presidential election, at county\n and state levels; Rogers & Cage, 2013), and linear, quadratic, and cubic effects of time of day. These covariates allowed us to statistically account for potential\n third variables that may have obscured or driven relationships between remoteness and use of particular word categories. For\n example, the total-word-count covariate allowed us to account for the possibility that time and spatial distance led to changes\n in the overall number of words used. The local-politics and population-density covariates allowed us to account for the possibility\n that social and political qualities of Twitter users’ local environments were related to distance from Newtown and also predictive\n of word use. The time-of-day covariates allowed us to account for circadian changes in word use.\n

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We tested exponential decay of tragedy-related tweet volume by taking the natural log transform of the tweets-per-second index\n and entering this transformed variable into an ordinary least squares model. Because the raw LIWC word-count variables followed\n overdispersed count distributions (i.e., with variance greater than the mean), we fit these data with negative binomial regression\n models (see Hilbe, 2011).\n

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Results

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Average word counts

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To characterize the affective content of the tweets in our data set, we computed word-count averages for the LIWC emotion\n categories, collapsing across time and distance. On average, the tweets in our data set had a total of 14.89 words (SE = 0.03) and 0.97 affect words (SE = 0.005). Within specific negative-emotion categories, the mean number of words was 0.16 for sadness words (SE = 0.002), 0.05 for anxiety words (SE = 0.001), and 0.26 for anger words (SE = 0.003).\n

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Effects on expression, immediacy, and overall affect

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As predicted by both the nonspecific distance hypothesis (which posits that remoteness has general effects on emotion) and\n the construal-level hypothesis (which posits that remoteness leads to more abstract forms of representation), we found that\n the passage of time led to an exponential decrease in tweet-per-second rate, b = −1.27, 95% confidence interval (CI) = [−1.28, −1.26], p < .001, and linear decreases in number of first-person pronouns, b = −0.062, 95% CI = [−0.082, −0.043], p < .001; present-tense verbs, b = −0.069, 95% CI = [−0.079, −0.059], p < .001; and affect words overall, b = −0.073, 95% CI = [−0.082, −0.064], p < .001. Increasing spatial distance brought about an independent and corresponding pattern, evoking an exponential decrease\n in the tweet-per-second rate, b = −0.040, 95% CI = [−0.056, −0.022], p < .001, as well as linear decreases in use of first-person pronouns, b = −0.049, 95% CI = [−0.081, −0.017], p < .005; present-tense verbs, b = −0.022, 95% CI = [−0.038, −0.006], p < .01; and affect words overall, b = −0.033, 95% CI = [−0.047, −0.020], p < .001. In summary, we observed time- and distance-related changes in word use suggesting decreases in posting of tragedy-related\n content, expression of psychological immediacy, and expression of emotion.\n

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Effects on sadness, anxiety, and causal thought

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Next, we considered changes in use of sadness, anxiety, and causality words, for which the construal-level hypothesis makes\n unique predictions. As predicted by this hypothesis, increasing time led to a decrease in use of sadness words, b = −0.377, 95% CI = [−0.405, −0.349], p < .001; an increase in use of anxiety words, b = 0.116, 95% CI = [0.079, 0.152], p < .001; and an increase in use of causality words, b = 0.021, 95% CI = [0.004, 0.038], p < .05 (see the graphs in Fig. 2). Similarly, increasing spatial distance brought about a decrease in use of sadness words, b = −0.057, 95% CI = [−0.091, −0.022], p < .001, and increases in use of anxiety words, b = 0.105, 95% CI = [0.044, 0.166], p < .001, and causality words, b = 0.050, 95% CI = [0.023, 0.077], p < .001. Follow-up analyses suggested that temporal patterns in word use were still evident when analyses were limited to\n sampling waves of equal duration (see the Supplemental Material).\n

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Fig. 2. \n \n

Results from Study 1: mean number of (a) sadness, (b) anxiety, and (c) causality words per tweet in tweets collected during\n the three sampling periods between December 14, 2012, and May 30, 2013. Effects of spatial distance are illustrated in the\n maps, which were derived from a series of three-dimensional spatial regression models; mean frequencies are indicated by color\n (and greater precision of the model’s predictions is represented by greater opacity). Effects of temporal distance are illustrated\n in the graphs, in which mean frequencies are plotted as a function of time since the Newtown shooting (aggregated in 24-hr\n bins); error bars represent 95% confidence intervals.\n

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Moreover, a path model (with time and distance as predictors, number of causality words as a mediator, number of anxiety words\n as the outcome, and total tweet word count as a covariate) revealed that the increase in use of anxiety words with increasing\n time and spatial distance was partially mediated by an associated increase in use of causality words, indirect effect of time\n = 0.006, 95% CI = [0.003, 0.009], p < .001; indirect effect of spatial distance = 0.005, 95% CI = [0.000, 0.009], p < .05. An analogous path model with use of sadness words as the outcome indicated that number of causality words did not\n significantly mediate either the effect of time on use of sadness words, indirect effect = −0.0006, 95% CI = [−0.002, 0.0004],\n p = .24, or the effect of spatial distance on use of sadness words, indirect effect = −0.002, 95% CI = [−0.004, 0.001], p = .23. These two path models were implemented via the gsem (generalized structural equation modeling) command in Stata 13,\n with family set to “negative binomial.” Significance of indirect paths was assessed with the nlcom command (which computes\n delta-method standard errors; StataCorp, 2013).\n

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Effects on anger

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For comparison purposes, we also investigated effects of time and spatial distance on anger, an emotion previously identified\n as a key component of the societal-level reaction to violent tragedy (e.g., Lerner, Gonzalez, Small, & Fischhoff, 2003). We found that use of anger words did not change significantly across time, b = −0.01, 95% CI = [−0.03, 0.01], p = .37, but did increase significantly with increasing spatial distance, b = 0.10, 95% CI = [0.07, 0.13], p < .001. (For additional information about the magnitude of the effects of time and spatial distance, see Tables S2 and S3\n in the Supplemental Material.)\n

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Mapping patterns of use of sadness, anxiety, and causality words

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To more thoroughly model and visualize patterns of word use across space, we ran a series of three-dimensional spatial regression\n models. In each model, a smooth surface was fitted to the observed data to predict a tweet feature (y) across the continental United States as a function of latitude (x\n 1) and longitude (x\n 2). To define these surfaces, we implemented a penalized thin-plate regression spline method using the bam function within the mgcv package in R (Wood, 2003). The mapped surfaces (see Fig. 2) represent levels of word use with variations in color and model precision (i.e., the inverse of prediction standard error,\n determined in part by data density) with variations in opacity. As expected, these mapped models are consistent with the linear\n regression analyses reported earlier (which collapsed latitude and longitude into a single distance dimension), but they provide\n more information about the spatial patterns of change in use of sadness, anxiety, and causality words.\n

\n \n
\n \n
\n \n

Word-level analyses

\n \n

To characterize the nature of these relationships at the level of individual words, we correlated time (in seconds) and approximate\n distance (in miles) with frequencies of each of the words in the LIWC sadness, anxiety, and causality categories. Table 1 summarizes the results of these analyses by showing, for each category, the five words whose usage was most strongly associated\n with spatial distance and the five words whose usage was most strongly associated with the passage of time. We corrected for\n multiple comparisons within word category using the false-discovery-rate procedure (Benjamini & Hochberg, 1995). (For additional information about word-level patterns in use of affective words, see Fig. S1 in the Supplemental Material.)\n

\n \n
\n
\n \n
\n
Table 1. \n \n

Individual Sadness, Anxiety, and Causality Words Most Strongly Associated With Increasing Time and Spatial Distance From the\n Newtown Tragedy\n

\n \n
\n
\n
\n \n
\n \n
\n \n " + ] + }, + "results_html": { + "value": [ + "\n \n

Outcome variables

\n \n

We derived several outcome variables of psychological relevance on a tweet-by-tweet basis. For an index of the societal-level\n expression of thoughts related to this tragedy across time and space, we estimated tragedy-related tweet volume for each tweet\n in our data set. Specifically, we determined the per-second rate of publication of tragedy-related tweets at the moment the\n tweet was published. We refer to this variable as the tweet-per-second rate. We next quantified the emotional and cognitive content of the tweets using Linguistic Inquiry and Word Count (LIWC), a prominent\n lexicon and software package that computes frequencies of words reflective of particular psychological states (Pennebaker, Chung, Ireland, Gonzales, & Booth, 2007). The LIWC dictionary includes multiple word categories that have been validated against human judgments of texts’ psychological\n content. We focused on three broad classes of content. First, we considered present-tense verbs and first-person pronouns,\n which indicate attention to one’s self and one’s present temporal context and thus reflect a sense of psychological immediacy\n (Tausczik & Pennebaker, 2010). Second, we considered affect words, which are reflective of experience and expression of emotional states in general (Kahn, Tobin, Massey, & Anderson, 2007), as well as sadness words, anxiety words, and anger words, categories that reflect particular kinds of negative emotion\n (Tausczik & Pennebaker, 2010; Tov, Ng, Lin, & Qiu, 2013). Third, we looked at words that reflect attention to causal processes, which in the context of traumatic events are known\n to mark a relatively complex and abstract style of thought focused on creating causal explanations (Boals & Klein, 2005; Tausczik & Pennebaker, 2010).\n

\n \n " + ] + }, + "discussion_html": { + "value": [ + "\n \n

Analyses

\n \n

We used regression models to quantify independent effects of time (rescaled for interpretation as number of months) and approximate\n distance (rescaled for interpretation as thousands of miles) on tweet features; rescalings were conducted via multiplication\n by a conversion factor. We simultaneously included covariates of no interest to model effects of total tweet word count, county-level\n population density (U.S. Census Bureau, 2013), local politics (i.e., percentage of the popular vote Mitt Romney received in the 2012 presidential election, at county\n and state levels; Rogers & Cage, 2013), and linear, quadratic, and cubic effects of time of day. These covariates allowed us to statistically account for potential\n third variables that may have obscured or driven relationships between remoteness and use of particular word categories. For\n example, the total-word-count covariate allowed us to account for the possibility that time and spatial distance led to changes\n in the overall number of words used. The local-politics and population-density covariates allowed us to account for the possibility\n that social and political qualities of Twitter users’ local environments were related to distance from Newtown and also predictive\n of word use. The time-of-day covariates allowed us to account for circadian changes in word use.\n

\n \n

We tested exponential decay of tragedy-related tweet volume by taking the natural log transform of the tweets-per-second index\n and entering this transformed variable into an ordinary least squares model. Because the raw LIWC word-count variables followed\n overdispersed count distributions (i.e., with variance greater than the mean), we fit these data with negative binomial regression\n models (see Hilbe, 2011).\n

\n \n " + ] + }, + "conclusions_html": { + "value": [ + "\n \n

Results

\n \n
\n \n

Average word counts

\n \n

To characterize the affective content of the tweets in our data set, we computed word-count averages for the LIWC emotion\n categories, collapsing across time and distance. On average, the tweets in our data set had a total of 14.89 words (SE = 0.03) and 0.97 affect words (SE = 0.005). Within specific negative-emotion categories, the mean number of words was 0.16 for sadness words (SE = 0.002), 0.05 for anxiety words (SE = 0.001), and 0.26 for anger words (SE = 0.003).\n

\n \n
\n \n
\n \n

Effects on expression, immediacy, and overall affect

\n \n

As predicted by both the nonspecific distance hypothesis (which posits that remoteness has general effects on emotion) and\n the construal-level hypothesis (which posits that remoteness leads to more abstract forms of representation), we found that\n the passage of time led to an exponential decrease in tweet-per-second rate, b = −1.27, 95% confidence interval (CI) = [−1.28, −1.26], p < .001, and linear decreases in number of first-person pronouns, b = −0.062, 95% CI = [−0.082, −0.043], p < .001; present-tense verbs, b = −0.069, 95% CI = [−0.079, −0.059], p < .001; and affect words overall, b = −0.073, 95% CI = [−0.082, −0.064], p < .001. Increasing spatial distance brought about an independent and corresponding pattern, evoking an exponential decrease\n in the tweet-per-second rate, b = −0.040, 95% CI = [−0.056, −0.022], p < .001, as well as linear decreases in use of first-person pronouns, b = −0.049, 95% CI = [−0.081, −0.017], p < .005; present-tense verbs, b = −0.022, 95% CI = [−0.038, −0.006], p < .01; and affect words overall, b = −0.033, 95% CI = [−0.047, −0.020], p < .001. In summary, we observed time- and distance-related changes in word use suggesting decreases in posting of tragedy-related\n content, expression of psychological immediacy, and expression of emotion.\n

\n \n
\n \n
\n \n

Effects on sadness, anxiety, and causal thought

\n \n

Next, we considered changes in use of sadness, anxiety, and causality words, for which the construal-level hypothesis makes\n unique predictions. As predicted by this hypothesis, increasing time led to a decrease in use of sadness words, b = −0.377, 95% CI = [−0.405, −0.349], p < .001; an increase in use of anxiety words, b = 0.116, 95% CI = [0.079, 0.152], p < .001; and an increase in use of causality words, b = 0.021, 95% CI = [0.004, 0.038], p < .05 (see the graphs in Fig. 2). Similarly, increasing spatial distance brought about a decrease in use of sadness words, b = −0.057, 95% CI = [−0.091, −0.022], p < .001, and increases in use of anxiety words, b = 0.105, 95% CI = [0.044, 0.166], p < .001, and causality words, b = 0.050, 95% CI = [0.023, 0.077], p < .001. Follow-up analyses suggested that temporal patterns in word use were still evident when analyses were limited to\n sampling waves of equal duration (see the Supplemental Material).\n

\n \n
\n
\"Fig.
View larger version:\n \n
\n
\n
Fig. 2. \n \n

Results from Study 1: mean number of (a) sadness, (b) anxiety, and (c) causality words per tweet in tweets collected during\n the three sampling periods between December 14, 2012, and May 30, 2013. Effects of spatial distance are illustrated in the\n maps, which were derived from a series of three-dimensional spatial regression models; mean frequencies are indicated by color\n (and greater precision of the model’s predictions is represented by greater opacity). Effects of temporal distance are illustrated\n in the graphs, in which mean frequencies are plotted as a function of time since the Newtown shooting (aggregated in 24-hr\n bins); error bars represent 95% confidence intervals.\n

\n \n
\n
\n
\n \n

Moreover, a path model (with time and distance as predictors, number of causality words as a mediator, number of anxiety words\n as the outcome, and total tweet word count as a covariate) revealed that the increase in use of anxiety words with increasing\n time and spatial distance was partially mediated by an associated increase in use of causality words, indirect effect of time\n = 0.006, 95% CI = [0.003, 0.009], p < .001; indirect effect of spatial distance = 0.005, 95% CI = [0.000, 0.009], p < .05. An analogous path model with use of sadness words as the outcome indicated that number of causality words did not\n significantly mediate either the effect of time on use of sadness words, indirect effect = −0.0006, 95% CI = [−0.002, 0.0004],\n p = .24, or the effect of spatial distance on use of sadness words, indirect effect = −0.002, 95% CI = [−0.004, 0.001], p = .23. These two path models were implemented via the gsem (generalized structural equation modeling) command in Stata 13,\n with family set to “negative binomial.” Significance of indirect paths was assessed with the nlcom command (which computes\n delta-method standard errors; StataCorp, 2013).\n

\n \n
\n \n
\n \n

Effects on anger

\n \n

For comparison purposes, we also investigated effects of time and spatial distance on anger, an emotion previously identified\n as a key component of the societal-level reaction to violent tragedy (e.g., Lerner, Gonzalez, Small, & Fischhoff, 2003). We found that use of anger words did not change significantly across time, b = −0.01, 95% CI = [−0.03, 0.01], p = .37, but did increase significantly with increasing spatial distance, b = 0.10, 95% CI = [0.07, 0.13], p < .001. (For additional information about the magnitude of the effects of time and spatial distance, see Tables S2 and S3\n in the Supplemental Material.)\n

\n \n
\n \n
\n \n

Mapping patterns of use of sadness, anxiety, and causality words

\n \n

To more thoroughly model and visualize patterns of word use across space, we ran a series of three-dimensional spatial regression\n models. In each model, a smooth surface was fitted to the observed data to predict a tweet feature (y) across the continental United States as a function of latitude (x\n 1) and longitude (x\n 2). To define these surfaces, we implemented a penalized thin-plate regression spline method using the bam function within the mgcv package in R (Wood, 2003). The mapped surfaces (see Fig. 2) represent levels of word use with variations in color and model precision (i.e., the inverse of prediction standard error,\n determined in part by data density) with variations in opacity. As expected, these mapped models are consistent with the linear\n regression analyses reported earlier (which collapsed latitude and longitude into a single distance dimension), but they provide\n more information about the spatial patterns of change in use of sadness, anxiety, and causality words.\n

\n \n
\n \n
\n \n

Word-level analyses

\n \n

To characterize the nature of these relationships at the level of individual words, we correlated time (in seconds) and approximate\n distance (in miles) with frequencies of each of the words in the LIWC sadness, anxiety, and causality categories. Table 1 summarizes the results of these analyses by showing, for each category, the five words whose usage was most strongly associated\n with spatial distance and the five words whose usage was most strongly associated with the passage of time. We corrected for\n multiple comparisons within word category using the false-discovery-rate procedure (Benjamini & Hochberg, 1995). (For additional information about word-level patterns in use of affective words, see Fig. S1 in the Supplemental Material.)\n

\n \n
\n
\n \n
\n
Table 1. \n \n

Individual Sadness, Anxiety, and Causality Words Most Strongly Associated With Increasing Time and Spatial Distance From the\n Newtown Tragedy\n

\n \n
\n
\n
\n \n
\n \n " + ] + }, + "acknowledgements_html": { + "value": [ + "\n \n

Acknowledgments

\n \n

We thank Daisy Burr, Ehjeen Kim, and Theodore Stephano for research assistance and David Sparks for sharing visualization\n code.\n

\n \n " + ] + }, + "competing_interests_html": { + "value": [ + "\n \n \n

Supplemental Material Additional supporting information can be found at http://pss.sagepub.com/content/by/supplemental-data\n \n

\n \n " + ] + }, + "financial_disclosure_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\n \n

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    (2003). Thin plate regression splines. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 65, 95114.
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\n " + ] + }, + "copyright": { + "value": [ + "© The Author(s) 2015" + ] + }, + "onlinefirst_published": { + "value": [ + "\n \t April 2015 \n " + ] + }, + "author_contrib_html": { + "value": [ + "\n \n \n

Author Contributions B. Doré and K. N. Ochsner designed the research. B. Doré, L. Ort, and O. Braverman collected and managed the data. B. Doré\n analyzed and visualized the data. B. Doré wrote the manuscript, and K. N. Ochsner provided critical revisions.\n

\n \n " + ] + }, + "author_corresp_html": { + "value": [ + "Bruce Doré, Psychology Department, Columbia University, 324 Schermerhorn, New York, NY 10027 E-mail: bpd2108{at}columbia.edu\n \n " + ] + }, + "file_hashes": [ + { + "fulltext.html": "6dfe67984637b87391ddaa42af355b36" + }, + { + "fulltext.pdf": "b020dd13278df6e824157c89aeb74659" + } + ] + }, + "http://pss.sagepub.com/content/26/4/385.full": { + "public_url": { + "value": [ + "http://pss.sagepub.com/content/26/4/385" + ] + }, + "title": { + "value": [ + "Bogus Visual Feedback Alters Onset of Movement-Evoked Pain in People With Neck Pain" + ] + }, + "doi": { + "value": [ + "10.1177/0956797614563339" + ] + }, + "pmid": { + "value": [ + "25691362" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "publisher": { + "value": [ + "SAGE Publications" + ] + }, + "journal": { + "value": [ + "Psychological Science" + ] + }, + "journal_issn": { + "value": [ + "0956-7976", + "1467-9280" + ] + }, + "author_name": { + "value": [ + "Daniel S. Harvie", + "Markus Broecker", + "Ross T. Smith", + "Ann Meulders", + "Victoria J. Madden", + "G. Lorimer Moseley" + ] + }, + "author_institution": { + "value": [ + "\n 1Sansom Institute for Health Research, University of South Australia", + "\n 2School of Information Technology and Mathematical Science, University of South Australia", + "\n 2School of Information Technology and Mathematical Science, University of South Australia", + "\n 3Research Group on Health Psychology, University of Leuven", + "\n 1Sansom Institute for Health Research, University of South Australia", + "\n 1Sansom Institute for Health Research, University of South Australia" + ] + }, + "volume": { + "value": [ + "26" + ] + }, + "issue": { + "value": [ + "4" + ] + }, + "firstpage": { + "value": [ + "385" + ] + }, + "article_type": { + "value": [ + "Research Articles" + ] + }, + "fulltext_html": { + "value": [ + "http://pss.sagepub.com/content/26/4/385.full" + ] + }, + "fulltext_pdf": { + "value": [ + "http://pss.sagepub.com/content/26/4/385.full.pdf" + ] + }, + "abstract_html": { + "value": [ + "\n \n

Abstract

\n \n

Pain is a protective perceptual response shaped by contextual, psychological, and sensory inputs that suggest danger to the\n body. Sensory cues suggesting that a body part is moving toward a painful position may credibly signal the threat and thereby\n modulate pain. In this experiment, we used virtual reality to investigate whether manipulating visual proprioceptive cues\n could alter movement-evoked pain in 24 people with neck pain. We hypothesized that pain would occur at a lesser degree of\n head rotation when visual feedback overstated true rotation and at a greater degree of rotation when visual feedback understated\n true rotation. Our hypothesis was clearly supported: When vision overstated the amount of rotation, pain occurred at 7% less\n rotation than under conditions of accurate visual feedback, and when vision understated rotation, pain occurred at 6% greater\n rotation than under conditions of accurate visual feedback. We concluded that visual-proprioceptive information modulated\n the threshold for movement-evoked pain, which suggests that stimuli that become associated with pain can themselves trigger\n pain.\n

\n \n " + ] + }, + "methods_html": { + "value": [ + "\n \n \n

Method

\n \n
\n \n

Participants

\n \n

Twenty-four individuals (6 men, 18 women; mean age = 45 years, SD = 15) volunteered to participate in this study. Sample size was determined a priori to enable detection of a small- to medium-sized\n effect (ηp\n 2 = .04) with 80% power, conservatively assuming a 60% correlation among repeated measures. The average duration of complaint\n was 11 years (SD = 11; range: 2 months to 45 years), and the participants’ pain conditions resulted primarily from posture, tension, or repeated\n strain (n = 9); whiplash (n = 7); degeneration (n = 5); trauma (n = 2); and scoliosis (n = 1). Participants were mildly to moderately disabled (Neck Pain Disability Index score = 29%, SD = 13%). Participants were recruited through local physiotherapy clinics and were reimbursed AU$20 for their participation.\n Participants were excluded if they had pain-free neck rotation, were unable to tolerate repeated rotation to the position\n at which they experienced the onset of pain, had severely impaired vision, or were under the age of 18. Participants were\n also excluded if a physiotherapist had identified significant neurological impairments, such as sensory or motor deficits\n and easily provoked, constant, or progressive upper-limb dysesthesia. The protocol was approved by the Human Research Ethics\n Committee of the University of South Australia (Protocol Number 31537).\n

\n \n
\n \n
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Stimulus material and apparatus

\n \n

A virtual-reality (VR) technique known as redirected walking modulates visual-proprioceptive feedback by tracking real-world movement and then feeding this back into the virtual environment\n in an understated or overstated form. Rotation gain (the factor by which real rotation is translated to virtual rotation) can be manipulated such that virtual and physical rotation\n differ. This process creates the illusion of either more or less movement than is actually happening. Within certain limits,\n participants remain unaware of the manipulation (Steinicke, Bruder, Jerald, Frenz, & Lappe, 2008). We used a VR head-mounted display (HMD) designed for immersive VR environments (Oculus Rift; Oculus VR, Irvine, CA). The\n HMD shown in Figure 1 displayed a virtual world and recorded head movement using internal gyroscopes. Customized software was used to map each\n of six scenes to the virtual template and apply the selected rotation gains. The six scenes included four outdoor scenes (a\n park, a mountain, a countryside, and church grounds) and two indoor scenes (a dining room and a living room).\n

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View larger version:\n \n
\n
\n
Fig. 1. \n \n

Virtual reality equipment. Participants sat in supportive chairs that prevented trunk movement (i.e., a seat belt around their\n shoulders) and wore headphones and head-mounted displays. A 360° (cylindrical) virtual template accommodated six virtual scenes.\n

\n \n
\n
\n
\n \n
\n \n
\n \n

Experimental design

\n \n

We used a within-subjects, randomized, double-blinded, repeated-measures design. The distance from center position to the\n left or right position at which participants experienced the onset of pain (i.e., the pain-free range of motion) was quantified in three conditions. Virtual rotation was (a) 20% less than actual physical rotation (rotation gain = 0.8),\n (b) equal to actual physical rotation (rotation gain = 1), or (c) 20% greater than actual physical rotation (rotation gain\n = 1.2). The order of the three conditions was counterbalanced across participants, which created six possible orders in which\n conditions could be presented. Four participants were randomly assigned to each order. Participants were blinded to the experimental\n manipulation and study purpose, and the files relating to the three VR conditions were coded, thereby blinding the experimenter\n to the order of conditions. The measurement of neck rotation was automated, and data were extracted only after collection\n was completed.\n

\n \n
\n \n
\n \n

Measurement

\n \n

Pain-free range of motion for axial neck rotation was measured in degrees. Because participants stopped at the onset of pain\n in each trial, the distance from center position to the left or right position at which participants experienced the onset\n of pain was defined as the peak rotation for each trial. This measure was extracted from each automated trial output by a\n blinded assessor.\n

\n \n
\n \n
\n \n

Protocol

\n \n

To prevent changes in postural alignment and to isolate neck movement, we asked participants to sit in a supportive chair,\n and their torsos were fixed in place by a seat belt at the level of the shoulders (see Fig. 1). A laser pointer was affixed to the HMD; the dot it produced was used to mark the starting position on the wall as a physical\n reference point for zeroing of the gyroscopes between measures and conditions. Participants wore headphones that emitted white\n noise to counter any incidental noise that might inform head orientation and disrupt the illusion.\n

\n \n

For each of the three conditions, participants were asked to rotate their heads slowly to the left and to stop at the onset\n of pain. They then returned their heads to the center, at which point the next trial was loaded, and the task was repeated\n on the right side. Each condition consisted of six measures of left rotation and six measures of right rotation. After each\n condition, participants were asked to rate the average pain intensity experienced for each rotation direction. This allowed\n for subsequent assessment of any overall differences in pain intensity between conditions. Pain was rated on an 11-point numerical\n scale (0 = no pain, 10 = the worst imaginable pain). To minimize the possibility that subjects would become aware of the different rotation settings and thus directly compare\n them, we used a 3-min interval between conditions. In addition, the six different VR scenes acted as a distraction from the\n actual study purpose and reduced the risk of participants’ anchoring their rotation to a previous visual cue within a VR scene.\n To assess blinding, at the end of the experiment we asked participants whether they noticed anything different between the\n three conditions.\n

\n \n
\n \n
\n \n

Manipulation Check 1: setting boundaries for altered visual-proprioceptive feedback

\n \n

To blind participants to this manipulation, we based the upper and lower limits of the rotation gain on the results of a pilot\n study. During this pilot study, an independent cohort of 9 healthy participants (7 men, 2 women; mean age = 32 years, SD = 12) were presented with a range of rotation-gain settings and asked to rotate their heads. They were to indicate when a\n difference between real and virtual rotation occurred by rating the observed rotation as slower than, equal to, or faster\n than the true physical rotation. We aimed to determine the rotation gain at which participants were more likely to judge the\n virtual and real rotation to be equal than they were to judge them to be different. As shown in Figure 2, the rotation gains that corresponded to these points were 0.72 and 1.18. As a result, our experimental gain settings were\n chosen to fall between 0.8 and 1.2, and additional controls were implemented to ensure that participants in the main study\n remained blinded.\n

\n \n
\n
\"Fig.
View larger version:\n \n
\n
\n
Fig. 2. \n \n

Results from the pilot study. The graph shows the percentage of rotations rated as slower than, equal to, or faster than the\n true physical rotation as a function of rotation gain. The double-headed arrow indicates the range of rotation-gain settings\n at which virtual movement speeds were more often perceived as equal to, rather than faster or slower than, real-world movement\n speeds.\n

\n \n
\n
\n
\n \n
\n \n
\n \n

Manipulation Check 2: reliability and validity of measurement

\n \n

The reliability of the gyroscopic measurement of rotation was tested by attaching the HMD to a mechanical (goniometric) arm\n and testing its ability to repeatedly and accurately measure three set angles (20°, 40°, and 60°). Initial observation of\n repeated measures revealed that the measurement was highly precise over a small number of trials, but error gradually increased\n as the number of trials increased. Therefore, a protocol was developed that required the virtual compass to be zeroed every\n five trials. To further prevent accumulation of error, we refreshed the program between conditions. This protocol enabled\n rotation as measured by the HMD to be correlated with actual rotation, r = .994, and produced a high degree of precision in the HDM’s measurements of rotations of 20° (M = 19.8°, SD = 0.8), 40° (M = 39.6°, SD = 0.3), and 60° (M = 59.1°, SD = 2.5).\n

\n \n
\n \n
\n \n

Data extraction and statistical-analysis overview

\n \n

To test our main hypothesis (i.e., that visual information that overstates or understates true rotation can affect movement-evoked\n pain), we compared pain-free range of motion across the three conditions. We used repeated measures analysis of variance (ANOVA)\n with Bonferroni-corrected pairwise comparisons. To account for between-subject differences in range of motion, we transformed\n data for each participant to a proportion of the average range of motion demonstrated in the neutral condition. Alpha was\n set at p < .05, and we used Cohen’s guidelines (Cohen, 1988) to interpret the effect sizes ηp\n 2 (.01 = small, .059 = medium, and .138 = large) and Cohen’s d (0.2 = small, 0.5 = medium, and 0.8 = large). As a manipulation check, each participant’s average movement-evoked pain for\n each condition was normalized to a proportion of their average across conditions. Normalized pain ratings were then compared\n among conditions using repeated measures ANOVA.\n

\n \n
\n \n " + ] + }, + "results_html": { + "value": [ + "\n \n

Measurement

\n \n

Pain-free range of motion for axial neck rotation was measured in degrees. Because participants stopped at the onset of pain\n in each trial, the distance from center position to the left or right position at which participants experienced the onset\n of pain was defined as the peak rotation for each trial. This measure was extracted from each automated trial output by a\n blinded assessor.\n

\n \n " + ] + }, + "discussion_html": { + "value": [ + "\n \n

Protocol

\n \n

To prevent changes in postural alignment and to isolate neck movement, we asked participants to sit in a supportive chair,\n and their torsos were fixed in place by a seat belt at the level of the shoulders (see Fig. 1). A laser pointer was affixed to the HMD; the dot it produced was used to mark the starting position on the wall as a physical\n reference point for zeroing of the gyroscopes between measures and conditions. Participants wore headphones that emitted white\n noise to counter any incidental noise that might inform head orientation and disrupt the illusion.\n

\n \n

For each of the three conditions, participants were asked to rotate their heads slowly to the left and to stop at the onset\n of pain. They then returned their heads to the center, at which point the next trial was loaded, and the task was repeated\n on the right side. Each condition consisted of six measures of left rotation and six measures of right rotation. After each\n condition, participants were asked to rate the average pain intensity experienced for each rotation direction. This allowed\n for subsequent assessment of any overall differences in pain intensity between conditions. Pain was rated on an 11-point numerical\n scale (0 = no pain, 10 = the worst imaginable pain). To minimize the possibility that subjects would become aware of the different rotation settings and thus directly compare\n them, we used a 3-min interval between conditions. In addition, the six different VR scenes acted as a distraction from the\n actual study purpose and reduced the risk of participants’ anchoring their rotation to a previous visual cue within a VR scene.\n To assess blinding, at the end of the experiment we asked participants whether they noticed anything different between the\n three conditions.\n

\n \n " + ] + }, + "conclusions_html": { + "value": [ + "\n \n

Manipulation Check 1: setting boundaries for altered visual-proprioceptive feedback

\n \n

To blind participants to this manipulation, we based the upper and lower limits of the rotation gain on the results of a pilot\n study. During this pilot study, an independent cohort of 9 healthy participants (7 men, 2 women; mean age = 32 years, SD = 12) were presented with a range of rotation-gain settings and asked to rotate their heads. They were to indicate when a\n difference between real and virtual rotation occurred by rating the observed rotation as slower than, equal to, or faster\n than the true physical rotation. We aimed to determine the rotation gain at which participants were more likely to judge the\n virtual and real rotation to be equal than they were to judge them to be different. As shown in Figure 2, the rotation gains that corresponded to these points were 0.72 and 1.18. As a result, our experimental gain settings were\n chosen to fall between 0.8 and 1.2, and additional controls were implemented to ensure that participants in the main study\n remained blinded.\n

\n \n
\n
\"Fig.
View larger version:\n \n
\n
\n
Fig. 2. \n \n

Results from the pilot study. The graph shows the percentage of rotations rated as slower than, equal to, or faster than the\n true physical rotation as a function of rotation gain. The double-headed arrow indicates the range of rotation-gain settings\n at which virtual movement speeds were more often perceived as equal to, rather than faster or slower than, real-world movement\n speeds.\n

\n \n
\n
\n
\n \n " + ] + }, + "acknowledgements_html": { + "value": [ + "\n \n

Acknowledgments

\n \n

For assistance with recruitment, we thank Julie Peacock, Jonathon Schubert, William Kuang, and Ellie Magarey (Marion Physiotherapy);\n Di Wilson, Peter Roberts, Eva Boesch, and Toby Moen (Roberts Physiotherapy); and Jason Collins and Glen Kocher (Northcare\n Physiotherapy). We thank Anthony Ikiosoglous for acting as a blind assessor for data extraction.\n

\n \n " + ] + }, + "competing_interests_html": { + "value": [ + + ] + }, + "financial_disclosure_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\n \n

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\n " + ] + }, + "copyright": { + "value": [ + "© The Author(s) 2015" + ] + }, + "onlinefirst_published": { + "value": [ + "\n \t April 2015 \n " + ] + }, + "author_contrib_html": { + "value": [ + "\n \n \n

Author Contributions D. S. Harvie and G. L. Moseley developed the study concept; contributed to design, data analysis, and interpretation; and\n helped write the manuscript. D. S. Harvie collected the data. V. J. Madden contributed to study design and helped write the\n manuscript. M. Broecker and R. T. Smith contributed to study design and provided technical expertise for the virtual reality\n setup. A. Meulders contributed to interpretation and helped write the manuscript. All authors approved the final version of\n the manuscript for submission.\n

\n \n " + ] + }, + "author_corresp_html": { + "value": [ + "G. Lorimer Moseley, University of South Australia, GPO Box 2471, Adelaide, South Australia 5001, Australia E-mail: lorimer.moseley{at}gmail.com\n \n " + ] + }, + "file_hashes": [ + { + "fulltext.html": "3d4e3979ea58f430f5a7f9ed30612ed8" + }, + { + "fulltext.pdf": "d95ae8194cef4bab791edbf9f85ebf0b" + } + ] + }, + "http://pss.sagepub.com/content/26/4/424.full": { + "public_url": { + "value": [ + "http://pss.sagepub.com/content/26/4/424" + ] + }, + "title": { + "value": [ + "Chinese Kindergartners Learn to Read Characters Analytically" + ] + }, + "doi": { + "value": [ + "10.1177/0956797614567203" + ] + }, + "pmid": { + "value": [ + "25711130" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "publisher": { + "value": [ + "SAGE Publications" + ] + }, + "journal": { + "value": [ + "Psychological Science" + ] + }, + "journal_issn": { + "value": [ + "0956-7976", + "1467-9280" + ] + }, + "author_name": { + "value": [ + "Li Yin", + "Catherine McBride" + ] + }, + "author_institution": { + "value": [ + "\n 1Tsinghua University", + "\n 2The Chinese University of Hong Kong" + ] + }, + "volume": { + "value": [ + "26" + ] + }, + "issue": { + "value": [ + "4" + ] + }, + "firstpage": { + "value": [ + "424" + ] + }, + "article_type": { + "value": [ + "Research Articles" + ] + }, + "fulltext_html": { + "value": [ + "http://pss.sagepub.com/content/26/4/424.full" + ] + }, + "fulltext_pdf": { + "value": [ + "http://pss.sagepub.com/content/26/4/424.full.pdf" + ] + }, + "abstract_html": { + "value": [ + "\n \n

Abstract

\n \n

Do Chinese children implicitly extract information from Chinese print before they are formally taught to read? We examined\n Chinese kindergartners’ sensitivity to regularities in Chinese characters and the relationship between such sensitivity and\n later literacy ability. Eighty-five kindergartners from Beijing were given a character-learning task and assessed on word\n reading and word writing twice within a 1-year interval. Sensitivity to the structural and phonetic regularities in Chinese\n appeared in 4-year-olds, and sensitivity to the positions of radicals in Chinese characters emerged in 5-year-olds. Such sensitivities\n explained unique variance in Chinese word reading and writing 1 year later, with age and nonverbal IQ statistically controlled.\n Young children detected regularities in written Chinese before they received formal instruction in it, which underscores both\n the importance of early statistical learning for literacy development and the analytic properties of Chinese print.\n

\n \n " + ] + }, + "methods_html": { + "value": [ + "\n \n \n

Method

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Participants

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Eighty-five native Chinese-speaking children (46 boys, 39 girls) from a public kindergarten in Beijing participated at Time\n 1. Forty-two children were from second-year kindergarten (K2; range = 4 years,1 month to 5 years, 2 months; mean age = 4 years,\n 7 months; SD = 3.0 months), and 43 children were from third-year kindergarten (K3; range = 5 years, 1 month to 6 years, 2 months; mean\n age = 5 years, 5 months; SD = 4.1 months). The kindergarten follows the governmental guidelines for preschool education in China. Children are not formally\n taught to read and write at school. Teachers read aloud to children often, and children have the opportunity to look at books\n on their own. They see characters on walls, food packages, product labels, and furniture, and in many other locations. Teachers\n identify characters for children if they ask but do not provide systematic instruction on how to read and write. One year\n later, 73 of the children were tested again for reading and writing at Time 2; 12 additional children who were tested at Time\n 1 were excluded from the study because contact information was unavailable for them at Time 2.\n

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Measures

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\n \n

Character-learning task

\n \n

In the character-learning task, children were taught to pronounce novel characters (written stimuli) that were based on three\n orthographic conditions (random strokes, noncharacter, and pseudocharacter) and two phonetic-cue conditions (available and\n not available). In the random-strokes condition, the stimuli contained real strokes, but they were not always organized into\n radicals, and they were in arbitrary positions (e.g., “\"Graphic\"”). In the noncharacter condition, the stimuli contained real radicals in illegal positions (e.g., “\"Graphic\"”). In the pseudocharacter condition, the stimuli contained real radicals in legal positions (e.g., “\"Graphic\"”).\n

\n \n

Six sets of stimuli, each consisting of five items, were constructed. In three sets, there were phonetic cues in the pseudocharacter\n and noncharacter conditions, that is, the pronunciation of the whole stimulus was the same as the pronunciation of the phonetic\n radical contained in the stimulus (e.g., the whole-stimulus pronunciation was “yang” for “\"Graphic\"” and “\"Graphic\",” where the real phonetic radical “\"Graphic\"” is also pronounced “yang”). In the other three sets, there were no phonetic cues. The radicals used to construct the pseudocharacters\n and noncharacters were taken from characters familiar to children of this age range, as judged by the schoolteachers, and\n the pronunciations were taken from vocabulary familiar to children. Visual complexity (indexed by the number of strokes) was\n balanced across conditions. Table 1 shows sample stimuli and pronunciations (shown in pinyin, a phonological coding system in which Chinese characters are transcribed in Roman alphabet letters and lexical tones).\n

\n \n
\n
\n \n
\n
Table 1. \n \n

Sample Written Stimuli and Pronunciations Used in the Character-Learning Task

\n \n
\n
\n
\n \n

The character-learning task consisted of a demonstration phase and up to eight learning trials. The experimenters began by\n saying that they would play a character-learning game with the child and that the characters to be learned were unfamiliar,\n but the child should try his or her best to learn. In the demonstration phase, the experimenter showed the child a card displaying\n the character and pronounced it aloud, running his or her fingers under the character. The experimenter then asked the child\n to follow by saying, “This character is read . . . ,” prompting the child to pronounce the character. The procedure was repeated\n for all five stimuli in each set, and the order of demonstration was randomized for each child. Once all five stimuli had\n been introduced, the first learning trial began: The experimenter showed the child one of the cards and asked the child to\n give the pronunciation of the character to which it corresponded. The experimenter praised the child if he or she named the\n character correctly and provided the correct answer if the child named it incorrectly or did not remember. This process was\n repeated for each of the five characters, and the order of learning was randomized for each child. Learning trials continued\n until the child achieved the criterion of responding correctly to all five items on two consecutive trials.\n

\n \n
\n \n
\n \n

Chinese word reading

\n \n

Children were asked to read aloud 50 Chinese single-character words presented in order of increasing difficulty (Lin et al., 2010). Testing was discontinued when children failed to read 10 characters consecutively. One point was given for each correctly\n read item. The maximum score was 50. The internal consistency for this task was .96 at Time 1 and .91 at Time 2.\n

\n \n
\n \n
\n \n

Chinese word writing

\n \n

Children were asked to write 10 Chinese words (Wang, McBride-Chang, & Chan, 2014): 3 single-character words and 7 two-character words, totaling 17 characters. All words were orally familiar to children.\n The experimenter read each word twice, putting it in a sentence each time, and then asked the children to try their best to\n write the target word. One point was given for each correctly written character, and the maximum score was 17. The internal\n consistency for this task was .82 at Time 1 and .86 at Time 2.\n

\n \n
\n \n
\n \n

Nonverbal IQ

\n \n

Sets A and B of Raven’s Standard Progressive Matrices (Raven, Court, & Raven, 1996) were used to measure children’s nonverbal IQ at Time 1 only. The maximum score was 24 points.\n

\n \n
\n \n
\n \n
\n \n

Procedure

\n \n

Testing took place in the middle of the school year. Tasks were administered by trained graduates with degrees in psychology\n or linguistics. At Time 1, each child participated in four sessions, each on separate days over a 3-week period, and was tested\n individually in a quiet room. In Sessions 1 to 3, children took completed each of the three orthographic conditions (with\n and without phonetic cues). The order of conditions was balanced across children, and a different stimulus set was used for\n each orthographic condition. In Session 4, children completed the measures of Chinese word reading, Chinese word spelling,\n and nonverbal IQ, with the order of testing balanced across children. At Time 2, children were tested on Chinese word reading\n and Chinese word writing again.\n

\n \n
\n \n " + ] + }, + "results_html": { + "value": [ + "\n \n

Chinese word reading

\n \n

Children were asked to read aloud 50 Chinese single-character words presented in order of increasing difficulty (Lin et al., 2010). Testing was discontinued when children failed to read 10 characters consecutively. One point was given for each correctly\n read item. The maximum score was 50. The internal consistency for this task was .96 at Time 1 and .91 at Time 2.\n

\n \n " + ] + }, + "discussion_html": { + "value": [ + "\n \n

Chinese word writing

\n \n

Children were asked to write 10 Chinese words (Wang, McBride-Chang, & Chan, 2014): 3 single-character words and 7 two-character words, totaling 17 characters. All words were orally familiar to children.\n The experimenter read each word twice, putting it in a sentence each time, and then asked the children to try their best to\n write the target word. One point was given for each correctly written character, and the maximum score was 17. The internal\n consistency for this task was .82 at Time 1 and .86 at Time 2.\n

\n \n " + ] + }, + "conclusions_html": { + "value": [ + "\n \n

Nonverbal IQ

\n \n

Sets A and B of Raven’s Standard Progressive Matrices (Raven, Court, & Raven, 1996) were used to measure children’s nonverbal IQ at Time 1 only. The maximum score was 24 points.\n

\n \n " + ] + }, + "acknowledgements_html": { + "value": [ + "\n \n

Acknowledgments

\n \n

We thank all participating children, as well as Xiuhong Tong for her help in calculating perimetric-complexity statistics.

\n \n " + ] + }, + "competing_interests_html": { + "value": [ + + ] + }, + "financial_disclosure_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\n \n

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\n " + ] + }, + "copyright": { + "value": [ + "© The Author(s) 2015" + ] + }, + "onlinefirst_published": { + "value": [ + "\n \t April 2015 \n " + ] + }, + "author_contrib_html": { + "value": [ + "\n \n \n

Author Contributions C. McBride developed the study concept. Both authors contributed to the study design and analyzed and interpreted the data.\n Testing and data collection were performed by L. Yin. L. Yin drafted the manuscript, and C. McBride provided critical revisions.\n Both authors approved the final version of the manuscript for submission.\n

\n \n " + ] + }, + "author_corresp_html": { + "value": [ + "\n Li Yin, Tsinghua University, Wen Nan Building, Room 103, Beijing, China 100084 E-mail: yinl{at}tsinghua.edu.cn\n \n " + ] + }, + "file_hashes": [ + { + "fulltext.html": "4511f278a274ea0c5cd7516db3bb6771" + }, + { + "fulltext.pdf": "7975416a17870afa5a2d13c1dc743d40" + } + ] + }, + "http://pss.sagepub.com/content/26/4/456.full": { + "public_url": { + "value": [ + "http://pss.sagepub.com/content/26/4/456" + ] + }, + "title": { + "value": [ + "Improving Vision Among Older Adults" + ] + }, + "doi": { + "value": [ + "10.1177/0956797614567510" + ] + }, + "pmid": { + "value": [ + "25749697" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "publisher": { + "value": [ + "SAGE Publications" + ] + }, + "journal": { + "value": [ + "Psychological Science" + ] + }, + "journal_issn": { + "value": [ + "0956-7976", + "1467-9280" + ] + }, + "author_name": { + "value": [ + "Denton J. DeLoss", + "Takeo Watanabe", + "George J. Andersen" + ] + }, + "author_institution": { + "value": [ + "\n 1University of California, Riverside", + "\n 2Brown University", + "\n 1University of California, Riverside" + ] + }, + "volume": { + "value": [ + "26" + ] + }, + "issue": { + "value": [ + "4" + ] + }, + "firstpage": { + "value": [ + "456" + ] + }, + "article_type": { + "value": [ + "Research Articles" + ] + }, + "fulltext_html": { + "value": [ + "http://pss.sagepub.com/content/26/4/456.full" + ] + }, + "fulltext_pdf": { + "value": [ + "http://pss.sagepub.com/content/26/4/456.full.pdf" + ] + }, + "abstract_html": { + "value": [ + "\n \n

Abstract

\n \n

A major problem for the rapidly growing population of older adults (age 65 and over) is age-related declines in vision, which\n have been associated with increased risk of falls and vehicle crashes. Research suggests that this increased risk is associated\n with declines in contrast sensitivity and visual acuity. We examined whether a perceptual-learning task could be used to improve\n age-related declines in contrast sensitivity. Older and younger adults were trained over 7 days using a forced-choice orientation-discrimination\n task with stimuli that varied in contrast with multiple levels of additive noise. Older adults performed as well after training\n as did college-age younger adults prior to training. Improvements transferred to performance for an untrained stimulus orientation\n and were not associated with changes in retinal illuminance. Improvements in far acuity in younger adults and in near acuity\n in older adults were also found. These findings indicate that behavioral interventions can greatly improve visual performance\n for older adults.\n

\n \n " + ] + }, + "methods_html": { + "value": [ + "\n \n \n

Method

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Subjects

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Sixteen younger adults (mean age = 22.43 years, SD = 1.16) from the University of California, Riverside (8 male and 8 female) and 16 older adults (mean age = 71.23 years, SD = 5.85) from the surrounding community (8 male and 8 female) participated in the study. The sample size was determined on\n the basis of pilot studies and previous research demonstrating an effect of training in older and younger adults (Andersen et al., 2010; Bower & Andersen, 2012; Bower et al., 2013; DeLoss et al., 2014). All subjects were compensated for their participation at a rate of $10 per hour. Older individuals received an additional\n $5 per hour to cover transportation costs to the campus. The sample size for each age group was comparable with sample sizes\n in other studies investigating the effects of perceptual learning. Subjects were naive to the purpose of the study, and all\n had normal or corrected-to-normal visual acuity.\n

\n \n

All subjects were screened using an array of cognitive and perceptual tests. This procedure ensured that the older group did\n not exhibit any early or atypical cognitive decline (e.g., Alzheimer’s disease) that could influence the results of the study.\n Demographic information for the subjects is presented in Table 1. One-way analyses of variance revealed that prior to training, there were significant differences between the two age groups\n in acuity and on the Matrix Reasoning subtest of the third edition of the Wechsler Adult Intelligence Scale (Wechsler, 1997; Fs ≤ 2.5, ps > .05). While the older group’s performance was significantly different from that of the younger group on Matrix Reasoning,\n their score was well above the age norm found in previous research (Ardila, 2007). Subjects were also screened for eye disease and neurological disorders.\n

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Table 1. \n \n

Demographic Information and Results From Cognitive and Perceptual Tests Administered Prior to the Start of the Study

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Apparatus

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Stimuli were presented on a 21-in. CRT monitor (Viewsonic P225F) at a resolution of 1,024 × 768 pixels; the monitor had a\n refresh rate of 100 Hz (noninterlaced) and a mean luminance value of 53.82 cd/m2. Stimuli were generated on a Dell Vostro 430 PC equipped with an Intel Core i5 750 processor using the Windows XP (Service\n Pack 3) operating system. A GeForce GTS 240 graphics card (NVIDIA, Santa Clara, CA) was used along with a Bits++ system (Cambridge\n Research Systems, Rochester, Kent, United Kingdom) to achieve 14-bit gray scale (16,384 gray-scale levels). Custom experimental\n software was written in MATLAB (The MathWorks, Natick, MA); Psychophysics Toolbox extensions were also utilized (Brainard, 1997; Pelli, 1997). The monitor was calibrated using a ColorCal2 colorimeter (Cambridge Research Systems). Gamma correction was performed through\n linearization of the color lookup table.\n

\n \n

Pupil size was measured on testing days using an EyeLink 1000 Tower Mount (SR Research, Ottawa, Ontario, Canada); subjects’\n head position was also stabilized with this device. Subjects’ far acuity was measured using the 2000 Series Revised ETDRS\n Chart 2 (Precision Vision, La Salle, IL) at a distance of 3 m. Subjects’ near acuity was measured using the 2000 series New\n ETDRS Chart 3 at a distance of 40 cm. Contrast sensitivity was measured using the Pelli-Robson Contrast Sensitivity Chart\n (Precision Vision).\n

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Stimuli and procedure

\n \n

The experiment consisted of 1.5 hr per day of testing and training over 7 days. Subjects were required to complete the study\n within 3 weeks of their first testing session. Stimuli were viewed binocularly on a monitor at a distance of 94 cm. Corrective\n lenses normally worn by the subjects were allowed during the experiment. All stimuli were viewed through a plano-convex glass\n collimation lens (45.7 cm diameter) with a 19% magnification factor to minimize any age-related differences in accommodative\n focus. The size of the stimuli was corrected to account for this magnification factor. The experiment was run in a darkened\n room; the only light source was the monitor. Stimuli were Gabor patches presented at 1.5 cycles per degree of visual angle\n (0.65° standard deviation of the Gaussian mask), and the phase of the Gabor was randomized ±180° on each trial.\n

\n \n
\n \n

Familiarization task

\n \n

On the first day of the study, before the experiment began, all subjects were given a 30-trial practice session to familiarize\n them with the task. These practice trials were presented without Gaussian noise. Subjects completed 15 trials in which the\n Gabor patch appeared in a standard orientation 45° clockwise off vertical and 15 trials in which the Gabor patch had a standard\n orientation 45° counterclockwise off vertical. At the beginning of each trial, subjects saw a fixation point in the center\n of the display for 1,600 ms. This fixation point alternated between black and white every 400 ms, to attract attention (Betts, Taylor, Sekuler, & Bennett, 2005). A Gabor patch then appeared at one of the two standard orientations for 100 ms. A second fixation point then appeared for\n 1,200 ms, alternating between black and white every 300 ms, followed by the target stimulus for 100 ms. During this phase,\n the target was rotated either 25° clockwise or 25° counterclockwise away from the standard orientation. After the target disappeared,\n the screen assumed a uniform midgray value indicating that the subject should judge whether the target stimulus was rotated\n clockwise or counterclockwise compared with the standard orientation (Fig. 1). Responses were made using the left and right arrow keys on the keyboard. Audio feedback was provided on each trial to indicate\n whether the subject was correct. Subjects were then prompted to “press any key to continue” to begin the next trial. During\n the familiarization task, subjects were instructed to get at least one trial incorrect to familiarize themselves with the\n corresponding auditory feedback.\n

\n \n
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\"Fig.
View larger version:\n \n
\n
\n
Fig. 1. \n \n

Example of the task used in the study. In each trial, subjects saw a Gabor patch at one of two standard orientations—25° clockwise\n (shown here) or 25° counterclockwise for training and testing trials, 45° clockwise or 45° counterclockwise for familiarization\n trials. After this Gabor patch disappeared, subjects saw a second stimulus and had to judge whether it was rotated clockwise\n or counterclockwise in comparison with the standard orientation (the examples shown here are rotated 15° clockwise and counterclockwise\n off the standard orientation, respectively).\n

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Testing

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Orientation-discrimination thresholds were tested during the first and last days (Days 1 and 7) of the experiment. During\n testing, the Gabor patches were embedded in additive Gaussian noise in four of the five testing blocks. The first block consisted\n of a no-noise condition with the standard deviation of the additive Gaussian noise set to zero; the standard deviation of\n the Gaussian distribution was then increased by 0.084375 in each successive block to a maximum of 0.3375 in Block 5.\n

\n \n

Standard stimulus orientations were either clockwise 25° or counterclockwise 25° off vertical (see Fig. 2 for an example of the stimuli). The testing order of these standard orientations was counterbalanced across subjects. These\n two orientations were chosen on the basis of previous research demonstrating that improvements in orientation sensitivity\n begin to degrade when the stimulus is rotated approximately 40° away from the trained orientation (Matthews, Liu, & Qian, 2001). These two specific standard orientations were chosen because they are 50° offset from one another.\n

\n \n
\n
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View larger version:\n \n
\n
\n
Fig. 2. \n \n

Example of contrast and noise levels used in the experiment. Gabor patches are displayed at 75% contrast in the top row and\n at 25% contrast in the bottom row. Stimuli were presented in five blocks (examples shown from left to right). There was no\n noise in the first block, but starting with the second block, stimuli were presented in Gaussian noise, with the noise level\n increasing in each subsequent block.\n

\n \n
\n
\n
\n \n

During Days 1 and 7, pretraining Michelson contrast thresholds for the trained and untrained standard orientations were assessed\n at five noise levels using the QUEST procedure (Watson & Pelli, 1983). QUEST was initialized with a criterion level of 0.75 (β = 1.4, δ = 0.025, γ = 0.5). On testing days, the estimated contrast\n values for QUEST for each successive noise level were 10%, 15%, 20%, 25%, and 30%, with a standard deviation of 5%. Subjects\n completed 60 trials at each noise level during testing. All stimuli were viewed through a circular annulus with a radius of\n 8 degrees of visual angle that was placed against the surface of the monitor. The annulus removed any edge cues that may have\n been used in the orientation-discrimination task. The background between trials and during interstimulus intervals consisted\n of the midgray value of the monitor (for no-noise blocks) or additive Gaussian noise with the mean set at the midgray level\n of the monitor and a standard deviation that matched the additive Gaussian noise (for blocks with external noise).\n

\n \n

Trials progressed in the same fashion as in the familiarization task. The orientation offset was fixed at 15° on all test\n trials. Posttraining thresholds for the trained and untrained orientations were measured on Day 7 using the same procedure\n as on Day 1. Pupil size was also measured on each trial during testing days to derive retinal-illuminance values.\n

\n \n
\n \n
\n \n

Training

\n \n

Training occurred on Days 2 through 6 using the same stimuli and a similar procedure as in the testing phase, with the key\n difference being that subjects were trained on only one standard orientation instead of the two they saw on testing days.\n During training, all subjects completed five blocks, one at each noise level. There were 150 trials per block, and subjects\n were allowed to take a short break after each block. During each training day, the QUEST procedure was run using the same\n parameters as during the testing days, but with one modification. The contrast threshold estimate for QUEST for each subject\n used the threshold derived on the previous day of testing or training as the initial estimate. Subsequent trials used the\n current threshold, taking into account each trial during the training sessions. Using this method, subjects were constantly\n trained at their threshold (75% correct) during each training day. This allowed training to be constantly optimized for any\n improvement that occurred between or within testing or training sessions. All subjects received 750 training trials per day,\n for a total of 3,750 training trials over the course of the experiment.\n

\n \n
\n \n
\n \n " + ] + }, + "results_html": { + "value": [ + "\n \n

Familiarization task

\n \n

On the first day of the study, before the experiment began, all subjects were given a 30-trial practice session to familiarize\n them with the task. These practice trials were presented without Gaussian noise. Subjects completed 15 trials in which the\n Gabor patch appeared in a standard orientation 45° clockwise off vertical and 15 trials in which the Gabor patch had a standard\n orientation 45° counterclockwise off vertical. At the beginning of each trial, subjects saw a fixation point in the center\n of the display for 1,600 ms. This fixation point alternated between black and white every 400 ms, to attract attention (Betts, Taylor, Sekuler, & Bennett, 2005). A Gabor patch then appeared at one of the two standard orientations for 100 ms. A second fixation point then appeared for\n 1,200 ms, alternating between black and white every 300 ms, followed by the target stimulus for 100 ms. During this phase,\n the target was rotated either 25° clockwise or 25° counterclockwise away from the standard orientation. After the target disappeared,\n the screen assumed a uniform midgray value indicating that the subject should judge whether the target stimulus was rotated\n clockwise or counterclockwise compared with the standard orientation (Fig. 1). Responses were made using the left and right arrow keys on the keyboard. Audio feedback was provided on each trial to indicate\n whether the subject was correct. Subjects were then prompted to “press any key to continue” to begin the next trial. During\n the familiarization task, subjects were instructed to get at least one trial incorrect to familiarize themselves with the\n corresponding auditory feedback.\n

\n \n
\n
\"Fig.
View larger version:\n \n
\n
\n
Fig. 1. \n \n

Example of the task used in the study. In each trial, subjects saw a Gabor patch at one of two standard orientations—25° clockwise\n (shown here) or 25° counterclockwise for training and testing trials, 45° clockwise or 45° counterclockwise for familiarization\n trials. After this Gabor patch disappeared, subjects saw a second stimulus and had to judge whether it was rotated clockwise\n or counterclockwise in comparison with the standard orientation (the examples shown here are rotated 15° clockwise and counterclockwise\n off the standard orientation, respectively).\n

\n \n
\n
\n
\n \n " + ] + }, + "discussion_html": { + "value": [ + "\n \n

Testing

\n \n

Orientation-discrimination thresholds were tested during the first and last days (Days 1 and 7) of the experiment. During\n testing, the Gabor patches were embedded in additive Gaussian noise in four of the five testing blocks. The first block consisted\n of a no-noise condition with the standard deviation of the additive Gaussian noise set to zero; the standard deviation of\n the Gaussian distribution was then increased by 0.084375 in each successive block to a maximum of 0.3375 in Block 5.\n

\n \n

Standard stimulus orientations were either clockwise 25° or counterclockwise 25° off vertical (see Fig. 2 for an example of the stimuli). The testing order of these standard orientations was counterbalanced across subjects. These\n two orientations were chosen on the basis of previous research demonstrating that improvements in orientation sensitivity\n begin to degrade when the stimulus is rotated approximately 40° away from the trained orientation (Matthews, Liu, & Qian, 2001). These two specific standard orientations were chosen because they are 50° offset from one another.\n

\n \n
\n
\"Fig.
View larger version:\n \n
\n
\n
Fig. 2. \n \n

Example of contrast and noise levels used in the experiment. Gabor patches are displayed at 75% contrast in the top row and\n at 25% contrast in the bottom row. Stimuli were presented in five blocks (examples shown from left to right). There was no\n noise in the first block, but starting with the second block, stimuli were presented in Gaussian noise, with the noise level\n increasing in each subsequent block.\n

\n \n
\n
\n
\n \n

During Days 1 and 7, pretraining Michelson contrast thresholds for the trained and untrained standard orientations were assessed\n at five noise levels using the QUEST procedure (Watson & Pelli, 1983). QUEST was initialized with a criterion level of 0.75 (β = 1.4, δ = 0.025, γ = 0.5). On testing days, the estimated contrast\n values for QUEST for each successive noise level were 10%, 15%, 20%, 25%, and 30%, with a standard deviation of 5%. Subjects\n completed 60 trials at each noise level during testing. All stimuli were viewed through a circular annulus with a radius of\n 8 degrees of visual angle that was placed against the surface of the monitor. The annulus removed any edge cues that may have\n been used in the orientation-discrimination task. The background between trials and during interstimulus intervals consisted\n of the midgray value of the monitor (for no-noise blocks) or additive Gaussian noise with the mean set at the midgray level\n of the monitor and a standard deviation that matched the additive Gaussian noise (for blocks with external noise).\n

\n \n

Trials progressed in the same fashion as in the familiarization task. The orientation offset was fixed at 15° on all test\n trials. Posttraining thresholds for the trained and untrained orientations were measured on Day 7 using the same procedure\n as on Day 1. Pupil size was also measured on each trial during testing days to derive retinal-illuminance values.\n

\n \n " + ] + }, + "conclusions_html": { + "value": [ + "\n \n

Training

\n \n

Training occurred on Days 2 through 6 using the same stimuli and a similar procedure as in the testing phase, with the key\n difference being that subjects were trained on only one standard orientation instead of the two they saw on testing days.\n During training, all subjects completed five blocks, one at each noise level. There were 150 trials per block, and subjects\n were allowed to take a short break after each block. During each training day, the QUEST procedure was run using the same\n parameters as during the testing days, but with one modification. The contrast threshold estimate for QUEST for each subject\n used the threshold derived on the previous day of testing or training as the initial estimate. Subsequent trials used the\n current threshold, taking into account each trial during the training sessions. Using this method, subjects were constantly\n trained at their threshold (75% correct) during each training day. This allowed training to be constantly optimized for any\n improvement that occurred between or within testing or training sessions. All subjects received 750 training trials per day,\n for a total of 3,750 training trials over the course of the experiment.\n

\n \n " + ] + }, + "acknowledgements_html": { + "value": [ + + ] + }, + "competing_interests_html": { + "value": [ + "\n \n \n

Funding This research was funded by National Institute on Aging Grant No. R01-AG031941.\n

\n \n " + ] + }, + "financial_disclosure_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\n \n

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\n " + ] + }, + "copyright": { + "value": [ + "© The Author(s) 2015" + ] + }, + "onlinefirst_published": { + "value": [ + "\n \t April 2015 \n " + ] + }, + "author_contrib_html": { + "value": [ + "\n \n \n

Author Contributions All authors contributed to the design of the study. Data were collected by D. J. DeLoss and analyzed by D. J. DeLoss and\n G. J. Andersen. D. J. DeLoss drafted the manuscript. G. J. Andersen and D. J. DeLoss provided revisions. All authors approved\n the final manuscript.\n

\n \n " + ] + }, + "author_corresp_html": { + "value": [ + "George J. Andersen, University of California, Riverside, Department of Psychology, 900 University Ave., Riverside, CA 92506\n E-mail: andersen{at}ucr.edu\n \n " + ] + }, + "file_hashes": [ + { + "fulltext.html": "4dde7038b74b5199c74cc76c7f10d318" + }, + { + "fulltext.pdf": "d8d20539b1d504b076eadf5b393fec9f" + } + ] + }, + "http://pss.sagepub.com/content/26/4/499.full": { + "public_url": { + "value": [ + "http://pss.sagepub.com/content/26/4/499" + ] + }, + "title": { + "value": [ + "Young Children Show the Bystander Effect in Helping Situations" + ] + }, + "doi": { + "value": [ + "10.1177/0956797615569579" + ] + }, + "pmid": { + "value": [ + "25792132" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "publisher": { + "value": [ + "SAGE Publications" + ] + }, + "journal": { + "value": [ + "Psychological Science" + ] + }, + "journal_issn": { + "value": [ + "0956-7976", + "1467-9280" + ] + }, + "author_name": { + "value": [ + "Maria Plötner", + "Harriet Over", + "Malinda Carpenter", + "Michael Tomasello" + ] + }, + "author_institution": { + "value": [ + "\n 1Department of Developmental and Comparative Psychology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany", + "\n 2Department of Psychology, University of York", + "\n 1Department of Developmental and Comparative Psychology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany", + "\n 3School of Psychology & Neuroscience, University of St Andrews", + "\n 1Department of Developmental and Comparative Psychology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany" + ] + }, + "volume": { + "value": [ + "26" + ] + }, + "issue": { + "value": [ + "4" + ] + }, + "firstpage": { + "value": [ + "499" + ] + }, + "article_type": { + "value": [ + "Research Articles" + ] + }, + "fulltext_html": { + "value": [ + "http://pss.sagepub.com/content/26/4/499.full" + ] + }, + "fulltext_pdf": { + "value": [ + "http://pss.sagepub.com/content/26/4/499.full.pdf" + ] + }, + "abstract_html": { + "value": [ + "\n \n

Abstract

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Much research in social psychology has shown that otherwise helpful people often fail to help when bystanders are present.\n Research in developmental psychology has shown that even very young children help and that the presence of others can actually\n increase helping in some cases. In the current study, in contrast, 5-year-old children helped an experimenter at very high\n levels when they were alone but helped significantly less often in the presence of bystanders who were potentially available\n to help. In another condition designed to elucidate the mechanism underlying the effect, children’s helping was not reduced\n when bystanders were present but confined behind a barrier and thus unable to help (a condition that has not been run in previous\n studies with adults). Young children thus show the bystander effect, and it is due not to social referencing or shyness to\n act in front of others but, rather, to a sense of a diffusion of responsibility.\n

\n \n " + ] + }, + "methods_html": { + "value": [ + "\n \n \n

Method

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Participants

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Participants were sixty 5-year-olds (mean age: 5 years 7 months; age range: 5 years 0 months–5 years 11 months). The sample\n size was specified prior to data collection, based on typical sample sizes in this field. In each condition, half of the participants\n were female and half were male. Children were recruited through a database of parents who had agreed to participate in studies\n on child development. Children were randomly assigned to one of the three conditions. A total of 12 peer confederates (mean\n age: 5 years 10 months; age range: 4 years 11 months–6 years 11 months) were assigned to mixed-sex dyads on the basis of their\n availability to participate in testing and their reliability as confederates. These children were bystanders in the bystander\n and the bystander-unavailable conditions and were always strangers to the participant.\n

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Four additional children were invited but not tested because they refused to participate. An additional 14 participants were\n tested but excluded from analyses for video-camera error (n = 1), experimenter error (n = 3), or confederate error (n = 10). Confederate error was coded if confederates deviated from their instructions in significant ways: if they gave hints\n to a participant that they knew what was going to happen next (n = 3), if they revealed that they had participated before (n = 4), if a participant noticed them looking toward him or her on more than two occasions during the test phase (n = 1), or if they talked excessively (n = 2). Interrater reliability on the decision to exclude participants because of confederate error was assessed for 12 randomly\n selected cases (including 6 of the 10 confederate errors) by a coder who was naive to the hypotheses of the study (κ = .83).\n The few disagreements were resolved by discussion.\n

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Setup and materials

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Testing was conducted in a room containing four child-sized tables and chairs, one for the experimenter and three for the\n participant and the two bystanders. The children’s tables stood next to each other (at a distance of 130 cm) in the back of\n the room, facing the experimenter’s table, and were separated by 135 cm × 80 cm barriers (which were opaque up to a height\n of 70 cm, i.e., approximately the shoulder height of the seated children). From the participant’s sitting position, both bystanders\n were equally visible in the bystander and the bystander-unavailable conditions (see Fig. 1). There was a pile of paper towels on the floor between children’s tables and the experimenter’s table (175 cm from each\n of the children’s tables). Other materials were a set of 10 different pictures for coloring, colored pencils, a 300 cm × 80\n cm cardboard wall, a cup of green paint, and a cup containing colored water and paintbrushes.\n

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View larger version:\n \n
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Fig. 1. \n \n

A re-creation of the experimental setup in the alone condition (a), the bystander condition (b), and the bystander-unavailable\n condition (c). The participant is seated on the left in each picture.\n

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Procedure

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Introduction

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Participants were told that they were going to color a picture. In the alone condition, participants were led to the testing\n room, where they were asked to choose a picture to color. In the bystander and bystander-unavailable conditions, participants\n met the two confederates in front of the testing room. They were introduced by name and said to be participating as well.\n All children and the experimenter then entered the testing room and chose a picture. Participants always were asked (seemingly\n randomly) to choose first, and then the confederates each chose different pictures.\n

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Familiarization phase

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In all conditions, the experimenter then noticed a puddle of water in the middle of the room, which she wiped up with some\n paper towels. She put the leftover paper towels on the floor, saying that she was doing so “in case something needs to be\n wiped up later.”\n

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Manipulation phase

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The children were asked to sit down to color. The experimenter then said that while the children colored their pictures, she\n would paint her cardboard wall and, to do that more easily, she would place it in a certain way. In the bystander condition,\n she put it to the side (against the right wall of the room). In the bystander-unavailable condition, she attached the cardboard\n wall to the barriers separating the two tables on the right, such that the two confederates were fenced in and unable to leave\n their compartments (see Fig. 1c). In this condition, the experimenter then commented on the wall with apparent surprise, saying, “Oh, I’ve just realized,\n now you two can’t get out of here. Well, you are fenced in now, briefly, but don’t worry, you can get out as soon as we’re\n finished here.” In the alone condition, the wall was put to the side (as in the bystander condition) for half of the participants\n and was attached to the barriers (as in the bystander-unavailable condition) for the other half. In all conditions, the participants\n were able to move freely. After this, all children were given pencils and were asked to start coloring while the experimenter\n painted her cardboard wall. After approximately a minute, the experimenter then said she needed to clean her paintbrushes\n and sat down at her table with the cup of water and the paintbrushes.\n

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Test phase

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After approximately half a minute, the experimenter “accidentally” knocked over the cup and spilled colored water all over\n her table. She tried to hold back the water with her forearms to prevent it from spilling onto the floor. During the first\n 15 s after spilling the water, the experimenter looked down at the water, said “Oops,” and groaned. She repeated this two\n more times. After those 15 s, if participants had not yet helped, she said, “My cup has fallen over.” After 30 s, the experimenter\n said, “The water is about to drip onto the floor.” After 45 s, she said “I need something to wipe it up” while looking back\n and forth between the water and the paper towels on the floor. After 60 s, she said, “I need the paper towels there,” looking\n at the paper towels, which were out of her reach. She then looked for the first time at the children, starting with the participant\n on the left and then moving her gaze to the right to each of the bystanders (or, in the alone condition, toward the empty\n tables), and did so twice. After 75 s, she said, “Could somebody give me the paper towels there?” while looking at the children\n again as described above. After 90 s, if the participant still had not brought her some paper towels, she appeared to realize\n that there were paper towels behind her that she could reach easily and used them to clean up the water herself.\n

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Confederates had been instructed to be friendly throughout the study but not to talk, and especially to give no hints about\n being confederates of the experimenter, about having participated in the study before, or about what would happen later. In\n the test phase, they were instructed to look at the experimenter neutrally from time to time but to continue drawing, and\n not to look at the participant. Details about the coding and analyses of confederates’ behavior to check that it was equivalent\n in the two bystander conditions can be found in the Supplemental Material available online. Confederates were told that they\n were just playacting for the sake of the study and that normally one should help in these situations.\n

\n \n
\n \n
\n \n

Interview

\n \n

We also interviewed participants after the main test phase was complete. This interview was based on the first four steps\n of Darley and Latané’s (1970) five-step model and also included a manipulation check. An assistant with whom participants had interacted briefly prior\n to the experiment interviewed them alone. She expressed her regret that she had missed the children’s drawing session, and\n to measure whether the children had noticed the accident, she asked what had happened and, in particular, whether there was\n anything that had happened to the experimenter (Step 1). To measure whether children had understood that the experimenter\n needed help, she asked whether the experimenter had really needed help in the situation (Step 2). To measure who children\n thought was responsible for helping, she asked whose job it was to help in the situation and how participants knew who should\n help (Step 3). To measure whether children knew appropriate means for helping, she asked if participants had known how to\n help the experimenter (Step 4). Finally, as a manipulation check to see whether the cardboard wall was a convincing barrier\n for participants in the bystander-unavailable condition, she asked if anybody else could have helped in the situation.\n

\n \n

At the very end of the test session, after the interview, the assistant emphasized to participants who had helped that it\n was good to help and to participants who had not helped that generally helping is good, but it was probably OK not to help\n in this case, since the experimenter was able to help herself eventually. Participants in the bystander condition were told\n that the bystanders had probably not helped because they had not noticed that the experimenter needed help.\n

\n \n
\n \n
\n \n
\n \n

Coding and reliability

\n \n
\n \n

Coding of helping

\n \n

For the helping situation, the main measure was whether participants did or did not help the experimenter by bringing her\n at least one paper towel within the 90-s response phase. In addition, we coded how quickly participants helped, using a 7-point\n scale that indicated the phase in which children had helped (phases corresponded to each 15-s step described above, during\n which the experimenter made her need for help increasingly more explicit). Children received a score of 1 if they helped spontaneously\n in the first part of the test phase, a score of 2 if they helped in the second part of the test phase, and so on up to the\n sixth and final part of the test phase; if they did not help, they were not included in the analyses on latency to help.\n

\n \n
\n \n
\n \n

Coding of social referencing

\n \n

For the bystander and bystander-unavailable conditions, we also took a measure of social referencing by coding how often participants\n looked toward the bystanders. The number of looks was divided by the helping phase to correct for the time it took children\n to help. This resulted in a mean number of looks per helping phase for each child.\n

\n \n
\n \n
\n \n

Coding of the interview

\n \n

For Step 1, we coded for whether participants mentioned the water-spilling incident or not. For Step 2, we coded for whether\n participants answered “[experimenter’s name] needed help” or “[experimenter’s name] did not need help.” For Step 3, we asked\n children whose job it had been to help and coded for whether they said “mine” (vs. “everybody’s,” “nobody’s,” or another answer);\n we also asked how they knew who should help and coded for whether they said “because I had to do it” (vs. “everybody could\n do it,” “nobody could do it,” or another answer). For Step 4, we coded for whether children answered “I knew how to help”\n or “I did not know how to help.” Finally, for the manipulation check, we coded for whether children mentioned the cardboard\n wall as a reason why nobody else could have helped.\n

\n \n
\n \n
\n \n

Reliability

\n \n

Videos of the helping situation and the interview were coded by the first author. Reliability coding for the full sample by\n a naive coder who was unaware of the hypotheses of the study revealed perfect agreement on whether or not children helped\n (κ = 1) and the phase in which children helped (rs\n = 1; no difference between coders, Mann-Whitney U test, p = 1) and excellent agreement on the number of times participants looked toward the bystanders (r = .95; no difference between coders, Mann-Whitney U test, p = .65) and the interview responses (all κs > .82). Disagreements were resolved through discussion.\n

\n \n
\n \n
\n \n " + ] + }, + "results_html": { + "value": [ + "\n \n

Introduction

\n \n

Participants were told that they were going to color a picture. In the alone condition, participants were led to the testing\n room, where they were asked to choose a picture to color. In the bystander and bystander-unavailable conditions, participants\n met the two confederates in front of the testing room. They were introduced by name and said to be participating as well.\n All children and the experimenter then entered the testing room and chose a picture. Participants always were asked (seemingly\n randomly) to choose first, and then the confederates each chose different pictures.\n

\n \n " + ] + }, + "discussion_html": { + "value": [ + "\n \n

Familiarization phase

\n \n

In all conditions, the experimenter then noticed a puddle of water in the middle of the room, which she wiped up with some\n paper towels. She put the leftover paper towels on the floor, saying that she was doing so “in case something needs to be\n wiped up later.”\n

\n \n " + ] + }, + "conclusions_html": { + "value": [ + "\n \n

Manipulation phase

\n \n

The children were asked to sit down to color. The experimenter then said that while the children colored their pictures, she\n would paint her cardboard wall and, to do that more easily, she would place it in a certain way. In the bystander condition,\n she put it to the side (against the right wall of the room). In the bystander-unavailable condition, she attached the cardboard\n wall to the barriers separating the two tables on the right, such that the two confederates were fenced in and unable to leave\n their compartments (see Fig. 1c). In this condition, the experimenter then commented on the wall with apparent surprise, saying, “Oh, I’ve just realized,\n now you two can’t get out of here. Well, you are fenced in now, briefly, but don’t worry, you can get out as soon as we’re\n finished here.” In the alone condition, the wall was put to the side (as in the bystander condition) for half of the participants\n and was attached to the barriers (as in the bystander-unavailable condition) for the other half. In all conditions, the participants\n were able to move freely. After this, all children were given pencils and were asked to start coloring while the experimenter\n painted her cardboard wall. After approximately a minute, the experimenter then said she needed to clean her paintbrushes\n and sat down at her table with the cup of water and the paintbrushes.\n

\n \n " + ] + }, + "acknowledgements_html": { + "value": [ + "\n \n

Acknowledgments

\n \n

We thank Robert Hepach for contributing to the study design and Jana Jurkat, Lydia Fiedler, Christian Biermann, Alex Call,\n and the confederates for their help with data collection.\n

\n \n " + ] + }, + "competing_interests_html": { + "value": [ + + ] + }, + "financial_disclosure_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\n \n

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\n " + ] + }, + "copyright": { + "value": [ + "© The Author(s) 2015" + ] + }, + "onlinefirst_published": { + "value": [ + "\n \t April 2015 \n " + ] + }, + "author_contrib_html": { + "value": [ + "\n \n \n

Author Contributions All authors contributed to the idea of the study and its design. Testing and data collection were performed by M. Plötner.\n M. Plötner analyzed the data under the supervision of H. Over, M. Carpenter, and M. Tomasello. M. Plötner drafted the manuscript,\n and H. Over, M. Carpenter, and M. Tomasello provided critical revisions. All authors approved the final version of the manuscript\n for submission.\n

\n \n " + ] + }, + "author_corresp_html": { + "value": [ + "Maria Plötner, Department of Developmental and Comparative Psychology, Max Planck Institute for Evolutionary Anthropology,\n Leipzig, Germany 04103 E-mail: maria_ploetner{at}eva.mpg.de\n \n " + ] + }, + "file_hashes": [ + { + "fulltext.html": "3a664c433dbd6958a3163c528fab6e07" + }, + { + "fulltext.pdf": "f3c64e0dccc7450507ef75618d44480f" + } + ] + }, + "http://pss.sagepub.com/content/17/8/670.full": { + "public_url": { + "value": [ + "http://pss.sagepub.com/content/17/8/670" + ] + }, + "title": { + "value": [ + "Naps Promote Abstraction in Language-Learning Infants" + ] + }, + "doi": { + "value": [ + "10.1111/j.1467-9280.2006.01764.x" + ] + }, + "pmid": { + "value": [ + "16913948" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "publisher": { + "value": [ + "SAGE Publications" + ] + }, + "journal": { + "value": [ + "Psychological Science" + ] + }, + "journal_issn": { + "value": [ + "0956-7976", + "1467-9280" + ] + }, + "author_name": { + "value": [ + "Rebecca L. Gómez", + "Richard R. Bootzin", + "Lynn Nadel" + ] + }, + "author_institution": { + "value": [ + + ] + }, + "volume": { + "value": [ + "17" + ] + }, + "issue": { + "value": [ + "8" + ] + }, + "firstpage": { + "value": [ + "670" + ] + }, + "article_type": { + "value": [ + "Research Reports" + ] + }, + "fulltext_html": { + "value": [ + "http://pss.sagepub.com/content/17/8/670.full" + ] + }, + "fulltext_pdf": { + "value": [ + "http://pss.sagepub.com/content/17/8/670.full.pdf" + ] + }, + "abstract_html": { + "value": [ + "\n \n

Abstract

\n \n

Infants engage in an extraordinary amount of learning during their waking hours even though much of their day is consumed\n by sleep. What role does sleep play in infant learning? Fifteen-month-olds were familiarized with an artificial language 4\n hr prior to a lab visit. Learning the language involved relating initial and final words in auditory strings by remembering\n the exact word dependencies or by remembering an abstract relation between initial and final words. One group napped during\n the interval between familiarization and test. Another group did not nap. Infants who napped appeared to remember a more abstract\n relation, one they could apply to stimuli that were similar but not identical to those from familiarization. Infants who did\n not nap showed a memory effect. Naps appear to promote a qualitative change in memory, one involving greater flexibility in\n learning.\n

\n \n " + ] + }, + "methods_html": { + "value": [ + "\n \n \n

METHOD

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Participants

\n \n

Forty-eight healthy 15-month-olds were recruited from the Tucson area and were randomly assigned to nap, no-nap, and nap-control\n conditions. Infants in the no-nap condition were not deprived of sleep, but were scheduled at times that were not expected\n to coincide with the usual time of their nap, whereas infants in the nap condition were scheduled such that their usual naptime\n would occur between exposure and test. The nap-control condition was included to eliminate the possibility that performance\n in the nap condition was due to one-trial learning (we describe the rationale fully in the Results section). These infants\n also napped between exposure and test, but unlike the other groups, they were exposed to a language with only a small set\n of elements used in the medial position. There were 8 males and 8 females in each condition. Fifteen additional infants were\n tested, but were withdrawn from consideration for various reasons. In several cases, infants were excluded from the analyses\n because their napping was inconsistent with their condition assignment. A nap was defined as 30 min or more of uninterrupted\n sleep in the 4-hr interval between familiarization and test. One infant in the nap-control group who did not meet this criterion\n was excluded, as were 8 infants in the no-nap group who exceeded it. Additionally, infants were excluded if they slept during\n familiarization (1 infant in the nap condition), a parent interfered with the test procedure (1 infant in the nap condition),\n they cried during the test procedure (3 infants in the no-nap condition), or they dozed during the test procedure (1 infant\n in the nap-control condition). Infants in the three groups were tested at similar times of day (see Table 1).\n

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TABLE 1 \n

Mean Looking Times (in Seconds)

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Materials

\n \n

Strings in the artificial language took the form pel-X-jic and vot-X-rud in Version A, and pel-X-rud and vot-X-jic in Version B. X elements for the experimental conditions were wadim, kicey, puser, fengle, coomo, loga, gople, taspu, hiftam, deecha, vamey, skiger, benez, gensim, feenam, laeljeen, chila, roosa, plizet, balip, malsig, suleb, nilbo, and wiffle. For the control condition, the X elements were wadim, kicey, and puser. Half of the infants in each condition were familiarized with Version A, and half with Version B.\n

\n \n \n

Familiarization Stimuli

\n \n

A female speaker recorded sample strings. Word tokens from the recorded strings were used to construct Version A and B strings\n (using the same tokens in both versions eliminates random differences in the pronunciation of words or strings in the two\n versions, so that the nonadjacent dependencies are the only source of difference). Strings were separated by 1,000-ms pauses.\n Infants in the nap and no-nap groups were familiarized with high variability (24 X items) and heard each of the 48 strings of their training language 5 times during familiarization. Infants in the nap-control\n group were familiarized with low variability (3 X items) and heard each of the 6 strings of their training language 40 times. Thus, all three groups heard each of the two\n nonadjacent word dependencies 120 times.\n

\n \n \n \n

Test Stimuli

\n \n

Six strings in each version of the language (the subset of strings used in the nap-control condition) were test items in all\n three conditions. Thus, infants in all groups were tested on the same materials. Four test sets were created—the Version A\n strings and Version B strings, each presented in two random orders. Each test set was presented four times (once in each of\n four test blocks), for a total of 16 trials (i.e., a trial consisted of the presentation of a test set). Test sets were 17\n s in duration.\n

\n \n \n \n \n

Procedure

\n \n

An experimenter visited each infant's home 4 hr prior to testing. She attached a Minimitter® Actiwatch with a memory chip to the infant's ankle in order to record body movements. Actigraphy has proven an accurate tool\n for monitoring infants' sleep behavior (Acebo et al., 2005; Gnidovec, Neubauer, & Zidar, 2002; Sadeh, Acebo, Seifer, Aytur, & Carskadon, 1995). As an extra check on accuracy, caregivers kept a log of their infant's activity, noting periods of sleep and externally\n produced motion. A small number of discrepancies between actigraph and log data (fewer than 9% of cases) were resolved by\n detailed comparison of the actigraph data and notes in the logs.\n

\n \n

Familiarization, which took place in the infant's home, lasted 15 min. During this time, the experimenter played quietly with\n the infant while the language played from a tape recorder in the periphery of the area where they were playing.\n

\n \n

Each infant was tested 4 hr later in the laboratory using the head-turn preference procedure (Kemler Nelson et al., 1995). The infant was seated on the caregiver's lap in an enclosed test booth. A center light, directly in front of the infant,\n was used to obtain his or her attention at the beginning of a trial. Two side lights, mounted directly underneath audio speakers\n on the infant's left and right, were used to draw the infant's attention to the speaker that would emit the stimulus on a\n given trial. Side of presentation was determined randomly, with familiar and unfamiliar test trials played from each side.\n

\n \n

An observer outside the booth monitored the infant's looking behavior using a computer program. The program initiated test\n trials in random order and recorded direction and duration of head-turn responses.\n

\n \n

Each of the 16 test trials began with the center light blinking. Once the infant fixated, the light was extinguished, initiating\n blinking of a side light. When the infant made a head turn of at least 30° in the direction of the blinking side light, the\n sample began to play, continuing until its completion or until the infant failed to maintain the minimum 30° head turn for\n 2 consecutive seconds (signaling the infant's loss of attention). The dependent measure was the amount of time the infant\n oriented toward the test stimulus.\n

\n \n \n " + ] + }, + "results_html": { + "value": [ + + ] + }, + "discussion_html": { + "value": [ + + ] + }, + "conclusions_html": { + "value": [ + "\n \n \n

RESULTS

\n \n

There were no differences in looking time as a function of gender or language version, so means were combined over these variables\n (see Table 1).\n

\n \n \n

Nap Condition

\n \n

The first postsleep trial set the direction of preference for the remaining trials. Mean looking-time difference between trials\n consistent with and inconsistent with the first test trial differed significantly from zero, t(15) = 5.15, p = .0001, prep = .996, d = 1.29 (14 of 16 infants showed this pattern).1 This difference was significant whether the first trial was familiar, M = 1.62 s, t(8) = 2.76, p = .024, prep = .923, d = 0.69, or unfamiliar, M = 2.84 s, t(6) = 5.45, p = .002, prep = .984, d = 1.36. In contrast, the difference between looking time to familiar strings and looking time to unfamiliar strings did not\n differ significantly from zero, t(15) < 1.\n

\n \n \n \n

No-Nap Condition

\n \n

The no-nap group showed the opposite pattern of effects, looking significantly longer to familiar than to unfamiliar strings,\n t(15) = 2.52, p = .024, prep = .923, d = 0.63, but exhibiting no pattern of preference based on the first test trial. The looking-time difference between trials\n consistent with and inconsistent with the first test trial did not deviate significantly from zero, t(15) = 1.13, p = .278, prep = .655, d = 0.28 (only 9 of 16 infants followed this pattern). The significant preference for familiar over unfamiliar strings is a\n replication of the effect reported when there is no delay between familiarization and test (Gómez & Maye, 2005) and is impressive given that familiarization occurred 4 hr earlier.\n

\n \n \n \n

Nap Versus No-Nap Conditions

\n \n

The looking-time difference between trials consistent with and inconsistent with the first test trial was significantly greater\n for the nap than for the no-nap condition, t(30) = 2.14, p = .04, prep = .894, d = 0.38, suggesting that sleep had an effect that was not found after the delay. The preference for familiar over unfamiliar\n strings was not significantly greater in the no-nap than in the nap condition, t(30) = 1.82, p = .079, prep = .838, d = 0.32.\n

\n \n \n \n

Nap-Control Condition

\n \n

Initial experience may have familiarized infants with general characteristics of the language (such as vocabulary) so that\n one-trial learning might take place. We needed a control group of infants who had equivalent prior experience and rest, but\n who were unlikely to have learned the nonadjacent dependency. The control group napped after exposure to a low-variability\n version of the language (middle element drawn from a set of three possible words) that does not promote learning of the nonadjacent\n dependency (Gómez, 2002). If performance in the nap group resulted from one-trial learning, the same pattern of effects would be found in the nap-control\n group. However, these infants did not show a pattern of preference based on the first trial, t(15) = 0.827, p = .421, prep = .553, d = 0.21. The nap group significantly outperformed the nap-control group on this measure, t(30) = 3.59, p = .001, prep = .985, d = 0.63.\n

\n \n \n " + ] + }, + "acknowledgements_html": { + "value": [ + "\n \n

Acknowledgments

\n \n

This research was funded by National Science Foundation CAREER Award BCS-0238584 to R.L.G. We thank L.A. Gerken, K. Fridel,\n J. Lany, and R. Schvaneveldt for helpful comments and suggestions; L. Curtis for help with data collection; K. Fridel for\n assistance with actigraphy analysis; and the parents and infants who participated in this study.\n

\n \n " + ] + }, + "competing_interests_html": { + "value": [ + + ] + }, + "financial_disclosure_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\n \n

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\n " + ] + }, + "copyright": { + "value": [ + "© 2006 Association for Psychological Science" + ] + }, + "onlinefirst_published": { + "value": [ + "\n \t August 2006 \n " + ] + }, + "author_contrib_html": { + "value": [ + + ] + }, + "author_corresp_html": { + "value": [ + "Address correspondence to Rebecca L. Gómez, Department of Psychology, 1503 E. University Ave., Room 312, University of Arizona,\n Tucson, AZ 85721–0068, e-mail: rgomez@u.arizona.edu.\n " + ] + }, + "file_hashes": [ + { + "fulltext.html": "cf13ce186e6d37d43590a8af3558ee89" + }, + { + "fulltext.pdf": "f8f2d254f7db8a4c5ccf98f08d0b3485" + } + ] + }, + "http://pss.sagepub.com/content/17/8/660.full": { + "public_url": { + "value": [ + "http://pss.sagepub.com/content/17/8/660" + ] + }, + "title": { + "value": [ + "How Do I Love Thee? Let Me Count the Words" + ] + }, + "doi": { + "value": [ + "10.1111/j.1467-9280.2006.01762.x" + ] + }, + "pmid": { + "value": [ + "16913946" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "publisher": { + "value": [ + "SAGE Publications" + ] + }, + "journal": { + "value": [ + "Psychological Science" + ] + }, + "journal_issn": { + "value": [ + "0956-7976", + "1467-9280" + ] + }, + "author_name": { + "value": [ + "Richard B. Slatcher", + "James W. Pennebaker" + ] + }, + "author_institution": { + "value": [ + + ] + }, + "volume": { + "value": [ + "17" + ] + }, + "issue": { + "value": [ + "8" + ] + }, + "firstpage": { + "value": [ + "660" + ] + }, + "article_type": { + "value": [ + "Research Reports" + ] + }, + "fulltext_html": { + "value": [ + "http://pss.sagepub.com/content/17/8/660.full" + ] + }, + "fulltext_pdf": { + "value": [ + "http://pss.sagepub.com/content/17/8/660.full.pdf" + ] + }, + "abstract_html": { + "value": [ + "\n \n

Abstract

\n \n

Writing about emotional experiences is associated with a host of positive outcomes. This study extended the expressive-writing\n paradigm to the realm of romantic relationships to examine the social effects of writing. For 3 consecutive days, one person\n from each of 86 dating couples either wrote about his or her deepest thoughts and feelings about the relationship or wrote\n about his or her daily activities. In the days before and after writing, instant messages were collected from the couples.\n Participants who wrote about their relationship were significantly more likely to still be dating their romantic partners\n 3 months later. Linguistic analyses of the instant messages revealed that participants and their partners used significantly\n more positive and negative emotion words in the days following the expressive-writing manipulation if the participants had\n written about their relationship than if they had written about their daily activities. Increases in positive emotion words\n partially mediated the relation between expressive writing and relationship stability.\n

\n \n " + ] + }, + "methods_html": { + "value": [ + "\n \n \n

METHOD

\n \n \n

Participants

\n \n

Eighty-six undergraduate psychology students (55 women, 31 men; mean age = 18.7, SD = 1.0) and their partners (31 women, 55 men; mean age = 19.3, SD = 1.6) were recruited on the basis that they were in a committed heterosexual romantic relationship and that they engaged\n in IM conversation with each other every day. The couples had been dating an average of 1.31 years (SD = 1.06).\n

\n \n \n \n

Procedure

\n \n

One member of each couple participated in the writing phase of the study. An experimenter met with participants individually\n or in small groups of 2 to 5 to give them an overview of the study. They were told that its purpose was to quantify the types\n of words that people use in writing and everyday interactions.\n

\n \n

Participants were instructed to forward to a secure e-mail address all daily IM conversations between themselves and their\n partners during the 10 days of the study. Considerable effort was taken during the introductory session to reassure participants\n that their messages would be completely confidential.\n

\n \n

Questionnaires assessing demographic information, relationship status, and relationship satisfaction were completed by participants\n and their partners on-line from home on the first day of the study. Satisfaction was measured using the Relationship Assessment\n Scale (RAS; Hendrick, 1988). The RAS consists of seven items, such as “In general, how satisfied are you with your relationship?” Ratings are made on\n a 7-point Likert scale.\n

\n \n

Participants were randomly assigned to the experimental (n = 44) or control (n = 42) writing condition and were instructed to set aside 20 min per day on the fourth, fifth, and sixth days of the study\n for completion of the on-line writing exercises. Participants in the experimental condition were instructed to write about\n their deepest thoughts and feelings about their current romantic relationship, “to really let go and explore your very deepest\n emotions and thoughts about your relationship.” Those in the control condition were instructed to write in detail about their\n daily activities—a standard control condition for expressive-writing studies. The purpose of the writing assignments was left\n intentionally vague to reduce the possibility of demand characteristics; participants were told that the writing assignments\n would be used to assess basic word use.\n

\n \n

Three months later, participants completed a brief on-line questionnaire that assessed relationship status and satisfaction.

\n \n \n \n

Linguistic Analysis

\n \n

The IM conversations were analyzed using the Linguistic Inquiry and Word Count program (LIWC; Pennebaker, Francis, & Booth, 2001). All conversations from couples in both conditions were spell-checked prior to being submitted to LIWC. They were converted\n to text files, categorized by speaker (participant or partner), and subcategorized according to whether they dated from before\n or after the writing manipulation, resulting in a total of four separate IM text files per couple.\n

\n \n \n " + ] + }, + "results_html": { + "value": [ + "\n \n \n

RESULTS

\n \n \n

Relationship Stability and Language Use

\n \n

Expressive writing was significantly related to the long-term stability of relationships, odds ratio = 3.09, prep = .95, Cohen's d = 0.54. Thirty-four participants (77%) in the experimental condition were still dating their partners at the 3-month follow-up\n mark, compared with 22 participants (52%) in the control condition. There were no significant differences in baseline relationship\n satisfaction between the conditions (experimental M = 6.21, SD = 0.63; control M = 6.01, SD = 0.66), nor was condition related to satisfaction at the 3-month follow-up (experimental M = 5.87, SD = 1.50; control M = 5.94, SD = 0.94). Note that the follow-up satisfaction measures are difficult to interpret because they were available only for couples\n still in their relationships.\n

\n \n

Hierarchical linear modeling (HLM; Raudenbush & Bryk, 2002) was employed to analyze changes in use of emotion words within couples' IM conversations as a function of experimental condition.\n Initial analyses focused on the effects of expressive writing on positive emotion words in couples' conversations. Level 1\n (individual-level) predictors were baseline use of positive emotion words and speaker (participant or partner). Only baseline\n use of positive emotion words was a significant Level 1 predictor, β1 = .51, prep > .99, d = 1.19. Level 2 (couple-level) predictors were gender of the participant, experimental condition, and a Gender × Condition\n interaction term. Only experimental condition was a significant Level 2 predictor, γ01 = .51, prep = .93, d = 0.46. Couples in the expressive-writing condition were more likely than those in the control condition to increase their\n use of positive emotion words with their romantic partners in the days following the manipulation. Additionally, participants\n and partners in the experimental condition increased their use of positive emotion words at similar rates as they communicated\n with each other via IM, even though only the participants were involved in the expressive-writing manipulation.\n

\n \n

Next, the effect of expressive writing on negative emotion words was analyzed. Level 1 predictors were baseline use of negative\n emotion words, as well as the speaker variable. Only baseline use of negative emotion words was a significant Level 1 predictor,\n β1 = .28, prep = .98, d = 0.46. Level 2 predictors were gender of the participant, experimental condition, and a Gender × Condition interaction term.\n Significant Level 2 predictors were experimental condition, γ01 = .54, prep = .98, d = 0.64, and the Gender × Condition interaction, γ02 = .52, prep = .97, d = 0.61. Compared with control couples, couples in the expressive-writing condition were more likely to increase their use\n of negative emotion words with their romantic partners in the days following the writing manipulation. This effect was moderated\n by the gender of the person in each couple who took part in the writing manipulation. Specifically, couples in which the male\n wrote about the relationship increased their use of negative emotion words significantly compared with control couples, whereas\n couples in which the female wrote about the relationship did not change in their use of negative emotion words compared with\n control couples.1

\n \n \n \n

Mediation Effects of Changes in Use of Emotion Words

\n \n

A strength of this design is that it allowed us to explore the degree to which measures of language may reflect the social\n psychological processes underlying the effects of expressive writing. Two sets of mediation analyses were conducted—one with\n positive emotion words as the potential mediator, the other with negative emotion words as the potential mediator. In both\n cases, the outcome measure was relationship stability at the 3-month follow-up. Means and standard deviations for couples'\n use of emotion words in their IM conversations are shown in Table 1.\n

\n \n
\n
\n \n
\n
TABLE 1 \n

Couples' Use of Emotion Words in Instant Messages as a Function of Time and Condition

\n
\n
\n
\n \n \n

Positive Emotion Words

\n \n

Experimental condition and use of positive emotion words before and after the writing manipulation were entered in separate\n steps into a logistic regression in which relationship stability was the dependent variable. Higher levels of postwriting\n positive emotion words were associated with higher levels of couple stability, odds ratio = 3.04, prep = .99, d = 0.95. After controlling for changes in positive emotion words, the effects of experimental condition on relationship stability\n were no longer significant, suggesting possible mediation. The results of a Sobel z test (Sobel, 1982) supported this analysis (z = 2.00, prep = .92). Thus, the salutary effects of writing about one's relationship were at least partially mediated by increases in use\n of positive emotion words in daily IM conversations.\n

\n \n \n \n

Negative Emotion Words

\n \n

No relationship was found between increases in negative emotion words and couple stability (prep < .50). This also was the case in a separate analysis for just those couples in which the male was the participant. The effects\n of expressive writing on stability therefore were not mediated by changes in use of negative emotion words.\n

\n \n \n \n " + ] + }, + "discussion_html": { + "value": [ + + ] + }, + "conclusions_html": { + "value": [ + + ] + }, + "acknowledgements_html": { + "value": [ + "\n \n

Acknowledgments

\n \n

Portions of this research were funded by a grant from the National Institutes of Health (MH52391). We would like to thank\n Greg Hixon, Amy Kaderka, and Girish Tembe for their assistance on this project and Amie Green, Timothy Loving, Matthew Newman,\n William Swann, and Simine Vazire for their helpful comments on an earlier draft of this article.\n

\n \n " + ] + }, + "competing_interests_html": { + "value": [ + + ] + }, + "financial_disclosure_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\n \n

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\n " + ] + }, + "copyright": { + "value": [ + "© 2006 Association for Psychological Science" + ] + }, + "onlinefirst_published": { + "value": [ + "\n \t August 2006 \n " + ] + }, + "author_contrib_html": { + "value": [ + + ] + }, + "author_corresp_html": { + "value": [ + "Address correspondence to Richard B. Slatcher, Department of Psychology A8000, The University of Texas at Austin, Austin,\n TX 78712, e-mail: slatcher@mail.utexas.edu.\n " + ] + }, + "file_hashes": [ + { + "fulltext.html": "54d035ed20578dfb18be1656e37ee608" + }, + { + "fulltext.pdf": "55b0c34fbd93bb286cdb6f60db449f79" + } + ] + }, + "http://pss.sagepub.com/content/17/8/654.full": { + "public_url": { + "value": [ + "http://pss.sagepub.com/content/17/8/654" + ] + }, + "title": { + "value": [ + "Reducing Sedentary Behavior" + ] + }, + "doi": { + "value": [ + "10.1111/j.1467-9280.2006.01761.x" + ] + }, + "pmid": { + "value": [ + "16913945" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "publisher": { + "value": [ + "SAGE Publications" + ] + }, + "journal": { + "value": [ + "Psychological Science" + ] + }, + "journal_issn": { + "value": [ + "0956-7976", + "1467-9280" + ] + }, + "author_name": { + "value": [ + "Leonard H. Epstein", + "Samina Raja", + "Samuel S. Gold", + "Rocco A. Paluch", + "Youngju Pak", + "James N. Roemmich" + ] + }, + "author_institution": { + "value": [ + + ] + }, + "volume": { + "value": [ + "17" + ] + }, + "issue": { + "value": [ + "8" + ] + }, + "firstpage": { + "value": [ + "654" + ] + }, + "article_type": { + "value": [ + "Research Reports" + ] + }, + "fulltext_html": { + "value": [ + "http://pss.sagepub.com/content/17/8/654.full" + ] + }, + "fulltext_pdf": { + "value": [ + "http://pss.sagepub.com/content/17/8/654.full.pdf" + ] + }, + "abstract_html": { + "value": [ + "\n \n

Abstract

\n \n

This study was designed to determine whether the characteristics of the neighborhood environment are related to the substitution\n of physical activity for sedentary behavior among youth. Fifty-eight 8- to 15-year-old youth were studied in a within-subjects\n crossover design with three phases: baseline, increased sedentary behavior, and decreased sedentary behavior. The relations\n between changes in physical activity and design, diversity, and density attributes of the neighborhood environment were determined\n using random coefficient models. Compared with girls, boys showed greater increases in physical activity when sedentary behaviors\n were reduced and greater decreases in physical activity when sedentary behaviors were increased. Greater access to parks was\n associated with greater physical activity when sedentary behaviors were reduced.\n

\n \n " + ] + }, + "methods_html": { + "value": [ + "\n \n \n

METHOD

\n \n \n

Participants

\n \n

Participants were fifty-eight 8- to 15-year-old youth recruited from the Buffalo-Niagara Falls Metropolitan Area, which is\n home to more than 1 million people. To be included, youth had to report engaging in 15 to 25 hr per week of targeted sedentary\n activities (watching television or videos, playing video games, or using a computer for recreation). Additional inclusion\n criteria were having no dietary, physical-activity, or medical restrictions and not experiencing systematic changes in factors\n that could influence energy intake or energy expenditure during the 9 weeks of the study (e.g., starting a newspaper route\n or beginning summer camp). Sixty percent of the population in the Buffalo-Niagara Falls Metropolitan Area resides in single-family\n detached housing; 40% lives in other housing types, including condominiums, multi-unit houses, and apartments. The city of\n Buffalo and its inner-ring suburbs offer a compact built environment, whereas newer outer-ring suburbs have larger lot sizes\n and lower housing density.\n

\n \n

The characteristics of the youth in this sample are summarized in Table 1 (see also Epstein, Roemmich, Paluch, & Raynor, 2005). Fifty-one (87.9%) of the participants were White, 4 (6.9%) were Black, 2 (3.4%) were Hispanic, and 1 (1.7%) reported “other”\n ethnicity. Parents of boys reported more pieces of exercise equipment in the home than did parents of girls (2.3 ± 1.8 vs.\n 1.1 ± 1.1, p = .006), and boys were more active than girls (518.9 ± 193.6 vs. 401.2 ± 182.5 accelerometer counts/min, p = .021).\n

\n \n
\n
\n \n
\n
TABLE 1 \n

Characteristics of the Participants

\n
\n
\n
\n \n

The consent form was approved by the institutional review board of the University at Buffalo School of Medicine and Biomedical\n Sciences. Written assent to participate was obtained from each child and adolescent, and written consent was obtained from\n their parents.\n

\n \n \n \n

Design and Procedure

\n \n

Families participated in a 9-week experiment, with a 3-week baseline, a 3-week phase in which sedentary behavior was increased,\n and a 3-week phase in which sedentary behavior was decreased. Order of the experimental phases was counterbalanced across\n families. Participants were asked to maintain their usual pattern of sedentary behavior, physical activity, and energy intake\n during baseline. During the experimental phases, the goal was a 25% to 50% increase or decrease from baseline in self-reported\n targeted sedentary behaviors (watching television and videos, playing video games, and using computers for recreation). Families\n could earn up to $475 for adherence to the protocol, and incentives were provided for recording sedentary behaviors and making\n recommended changes in targeted sedentary behaviors. No incentives were earned for changes in physical activity. Families\n attended three meetings, one for each phase of the study, at which we determined whether or not they had met their goals and\n completed all the required measurements. At these meetings, the families also were informed about their next phase and received\n help solving any problems related to the study. Three cohorts began the study in the summer, and two began it during the school\n year. The methods of this study are reported in greater detail elsewhere (Epstein, Roemmich, Paluch, & Raynor, 2005).\n

\n \n \n \n

Measurement

\n \n \n

Sedentary Behavior

\n \n

During 3 baseline days, the youth recorded in a habit book the time and duration of targeted sedentary behaviors (watching\n television or a video, playing video games, and using a computer for recreation). In addition, each family member, including\n the participating youth, recorded his or her television and computer use in a log that was attached to the device, and every\n television and computer was attached to a Brultech event logger (EL-100; Brultech Research, Inc., Port Colborne, Ontario,\n Canada) that recorded whether the appliance was turned on or off on a minute-by-minute basis. Family logs and the Brultech\n event logger were used during the baseline period to develop reliability data on the children's records. There was 90.6% agreement\n (κ = .72) between the youths' habit books and log recordings and 91.8% agreement (κ = .67) between the total time recorded\n on family logs and Brultech devices.\n

\n \n

The participating youth continued to record their targeted sedentary behavior daily throughout the study. Reported minutes\n of sedentary behavior on the 2 weekdays and 1 weekend day that activity data were collected (see the next paragraph) were\n used as the measure of targeted sedentary behavior. Parents reported the number of televisions, computers, and pieces of exercise\n equipment in the home.\n

\n \n \n \n

Physical Activity

\n \n

A unidirectional accelerometer, the Model 7164 Actigraph (formerly CSA; Health One Technology, Fort Walton Beach, FL), validated\n as a measure of physical activity in children (Ekelund et al., 2001; Janz, 1994; Janz, Witt, & Mahoney, 1995), was used to measure physical activity on 2 weekdays and 1 weekend day during the last week of each phase. Participants\n recorded when the Actigraph was put on and removed (e.g., for showering and swimming) on the Previous Day Physical Activity\n Recall (PD-PAR) form (Weston, Petosa, & Pate, 1997).\n

\n \n

Activity counts generated by the Actigraph were recorded in 1-min epochs over the day. The activity counts served as the primary\n dependent measure for the statistical analyses. In addition to activity counts, the number of minutes of moderate to vigorous\n physical activity (MVPA) was estimated. MVPA is defined as activity expenditure that is equal to or greater than 3 METS. One\n MET is equivalent to resting metabolic rate, and METS, measured in milliliters of oxygen consumed per kilogram of body mass\n per minute, are multiples of resting metabolic rate. Estimated activity energy expenditure was based on accelerometer counts\n (Puyau, Adolph, Vohra, & Butte, 2002), and resting metabolic rate was estimated on the basis of age, gender, and weight (Firouzbakhsh et al., 1993). METS values were calculated as follows: (activity energy expenditure + resting metabolic rate)/resting metabolic rate.\n Minutes when this value was greater than or equal to 3 were included as minutes of MVPA. Objective activity data were not\n available for 2 participants in one phase because of equipment malfunction. Their activity counts were estimated using the\n intercept and beta coefficient for the regression model relating Actigraph accelerometer counts and METS (based on PD-PAR\n self-reported activities).\n

\n \n \n \n

Body Mass Index

\n \n

Body mass index (BMI) was calculated from height and weight (kg/m2), with height measured using a stadiometer (Seca, Columbia, MD) and weight measured using a balance-beam scale (Healthometer,\n Bridgeview, IL) calibrated daily. Standardized z-BMI values were calculated by the following formula: (BMI − 50th percentile\n BMI)/SD of BMI, using the 50th-percentile BMI for the child's age and sex (Kuczmarski et al., 2002).\n

\n \n \n \n

Characteristics of the Neighborhood Environment

\n \n

A geographic information system (GIS) measured attributes of the neighborhood environment within a 0.5-mile radius around\n each child's residence using ArcGIS 8 and ArcView 3.3 (network analyst) software (ESRI, 2004). Each child's address was matched (geo-coded) to a unique parcel of land in a land-parcel data layer of either Erie or Niagara\n County in New York State. The attribute table accompanying the data layer was used to identify the type of housing (e.g.,\n single-family, two-family, garden apartment, or public housing project) in which the child lived. Variables related to housing\n density and age of housing in the block where a child's house was located were derived from block-group data from the 2000\n U.S. Census (retrieved from the Census Bureau's American FactFinder Web site, http://factfinder.census.gov, on December 13, 2005).\n

\n \n

On the basis of previous theoretical and conceptual work, we chose to focus on 4 of 67 neighborhood-environment variables\n for which we had data. These variables reflect density, diversity, and design of the neighborhood environment (Table 2; Ewing, 2005). Density, which is a measure of the compactness of an environment or the degree to which residences are located close to\n each other, was calculated as the number of housing units per residential acre. Design of the neighborhood environment includes,\n among other things, the degree to which the layout of the neighborhood facilitates connectivity through its transportation\n network. Design was assessed using a connectivity measure defined as the number of intersections divided by the length of\n the street network in feet. Finally, diversity in land use, the mix of land uses available in a neighborhood, was assessed\n by the percentage of residential parcels (i.e., number of residential parcels as a percentage of the total number of parcels\n accessible by the street network) and by the amount of park area accessible by the street network.\n

\n \n
\n
\n \n
\n
TABLE 2 \n

Neighborhood-Environment Variables

\n
\n
\n
\n \n \n \n \n

Analytic Plan

\n \n

We used analysis of variance to test differences in characteristics of the neighborhood environment by sex (boys vs. girls).\n Separate random coefficient models were built to predict activity changes from baseline in each of the experimental phases\n (i.e., decreasing sedentary behaviors and increasing sedentary behaviors), because previous studies have shown asymmetry in\n how decreasing and increasing sedentary behavior influence physical activity (Epstein, Roemmich, Paluch, & Raynor, 2005). We developed random coefficient models with daily accelerometer measures of physical activity as the dependent variable,\n with time-varying minutes of sedentary behavior and time-invariant age, sex, socioeconomic status, z-BMI, and built-environment\n variables as predictors. The models included a random intercept, with the predictors set as fixed effects. Random coefficient\n models were implemented using natural logs of the measures of activity and sedentary behavior to provide estimates of elasticity—the\n relation between proportional change in sedentary behaviors and proportional change in physical activity. Negative elasticity\n coefficients (e.g., as sedentary behavior decreases, physical activity increases) represent substitution of physical activity\n for sedentary behaviors. Initial models included interactions among the between-subjects variables and interactions between\n sedentary-behavior change and the between-subjects variables. The final models included only significant predictors.\n

\n \n

After the model to predict accelerometer counts was developed, a random regression model to predict minutes of MVPA was developed\n for the study sample using accelerometer counts, targeted sedentary behavior, age, sex, park area within 0.5 mile of the family's\n home, and the interaction of targeted sedentary behavior and sex as predictors.\n

\n \n

Both traditional probability levels and prep, the probability of replicating the results (Killeen, 2005), are reported. To measure effect sizes, we calculated r2 for the relation between the predictors and physical activity in univariate regression models and converted this value to\n d using the formula \"Formula\"\"Graphic\" (Rosnow & Rosenthal, 1996). Analyses were conducted using SYSTAT software (2004).\n

\n \n \n " + ] + }, + "results_html": { + "value": [ + + ] + }, + "discussion_html": { + "value": [ + + ] + }, + "conclusions_html": { + "value": [ + + ] + }, + "acknowledgements_html": { + "value": [ + "\n \n

Acknowledgments

\n \n

This research is supported in part by Grant R01 HD39778 from the National Institute of Child Health and Human Development\n to Leonard H. Epstein and by an award from the University at Buffalo Interdisciplinary Research and Creative Activities Fund\n to James Roemmich. We express our appreciation to Hollie Raynor and Rekha Trivikram for implementing the study.\n

\n \n " + ] + }, + "competing_interests_html": { + "value": [ + + ] + }, + "financial_disclosure_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\n \n

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\n " + ] + }, + "copyright": { + "value": [ + "© 2006 Association for Psychological Science" + ] + }, + "onlinefirst_published": { + "value": [ + "\n \t August 2006 \n " + ] + }, + "author_contrib_html": { + "value": [ + + ] + }, + "author_corresp_html": { + "value": [ + "Address correspondence to Leonard H. Epstein, Department of Pediatrics, School of Medicine and Biomedical Sciences, University\n at Buffalo, Farber Hall, Room G56, 3435 Main St., Building #26, Buffalo, NY 14214–3000, e-mail: lhenet@acsu.buffalo.edu.\n " + ] + }, + "file_hashes": [ + { + "fulltext.html": "47d607ac66c979599ab3d82d73d071af" + }, + { + "fulltext.pdf": "493b000b9e1cd71d8ed6d5aa0a082e69" + } + ] + }, + "http://pss.sagepub.com/content/17/12/1021.full": { + "public_url": { + "value": [ + "http://pss.sagepub.com/content/17/12/1021" + ] + }, + "title": { + "value": [ + "The Time Course of Orthographic and Phonological Code Activation" + ] + }, + "doi": { + "value": [ + "10.1111/j.1467-9280.2006.01821.x" + ] + }, + "pmid": { + "value": [ + "17201781" + ] + }, + "language": { + "value": [ + "en" + ] + }, + "publisher": { + "value": [ + "SAGE Publications" + ] + }, + "journal": { + "value": [ + "Psychological Science" + ] + }, + "journal_issn": { + "value": [ + "0956-7976", + "1467-9280" + ] + }, + "author_name": { + "value": [ + "Jonathan Grainger", + "Kristi Kiyonaga", + "Phillip J. Holcomb" + ] + }, + "author_institution": { + "value": [ + + ] + }, + "volume": { + "value": [ + "17" + ] + }, + "issue": { + "value": [ + "12" + ] + }, + "firstpage": { + "value": [ + "1021" + ] + }, + "article_type": { + "value": [ + "Research Reports" + ] + }, + "fulltext_html": { + "value": [ + "http://pss.sagepub.com/content/17/12/1021.full" + ] + }, + "fulltext_pdf": { + "value": [ + "http://pss.sagepub.com/content/17/12/1021.full.pdf" + ] + }, + "abstract_html": { + "value": [ + "\n \n

Abstract

\n \n

The present study used event-related potentials (ERPs) to examine the time course of orthographic and phonological priming\n in the masked priming paradigm. Participants monitored visual target words for occasional animal names, and ERPs to nonanimal\n critical items were recorded. These critical items were preceded by different types of primes: Orthographic priming was examined\n using transposed-letter (TL) primes (e.g., barin-BRAIN) and their controls (e.g., bosin-BRAIN); phonological priming was examined\n using pseudohomophone primes (e.g., brane-BRAIN) and their controls (e.g., brant-BRAIN). Both manipulations modulated the\n N250 ERP component, which is hypothesized to reflect sublexical processing during visual word recognition. Orthographic (TL)\n priming and phonological (pseudohomophone) priming were found to have distinct topographical distributions and different timing,\n with orthographic effects arising earlier than phonological effects.\n

\n \n " + ] + }, + "methods_html": { + "value": [ + "\n \n \n

METHOD

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Subjects

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Twenty volunteers (14 female; mean age = 20, SD = 1.71) from Tufts University were paid $25 to participate in this experiment. All reported being right-handed native speakers\n of English with normal or corrected-to-normal vision.\n

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Stimuli

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The critical stimuli for this experiment were formed from 332 five-letter words and their respective five-letter pseudohomophones.\n Fifteen subjects (who did not participate in the main experiment) rated each word-pseudohomophone pair for phonological similarity\n on a scale from 1 (low) to 7 (high), and the 200 most similar pairs were selected as stimuli for the main experiment (mean rating = 6.52, range = 4.75–7, SD = 0.57).\n

\n \n

Each of the 200 target words was paired with four prime stimuli: the pseudohomophone that was pretested (e.g., brane-BRAIN), a pseudohomophone control prime (e.g., brant-BRAIN), a TL prime (e.g., barin-BRAIN), and a TL control prime (e.g., bosin-BRAIN). Control primes for pseudohomophones were formed by replacing one letter of the pseudohomophone that did not overlap with\n the target word (e.g., the e in brane became a t in brant); the pseudohomophone primes and pseudohomophone control primes were therefore matched in terms of the number of letters\n shared by prime and target and the position of the shared letters. Control primes for TL primes had two different letters\n replacing the transposed letters. For purposes of counterbalancing, each participant was tested with one of four lists of\n prime-target pairings; each list included all four priming conditions, with each target word appearing only once. Thus, each\n target word was tested in all four priming conditions across different participants.\n

\n \n

Sixty noncritical trials were intermixed with the 200 critical trials. Thirty of the noncritical trials contained an animal\n name in the prime position and a filler word in the target position (e.g., horse-TABLE), and 30 contained an animal name in the target position and an unrelated pseudohomophone, TL, or corresponding control prime\n in the prime position (e.g., trane-HORSE, trian-HORSE, troun-HORSE). Each of 30 animal names was used once as a prime and once as a target in each list. The animal names served as probe items\n in a go/no-go semantic categorization task in which participants were instructed to rapidly press a button whenever they detected\n an animal name. Subjects were told to read all other words passively (i.e., critical stimuli did not require an overt response).\n The trials on which animal names were in the prime position provided a measure of prime awareness during the course of the\n experiment. A practice session was administered before the main experiment to familiarize the subjects with the procedure.\n

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Procedure

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Visual stimuli were presented on a 19-in. monitor set to a refresh rate of 60 Hz (which allows 16.67-ms resolution of stimulus\n control) and located 143 cm in front of the participant. Stimuli were displayed at high contrast as white letters (Arial font)\n on a black background (letter matrix was 30 pixels tall × 15 pixels wide). Each trial began with the termination of a fixation\n stimulus in the middle of the screen. After 500 ms, a forward mask of seven pound signs (#######) was presented for a duration\n of 500 ms. This forward mask was replaced at the same location on the screen by a five-letter prime, presented in lowercase\n letters for 50 ms. The prime was immediately replaced by a backward mask of seven random consonants (e.g., CFTRPQB). The backward\n mask remained on the screen for one retrace interval (16.67 ms) and was immediately replaced by the visual target, presented\n in uppercase letters for a duration of 500 ms. All target words were followed by a 1,000-ms black screen, which was replaced\n by a 2,000-ms fixation stimulus marking the end of the trial. The next trial followed a 500-ms blank screen. Subjects were\n asked to blink and move their eyes only when the fixation stimulus appeared on the screen.\n

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Electroencephalogram Recording

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Participants were seated in a comfortable chair in a sound-attenuated darkened room. The electroencephalogram (EEG) was recorded\n from 29 active tin electrodes held in place on the scalp by an elastic cap (Electrode-Cap International, Eaton, OH). Additional\n electrodes were attached below the left eye (to monitor for vertical eye movement or blinks), to the right of the right eye\n (to monitor for horizontal eye movements), over the left mastoid bone (reference), and over the right mastoid bone (recorded\n actively to monitor for differential mastoid activity). All EEG electrode impedances were maintained below 5 kΩ (impedance\n for eye electrodes was less than 10 kΩ). The EEG was amplified by an SA Bioamplifier with a band pass of 0.01 to 40 Hz, and\n the EEG was continuously sampled at a rate of 200 Hz throughout the experiment.\n

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Data Analysis

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Averaged ERPs were formed off-line from trials free of ocular and muscular artifact (less than 5% of trials). Separate waveforms\n were calculated by averaging compound-stimulus ERPs (i.e., the EEG time-locked to a point 100 ms before prime onset and lasting\n until 900 ms after target onset) for each of the four priming conditions. In order to carefully quantify the time course of\n the ERP effects, we measured mean amplitudes in three contiguous windows after target onset: 150 through 250 ms, 250 through\n 350 ms, and 350 through 550 ms. Repeated measures analyses of variance (ANOVAs) with within-participants factors of prime\n type (pseudohomophone vs. TL) and repetition (repeated vs. control) were used to analyze the ERP data. The Geisser and Greenhouse (1959) correction was applied to all repeated measures with more than one degree of freedom (corrected p values are reported). Three anterior (FP1, FPz, FP2), three middle (C3, Cz, C4), and three posterior (P3, Pz, P4) electrode\n sites were chosen for analysis; these sites provided ANOVA factors of laterality (left vs. center vs. right) and front-to-back\n extent (anterior vs. middle vs. posterior).\n

\n \n
\n \n " + ] + }, + "results_html": { + "value": [ + "\n \n

Electroencephalogram Recording

\n \n

Participants were seated in a comfortable chair in a sound-attenuated darkened room. The electroencephalogram (EEG) was recorded\n from 29 active tin electrodes held in place on the scalp by an elastic cap (Electrode-Cap International, Eaton, OH). Additional\n electrodes were attached below the left eye (to monitor for vertical eye movement or blinks), to the right of the right eye\n (to monitor for horizontal eye movements), over the left mastoid bone (reference), and over the right mastoid bone (recorded\n actively to monitor for differential mastoid activity). All EEG electrode impedances were maintained below 5 kΩ (impedance\n for eye electrodes was less than 10 kΩ). The EEG was amplified by an SA Bioamplifier with a band pass of 0.01 to 40 Hz, and\n the EEG was continuously sampled at a rate of 200 Hz throughout the experiment.\n

\n \n " + ] + }, + "discussion_html": { + "value": [ + "\n \n

Data Analysis

\n \n

Averaged ERPs were formed off-line from trials free of ocular and muscular artifact (less than 5% of trials). Separate waveforms\n were calculated by averaging compound-stimulus ERPs (i.e., the EEG time-locked to a point 100 ms before prime onset and lasting\n until 900 ms after target onset) for each of the four priming conditions. In order to carefully quantify the time course of\n the ERP effects, we measured mean amplitudes in three contiguous windows after target onset: 150 through 250 ms, 250 through\n 350 ms, and 350 through 550 ms. Repeated measures analyses of variance (ANOVAs) with within-participants factors of prime\n type (pseudohomophone vs. TL) and repetition (repeated vs. control) were used to analyze the ERP data. The Geisser and Greenhouse (1959) correction was applied to all repeated measures with more than one degree of freedom (corrected p values are reported). Three anterior (FP1, FPz, FP2), three middle (C3, Cz, C4), and three posterior (P3, Pz, P4) electrode\n sites were chosen for analysis; these sites provided ANOVA factors of laterality (left vs. center vs. right) and front-to-back\n extent (anterior vs. middle vs. posterior).\n

\n \n " + ] + }, + "conclusions_html": { + "value": [ + "\n \n \n

RESULTS

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ERPs for the pseudohomophone-, TL-, and control-prime conditions are plotted separately in Figures 1a and 1b for the nine electrodes used in the analyses presented here. Figure 2 presents the voltage maps (formed from all 29 scalp sites) for pseudohomophone and TL priming effects in each of the three\n analysis windows.\n

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\"Fig.
View larger version:\n \n
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\n
Fig. 1. \n

Event-related potentials time-locked to target onset in the pseudohomophone (a) and transposed-letter (b) conditions, plotted\n with the waveforms for their respective control conditions.\n

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\"Fig.
View larger version:\n \n
\n
\n
Fig. 2. \n

Voltage maps of the pseudohomophone (a) and transposed-letter (b) priming effects. Each effect was calculated by subtracting\n event-related potentials (ERPs) to the target in the priming condition from ERPs to the target in the control condition.\n

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150- to 250-Ms Target Epoch

\n \n

As can be seen in Figures 1 and 2, between about 150 and 250 ms, targets following TL primes showed an early priming effect over the more posterior electrode\n sites, but targets following pseudohomophone primes showed little evidence of a priming effect. ANOVA results were consistent\n with this observation: There was a significant interaction among prime type, repetition, anterior-posterior extent, and laterality,\n F(4, 76) = 4.59, p = .01, η2 = .195. Follow-up analyses confirmed that in the TL condition, there was a significant priming effect at posterior sites,\n F(1, 19) = 4.69, p = .043, η2 = .198, and a marginal effect at the middle sites, F(1, 19) = 3.41, p = .08, η2 = .152, but no effect at anterior sites (F < 1). There was no significant effect of priming for pseudohomophones at any location in this epoch (Fs < 1).\n

\n \n
\n \n
\n \n

250- to 350-Ms Target Epoch

\n \n

As can be seen in Figures 1 and 2, between 250 and 350 ms, it was targets following pseudohomophone primes that showed priming effects, whereas targets following\n TL primes showed little to no priming. This observation was supported by a significant interaction of prime type, repetition,\n laterality, and anterior-posterior extent, F(4, 76) = 3.24, p = .045, η2 = .146. Follow-up analyses demonstrated that whereas pseudohomophones showed a significant priming effect, F(1, 19) = 4.77, p = .042, η2 = .201, TL primes did not (F < 1). Moreover, the pseudohomophone effect was significant at anterior sites, F(1, 19) = 5.97, p = .025, η2 = .239, but was not reliable at middle or more posterior sites (ps < .1).\n

\n \n
\n \n
\n \n

350- to 550-Ms Target Epoch

\n \n

Examination of Figures 1 and 2 reveals that the third interval contained the bulk of the activity resembling the classic N400 component. This observation\n was confirmed by the presence of a large main effect of repetition, F(1, 19) = 7.78, p = .012, η2 = .291. Follow-up analyses indicated that priming effects were significant for pseudohomophones across the scalp. The effect\n of pseudohomophone priming was significant, F(1, 19) = 7.20, p = .015, η2 = .275, and remained significant in analyses of anterior sites, F(1, 19) = 7.24, p = .014, η2 = .276; middle sites, F(1, 19) = 5.31, p = .033, η2 = .218; and posterior sites, F(1, 19) = 5.89, p = .025, η2 = .237. In contrast, there was no significant TL priming (ps < .12).\n

\n \n
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\n \n

Time Course of Priming

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To better understand the time course of the effects, we also binned successive 50-ms epochs between 150 and 500 ms for the\n TL and pseudohomophone primes and their respective controls, and ran separate ANOVAs on each 50-ms epoch. The results are\n reported in Table 1 separately for anterior, middle, and posterior electrode sites. During the N250 epoch, TL priming began approximately 50\n ms earlier (200–250 ms vs. 250–300 ms) than pseudohomophone priming, and the scalp distribution of these earliest effects\n was posteriorly oriented for TL priming and anteriorly oriented for pseudohomophone priming. During the N400 epoch, it was\n pseudohomophone priming that started earlier (300–350 ms vs. 450–500 ms), and pseudohomophone priming was generally more robust\n than TL priming, although in this case the scalp distribution was similar for the two types of priming.\n

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\n
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TABLE 1 \n

Time Course of Priming Effects: Results of Tests of Significance for Three Anterior-Posterior Rows of Electrodes

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Behavioral Data

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Participants detected 91.3% (SD = 6.1) of animal probes in the target position and 2% (SD = 3.3) of animal probes in the prime position within a window from 200 to 1,200 ms after probe onset.\n

\n \n
\n \n " + ] + }, + "acknowledgements_html": { + "value": [ + "\n \n

Acknowledgments

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This research was supported by National Institutes of Health Grants HD25889 and HD043251.

\n \n " + ] + }, + "competing_interests_html": { + "value": [ + + ] + }, + "financial_disclosure_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "\n \n

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"article_type": { + "copyright": { "value": [ - "Research Articles" + "© The Author(s) 2015" ] }, "fulltext_html": { @@ -112,19 +119,14 @@ "\n \n

Results

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Average word counts

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To characterize the affective content of the tweets in our data set, we computed word-count averages for the LIWC emotion\n categories, collapsing across time and distance. On average, the tweets in our data set had a total of 14.89 words (SE = 0.03) and 0.97 affect words (SE = 0.005). Within specific negative-emotion categories, the mean number of words was 0.16 for sadness words (SE = 0.002), 0.05 for anxiety words (SE = 0.001), and 0.26 for anger words (SE = 0.003).\n

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Effects on expression, immediacy, and overall affect

\n \n

As predicted by both the nonspecific distance hypothesis (which posits that remoteness has general effects on emotion) and\n the construal-level hypothesis (which posits that remoteness leads to more abstract forms of representation), we found that\n the passage of time led to an exponential decrease in tweet-per-second rate, b = −1.27, 95% confidence interval (CI) = [−1.28, −1.26], p < .001, and linear decreases in number of first-person pronouns, b = −0.062, 95% CI = [−0.082, −0.043], p < .001; present-tense verbs, b = −0.069, 95% CI = [−0.079, −0.059], p < .001; and affect words overall, b = −0.073, 95% CI = [−0.082, −0.064], p < .001. Increasing spatial distance brought about an independent and corresponding pattern, evoking an exponential decrease\n in the tweet-per-second rate, b = −0.040, 95% CI = [−0.056, −0.022], p < .001, as well as linear decreases in use of first-person pronouns, b = −0.049, 95% CI = [−0.081, −0.017], p < .005; present-tense verbs, b = −0.022, 95% CI = [−0.038, −0.006], p < .01; and affect words overall, b = −0.033, 95% CI = [−0.047, −0.020], p < .001. In summary, we observed time- and distance-related changes in word use suggesting decreases in posting of tragedy-related\n content, expression of psychological immediacy, and expression of emotion.\n

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Effects on sadness, anxiety, and causal thought

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Next, we considered changes in use of sadness, anxiety, and causality words, for which the construal-level hypothesis makes\n unique predictions. As predicted by this hypothesis, increasing time led to a decrease in use of sadness words, b = −0.377, 95% CI = [−0.405, −0.349], p < .001; an increase in use of anxiety words, b = 0.116, 95% CI = [0.079, 0.152], p < .001; and an increase in use of causality words, b = 0.021, 95% CI = [0.004, 0.038], p < .05 (see the graphs in Fig. 2). Similarly, increasing spatial distance brought about a decrease in use of sadness words, b = −0.057, 95% CI = [−0.091, −0.022], p < .001, and increases in use of anxiety words, b = 0.105, 95% CI = [0.044, 0.166], p < .001, and causality words, b = 0.050, 95% CI = [0.023, 0.077], p < .001. Follow-up analyses suggested that temporal patterns in word use were still evident when analyses were limited to\n sampling waves of equal duration (see the Supplemental Material).\n

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\"Fig.
View larger version:\n \n
\n
\n
Fig. 2. \n \n

Results from Study 1: mean number of (a) sadness, (b) anxiety, and (c) causality words per tweet in tweets collected during\n the three sampling periods between December 14, 2012, and May 30, 2013. Effects of spatial distance are illustrated in the\n maps, which were derived from a series of three-dimensional spatial regression models; mean frequencies are indicated by color\n (and greater precision of the model’s predictions is represented by greater opacity). Effects of temporal distance are illustrated\n in the graphs, in which mean frequencies are plotted as a function of time since the Newtown shooting (aggregated in 24-hr\n bins); error bars represent 95% confidence intervals.\n

\n \n
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Moreover, a path model (with time and distance as predictors, number of causality words as a mediator, number of anxiety words\n as the outcome, and total tweet word count as a covariate) revealed that the increase in use of anxiety words with increasing\n time and spatial distance was partially mediated by an associated increase in use of causality words, indirect effect of time\n = 0.006, 95% CI = [0.003, 0.009], p < .001; indirect effect of spatial distance = 0.005, 95% CI = [0.000, 0.009], p < .05. An analogous path model with use of sadness words as the outcome indicated that number of causality words did not\n significantly mediate either the effect of time on use of sadness words, indirect effect = −0.0006, 95% CI = [−0.002, 0.0004],\n p = .24, or the effect of spatial distance on use of sadness words, indirect effect = −0.002, 95% CI = [−0.004, 0.001], p = .23. These two path models were implemented via the gsem (generalized structural equation modeling) command in Stata 13,\n with family set to “negative binomial.” Significance of indirect paths was assessed with the nlcom command (which computes\n delta-method standard errors; StataCorp, 2013).\n

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Effects on anger

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For comparison purposes, we also investigated effects of time and spatial distance on anger, an emotion previously identified\n as a key component of the societal-level reaction to violent tragedy (e.g., Lerner, Gonzalez, Small, & Fischhoff, 2003). We found that use of anger words did not change significantly across time, b = −0.01, 95% CI = [−0.03, 0.01], p = .37, but did increase significantly with increasing spatial distance, b = 0.10, 95% CI = [0.07, 0.13], p < .001. (For additional information about the magnitude of the effects of time and spatial distance, see Tables S2 and S3\n in the Supplemental Material.)\n

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Mapping patterns of use of sadness, anxiety, and causality words

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To more thoroughly model and visualize patterns of word use across space, we ran a series of three-dimensional spatial regression\n models. In each model, a smooth surface was fitted to the observed data to predict a tweet feature (y) across the continental United States as a function of latitude (x\n 1) and longitude (x\n 2). To define these surfaces, we implemented a penalized thin-plate regression spline method using the bam function within the mgcv package in R (Wood, 2003). The mapped surfaces (see Fig. 2) represent levels of word use with variations in color and model precision (i.e., the inverse of prediction standard error,\n determined in part by data density) with variations in opacity. As expected, these mapped models are consistent with the linear\n regression analyses reported earlier (which collapsed latitude and longitude into a single distance dimension), but they provide\n more information about the spatial patterns of change in use of sadness, anxiety, and causality words.\n

\n \n
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Word-level analyses

\n \n

To characterize the nature of these relationships at the level of individual words, we correlated time (in seconds) and approximate\n distance (in miles) with frequencies of each of the words in the LIWC sadness, anxiety, and causality categories. Table 1 summarizes the results of these analyses by showing, for each category, the five words whose usage was most strongly associated\n with spatial distance and the five words whose usage was most strongly associated with the passage of time. We corrected for\n multiple comparisons within word category using the false-discovery-rate procedure (Benjamini & Hochberg, 1995). (For additional information about word-level patterns in use of affective words, see Fig. S1 in the Supplemental Material.)\n

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\n
\n \n
\n
Table 1. \n \n

Individual Sadness, Anxiety, and Causality Words Most Strongly Associated With Increasing Time and Spatial Distance From the\n Newtown Tragedy\n

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\n \n " ] }, - "acknowledgements_html": { + "author_contrib_html": { "value": [ - "\n \n

Acknowledgments

\n \n

We thank Daisy Burr, Ehjeen Kim, and Theodore Stephano for research assistance and David Sparks for sharing visualization\n code.\n

\n \n " + "\n \n \n

Author Contributions B. Doré and K. N. Ochsner designed the research. B. Doré, L. Ort, and O. Braverman collected and managed the data. B. Doré\n analyzed and visualized the data. B. Doré wrote the manuscript, and K. N. Ochsner provided critical revisions.\n

\n \n " ] }, "competing_interests_html": { "value": [ - "\n \n \n

Supplemental Material Additional supporting information can be found at http://pss.sagepub.com/content/by/supplemental-data\n \n

\n \n " - ] - }, - "financial_disclosure_html": { - "value": [ - + "\n \n \n

Declaration of Conflicting Interests The authors declared that they had no conflicts of interest with respect to their authorship or the publication of this article.\n

\n \n " ] }, "references_html": { @@ -132,75 +134,50 @@ "\n \n

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\n " ] }, - "copyright": { - "value": [ - "© The Author(s) 2015" - ] - }, - "onlinefirst_published": { - "value": [ - "\n \t April 2015 \n " - ] - }, - "author_contrib_html": { - "value": [ - "\n \n \n

Author Contributions B. Doré and K. N. Ochsner designed the research. B. Doré, L. Ort, and O. Braverman collected and managed the data. B. Doré\n analyzed and visualized the data. B. Doré wrote the manuscript, and K. N. Ochsner provided critical revisions.\n

\n \n " - ] - }, - "author_corresp_html": { - "value": [ - "Bruce Doré, Psychology Department, Columbia University, 324 Schermerhorn, New York, NY 10027 E-mail: bpd2108{at}columbia.edu\n \n " - ] - }, "file_hashes": [ { - "fulltext.html": "6dfe67984637b87391ddaa42af355b36" + "fulltext.html": "6ed6cd9e0c522dad65896595b42d4af9" }, { - "fulltext.pdf": "b020dd13278df6e824157c89aeb74659" + "fulltext.pdf": "37da58bf1a2074a2b89eb444dee0ddd4" } ] }, "http://pss.sagepub.com/content/26/4/385.full": { - "public_url": { - "value": [ - "http://pss.sagepub.com/content/26/4/385" - ] - }, - "title": { + "publisher": { "value": [ - "Bogus Visual Feedback Alters Onset of Movement-Evoked Pain in People With Neck Pain" + "SAGE Publications" ] }, - "doi": { + "journal_name": { "value": [ - "10.1177/0956797614563339" + "Psychological Science" ] }, - "pmid": { + "journal_issn": { "value": [ - "25691362" + "0956-7976", + "1467-9280" ] }, - "language": { + "volume": { "value": [ - "en" + "26" ] }, - "publisher": { + "issue": { "value": [ - "SAGE Publications" + "4" ] }, - "journal": { + "firstpage": { "value": [ - "Psychological Science" + "385" ] }, - "journal_issn": { + "title": { "value": [ - "0956-7976", - "1467-9280" + "Bogus Visual Feedback Alters Onset of Movement-Evoked Pain in People With Neck Pain" ] }, "author_name": { @@ -223,24 +200,36 @@ "\n 1Sansom Institute for Health Research, University of South Australia" ] }, - "volume": { + "date_published": { "value": [ - "26" + "\n \t April 2015 \n " ] }, - "issue": { + "date_accepted": { "value": [ - "4" + "Accepted November 18, 2014.\n ", + "Accepted " ] }, - "firstpage": { + "date_submitted": { "value": [ - "385" + "Received July 15, 2014.\n ", + "Received " ] }, - "article_type": { + "doi": { "value": [ - "Research Articles" + "10.1177/0956797614563339" + ] + }, + "pmid": { + "value": [ + "25691362" + ] + }, + "copyright": { + "value": [ + "© The Author(s) 2015" ] }, "fulltext_html": { @@ -278,95 +267,65 @@ "\n \n

Manipulation Check 1: setting boundaries for altered visual-proprioceptive feedback

\n \n

To blind participants to this manipulation, we based the upper and lower limits of the rotation gain on the results of a pilot\n study. During this pilot study, an independent cohort of 9 healthy participants (7 men, 2 women; mean age = 32 years, SD = 12) were presented with a range of rotation-gain settings and asked to rotate their heads. They were to indicate when a\n difference between real and virtual rotation occurred by rating the observed rotation as slower than, equal to, or faster\n than the true physical rotation. We aimed to determine the rotation gain at which participants were more likely to judge the\n virtual and real rotation to be equal than they were to judge them to be different. As shown in Figure 2, the rotation gains that corresponded to these points were 0.72 and 1.18. As a result, our experimental gain settings were\n chosen to fall between 0.8 and 1.2, and additional controls were implemented to ensure that participants in the main study\n remained blinded.\n

\n \n
\n
\"Fig.
View larger version:\n \n
\n
\n
Fig. 2. \n \n

Results from the pilot study. The graph shows the percentage of rotations rated as slower than, equal to, or faster than the\n true physical rotation as a function of rotation gain. The double-headed arrow indicates the range of rotation-gain settings\n at which virtual movement speeds were more often perceived as equal to, rather than faster or slower than, real-world movement\n speeds.\n

\n \n
\n
\n
\n \n " ] }, - "acknowledgements_html": { + "author_contrib_html": { "value": [ - "\n \n

Acknowledgments

\n \n

For assistance with recruitment, we thank Julie Peacock, Jonathon Schubert, William Kuang, and Ellie Magarey (Marion Physiotherapy);\n Di Wilson, Peter Roberts, Eva Boesch, and Toby Moen (Roberts Physiotherapy); and Jason Collins and Glen Kocher (Northcare\n Physiotherapy). We thank Anthony Ikiosoglous for acting as a blind assessor for data extraction.\n

\n \n " + "\n \n \n

Author Contributions D. S. Harvie and G. L. Moseley developed the study concept; contributed to design, data analysis, and interpretation; and\n helped write the manuscript. D. S. Harvie collected the data. V. J. Madden contributed to study design and helped write the\n manuscript. M. Broecker and R. T. Smith contributed to study design and provided technical expertise for the virtual reality\n setup. A. Meulders contributed to interpretation and helped write the manuscript. All authors approved the final version of\n the manuscript for submission.\n

\n \n " ] }, "competing_interests_html": { "value": [ - - ] - }, - "financial_disclosure_html": { - "value": [ - + "\n \n \n

Declaration of Conflicting Interests The authors declared that they had no conflicts of interest with respect to their authorship or the publication of this article.\n

\n \n " ] }, "references_html": { "value": [ - "\n \n

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\n " - ] - }, - "copyright": { - "value": [ - "© The Author(s) 2015" - ] - }, - "onlinefirst_published": { - "value": [ - "\n \t April 2015 \n " - ] - }, - "author_contrib_html": { - "value": [ - "\n \n \n

Author Contributions D. S. Harvie and G. L. Moseley developed the study concept; contributed to design, data analysis, and interpretation; and\n helped write the manuscript. D. S. Harvie collected the data. V. J. Madden contributed to study design and helped write the\n manuscript. M. Broecker and R. T. Smith contributed to study design and provided technical expertise for the virtual reality\n setup. A. Meulders contributed to interpretation and helped write the manuscript. All authors approved the final version of\n the manuscript for submission.\n

\n \n " - ] - }, - "author_corresp_html": { - "value": [ - "G. Lorimer Moseley, University of South Australia, GPO Box 2471, Adelaide, South Australia 5001, Australia E-mail: lorimer.moseley{at}gmail.com\n \n " + "\n \n

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\n " ] }, "file_hashes": [ { - "fulltext.html": "3d4e3979ea58f430f5a7f9ed30612ed8" + "fulltext.html": "3fa5cf143b97ce4fbe0d7653c516dc8c" }, { - "fulltext.pdf": "d95ae8194cef4bab791edbf9f85ebf0b" + "fulltext.pdf": "69c828e0a026fa897671b55a40e4e657" } ] }, "http://pss.sagepub.com/content/26/4/424.full": { - "public_url": { - "value": [ - "http://pss.sagepub.com/content/26/4/424" - ] - }, - "title": { + "publisher": { "value": [ - "Chinese Kindergartners Learn to Read Characters Analytically" + "SAGE Publications" ] }, - "doi": { + "journal_name": { "value": [ - "10.1177/0956797614567203" + "Psychological Science" ] }, - "pmid": { + "journal_issn": { "value": [ - "25711130" + "0956-7976", + "1467-9280" ] }, - "language": { + "volume": { "value": [ - "en" + "26" ] }, - "publisher": { + "issue": { "value": [ - "SAGE Publications" + "4" ] }, - "journal": { + "firstpage": { "value": [ - "Psychological Science" + "424" ] }, - "journal_issn": { + "title": { "value": [ - "0956-7976", - "1467-9280" + "Chinese Kindergartners Learn to Read Characters Analytically" ] }, "author_name": { @@ -381,24 +340,36 @@ "\n 2The Chinese University of Hong Kong" ] }, - "volume": { + "date_published": { "value": [ - "26" + "\n \t April 2015 \n " ] }, - "issue": { + "date_accepted": { "value": [ - "4" + "Accepted December 13, 2014.\n ", + "Accepted " ] }, - "firstpage": { + "date_submitted": { "value": [ - "424" + "Received March 27, 2014.\n ", + "Received " + ] + }, + "doi": { + "value": [ + "10.1177/0956797614567203" + ] + }, + "pmid": { + "value": [ + "25711130" ] }, - "article_type": { + "copyright": { "value": [ - "Research Articles" + "© The Author(s) 2015" ] }, "fulltext_html": { @@ -436,95 +407,65 @@ "\n \n

Nonverbal IQ

\n \n

Sets A and B of Raven’s Standard Progressive Matrices (Raven, Court, & Raven, 1996) were used to measure children’s nonverbal IQ at Time 1 only. The maximum score was 24 points.\n

\n \n " ] }, - "acknowledgements_html": { + "author_contrib_html": { "value": [ - "\n \n

Acknowledgments

\n \n

We thank all participating children, as well as Xiuhong Tong for her help in calculating perimetric-complexity statistics.

\n \n " + "\n \n \n

Author Contributions C. McBride developed the study concept. Both authors contributed to the study design and analyzed and interpreted the data.\n Testing and data collection were performed by L. Yin. L. Yin drafted the manuscript, and C. McBride provided critical revisions.\n Both authors approved the final version of the manuscript for submission.\n

\n \n " ] }, "competing_interests_html": { "value": [ - - ] - }, - "financial_disclosure_html": { - "value": [ - + "\n \n \n

Declaration of Conflicting Interests The authors declared that they had no conflicts of interest with respect to their authorship or the publication of this article.\n

\n \n " ] }, "references_html": { "value": [ - "\n \n

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\n " - ] - }, - "copyright": { - "value": [ - "© The Author(s) 2015" - ] - }, - "onlinefirst_published": { - "value": [ - "\n \t April 2015 \n " - ] - }, - "author_contrib_html": { - "value": [ - "\n \n \n

Author Contributions C. McBride developed the study concept. Both authors contributed to the study design and analyzed and interpreted the data.\n Testing and data collection were performed by L. Yin. L. Yin drafted the manuscript, and C. McBride provided critical revisions.\n Both authors approved the final version of the manuscript for submission.\n

\n \n " - ] - }, - "author_corresp_html": { - "value": [ - "\n Li Yin, Tsinghua University, Wen Nan Building, Room 103, Beijing, China 100084 E-mail: yinl{at}tsinghua.edu.cn\n \n " + "\n \n

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Training

\n \n

Training occurred on Days 2 through 6 using the same stimuli and a similar procedure as in the testing phase, with the key\n difference being that subjects were trained on only one standard orientation instead of the two they saw on testing days.\n During training, all subjects completed five blocks, one at each noise level. There were 150 trials per block, and subjects\n were allowed to take a short break after each block. During each training day, the QUEST procedure was run using the same\n parameters as during the testing days, but with one modification. The contrast threshold estimate for QUEST for each subject\n used the threshold derived on the previous day of testing or training as the initial estimate. Subsequent trials used the\n current threshold, taking into account each trial during the training sessions. Using this method, subjects were constantly\n trained at their threshold (75% correct) during each training day. This allowed training to be constantly optimized for any\n improvement that occurred between or within testing or training sessions. All subjects received 750 training trials per day,\n for a total of 3,750 training trials over the course of the experiment.\n

\n \n " ] }, - "acknowledgements_html": { + "author_contrib_html": { "value": [ - + "\n \n \n

Author Contributions All authors contributed to the design of the study. Data were collected by D. J. DeLoss and analyzed by D. J. DeLoss and\n G. J. Andersen. D. J. DeLoss drafted the manuscript. G. J. Andersen and D. J. DeLoss provided revisions. All authors approved\n the final manuscript.\n

\n \n " ] }, "competing_interests_html": { "value": [ - "\n \n \n

Funding This research was funded by National Institute on Aging Grant No. R01-AG031941.\n

\n \n " - ] - }, - "financial_disclosure_html": { - "value": [ - + "\n \n \n

Declaration of Conflicting Interests The authors declared that they had no conflicts of interest with respect to their authorship or the publication of this article.\n

\n \n " ] }, "references_html": { @@ -616,75 +564,50 @@ "\n \n

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\n " ] }, - "copyright": { - "value": [ - "© The Author(s) 2015" - ] - }, - "onlinefirst_published": { - "value": [ - "\n \t April 2015 \n " - ] - }, - "author_contrib_html": { - "value": [ - "\n \n \n

Author Contributions All authors contributed to the design of the study. Data were collected by D. J. DeLoss and analyzed by D. J. DeLoss and\n G. J. Andersen. D. J. DeLoss drafted the manuscript. G. J. Andersen and D. J. DeLoss provided revisions. All authors approved\n the final manuscript.\n

\n \n " - ] - }, - "author_corresp_html": { - "value": [ - "George J. Andersen, University of California, Riverside, Department of Psychology, 900 University Ave., Riverside, CA 92506\n E-mail: andersen{at}ucr.edu\n \n " - ] - }, "file_hashes": [ { - "fulltext.html": "4dde7038b74b5199c74cc76c7f10d318" + "fulltext.html": "8dba5cddc4478a8192d1a82fb8d3fe19" }, { - "fulltext.pdf": "d8d20539b1d504b076eadf5b393fec9f" + "fulltext.pdf": "a5b3005e8626bc1ed65f61da553c274c" } ] }, "http://pss.sagepub.com/content/26/4/499.full": { - "public_url": { - "value": [ - "http://pss.sagepub.com/content/26/4/499" - ] - }, - "title": { + "publisher": { "value": [ - "Young Children Show the Bystander Effect in Helping Situations" + "SAGE Publications" ] }, - "doi": { + "journal_name": { "value": [ - "10.1177/0956797615569579" + "Psychological Science" ] }, - "pmid": { + "journal_issn": { "value": [ - "25792132" + "0956-7976", + "1467-9280" ] }, - "language": { + "volume": { "value": [ - "en" + "26" ] }, - "publisher": { + "issue": { "value": [ - "SAGE Publications" + "4" ] }, - "journal": { + "firstpage": { "value": [ - "Psychological Science" + "499" ] }, - "journal_issn": { + "title": { "value": [ - "0956-7976", - "1467-9280" + "Young Children Show the Bystander Effect in Helping Situations" ] }, "author_name": { @@ -704,24 +627,36 @@ "\n 1Department of Developmental and Comparative Psychology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany" ] }, - "volume": { + "date_published": { "value": [ - "26" + "\n \t April 2015 \n " ] }, - "issue": { + "date_accepted": { "value": [ - "4" + "Accepted January 6, 2015.\n ", + "Accepted " ] }, - "firstpage": { + "date_submitted": { "value": [ - "499" + "Received April 15, 2014.\n ", + "Received " + ] + }, + "doi": { + "value": [ + "10.1177/0956797615569579" + ] + }, + "pmid": { + "value": [ + "25792132" ] }, - "article_type": { + "copyright": { "value": [ - "Research Articles" + "© The Author(s) 2015" ] }, "fulltext_html": { @@ -759,95 +694,65 @@ "\n \n

Manipulation phase

\n \n

The children were asked to sit down to color. The experimenter then said that while the children colored their pictures, she\n would paint her cardboard wall and, to do that more easily, she would place it in a certain way. In the bystander condition,\n she put it to the side (against the right wall of the room). In the bystander-unavailable condition, she attached the cardboard\n wall to the barriers separating the two tables on the right, such that the two confederates were fenced in and unable to leave\n their compartments (see Fig. 1c). In this condition, the experimenter then commented on the wall with apparent surprise, saying, “Oh, I’ve just realized,\n now you two can’t get out of here. Well, you are fenced in now, briefly, but don’t worry, you can get out as soon as we’re\n finished here.” In the alone condition, the wall was put to the side (as in the bystander condition) for half of the participants\n and was attached to the barriers (as in the bystander-unavailable condition) for the other half. In all conditions, the participants\n were able to move freely. After this, all children were given pencils and were asked to start coloring while the experimenter\n painted her cardboard wall. After approximately a minute, the experimenter then said she needed to clean her paintbrushes\n and sat down at her table with the cup of water and the paintbrushes.\n

\n \n " ] }, - "acknowledgements_html": { + "author_contrib_html": { "value": [ - "\n \n

Acknowledgments

\n \n

We thank Robert Hepach for contributing to the study design and Jana Jurkat, Lydia Fiedler, Christian Biermann, Alex Call,\n and the confederates for their help with data collection.\n

\n \n " + "\n \n \n

Author Contributions All authors contributed to the idea of the study and its design. Testing and data collection were performed by M. Plötner.\n M. Plötner analyzed the data under the supervision of H. Over, M. Carpenter, and M. Tomasello. M. Plötner drafted the manuscript,\n and H. Over, M. Carpenter, and M. Tomasello provided critical revisions. All authors approved the final version of the manuscript\n for submission.\n

\n \n " ] }, "competing_interests_html": { "value": [ - - ] - }, - "financial_disclosure_html": { - "value": [ - + "\n \n \n

Declaration of Conflicting Interests The authors declared that they had no conflicts of interest with respect to their authorship or the publication of this article.\n

\n \n " ] }, "references_html": { "value": [ - "\n \n

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\n " - ] - }, - "copyright": { - "value": [ - "© The Author(s) 2015" - ] - }, - "onlinefirst_published": { - "value": [ - "\n \t April 2015 \n " - ] - }, - "author_contrib_html": { - "value": [ - "\n \n \n

Author Contributions All authors contributed to the idea of the study and its design. Testing and data collection were performed by M. Plötner.\n M. Plötner analyzed the data under the supervision of H. Over, M. Carpenter, and M. Tomasello. M. Plötner drafted the manuscript,\n and H. Over, M. Carpenter, and M. Tomasello provided critical revisions. All authors approved the final version of the manuscript\n for submission.\n

\n \n " - ] - }, - "author_corresp_html": { - "value": [ - "Maria Plötner, Department of Developmental and Comparative Psychology, Max Planck Institute for Evolutionary Anthropology,\n Leipzig, Germany 04103 E-mail: maria_ploetner{at}eva.mpg.de\n \n " + "\n \n

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\n " ] }, "file_hashes": [ { - "fulltext.html": "3a664c433dbd6958a3163c528fab6e07" + "fulltext.html": "6f62b7b7bf8a69a60da33876a5a7aa07" }, { - "fulltext.pdf": "f3c64e0dccc7450507ef75618d44480f" + "fulltext.pdf": "59a92b6aa0247154202a982f6d5ec379" } ] }, "http://pss.sagepub.com/content/17/8/670.full": { - "public_url": { - "value": [ - "http://pss.sagepub.com/content/17/8/670" - ] - }, - "title": { + "publisher": { "value": [ - "Naps Promote Abstraction in Language-Learning Infants" + "SAGE Publications" ] }, - "doi": { + "journal_name": { "value": [ - "10.1111/j.1467-9280.2006.01764.x" + "Psychological Science" ] }, - "pmid": { + "journal_issn": { "value": [ - "16913948" + "0956-7976", + "1467-9280" ] }, - "language": { + "volume": { "value": [ - "en" + "17" ] }, - "publisher": { + "issue": { "value": [ - "SAGE Publications" + "8" ] }, - "journal": { + "firstpage": { "value": [ - "Psychological Science" + "670" ] }, - "journal_issn": { + "title": { "value": [ - "0956-7976", - "1467-9280" + "Naps Promote Abstraction in Language-Learning Infants" ] }, "author_name": { @@ -862,24 +767,36 @@ ] }, - "volume": { + "date_published": { "value": [ - "17" + "\n \t August 2006 \n " ] }, - "issue": { + "date_accepted": { "value": [ - "8" + "Accepted November 8, 2005.\n ", + "Accepted " ] }, - "firstpage": { + "date_submitted": { "value": [ - "670" + "Received September 26, 2005.\n ", + "Received " + ] + }, + "doi": { + "value": [ + "10.1111/j.1467-9280.2006.01764.x" + ] + }, + "pmid": { + "value": [ + "16913948" ] }, - "article_type": { + "copyright": { "value": [ - "Research Reports" + "© 2006 Association for Psychological Science" ] }, "fulltext_html": { @@ -917,95 +834,65 @@ "\n \n \n

RESULTS

\n \n

There were no differences in looking time as a function of gender or language version, so means were combined over these variables\n (see Table 1).\n

\n \n \n

Nap Condition

\n \n

The first postsleep trial set the direction of preference for the remaining trials. Mean looking-time difference between trials\n consistent with and inconsistent with the first test trial differed significantly from zero, t(15) = 5.15, p = .0001, prep = .996, d = 1.29 (14 of 16 infants showed this pattern).1 This difference was significant whether the first trial was familiar, M = 1.62 s, t(8) = 2.76, p = .024, prep = .923, d = 0.69, or unfamiliar, M = 2.84 s, t(6) = 5.45, p = .002, prep = .984, d = 1.36. In contrast, the difference between looking time to familiar strings and looking time to unfamiliar strings did not\n differ significantly from zero, t(15) < 1.\n

\n \n \n \n

No-Nap Condition

\n \n

The no-nap group showed the opposite pattern of effects, looking significantly longer to familiar than to unfamiliar strings,\n t(15) = 2.52, p = .024, prep = .923, d = 0.63, but exhibiting no pattern of preference based on the first test trial. The looking-time difference between trials\n consistent with and inconsistent with the first test trial did not deviate significantly from zero, t(15) = 1.13, p = .278, prep = .655, d = 0.28 (only 9 of 16 infants followed this pattern). The significant preference for familiar over unfamiliar strings is a\n replication of the effect reported when there is no delay between familiarization and test (Gómez & Maye, 2005) and is impressive given that familiarization occurred 4 hr earlier.\n

\n \n \n \n

Nap Versus No-Nap Conditions

\n \n

The looking-time difference between trials consistent with and inconsistent with the first test trial was significantly greater\n for the nap than for the no-nap condition, t(30) = 2.14, p = .04, prep = .894, d = 0.38, suggesting that sleep had an effect that was not found after the delay. The preference for familiar over unfamiliar\n strings was not significantly greater in the no-nap than in the nap condition, t(30) = 1.82, p = .079, prep = .838, d = 0.32.\n

\n \n \n \n

Nap-Control Condition

\n \n

Initial experience may have familiarized infants with general characteristics of the language (such as vocabulary) so that\n one-trial learning might take place. We needed a control group of infants who had equivalent prior experience and rest, but\n who were unlikely to have learned the nonadjacent dependency. The control group napped after exposure to a low-variability\n version of the language (middle element drawn from a set of three possible words) that does not promote learning of the nonadjacent\n dependency (Gómez, 2002). If performance in the nap group resulted from one-trial learning, the same pattern of effects would be found in the nap-control\n group. However, these infants did not show a pattern of preference based on the first trial, t(15) = 0.827, p = .421, prep = .553, d = 0.21. The nap group significantly outperformed the nap-control group on this measure, t(30) = 3.59, p = .001, prep = .985, d = 0.63.\n

\n \n \n " ] }, - "acknowledgements_html": { - "value": [ - "\n \n

Acknowledgments

\n \n

This research was funded by National Science Foundation CAREER Award BCS-0238584 to R.L.G. We thank L.A. Gerken, K. Fridel,\n J. Lany, and R. Schvaneveldt for helpful comments and suggestions; L. Curtis for help with data collection; K. Fridel for\n assistance with actigraphy analysis; and the parents and infants who participated in this study.\n

\n \n " - ] - }, - "competing_interests_html": { + "author_contrib_html": { "value": [ ] }, - "financial_disclosure_html": { + "competing_interests_html": { "value": [ ] }, "references_html": { "value": [ - "\n \n

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\n " - ] - }, - "copyright": { - "value": [ - "© 2006 Association for Psychological Science" - ] - }, - "onlinefirst_published": { - "value": [ - "\n \t August 2006 \n " - ] - }, - "author_contrib_html": { - "value": [ - - ] - }, - "author_corresp_html": { - "value": [ - "Address correspondence to Rebecca L. Gómez, Department of Psychology, 1503 E. University Ave., Room 312, University of Arizona,\n Tucson, AZ 85721–0068, e-mail: rgomez@u.arizona.edu.\n " + "\n \n

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Acknowledgments

\n \n

Portions of this research were funded by a grant from the National Institutes of Health (MH52391). We would like to thank\n Greg Hixon, Amy Kaderka, and Girish Tembe for their assistance on this project and Amie Green, Timothy Loving, Matthew Newman,\n William Swann, and Simine Vazire for their helpful comments on an earlier draft of this article.\n

\n \n " - ] - }, - "competing_interests_html": { + "author_contrib_html": { "value": [ ] }, - "financial_disclosure_html": { + "competing_interests_html": { "value": [ ] }, "references_html": { "value": [ - "\n \n

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Acknowledgments

\n \n

This research is supported in part by Grant R01 HD39778 from the National Institute of Child Health and Human Development\n to Leonard H. Epstein and by an award from the University at Buffalo Interdisciplinary Research and Creative Activities Fund\n to James Roemmich. We express our appreciation to Hollie Raynor and Rekha Trivikram for implementing the study.\n

\n \n " - ] - }, - "competing_interests_html": { + "author_contrib_html": { "value": [ ] }, - "financial_disclosure_html": { + "competing_interests_html": { "value": [ ] }, "references_html": { "value": [ - "\n \n

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\n " - ] - }, - "copyright": { - "value": [ - "© 2006 Association for Psychological Science" - ] - }, - "onlinefirst_published": { - "value": [ - "\n \t August 2006 \n " - ] - }, - "author_contrib_html": { - "value": [ - - ] - }, - "author_corresp_html": { - "value": [ - "Address correspondence to Leonard H. Epstein, Department of Pediatrics, School of Medicine and Biomedical Sciences, University\n at Buffalo, Farber Hall, Room G56, 3435 Main St., Building #26, Buffalo, NY 14214–3000, e-mail: lhenet@acsu.buffalo.edu.\n " + "\n \n

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\n " ] }, "file_hashes": [ { - "fulltext.html": "47d607ac66c979599ab3d82d73d071af" + "fulltext.html": "4287086772b5f8c208b09e3f7aebb7f3" }, { - "fulltext.pdf": "493b000b9e1cd71d8ed6d5aa0a082e69" + "fulltext.pdf": "bf30f304a49a461f2f1e4a22cfb8d5fb" } ] }, "http://pss.sagepub.com/content/17/12/1021.full": { - "public_url": { - "value": [ - "http://pss.sagepub.com/content/17/12/1021" - ] - }, - "title": { + "publisher": { "value": [ - "The Time Course of Orthographic and Phonological Code Activation" + "SAGE Publications" ] }, - "doi": { + "journal_name": { "value": [ - "10.1111/j.1467-9280.2006.01821.x" + "Psychological Science" ] }, - "pmid": { + "journal_issn": { "value": [ - "17201781" + "0956-7976", + "1467-9280" ] }, - "language": { + "volume": { "value": [ - "en" + "17" ] }, - "publisher": { + "issue": { "value": [ - "SAGE Publications" + "12" ] }, - "journal": { + "firstpage": { "value": [ - "Psychological Science" + "1021" ] }, - "journal_issn": { + "title": { "value": [ - "0956-7976", - "1467-9280" + "The Time Course of Orthographic and Phonological Code Activation" ] }, "author_name": { @@ -1338,24 +1189,36 @@ ] }, - "volume": { + "date_published": { "value": [ - "17" + "\n \t December 2006 \n " ] }, - "issue": { + "date_accepted": { "value": [ - "12" + "Accepted May 3, 2006.\n ", + "Accepted " ] }, - "firstpage": { + "date_submitted": { "value": [ - "1021" + "Received December 9, 2005.\n ", + "Received " + ] + }, + "doi": { + "value": [ + "10.1111/j.1467-9280.2006.01821.x" + ] + }, + "pmid": { + "value": [ + "17201781" ] }, - "article_type": { + "copyright": { "value": [ - "Research Reports" + "© 2006 Association for Psychological Science" ] }, "fulltext_html": { @@ -1393,52 +1256,27 @@ "\n \n \n

RESULTS

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ERPs for the pseudohomophone-, TL-, and control-prime conditions are plotted separately in Figures 1a and 1b for the nine electrodes used in the analyses presented here. Figure 2 presents the voltage maps (formed from all 29 scalp sites) for pseudohomophone and TL priming effects in each of the three\n analysis windows.\n

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View larger version:\n \n
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Fig. 1. \n

Event-related potentials time-locked to target onset in the pseudohomophone (a) and transposed-letter (b) conditions, plotted\n with the waveforms for their respective control conditions.\n

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Fig. 2. \n

Voltage maps of the pseudohomophone (a) and transposed-letter (b) priming effects. Each effect was calculated by subtracting\n event-related potentials (ERPs) to the target in the priming condition from ERPs to the target in the control condition.\n

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150- to 250-Ms Target Epoch

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As can be seen in Figures 1 and 2, between about 150 and 250 ms, targets following TL primes showed an early priming effect over the more posterior electrode\n sites, but targets following pseudohomophone primes showed little evidence of a priming effect. ANOVA results were consistent\n with this observation: There was a significant interaction among prime type, repetition, anterior-posterior extent, and laterality,\n F(4, 76) = 4.59, p = .01, η2 = .195. Follow-up analyses confirmed that in the TL condition, there was a significant priming effect at posterior sites,\n F(1, 19) = 4.69, p = .043, η2 = .198, and a marginal effect at the middle sites, F(1, 19) = 3.41, p = .08, η2 = .152, but no effect at anterior sites (F < 1). There was no significant effect of priming for pseudohomophones at any location in this epoch (Fs < 1).\n

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250- to 350-Ms Target Epoch

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As can be seen in Figures 1 and 2, between 250 and 350 ms, it was targets following pseudohomophone primes that showed priming effects, whereas targets following\n TL primes showed little to no priming. This observation was supported by a significant interaction of prime type, repetition,\n laterality, and anterior-posterior extent, F(4, 76) = 3.24, p = .045, η2 = .146. Follow-up analyses demonstrated that whereas pseudohomophones showed a significant priming effect, F(1, 19) = 4.77, p = .042, η2 = .201, TL primes did not (F < 1). Moreover, the pseudohomophone effect was significant at anterior sites, F(1, 19) = 5.97, p = .025, η2 = .239, but was not reliable at middle or more posterior sites (ps < .1).\n

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350- to 550-Ms Target Epoch

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Examination of Figures 1 and 2 reveals that the third interval contained the bulk of the activity resembling the classic N400 component. This observation\n was confirmed by the presence of a large main effect of repetition, F(1, 19) = 7.78, p = .012, η2 = .291. Follow-up analyses indicated that priming effects were significant for pseudohomophones across the scalp. The effect\n of pseudohomophone priming was significant, F(1, 19) = 7.20, p = .015, η2 = .275, and remained significant in analyses of anterior sites, F(1, 19) = 7.24, p = .014, η2 = .276; middle sites, F(1, 19) = 5.31, p = .033, η2 = .218; and posterior sites, F(1, 19) = 5.89, p = .025, η2 = .237. In contrast, there was no significant TL priming (ps < .12).\n

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Time Course of Priming

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To better understand the time course of the effects, we also binned successive 50-ms epochs between 150 and 500 ms for the\n TL and pseudohomophone primes and their respective controls, and ran separate ANOVAs on each 50-ms epoch. The results are\n reported in Table 1 separately for anterior, middle, and posterior electrode sites. During the N250 epoch, TL priming began approximately 50\n ms earlier (200–250 ms vs. 250–300 ms) than pseudohomophone priming, and the scalp distribution of these earliest effects\n was posteriorly oriented for TL priming and anteriorly oriented for pseudohomophone priming. During the N400 epoch, it was\n pseudohomophone priming that started earlier (300–350 ms vs. 450–500 ms), and pseudohomophone priming was generally more robust\n than TL priming, although in this case the scalp distribution was similar for the two types of priming.\n

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TABLE 1 \n

Time Course of Priming Effects: Results of Tests of Significance for Three Anterior-Posterior Rows of Electrodes

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Behavioral Data

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Participants detected 91.3% (SD = 6.1) of animal probes in the target position and 2% (SD = 3.3) of animal probes in the prime position within a window from 200 to 1,200 ms after probe onset.\n

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\n \n " ] }, - "acknowledgements_html": { - "value": [ - "\n \n

Acknowledgments

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This research was supported by National Institutes of Health Grants HD25889 and HD043251.

\n \n " - ] - }, - "competing_interests_html": { + "author_contrib_html": { "value": [ ] }, - "financial_disclosure_html": { + "competing_interests_html": { "value": [ ] }, "references_html": { "value": [ - "\n \n

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    2. \n
    3. Brysbaert M.
    4. \n
    (in press). Masked phonological priming effects in English: Are they real? Do they matter?Cognitive Psychology.
    \n \n
    \n
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      \n
    1. Schoonbaert S., \n
    2. \n
    3. Grainger J.
    4. \n
    (2004). Letter position coding in printed word perception: Effects of repeated and transposed letters. Language and Cognitive Processes, 19, 333367.
    \n \n
    \n
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      \n
    1. Van Assche E., \n
    2. \n
    3. Grainger J.
    4. \n
    (2006). A study of relative-position priming with superset primes. Journal of Experimental Psychology: Learning, Memory, and Cognition, 32, 399415.
    \n \n
    \n
  42. \n
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      \n
    1. Ziegler J., \n
    2. \n
    3. Ferrand L., \n
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    5. Jacobs A.M., \n
    6. \n
    7. Rey A., \n
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    9. Grainger J.
    10. \n
    (2000). Visual and phonological codes in letter and word recognition: Evidence from incremental priming. Quarterly Journal of Experimental Psychology, 53A, 671692.
    \n \n
    \n
  44. \n
\n " - ] - }, - "copyright": { - "value": [ - "© 2006 Association for Psychological Science" - ] - }, - "onlinefirst_published": { - "value": [ - "\n \t December 2006 \n " - ] - }, - "author_contrib_html": { - "value": [ - - ] - }, - "author_corresp_html": { - "value": [ - "Jonathan Grainger, Laboratoire de Psychologie Cognitive, Université de Provence, 3 pl. Victor Hugo, 13331 Marseille, France,\n e-mail: grainger{at}up.univ-mrs.fr.\n " + "\n \n

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\n " ] }, "file_hashes": [ { - "fulltext.html": "b9378eb561244adc83edee20e66bdffa" + "fulltext.html": "bd3901737511983a269808b667301297" }, { - "fulltext.pdf": "b76ae204fce0e9965f9eea630d99555a" + "fulltext.pdf": "01c434ff99c65790cdfc739bae8a3d0c" } ] } From 1be754a1321275fd696e9b11a19f74a8415ac751 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 16 Aug 2015 05:17:00 +0100 Subject: [PATCH 140/154] Upgrade to new container-based Travis CI --- .travis.yml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 2009726..cc40fd2 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,10 +1,13 @@ language: ruby rvm: - 2.1.0 +addons: + apt: + packages: + - software-properties-common + - build-essential + - libfontconfig before_install: - - sudo apt-get update -qq - - sudo apt-get install -y software-properties-common - - sudo apt-get install -y build-essential libfontconfig - nvm install 0.10.32 - nvm use 0.10.32 - npm update npm -g @@ -12,3 +15,4 @@ install: - npm install --global quickscrape@0.3.3 script: - ruby test/test_all.rb +sudo: false From c92010e44329879296c0e55c14260f1fafc72ca4 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 16 Aug 2015 05:19:26 +0100 Subject: [PATCH 141/154] Remove unnecessary setup --- .travis.yml | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/.travis.yml b/.travis.yml index cc40fd2..f56228d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,18 +1,12 @@ language: ruby rvm: - 2.1.0 -addons: - apt: - packages: - - software-properties-common - - build-essential - - libfontconfig before_install: - nvm install 0.10.32 - nvm use 0.10.32 - npm update npm -g install: - - npm install --global quickscrape@0.3.3 + - npm install --global quickscrape@0.4.6 script: - ruby test/test_all.rb sudo: false From 252e17f19d03e7e48721d57528a9fa59eb7e5691 Mon Sep 17 00:00:00 2001 From: Richard Smith-Unna Date: Sun, 16 Aug 2015 05:22:26 +0100 Subject: [PATCH 142/154] Flushing test changes --- scripts/check_completeness.rb | 0 scripts/make_tests.rb | 8 +- test/elife.json | 52 +- test/peerj.json | 692 ++++++++--------- test/plos.json | 1384 ++++++++++++++++++++++++++++++--- test/test_all.rb | 13 +- 6 files changed, 1665 insertions(+), 484 deletions(-) create mode 100644 scripts/check_completeness.rb diff --git a/scripts/check_completeness.rb b/scripts/check_completeness.rb new file mode 100644 index 0000000..e69de29 diff --git a/scripts/make_tests.rb b/scripts/make_tests.rb index 13d988b..652900f 100755 --- a/scripts/make_tests.rb +++ b/scripts/make_tests.rb @@ -8,7 +8,7 @@ parser = Trollop::Parser.new do banner <<-EOS make_tests.rb - ScraperJSON test generator script -by Richard Smith-Unna for ContentMine.org +by Richard Smith-Unna for ContentMine.org This script generates a test file from a ScraperJSON scraper definition and a list of URLs the scraper applies to. @@ -68,11 +68,11 @@ results = JSON.load(File.open 'results.json') files = Dir['*'] files = files.keep_if { |f| f != 'results.json' } - file_hashes = [] + file_sizes = [] files.each do |f| - file_hashes << { f => Digest::MD5.file(f).hexdigest } + file_sizes << { f => File.size(f) } end - results['file_hashes'] = file_hashes + results['file_sizes'] = file_sizes end if (index + 1) < urls.length puts "waiting 5 seconds before next scrape" diff --git a/test/elife.json b/test/elife.json index ba17aaf..9085a5b 100644 --- a/test/elife.json +++ b/test/elife.json @@ -55,7 +55,7 @@ }, "description": { "value": [ - "eLife - Open access to the most promising advances in science" + "The molecular mechanism behind how emetine inhibits the ribosome of the human malaria parasite, along with structural details of the complex formed, is revealed at high resolution using cryo-electron microscopy." ] }, "abstract": { @@ -70,7 +70,7 @@ }, "fulltext_pdf": { "value": [ - "http://elifesciences.org/content/elife/3/e03080.full.pdf" + "http://elifesciences.org/content/3/e03080.full.pdf" ] }, "fulltext_xml": { @@ -103,12 +103,12 @@ "" ] }, - "file_hashes": [ + "file_sizes": [ { - "fulltext.pdf": "851eb256466737ecd1de664e99151b1e" + "fulltext.pdf": 1584602 }, { - "fulltext.xml": "8e51231098b99ae7a87e9f635e0ffb18" + "fulltext.xml": 265268 } ] }, @@ -169,7 +169,7 @@ }, "description": { "value": [ - "eLife - Open access to the most promising advances in science" + "The number of CENP-A molecules at human centromeres helps to explain how this structure is built and epigenetically inherited." ] }, "abstract": { @@ -184,7 +184,7 @@ }, "fulltext_pdf": { "value": [ - "http://elifesciences.org/content/elife/3/e02137.full.pdf" + "http://elifesciences.org/content/3/e02137.full.pdf" ] }, "fulltext_xml": { @@ -217,12 +217,12 @@ "" ] }, - "file_hashes": [ + "file_sizes": [ { - "fulltext.pdf": "99eeed6d3488672365d3ccaabcc828b0" + "fulltext.pdf": 2756614 }, { - "fulltext.xml": "9b1d02beb7f46567507afb00b746698b" + "fulltext.xml": 336749 } ] }, @@ -281,7 +281,7 @@ }, "description": { "value": [ - "eLife - Open access to the most promising advances in science" + "In addition to its cytoplasmic role for translation, the seryl-tRNA synthetase also antagonizes the c-Myc transcription factor in the nucleus to transcriptionally repress the growth factor VEGFA and ensure proper development of the vasculature in vertebrates." ] }, "abstract": { @@ -296,7 +296,7 @@ }, "fulltext_pdf": { "value": [ - "http://elifesciences.org/content/elife/3/e02349.full.pdf" + "http://elifesciences.org/content/3/e02349.full.pdf" ] }, "fulltext_xml": { @@ -329,12 +329,12 @@ "" ] }, - "file_hashes": [ + "file_sizes": [ { - "fulltext.pdf": "7d8c1c8c30073ee4835035f0edab70a6" + "fulltext.pdf": 6826005 }, { - "fulltext.xml": "9de87984f8608b2fa85d50cd99064194" + "fulltext.xml": 184217 } ] }, @@ -408,7 +408,7 @@ }, "description": { "value": [ - "eLife - Open access to the most promising advances in science" + "One-quarter of the Chondrichthyes have an elevated risk of extinction, mainly as a result of overfishing." ] }, "abstract": { @@ -423,7 +423,7 @@ }, "fulltext_pdf": { "value": [ - "http://elifesciences.org/content/elife/3/e00590.full.pdf" + "http://elifesciences.org/content/3/e00590.full.pdf" ] }, "fulltext_xml": { @@ -456,12 +456,12 @@ "" ] }, - "file_hashes": [ + "file_sizes": [ { - "fulltext.pdf": "0346be2f1154e0bd608459b19682a08b" + "fulltext.pdf": 3862063 }, { - "fulltext.xml": "4890527e549d9f9ee3f8ec22ea06f414" + "fulltext.xml": 458687 } ] }, @@ -495,7 +495,7 @@ "Dung T Le", "Evan J Lipson", "Paul B Chapman", - "Luis A Diaz, Jr", + "Luis A Diaz", "Bert Vogelstein", "Martin A Nowak" ] @@ -527,7 +527,7 @@ }, "description": { "value": [ - "eLife - Open access to the most promising advances in science" + "A study that models the evolution of drug resistance in tumors reveals that drugs are more effective when given in combination than sequentially, and that cure is much more likely when the drugs target different pathways." ] }, "abstract": { @@ -542,7 +542,7 @@ }, "fulltext_pdf": { "value": [ - "http://elifesciences.org/content/elife/2/e00747.full.pdf" + "http://elifesciences.org/content/2/e00747.full.pdf" ] }, "fulltext_xml": { @@ -575,12 +575,12 @@ "" ] }, - "file_hashes": [ + "file_sizes": [ { - "fulltext.pdf": "c8e8c52362bbb1663c7d4c98cfbd0a56" + "fulltext.pdf": 3358321 }, { - "fulltext.xml": "77ac1d3b2d9bb7ba0c55daa06bf63e3e" + "fulltext.xml": 187697 } ] } diff --git a/test/peerj.json b/test/peerj.json index 74ed8e8..0362579 100644 --- a/test/peerj.json +++ b/test/peerj.json @@ -65,7 +65,7 @@ }, "date_accepted": { "value": [ - "2013-06-21" + ] }, "date_submitted": { @@ -105,7 +105,7 @@ }, "introduction_html": { "value": [ - "

Introduction

\n

The aim of this randomized controlled trial was to investigate the efficacy of an Internet-delivered psychodynamic guided self-help treatment for depression and anxiety disorders that was based on the affect-phobia model of psychopathology (McCullough et al., 2003). The project extends previous research on Internet-delivered psychological treatments in general, and that of Internet-delivered psychodynamic psychotherapy in particular (Andersson et al., 2012; Johansson et al., 2012). An overview of the trial can be seen in Fig. 1.

\n
\"CONSORT
\n

\nFigure 1: CONSORT flowchart.

\n

Depression and anxiety disorders are major world-wide health problems which lower the quality of life for the individual and generate large costs for society (Ebmeier, Donaghey & Steele, 2006; Smit et al., 2006). Lifetime prevalence for mood disorders and anxiety disorders in the US have been estimated to be 20.8% and 28.8%, respectively (Kessler et al., 2005).

\n

Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base (Town et al., 2012), with research support for e.g., depression (Driessen et al., 2010), social anxiety disorder (Leichsenring et al., 2013), panic disorder (Milrod et al., 2007), and generalized anxiety disorder (Leichsenring et al., 2009). There is a variation among the psychodynamic therapies in the degree to which they focus on expression and experience of affect. Diener, Hilsenroth & Weinberger (2007) conducted a meta-analysis of high-quality studies that had examined the role of therapist focus on affect in psychodynamic psychotherapy. The results indicated that the more therapists facilitated the affective experience/expression in psychodynamic therapy, the more patients improved (Diener, Hilsenroth & Weinberger, 2007). Thus, keeping a focus on affect may be one way of enhancing psychodynamic psychotherapies.

\n

One psychodynamic treatment that has a strong focus on expression and experience of affect is affect-phobia therapy (APT), developed by McCullough et al. (2003). APT follows a treatment model which adheres to the fundamental structure of psychodynamic psychotherapy as outlined by Malan’s triangle of conflict (i.e., the experience/expression of feelings (F) is blocked by defenses (D) and anxieties (A)) and triangle of person (i.e., conflicted patterns began with past persons (P), are maintained with current persons (C), and can be enacted with a therapist (T)), as illustrated in Fig. 2 (Malan, 1995). Typically in APT, the therapist clarifies a client’s defenses, helps the client to observe and experience the underlying affects, and helps the client to regulate associated anxiety (McCullough et al., 2003). Formally, the treatment includes three main treatment objectives: defense restructuring (recognizing and relinquishing maladaptive defenses), affect restructuring (desensitization of affects through exposure to conflicted feeling), and self/other restructuring (improvement in sense of self and relationship with others). The main goal of psychodynamic psychotherapy based on the APT model is to help clients experience and to adaptively express previously avoided feelings (McCullough et al., 2003). That goal is shared with an entire set of psychodynamic psychotherapies that are grouped under the umbrella term experiential dynamic therapies (Osimo & Stein, 2012), which in addition to APT includes, for example, Intensive Short-Term Dynamic Psychotherapy (Abbass, Town & Driessen, 2012; Davanloo, 2000), and Accelerated Experiential Dynamic Psychotherapy (Fosha, 2000). Two randomized trials, investigating the efficacy of APT in the treatment of personality disorders, found that APT can be effective in reducing general psychiatric symptoms (Svartberg, Stiles & Seltzer, 2004; Winston et al., 1994). However, except for case-series and some small uncontrolled studies (e.g., Dornelas et al., 2010), to date no trial has investigated the efficacy of APT for patients with a principal Axis I disorder.

\n
\"Malan’s
\n

\nFigure 2: Malan’s two triangles - the triangle of conflict and the triangle of person.

\nThe two triangles (Malan, 1995) represent what David Malan called “the universal principle of psychodynamic psychotherapy”. That is, defenses (D) and anxieties (A) can block the expression of true feelings (F). These patterns began with past persons (P), are maintained with current persons (C), and are often enacted with the therapist (T).

During the last decade, numerous trials on guided self-help and Internet-delivered cognitive behavior therapy (CBT) for various psychiatric disorders have been conducted (Andersson, 2009; Hedman, Ljótsson & Lindefors, 2012; Johansson & Andersson, 2012). For mild to moderate depression and anxiety disorders, it seems safe to conclude that these treatments are as effective as face-to-face treatments (Cuijpers et al., 2010). While most research regarding Internet-based psychological treatments have concerned CBT, there are exceptions. Results from two recent randomized controlled trials focusing on the treatment of depression and generalized anxiety disorder indicate that psychodynamic treatments can also be delivered via the Internet (Andersson et al., 2012; Johansson et al., 2012).

\n

This randomized controlled trial aimed to examine the effects of an Internet-delivered psychodynamic treatment based on the affect-phobia model of psychopathology. Participants had depression and anxiety disorders. The treatment was given as self-help with additional therapist support via the Internet, and compared to a control group who also received online support. As compared with the control condition, a significant effect of treatment was expected both on measures of depression and anxiety for the full sample. In addition, a larger effect was expected on measures of depression for participants with depression as their main presenting problem as compared with those who did not have this as the main problem. Similar, a larger effect on anxiety measures was expected for participants with a principal anxiety diagnosis as compared with those who did not have such a diagnosis. We also investigated the uncontrolled effects of the treatment 7 months following the completion of the treatment.

" + "

Introduction

\n

The aim of this randomized controlled trial was to investigate the efficacy of an Internet-delivered psychodynamic guided self-help treatment for depression and anxiety disorders that was based on the affect-phobia model of psychopathology (McCullough et al., 2003). The project extends previous research on Internet-delivered psychological treatments in general, and that of Internet-delivered psychodynamic psychotherapy in particular (Andersson et al., 2012; Johansson et al., 2012). An overview of the trial can be seen in Fig. 1.

\n
\"CONSORT
\n

\nFigure 1: CONSORT flowchart.

\n

Depression and anxiety disorders are major world-wide health problems which lower the quality of life for the individual and generate large costs for society (Ebmeier, Donaghey & Steele, 2006; Smit et al., 2006). Lifetime prevalence for mood disorders and anxiety disorders in the US have been estimated to be 20.8% and 28.8%, respectively (Kessler et al., 2005).

\n

Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base (Town et al., 2012), with research support for e.g., depression (Driessen et al., 2010), social anxiety disorder (Leichsenring et al., 2013), panic disorder (Milrod et al., 2007), and generalized anxiety disorder (Leichsenring et al., 2009). There is a variation among the psychodynamic therapies in the degree to which they focus on expression and experience of affect. Diener, Hilsenroth & Weinberger (2007) conducted a meta-analysis of high-quality studies that had examined the role of therapist focus on affect in psychodynamic psychotherapy. The results indicated that the more therapists facilitated the affective experience/expression in psychodynamic therapy, the more patients improved (Diener, Hilsenroth & Weinberger, 2007). Thus, keeping a focus on affect may be one way of enhancing psychodynamic psychotherapies.

\n

One psychodynamic treatment that has a strong focus on expression and experience of affect is affect-phobia therapy (APT), developed by McCullough et al. (2003). APT follows a treatment model which adheres to the fundamental structure of psychodynamic psychotherapy as outlined by Malan’s triangle of conflict (i.e., the experience/expression of feelings (F) is blocked by defenses (D) and anxieties (A)) and triangle of person (i.e., conflicted patterns began with past persons (P), are maintained with current persons (C), and can be enacted with a therapist (T)), as illustrated in Fig. 2 (Malan, 1995). Typically in APT, the therapist clarifies a client’s defenses, helps the client to observe and experience the underlying affects, and helps the client to regulate associated anxiety (McCullough et al., 2003). Formally, the treatment includes three main treatment objectives: defense restructuring (recognizing and relinquishing maladaptive defenses), affect restructuring (desensitization of affects through exposure to conflicted feeling), and self/other restructuring (improvement in sense of self and relationship with others). The main goal of psychodynamic psychotherapy based on the APT model is to help clients experience and to adaptively express previously avoided feelings (McCullough et al., 2003). That goal is shared with an entire set of psychodynamic psychotherapies that are grouped under the umbrella term experiential dynamic therapies (Osimo & Stein, 2012), which in addition to APT includes, for example, Intensive Short-Term Dynamic Psychotherapy (Abbass, Town & Driessen, 2012; Davanloo, 2000), and Accelerated Experiential Dynamic Psychotherapy (Fosha, 2000). Two randomized trials, investigating the efficacy of APT in the treatment of personality disorders, found that APT can be effective in reducing general psychiatric symptoms (Svartberg, Stiles & Seltzer, 2004; Winston et al., 1994). However, except for case-series and some small uncontrolled studies (e.g., Dornelas et al., 2010), to date no trial has investigated the efficacy of APT for patients with a principal Axis I disorder.

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\"Malan’s
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\nFigure 2: Malan’s two triangles - the triangle of conflict and the triangle of person.

\nThe two triangles (Malan, 1995) represent what David Malan called “the universal principle of psychodynamic psychotherapy”. That is, defenses (D) and anxieties (A) can block the expression of true feelings (F). These patterns began with past persons (P), are maintained with current persons (C), and are often enacted with the therapist (T).

During the last decade, numerous trials on guided self-help and Internet-delivered cognitive behavior therapy (CBT) for various psychiatric disorders have been conducted (Andersson, 2009; Hedman, Ljótsson & Lindefors, 2012; Johansson & Andersson, 2012). For mild to moderate depression and anxiety disorders, it seems safe to conclude that these treatments are as effective as face-to-face treatments (Cuijpers et al., 2010). While most research regarding Internet-based psychological treatments have concerned CBT, there are exceptions. Results from two recent randomized controlled trials focusing on the treatment of depression and generalized anxiety disorder indicate that psychodynamic treatments can also be delivered via the Internet (Andersson et al., 2012; Johansson et al., 2012).

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This randomized controlled trial aimed to examine the effects of an Internet-delivered psychodynamic treatment based on the affect-phobia model of psychopathology. Participants had depression and anxiety disorders. The treatment was given as self-help with additional therapist support via the Internet, and compared to a control group who also received online support. As compared with the control condition, a significant effect of treatment was expected both on measures of depression and anxiety for the full sample. In addition, a larger effect was expected on measures of depression for participants with depression as their main presenting problem as compared with those who did not have this as the main problem. Similar, a larger effect on anxiety measures was expected for participants with a principal anxiety diagnosis as compared with those who did not have such a diagnosis. We also investigated the uncontrolled effects of the treatment 7 months following the completion of the treatment.

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Results

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Enrollment and baseline characteristics

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One hundred individuals with depression and/or anxiety disorders were enrolled in the study. There were no significant pre-treatment mean differences between the treatment group and the control group on any outcome measures (all t’s < 0.97, all p’s > .33). Additionally, there were no significant differences between the groups on any demographic data or current/past treatment with medication and/or psychological treatment. A complete description of demographic data of included participants is available in Table 1.

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\nTable 1:
Demographic description of the participants.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Treatment groupControl groupTotal
GenderMale8 (16%)10 (20%)18 (18%)
Female42 (84%)40 (80%)82 (82%)
AgeMean (SD)43.1 (13.9)46.6 (12.1)44.9 (13.1)
Min-Max19–7223–7719–77
Marital statusMarried or co-habiting31 (62%)36 (72%)67 (67%)
Other19 (38%)14 (28%)33 (33%)
Educational levelCollege or university, at least 3 years27 (54%)29 (58%)56 (56%)
Other23 (46%)21 (42%)44 (44%)
Employment statusEmployed or student41 (82%)33 (66%)74 (74%)
Other9 (18%)17 (34%)26 (26%)
Psychological treatmentNo experience15 (30%)16 (32%)31 (31%)
Prior experience35 (70%)31 (62%)66 (66%)
Ongoing0 (0%)3 (6%)3 (3%)
Pharmacological treatmentNo experience27 (54%)22 (44%)49 (49%)
Prior experience14 (28%)12 (24%)26 (26%)
Ongoing9 (18%)16 (32%)25 (25%)
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Regarding subgroups of principal depression and anxiety, there was a difference between subgroups in the number of participants in an acute episode of depression, χ2(N = 100, d f = 1) = 39.4, p < .001, with 55/57 (96.5%; two participants had depression not otherwise specified) compared to 17/43 (39.5%) for subgroups of depression and anxiety, respectively. Similarly, there were significantly more participants with a principal anxiety disorder that had GAD (67.4%) compared to 35.1% from the depression subgroup, χ2(N = 100, d f = 1) = 10.3, p < .001. There were no differences between subgroups regarding diagnoses of panic disorder and social phobia. Also, there were no differences in any demographics. However, there was a significant difference between subgroups in depression severity as measured by the PHQ-9 at baseline, t(98) = 3.70, p < .001. However, no significant baseline difference on the GAD-7 was found t(98) = 1.23, p = .22.

Attrition and adherence

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At post-treatment, 100% of the data was collected. At the 7-month follow-up, 47/50 (94%) of the self-report measures and 40/50 (80%) of the data from the follow-up interviews (i.e., diagnostic data and estimates of global improvement) were collected. Adherence to treatment was defined as the number of modules completed. A module was only considered completed if the homework assignment had been sent to the therapist. Out of the 50 participants receiving treatment, 42 (84%) completed all modules. Only 4 participants (8%) completed less than half of the program.

Outcome and process measures

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Means, standard deviations and effect sizes within and between groups for the self-report measures are presented in Tables 2 and 3. Both the treatment group and the control group had substantial within-group effects after the 10-week period. Mixed models analyses revealed significant interaction effects of treatment group and time on the PHQ-9, F(1, 102.1) = 19.94, p < .001, and the GAD-7, F(1, 105.1) = 7.86, p < .01. Both interaction effects were significant at the Bonferroni-corrected alpha level of p < .0125. Estimates of fixed effects for the PHQ-9 and the GAD-7 were as follows. Intercept: 12.37 and 10.71 (p’s < .001); Group: 0.11 and 0.14 (p’s > .85); Time: −0.64 and −0.49 (p’s < .001); Group × Time: 0.40 and 0.23 (p’s < .01). Random effects for the PHQ-9 and the GAD-7 were estimated as follows. Intercept: 14.33 and 12.78 (p’s < .001); Time: 0.15 and 0.12 (p’s < .001). Between-group effect sizes at post-treatment was large (d = 0.77) for depression and moderate (d = 0.48) for anxiety, favoring treatment over control. The continuous within-group changes on the PHQ-9 and the GAD-7 are illustrated in Fig. 3. At the 7-month follow-up, the treatment effect was stable. Paired t-tests conducted post hoc showed that there were significant post-treatment versus follow-up decrease on the GAD-7, t(46) = 2.03, p < .05, and a trend towards a significant decrease on the PHQ-9, t(46) = 1.42, p = .16. For the EPS-25 and the FFMQ, there were also significant interaction effects of treatment group and time (F(1, 104.5) = 26.5 and F(1, 101.2) = 29.9, respectively; Both p’s < .001). Both these interaction effects were significant at the Bonferroni-corrected alpha level of p < .0125. Fixed effects for the EPS-25 and the FFMQ were estimated as follows. Intercept: 4.70 and 72.76 (p’s < .001); Group: −0.16 and 3.67 (p’s > .15); Time: −0.18 and 1.39 (p’s < .001); Group × Time: 0.13 and −1.17 (p’s < .001). Estimates of random effects for the EPS-25 and the FFMQ were as follows. Intercept: 1.25 and 156.37 (p’s < .001); Time: 0.013 and 0.98 (p’s < .001). The between-group effect at post-treatment was large for the EPS-25 (d = 0.82) and moderate to large (d = 0.65) for the FFMQ.

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\nTable 2:
Means, SDs and effect sizes (Cohen’s d) for measures of depression and anxiety.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Mean (SD)Effect size Cohen’s d (95% CI)Linear mixed models
Measure and groupPre-treatmentPost-treatment7-month
follow-up
Between-group,
post-treatment
Within-group
pre-post-treatment
Within-group
pre-7-month follow-up
Effect\n p\n
\n PHQ-9\n
Treatment group
(n = 50)
13.90 (3.6)6.32 (4.2)5.55 (3.5)0.77 (0.37–1.18)1.93 (1.31–2.55)2.43 (1.72–3.14)Group.89
Depression subgroup
(n = 28)
15.32 (3.3)5.89 (2.8)5.96 (3.5)0.95 (0.40–1.50)3.10 (1.87–4.32)2.82 (1.78–3.87)Time < .001
Anxiety subgroup
(n = 22)
12.09 (3.3)6.86 (5.5)5.00 (3.4)0.55 (−0.06–1.16)1.12 (0.49–1.75)2.17 (1.11–3.24)G × T < .001
Control group
(n = 50)
13.96 (4.7)10.26 (5.9)0.69 (0.40–0.97)
Depression subgroup
(n = 29)
15.07 (4.4)10.59 (6.4)0.79 (0.37–1.22)
Anxiety subgroup
(n = 21)
12.43 (4.7)9.81 (5.2)0.53 (0.20–0.85)
\n GAD-7\n
Treatment group
(n = 50)
11.46 (4.0)6.12 (4.5)5.34 (4.1)0.48 (0.08–0.87)1.25 (0.79–1.71)1.51 (0.97–2.06)Group.85
Depression subgroup
(n = 28)
10.86 (4.1)5.46 (3.9)5.19 (4.1)0.56 (0.03–1.09)1.35 (0.75–1.95)1.43 (0.73–2.10)Time < .001
Anxiety subgroup
(n = 22)
12.23 (3.8)6.95 (5.3)5.55 (4.2)0.39 (−0.21–0.99)1.15 (0.44–1.86)1.62 (0.72–2.52)G × T < .01
Control group
(n = 50)
12.26 (4.2)8.40 (5.0)0.82 (0.51–1.13)
Depression subgroup
(n = 29)
11.97 (5.0)8.03 (5.3)0.76 (0.39–1.13)
Anxiety subgroup
(n = 21)
12.67 (2.8)8.90 (4.7)0.93 (0.36–1.50)
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Notes:

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The confidence intervals were calculated using the standard error and an alpha level of 0.05. A confidence interval that do not overlap zero indicates a significance of p < .05. p values are given for linear mixed models using data from pre-treatment and post-treatment and all individuals (N = 100). The p value associated with the main effect of group denotes significance of average difference between groups at the pre-treatment assessment. The p value associated with the effect of time denotes the significance of average change over all assessment periods across treatment. The p value associated with the effect of G × T (group × time) denotes significance of difference between the treatment group and the control group in change over all assessment periods. Effect sizes are calculated as standardized mean differences. PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.

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\nTable 3:
Means, SDs and effect sizes (Cohen’s d) for measures of emotional processing and mindfulness skills.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Mean (SD)Effect size Cohen’s d (95% CI)Linear mixed models
Measure and groupPre-treatmentPost-treatment7-month
follow-up
Between-group,
post-treatment
Within-group
pre-post-treatment
Within-group
pre-7-month follow-up
Effect\n p\n
\n EPS-25\n Group.50
Treatment group
(n = 50)
5.00 (1.03)2.86 (1.48)2.84 (1.65)0.82 (0.41–1.23)1.67 (1.13–2.21)1.51 (1.00–2.01)Time < .001
Control group
(n = 50)
4.93 (1.01)4.17 (1.73)0.50 (0.22–0.77)G × T < .001
\n FFMQ\n Group.15
Treatment group
(n = 50)
76.70 (10.9)88.00 (12.0)88.98 (13.3)0.65 (0.25–1.05)0.98 (0.65–1.31)0.99 (0.59–1.39)Time < .001
Control group
(n = 50)
77.18 (14.1)78.44 (17.1)0.08 (−0.11–0.27)G × T < .001
\n\n
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Notes:

\n

The confidence intervals were calculated using the standard error and an alpha level of 0.05. A confidence interval that do not overlap zero indicates a significance of p < .05. p values are given for linear mixed models using data from pre-treatment and post-treatment and all individuals (N = 100). The p value associated with the main effect of group denotes significance of average difference between groups at the pre-treatment assessment. The p value associated with the effect of time denotes the significance of average change over all assessment periods across treatment. The p value associated with the effect of G × T (group × time) denotes significance of difference between the treatment group and the control group in change over all assessment periods. Effect sizes are calculated as standardized mean differences. EPS-25: Emotional Processing Scale; FFMQ: Five Facets of Mindfulness Questionnaire.

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\"Weekly
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\nFigure 3: Weekly PHQ-9 and GAD-7 scores.

\nWeekly scores on the PHQ-9 and the GAD-7 for both groups. Vertical bars denote 95% confidence intervals (CI). PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.

Diagnoses

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The number of diagnoses among participants at pre-treatment, post-treatment and at the 7-month follow-up are illustrated in Table 4. At post-treatment, there were significantly fewer participants with a diagnosis of major depression in the treatment group (10%) than in the control group (32%). The difference was significant (χ2(N = 100, d f = 1) = 7.3, p < .01). Reductions in the number of diagnoses of GAD, SP or PD were not significantly different between groups at post-treatment.

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\nTable 4:
Frequency data of DSM-IV diagnoses.
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\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Treatment groupControl group
DiagnosisPre-treatmentPost-treatment7-month follow-upPre-treatmentPost-treatment
DEP35 (70%)5 (10%)6 (12%)37 (74%)16 (32%)
GAD23 (46%)13 (26%)10 (20%)26 (52%)18 (36%)
SP19 (38%)10 (20%)9 (18%)17 (34%)13 (26%)
PD11 (22%)5 (10%)6 (12%)9 (18%)5 (10%)
\n Number of diagnoses\n
04 (8%)28 (56%)31 (62%)0 (0%)18 (36%)
116 (32%)13 (26%)8 (16%)23 (46%)18 (36%)
219 (38%)7 (14%)10 (20%)16 (32%)9 (18%)
310 (20%)2 (4%)1 (2%)10 (20%)4 (8%)
41 (2%)0 (0%)0 (0%)1 (2%)1 (2%)
Total number of diagnoses8833318949
\n\n
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Notes:

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The four participants with zero diagnoses listed at pre-treatment fulfilled DSM-IV criteria for depression and anxiety, not otherwise specified. DEP, GAD, SP, PD: Diagnoses of major depression, generalized anxiety disorder, social phobia and panic disorder.

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Recovery after treatment and clinical global improvement

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Categorical rates of recovery after treatment (i.e., a participant who did not fulfill criteria for any DSM-IV diagnosis and reached a score less than 10 on both the PHQ-9 and the GAD-7) were significantly different at post-treatment between the treatment group (n = 26; 52.0%) and the control group (n = 12; 24.0%), χ2(N = 100, d f = 1) = 8.3, p < .01. At follow-up there were 25 participants (50.0%) from the treatment group who met the criteria for recovery.

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Post-treatment interviews resulted in estimates of clinical global improvement according to the CGI-I (Guy, 1976). In the treatment group, 28 participants (56.0%) were much or very much improved while this was only true for 11 (22.0%) in the control group. This difference was significant, χ2(N = 100, d f = 1) = 12.1, p < .001. At follow-up, this figure was 52% (n = 26) in the treatment group.

Subgroups of principal depression and anxiety

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There were no significant interaction effect of group, subgroup and time on neither the PHQ-9 nor the GAD-7. This was despite the fact that the treatment had a very large within-group group effect (d = 3.10) on the PHQ-9 in the depression subgroup, compared to for those in the anxiety subgroup (d = 1.12). Thus, there were no indications that the treatment was more effective in reducing symptoms of depression among participants with a principal diagnosis of depression, or analogously for anxiety symptoms.

Therapist time

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In the treatment group, the average therapist time per client and week was 9.5 min (S D = 4.0). While there was a significant difference in average therapist time per week between therapists (F(2, 47) = 7.73, p < .001), there were no correlations between therapist time and change scores on any of the outcome measures (all r’s < .19, all p’s > .18). The average therapist time per client and week was 2.3 min (S D = 0.86) in the control group. As expected, therapist time was significantly less in the control group than in the treatment group, t(98) = 12.4, p < .001.

Participants’ evaluation of the treatment

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Most participants were satisfied (46%) or very satisfied (36%) with the overall treatment they had received. Nine (18%) were indifferent or mildly dissatisfied, and no one was clearly dissatisfied. An absolute majority (82%) thought that the amount of text was appropriate. A similar amount of participants considered the text interesting and relevant, all the time (46%) or most of the time (40%). Most participants considered the treatment to be very demanding (28%), demanding (42%) or somewhat demanding (26%). Importantly though, a majority considered the treatment very much worth the effort (52%) or worth the effort (38%).

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Results

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Enrollment and baseline characteristics

\n

One hundred individuals with depression and/or anxiety disorders were enrolled in the study. There were no significant pre-treatment mean differences between the treatment group and the control group on any outcome measures (all t’s < 0.97, all p’s > .33). Additionally, there were no significant differences between the groups on any demographic data or current/past treatment with medication and/or psychological treatment. A complete description of demographic data of included participants is available in Table 1.

\n
\nTable 1:
Demographic description of the participants.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Treatment groupControl groupTotal
GenderMale8 (16%)10 (20%)18 (18%)
Female42 (84%)40 (80%)82 (82%)
AgeMean (SD)43.1 (13.9)46.6 (12.1)44.9 (13.1)
Min-Max19–7223–7719–77
Marital statusMarried or co-habiting31 (62%)36 (72%)67 (67%)
Other19 (38%)14 (28%)33 (33%)
Educational levelCollege or university, at least 3 years27 (54%)29 (58%)56 (56%)
Other23 (46%)21 (42%)44 (44%)
Employment statusEmployed or student41 (82%)33 (66%)74 (74%)
Other9 (18%)17 (34%)26 (26%)
Psychological treatmentNo experience15 (30%)16 (32%)31 (31%)
Prior experience35 (70%)31 (62%)66 (66%)
Ongoing0 (0%)3 (6%)3 (3%)
Pharmacological treatmentNo experience27 (54%)22 (44%)49 (49%)
Prior experience14 (28%)12 (24%)26 (26%)
Ongoing9 (18%)16 (32%)25 (25%)
\n

Regarding subgroups of principal depression and anxiety, there was a difference between subgroups in the number of participants in an acute episode of depression, χ2(N = 100, d f = 1) = 39.4, p < .001, with 55/57 (96.5%; two participants had depression not otherwise specified) compared to 17/43 (39.5%) for subgroups of depression and anxiety, respectively. Similarly, there were significantly more participants with a principal anxiety disorder that had GAD (67.4%) compared to 35.1% from the depression subgroup, χ2(N = 100, d f = 1) = 10.3, p < .001. There were no differences between subgroups regarding diagnoses of panic disorder and social phobia. Also, there were no differences in any demographics. However, there was a significant difference between subgroups in depression severity as measured by the PHQ-9 at baseline, t(98) = 3.70, p < .001. However, no significant baseline difference on the GAD-7 was found t(98) = 1.23, p = .22.

Attrition and adherence

\n

At post-treatment, 100% of the data was collected. At the 7-month follow-up, 47/50 (94%) of the self-report measures and 40/50 (80%) of the data from the follow-up interviews (i.e., diagnostic data and estimates of global improvement) were collected. Adherence to treatment was defined as the number of modules completed. A module was only considered completed if the homework assignment had been sent to the therapist. Out of the 50 participants receiving treatment, 42 (84%) completed all modules. Only 4 participants (8%) completed less than half of the program.

Outcome and process measures

\n

Means, standard deviations and effect sizes within and between groups for the self-report measures are presented in Tables 2 and 3. Both the treatment group and the control group had substantial within-group effects after the 10-week period. Mixed models analyses revealed significant interaction effects of treatment group and time on the PHQ-9, F(1, 102.1) = 19.94, p < .001, and the GAD-7, F(1, 105.1) = 7.86, p < .01. Both interaction effects were significant at the Bonferroni-corrected alpha level of p < .0125. Estimates of fixed effects for the PHQ-9 and the GAD-7 were as follows. Intercept: 12.37 and 10.71 (p’s < .001); Group: 0.11 and 0.14 (p’s > .85); Time: −0.64 and −0.49 (p’s < .001); Group × Time: 0.40 and 0.23 (p’s < .01). Random effects for the PHQ-9 and the GAD-7 were estimated as follows. Intercept: 14.33 and 12.78 (p’s < .001); Time: 0.15 and 0.12 (p’s < .001). Between-group effect sizes at post-treatment was large (d = 0.77) for depression and moderate (d = 0.48) for anxiety, favoring treatment over control. The continuous within-group changes on the PHQ-9 and the GAD-7 are illustrated in Fig. 3. At the 7-month follow-up, the treatment effect was stable. Paired t-tests conducted post hoc showed that there were significant post-treatment versus follow-up decrease on the GAD-7, t(46) = 2.03, p < .05, and a trend towards a significant decrease on the PHQ-9, t(46) = 1.42, p = .16. For the EPS-25 and the FFMQ, there were also significant interaction effects of treatment group and time (F(1, 104.5) = 26.5 and F(1, 101.2) = 29.9, respectively; Both p’s < .001). Both these interaction effects were significant at the Bonferroni-corrected alpha level of p < .0125. Fixed effects for the EPS-25 and the FFMQ were estimated as follows. Intercept: 4.70 and 72.76 (p’s < .001); Group: −0.16 and 3.67 (p’s > .15); Time: −0.18 and 1.39 (p’s < .001); Group × Time: 0.13 and −1.17 (p’s < .001). Estimates of random effects for the EPS-25 and the FFMQ were as follows. Intercept: 1.25 and 156.37 (p’s < .001); Time: 0.013 and 0.98 (p’s < .001). The between-group effect at post-treatment was large for the EPS-25 (d = 0.82) and moderate to large (d = 0.65) for the FFMQ.

\n
\nTable 2:
Means, SDs and effect sizes (Cohen’s d) for measures of depression and anxiety.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Mean (SD)Effect size Cohen’s d (95% CI)Linear mixed models
Measure and groupPre-treatmentPost-treatment7-month
follow-up
Between-group,
post-treatment
Within-group
pre-post-treatment
Within-group
pre-7-month follow-up
Effect\n p\n
\n PHQ-9\n
Treatment group
(n = 50)
13.90 (3.6)6.32 (4.2)5.55 (3.5)0.77 (0.37–1.18)1.93 (1.31–2.55)2.43 (1.72–3.14)Group.89
Depression subgroup
(n = 28)
15.32 (3.3)5.89 (2.8)5.96 (3.5)0.95 (0.40–1.50)3.10 (1.87–4.32)2.82 (1.78–3.87)Time < .001
Anxiety subgroup
(n = 22)
12.09 (3.3)6.86 (5.5)5.00 (3.4)0.55 (−0.06–1.16)1.12 (0.49–1.75)2.17 (1.11–3.24)G × T < .001
Control group
(n = 50)
13.96 (4.7)10.26 (5.9)0.69 (0.40–0.97)
Depression subgroup
(n = 29)
15.07 (4.4)10.59 (6.4)0.79 (0.37–1.22)
Anxiety subgroup
(n = 21)
12.43 (4.7)9.81 (5.2)0.53 (0.20–0.85)
\n GAD-7\n
Treatment group
(n = 50)
11.46 (4.0)6.12 (4.5)5.34 (4.1)0.48 (0.08–0.87)1.25 (0.79–1.71)1.51 (0.97–2.06)Group.85
Depression subgroup
(n = 28)
10.86 (4.1)5.46 (3.9)5.19 (4.1)0.56 (0.03–1.09)1.35 (0.75–1.95)1.43 (0.73–2.10)Time < .001
Anxiety subgroup
(n = 22)
12.23 (3.8)6.95 (5.3)5.55 (4.2)0.39 (−0.21–0.99)1.15 (0.44–1.86)1.62 (0.72–2.52)G × T < .01
Control group
(n = 50)
12.26 (4.2)8.40 (5.0)0.82 (0.51–1.13)
Depression subgroup
(n = 29)
11.97 (5.0)8.03 (5.3)0.76 (0.39–1.13)
Anxiety subgroup
(n = 21)
12.67 (2.8)8.90 (4.7)0.93 (0.36–1.50)
\n\n
\n

Notes:

\n

The confidence intervals were calculated using the standard error and an alpha level of 0.05. A confidence interval that do not overlap zero indicates a significance of p < .05. p values are given for linear mixed models using data from pre-treatment and post-treatment and all individuals (N = 100). The p value associated with the main effect of group denotes significance of average difference between groups at the pre-treatment assessment. The p value associated with the effect of time denotes the significance of average change over all assessment periods across treatment. The p value associated with the effect of G × T (group × time) denotes significance of difference between the treatment group and the control group in change over all assessment periods. Effect sizes are calculated as standardized mean differences. PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.

\n
\nTable 3:
Means, SDs and effect sizes (Cohen’s d) for measures of emotional processing and mindfulness skills.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Mean (SD)Effect size Cohen’s d (95% CI)Linear mixed models
Measure and groupPre-treatmentPost-treatment7-month
follow-up
Between-group,
post-treatment
Within-group
pre-post-treatment
Within-group
pre-7-month follow-up
Effect\n p\n
\n EPS-25\n Group.50
Treatment group
(n = 50)
5.00 (1.03)2.86 (1.48)2.84 (1.65)0.82 (0.41–1.23)1.67 (1.13–2.21)1.51 (1.00–2.01)Time < .001
Control group
(n = 50)
4.93 (1.01)4.17 (1.73)0.50 (0.22–0.77)G × T < .001
\n FFMQ\n Group.15
Treatment group
(n = 50)
76.70 (10.9)88.00 (12.0)88.98 (13.3)0.65 (0.25–1.05)0.98 (0.65–1.31)0.99 (0.59–1.39)Time < .001
Control group
(n = 50)
77.18 (14.1)78.44 (17.1)0.08 (−0.11–0.27)G × T < .001
\n\n
\n

Notes:

\n

The confidence intervals were calculated using the standard error and an alpha level of 0.05. A confidence interval that do not overlap zero indicates a significance of p < .05. p values are given for linear mixed models using data from pre-treatment and post-treatment and all individuals (N = 100). The p value associated with the main effect of group denotes significance of average difference between groups at the pre-treatment assessment. The p value associated with the effect of time denotes the significance of average change over all assessment periods across treatment. The p value associated with the effect of G × T (group × time) denotes significance of difference between the treatment group and the control group in change over all assessment periods. Effect sizes are calculated as standardized mean differences. EPS-25: Emotional Processing Scale; FFMQ: Five Facets of Mindfulness Questionnaire.

\n
\"Weekly
\n

\nFigure 3: Weekly PHQ-9 and GAD-7 scores.

\nWeekly scores on the PHQ-9 and the GAD-7 for both groups. Vertical bars denote 95% confidence intervals (CI). PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.

Diagnoses

\n

The number of diagnoses among participants at pre-treatment, post-treatment and at the 7-month follow-up are illustrated in Table 4. At post-treatment, there were significantly fewer participants with a diagnosis of major depression in the treatment group (10%) than in the control group (32%). The difference was significant (χ2(N = 100, d f = 1) = 7.3, p < .01). Reductions in the number of diagnoses of GAD, SP or PD were not significantly different between groups at post-treatment.

\n
\nTable 4:
Frequency data of DSM-IV diagnoses.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Treatment groupControl group
DiagnosisPre-treatmentPost-treatment7-month follow-upPre-treatmentPost-treatment
DEP35 (70%)5 (10%)6 (12%)37 (74%)16 (32%)
GAD23 (46%)13 (26%)10 (20%)26 (52%)18 (36%)
SP19 (38%)10 (20%)9 (18%)17 (34%)13 (26%)
PD11 (22%)5 (10%)6 (12%)9 (18%)5 (10%)
\n Number of diagnoses\n
04 (8%)28 (56%)31 (62%)0 (0%)18 (36%)
116 (32%)13 (26%)8 (16%)23 (46%)18 (36%)
219 (38%)7 (14%)10 (20%)16 (32%)9 (18%)
310 (20%)2 (4%)1 (2%)10 (20%)4 (8%)
41 (2%)0 (0%)0 (0%)1 (2%)1 (2%)
Total number of diagnoses8833318949
\n\n
\n

Notes:

\n

The four participants with zero diagnoses listed at pre-treatment fulfilled DSM-IV criteria for depression and anxiety, not otherwise specified. DEP, GAD, SP, PD: Diagnoses of major depression, generalized anxiety disorder, social phobia and panic disorder.

\n

Recovery after treatment and clinical global improvement

\n

Categorical rates of recovery after treatment (i.e., a participant who did not fulfill criteria for any DSM-IV diagnosis and reached a score less than 10 on both the PHQ-9 and the GAD-7) were significantly different at post-treatment between the treatment group (n = 26; 52.0%) and the control group (n = 12; 24.0%), χ2(N = 100, d f = 1) = 8.3, p < .01. At follow-up there were 25 participants (50.0%) from the treatment group who met the criteria for recovery.

\n

Post-treatment interviews resulted in estimates of clinical global improvement according to the CGI-I (Guy, 1976). In the treatment group, 28 participants (56.0%) were much or very much improved while this was only true for 11 (22.0%) in the control group. This difference was significant, χ2(N = 100, d f = 1) = 12.1, p < .001. At follow-up, this figure was 52% (n = 26) in the treatment group.

Subgroups of principal depression and anxiety

\n

There were no significant interaction effect of group, subgroup and time on neither the PHQ-9 nor the GAD-7. This was despite the fact that the treatment had a very large within-group group effect (d = 3.10) on the PHQ-9 in the depression subgroup, compared to for those in the anxiety subgroup (d = 1.12). Thus, there were no indications that the treatment was more effective in reducing symptoms of depression among participants with a principal diagnosis of depression, or analogously for anxiety symptoms.

Therapist time

\n

In the treatment group, the average therapist time per client and week was 9.5 min (S D = 4.0). While there was a significant difference in average therapist time per week between therapists (F(2, 47) = 7.73, p < .001), there were no correlations between therapist time and change scores on any of the outcome measures (all r’s < .19, all p’s > .18). The average therapist time per client and week was 2.3 min (S D = 0.86) in the control group. As expected, therapist time was significantly less in the control group than in the treatment group, t(98) = 12.4, p < .001.

Participants’ evaluation of the treatment

\n

Most participants were satisfied (46%) or very satisfied (36%) with the overall treatment they had received. Nine (18%) were indifferent or mildly dissatisfied, and no one was clearly dissatisfied. An absolute majority (82%) thought that the amount of text was appropriate. A similar amount of participants considered the text interesting and relevant, all the time (46%) or most of the time (40%). Most participants considered the treatment to be very demanding (28%), demanding (42%) or somewhat demanding (26%). Importantly though, a majority considered the treatment very much worth the effort (52%) or worth the effort (38%).

" ] }, "discussion_html": { "value": [ - "

Discussion

\n

This randomized controlled trial aimed to evaluate the effects of affect-phobia therapy in the format of guided self-help through the Internet in a sample of participants with depression and anxiety disorders. The results indicated that the treatment was effective in reducing symptoms of depression and anxiety, and also in facilitating emotional processing and mindfulness skills. Subgroup analyses gave no indications of differential efficacy between participants with a principal diagnosis of depression and those with principal anxiety. Treatment gains were maintained in the 7-month follow-up.

\n

The treatment manual used in this study aimed to implement a psychodynamic treatment based on the affect-phobia model in self-help format. This approach calls for a discussion on similarities and differences to the original APT manual. An assumption of this implementation was that the core principles of affect-phobia treatment manual could be retained. This included the general model of psychopathology (i.e., as illustrated by the triangle of conflict in Fig. 2) and the overall structure of the therapy. While the treatment emphasized how affect-phobic patterns in a person’s current life (C) began with past persons (P), as illustrated in Malan’s triangle of person, the treatment did not address how these patterns could potentially be enacted with the therapist (T). Importantly, these patterns were not regarded as non-existing, but rather the treatment material did not address them nor was it part of the role of the therapists to address these patterns. While the therapist role might overlap between guided self-help and face-to-face therapy in several aspects (Paxling et al., 2013), there is a difference in the present study in how the treatment material taught “emotional mindfulness” as a way of conducting exposure to one’s feelings without the therapist being present. Some authors have suggested that exposure with response prevention may result in better effects of treatment when patients conduct the exposure by themselves, in their natural environment (Röper & Rachman, 1976; Salkovskis, 1985). If this is also the case in affect-phobia therapy and how that would affect outcome is a question for further research, but it is possible that self-exposure to feelings is at least as effective as exposure with a therapist present. Importantly, as exposure with response prevention is assumed to be an active mechanism in the treatment tested in this study, this would imply similarities in working mechanisms in affect-focused psychodynamic treatment and cognitive behavioral therapy based on principles of exposure. Similarly, several contemporary CBT treatments have components of emotion regulation techniques (e.g., Berking et al., 2013; Bryant et al., 2013), that seem overlapping to affect-phobia treatment. Future research should investigate further similarities and differences between affect-focused psychodynamic therapy and various CBT models. Summing up, despite the aforementioned differences to the original APT manual, we believe that the manual used in the current study is indeed a valid implementation of a psychodynamic therapy based on the affect-phobia model.

\n

In affect-phobia therapy, the model of psychopathology is the same across disorders, i.e., the triangle of conflict is assumed to explain both etiology and maintenance of for example depression and anxiety disorders (McCullough et al., 2003). This aim is similar to transdiagnostic and unified protocols where the treatment material has been arranged to fit a broader range of patients (Barlow, Allen & Choate, 2004; Craske, 2012). Hence, affect-phobia therapy could be described as a transdiagnostic treatment. While there are several studies on the efficacy of cognitive behavioral transdiagnostic treatments for anxiety disorders (Farchione et al., 2012; McEvoy, Nathan & Norton, 2009), few exist that explicitly target both depression and anxiety. However, one uncontrolled trial testing the effectiveness of a group-based intervention (McEvoy & Nathan, 2007) resulted in promising outcomes and showed comparable efficacy to several disorder-specific treatments. More recently, Titov et al. (2011) provided evidence of the efficacy of an Internet-delivered transdiagnostic program that targeted both anxiety and depression, when compared to a waiting-list. Both these treatments yielded within-group effect sizes of Cohen’s d around 1.0 for measures of depression and anxiety. Hence, the affect-phobia treatment tested in this study, seems to stand well when compared to other transdiagnostic treatments tested.

\n

There are methodological limitations that need to be considered. First, as we recruited participants from the community and not from, for example, a treatment clinic, the external validity of the findings are challenging to interpret. While there are studies on ICBT that suggests generalizability to clinical settings (e.g., Bergström et al., 2010; Hedman et al., 2013), this has yet to be proven for Internet-delivered psychodynamic therapy. Moreover, more than half of the participants in the present study had three years or more of university education. While this factor might have biased the results, the average severity of depression and anxiety symptoms was moderate to moderately severe (Kroenke et al., 2010), and more than half of the participants had comorbid disorders, suggesting clinical representativity (Kessler, Merikangas & Wang, 2007). A second methodological limitation concerns the substantial within-group effects in the control group that make the results harder to interpret. These effects are probably due to the weekly clinical monitoring and supportive contact with the therapists in addition to the extensive test procedures such as telephone interviews before and after the treatment period. While these aspects might have biased the results, it also highlights the need for research regarding specific factors in guided self-help treatments. A third limitation concerns how missing data were handled at the 7-month follow-up for the categorical measure of recovery. For that measure, missing data at follow-up were replaced by that from post-treatment. When using that approach in longitudinal analysis, there is a known risk for estimation bias (Gueorguieva & Krystal, 2004). While we did not compare the recovery rates over time (i.e., did not include this measure in any longitudinal analysis) we still acknowledge that some method of multiple imputation could have been used to account for the missing data (Graham, 2009). Another limitation concerns the subgroup analyses. As the total sample size was appropriate for the comparison between treatment and control, it seemed not to have been adequate for the analyses regarding subgroups of principal depression and anxiety. This implies that a larger sample size would be needed in future research if investigating the effect of a transdiagnostic treatment on specific diagnoses in a sample with multiple disorders. A related limitation concerns the definition of the subgroups in this study. The group with principal anxiety disorders is a heterogeneous group, e.g., in the sense that it includes both fear disorders (e.g., panic disorder) and worry disorders (GAD). This may have confounded the subgroup analyses. A final limitation that needs to be addressed concerns the therapists in the study, all of whom were psychologists in training, albeit during the last semester of training in a five year program and under regular supervision. It is possible that more experienced therapists would have enabled even larger treatment effects. A related concern is that psychologists in training conducted all diagnostic interviews. While the psychologists were explicitly trained in the diagnostic procedures and received supervision, there is a possibility that their level of experience may have affected how the diagnostic categories were defined. Importantly though, the MINI interview has been designed to be administered by non-experts.

" + "

Discussion

\n

This randomized controlled trial aimed to evaluate the effects of affect-phobia therapy in the format of guided self-help through the Internet in a sample of participants with depression and anxiety disorders. The results indicated that the treatment was effective in reducing symptoms of depression and anxiety, and also in facilitating emotional processing and mindfulness skills. Subgroup analyses gave no indications of differential efficacy between participants with a principal diagnosis of depression and those with principal anxiety. Treatment gains were maintained in the 7-month follow-up.

\n

The treatment manual used in this study aimed to implement a psychodynamic treatment based on the affect-phobia model in self-help format. This approach calls for a discussion on similarities and differences to the original APT manual. An assumption of this implementation was that the core principles of affect-phobia treatment manual could be retained. This included the general model of psychopathology (i.e., as illustrated by the triangle of conflict in Fig. 2) and the overall structure of the therapy. While the treatment emphasized how affect-phobic patterns in a person’s current life (C) began with past persons (P), as illustrated in Malan’s triangle of person, the treatment did not address how these patterns could potentially be enacted with the therapist (T). Importantly, these patterns were not regarded as non-existing, but rather the treatment material did not address them nor was it part of the role of the therapists to address these patterns. While the therapist role might overlap between guided self-help and face-to-face therapy in several aspects (Paxling et al., 2013), there is a difference in the present study in how the treatment material taught “emotional mindfulness” as a way of conducting exposure to one’s feelings without the therapist being present. Some authors have suggested that exposure with response prevention may result in better effects of treatment when patients conduct the exposure by themselves, in their natural environment (Röper & Rachman, 1976; Salkovskis, 1985). If this is also the case in affect-phobia therapy and how that would affect outcome is a question for further research, but it is possible that self-exposure to feelings is at least as effective as exposure with a therapist present. Importantly, as exposure with response prevention is assumed to be an active mechanism in the treatment tested in this study, this would imply similarities in working mechanisms in affect-focused psychodynamic treatment and cognitive behavioral therapy based on principles of exposure. Similarly, several contemporary CBT treatments have components of emotion regulation techniques (e.g., Berking et al., 2013; Bryant et al., 2013), that seem overlapping to affect-phobia treatment. Future research should investigate further similarities and differences between affect-focused psychodynamic therapy and various CBT models. Summing up, despite the aforementioned differences to the original APT manual, we believe that the manual used in the current study is indeed a valid implementation of a psychodynamic therapy based on the affect-phobia model.

\n

In affect-phobia therapy, the model of psychopathology is the same across disorders, i.e., the triangle of conflict is assumed to explain both etiology and maintenance of for example depression and anxiety disorders (McCullough et al., 2003). This aim is similar to transdiagnostic and unified protocols where the treatment material has been arranged to fit a broader range of patients (Barlow, Allen & Choate, 2004; Craske, 2012). Hence, affect-phobia therapy could be described as a transdiagnostic treatment. While there are several studies on the efficacy of cognitive behavioral transdiagnostic treatments for anxiety disorders (Farchione et al., 2012; McEvoy, Nathan & Norton, 2009), few exist that explicitly target both depression and anxiety. However, one uncontrolled trial testing the effectiveness of a group-based intervention (McEvoy & Nathan, 2007) resulted in promising outcomes and showed comparable efficacy to several disorder-specific treatments. More recently, Titov et al. (2011) provided evidence of the efficacy of an Internet-delivered transdiagnostic program that targeted both anxiety and depression, when compared to a waiting-list. Both these treatments yielded within-group effect sizes of Cohen’s d around 1.0 for measures of depression and anxiety. Hence, the affect-phobia treatment tested in this study, seems to stand well when compared to other transdiagnostic treatments tested.

\n

There are methodological limitations that need to be considered. First, as we recruited participants from the community and not from, for example, a treatment clinic, the external validity of the findings are challenging to interpret. While there are studies on ICBT that suggests generalizability to clinical settings (e.g., Bergström et al., 2010; Hedman et al., 2013), this has yet to be proven for Internet-delivered psychodynamic therapy. Moreover, more than half of the participants in the present study had three years or more of university education. While this factor might have biased the results, the average severity of depression and anxiety symptoms was moderate to moderately severe (Kroenke et al., 2010), and more than half of the participants had comorbid disorders, suggesting clinical representativity (Kessler, Merikangas & Wang, 2007). A second methodological limitation concerns the substantial within-group effects in the control group that make the results harder to interpret. These effects are probably due to the weekly clinical monitoring and supportive contact with the therapists in addition to the extensive test procedures such as telephone interviews before and after the treatment period. While these aspects might have biased the results, it also highlights the need for research regarding specific factors in guided self-help treatments. A third limitation concerns how missing data were handled at the 7-month follow-up for the categorical measure of recovery. For that measure, missing data at follow-up were replaced by that from post-treatment. When using that approach in longitudinal analysis, there is a known risk for estimation bias (Gueorguieva & Krystal, 2004). While we did not compare the recovery rates over time (i.e., did not include this measure in any longitudinal analysis) we still acknowledge that some method of multiple imputation could have been used to account for the missing data (Graham, 2009). Another limitation concerns the subgroup analyses. As the total sample size was appropriate for the comparison between treatment and control, it seemed not to have been adequate for the analyses regarding subgroups of principal depression and anxiety. This implies that a larger sample size would be needed in future research if investigating the effect of a transdiagnostic treatment on specific diagnoses in a sample with multiple disorders. A related limitation concerns the definition of the subgroups in this study. The group with principal anxiety disorders is a heterogeneous group, e.g., in the sense that it includes both fear disorders (e.g., panic disorder) and worry disorders (GAD). This may have confounded the subgroup analyses. A final limitation that needs to be addressed concerns the therapists in the study, all of whom were psychologists in training, albeit during the last semester of training in a five year program and under regular supervision. It is possible that more experienced therapists would have enabled even larger treatment effects. A related concern is that psychologists in training conducted all diagnostic interviews. While the psychologists were explicitly trained in the diagnostic procedures and received supervision, there is a possibility that their level of experience may have affected how the diagnostic categories were defined. Importantly though, the MINI interview has been designed to be administered by non-experts.

" ] }, "conclusion_html": { @@ -140,77 +140,77 @@ }, "references_html": { "value": [ - "\nAbbass A, Town J, Driessen E. 2012. Intensive short-term dynamic psychotherapy: a systematic review and meta-analysis of outcome research. Harvard Review of Psychiatry 20:97-108 \n", - "\nAndersson G. 2009. Using the Internet to provide cognitive behaviour therapy. Behaviour Research and Therapy 47:175-180 \n", - "\nAndersson G, Paxling B, Roch-Norlund P, Östman G, Norgren A, Almlöv J, Georén L, Breitholtz E, Dahlin M, Cuijpers P, Carlbring P, Silverberg F. 2012. Internet-based psychodynamic vs. cognitive behavioural guided self-help for generalized anxiety disorder: a randomised controlled trial. Psychotherapy and Psychosomatics 81:344-355 \n", - "\nBaer RA, Smith GT, Hopkins J, Krietemeyer J, Toney L. 2006. Using self-report assessment methods to explore facets of mindfulness. Assessment 13:27-45 \n", - "\nBaker R, Thomas S, Thomas PW, Gower P, Santonastaso M, Whittlesea A. 2010. The emotional processing scale: scale refinement and abridgement (EPS-25) Journal of Psychosomatic Research 68:83-88 \n", - "\nBarlow DH, Allen LB, Choate ML. 2004. Toward a unified treatment for emotional disorders. Behavior Therapy 35:205-230 \n", - "\nBergström J, Andersson G, Ljótsson B, Rück C, Andréewitch S, Karlsson A, Carlbring P, Andersson E, Lindefors N. 2010. Internet-versus group-administered cognitive behaviour therapy for panic disorder in a psychiatric setting: a randomised trial. BMC Psychiatry 10:54 \n", - "\nBerking M, Ebert D, Cuijpers P, Hofmann SG. 2013. Emotion regulation skills training enhances the efficacy of inpatient cognitive behavioral therapy for major depressive disorder: a randomized controlled trial. Psychotherapy and Psychosomatics 82:234-245 \n", - "\nBorenstein M, Hedges LV, Higgins JPT, Rothstein HR. 2009. Introduction to meta-analysis. Chichester: John Wiley & Sons. \n", - "\nBryant RA, Mastrodomenico J, Hopwood S, Kenny L, Cahill C, Kandris E, Taylor K. 2013. Augmenting cognitive behaviour therapy for post-traumatic stress disorder with emotion tolerance training: a randomized controlled trial. Psychological Medicine 1-8 \n", - "\nCohen J. 1988. Statistical power analysis for the behavioral sciences (2nd ed). Hillsdale: Lawrence Erlbaum Associates. \n", - "\nCraske MG. 2012. Transdiagnostic treatment for anxiety and depression. Depression and Anxiety 29:749-753 \n", - "\nCuijpers P, Donker T, Van Straten A, Li J, Andersson G. 2010. Is guided self-help as effective as face-to-face psychotherapy for depression and anxiety disorders? A systematic review and meta-analysis of comparative outcome studies. Psychological Medicine 40:1943-1957 \n", - "\nDavanloo H. 2000. Intensive short-term dynamic psychotherapy: selected papers of Habib Davanloo. Chichester: Wiley. \n", - "\nDiener MJ, Hilsenroth MJ, Weinberger J. 2007. Therapist affect focus and patient outcomes in psychodynamic psychotherapy: a meta-analysis. The American Journal of Psychiatry 164:936-941 \n", - "\nDornelas E, Ferrand J, Stepnowski R, Barbagallo J, McCullough L. 2010. A pilot study of affect-focused psychotherapy for antepartum depression. Journal of Psychotherapy Integration 20:364-382 \n", - "\nDriessen E, Cuijpers P, De Maat SCM, Abbass A, De Jonghe F, Dekker JJM. 2010. The efficacy of short-term psychodynamic psychotherapy for depression: a meta-analysis. Clinical Psychology Review 30:25-36 \n", - "\nEbmeier KP, Donaghey C, Steele JD. 2006. Recent developments and current controversies in depression. Lancet 367:153-167 \n", - "\nFann JR, Berry DL, Wolpin S, Austin-Seymour M, Bush N, Halpenny B, Lober WB, McCorkle R. 2009. Depression screening using the Patient Health Questionnaire-9 administered on a touch screen computer. Psycho-oncology 18:14-22 \n", - "\nFarchione TJ, Fairholme CP, Ellard KK, Boisseau CL, Thompson-Hollands J, Carl JR, Gallagher MW, Barlow DH. 2012. Unified protocol for transdiagnostic treatment of emotional disorders: a randomized controlled trial. Behavior Therapy 43:666-678 \n", - "\nFosha D. 2000. The transforming power of affect: a model for accelerated change. New York: BasicBooks. \n", - "\nFrederick RJ. 2009. Living like you mean it: use the wisdom and power of your emotions to get the life you really want. San Francisco: Jossey-Bass. \n", - "\nGraham JW. 2009. Missing data analysis: making it work in the real world. Annual Review of Psychology 60:549-576 \n", - "\nGueorguieva R, Krystal JH. 2004. Move over ANOVA: progress in analyzing repeated-measures data and its reflection in papers published in the Archives of General Psychiatry. Archives of General Psychiatry 61:310-317 \n", - "\nGuy W. 1976. Clinical global impressions. ECDEU assessment manual for psychopharmacology. Rockville: NIMH. \n", - "\nHedman E, Ljótsson B, Lindefors N. 2012. Cognitive behavior therapy via the Internet: a systematic review of applications, clinical efficacy and cost-effectiveness. Expert Review of Pharmacoeconomics & Outcomes Research 12:745-764 \n", - "\nHedman E, Ljótsson B, Rück C, Bergström J, Andersson G, Kaldo V, Jansson L, Andersson E, Blom K, El Alaoui S, Falk L, Ivarsson J, Nasri B, Rydh S, Lindefors N. 2013. Effectiveness of Internet-based cognitive behaviour therapy for panic disorder in routine psychiatric care. Acta Psychiatrica Scandinavica Epub ahead of print Feb 14 2013\n", - "\nJohansson R, Andersson G. 2012. Internet-based psychological treatments for depression. Expert Review of Neurotherapeutics 12:861-870 \n", - "\nJohansson R, Ekbladh S, Hebert A, Lindström M, Möller S, Petitt E, Poysti S, Larsson MH, Rousseau A, Carlbring P, Cuijpers P, Andersson G. 2012. Psychodynamic guided self-help for adult depression through the internet: a randomised controlled trial. PLoS ONE 7:e38021 \n", - "\nKessler RC, Berglund P, Demler O, Jin R, Merikangas KR, Walters EE. 2005. Lifetime prevalence and age-of-onset distributions of DSM-IV disorders in the National Comorbidity Survey Replication. Archives of General Psychiatry 62:593-602 \n", - "\nKessler RC, Merikangas KR, Wang PS. 2007. Prevalence, comorbidity, and service utilization for mood disorders in the United States at the beginning of the twenty-first century. Annual Review of Clinical Psychology 3:137-158 \n", - "\nKroenke K, Spitzer RL, Williams JB. 2001. The PHQ-9: validity of a brief depression severity measure. Journal of General Internal Medicine 16:606-613 \n", - "\nKroenke K, Spitzer RL, Williams JBW, Löwe B. 2010. The patient health questionnaire somatic, anxiety, and depressive symptom scales: a systematic review. General Hospital Psychiatry 32:345-359 \n", - "\nLeichsenring F, Salzer S, Beutel ME, Herpertz S, Hiller W, Hoyer J, Huesing J, Joraschky P, Nolting B, Poehlmann K, Ritter V, Stangier U, Strauss B, Stuhldreher N, Tefikow S, Teismann T, Willutzki U, Wiltink J, Leibing E. 2013. Psychodynamic therapy and cognitive-behavioral therapy in social anxiety disorder: a multicenter randomized controlled trial. The American Journal of Psychiatry Epub ahead of print May 17 2013\n", - "\nLeichsenring F, Salzer S, Jaeger U, Kächele H, Kreische R, Leweke F, Rüger U, Winkelbach C, Leibing E. 2009. Short-term psychodynamic psychotherapy and cognitive-behavioral therapy in generalized anxiety disorder: a randomized, controlled trial. The American Journal of Psychiatry 166:875-881 \n", - "\nLilja JL, Frodi-Lundgren A, Hanse JJ, Josefsson T, Lundh L-G, Sköld C, Hansen E, Broberg AG. 2011. Five Facets Mindfulness Questionnaire - reliability and factor structure: a Swedish version. Cognitive Behaviour Therapy 40:291-303 \n", - "\nMalan D. 1995. Individual psychotherapy and the science of psychodynamics (2nd ed). Oxford: Butterworth-Heinemann. \n", - "\nMallinckrodt CH, Clark WS, David SR. 2001. Accounting for dropout bias using mixed-effects models. Journal of Biopharmaceutical Statistics 11:9-21 \n", - "\nMcCullough L, Kuhn N, Andrews S, Kaplan A, Wolf J, Hurley CL. 2003. Treating affect phobia: a manual for short-term dynamic psychotherapy. New York: Guilford Press. \n", - "\nMcEvoy P, Nathan P. 2007. Effectiveness of cognitive behavior therapy for diagnostically heterogeneous groups: a benchmarking study. Journal of Consulting and Clinical Psychology 75:344-350 \n", - "\nMcEvoy P, Nathan P, Norton P. 2009. Efficacy of transdiagnostic treatments: a review of published outcome studies and future research directions. Journal of Cognitive Psychotherapy: An International Quarterly 23:20-33 \n", - "\nMilrod B, Leon AC, Busch F, Rudden M, Schwalberg M, Clarkin J, Aronson A, Singer M, Turchin W, Klass ET, Graf E, Teres JJ, Shear MK. 2007. A randomized controlled clinical trial of psychoanalytic psychotherapy for panic disorder. The American Journal of Psychiatry 164:265-272 \n", - "\nOsimo F, Stein MJ. 2012. Theory and practice of experiential dynamic psychotherapy. London: Karnac. \n", - "\nPaxling B, Lundgren S, Norman A, Almlöv J, Carlbring P, Cuijpers P, Andersson G. 2013. Therapist behaviours in internet-delivered cognitive behaviour therapy: analyses of e-mail correspondence in the treatment of generalized anxiety disorder. Behavioural and Cognitive Psychotherapy 41:280-289 \n", - "\nRöper G, Rachman S. 1976. Obsessional-compulsive checking: experimental replication and development. Behaviour Research and Therapy 14:25-32 \n", - "\nSalkovskis PM. 1985. Obsessional-compulsive problems: a cognitive-behavioural analysis. Behaviour Research and Therapy 23:571-583 \n", - "\nSchulz KF, Altman DG, Moher D. 2010. CONSORT 2010 statement: updated guidelines for reporting parallel group randomised trials. PLoS Medicine 7:e1000251 \n", - "\nShapiro S, Wilk M. 1965. An analysis of variance test for normality (complete samples) Biometrika 52:591-611 \n", - "\nSheehan DV, Lecrubier Y, Sheehan KH, Amorim P, Janavs J, Weiller E, Hergueta T, Baker R, Dunbar GC. 1998. The Mini-International Neuropsychiatric Interview (M.I.N.I.): the development and validation of a structured diagnostic psychiatric interview for DSM-IV and ICD-10. The Journal of Clinical Psychiatry 59(Suppl 2):22-33 Quiz 34–57\n", - "\nSmit F, Cuijpers P, Oostenbrink J, Batelaan N, De Graaf R, Beekman A. 2006. Costs of nine common mental disorders: implications for curative and preventive psychiatry. The Journal of Mental Health Policy and Economics 9:193-200 \n", - "\nSpitzer RL, Kroenke K, Williams JBW, Löwe B. 2006. A brief measure for assessing generalized anxiety disorder: the GAD-7. Archives of Internal Medicine 166:1092-1097 \n", - "\nSvartberg M, Stiles TC, Seltzer MH. 2004. Randomized, controlled trial of the effectiveness of short-term dynamic psychotherapy and cognitive therapy for cluster C personality disorders. The American Journal of Psychiatry 161:810-817 \n", - "\nTitov N, Dear BF, Schwencke G, Andrews G, Johnston L, Craske MG, McEvoy P. 2011. Transdiagnostic internet treatment for anxiety and depression: a randomised controlled trial. Behaviour Research and Therapy 49:441-452 \n", - "\nTown JM, Diener MJ, Abbass A, Leichsenring F, Driessen E, Rabung S. 2012. A meta-analysis of psychodynamic psychotherapy outcomes: evaluating the effects of research-specific procedures. Psychotherapy (Chicago, Ill.) 49:276-290 \n", - "\nVerbeke G, Molenberghs G. 2000. Linear mixed models for longitudinal data. New York: Springer. \n", - "\nWinston A, Laikin M, Pollack J, Samstag LW, McCullough L, Muran JC. 1994. Short-term psychotherapy of personality disorders. The American Journal of Psychiatry 151:190-194 \n" + "\nAbbass A, Town J, Driessen E. 2012. Intensive short-term dynamic psychotherapy: a systematic review and meta-analysis of outcome research. Harvard Review of Psychiatry 20:97-108 \n", + "\nAndersson G. 2009. Using the Internet to provide cognitive behaviour therapy. Behaviour Research and Therapy 47:175-180 \n", + "\nAndersson G, Paxling B, Roch-Norlund P, Östman G, Norgren A, Almlöv J, Georén L, Breitholtz E, Dahlin M, Cuijpers P, Carlbring P, Silverberg F. 2012. Internet-based psychodynamic vs. cognitive behavioural guided self-help for generalized anxiety disorder: a randomised controlled trial. Psychotherapy and Psychosomatics 81:344-355 \n", + "\nBaer RA, Smith GT, Hopkins J, Krietemeyer J, Toney L. 2006. Using self-report assessment methods to explore facets of mindfulness. Assessment 13:27-45 \n", + "\nBaker R, Thomas S, Thomas PW, Gower P, Santonastaso M, Whittlesea A. 2010. The emotional processing scale: scale refinement and abridgement (EPS-25) Journal of Psychosomatic Research 68:83-88 \n", + "\nBarlow DH, Allen LB, Choate ML. 2004. Toward a unified treatment for emotional disorders. Behavior Therapy 35:205-230 \n", + "\nBergström J, Andersson G, Ljótsson B, Rück C, Andréewitch S, Karlsson A, Carlbring P, Andersson E, Lindefors N. 2010. Internet-versus group-administered cognitive behaviour therapy for panic disorder in a psychiatric setting: a randomised trial. BMC Psychiatry 10:54 \n", + "\nBerking M, Ebert D, Cuijpers P, Hofmann SG. 2013. Emotion regulation skills training enhances the efficacy of inpatient cognitive behavioral therapy for major depressive disorder: a randomized controlled trial. Psychotherapy and Psychosomatics 82:234-245 \n", + "\nBorenstein M, Hedges LV, Higgins JPT, Rothstein HR. 2009. Introduction to meta-analysis. Chichester: John Wiley & Sons. \n", + "\nBryant RA, Mastrodomenico J, Hopwood S, Kenny L, Cahill C, Kandris E, Taylor K. 2013. Augmenting cognitive behaviour therapy for post-traumatic stress disorder with emotion tolerance training: a randomized controlled trial. Psychological Medicine 1-8 \n", + "\nCohen J. 1988. Statistical power analysis for the behavioral sciences (2nd ed). Hillsdale: Lawrence Erlbaum Associates. \n", + "\nCraske MG. 2012. Transdiagnostic treatment for anxiety and depression. Depression and Anxiety 29:749-753 \n", + "\nCuijpers P, Donker T, Van Straten A, Li J, Andersson G. 2010. Is guided self-help as effective as face-to-face psychotherapy for depression and anxiety disorders? A systematic review and meta-analysis of comparative outcome studies. Psychological Medicine 40:1943-1957 \n", + "\nDavanloo H. 2000. Intensive short-term dynamic psychotherapy: selected papers of Habib Davanloo. Chichester: Wiley. \n", + "\nDiener MJ, Hilsenroth MJ, Weinberger J. 2007. Therapist affect focus and patient outcomes in psychodynamic psychotherapy: a meta-analysis. The American Journal of Psychiatry 164:936-941 \n", + "\nDornelas E, Ferrand J, Stepnowski R, Barbagallo J, McCullough L. 2010. A pilot study of affect-focused psychotherapy for antepartum depression. Journal of Psychotherapy Integration 20:364-382 \n", + "\nDriessen E, Cuijpers P, De Maat SCM, Abbass A, De Jonghe F, Dekker JJM. 2010. The efficacy of short-term psychodynamic psychotherapy for depression: a meta-analysis. Clinical Psychology Review 30:25-36 \n", + "\nEbmeier KP, Donaghey C, Steele JD. 2006. Recent developments and current controversies in depression. Lancet 367:153-167 \n", + "\nFann JR, Berry DL, Wolpin S, Austin-Seymour M, Bush N, Halpenny B, Lober WB, McCorkle R. 2009. Depression screening using the Patient Health Questionnaire-9 administered on a touch screen computer. Psycho-oncology 18:14-22 \n", + "\nFarchione TJ, Fairholme CP, Ellard KK, Boisseau CL, Thompson-Hollands J, Carl JR, Gallagher MW, Barlow DH. 2012. Unified protocol for transdiagnostic treatment of emotional disorders: a randomized controlled trial. Behavior Therapy 43:666-678 \n", + "\nFosha D. 2000. The transforming power of affect: a model for accelerated change. New York: BasicBooks. \n", + "\nFrederick RJ. 2009. Living like you mean it: use the wisdom and power of your emotions to get the life you really want. San Francisco: Jossey-Bass. \n", + "\nGraham JW. 2009. Missing data analysis: making it work in the real world. Annual Review of Psychology 60:549-576 \n", + "\nGueorguieva R, Krystal JH. 2004. Move over ANOVA: progress in analyzing repeated-measures data and its reflection in papers published in the Archives of General Psychiatry. Archives of General Psychiatry 61:310-317 \n", + "\nGuy W. 1976. Clinical global impressions. ECDEU assessment manual for psychopharmacology. Rockville: NIMH. \n", + "\nHedman E, Ljótsson B, Lindefors N. 2012. Cognitive behavior therapy via the Internet: a systematic review of applications, clinical efficacy and cost-effectiveness. Expert Review of Pharmacoeconomics & Outcomes Research 12:745-764 \n", + "\nHedman E, Ljótsson B, Rück C, Bergström J, Andersson G, Kaldo V, Jansson L, Andersson E, Blom K, El Alaoui S, Falk L, Ivarsson J, Nasri B, Rydh S, Lindefors N. 2013. Effectiveness of Internet-based cognitive behaviour therapy for panic disorder in routine psychiatric care. Acta Psychiatrica Scandinavica Epub ahead of print Feb 14 2013\n", + "\nJohansson R, Andersson G. 2012. Internet-based psychological treatments for depression. Expert Review of Neurotherapeutics 12:861-870 \n", + "\nJohansson R, Ekbladh S, Hebert A, Lindström M, Möller S, Petitt E, Poysti S, Larsson MH, Rousseau A, Carlbring P, Cuijpers P, Andersson G. 2012. Psychodynamic guided self-help for adult depression through the internet: a randomised controlled trial. PLoS ONE 7:e38021 \n", + "\nKessler RC, Berglund P, Demler O, Jin R, Merikangas KR, Walters EE. 2005. Lifetime prevalence and age-of-onset distributions of DSM-IV disorders in the National Comorbidity Survey Replication. Archives of General Psychiatry 62:593-602 \n", + "\nKessler RC, Merikangas KR, Wang PS. 2007. Prevalence, comorbidity, and service utilization for mood disorders in the United States at the beginning of the twenty-first century. Annual Review of Clinical Psychology 3:137-158 \n", + "\nKroenke K, Spitzer RL, Williams JB. 2001. The PHQ-9: validity of a brief depression severity measure. Journal of General Internal Medicine 16:606-613 \n", + "\nKroenke K, Spitzer RL, Williams JBW, Löwe B. 2010. The patient health questionnaire somatic, anxiety, and depressive symptom scales: a systematic review. General Hospital Psychiatry 32:345-359 \n", + "\nLeichsenring F, Salzer S, Beutel ME, Herpertz S, Hiller W, Hoyer J, Huesing J, Joraschky P, Nolting B, Poehlmann K, Ritter V, Stangier U, Strauss B, Stuhldreher N, Tefikow S, Teismann T, Willutzki U, Wiltink J, Leibing E. 2013. Psychodynamic therapy and cognitive-behavioral therapy in social anxiety disorder: a multicenter randomized controlled trial. The American Journal of Psychiatry Epub ahead of print May 17 2013\n", + "\nLeichsenring F, Salzer S, Jaeger U, Kächele H, Kreische R, Leweke F, Rüger U, Winkelbach C, Leibing E. 2009. Short-term psychodynamic psychotherapy and cognitive-behavioral therapy in generalized anxiety disorder: a randomized, controlled trial. The American Journal of Psychiatry 166:875-881 \n", + "\nLilja JL, Frodi-Lundgren A, Hanse JJ, Josefsson T, Lundh L-G, Sköld C, Hansen E, Broberg AG. 2011. Five Facets Mindfulness Questionnaire - reliability and factor structure: a Swedish version. Cognitive Behaviour Therapy 40:291-303 \n", + "\nMalan D. 1995. Individual psychotherapy and the science of psychodynamics (2nd ed). Oxford: Butterworth-Heinemann. \n", + "\nMallinckrodt CH, Clark WS, David SR. 2001. Accounting for dropout bias using mixed-effects models. Journal of Biopharmaceutical Statistics 11:9-21 \n", + "\nMcCullough L, Kuhn N, Andrews S, Kaplan A, Wolf J, Hurley CL. 2003. Treating affect phobia: a manual for short-term dynamic psychotherapy. New York: Guilford Press. \n", + "\nMcEvoy P, Nathan P. 2007. Effectiveness of cognitive behavior therapy for diagnostically heterogeneous groups: a benchmarking study. Journal of Consulting and Clinical Psychology 75:344-350 \n", + "\nMcEvoy P, Nathan P, Norton P. 2009. Efficacy of transdiagnostic treatments: a review of published outcome studies and future research directions. Journal of Cognitive Psychotherapy: An International Quarterly 23:20-33 \n", + "\nMilrod B, Leon AC, Busch F, Rudden M, Schwalberg M, Clarkin J, Aronson A, Singer M, Turchin W, Klass ET, Graf E, Teres JJ, Shear MK. 2007. A randomized controlled clinical trial of psychoanalytic psychotherapy for panic disorder. The American Journal of Psychiatry 164:265-272 \n", + "\nOsimo F, Stein MJ. 2012. Theory and practice of experiential dynamic psychotherapy. London: Karnac. \n", + "\nPaxling B, Lundgren S, Norman A, Almlöv J, Carlbring P, Cuijpers P, Andersson G. 2013. Therapist behaviours in internet-delivered cognitive behaviour therapy: analyses of e-mail correspondence in the treatment of generalized anxiety disorder. Behavioural and Cognitive Psychotherapy 41:280-289 \n", + "\nRöper G, Rachman S. 1976. Obsessional-compulsive checking: experimental replication and development. Behaviour Research and Therapy 14:25-32 \n", + "\nSalkovskis PM. 1985. Obsessional-compulsive problems: a cognitive-behavioural analysis. Behaviour Research and Therapy 23:571-583 \n", + "\nSchulz KF, Altman DG, Moher D. 2010. CONSORT 2010 statement: updated guidelines for reporting parallel group randomised trials. PLoS Medicine 7:e1000251 \n", + "\nShapiro S, Wilk M. 1965. An analysis of variance test for normality (complete samples) Biometrika 52:591-611 \n", + "\nSheehan DV, Lecrubier Y, Sheehan KH, Amorim P, Janavs J, Weiller E, Hergueta T, Baker R, Dunbar GC. 1998. The Mini-International Neuropsychiatric Interview (M.I.N.I.): the development and validation of a structured diagnostic psychiatric interview for DSM-IV and ICD-10. The Journal of Clinical Psychiatry 59(Suppl 2):22-33 Quiz 34–57\n", + "\nSmit F, Cuijpers P, Oostenbrink J, Batelaan N, De Graaf R, Beekman A. 2006. Costs of nine common mental disorders: implications for curative and preventive psychiatry. The Journal of Mental Health Policy and Economics 9:193-200 \n", + "\nSpitzer RL, Kroenke K, Williams JBW, Löwe B. 2006. A brief measure for assessing generalized anxiety disorder: the GAD-7. Archives of Internal Medicine 166:1092-1097 \n", + "\nSvartberg M, Stiles TC, Seltzer MH. 2004. Randomized, controlled trial of the effectiveness of short-term dynamic psychotherapy and cognitive therapy for cluster C personality disorders. The American Journal of Psychiatry 161:810-817 \n", + "\nTitov N, Dear BF, Schwencke G, Andrews G, Johnston L, Craske MG, McEvoy P. 2011. Transdiagnostic internet treatment for anxiety and depression: a randomised controlled trial. Behaviour Research and Therapy 49:441-452 \n", + "\nTown JM, Diener MJ, Abbass A, Leichsenring F, Driessen E, Rabung S. 2012. A meta-analysis of psychodynamic psychotherapy outcomes: evaluating the effects of research-specific procedures. Psychotherapy (Chicago, Ill.) 49:276-290 \n", + "\nVerbeke G, Molenberghs G. 2000. Linear mixed models for longitudinal data. New York: Springer. \n", + "\nWinston A, Laikin M, Pollack J, Samstag LW, McCullough L, Muran JC. 1994. Short-term psychotherapy of personality disorders. The American Journal of Psychiatry 151:190-194 \n" ] }, "figures_html": { "value": [ - "
\"CONSORT
\n

\nFigure 1: CONSORT flowchart.

\n
", - "
\"Malan’s
\n

\nFigure 2: Malan’s two triangles - the triangle of conflict and the triangle of person.

\nThe two triangles (Malan, 1995) represent what David Malan called “the universal principle of psychodynamic psychotherapy”. That is, defenses (D) and anxieties (A) can block the expression of true feelings (F). These patterns began with past persons (P), are maintained with current persons (C), and are often enacted with the therapist (T).
", - "
\"Weekly
\n

\nFigure 3: Weekly PHQ-9 and GAD-7 scores.

\nWeekly scores on the PHQ-9 and the GAD-7 for both groups. Vertical bars denote 95% confidence intervals (CI). PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.
" + "
\"CONSORT
\n

\nFigure 1: CONSORT flowchart.

\n
", + "
\"Malan’s
\n

\nFigure 2: Malan’s two triangles - the triangle of conflict and the triangle of person.

\nThe two triangles (Malan, 1995) represent what David Malan called “the universal principle of psychodynamic psychotherapy”. That is, defenses (D) and anxieties (A) can block the expression of true feelings (F). These patterns began with past persons (P), are maintained with current persons (C), and are often enacted with the therapist (T).
", + "
\"Weekly
\n

\nFigure 3: Weekly PHQ-9 and GAD-7 scores.

\nWeekly scores on the PHQ-9 and the GAD-7 for both groups. Vertical bars denote 95% confidence intervals (CI). PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.
" ] }, "tables_html": { "value": [ - "
\nTable 1:
Demographic description of the participants.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Treatment groupControl groupTotal
GenderMale8 (16%)10 (20%)18 (18%)
Female42 (84%)40 (80%)82 (82%)
AgeMean (SD)43.1 (13.9)46.6 (12.1)44.9 (13.1)
Min-Max19–7223–7719–77
Marital statusMarried or co-habiting31 (62%)36 (72%)67 (67%)
Other19 (38%)14 (28%)33 (33%)
Educational levelCollege or university, at least 3 years27 (54%)29 (58%)56 (56%)
Other23 (46%)21 (42%)44 (44%)
Employment statusEmployed or student41 (82%)33 (66%)74 (74%)
Other9 (18%)17 (34%)26 (26%)
Psychological treatmentNo experience15 (30%)16 (32%)31 (31%)
Prior experience35 (70%)31 (62%)66 (66%)
Ongoing0 (0%)3 (6%)3 (3%)
Pharmacological treatmentNo experience27 (54%)22 (44%)49 (49%)
Prior experience14 (28%)12 (24%)26 (26%)
Ongoing9 (18%)16 (32%)25 (25%)
\n", - "
\nTable 2:
Means, SDs and effect sizes (Cohen’s d) for measures of depression and anxiety.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Mean (SD)Effect size Cohen’s d (95% CI)Linear mixed models
Measure and groupPre-treatmentPost-treatment7-month
follow-up
Between-group,
post-treatment
Within-group
pre-post-treatment
Within-group
pre-7-month follow-up
Effect\n p\n
\n PHQ-9\n
Treatment group
(n = 50)
13.90 (3.6)6.32 (4.2)5.55 (3.5)0.77 (0.37–1.18)1.93 (1.31–2.55)2.43 (1.72–3.14)Group.89
Depression subgroup
(n = 28)
15.32 (3.3)5.89 (2.8)5.96 (3.5)0.95 (0.40–1.50)3.10 (1.87–4.32)2.82 (1.78–3.87)Time < .001
Anxiety subgroup
(n = 22)
12.09 (3.3)6.86 (5.5)5.00 (3.4)0.55 (−0.06–1.16)1.12 (0.49–1.75)2.17 (1.11–3.24)G × T < .001
Control group
(n = 50)
13.96 (4.7)10.26 (5.9)0.69 (0.40–0.97)
Depression subgroup
(n = 29)
15.07 (4.4)10.59 (6.4)0.79 (0.37–1.22)
Anxiety subgroup
(n = 21)
12.43 (4.7)9.81 (5.2)0.53 (0.20–0.85)
\n GAD-7\n
Treatment group
(n = 50)
11.46 (4.0)6.12 (4.5)5.34 (4.1)0.48 (0.08–0.87)1.25 (0.79–1.71)1.51 (0.97–2.06)Group.85
Depression subgroup
(n = 28)
10.86 (4.1)5.46 (3.9)5.19 (4.1)0.56 (0.03–1.09)1.35 (0.75–1.95)1.43 (0.73–2.10)Time < .001
Anxiety subgroup
(n = 22)
12.23 (3.8)6.95 (5.3)5.55 (4.2)0.39 (−0.21–0.99)1.15 (0.44–1.86)1.62 (0.72–2.52)G × T < .01
Control group
(n = 50)
12.26 (4.2)8.40 (5.0)0.82 (0.51–1.13)
Depression subgroup
(n = 29)
11.97 (5.0)8.03 (5.3)0.76 (0.39–1.13)
Anxiety subgroup
(n = 21)
12.67 (2.8)8.90 (4.7)0.93 (0.36–1.50)
\n\n
\n

Notes:

\n

The confidence intervals were calculated using the standard error and an alpha level of 0.05. A confidence interval that do not overlap zero indicates a significance of p < .05. p values are given for linear mixed models using data from pre-treatment and post-treatment and all individuals (N = 100). The p value associated with the main effect of group denotes significance of average difference between groups at the pre-treatment assessment. The p value associated with the effect of time denotes the significance of average change over all assessment periods across treatment. The p value associated with the effect of G × T (group × time) denotes significance of difference between the treatment group and the control group in change over all assessment periods. Effect sizes are calculated as standardized mean differences. PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.

\n
", - "
\nTable 3:
Means, SDs and effect sizes (Cohen’s d) for measures of emotional processing and mindfulness skills.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Mean (SD)Effect size Cohen’s d (95% CI)Linear mixed models
Measure and groupPre-treatmentPost-treatment7-month
follow-up
Between-group,
post-treatment
Within-group
pre-post-treatment
Within-group
pre-7-month follow-up
Effect\n p\n
\n EPS-25\n Group.50
Treatment group
(n = 50)
5.00 (1.03)2.86 (1.48)2.84 (1.65)0.82 (0.41–1.23)1.67 (1.13–2.21)1.51 (1.00–2.01)Time < .001
Control group
(n = 50)
4.93 (1.01)4.17 (1.73)0.50 (0.22–0.77)G × T < .001
\n FFMQ\n Group.15
Treatment group
(n = 50)
76.70 (10.9)88.00 (12.0)88.98 (13.3)0.65 (0.25–1.05)0.98 (0.65–1.31)0.99 (0.59–1.39)Time < .001
Control group
(n = 50)
77.18 (14.1)78.44 (17.1)0.08 (−0.11–0.27)G × T < .001
\n\n
\n

Notes:

\n

The confidence intervals were calculated using the standard error and an alpha level of 0.05. A confidence interval that do not overlap zero indicates a significance of p < .05. p values are given for linear mixed models using data from pre-treatment and post-treatment and all individuals (N = 100). The p value associated with the main effect of group denotes significance of average difference between groups at the pre-treatment assessment. The p value associated with the effect of time denotes the significance of average change over all assessment periods across treatment. The p value associated with the effect of G × T (group × time) denotes significance of difference between the treatment group and the control group in change over all assessment periods. Effect sizes are calculated as standardized mean differences. EPS-25: Emotional Processing Scale; FFMQ: Five Facets of Mindfulness Questionnaire.

\n
", - "
\nTable 4:
Frequency data of DSM-IV diagnoses.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Treatment groupControl group
DiagnosisPre-treatmentPost-treatment7-month follow-upPre-treatmentPost-treatment
DEP35 (70%)5 (10%)6 (12%)37 (74%)16 (32%)
GAD23 (46%)13 (26%)10 (20%)26 (52%)18 (36%)
SP19 (38%)10 (20%)9 (18%)17 (34%)13 (26%)
PD11 (22%)5 (10%)6 (12%)9 (18%)5 (10%)
\n Number of diagnoses\n
04 (8%)28 (56%)31 (62%)0 (0%)18 (36%)
116 (32%)13 (26%)8 (16%)23 (46%)18 (36%)
219 (38%)7 (14%)10 (20%)16 (32%)9 (18%)
310 (20%)2 (4%)1 (2%)10 (20%)4 (8%)
41 (2%)0 (0%)0 (0%)1 (2%)1 (2%)
Total number of diagnoses8833318949
\n\n
\n

Notes:

\n

The four participants with zero diagnoses listed at pre-treatment fulfilled DSM-IV criteria for depression and anxiety, not otherwise specified. DEP, GAD, SP, PD: Diagnoses of major depression, generalized anxiety disorder, social phobia and panic disorder.

\n
" + "
\nTable 1:
Demographic description of the participants.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Treatment groupControl groupTotal
GenderMale8 (16%)10 (20%)18 (18%)
Female42 (84%)40 (80%)82 (82%)
AgeMean (SD)43.1 (13.9)46.6 (12.1)44.9 (13.1)
Min-Max19–7223–7719–77
Marital statusMarried or co-habiting31 (62%)36 (72%)67 (67%)
Other19 (38%)14 (28%)33 (33%)
Educational levelCollege or university, at least 3 years27 (54%)29 (58%)56 (56%)
Other23 (46%)21 (42%)44 (44%)
Employment statusEmployed or student41 (82%)33 (66%)74 (74%)
Other9 (18%)17 (34%)26 (26%)
Psychological treatmentNo experience15 (30%)16 (32%)31 (31%)
Prior experience35 (70%)31 (62%)66 (66%)
Ongoing0 (0%)3 (6%)3 (3%)
Pharmacological treatmentNo experience27 (54%)22 (44%)49 (49%)
Prior experience14 (28%)12 (24%)26 (26%)
Ongoing9 (18%)16 (32%)25 (25%)
\n", + "
\nTable 2:
Means, SDs and effect sizes (Cohen’s d) for measures of depression and anxiety.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Mean (SD)Effect size Cohen’s d (95% CI)Linear mixed models
Measure and groupPre-treatmentPost-treatment7-month
follow-up
Between-group,
post-treatment
Within-group
pre-post-treatment
Within-group
pre-7-month follow-up
Effect\n p\n
\n PHQ-9\n
Treatment group
(n = 50)
13.90 (3.6)6.32 (4.2)5.55 (3.5)0.77 (0.37–1.18)1.93 (1.31–2.55)2.43 (1.72–3.14)Group.89
Depression subgroup
(n = 28)
15.32 (3.3)5.89 (2.8)5.96 (3.5)0.95 (0.40–1.50)3.10 (1.87–4.32)2.82 (1.78–3.87)Time < .001
Anxiety subgroup
(n = 22)
12.09 (3.3)6.86 (5.5)5.00 (3.4)0.55 (−0.06–1.16)1.12 (0.49–1.75)2.17 (1.11–3.24)G × T < .001
Control group
(n = 50)
13.96 (4.7)10.26 (5.9)0.69 (0.40–0.97)
Depression subgroup
(n = 29)
15.07 (4.4)10.59 (6.4)0.79 (0.37–1.22)
Anxiety subgroup
(n = 21)
12.43 (4.7)9.81 (5.2)0.53 (0.20–0.85)
\n GAD-7\n
Treatment group
(n = 50)
11.46 (4.0)6.12 (4.5)5.34 (4.1)0.48 (0.08–0.87)1.25 (0.79–1.71)1.51 (0.97–2.06)Group.85
Depression subgroup
(n = 28)
10.86 (4.1)5.46 (3.9)5.19 (4.1)0.56 (0.03–1.09)1.35 (0.75–1.95)1.43 (0.73–2.10)Time < .001
Anxiety subgroup
(n = 22)
12.23 (3.8)6.95 (5.3)5.55 (4.2)0.39 (−0.21–0.99)1.15 (0.44–1.86)1.62 (0.72–2.52)G × T < .01
Control group
(n = 50)
12.26 (4.2)8.40 (5.0)0.82 (0.51–1.13)
Depression subgroup
(n = 29)
11.97 (5.0)8.03 (5.3)0.76 (0.39–1.13)
Anxiety subgroup
(n = 21)
12.67 (2.8)8.90 (4.7)0.93 (0.36–1.50)
\n\n
\n

Notes:

\n

The confidence intervals were calculated using the standard error and an alpha level of 0.05. A confidence interval that do not overlap zero indicates a significance of p < .05. p values are given for linear mixed models using data from pre-treatment and post-treatment and all individuals (N = 100). The p value associated with the main effect of group denotes significance of average difference between groups at the pre-treatment assessment. The p value associated with the effect of time denotes the significance of average change over all assessment periods across treatment. The p value associated with the effect of G × T (group × time) denotes significance of difference between the treatment group and the control group in change over all assessment periods. Effect sizes are calculated as standardized mean differences. PHQ-9: 9-item Patient Health Questionnaire Depression Scale; GAD-7: 7-item Generalized Anxiety Disorder Scale.

\n
", + "
\nTable 3:
Means, SDs and effect sizes (Cohen’s d) for measures of emotional processing and mindfulness skills.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Mean (SD)Effect size Cohen’s d (95% CI)Linear mixed models
Measure and groupPre-treatmentPost-treatment7-month
follow-up
Between-group,
post-treatment
Within-group
pre-post-treatment
Within-group
pre-7-month follow-up
Effect\n p\n
\n EPS-25\n Group.50
Treatment group
(n = 50)
5.00 (1.03)2.86 (1.48)2.84 (1.65)0.82 (0.41–1.23)1.67 (1.13–2.21)1.51 (1.00–2.01)Time < .001
Control group
(n = 50)
4.93 (1.01)4.17 (1.73)0.50 (0.22–0.77)G × T < .001
\n FFMQ\n Group.15
Treatment group
(n = 50)
76.70 (10.9)88.00 (12.0)88.98 (13.3)0.65 (0.25–1.05)0.98 (0.65–1.31)0.99 (0.59–1.39)Time < .001
Control group
(n = 50)
77.18 (14.1)78.44 (17.1)0.08 (−0.11–0.27)G × T < .001
\n\n
\n

Notes:

\n

The confidence intervals were calculated using the standard error and an alpha level of 0.05. A confidence interval that do not overlap zero indicates a significance of p < .05. p values are given for linear mixed models using data from pre-treatment and post-treatment and all individuals (N = 100). The p value associated with the main effect of group denotes significance of average difference between groups at the pre-treatment assessment. The p value associated with the effect of time denotes the significance of average change over all assessment periods across treatment. The p value associated with the effect of G × T (group × time) denotes significance of difference between the treatment group and the control group in change over all assessment periods. Effect sizes are calculated as standardized mean differences. EPS-25: Emotional Processing Scale; FFMQ: Five Facets of Mindfulness Questionnaire.

\n
", + "
\nTable 4:
Frequency data of DSM-IV diagnoses.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Treatment groupControl group
DiagnosisPre-treatmentPost-treatment7-month follow-upPre-treatmentPost-treatment
DEP35 (70%)5 (10%)6 (12%)37 (74%)16 (32%)
GAD23 (46%)13 (26%)10 (20%)26 (52%)18 (36%)
SP19 (38%)10 (20%)9 (18%)17 (34%)13 (26%)
PD11 (22%)5 (10%)6 (12%)9 (18%)5 (10%)
\n Number of diagnoses\n
04 (8%)28 (56%)31 (62%)0 (0%)18 (36%)
116 (32%)13 (26%)8 (16%)23 (46%)18 (36%)
219 (38%)7 (14%)10 (20%)16 (32%)9 (18%)
310 (20%)2 (4%)1 (2%)10 (20%)4 (8%)
41 (2%)0 (0%)0 (0%)1 (2%)1 (2%)
Total number of diagnoses8833318949
\n\n
\n

Notes:

\n

The four participants with zero diagnoses listed at pre-treatment fulfilled DSM-IV criteria for depression and anxiety, not otherwise specified. DEP, GAD, SP, PD: Diagnoses of major depression, generalized anxiety disorder, social phobia and panic disorder.

\n
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Introduction

\n

Until the recent discoveries from the Jehol Group (Zhou & Zhang, 2007; Chiappe, 2007; O’Connor, Chiappe & Bell, 2011; Zhou, Zhou & O’Connor, 2012) and other Early Cretaceous sites (You et al., 2006) in northern China, the morphological and taxonomical diversity of the basal Ornithuromorpha—which advanced members include all living birds—remained one of the most poorly understood chapters of avian evolutionary history. The global record of these Cretaceous birds was sparse and limited to either incompletely known taxa such as Ambiortus dementjevi (Kurochkin, 1982), Vorona berivotrensis (Forster et al., 1996), or Ichthyornis dispar (Marsh, 1880; Clarke, 2004), or highly specialized forms such as the flightless Patagopteryx deferrariisi (Alvarenga & Bonaparte, 1992; Chiappe, 2002) and the foot-propelled diving hesperornithiforms (Marsh, 1880; Martin & Tate, 1976). The abundant discoveries from the Early Cretaceous Jehol Group of northern China have resulted in the recognition of a diversity of basal ornithuromorph taxa (e.g., Yanornis martini, Yixianornis grabaui, Gansus yumenensis, Hongshanornis longicresta, Archaeorhynchus spathula, Longicrusavis houi, Parahongshanornis chaoyangensis, Jianchangornis microdonta, Schizooura lii, Piscivoravis lii) (Zhou & Zhang, 2001; Zhou & Zhang, 2005; Zhou & Zhang, 2006; Clarke, Zhou & Zhang, 2006; You et al., 2006; Zhou, Zhang & Li, 2009; O’Connor, Gao & Chiappe, 2010; Li et al., 2010; Zhou, Zhou & O’Connor, 2012; Zhou, Zhou & O’Connor, 2013a), which are known by nearly complete specimens (albeit for the most part preserved bi-dimensionally) and in some instances by multiple specimens (e.g., Yanornis martini, Gansus yumenensis, Archaeorhynchus spathula). These specimens have significantly helped to refine our understanding of basal ornithuromorph morphology but despite these recent advances, specimens of these birds remain relatively rare, the vast majority of the Chinese Early Cretaceous birds belong to more primitive groups such as Enantiornithes and basal pygostylians (e.g., Confuciusornithidae, Sapeornithidae).

\n

Among the newly unearthed avifauna of Chinese basal ornithuromorphs are the hongshanornithids, which are particularly noticeable because of their small size (Table 1) and because they are the only lineage of basal ornithuromorphs known from both the Yixian and Jiufotang formations of the Jehol Group. Originally recognized by the discovery of the holotype of Hongshanornis longicresta (Zhou & Zhang, 2005), subsequent discoveries have added the closely related species Longicrusavis houi (O’Connor, Gao & Chiappe, 2010) and Parahongshanornis chaoyangensis (Li, Zhou & Clarke, 2011). To date, while two additional specimens of Hongshanornis longicresta have been recognized in the literature (Li, Zhou & Clarke, 2011; Zheng et al., 2011), the published anatomical information on this taxon is still limited to the preliminary description of the holotype, which skeleton is entirely preserved as voids on two slabs (Zhou & Zhang, 2005). Here we provide a detailed description of the anatomy of another specimen of Hongshanornis longicresta, DNHM D2945/6 (Figs. 14), which preservation provides critical evidence for understanding better the morphology and function of these birds. Furthermore, despite the new discoveries of basal ornithuromorphs, the integument of these birds has remained poorly known in comparison to other basal avians from the Jehol Biota, in particular what refers to the rectricial morphology (Zhou, Zhou & O’Connor, 2012). The complete wing and tail surfaces of DNHM D2945/6, which arguably boasts one of the best-preserved fan-shaped tails from the Mesozoic, reveals important new information about the integumentary evolution and flight capabilities of basal ornithuromorphs.

\n
\nTable 1:
Comparisons of selective measurements in hongshanornithids.
\nThe values highlight the similar sizes and proportions of the three named species of hongshanornithids: Hongshanornis longicresta (DNHM D2945/6 and IVPP V14533), Parahongshanornis chaoyangensis (PMOL-AB00161), and Longicrusavis houi (PKUP 1069).\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
ElementDNHM D2945/6IVPP V14533PMOL-AB00161PKUP 1069
Skull30.530.7
Humerus24.626.029.026.0
Ulna24.524.027.025.0
Carpometacarpus13.013.012.313.1
Manual digit II18.117.7
Femur22.022.024.024.3
Tibiotarsus35.538.038.037.6
Tarsometatarsus20.622.022.021.5
Pedal digit III20.0
\n
\"Photograph
\n

\nFigure 1: Photograph of DNHM D2945.

\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.
\"Interpretive
\n

\nFigure 2: Interpretive drawing of DNHM D2945.

\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pt, proximal tarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.
\"Photograph
\n

\nFigure 3: Photograph of DNHM D2946.

\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.
\"Interpretive
\n

\nFigure 4: Interpretive drawing of DNHM D2946.

\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; st, sternum; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.
" + "

Introduction

\n

Until the recent discoveries from the Jehol Group (Zhou & Zhang, 2007; Chiappe, 2007; O’Connor, Chiappe & Bell, 2011; Zhou, Zhou & O’Connor, 2012) and other Early Cretaceous sites (You et al., 2006) in northern China, the morphological and taxonomical diversity of the basal Ornithuromorpha—which advanced members include all living birds—remained one of the most poorly understood chapters of avian evolutionary history. The global record of these Cretaceous birds was sparse and limited to either incompletely known taxa such as Ambiortus dementjevi (Kurochkin, 1982), Vorona berivotrensis (Forster et al., 1996), or Ichthyornis dispar (Marsh, 1880; Clarke, 2004), or highly specialized forms such as the flightless Patagopteryx deferrariisi (Alvarenga & Bonaparte, 1992; Chiappe, 2002) and the foot-propelled diving hesperornithiforms (Marsh, 1880; Martin & Tate, 1976). The abundant discoveries from the Early Cretaceous Jehol Group of northern China have resulted in the recognition of a diversity of basal ornithuromorph taxa (e.g., Yanornis martini, Yixianornis grabaui, Gansus yumenensis, Hongshanornis longicresta, Archaeorhynchus spathula, Longicrusavis houi, Parahongshanornis chaoyangensis, Jianchangornis microdonta, Schizooura lii, Piscivoravis lii) (Zhou & Zhang, 2001; Zhou & Zhang, 2005; Zhou & Zhang, 2006; Clarke, Zhou & Zhang, 2006; You et al., 2006; Zhou, Zhang & Li, 2009; O’Connor, Gao & Chiappe, 2010; Li et al., 2010; Zhou, Zhou & O’Connor, 2012; Zhou, Zhou & O’Connor, 2013a), which are known by nearly complete specimens (albeit for the most part preserved bi-dimensionally) and in some instances by multiple specimens (e.g., Yanornis martini, Gansus yumenensis, Archaeorhynchus spathula). These specimens have significantly helped to refine our understanding of basal ornithuromorph morphology but despite these recent advances, specimens of these birds remain relatively rare, the vast majority of the Chinese Early Cretaceous birds belong to more primitive groups such as Enantiornithes and basal pygostylians (e.g., Confuciusornithidae, Sapeornithidae).

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Among the newly unearthed avifauna of Chinese basal ornithuromorphs are the hongshanornithids, which are particularly noticeable because of their small size (Table 1) and because they are the only lineage of basal ornithuromorphs known from both the Yixian and Jiufotang formations of the Jehol Group. Originally recognized by the discovery of the holotype of Hongshanornis longicresta (Zhou & Zhang, 2005), subsequent discoveries have added the closely related species Longicrusavis houi (O’Connor, Gao & Chiappe, 2010) and Parahongshanornis chaoyangensis (Li, Zhou & Clarke, 2011). To date, while two additional specimens of Hongshanornis longicresta have been recognized in the literature (Li, Zhou & Clarke, 2011; Zheng et al., 2011), the published anatomical information on this taxon is still limited to the preliminary description of the holotype, which skeleton is entirely preserved as voids on two slabs (Zhou & Zhang, 2005). Here we provide a detailed description of the anatomy of another specimen of Hongshanornis longicresta, DNHM D2945/6 (Figs. 14), which preservation provides critical evidence for understanding better the morphology and function of these birds. Furthermore, despite the new discoveries of basal ornithuromorphs, the integument of these birds has remained poorly known in comparison to other basal avians from the Jehol Biota, in particular what refers to the rectricial morphology (Zhou, Zhou & O’Connor, 2012). The complete wing and tail surfaces of DNHM D2945/6, which arguably boasts one of the best-preserved fan-shaped tails from the Mesozoic, reveals important new information about the integumentary evolution and flight capabilities of basal ornithuromorphs.

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\nTable 1:
Comparisons of selective measurements in hongshanornithids.
\nThe values highlight the similar sizes and proportions of the three named species of hongshanornithids: Hongshanornis longicresta (DNHM D2945/6 and IVPP V14533), Parahongshanornis chaoyangensis (PMOL-AB00161), and Longicrusavis houi (PKUP 1069).\n
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\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
ElementDNHM D2945/6IVPP V14533PMOL-AB00161PKUP 1069
Skull30.530.7
Humerus24.626.029.026.0
Ulna24.524.027.025.0
Carpometacarpus13.013.012.313.1
Manual digit II18.117.7
Femur22.022.024.024.3
Tibiotarsus35.538.038.037.6
Tarsometatarsus20.622.022.021.5
Pedal digit III20.0
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\nFigure 1: Photograph of DNHM D2945.

\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.
\"Interpretive
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\nFigure 2: Interpretive drawing of DNHM D2945.

\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pt, proximal tarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.
\"Photograph
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\nFigure 3: Photograph of DNHM D2946.

\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.
\"Interpretive
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\nFigure 4: Interpretive drawing of DNHM D2946.

\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; st, sternum; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.
" ] }, "methods_html": { @@ -393,12 +393,12 @@ }, "results_html": { "value": [ - "

Results

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Description

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In this description we primarily highlight morphological information from the new specimen (DNHM D2945/6) that either supplements or contradicts the description of the holotype (Zhou & Zhang, 2005). Anatomical nomenclature mainly follows Baumel & Witmer (1993); certain structures not cited therein follow Howard (1929). While the Latin terminology used by Baumel & Witmer (1993) is retained for muscles and ligaments, osteological structures are described using the English equivalents of the Latin terms.

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The entire skeleton of DNHM D2945/6 is preserved and visible in two slabs; the bones are broken between the two, leaving clear voids. DNHM D2945 preserves the bones of the skull, most of the axial skeleton, right radius, major digit and tibiotarsus, and both feet (Figs. 1 and 2). DNHM D2946 preserves most of the bones of the wings and thoracic girdle, both femora, the left tibiotarsus, and the distal ends of the pubes (Figs. 3 and 4).

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Skull

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The skull is rather poorly preserved, embedded in a well-indurated rusty concretion; the shape of the skull is well preserved, but few anatomical details can be discerned (Fig. 5). As in the holotype, the skull constricts abruptly into a low and pointed rostrum, different from the more robust rostrum of Longicrusavis houi (O’Connor, Gao & Chiappe, 2010). Impressions of five teeth can be clearly identified in the maxilla (Fig. 5), contradicting the previous description of Hongshanornis longicresta as edentulous (Zhou & Zhang, 2005; Zheng et al., 2011). Teeth were suggested for hongshanornithids on the basis of structures that appeared to be alveoli preserved in the upper jaw of Longicrusavis houi (O’Connor, Gao & Chiappe, 2010). The presence of teeth in the premaxilla, however, cannot be determined in DNHM D2945. There are no obvious pits or scaring on the maxilla or premaxilla to indicate that a beak was present, as in the edentulous Archaeorhynchus spathula (Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2013b).

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\nFigure 5: Close up photograph of the skull of DNHM D2945 in right lateral view and detail (inset) of the central portion of its maxilla.
\nAbbreviations: al, alveoli.

The mandibular symphysial ossification (predentary bone of Zhou & Martin, 2011) is visible as a void in DNHM D2945. The fragmentary remains of two to four teeth are preserved set in the dentary. This confirms the presence of teeth in the dentary of hongshanornithids, which was hypothesized by O’Connor, Gao & Chiappe (2010). Crowns cannot be discerned, but the dentary teeth appear to be smaller than those preserved in the maxilla. The dentary is caudally unforked and unfused to the surangular, as in other basal ornithuromorphs.

Axial skeleton

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The cervical vertebrae are poorly preserved, revealing little more than the remnants of low neural spines. The anterior dorsal vertebrae (visible in ventral view in DNHM D2945) bear compressed centra lacking ventral processes; the posterior dorsals have thicker centra. The articulations are amphyplatan or amphicoelic and the elements are not fused in a notarium. The lateral surfaces of the dorsal vertebrae are excavated by a broad fossa, as in other basal ornithuromorphs (e.g., Yanornis martini, Longicrusavis houi).

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The synsacrum is incomplete and broken between the two slabs (dorsally exposed in DNHM D2946 and ventrally exposed in DNHM D2945) (Figs. 14). A number of well-differentiated costal processes project from the side of the synsacrum—these processes have expanded distal ends for their attachment to the ilium. Judging by the number of costal processes articulated to the ilium, the synsacrum was composed of no less than nine vertebrae (the synsacral count cannot be determined in either the holotype of Hongshanornis longicresta or Longicrusavis houi), which is comparable to other basal ornithuromorphs and more than is typical of the more primitive enantiornithines (Chiappe, 1996). The ventral surface of the synsacrum (anterior half preserved in DNHM D2945) is smooth, lacking a distinct groove (e.g., Archaeorhynchus spathula, Patagopteryx deferrariisi). Dorsally, the portion of synsacrum preserved in slab DNHM D2946—corresponding largely to the postacetabular portion—is longitudinally scarred by a pair of shallow grooves.

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At least four uncinate processes can be discerned, including one that is completely preserved (DNHM D2946). These ossifications are long (extending across two ribs) with broad bases and tapered outlines (Fig. 6). The uncinate processes appear not to be fused to the ribs, as in the holotype. Several ventral ribs are preserved in articulation with the sternum (DNHM D2946). The proximal ends of the thoracic ribs are very robust, the expanded proximal portion abruptly narrows towards the much thinner shaft (Fig. 6).

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\nFigure 6: Photograph (A) and interpretive drawing (B) of the thoracic girdle and vertebral series, rib cage, and humeri of DNHM D2946.
\nAbbreviations: co, coracoid; fu, furcula; hu, humerus; lt, lateral trabecular; ra, radius; rb, ribs; sc, scapula; sp, supracondylar process; st, sternum; up, uncinate process.

Appendicular skeleton

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The furcula is delicate and U-shaped as in many other basal ornithuromorpha (e.g., Clarke, Zhou & Zhang, 2006; You et al., 2006; Zhou, Zhang & Li, 2009; Zhou, Zhou & O’Connor, 2013b). The interclavicular angle is estimated to be approximately 45°(Fig. 6). The rami are transversely compressed proximally, becoming more dorsoventrally compressed and wider towards the symphysis. The caudal surface of the bone exhibits a distinct trough running along the distal half of the rami and converging towards the symphysial region. The proximal compression and caudal groove of the furcula of DNHM D2946 are comparable to that reported by Li, Wang & Hou (2011) as diagnostic characters of Parahongshanornis chaoyangensis. The presence of these conditions in DNHM D2946 indicates that such characters are unlikely to be diagnostic of the latter taxon. A cross section of the furcula in slab DNHM D2945 indicates the bone may have been hollow. No long hypocleidium like that reported in the holotype of Hongshanornis longicresta (IVPP V14533) is visible but the symphysial region of DNHM D2945/46 is covered by the distal portion of the left coracoid, thus making it unclear if a hypocleidium was present or not. The similarity between the furcula of DNHM D2945/46 and that of Longicrusavis houi and Parahongshanornis chaoyangensis, taxa lacking a long hypocleidium and possessing only a small tubercle at the symphysis (O’Connor, Gao & Chiappe, 2010; Li, Wang & Hou, 2011), suggests that the furcula of hongshanornithids possibly lacked a well-developed hypocleidium.

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The sternum, primarily preserved in DNHM D2946 in dorsal view, has a slightly rounded cranial margin (Fig. 6). Distally on the left side of the sternum, a bony bar with a terminal expansion is preserved. Damage makes it difficult to interpret this region of the sternum. One alternative is that this bar corresponds to a slightly displaced, lateral trabecula with an expanded distal end; the lateral trabecula of the sternum of various basal ornithuromorphs (e.g., Archaeorhynchus spathula, Jianchangornis microdonta, Yixianornis grabaui, Yanornis martini) is distally expanded in varying degrees (Zhou, Zhou & O’Connor, 2013b). Alternatively, it may represent the lateral margin of a sternal fenestra, such as those present in the basal ornithuromorphs Songlingornis linghensis, Yixianornis grabaui, and Yanornis martini (Clarke, Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2013b), a feature apparently absent in the sternum of the holotype of Hongshanornis longicresta. Zhou & Zhang (2005) described the sternum of the latter with lateral processes lacking a distal expansion; however the sternum of this specimen is too poorly preserved to confidently support the absence of such expansion.

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The strut-like coracoids articulate adjacent to each other on the cranial margin of the sternum, nearly touching each other if not slightly overlapping (Fig. 6). There is a depression (possibly corresponding to the impression of the m. sternocoracoidei of modern birds) on the dorsal surface of the sternal half of these bones (also present in Jehol ornithuromorphs such Jianchangornis microdonta and Yixianornis grabaui). This feature in ornithuromorphs is not as pronounced as the dorsal fossa that excavates the coracoids of many Late Cretaceous enantiornithines (Chiappe & Walker, 2002). The proximal ends of the coracoids are poorly preserved so that a procoracoid process cannot be identified—the presence of this process in Hongshanornis longicresta is not as clear as was suggested by Zhou & Zhang (2005) and remains equivocal in this taxon. However, a procoracoid process is known in almost every other Early Cretaceous ornithuromorph (e.g., Jianchangornis microdonta, Yixianornis grabaui, Yanornis martini, Gansus yumenensis) (Zhou & Zhang, 2001; Clarke, Zhou & Zhang, 2006; You et al., 2006; Zhou, Zhou & O’Connor, 2012). The body of the coracoid exhibits no evidence of either a supracoracoid nerve foramen or medial notch (incisura n. supracoracoidei). Both the lateral and medial borders of this bone are clearly concave, indicating that the convex lateral margin described by Zhou & Zhang (2005) for the poorly preserved holotype is incorrect. A lateral process is present; its squared off morphology is consistent with that of other Early Cretaceous ornithuromorphs (e.g., Ambiortus dementjevi, Yixianornis grabaui, Gansus yumenensis) (Clarke, Zhou & Zhang, 2006; Kurochkin, 1982; You et al., 2006).

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Both humeri are exposed in caudal view in DNHM D2946 (Fig. 6). The head is prominent—largely projected caudally—and proximally flat. Such design is more reminiscent to that of the humeral head of Patagopteryx deferrariisi and other basal ornithuromorphs (i.e., Archaeorhynchus spathula, Jianchangornis microdonta) and it differs from the domed-head of modern birds (Chiappe, 2002). The proximal third of the humerus appears to be very broad, expanded as in the holotype of Hongshanornis longicresta, Ichthyornis dispar and Ambiortus dementjevi (Kurochkin, 1985; Clarke, 2004) (Fig. 6). The caudal surface is not perforated by a pneumotricipital foramen and the pneumotricipital fossa is minimally developed. A distinct furrow—presumably the capital incisure—separates the ventral margin of the head from the ventral tubercle. Ventral to the latter, on the ventroproximal corner (and the bicipital area) of the bone, there is a shallow circular depression also present in Ichthyornis dispar, possibly corresponding to the attachment site of the m. pectoralis superficialis (Clarke, 2004). The deltopectoral crest is large—extending longitudinally for more than 1/3 the length of the bone (Fig. 6)—and rounded, lacking the cranial deflection of more advanced ornithuromorphs (neornithines). Distally, the margin of the crest gradually diminishes along the dorsal border of the shaft, typical of Cretaceous ornithuromorphs (e.g., Jianchangornis microdonta, Yixianornis grabaui, Archaeorhynchus spathula), as opposed to the rapid step-like constriction of this crest in most basal birds (e.g., Confuciusornis sanctus, Sapeornis chaoyangensis, Rapaxavis pani) and some basal ornithuromorphs (e.g., Schizooura lii, Zhongjianornis yangi).

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In caudal view (DNHM D2946) the distal humeri bear no evidence of humerotriciptial or scapulotricipital grooves (Fig. 6). The olecranon fossa is present but poorly developed. A well-developed dorsal supracondylar process is present, clearest on the right humerus (DNHM D2946) as in Longicrusavis houi (O’Connor, Gao & Chiappe, 2010) and Ichthyornis dispar (Clarke, 2004). The flexor process is small and poorly developed; the transversal distal margin is roughly perpendicular from the longitudinal axis of the shaft as in other ornithuromorphs, not angled as in many enantiornithines (Chiappe & Walker, 2002). The cranial surfaces of the humeri are not visible, planted in the matrix.

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The radius is straight and roughly half the width of the ulna. The ulna, comparable in length to that of the humerus (Table 1), is exposed in caudal-dorsal view. Remige papillae are absent. The olecranon process is weakly developed. Distally, the ulna’s dorsal condyle is rounded in caudal view. Near its articulation with the radius, it exhibits a small circular depression that may correspond to the radial depression of living birds (Baumel & Witmer, 1993).

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The radius and ulna are in articulation with the proximal carpals and the carpometacarpus (Fig. 7). The radiale is in articulation with the radius. The left carpometacarpus, exposed dorsally in DNHM D2946, is completely fused, proximally and distally. Close to the contact between the major (II) and alular (I) metacarpals there is a raised area. Both the major (II) and minor (III) metacarpals are straight (Fig. 7). Proximally, there is a small depression on the minor metacarpal. The proximal end of the intermetacarpal space extends proximal to the level of the distal end of the alular metacarpal (Fig. 7). The alular (I) metacarpal is subrectangular. An extensor process is not absent, only minimally developed in such a way that the proximal end of the alular metacarpal is slightly more expanded than its distal end (Fig. 7), as in some other Cretaceous ornithurmorphs (e.g., Jianchangornis microdonta, Gansus yumenensis, Yixianornis grabaui).

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\nFigure 7: Photograph of the left manus of DNHM D2945/6 in ventral (A; DNHM D2945) and dorsal (B; DNHM D2946) views.
\nAbbreviations: mc I-III, metacarpals I-III; p1-I, phalanx 1 (proximal) of digit I (alular digit); p2-I, phalanx 2 (ungual) of digit I (alular digit); p1-II, phalanx 1 (proximal) of digit II (major digit); p2-II, phalanx 2 (intermediate) of digit II (major digit); p3-II, phalanx 3 (ungual) of digit II (major digit); p1-III, phalanx 1 (proximal) of digit III (minor digit); p2-III, phalanx 2 of digit III (minor digit); ra, radius; sl, semilunate carpal; ul, ulna.

The alular digit bears two phalanges. The second phalanx, a claw, extends slightly past the distal end of the major metacarpal, as described by Zhou & Zhang (2005) for the holotype. The major digit has three phalanges; the proximal phalanx is broad bearing a well-developed, sinusoidal lateral flange (Fig. 7). As in the holotype, the intermediate phalanx is S-shaped (Zhou & Zhang, 2005). The claw of the major digit is much smaller than that of the alular digit. The minor digit bears a single, wedge-shaped phalanx that tapers distally; Longicrusavis houi and the Hongshanornis longicresta holotype bear two phalanges on this digit, the second being extremely reduced (and not an ungual) suggesting that this small phalanx is simply not preserved in DNHM D2945/6.

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The ilia are poorly preserved and broken between the two slabs; the left is visible in medial view in DNHM D2945, while portions of the right are preserved in DNHM D2946 in dorsal view. The preacetabular wing has a straight dorsal margin that tapers cranially. The caudal half of the ventral margin of the preacetabular wing defines a broad notch, a condition observed in other Jehol ornithuromorphs (e.g., Archaeorhynchus spathula, Schizooura lii) (Zhou, Zhou & O’Connor, 2012; Zhou, Zhou & O’Connor, 2013b).

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A fragment of the pubis is preserved near the midshaft of the right tibiotarsus in DNHM D2946 (Figs. 14 and 8). The distal ends of both pubes are in contact and only slightly disarticulated. They are not fused but their flat medial surfaces form a short, expanded symphysis, although a distinct ‘boot’, with a prominent caudal projection, like that of some enantiornithines is absent (Chiappe & Walker, 2002) (Fig. 8). The presence of this distal pubic expansion, identical to that present in Parahongshanornis chaoyangensis, indicates that unlike what was claimed by Li, Wang & Hou (2011), this feature is not diagnostic of the latter species. The cross-section of the shaft of the distal portion of the pubis is oval, with the main axis oriented craniocaudally. No pygostyle or caudal vertebrae are preserved in DNHM D2945/6.

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\nFigure 8: Close up photograph of the right knee (medial view) and pubic symphysis (left laterocaudal view) of DNHM D2946.
\nNote the detail of the gastroliths. Abbreviations: fe, femur; fi, fibula; gl, gastroliths, pu, pubis; ti, tibia. (l) and (r) refer to the left and right pubis, respectively.

The elongate hindlimbs are completely preserved in both slabs as partly bone and partly void (Figs. 14). The left femur is preserved in articulation with the left ilium in DNHM D2945—its rounded head is visible through the acetabulum, which is exposed medially. The femoral shaft is only slightly bowed craniocaudally. Its laterodistal end is exposed in DNHM D2946; similar to other Jehol ornithuromorphs (e.g., Yixianornis grabaui), there is minimal development of the fibular trochlea and tibiofibular crest, which are developed in Patagopteryx deferrariisi and ornithurines (Chiappe, 2002; Clarke, 2004).

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The tibiotarsus is more than 150% the length of the femur (tibiotarsus: femur = 1.6) (Table 1). The right element is in articulation with the fibula, which is exposed caudally in DNHM D2946. Proximally, the tibiotarsus exhibits a large, well-developed cnemial crest (Fig. 9). This crest, exposed laterally in DNHM D2946, is limited proximally, and projects proximally beyond the proximal articular surface of the tibiotarsus. Its cranial edge develops into an inflated quadrangular prominence that projects laterally (Fig. 9). The morphology of this crest is comparable to that of other Early Cretaceous ornithuromorphs (e.g., Schizooura lii, Yixianornis grabaui) (Clarke, Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2012). This cranial prominence is separated by a lateral trough from the proximal articular surface of the tibiotarsus. It is not possible to determine whether the tibiotarsus had one or two cnemial crests; if a cranial cnemial crest were present, it would be embedded in sediment and obstructed by the lateral cnemial crest. In caudal view, the proximal fourth of the tibiotarsus is marked by a robust ridge that slants towards the proximomedial corner of the bone—this feature is not present in Longicrusavis houi, further distinguishing this taxon from Hongshanornis longicresta.

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\nFigure 9: Close up photograph of the left knee (lateral view) of DNHM D2946.
\nAbbreviations: cn, cnemial crest; fc, fibular condyle; fe, femur; fi, fibula; ld, lateral articular facet of tibia; md, medial articular facet of tibia; ti, tibia.

Distally, the tibia is largely fused to the distal tarsals, however the suture of an ample ascending process of the astragalus remains visible on both the left (DNHM D2946) and right (DNHM D2945) tibiotarsi. The distal condyles are preserved in cranial view in DNHM D2945. The lateral condyle is larger than the medial condyle, as in other basal ornithuromorphs (Chiappe, 1996; Zhou & Zhang, 2006), and separated by a wide intercondylar groove (incisura intercondylaris). The cranial surface of the distal end is scarred by a deep extensor sulcus, which ends near a raised area just proximal to the intercondylar groove—a supratendinal bridge like that of more advanced ornithurines is not developed. The lateral epicondyle is minimally developed and there is only a slightly developed, crescent-like lateral epicondylar depression. Caudally, neither the lateral nor medial crests of the cartilaginous trochlea of the tibia (trochlea cartilaginous tibialis) are developed. These crests are slightly developed in Yixianornis grabaui and well developed in Apsaravis ukhaana (Norell & Clark, 2001; Clarke, Zhou & Zhang, 2006). The fibula is very slender (Figs. 8 and 9)—its distal end does not seem to extend beyond the midpoint of the tibiotarsus.

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Both tarsometatarsi are well-exposed in cranial view in DNHM D2945. As reported in the holotype of Hongshanornis longicresta (Zhou & Zhang, 2005), metatarsals II–IV are completely fused to one another. The intercotylar prominence is at best minimally developed. The proximal cotyla are slightly concave—the lateral one is slightly more distally placed than the medial one. Metatarsal III is plantarly displaced so that proximally, metatarsal II and metatarsal IV form ridges defining a recess excavating the central portion of the tarsometatarsus. Such morphology is consistent with that of other basal ornithuromorphs (e.g., Yanornis martini, Yixianornis grabaui, Gansus yumenensis, Ichthyornis dispar). Inside this proximocentral recess there is a foramen located between metatarsals III and IV, and medial to it, a tubercle on metatarsal II (possibly corresponding to the m. tibialis cranialis tuberosity of modern birds). Metatarsal III is the longest; metatarsal IV is slightly shorter, followed by the even shorter metatarsal II (Fig. 10). Metatarsal I is robust and fairly straight, with a concave medial margin. A distal vascular foramen is located between metatarsals III and IV as in Longicrusavis houi; the distal margin of the foramen is raised. The foramen seems to penetrate the bone at an oblique angle—from cranial to plantar surfaces. All trochleae appear to be ginglymous.

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\nFigure 10: Close up photograph of the feet and rectrices of DNHM D2945.
\nAbbreviations: mt, metatarsals; re, rectrices; I-IV, digits I-IV.

Digit III is the longest (Table 1); digit II is substantially shorter than IV (Fig. 10). Digit I is short and slender. All the pedal phalanges are long and slender and decrease in length distally. The phalanges of the second and third digits are approximately 2/3 the length of the preceding phalanx. The phalanges of digit IV are subequal, but still slightly decrease in length distally. The ungual phalanges bear distinct flexor tubercles. The morphology of the distal tarsometatarsus and the proportions of the pedal phalanges are consistent with cursorial function (Hopson, 2001), as in other Early Cretaceous ornithuromorphs.

Plumage

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DNHM D2945/6 preserves significant portions of the plumage of the wing, tail, and around the skull and neck. The feathers preserved over the skull question the assumption that this species was characterized by the presence of a feathery crest projecting from the head (Zhou & Zhang, 2005). DNHM D2945/6 shows nothing of that sort. The relatively short feathers of the head become gradually shorter until the plumage ends at the junction of the rostrum and the orbit, thus indicating that the culmen was devoid of feathers (whether it was covered by skin or a corneous beak is unknown). Furthermore, contrary to what was suggested by Zheng et al. (2011) for another specimen putatively identified as Hongshanornis longicresta (STM 35-3), DNHM D2945/6 indicates that these birds had relatively broad, but long and tapered, wings (Figs. 14 and 11).

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\"Interpretive
\n
\nFigure 11: Interpretive drawing of the outline of the wings and feathered tail of DNHM D2945/6 (see Figs. 1 and 3 for the maximum extent of the primaries and secondaries).
\nThe aerodynamic parameters used in this study were derived from this reconstruction (see Materials and Methods).

The most distal primaries are clearly much shorter than the remaining primaries. Based on the well-preserved outline of the wing, our estimation of the wingspan of DNHM D2945/6 is approximately 0.32 m and the wing area is 0.016 m2 (Fig. 11). There is exquisite evidence of rectrices forming a fan-like tail preserved in natural orientation, about the extended feet. Although visualization of individual feathers is difficult due to overlap, the tail appears to be composed of at least 10 vaned rectrices. The precise degree of asymmetry of these feathers cannot be ascertained but it is clear that none of them were strongly asymmetric (Fig. 10). The caudal margin of the feathered tail is rounded and the pair of central rectrices projects distally more than the feathers on either side, thus suggesting a gently graded tail (comparable to the one described for Piscivoravis lii; see Zhou, Zhou & O’Connor, 2013a). The holotype of Hongshanornis longicresta also shows evidence of an extensive feathered tail as a series of partially preserved vaned feathers between the feet (IVPP V14533A); these are very faint and were not described in the original description (see O’Connor, Gao & Chiappe, 2010). In the holotype of Hongshanornis longicresta, the tail is clearly incomplete and only four feathers can be discerned; the tail in DNHM D2945/6 appears complete. The number of preserved feathers is thus greater than the one described in the younger ornithuromorphs Yixianornis grabaui (minimum of eight described) and Piscivoravis lii (at least six described) from the Jiufotang Formation (Clarke, Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2013a).

Gastroliths

\n

At least 11 small geo-gastroliths are clustered in the visceral and pelvic region of DNHM D2945/6. Some of these ‘stomach stones’ are still in place while others are represented by the voids left on the slabs (Figs. 14 and 8). The smallest of the stones is nearly half the size the largest (1.71 mm to 3.08 mm) with the mean being 2.2 mm (Table 2). They range in shape from subspherical to oblong. It is unclear whether gastroliths were preserved with the holotype (IVPP V14533A), although more than 50 small (∼1 mm) geo-gastroliths were reported in the poorly preserved STM 35-3, a specimen identified as of Hongshanornis longicresta by Zheng et al. (2011). Despite the fact that Zheng et al. (2011) did not provide any anatomical evidence supporting the identification of STM 35-5 as Hongshanornis longicresta, the discovery of DNHM D2945/6 provides unquestionable evidence of the behavior of ingesting grit by this basal ornithuromorph species.

\n
\nTable 2:
Measurements (mm) of the gastroliths of DNHM D2945/6.
\nLeft column numbers correspond to numbers on Figs. 2 and 4.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
D2945D2946Mean value
12.212.272.24
23.063.093.08
32.312.072.19
42.052.152.10
52.152.112.13
62.902.592.75
71.841.761.80
81.761.791.78
91.742.081.91
101.841.561.70
112.513.132.82
\n
" + "

Results

\n

Description

\n

In this description we primarily highlight morphological information from the new specimen (DNHM D2945/6) that either supplements or contradicts the description of the holotype (Zhou & Zhang, 2005). Anatomical nomenclature mainly follows Baumel & Witmer (1993); certain structures not cited therein follow Howard (1929). While the Latin terminology used by Baumel & Witmer (1993) is retained for muscles and ligaments, osteological structures are described using the English equivalents of the Latin terms.

\n

The entire skeleton of DNHM D2945/6 is preserved and visible in two slabs; the bones are broken between the two, leaving clear voids. DNHM D2945 preserves the bones of the skull, most of the axial skeleton, right radius, major digit and tibiotarsus, and both feet (Figs. 1 and 2). DNHM D2946 preserves most of the bones of the wings and thoracic girdle, both femora, the left tibiotarsus, and the distal ends of the pubes (Figs. 3 and 4).

\n

Skull

\n

The skull is rather poorly preserved, embedded in a well-indurated rusty concretion; the shape of the skull is well preserved, but few anatomical details can be discerned (Fig. 5). As in the holotype, the skull constricts abruptly into a low and pointed rostrum, different from the more robust rostrum of Longicrusavis houi (O’Connor, Gao & Chiappe, 2010). Impressions of five teeth can be clearly identified in the maxilla (Fig. 5), contradicting the previous description of Hongshanornis longicresta as edentulous (Zhou & Zhang, 2005; Zheng et al., 2011). Teeth were suggested for hongshanornithids on the basis of structures that appeared to be alveoli preserved in the upper jaw of Longicrusavis houi (O’Connor, Gao & Chiappe, 2010). The presence of teeth in the premaxilla, however, cannot be determined in DNHM D2945. There are no obvious pits or scaring on the maxilla or premaxilla to indicate that a beak was present, as in the edentulous Archaeorhynchus spathula (Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2013b).

\n
\"Close
\n
\nFigure 5: Close up photograph of the skull of DNHM D2945 in right lateral view and detail (inset) of the central portion of its maxilla.
\nAbbreviations: al, alveoli.

The mandibular symphysial ossification (predentary bone of Zhou & Martin, 2011) is visible as a void in DNHM D2945. The fragmentary remains of two to four teeth are preserved set in the dentary. This confirms the presence of teeth in the dentary of hongshanornithids, which was hypothesized by O’Connor, Gao & Chiappe (2010). Crowns cannot be discerned, but the dentary teeth appear to be smaller than those preserved in the maxilla. The dentary is caudally unforked and unfused to the surangular, as in other basal ornithuromorphs.

Axial skeleton

\n

The cervical vertebrae are poorly preserved, revealing little more than the remnants of low neural spines. The anterior dorsal vertebrae (visible in ventral view in DNHM D2945) bear compressed centra lacking ventral processes; the posterior dorsals have thicker centra. The articulations are amphyplatan or amphicoelic and the elements are not fused in a notarium. The lateral surfaces of the dorsal vertebrae are excavated by a broad fossa, as in other basal ornithuromorphs (e.g., Yanornis martini, Longicrusavis houi).

\n

The synsacrum is incomplete and broken between the two slabs (dorsally exposed in DNHM D2946 and ventrally exposed in DNHM D2945) (Figs. 14). A number of well-differentiated costal processes project from the side of the synsacrum—these processes have expanded distal ends for their attachment to the ilium. Judging by the number of costal processes articulated to the ilium, the synsacrum was composed of no less than nine vertebrae (the synsacral count cannot be determined in either the holotype of Hongshanornis longicresta or Longicrusavis houi), which is comparable to other basal ornithuromorphs and more than is typical of the more primitive enantiornithines (Chiappe, 1996). The ventral surface of the synsacrum (anterior half preserved in DNHM D2945) is smooth, lacking a distinct groove (e.g., Archaeorhynchus spathula, Patagopteryx deferrariisi). Dorsally, the portion of synsacrum preserved in slab DNHM D2946—corresponding largely to the postacetabular portion—is longitudinally scarred by a pair of shallow grooves.

\n

At least four uncinate processes can be discerned, including one that is completely preserved (DNHM D2946). These ossifications are long (extending across two ribs) with broad bases and tapered outlines (Fig. 6). The uncinate processes appear not to be fused to the ribs, as in the holotype. Several ventral ribs are preserved in articulation with the sternum (DNHM D2946). The proximal ends of the thoracic ribs are very robust, the expanded proximal portion abruptly narrows towards the much thinner shaft (Fig. 6).

\n
\"Photograph
\n
\nFigure 6: Photograph (A) and interpretive drawing (B) of the thoracic girdle and vertebral series, rib cage, and humeri of DNHM D2946.
\nAbbreviations: co, coracoid; fu, furcula; hu, humerus; lt, lateral trabecular; ra, radius; rb, ribs; sc, scapula; sp, supracondylar process; st, sternum; up, uncinate process.

Appendicular skeleton

\n

The furcula is delicate and U-shaped as in many other basal ornithuromorpha (e.g., Clarke, Zhou & Zhang, 2006; You et al., 2006; Zhou, Zhang & Li, 2009; Zhou, Zhou & O’Connor, 2013b). The interclavicular angle is estimated to be approximately 45°(Fig. 6). The rami are transversely compressed proximally, becoming more dorsoventrally compressed and wider towards the symphysis. The caudal surface of the bone exhibits a distinct trough running along the distal half of the rami and converging towards the symphysial region. The proximal compression and caudal groove of the furcula of DNHM D2946 are comparable to that reported by Li, Wang & Hou (2011) as diagnostic characters of Parahongshanornis chaoyangensis. The presence of these conditions in DNHM D2946 indicates that such characters are unlikely to be diagnostic of the latter taxon. A cross section of the furcula in slab DNHM D2945 indicates the bone may have been hollow. No long hypocleidium like that reported in the holotype of Hongshanornis longicresta (IVPP V14533) is visible but the symphysial region of DNHM D2945/46 is covered by the distal portion of the left coracoid, thus making it unclear if a hypocleidium was present or not. The similarity between the furcula of DNHM D2945/46 and that of Longicrusavis houi and Parahongshanornis chaoyangensis, taxa lacking a long hypocleidium and possessing only a small tubercle at the symphysis (O’Connor, Gao & Chiappe, 2010; Li, Wang & Hou, 2011), suggests that the furcula of hongshanornithids possibly lacked a well-developed hypocleidium.

\n

The sternum, primarily preserved in DNHM D2946 in dorsal view, has a slightly rounded cranial margin (Fig. 6). Distally on the left side of the sternum, a bony bar with a terminal expansion is preserved. Damage makes it difficult to interpret this region of the sternum. One alternative is that this bar corresponds to a slightly displaced, lateral trabecula with an expanded distal end; the lateral trabecula of the sternum of various basal ornithuromorphs (e.g., Archaeorhynchus spathula, Jianchangornis microdonta, Yixianornis grabaui, Yanornis martini) is distally expanded in varying degrees (Zhou, Zhou & O’Connor, 2013b). Alternatively, it may represent the lateral margin of a sternal fenestra, such as those present in the basal ornithuromorphs Songlingornis linghensis, Yixianornis grabaui, and Yanornis martini (Clarke, Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2013b), a feature apparently absent in the sternum of the holotype of Hongshanornis longicresta. Zhou & Zhang (2005) described the sternum of the latter with lateral processes lacking a distal expansion; however the sternum of this specimen is too poorly preserved to confidently support the absence of such expansion.

\n

The strut-like coracoids articulate adjacent to each other on the cranial margin of the sternum, nearly touching each other if not slightly overlapping (Fig. 6). There is a depression (possibly corresponding to the impression of the m. sternocoracoidei of modern birds) on the dorsal surface of the sternal half of these bones (also present in Jehol ornithuromorphs such Jianchangornis microdonta and Yixianornis grabaui). This feature in ornithuromorphs is not as pronounced as the dorsal fossa that excavates the coracoids of many Late Cretaceous enantiornithines (Chiappe & Walker, 2002). The proximal ends of the coracoids are poorly preserved so that a procoracoid process cannot be identified—the presence of this process in Hongshanornis longicresta is not as clear as was suggested by Zhou & Zhang (2005) and remains equivocal in this taxon. However, a procoracoid process is known in almost every other Early Cretaceous ornithuromorph (e.g., Jianchangornis microdonta, Yixianornis grabaui, Yanornis martini, Gansus yumenensis) (Zhou & Zhang, 2001; Clarke, Zhou & Zhang, 2006; You et al., 2006; Zhou, Zhou & O’Connor, 2012). The body of the coracoid exhibits no evidence of either a supracoracoid nerve foramen or medial notch (incisura n. supracoracoidei). Both the lateral and medial borders of this bone are clearly concave, indicating that the convex lateral margin described by Zhou & Zhang (2005) for the poorly preserved holotype is incorrect. A lateral process is present; its squared off morphology is consistent with that of other Early Cretaceous ornithuromorphs (e.g., Ambiortus dementjevi, Yixianornis grabaui, Gansus yumenensis) (Clarke, Zhou & Zhang, 2006; Kurochkin, 1982; You et al., 2006).

\n

Both humeri are exposed in caudal view in DNHM D2946 (Fig. 6). The head is prominent—largely projected caudally—and proximally flat. Such design is more reminiscent to that of the humeral head of Patagopteryx deferrariisi and other basal ornithuromorphs (i.e., Archaeorhynchus spathula, Jianchangornis microdonta) and it differs from the domed-head of modern birds (Chiappe, 2002). The proximal third of the humerus appears to be very broad, expanded as in the holotype of Hongshanornis longicresta, Ichthyornis dispar and Ambiortus dementjevi (Kurochkin, 1985; Clarke, 2004) (Fig. 6). The caudal surface is not perforated by a pneumotricipital foramen and the pneumotricipital fossa is minimally developed. A distinct furrow—presumably the capital incisure—separates the ventral margin of the head from the ventral tubercle. Ventral to the latter, on the ventroproximal corner (and the bicipital area) of the bone, there is a shallow circular depression also present in Ichthyornis dispar, possibly corresponding to the attachment site of the m. pectoralis superficialis (Clarke, 2004). The deltopectoral crest is large—extending longitudinally for more than 1/3 the length of the bone (Fig. 6)—and rounded, lacking the cranial deflection of more advanced ornithuromorphs (neornithines). Distally, the margin of the crest gradually diminishes along the dorsal border of the shaft, typical of Cretaceous ornithuromorphs (e.g., Jianchangornis microdonta, Yixianornis grabaui, Archaeorhynchus spathula), as opposed to the rapid step-like constriction of this crest in most basal birds (e.g., Confuciusornis sanctus, Sapeornis chaoyangensis, Rapaxavis pani) and some basal ornithuromorphs (e.g., Schizooura lii, Zhongjianornis yangi).

\n

In caudal view (DNHM D2946) the distal humeri bear no evidence of humerotriciptial or scapulotricipital grooves (Fig. 6). The olecranon fossa is present but poorly developed. A well-developed dorsal supracondylar process is present, clearest on the right humerus (DNHM D2946) as in Longicrusavis houi (O’Connor, Gao & Chiappe, 2010) and Ichthyornis dispar (Clarke, 2004). The flexor process is small and poorly developed; the transversal distal margin is roughly perpendicular from the longitudinal axis of the shaft as in other ornithuromorphs, not angled as in many enantiornithines (Chiappe & Walker, 2002). The cranial surfaces of the humeri are not visible, planted in the matrix.

\n

The radius is straight and roughly half the width of the ulna. The ulna, comparable in length to that of the humerus (Table 1), is exposed in caudal-dorsal view. Remige papillae are absent. The olecranon process is weakly developed. Distally, the ulna’s dorsal condyle is rounded in caudal view. Near its articulation with the radius, it exhibits a small circular depression that may correspond to the radial depression of living birds (Baumel & Witmer, 1993).

\n

The radius and ulna are in articulation with the proximal carpals and the carpometacarpus (Fig. 7). The radiale is in articulation with the radius. The left carpometacarpus, exposed dorsally in DNHM D2946, is completely fused, proximally and distally. Close to the contact between the major (II) and alular (I) metacarpals there is a raised area. Both the major (II) and minor (III) metacarpals are straight (Fig. 7). Proximally, there is a small depression on the minor metacarpal. The proximal end of the intermetacarpal space extends proximal to the level of the distal end of the alular metacarpal (Fig. 7). The alular (I) metacarpal is subrectangular. An extensor process is not absent, only minimally developed in such a way that the proximal end of the alular metacarpal is slightly more expanded than its distal end (Fig. 7), as in some other Cretaceous ornithurmorphs (e.g., Jianchangornis microdonta, Gansus yumenensis, Yixianornis grabaui).

\n
\"Photograph
\n
\nFigure 7: Photograph of the left manus of DNHM D2945/6 in ventral (A; DNHM D2945) and dorsal (B; DNHM D2946) views.
\nAbbreviations: mc I-III, metacarpals I-III; p1-I, phalanx 1 (proximal) of digit I (alular digit); p2-I, phalanx 2 (ungual) of digit I (alular digit); p1-II, phalanx 1 (proximal) of digit II (major digit); p2-II, phalanx 2 (intermediate) of digit II (major digit); p3-II, phalanx 3 (ungual) of digit II (major digit); p1-III, phalanx 1 (proximal) of digit III (minor digit); p2-III, phalanx 2 of digit III (minor digit); ra, radius; sl, semilunate carpal; ul, ulna.

The alular digit bears two phalanges. The second phalanx, a claw, extends slightly past the distal end of the major metacarpal, as described by Zhou & Zhang (2005) for the holotype. The major digit has three phalanges; the proximal phalanx is broad bearing a well-developed, sinusoidal lateral flange (Fig. 7). As in the holotype, the intermediate phalanx is S-shaped (Zhou & Zhang, 2005). The claw of the major digit is much smaller than that of the alular digit. The minor digit bears a single, wedge-shaped phalanx that tapers distally; Longicrusavis houi and the Hongshanornis longicresta holotype bear two phalanges on this digit, the second being extremely reduced (and not an ungual) suggesting that this small phalanx is simply not preserved in DNHM D2945/6.

\n

The ilia are poorly preserved and broken between the two slabs; the left is visible in medial view in DNHM D2945, while portions of the right are preserved in DNHM D2946 in dorsal view. The preacetabular wing has a straight dorsal margin that tapers cranially. The caudal half of the ventral margin of the preacetabular wing defines a broad notch, a condition observed in other Jehol ornithuromorphs (e.g., Archaeorhynchus spathula, Schizooura lii) (Zhou, Zhou & O’Connor, 2012; Zhou, Zhou & O’Connor, 2013b).

\n

A fragment of the pubis is preserved near the midshaft of the right tibiotarsus in DNHM D2946 (Figs. 14 and 8). The distal ends of both pubes are in contact and only slightly disarticulated. They are not fused but their flat medial surfaces form a short, expanded symphysis, although a distinct ‘boot’, with a prominent caudal projection, like that of some enantiornithines is absent (Chiappe & Walker, 2002) (Fig. 8). The presence of this distal pubic expansion, identical to that present in Parahongshanornis chaoyangensis, indicates that unlike what was claimed by Li, Wang & Hou (2011), this feature is not diagnostic of the latter species. The cross-section of the shaft of the distal portion of the pubis is oval, with the main axis oriented craniocaudally. No pygostyle or caudal vertebrae are preserved in DNHM D2945/6.

\n
\"Close
\n
\nFigure 8: Close up photograph of the right knee (medial view) and pubic symphysis (left laterocaudal view) of DNHM D2946.
\nNote the detail of the gastroliths. Abbreviations: fe, femur; fi, fibula; gl, gastroliths, pu, pubis; ti, tibia. (l) and (r) refer to the left and right pubis, respectively.

The elongate hindlimbs are completely preserved in both slabs as partly bone and partly void (Figs. 14). The left femur is preserved in articulation with the left ilium in DNHM D2945—its rounded head is visible through the acetabulum, which is exposed medially. The femoral shaft is only slightly bowed craniocaudally. Its laterodistal end is exposed in DNHM D2946; similar to other Jehol ornithuromorphs (e.g., Yixianornis grabaui), there is minimal development of the fibular trochlea and tibiofibular crest, which are developed in Patagopteryx deferrariisi and ornithurines (Chiappe, 2002; Clarke, 2004).

\n

The tibiotarsus is more than 150% the length of the femur (tibiotarsus: femur = 1.6) (Table 1). The right element is in articulation with the fibula, which is exposed caudally in DNHM D2946. Proximally, the tibiotarsus exhibits a large, well-developed cnemial crest (Fig. 9). This crest, exposed laterally in DNHM D2946, is limited proximally, and projects proximally beyond the proximal articular surface of the tibiotarsus. Its cranial edge develops into an inflated quadrangular prominence that projects laterally (Fig. 9). The morphology of this crest is comparable to that of other Early Cretaceous ornithuromorphs (e.g., Schizooura lii, Yixianornis grabaui) (Clarke, Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2012). This cranial prominence is separated by a lateral trough from the proximal articular surface of the tibiotarsus. It is not possible to determine whether the tibiotarsus had one or two cnemial crests; if a cranial cnemial crest were present, it would be embedded in sediment and obstructed by the lateral cnemial crest. In caudal view, the proximal fourth of the tibiotarsus is marked by a robust ridge that slants towards the proximomedial corner of the bone—this feature is not present in Longicrusavis houi, further distinguishing this taxon from Hongshanornis longicresta.

\n
\"Close
\n
\nFigure 9: Close up photograph of the left knee (lateral view) of DNHM D2946.
\nAbbreviations: cn, cnemial crest; fc, fibular condyle; fe, femur; fi, fibula; ld, lateral articular facet of tibia; md, medial articular facet of tibia; ti, tibia.

Distally, the tibia is largely fused to the distal tarsals, however the suture of an ample ascending process of the astragalus remains visible on both the left (DNHM D2946) and right (DNHM D2945) tibiotarsi. The distal condyles are preserved in cranial view in DNHM D2945. The lateral condyle is larger than the medial condyle, as in other basal ornithuromorphs (Chiappe, 1996; Zhou & Zhang, 2006), and separated by a wide intercondylar groove (incisura intercondylaris). The cranial surface of the distal end is scarred by a deep extensor sulcus, which ends near a raised area just proximal to the intercondylar groove—a supratendinal bridge like that of more advanced ornithurines is not developed. The lateral epicondyle is minimally developed and there is only a slightly developed, crescent-like lateral epicondylar depression. Caudally, neither the lateral nor medial crests of the cartilaginous trochlea of the tibia (trochlea cartilaginous tibialis) are developed. These crests are slightly developed in Yixianornis grabaui and well developed in Apsaravis ukhaana (Norell & Clark, 2001; Clarke, Zhou & Zhang, 2006). The fibula is very slender (Figs. 8 and 9)—its distal end does not seem to extend beyond the midpoint of the tibiotarsus.

\n

Both tarsometatarsi are well-exposed in cranial view in DNHM D2945. As reported in the holotype of Hongshanornis longicresta (Zhou & Zhang, 2005), metatarsals II–IV are completely fused to one another. The intercotylar prominence is at best minimally developed. The proximal cotyla are slightly concave—the lateral one is slightly more distally placed than the medial one. Metatarsal III is plantarly displaced so that proximally, metatarsal II and metatarsal IV form ridges defining a recess excavating the central portion of the tarsometatarsus. Such morphology is consistent with that of other basal ornithuromorphs (e.g., Yanornis martini, Yixianornis grabaui, Gansus yumenensis, Ichthyornis dispar). Inside this proximocentral recess there is a foramen located between metatarsals III and IV, and medial to it, a tubercle on metatarsal II (possibly corresponding to the m. tibialis cranialis tuberosity of modern birds). Metatarsal III is the longest; metatarsal IV is slightly shorter, followed by the even shorter metatarsal II (Fig. 10). Metatarsal I is robust and fairly straight, with a concave medial margin. A distal vascular foramen is located between metatarsals III and IV as in Longicrusavis houi; the distal margin of the foramen is raised. The foramen seems to penetrate the bone at an oblique angle—from cranial to plantar surfaces. All trochleae appear to be ginglymous.

\n
\"Close
\n
\nFigure 10: Close up photograph of the feet and rectrices of DNHM D2945.
\nAbbreviations: mt, metatarsals; re, rectrices; I-IV, digits I-IV.

Digit III is the longest (Table 1); digit II is substantially shorter than IV (Fig. 10). Digit I is short and slender. All the pedal phalanges are long and slender and decrease in length distally. The phalanges of the second and third digits are approximately 2/3 the length of the preceding phalanx. The phalanges of digit IV are subequal, but still slightly decrease in length distally. The ungual phalanges bear distinct flexor tubercles. The morphology of the distal tarsometatarsus and the proportions of the pedal phalanges are consistent with cursorial function (Hopson, 2001), as in other Early Cretaceous ornithuromorphs.

Plumage

\n

DNHM D2945/6 preserves significant portions of the plumage of the wing, tail, and around the skull and neck. The feathers preserved over the skull question the assumption that this species was characterized by the presence of a feathery crest projecting from the head (Zhou & Zhang, 2005). DNHM D2945/6 shows nothing of that sort. The relatively short feathers of the head become gradually shorter until the plumage ends at the junction of the rostrum and the orbit, thus indicating that the culmen was devoid of feathers (whether it was covered by skin or a corneous beak is unknown). Furthermore, contrary to what was suggested by Zheng et al. (2011) for another specimen putatively identified as Hongshanornis longicresta (STM 35-3), DNHM D2945/6 indicates that these birds had relatively broad, but long and tapered, wings (Figs. 14 and 11).

\n
\"Interpretive
\n
\nFigure 11: Interpretive drawing of the outline of the wings and feathered tail of DNHM D2945/6 (see Figs. 1 and 3 for the maximum extent of the primaries and secondaries).
\nThe aerodynamic parameters used in this study were derived from this reconstruction (see Materials and Methods).

The most distal primaries are clearly much shorter than the remaining primaries. Based on the well-preserved outline of the wing, our estimation of the wingspan of DNHM D2945/6 is approximately 0.32 m and the wing area is 0.016 m2 (Fig. 11). There is exquisite evidence of rectrices forming a fan-like tail preserved in natural orientation, about the extended feet. Although visualization of individual feathers is difficult due to overlap, the tail appears to be composed of at least 10 vaned rectrices. The precise degree of asymmetry of these feathers cannot be ascertained but it is clear that none of them were strongly asymmetric (Fig. 10). The caudal margin of the feathered tail is rounded and the pair of central rectrices projects distally more than the feathers on either side, thus suggesting a gently graded tail (comparable to the one described for Piscivoravis lii; see Zhou, Zhou & O’Connor, 2013a). The holotype of Hongshanornis longicresta also shows evidence of an extensive feathered tail as a series of partially preserved vaned feathers between the feet (IVPP V14533A); these are very faint and were not described in the original description (see O’Connor, Gao & Chiappe, 2010). In the holotype of Hongshanornis longicresta, the tail is clearly incomplete and only four feathers can be discerned; the tail in DNHM D2945/6 appears complete. The number of preserved feathers is thus greater than the one described in the younger ornithuromorphs Yixianornis grabaui (minimum of eight described) and Piscivoravis lii (at least six described) from the Jiufotang Formation (Clarke, Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2013a).

Gastroliths

\n

At least 11 small geo-gastroliths are clustered in the visceral and pelvic region of DNHM D2945/6. Some of these ‘stomach stones’ are still in place while others are represented by the voids left on the slabs (Figs. 14 and 8). The smallest of the stones is nearly half the size the largest (1.71 mm to 3.08 mm) with the mean being 2.2 mm (Table 2). They range in shape from subspherical to oblong. It is unclear whether gastroliths were preserved with the holotype (IVPP V14533A), although more than 50 small (∼1 mm) geo-gastroliths were reported in the poorly preserved STM 35-3, a specimen identified as of Hongshanornis longicresta by Zheng et al. (2011). Despite the fact that Zheng et al. (2011) did not provide any anatomical evidence supporting the identification of STM 35-5 as Hongshanornis longicresta, the discovery of DNHM D2945/6 provides unquestionable evidence of the behavior of ingesting grit by this basal ornithuromorph species.

\n
\nTable 2:
Measurements (mm) of the gastroliths of DNHM D2945/6.
\nLeft column numbers correspond to numbers on Figs. 2 and 4.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
D2945D2946Mean value
12.212.272.24
23.063.093.08
32.312.072.19
42.052.152.10
52.152.112.13
62.902.592.75
71.841.761.80
81.761.791.78
91.742.081.91
101.841.561.70
112.513.132.82
\n
" ] }, "discussion_html": { "value": [ - "

Discussion

\n

The specimen described here, DNHM D2945/6, is indistinguishable from the holotype of Hongshanornis longicresta and is thus referred to this taxon. DNHM D2945/6 is from the same locality and formation (Yixian) that yielded the closely related Longicrusavis houi (PKVP 1069; O’Connor, Gao & Chiappe, 2010). The coexistence of these two closely related taxa in a single fauna suggests that Hongshanornithidae was a diverse component of the avifauna of the Yixian Formation.

\n

DNHM D2945/6 reveals important new information regarding the morphology, diet, and ecology of Hongshanornis longicresta and other Early Cretaceous ornithuromorphs. The new specimen of Hongshanornis longicresta preserves actual fossilized bone rather than voids of bone, as in the holotype (IVPP V 14533), and as such this new specimen helps clarify the osteology of the taxon. DNHM D2945/6 documents the presence of two different skull morphologies within Hongshanornithidae. It also confirms that the upper and lower jaws of these birds were toothed, a conclusion previously suggested by morphologies preserved in the holotype of Longicrusavis houi (O’Connor, Gao & Chiappe, 2010). Additionally, DNHM D2945/6 shows that the lateral margin of the coracoid of hongshanornithids was concave, as is typical of other basal ornithuromorphs, and not convex as reported by Zhou & Zhang (2005). DNHM D2945/6 also preserves a dorsal supracondylar process, a feature present in Longicrusavis houi and many extant shorebirds.

\n

The presence of a hypocleidium in Hongshanornis longicresta is still controversial. This process does not appear present in DNHM D2945/6, however preservation prevents us from making an unequivocal statement. While most known Early Cretaceous ornithuromorphs do not possess even the smallest hypocleidium, basal ornithuromorphs with furculae bearing a distinct hypocleidium have been recently reported (Zhou, Zhou & O’Connor, 2012). Such discoveries lend credibility to Zhou and Zhang’s (2005) claim that the furcula of Hongshanornis longicresta possessed a hypocleidium, although well-preserved specimens are necessary to corroborate such a claim.

\n

Furthermore, the anatomy of DNHM D2945/6 partially undermines the anatomical basis used by Li, Wang & Hou (2011) to diagnose the hongshanornithid Parahongshanornis chaoyangensis. The compression of the proximal portion of the furcula and caudal groove of this bone in DNHM D2945/6 indicate that these characters cannot be considered as diagnostic of Parahongshanornis chaoyangensis. This is the same for the distal expansion of the pubes, a condition that is identical in DNHM D2945/6 and the holotype of Parahongshanornis chaoyangensis.

\n

Diet

\n

The presence of teeth on both the maxilla and the dentary, and the reinterpretation of the hongshanornithids as toothed birds, impact earlier ecological inferences for the clade, suggesting they were less specialized trophically than previously imagined. The presence of at least two distinct skull morphologies within Hongshanornithidae indicates intraclade trophic diversity, and niche partitioning within the specialized wading ecology inferred to have been occupied by this clade.

\n

The geo-gastroliths preserved associated with the visceral region of DNHM D2945/6 offer a glimpse into the digestive system and dietary preferences of hongshanornithids. A variety of aquatic and terrestrial organisms regularly ingest sand, fine gravel, or coarse sand. These ‘stomach stones’ or grit are assumed to perform a variety of functions ranging from acting like ballast in aquatic animals to parasite control and hunger placation (Wings, 2007). Most typically, however, geo-gastroliths are interpreted as grinding devices assisting the digestion of hard food items. Geo-gastroliths are not only common among living crocodiles (Taylor, 1993; Henderson, 2003) and birds (Gionfriddo & Best, 1999) but they also have been documented in a variety of extinct archosaurian clades, including pterosaurs (Codorniú, Chiappe & Cid, 2013) and every major group of dinosaurs (Osborn, 1924; Ji et al., 1998; Weems, Culp & Wings, 2007; Wings & Sander, 2007). Geo-gastroliths have also been discovered in association with the skeletons of a number of Early Cretaceous ornithuromorphs from China (e.g., Yanornis martini, Gansus yumenensis, Archaeorhynchus spathula) (Zhou et al., 2004; You et al., 2006; Zhou, Zhou & O’Connor, 2013b). The presence of geo-gastroliths in fossil dinosaurs (including birds) is generally regarded as indicative of herbivory (Ji et al., 1998; Gionfriddo & Best, 1999; Kobayashi et al., 1999; Wings, 2007; Xu et al., 2009; Zanno & Makovicky, 2011; Brusatte, 2012), however such a correlation is not as consistent as often assumed. In the case of DNHM D2945/6, the closely associated cluster of fairly evenly sized stones located in the abdominal cavity distal to the sternum but proximal to the pelvic girdle, is consistent with the interpretation of these geo-gastroliths as gizzard stones. Furthermore, the report by Zheng et al. (2011) of a specimen (STM 35-3, identified as of Hongshanornis longicresta) containing seeds in a crop provides evidence that these birds were granivorous. Such evidence is consistent with both the preservation of geo-gastroliths in DNHM D2945/6 and STM 35-3, and the functional interpretation that highlights the role these stones play in processing hard foods.

Caudal plumage

\n

Very little is known about the rectrices of basal ornithuromorphs and DNHM D2945/6 represents what is possibly the most informative example for understanding the morphology of the tail of these birds. Only two types of feathered tails—fan-shaped and forked—have been reported for basal ornithuromorphs (Zhou & Zhang, 2001; Clarke, Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2012; Zhou, Zhou & O’Connor, 2013a). Such limited diversity contrasts with what is known for their sister-group, the Enantiornithes, in which a larger number of tail morphologies (including one inferred to be aerodynamic; O’Connor et al., 2009) are known (Zhang & Zhou, 2000; Zheng, Zhang & Hou, 2007; O’Connor, Gao & Chiappe, 2010; O’Connor et al., 2012).

\n

DNHM D2945/6 provides evidence that as early as 125 million year ago, basal ornithuromorphs had evolved a feathered tail comparable in size and design to those of many modern birds. Such tail had rectrices suitable of fanning and capable of generating aerodynamic forces much greater than those of more basal birds (Gatesy & Dial, 1996).

\n

In living birds, all but the central pair of rectrices of a fan-shaped tail anchor on a musculo-adipose organ, the rectricial bulb, which controls the fanning of the feathers and as such, plays a critical role in flight (Gatesy & Dial, 1996). The rectricial bulb is in turn supported by, and intimately connected to, the pygostyle. Nonetheless, because no direct evidence of a rectricial bulb has ever been found in any Mesozoic bird, whether the pygostyle is a reliable osteological correlate of the rectricial bulb has been questioned (Clarke, Zhou & Zhang, 2006). The morphology of the pygostyle of basal ornithuromorphs (and of their living relatives) differs from that typical of more basal birds, which commonly possess a long, robust, and club-shaped pygostyle (e.g., Confuciusornithidae, Enantiornithes). In contrast, the pygostyle of ornithuromorphs is relatively small, more delicate, and plough-shaped—even if the pygostyle of hongshanornithids is poorly known (and missing in DNHM 2945/6), its morphology seems to agree with that of other basal ornithuromorphs (Zhou & Zhang, 2005). The morphological difference between the pygostyle of ornithuromorphs and that of more basal birds led Clarke, Zhou & Zhang (2006) to hypothesize that the rectricial bulb evolved in concert with both the modern avian pygostyle (plough-shaped) and aerodynamic tail morphologies such as those known for basal ornithuromorph taxa. This hypothesis, however, has been somewhat challenged by the recent report of a tail formed by long, shafted rectrices in the enantiornithine Shanweiniao cooperorum (O’Connor et al., 2009). In the holotype and only known specimen of this taxon, the impressions of four vaned feathers can be seen projecting from the end of the caudal vertebral series. Such evidence suggests that the presence of a large and club-shaped pygostyle, like the one characteristic of enantiornithines, might not have excluded the development of a fan-shaped feather tail among non-ornithuromorph birds from such tail feather morphologies (O’Connor et al., 2009), and therefore that a rectricial bulb might have evolved either prior to the origin of the Ornithuromorpha or independently in more than one clade of birds (e.g., Ornithuromorpha and Enantiornithes). The derived phylogenetic position of Shanweiniao cooperorum, nested among advanced enantiornithines (O’Connor & Zhou, 2012), and the widespread presence of pintail morphologies lacking vaned rectrices capable of fanning among other enantiornithines (O’Connor et al., 2012) favor interpretations of the aerodynamic tail of Shanweiniao (and presumably the rectricial bulb that operated the fanning of its rectrices) as an independent evolutionary event. Likewise, the presence of fan-shaped feathered tails and modern-like pygostyles in a variety of basal ornithuromorphs (e.g., Hongshanornis longicresta, Yixianornis grabaui, Yanornis martini, Piscivoravis lii) supports the argument that such morphologies are ancestral for Ornithuromorpha (Clarke, Zhou & Zhang, 2006).

Aerodynamics

\n

DNHM D2945/6 possesses relatively broad, but tapered wings. Compared to a general regression of mass against wing area for birds (data taken from Greenewalt, 1962), the relative wing area for DNHM D2945/6 is somewhat larger than average, when using the mean body mass estimate (42 g; residual of −0.37) (see Materials and Methods). However, using the heaviest mass estimate for DNHM D2945/6 (65 g) (see Materials and Methods) yields an average wing area, and therefore a typical wing loading compared to a modern bird of similar size (residual of −0.04).

\n

The overall size of DNHM D2945/6, along with its wing shape, is qualitatively similar to that of some living passerines with flexible diets (e.g., Monticola solitarius, Sturnus vulgaris, Turdus naumanni). These same living birds also tend to have somewhat tapering wings without extensive wing tip slotting. As a result, we tentatively suggest that DNHM D2945/6 may have lacked extensive wingtip slotting, even if direct evidence of this is not available in the specimen. Additional specimens will be required to confirm this prediction. Tip slots are most effective at slow speeds, where they can increase effective aspect ratio in wings with low geometric aspect ratio (Tucker, 1993). As a result, it is generally expected that birds without tip slots tend to either have high geometric aspect ratio (which is not relevant to DNHM D2945/6), or else tend to fly at relatively high speeds. Based on its intermediate size and moderate aspect ratio, DNHM D2945/6 would be expected to flap continuously at low speeds, but may have switched to flap-bounding (a cycle of flapping and bounding with the wings flexed) at higher rates of travel, since this type of gait transition is seen among modern birds with similar wing shape and body size to DNHM D2945/6. We note that such gait transitions are related to flight speed and cost of transport, both of which relate to total body size and wing loading (Tobalske, Peacock & Dial, 1999; Tobalske, 2001). Since we have reliable measurements of the specimen dimensions, conservative predictions of gait are possible for DNHM D2945/6, even though the wings of the specimen lack feather details. For the same reasons, we do not expect that these gait transitions would be particularly sensitive to specifics of osteology (i.e., differences in skeletal structure between basal ornithuromorphs and modern birds). So long as DNHM D2945/6 was able to fly continuously for significant distances, the same basic patterns of cost of transport relative to size and flight speed should apply to both living neornithines and DNHM D2945/6.

\n

Tail positioning and effective functional area are more difficult to estimate in fossil taxa than the same variables for the wings, because avian tails can be used at extremely fanned or collapsed states (or any number of positions in between). While the degree of asymmetry of the rectrices is unclear, the lateral feathers of the tail in DNHM D2945/6 appear to be less asymmetrical than it would expected if these feathers were regularly oriented with their long axis fully transverse to the air flow (as would be the case for primary feathers on the wings or the lateral rectrices in a fully fanned tail). This suggests that the tail was typically deployed as a partially fanned “wedge”, rather than a full fan. This is not uncommon among modern birds with long tails, such as flycatchers, accipiters, and sunbitterns (M Habib, pers. observation).

\n

The preserved plumage of DNHM D2945/6 indicates that hongshanornithids had wing and tail surfaces comparable to those of living birds of similar sizes. In general, the morphology of the wing and feathered tail of DNHM D2945/6, combined with estimates of its weight, is indicative of a flight mode comparable to the intermittent flight of many medium-sized passerines and congruent with the conclusions reached by Close & Rayfield (2012), whose geometric morphometric analysis of furculae interpreted Hongshanornis longicresta as a continuous flapper.

" + "

Discussion

\n

The specimen described here, DNHM D2945/6, is indistinguishable from the holotype of Hongshanornis longicresta and is thus referred to this taxon. DNHM D2945/6 is from the same locality and formation (Yixian) that yielded the closely related Longicrusavis houi (PKVP 1069; O’Connor, Gao & Chiappe, 2010). The coexistence of these two closely related taxa in a single fauna suggests that Hongshanornithidae was a diverse component of the avifauna of the Yixian Formation.

\n

DNHM D2945/6 reveals important new information regarding the morphology, diet, and ecology of Hongshanornis longicresta and other Early Cretaceous ornithuromorphs. The new specimen of Hongshanornis longicresta preserves actual fossilized bone rather than voids of bone, as in the holotype (IVPP V 14533), and as such this new specimen helps clarify the osteology of the taxon. DNHM D2945/6 documents the presence of two different skull morphologies within Hongshanornithidae. It also confirms that the upper and lower jaws of these birds were toothed, a conclusion previously suggested by morphologies preserved in the holotype of Longicrusavis houi (O’Connor, Gao & Chiappe, 2010). Additionally, DNHM D2945/6 shows that the lateral margin of the coracoid of hongshanornithids was concave, as is typical of other basal ornithuromorphs, and not convex as reported by Zhou & Zhang (2005). DNHM D2945/6 also preserves a dorsal supracondylar process, a feature present in Longicrusavis houi and many extant shorebirds.

\n

The presence of a hypocleidium in Hongshanornis longicresta is still controversial. This process does not appear present in DNHM D2945/6, however preservation prevents us from making an unequivocal statement. While most known Early Cretaceous ornithuromorphs do not possess even the smallest hypocleidium, basal ornithuromorphs with furculae bearing a distinct hypocleidium have been recently reported (Zhou, Zhou & O’Connor, 2012). Such discoveries lend credibility to Zhou and Zhang’s (2005) claim that the furcula of Hongshanornis longicresta possessed a hypocleidium, although well-preserved specimens are necessary to corroborate such a claim.

\n

Furthermore, the anatomy of DNHM D2945/6 partially undermines the anatomical basis used by Li, Wang & Hou (2011) to diagnose the hongshanornithid Parahongshanornis chaoyangensis. The compression of the proximal portion of the furcula and caudal groove of this bone in DNHM D2945/6 indicate that these characters cannot be considered as diagnostic of Parahongshanornis chaoyangensis. This is the same for the distal expansion of the pubes, a condition that is identical in DNHM D2945/6 and the holotype of Parahongshanornis chaoyangensis.

\n

Diet

\n

The presence of teeth on both the maxilla and the dentary, and the reinterpretation of the hongshanornithids as toothed birds, impact earlier ecological inferences for the clade, suggesting they were less specialized trophically than previously imagined. The presence of at least two distinct skull morphologies within Hongshanornithidae indicates intraclade trophic diversity, and niche partitioning within the specialized wading ecology inferred to have been occupied by this clade.

\n

The geo-gastroliths preserved associated with the visceral region of DNHM D2945/6 offer a glimpse into the digestive system and dietary preferences of hongshanornithids. A variety of aquatic and terrestrial organisms regularly ingest sand, fine gravel, or coarse sand. These ‘stomach stones’ or grit are assumed to perform a variety of functions ranging from acting like ballast in aquatic animals to parasite control and hunger placation (Wings, 2007). Most typically, however, geo-gastroliths are interpreted as grinding devices assisting the digestion of hard food items. Geo-gastroliths are not only common among living crocodiles (Taylor, 1993; Henderson, 2003) and birds (Gionfriddo & Best, 1999) but they also have been documented in a variety of extinct archosaurian clades, including pterosaurs (Codorniú, Chiappe & Cid, 2013) and every major group of dinosaurs (Osborn, 1924; Ji et al., 1998; Weems, Culp & Wings, 2007; Wings & Sander, 2007). Geo-gastroliths have also been discovered in association with the skeletons of a number of Early Cretaceous ornithuromorphs from China (e.g., Yanornis martini, Gansus yumenensis, Archaeorhynchus spathula) (Zhou et al., 2004; You et al., 2006; Zhou, Zhou & O’Connor, 2013b). The presence of geo-gastroliths in fossil dinosaurs (including birds) is generally regarded as indicative of herbivory (Ji et al., 1998; Gionfriddo & Best, 1999; Kobayashi et al., 1999; Wings, 2007; Xu et al., 2009; Zanno & Makovicky, 2011; Brusatte, 2012), however such a correlation is not as consistent as often assumed. In the case of DNHM D2945/6, the closely associated cluster of fairly evenly sized stones located in the abdominal cavity distal to the sternum but proximal to the pelvic girdle, is consistent with the interpretation of these geo-gastroliths as gizzard stones. Furthermore, the report by Zheng et al. (2011) of a specimen (STM 35-3, identified as of Hongshanornis longicresta) containing seeds in a crop provides evidence that these birds were granivorous. Such evidence is consistent with both the preservation of geo-gastroliths in DNHM D2945/6 and STM 35-3, and the functional interpretation that highlights the role these stones play in processing hard foods.

Caudal plumage

\n

Very little is known about the rectrices of basal ornithuromorphs and DNHM D2945/6 represents what is possibly the most informative example for understanding the morphology of the tail of these birds. Only two types of feathered tails—fan-shaped and forked—have been reported for basal ornithuromorphs (Zhou & Zhang, 2001; Clarke, Zhou & Zhang, 2006; Zhou, Zhou & O’Connor, 2012; Zhou, Zhou & O’Connor, 2013a). Such limited diversity contrasts with what is known for their sister-group, the Enantiornithes, in which a larger number of tail morphologies (including one inferred to be aerodynamic; O’Connor et al., 2009) are known (Zhang & Zhou, 2000; Zheng, Zhang & Hou, 2007; O’Connor, Gao & Chiappe, 2010; O’Connor et al., 2012).

\n

DNHM D2945/6 provides evidence that as early as 125 million year ago, basal ornithuromorphs had evolved a feathered tail comparable in size and design to those of many modern birds. Such tail had rectrices suitable of fanning and capable of generating aerodynamic forces much greater than those of more basal birds (Gatesy & Dial, 1996).

\n

In living birds, all but the central pair of rectrices of a fan-shaped tail anchor on a musculo-adipose organ, the rectricial bulb, which controls the fanning of the feathers and as such, plays a critical role in flight (Gatesy & Dial, 1996). The rectricial bulb is in turn supported by, and intimately connected to, the pygostyle. Nonetheless, because no direct evidence of a rectricial bulb has ever been found in any Mesozoic bird, whether the pygostyle is a reliable osteological correlate of the rectricial bulb has been questioned (Clarke, Zhou & Zhang, 2006). The morphology of the pygostyle of basal ornithuromorphs (and of their living relatives) differs from that typical of more basal birds, which commonly possess a long, robust, and club-shaped pygostyle (e.g., Confuciusornithidae, Enantiornithes). In contrast, the pygostyle of ornithuromorphs is relatively small, more delicate, and plough-shaped—even if the pygostyle of hongshanornithids is poorly known (and missing in DNHM 2945/6), its morphology seems to agree with that of other basal ornithuromorphs (Zhou & Zhang, 2005). The morphological difference between the pygostyle of ornithuromorphs and that of more basal birds led Clarke, Zhou & Zhang (2006) to hypothesize that the rectricial bulb evolved in concert with both the modern avian pygostyle (plough-shaped) and aerodynamic tail morphologies such as those known for basal ornithuromorph taxa. This hypothesis, however, has been somewhat challenged by the recent report of a tail formed by long, shafted rectrices in the enantiornithine Shanweiniao cooperorum (O’Connor et al., 2009). In the holotype and only known specimen of this taxon, the impressions of four vaned feathers can be seen projecting from the end of the caudal vertebral series. Such evidence suggests that the presence of a large and club-shaped pygostyle, like the one characteristic of enantiornithines, might not have excluded the development of a fan-shaped feather tail among non-ornithuromorph birds from such tail feather morphologies (O’Connor et al., 2009), and therefore that a rectricial bulb might have evolved either prior to the origin of the Ornithuromorpha or independently in more than one clade of birds (e.g., Ornithuromorpha and Enantiornithes). The derived phylogenetic position of Shanweiniao cooperorum, nested among advanced enantiornithines (O’Connor & Zhou, 2012), and the widespread presence of pintail morphologies lacking vaned rectrices capable of fanning among other enantiornithines (O’Connor et al., 2012) favor interpretations of the aerodynamic tail of Shanweiniao (and presumably the rectricial bulb that operated the fanning of its rectrices) as an independent evolutionary event. Likewise, the presence of fan-shaped feathered tails and modern-like pygostyles in a variety of basal ornithuromorphs (e.g., Hongshanornis longicresta, Yixianornis grabaui, Yanornis martini, Piscivoravis lii) supports the argument that such morphologies are ancestral for Ornithuromorpha (Clarke, Zhou & Zhang, 2006).

Aerodynamics

\n

DNHM D2945/6 possesses relatively broad, but tapered wings. Compared to a general regression of mass against wing area for birds (data taken from Greenewalt, 1962), the relative wing area for DNHM D2945/6 is somewhat larger than average, when using the mean body mass estimate (42 g; residual of −0.37) (see Materials and Methods). However, using the heaviest mass estimate for DNHM D2945/6 (65 g) (see Materials and Methods) yields an average wing area, and therefore a typical wing loading compared to a modern bird of similar size (residual of −0.04).

\n

The overall size of DNHM D2945/6, along with its wing shape, is qualitatively similar to that of some living passerines with flexible diets (e.g., Monticola solitarius, Sturnus vulgaris, Turdus naumanni). These same living birds also tend to have somewhat tapering wings without extensive wing tip slotting. As a result, we tentatively suggest that DNHM D2945/6 may have lacked extensive wingtip slotting, even if direct evidence of this is not available in the specimen. Additional specimens will be required to confirm this prediction. Tip slots are most effective at slow speeds, where they can increase effective aspect ratio in wings with low geometric aspect ratio (Tucker, 1993). As a result, it is generally expected that birds without tip slots tend to either have high geometric aspect ratio (which is not relevant to DNHM D2945/6), or else tend to fly at relatively high speeds. Based on its intermediate size and moderate aspect ratio, DNHM D2945/6 would be expected to flap continuously at low speeds, but may have switched to flap-bounding (a cycle of flapping and bounding with the wings flexed) at higher rates of travel, since this type of gait transition is seen among modern birds with similar wing shape and body size to DNHM D2945/6. We note that such gait transitions are related to flight speed and cost of transport, both of which relate to total body size and wing loading (Tobalske, Peacock & Dial, 1999; Tobalske, 2001). Since we have reliable measurements of the specimen dimensions, conservative predictions of gait are possible for DNHM D2945/6, even though the wings of the specimen lack feather details. For the same reasons, we do not expect that these gait transitions would be particularly sensitive to specifics of osteology (i.e., differences in skeletal structure between basal ornithuromorphs and modern birds). So long as DNHM D2945/6 was able to fly continuously for significant distances, the same basic patterns of cost of transport relative to size and flight speed should apply to both living neornithines and DNHM D2945/6.

\n

Tail positioning and effective functional area are more difficult to estimate in fossil taxa than the same variables for the wings, because avian tails can be used at extremely fanned or collapsed states (or any number of positions in between). While the degree of asymmetry of the rectrices is unclear, the lateral feathers of the tail in DNHM D2945/6 appear to be less asymmetrical than it would expected if these feathers were regularly oriented with their long axis fully transverse to the air flow (as would be the case for primary feathers on the wings or the lateral rectrices in a fully fanned tail). This suggests that the tail was typically deployed as a partially fanned “wedge”, rather than a full fan. This is not uncommon among modern birds with long tails, such as flycatchers, accipiters, and sunbitterns (M Habib, pers. observation).

\n

The preserved plumage of DNHM D2945/6 indicates that hongshanornithids had wing and tail surfaces comparable to those of living birds of similar sizes. In general, the morphology of the wing and feathered tail of DNHM D2945/6, combined with estimates of its weight, is indicative of a flight mode comparable to the intermittent flight of many medium-sized passerines and congruent with the conclusions reached by Close & Rayfield (2012), whose geometric morphometric analysis of furculae interpreted Hongshanornis longicresta as a continuous flapper.

" ] }, "conclusion_html": { @@ -418,93 +418,93 @@ }, "references_html": { "value": [ - "\nAlexander RMcN. 1983. Allometry of the leg bones of moas (Dinornithes) and other birds. Journal of Zoology 200:215-223 \n", - "\nAlvarenga HM, Bonaparte JF. 1992. A new flightless land bird from the Cretaceous of Patagonia. In: Campbell KC, ed. Papers in avian paleontology honoring pierce brodkorb. Los Angeles: Natural History Museum of Los Angeles County. 51-64 \n", - "\nBaumel JJ, Witmer LM. 1993. Osteologia. In: Baumel JJ, King AS, Breazile JE, Evans HE, Vanden Berge JC, eds. Handbook of avian anatomy: nomina anatomica avium (Second Edition). Cambridge: Nuttall Ornithological Club. 45-132 \n", - "\nBrusatte SL. 2012. Dinosaur paleobiology. Chichester: Wiley-Blackwell. 322 \n", - "\nChang S, Zhang H, Renne PR, Fang Y. 2009. High-precision 40Ar/39Ar age for the Jehol Biota. Palaeogeography, Palaeoclimatology, Palaeoecology 280:94-104 \n", - "\nChiappe LM. 1996. Late Cretaceous birds of southern South America: anatomy and systematics of Enantiornithes and Patagopteryx deferrariisi. Münchner Geowissenschaftliche Abhandlungen 30:203-244 \n", - "\nChiappe LM. 2002. Basal bird phylogeny: problems and solutions. In: Chiappe LM, Witmer LM, eds. Mesozoic birds: above the heads of dinosaurs. Berkeley: University of California Press. 448-472 \n", - "\nChiappe LM. 2007. Glorified dinosaurs: the origin and early evolution of birds. Hoboken: John Wiley & Sons. 263 \n", - "\nChiappe LM, Walker CA. 2002. Skeletal morphology and systematics of the Cretaceous Euenantiornithes (Ornithothoraces: Enantiornithes) In: Chiappe LM, Witmer LM, eds. Mesozoic birds: above the heads of dinosaurs. Berkeley: University of California Press. 240-267 \n", - "\nClarke JA. 2004. Morphology, phylogenetic taxonomy, and systematics of Ichthyornis and Apatornis (Avialae: Ornithurae) Bulletin of the American Museum of Natural History 286:1-179 \n", - "\nClarke JA, Zhou Z, Zhang F. 2006. Insight into the evolution of avian flight from a new clade of Early Cretaceous ornithurines from China and the morphology of Yixianornis grabaui. Journal of Anatomy 208:287-308 \n", - "\nClose RA, Rayfield EJ. 2012. Functional morphometric analysis of the furcula in Mesozoic birds. PLoS ONE 7(5):e36664 \n", - "\nCodorniú L, Chiappe LM, Cid FD. 2013. First occurrence of stomach stones in pterosaurs. Journal of Vertebrate Paleontology 33:647-654 \n", - "\nDunning JB. 2008. CRC handbook of avian body masses (Second Edition). Boca Raton: CRC Press. 655 \n", - "\nForster CA, Chiappe LM, Krause DW, Sampson SD. 1996. The first Cretaceous bird from Madagascar. Nature 382:532-534 \n", - "\nGatesy SM, Dial KP. 1996. From frond to fan: Archaeopteryx and the evolution of short tailed birds. Evolution 50:2037-2048 \n", - "\nGionfriddo JP, Best LB. 1999. Grit use by birds: a review. Current Ornithology 15:89-148 \n", - "\nGreenewalt CH. 1962. Dimensional relationships for flying animals. Smithsonian Miscellaneous Collections 144(2):1-46 \n", - "\nHenderson DM. 2003. Effects of stomach stones on the buoyancy and equilibrium of a floating crocodilian: a computational analysis. Canadian Journal of Zoology 81:1346-1357 \n", - "\nHone DW, Dyke GJ, Haden M, Benton MJ. 2008. Body size evolution in Mesozoic birds. Journal of Evolutionary Biology 21:618-624 \n", - "\nHopson JA. 2001. Ecomorpology of avian and nonavian theropod phalangeal proportions: implications for the arboreal versus terrestrial origin of bird flight. In: Gauthier J, Gall LF, eds. New perspectives on the origins and early evolution of birds. New Haven: Peabody Museum of Natural History. 211-235 \n", - "\nHoward H. 1929. The avifauna of Emeryville shellmound. University of California Publications in Zoology 32(2):301-394 \n", - "\nJi Q, Currie PJ, Norell MA, Ji SA. 1998. Two feathered dinosaurs from northeastern China. Nature 393:753-761 \n", - "\nKobayashi Y, Lu JC, Dong ZM, Barsbold R, Azuma Y. 1999. Herbivorous diet in an ornithomimid dinosaur. Nature 402:480-481 \n", - "\nKurochkin EN. 1982. New order of birds from the Lower Cretaceous in Mongolia. Paleontological Journal 1982:215-218 \n", - "\nKurochkin EN. 1985. A true carinate bird from Lower Cretaceous deposits in Mongolia and other evidence of early Cretaceous birds in Asia. Cretaceous Research 6:271-278 \n", - "\nLi DS, Sullivan C, Zhou AH, Zhang FC. 2010. Basal birds from China: a brief review. Chinese Birds 1:83-96 \n", - "\nLi L, Wang J, Hou S. 2011. A new ornithurine bird (Hongshanornithidae) from the Jiufotang Formation of Chaoyang, Liaoning, China. Vertebrata PalAsiatica 49(2):195-200 \n", - "\nLi Z, Zhou Z, Clarke JA. 2011. A reevaluation of the relationships among basal ornithurine birds from China and new information on the anatomy of Hongshanornis longicresta. In: 71st annual meeting, society of vertebrate paleontology (November 2011), Supplement to the online Journal of Vertebrate Paleontology. 144 \n", - "\nMaloiy GMO, Alexander RM, Njau R, Jayes AS. 1979. Allometry of the legs of running birds. Journal of Zoology 187:161-167 \n", - "\nMarsh OC. 1880. Odontornithes: a monograph on the extinct birds of North America. Washington: Government Printing Office. 312 \n", - "\nMartin LD, Tate J. 1976. The skeleton of Baptornis advenus (Aves: Hesperornithiformes) Smithsonian Contributions to Paleobiology 27:35-66 \n", - "\nNorell MA, Clark JA. 2001. Fossil that fills a critical gap in avian evolution. Nature 409:181-182 \n", - "\nO’Connor JK, Chiappe LM, Bell A. 2011. Pre-modern birds: avian divergences in the Mesozoic. In: Dyke GD, Kaiser G, eds. Living dinosaurs: the evolutionary history of birds. New Jersey: J. Wiley & Sons. 39-114 \n", - "\nO’Connor JK, Chiappe LM, Chuong CM, Bottjer D, You H. 2012. Homology and potential cellular and molecular mechanisms for the development of unique feather morphologies in early birds. Geosciences 2(3):157-177 \n", - "\nO’Connor JK, Gao KQ, Chiappe LM. 2010. A new ornithuromorph (Aves: Ornithothoraces) bird from the Jehol Group indicative of higher-level diversity. Journal of Vertebrate Paleontology 30:311-321 \n", - "\nO’Connor JK, Wang XR, Chiappe LM, Gao CH, Meng QJ, Cheng XD, Liu JY. 2009. Phylogenetic support for a specialized clade of Cretaceous enantiornithine birds with information from a new species. Journal of Vertebrate Paleontology 29:188-204 \n", - "\nO’Connor JK, Zhou Z. 2012. A redescription of Chaoyangia beishanensis (Aves) and a comprehensive phylogeny of Mesozoic birds. Journal of Systematic Palaeontology 2(7):889-906 \n", - "\nOsborn HF. 1924. Psittacosaurus and protiguanodon: two lower Cretaceous iguanodonts from Mongolia. American Museum Novitates 127:1-16 \n", - "\nPennycuick C. 2008. Modeling the flying bird. London: Academic Press. 480 \n", - "\nPeters WS, Peters DS. 2009. Life history, sexual dimorphism and ‘ornamental’ feathers in the Mesozoic bird Confuciusornis sanctus. Biology Letters 5:817-882 \n", - "\nSwisher CC, Wang X, Zhou Z, Wang YE, Jin F, Zhang J, Xu X, Zhang F, Wang Y. 2002. Further support for a Cretaceous age for the feathered-dinosaur beds of Liaoning, China: new 40Ar/39Ar dating of the Yixian and Tuchengzi formations. Chinese Science Bulletin 47:135-138 \n", - "\nTaylor MA. 1993. Stomach stones for feeding or buoyancy? The occurrence and function of gastroliths in marine tetrapods. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 341:163-175 \n", - "\nTobalske BW. 2001. Morphology, velocity, and intermittent flight in birds. American Zoology 41:177-187 \n", - "\nTobalske BW, Peacock W, Dial KP. 1999. Kinematics of flap-bounding flight in the zebra finch over a wide range of speeds. Journal of Experimental Biology 202:1725-1739 \n", - "\nTucker VA. 1993. Gliding birds: reduction of induced drag by wing tip slots between primary feathers. Journal of Experimental Biology 180:285-310 \n", - "\nWeems RE, Culp MJ, Wings O. 2007. Evidence for prosauropod dinosaur gastroliths in the Bull Run Formation (Upper Triassic, Norian) of Virginia. Ichnos 14:271-295 \n", - "\nWings O. 2007. A review of gastrolith function with implications for fossil vertebrates and a revised classification. Acta Palaeontologica Polonica 52:1-16 \n", - "\nWings O, Sander PM. 2007. No gastric mill in sauropod dinosaurs: new evidence from analysis of gastrolith mass and function in ostriches. Proceedings of the Royal Society B: Biological Sciences 274:635-640 \n", - "\nXu X, Clark JM, Mo J, Choiniere J, Forster CA, Erickson GM, Hone DWE, Sullivan C, Eberth DA, Nesbitt S, Zhao Q, Hernandez R, Jia CK, Han FL, Guo Y. 2009. A Jurassic ceratosaur from China helps clarify avian digital homologies. Nature 459:940-944 \n", - "\nYang W, Li S, Jiang B. 2007. New evidence for Cretaceous age of the feathered dinosaurs of Liaoning: zircon U-Pb SHRIMP dating of the Yixian Formation in Sihetun, Northeast China. Cretaceous Research 28:177-182 \n", - "\nYou HL, Lamanna MC, Harris JD, Chiappe LM, O’Connor JK, Ji SA, Lu JC, Yuan CX, Li DQ, Zhang X, Lacovara KJ, Dodson P, Ji Q. 2006. A nearly modern amphibious bird from the Early Cretaceous of northwestern China. Science 312:1640-1643 \n", - "\nZanno L, Makovicky P. 2011. Herbivorous ecomorphology and specialization patterns in theropod dinosaur evolution. Proceedings of the National Academy of Sciences 108:232-237 \n", - "\nZhang F, Zhou Z. 2000. A primitive enantiornithine bird and the origin of feathers. Science 290:1955-1960 \n", - "\nZheng X, Zhang Z, Hou L. 2007. A new enantiornitine bird with four long rectrices from the Early Cretaceous of northern Hebei, China. Acta Geologica Sinica 81:703-708 \n", - "\nZheng XT, Martin LD, Zhou ZH, Burnham DA, Zhang FC, Miao D. 2011. Fossil evidence of avian crops from the Early Cretaceous of China. Proceedings of the National Academy of Sciences of the United States of America 108:15904-15907 \n", - "\nZhou ZH, Clarke J, Zhang F, Wings O. 2004. Gastroliths in Yanornis: an indication of the earliest radical diet-switching and gizzard plasticity in the lineage leading to living birds. Naturwissenschaften 91:571-574 \n", - "\nZhou ZH, Martin LD. 2011. Distribution of the predentary bone in Mesozoic ornithurine birds. Journal of Systematic Palaeontology 9:25-31 \n", - "\nZhou ZH, Zhang F. 2001. Two new ornithurine birds from the Early Cretaceous of western Liaoning, China. Kexue Tongbao 46:371-377 \n", - "\nZhou ZH, Zhang F. 2005. Discovery of an ornithurine bird and its implication for Early Cretaceous avian radiation. Proceedings of the National Academy of Sciences 102:18998-19002 \n", - "\nZhou ZH, Zhang FC. 2006. A beaked basal ornithurine bird (Aves, Ornithurae) from the Lower Cretaceous of China. Zoologica Scripta 35:363-373 \n", - "\nZhou ZH, Zhang FC. 2007. Mesozoic birds of China – a synoptic review. Frontiers of Biology in China 2(1):1-14 \n", - "\nZhou ZH, Zhang FC, Li ZH. 2009. A New Basal Ornithurine Bird (Jianchangornis microdonta gen. et sp. nov.) from the Lower Cretaceous of China. Vertebrata PalAsiatica 47(4):299-310 \n", - "\nZhou S, Zhou ZH, O’Connor JK. 2012. A new toothless ornithurine bird (Schizooura lii gen. et sp. nov.) from the Lower Cretaceous of China. Vertebrata Palasiatica 50(1):9-24 \n", - "\nZhou S, Zhou ZH, O’Connor JK. 2013a. A new piscivorous ornithuromorph from the Jehol Biota. Historical Biology: An International Journal of Paleobiology \n", - "\nZhou S, Zhou ZH, O’Connor JK. 2013b. Anatomy of the Basal Ornithuromorph Bird Archaeorhynchus spathula from the Early Cretaceous of Liaoning, China. Journal of Vertebrate Paleontology 33(1):141-152 \n" + "\nAlexander RMcN. 1983. Allometry of the leg bones of moas (Dinornithes) and other birds. Journal of Zoology 200:215-223 \n", + "\nAlvarenga HM, Bonaparte JF. 1992. A new flightless land bird from the Cretaceous of Patagonia. In: Campbell KC, ed. Papers in avian paleontology honoring pierce brodkorb. Los Angeles: Natural History Museum of Los Angeles County. 51-64 \n", + "\nBaumel JJ, Witmer LM. 1993. Osteologia. In: Baumel JJ, King AS, Breazile JE, Evans HE, Vanden Berge JC, eds. Handbook of avian anatomy: nomina anatomica avium (Second Edition). Cambridge: Nuttall Ornithological Club. 45-132 \n", + "\nBrusatte SL. 2012. Dinosaur paleobiology. Chichester: Wiley-Blackwell. 322 \n", + "\nChang S, Zhang H, Renne PR, Fang Y. 2009. High-precision 40Ar/39Ar age for the Jehol Biota. Palaeogeography, Palaeoclimatology, Palaeoecology 280:94-104 \n", + "\nChiappe LM. 1996. Late Cretaceous birds of southern South America: anatomy and systematics of Enantiornithes and Patagopteryx deferrariisi. Münchner Geowissenschaftliche Abhandlungen 30:203-244 \n", + "\nChiappe LM. 2002. Basal bird phylogeny: problems and solutions. In: Chiappe LM, Witmer LM, eds. Mesozoic birds: above the heads of dinosaurs. Berkeley: University of California Press. 448-472 \n", + "\nChiappe LM. 2007. Glorified dinosaurs: the origin and early evolution of birds. Hoboken: John Wiley & Sons. 263 \n", + "\nChiappe LM, Walker CA. 2002. Skeletal morphology and systematics of the Cretaceous Euenantiornithes (Ornithothoraces: Enantiornithes) In: Chiappe LM, Witmer LM, eds. Mesozoic birds: above the heads of dinosaurs. Berkeley: University of California Press. 240-267 \n", + "\nClarke JA. 2004. Morphology, phylogenetic taxonomy, and systematics of Ichthyornis and Apatornis (Avialae: Ornithurae) Bulletin of the American Museum of Natural History 286:1-179 \n", + "\nClarke JA, Zhou Z, Zhang F. 2006. Insight into the evolution of avian flight from a new clade of Early Cretaceous ornithurines from China and the morphology of Yixianornis grabaui. Journal of Anatomy 208:287-308 \n", + "\nClose RA, Rayfield EJ. 2012. Functional morphometric analysis of the furcula in Mesozoic birds. PLoS ONE 7(5):e36664 \n", + "\nCodorniú L, Chiappe LM, Cid FD. 2013. First occurrence of stomach stones in pterosaurs. Journal of Vertebrate Paleontology 33:647-654 \n", + "\nDunning JB. 2008. CRC handbook of avian body masses (Second Edition). Boca Raton: CRC Press. 655 \n", + "\nForster CA, Chiappe LM, Krause DW, Sampson SD. 1996. The first Cretaceous bird from Madagascar. Nature 382:532-534 \n", + "\nGatesy SM, Dial KP. 1996. From frond to fan: Archaeopteryx and the evolution of short tailed birds. Evolution 50:2037-2048 \n", + "\nGionfriddo JP, Best LB. 1999. Grit use by birds: a review. Current Ornithology 15:89-148 \n", + "\nGreenewalt CH. 1962. Dimensional relationships for flying animals. Smithsonian Miscellaneous Collections 144(2):1-46 \n", + "\nHenderson DM. 2003. Effects of stomach stones on the buoyancy and equilibrium of a floating crocodilian: a computational analysis. Canadian Journal of Zoology 81:1346-1357 \n", + "\nHone DW, Dyke GJ, Haden M, Benton MJ. 2008. Body size evolution in Mesozoic birds. Journal of Evolutionary Biology 21:618-624 \n", + "\nHopson JA. 2001. Ecomorpology of avian and nonavian theropod phalangeal proportions: implications for the arboreal versus terrestrial origin of bird flight. In: Gauthier J, Gall LF, eds. New perspectives on the origins and early evolution of birds. New Haven: Peabody Museum of Natural History. 211-235 \n", + "\nHoward H. 1929. The avifauna of Emeryville shellmound. University of California Publications in Zoology 32(2):301-394 \n", + "\nJi Q, Currie PJ, Norell MA, Ji SA. 1998. Two feathered dinosaurs from northeastern China. Nature 393:753-761 \n", + "\nKobayashi Y, Lu JC, Dong ZM, Barsbold R, Azuma Y. 1999. Herbivorous diet in an ornithomimid dinosaur. Nature 402:480-481 \n", + "\nKurochkin EN. 1982. New order of birds from the Lower Cretaceous in Mongolia. Paleontological Journal 1982:215-218 \n", + "\nKurochkin EN. 1985. A true carinate bird from Lower Cretaceous deposits in Mongolia and other evidence of early Cretaceous birds in Asia. Cretaceous Research 6:271-278 \n", + "\nLi DS, Sullivan C, Zhou AH, Zhang FC. 2010. Basal birds from China: a brief review. Chinese Birds 1:83-96 \n", + "\nLi L, Wang J, Hou S. 2011. A new ornithurine bird (Hongshanornithidae) from the Jiufotang Formation of Chaoyang, Liaoning, China. Vertebrata PalAsiatica 49(2):195-200 \n", + "\nLi Z, Zhou Z, Clarke JA. 2011. A reevaluation of the relationships among basal ornithurine birds from China and new information on the anatomy of Hongshanornis longicresta. In: 71st annual meeting, society of vertebrate paleontology (November 2011), Supplement to the online Journal of Vertebrate Paleontology. 144 \n", + "\nMaloiy GMO, Alexander RM, Njau R, Jayes AS. 1979. Allometry of the legs of running birds. Journal of Zoology 187:161-167 \n", + "\nMarsh OC. 1880. Odontornithes: a monograph on the extinct birds of North America. Washington: Government Printing Office. 312 \n", + "\nMartin LD, Tate J. 1976. The skeleton of Baptornis advenus (Aves: Hesperornithiformes) Smithsonian Contributions to Paleobiology 27:35-66 \n", + "\nNorell MA, Clark JA. 2001. Fossil that fills a critical gap in avian evolution. Nature 409:181-182 \n", + "\nO’Connor JK, Chiappe LM, Bell A. 2011. Pre-modern birds: avian divergences in the Mesozoic. In: Dyke GD, Kaiser G, eds. Living dinosaurs: the evolutionary history of birds. New Jersey: J. Wiley & Sons. 39-114 \n", + "\nO’Connor JK, Chiappe LM, Chuong CM, Bottjer D, You H. 2012. Homology and potential cellular and molecular mechanisms for the development of unique feather morphologies in early birds. Geosciences 2(3):157-177 \n", + "\nO’Connor JK, Gao KQ, Chiappe LM. 2010. A new ornithuromorph (Aves: Ornithothoraces) bird from the Jehol Group indicative of higher-level diversity. Journal of Vertebrate Paleontology 30:311-321 \n", + "\nO’Connor JK, Wang XR, Chiappe LM, Gao CH, Meng QJ, Cheng XD, Liu JY. 2009. Phylogenetic support for a specialized clade of Cretaceous enantiornithine birds with information from a new species. Journal of Vertebrate Paleontology 29:188-204 \n", + "\nO’Connor JK, Zhou Z. 2012. A redescription of Chaoyangia beishanensis (Aves) and a comprehensive phylogeny of Mesozoic birds. Journal of Systematic Palaeontology 2(7):889-906 \n", + "\nOsborn HF. 1924. Psittacosaurus and protiguanodon: two lower Cretaceous iguanodonts from Mongolia. American Museum Novitates 127:1-16 \n", + "\nPennycuick C. 2008. Modeling the flying bird. London: Academic Press. 480 \n", + "\nPeters WS, Peters DS. 2009. Life history, sexual dimorphism and ‘ornamental’ feathers in the Mesozoic bird Confuciusornis sanctus. Biology Letters 5:817-882 \n", + "\nSwisher CC, Wang X, Zhou Z, Wang YE, Jin F, Zhang J, Xu X, Zhang F, Wang Y. 2002. Further support for a Cretaceous age for the feathered-dinosaur beds of Liaoning, China: new 40Ar/39Ar dating of the Yixian and Tuchengzi formations. Chinese Science Bulletin 47:135-138 \n", + "\nTaylor MA. 1993. Stomach stones for feeding or buoyancy? The occurrence and function of gastroliths in marine tetrapods. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 341:163-175 \n", + "\nTobalske BW. 2001. Morphology, velocity, and intermittent flight in birds. American Zoology 41:177-187 \n", + "\nTobalske BW, Peacock W, Dial KP. 1999. Kinematics of flap-bounding flight in the zebra finch over a wide range of speeds. Journal of Experimental Biology 202:1725-1739 \n", + "\nTucker VA. 1993. Gliding birds: reduction of induced drag by wing tip slots between primary feathers. Journal of Experimental Biology 180:285-310 \n", + "\nWeems RE, Culp MJ, Wings O. 2007. Evidence for prosauropod dinosaur gastroliths in the Bull Run Formation (Upper Triassic, Norian) of Virginia. Ichnos 14:271-295 \n", + "\nWings O. 2007. A review of gastrolith function with implications for fossil vertebrates and a revised classification. Acta Palaeontologica Polonica 52:1-16 \n", + "\nWings O, Sander PM. 2007. No gastric mill in sauropod dinosaurs: new evidence from analysis of gastrolith mass and function in ostriches. Proceedings of the Royal Society B: Biological Sciences 274:635-640 \n", + "\nXu X, Clark JM, Mo J, Choiniere J, Forster CA, Erickson GM, Hone DWE, Sullivan C, Eberth DA, Nesbitt S, Zhao Q, Hernandez R, Jia CK, Han FL, Guo Y. 2009. A Jurassic ceratosaur from China helps clarify avian digital homologies. Nature 459:940-944 \n", + "\nYang W, Li S, Jiang B. 2007. New evidence for Cretaceous age of the feathered dinosaurs of Liaoning: zircon U-Pb SHRIMP dating of the Yixian Formation in Sihetun, Northeast China. Cretaceous Research 28:177-182 \n", + "\nYou HL, Lamanna MC, Harris JD, Chiappe LM, O’Connor JK, Ji SA, Lu JC, Yuan CX, Li DQ, Zhang X, Lacovara KJ, Dodson P, Ji Q. 2006. A nearly modern amphibious bird from the Early Cretaceous of northwestern China. Science 312:1640-1643 \n", + "\nZanno L, Makovicky P. 2011. Herbivorous ecomorphology and specialization patterns in theropod dinosaur evolution. Proceedings of the National Academy of Sciences 108:232-237 \n", + "\nZhang F, Zhou Z. 2000. A primitive enantiornithine bird and the origin of feathers. Science 290:1955-1960 \n", + "\nZheng X, Zhang Z, Hou L. 2007. A new enantiornitine bird with four long rectrices from the Early Cretaceous of northern Hebei, China. Acta Geologica Sinica 81:703-708 \n", + "\nZheng XT, Martin LD, Zhou ZH, Burnham DA, Zhang FC, Miao D. 2011. Fossil evidence of avian crops from the Early Cretaceous of China. Proceedings of the National Academy of Sciences of the United States of America 108:15904-15907 \n", + "\nZhou ZH, Clarke J, Zhang F, Wings O. 2004. Gastroliths in Yanornis: an indication of the earliest radical diet-switching and gizzard plasticity in the lineage leading to living birds. Naturwissenschaften 91:571-574 \n", + "\nZhou ZH, Martin LD. 2011. Distribution of the predentary bone in Mesozoic ornithurine birds. Journal of Systematic Palaeontology 9:25-31 \n", + "\nZhou ZH, Zhang F. 2001. Two new ornithurine birds from the Early Cretaceous of western Liaoning, China. Kexue Tongbao 46:371-377 \n", + "\nZhou ZH, Zhang F. 2005. Discovery of an ornithurine bird and its implication for Early Cretaceous avian radiation. Proceedings of the National Academy of Sciences 102:18998-19002 \n", + "\nZhou ZH, Zhang FC. 2006. A beaked basal ornithurine bird (Aves, Ornithurae) from the Lower Cretaceous of China. Zoologica Scripta 35:363-373 \n", + "\nZhou ZH, Zhang FC. 2007. Mesozoic birds of China – a synoptic review. Frontiers of Biology in China 2(1):1-14 \n", + "\nZhou ZH, Zhang FC, Li ZH. 2009. A New Basal Ornithurine Bird (Jianchangornis microdonta gen. et sp. nov.) from the Lower Cretaceous of China. Vertebrata PalAsiatica 47(4):299-310 \n", + "\nZhou S, Zhou ZH, O’Connor JK. 2012. A new toothless ornithurine bird (Schizooura lii gen. et sp. nov.) from the Lower Cretaceous of China. Vertebrata Palasiatica 50(1):9-24 \n", + "\nZhou S, Zhou ZH, O’Connor JK. 2013a. A new piscivorous ornithuromorph from the Jehol Biota. Historical Biology: An International Journal of Paleobiology \n", + "\nZhou S, Zhou ZH, O’Connor JK. 2013b. Anatomy of the Basal Ornithuromorph Bird Archaeorhynchus spathula from the Early Cretaceous of Liaoning, China. Journal of Vertebrate Paleontology 33(1):141-152 \n" ] }, "figures_html": { "value": [ - "
\"Photograph
\n

\nFigure 1: Photograph of DNHM D2945.

\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.
", - "
\"Interpretive
\n

\nFigure 2: Interpretive drawing of DNHM D2945.

\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pt, proximal tarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.
", - "
\"Photograph
\n

\nFigure 3: Photograph of DNHM D2946.

\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.
", - "
\"Interpretive
\n

\nFigure 4: Interpretive drawing of DNHM D2946.

\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; st, sternum; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.
", - "
\"Close
\n
\nFigure 5: Close up photograph of the skull of DNHM D2945 in right lateral view and detail (inset) of the central portion of its maxilla.
\nAbbreviations: al, alveoli.
", - "
\"Photograph
\n
\nFigure 6: Photograph (A) and interpretive drawing (B) of the thoracic girdle and vertebral series, rib cage, and humeri of DNHM D2946.
\nAbbreviations: co, coracoid; fu, furcula; hu, humerus; lt, lateral trabecular; ra, radius; rb, ribs; sc, scapula; sp, supracondylar process; st, sternum; up, uncinate process.
", - "
\"Photograph
\n
\nFigure 7: Photograph of the left manus of DNHM D2945/6 in ventral (A; DNHM D2945) and dorsal (B; DNHM D2946) views.
\nAbbreviations: mc I-III, metacarpals I-III; p1-I, phalanx 1 (proximal) of digit I (alular digit); p2-I, phalanx 2 (ungual) of digit I (alular digit); p1-II, phalanx 1 (proximal) of digit II (major digit); p2-II, phalanx 2 (intermediate) of digit II (major digit); p3-II, phalanx 3 (ungual) of digit II (major digit); p1-III, phalanx 1 (proximal) of digit III (minor digit); p2-III, phalanx 2 of digit III (minor digit); ra, radius; sl, semilunate carpal; ul, ulna.
", - "
\"Close
\n
\nFigure 8: Close up photograph of the right knee (medial view) and pubic symphysis (left laterocaudal view) of DNHM D2946.
\nNote the detail of the gastroliths. Abbreviations: fe, femur; fi, fibula; gl, gastroliths, pu, pubis; ti, tibia. (l) and (r) refer to the left and right pubis, respectively.
", - "
\"Close
\n
\nFigure 9: Close up photograph of the left knee (lateral view) of DNHM D2946.
\nAbbreviations: cn, cnemial crest; fc, fibular condyle; fe, femur; fi, fibula; ld, lateral articular facet of tibia; md, medial articular facet of tibia; ti, tibia.
", - "
\"Close
\n
\nFigure 10: Close up photograph of the feet and rectrices of DNHM D2945.
\nAbbreviations: mt, metatarsals; re, rectrices; I-IV, digits I-IV.
", - "
\"Interpretive
\n
\nFigure 11: Interpretive drawing of the outline of the wings and feathered tail of DNHM D2945/6 (see Figs. 1 and 3 for the maximum extent of the primaries and secondaries).
\nThe aerodynamic parameters used in this study were derived from this reconstruction (see Materials and Methods).
" + "
\"Photograph
\n

\nFigure 1: Photograph of DNHM D2945.

\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.
", + "
\"Interpretive
\n

\nFigure 2: Interpretive drawing of DNHM D2945.

\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pt, proximal tarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.
", + "
\"Photograph
\n

\nFigure 3: Photograph of DNHM D2946.

\nRed and white arrows point at the maximum extent of the primary and secondary feathers of the wing.
", + "
\"Interpretive
\n

\nFigure 4: Interpretive drawing of DNHM D2946.

\nAbbreviations: ce, cervical vertebrae; co, coracoid; fe, femur; fi, fibula; fu, furcula; gl, gastroliths; hu, humerus; il, ilium; mc, metacarpals; mt, metatarsals; pu, pubis; ra, radius; rb, ribs; re, rectrices; sc, scapula; st, sternum; sy, synsacrum; ti, tibia; ul, ulna; I–IV, digits (manual or pedal) I–IV. Numbers in inset (close up of gastrolith cluster) refer to those in Table 2.
", + "
\"Close
\n
\nFigure 5: Close up photograph of the skull of DNHM D2945 in right lateral view and detail (inset) of the central portion of its maxilla.
\nAbbreviations: al, alveoli.
", + "
\"Photograph
\n
\nFigure 6: Photograph (A) and interpretive drawing (B) of the thoracic girdle and vertebral series, rib cage, and humeri of DNHM D2946.
\nAbbreviations: co, coracoid; fu, furcula; hu, humerus; lt, lateral trabecular; ra, radius; rb, ribs; sc, scapula; sp, supracondylar process; st, sternum; up, uncinate process.
", + "
\"Photograph
\n
\nFigure 7: Photograph of the left manus of DNHM D2945/6 in ventral (A; DNHM D2945) and dorsal (B; DNHM D2946) views.
\nAbbreviations: mc I-III, metacarpals I-III; p1-I, phalanx 1 (proximal) of digit I (alular digit); p2-I, phalanx 2 (ungual) of digit I (alular digit); p1-II, phalanx 1 (proximal) of digit II (major digit); p2-II, phalanx 2 (intermediate) of digit II (major digit); p3-II, phalanx 3 (ungual) of digit II (major digit); p1-III, phalanx 1 (proximal) of digit III (minor digit); p2-III, phalanx 2 of digit III (minor digit); ra, radius; sl, semilunate carpal; ul, ulna.
", + "
\"Close
\n
\nFigure 8: Close up photograph of the right knee (medial view) and pubic symphysis (left laterocaudal view) of DNHM D2946.
\nNote the detail of the gastroliths. Abbreviations: fe, femur; fi, fibula; gl, gastroliths, pu, pubis; ti, tibia. (l) and (r) refer to the left and right pubis, respectively.
", + "
\"Close
\n
\nFigure 9: Close up photograph of the left knee (lateral view) of DNHM D2946.
\nAbbreviations: cn, cnemial crest; fc, fibular condyle; fe, femur; fi, fibula; ld, lateral articular facet of tibia; md, medial articular facet of tibia; ti, tibia.
", + "
\"Close
\n
\nFigure 10: Close up photograph of the feet and rectrices of DNHM D2945.
\nAbbreviations: mt, metatarsals; re, rectrices; I-IV, digits I-IV.
", + "
\"Interpretive
\n
\nFigure 11: Interpretive drawing of the outline of the wings and feathered tail of DNHM D2945/6 (see Figs. 1 and 3 for the maximum extent of the primaries and secondaries).
\nThe aerodynamic parameters used in this study were derived from this reconstruction (see Materials and Methods).
" ] }, "tables_html": { "value": [ - "
\nTable 1:
Comparisons of selective measurements in hongshanornithids.
\nThe values highlight the similar sizes and proportions of the three named species of hongshanornithids: Hongshanornis longicresta (DNHM D2945/6 and IVPP V14533), Parahongshanornis chaoyangensis (PMOL-AB00161), and Longicrusavis houi (PKUP 1069).\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
ElementDNHM D2945/6IVPP V14533PMOL-AB00161PKUP 1069
Skull30.530.7
Humerus24.626.029.026.0
Ulna24.524.027.025.0
Carpometacarpus13.013.012.313.1
Manual digit II18.117.7
Femur22.022.024.024.3
Tibiotarsus35.538.038.037.6
Tarsometatarsus20.622.022.021.5
Pedal digit III20.0
\n", - "
\nTable 2:
Measurements (mm) of the gastroliths of DNHM D2945/6.
\nLeft column numbers correspond to numbers on Figs. 2 and 4.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
D2945D2946Mean value
12.212.272.24
23.063.093.08
32.312.072.19
42.052.152.10
52.152.112.13
62.902.592.75
71.841.761.80
81.761.791.78
91.742.081.91
101.841.561.70
112.513.132.82
\n" + "
\nTable 1:
Comparisons of selective measurements in hongshanornithids.
\nThe values highlight the similar sizes and proportions of the three named species of hongshanornithids: Hongshanornis longicresta (DNHM D2945/6 and IVPP V14533), Parahongshanornis chaoyangensis (PMOL-AB00161), and Longicrusavis houi (PKUP 1069).\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
ElementDNHM D2945/6IVPP V14533PMOL-AB00161PKUP 1069
Skull30.530.7
Humerus24.626.029.026.0
Ulna24.524.027.025.0
Carpometacarpus13.013.012.313.1
Manual digit II18.117.7
Femur22.022.024.024.3
Tibiotarsus35.538.038.037.6
Tarsometatarsus20.622.022.021.5
Pedal digit III20.0
\n", + "
\nTable 2:
Measurements (mm) of the gastroliths of DNHM D2945/6.
\nLeft column numbers correspond to numbers on Figs. 2 and 4.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
D2945D2946Mean value
12.212.272.24
23.063.093.08
32.312.072.19
42.052.152.10
52.152.112.13
62.902.592.75
71.841.761.80
81.761.791.78
91.742.081.91
101.841.561.70
112.513.132.82
\n" ] }, "fulltext_html": { @@ -519,7 +519,7 @@ }, "fulltext_xml": { "value": [ - "/articles/234.xml" + "https://peerj.com/articles/234.xml" ] }, "supplementary_file": { @@ -552,48 +552,48 @@ "© 2014 Chiappe et al.\n" ] }, - "file_hashes": [ + "file_sizes": [ { - "fig-1-full.png": "5870a310df205fb7216bd358568a11d9" + "fig-1-full.png": 13473326 }, { - "fig-10-full.png": "d3d1eadb360073c696eef317130004e8" + "fig-10-full.png": 6633314 }, { - "fig-11-full.png": "0ce3c5edbe7822a1c6b5ea26f6cfd1c4" + "fig-11-full.png": 145753 }, { - "fig-2-full.png": "af0dbb6dbbdd9dc38ba8fdb5a4409d26" + "fig-2-full.png": 1503450 }, { - "fig-3-full.png": "165114a6bd917393af1c628e4f15cc23" + "fig-3-full.png": 12412711 }, { - "fig-4-full.png": "9e43600b181b87de53f52d1ee145aec8" + "fig-4-full.png": 1799469 }, { - "fig-5-full.png": "95ed20e2b3abffa642caccf50c73941d" + "fig-5-full.png": 6907888 }, { - "fig-6-full.png": "28860f72dcafe1bae43e29c49374e644" + "fig-6-full.png": 8116810 }, { - "fig-7-full.png": "7040496f9de9004852cf2bae90034fe7" + "fig-7-full.png": 8590384 }, { - "fig-8-full.png": "73da14b5d45b36d95a9fa8a206651336" + "fig-8-full.png": 9793225 }, { - "fig-9-full.png": "3d3868736ac56e4f2e8e6395d05df051" + "fig-9-full.png": 5894432 }, { - "fulltext.html": "d9f257ed6908df4c56ae1be06e501e89" + "fulltext.html": 358542 }, { - "fulltext.pdf": "3aa12392730333dd193322c7fb7ac72c" + "fulltext.pdf": 10641118 }, { - "fulltext.xml": "a322b65a64bb8bcb3c5756b49eeb0ad6" + "fulltext.xml": 142200 } ] }, @@ -665,7 +665,7 @@ }, "date_accepted": { "value": [ - "2014-01-26" + ] }, "date_submitted": { @@ -705,12 +705,12 @@ }, "introduction_html": { "value": [ - "

Introduction

\n

Operation of most of the glucose biosensors for continuous, non-invasive glucose monitoring in biological fluids is based on specific enzymatic glucose oxidation by glucose oxidase (Tang et al., 2004) or phosphorylation by glucokinase (Katsube et al., 1990). The main drawback of such sensors is that its sensitive element is consumable due to the irreversible nature of the reaction of sensitive elements with analyte. A more promising direction for non-invasive glucometer design is the development of a biosensor system with a protein-sensitive element those reaction with glucose is reversible. Such proteins are concanavalin A and the D-glucose/D-galactose-binding protein (GGBP). The application of GGBP is promising because the protein–glucose binding promotes a significant change in the tertiary structure of GGBP (Amiss et al., 2007; Sakaguchi-Mikami et al., 2008; Saxl et al., 2009; Yesylevskyy, Kharkyanen & Demchenko, 2006). One of the most common methods for detecting conformational changes in proteins is fluorescence. Despite the significant structural changes of GGBP that occur when it interacts with glucose the intrinsic UV fluorescence characteristics remains practically unchanged (Stepanenko et al., 2011a; Stepanenko et al., 2011b). Thus, the fluorescent response to glucose binding to GGBP could be obtained using fluorescence of dye linked to protein (Amiss et al., 2007; Khan, Gnudi & Pickup, 2008; Khan, Saxl & Pickup, 2010; Sakaguchi-Mikami et al., 2008; Saxl et al., 2011; Saxl et al., 2009) or the changes of FRET signal of chimeric constructs based on GGBP and fluorescent proteins (Ge, Tolosa & Rao, 2004; Ye & Schultz, 2003).

\n

One of the promising candidates for the role of a glucose biosensor system sensitive element is the GGBP/H152C mutant form of GGBP in which the histidine at position 152 has been replaced with a cysteine and fluorescent dye BADAN linked to the Cys 152 (Khan, Gnudi & Pickup, 2008). It was shown that the fluorescence intensity of the dye linked to the protein increased three-fold in response to binding of GGBP/H152C with glucose (the transition of GGBP/H152C from its open to closed forms) (Khan, Gnudi & Pickup, 2008; Khan, Saxl & Pickup, 2010). The replacement of histidine 152 with cysteine was used for labeling with the fluorescent dye of series of GGBP mutant forms for glucose monitoring (Khan, Saxl & Pickup, 2010; Saxl et al., 2011). Continuous glucose concentration measurements in analyzable mediums could be achieved using a protein-sensitive element having as much as possible, a high stability, and which properties do not significantly change on the possible composition variations of the biological fluids, in which to determine glucose.

\n

In this connection aim of this work was to study the effect of different external factors (i.e., changing the pH, viscosity, ionic strength of solution) on the fluorescence characteristics of the GGBP/H152C mutant in its open and closed forms and on the response time of the recorded signal to glucose change in the assay medium. One way to assess the stability of proteins is to study their unfolding under the action of chemical denaturants. Thus we also investigated denaturation GGBP/H152C under the GdnHCl and urea action.

" + "

Introduction

\n

Operation of most of the glucose biosensors for continuous, non-invasive glucose monitoring in biological fluids is based on specific enzymatic glucose oxidation by glucose oxidase (Tang et al., 2004) or phosphorylation by glucokinase (Katsube et al., 1990). The main drawback of such sensors is that its sensitive element is consumable due to the irreversible nature of the reaction of sensitive elements with analyte. A more promising direction for non-invasive glucometer design is the development of a biosensor system with a protein-sensitive element those reaction with glucose is reversible. Such proteins are concanavalin A and the D-glucose/D-galactose-binding protein (GGBP). The application of GGBP is promising because the protein–glucose binding promotes a significant change in the tertiary structure of GGBP (Amiss et al., 2007; Sakaguchi-Mikami et al., 2008; Saxl et al., 2009; Yesylevskyy, Kharkyanen & Demchenko, 2006). One of the most common methods for detecting conformational changes in proteins is fluorescence. Despite the significant structural changes of GGBP that occur when it interacts with glucose the intrinsic UV fluorescence characteristics remains practically unchanged (Stepanenko et al., 2011a; Stepanenko et al., 2011b). Thus, the fluorescent response to glucose binding to GGBP could be obtained using fluorescence of dye linked to protein (Amiss et al., 2007; Khan, Gnudi & Pickup, 2008; Khan, Saxl & Pickup, 2010; Sakaguchi-Mikami et al., 2008; Saxl et al., 2011; Saxl et al., 2009) or the changes of FRET signal of chimeric constructs based on GGBP and fluorescent proteins (Ge, Tolosa & Rao, 2004; Ye & Schultz, 2003).

\n

One of the promising candidates for the role of a glucose biosensor system sensitive element is the GGBP/H152C mutant form of GGBP in which the histidine at position 152 has been replaced with a cysteine and fluorescent dye BADAN linked to the Cys 152 (Khan, Gnudi & Pickup, 2008). It was shown that the fluorescence intensity of the dye linked to the protein increased three-fold in response to binding of GGBP/H152C with glucose (the transition of GGBP/H152C from its open to closed forms) (Khan, Gnudi & Pickup, 2008; Khan, Saxl & Pickup, 2010). The replacement of histidine 152 with cysteine was used for labeling with the fluorescent dye of series of GGBP mutant forms for glucose monitoring (Khan, Saxl & Pickup, 2010; Saxl et al., 2011). Continuous glucose concentration measurements in analyzable mediums could be achieved using a protein-sensitive element having as much as possible, a high stability, and which properties do not significantly change on the possible composition variations of the biological fluids, in which to determine glucose.

\n

In this connection aim of this work was to study the effect of different external factors (i.e., changing the pH, viscosity, ionic strength of solution) on the fluorescence characteristics of the GGBP/H152C mutant in its open and closed forms and on the response time of the recorded signal to glucose change in the assay medium. One way to assess the stability of proteins is to study their unfolding under the action of chemical denaturants. Thus we also investigated denaturation GGBP/H152C under the GdnHCl and urea action.

" ] }, "methods_html": { "value": [ - "

Materials and Methods

\n

Materials

\n

D-glucose, acetonitrile (Sigma, USA), NaCl (Vekton, Russia), fluorescent dyes BADAN and quinine sulfate (AnaSpec, USA), guanidine hydrochloride (Nacalai Tesque, Japan), and glycerol (Merck, Germany) were used without further purification. The mutant form of the D-glucose/D-galactose–binding protein GGBP/H152C was obtained, separated and purified as described previously (Stepanenko et al., 2011a). The labeling of GGBP/H152C with the fluorescent dye BADAN was performed as described by Khan, Saxl & Pickup (2010). The experiments were performed in solutions with protein concentrations ranging from 0.2 to 0.8 mg/ml. For the formation of the protein-ligand complex, 5 µM–20 mM of D-glucose was added to the protein solution. The measurements were made in buffer solutions containing citric acid and Na2HPO4 (pH 2.8, 4.2, 6.0, 7.1), PBS (pH 7.4) and TrisHCl (pH 7.2, 9.6).

Fluorescence measurements

\n

The fluorescence experiments were carried out using Cary Eclipse (Agilent, Australia) and homemade (Turoverov et al., 1998) spectrofluorimeters. The kinetics of GGBP/H152C-BADAN binding with glucose was measured using a stopped flow apparatus MOS 450 (Bio-Logic, France). The excitation wavelengths for the intrinsic protein fluorescence spectra were 297 or 280 nm. The dye fluorescence was excited at 387 or 405 nm. The position and form of the fluorescence spectra were characterized by the parameter A = I320/I365, where I320 and I365 are the fluorescence intensities measured at emission wavelengths of 320 and 365 nm, respectively (Kuznetsova, Yakusheva & Turoverov, 1999; Turoverov & Kuznetsova, 2003). The values of parameter A and the fluorescence spectra were corrected using the instrument’s spectral sensitivity. The quantum yield of BADAN fluorescence was determined according to the procedure described previously (Kuznetsova et al., 2012b). Quinine sulfate in 0.1 M H2SO4 was used as a reference solution. The measurements were made at 23°C with micro-cells (10 × 10 × 4 mm; Starna, Great Britain).

Determination of protein-ligand dissociation constant

\n

The fluorescence intensity of protein solution in the ligand presence can be determined by equation (1)IC0=αFC0IF+αBC0IB\n where IF and IB are the fluorescence intensity of protein in free state and bounded with ligand, respectively, and αF(C0) and αB(C0) are the relative fraction of this protein states in the solution at concentration of added ligand C0, αF(C0) + αB(C0) = 1. Thus, the fraction of bounded protein is determined as: (2)αB=IC0IFIBIF=CbCp\n where Cp is the total protein concentration and Cb is the concentration of protein bounded with ligand. The dissociation constant, Kd can be expressed as follows (Kuznetsova et al., 2012a): (3)Kd=receptor×ligandcomplex=CpCb×CfCb\n where Cf is concentration of free ligand, which can be calculated from the equation: (4)Cb=C0Cf\n here C0 is concentration of added ligand. Eliminating Cf from the Eq. (3), we can obtain the next equation for Cb: (5)Cb=Kd+Cp+C0Kd+Cp+C024Cp×C02.\n Combining the Eqs. (2) and (5), we have the equation for definition of Kd, using the difference of fluorescence intensity of mutant proteins in the presence and in the absence of glucose: (6)IC0=IF+IBIF×Kd+Cp+C0Kd+Cp+C024Cp×C02Cp.\n The wavelength of registration was chosen as that of the maximal difference in the fluorescence intensity of the ligand-free and bound states of the studied protein. Approximation of experimental data was performed via the nonlinear regression method using Sigma Plot program.

" + "

Materials and Methods

\n

Materials

\n

D-glucose, acetonitrile (Sigma, USA), NaCl (Vekton, Russia), fluorescent dyes BADAN and quinine sulfate (AnaSpec, USA), guanidine hydrochloride (Nacalai Tesque, Japan), and glycerol (Merck, Germany) were used without further purification. The mutant form of the D-glucose/D-galactose–binding protein GGBP/H152C was obtained, separated and purified as described previously (Stepanenko et al., 2011a). The labeling of GGBP/H152C with the fluorescent dye BADAN was performed as described by Khan, Saxl & Pickup (2010). The experiments were performed in solutions with protein concentrations ranging from 0.2 to 0.8 mg/ml. For the formation of the protein-ligand complex, 5 µM–20 mM of D-glucose was added to the protein solution. The measurements were made in buffer solutions containing citric acid and Na2HPO4 (pH 2.8, 4.2, 6.0, 7.1), PBS (pH 7.4) and TrisHCl (pH 7.2, 9.6).

Fluorescence measurements

\n

The fluorescence experiments were carried out using Cary Eclipse (Agilent, Australia) and homemade (Turoverov et al., 1998) spectrofluorimeters. The kinetics of GGBP/H152C-BADAN binding with glucose was measured using a stopped flow apparatus MOS 450 (Bio-Logic, France). The excitation wavelengths for the intrinsic protein fluorescence spectra were 297 or 280 nm. The dye fluorescence was excited at 387 or 405 nm. The position and form of the fluorescence spectra were characterized by the parameter A = I320/I365, where I320 and I365 are the fluorescence intensities measured at emission wavelengths of 320 and 365 nm, respectively (Kuznetsova, Yakusheva & Turoverov, 1999; Turoverov & Kuznetsova, 2003). The values of parameter A and the fluorescence spectra were corrected using the instrument’s spectral sensitivity. The quantum yield of BADAN fluorescence was determined according to the procedure described previously (Kuznetsova et al., 2012b). Quinine sulfate in 0.1 M H2SO4 was used as a reference solution. The measurements were made at 23°C with micro-cells (10 × 10 × 4 mm; Starna, Great Britain).

Determination of protein-ligand dissociation constant

\n

The fluorescence intensity of protein solution in the ligand presence can be determined by equation (1)IC0=αFC0IF+αBC0IB\n where IF and IB are the fluorescence intensity of protein in free state and bounded with ligand, respectively, and αF(C0) and αB(C0) are the relative fraction of this protein states in the solution at concentration of added ligand C0, αF(C0) + αB(C0) = 1. Thus, the fraction of bounded protein is determined as: (2)αB=IC0IFIBIF=CbCp\n where Cp is the total protein concentration and Cb is the concentration of protein bounded with ligand. The dissociation constant, Kd can be expressed as follows (Kuznetsova et al., 2012a): (3)Kd=receptor×ligandcomplex=CpCb×CfCb\n where Cf is concentration of free ligand, which can be calculated from the equation: (4)Cb=C0Cf\n here C0 is concentration of added ligand. Eliminating Cf from the Eq. (3), we can obtain the next equation for Cb: (5)Cb=Kd+Cp+C0Kd+Cp+C024Cp×C02.\n Combining the Eqs. (2) and (5), we have the equation for definition of Kd, using the difference of fluorescence intensity of mutant proteins in the presence and in the absence of glucose: (6)IC0=IF+IBIF×Kd+Cp+C0Kd+Cp+C024Cp×C02Cp.\n The wavelength of registration was chosen as that of the maximal difference in the fluorescence intensity of the ligand-free and bound states of the studied protein. Approximation of experimental data was performed via the nonlinear regression method using Sigma Plot program.

" ] }, "results_html": { @@ -740,53 +740,53 @@ }, "references_html": { "value": [ - "\nAmiss TJ, Sherman DB, Nycz CM, Andaluz SA, Pitner JB. 2007. Engineering and rapid selection of a low-affinity glucose/galactose-binding protein for a glucose biosensor. Protein Science 16:2350-2359 \n", - "\nBongrand P. 1999. Ligand–receptor interactions. Reports on Progress in Physics 62:921-968 \n", - "\nBorrok MJ, Kiessling LL, Forest KT. 2007. Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures. Protein Science 16:1032-1041 \n", - "\nDintenfass L. 1985. Blood viscosity, hyperviscosity, and hyperviscosaemia. Netherlands: Kluwer Academic Publishers Group. \n", - "\nGe X, Rao G, Tolosa L. 2008. On the possibility of real-time monitoring of glucose in cell culture by microdialysis using a fluorescent glucose binding protein sensor. Biotechnology Progress 24:691-697 \n", - "\nGe X, Tolosa L, Rao G. 2004. Dual-labeled glucose binding protein for ratiometric measurements of glucose. Analytical Chemistry 76:1403-1410 \n", - "\nHeinemann L. 2003. Continuous glucose monitoring by means of the microdialysis technique: underlying fundamental aspects. Diabetes Technology & Therapeutics 5:545-561 \n", - "\nKatsube T, Katoh M, Maekawa H, Hara M, Yamaguchi S, Uchida N, Shimomura T. 1990. Stabilization of an FET glucose sensor with the thermophilic enzyme glucokinase. Sensors and Actuators B: Chemical 1:504-507 \n", - "\nKhan F, Gnudi L, Pickup JC. 2008. Fluorescence-based sensing of glucose using engineered glucose/galactose-binding protein: a comparison of fluorescence resonance energy transfer and environmentally sensitive dye labelling strategies. Biochemical and Biophysical Research Communications 365:102-106 \n", - "\nKhan F, Saxl TE, Pickup JC. 2010. Fluorescence intensity- and lifetime-based glucose sensing using an engineered high-Kd mutant of glucose/galactose-binding protein. Analytical Biochemistry 399:39-43 \n", - "\nKoehorst RB, Spruijt RB, Hemminga MA. 2008. Site-directed fluorescence labeling of a membrane protein with BADAN: probing protein topology and local environment. Biophysical Journal 94:3945-3955 \n", - "\nKost J, Mitragotri S, Gabbay RA, Pishko M, Langer R. 2000. Transdermal monitoring of glucose and other analytes using ultrasound. Nature Medicine 6:347-350 \n", - "\nKuznetsova IM, Stepanenko Olga V, Turoverov KK, Zhu L, Zhou JM, Fink AL, Uversky VN. 2002. Unraveling multistate unfolding of rabbit muscle creatine kinase. Biochimica et Biophysica Acta/Protein Structure and Molecular Enzimology 1596:138-155 \n", - "\nKuznetsova IM, Sulatskaya AI, Povarova OI, Turoverov KK. 2012a. Reevaluation of ANS binding to human and bovine serum albumins: key role of equilibrium microdialysis in ligand-receptor binding characterization. PLoS ONE 7:e40845 \n", - "\nKuznetsova IM, Sulatskaya AI, Uversky VN, Turoverov KK. 2012b. A new trend in the experimental methodology for the analysis of the thioflavin T binding to amyloid fibrils. Molecular Neurobiology 45:488-498 \n", - "\nKuznetsova IM, Yakusheva TA, Turoverov KK. 1999. Contribution of separate tryptophan residues to intrinsic fluorescence of actin. Analysis of 3D structure. FEBS Letters 452:205-210 \n", - "\nLoutfy RO, Arnold BA. 1982. Effect of viscosity and temperature on torsional relaxation of molecular rotors. The Journal of Physical Chemistry 86:4205-4211 \n", - "\nOliver NS, Toumazou C, Cass AE, Johnston DG. 2009. Glucose sensors: a review of current and emerging technology. Diabetic Medicine 26:197-210 \n", - "\nOwenius R, Osterlund M, Lindgren M, Svensson M, Olsen OH, Persson E, Freskgard PO, Carlsson U. 1999. Properties of spin and fluorescent labels at a receptor–ligand interface. Biophysical Journal 77:2237-2250 \n", - "\nPovarova OI, Kuznetsova IM, Turoverov KK. 2010. Differences in the pathways of proteins unfolding induced by urea and guanidine hydrochloride: molten globule state and aggregates. PLoS ONE 5:e15035 \n", - "\nRenard E. 2005. Monitoring glycemic control: the importance of self-monitoring of blood glucose. American Journal of Medicine 118:12S-19S \n", - "\nRhee SY, Chon S, Koh G, Paeng JR, Oh S, Woo JT, Kim SW, Kim JW, Kim YS. 2007. Clinical experience of an iontophoresis based glucose measuring system. Journal of Korean Medical Science 22:70-73 \n", - "\nSakaguchi-Mikami A, Taneoka A, Yamoto R, Ferri S, Sode K. 2008. Engineering of ligand specificity of periplasmic binding protein for glucose sensing. Biotechnology Letters 30:1453-1460 \n", - "\nSaxl T, Khan F, Ferla M, Birch D, Pickup J. 2011. A fluorescence lifetime-based fibre-optic glucose sensor using glucose/galactose-binding protein. Analyst 136:968-972 \n", - "\nSaxl T, Khan F, Matthews DR, Zhi ZL, Rolinski O, Ameer-Beg S, Pickup J. 2009. Fluorescence lifetime spectroscopy and imaging of nano-engineered glucose sensor microcapsules based on glucose/galactose-binding protein. Biosensors and Bioelectronics 24:3229-3234 \n", - "\nStepanenko Olga V, Fonin AV, Morozova KS, Verkhusha VV, Kuznetsova IM, Turoverov KK, Staiano M, D’Auria S. 2011a. New insight in protein-ligand interactions. 2. Stability and properties of two mutant forms of the D-galactose/D-glucose-binding protein from E. coli. The Journal of Physical Chemistry B 115:9022-9032 \n", - "\nStepanenko Olga V, Povarova OI, Fonin AV, Kuznetsova IM, Turoverov KK, Staiano M, Varriale A, D’Auria S. 2011b. New insight into protein-ligand interactions. The case of the D-galactose/D-glucose-binding protein from Escherichia coli. The Journal of Physical Chemistry B 115:2765-2773 \n", - "\nStepanenko Olesya V, Verkhusha VV, Kazakov VI, Shavlovsky MM, Kuznetsova IM, Uversky VN, Turoverov KK. 2004. Comparative studies on the structure and stability of fluorescent proteins EGFP, zFP506, mRFP1, “dimer2”, and DsRed1. Biochemistry 43:14913-14923 \n", - "\nTang H, Chen J, Yao S, Nie L, Deng G, Kuang Y. 2004. Amperometric glucose biosensor based on adsorption of glucose oxidase at platinum nanoparticle-modified carbon nanotube electrode. Analytical Biochemistry 331:89-97 \n", - "\nTolosa L, Gryczynski I, Eichhorn LR, Dattelbaum JD, Castellano FN, Rao G, Lakowicz JR. 1999. Glucose sensor for low-cost lifetime-based sensing using a genetically engineered protein. Analytical Biochemistry 267:114-120 \n", - "\nTuroverov KK, Biktashev AG, Dorofeiuk AV, Kuznetsova IM. 1998. A complex of apparatus and programs for the measurement of spectral, polarization and kinetic characteristics of fluorescence in solution. Tsitologiia 40:806-817 \n", - "\nTuroverov KK, Kuznetsova IM. 2003. Intrinsic fluorescence of actin. Journal of Fluorescence 13:41-57 \n", - "\nVerkhusha VV, Kuznetsova IM, Stepanenko Olesya V, Zaraisky AG, Shavlovsky MM, Turoverov KK, Uversky VN. 2003. High stability of Discosoma DsRed as compared to Aequorea EGFP. Biochemistry 42:7879-7884 \n", - "\nVyas NK, Vyas MN, Quiocho FA. 1988. Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. Science 242:1290-1295 \n", - "\nYe K, Schultz JS. 2003. Genetic engineering of an allosterically based glucose indicator protein for continuous glucose monitoring by fluorescence resonance energy transfer. Analytical Chemistry 75:3451-3459 \n", - "\nYesylevskyy SO, Kharkyanen VN, Demchenko AP. 2006. The change of protein intradomain mobility on ligand binding: is it a commonly observed phenomenon? Biophysical Journal 91:3002-3013 \n" + "\nAmiss TJ, Sherman DB, Nycz CM, Andaluz SA, Pitner JB. 2007. Engineering and rapid selection of a low-affinity glucose/galactose-binding protein for a glucose biosensor. Protein Science 16:2350-2359 \n", + "\nBongrand P. 1999. Ligand–receptor interactions. Reports on Progress in Physics 62:921-968 \n", + "\nBorrok MJ, Kiessling LL, Forest KT. 2007. Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures. Protein Science 16:1032-1041 \n", + "\nDintenfass L. 1985. Blood viscosity, hyperviscosity, and hyperviscosaemia. Netherlands: Kluwer Academic Publishers Group. \n", + "\nGe X, Rao G, Tolosa L. 2008. On the possibility of real-time monitoring of glucose in cell culture by microdialysis using a fluorescent glucose binding protein sensor. Biotechnology Progress 24:691-697 \n", + "\nGe X, Tolosa L, Rao G. 2004. Dual-labeled glucose binding protein for ratiometric measurements of glucose. Analytical Chemistry 76:1403-1410 \n", + "\nHeinemann L. 2003. Continuous glucose monitoring by means of the microdialysis technique: underlying fundamental aspects. Diabetes Technology & Therapeutics 5:545-561 \n", + "\nKatsube T, Katoh M, Maekawa H, Hara M, Yamaguchi S, Uchida N, Shimomura T. 1990. Stabilization of an FET glucose sensor with the thermophilic enzyme glucokinase. Sensors and Actuators B: Chemical 1:504-507 \n", + "\nKhan F, Gnudi L, Pickup JC. 2008. Fluorescence-based sensing of glucose using engineered glucose/galactose-binding protein: a comparison of fluorescence resonance energy transfer and environmentally sensitive dye labelling strategies. Biochemical and Biophysical Research Communications 365:102-106 \n", + "\nKhan F, Saxl TE, Pickup JC. 2010. Fluorescence intensity- and lifetime-based glucose sensing using an engineered high-Kd mutant of glucose/galactose-binding protein. Analytical Biochemistry 399:39-43 \n", + "\nKoehorst RB, Spruijt RB, Hemminga MA. 2008. Site-directed fluorescence labeling of a membrane protein with BADAN: probing protein topology and local environment. Biophysical Journal 94:3945-3955 \n", + "\nKost J, Mitragotri S, Gabbay RA, Pishko M, Langer R. 2000. Transdermal monitoring of glucose and other analytes using ultrasound. Nature Medicine 6:347-350 \n", + "\nKuznetsova IM, Stepanenko Olga V, Turoverov KK, Zhu L, Zhou JM, Fink AL, Uversky VN. 2002. Unraveling multistate unfolding of rabbit muscle creatine kinase. Biochimica et Biophysica Acta/Protein Structure and Molecular Enzimology 1596:138-155 \n", + "\nKuznetsova IM, Sulatskaya AI, Povarova OI, Turoverov KK. 2012a. Reevaluation of ANS binding to human and bovine serum albumins: key role of equilibrium microdialysis in ligand-receptor binding characterization. PLoS ONE 7:e40845 \n", + "\nKuznetsova IM, Sulatskaya AI, Uversky VN, Turoverov KK. 2012b. A new trend in the experimental methodology for the analysis of the thioflavin T binding to amyloid fibrils. Molecular Neurobiology 45:488-498 \n", + "\nKuznetsova IM, Yakusheva TA, Turoverov KK. 1999. Contribution of separate tryptophan residues to intrinsic fluorescence of actin. Analysis of 3D structure. FEBS Letters 452:205-210 \n", + "\nLoutfy RO, Arnold BA. 1982. Effect of viscosity and temperature on torsional relaxation of molecular rotors. The Journal of Physical Chemistry 86:4205-4211 \n", + "\nOliver NS, Toumazou C, Cass AE, Johnston DG. 2009. Glucose sensors: a review of current and emerging technology. Diabetic Medicine 26:197-210 \n", + "\nOwenius R, Osterlund M, Lindgren M, Svensson M, Olsen OH, Persson E, Freskgard PO, Carlsson U. 1999. Properties of spin and fluorescent labels at a receptor–ligand interface. Biophysical Journal 77:2237-2250 \n", + "\nPovarova OI, Kuznetsova IM, Turoverov KK. 2010. Differences in the pathways of proteins unfolding induced by urea and guanidine hydrochloride: molten globule state and aggregates. PLoS ONE 5:e15035 \n", + "\nRenard E. 2005. Monitoring glycemic control: the importance of self-monitoring of blood glucose. American Journal of Medicine 118:12S-19S \n", + "\nRhee SY, Chon S, Koh G, Paeng JR, Oh S, Woo JT, Kim SW, Kim JW, Kim YS. 2007. Clinical experience of an iontophoresis based glucose measuring system. Journal of Korean Medical Science 22:70-73 \n", + "\nSakaguchi-Mikami A, Taneoka A, Yamoto R, Ferri S, Sode K. 2008. Engineering of ligand specificity of periplasmic binding protein for glucose sensing. Biotechnology Letters 30:1453-1460 \n", + "\nSaxl T, Khan F, Ferla M, Birch D, Pickup J. 2011. A fluorescence lifetime-based fibre-optic glucose sensor using glucose/galactose-binding protein. Analyst 136:968-972 \n", + "\nSaxl T, Khan F, Matthews DR, Zhi ZL, Rolinski O, Ameer-Beg S, Pickup J. 2009. Fluorescence lifetime spectroscopy and imaging of nano-engineered glucose sensor microcapsules based on glucose/galactose-binding protein. Biosensors and Bioelectronics 24:3229-3234 \n", + "\nStepanenko Olga V, Fonin AV, Morozova KS, Verkhusha VV, Kuznetsova IM, Turoverov KK, Staiano M, D’Auria S. 2011a. New insight in protein-ligand interactions. 2. Stability and properties of two mutant forms of the D-galactose/D-glucose-binding protein from E. coli. The Journal of Physical Chemistry B 115:9022-9032 \n", + "\nStepanenko Olga V, Povarova OI, Fonin AV, Kuznetsova IM, Turoverov KK, Staiano M, Varriale A, D’Auria S. 2011b. New insight into protein-ligand interactions. The case of the D-galactose/D-glucose-binding protein from Escherichia coli. The Journal of Physical Chemistry B 115:2765-2773 \n", + "\nStepanenko Olesya V, Verkhusha VV, Kazakov VI, Shavlovsky MM, Kuznetsova IM, Uversky VN, Turoverov KK. 2004. Comparative studies on the structure and stability of fluorescent proteins EGFP, zFP506, mRFP1, “dimer2”, and DsRed1. Biochemistry 43:14913-14923 \n", + "\nTang H, Chen J, Yao S, Nie L, Deng G, Kuang Y. 2004. Amperometric glucose biosensor based on adsorption of glucose oxidase at platinum nanoparticle-modified carbon nanotube electrode. Analytical Biochemistry 331:89-97 \n", + "\nTolosa L, Gryczynski I, Eichhorn LR, Dattelbaum JD, Castellano FN, Rao G, Lakowicz JR. 1999. Glucose sensor for low-cost lifetime-based sensing using a genetically engineered protein. Analytical Biochemistry 267:114-120 \n", + "\nTuroverov KK, Biktashev AG, Dorofeiuk AV, Kuznetsova IM. 1998. A complex of apparatus and programs for the measurement of spectral, polarization and kinetic characteristics of fluorescence in solution. Tsitologiia 40:806-817 \n", + "\nTuroverov KK, Kuznetsova IM. 2003. Intrinsic fluorescence of actin. Journal of Fluorescence 13:41-57 \n", + "\nVerkhusha VV, Kuznetsova IM, Stepanenko Olesya V, Zaraisky AG, Shavlovsky MM, Turoverov KK, Uversky VN. 2003. High stability of Discosoma DsRed as compared to Aequorea EGFP. Biochemistry 42:7879-7884 \n", + "\nVyas NK, Vyas MN, Quiocho FA. 1988. Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. Science 242:1290-1295 \n", + "\nYe K, Schultz JS. 2003. Genetic engineering of an allosterically based glucose indicator protein for continuous glucose monitoring by fluorescence resonance energy transfer. Analytical Chemistry 75:3451-3459 \n", + "\nYesylevskyy SO, Kharkyanen VN, Demchenko AP. 2006. The change of protein intradomain mobility on ligand binding: is it a commonly observed phenomenon? Biophysical Journal 91:3002-3013 \n" ] }, "figures_html": { "value": [ - "
\"Determination
\n

\nFigure 1: Determination of the dissociation constant (Kd) of the complex of GGBP/H152C-BADAN with glucose (Glc).

\nThe excitation wavelength was 387 nm, the emission wavelength was 545 nm.
", - "
\"The
\n

\nFigure 2: The kinetics of Glc binding to GGBP/H152C-BADAN in solutions with different viscosities.

\nGlc concentration was 20 mM. The excitation wavelength was 405 nm. Curve 1, 2 and 3 represents the control, Glc binding to GGBP/H152C-BADAN in a PBS solution, and in PBS-glycerol solution with viscosity equal to 4.0 cP. Inset: The kinetic curves 1 and 2 in interval from 0.01 to 0.08 s are given.
", - "
\"The
\n

\nFigure 3: The effect of solvent viscosity and temperature on the fluorescence quantum yield of the GGBP/H152C-BADAN in the open (circles) and closed (triangles) forms.

\nThe excitation wavelength was 387 nm.
", - "
\"GdnHCl-induced
\n

\nFigure 4: GdnHCl-induced (A, B) and urea-induced (C, D) conformational changing of GGBP/H152C-BADAN structure in open (circles) and closed forms (triangles).

\n(A) and (C) represents the dependence of the fluorescence intensity (the excitation wavelength was 387 nm, the emission wavelength was 545 nm) on the denaturants concentration. (B) and (D) represents the dependence of the parameter A = I320/I365 (I320 and I365 fluorescence intensities recorded at 320 and 365 nm, respectively) on the denaturants concentration (the excitation wavelength was 297 nm).
", - "
\"Changes
\n

\nFigure 5: Changes of ellipticity at 222 nm of GGBP/H152C-BADAN and GGBP/H152C-BADAN–Glc on the GdnHCl concentration.

\n
", - "
\"The
\n

\nFigure 6: The effect of the pH solution on the fluorescent characteristics of GGBP/H152C-BADAN in the open (the solid curves) and closed (the dashed curves) forms.

\n(A) The excitation wavelength was 297 nm. (B) The excitation wavelength was 387 nm. The pH values of the solution were 2.8 (black curves), 4.2 (red curves), 6.4 (blue curves), 7.4 (dark green curves) and 9.6 (dark red curves).
", - "
\"The
\n

\nFigure 7: The effect of NaCl and MgCl2 on the fluorescent characteristics of GGBP/H152C-BADAN in open (solid curves) and closed (dashed curves) forms.

\n(A) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.8 M NaCl (red curve) and 2.5 M NaCl (blue curve). (B) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.1 M MgCl2 (red curve) and 0.5 M MgCl2 (blue curve). The fluorescence spectra of GGBP/H152C-BADAN in PBS solution appear in black. (The excitation wavelength was 387 nm.)
" + "
\"Determination
\n

\nFigure 1: Determination of the dissociation constant (Kd) of the complex of GGBP/H152C-BADAN with glucose (Glc).

\nThe excitation wavelength was 387 nm, the emission wavelength was 545 nm.
", + "
\"The
\n

\nFigure 2: The kinetics of Glc binding to GGBP/H152C-BADAN in solutions with different viscosities.

\nGlc concentration was 20 mM. The excitation wavelength was 405 nm. Curve 1, 2 and 3 represents the control, Glc binding to GGBP/H152C-BADAN in a PBS solution, and in PBS-glycerol solution with viscosity equal to 4.0 cP. Inset: The kinetic curves 1 and 2 in interval from 0.01 to 0.08 s are given.
", + "
\"The
\n

\nFigure 3: The effect of solvent viscosity and temperature on the fluorescence quantum yield of the GGBP/H152C-BADAN in the open (circles) and closed (triangles) forms.

\nThe excitation wavelength was 387 nm.
", + "
\"GdnHCl-induced
\n

\nFigure 4: GdnHCl-induced (A, B) and urea-induced (C, D) conformational changing of GGBP/H152C-BADAN structure in open (circles) and closed forms (triangles).

\n(A) and (C) represents the dependence of the fluorescence intensity (the excitation wavelength was 387 nm, the emission wavelength was 545 nm) on the denaturants concentration. (B) and (D) represents the dependence of the parameter A = I320/I365 (I320 and I365 fluorescence intensities recorded at 320 and 365 nm, respectively) on the denaturants concentration (the excitation wavelength was 297 nm).
", + "
\"Changes
\n

\nFigure 5: Changes of ellipticity at 222 nm of GGBP/H152C-BADAN and GGBP/H152C-BADAN–Glc on the GdnHCl concentration.

\n
", + "
\"The
\n

\nFigure 6: The effect of the pH solution on the fluorescent characteristics of GGBP/H152C-BADAN in the open (the solid curves) and closed (the dashed curves) forms.

\n(A) The excitation wavelength was 297 nm. (B) The excitation wavelength was 387 nm. The pH values of the solution were 2.8 (black curves), 4.2 (red curves), 6.4 (blue curves), 7.4 (dark green curves) and 9.6 (dark red curves).
", + "
\"The
\n

\nFigure 7: The effect of NaCl and MgCl2 on the fluorescent characteristics of GGBP/H152C-BADAN in open (solid curves) and closed (dashed curves) forms.

\n(A) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.8 M NaCl (red curve) and 2.5 M NaCl (blue curve). (B) Fluorescence spectra of GGBP/H152C-BADAN in solutions with 0.1 M MgCl2 (red curve) and 0.5 M MgCl2 (blue curve). The fluorescence spectra of GGBP/H152C-BADAN in PBS solution appear in black. (The excitation wavelength was 387 nm.)
" ] }, "tables_html": { @@ -806,7 +806,7 @@ }, "fulltext_xml": { "value": [ - "/articles/275.xml" + "https://peerj.com/articles/275.xml" ] }, "supplementary_file": { @@ -835,36 +835,36 @@ "© 2014 Fonin et al.\n" ] }, - "file_hashes": [ + "file_sizes": [ { - "fig-1-full.png": "3698cf17a11ba9ef9183634bd3801b49" + "fig-1-full.png": 49431 }, { - "fig-2-full.png": "90442c7e0490029e4d59193979537f6a" + "fig-2-full.png": 86562 }, { - "fig-3-full.png": "c41e4a8c837cfe6aeabff81982844a98" + "fig-3-full.png": 59437 }, { - "fig-4-full.png": "e3ea581b9d3ae478cc5c7e3c630576e8" + "fig-4-full.png": 228283 }, { - "fig-5-full.png": "97904c56a6215db7065fd1830624f708" + "fig-5-full.png": 91615 }, { - "fig-6-full.png": "fff6b0de359e83441f6b5838d862fd93" + "fig-6-full.png": 424165 }, { - "fig-7-full.png": "b76d31a596a07e5ef4fe238d687c5729" + "fig-7-full.png": 336068 }, { - "fulltext.html": "bda96b3c9b38dda43393d8f36acf393c" + "fulltext.html": 212387 }, { - "fulltext.pdf": "6b554c704f1ed7a8129863a2869036eb" + "fulltext.pdf": 1036931 }, { - "fulltext.xml": "033fb090781f7a84c4e7b5ac43dec2b6" + "fulltext.xml": 94055 } ] }, @@ -920,7 +920,7 @@ }, "date_accepted": { "value": [ - "2014-02-26" + ] }, "date_submitted": { @@ -960,22 +960,22 @@ }, "introduction_html": { "value": [ - "

Introduction

\n

Attendance at religious services is usually reported to be inversely related to depression (Baetz et al., 2004; Balbuena, Baetz & Bowen, 2013; Hayward et al., 2012; Maselko, Gilman & Buka, 2009). However, as with many findings in the literature on religion and depression, the results have not been consistent, with other studies reporting a null (Ellison & Flannelly, 2009; Miller et al., 2012; Schnittker, 2001) or curvilinear relationship of attendance and depression (Taylor, Chatters & Nguyen, 2013). This inconsistency has been due in part to the predominance of cross-sectional designs, which cannot establish causation. We are aware of only three longitudinal studies examining the relation of depression to subsequent religious attendance. Recently, it was reported (Maselko et al., 2012) that women having an onset of depression prior to age 18 were more likely to stop attending religious services as adults compared to those with adult-onset MDE and those with no lifetime MDE. Similarly, a longitudinal study (Horowitz & Garber, 2003) reported that depressive episodes in grades 7–11 predicted lower levels of religious attendance in grade 12. The latter result is ambiguous because religious attendance in grade 6 also predicted lower odds of depression in grades 7–12, although the effect was just shy of statistical significance. Miller and colleagues (2002) followed a cohort of 146 individuals who had an MDE in childhood together with a control group of 123 who had no psychiatric disorder over 11 years. At follow-up, the rates of religious attendance between groups did not differ by childhood depression status. It is noteworthy that these studies covered the adolescence-to-adult transition period. Late adolescence is generally a time of profound change. The quest to establish one’s identity and career (Arnett, 2000) and experimentation with cohabitation, drugs, and alcohol (Benda & Corwyn, 1997; Thornton, Axinn & Hill, 1992; Uecker, Regnerus & Vaaler, 2007) could precipitate internal conflicts with religious doctrine, leading to declines in religious attendance. In short, the developmental processes occurring during adolescence confounds the relation of depression with religious attendance, in either causal direction.

\n

Selection effects might work in two ways to confound the relation of depression with subsequent religious attendance. First, depressed individuals may withdraw from public worship as part of the overall social disengagement that occurs in depression (Maselko et al., 2012). Secondly, churchgoers might be less susceptible to depression. A meta-analysis of 94 studies reported a positive correlation of agreeableness, conscientiousness, and sociability with religious social investment (Lodi-Smith & Roberts, 2007). In summary, theory suggests that depressed individuals select themselves out of the churchgoing demographic while healthy ones select themselves into it. These selection effects, if operative, would likely overestimate the protective value of religion for mental health.

\n

The protective value of religiosity does have empirical support. Coping with adversity through religion is well-documented in the literature (Pargament, 1997). “Turning to God or religion” as a coping strategy has been reported in cancer patients (Bussing, Ostermann & Koenig, 2007), newly bereaved individuals (Brown et al., 2004), and new immigrants (Connor, 2009). A study comparing religiosity and spirituality before and after HIV patients were informed of the diagnosis (Ironson, Stuetzle & Fletcher, 2006) reported that religiosity (including attendance) increased after the diagnosis became known. Furthermore, increased religiosity was associated with greater CD4 helper cells in the blood, indicating slower HIV progression (Ironson, Stuetzle & Fletcher, 2006). A US longitudinal study reported that depressed individuals were more likely to seek religious consolation—defined as searching for meaning in problems and difficulties (Ferraro & Kelley-Moore, 2000). Importantly, even those with no initial religious affiliation sought religious consolation after depression. This finding seems to support the “no atheists in foxholes” aphorism. However, adversity or trauma can also cause individuals to turn away from God or religion (Chen & Koenig, 2006; Fontana & Rosenheck, 2004). We are not aware of longitudinal studies reporting changes to religious attendance per se (vis-a-vis religiosity broadly speaking) after a depressive episode aside from the three studies in adolescence (Horowitz & Garber, 2003; Maselko et al., 2012; Miller et al., 2002) already mentioned.

\n

In this paper, our main objective was to study whether elevated depressive symptoms introduce selection bias in a longitudinal follow-up of religious attendance. Our research questions were as follows. First, do religious attenders who develop elevated depressive symptoms subsequently decrease their attendance level? Second, do non-attenders who develop elevated symptoms begin to attend services?

" + "

Introduction

\n

Attendance at religious services is usually reported to be inversely related to depression (Baetz et al., 2004; Balbuena, Baetz & Bowen, 2013; Hayward et al., 2012; Maselko, Gilman & Buka, 2009). However, as with many findings in the literature on religion and depression, the results have not been consistent, with other studies reporting a null (Ellison & Flannelly, 2009; Miller et al., 2012; Schnittker, 2001) or curvilinear relationship of attendance and depression (Taylor, Chatters & Nguyen, 2013). This inconsistency has been due in part to the predominance of cross-sectional designs, which cannot establish causation. We are aware of only three longitudinal studies examining the relation of depression to subsequent religious attendance. Recently, it was reported (Maselko et al., 2012) that women having an onset of depression prior to age 18 were more likely to stop attending religious services as adults compared to those with adult-onset MDE and those with no lifetime MDE. Similarly, a longitudinal study (Horowitz & Garber, 2003) reported that depressive episodes in grades 7–11 predicted lower levels of religious attendance in grade 12. The latter result is ambiguous because religious attendance in grade 6 also predicted lower odds of depression in grades 7–12, although the effect was just shy of statistical significance. Miller and colleagues (2002) followed a cohort of 146 individuals who had an MDE in childhood together with a control group of 123 who had no psychiatric disorder over 11 years. At follow-up, the rates of religious attendance between groups did not differ by childhood depression status. It is noteworthy that these studies covered the adolescence-to-adult transition period. Late adolescence is generally a time of profound change. The quest to establish one’s identity and career (Arnett, 2000) and experimentation with cohabitation, drugs, and alcohol (Benda & Corwyn, 1997; Thornton, Axinn & Hill, 1992; Uecker, Regnerus & Vaaler, 2007) could precipitate internal conflicts with religious doctrine, leading to declines in religious attendance. In short, the developmental processes occurring during adolescence confounds the relation of depression with religious attendance, in either causal direction.

\n

Selection effects might work in two ways to confound the relation of depression with subsequent religious attendance. First, depressed individuals may withdraw from public worship as part of the overall social disengagement that occurs in depression (Maselko et al., 2012). Secondly, churchgoers might be less susceptible to depression. A meta-analysis of 94 studies reported a positive correlation of agreeableness, conscientiousness, and sociability with religious social investment (Lodi-Smith & Roberts, 2007). In summary, theory suggests that depressed individuals select themselves out of the churchgoing demographic while healthy ones select themselves into it. These selection effects, if operative, would likely overestimate the protective value of religion for mental health.

\n

The protective value of religiosity does have empirical support. Coping with adversity through religion is well-documented in the literature (Pargament, 1997). “Turning to God or religion” as a coping strategy has been reported in cancer patients (Bussing, Ostermann & Koenig, 2007), newly bereaved individuals (Brown et al., 2004), and new immigrants (Connor, 2009). A study comparing religiosity and spirituality before and after HIV patients were informed of the diagnosis (Ironson, Stuetzle & Fletcher, 2006) reported that religiosity (including attendance) increased after the diagnosis became known. Furthermore, increased religiosity was associated with greater CD4 helper cells in the blood, indicating slower HIV progression (Ironson, Stuetzle & Fletcher, 2006). A US longitudinal study reported that depressed individuals were more likely to seek religious consolation—defined as searching for meaning in problems and difficulties (Ferraro & Kelley-Moore, 2000). Importantly, even those with no initial religious affiliation sought religious consolation after depression. This finding seems to support the “no atheists in foxholes” aphorism. However, adversity or trauma can also cause individuals to turn away from God or religion (Chen & Koenig, 2006; Fontana & Rosenheck, 2004). We are not aware of longitudinal studies reporting changes to religious attendance per se (vis-a-vis religiosity broadly speaking) after a depressive episode aside from the three studies in adolescence (Horowitz & Garber, 2003; Maselko et al., 2012; Miller et al., 2002) already mentioned.

\n

In this paper, our main objective was to study whether elevated depressive symptoms introduce selection bias in a longitudinal follow-up of religious attendance. Our research questions were as follows. First, do religious attenders who develop elevated depressive symptoms subsequently decrease their attendance level? Second, do non-attenders who develop elevated symptoms begin to attend services?

" ] }, "methods_html": { "value": [ - "

Materials and Methods

\n

Sample

\n

The data is from the Longitudinal Internet Studies for the Social Sciences (LISS) panel, a random sample of adults living in the Netherlands (Scherpenzeel, 2011). The panel of almost 8,000 individuals was drawn from the Dutch-speaking population based on a list of addresses provided by Statistics Netherlands. The recruitment strategy is described in more detail elsewhere (Scherpenzeel, 2011). LISS is a continuing study in which participants complete online questionnaires monthly on topics including family, economic situation, health, and religion. Each LISS participant has a unique member ID, so it is possible to combine their responses across different survey modules and from one wave to another. For the purpose of our study, we merged the religion (n = 7, 418) and mental health (n = 1, 804) modules, narrowing our sample to those who responded to both surveys (n = 1, 718) (see Fig. 1A). Waves of religion and depression assessments were not simultaneous, so hereafter, use the notations Ri and Di to refer to religion and depression waves, respectively (see Fig. 1B). Our research question requires the following temporal sequence: R1 → D2 to D4 → R2. By comparing attendance level at R2 with R1, we can test whether depression predicts a relative decrease at R2. This design requirement forced us to exclude those individuals (n = 41) who had a different sequence of assessments:

\n

D1 → D2 → R1 → D2 to D4 since for these individuals, one cannot compare attendance levels before and after depression. Our effective sample size was 1,673.

\n
\"Subjects.\"
\n

\nFigure 1: Subjects.

\n(A) LISS datasets used and participant flowchart; (B) schedule of religion and depression assessments.

In the sample, 887 individuals did not attend services and 786 attended services at R1. (Explained in Measures section below.) The characteristics of these groups are described in Table 1. After baseline assessment, D1, depression was assessed during a seven-month span from March to September 2008 while attendance was assessed another four times in addition to R1, and these assessments occurred on each January from 2009 to 2012. Our main analytic strategy was to compare the proportion of individuals that changed their attendance level, stratified by baseline attendance. The change in attendance level was indexed to R1 attendance since there were no further depression assessments after September 2008.

\n
\nTable 1:
Comparison of attenders and non-attenders.
\nCharacteristics of Dutch individuals who responded to mental health (Wave 1) and religious attendance (Wave 1–Jan 2008) of the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands (n = 1, 673).\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Service attenders at R1Non-attenders of service at R1\np of the difference
\n n\n 786887
Mean age (sd)49.60 (18.22)45.90 (17.21)<.001
Civil status
\n Unmarried\n 323 (41)443 (50)<.001
\n Married\n 463 (59)444 (50)
Monthly income
\n Low income (0–500 € per month)\n 77 (10)65 (7).07
\n Not low income (>500 € per month)\n 709 (90)822 (93)
Mean self-rated health (sd)*\n3.12 (0.76)3.13 (0.76).68
With a chronic condition
\n Yes\n 232 (32)227 (27)
\n No\n 497 (68)600 (73).06
Baseline distribution of BSI depression normative scores
\n Very low\n 0 (0)0 (0).38
\n Low\n 0 (0)0 (0)
\n Below average\n 113 (14)145 (16)
\n Average\n 196 (25)234 (26)
\n Above average\n 284 (36)324 (37)
\n High\n 168 (21)162 (18)
\n Very high\n 25 (3)22 (2)
\n\n
\n

Notes:

\n

Figures in this table are n (%) except for age and self-rated health which are mean (sd).

\n
\n*Rated on a scale of 1–5, with higher scores indicating better health.\n
\n

Measures

\n

Religious attendance was assessed with the single question, “Aside from special occasions such as weddings and funerals, how often do you attend religious gatherings nowadays?” This was answered on a 7-point Likert scale coded as 1 = everyday, 2 = more than once a week, 3 = once a week, 4 = at least once a month, 5 = only on special religious days, 6 = less often, and 7 = never. We reverse coded the scale for ease of interpretation—i.e., larger number indicated higher attendance. Among attenders, we used a dichotomous attendance variable for decreased (coded 0) and same/increased (coded 1) and a categorical version: decreased, unchanged, and increased attendance. These categories were formed by subtracting the R1 attendance level from a given follow-up assessment. For non-attenders in R1, a dichotomous variable with unchanged (coded 0) and increased (coded 1) was used.

\n

Our substantive predictor was assessed using the Depression subscale of the Brief Symptom Inventory (Derogatis, 1975). The subscale consists of 6 items rated on a 5-point scale from “Not at all” to “Extremely”. The BSI is itself a short version of the SCL-90 (Derogatis & Melisaratos, 1983). BSI Depression had an internal reliability ranging from 0.70 to 0.92 in four different studies (Boulet & Boss, 1991; Derogatis & Melisaratos, 1983; Johnson et al., 2008; Kellett et al., 2003) and correlated with the Beck Depression Inventory, r = .71 and r = .77, in two other studies (Stukenberg, Dura & Kiecolt-Glaser, 1990; Prinz et al., 2013). Two studies validated BSI Depression against either DSM-III or DSM-IV-TR major depression (Stukenberg, Dura & Kiecolt-Glaser, 1990; Johnson et al., 2008). ROC analyses reported area under the curve as 0.83 in community dwelling older adults, but a more modest 0.65 among psychiatric inpatients.

\n

For copyright reasons, the LISS dataset only provided the normative category of each respondent and not the responses to individual questions. These normative categories of BSI depression were: 1 = very low, 2 = low, 3 = below average, 4 = average, and 5 = above average, 6 = high, 7 = very high. We dichotomized them into low (very low to above average) and elevated (high to very high). The cut-off was chosen because it resulted in a better approximation of the prevalence of depression in the Netherlands (Bijl, Ravelli & van Zessen, 1998) compared to alternative cut-offs.

Covariates

\n

We controlled for possible confounders including chronic health conditions, income, marital status, age, and gender. Chronic conditions were assessed with the single question, “Do you suffer from any kind of long-standing disease, affliction or handicap, or do you suffer from the consequences of an accident?” Income was assessed using a monthly personal gross income with five categories: 0–500, 501–1500, 1501–2500, 2501–3500, and 3501 and higher Euros per month. Marital status was used as an index of social support and was categorized into 1 = Married; 2 = Separated/Divorced/Widowed; 3 = Not Married. All covariates were measured between December 2007 and January 2008.

Statistical analysis

\n

We first compared demographic characteristics of attenders and non-attenders at baseline. To examine whether elevated depressive symptoms predicted subsequent decreased attendance, we crosstabulated dichotomized attendance with level of symptoms among attenders, for each religion follow-up year. Chi-square tests of association were performed. To examine change longitudinally and control for confounders, we created a multinomial logistic regression model among attenders. Relative risk ratios of decreasing or increasing attendance over maintaining attendance were calculated.

\n

To examine if non-attenders start attending services after elevated depression, a binary logistic regression model was created with change in attendance (0 = no change; 1 = attended) as dependent variable. We entered the covariates in all regression models to control for confounding and robust standard errors were calculated to account for correlated errors in repeated observations.

Missing data

\n

Missing values for the covariates at baseline did not differ between attenders and non-attenders. To examine whether our results would be biased by differential attrition between attenders and non-attenders, we performed multiple imputation on our dependent and predictor variables using a set of 15 socio-demographic and psychological variables assessed at baseline. (These variables are available from the authors upon request.) The imputation procedure was implemented using REALCOM-IMPUTE (Carpenter, Goldstein & Kenward, 2011) software and 10 imputed datasets were generated, which were then analyzed using Stata 12.1. Our regression models were then repeated using the multiply imputed data.

" + "

Materials and Methods

\n

Sample

\n

The data is from the Longitudinal Internet Studies for the Social Sciences (LISS) panel, a random sample of adults living in the Netherlands (Scherpenzeel, 2011). The panel of almost 8,000 individuals was drawn from the Dutch-speaking population based on a list of addresses provided by Statistics Netherlands. The recruitment strategy is described in more detail elsewhere (Scherpenzeel, 2011). LISS is a continuing study in which participants complete online questionnaires monthly on topics including family, economic situation, health, and religion. Each LISS participant has a unique member ID, so it is possible to combine their responses across different survey modules and from one wave to another. For the purpose of our study, we merged the religion (n = 7, 418) and mental health (n = 1, 804) modules, narrowing our sample to those who responded to both surveys (n = 1, 718) (see Fig. 1A). Waves of religion and depression assessments were not simultaneous, so hereafter, use the notations Ri and Di to refer to religion and depression waves, respectively (see Fig. 1B). Our research question requires the following temporal sequence: R1 → D2 to D4 → R2. By comparing attendance level at R2 with R1, we can test whether depression predicts a relative decrease at R2. This design requirement forced us to exclude those individuals (n = 41) who had a different sequence of assessments:

\n

D1 → D2 → R1 → D2 to D4 since for these individuals, one cannot compare attendance levels before and after depression. Our effective sample size was 1,673.

\n
\"Subjects.\"
\n

\nFigure 1: Subjects.

\n(A) LISS datasets used and participant flowchart; (B) schedule of religion and depression assessments.

In the sample, 887 individuals did not attend services and 786 attended services at R1. (Explained in Measures section below.) The characteristics of these groups are described in Table 1. After baseline assessment, D1, depression was assessed during a seven-month span from March to September 2008 while attendance was assessed another four times in addition to R1, and these assessments occurred on each January from 2009 to 2012. Our main analytic strategy was to compare the proportion of individuals that changed their attendance level, stratified by baseline attendance. The change in attendance level was indexed to R1 attendance since there were no further depression assessments after September 2008.

\n
\nTable 1:
Comparison of attenders and non-attenders.
\nCharacteristics of Dutch individuals who responded to mental health (Wave 1) and religious attendance (Wave 1–Jan 2008) of the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands (n = 1, 673).\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Service attenders at R1Non-attenders of service at R1\np of the difference
\n n\n 786887
Mean age (sd)49.60 (18.22)45.90 (17.21)<.001
Civil status
\n Unmarried\n 323 (41)443 (50)<.001
\n Married\n 463 (59)444 (50)
Monthly income
\n Low income (0–500 € per month)\n 77 (10)65 (7).07
\n Not low income (>500 € per month)\n 709 (90)822 (93)
Mean self-rated health (sd)*\n3.12 (0.76)3.13 (0.76).68
With a chronic condition
\n Yes\n 232 (32)227 (27)
\n No\n 497 (68)600 (73).06
Baseline distribution of BSI depression normative scores
\n Very low\n 0 (0)0 (0).38
\n Low\n 0 (0)0 (0)
\n Below average\n 113 (14)145 (16)
\n Average\n 196 (25)234 (26)
\n Above average\n 284 (36)324 (37)
\n High\n 168 (21)162 (18)
\n Very high\n 25 (3)22 (2)
\n\n
\n

Notes:

\n

Figures in this table are n (%) except for age and self-rated health which are mean (sd).

\n
\n*Rated on a scale of 1–5, with higher scores indicating better health.\n
\n

Measures

\n

Religious attendance was assessed with the single question, “Aside from special occasions such as weddings and funerals, how often do you attend religious gatherings nowadays?” This was answered on a 7-point Likert scale coded as 1 = everyday, 2 = more than once a week, 3 = once a week, 4 = at least once a month, 5 = only on special religious days, 6 = less often, and 7 = never. We reverse coded the scale for ease of interpretation—i.e., larger number indicated higher attendance. Among attenders, we used a dichotomous attendance variable for decreased (coded 0) and same/increased (coded 1) and a categorical version: decreased, unchanged, and increased attendance. These categories were formed by subtracting the R1 attendance level from a given follow-up assessment. For non-attenders in R1, a dichotomous variable with unchanged (coded 0) and increased (coded 1) was used.

\n

Our substantive predictor was assessed using the Depression subscale of the Brief Symptom Inventory (Derogatis, 1975). The subscale consists of 6 items rated on a 5-point scale from “Not at all” to “Extremely”. The BSI is itself a short version of the SCL-90 (Derogatis & Melisaratos, 1983). BSI Depression had an internal reliability ranging from 0.70 to 0.92 in four different studies (Boulet & Boss, 1991; Derogatis & Melisaratos, 1983; Johnson et al., 2008; Kellett et al., 2003) and correlated with the Beck Depression Inventory, r = .71 and r = .77, in two other studies (Stukenberg, Dura & Kiecolt-Glaser, 1990; Prinz et al., 2013). Two studies validated BSI Depression against either DSM-III or DSM-IV-TR major depression (Stukenberg, Dura & Kiecolt-Glaser, 1990; Johnson et al., 2008). ROC analyses reported area under the curve as 0.83 in community dwelling older adults, but a more modest 0.65 among psychiatric inpatients.

\n

For copyright reasons, the LISS dataset only provided the normative category of each respondent and not the responses to individual questions. These normative categories of BSI depression were: 1 = very low, 2 = low, 3 = below average, 4 = average, and 5 = above average, 6 = high, 7 = very high. We dichotomized them into low (very low to above average) and elevated (high to very high). The cut-off was chosen because it resulted in a better approximation of the prevalence of depression in the Netherlands (Bijl, Ravelli & van Zessen, 1998) compared to alternative cut-offs.

Covariates

\n

We controlled for possible confounders including chronic health conditions, income, marital status, age, and gender. Chronic conditions were assessed with the single question, “Do you suffer from any kind of long-standing disease, affliction or handicap, or do you suffer from the consequences of an accident?” Income was assessed using a monthly personal gross income with five categories: 0–500, 501–1500, 1501–2500, 2501–3500, and 3501 and higher Euros per month. Marital status was used as an index of social support and was categorized into 1 = Married; 2 = Separated/Divorced/Widowed; 3 = Not Married. All covariates were measured between December 2007 and January 2008.

Statistical analysis

\n

We first compared demographic characteristics of attenders and non-attenders at baseline. To examine whether elevated depressive symptoms predicted subsequent decreased attendance, we crosstabulated dichotomized attendance with level of symptoms among attenders, for each religion follow-up year. Chi-square tests of association were performed. To examine change longitudinally and control for confounders, we created a multinomial logistic regression model among attenders. Relative risk ratios of decreasing or increasing attendance over maintaining attendance were calculated.

\n

To examine if non-attenders start attending services after elevated depression, a binary logistic regression model was created with change in attendance (0 = no change; 1 = attended) as dependent variable. We entered the covariates in all regression models to control for confounding and robust standard errors were calculated to account for correlated errors in repeated observations.

Missing data

\n

Missing values for the covariates at baseline did not differ between attenders and non-attenders. To examine whether our results would be biased by differential attrition between attenders and non-attenders, we performed multiple imputation on our dependent and predictor variables using a set of 15 socio-demographic and psychological variables assessed at baseline. (These variables are available from the authors upon request.) The imputation procedure was implemented using REALCOM-IMPUTE (Carpenter, Goldstein & Kenward, 2011) software and 10 imputed datasets were generated, which were then analyzed using Stata 12.1. Our regression models were then repeated using the multiply imputed data.

" ] }, "results_html": { "value": [ - "

Results

\n

Religious attenders were more likely to be female, older, and married as compared to non-attenders. Attenders and non-attenders were similar in self-rated health, in the proportion having chronic conditions, and in the distribution of BSI Depression normative scores. From March to September 2008, 491 individuals developed elevated depression. The chi-square tests in each of the four follow-up waves showed no association between depression status and subsequent decrease in attendance with one exception. In 2012, those with elevated BSI Depression among baseline attenders were more likely to keep or increase their 2008 attendance levels. In post-hoc analysis, we repeated the change in attendance analysis by depression category stratified first by gender and then by age category. In gender-stratified analysis, no associations were found in each attendance follow-up. In age-stratified analysis, no associations were found in the first two years after depression assessments took place. In both R3 and R4, those 48 years old and above and with elevated depression were more likely to maintain or increase attendance levels (both p’s < .05). (See Table 2. The tables stratified by gender or age category are available from the authors by request.)

\n
\nTable 2:
Change in attendance by depression status.
\nBSI depression vs changes in attendance in the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Service attenders at R1Non-attenders of service at R1
\n 2009 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2009 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase371 (73)184 (78)2.31.13Same394 (67)177 (69).47.49
Decrease139 (27)52 (22)Increase194 (33)78 (31)
\n 2010 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2010 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase392 (77)191 (81)1.56.21Same348 (59)154 (60).11.74
Decrease118 (23)45 (19)Increase240 (41)101 (40)
\n 2011 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2011 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase390 (76)189 (80)1.22.27Same315 (54)142 (56).32.57
Decrease120 (24)47 (20)Increase273 (46)113 (44)
\n 2012 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2012 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase367 (72)189 (80)5.61\n .02\n Same291 (49)136 (53)1.05.31
Decrease143 (28)47 (20)Increase297 (50)119 (47)
\n\n
\n

Notes:

\n

If the individual had a norm-referenced score of “high” or “very high” in any of the three assessments in 2008, the individual was assigned to elevated and otherwise to unelevated.

\n

\n

\n
BSI
\n

Brief Symptom Inventory

\n
\n

\n

In multinomial logistic regression modeling, elevated symptoms predicted lower probability of a decrease in attendance (relative risk ratio = 0.55, 95% CI [0.38–0.79]) relative to baseline attendance levels among attenders (see Table 3 and Fig. 2). Among non-attenders, elevated symptoms were unrelated to a subsequent increase in attendance with one exception. The estimates were not materially different when the models were run using multiply imputed data.

\n
\nTable 3:
Regression models.
\nLogistic models of change in religious attendance levels over 5 years from the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Religious attenders at baselineNon-attenders at baseline
Model 1a:
complete cases
Model 1Aa:
multiply imputed data
(10 imputations)
Model 2a:
complete cases
Model 2Aa:
multiply imputed data
(10 imputations)
Relative risk ratio
(95% CI)
Relative risk ratio
(95% CI)
Odds ratio
(95% CI)
Odds ratio
(95% CI)
\n Outcome: decreased attendance\n
Predictor: elevated depression\n 0.55 (0.38–0.79)\n \n **\n \n \n 0.58 (0.41–0.83)\n \n **\n \n N/AN/A
\n Outcome: same attendance\n \n (Reference category)\n \n (Reference category)\n
\n Outcome: increased attendance\n
Predictor: elevated depression0.90 (0.68–1.19)1.27 (0.78–2.07)0.93 (0.73–1.18)1.10 (0.55–2.21)
\n\n
\n

Notes:

\n
\naIn these models, the following covariates have been controlled: existing chronic condition, gender, marital status, income, and age.\n
\n
\n**p values: .01.\n
\n
\"Probabilities.\"
\n

\nFigure 2: Probabilities.

\nPredicted probabilities of a decrease, same, and increase in religious attendance (95% CI).
" + "

Results

\n

Religious attenders were more likely to be female, older, and married as compared to non-attenders. Attenders and non-attenders were similar in self-rated health, in the proportion having chronic conditions, and in the distribution of BSI Depression normative scores. From March to September 2008, 491 individuals developed elevated depression. The chi-square tests in each of the four follow-up waves showed no association between depression status and subsequent decrease in attendance with one exception. In 2012, those with elevated BSI Depression among baseline attenders were more likely to keep or increase their 2008 attendance levels. In post-hoc analysis, we repeated the change in attendance analysis by depression category stratified first by gender and then by age category. In gender-stratified analysis, no associations were found in each attendance follow-up. In age-stratified analysis, no associations were found in the first two years after depression assessments took place. In both R3 and R4, those 48 years old and above and with elevated depression were more likely to maintain or increase attendance levels (both p’s < .05). (See Table 2. The tables stratified by gender or age category are available from the authors by request.)

\n
\nTable 2:
Change in attendance by depression status.
\nBSI depression vs changes in attendance in the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Service attenders at R1Non-attenders of service at R1
\n 2009 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2009 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase371 (73)184 (78)2.31.13Same394 (67)177 (69).47.49
Decrease139 (27)52 (22)Increase194 (33)78 (31)
\n 2010 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2010 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase392 (77)191 (81)1.56.21Same348 (59)154 (60).11.74
Decrease118 (23)45 (19)Increase240 (41)101 (40)
\n 2011 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2011 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase390 (76)189 (80)1.22.27Same315 (54)142 (56).32.57
Decrease120 (24)47 (20)Increase273 (46)113 (44)
\n 2012 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2012 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase367 (72)189 (80)5.61\n .02\n Same291 (49)136 (53)1.05.31
Decrease143 (28)47 (20)Increase297 (50)119 (47)
\n\n
\n

Notes:

\n

If the individual had a norm-referenced score of “high” or “very high” in any of the three assessments in 2008, the individual was assigned to elevated and otherwise to unelevated.

\n

\n

\n
BSI
\n

Brief Symptom Inventory

\n
\n

\n

In multinomial logistic regression modeling, elevated symptoms predicted lower probability of a decrease in attendance (relative risk ratio = 0.55, 95% CI [0.38–0.79]) relative to baseline attendance levels among attenders (see Table 3 and Fig. 2). Among non-attenders, elevated symptoms were unrelated to a subsequent increase in attendance with one exception. The estimates were not materially different when the models were run using multiply imputed data.

\n
\nTable 3:
Regression models.
\nLogistic models of change in religious attendance levels over 5 years from the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Religious attenders at baselineNon-attenders at baseline
Model 1a:
complete cases
Model 1Aa:
multiply imputed data
(10 imputations)
Model 2a:
complete cases
Model 2Aa:
multiply imputed data
(10 imputations)
Relative risk ratio
(95% CI)
Relative risk ratio
(95% CI)
Odds ratio
(95% CI)
Odds ratio
(95% CI)
\n Outcome: decreased attendance\n
Predictor: elevated depression\n 0.55 (0.38–0.79)\n \n **\n \n \n 0.58 (0.41–0.83)\n \n **\n \n N/AN/A
\n Outcome: same attendance\n \n (Reference category)\n \n (Reference category)\n
\n Outcome: increased attendance\n
Predictor: elevated depression0.90 (0.68–1.19)1.27 (0.78–2.07)0.93 (0.73–1.18)1.10 (0.55–2.21)
\n\n
\n

Notes:

\n
\naIn these models, the following covariates have been controlled: existing chronic condition, gender, marital status, income, and age.\n
\n
\n**p values: .01.\n
\n
\"Probabilities.\"
\n

\nFigure 2: Probabilities.

\nPredicted probabilities of a decrease, same, and increase in religious attendance (95% CI).
" ] }, "discussion_html": { "value": [ - "

Discussion

\n

The main finding in this study is that elevated BSI depression does not cause a subsequent decrease in attendance. On the contrary, elevated BSI depression predicts same or increased levels of attendance as compared with prior to elevated BSI depression. None of our results across three analytical strategies showed a decrease in attendance. Although unstratified analyses did not yield a significant association, gender and age-stratified results indicated an association of continued or increased attendance with elevated symptoms. We do not interpret this association because other variables could possibly explain the association. The multinomial logistic model among attenders, with covariates controlled for, indicated that elevated symptoms predicted same or increased attendance. As a secondary finding, non-attenders were not likely to seek recourse in religion by starting to attend services.

\n

Our main finding addresses the issue of selection bias in studies of religious attendance and mental health. To recap, when depressed individuals stop attending services, the apparent protection afforded by attendance would be inflated. This selection bias would be most pronounced in cross-sectional studies. In longitudinal epidemiologic studies, bias remains an issue because there might be differential attrition in attendance by depression status. Since we found that attenders who develop elevated symptoms become less likely to drop out of worship, then they might in effect be overrepresented among churchgoers. Therefore, the protective effect of religious attendance might in fact be underestimated, contrary to the reverse causation argument.

\n

Religious individuals turn to their faith in times of distress as a means of coping (Brown et al., 2004; Bussing, Ostermann & Koenig, 2007; Ironson, Stuetzle & Fletcher, 2006). Religious worship is a source of social support and allows individuals to cope with life-threatening conditions by providing “medicine for the spirit” (Cummings & Pargament, 2010). A longitudinal study (Li & Ferraro, 2005) on depression and volunteering among older adults reported that elevated depression at wave 2 predicted seeking out volunteering opportunities at wave 3. This was explained as a compensatory mechanism to alleviate negative affect, via social integration. These older adults had physical health problems in addition to depression and the physical health problems were the operative barriers. Consistent with this finding, Chen & Koenig (2006) reported that in elderly, medically ill individuals, an increased severity of physical illness predicted a decrease in organizational religiousness. Importantly, the association was completely mediated by physical activity limitations. Together with our own results, these suggest that it is not depression per se that causes a disengagement from participation in religious service. In effect, reverse causation and non-random attrition might be more relevant to studies examining religious attendance and physical health.

\n

The null association of elevated depression with subsequent attendance among non-attenders indicates that non-attenders do not start attending in the face of adversity. By contrast, Ferraro & Kelley-Moore (2000) reported that depression, cancer, and chronic conditions lead to consolation-seeking even among those with no religious affiliation. The two points of view can be reconciled because attendance is not necessary for consolation-seeking. The need to find meaning in illness is shared by believers and non-believers who may turn to nature, arts, music, and relationships (Burnard, 1988).

\n

An intriguing study (Farias et al., 2013) reported that rowers about to enter a competition reported greater belief in science as compared with those in a training session. The authors concluded that affirming one’s secular worldview serves a similar function as religious faith in moments of stress or existential anxiety. Hence, affiliated individuals cope by means of religion while non-attending ones seek support and meaning elsewhere. It appears that depressive symptoms are not a strong driver of entry into or exit from the churchgoing demographic. More empirical research is needed to validate this interpretation.

\n

Our study has several important limitations. First, we relied on the depression subscale of the BSI to assess depressive symptoms. It has been argued that although the global BSI scale is a valid measure of distress, it is not intended to screen for particular psychiatric disorders (Asner-Self, Schreiber & Marotta, 2006). We set the BSI cut-off for depression at “high” or “very high” but there is no way to tell whether this is in concordance with clinically diagnosed depression. We therefore allow for the possibility that the depressed group that we studied might differ from a group with formally diagnosed major depression (Sareen et al., 2013). Secondly, there were no assessments of depression from 2009 to 2012—the period during which religious attendance was compared to initial attendance. As such, all religious attendance changes were indexed to depression levels in 2008 only. We cannot rule out the possibility that attendance levels after 2008 were related to unmeasured elevated symptoms after 2008. Third, the sample that we worked with was restricted to LISS participants who responded to both religion and mental health modules and might not be representative of the Dutch national population. Fourth, while we have ruled out sampling bias in terms of attrition in attendance, we could not address whether personality traits such as greater resilience to depression characterized attenders in the first place. Finally, other health-related reasons, including physical disability, might be correlated with depression and could cause selection bias. This is beyond the scope of our study. The major strength of this study was that depression assessments were proximal to those of religion. Our sample also consisted of a small fraction (5%) of late adolescents and is less affected by the well-reported decline in religious attendance in adolescence.

\n

Within the limitations of our study, we conclude that elevated depressive symptoms do not cause religiously affiliated individuals to subsequently decrease attendance at religious services.

" + "

Discussion

\n

The main finding in this study is that elevated BSI depression does not cause a subsequent decrease in attendance. On the contrary, elevated BSI depression predicts same or increased levels of attendance as compared with prior to elevated BSI depression. None of our results across three analytical strategies showed a decrease in attendance. Although unstratified analyses did not yield a significant association, gender and age-stratified results indicated an association of continued or increased attendance with elevated symptoms. We do not interpret this association because other variables could possibly explain the association. The multinomial logistic model among attenders, with covariates controlled for, indicated that elevated symptoms predicted same or increased attendance. As a secondary finding, non-attenders were not likely to seek recourse in religion by starting to attend services.

\n

Our main finding addresses the issue of selection bias in studies of religious attendance and mental health. To recap, when depressed individuals stop attending services, the apparent protection afforded by attendance would be inflated. This selection bias would be most pronounced in cross-sectional studies. In longitudinal epidemiologic studies, bias remains an issue because there might be differential attrition in attendance by depression status. Since we found that attenders who develop elevated symptoms become less likely to drop out of worship, then they might in effect be overrepresented among churchgoers. Therefore, the protective effect of religious attendance might in fact be underestimated, contrary to the reverse causation argument.

\n

Religious individuals turn to their faith in times of distress as a means of coping (Brown et al., 2004; Bussing, Ostermann & Koenig, 2007; Ironson, Stuetzle & Fletcher, 2006). Religious worship is a source of social support and allows individuals to cope with life-threatening conditions by providing “medicine for the spirit” (Cummings & Pargament, 2010). A longitudinal study (Li & Ferraro, 2005) on depression and volunteering among older adults reported that elevated depression at wave 2 predicted seeking out volunteering opportunities at wave 3. This was explained as a compensatory mechanism to alleviate negative affect, via social integration. These older adults had physical health problems in addition to depression and the physical health problems were the operative barriers. Consistent with this finding, Chen & Koenig (2006) reported that in elderly, medically ill individuals, an increased severity of physical illness predicted a decrease in organizational religiousness. Importantly, the association was completely mediated by physical activity limitations. Together with our own results, these suggest that it is not depression per se that causes a disengagement from participation in religious service. In effect, reverse causation and non-random attrition might be more relevant to studies examining religious attendance and physical health.

\n

The null association of elevated depression with subsequent attendance among non-attenders indicates that non-attenders do not start attending in the face of adversity. By contrast, Ferraro & Kelley-Moore (2000) reported that depression, cancer, and chronic conditions lead to consolation-seeking even among those with no religious affiliation. The two points of view can be reconciled because attendance is not necessary for consolation-seeking. The need to find meaning in illness is shared by believers and non-believers who may turn to nature, arts, music, and relationships (Burnard, 1988).

\n

An intriguing study (Farias et al., 2013) reported that rowers about to enter a competition reported greater belief in science as compared with those in a training session. The authors concluded that affirming one’s secular worldview serves a similar function as religious faith in moments of stress or existential anxiety. Hence, affiliated individuals cope by means of religion while non-attending ones seek support and meaning elsewhere. It appears that depressive symptoms are not a strong driver of entry into or exit from the churchgoing demographic. More empirical research is needed to validate this interpretation.

\n

Our study has several important limitations. First, we relied on the depression subscale of the BSI to assess depressive symptoms. It has been argued that although the global BSI scale is a valid measure of distress, it is not intended to screen for particular psychiatric disorders (Asner-Self, Schreiber & Marotta, 2006). We set the BSI cut-off for depression at “high” or “very high” but there is no way to tell whether this is in concordance with clinically diagnosed depression. We therefore allow for the possibility that the depressed group that we studied might differ from a group with formally diagnosed major depression (Sareen et al., 2013). Secondly, there were no assessments of depression from 2009 to 2012—the period during which religious attendance was compared to initial attendance. As such, all religious attendance changes were indexed to depression levels in 2008 only. We cannot rule out the possibility that attendance levels after 2008 were related to unmeasured elevated symptoms after 2008. Third, the sample that we worked with was restricted to LISS participants who responded to both religion and mental health modules and might not be representative of the Dutch national population. Fourth, while we have ruled out sampling bias in terms of attrition in attendance, we could not address whether personality traits such as greater resilience to depression characterized attenders in the first place. Finally, other health-related reasons, including physical disability, might be correlated with depression and could cause selection bias. This is beyond the scope of our study. The major strength of this study was that depression assessments were proximal to those of religion. Our sample also consisted of a small fraction (5%) of late adolescents and is less affected by the well-reported decline in religious attendance in adolescence.

\n

Within the limitations of our study, we conclude that elevated depressive symptoms do not cause religiously affiliated individuals to subsequently decrease attendance at religious services.

" ] }, "conclusion_html": { @@ -995,59 +995,59 @@ }, "references_html": { "value": [ - "\nArnett JJ. 2000. Emerging adulthood—a theory of development from the late teens through the twenties. American Psychologist 55:469-480 \n", - "\nAsner-Self KK, Schreiber JB, Marotta SA. 2006. A cross-cultural analysis of the Brief Symptom Inventory-18. Cultural Diversity & Ethnic Minority Psychology 12:367-375 \n", - "\nBaetz M, Griffin R, Bowen R, Koenig HG, Marcoux E. 2004. The association between spiritual and religious involvement and depressive symptoms in a Canadian population. Journal of Nervous and Mental Disease 192:818-822 \n", - "\nBalbuena L, Baetz M, Bowen R. 2013. Religious attendance, spirituality, and major depression in Canada: a 14-year follow-up study. Canadian Journal of Psychiatry 58:225-232 \n", - "\nBenda BB, Corwyn RF. 1997. A test of a model with reciprocal effects between religiosity and various forms of delinquency using 2-stage least squares regression. Journal of Social Service Research 22:27-52 \n", - "\nBijl RV, Ravelli A, van Zessen G. 1998. Prevalence of psychiatric disorder in the general population: results of the Netherlands Mental Health Survey and Incidence Study (NEMESIS) Social Psychiatry and Psychiatric Epidemiology 33:587-595 \n", - "\nBoulet J, Boss M. 1991. Reliability and validity of the Brief Symptom Inventory. Psychological Assessment: A Journal of Consulting & Clinical Psychology 3:433-437 \n", - "\nBrown SL, Nesse RM, House JS, Utz RL. 2004. Religion and emotional compensation: results from a prospective study of widowhood. Personality and Social Psychology Bulletin 30:1165-1174 \n", - "\nBurnard P. 1988. The spiritual needs of atheists and agnostics. Professional Nurse 4:130-132 \n", - "\nBussing A, Ostermann T, Koenig HG. 2007. Relevance of religion and spirituality in German patients with chronic diseases. International Journal of Psychiatry in Medicine 37:39-57 \n", - "\nCarpenter JR, Goldstein H, Kenward MG. 2011. REALCOM-IMPUTE software for multilevel multiple imputation with mixed response types. Journal of Statistical Software 45:1-14 \n", - "\nChen YY, Koenig HG. 2006. Do people turn to religion in times of stress?: an examination of change in religiousness among elderly, medically ill patients. Journal of Nervous and Mental Disease 194:114-120 \n", - "\nConnor P. 2009. Immigrant religiosity in Canada: multiple trajectories. International Migration & Integration 10:159-175 \n", - "\nCummings JP, Pargament KI. 2010. Medicine for the spirit: religious coping in individuals with medical conditions. Religions 1:28-53 \n", - "\nDerogatis LR. 1975. Brief Symptom Inventory. Baltimore: Clinical Psychometric Research. \n", - "\nDerogatis LR, Melisaratos N. 1983. The Brief Symptom Inventory—an introductory report. Psychological Medicine 13:595-605 \n", - "\nEllison CG, Flannelly KJ. 2009. Religious involvement and risk of major depression in a prospective nationwide study of African American adults. Journal of Nervous and Mental Disease 197:568-573 \n", - "\nFarias M, Newheiser AK, Kahane G, de Toledo Z. 2013. Scientific faith: belief in science increases in the face of stress and existential anxiety. Journal of Experimental Social Psychology 49:1210-1213 \n", - "\nFerraro KF, Kelley-Moore JA. 2000. Religious consolation among men and women: do health problems spur seeking? Journal for the Scientific Study of Religion 39:220-234 \n", - "\nFontana A, Rosenheck R. 2004. Trauma, change in strength of religious faith, and mental health service use among veterans treated for PTSD. Journal of Nervous and Mental Disease 192:579-584 \n", - "\nHayward RD, Owen AD, Koenig HG, Steffens DC, Payne ME. 2012. Religion and the presence and severity of depression in older adults. American Journal of Geriatric Psychiatry 20:188-192 \n", - "\nHorowitz JL, Garber J. 2003. Relation of intelligence and religiosity to depressive disorders in offspring of depressed and nondepressed mothers. Journal of the American Academy of Child and Adolescent Psychiatry 42:578-586 \n", - "\nIronson G, Stuetzle R, Fletcher MA. 2006. An increase in religiousness/spirituality occurs after HIV diagnosis and predicts slower disease progression over 4 years in people with HIV. Journal of General Internal Medicine 21(Suppl 5):S62-S68 \n", - "\nJohnson ME, Chipp CL, Brems C, Neal DB. 2008. Receiver operating characteristics for the brief symptom inventory depression, paranoid ideation, and psychoticism scales in a large sample of clinical inpatients. Psychological Reports 102:695-705 \n", - "\nKellett S, Beail N, Newman DW, Frankish P. 2003. Utility of the brief symptom inventory in the assessment of psychological distress. Journal of Applied Research in Intellectual Disabilities 16:127-134 \n", - "\nLi YQ, Ferraro KF. 2005. Volunteering and depression in later life: social benefit or selection processes? Journal of Health and Social Behavior 46:68-84 \n", - "\nLodi-Smith J, Roberts BW. 2007. Social investment and personality: a meta-analysis of the relationship of personality traits to investment in work, family, religion, and volunteerism. Personality and Social Psychology Review 11:68-86 \n", - "\nMaselko J, Gilman SE, Buka S. 2009. Religious service attendance and spiritual well-being are differentially associated with risk of major depression. Psychological Medicine 39:1009-1017 \n", - "\nMaselko J, Hayward RD, Hanlon A, Buka S, Meador K. 2012. Religious service attendance and major depression: a case of reverse causality? American Journal of Epidemiology 175:576-583 \n", - "\nMiller L, Weissman M, Gur M, Greenwald S. 2002. Adult religiousness and history of childhood depression: eleven-year follow-up study. Journal of Nervous and Mental Disease 190:86-93 \n", - "\nMiller L, Wickramaratne P, Gameroff MJ, Sage M, Tenke CE, Weissman MM. 2012. Religiosity and major depression in adults at high risk: a ten-year prospective study. American Journal of Psychiatry 169:89-94 \n", - "\nPargament KI. 1997. The psychology of religion and coping: theory, research, practice. New York, London: Guilford Press. \n", - "\nPrinz U, Nutzinger DO, Schulz H, Petermann F, Braukhaus C, Andreas S. 2013. Comparative psychometric analyses of the SCL-90-R and its short versions in patients with affective disorders. BMC Psychiatry 13:104 \n", - "\nSareen J, Henriksen CA, Stein MB, Afifi TO, Lix LM, Enns MW. 2013. Common mental disorder diagnosis and need for treatment are not the same: findings from a population-based longitudinal survey. Psychological Medicine 43:1941-1951 \n", - "\nScherpenzeel A. 2011. Data collection in a probability-based internet panel: how the LISS panel was built and how it can be used. Bulletin of Sociological Methodology 109:56-61 \n", - "\nSchnittker J. 2001. When is faith enough? The effects of religious involvement on depression. Journal for the Scientific Study of Religion 40:393-411 \n", - "\nStukenberg KW, Dura JR, Kiecolt-Glaser JK. 1990. Depression screening scale validation in an elderly, community-dwelling population. Psychological Assessment: A Journal of Consulting & Clinical Psychology 2:134-138 \n", - "\nTaylor RJ, Chatters LM, Nguyen AW. 2013. Religious participation and DSM IV major depressive disorder among Black Caribbeans in the United States. Journal of Immigrant and Minority Health 15:903-909 \n", - "\nThornton A, Axinn WG, Hill DH. 1992. Reciprocal effects of religiosity, cohabitation, and marriage. American Journal of Sociology 98:628-651 \n", - "\nUecker JE, Regnerus MD, Vaaler ML. 2007. Losing my religion: the social sources of religious decline in early adulthood. Social Forces 85:1667-1692 \n" + "\nArnett JJ. 2000. Emerging adulthood—a theory of development from the late teens through the twenties. American Psychologist 55:469-480 \n", + "\nAsner-Self KK, Schreiber JB, Marotta SA. 2006. A cross-cultural analysis of the Brief Symptom Inventory-18. Cultural Diversity & Ethnic Minority Psychology 12:367-375 \n", + "\nBaetz M, Griffin R, Bowen R, Koenig HG, Marcoux E. 2004. The association between spiritual and religious involvement and depressive symptoms in a Canadian population. Journal of Nervous and Mental Disease 192:818-822 \n", + "\nBalbuena L, Baetz M, Bowen R. 2013. Religious attendance, spirituality, and major depression in Canada: a 14-year follow-up study. Canadian Journal of Psychiatry 58:225-232 \n", + "\nBenda BB, Corwyn RF. 1997. A test of a model with reciprocal effects between religiosity and various forms of delinquency using 2-stage least squares regression. Journal of Social Service Research 22:27-52 \n", + "\nBijl RV, Ravelli A, van Zessen G. 1998. Prevalence of psychiatric disorder in the general population: results of the Netherlands Mental Health Survey and Incidence Study (NEMESIS) Social Psychiatry and Psychiatric Epidemiology 33:587-595 \n", + "\nBoulet J, Boss M. 1991. Reliability and validity of the Brief Symptom Inventory. Psychological Assessment: A Journal of Consulting & Clinical Psychology 3:433-437 \n", + "\nBrown SL, Nesse RM, House JS, Utz RL. 2004. Religion and emotional compensation: results from a prospective study of widowhood. Personality and Social Psychology Bulletin 30:1165-1174 \n", + "\nBurnard P. 1988. The spiritual needs of atheists and agnostics. Professional Nurse 4:130-132 \n", + "\nBussing A, Ostermann T, Koenig HG. 2007. Relevance of religion and spirituality in German patients with chronic diseases. International Journal of Psychiatry in Medicine 37:39-57 \n", + "\nCarpenter JR, Goldstein H, Kenward MG. 2011. REALCOM-IMPUTE software for multilevel multiple imputation with mixed response types. Journal of Statistical Software 45:1-14 \n", + "\nChen YY, Koenig HG. 2006. Do people turn to religion in times of stress?: an examination of change in religiousness among elderly, medically ill patients. Journal of Nervous and Mental Disease 194:114-120 \n", + "\nConnor P. 2009. Immigrant religiosity in Canada: multiple trajectories. International Migration & Integration 10:159-175 \n", + "\nCummings JP, Pargament KI. 2010. Medicine for the spirit: religious coping in individuals with medical conditions. Religions 1:28-53 \n", + "\nDerogatis LR. 1975. Brief Symptom Inventory. Baltimore: Clinical Psychometric Research. \n", + "\nDerogatis LR, Melisaratos N. 1983. The Brief Symptom Inventory—an introductory report. Psychological Medicine 13:595-605 \n", + "\nEllison CG, Flannelly KJ. 2009. Religious involvement and risk of major depression in a prospective nationwide study of African American adults. Journal of Nervous and Mental Disease 197:568-573 \n", + "\nFarias M, Newheiser AK, Kahane G, de Toledo Z. 2013. Scientific faith: belief in science increases in the face of stress and existential anxiety. Journal of Experimental Social Psychology 49:1210-1213 \n", + "\nFerraro KF, Kelley-Moore JA. 2000. Religious consolation among men and women: do health problems spur seeking? Journal for the Scientific Study of Religion 39:220-234 \n", + "\nFontana A, Rosenheck R. 2004. Trauma, change in strength of religious faith, and mental health service use among veterans treated for PTSD. Journal of Nervous and Mental Disease 192:579-584 \n", + "\nHayward RD, Owen AD, Koenig HG, Steffens DC, Payne ME. 2012. Religion and the presence and severity of depression in older adults. American Journal of Geriatric Psychiatry 20:188-192 \n", + "\nHorowitz JL, Garber J. 2003. Relation of intelligence and religiosity to depressive disorders in offspring of depressed and nondepressed mothers. Journal of the American Academy of Child and Adolescent Psychiatry 42:578-586 \n", + "\nIronson G, Stuetzle R, Fletcher MA. 2006. An increase in religiousness/spirituality occurs after HIV diagnosis and predicts slower disease progression over 4 years in people with HIV. Journal of General Internal Medicine 21(Suppl 5):S62-S68 \n", + "\nJohnson ME, Chipp CL, Brems C, Neal DB. 2008. Receiver operating characteristics for the brief symptom inventory depression, paranoid ideation, and psychoticism scales in a large sample of clinical inpatients. Psychological Reports 102:695-705 \n", + "\nKellett S, Beail N, Newman DW, Frankish P. 2003. Utility of the brief symptom inventory in the assessment of psychological distress. Journal of Applied Research in Intellectual Disabilities 16:127-134 \n", + "\nLi YQ, Ferraro KF. 2005. Volunteering and depression in later life: social benefit or selection processes? Journal of Health and Social Behavior 46:68-84 \n", + "\nLodi-Smith J, Roberts BW. 2007. Social investment and personality: a meta-analysis of the relationship of personality traits to investment in work, family, religion, and volunteerism. Personality and Social Psychology Review 11:68-86 \n", + "\nMaselko J, Gilman SE, Buka S. 2009. Religious service attendance and spiritual well-being are differentially associated with risk of major depression. Psychological Medicine 39:1009-1017 \n", + "\nMaselko J, Hayward RD, Hanlon A, Buka S, Meador K. 2012. Religious service attendance and major depression: a case of reverse causality? American Journal of Epidemiology 175:576-583 \n", + "\nMiller L, Weissman M, Gur M, Greenwald S. 2002. Adult religiousness and history of childhood depression: eleven-year follow-up study. Journal of Nervous and Mental Disease 190:86-93 \n", + "\nMiller L, Wickramaratne P, Gameroff MJ, Sage M, Tenke CE, Weissman MM. 2012. Religiosity and major depression in adults at high risk: a ten-year prospective study. American Journal of Psychiatry 169:89-94 \n", + "\nPargament KI. 1997. The psychology of religion and coping: theory, research, practice. New York, London: Guilford Press. \n", + "\nPrinz U, Nutzinger DO, Schulz H, Petermann F, Braukhaus C, Andreas S. 2013. Comparative psychometric analyses of the SCL-90-R and its short versions in patients with affective disorders. BMC Psychiatry 13:104 \n", + "\nSareen J, Henriksen CA, Stein MB, Afifi TO, Lix LM, Enns MW. 2013. Common mental disorder diagnosis and need for treatment are not the same: findings from a population-based longitudinal survey. Psychological Medicine 43:1941-1951 \n", + "\nScherpenzeel A. 2011. Data collection in a probability-based internet panel: how the LISS panel was built and how it can be used. Bulletin of Sociological Methodology 109:56-61 \n", + "\nSchnittker J. 2001. When is faith enough? The effects of religious involvement on depression. Journal for the Scientific Study of Religion 40:393-411 \n", + "\nStukenberg KW, Dura JR, Kiecolt-Glaser JK. 1990. Depression screening scale validation in an elderly, community-dwelling population. Psychological Assessment: A Journal of Consulting & Clinical Psychology 2:134-138 \n", + "\nTaylor RJ, Chatters LM, Nguyen AW. 2013. Religious participation and DSM IV major depressive disorder among Black Caribbeans in the United States. Journal of Immigrant and Minority Health 15:903-909 \n", + "\nThornton A, Axinn WG, Hill DH. 1992. Reciprocal effects of religiosity, cohabitation, and marriage. American Journal of Sociology 98:628-651 \n", + "\nUecker JE, Regnerus MD, Vaaler ML. 2007. Losing my religion: the social sources of religious decline in early adulthood. Social Forces 85:1667-1692 \n" ] }, "figures_html": { "value": [ - "
\"Subjects.\"
\n

\nFigure 1: Subjects.

\n(A) LISS datasets used and participant flowchart; (B) schedule of religion and depression assessments.
", - "
\"Probabilities.\"
\n

\nFigure 2: Probabilities.

\nPredicted probabilities of a decrease, same, and increase in religious attendance (95% CI).
" + "
\"Subjects.\"
\n

\nFigure 1: Subjects.

\n(A) LISS datasets used and participant flowchart; (B) schedule of religion and depression assessments.
", + "
\"Probabilities.\"
\n

\nFigure 2: Probabilities.

\nPredicted probabilities of a decrease, same, and increase in religious attendance (95% CI).
" ] }, "tables_html": { "value": [ - "
\nTable 1:
Comparison of attenders and non-attenders.
\nCharacteristics of Dutch individuals who responded to mental health (Wave 1) and religious attendance (Wave 1–Jan 2008) of the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands (n = 1, 673).\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Service attenders at R1Non-attenders of service at R1\np of the difference
\n n\n 786887
Mean age (sd)49.60 (18.22)45.90 (17.21)<.001
Civil status
\n Unmarried\n 323 (41)443 (50)<.001
\n Married\n 463 (59)444 (50)
Monthly income
\n Low income (0–500 € per month)\n 77 (10)65 (7).07
\n Not low income (>500 € per month)\n 709 (90)822 (93)
Mean self-rated health (sd)*\n3.12 (0.76)3.13 (0.76).68
With a chronic condition
\n Yes\n 232 (32)227 (27)
\n No\n 497 (68)600 (73).06
Baseline distribution of BSI depression normative scores
\n Very low\n 0 (0)0 (0).38
\n Low\n 0 (0)0 (0)
\n Below average\n 113 (14)145 (16)
\n Average\n 196 (25)234 (26)
\n Above average\n 284 (36)324 (37)
\n High\n 168 (21)162 (18)
\n Very high\n 25 (3)22 (2)
\n\n
\n

Notes:

\n

Figures in this table are n (%) except for age and self-rated health which are mean (sd).

\n
\n*Rated on a scale of 1–5, with higher scores indicating better health.\n
\n
", - "
\nTable 2:
Change in attendance by depression status.
\nBSI depression vs changes in attendance in the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Service attenders at R1Non-attenders of service at R1
\n 2009 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2009 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase371 (73)184 (78)2.31.13Same394 (67)177 (69).47.49
Decrease139 (27)52 (22)Increase194 (33)78 (31)
\n 2010 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2010 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase392 (77)191 (81)1.56.21Same348 (59)154 (60).11.74
Decrease118 (23)45 (19)Increase240 (41)101 (40)
\n 2011 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2011 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase390 (76)189 (80)1.22.27Same315 (54)142 (56).32.57
Decrease120 (24)47 (20)Increase273 (46)113 (44)
\n 2012 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2012 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase367 (72)189 (80)5.61\n .02\n Same291 (49)136 (53)1.05.31
Decrease143 (28)47 (20)Increase297 (50)119 (47)
\n\n
\n

Notes:

\n

If the individual had a norm-referenced score of “high” or “very high” in any of the three assessments in 2008, the individual was assigned to elevated and otherwise to unelevated.

\n

\n

\n
BSI
\n

Brief Symptom Inventory

\n
\n

\n
", - "
\nTable 3:
Regression models.
\nLogistic models of change in religious attendance levels over 5 years from the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Religious attenders at baselineNon-attenders at baseline
Model 1a:
complete cases
Model 1Aa:
multiply imputed data
(10 imputations)
Model 2a:
complete cases
Model 2Aa:
multiply imputed data
(10 imputations)
Relative risk ratio
(95% CI)
Relative risk ratio
(95% CI)
Odds ratio
(95% CI)
Odds ratio
(95% CI)
\n Outcome: decreased attendance\n
Predictor: elevated depression\n 0.55 (0.38–0.79)\n \n **\n \n \n 0.58 (0.41–0.83)\n \n **\n \n N/AN/A
\n Outcome: same attendance\n \n (Reference category)\n \n (Reference category)\n
\n Outcome: increased attendance\n
Predictor: elevated depression0.90 (0.68–1.19)1.27 (0.78–2.07)0.93 (0.73–1.18)1.10 (0.55–2.21)
\n\n
\n

Notes:

\n
\naIn these models, the following covariates have been controlled: existing chronic condition, gender, marital status, income, and age.\n
\n
\n**p values: .01.\n
\n
" + "
\nTable 1:
Comparison of attenders and non-attenders.
\nCharacteristics of Dutch individuals who responded to mental health (Wave 1) and religious attendance (Wave 1–Jan 2008) of the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands (n = 1, 673).\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Service attenders at R1Non-attenders of service at R1\np of the difference
\n n\n 786887
Mean age (sd)49.60 (18.22)45.90 (17.21)<.001
Civil status
\n Unmarried\n 323 (41)443 (50)<.001
\n Married\n 463 (59)444 (50)
Monthly income
\n Low income (0–500 € per month)\n 77 (10)65 (7).07
\n Not low income (>500 € per month)\n 709 (90)822 (93)
Mean self-rated health (sd)*\n3.12 (0.76)3.13 (0.76).68
With a chronic condition
\n Yes\n 232 (32)227 (27)
\n No\n 497 (68)600 (73).06
Baseline distribution of BSI depression normative scores
\n Very low\n 0 (0)0 (0).38
\n Low\n 0 (0)0 (0)
\n Below average\n 113 (14)145 (16)
\n Average\n 196 (25)234 (26)
\n Above average\n 284 (36)324 (37)
\n High\n 168 (21)162 (18)
\n Very high\n 25 (3)22 (2)
\n\n
\n

Notes:

\n

Figures in this table are n (%) except for age and self-rated health which are mean (sd).

\n
\n*Rated on a scale of 1–5, with higher scores indicating better health.\n
\n
", + "
\nTable 2:
Change in attendance by depression status.
\nBSI depression vs changes in attendance in the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Service attenders at R1Non-attenders of service at R1
\n 2009 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2009 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase371 (73)184 (78)2.31.13Same394 (67)177 (69).47.49
Decrease139 (27)52 (22)Increase194 (33)78 (31)
\n 2010 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2010 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase392 (77)191 (81)1.56.21Same348 (59)154 (60).11.74
Decrease118 (23)45 (19)Increase240 (41)101 (40)
\n 2011 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2011 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase390 (76)189 (80)1.22.27Same315 (54)142 (56).32.57
Decrease120 (24)47 (20)Increase273 (46)113 (44)
\n 2012 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n \n 2012 attendance vs 2008\n Unelevated BSI depression n (%)Elevated BSI depression n (%)\n χ\n 2\n \n p\n
Same or increase367 (72)189 (80)5.61\n .02\n Same291 (49)136 (53)1.05.31
Decrease143 (28)47 (20)Increase297 (50)119 (47)
\n\n
\n

Notes:

\n

If the individual had a norm-referenced score of “high” or “very high” in any of the three assessments in 2008, the individual was assigned to elevated and otherwise to unelevated.

\n

\n

\n
BSI
\n

Brief Symptom Inventory

\n
\n

\n
", + "
\nTable 3:
Regression models.
\nLogistic models of change in religious attendance levels over 5 years from the Longitudinal Internet Studies for the Social Sciences (LISS), Netherlands.\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Religious attenders at baselineNon-attenders at baseline
Model 1a:
complete cases
Model 1Aa:
multiply imputed data
(10 imputations)
Model 2a:
complete cases
Model 2Aa:
multiply imputed data
(10 imputations)
Relative risk ratio
(95% CI)
Relative risk ratio
(95% CI)
Odds ratio
(95% CI)
Odds ratio
(95% CI)
\n Outcome: decreased attendance\n
Predictor: elevated depression\n 0.55 (0.38–0.79)\n \n **\n \n \n 0.58 (0.41–0.83)\n \n **\n \n N/AN/A
\n Outcome: same attendance\n \n (Reference category)\n \n (Reference category)\n
\n Outcome: increased attendance\n
Predictor: elevated depression0.90 (0.68–1.19)1.27 (0.78–2.07)0.93 (0.73–1.18)1.10 (0.55–2.21)
\n\n
\n

Notes:

\n
\naIn these models, the following covariates have been controlled: existing chronic condition, gender, marital status, income, and age.\n
\n
\n**p values: .01.\n
\n
" ] }, "fulltext_html": { @@ -1062,7 +1062,7 @@ }, "fulltext_xml": { "value": [ - "/articles/311.xml" + "https://peerj.com/articles/311.xml" ] }, "supplementary_file": { @@ -1086,21 +1086,21 @@ "© 2014 Balbuena et al.\n" ] }, - "file_hashes": [ + "file_sizes": [ { - "fig-1-full.png": "3ff19ca931ac3850d2e6d045efb5d213" + "fig-1-full.png": 1047086 }, { - "fig-2-full.png": "b6a99fff0a72af9fde1e550f80d43799" + "fig-2-full.png": 514084 }, { - "fulltext.html": "b1926638ed43aa476351c64095ce6b54" + "fulltext.html": 178969 }, { - "fulltext.pdf": "8aa4a538c24c0f3bfcc8b9fa5cd63d7c" + "fulltext.pdf": 792375 }, { - "fulltext.xml": "c7b28594cefc8f9bd2fd61bc226056a9" + "fulltext.xml": 87236 } ] }, @@ -1163,7 +1163,7 @@ }, "date_accepted": { "value": [ - "2014-04-25" + ] }, "date_submitted": { @@ -1203,22 +1203,22 @@ }, "introduction_html": { "value": [ - "

Introduction

\n

Hearing loss is a common congenital defect. The estimated incidence of permanent hearing loss at birth, defined as a sensorineural loss of 35 dB or more in the U.S., is one in 500 newborns (Morton & Nance, 2006). The origins of hearing loss may be genetic, environmental or multifactorial, with at least 50% of prelingual hearing loss in industrialized countries attributable to genetic abnormalities (Vele & Schrijver, 2008). Approximately 70% of prelingual hearing loss is non-syndromic; the remaining 30% is accompanied by additional clinical findings and is considered syndromic (Hilgert, Smith & Van Camp, 2009). Inheritance of hearing loss can be recessive, dominant, X-linked or mitochondrial, with autosomal recessive inheritance constituting roughly 80% of non-syndromic sensorineural hearing loss (SNHL). Mutations of a single gene, GJB2 (OMIM *121011), which encodes the connexin 26 protein, account for the majority of autosomal recessive non-syndromic SNHL (Kenneson, Van Naarden Braun & Boyle, 2002). Mutations of the SLC26A4 gene (OMIM *605646) are the second most frequent cause of autosomal recessive non-syndromic SNHL (Hilgert, Smith & Van Camp, 2009) and produce a phenotypic spectrum of hearing loss disorders encompassing both Pendred syndrome (PDS; OMIM #274600) and DFNB4 (OMIM #600791) (Everett et al., 1997; Li et al., 1998). SLC26A4 is composed of 21 exons and encodes the 780 amino acid transmembrane anion transporter protein pendrin (Everett et al., 1997; Everett et al., 1999; Royaux et al., 2000; Royaux et al., 2001), which plays a key role in maintaining the endocochlear potential (Everett et al., 1999; Royaux et al., 2003).

\n

PDS and DFNB4 are typically characterized by congenital, bilateral sensorineural hearing loss which can be progressive and is usually severe to profound. There is considerable variability of symptoms. Vestibular dysfunction as well as non-pathognomonic temporal bone abnormalities, in particular enlargement of the vestibular aqueduct (EVA), can also be present in these conditions. DFNB4, also known as non-syndromic enlarged vestibular aqueduct (NS-EVA), is not associated with other clinical findings. PDS, in contrast, classically manifests additional symptoms such as the development of an incompletely penetrant euthyroid goiter, which can be present at birth but is more likely to develop in late childhood to early adulthood. PDS is also typically accompanied by Mondini dysplasia, a reduction of the number of turns of the cochlea combined with the characteristic bilateral EVA (Schrijver & Gardner, 2006). Although the Mondini malformation can be used as a criterion for diagnosis, it is thought to be clinically heterogeneous and it remains uncertain what proportion of Mondini malformations are linked to Pendred syndrome (Reardon et al., 1997). Other, less well defined, temporal bone abnormalities can (and typically are) seen in those individuals lacking Mondini dysplasia.

\n

PDS was originally estimated to be responsible for 7.5% of hereditary hearing loss cases (Fraser, 1965) but the actual incidence has not been determined due to difficulties inherent in diagnosing PDS, the degree of phenotypic variability (i.e., isolated hearing loss versus multisystem involvement), the frequently late onset and reduced penetrance of the goiter, and the lack of pathognomonic findings (Blons et al., 2004). Nevertheless, PDS is thought to be one of the most common forms of syndromic deafness and mutations of SLC26A4 were reported to be the second most frequent cause of autosomal recessive non-syndromic sensorineural hearing loss worldwide (Hilgert, Smith & Van Camp, 2009).

\n

More than 260 mutations in the SLC26A4 gene have been identified to date (http://www.hgmd.cf.ac.uk/ac/gene.php?gene=SLC26A4), including deletions spanning multiple exons (Park et al., 2003; Hu et al., 2007; Pera et al., 2008a; Anwar et al., 2009; Siem et al., 2010). Until recently, however, individuals with SNHL and possible PDS or DFNB4 were not systematically analyzed for the presence of multiexon deletions and duplications. Multiplex Ligation-dependent Probe Amplification (MLPA) analysis of 37 probands in a Scandinavian cohort of 109 patients suspected to have PDS/DFNB4 identified a homozygous SLC26A4 deletion of exons 4–6 in one individual, indicating that intragenic deletions and duplications may contribute to the phenotype (Rendtorff et al., 2013). Mutations of the FOXI1 and the KCNJ10 genes have also been associated with PDS/DFNB4 and were reported to be digenically inherited with heterozygous mutations in SLC26A4 (Yang et al., 2007; Yang et al., 2009). FOXI1 encodes a transcription factor that binds to the promoter region of SLC26A4 and is responsible for upstream regulation of the gene. KCNJ10 encodes an inwardly rectifying potassium (K+) channel that is involved in generating and maintaining the endocochlear potential (Marcus et al., 2002). Intragenic deletions of SLC26A4 as well as digenic mutations with either FOXI1 or KCNJ10 have all been implicated in PDS/DFNB4 pathogenesis but the extent of their involvement as well as their clinical relevance for SNHL remains unclear.

\n

We investigated the contribution of intragenic SLC26A4 copy number changes by performing MLPA analysis on DNA samples from 107 probands with congenital SNHL who had only one identified SLC26A4 mutation. Although it has been recommended to consider SLC26A4 mutation analysis if there is progressive hearing loss, goiter, Mondini dysplasia, or EVA (Hilgert, Smith & Van Camp, 2009), the clinical testing strategy often adheres to the following algorithm: For individuals with congenital hearing loss that is consistent with autosomal recessive inheritance and that appears non-syndromic, diagnostic testing typically starts with GJB2 sequence analysis. If clinical testing does not identify two pathogenic mutations, then inner ear imaging studies by MRI or CT for temporal bone anomalies may be performed. However, clinical testing of SLC26A4 without MRI or CT is also considered acceptable because mutations in this gene are thought to be a frequent cause of SNHL (Alasti, Van Camp & Smith, 1998, updated 2012). This approach to the clinical work-up is quite common in the U.S., in part because the same DNA specimen can be used for both molecular tests sequentially and in part because imaging studies in the pediatric population can be challenging. As a result, our patients were selected based on the presence of congenital SNHL compatible with autosomal recessive inheritance, absence of two hearing loss-associated GJB2 mutations, and the presence of only one known mutation in SLC26A4. In these individuals, we performed MLPA of SLC26A4 and in a subset we also sequenced the coding regions and splice sites of FOXI1 and KCNJ10 to evaluate alternative etiologies.

" + "

Introduction

\n

Hearing loss is a common congenital defect. The estimated incidence of permanent hearing loss at birth, defined as a sensorineural loss of 35 dB or more in the U.S., is one in 500 newborns (Morton & Nance, 2006). The origins of hearing loss may be genetic, environmental or multifactorial, with at least 50% of prelingual hearing loss in industrialized countries attributable to genetic abnormalities (Vele & Schrijver, 2008). Approximately 70% of prelingual hearing loss is non-syndromic; the remaining 30% is accompanied by additional clinical findings and is considered syndromic (Hilgert, Smith & Van Camp, 2009). Inheritance of hearing loss can be recessive, dominant, X-linked or mitochondrial, with autosomal recessive inheritance constituting roughly 80% of non-syndromic sensorineural hearing loss (SNHL). Mutations of a single gene, GJB2 (OMIM *121011), which encodes the connexin 26 protein, account for the majority of autosomal recessive non-syndromic SNHL (Kenneson, Van Naarden Braun & Boyle, 2002). Mutations of the SLC26A4 gene (OMIM *605646) are the second most frequent cause of autosomal recessive non-syndromic SNHL (Hilgert, Smith & Van Camp, 2009) and produce a phenotypic spectrum of hearing loss disorders encompassing both Pendred syndrome (PDS; OMIM #274600) and DFNB4 (OMIM #600791) (Everett et al., 1997; Li et al., 1998). SLC26A4 is composed of 21 exons and encodes the 780 amino acid transmembrane anion transporter protein pendrin (Everett et al., 1997; Everett et al., 1999; Royaux et al., 2000; Royaux et al., 2001), which plays a key role in maintaining the endocochlear potential (Everett et al., 1999; Royaux et al., 2003).

\n

PDS and DFNB4 are typically characterized by congenital, bilateral sensorineural hearing loss which can be progressive and is usually severe to profound. There is considerable variability of symptoms. Vestibular dysfunction as well as non-pathognomonic temporal bone abnormalities, in particular enlargement of the vestibular aqueduct (EVA), can also be present in these conditions. DFNB4, also known as non-syndromic enlarged vestibular aqueduct (NS-EVA), is not associated with other clinical findings. PDS, in contrast, classically manifests additional symptoms such as the development of an incompletely penetrant euthyroid goiter, which can be present at birth but is more likely to develop in late childhood to early adulthood. PDS is also typically accompanied by Mondini dysplasia, a reduction of the number of turns of the cochlea combined with the characteristic bilateral EVA (Schrijver & Gardner, 2006). Although the Mondini malformation can be used as a criterion for diagnosis, it is thought to be clinically heterogeneous and it remains uncertain what proportion of Mondini malformations are linked to Pendred syndrome (Reardon et al., 1997). Other, less well defined, temporal bone abnormalities can (and typically are) seen in those individuals lacking Mondini dysplasia.

\n

PDS was originally estimated to be responsible for 7.5% of hereditary hearing loss cases (Fraser, 1965) but the actual incidence has not been determined due to difficulties inherent in diagnosing PDS, the degree of phenotypic variability (i.e., isolated hearing loss versus multisystem involvement), the frequently late onset and reduced penetrance of the goiter, and the lack of pathognomonic findings (Blons et al., 2004). Nevertheless, PDS is thought to be one of the most common forms of syndromic deafness and mutations of SLC26A4 were reported to be the second most frequent cause of autosomal recessive non-syndromic sensorineural hearing loss worldwide (Hilgert, Smith & Van Camp, 2009).

\n

More than 260 mutations in the SLC26A4 gene have been identified to date (http://www.hgmd.cf.ac.uk/ac/gene.php?gene=SLC26A4), including deletions spanning multiple exons (Park et al., 2003; Hu et al., 2007; Pera et al., 2008a; Anwar et al., 2009; Siem et al., 2010). Until recently, however, individuals with SNHL and possible PDS or DFNB4 were not systematically analyzed for the presence of multiexon deletions and duplications. Multiplex Ligation-dependent Probe Amplification (MLPA) analysis of 37 probands in a Scandinavian cohort of 109 patients suspected to have PDS/DFNB4 identified a homozygous SLC26A4 deletion of exons 4–6 in one individual, indicating that intragenic deletions and duplications may contribute to the phenotype (Rendtorff et al., 2013). Mutations of the FOXI1 and the KCNJ10 genes have also been associated with PDS/DFNB4 and were reported to be digenically inherited with heterozygous mutations in SLC26A4 (Yang et al., 2007; Yang et al., 2009). FOXI1 encodes a transcription factor that binds to the promoter region of SLC26A4 and is responsible for upstream regulation of the gene. KCNJ10 encodes an inwardly rectifying potassium (K+) channel that is involved in generating and maintaining the endocochlear potential (Marcus et al., 2002). Intragenic deletions of SLC26A4 as well as digenic mutations with either FOXI1 or KCNJ10 have all been implicated in PDS/DFNB4 pathogenesis but the extent of their involvement as well as their clinical relevance for SNHL remains unclear.

\n

We investigated the contribution of intragenic SLC26A4 copy number changes by performing MLPA analysis on DNA samples from 107 probands with congenital SNHL who had only one identified SLC26A4 mutation. Although it has been recommended to consider SLC26A4 mutation analysis if there is progressive hearing loss, goiter, Mondini dysplasia, or EVA (Hilgert, Smith & Van Camp, 2009), the clinical testing strategy often adheres to the following algorithm: For individuals with congenital hearing loss that is consistent with autosomal recessive inheritance and that appears non-syndromic, diagnostic testing typically starts with GJB2 sequence analysis. If clinical testing does not identify two pathogenic mutations, then inner ear imaging studies by MRI or CT for temporal bone anomalies may be performed. However, clinical testing of SLC26A4 without MRI or CT is also considered acceptable because mutations in this gene are thought to be a frequent cause of SNHL (Alasti, Van Camp & Smith, 1998, updated 2012). This approach to the clinical work-up is quite common in the U.S., in part because the same DNA specimen can be used for both molecular tests sequentially and in part because imaging studies in the pediatric population can be challenging. As a result, our patients were selected based on the presence of congenital SNHL compatible with autosomal recessive inheritance, absence of two hearing loss-associated GJB2 mutations, and the presence of only one known mutation in SLC26A4. In these individuals, we performed MLPA of SLC26A4 and in a subset we also sequenced the coding regions and splice sites of FOXI1 and KCNJ10 to evaluate alternative etiologies.

" ] }, "methods_html": { "value": [ - "

Materials and Methods

\n

Study subjects

\n

A total of 107 individuals participated in this study. Participants provided written informed consent as appropriate. All were enrolled with IRB approval from the Stanford University Administrative Panels for the Protection of Human Subjects (IRB Approval Numbers IRB-14011 and IRB-8353). Participants included individuals from Stanford University Medical Center (n = 60, Stanford, CA), the Center for Genetic Testing at Saint Francis Hospital (n = 30, Tulsa, OK) and Cincinnati Children’s Hospital Medical Center (n = 17, Cincinnati, OH). All participants were probands presenting with congenital SNHL who prior to enrollment, had all received GJB2 testing and been sequenced for mutations in the exons, splice sites and promoter region of the SLC26A4 gene (GenBank: NC_000007.13) as part of routine clinical care. Patients who did not have two pathogenic GJB2 mutations and who had only one identified SLC26A4 mutation were then eligible for additional genetic testing by MLPA in an effort to identify a second disease-causing mutation. FOXI1 (GenBank: NG_012068.1) and KCNJ10 (GenBank: NG_016411.1) were also sequenced in a subset of the Stanford patient group (n = 29/60) for whom sample was available.

\n

Because imaging analysis is not routinely ordered on children with phenotypically non-syndromic SNHL prior to SLC26A4 sequencing, imaging analysis results were available for only a portion of the subjects (n = 46/107; 43%) and indicated the presence of EVA in 56% (n = 26/46) and Mondini malformation in none of the probands. Vestibular dysfunction complaints were noted in only one of 54 participants for whom this information was reported. Thyroid manifestations were reported in none of the Stanford probands for whom this information was available (n = 0/37), including five individuals older than 13 years of age.

Detection and characterization of intragenic rearrangements

\n

Genomic DNA samples extracted from peripheral blood by standard methods were analyzed for copy number mutations by MLPA, using the SALSA MLPA kit P280 Pendred-SLC26A4 (MRC-Holland, Amsterdam, the Netherlands) according to the manufacturer’s protocol. Capillary electrophoresis of PCR products was performed using either an ABI 310 or an ABI 3500 Genetic Analyzer (Life Technologies, Grand Island, NY, USA) and the resulting data were analyzed using GeneMarker 1.51 software (SoftGenetics, LLC., State College, PA, USA).

\n

For breakpoint analysis in the single proband with an identified SLC26A4 deletion, PCR products were electrophoresed on an agarose gel and the 494 base pair (bp) fragment corresponding to the deletion was excised and purified using the QIAquick Gel Extraction Kit (Qiagen, Germantown, MD). The amplicon was then sequenced on an ABI 3730xl Genetic Analyzer (Life Technologies, Grand Island, NY, USA) to confirm the breakpoints of the deletion.

\nFOXI1 and KCNJ10 sequencing

\n

Almost half (n = 29/60) of the Stanford University proband samples had direct DNA sequencing of the coding exons, including intron/exon boundaries ±20 bp into the introns, of FOXI1 and KCNJ10. Primers were designed to amplify and sequence exons 1 and 2 of FOXI1 and exon 2 of KCNJ10 (Table 1). Amplicons were purified using the QIAquick PCR Purification Kit (Qiagen, Germantown, MD) and then sequenced on an ABI 3730xl Genetic Analyzer (Life Technologies, Grand Island, NY, USA). Sequences were compared against either the FOXI1 (GenBank: NG_012068.1) or the KCNJ10 (GenBank: NG_016411.1) reference sequence using Mutation Surveyor 2.51 software (SoftGenetics, LLC., State College, PA, USA). Nonsynonymous sequence variants detected in the coding regions of the FOXI1 and KCNJ10 genes were further analyzed using the mutation interpretation tools SIFT (Sorting Intolerant From Tolerant, http://sift.jcvi.org/) and PolyPhen-2 (Polymorphism Phenotyping v2, http://genetics.bwh.harvard.edu/pph2/), which predict the effect of an amino acid substitution on protein function.

\n
\nTable 1:
Primers used for the amplification of FOXI1 and KCNJ10.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GeneExonPrimer namePrimer sequence (5′ to 3′)\n T\n \n a\n \n
\n FOXI1\n 1FOXI1-1FTGAGCACCTGTCAGGGGCAG61
\n FOXI1\n 1FOXI1-1RGAACTTTCTAGAATGGGGTCTTG61
\n FOXI1\n 1FOXI1-1RintCCCTGTGGGTGGAAGAAGT55
\n FOXI1\n 2FOXI1-2FGACAATAAGGAGGAACAGAAG55
\n FOXI1\n 2FOXI1-2RGCATGGAGGACCTCTACTG55
\n KCNJ10\n 2KCNJ10-2aFGTTAATTCCTCCCTCCCATGG59
\n KCNJ10\n 2KCNJ10-2aRGTTCTCCCCTTCCTTGGTTTG59
\n KCNJ10\n 2KCNJ10-2bFGAGACCATTCGTTTCAGCCAG59
\n KCNJ10\n 2KCNJ10-2bRAAGAAGAGGGAGTGGAGGATG59
\n
" + "

Materials and Methods

\n

Study subjects

\n

A total of 107 individuals participated in this study. Participants provided written informed consent as appropriate. All were enrolled with IRB approval from the Stanford University Administrative Panels for the Protection of Human Subjects (IRB Approval Numbers IRB-14011 and IRB-8353). Participants included individuals from Stanford University Medical Center (n = 60, Stanford, CA), the Center for Genetic Testing at Saint Francis Hospital (n = 30, Tulsa, OK) and Cincinnati Children’s Hospital Medical Center (n = 17, Cincinnati, OH). All participants were probands presenting with congenital SNHL who prior to enrollment, had all received GJB2 testing and been sequenced for mutations in the exons, splice sites and promoter region of the SLC26A4 gene (GenBank: NC_000007.13) as part of routine clinical care. Patients who did not have two pathogenic GJB2 mutations and who had only one identified SLC26A4 mutation were then eligible for additional genetic testing by MLPA in an effort to identify a second disease-causing mutation. FOXI1 (GenBank: NG_012068.1) and KCNJ10 (GenBank: NG_016411.1) were also sequenced in a subset of the Stanford patient group (n = 29/60) for whom sample was available.

\n

Because imaging analysis is not routinely ordered on children with phenotypically non-syndromic SNHL prior to SLC26A4 sequencing, imaging analysis results were available for only a portion of the subjects (n = 46/107; 43%) and indicated the presence of EVA in 56% (n = 26/46) and Mondini malformation in none of the probands. Vestibular dysfunction complaints were noted in only one of 54 participants for whom this information was reported. Thyroid manifestations were reported in none of the Stanford probands for whom this information was available (n = 0/37), including five individuals older than 13 years of age.

Detection and characterization of intragenic rearrangements

\n

Genomic DNA samples extracted from peripheral blood by standard methods were analyzed for copy number mutations by MLPA, using the SALSA MLPA kit P280 Pendred-SLC26A4 (MRC-Holland, Amsterdam, the Netherlands) according to the manufacturer’s protocol. Capillary electrophoresis of PCR products was performed using either an ABI 310 or an ABI 3500 Genetic Analyzer (Life Technologies, Grand Island, NY, USA) and the resulting data were analyzed using GeneMarker 1.51 software (SoftGenetics, LLC., State College, PA, USA).

\n

For breakpoint analysis in the single proband with an identified SLC26A4 deletion, PCR products were electrophoresed on an agarose gel and the 494 base pair (bp) fragment corresponding to the deletion was excised and purified using the QIAquick Gel Extraction Kit (Qiagen, Germantown, MD). The amplicon was then sequenced on an ABI 3730xl Genetic Analyzer (Life Technologies, Grand Island, NY, USA) to confirm the breakpoints of the deletion.

\nFOXI1 and KCNJ10 sequencing

\n

Almost half (n = 29/60) of the Stanford University proband samples had direct DNA sequencing of the coding exons, including intron/exon boundaries ±20 bp into the introns, of FOXI1 and KCNJ10. Primers were designed to amplify and sequence exons 1 and 2 of FOXI1 and exon 2 of KCNJ10 (Table 1). Amplicons were purified using the QIAquick PCR Purification Kit (Qiagen, Germantown, MD) and then sequenced on an ABI 3730xl Genetic Analyzer (Life Technologies, Grand Island, NY, USA). Sequences were compared against either the FOXI1 (GenBank: NG_012068.1) or the KCNJ10 (GenBank: NG_016411.1) reference sequence using Mutation Surveyor 2.51 software (SoftGenetics, LLC., State College, PA, USA). Nonsynonymous sequence variants detected in the coding regions of the FOXI1 and KCNJ10 genes were further analyzed using the mutation interpretation tools SIFT (Sorting Intolerant From Tolerant, http://sift.jcvi.org/) and PolyPhen-2 (Polymorphism Phenotyping v2, http://genetics.bwh.harvard.edu/pph2/), which predict the effect of an amino acid substitution on protein function.

\n
\nTable 1:
Primers used for the amplification of FOXI1 and KCNJ10.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GeneExonPrimer namePrimer sequence (5′ to 3′)\n T\n \n a\n \n
\n FOXI1\n 1FOXI1-1FTGAGCACCTGTCAGGGGCAG61
\n FOXI1\n 1FOXI1-1RGAACTTTCTAGAATGGGGTCTTG61
\n FOXI1\n 1FOXI1-1RintCCCTGTGGGTGGAAGAAGT55
\n FOXI1\n 2FOXI1-2FGACAATAAGGAGGAACAGAAG55
\n FOXI1\n 2FOXI1-2RGCATGGAGGACCTCTACTG55
\n KCNJ10\n 2KCNJ10-2aFGTTAATTCCTCCCTCCCATGG59
\n KCNJ10\n 2KCNJ10-2aRGTTCTCCCCTTCCTTGGTTTG59
\n KCNJ10\n 2KCNJ10-2bFGAGACCATTCGTTTCAGCCAG59
\n KCNJ10\n 2KCNJ10-2bRAAGAAGAGGGAGTGGAGGATG59
\n
" ] }, "results_html": { "value": [ - "

Results

\n

In order to assess the potential diagnostic benefits of deletion/duplication analysis of the SLC26A4 gene, we performed MLPA on genomic DNA samples from 107 patients with congenital hearing loss in whom only one SLC26A4 mutation had been found by sequencing. Only one individual, PDS41, (1/107 unknown alleles; 0.93%) had MLPA results indicative of such a copy number variation—a putative heterozygous deletion spanning exons 4–6 of the gene (Fig. 1). Because deletions of these same SLC26A4 exons were previously described in a Spanish patient (Pera et al., 2008a) and in two Norwegian patients of Lebanese descent (Siem et al., 2010; Rendtorff et al., 2013), we investigated the possibility that our MLPA assay had detected a known rearrangement in our proband. Flanking PCR primers were designed to analyze the breakpoints of the deletion (PDS IVS3 Forward: 5′-ACAATGTCCATGCCACAACC-3′ and PDS IVS6 Reverse: 5′-ACAGAGACCATTACATACATAC-3′). A duplex reaction including both the breakpoint primers and a set of control primers for the amplification of exon 4 (PDS Ex4 Forward: 5′-AGGCAAAGTCATAAGTGGAAC-3′ and PDS Ex4 Reverse: 5′-ACCTAATAGAGGTATAATGCAC-3′) resulted in two products: a 494 bp fragment corresponding to the deletion and a 289 bp fragment amplified from the control primers (data not shown). The presence of the 289 bp amplicon indicated that the deletion was indeed heterozygous. Subsequent sequencing of the 494 bp amplicon confirmed the presence of g.8091T-22145Cdel (Fig. 1). This deletion removes 14,053 bp from the SLC26A4 gene, disrupting the open reading frame and truncating the protein at amino acid residue 105 in the first transmembrane domain.

\n
\"Identification
\n

\nFigure 1: Identification of the heterozygous SLC26A4 deletion g.8091T-22145Cdel in subject PDS41.

\n(A) The SLC26A4 MLPA probe mix includes probes for the 21 SLC26A4 exons, 14 reference probes and three probes specific for the point mutations c.1001+1G>A (IV S8+1G>A), c.707T>C (p.Leu236Pro) and c.1246A>C (p.Thr416Pro). Subject PDS41 is heterozygous for a deletion (g.8091T-22145Cdel) spanning exons 4–6 in SLC26A4, as evidenced by the reproducible reduction in peak height for these three exon probes (peaks labeled 4, 5, 6) relative to the control. PDS41 also has a heterozygous c.1246A>C (p.Thr416Pro) mutation that was previously identified by sequencing and confirmed by these MLPA results (peak labeled p.T416P). (B) Sequencing chromatogram of the deletion breakpoints in SLC26A4 IVS3 and IVS6. The deletion removes a total of 14,053 bp. IVS, intervening sequence.

In addition to performing MLPA analysis on samples from our patient cohort, we investigated other genes potentially contributing to their SNHL by sequencing 29 probands for variants in the coding regions of the FOXI1 and KCNJ10 genes. We identified a heterozygous variant of FOXI1, c.677C>T (p.Thr226Ile), in one patient, PDS29 (1/29 unknown alleles; 3.4%). This FOXI1 substitution has not been previously described in SNHL. It represents a rare variant (dbSNP:rs115399307; minor allele frequency of 0.3%, http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=115399307) of unknown clinical significance. The SIFT and PolyPhen-2 programs predicted the substitution to be “tolerated” and “benign”, respectively. Two heterozygous variants of KCNJ10 were also detected in this group (2/29 unknown alleles; 6.9%), each in a separate proband. The substitution c.812G> A(p.Arg271His) in PDS21 was predicted by SIFT and PolyPhen-2 to be “tolerated” and “benign”, respectively. This substitution is also a rare sequence variant (dbSNP: rs3795339; minor allele frequency of 0.6%, http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3795339) of uncertain clinical significance that has been reported previously in a single heterozygous Chinese proband with non-syndromic EVA and zero mutations of SLC26A4 (Chai et al., 2013). In that same study, however, the c.812G>A (p.Arg271His) variant was found in 10/200 or 5% of normal hearing controls, suggesting that this substitution may be a polymorphism in the Chinese population. The other KCNJ10 variant, c.811C>T (p.Arg271Cys), was discovered in patient PDS23 and it also affects amino acid residue 271. Although this substitution is predicted to “affect protein function” by SIFT and to be “possibly damaging” by PolyPhen-2, it is a reported polymorphism of unknown clinical significance (dbSNP: rs1130183) with a minor allele frequency of 2.3% (dbSNP: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type= rs&rs=1130183). This substitution has been previously reported in three Italian individuals affected with SNHL, who also had bilateral inner ear malformations (Cirello et al., 2012) and has been associated with seizure susceptibility (Buono et al., 2004; Lenzen et al., 2005).

" + "

Results

\n

In order to assess the potential diagnostic benefits of deletion/duplication analysis of the SLC26A4 gene, we performed MLPA on genomic DNA samples from 107 patients with congenital hearing loss in whom only one SLC26A4 mutation had been found by sequencing. Only one individual, PDS41, (1/107 unknown alleles; 0.93%) had MLPA results indicative of such a copy number variation—a putative heterozygous deletion spanning exons 4–6 of the gene (Fig. 1). Because deletions of these same SLC26A4 exons were previously described in a Spanish patient (Pera et al., 2008a) and in two Norwegian patients of Lebanese descent (Siem et al., 2010; Rendtorff et al., 2013), we investigated the possibility that our MLPA assay had detected a known rearrangement in our proband. Flanking PCR primers were designed to analyze the breakpoints of the deletion (PDS IVS3 Forward: 5′-ACAATGTCCATGCCACAACC-3′ and PDS IVS6 Reverse: 5′-ACAGAGACCATTACATACATAC-3′). A duplex reaction including both the breakpoint primers and a set of control primers for the amplification of exon 4 (PDS Ex4 Forward: 5′-AGGCAAAGTCATAAGTGGAAC-3′ and PDS Ex4 Reverse: 5′-ACCTAATAGAGGTATAATGCAC-3′) resulted in two products: a 494 bp fragment corresponding to the deletion and a 289 bp fragment amplified from the control primers (data not shown). The presence of the 289 bp amplicon indicated that the deletion was indeed heterozygous. Subsequent sequencing of the 494 bp amplicon confirmed the presence of g.8091T-22145Cdel (Fig. 1). This deletion removes 14,053 bp from the SLC26A4 gene, disrupting the open reading frame and truncating the protein at amino acid residue 105 in the first transmembrane domain.

\n
\"Identification
\n

\nFigure 1: Identification of the heterozygous SLC26A4 deletion g.8091T-22145Cdel in subject PDS41.

\n(A) The SLC26A4 MLPA probe mix includes probes for the 21 SLC26A4 exons, 14 reference probes and three probes specific for the point mutations c.1001+1G>A (IV S8+1G>A), c.707T>C (p.Leu236Pro) and c.1246A>C (p.Thr416Pro). Subject PDS41 is heterozygous for a deletion (g.8091T-22145Cdel) spanning exons 4–6 in SLC26A4, as evidenced by the reproducible reduction in peak height for these three exon probes (peaks labeled 4, 5, 6) relative to the control. PDS41 also has a heterozygous c.1246A>C (p.Thr416Pro) mutation that was previously identified by sequencing and confirmed by these MLPA results (peak labeled p.T416P). (B) Sequencing chromatogram of the deletion breakpoints in SLC26A4 IVS3 and IVS6. The deletion removes a total of 14,053 bp. IVS, intervening sequence.

In addition to performing MLPA analysis on samples from our patient cohort, we investigated other genes potentially contributing to their SNHL by sequencing 29 probands for variants in the coding regions of the FOXI1 and KCNJ10 genes. We identified a heterozygous variant of FOXI1, c.677C>T (p.Thr226Ile), in one patient, PDS29 (1/29 unknown alleles; 3.4%). This FOXI1 substitution has not been previously described in SNHL. It represents a rare variant (dbSNP:rs115399307; minor allele frequency of 0.3%, http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=115399307) of unknown clinical significance. The SIFT and PolyPhen-2 programs predicted the substitution to be “tolerated” and “benign”, respectively. Two heterozygous variants of KCNJ10 were also detected in this group (2/29 unknown alleles; 6.9%), each in a separate proband. The substitution c.812G> A(p.Arg271His) in PDS21 was predicted by SIFT and PolyPhen-2 to be “tolerated” and “benign”, respectively. This substitution is also a rare sequence variant (dbSNP: rs3795339; minor allele frequency of 0.6%, http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=3795339) of uncertain clinical significance that has been reported previously in a single heterozygous Chinese proband with non-syndromic EVA and zero mutations of SLC26A4 (Chai et al., 2013). In that same study, however, the c.812G>A (p.Arg271His) variant was found in 10/200 or 5% of normal hearing controls, suggesting that this substitution may be a polymorphism in the Chinese population. The other KCNJ10 variant, c.811C>T (p.Arg271Cys), was discovered in patient PDS23 and it also affects amino acid residue 271. Although this substitution is predicted to “affect protein function” by SIFT and to be “possibly damaging” by PolyPhen-2, it is a reported polymorphism of unknown clinical significance (dbSNP: rs1130183) with a minor allele frequency of 2.3% (dbSNP: http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type= rs&rs=1130183). This substitution has been previously reported in three Italian individuals affected with SNHL, who also had bilateral inner ear malformations (Cirello et al., 2012) and has been associated with seizure susceptibility (Buono et al., 2004; Lenzen et al., 2005).

" ] }, "discussion_html": { "value": [ - "

Discussion

\n

The autosomal recessive inheritance of PDS and DFNB4 is well established and yet, for many affected individuals, analysis of the coding sequences and splice sites of the SLC26A4 gene has failed to identify one or both of the mutations required to cause these disorders (Campbell et al., 2001; Tsukamoto et al., 2003; Pryor et al., 2005; Albert et al., 2006; Yang et al., 2007; Wu et al., 2010). In fact, an analysis of six studies with a total enrollment of 769 hearing impaired probands with EVA, a non-pathognomonic clinical finding that is a hallmark of PDS and DFNB4, reveals that only 25% have biallelic SLC26A4 mutations (Table 2). Of these same probands, 45% have at least one SLC26A4 mutation, a percentage slightly lower than the 50% reported by GeneReviews as the proportion of PDS/DFNB4 accounted for by mutations in SLC26A4 (http://www.ncbi.nlm.nih.gov/books/NBK1467/). Among the six included studies, there are considerable differences in the reported percentages of individuals segregating monoallelic or biallelic SLC26A4 mutations. The proportion of probands for whom at least one SLC26A4 mutation is detected ranges from as low as 30–40% (Campbell et al., 2001; Albert et al., 2006; Yang et al., 2007) to as high as 80–90% (Tsukamoto et al., 2003; Wu et al., 2010). The percentage of probands in whom biallelic mutations are found varies accordingly, from a low of 13% (Yang et al., 2007) to a high of 62% (Wu et al., 2010). This variation may be attributed to differences in the selection criteria of each study and/or to the patient population being tested; however, in all cases, there is a substantial proportion of individuals for whom the genotype is either incomplete or for whom no mutations in SLC26A4 were identified at all. This has implications for genetic counseling regarding recurrence risk, whether to pursue imaging, and, more broadly, understanding of disease pathogenesis. The inability to identify both mutations in individuals suspected of having a PDS/DFNB4 hearing loss etiology suggests the possible involvement of (1) mutations in unexamined regions of SLC26A4; (2) mutations in other, as yet to be implicated genes; or (3) other factors, such as those that may regulate gene expression.

\n
\nTable 2:
Percentages of PDS/DFNB4 probands with SLC26A4 mutations.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
ReferenceProbands2 Mutations1 Mutation0 MutationsStudy selection criteria
\n Campbell et al., 2001\n 589 (16%)14 (24%)35 (60%)Recessive HL with DVA or Mondini dysplasia
\n Tsukamoto et al., 2003\n 4224 (57%)10 (24%)8 (19%)Pendred (goiter) or bilateral HL with EVA
\n Pryor et al., 2005\n 3914 (36%)14 (36%)11 (28%)EVA in at least one ear
\n Albert et al., 2006\n 10024 (24%)16 (16%)60 (60%)Bilateral, recessive HL; EVA; no GJB2 mutations
\n Yang et al., 2007\n 42957 (13%)75 (17%)297 (69%)HL with EVA
\n Wu et al., 2010\n 10163 (62%)24 (24%)14 (14%)Bilateral EVA
\n Total\n 769191 (25%)153 (20%)425 (55%)
\n\n
\n

Notes:

\n

\n

\n
HL
\n

hearing loss

\n
DVA
\n

dilated vestibular aqueduct

\n
EVA
\n

enlarged vestibular aqueduct

\n
\n

\n

The selection of study subjects is an important factor that is not consistent between studies. Our patient selection was based primarily on the genetic testing of GJB2 and SLC26A4 as is common in the clinical work-up for children with SNHL in the U.S., with imaging studies performed on only a subset of patients. Even in this relatively general SNHL patient population, however, we saw a considerable enrichment for probands with single SLC26A4 mutations, compared to unaffected individuals. In the experience of the Stanford Molecular Pathology Laboratory, the frequency of heterozygous SLC26A4 mutations in probands tested with a GJB2 and SLC26A4 algorithm and in whom two pathogenic mutations are not identified is 12.3%, which is significantly higher (p < 0.001) than the expected carrier frequency. Using a frequency of 1/500 for congenital bilateral hearing loss of ≥40 dB (Hilgert, Smith & Van Camp, 2009), and the estimate that SLC26A4 related SNHL would account for up to 7.5%, then the frequency of such hearing loss could approximate one in 7,000. Assuming Hardy–Weinberg equilibrium, the carrier frequency would be about 1:50 (2%). This is congruent with a study in which pathogenic or possibly pathogenic mutations were identified in 1.9% of normal-hearing controls (8/428 controls; p.E29Q, p.F354S, p.F667C, p.D724G, p.G740S) (Pera et al., 2008b). An “excess” of heterozygous mutations in individuals with SNHL compared to controls has also been observed for GJB2 (Putcha et al., 2007), a gene for which neighboring deletions can affect gene expression (Rodriguez-Paris & Schrijver, 2009).

\n

Given that SLC26A4 related SNHL is autosomal recessive, we postulated that these ‘missing’ SLC26A4 mutations may be the result of intragenic deletions or duplications of one or more exons for which patients are not routinely tested. We selected 107 individuals with SNHL and monoallelic mutations of SLC26A4 for MLPA analysis of the SLC26A4 gene to explore this further. A handful of multiexon SLC26A4 deletions have been described in the literature (Park et al., 2003; Hu et al., 2007; Pera et al., 2008a; Anwar et al., 2009; Siem et al., 2010) but it is unclear how many of the probands in these cohorts were tested for intragenic deletions and duplications. Recently, however, in a study of 109 Scandinavian probands with suspected PDS/DFNB4, 37 individuals with only one or zero mutations of SLC26A4 were systematically screened for copy number variants by MLPA (Rendtorff et al., 2013). Only one harbored a homozygous deletion, of exons 4–6 (n = 2/63 unknown alleles; 3.2%). In our study of hearing impaired individuals with one previously identified SLC26A4 mutation, we found an intragenic deletion in a single individual only (n = 1/107 unknown alleles; 0.93%). This deletion also spanned exons 4–6 of the SLC26A4 gene and was previously detected in a patient of Spanish descent (Pera et al., 2008a). An analysis of the deletion breakpoints confirmed that our subject carried a heterozygous copy of g.8091T-22145Cdel (Fig. 1). To date, deletions and duplications seem to represent approximately 1.8% of missing SLC26A4 mutations overall (n = 3/170 unknown alleles) (Rendtorff et al., 2013; this study). Despite accounting for a low percentage of the ‘missing’ mutations, clinical testing for multiexon deletions and duplications of additional patients with potential PDS/DFNB4 etiology may remain warranted in order to more firmly establish frequencies and elucidate their relative contribution to the phenotype.

\n

Alternatively, unrecognized mutations in unexamined, noncoding regions of the gene may be responsible for the ‘missing’ SLC26A4 mutations and contribute to the PDS/DFNB4 phenotype. For example, intronic mutations may create cryptic splice sites and mutations in the promoter region may disrupt the binding of regulatory elements. Indeed, a cis-regulatory element that binds transcription factor FOXI1 has been described in the SLC26A4 promoter region (Yang et al., 2007). The regulatory element consists of two head-to-head binding sites, FBS1 and FBS2, and a mutation within this cis-element, c.-103T>C, has been shown to disrupt transcriptional activation of the gene by FOXI1. However, none of the probands included in this study carried mutations in the promoter region.

\n

Mutations of the FOXI1 gene itself have also been implicated in PDS and DFNB4. Monoallelic variants of FOXI1 were documented in six patients with either PDS or non-syndromic EVA and were shown to compromise the ability of FOXI1 to transcriptionally activate SLC26A4 (Yang et al., 2007). One of these six probands segregated the DFNB4 phenotype with one heterozygous mutation each of FOXI1 and SLC26A4. This finding was consistent with the EVA phenotype observed in the Slc26a4+/−; Foxi1+/− double-heterozygous mouse model and suggests that the transcriptional regulatory machinery of SLC26A4 plays a role in PDS/DFNB4 pathogenesis. Mutations of KCNJ10, a gene that encodes a K+ channel protein, have also been associated with PDS/DFNB4 (Marcus et al., 2002). Protein expression studies in SLC26A4 knockout mice have indicated that the absence of pendrin expression reduces KCNJ10 protein levels, supporting the hypothesis that deafness in the mouse model is secondary to loss of KCNJ10 function (Wangemann et al., 2004). A similar reduction of KCNJ10 expression was observed in the stria vascularis of the inner ear in the haploinsufficient Slc26a4+/− mouse mutant (Yang et al., 2009). In that same study, two individuals with the PDS/DFNB4 phenotype were reported to be double heterozygous for mutations of the SLC26A4 and KCNJ10 genes, further supporting a digenic model of inheritance.

\n

We examined to what extent digenic inheritance may contribute to the PDS/DFNB4 phenotype by sequencing the coding regions and splice sites of FOXI1 and KCNJ10 in about half (n = 29/60) of the Stanford University probands enrolled in the study for whom enough sample was available for the additional analysis. Our initial sequencing of FOXI1 and KCNJ10 in these subjects resulted in three nonsynonymous variants overall; all three of these heterozygous substitutions are listed in the dbSNP database as having unknown clinical significance. Nonetheless, functional studies must be conducted to investigate the effects of the FOXI1 variant on SLC26A4 transcriptional activation and the impact of the two KCNJ10 variants on K+ channel conductance before a determination of the pathogenicity of these three variants and their effect on SNHL phenotypes can be more definitively made.

\n

Although unlikely, if the FOXI1 variant and the two KCNJ10 variants detected in our probands are indeed digenic mutations acting in conjunction with mutations of SLC26A4, then 3.4% and 6.9% of the missing mutant alleles in our SNHL patients would be attributable to variants in FOXI1 and KCNJ10, respectively. However, the number of patients tested for FOXI1 and KCNJ10 variants (n = 29/107 total probands) is too small a sample size to merit this conclusion. Consequently, a meta-analysis of published studies in which FOXI1 and KCNJ10 were sequenced in SNHL patients with inner ear malformations was conducted. The meta-analysis does not support the frequencies observed in our patients (Table 3) and shows instead that, overall, 1.3% and 3.1% of suspected PDS/DFNB4 patients have variants in FOXI1 and KCNJ10, respectively. In fact, considering that the KCNJ10 variant c.812G>A (p.Arg271His) may be a polymorphism in the Chinese population and the KCNJ10 variant c.811C>T (p.Arg271Cys) is a reported polymorphism in the dbSNP database, the frequency of KCNJ10 variants in PDS/DFNB4 patients may be inflated by the inclusion of the Chinese and Italian probands carrying these substitutions and may actually be lower. The great majority of reported FOXI1 and KCNJ10 variants are from the initial studies that implicated the genes in the digenic inheritance of PDS/DFNB4 (Yang et al., 2007; Yang et al., 2009). However, the actual contribution of FOXI1 and KCNJ10 mutations to SNHL may be more limited, as illustrated by several subsequent studies in which either no FOXI1 variants (Wu et al., 2010; Mercer, Mutton & Dahl, 2011; Lai et al., 2012; Chen et al., 2012; Chai et al., 2013), or no KCNJ10 variants (Mercer, Mutton & Dahl, 2011; Chen et al., 2012) were identified.

\n
\nTable 3:
Meta-analysis of the frequency of FOXI1 and KCNJ10 variants in PDS/DFNB4 probands.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GenePopulation
origin
ReferenceControls1\nInclusion criteria for SLC26A4 sequencingSelection criteria for
FOXI1 sequencing
Subjects with nonsynonymous variants
\n FOXI1\n US/Sweden\n Yang et al., 2007\n 250EVA with or without Mondini dysplasia0 or 1 SLC26A4 mutations6/372 (1.6%)2\n
\n FOXI1\n Taiwan\n Wu et al., 2010\n 100Bilateral EVA with or without other IEMs0 or 1 SLC26A4 mutations0/38 (0.0%)
\n FOXI1\n Australia\n Mercer, Mutton & Dahl, 2011\n 96EVAPhenotype only0/44 (0.0%)
\n FOXI1\n Italy\n Cirello et al., 2012\n 80Bilateral IEMs/family history of PS/goiter0 or 1 SLC26A4 mutations1/14 (7.1%)3\n
\n FOXI1\n China\n Lai et al., 2012\n 100EVA0 or 1 SLC26A4 mutations0/8 (0.0%)
\n FOXI1\n China\n Chen et al., 2012\n IEM’s0 or 1 SLC26A4 mutations0/15 (0.0%)
\n FOXI1\n China\n Chai et al., 2013\n 200Nonsyndromic EVA0 or 1 SLC26A4 mutations0/33 (0.0%)
\nReported FOXI1 frequency= 7/524 (1.3%)\n
\n FOXI1\n USThis studySensorineural hearing loss1 SLC26A4 mutation1/29 (3.4%)
\nTotal combined FOXI1 frequency= 8/553 (1.4%)\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GenePopulation
origin
ReferenceControls1\nInclusion criteria for
SLC26A4 sequencing
Selection criteria for
KCNJ10 sequencing
Subjects with nonsynonymous variants
\n KCNJ10\n China/US/
Canada
\n Yang et al., 2009\n 400EVA with or without Mondini dysplasia1 SLC26A4 mutation2/89 (2.2%)4\n
\n KCNJ10\n Australia\n Mercer, Mutton & Dahl, 2011\n 96EVAPhenotype only0/44 (0.0%)
\n KCNJ10\n Italy\n Cirello et al., 2012\n 80Bilateral IEMs/family history of PS/goiter0 or 1 SLC26A4 mutations3/14 (21.4%)5\n
\n KCNJ10\n China\n Chen et al., 2012\n IEM’s0 or 1 SLC26A4 mutations0/15 (0.0%)
\n KCNJ10\n China\n Chai et al., 2013\n 200Nonsyndromic EVA0 or 1 SLC26A4 mutations1/33 (3.0%)6\n
\nReported KCNJ10 frequency = 6/195 (3.1%)\n
\n KCNJ10\n USThis studySensorineural hearing loss1 SLC26A4 mutation2/29 (6.9%)
\nTotal combined KCNJ10 frequency= 8/224 (3.6%)\n
\n
\n\n
\n

Notes:

\n
\n1All controls had normal hearing and, unless otherwise noted, none harbored any of the novel variants.\n
\n
\n2Five variants (p.G258E, p.N161del, p.G258R, p.R267Q and p.G335V) were detected in six probands and were shown to compromise SLC26A4 transcriptional activation.\n
\n
\n3Functional analysis of the identified novel variant (p.P239L) showed no impairment of SLC26A4 transcriptional activation.\n
\n
\n4Two identified missense mutations (p.P194H and p.R348C) were shown to impair K+ channel conductance.\n
\n
\n5One previously reported variant (p.R271C) was identified in 3 probands.\n
\n
\n6One heterozygous variant (p.R271H) was detected in a single proband; this variant was also found in 10/200 normal hearing controls.\n
\n

\n

\n
EVA
\n

Enlarged vestibular aqueduct

\n
IEM
\n

Inner ear malformation

\n
PS
\n

Pendred syndrome

\n
\n

\n

The genetic basis of hearing loss is diagnostically challenging with over 100 genes implicated (http://hereditaryhearingloss.org). The phenotypic variability observed within the PDS/DFNB4 spectrum also complicates diagnosis with changes in the same gene, SLC26A4, responsible for syndromic as well as non-syndromic hearing loss. Most clinical centers have historically utilized tiered testing in the assessment of hearing loss genetic etiology. However, with the advent of large-scale massively parallel sequencing (MPS), future approaches will likely employ testing platforms that are more comprehensive, cost effective and efficient (Shearer & Smith, 2012). Additional sources of genetic mutation, such as deletions and duplications, will need to be included in these new testing approaches.

" + "

Discussion

\n

The autosomal recessive inheritance of PDS and DFNB4 is well established and yet, for many affected individuals, analysis of the coding sequences and splice sites of the SLC26A4 gene has failed to identify one or both of the mutations required to cause these disorders (Campbell et al., 2001; Tsukamoto et al., 2003; Pryor et al., 2005; Albert et al., 2006; Yang et al., 2007; Wu et al., 2010). In fact, an analysis of six studies with a total enrollment of 769 hearing impaired probands with EVA, a non-pathognomonic clinical finding that is a hallmark of PDS and DFNB4, reveals that only 25% have biallelic SLC26A4 mutations (Table 2). Of these same probands, 45% have at least one SLC26A4 mutation, a percentage slightly lower than the 50% reported by GeneReviews as the proportion of PDS/DFNB4 accounted for by mutations in SLC26A4 (http://www.ncbi.nlm.nih.gov/books/NBK1467/). Among the six included studies, there are considerable differences in the reported percentages of individuals segregating monoallelic or biallelic SLC26A4 mutations. The proportion of probands for whom at least one SLC26A4 mutation is detected ranges from as low as 30–40% (Campbell et al., 2001; Albert et al., 2006; Yang et al., 2007) to as high as 80–90% (Tsukamoto et al., 2003; Wu et al., 2010). The percentage of probands in whom biallelic mutations are found varies accordingly, from a low of 13% (Yang et al., 2007) to a high of 62% (Wu et al., 2010). This variation may be attributed to differences in the selection criteria of each study and/or to the patient population being tested; however, in all cases, there is a substantial proportion of individuals for whom the genotype is either incomplete or for whom no mutations in SLC26A4 were identified at all. This has implications for genetic counseling regarding recurrence risk, whether to pursue imaging, and, more broadly, understanding of disease pathogenesis. The inability to identify both mutations in individuals suspected of having a PDS/DFNB4 hearing loss etiology suggests the possible involvement of (1) mutations in unexamined regions of SLC26A4; (2) mutations in other, as yet to be implicated genes; or (3) other factors, such as those that may regulate gene expression.

\n
\nTable 2:
Percentages of PDS/DFNB4 probands with SLC26A4 mutations.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
ReferenceProbands2 Mutations1 Mutation0 MutationsStudy selection criteria
\n Campbell et al., 2001\n 589 (16%)14 (24%)35 (60%)Recessive HL with DVA or Mondini dysplasia
\n Tsukamoto et al., 2003\n 4224 (57%)10 (24%)8 (19%)Pendred (goiter) or bilateral HL with EVA
\n Pryor et al., 2005\n 3914 (36%)14 (36%)11 (28%)EVA in at least one ear
\n Albert et al., 2006\n 10024 (24%)16 (16%)60 (60%)Bilateral, recessive HL; EVA; no GJB2 mutations
\n Yang et al., 2007\n 42957 (13%)75 (17%)297 (69%)HL with EVA
\n Wu et al., 2010\n 10163 (62%)24 (24%)14 (14%)Bilateral EVA
\n Total\n 769191 (25%)153 (20%)425 (55%)
\n\n
\n

Notes:

\n

\n

\n
HL
\n

hearing loss

\n
DVA
\n

dilated vestibular aqueduct

\n
EVA
\n

enlarged vestibular aqueduct

\n
\n

\n

The selection of study subjects is an important factor that is not consistent between studies. Our patient selection was based primarily on the genetic testing of GJB2 and SLC26A4 as is common in the clinical work-up for children with SNHL in the U.S., with imaging studies performed on only a subset of patients. Even in this relatively general SNHL patient population, however, we saw a considerable enrichment for probands with single SLC26A4 mutations, compared to unaffected individuals. In the experience of the Stanford Molecular Pathology Laboratory, the frequency of heterozygous SLC26A4 mutations in probands tested with a GJB2 and SLC26A4 algorithm and in whom two pathogenic mutations are not identified is 12.3%, which is significantly higher (p < 0.001) than the expected carrier frequency. Using a frequency of 1/500 for congenital bilateral hearing loss of ≥40 dB (Hilgert, Smith & Van Camp, 2009), and the estimate that SLC26A4 related SNHL would account for up to 7.5%, then the frequency of such hearing loss could approximate one in 7,000. Assuming Hardy–Weinberg equilibrium, the carrier frequency would be about 1:50 (2%). This is congruent with a study in which pathogenic or possibly pathogenic mutations were identified in 1.9% of normal-hearing controls (8/428 controls; p.E29Q, p.F354S, p.F667C, p.D724G, p.G740S) (Pera et al., 2008b). An “excess” of heterozygous mutations in individuals with SNHL compared to controls has also been observed for GJB2 (Putcha et al., 2007), a gene for which neighboring deletions can affect gene expression (Rodriguez-Paris & Schrijver, 2009).

\n

Given that SLC26A4 related SNHL is autosomal recessive, we postulated that these ‘missing’ SLC26A4 mutations may be the result of intragenic deletions or duplications of one or more exons for which patients are not routinely tested. We selected 107 individuals with SNHL and monoallelic mutations of SLC26A4 for MLPA analysis of the SLC26A4 gene to explore this further. A handful of multiexon SLC26A4 deletions have been described in the literature (Park et al., 2003; Hu et al., 2007; Pera et al., 2008a; Anwar et al., 2009; Siem et al., 2010) but it is unclear how many of the probands in these cohorts were tested for intragenic deletions and duplications. Recently, however, in a study of 109 Scandinavian probands with suspected PDS/DFNB4, 37 individuals with only one or zero mutations of SLC26A4 were systematically screened for copy number variants by MLPA (Rendtorff et al., 2013). Only one harbored a homozygous deletion, of exons 4–6 (n = 2/63 unknown alleles; 3.2%). In our study of hearing impaired individuals with one previously identified SLC26A4 mutation, we found an intragenic deletion in a single individual only (n = 1/107 unknown alleles; 0.93%). This deletion also spanned exons 4–6 of the SLC26A4 gene and was previously detected in a patient of Spanish descent (Pera et al., 2008a). An analysis of the deletion breakpoints confirmed that our subject carried a heterozygous copy of g.8091T-22145Cdel (Fig. 1). To date, deletions and duplications seem to represent approximately 1.8% of missing SLC26A4 mutations overall (n = 3/170 unknown alleles) (Rendtorff et al., 2013; this study). Despite accounting for a low percentage of the ‘missing’ mutations, clinical testing for multiexon deletions and duplications of additional patients with potential PDS/DFNB4 etiology may remain warranted in order to more firmly establish frequencies and elucidate their relative contribution to the phenotype.

\n

Alternatively, unrecognized mutations in unexamined, noncoding regions of the gene may be responsible for the ‘missing’ SLC26A4 mutations and contribute to the PDS/DFNB4 phenotype. For example, intronic mutations may create cryptic splice sites and mutations in the promoter region may disrupt the binding of regulatory elements. Indeed, a cis-regulatory element that binds transcription factor FOXI1 has been described in the SLC26A4 promoter region (Yang et al., 2007). The regulatory element consists of two head-to-head binding sites, FBS1 and FBS2, and a mutation within this cis-element, c.-103T>C, has been shown to disrupt transcriptional activation of the gene by FOXI1. However, none of the probands included in this study carried mutations in the promoter region.

\n

Mutations of the FOXI1 gene itself have also been implicated in PDS and DFNB4. Monoallelic variants of FOXI1 were documented in six patients with either PDS or non-syndromic EVA and were shown to compromise the ability of FOXI1 to transcriptionally activate SLC26A4 (Yang et al., 2007). One of these six probands segregated the DFNB4 phenotype with one heterozygous mutation each of FOXI1 and SLC26A4. This finding was consistent with the EVA phenotype observed in the Slc26a4+/−; Foxi1+/− double-heterozygous mouse model and suggests that the transcriptional regulatory machinery of SLC26A4 plays a role in PDS/DFNB4 pathogenesis. Mutations of KCNJ10, a gene that encodes a K+ channel protein, have also been associated with PDS/DFNB4 (Marcus et al., 2002). Protein expression studies in SLC26A4 knockout mice have indicated that the absence of pendrin expression reduces KCNJ10 protein levels, supporting the hypothesis that deafness in the mouse model is secondary to loss of KCNJ10 function (Wangemann et al., 2004). A similar reduction of KCNJ10 expression was observed in the stria vascularis of the inner ear in the haploinsufficient Slc26a4+/− mouse mutant (Yang et al., 2009). In that same study, two individuals with the PDS/DFNB4 phenotype were reported to be double heterozygous for mutations of the SLC26A4 and KCNJ10 genes, further supporting a digenic model of inheritance.

\n

We examined to what extent digenic inheritance may contribute to the PDS/DFNB4 phenotype by sequencing the coding regions and splice sites of FOXI1 and KCNJ10 in about half (n = 29/60) of the Stanford University probands enrolled in the study for whom enough sample was available for the additional analysis. Our initial sequencing of FOXI1 and KCNJ10 in these subjects resulted in three nonsynonymous variants overall; all three of these heterozygous substitutions are listed in the dbSNP database as having unknown clinical significance. Nonetheless, functional studies must be conducted to investigate the effects of the FOXI1 variant on SLC26A4 transcriptional activation and the impact of the two KCNJ10 variants on K+ channel conductance before a determination of the pathogenicity of these three variants and their effect on SNHL phenotypes can be more definitively made.

\n

Although unlikely, if the FOXI1 variant and the two KCNJ10 variants detected in our probands are indeed digenic mutations acting in conjunction with mutations of SLC26A4, then 3.4% and 6.9% of the missing mutant alleles in our SNHL patients would be attributable to variants in FOXI1 and KCNJ10, respectively. However, the number of patients tested for FOXI1 and KCNJ10 variants (n = 29/107 total probands) is too small a sample size to merit this conclusion. Consequently, a meta-analysis of published studies in which FOXI1 and KCNJ10 were sequenced in SNHL patients with inner ear malformations was conducted. The meta-analysis does not support the frequencies observed in our patients (Table 3) and shows instead that, overall, 1.3% and 3.1% of suspected PDS/DFNB4 patients have variants in FOXI1 and KCNJ10, respectively. In fact, considering that the KCNJ10 variant c.812G>A (p.Arg271His) may be a polymorphism in the Chinese population and the KCNJ10 variant c.811C>T (p.Arg271Cys) is a reported polymorphism in the dbSNP database, the frequency of KCNJ10 variants in PDS/DFNB4 patients may be inflated by the inclusion of the Chinese and Italian probands carrying these substitutions and may actually be lower. The great majority of reported FOXI1 and KCNJ10 variants are from the initial studies that implicated the genes in the digenic inheritance of PDS/DFNB4 (Yang et al., 2007; Yang et al., 2009). However, the actual contribution of FOXI1 and KCNJ10 mutations to SNHL may be more limited, as illustrated by several subsequent studies in which either no FOXI1 variants (Wu et al., 2010; Mercer, Mutton & Dahl, 2011; Lai et al., 2012; Chen et al., 2012; Chai et al., 2013), or no KCNJ10 variants (Mercer, Mutton & Dahl, 2011; Chen et al., 2012) were identified.

\n
\nTable 3:
Meta-analysis of the frequency of FOXI1 and KCNJ10 variants in PDS/DFNB4 probands.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GenePopulation
origin
ReferenceControls1\nInclusion criteria for SLC26A4 sequencingSelection criteria for
FOXI1 sequencing
Subjects with nonsynonymous variants
\n FOXI1\n US/Sweden\n Yang et al., 2007\n 250EVA with or without Mondini dysplasia0 or 1 SLC26A4 mutations6/372 (1.6%)2\n
\n FOXI1\n Taiwan\n Wu et al., 2010\n 100Bilateral EVA with or without other IEMs0 or 1 SLC26A4 mutations0/38 (0.0%)
\n FOXI1\n Australia\n Mercer, Mutton & Dahl, 2011\n 96EVAPhenotype only0/44 (0.0%)
\n FOXI1\n Italy\n Cirello et al., 2012\n 80Bilateral IEMs/family history of PS/goiter0 or 1 SLC26A4 mutations1/14 (7.1%)3\n
\n FOXI1\n China\n Lai et al., 2012\n 100EVA0 or 1 SLC26A4 mutations0/8 (0.0%)
\n FOXI1\n China\n Chen et al., 2012\n IEM’s0 or 1 SLC26A4 mutations0/15 (0.0%)
\n FOXI1\n China\n Chai et al., 2013\n 200Nonsyndromic EVA0 or 1 SLC26A4 mutations0/33 (0.0%)
\nReported FOXI1 frequency= 7/524 (1.3%)\n
\n FOXI1\n USThis studySensorineural hearing loss1 SLC26A4 mutation1/29 (3.4%)
\nTotal combined FOXI1 frequency= 8/553 (1.4%)\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GenePopulation
origin
ReferenceControls1\nInclusion criteria for
SLC26A4 sequencing
Selection criteria for
KCNJ10 sequencing
Subjects with nonsynonymous variants
\n KCNJ10\n China/US/
Canada
\n Yang et al., 2009\n 400EVA with or without Mondini dysplasia1 SLC26A4 mutation2/89 (2.2%)4\n
\n KCNJ10\n Australia\n Mercer, Mutton & Dahl, 2011\n 96EVAPhenotype only0/44 (0.0%)
\n KCNJ10\n Italy\n Cirello et al., 2012\n 80Bilateral IEMs/family history of PS/goiter0 or 1 SLC26A4 mutations3/14 (21.4%)5\n
\n KCNJ10\n China\n Chen et al., 2012\n IEM’s0 or 1 SLC26A4 mutations0/15 (0.0%)
\n KCNJ10\n China\n Chai et al., 2013\n 200Nonsyndromic EVA0 or 1 SLC26A4 mutations1/33 (3.0%)6\n
\nReported KCNJ10 frequency = 6/195 (3.1%)\n
\n KCNJ10\n USThis studySensorineural hearing loss1 SLC26A4 mutation2/29 (6.9%)
\nTotal combined KCNJ10 frequency= 8/224 (3.6%)\n
\n
\n\n
\n

Notes:

\n
\n1All controls had normal hearing and, unless otherwise noted, none harbored any of the novel variants.\n
\n
\n2Five variants (p.G258E, p.N161del, p.G258R, p.R267Q and p.G335V) were detected in six probands and were shown to compromise SLC26A4 transcriptional activation.\n
\n
\n3Functional analysis of the identified novel variant (p.P239L) showed no impairment of SLC26A4 transcriptional activation.\n
\n
\n4Two identified missense mutations (p.P194H and p.R348C) were shown to impair K+ channel conductance.\n
\n
\n5One previously reported variant (p.R271C) was identified in 3 probands.\n
\n
\n6One heterozygous variant (p.R271H) was detected in a single proband; this variant was also found in 10/200 normal hearing controls.\n
\n

\n

\n
EVA
\n

Enlarged vestibular aqueduct

\n
IEM
\n

Inner ear malformation

\n
PS
\n

Pendred syndrome

\n
\n

\n

The genetic basis of hearing loss is diagnostically challenging with over 100 genes implicated (http://hereditaryhearingloss.org). The phenotypic variability observed within the PDS/DFNB4 spectrum also complicates diagnosis with changes in the same gene, SLC26A4, responsible for syndromic as well as non-syndromic hearing loss. Most clinical centers have historically utilized tiered testing in the assessment of hearing loss genetic etiology. However, with the advent of large-scale massively parallel sequencing (MPS), future approaches will likely employ testing platforms that are more comprehensive, cost effective and efficient (Shearer & Smith, 2012). Additional sources of genetic mutation, such as deletions and duplications, will need to be included in these new testing approaches.

" ] }, "conclusion_html": { @@ -1239,58 +1239,58 @@ "references_html": { "value": [ "\nAlasti F, Van Camp G, Smith RJH. 1998 (Updated 2012). Pendred Syndrome/DFNB4. In: Pagon RA, Adam MP, Ardinger HH, et al. eds. Seattle, WA: University of Washington. Available at http://www.ncbi.nlm.nih.gov/books/NBK1467/\n", - "\nAlbert S, Blons H, Jonard L, Feldmann D, Chauvin P, Loundon N, Sergent-Allaoui A, Houang M, Joannard A, Schmerber S, Delobel B, Leman J, Journel H, Catros H, Dollfus H, Eliot MM, David A, Calais C, Drouin-Garraud V, Obstoy MF, Tran Ba Huy P, Lacombe D, Duriez F, Francannet C, Bitoun P, Petit C, Garabédian EN, Couderc R, Marlin S, Denoyelle F. 2006. SLC26A4 gene is frequently involved in nonsyndromic hearing impairment with enlarged vestibular aqueduct in Caucasian populations. European Journal of Human Genetics 14:773-779 \n", - "\nAnwar S, Riazuddin S, Ahmed ZM, Tasneem S, Ateeq-ul-Jaleel Khan SY, Griffith AJ, Friedman TB, Riazuddin S. 2009. SLC26A4 mutation spectrum associated with DFNB4 deafness and Pendred’s syndrome in Pakistanis. Journal of Human Genetics 54:266-270 \n", - "\nBlons H, Feldmann D, Duval V, Messaz O, Denoyelle F, Loundon N, Sergout-Allaoui A, Houang M, Duriez F, Lacombe D, Delobel B, Leman J, Catros H, Journel H, Drouin-Garraud V, Obstoy MF, Toutain A, Oden S, Toublanc JE, Couderc R, Petit C, Garabédian EN, Marlin S. 2004. Screening of SLC26A4 (PDS) gene in Pendred’s syndrome: a large spectrum of mutations in France and phenotypic heterogeneity. Clinical Genetics 66:333-340 \n", - "\nBuono RJ, Lohoff FW, Sander T, Sperling MR, O’Connor MJ, Dlugos DJ, Ryan SG, Golden GT, Zhao H, Scattergood TM, Berrettini WH, Ferraro TN. 2004. Association between variation in the human KCNJ10 potassium ion channel gene and seizure susceptibility. Epilepsy Research 58:175-183 \n", - "\nCampbell C, Cucci RA, Prasad S, Green GE, Edeal JB, Galer CE, Karniski LP, Sheffield VC, Smith RJ. 2001. Pendred syndrome, DFNB4, and PDS/SLC26A4 identification of eight novel mutations and possible genotype-phenotype correlations. Human Mutation 17:403-411 \n", - "\nChai Y, Huang Z, Tao Z, Li X, Li L, Li Y, Wu H, Yang T. 2013. Molecular etiology of hearing impairment associated with nonsyndromic enlarged vestibular aqueduct in East China. American Journal of Medical Genetics Part A 161:2226-2233 \n", - "\nChen K, Wang X, Sun L, Jiang H. 2012. Screening of SLC26A4, FOXI1, KCNJ10, and GJB2 in bilateral deafness patients with inner ear malformation. Otolaryngology Head and Neck Surgery 146:972-978 \n", - "\nCirello V, Bazzini C, Vezzoli V, Muzza M, Rodighiero S, Castorina P, Maffini A, Bottà G, Persani L, Beck-Peccoz P, Meyer G, Fugazzola L. 2012. Molecular and functional studies of 4 candidate loci in Pendred syndrome and nonsyndromic hearing loss. Molecular and Cellular Endocrinology 351:342-350 \n", - "\nEverett LA, Glaser B, Beck JC, Idol JR, Buchs A, Heyman M, Adawi F, Hazani E, Nassir E, Baxevanis AD, Sheffield VC, Green ED. 1997. Pendred syndrome is caused by mutations in a putative sulphate transporter gene (PDS) Nature Genetics 17:411-422 \n", - "\nEverett LA, Morsli H, Wu DK, Green ED. 1999. Expression pattern of the mouse ortholog of the Pendred’s syndrome gene (Pds) suggests a key role for pendrin in the inner ear. Proceedings of the National Academy of Sciences of the United States of America 96:9727-9732 \n", - "\nFraser GR. 1965. Association of congenital deafness with goitre (Pendred’s syndrome), a study of 207 families. Annals of Human Genetics 28:201-249 \n", - "\nHilgert N, Smith RJ, Van Camp G. 2009. Forty-six genes causing nonsyndromic hearing impairment: which ones should be analyzed in DNA diagnostics? Mutation Research 681:189-196 \n", - "\nHu H, Wu L, Feng Y, Pan Q, Long Z, Li J, Dai H, Xia K, Liang D, Niikawa N, Xia J. 2007. Molecular analysis of hearing loss associated with enlarged vestibular aqueduct in the mainland Chinese: a unique SLC26A4 mutation spectrum. Journal of Human Genetics 52:492-497 \n", - "\nKenneson A, Van Naarden Braun K, Boyle C. 2002. GJB2 (connexin 26) variants and nonsyndromic sensorineural hearing loss: a HuGE review. Genetics in Medicine 4:258-274 \n", - "\nLai R, Hu P, Zhu F, Zhu G, Vivero R, Peng A, Wu W, Xiao Z, Liu X, Xie D. 2012. Genetic diagnosis and cochlear implantation for patients with nonsyndromic hearing loss and enlarged vestibular aqueduct. The Journal of Laryngology & Otology 126:349-355 \n", - "\nLenzen KP, Heils A, Lorenz S, Hempelmann A, Höfels S, Lohoff FW, Schmitz B, Sander T. 2005. Supportive evidence for an allelic association of the human KCNJ10 potassium channel gene with idiopathic generalized epilepsy. Epilepsy Research 63:113-118 \n", - "\nLi XC, Everett LA, Lalwani AK, Desmukh D, Friedman TB, Green ED, Wilcox ER. 1998. A mutation in PDS causes non-syndromic recessive deafness. Nature Genetics 18:215-217 \n", - "\nMarcus DC, Wu T, Wangemann P, Kofuji P. 2002. KCNJ10 (Kir4.1) potassium channel knockout abolishes endocochlear potential. American Journal of Physiology Cell Physiology 282:C403-C407 \n", - "\nMercer S, Mutton P, Dahl HH. 2011. Identification of SLC26A4 mutations in patients with hearing loss and enlarged vestibular aqueduct using high-resolution melting curve analysis. Genetic Testing and Molecular Biomarkers 15:365-368 \n", - "\nMorton CC, Nance WE. 2006. Newborn hearing screening—a silent revolution. New England Journal of Medicine 354:2151-2164 \n", - "\nPark HJ, Shaukat S, Liu XZ, Hahn SH, Naz S, Ghosh M, Kim HN, Moon SK, Abe S, Tukamoto K, Riazuddin S, Kabra M, Erdenetungalag R, Radnaabazar J, Khan S, Pandya A, Usami SI, Nance WE, Wilcox ER, Riazuddin S, Griffith AJ. 2003. Origins and frequencies of SLC26A4 (PDS) mutations in east and south Asians: global implications for the epidemiology of deafness. Journal of Medical Genetics 40:242-248 \n", - "\nPera A, Villamar M, Viñuela A, Gandía M, Medà C, Moreno F, Hernández-Chico C. 2008a. A mutational analysis of the SLC26A4 gene in Spanish hearing-impaired families provides new insights into the genetic causes of Pendred syndrome and DFNB4 hearing loss. European Journal of Human Genetics 16:888-896 \n", - "\nPera A, Dossena S, Rodighiero S, Gandía M, Bottà G, Meyer G, Moreno F, Nofziger C, Hernández-Chico C, Paulmichl M. 2008b. Functional assessment of allelic variants in the SLC26A4 gene involved in Pendred syndrome and nonsyndromic EVA. Proceedings of the National Academy of Sciences of the United States of America 105:18608-18613 \n", - "\nPryor SP, Madeo AC, Reynolds JC, Sarlis NJ, Arnos KS, Nance WE, Yang Y, Zalewski CK, Brewer CC, Butman JA, Griffith AJ. 2005. SLC26A4/PDS genotype–phenotype correlation in hearing loss with enlargement of the vestibular aqueduct (EVA): evidence that Pendred syndrome and non-syndromic EVA are distinct clinical and genetic entities. Journal of Medical Genetics 42:159-165 \n", - "\nPutcha GV, Bejjani BA, Bleoo S, Booker JK, Carey JC, Carson N, Das S, Dempsey MA, Gastier-Foster JM, Greinwald JH, Hoffmann ML, Jeng LJ, Kenna MA, Khababa I, Lilley M, Mao R, Muralidharan K, Otani IM, Rehm HL, Schaefer F, Seltzer WK, Spector EB, Springer MA, Weck KE, Wenstrup RJ, Withrow S, Wu BL, Zariwala MA, Schrijver I. 2007. A multicenter study of the frequency and distribution of GJB2 and GJB6 mutations in a large North American cohort. Genetics in Medicine 9:413-426 \n", - "\nReardon W, Coffey R, Phelps PD, Luxon LM, Stephens D, Kendall-Taylor P, Britton KE, Grossman A, Trembath R. 1997. Pendred syndrome—100 years of underascertainment? QJM 90:443-447 \n", - "\nRendtorff N, Schrijver I, Lodahl M, Rodriguez-Paris J, Johnsen T, Hansén E, Nickelsen L, Tümer Z, Fagerheim T, Wetke R, Tranebjaerg L. 2013. SLC26A4 mutation frequency and spectrum in 109 Danish Pendred syndrome/DFNB4 probands and a report of nine novel mutations. Clinical Genetics 84(4):388-391 \n", - "\nRodriguez-Paris J, Schrijver I. 2009. The digenic hypothesis unraveled: the GJB6 del(GJB6-D13S1830) mutation causes allele-specific loss of GJB2 expression in cis. Biochemical and Biophysical Research Communications 389:354-359 \n", - "\nRoyaux IE, Suzuki K, Mori A, Katoh R, Everett LA, Kohn LD, Green ED. 2000. Pendrin, the protein encoded by the Pendred syndrome gene (PDS), is an apical porter of iodide in the thyroid and is regulated by thyroglobulin in FRTL-5 cells. Endocrinology 141:839-845 \n", - "\nRoyaux IE, Wall SM, Karniski LP, Everett LA, Suzuki K, Knepper MA, Green ED. 2001. Pendrin, encoded by the Pendred syndrome gene, resides in the apical region of renal intercalated cells and mediates bicarbonate secretion. Proceedings of the National Academy of Sciences of the United States of America 98:4221-4226 \n", - "\nRoyaux IE, Belyantseva IA, Wu T, Kachar B, Everett LA, Marcus DC, Green ED. 2003. Localization and functional studies of pendrin in the mouse inner ear provide insight about the etiology of deafness in pendred syndrome. Journal of the Association for Research in Otolaryngology 4:394-404 \n", - "\nSchrijver I, Gardner P. 2006. Hereditary sensorineural hearing loss: advances in molecular genetics and mutation analysis. Expert Review of Molecular Diagnostics 6:375-386 \n", - "\nShearer AE, Smith RJ. 2012. Genetics: advances in genetic testing for deafness. Current Opinion in Pediatrics 24:679-686 \n", - "\nSiem G, Fagerheim T, Jonsrud C, Laurent C, Teig E, Harris S, Leren TP, Früh A, Heimdal K. 2010. Causes of hearing impairment in the Norwegian paediatric cochlear implant program. International Journal of Audiology 49:596-605 \n", - "\nTsukamoto K, Suzuki H, Harada D, Namba A, Abe S, Usami S. 2003. Distribution and frequencies of PDS (SLC26A4) mutations in Pendred syndrome and nonsyndromic hearing loss associated with enlarged vestibular aqueduct: a unique spectrum of mutations in Japanese. European Journal of Human Genetics 11:916-922 \n", - "\nVele O, Schrijver I. 2008. Inherited hearing loss: molecular genetics and diagnostic testing. Expert Opinion on Medical Diagnostics 2:231-248 \n", - "\nWangemann P, Itza EM, Albrecht B, Wu T, Jabba SV, Maganti RJ, Lee JH, Everett LA, Wall SM, Royaux IE, Green ED, Marcus DC. 2004. Loss of KCNJ10 protein expression abolishes endocochlear potential and causes deafness in Pendred syndrome mouse model. BMC Medicine 2:30 \n", - "\nWu CC, Lu YC, Chen PJ, Yeh PL, Su YN, Hwu WL, Hsu CJ. 2010. Phenotypic analyses and mutation screening of the SLC26A4 and FOXI1 genes in 101 Taiwanese families with bilateral nonsyndromic enlarged vestibular aqueduct (DFNB4) or Pendred syndrome. Audiology & Neurotology 15:57-66 \n", - "\nYang T, Vidarsson H, Rodrigo-Blomqvist S, Rosengren SS, Enerback S, Smith RJ. 2007. Transcriptional control of SLC26A4 is involved in Pendred syndrome and nonsyndromic enlargement of vestibular aqueduct (DFNB4) The American Journal of Human Genetics 80:1055-1063 \n", - "\nYang T, Gurrola JG, Wu H, Chiu SM, Wangemann P, Snyder PM, Smith RJ. 2009. Mutations of KCNJ10 together with mutations of SLC26A4 cause digenic nonsyndromic hearing loss associated with enlarged vestibular aqueduct syndrome. The American Journal of Human Genetics 84:651-657 \n" + "\nAlbert S, Blons H, Jonard L, Feldmann D, Chauvin P, Loundon N, Sergent-Allaoui A, Houang M, Joannard A, Schmerber S, Delobel B, Leman J, Journel H, Catros H, Dollfus H, Eliot MM, David A, Calais C, Drouin-Garraud V, Obstoy MF, Tran Ba Huy P, Lacombe D, Duriez F, Francannet C, Bitoun P, Petit C, Garabédian EN, Couderc R, Marlin S, Denoyelle F. 2006. SLC26A4 gene is frequently involved in nonsyndromic hearing impairment with enlarged vestibular aqueduct in Caucasian populations. European Journal of Human Genetics 14:773-779 \n", + "\nAnwar S, Riazuddin S, Ahmed ZM, Tasneem S, Ateeq-ul-Jaleel Khan SY, Griffith AJ, Friedman TB, Riazuddin S. 2009. SLC26A4 mutation spectrum associated with DFNB4 deafness and Pendred’s syndrome in Pakistanis. Journal of Human Genetics 54:266-270 \n", + "\nBlons H, Feldmann D, Duval V, Messaz O, Denoyelle F, Loundon N, Sergout-Allaoui A, Houang M, Duriez F, Lacombe D, Delobel B, Leman J, Catros H, Journel H, Drouin-Garraud V, Obstoy MF, Toutain A, Oden S, Toublanc JE, Couderc R, Petit C, Garabédian EN, Marlin S. 2004. Screening of SLC26A4 (PDS) gene in Pendred’s syndrome: a large spectrum of mutations in France and phenotypic heterogeneity. Clinical Genetics 66:333-340 \n", + "\nBuono RJ, Lohoff FW, Sander T, Sperling MR, O’Connor MJ, Dlugos DJ, Ryan SG, Golden GT, Zhao H, Scattergood TM, Berrettini WH, Ferraro TN. 2004. Association between variation in the human KCNJ10 potassium ion channel gene and seizure susceptibility. Epilepsy Research 58:175-183 \n", + "\nCampbell C, Cucci RA, Prasad S, Green GE, Edeal JB, Galer CE, Karniski LP, Sheffield VC, Smith RJ. 2001. Pendred syndrome, DFNB4, and PDS/SLC26A4 identification of eight novel mutations and possible genotype-phenotype correlations. Human Mutation 17:403-411 \n", + "\nChai Y, Huang Z, Tao Z, Li X, Li L, Li Y, Wu H, Yang T. 2013. Molecular etiology of hearing impairment associated with nonsyndromic enlarged vestibular aqueduct in East China. American Journal of Medical Genetics Part A 161:2226-2233 \n", + "\nChen K, Wang X, Sun L, Jiang H. 2012. Screening of SLC26A4, FOXI1, KCNJ10, and GJB2 in bilateral deafness patients with inner ear malformation. Otolaryngology Head and Neck Surgery 146:972-978 \n", + "\nCirello V, Bazzini C, Vezzoli V, Muzza M, Rodighiero S, Castorina P, Maffini A, Bottà G, Persani L, Beck-Peccoz P, Meyer G, Fugazzola L. 2012. Molecular and functional studies of 4 candidate loci in Pendred syndrome and nonsyndromic hearing loss. Molecular and Cellular Endocrinology 351:342-350 \n", + "\nEverett LA, Glaser B, Beck JC, Idol JR, Buchs A, Heyman M, Adawi F, Hazani E, Nassir E, Baxevanis AD, Sheffield VC, Green ED. 1997. Pendred syndrome is caused by mutations in a putative sulphate transporter gene (PDS) Nature Genetics 17:411-422 \n", + "\nEverett LA, Morsli H, Wu DK, Green ED. 1999. Expression pattern of the mouse ortholog of the Pendred’s syndrome gene (Pds) suggests a key role for pendrin in the inner ear. Proceedings of the National Academy of Sciences of the United States of America 96:9727-9732 \n", + "\nFraser GR. 1965. Association of congenital deafness with goitre (Pendred’s syndrome), a study of 207 families. Annals of Human Genetics 28:201-249 \n", + "\nHilgert N, Smith RJ, Van Camp G. 2009. Forty-six genes causing nonsyndromic hearing impairment: which ones should be analyzed in DNA diagnostics? Mutation Research 681:189-196 \n", + "\nHu H, Wu L, Feng Y, Pan Q, Long Z, Li J, Dai H, Xia K, Liang D, Niikawa N, Xia J. 2007. Molecular analysis of hearing loss associated with enlarged vestibular aqueduct in the mainland Chinese: a unique SLC26A4 mutation spectrum. Journal of Human Genetics 52:492-497 \n", + "\nKenneson A, Van Naarden Braun K, Boyle C. 2002. GJB2 (connexin 26) variants and nonsyndromic sensorineural hearing loss: a HuGE review. Genetics in Medicine 4:258-274 \n", + "\nLai R, Hu P, Zhu F, Zhu G, Vivero R, Peng A, Wu W, Xiao Z, Liu X, Xie D. 2012. Genetic diagnosis and cochlear implantation for patients with nonsyndromic hearing loss and enlarged vestibular aqueduct. The Journal of Laryngology & Otology 126:349-355 \n", + "\nLenzen KP, Heils A, Lorenz S, Hempelmann A, Höfels S, Lohoff FW, Schmitz B, Sander T. 2005. Supportive evidence for an allelic association of the human KCNJ10 potassium channel gene with idiopathic generalized epilepsy. Epilepsy Research 63:113-118 \n", + "\nLi XC, Everett LA, Lalwani AK, Desmukh D, Friedman TB, Green ED, Wilcox ER. 1998. A mutation in PDS causes non-syndromic recessive deafness. Nature Genetics 18:215-217 \n", + "\nMarcus DC, Wu T, Wangemann P, Kofuji P. 2002. KCNJ10 (Kir4.1) potassium channel knockout abolishes endocochlear potential. American Journal of Physiology Cell Physiology 282:C403-C407 \n", + "\nMercer S, Mutton P, Dahl HH. 2011. Identification of SLC26A4 mutations in patients with hearing loss and enlarged vestibular aqueduct using high-resolution melting curve analysis. Genetic Testing and Molecular Biomarkers 15:365-368 \n", + "\nMorton CC, Nance WE. 2006. Newborn hearing screening—a silent revolution. New England Journal of Medicine 354:2151-2164 \n", + "\nPark HJ, Shaukat S, Liu XZ, Hahn SH, Naz S, Ghosh M, Kim HN, Moon SK, Abe S, Tukamoto K, Riazuddin S, Kabra M, Erdenetungalag R, Radnaabazar J, Khan S, Pandya A, Usami SI, Nance WE, Wilcox ER, Riazuddin S, Griffith AJ. 2003. Origins and frequencies of SLC26A4 (PDS) mutations in east and south Asians: global implications for the epidemiology of deafness. Journal of Medical Genetics 40:242-248 \n", + "\nPera A, Villamar M, Viñuela A, Gandía M, Medà C, Moreno F, Hernández-Chico C. 2008a. A mutational analysis of the SLC26A4 gene in Spanish hearing-impaired families provides new insights into the genetic causes of Pendred syndrome and DFNB4 hearing loss. European Journal of Human Genetics 16:888-896 \n", + "\nPera A, Dossena S, Rodighiero S, Gandía M, Bottà G, Meyer G, Moreno F, Nofziger C, Hernández-Chico C, Paulmichl M. 2008b. Functional assessment of allelic variants in the SLC26A4 gene involved in Pendred syndrome and nonsyndromic EVA. Proceedings of the National Academy of Sciences of the United States of America 105:18608-18613 \n", + "\nPryor SP, Madeo AC, Reynolds JC, Sarlis NJ, Arnos KS, Nance WE, Yang Y, Zalewski CK, Brewer CC, Butman JA, Griffith AJ. 2005. SLC26A4/PDS genotype–phenotype correlation in hearing loss with enlargement of the vestibular aqueduct (EVA): evidence that Pendred syndrome and non-syndromic EVA are distinct clinical and genetic entities. Journal of Medical Genetics 42:159-165 \n", + "\nPutcha GV, Bejjani BA, Bleoo S, Booker JK, Carey JC, Carson N, Das S, Dempsey MA, Gastier-Foster JM, Greinwald JH, Hoffmann ML, Jeng LJ, Kenna MA, Khababa I, Lilley M, Mao R, Muralidharan K, Otani IM, Rehm HL, Schaefer F, Seltzer WK, Spector EB, Springer MA, Weck KE, Wenstrup RJ, Withrow S, Wu BL, Zariwala MA, Schrijver I. 2007. A multicenter study of the frequency and distribution of GJB2 and GJB6 mutations in a large North American cohort. Genetics in Medicine 9:413-426 \n", + "\nReardon W, Coffey R, Phelps PD, Luxon LM, Stephens D, Kendall-Taylor P, Britton KE, Grossman A, Trembath R. 1997. Pendred syndrome—100 years of underascertainment? QJM 90:443-447 \n", + "\nRendtorff N, Schrijver I, Lodahl M, Rodriguez-Paris J, Johnsen T, Hansén E, Nickelsen L, Tümer Z, Fagerheim T, Wetke R, Tranebjaerg L. 2013. SLC26A4 mutation frequency and spectrum in 109 Danish Pendred syndrome/DFNB4 probands and a report of nine novel mutations. Clinical Genetics 84(4):388-391 \n", + "\nRodriguez-Paris J, Schrijver I. 2009. The digenic hypothesis unraveled: the GJB6 del(GJB6-D13S1830) mutation causes allele-specific loss of GJB2 expression in cis. Biochemical and Biophysical Research Communications 389:354-359 \n", + "\nRoyaux IE, Suzuki K, Mori A, Katoh R, Everett LA, Kohn LD, Green ED. 2000. Pendrin, the protein encoded by the Pendred syndrome gene (PDS), is an apical porter of iodide in the thyroid and is regulated by thyroglobulin in FRTL-5 cells. Endocrinology 141:839-845 \n", + "\nRoyaux IE, Wall SM, Karniski LP, Everett LA, Suzuki K, Knepper MA, Green ED. 2001. Pendrin, encoded by the Pendred syndrome gene, resides in the apical region of renal intercalated cells and mediates bicarbonate secretion. Proceedings of the National Academy of Sciences of the United States of America 98:4221-4226 \n", + "\nRoyaux IE, Belyantseva IA, Wu T, Kachar B, Everett LA, Marcus DC, Green ED. 2003. Localization and functional studies of pendrin in the mouse inner ear provide insight about the etiology of deafness in pendred syndrome. Journal of the Association for Research in Otolaryngology 4:394-404 \n", + "\nSchrijver I, Gardner P. 2006. Hereditary sensorineural hearing loss: advances in molecular genetics and mutation analysis. Expert Review of Molecular Diagnostics 6:375-386 \n", + "\nShearer AE, Smith RJ. 2012. Genetics: advances in genetic testing for deafness. Current Opinion in Pediatrics 24:679-686 \n", + "\nSiem G, Fagerheim T, Jonsrud C, Laurent C, Teig E, Harris S, Leren TP, Früh A, Heimdal K. 2010. Causes of hearing impairment in the Norwegian paediatric cochlear implant program. International Journal of Audiology 49:596-605 \n", + "\nTsukamoto K, Suzuki H, Harada D, Namba A, Abe S, Usami S. 2003. Distribution and frequencies of PDS (SLC26A4) mutations in Pendred syndrome and nonsyndromic hearing loss associated with enlarged vestibular aqueduct: a unique spectrum of mutations in Japanese. European Journal of Human Genetics 11:916-922 \n", + "\nVele O, Schrijver I. 2008. Inherited hearing loss: molecular genetics and diagnostic testing. Expert Opinion on Medical Diagnostics 2:231-248 \n", + "\nWangemann P, Itza EM, Albrecht B, Wu T, Jabba SV, Maganti RJ, Lee JH, Everett LA, Wall SM, Royaux IE, Green ED, Marcus DC. 2004. Loss of KCNJ10 protein expression abolishes endocochlear potential and causes deafness in Pendred syndrome mouse model. BMC Medicine 2:30 \n", + "\nWu CC, Lu YC, Chen PJ, Yeh PL, Su YN, Hwu WL, Hsu CJ. 2010. Phenotypic analyses and mutation screening of the SLC26A4 and FOXI1 genes in 101 Taiwanese families with bilateral nonsyndromic enlarged vestibular aqueduct (DFNB4) or Pendred syndrome. Audiology & Neurotology 15:57-66 \n", + "\nYang T, Vidarsson H, Rodrigo-Blomqvist S, Rosengren SS, Enerback S, Smith RJ. 2007. Transcriptional control of SLC26A4 is involved in Pendred syndrome and nonsyndromic enlargement of vestibular aqueduct (DFNB4) The American Journal of Human Genetics 80:1055-1063 \n", + "\nYang T, Gurrola JG, Wu H, Chiu SM, Wangemann P, Snyder PM, Smith RJ. 2009. Mutations of KCNJ10 together with mutations of SLC26A4 cause digenic nonsyndromic hearing loss associated with enlarged vestibular aqueduct syndrome. The American Journal of Human Genetics 84:651-657 \n" ] }, "figures_html": { "value": [ - "
\"Identification
\n

\nFigure 1: Identification of the heterozygous SLC26A4 deletion g.8091T-22145Cdel in subject PDS41.

\n(A) The SLC26A4 MLPA probe mix includes probes for the 21 SLC26A4 exons, 14 reference probes and three probes specific for the point mutations c.1001+1G>A (IV S8+1G>A), c.707T>C (p.Leu236Pro) and c.1246A>C (p.Thr416Pro). Subject PDS41 is heterozygous for a deletion (g.8091T-22145Cdel) spanning exons 4–6 in SLC26A4, as evidenced by the reproducible reduction in peak height for these three exon probes (peaks labeled 4, 5, 6) relative to the control. PDS41 also has a heterozygous c.1246A>C (p.Thr416Pro) mutation that was previously identified by sequencing and confirmed by these MLPA results (peak labeled p.T416P). (B) Sequencing chromatogram of the deletion breakpoints in SLC26A4 IVS3 and IVS6. The deletion removes a total of 14,053 bp. IVS, intervening sequence.
" + "
\"Identification
\n

\nFigure 1: Identification of the heterozygous SLC26A4 deletion g.8091T-22145Cdel in subject PDS41.

\n(A) The SLC26A4 MLPA probe mix includes probes for the 21 SLC26A4 exons, 14 reference probes and three probes specific for the point mutations c.1001+1G>A (IV S8+1G>A), c.707T>C (p.Leu236Pro) and c.1246A>C (p.Thr416Pro). Subject PDS41 is heterozygous for a deletion (g.8091T-22145Cdel) spanning exons 4–6 in SLC26A4, as evidenced by the reproducible reduction in peak height for these three exon probes (peaks labeled 4, 5, 6) relative to the control. PDS41 also has a heterozygous c.1246A>C (p.Thr416Pro) mutation that was previously identified by sequencing and confirmed by these MLPA results (peak labeled p.T416P). (B) Sequencing chromatogram of the deletion breakpoints in SLC26A4 IVS3 and IVS6. The deletion removes a total of 14,053 bp. IVS, intervening sequence.
" ] }, "tables_html": { "value": [ - "
\nTable 1:
Primers used for the amplification of FOXI1 and KCNJ10.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GeneExonPrimer namePrimer sequence (5′ to 3′)\n T\n \n a\n \n
\n FOXI1\n 1FOXI1-1FTGAGCACCTGTCAGGGGCAG61
\n FOXI1\n 1FOXI1-1RGAACTTTCTAGAATGGGGTCTTG61
\n FOXI1\n 1FOXI1-1RintCCCTGTGGGTGGAAGAAGT55
\n FOXI1\n 2FOXI1-2FGACAATAAGGAGGAACAGAAG55
\n FOXI1\n 2FOXI1-2RGCATGGAGGACCTCTACTG55
\n KCNJ10\n 2KCNJ10-2aFGTTAATTCCTCCCTCCCATGG59
\n KCNJ10\n 2KCNJ10-2aRGTTCTCCCCTTCCTTGGTTTG59
\n KCNJ10\n 2KCNJ10-2bFGAGACCATTCGTTTCAGCCAG59
\n KCNJ10\n 2KCNJ10-2bRAAGAAGAGGGAGTGGAGGATG59
\n", - "
\nTable 2:
Percentages of PDS/DFNB4 probands with SLC26A4 mutations.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
ReferenceProbands2 Mutations1 Mutation0 MutationsStudy selection criteria
\n Campbell et al., 2001\n 589 (16%)14 (24%)35 (60%)Recessive HL with DVA or Mondini dysplasia
\n Tsukamoto et al., 2003\n 4224 (57%)10 (24%)8 (19%)Pendred (goiter) or bilateral HL with EVA
\n Pryor et al., 2005\n 3914 (36%)14 (36%)11 (28%)EVA in at least one ear
\n Albert et al., 2006\n 10024 (24%)16 (16%)60 (60%)Bilateral, recessive HL; EVA; no GJB2 mutations
\n Yang et al., 2007\n 42957 (13%)75 (17%)297 (69%)HL with EVA
\n Wu et al., 2010\n 10163 (62%)24 (24%)14 (14%)Bilateral EVA
\n Total\n 769191 (25%)153 (20%)425 (55%)
\n\n
\n

Notes:

\n

\n

\n
HL
\n

hearing loss

\n
DVA
\n

dilated vestibular aqueduct

\n
EVA
\n

enlarged vestibular aqueduct

\n
\n

\n
", - "
\nTable 3:
Meta-analysis of the frequency of FOXI1 and KCNJ10 variants in PDS/DFNB4 probands.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GenePopulation
origin
ReferenceControls1\nInclusion criteria for SLC26A4 sequencingSelection criteria for
FOXI1 sequencing
Subjects with nonsynonymous variants
\n FOXI1\n US/Sweden\n Yang et al., 2007\n 250EVA with or without Mondini dysplasia0 or 1 SLC26A4 mutations6/372 (1.6%)2\n
\n FOXI1\n Taiwan\n Wu et al., 2010\n 100Bilateral EVA with or without other IEMs0 or 1 SLC26A4 mutations0/38 (0.0%)
\n FOXI1\n Australia\n Mercer, Mutton & Dahl, 2011\n 96EVAPhenotype only0/44 (0.0%)
\n FOXI1\n Italy\n Cirello et al., 2012\n 80Bilateral IEMs/family history of PS/goiter0 or 1 SLC26A4 mutations1/14 (7.1%)3\n
\n FOXI1\n China\n Lai et al., 2012\n 100EVA0 or 1 SLC26A4 mutations0/8 (0.0%)
\n FOXI1\n China\n Chen et al., 2012\n IEM’s0 or 1 SLC26A4 mutations0/15 (0.0%)
\n FOXI1\n China\n Chai et al., 2013\n 200Nonsyndromic EVA0 or 1 SLC26A4 mutations0/33 (0.0%)
\nReported FOXI1 frequency= 7/524 (1.3%)\n
\n FOXI1\n USThis studySensorineural hearing loss1 SLC26A4 mutation1/29 (3.4%)
\nTotal combined FOXI1 frequency= 8/553 (1.4%)\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GenePopulation
origin
ReferenceControls1\nInclusion criteria for
SLC26A4 sequencing
Selection criteria for
KCNJ10 sequencing
Subjects with nonsynonymous variants
\n KCNJ10\n China/US/
Canada
\n Yang et al., 2009\n 400EVA with or without Mondini dysplasia1 SLC26A4 mutation2/89 (2.2%)4\n
\n KCNJ10\n Australia\n Mercer, Mutton & Dahl, 2011\n 96EVAPhenotype only0/44 (0.0%)
\n KCNJ10\n Italy\n Cirello et al., 2012\n 80Bilateral IEMs/family history of PS/goiter0 or 1 SLC26A4 mutations3/14 (21.4%)5\n
\n KCNJ10\n China\n Chen et al., 2012\n IEM’s0 or 1 SLC26A4 mutations0/15 (0.0%)
\n KCNJ10\n China\n Chai et al., 2013\n 200Nonsyndromic EVA0 or 1 SLC26A4 mutations1/33 (3.0%)6\n
\nReported KCNJ10 frequency = 6/195 (3.1%)\n
\n KCNJ10\n USThis studySensorineural hearing loss1 SLC26A4 mutation2/29 (6.9%)
\nTotal combined KCNJ10 frequency= 8/224 (3.6%)\n
\n
\n\n
\n

Notes:

\n
\n1All controls had normal hearing and, unless otherwise noted, none harbored any of the novel variants.\n
\n
\n2Five variants (p.G258E, p.N161del, p.G258R, p.R267Q and p.G335V) were detected in six probands and were shown to compromise SLC26A4 transcriptional activation.\n
\n
\n3Functional analysis of the identified novel variant (p.P239L) showed no impairment of SLC26A4 transcriptional activation.\n
\n
\n4Two identified missense mutations (p.P194H and p.R348C) were shown to impair K+ channel conductance.\n
\n
\n5One previously reported variant (p.R271C) was identified in 3 probands.\n
\n
\n6One heterozygous variant (p.R271H) was detected in a single proband; this variant was also found in 10/200 normal hearing controls.\n
\n

\n

\n
EVA
\n

Enlarged vestibular aqueduct

\n
IEM
\n

Inner ear malformation

\n
PS
\n

Pendred syndrome

\n
\n

\n
" + "
\nTable 1:
Primers used for the amplification of FOXI1 and KCNJ10.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GeneExonPrimer namePrimer sequence (5′ to 3′)\n T\n \n a\n \n
\n FOXI1\n 1FOXI1-1FTGAGCACCTGTCAGGGGCAG61
\n FOXI1\n 1FOXI1-1RGAACTTTCTAGAATGGGGTCTTG61
\n FOXI1\n 1FOXI1-1RintCCCTGTGGGTGGAAGAAGT55
\n FOXI1\n 2FOXI1-2FGACAATAAGGAGGAACAGAAG55
\n FOXI1\n 2FOXI1-2RGCATGGAGGACCTCTACTG55
\n KCNJ10\n 2KCNJ10-2aFGTTAATTCCTCCCTCCCATGG59
\n KCNJ10\n 2KCNJ10-2aRGTTCTCCCCTTCCTTGGTTTG59
\n KCNJ10\n 2KCNJ10-2bFGAGACCATTCGTTTCAGCCAG59
\n KCNJ10\n 2KCNJ10-2bRAAGAAGAGGGAGTGGAGGATG59
\n", + "
\nTable 2:
Percentages of PDS/DFNB4 probands with SLC26A4 mutations.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
ReferenceProbands2 Mutations1 Mutation0 MutationsStudy selection criteria
\n Campbell et al., 2001\n 589 (16%)14 (24%)35 (60%)Recessive HL with DVA or Mondini dysplasia
\n Tsukamoto et al., 2003\n 4224 (57%)10 (24%)8 (19%)Pendred (goiter) or bilateral HL with EVA
\n Pryor et al., 2005\n 3914 (36%)14 (36%)11 (28%)EVA in at least one ear
\n Albert et al., 2006\n 10024 (24%)16 (16%)60 (60%)Bilateral, recessive HL; EVA; no GJB2 mutations
\n Yang et al., 2007\n 42957 (13%)75 (17%)297 (69%)HL with EVA
\n Wu et al., 2010\n 10163 (62%)24 (24%)14 (14%)Bilateral EVA
\n Total\n 769191 (25%)153 (20%)425 (55%)
\n\n
\n

Notes:

\n

\n

\n
HL
\n

hearing loss

\n
DVA
\n

dilated vestibular aqueduct

\n
EVA
\n

enlarged vestibular aqueduct

\n
\n

\n
", + "
\nTable 3:
Meta-analysis of the frequency of FOXI1 and KCNJ10 variants in PDS/DFNB4 probands.
\n
\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GenePopulation
origin
ReferenceControls1\nInclusion criteria for SLC26A4 sequencingSelection criteria for
FOXI1 sequencing
Subjects with nonsynonymous variants
\n FOXI1\n US/Sweden\n Yang et al., 2007\n 250EVA with or without Mondini dysplasia0 or 1 SLC26A4 mutations6/372 (1.6%)2\n
\n FOXI1\n Taiwan\n Wu et al., 2010\n 100Bilateral EVA with or without other IEMs0 or 1 SLC26A4 mutations0/38 (0.0%)
\n FOXI1\n Australia\n Mercer, Mutton & Dahl, 2011\n 96EVAPhenotype only0/44 (0.0%)
\n FOXI1\n Italy\n Cirello et al., 2012\n 80Bilateral IEMs/family history of PS/goiter0 or 1 SLC26A4 mutations1/14 (7.1%)3\n
\n FOXI1\n China\n Lai et al., 2012\n 100EVA0 or 1 SLC26A4 mutations0/8 (0.0%)
\n FOXI1\n China\n Chen et al., 2012\n IEM’s0 or 1 SLC26A4 mutations0/15 (0.0%)
\n FOXI1\n China\n Chai et al., 2013\n 200Nonsyndromic EVA0 or 1 SLC26A4 mutations0/33 (0.0%)
\nReported FOXI1 frequency= 7/524 (1.3%)\n
\n FOXI1\n USThis studySensorineural hearing loss1 SLC26A4 mutation1/29 (3.4%)
\nTotal combined FOXI1 frequency= 8/553 (1.4%)\n
\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
GenePopulation
origin
ReferenceControls1\nInclusion criteria for
SLC26A4 sequencing
Selection criteria for
KCNJ10 sequencing
Subjects with nonsynonymous variants
\n KCNJ10\n China/US/
Canada
\n Yang et al., 2009\n 400EVA with or without Mondini dysplasia1 SLC26A4 mutation2/89 (2.2%)4\n
\n KCNJ10\n Australia\n Mercer, Mutton & Dahl, 2011\n 96EVAPhenotype only0/44 (0.0%)
\n KCNJ10\n Italy\n Cirello et al., 2012\n 80Bilateral IEMs/family history of PS/goiter0 or 1 SLC26A4 mutations3/14 (21.4%)5\n
\n KCNJ10\n China\n Chen et al., 2012\n IEM’s0 or 1 SLC26A4 mutations0/15 (0.0%)
\n KCNJ10\n China\n Chai et al., 2013\n 200Nonsyndromic EVA0 or 1 SLC26A4 mutations1/33 (3.0%)6\n
\nReported KCNJ10 frequency = 6/195 (3.1%)\n
\n KCNJ10\n USThis studySensorineural hearing loss1 SLC26A4 mutation2/29 (6.9%)
\nTotal combined KCNJ10 frequency= 8/224 (3.6%)\n
\n
\n\n
\n

Notes:

\n
\n1All controls had normal hearing and, unless otherwise noted, none harbored any of the novel variants.\n
\n
\n2Five variants (p.G258E, p.N161del, p.G258R, p.R267Q and p.G335V) were detected in six probands and were shown to compromise SLC26A4 transcriptional activation.\n
\n
\n3Functional analysis of the identified novel variant (p.P239L) showed no impairment of SLC26A4 transcriptional activation.\n
\n
\n4Two identified missense mutations (p.P194H and p.R348C) were shown to impair K+ channel conductance.\n
\n
\n5One previously reported variant (p.R271C) was identified in 3 probands.\n
\n
\n6One heterozygous variant (p.R271H) was detected in a single proband; this variant was also found in 10/200 normal hearing controls.\n
\n

\n

\n
EVA
\n

Enlarged vestibular aqueduct

\n
IEM
\n

Inner ear malformation

\n
PS
\n

Pendred syndrome

\n
\n

\n
" ] }, "fulltext_html": { @@ -1305,7 +1305,7 @@ }, "fulltext_xml": { "value": [ - "/articles/384.xml" + "https://peerj.com/articles/384.xml" ] }, "supplementary_file": { @@ -1328,18 +1328,18 @@ "© 2014 Pique et al.\n" ] }, - "file_hashes": [ + "file_sizes": [ { - "fig-1-full.png": "6ee6bf8676df1087e9d724bfdc9178e8" + "fig-1-full.png": 736091 }, { - "fulltext.html": "022bdb4b899eaedf165ad2693e1aa401" + "fulltext.html": 264861 }, { - "fulltext.pdf": "b2020a8f8037228e6face4a220751932" + "fulltext.pdf": 776033 }, { - "fulltext.xml": "03352087dcff14b9fba0271c47574759" + "fulltext.xml": 123052 } ] } diff --git a/test/plos.json b/test/plos.json index bec8ed0..db2ee03 100644 --- a/test/plos.json +++ b/test/plos.json @@ -1,18 +1,18 @@ { "http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001874": { - "fulltext_pdf": { + "publisher": { "value": [ - "http://dx.plos.org/10.1371/journal.pbio.1001874.pdf" + ] }, - "fulltext_html": { + "journal_name": { "value": [ - + "PLOS Biology" ] }, - "fulltext_xml": { + "journal_issn": { "value": [ - "/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pbio.1001874&representation=XML" + "1545-7885" ] }, "title": { @@ -20,7 +20,12 @@ "Extracellular Vesicle-Mediated Transfer of Genetic Information between the Hematopoietic System and the Brain in Response to Inflammation" ] }, - "author": { + "keywords": { + "value": [ + + ] + }, + "author_name": { "value": [ "Kirsten Ridder", "Sascha Keller", @@ -42,9 +47,35 @@ "Stefan Momma" ] }, - "date": { + "author_institution": { + "value": [ + + ] + }, + "editor_name": { + "value": [ + + ] + }, + "date_published": { + "value": [ + [ + " June 3, 2014" + ] + ] + }, + "date_accepted": { + "value": [ + [ + "April 24, 2014" + ] + ] + }, + "date_submitted": { "value": [ - "2014/6/3" + [ + "February 24, 2014" + ] ] }, "doi": { @@ -67,40 +98,213 @@ "e1001874" ] }, - "description": { + "abstract": { "value": [ - "PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines." + ] }, - "abstract": { + "abstract_html": { "value": [ - "AbstractMechanisms behind how the immune system signals to the brain in response to systemic inflammation are not fully understood. Transgenic mice expressing Cre recombinase specifically in the hematopoietic lineage in a Cre reporter background display recombination and marker gene expression in Purkinje neurons. Here we show that reportergene expression in neurons is caused by intercellular transfer of functional Cre recombinase messenger RNA from immune cells into neurons in the absence of cell fusion. In vitro purified secreted extracellular vesicles (EVs) from blood cells contain Cre mRNA, which induces recombination in neurons when injected into the brain. Although Cre-mediated recombination events in the brain occur very rarely in healthy animals, their number increases considerably in different injury models, particularly under inflammatory conditions, and extend beyond Purkinje neurons to other neuronal populations in cortex, hippocampus, and substantia nigra. Recombined Purkinje neurons differ in their miRNA profile from their nonrecombined counterparts, indicating physiological significance. These observations reveal the existence of a previously unrecognized mechanism to communicate RNA-based signals between the hematopoietic system and various organs, including the brain, in response to inflammation.\n", - "\nAuthor Summary\nPeripheral infections leading to an inflammatory response can initiate signaling from the hematopoietic system to various organs including the brain. The traditional view of this communication between blood and brain is that individual factors are released by immune cells that in turn bind to neuronal or nonneuronal target cells in the brain where they exert their effects. By using a genetic tracing system, we now show that extracellular vesicles, small membrane structures that can contain a multitude of different molecules, can transfer functional RNA directly from blood cells to neurons. Although this type of signaling is highly restricted in the healthy animal, inflammatory injuries increase both the frequency of transfer and the range of the neuronal target populations in the brain. By showing altered miRNA profiles in neurons receiving extracellular vesicle cargo, we predict a complex regulation of gene expression in neural cells in response to peripheral inflammation.\n" + "

Abstract

Mechanisms behind how the immune system signals to the brain in response to systemic inflammation are not fully understood. Transgenic mice expressing Cre recombinase specifically in the hematopoietic lineage in a Cre reporter background display recombination and marker gene expression in Purkinje neurons. Here we show that reportergene expression in neurons is caused by intercellular transfer of functional Cre recombinase messenger RNA from immune cells into neurons in the absence of cell fusion. In vitro purified secreted extracellular vesicles (EVs) from blood cells contain Cre mRNA, which induces recombination in neurons when injected into the brain. Although Cre-mediated recombination events in the brain occur very rarely in healthy animals, their number increases considerably in different injury models, particularly under inflammatory conditions, and extend beyond Purkinje neurons to other neuronal populations in cortex, hippocampus, and substantia nigra. Recombined Purkinje neurons differ in their miRNA profile from their nonrecombined counterparts, indicating physiological significance. These observations reveal the existence of a previously unrecognized mechanism to communicate RNA-based signals between the hematopoietic system and various organs, including the brain, in response to inflammation.

\n", + "\n

Author Summary

\n

Peripheral infections leading to an inflammatory response can initiate signaling from the hematopoietic system to various organs including the brain. The traditional view of this communication between blood and brain is that individual factors are released by immune cells that in turn bind to neuronal or nonneuronal target cells in the brain where they exert their effects. By using a genetic tracing system, we now show that extracellular vesicles, small membrane structures that can contain a multitude of different molecules, can transfer functional RNA directly from blood cells to neurons. Although this type of signaling is highly restricted in the healthy animal, inflammatory injuries increase both the frequency of transfer and the range of the neuronal target populations in the brain. By showing altered miRNA profiles in neurons receiving extracellular vesicle cargo, we predict a complex regulation of gene expression in neural cells in response to peripheral inflammation.

\n" + ] + }, + "abstract_text": { + "value": [ + ] }, - "file_hashes": [ + "introduction_html": { + "value": [ + + ] + }, + "methods_html": { + "value": [ + + ] + }, + "results_html": { + "value": [ + + ] + }, + "discussion_html": { + "value": [ + + ] + }, + "author_contrib_html": { + "value": [ + "The author(s) have made the following declarations about their contributions: Conceived and designed the experiments: SK DD KD CD BA GH HS PA SM. Performed the experiments: KR SK MD AR JSc JSt JM DK KD CD BL SM. Analyzed the data: KR SK MD AR JSc DD JSt JM KD GH KP HS PA SM. Contributed reagents/materials/analysis tools: KP. Wrote the paper: PA SM." + ] + }, + "references_html": { + "value": [ + "1.\n Glass CK, Saijo K, Winner B, Marchetto MC, Gage FH (2010) Mechanisms underlying inflammation in neurodegeneration. Cell 140: 918–934. ", + "2.\n Terada N, Hamazaki T, Oka M, Hoki M, Mastalerz DM, et al. (2002) Bone marrow cells adopt the phenotype of other cells by spontaneous cell fusion. Nature 416: 542–545. ", + "3.\n Ying QL, Nichols J, Evans EP, Smith AG (2002) Changing potency by spontaneous fusion. Nature 416: 545–548. ", + "4.\n Alvarez-Dolado M, Pardal R, Garcia-Verdugo JM, Fike JR, Lee HO, et al. (2003) Fusion of bone-marrow-derived cells with Purkinje neurons, cardiomyocytes and hepatocytes. Nature 425: 968–973. ", + "5.\n Johansson CB, Youssef S, Koleckar K, Holbrook C, Doyonnas R, et al. (2008) Extensive fusion of haematopoietic cells with Purkinje neurons in response to chronic inflammation. Nat Cell Biol 10: 575–583. ", + "6.\n de Boer J, Williams A, Skavdis G, Harker N, Coles M, et al. (2003) Transgenic mice with hematopoietic and lymphoid specific expression of Cre. Eur J Immunol 33: 314–325. ", + "7.\n Nern C, Wolff I, Macas J, von Randow J, Scharenberg C, et al. (2009) Fusion of hematopoietic cells with Purkinje neurons does not lead to stable heterokaryon formation under noninvasive conditions. J Neurosci 29: 3799–3807. ", + "8.\n Koni PA, Joshi SK, Temann UA, Olson D, Burkly L, et al. (2001) Conditional vascular cell adhesion molecule 1 deletion in mice: impaired lymphocyte migration to bone marrow. J Exp Med 193: 741–754. ", + "9.\n Thery C, Ostrowski M, Segura E (2009) Membrane vesicles as conveyors of immune responses. Nat Rev Immunol 9: 581–593. ", + "10.\n Valadi H, Ekstrom K, Bossios A, Sjostrand M, Lee JJ, et al. (2007) Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol 9: 654–659. ", + "11.\n Thery C, Amigorena S, Raposo G, Clayton A (2006) Isolation and characterization of exosomes from cell culture supernatants and biological fluids. Curr Protoc Cell Biol Chapter 3 : Unit 3 22.
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(1998) Transcriptional regulation of vav, a gene expressed throughout the hematopoietic compartment. Blood 91: 419–430. ", + "33.\n De Palma M, Venneri MA, Galli R, Sergi Sergi L, Politi LS, et al. (2005) Tie2 identifies a hematopoietic lineage of proangiogenic monocytes required for tumor vessel formation and a mesenchymal population of pericyte progenitors. Cancer Cell 8: 211–226. ", + "34.\n Puri MC, Bernstein A (2003) Requirement for the TIE family of receptor tyrosine kinases in adult but not fetal hematopoiesis. Proc Natl Acad Sci U S A 100: 12753–12758. ", + "35.\n Fitzner D, Schnaars M, van Rossum D, Krishnamoorthy G, Dibaj P, et al. (2011) Selective transfer of exosomes from oligodendrocytes to microglia by macropinocytosis. J Cell Sci 124: 447–458. ", + "36.\n El-Andaloussi S, Lee Y, Lakhal-Littleton S, Li J, Seow Y, et al. (2012) Exosome-mediated delivery of siRNA in vitro and in vivo. Nat Protoc 7: 2112–2126. ", + "37.\n Feng D, Zhao WL, Ye YY, Bai XC, Liu RQ, et al. (2010) Cellular internalization of exosomes occurs through phagocytosis. Traffic 11: 675–687. ", + "38.\n Hickey WF, Hsu BL, Kimura H (1991) T-lymphocyte entry into the central nervous system. J Neurosci Res 28: 254–260. ", + "39.\n Grivennikov SI, Greten FR, Karin M (2010) Immunity, inflammation, and cancer. Cell 140: 883–899. ", + "40.\n Schratt G (2009) Fine-tuning neural gene expression with microRNAs. Curr Opin Neurobiol 19: 213–219. ", + "41.\n Fruhbeis C, Frohlich D, Kuo WP, Amphornrat J, Thilemann S, et al. (2013) Neurotransmitter-triggered transfer of exosomes mediates oligodendrocyte-neuron communication. PLoS Biol 11: e1001604. ", + "42.\n Kawahara Y, Mieda-Sato A (2012) TDP-43 promotes microRNA biogenesis as a component of the Drosha and Dicer complexes. Proc Natl Acad Sci U S A 109: 3347–3352. ", + "43.\n Freischmidt A, Muller K, Ludolph AC, Weishaupt JH (2013) Systemic dysregulation of TDP-43 binding microRNAs in amyotrophic lateral sclerosis. Acta Neuropathol Commun 1: 42. ", + "44.\n Baralle M, Buratti E, Baralle FE (2013) The role of TDP-43 in the pathogenesis of ALS and FTLD. Biochem Soc Trans 41: 1536–1540. ", + "45.\n Wang K, Long B, Jiao JQ, Wang JX, Liu JP, et al. (2012) miR-484 regulates mitochondrial network through targeting Fis1. Nat Commun 3: 781. ", + "46.\n Baudry A, Mouillet-Richard S, Schneider B, Launay JM, Kellermann O (2010) miR-16 targets the serotonin transporter: a new facet for adaptive responses to antidepressants. Science 329: 1537–1541. ", + "47.\n Aranha MM, Santos DM, Xavier JM, Low WC, Steer CJ, et al. (2010) Apoptosis-associated microRNAs are modulated in mouse, rat and human neural differentiation. BMC Genomics 11: 514. ", + "48.\n Emmanouilidou E, Melachroinou K, Roumeliotis T, Garbis SD, Ntzouni M, et al. (2010) Cell-produced alpha-synuclein is secreted in a calcium-dependent manner by exosomes and impacts neuronal survival. J Neurosci 30: 6838–6851. ", + "49.\n Saman S, Kim W, Raya M, Visnick Y, Miro S, et al. (2012) Exosome-associated tau is secreted in tauopathy models and is selectively phosphorylated in cerebrospinal fluid (CSF) in early Alzheimer's disease. J Biol Chem 287(6): 3842–3849. ", + "50.\n Clavaguera F, Bolmont T, Crowther RA, Abramowski D, Frank S, et al. (2009) Transmission and spreading of tauopathy in transgenic mouse brain. Nat Cell Biol 11: 909–913. ", + "51.\n Dunning CJ, Reyes JF, Steiner JA, Brundin P (2011) Can Parkinson's disease pathology be propagated from one neuron to another? Prog Neurobiol 97(2): 205–219. ", + "52.\n Del Turco D, Woods AG, Gebhardt C, Phinney AL, Jucker M, et al. (2003) Comparison of commissural sprouting in the mouse and rat fascia dentata after entorhinal cortex lesion. Hippocampus 13: 685–699. ", + "53.\n Stoppini L, Buchs PA, Muller D (1991) A simple method for organotypic cultures of nervous tissue. J Neurosci Methods 37: 173–182. ", + "54.\n Keller S, Rupp C, Stoeck A, Runz S, Fogel M, et al. (2007) CD24 is a marker of exosomes secreted into urine and amniotic fluid. Kidney Int 72: 1095–1102. " + ] + }, + "figures_html": { + "value": [ + "
    \"thumbnail\"
    Figure 1. Noninvasive tracing of hematopoietic Cre recombinase activity.

    (A) Expressing Cre recombinase specifically in the hematopoietic lineage reveals the contribution of hematopoietic cells to nonhematopoietic tissues by irreversibly switching on reporter gene expression after excision of a floxed stop codon. β-galactosidase expression after recombination can be observed in multiple tissues such as liver (B), lung epithelia (C), and small intestine (D). In the intestine, the labeling of an entire crypt indicates recombination of an intestinal stem cell with concomitant inheritance of the marker to all progeny. (E) Overview of a cerebellar section showing a single recombined Purkinje neuron expressing GFP (green). (F) High magnification of a Purkinje neuron in serial section confocal analysis confirming absence of a second nucleus, excluding cell fusion. Scale bar, 50 µm (B), 20 µm (C), 50 µm (D), 50 µm (E), and 10 µm (F).

    \n

    doi:10.1371/journal.pbio.1001874.g001

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 2. Cre mRNA is present in the blood plasma of Vav-iCre mice and contained in EVs including exosomes.

    (A) Cre mRNA can be detected in vesicle preparations enriched for exosomes from the blood plasma of Vav-iCre mice by RT-PCR. Each lane represents a result from an individual animal. For detection of Cre mRNA, nested primer PCR was used. The PCR product at 100 bp represents the signal after the second round of amplification. (B) Cre mRNA is localized in the pellet but not in the supernatant after ultracentrifugation of conditioned medium from primary Vav-iCre–positive hematopoietic cells after stimulation by LPS in vitro. Cre mRNA was resistant to RNaseA treatment in all experiments. (C) After treatment with Triton-X to lyse EVs in combination with RNaseA digestion, Cre mRNA is no longer detectable in contrast to RNaseA treatment alone. (D) Vesicular structures between 50 and 100 nm in size were visualized in electron micrographs from Vav-iCre hematopoietic-cell-derived vesicle preparations (scale bar, 50 nm). (E and F) Secreted membrane vesicle subspecies can be separated by density by sucrose gradient ultracentrifugation. Exosomal identity was confirmed by blotting against the specific protein markers ADAM10 and CD9 for all subfractions. (G) Cre protein could not be detected in any of the fractions. Positive controls for all antibodies are shown in boxes to the right. (H) Cre mRNA is present in the exosomal fractions 2–7. The nonexosomal vesicles fractions or apoptotic bodies are characterized by their variability of positive subfractions to complete absence of Cre mRNA. In this experiment, subfractions 9 and 10 are positive, whereas 8, 11, and 12 do not contain any Cre RNA.

    \n

    doi:10.1371/journal.pbio.1001874.g002

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 3. EVs containing Cre mRNA are sufficient to induce recombination in Purkinje neurons after intracerebellar injection in vivo.

    (A) EV preparations enriched for exosomes prepared from the peripheral blood and bone marrow of Vav-iCre mice were brought into the circulation by tail vein injection or were directly injected into the cerebellum. Injection of Cre RNA-containing EVs into tail veins did not lead to recombination events in the brain (n = 4). (B) β-galactosidase–positive Purkinje neuron in the cerebellum of a reporter mouse 4 d after intracerebellar injection of EVs. (C) Other reporter-gene–positive cells with a shape and size reminiscent of glial cells in proximity to the Purkinje cell layer. (D) Reporter-gene–positive cells displaying a microglia-like morphology. (E) Quantification of reporter-gene–expressing Purkinje neurons after intracerebellar injection of vesicle preparations from Vav-iCre–positive peripheral blood. Control mice (shaded part) were injected with 1 µl purified Cre-recombinase protein at 1 U/µl (light grey) or lysate prepared from Vav-iCre bone marrow (dark grey) and never showed any recombined cells. Scale bar, 50 µm (B and C) and 25 µm (D).

    \n

    doi:10.1371/journal.pbio.1001874.g003

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 4. Transfer of Cre mRNA in blood chimeras.

    (A) Schematic drawings of the experimental strategies to test for recombination events in blood chimeras. Lethally irradiated ROSA26-LacZ mice receive BM cells from Vav-iCre-ROSA-GFP mice. The bone marrow of recipient mice was tested for engraftment by flow cytometry analysis of GFP expression (representative analysis in right panel; wild-type bone marrow, red line; Vav-iCre-ROSA-GFP donor bone marrow, green line; bone marrow of ROSA26-LacZ recipient mouse after engraftment, blue line). For adoptive transfer experiments, the same combination of transgenes was used with spleen and lymph node cells as donor organs. Representative flow cytometry analysis of GFP expression of donor (green line) compared to wild-type cells (red line). At the time of analysis, GFP-positive cells were undetectable in recipient spleens (blue line). Two months after bone marrow transplantation, recombined cells can be detected in the liver (B), granular cell layer (C), and Purkinje cell layer (D), as well as associated with blood vessels (E). None of the recombined LacZ-/X-Gal–positive cells were positive for GFP, excluding cell fusion. Scale bar, 10 µm (B–E).

    \n

    doi:10.1371/journal.pbio.1001874.g004

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 5. Peripheral inflammation increases the number of recombined Purkinje neurons.

    The number of recombined Purkinje neurons is low in healthy animals (A) but increases dramatically after peripheral inflammatory conditions (B). Inflammatory injuries were induced by subcutaneous injection of LLC2s or peritonitis. Animals were analyzed 12 d after injection when tumors were formed. Peritonitis was induced by a single i.p. injection of thioglycolate broth (1 ml in 3% PBS). Mice with peritonitis and ECL were analyzed 4 d after injection. (C) Filled bars represent results from Vav-iCre and empty bars from Tie2-Cre reporter mice. The p values were calculated by two-tailed t test for groups with unequal variance. (D and E) We did not observe any recombined Purkinje neurons that were binucleated in either transgenic mouse line after induction of an inflammation. (F and G) Microglia (white arrows) were always negative for the marker gene in healthy animals as well as after an inflammation. (H and I) Transendothelial electrical resistance (TEER, top panel) decreases and the corresponding capacitance (Ccl, bottom panel) of the bEnd5 endothelial monolayers increases significantly 24 h and 48 h after addition of bone-marrow-derived EVs compared to conditioned medium supernatant after ultracentrifugation. Vertical line at 0 h indicates media exchange. Scale bar, 100 µm (A and B), 50 µm (D and F), 10 µm (E), and 5 µm (G).

    \n

    doi:10.1371/journal.pbio.1001874.g005

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 6. Reporter-gene–positive neurons can be found in multiple areas of the brain.

    (A and B) β-galactosidase–positive cells in the SN/VTA that can be TH-positive dopaminergic neurons as well as TH-negative cells with neuronal morphology (C). (D–F) β-galactosidase–positive cells in the cortex are also positive for NeuN. (G–I) Overview of the dentate gyrus in the hippocampus with recombined neurons in the granular cell layer that are positive for the neuronal marker NeuN. (J and K) Recombined neurons after ECL in hippocampal areas CA2 and CA3 and nonneuronal GFAP-negative recombined cells at the lesion site (L). Scale bar, 100 µm (D, G, H, and J), 50 µm (A, E, K, and L), and 10 µm (B, C, F, and I).

    \n

    doi:10.1371/journal.pbio.1001874.g006

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 7. Recombined Purkinje neurons display a different miRNA profile compared to nonrecombined neighboring neurons.

    (A) Example for an X-Gal–positive neuron and corresponding nonrecombined Purkinje neuron that were collected by LCM for miRNA analysis. Cells were identified based on morphology and location in the Purkinje cell layer. Nonrecombined Purkinje neurons in the direct vicinity were cut out as references, depicted below. (B) Pairwise comparison of nonrecombined versus recombined Purkinje neurons from the same animal. Each symbol represents an individual miRNA; colored symbols represent miRNAs that could only be detected in one pool. Symbols representing higher expressed miRNAs are at the top; those representing lower expressed miRNAs are at the bottom of each column. The comparison of recombined versus nonrecombined PKNs from the same animals reveals significant differences in their miRNA profile. (C) Venn diagram depicting miRNAs specific for recombined PKNs. The three miRNAs displayed in the box are those that can be found in both samples of the recombined PKNs but not in any sample of the nonrecombined PKN. (D) EVs isolated from the serum of mice with peritonitis display a different miRNA content than those of healthy control animals.

    \n

    doi:10.1371/journal.pbio.1001874.g007

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 8. Model for EV transfer of RNA from immune cells to the brain.

    Possible modes of RNA transfer from blood to brain: (A) EVs are released from blood cells into the blood stream, where they can cross the BBB and fuse with neurons. (B) Alternatively, leukocytes enter the brain and only EVs released in short distance to the target cell are able to bind and release their content. This direct signaling of immune cells to the brain is independent of microglia.

    \n

    doi:10.1371/journal.pbio.1001874.g008

    ", + "\n Download:\n " + ] + }, + "tables_html": { + "value": [ + "
    \"thumbnail\"
    Figure 1. Noninvasive tracing of hematopoietic Cre recombinase activity.

    (A) Expressing Cre recombinase specifically in the hematopoietic lineage reveals the contribution of hematopoietic cells to nonhematopoietic tissues by irreversibly switching on reporter gene expression after excision of a floxed stop codon. β-galactosidase expression after recombination can be observed in multiple tissues such as liver (B), lung epithelia (C), and small intestine (D). In the intestine, the labeling of an entire crypt indicates recombination of an intestinal stem cell with concomitant inheritance of the marker to all progeny. (E) Overview of a cerebellar section showing a single recombined Purkinje neuron expressing GFP (green). (F) High magnification of a Purkinje neuron in serial section confocal analysis confirming absence of a second nucleus, excluding cell fusion. Scale bar, 50 µm (B), 20 µm (C), 50 µm (D), 50 µm (E), and 10 µm (F).

    \n

    doi:10.1371/journal.pbio.1001874.g001

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 2. Cre mRNA is present in the blood plasma of Vav-iCre mice and contained in EVs including exosomes.

    (A) Cre mRNA can be detected in vesicle preparations enriched for exosomes from the blood plasma of Vav-iCre mice by RT-PCR. Each lane represents a result from an individual animal. For detection of Cre mRNA, nested primer PCR was used. The PCR product at 100 bp represents the signal after the second round of amplification. (B) Cre mRNA is localized in the pellet but not in the supernatant after ultracentrifugation of conditioned medium from primary Vav-iCre–positive hematopoietic cells after stimulation by LPS in vitro. Cre mRNA was resistant to RNaseA treatment in all experiments. (C) After treatment with Triton-X to lyse EVs in combination with RNaseA digestion, Cre mRNA is no longer detectable in contrast to RNaseA treatment alone. (D) Vesicular structures between 50 and 100 nm in size were visualized in electron micrographs from Vav-iCre hematopoietic-cell-derived vesicle preparations (scale bar, 50 nm). (E and F) Secreted membrane vesicle subspecies can be separated by density by sucrose gradient ultracentrifugation. Exosomal identity was confirmed by blotting against the specific protein markers ADAM10 and CD9 for all subfractions. (G) Cre protein could not be detected in any of the fractions. Positive controls for all antibodies are shown in boxes to the right. (H) Cre mRNA is present in the exosomal fractions 2–7. The nonexosomal vesicles fractions or apoptotic bodies are characterized by their variability of positive subfractions to complete absence of Cre mRNA. In this experiment, subfractions 9 and 10 are positive, whereas 8, 11, and 12 do not contain any Cre RNA.

    \n

    doi:10.1371/journal.pbio.1001874.g002

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 3. EVs containing Cre mRNA are sufficient to induce recombination in Purkinje neurons after intracerebellar injection in vivo.

    (A) EV preparations enriched for exosomes prepared from the peripheral blood and bone marrow of Vav-iCre mice were brought into the circulation by tail vein injection or were directly injected into the cerebellum. Injection of Cre RNA-containing EVs into tail veins did not lead to recombination events in the brain (n = 4). (B) β-galactosidase–positive Purkinje neuron in the cerebellum of a reporter mouse 4 d after intracerebellar injection of EVs. (C) Other reporter-gene–positive cells with a shape and size reminiscent of glial cells in proximity to the Purkinje cell layer. (D) Reporter-gene–positive cells displaying a microglia-like morphology. (E) Quantification of reporter-gene–expressing Purkinje neurons after intracerebellar injection of vesicle preparations from Vav-iCre–positive peripheral blood. Control mice (shaded part) were injected with 1 µl purified Cre-recombinase protein at 1 U/µl (light grey) or lysate prepared from Vav-iCre bone marrow (dark grey) and never showed any recombined cells. Scale bar, 50 µm (B and C) and 25 µm (D).

    \n

    doi:10.1371/journal.pbio.1001874.g003

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 4. Transfer of Cre mRNA in blood chimeras.

    (A) Schematic drawings of the experimental strategies to test for recombination events in blood chimeras. Lethally irradiated ROSA26-LacZ mice receive BM cells from Vav-iCre-ROSA-GFP mice. The bone marrow of recipient mice was tested for engraftment by flow cytometry analysis of GFP expression (representative analysis in right panel; wild-type bone marrow, red line; Vav-iCre-ROSA-GFP donor bone marrow, green line; bone marrow of ROSA26-LacZ recipient mouse after engraftment, blue line). For adoptive transfer experiments, the same combination of transgenes was used with spleen and lymph node cells as donor organs. Representative flow cytometry analysis of GFP expression of donor (green line) compared to wild-type cells (red line). At the time of analysis, GFP-positive cells were undetectable in recipient spleens (blue line). Two months after bone marrow transplantation, recombined cells can be detected in the liver (B), granular cell layer (C), and Purkinje cell layer (D), as well as associated with blood vessels (E). None of the recombined LacZ-/X-Gal–positive cells were positive for GFP, excluding cell fusion. Scale bar, 10 µm (B–E).

    \n

    doi:10.1371/journal.pbio.1001874.g004

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 5. Peripheral inflammation increases the number of recombined Purkinje neurons.

    The number of recombined Purkinje neurons is low in healthy animals (A) but increases dramatically after peripheral inflammatory conditions (B). Inflammatory injuries were induced by subcutaneous injection of LLC2s or peritonitis. Animals were analyzed 12 d after injection when tumors were formed. Peritonitis was induced by a single i.p. injection of thioglycolate broth (1 ml in 3% PBS). Mice with peritonitis and ECL were analyzed 4 d after injection. (C) Filled bars represent results from Vav-iCre and empty bars from Tie2-Cre reporter mice. The p values were calculated by two-tailed t test for groups with unequal variance. (D and E) We did not observe any recombined Purkinje neurons that were binucleated in either transgenic mouse line after induction of an inflammation. (F and G) Microglia (white arrows) were always negative for the marker gene in healthy animals as well as after an inflammation. (H and I) Transendothelial electrical resistance (TEER, top panel) decreases and the corresponding capacitance (Ccl, bottom panel) of the bEnd5 endothelial monolayers increases significantly 24 h and 48 h after addition of bone-marrow-derived EVs compared to conditioned medium supernatant after ultracentrifugation. Vertical line at 0 h indicates media exchange. Scale bar, 100 µm (A and B), 50 µm (D and F), 10 µm (E), and 5 µm (G).

    \n

    doi:10.1371/journal.pbio.1001874.g005

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 6. Reporter-gene–positive neurons can be found in multiple areas of the brain.

    (A and B) β-galactosidase–positive cells in the SN/VTA that can be TH-positive dopaminergic neurons as well as TH-negative cells with neuronal morphology (C). (D–F) β-galactosidase–positive cells in the cortex are also positive for NeuN. (G–I) Overview of the dentate gyrus in the hippocampus with recombined neurons in the granular cell layer that are positive for the neuronal marker NeuN. (J and K) Recombined neurons after ECL in hippocampal areas CA2 and CA3 and nonneuronal GFAP-negative recombined cells at the lesion site (L). Scale bar, 100 µm (D, G, H, and J), 50 µm (A, E, K, and L), and 10 µm (B, C, F, and I).

    \n

    doi:10.1371/journal.pbio.1001874.g006

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 7. Recombined Purkinje neurons display a different miRNA profile compared to nonrecombined neighboring neurons.

    (A) Example for an X-Gal–positive neuron and corresponding nonrecombined Purkinje neuron that were collected by LCM for miRNA analysis. Cells were identified based on morphology and location in the Purkinje cell layer. Nonrecombined Purkinje neurons in the direct vicinity were cut out as references, depicted below. (B) Pairwise comparison of nonrecombined versus recombined Purkinje neurons from the same animal. Each symbol represents an individual miRNA; colored symbols represent miRNAs that could only be detected in one pool. Symbols representing higher expressed miRNAs are at the top; those representing lower expressed miRNAs are at the bottom of each column. The comparison of recombined versus nonrecombined PKNs from the same animals reveals significant differences in their miRNA profile. (C) Venn diagram depicting miRNAs specific for recombined PKNs. The three miRNAs displayed in the box are those that can be found in both samples of the recombined PKNs but not in any sample of the nonrecombined PKN. (D) EVs isolated from the serum of mice with peritonitis display a different miRNA content than those of healthy control animals.

    \n

    doi:10.1371/journal.pbio.1001874.g007

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 8. Model for EV transfer of RNA from immune cells to the brain.

    Possible modes of RNA transfer from blood to brain: (A) EVs are released from blood cells into the blood stream, where they can cross the BBB and fuse with neurons. (B) Alternatively, leukocytes enter the brain and only EVs released in short distance to the target cell are able to bind and release their content. This direct signaling of immune cells to the brain is independent of microglia.

    \n

    doi:10.1371/journal.pbio.1001874.g008

    ", + "\n Download:\n " + ] + }, + "fulltext_html": { + "value": [ + "http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001874" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.plosbiology.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pbio.1001874&representation=PDF" + ] + }, + "fulltext_xml": { + "value": [ + "http://www.plosbiology.org/article/article/asset?id=10.1371/journal.pbio.1001874.XML" + ] + }, + "supplementary_file": { + "value": [ + + ] + }, + "figures_image": { + "value": [ + "article/figure/image?size=large&id=info:doi/10.1371/journal.pbio.1001874.g001", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pbio.1001874.g002", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pbio.1001874.g003", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pbio.1001874.g004", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pbio.1001874.g005", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pbio.1001874.g006", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pbio.1001874.g007", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pbio.1001874.g008" + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_sizes": [ + { + "fulltext.html": 247534 + }, { - "fulltext.pdf": "c730b7b2434f950ea409d74a78c30316" + "fulltext.pdf": 3691810 }, { - "fulltext.xml": "40397e5bedf709fd1e98d19dc8a8a8fb" + "fulltext.xml": 11900 } ] }, "http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001882": { - "fulltext_pdf": { + "publisher": { "value": [ - "http://dx.plos.org/10.1371/journal.pbio.1001882.pdf" + ] }, - "fulltext_html": { + "journal_name": { "value": [ - + "PLOS Biology" ] }, - "fulltext_xml": { + "journal_issn": { "value": [ - "/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pbio.1001882&representation=XML" + "1545-7885" ] }, "title": { @@ -108,14 +312,41 @@ "The Billion Cell Construct: Will Three-Dimensional Printing Get Us There?" ] }, - "author": { + "keywords": { + "value": [ + + ] + }, + "author_name": { "value": [ "Jordan S. Miller" ] }, - "date": { + "author_institution": { + "value": [ + + ] + }, + "editor_name": { + "value": [ + + ] + }, + "date_published": { "value": [ - "2014/6/17" + [ + " June 17, 2014" + ] + ] + }, + "date_accepted": { + "value": [ + + ] + }, + "date_submitted": { + "value": [ + ] }, "doi": { @@ -138,47 +369,237 @@ "e1001882" ] }, - "description": { + "abstract": { "value": [ - "PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines." + ] }, - "abstract": { + "abstract_html": { + "value": [ + "

    Abstract

    How structure relates to function—across spatial scales, from the single molecule to the whole organism—is a central theme in biology. Bioengineers, however, wrestle with the converse question: will function follow form? That is, we struggle to approximate the architecture of living tissues experimentally, hoping that the structure we create will lead to the function we desire. A new means to explore the relationship between form and function in living tissue has arrived with three-dimensional printing, but the technology is not without limitations.

    \n" + ] + }, + "abstract_text": { + "value": [ + + ] + }, + "introduction_html": { + "value": [ + + ] + }, + "methods_html": { + "value": [ + + ] + }, + "results_html": { + "value": [ + + ] + }, + "discussion_html": { + "value": [ + + ] + }, + "author_contrib_html": { + "value": [ + + ] + }, + "references_html": { + "value": [ + "1.\n Lipetz LE (1961) Bionics. Science 133: 588–593.\n doi:\n 10.1126/science.133.3452.588 ", + "2.\n Kung TA, Bueno RA, Alkhalefah GK, Langhals NB, Urbanchek MG, et al. (2013) Innovations in prosthetic interfaces for the upper extremity. Plast Reconstr Surg 132: 1515–1523.\n doi:\n 10.1097/prs.0b013e3182a97e5f ", + "3.\n Eiber CD, Lovell NH, Suaning GJ (2013) Attaining higher resolution visual prosthetics: a review of the factors and limitations. J Neural Eng 10: 011002.\n doi:\n 10.1088/1741-2560/10/1/011002 ", + "4.\n Sauer IM, Kardassis D, Zeillinger K, Pascher A, Gruenwald A, et al. (2003) Clinical extracorporeal hybrid liver support–phase I study with primary porcine liver cells. Xenotransplantation 10: 460–469.\n doi:\n 10.1034/j.1399-3089.2003.00062.x ", + "5.\n Thiel K, Schenk M, Etspüler A, Schenk T, Morgalla MH, et al. (2011) A simple dummy liver assist device prolongs anhepatic survival in a porcine model of total hepatectomy by slight hypothermia. BMC Gastroenterol 11: 79.\n doi:\n 10.1186/1471-230x-11-79 ", + "6.\n Herrera M, Mirotsou M (2014) Stem cells: potential and challenges for kidney repair. Am J Physiol Renal Physiol 306: F12–F23.\n doi:\n 10.1152/ajprenal.00238.2013 ", + "7.\n Wagner FM (2011) Donor heart preservation and perfusion. Appl Cardiopulm Pathophysiol 15: 198–206. ", + "8.\n Valenza F, Rosso L, Gatti S, Coppola S, Froio S, et al. (2012) Extracorporeal lung perfusion and ventilation to improve donor lung function and increase the number of organs available for transplantation. Transplant Proc 44: 1826–1829.\n doi:\n 10.1016/j.transproceed.2012.06.023 ", + "9.\n Ohashi K, Yokoyama T, Yamato M, Kuge H, Kanehiro H, et al. (2007) Engineering functional two- and three-dimensional liver systems in vivo using hepatic tissue sheets. Nat Med 13: 880–885.\n doi:\n 10.1038/nm1576 ", + "10.\n Chen AA, Thomas DK, Ong LL, Schwartz RE, Golub TR, et al. (2011) Humanized mice with ectopic artificial liver tissues. Proc Natl Acad Sci U S A 108: 11842–11847.\n doi:\n 10.1073/pnas.1101791108 ", + "11.\n Hoppo T, Komori J, Manohar R, Stolz DB, Lagasse E (2011) Rescue of lethal hepatic failure by hepatized lymph nodes in mice. Gastroenterology 140: 656–666.e2.\n doi:\n 10.1053/j.gastro.2010.11.006 ", + "12.\n Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. 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Continuous Digital Light Processing (cDLP): Highly Accurate Additive Manufacturing of Tissue Engineered Bone Scaffolds. Virtual Phys Prototyp 7: 13–24.\n doi:\n 10.1080/17452759.2012.673152 ", + "35.\n Marga F, Jakab K, Khatiwala C, Shepherd B, Dorfman S, et al. (2012) Toward engineering functional organ modules by additive manufacturing. Biofabrication 4: 022001.\n doi:\n 10.1088/1758-5082/4/2/022001 ", + "36.\n Jones N (2012) Science in three dimensions: the print revolution. Nature 487: 22–23.\n doi:\n 10.1038/487022a ", + "37.\n Cui X, Boland T (2009) Human microvasculature fabrication using thermal inkjet printing technology. Biomaterials 30: 6221–6227.\n doi:\n 10.1016/j.biomaterials.2009.07.056 ", + "38.\n Mironov V, Visconti RP, Kasyanov V, Forgacs G, Drake CJ, et al. (2009) Organ printing: tissue spheroids as building blocks. Biomaterials 30: 2164–2174.\n doi:\n 10.1016/j.biomaterials.2008.12.084 ", + "39.\n Duan B, Hockaday LA, Kang KH, Butcher JT (2013) 3D bioprinting of heterogeneous aortic valve conduits with alginate/gelatin hydrogels. J Biomed Mater Res A 101: 1255–1264.\n doi:\n 10.1002/jbm.a.34420 ", + "40.\n Derby B (2010) Inkjet printing of functional and structural materials: fluid property requirements, feature stability, and resolution. Annu Rev Mater Res 40: 395–414.\n doi:\n 10.1146/annurev-matsci-070909-104502 ", + "41.\n Cui X, Dean D, Ruggeri ZM, Boland T (2010) Cell damage evaluation of thermal inkjet printed Chinese hamster ovary cells. Biotechnol Bioeng 106: 963–969.\n doi:\n 10.1002/bit.22762 ", + "42.\n Kikuchi T, Shimizu T, Wada M, Yamato M, Okano T (2014) Automatic fabrication of 3-dimensional tissues using cell sheet manipulator technique. 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(2014) 3D Bioprinting of Vascularized, Heterogeneous Cell-Laden Tissue Constructs. Adv Mater 26: 3124–3130.\n doi:\n 10.1002/adma.201305506 ", + "48.\n Symes MD, Kitson PJ, Yan J, Richmond CJ, Cooper GJ, et al. (2012) Integrated 3D-printed reactionware for chemical synthesis and analysis. Nat Chem 4: 349–354.\n doi:\n 10.1038/nchem.1313 ", + "49.\n Pham QP, Kasper FK, Scott Baggett L, Raphael RM, Jansen JA, et al. (2008) The influence of an in vitro generated bone-like extracellular matrix on osteoblastic gene expression of marrow stromal cells. Biomaterials 29: 2729–2739.\n doi:\n 10.1016/j.biomaterials.2008.02.025 ", + "50.\n McGuigan AP, Sefton MV (2007) The influence of biomaterials on endothelial cell thrombogenicity. Biomaterials 28: 2547–2571.\n doi:\n 10.1016/j.biomaterials.2007.01.039 ", + "51.\n Koike N, Fukumura D, Gralla O, Au P, Schechner JS, et al. (2004) Tissue engineering: creation of long-lasting blood vessels. Nature 428: 138–139.\n doi:\n 10.1038/428138a ", + "52.\n Koffler J, Kaufman-Francis K, Shandalov Y, Egozi D, Pavlov DA, et al. (2011) Improved vascular organization enhances functional integration of engineered skeletal muscle grafts. Proc Natl Acad Sci U S A 108: 14789–14794.\n doi:\n 10.1073/pnas.1017825108 ", + "53.\n Baranski JD, Chaturvedi RR, Stevens KR, Eyckmans J, Carvalho B, et al. (2013) Geometric control of vascular networks to enhance engineered tissue integration and function. Proc Natl Acad Sci U S A 110: 7586–7591.\n doi:\n 10.1073/pnas.1217796110 ", + "54.\n Zhong TP, Childs S, Leu JP, Fishman MC (2001) Gridlock signalling pathway fashions the first embryonic artery. Nature 414: 216–220.\n doi:\n 10.1038/35102599 ", + "55.\n Lu X, Le Noble F, Yuan L, Jiang Q, De Lafarge B, et al. (2004) The netrin receptor UNC5B mediates guidance events controlling morphogenesis of the vascular system. 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Biomed Opt Express 4: 2269–2283.\n doi:\n 10.1364/boe.4.002269 ", + "61.\n Shikata H, McLennan G, Hoffman EA, Sonka M (2009) Segmentation of Pulmonary Vascular Trees from Thoracic 3D CT Images. Int J Biomed Imaging 2009: 636240.\n doi:\n 10.1155/2009/636240 ", + "62.\n Chang DR, Martinez Alanis D, Miller RK, Ji H, Akiyama H, et al. (2013) Lung epithelial branching program antagonizes alveolar differentiation. Proc Natl Acad Sci U S A 110: 18042–18051.\n doi:\n 10.1073/pnas.1311760110 ", + "63.\n Sprinzak D, Lakhanpal A, Lebon L, Santat LA, Fontes ME, et al. (2010) Cis-interactions between Notch and Delta generate mutually exclusive signalling states. Nature 465: 86–90.\n doi:\n 10.1038/nature08959 ", + "64.\n Hester SD, Belmonte JM, Gens JS, Clendenon SG, Glazier JA (2011) A multi-cell, multi-scale model of vertebrate segmentation and somite formation. PLoS Comput Biol 7: e1002155.\n doi:\n 10.1371/journal.pcbi.1002155 ", + "65.\n Vedula SRK, Leong MC, Lai TL, Hersen P, Kabla AJ, et al. (2012) Emerging modes of collective cell migration induced by geometrical constraints. Proc Natl Acad Sci U S A 109: 12974–12979.\n doi:\n 10.1073/pnas.1119313109 ", + "66.\n Desai RA, Gopal SB, Chen S, Chen CS (2013) Contact inhibition of locomotion probabilities drive solitary versus collective cell migration. J R Soc Interface 10: 20130717.\n doi:\n 10.1098/rsif.2013.0717 ", + "67.\n Nawroth JC, Lee H, Feinberg AW, Ripplinger CM, McCain ML, et al. (2012) A tissue-engineered jellyfish with biomimetic propulsion. Nat Biotechnol 30: 792–797.\n doi:\n 10.1038/nbt.2269 ", + "68.\n Rekhi R, Qutub AA (2013) Systems approaches for synthetic biology: a pathway toward mammalian design. 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Am J Physiol Heart Circ Physiol 303: H903–H909.\n doi:\n 10.1152/ajpheart.00263.2012 ", + "73.\n Ghajar CM, Bissell MJ (2010) Tumor engineering: the other face of tissue engineering. Tissue Eng Part A 16: 2153–2156.\n doi:\n 10.1089/ten.tea.2010.0135 ", + "74.\n Hutmacher DW, Loessner D, Rizzi S, Kaplan DL, Mooney DJ, et al. (2010) Can tissue engineering concepts advance tumor biology research? Trends Biotechnol 28: 125–133.\n doi:\n 10.1016/j.tibtech.2009.12.001 ", + "75.\n Ghajar CM, Peinado H, Mori H, Matei IR, Evason KJ, et al. (2013) The perivascular niche regulates breast tumour dormancy. Nat Cell Biol 15: 807–817.\n doi:\n 10.1038/ncb2767 ", + "76.\n Jain RK (1987) Transport of molecules across tumor vasculature. Cancer Metastasis Rev 6: 559–593.\n doi:\n 10.1007/bf00047468 ", + "77.\n Jain RK (2005) Normalization of tumor vasculature: an emerging concept in antiangiogenic therapy. 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Proc Natl Acad Sci U S A 110: 14266–14271.\n doi:\n 10.1073/pnas.1300619110 " + ] + }, + "figures_html": { + "value": [ + "
    \"thumbnail\"
    Figure 1. Anatomical complexity remains unsolved.

    (A) Leonardo da Vinci famously recognized the interpenetrating networks of lung vasculature and branched airways with his detailed drawings (c. 1500). Image courtesy of the European Union Leonardo Digitale. (B) Whole-lung vasculature can be reconstructed and visualized from computed tomography (CT) scans. Reprinted with permission from [61]. (C) Air sac architecture of adult rat lung (electron micrograph of decellularized resin cast). Image courtesy of Laura Niklason, additional research available via [25], scale bar = 1 mm. (D) Optical projection tomography image of an embryonic day 15 mouse lung undergoing branching morphogenesis. Epithelium (E-Cadherin, magenta), future conducting airways (SOX2, white). Image courtesy of Jichao Chen, additional research available via [62], scale bar = 500 m.

    \n

    doi:10.1371/journal.pbio.1001882.g001

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 2. Tissue engineering.

    Investigations with engineered tissue constructs currently span at least eight orders of magnitude. Yet, the minimum therapeutic threshold for recapitulating solid organ function in humans is estimated at the level of 1–10 billion functioning parenchymal cells. We still have a ways to go.

    \n

    doi:10.1371/journal.pbio.1001882.g002

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 3. Overview of 3D printing.

    (A) A 3D model can be generated and visualized in a wide range of software packages. 3D model available under Creative Commons license via Thingiverse.com, courtesy of artists Barak Moshe and Faberdashery. (B) The surface topology is simplified to a mesh comprising a series of 3D coordinates (vertices) and the triangles (faces) that connect them. (C) The surface mesh is computationally sliced layer-by-layer to calculate machine instructions suitable for 3D printing. Machine instructions can be visualized en face or in cross-section (inset). (D) 3D printing via melt extrusion (inset) can easily achieve layer heights which surpass the resolution of human fingerprints. Scale bar = 1 mm. (E) A selection of the diverse parameter space of 3D printing technologies. Many dozens of different combinations are in practice today.

    \n

    doi:10.1371/journal.pbio.1001882.g003

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 4. Journey of a molecular nutrient through native tissues.

    Cellular organization in vascularized tissues is commonly simplified into four regimes, which are rarely recapitulated together in engineered tissue constructs. Soluble blood components vary dramatically in size, concentration, and biochemistry, and each has distinct targets and mechanisms for negotiating tissue architecture. Artwork render and animation (Movie S1) performed with Blender.org open-source software.

    \n

    doi:10.1371/journal.pbio.1001882.g004

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 5. Recapitulating whole organ vasculature.

    It should be possible to create whole vascularized organoids by merging current anatomical mapping technologies with 3D printing. (A) A tissue or organ of interest is scanned via microcomputed tomography (micro-CT). Source 2D liver scans courtesy of Chris Chen and Sangeeta Bhatia, additional research available via [10]. The resulting voxels (volumetric pixels) can be visualized and converted into a 3D surface topology. (B) Optionally, the 3D surface mesh can be fully parametrized in order to generate, de novo, similar vascular architectures as a new topology. (C) Native or synthetically generated vascular architectures are then computationally sliced and prepared for 3D printing directly (in sacrificial ink) or by boolean volumetric subtraction (in additive ink). After physical cleanup, 3D printing can yield cell-laden hydrogels containing living cells and perfusable vasculature. Shown here for clarity is an architecture with one inlet and zero outlets, but more complete or complex architectures with multiple inlets and outlets could be achieved with this same workflow.

    \n

    doi:10.1371/journal.pbio.1001882.g005

    ", + "\n Download:\n " + ] + }, + "tables_html": { + "value": [ + "
    \"thumbnail\"
    Figure 1. Anatomical complexity remains unsolved.

    (A) Leonardo da Vinci famously recognized the interpenetrating networks of lung vasculature and branched airways with his detailed drawings (c. 1500). Image courtesy of the European Union Leonardo Digitale. (B) Whole-lung vasculature can be reconstructed and visualized from computed tomography (CT) scans. Reprinted with permission from [61]. (C) Air sac architecture of adult rat lung (electron micrograph of decellularized resin cast). Image courtesy of Laura Niklason, additional research available via [25], scale bar = 1 mm. (D) Optical projection tomography image of an embryonic day 15 mouse lung undergoing branching morphogenesis. Epithelium (E-Cadherin, magenta), future conducting airways (SOX2, white). Image courtesy of Jichao Chen, additional research available via [62], scale bar = 500 m.

    \n

    doi:10.1371/journal.pbio.1001882.g001

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 2. Tissue engineering.

    Investigations with engineered tissue constructs currently span at least eight orders of magnitude. Yet, the minimum therapeutic threshold for recapitulating solid organ function in humans is estimated at the level of 1–10 billion functioning parenchymal cells. We still have a ways to go.

    \n

    doi:10.1371/journal.pbio.1001882.g002

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 3. Overview of 3D printing.

    (A) A 3D model can be generated and visualized in a wide range of software packages. 3D model available under Creative Commons license via Thingiverse.com, courtesy of artists Barak Moshe and Faberdashery. (B) The surface topology is simplified to a mesh comprising a series of 3D coordinates (vertices) and the triangles (faces) that connect them. (C) The surface mesh is computationally sliced layer-by-layer to calculate machine instructions suitable for 3D printing. Machine instructions can be visualized en face or in cross-section (inset). (D) 3D printing via melt extrusion (inset) can easily achieve layer heights which surpass the resolution of human fingerprints. Scale bar = 1 mm. (E) A selection of the diverse parameter space of 3D printing technologies. Many dozens of different combinations are in practice today.

    \n

    doi:10.1371/journal.pbio.1001882.g003

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 4. Journey of a molecular nutrient through native tissues.

    Cellular organization in vascularized tissues is commonly simplified into four regimes, which are rarely recapitulated together in engineered tissue constructs. Soluble blood components vary dramatically in size, concentration, and biochemistry, and each has distinct targets and mechanisms for negotiating tissue architecture. Artwork render and animation (Movie S1) performed with Blender.org open-source software.

    \n

    doi:10.1371/journal.pbio.1001882.g004

    ", + "\n Download:\n ", + "
    \"thumbnail\"
    Figure 5. Recapitulating whole organ vasculature.

    It should be possible to create whole vascularized organoids by merging current anatomical mapping technologies with 3D printing. (A) A tissue or organ of interest is scanned via microcomputed tomography (micro-CT). Source 2D liver scans courtesy of Chris Chen and Sangeeta Bhatia, additional research available via [10]. The resulting voxels (volumetric pixels) can be visualized and converted into a 3D surface topology. (B) Optionally, the 3D surface mesh can be fully parametrized in order to generate, de novo, similar vascular architectures as a new topology. (C) Native or synthetically generated vascular architectures are then computationally sliced and prepared for 3D printing directly (in sacrificial ink) or by boolean volumetric subtraction (in additive ink). After physical cleanup, 3D printing can yield cell-laden hydrogels containing living cells and perfusable vasculature. Shown here for clarity is an architecture with one inlet and zero outlets, but more complete or complex architectures with multiple inlets and outlets could be achieved with this same workflow.

    \n

    doi:10.1371/journal.pbio.1001882.g005

    ", + "\n Download:\n " + ] + }, + "fulltext_html": { + "value": [ + "http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001882" + ] + }, + "fulltext_pdf": { "value": [ - "AbstractHow structure relates to function—across spatial scales, from the single molecule to the whole organism—is a central theme in biology. Bioengineers, however, wrestle with the converse question: will function follow form? That is, we struggle to approximate the architecture of living tissues experimentally, hoping that the structure we create will lead to the function we desire. A new means to explore the relationship between form and function in living tissue has arrived with three-dimensional printing, but the technology is not without limitations.\n" + "http://www.plosbiology.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pbio.1001882&representation=PDF" + ] + }, + "fulltext_xml": { + "value": [ + "http://www.plosbiology.org/article/article/asset?id=10.1371/journal.pbio.1001882.XML" + ] + }, + "supplementary_file": { + "value": [ + ] }, - "file_hashes": [ + "figures_image": { + "value": [ + "article/figure/image?size=large&id=info:doi/10.1371/journal.pbio.1001882.g001", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pbio.1001882.g002", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pbio.1001882.g003", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pbio.1001882.g004", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pbio.1001882.g005" + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_sizes": [ { - "fulltext.pdf": "b1a6bb4e193cb39cc6aef1b1866dcb3b" + "fulltext.html": 210809 }, { - "fulltext.xml": "cc5a11cbce83bca1b9f4718f0ff90f56" + "fulltext.pdf": 6538480 + }, + { + "fulltext.xml": 11900 } ] }, "http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004441": { - "fulltext_pdf": { + "publisher": { "value": [ - "http://dx.plos.org/10.1371/journal.pgen.1004441.pdf" + ] }, - "fulltext_html": { + "journal_name": { "value": [ - + "PLOS Genetics" ] }, - "fulltext_xml": { + "journal_issn": { "value": [ - "/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pgen.1004441&representation=XML" + "1553-7404" ] }, "title": { "value": [ - "An Operon of Three Transcriptional Regulators Controls Horizontal Gene Transfer of the Integrative and Conjugative Element ICEclc in Pseudomonas knackmussii B13" + "An Operon of Three Transcriptional Regulators Controls Horizontal Gene Transfer of the Integrative and Conjugative Element ICE clc in Pseudomonas knackmussii B13" + ] + }, + "keywords": { + "value": [ + ] }, - "author": { + "author_name": { "value": [ "Nicolas Pradervand", "Sandra Sulser", @@ -188,9 +609,35 @@ "Jan Roelof van der Meer" ] }, - "date": { + "author_institution": { "value": [ - "2014/6/19" + + ] + }, + "editor_name": { + "value": [ + + ] + }, + "date_published": { + "value": [ + [ + " June 19, 2014" + ] + ] + }, + "date_accepted": { + "value": [ + [ + "April 30, 2014" + ] + ] + }, + "date_submitted": { + "value": [ + [ + "February 12, 2014" + ] ] }, "doi": { @@ -213,48 +660,227 @@ "e1004441" ] }, - "description": { + "abstract": { "value": [ - "PLOS Genetics is an open-access" + ] }, - "abstract": { + "abstract_html": { + "value": [ + "

    Abstract

    The integrative and conjugative element ICEclc is a mobile genetic element in Pseudomonas knackmussii B13, and an experimental model for a widely distributed group of elements in Proteobacteria. ICEclc is transferred from specialized transfer competent cells, which arise at a frequency of 3-5% in a population at stationary phase. Very little is known about the different factors that control the transfer frequency of this ICE family. Here we report the discovery of a three-gene operon encoded by ICEclc, which exerts global control on transfer initiation. The operon consists of three consecutive regulatory genes, encoding a TetR-type repressor MfsR, a MarR-type regulator and a LysR-type activator TciR. We show that MfsR autoregulates expression of the operon, whereas TciR is a global activator of ICEclc gene expression, but no clear role was yet found for MarR. Deletion of mfsR increases expression of tciR and marR, causing the proportion of transfer competent cells to reach almost 100% and transfer frequencies to approach 1 per donor. mfsR deletion also caused a two orders of magnitude loss in population viability, individual cell growth arrest and loss of ICEclc. This indicates that autoregulation is an important feature maintaining ICE transfer but avoiding fitness loss. Bioinformatic analysis showed that the mfsR-marR-tciR operon is unique for ICEclc and a few highly related ICE, whereas tciR orthologues occur more widely in a large variety of suspected ICE among Proteobacteria.

    \n", + "\n

    Author Summary

    \n

    Integrative and conjugative elements (ICEs) are a relatively newly recognized class of mobile elements in bacteria, which integrate at one or more positions in a host chromosome, can be excised, circularized, and transfer by conjugation to a new recipient cell. Genome sequencing indicated that ICEs often carry genes with potential adaptive functions for the host. Various ICE-types have been described and ICEclc is a useful model for a wide class of elements found in Beta- and Gammaproteobacteria. Because ICEs normally remain “silent” in the host chromosome and often lack selectable markers, their lifestyle is difficult to study. One of the characteristics of ICEclc is that transfer is initiated in only 3-5% of donor cells in a population during stationary phase. Here, we describe an operon of three regulatory genes, two of which control the transfer initiation of ICEclc. Our findings suggest that the low transfer rate results from the repression of an activator and that this is essential to minimize the deleterious effect of hyper-activation of transfer initiation. While the individual regulatory genes are quite common on ICEs, they rarely occur in this configuration.

    \n" + ] + }, + "abstract_text": { + "value": [ + + ] + }, + "introduction_html": { + "value": [ + + ] + }, + "methods_html": { + "value": [ + + ] + }, + "results_html": { + "value": [ + + ] + }, + "discussion_html": { + "value": [ + + ] + }, + "author_contrib_html": { + "value": [ + "Conceived and designed the experiments: NP SS FD JRvdM. Performed the experiments: NP SS FD IL RM JRvdM. Analyzed the data: NP SS FD RM JRvdM. Contributed reagents/materials/analysis tools: RM NP. Wrote the paper: NP JRvdM FD." + ] + }, + "references_html": { + "value": [ + "1.\n Koonin EV, Wolf YI (2008) Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36: 6688–6719.\n doi:\n 10.1093/nar/gkn668 ", + "2.\n Kloesges T, Popa O, Martin W, Dagan T (2011) Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol Biol Evol 28: 1057–1074.\n doi:\n 10.1093/molbev/msq297 ", + "3.\n Rankin DJ, Rocha EP, Brown SP (2011) What traits are carried on mobile genetic elements, and why? Heredity 106: 1–10.\n doi:\n 10.1038/hdy.2010.24 ", + "4.\n Beiko RG, Harlow TJ, Ragan MA (2005) Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A 102: 14332–14337.\n doi:\n 10.1073/pnas.0504068102 ", + "5.\n Gogarten JP, Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3: 679–682.\n doi:\n 10.1038/nrmicro1204 ", + "6.\n Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3: 722–732.\n doi:\n 10.1038/nrmicro1235 ", + "7.\n Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3: 711–721.\n doi:\n 10.1038/nrmicro1234 ", + "8.\n Juhas M, van der Meer JR, Gaillard M, Harding RM, Hood DW, et al. (2009) Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev 33: 376–393.\n doi:\n 10.1111/j.1574-6976.2008.00136.x ", + "9.\n Guglielmini J, Quintais L, Garcillan-Barcia MP, de la Cruz F, Rocha EPC (2011) The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet 7: e1002222.\n doi:\n 10.1371/journal.pgen.1002222 ", + "10.\n Wozniak RA, Waldor MK (2010) Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 8: 552–563.\n doi:\n 10.1038/nrmicro2382 ", + "11.\n Burrus V, Waldor MK (2004) Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol 155: 376–386.\n doi:\n 10.1016/j.resmic.2004.01.012 ", + "12.\n Burrus V, Pavlovic G, Decaris B, Guédon G (2002) Conjugative transposons: the tip of the iceberg. Mol Microbiol 46: 601–610.\n doi:\n 10.1046/j.1365-2958.2002.03191.x ", + "13.\n Dobrindt U, Hochhut B, Hentschel U, Hacker J (2004) Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2: 414–424.\n doi:\n 10.1038/nrmicro884 ", + "14.\n Bellanger X, Payot S, Leblond-Bourget N, Guedon G (2013) Conjugative and mobilizable genomic islands in bacteria: evolution and diversity. FEMS Microbiol Rev. 10.1111/1574-6976.12058 [epub ahead of print].
      ", + "15.\n Klockgether J, Reva O, Larbig K, Tümmler B (2004) Sequence analysis of the mobile genome island pKLC102 of Pseudomonas aeruginosa C. J Bacteriol. 186: 518–534.\n doi:\n 10.1128/jb.186.2.518-534.2004 ", + "16.\n Klockgether J, Würdemann D, Reva O, Wiehlmann L, Tümmler B (2007) Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa. J Bacteriol 189: 2443–2459.\n doi:\n 10.1128/jb.01688-06 ", + "17.\n Lee CA, Babic A, Grossman AD (2010) Autonomous plasmid-like replication of a conjugative transposon. Mol Microbiol 75: 268–279.\n doi:\n 10.1111/j.1365-2958.2009.06985.x ", + "18.\n Auchtung JM, Lee CA, Monson RE, Lehman AP, Grossman AD (2005) Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response. Proc Natl Acad Sci U S A 102: 12554–12559.\n doi:\n 10.1073/pnas.0505835102 ", + "19.\n Beaber JW, Waldor MK (2004) Identification of operators and promoters that control SXT conjugative transfer. J Bacteriol 186: 5945–5949.\n doi:\n 10.1128/jb.186.17.5945-5949.2004 ", + "20.\n Burrus V, Waldor MK (2003) Control of SXT integration and excision. J Bacteriol 185: 5045–5054.\n doi:\n 10.1128/jb.185.17.5045-5054.2003 ", + "21.\n Sezonov G, Hagège J, Friedmann A, Guérineau M (1995) Characterization of pra, a gene for replication control in pSAM2, the integrating element of Streptomyces ambofaciens. Mol Microbiol 17: 533–544.\n doi:\n 10.1111/j.1365-2958.1995.mmi_17030533.x ", + "22.\n Sezonov G, Duchêne A-M, Friedmann A, Guérineau M, Pernodet J-L (1998) Replicase, excisionase, and integrase genes of the Streptomyces element pSAM2 constitute an operon positively regulated by the pra gene. J Bacteriol 180: 3056–3061. ", + "23.\n Sezonov G, Possoz C, Friedmann A, Pernodet J-L, Guérineau M (2000) KorSA from the Streptomyces integrative element pSAM2 is a central transcriptional repressor: target genes and binding sites. J Bacteriol 182: 1243–1250.\n doi:\n 10.1128/jb.182.5.1243-1250.2000 ", + "24.\n Ramsay JP, Sullivan JT, Jambari N, Ortori CA, Heeb S, et al. (2009) A LuxRI-family regulatory system controls excision and transfer of the Mesorhizobium loti strain R7A symbiosis island by activating expression of two conserved hypothetical genes. Mol Microbiol 73: 1141–1155.\n doi:\n 10.1111/j.1365-2958.2009.06843.x ", + "25.\n Ramsay JP, Major AS, Komarovsky VM, Sullivan JT, Dy RL, et al. (2013) A widely conserved molecular switch controls quorum sensing and symbiosis island transfer in Mesorhizobium loti through expression of a novel antiactivator. Mol Microbiol 87: 1–13.\n doi:\n 10.1111/mmi.12079 ", + "26.\n Minoia M, Gaillard M, Reinhard F, Stojanov M, Sentchilo V, et al. (2008) Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas. Proc Natl Acad Sci U S A 105: 20792–20797.\n doi:\n 10.1073/pnas.0806164106 ", + "27.\n Gaillard M, Vallaeys T, Vorhölter FJ, Minoia M, Werlen C, et al. (2006) The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties. J Bacteriol 188: 1999–2013.\n doi:\n 10.1128/jb.188.5.1999-2013.2006 ", + "28.\n Miyazaki R, Minoia M, Pradervand N, Sentchilo V, Sulser S, et al.. (2011) The clc element and related genomic islands in Proteobacteria. In: Roberts AP, Mullany P, editors. Bacterial integrative mobile genetic elements: Landes Bioscience.
        ", + "29.\n Miyazaki R, Minoia M, Pradervand N, Sulser S, Reinhard F, et al. (2012) Cellular variability of RpoS expression underlies subpopulation activation of an integrative and conjugative element. PLoS Genet 8: e1002818.\n doi:\n 10.1371/journal.pgen.1002818 ", + "30.\n Reinhard F, Miyazaki R, Pradervand N, van der Meer JR (2013) Cell differentiation to “mating bodies” induced by an integrating and conjugative element in free-living bacteria. Curr Biol 23: 255–259.\n doi:\n 10.1016/j.cub.2012.12.025 ", + "31.\n Larsen RA, Wilson MM, Guss AM, Metcalf WW (2002) Genetic analysis of pigment biosynthesis in Xanthobacter autotrophicus Py2 using a new, highly efficient transposon mutagenesis system that is functional in a wide variety of bacteria. Arch Microbiol 178: 193–201.\n doi:\n 10.1007/s00203-002-0442-2 ", + "32.\n Gaillard M, Pradervand N, Minoia M, Sentchilo V, Johnson DR, et al. (2010) Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13. BMC Microbiol 10: 153.\n doi:\n 10.1186/1471-2180-10-153 ", + "33.\n Miyazaki R, van der Meer JR (2011) A dual functional origin of transfer in the ICEclc genomic island of Pseudomonas knackmussii B13. Mol Microbiol 79: 743–758.\n doi:\n 10.1111/j.1365-2958.2010.07484.x ", + "34.\n Sentchilo VS, Ravatn R, Werlen C, Zehnder AJB, van der Meer JR (2003) Unusual integrase gene expression on the clc genomic island of Pseudomonas sp. strain B13. J Bacteriol 185: 4530–4538.\n doi:\n 10.1128/jb.185.15.4530-4538.2003 ", + "35.\n Lechner M, Schmitt K, Bauer S, Hot D, Hubans C, et al. (2009) Genomic island excisions in Bordetella petrii. BMC Microbiol 9: 141.\n doi:\n 10.1186/1471-2180-9-141 ", + "36.\n Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor: Cold Spring Harbor Laboratory Press.
          ", + "37.\n Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA, et al., editors (1981) Manual of methods for general bacteriology. Washington, D.C.: American Society for Microbiology.
            ", + "38.\n Martinez-Garcia E, de Lorenzo V (2011) Engineering multiple genomic deletions in Gram-negative bacteria: analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440. Environ Microbiol 13: 2702–2716.\n doi:\n 10.1111/j.1462-2920.2011.02538.x ", + "39.\n Choi KH, Gaynor JB, White KG, Lopez C, Bosio CM, et al. (2005) A Tn7-based broad-range bacterial cloning and expression system. Nat Methods 2: 443–448.\n doi:\n 10.1038/nmeth765 ", + "40.\n Koch B, Jensen LE, Nybroe O (2001) A panel of Tn7-based vectors for insertion of the gfp marker gene or for delivery of cloned DNA into Gram-negative bacteria at a neutral chromosomal site. J Microbiol Methods 45: 187–195.\n doi:\n 10.1016/s0167-7012(01)00246-9 ", + "41.\n Reinhard F, van der Meer JR (2010) Microcolony growth assays In: Timmis KN, de Lorenzo V, McGenity T, van der Meer JR, editors. Handbook of Hydrocarbon and Lipid Microbiology: Springer Verlag. pp. 3562-3570.
              ", + "42.\n Abbott JC, Aanensen DM, Bentley SD (2007) WebACT: an online genome comparison suite. Methods Mol Biol 395: 57–74.\n doi:\n 10.1385/1-59745-514-8:57 ", + "43.\n Dorn E, Hellwig M, Reineke W, Knackmuss H-J (1974) Isolation and characterization of a 3-chlorobenzoate degrading Pseudomonad. Arch Microbiol 99: 61–70.\n doi:\n 10.1007/bf00696222 ", + "44.\n McClure NC, Weightman AJ, Fry JC (1989) Survival of Pseudomonas putida UWC1 containing cloned catabolic genes in a model activated-sludge unit. Appl Environ Microbiol 55: 2627–2634. ", + "45.\n Sentchilo V, Czechowska K, Pradervand N, Minoia M, Miyazaki R, et al. (2009) Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13. Mol Microbiol 72: 1293–1306.\n doi:\n 10.1111/j.1365-2958.2009.06726.x " + ] + }, + "figures_html": { + "value": [ + "
              \"thumbnail\"
              Figure 1. Schematic overview of ICEclc and the location of the genes relevant to this study.

              (A) ICEclc integrated form with the two flanking 18-bp repeats (as black rectangles, attR and attL). Previously determined gene regions are placed at their approximate location. Important functional regions are depicted as grey boxes accompanied by legends. + or -, indicate the orientation of the coding strand for the respective gene(s) (the + strand being the one of intB13). clc genes, chlorocatechol degradation; amn genes, 2-aminophenol degradation. kb, kilo-basepairs. (B) Detail of the mfsR operon. Arrows, predicted open reading frames (the right-to-left orientation indicates the minus strand). Triangles, positions of the Tn5-mediated kanamycin gene insertions (nucleotide positions indicated below, according to the AJ617740.2 numbering). Regions deleted in this study are displayed as white bars with the names of the mutations noted below. The hooked arrow indicates repression by the mfsR gene product on the PmfsR promoter. (C) Detail of the fragments inserted by mini-Tn7 delivery for complementation of mfsR and tciR deletions. (D) BlastP-predicted domains for each of the three regulatory genes in the mfsR operon. C and N, carboxy and amino terminus, respectively.

              \n

              doi:10.1371/journal.pgen.1004441.g001

              ", + "\n Download:\n ", + "
              \"thumbnail\"
              Figure 2. ICEclc transfer frequencies from P. putida UWC1 donors with different ICEclc genotypes.

              (A) and (B), Independently carried out transfer experiments using the indicated strain sets. Bars show mean transfer frequencies as transconjugant colony forming units (CFU/ml, growing on 3CBA, Km- or Gm-resistant) per donor CFU/ml from biological triplicates, and the corresponding standard deviations. Letters above bars indicate statistically significantly different groups per panel in an Anova with post hoc Tukey-Kramer test (P<0.001), with the same letter pointing to the absence of statistically significant differences.

              \n

              doi:10.1371/journal.pgen.1004441.g002

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              \"thumbnail\"
              Table 1. Strains used in this study and their specifications.

              doi:10.1371/journal.pgen.1004441.t001

              ", + "\n Download:\n ", + "
              \"thumbnail\"
              Figure 3. Differential expression of the ICEclc gene region from micro-array data in selected mutant ICEclc versus wild type in P. putida UWC1.

              (A) Differential expression of the ICEclc region between stationary and exponential phase cells of wild type P. putida UWC1 (ICEclc). (B) Differential expression of the ICEclc region between the mfsR deletion mutant and wild-type, in exponentially growing cells. (C) Comparison of the tciR deletion mutant and wild-type, in stationary phase cells. (D) Comparison of the mfsR transposon insertion mutant versus wild-type, in stationary phase cells. Dots indicate the 2log-fold change of hybridization signal per microarray probe in the comparison, plotted at their distance along the ICEclc sequence (X-axis; in kb). Regions of interest on ICEclc are redrawn as grey boxes at the bottom of each section (+ or - indicate the DNA strand on which the region is encoded). Separate displays indicate expression differences on the plus- (open symbols) or the minus-strand (closed symbols). Grey bars in the background indicate the two-fold cut-off level. For a complete set of microarray results, see Figures S3 and S4.

              \n

              doi:10.1371/journal.pgen.1004441.g003

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              \"thumbnail\"
              Figure 4. Detailed view on the differential expression of the mfsR operon in P. putida ICEclc wild-type or mutants.

              (A) MarR deletion mutant versus wild-type. (B) mfsR deletion mutant versus wild type. (C) tciR deletion mutant versus wild-type. (D) mfsR-'marR deletion mutant versus wild-type. (E) marR versus tciR deletions. (F) mfsR-transposon insertion mutant versus wild-type. Panels show 2log-fold change of expression level per microarray probe in this region of ICEclc for exponential (dark dots) and stationary phase cells (white dots). Genetic map of the region drawn at the bottom of each section for clarity. Arrows represent genes, deleted regions are indicated by stippled bars and corresponding probes are within brackets.

              \n

              doi:10.1371/journal.pgen.1004441.g004

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              \"thumbnail\"
              Figure 5. Effect of mutations in the mfsR region on the expression of the PmfsR-, Pint- and PinR-promoters of ICEclc in P. putida UWC1.

              (A) mCherry expression from the mfsR promoter added in single copy to the chromosome of the indicated P. putida UWC1 strains (relevant genotypes and strain numbers specified below the graph). mCherry expression measured on individual cells (n = 1000) by epifluorescence microscopy in late exponential phase of cultures grown on 10 mM succinate and expressed as box plots (AU, arbitrary units at 20 ms exposure time). (B) Scatter plot of GFP and mcherry fluorescence in single cells of P. putida UWC1 (ICEclc) wild-type, ΔmfsR, ΔtciR or ΔmarR deletions, equipped with a single copy mini-transposon containing the Pint-egfp and PinR-mcherry fusions. Panels show expression of both markers at different growth phases, as indicated, with colors representing genotypes with independent mini-Tn5 insertions. Note as example the subpopulation of wild-type cells (dotted ellips) expressing both reporters, compared to the majority of cells in the mfsR deletion mutant but a complete absence of such subpopulation in the tciR and marR deletion mutants.

              \n

              doi:10.1371/journal.pgen.1004441.g005

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              \"thumbnail\"
              Figure 6. Fitness loss of P. putida UWC1 (ICEclc) caused by the mfsR deletion.

              (A) Survival of P. putida UWC1 (ICEclc, 2737) and P. putida UWC1 (ICEclcmfsR, 4322) pregrown in suspended culture to stationary phase on 3-chlorobenzoate (3CBA) or succinate (succ), and plated from there on 3CBA or succinate agar. (E.g., 3CBA-3CBA, suspended culture on 3CBA, plated on 3CBA agar). Survival expressed as colony forming units (CFU) on the agar plate per ml of stationary phase culture. Data bars indicate the average from independent biological triplicates. Error bars indicate the calculated standard deviation from the average. (B) Phase-contrast micrographs at 1000-fold magnification of microcolonies of P. putida UWC1 (ICEclc) and P. putida (ICEclcmfsR Pint-egfp, 4612) growing on agarose surface supplemented with 0.1 mM 3CBA. Shown are a regular stationary phase microcolony of P. putida with wild-type ICEclc and a transfer competent microcolony (tcm), occurring at 1-3% frequency as reported previously [30]. For comparison, massive lysis (white arrows) and cellular malformations formed in many microcolonies of P. putida UWC1 with the mfsR deletion.

              \n

              doi:10.1371/journal.pgen.1004441.g006

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              \"thumbnail\"
              Table 2. Effects of the mfsR deletion on the growth characteristics of P. putida UWC1 carrying ICEclc.

              doi:10.1371/journal.pgen.1004441.t002

              ", + "\n Download:\n ", + "
              \"thumbnail\"
              Figure 7. Conservation of tciR analogues in putative ICEclc-like regions in a variety of other bacterial genomes.

              Illustration represents tciR analogues (identified on the basis of a BLASTN E-value lower than 1·10-15), and surrounding relevant gene regions in the indicated bacterial genomes (species name, accession numbers) compared to ICEclc. Genes are indicated as in the respective genome accession. Rectangles show annotated genes and their orientation (top, orientation towards the left; bottom, gene orientation towards to right); common colors indicate similar predicted functions. Stippled rectangles indicate common gene regions inferred from Artemis comparison, but not present in the respective annotation. ICE were inferred from (i) more than 75% nucleotide identities across the complete core region of ICEclc, and within a 1-100 kb window from the tciR position, and (ii) the presence of an integrase gene (in brown) within a 5-20 kb window from the tciR-analogue. Note how some genomes carry multiple different ICE from the same family (e.g., Achromobacter xylosoxidans, Acidovorax sp. strain JS42), and further how pair-wise identical ICE regions (shaded in grey) occur between different genomes. Finally note how the tciR-analogues often co-occur with a xer-type regulatory gene on the other strand (light green), and a further lysR gene member (yellow), but in none of the cases shown here with an mfsR counterpart (in red).

              \n

              doi:10.1371/journal.pgen.1004441.g007

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              \"thumbnail\"
              Figure 8. Model for regulation of ICEclc transfer competence.

              MfsR autoregulates expression of itself and of the TciR activator, without which ICEclc transfer decreases by 2·103-fold. TciR may activate specifically one or more promoters on ICEclc, such as the RpoS-dependent PinR-promoter [29], or a promoter upstream of the parA-like gene [32]. Expression of the PinR-promoter occurs preferentially in cells having highest RpoS levels, and only 1-3% of cells in a population in stationary phase visibly express reporter gene from PinR [29]. InrR transmits bistable activation through an unknown process to the intB13 promoter [26], and possibly simultaneously to other promoters for the genes for the conjugative system in the ICEclc core region [32]. The exact mechanism of arisal of bistability is unclear as yet. For gene locations on ICEclc, see Figure 1A.

              \n

              doi:10.1371/journal.pgen.1004441.g008

              ", + "\n Download:\n " + ] + }, + "tables_html": { + "value": [ + "
              \"thumbnail\"
              Figure 1. Schematic overview of ICEclc and the location of the genes relevant to this study.

              (A) ICEclc integrated form with the two flanking 18-bp repeats (as black rectangles, attR and attL). Previously determined gene regions are placed at their approximate location. Important functional regions are depicted as grey boxes accompanied by legends. + or -, indicate the orientation of the coding strand for the respective gene(s) (the + strand being the one of intB13). clc genes, chlorocatechol degradation; amn genes, 2-aminophenol degradation. kb, kilo-basepairs. (B) Detail of the mfsR operon. Arrows, predicted open reading frames (the right-to-left orientation indicates the minus strand). Triangles, positions of the Tn5-mediated kanamycin gene insertions (nucleotide positions indicated below, according to the AJ617740.2 numbering). Regions deleted in this study are displayed as white bars with the names of the mutations noted below. The hooked arrow indicates repression by the mfsR gene product on the PmfsR promoter. (C) Detail of the fragments inserted by mini-Tn7 delivery for complementation of mfsR and tciR deletions. (D) BlastP-predicted domains for each of the three regulatory genes in the mfsR operon. C and N, carboxy and amino terminus, respectively.

              \n

              doi:10.1371/journal.pgen.1004441.g001

              ", + "\n Download:\n ", + "
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              Figure 2. ICEclc transfer frequencies from P. putida UWC1 donors with different ICEclc genotypes.

              (A) and (B), Independently carried out transfer experiments using the indicated strain sets. Bars show mean transfer frequencies as transconjugant colony forming units (CFU/ml, growing on 3CBA, Km- or Gm-resistant) per donor CFU/ml from biological triplicates, and the corresponding standard deviations. Letters above bars indicate statistically significantly different groups per panel in an Anova with post hoc Tukey-Kramer test (P<0.001), with the same letter pointing to the absence of statistically significant differences.

              \n

              doi:10.1371/journal.pgen.1004441.g002

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              Table 1. Strains used in this study and their specifications.

              doi:10.1371/journal.pgen.1004441.t001

              ", + "\n Download:\n ", + "
              \"thumbnail\"
              Figure 3. Differential expression of the ICEclc gene region from micro-array data in selected mutant ICEclc versus wild type in P. putida UWC1.

              (A) Differential expression of the ICEclc region between stationary and exponential phase cells of wild type P. putida UWC1 (ICEclc). (B) Differential expression of the ICEclc region between the mfsR deletion mutant and wild-type, in exponentially growing cells. (C) Comparison of the tciR deletion mutant and wild-type, in stationary phase cells. (D) Comparison of the mfsR transposon insertion mutant versus wild-type, in stationary phase cells. Dots indicate the 2log-fold change of hybridization signal per microarray probe in the comparison, plotted at their distance along the ICEclc sequence (X-axis; in kb). Regions of interest on ICEclc are redrawn as grey boxes at the bottom of each section (+ or - indicate the DNA strand on which the region is encoded). Separate displays indicate expression differences on the plus- (open symbols) or the minus-strand (closed symbols). Grey bars in the background indicate the two-fold cut-off level. For a complete set of microarray results, see Figures S3 and S4.

              \n

              doi:10.1371/journal.pgen.1004441.g003

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              Figure 4. Detailed view on the differential expression of the mfsR operon in P. putida ICEclc wild-type or mutants.

              (A) MarR deletion mutant versus wild-type. (B) mfsR deletion mutant versus wild type. (C) tciR deletion mutant versus wild-type. (D) mfsR-'marR deletion mutant versus wild-type. (E) marR versus tciR deletions. (F) mfsR-transposon insertion mutant versus wild-type. Panels show 2log-fold change of expression level per microarray probe in this region of ICEclc for exponential (dark dots) and stationary phase cells (white dots). Genetic map of the region drawn at the bottom of each section for clarity. Arrows represent genes, deleted regions are indicated by stippled bars and corresponding probes are within brackets.

              \n

              doi:10.1371/journal.pgen.1004441.g004

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              Figure 5. Effect of mutations in the mfsR region on the expression of the PmfsR-, Pint- and PinR-promoters of ICEclc in P. putida UWC1.

              (A) mCherry expression from the mfsR promoter added in single copy to the chromosome of the indicated P. putida UWC1 strains (relevant genotypes and strain numbers specified below the graph). mCherry expression measured on individual cells (n = 1000) by epifluorescence microscopy in late exponential phase of cultures grown on 10 mM succinate and expressed as box plots (AU, arbitrary units at 20 ms exposure time). (B) Scatter plot of GFP and mcherry fluorescence in single cells of P. putida UWC1 (ICEclc) wild-type, ΔmfsR, ΔtciR or ΔmarR deletions, equipped with a single copy mini-transposon containing the Pint-egfp and PinR-mcherry fusions. Panels show expression of both markers at different growth phases, as indicated, with colors representing genotypes with independent mini-Tn5 insertions. Note as example the subpopulation of wild-type cells (dotted ellips) expressing both reporters, compared to the majority of cells in the mfsR deletion mutant but a complete absence of such subpopulation in the tciR and marR deletion mutants.

              \n

              doi:10.1371/journal.pgen.1004441.g005

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              Figure 6. Fitness loss of P. putida UWC1 (ICEclc) caused by the mfsR deletion.

              (A) Survival of P. putida UWC1 (ICEclc, 2737) and P. putida UWC1 (ICEclcmfsR, 4322) pregrown in suspended culture to stationary phase on 3-chlorobenzoate (3CBA) or succinate (succ), and plated from there on 3CBA or succinate agar. (E.g., 3CBA-3CBA, suspended culture on 3CBA, plated on 3CBA agar). Survival expressed as colony forming units (CFU) on the agar plate per ml of stationary phase culture. Data bars indicate the average from independent biological triplicates. Error bars indicate the calculated standard deviation from the average. (B) Phase-contrast micrographs at 1000-fold magnification of microcolonies of P. putida UWC1 (ICEclc) and P. putida (ICEclcmfsR Pint-egfp, 4612) growing on agarose surface supplemented with 0.1 mM 3CBA. Shown are a regular stationary phase microcolony of P. putida with wild-type ICEclc and a transfer competent microcolony (tcm), occurring at 1-3% frequency as reported previously [30]. For comparison, massive lysis (white arrows) and cellular malformations formed in many microcolonies of P. putida UWC1 with the mfsR deletion.

              \n

              doi:10.1371/journal.pgen.1004441.g006

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              Table 2. Effects of the mfsR deletion on the growth characteristics of P. putida UWC1 carrying ICEclc.

              doi:10.1371/journal.pgen.1004441.t002

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              Figure 7. Conservation of tciR analogues in putative ICEclc-like regions in a variety of other bacterial genomes.

              Illustration represents tciR analogues (identified on the basis of a BLASTN E-value lower than 1·10-15), and surrounding relevant gene regions in the indicated bacterial genomes (species name, accession numbers) compared to ICEclc. Genes are indicated as in the respective genome accession. Rectangles show annotated genes and their orientation (top, orientation towards the left; bottom, gene orientation towards to right); common colors indicate similar predicted functions. Stippled rectangles indicate common gene regions inferred from Artemis comparison, but not present in the respective annotation. ICE were inferred from (i) more than 75% nucleotide identities across the complete core region of ICEclc, and within a 1-100 kb window from the tciR position, and (ii) the presence of an integrase gene (in brown) within a 5-20 kb window from the tciR-analogue. Note how some genomes carry multiple different ICE from the same family (e.g., Achromobacter xylosoxidans, Acidovorax sp. strain JS42), and further how pair-wise identical ICE regions (shaded in grey) occur between different genomes. Finally note how the tciR-analogues often co-occur with a xer-type regulatory gene on the other strand (light green), and a further lysR gene member (yellow), but in none of the cases shown here with an mfsR counterpart (in red).

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              doi:10.1371/journal.pgen.1004441.g007

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              Figure 8. Model for regulation of ICEclc transfer competence.

              MfsR autoregulates expression of itself and of the TciR activator, without which ICEclc transfer decreases by 2·103-fold. TciR may activate specifically one or more promoters on ICEclc, such as the RpoS-dependent PinR-promoter [29], or a promoter upstream of the parA-like gene [32]. Expression of the PinR-promoter occurs preferentially in cells having highest RpoS levels, and only 1-3% of cells in a population in stationary phase visibly express reporter gene from PinR [29]. InrR transmits bistable activation through an unknown process to the intB13 promoter [26], and possibly simultaneously to other promoters for the genes for the conjugative system in the ICEclc core region [32]. The exact mechanism of arisal of bistability is unclear as yet. For gene locations on ICEclc, see Figure 1A.

              \n

              doi:10.1371/journal.pgen.1004441.g008

              ", + "\n Download:\n " + ] + }, + "fulltext_html": { + "value": [ + "http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004441" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004441&representation=PDF" + ] + }, + "fulltext_xml": { + "value": [ + "http://www.plosgenetics.org/article/article/asset?id=10.1371/journal.pgen.1004441.XML" + ] + }, + "supplementary_file": { + "value": [ + + ] + }, + "figures_image": { + "value": [ + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004441.g001", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004441.g002", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004441.t001", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004441.g003", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004441.g004", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004441.g005", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004441.g006", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004441.t002", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004441.g007", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004441.g008" + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { "value": [ - "AbstractThe integrative and conjugative element ICEclc is a mobile genetic element in Pseudomonas knackmussii B13, and an experimental model for a widely distributed group of elements in Proteobacteria. ICEclc is transferred from specialized transfer competent cells, which arise at a frequency of 3-5% in a population at stationary phase. Very little is known about the different factors that control the transfer frequency of this ICE family. Here we report the discovery of a three-gene operon encoded by ICEclc, which exerts global control on transfer initiation. The operon consists of three consecutive regulatory genes, encoding a TetR-type repressor MfsR, a MarR-type regulator and a LysR-type activator TciR. We show that MfsR autoregulates expression of the operon, whereas TciR is a global activator of ICEclc gene expression, but no clear role was yet found for MarR. Deletion of mfsR increases expression of tciR and marR, causing the proportion of transfer competent cells to reach almost 100% and transfer frequencies to approach 1 per donor. mfsR deletion also caused a two orders of magnitude loss in population viability, individual cell growth arrest and loss of ICEclc. This indicates that autoregulation is an important feature maintaining ICE transfer but avoiding fitness loss. Bioinformatic analysis showed that the mfsR-marR-tciR operon is unique for ICEclc and a few highly related ICE, whereas tciR orthologues occur more widely in a large variety of suspected ICE among Proteobacteria.\n", - "\nAuthor Summary\nIntegrative and conjugative elements (ICEs) are a relatively newly recognized class of mobile elements in bacteria, which integrate at one or more positions in a host chromosome, can be excised, circularized, and transfer by conjugation to a new recipient cell. Genome sequencing indicated that ICEs often carry genes with potential adaptive functions for the host. Various ICE-types have been described and ICEclc is a useful model for a wide class of elements found in Beta- and Gammaproteobacteria. Because ICEs normally remain “silent” in the host chromosome and often lack selectable markers, their lifestyle is difficult to study. One of the characteristics of ICEclc is that transfer is initiated in only 3-5% of donor cells in a population during stationary phase. Here, we describe an operon of three regulatory genes, two of which control the transfer initiation of ICEclc. Our findings suggest that the low transfer rate results from the repression of an activator and that this is essential to minimize the deleterious effect of hyper-activation of transfer initiation. While the individual regulatory genes are quite common on ICEs, they rarely occur in this configuration.\n" + ] }, - "file_hashes": [ + "file_sizes": [ + { + "fulltext.html": 219745 + }, { - "fulltext.pdf": "037d0a292bcca909943daf27a1e51f77" + "fulltext.pdf": 1423552 }, { - "fulltext.xml": "09305c9e8d09f37ba7107df1fd0c7cd0" + "fulltext.xml": 11133 } ] }, "http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004433": { - "fulltext_pdf": { + "publisher": { "value": [ - "http://dx.plos.org/10.1371/journal.pgen.1004433.pdf" + ] }, - "fulltext_html": { + "journal_name": { "value": [ - + "PLOS Genetics" ] }, - "fulltext_xml": { + "journal_issn": { "value": [ - "/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pgen.1004433&representation=XML" + "1553-7404" ] }, "title": { "value": [ - "A Novel Peptidoglycan Binding Protein Crucial for PBP1A-Mediated Cell Wall Biogenesis in Vibrio cholerae" + "A Novel Peptidoglycan Binding Protein Crucial for PBP1A-Mediated Cell Wall Biogenesis in Vibrio cholerae " ] }, - "author": { + "keywords": { + "value": [ + + ] + }, + "author_name": { "value": [ "Tobias Dörr", "Hubert Lam", @@ -264,9 +890,35 @@ "Matthew K. Waldor" ] }, - "date": { + "author_institution": { + "value": [ + + ] + }, + "editor_name": { + "value": [ + + ] + }, + "date_published": { + "value": [ + [ + " June 19, 2014" + ] + ] + }, + "date_accepted": { "value": [ - "2014/6/19" + [ + "April 25, 2014" + ] + ] + }, + "date_submitted": { + "value": [ + [ + "March 13, 2014" + ] ] }, "doi": { @@ -289,40 +941,195 @@ "e1004433" ] }, - "description": { + "abstract": { "value": [ - "PLOS Genetics is an open-access" + ] }, - "abstract": { + "abstract_html": { + "value": [ + "

              Abstract

              The bacterial cell wall, which is comprised of a mesh of polysaccharide strands crosslinked via peptide bridges (peptidoglycan, PG), is critical for maintenance of cell shape and survival. PG assembly is mediated by a variety of Penicillin Binding Proteins (PBP) whose fundamental activities have been characterized in great detail; however, there is limited knowledge of the factors that modulate their activities in different environments or growth phases. In Vibrio cholerae, the cause of cholera, PG synthesis during the transition into stationary phase is primarily mediated by the bifunctional enzyme PBP1A. Here, we screened an ordered V. cholerae transposon library for mutants that are sensitive to growth inhibition by non-canonical D-amino acids (DAA), which prevent growth and maintenance of cell shape in PBP1A-deficient V. cholerae. In addition to PBP1A and its lipoprotein activator LpoA, we found that CsiV, a small periplasmic protein with no previously described function, is essential for growth in the presence of DAA. Deletion of csiV, like deletion of lpoA or the PBP1A–encoding gene mrcA, causes cells to lose their rod shape in the presence of DAA or the beta-lactam antibiotic cefsulodin, and all three mutations are synthetically lethal with deletion of mrcB, which encodes PBP1B, V. cholerae's second key bifunctional PBP. CsiV interacts with LpoA and PG but apparently not with PBP1A, supporting the hypothesis that CsiV promotes LpoA's role as an activator of PBP1A, and thereby modulates V. cholerae PG biogenesis. Finally, the requirement for CsiV in PBP1A-mediated growth of V. cholerae can be overcome either by augmenting PG synthesis or by reducing PG degradation, thereby highlighting the importance of balancing these two processes for bacterial survival.

              \n", + "\n

              Author Summary

              \n

              Bacteria surround themselves with a mesh-like peptidoglycan (PG) cell wall, which is essential for maintenance of cell shape and survival. While the enzymes that catalyze the assembly of the cell wall (aka penicillin-binding proteins (PBPs)) have been extensively characterized, our understanding of the factors that modulate the activities of these enzymes is less developed. Here, using a genetic screen, we identified a gene of unknown function that plays a crucial role in PBP1A-mediated cell wall synthesis in Vibrio cholerae, the bacterium causing cholera. V. cholerae mutants lacking this gene, whose protein product was re-named CsiV (for Cell shape integrity Vibrio), share many phenotypes with PBP1A mutants, including becoming spherical during stationary phase. We show that CsiV interacts with LpoA, a lipoprotein activator of PBP1A, as well as with PG. CsiV, LpoA, or PBP1A are all required for survival of V. cholerae lacking PBP1B, and mutants lacking any of these factors show marked changes in PG content in stationary phase. Collectively, our data suggest that CsiV acts through LpoA to promote PG biogenesis in V. cholerae and other vibrio species as well as in the other genera where this protein is found.

              \n" + ] + }, + "abstract_text": { + "value": [ + + ] + }, + "introduction_html": { + "value": [ + + ] + }, + "methods_html": { + "value": [ + + ] + }, + "results_html": { + "value": [ + + ] + }, + "discussion_html": { + "value": [ + + ] + }, + "author_contrib_html": { + "value": [ + "Conceived and designed the experiments: TD HL FC BMD MKW. Performed the experiments: TD HL LA. Analyzed the data: TD FC BMD MKW. Contributed reagents/materials/analysis tools: TD HL FC. Contributed to the writing of the manuscript: TD BMD MKW." + ] + }, + "references_html": { + "value": [ + "1.\n Vollmer W, Bertsche U (2008) Murein (peptidoglycan) structure, architecture and biosynthesis in Escherichia coli. Biochim Biophys Acta 1778: 1714–1734.\n doi:\n 10.1016/j.bbamem.2007.06.007 ", + "2.\n Glauner B, Holtje JV, Schwarz U (1988) The composition of the murein of Escherichia coli. J Biol Chem 263: 10088–10095. ", + "3.\n Gan L, Chen S, Jensen GJ (2008) Molecular organization of Gram-negative peptidoglycan. Proc Natl Acad Sci U S A 105: 18953–18957.\n doi:\n 10.1073/pnas.0808035105 ", + "4.\n Young KD (2010) Bacterial shape: two-dimensional questions and possibilities. Annu Rev Microbiol 64: 223–240.\n doi:\n 10.1146/annurev.micro.112408.134102 ", + "5.\n Sycuro LK, Pincus Z, Gutierrez KD, Biboy J, Stern CA, et al. (2010) Peptidoglycan crosslinking relaxation promotes Helicobacter pylori's helical shape and stomach colonization. Cell 141: 822–833.\n doi:\n 10.1016/j.cell.2010.03.046 ", + "6.\n Lawler ML, Brun YV (2007) Advantages and mechanisms of polarity and cell shape determination in Caulobacter crescentus. Curr Opin Microbiol 10: 630–637.\n doi:\n 10.1016/j.mib.2007.09.007 ", + "7.\n Schneider T, Sahl HG (2010) An oldie but a goodie - cell wall biosynthesis as antibiotic target pathway. Int J Med Microbiol 300: 161–169.\n doi:\n 10.1016/j.ijmm.2009.10.005 ", + "8.\n Typas A, Banzhaf M, Gross CA, Vollmer W (2011) From the regulation of peptidoglycan synthesis to bacterial growth and morphology. Nat Rev Microbiol 10: 123–136.\n doi:\n 10.1038/nrmicro2677 ", + "9.\n Sauvage E, Kerff F, Terrak M, Ayala JA, Charlier P (2008) The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis. FEMS Microbiol Rev 32: 234–258.\n doi:\n 10.1111/j.1574-6976.2008.00105.x ", + "10.\n Kato J, Suzuki H, Hirota Y (1985) Dispensability of either penicillin-binding protein-1a or -1b involved in the essential process for cell elongation in Escherichia coli. Mol Gen Genet 200: 272–277.\n doi:\n 10.1007/bf00425435 ", + "11.\n Yousif SY, Broome-Smith JK, Spratt BG (1985) Lysis of Escherichia coli by beta-lactam antibiotics: deletion analysis of the role of penicillin-binding proteins 1A and 1B. J Gen Microbiol 131: 2839–2845.\n doi:\n 10.1099/00221287-131-10-2839 ", + "12.\n Typas A, Banzhaf M, van den Berg van Saparoea B, Verheul J, Biboy J, et al. (2011) Regulation of peptidoglycan synthesis by outer-membrane proteins. Cell 143: 1097–1109.\n doi:\n 10.1016/j.cell.2010.11.038 ", + "13.\n Paradis-Bleau C, Markovski M, Uehara T, Lupoli TJ, Walker S, et al. (2011) Lipoprotein cofactors located in the outer membrane activate bacterial cell wall polymerases. Cell 143: 1110–1120.\n doi:\n 10.1016/j.cell.2010.11.037 ", + "14.\n Lupoli TJ, Lebar MD, Markovski M, Bernhardt T, Kahne D, et al. (2013) Lipoprotein activators stimulate Escherichia coli penicillin-binding proteins by different mechanisms. J Am Chem Soc 136: 52–55.\n doi:\n 10.1021/ja410813j ", + "15.\n Holtje JV (1998) Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli. Microbiol Mol Biol Rev 62: 181–203. ", + "16.\n Dörr T, Cava F, Lam H, Davis BM, Waldor MK (2013) Substrate specificity of an elongation-specific peptidoglycan endopeptidase and its implications for cell wall architecture and growth of Vibrio cholerae. Mol Microbiol 89: 949–962.\n doi:\n 10.1111/mmi.12323 ", + "17.\n Singh SK, SaiSree L, Amrutha RN, Reddy M (2012) Three redundant murein endopeptidases catalyse an essential cleavage step in peptidoglycan synthesis of Escherichia coli K12. Mol Microbiol 86: 1036–1051.\n doi:\n 10.1111/mmi.12058 ", + "18.\n Dörr T, Möll A, Chao MC, Lam H, Cava F, et al. (2014) Differential Requirement for PBP1A and PBP1B in In Vivo and In Vitro Fitness of Vibrio cholerae. Infect Immun 82: 2115–2124.\n doi:\n 10.1128/iai.00012-14 ", + "19.\n Lam H, Oh DC, Cava F, Takacs CN, Clardy J, et al. (2009) D-amino acids govern stationary phase cell wall remodeling in bacteria. Science 325: 1552–1555.\n doi:\n 10.1126/science.1178123 ", + "20.\n Cava F, de Pedro MA, Lam H, Davis BM, Waldor MK (2010) Distinct pathways for modification of the bacterial cell wall by non-canonical D-amino acids. EMBO J 30: 3442–3453.\n doi:\n 10.1038/emboj.2011.246 ", + "21.\n Kuru E, Hughes HV, Brown PJ, Hall E, Tekkam S, et al. (2012) In Situ probing of newly synthesized peptidoglycan in live bacteria with fluorescent D-amino acids. Angew Chem Int Ed Engl 51: 12519–12523.\n doi:\n 10.1002/anie.201206749 ", + "22.\n Ursinus A, van den Ent F, Brechtel S, de Pedro M, Holtje JV, et al. (2004) Murein (peptidoglycan) binding property of the essential cell division protein FtsN from Escherichia coli. J Bacteriol 186: 6728–6737.\n doi:\n 10.1128/jb.186.20.6728-6737.2004 ", + "23.\n Lee TK, Tropini C, Hsin J, Desmarais SM, Ursell TS, et al. (2014) A dynamically assembled cell wall synthesis machinery buffers cell growth. Proc Natl Acad Sci U S A 111: 4355–4356.\n doi:\n 10.1073/pnas.1313826111 ", + "24.\n Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, et al. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6: 343–345.\n doi:\n 10.1038/nmeth.1318 ", + "25.\n Donnenberg MS, Kaper JB (1991) Construction of an eae deletion mutant of enteropathogenic Escherichia coli by using a positive-selection suicide vector. Infect Immun 59: 4310–4317. ", + "26.\n Butterton JR, Beattie DT, Gardel CL, Carroll PA, Hyman T, et al. (1995) Heterologous antigen expression in Vibrio cholerae vector strains. Infect Immun 63: 2689–2696. ", + "27.\n Cameron DE, Urbach JM, Mekalanos JJ (2008) A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae. Proc Natl Acad Sci U S A 105: 8736–8741.\n doi:\n 10.1073/pnas.0803281105 ", + "28.\n Desmarais SM, De Pedro MA, Cava F, Huang KC (2013) Peptidoglycan at its peaks: how chromatographic analyses can reveal bacterial cell wall structure and assembly. Mol Microbiol 89: 1–13.\n doi:\n 10.1111/mmi.12266 ", + "29.\n Work E (1957) Reaction of ninhydrin in acid solution with straight-chain amino acids containing two amino groups and its application to the estimation of alpha epsilon-diaminopimelic acid. Biochem J 67: 416–423. ", + "30.\n Karimova G, Pidoux J, Ullmann A, Ladant D (1998) A bacterial two-hybrid system based on a reconstituted signal transduction pathway. Proc Natl Acad Sci U S A 95: 5752–5756.\n doi:\n 10.1073/pnas.95.10.5752 ", + "31.\n Moll A, Schlimpert S, Briegel A, Jensen GJ, Thanbichler M (2010) DipM, a new factor required for peptidoglycan remodelling during cell division in Caulobacter crescentus. Mol Microbiol 77: 90–107.\n doi:\n 10.1111/j.1365-2958.2010.07224.x " + ] + }, + "figures_html": { + "value": [ + "
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              Figure 1. Identification and complementation of PBP1A pathway mutants using a chemical genetic screen.

              (A) For the screen, an ordered V. cholerae transposon library was pintooled onto LB agar +/−5 mM D-Met and scored for growth deficiency in the presence of D-Met. (B) Growth of V. cholerae PBP1A pathway mutants containing either an empty vector (pHL) or a plasmid enabling inducible expression of the deleted gene (pHLorf) on plates containing inducer and 5 mM D-Met confirms that their growth deficiencies on D-Met are due to deletion of the indicated genes.

              \n

              doi:10.1371/journal.pgen.1004433.g001

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              Figure 2. CsiV is a periplasmic protein of unknown function.

              (A) Domain architecture of CsiV (VC1887). The signal sequence is predicted to be cleaved off between A30 and R31. DUF2803 is not associated with any function. (B) Fluorescence microscopy analysis of V. cholerae producing plasmid-encoded CsiV-mCherry, a functional fusion protein that localizes to the cell periphery. Scale bar = 5 µm.

              \n

              doi:10.1371/journal.pgen.1004433.g002

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              Figure 3. A csiV mutant phenocopies the growth deficiencies of mrcA and lpoA mutants.

              The minimum inhibitory concentration (MIC) of (A) deoxycholate, (B) cefsulodin and (C) DAA are shown for wt V. cholerae and PBP1A pathway mutants. MIC data reflect values obtained with two biological replicates done in technical quadruplicates for each strain. Absence of error reflects that the same values were obtained for all experiments (D) Morphological changes induced by DAA. The indicated V. cholerae strains were grown in the absence of DAA until OD600~0.3 and then applied to 0.8% agarose pads containing 4 mM D-Met. Scale bar = 5 µm.

              \n

              doi:10.1371/journal.pgen.1004433.g003

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              Figure 4. Muropeptide analysis of the csiV, mrcA and lpoA mutants.

              Cell wall content was estimated by colorimetric quantification of DAP in PG extracted from (A) exponential phase or (B) stationary phase cultures. (C–F) UPLC analysis of the degree of crosslinking (C,D) and average chain length (E, F) in cell wall extracted from exponential phase (C,E) and stationary phase (D,F) cultures. Data are averages of two (exponential phase) or three (stationary phase) biological replicates, error bars indicate standard deviation. ** = p<0.01 (t-test). S481T is a PBP1A transpeptidase mutant expressed from its native chromosomal locus, where the S residue at position 481 (in the active site) is replaced by a T.

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              doi:10.1371/journal.pgen.1004433.g004

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              Figure 5. Deletion of csiV is synthetically lethal with deletion of mrcB but not lpoB.

              (A) Growth curves, based on OD600, for the indicated V. cholerae strains grown in LB. Data represent averages of technical triplicates and are representative of two experiments with similar results. (B) Cells in which PBP1B's native promoter was replaced by an arabinose-inducible promoter (PARA) were initially grown in the presence of arabinose (Ara+), then grown for 1 h in fresh medium without arabinose (Ara).

              \n

              doi:10.1371/journal.pgen.1004433.g005

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              Figure 6. V. cholerae PBP1A is partially functional in the absence of CsiV.

              (A) Morphological changes of V. cholerae strains grown in the presence of the PBP1B inhibitor cefsulodin. Frames are 5 min apart. (B) Growth (OD600) of ΔcsiV, ΔmrcA and ΔlpoA strains ectopically expressing mrcA or mrcB and cultured in the presence of cefsulodin. Data are averages of three experiments, error bars represent standard deviation.

              \n

              doi:10.1371/journal.pgen.1004433.g006

              ", + "\n Download:\n ", + "
              \"thumbnail\"
              Figure 7. The absence of the endopeptidase ShyA enables PBP1B-independent growth of CsiV-deficient V. cholerae.

              (A) Growth curves, based on OD600, for cultures containing the PBP1B inhibitor cefsulodin. Data are averages of technical quadruplicates and representative of 4 experiments with similar results, error bars represent standard deviation (B) Single-cell dynamics of ΔcsiV and the ΔcsiV ΔshyA double mutant in the presence of cefsulodin. Cells were grown to OD600~0.3 and then applied to agarose pads containing 100 µg/ml cefsulodin. Arrowheads point to blebs (C) ΔcsiV ΔshyA or ΔlpoA ΔshyA cells in which PBP1B's native promoter was replaced with an arabinose-inducible promoter (PARA) were treated as described in Fig. 5B.

              \n

              doi:10.1371/journal.pgen.1004433.g007

              ", + "\n Download:\n ", + "
              \"thumbnail\"
              Figure 8. CsiV interacts with LpoA.

              (A) Lysates from a csiV::csiV-his lpoA::lpoA-mCherry strain and a ΔlpoA::lpoA-mCherry strain were affinity purified on NiNTA resin, then Western blotted with anti His and anti-mCherry antibodies to show copurification of CsiV and LpoA. (B) Purified MalE-His (10 µM) and either LpoA-His77-653 (2.5 µM) or PBP1A-His (2.5 µM) were mixed with CsiV-His31-266 covalently attached to NHS-activated sepharose. Protein associations were assessed via western blotting (anti-His) of Input (IN), flowthrough (F), third wash (W3), and eluate from boiled beads (E). (C) Bacterial two-hybrid analysis of CsiV-LpoA and CsiV-PBP1A interactions. All constructs are truncated downstream of their signal sequences to allow for cytoplasmic BACTH.

              \n

              doi:10.1371/journal.pgen.1004433.g008

              ", + "\n Download:\n ", + "
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              Figure 9. CsiV interacts with peptidoglycan.

              Purified proteins were incubated with SDS-extracted PG, then ultracentrifuged to pellet PG and associated proteins. Proteins were visualized by anti-His Western blot. For the lysozyme control, 1 mg/ml lysozyme was added simultaneously with the addition of CsiV-His.

              \n

              doi:10.1371/journal.pgen.1004433.g009

              ", + "\n Download:\n " + ] + }, + "tables_html": { + "value": [ + "
              \"thumbnail\"
              Figure 1. Identification and complementation of PBP1A pathway mutants using a chemical genetic screen.

              (A) For the screen, an ordered V. cholerae transposon library was pintooled onto LB agar +/−5 mM D-Met and scored for growth deficiency in the presence of D-Met. (B) Growth of V. cholerae PBP1A pathway mutants containing either an empty vector (pHL) or a plasmid enabling inducible expression of the deleted gene (pHLorf) on plates containing inducer and 5 mM D-Met confirms that their growth deficiencies on D-Met are due to deletion of the indicated genes.

              \n

              doi:10.1371/journal.pgen.1004433.g001

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              Figure 2. CsiV is a periplasmic protein of unknown function.

              (A) Domain architecture of CsiV (VC1887). The signal sequence is predicted to be cleaved off between A30 and R31. DUF2803 is not associated with any function. (B) Fluorescence microscopy analysis of V. cholerae producing plasmid-encoded CsiV-mCherry, a functional fusion protein that localizes to the cell periphery. Scale bar = 5 µm.

              \n

              doi:10.1371/journal.pgen.1004433.g002

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              Figure 3. A csiV mutant phenocopies the growth deficiencies of mrcA and lpoA mutants.

              The minimum inhibitory concentration (MIC) of (A) deoxycholate, (B) cefsulodin and (C) DAA are shown for wt V. cholerae and PBP1A pathway mutants. MIC data reflect values obtained with two biological replicates done in technical quadruplicates for each strain. Absence of error reflects that the same values were obtained for all experiments (D) Morphological changes induced by DAA. The indicated V. cholerae strains were grown in the absence of DAA until OD600~0.3 and then applied to 0.8% agarose pads containing 4 mM D-Met. Scale bar = 5 µm.

              \n

              doi:10.1371/journal.pgen.1004433.g003

              ", + "\n Download:\n ", + "
              \"thumbnail\"
              Figure 4. Muropeptide analysis of the csiV, mrcA and lpoA mutants.

              Cell wall content was estimated by colorimetric quantification of DAP in PG extracted from (A) exponential phase or (B) stationary phase cultures. (C–F) UPLC analysis of the degree of crosslinking (C,D) and average chain length (E, F) in cell wall extracted from exponential phase (C,E) and stationary phase (D,F) cultures. Data are averages of two (exponential phase) or three (stationary phase) biological replicates, error bars indicate standard deviation. ** = p<0.01 (t-test). S481T is a PBP1A transpeptidase mutant expressed from its native chromosomal locus, where the S residue at position 481 (in the active site) is replaced by a T.

              \n

              doi:10.1371/journal.pgen.1004433.g004

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              \"thumbnail\"
              Figure 5. Deletion of csiV is synthetically lethal with deletion of mrcB but not lpoB.

              (A) Growth curves, based on OD600, for the indicated V. cholerae strains grown in LB. Data represent averages of technical triplicates and are representative of two experiments with similar results. (B) Cells in which PBP1B's native promoter was replaced by an arabinose-inducible promoter (PARA) were initially grown in the presence of arabinose (Ara+), then grown for 1 h in fresh medium without arabinose (Ara).

              \n

              doi:10.1371/journal.pgen.1004433.g005

              ", + "\n Download:\n ", + "
              \"thumbnail\"
              Figure 6. V. cholerae PBP1A is partially functional in the absence of CsiV.

              (A) Morphological changes of V. cholerae strains grown in the presence of the PBP1B inhibitor cefsulodin. Frames are 5 min apart. (B) Growth (OD600) of ΔcsiV, ΔmrcA and ΔlpoA strains ectopically expressing mrcA or mrcB and cultured in the presence of cefsulodin. Data are averages of three experiments, error bars represent standard deviation.

              \n

              doi:10.1371/journal.pgen.1004433.g006

              ", + "\n Download:\n ", + "
              \"thumbnail\"
              Figure 7. The absence of the endopeptidase ShyA enables PBP1B-independent growth of CsiV-deficient V. cholerae.

              (A) Growth curves, based on OD600, for cultures containing the PBP1B inhibitor cefsulodin. Data are averages of technical quadruplicates and representative of 4 experiments with similar results, error bars represent standard deviation (B) Single-cell dynamics of ΔcsiV and the ΔcsiV ΔshyA double mutant in the presence of cefsulodin. Cells were grown to OD600~0.3 and then applied to agarose pads containing 100 µg/ml cefsulodin. Arrowheads point to blebs (C) ΔcsiV ΔshyA or ΔlpoA ΔshyA cells in which PBP1B's native promoter was replaced with an arabinose-inducible promoter (PARA) were treated as described in Fig. 5B.

              \n

              doi:10.1371/journal.pgen.1004433.g007

              ", + "\n Download:\n ", + "
              \"thumbnail\"
              Figure 8. CsiV interacts with LpoA.

              (A) Lysates from a csiV::csiV-his lpoA::lpoA-mCherry strain and a ΔlpoA::lpoA-mCherry strain were affinity purified on NiNTA resin, then Western blotted with anti His and anti-mCherry antibodies to show copurification of CsiV and LpoA. (B) Purified MalE-His (10 µM) and either LpoA-His77-653 (2.5 µM) or PBP1A-His (2.5 µM) were mixed with CsiV-His31-266 covalently attached to NHS-activated sepharose. Protein associations were assessed via western blotting (anti-His) of Input (IN), flowthrough (F), third wash (W3), and eluate from boiled beads (E). (C) Bacterial two-hybrid analysis of CsiV-LpoA and CsiV-PBP1A interactions. All constructs are truncated downstream of their signal sequences to allow for cytoplasmic BACTH.

              \n

              doi:10.1371/journal.pgen.1004433.g008

              ", + "\n Download:\n ", + "
              \"thumbnail\"
              Figure 9. CsiV interacts with peptidoglycan.

              Purified proteins were incubated with SDS-extracted PG, then ultracentrifuged to pellet PG and associated proteins. Proteins were visualized by anti-His Western blot. For the lysozyme control, 1 mg/ml lysozyme was added simultaneously with the addition of CsiV-His.

              \n

              doi:10.1371/journal.pgen.1004433.g009

              ", + "\n Download:\n " + ] + }, + "fulltext_html": { + "value": [ + "http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004433" + ] + }, + "fulltext_pdf": { "value": [ - "AbstractThe bacterial cell wall, which is comprised of a mesh of polysaccharide strands crosslinked via peptide bridges (peptidoglycan, PG), is critical for maintenance of cell shape and survival. PG assembly is mediated by a variety of Penicillin Binding Proteins (PBP) whose fundamental activities have been characterized in great detail; however, there is limited knowledge of the factors that modulate their activities in different environments or growth phases. In Vibrio cholerae, the cause of cholera, PG synthesis during the transition into stationary phase is primarily mediated by the bifunctional enzyme PBP1A. Here, we screened an ordered V. cholerae transposon library for mutants that are sensitive to growth inhibition by non-canonical D-amino acids (DAA), which prevent growth and maintenance of cell shape in PBP1A-deficient V. cholerae. In addition to PBP1A and its lipoprotein activator LpoA, we found that CsiV, a small periplasmic protein with no previously described function, is essential for growth in the presence of DAA. Deletion of csiV, like deletion of lpoA or the PBP1A–encoding gene mrcA, causes cells to lose their rod shape in the presence of DAA or the beta-lactam antibiotic cefsulodin, and all three mutations are synthetically lethal with deletion of mrcB, which encodes PBP1B, V. cholerae's second key bifunctional PBP. CsiV interacts with LpoA and PG but apparently not with PBP1A, supporting the hypothesis that CsiV promotes LpoA's role as an activator of PBP1A, and thereby modulates V. cholerae PG biogenesis. Finally, the requirement for CsiV in PBP1A-mediated growth of V. cholerae can be overcome either by augmenting PG synthesis or by reducing PG degradation, thereby highlighting the importance of balancing these two processes for bacterial survival.\n", - "\nAuthor Summary\nBacteria surround themselves with a mesh-like peptidoglycan (PG) cell wall, which is essential for maintenance of cell shape and survival. While the enzymes that catalyze the assembly of the cell wall (aka penicillin-binding proteins (PBPs)) have been extensively characterized, our understanding of the factors that modulate the activities of these enzymes is less developed. Here, using a genetic screen, we identified a gene of unknown function that plays a crucial role in PBP1A-mediated cell wall synthesis in Vibrio cholerae, the bacterium causing cholera. V. cholerae mutants lacking this gene, whose protein product was re-named CsiV (for Cell shape integrity Vibrio), share many phenotypes with PBP1A mutants, including becoming spherical during stationary phase. We show that CsiV interacts with LpoA, a lipoprotein activator of PBP1A, as well as with PG. CsiV, LpoA, or PBP1A are all required for survival of V. cholerae lacking PBP1B, and mutants lacking any of these factors show marked changes in PG content in stationary phase. Collectively, our data suggest that CsiV acts through LpoA to promote PG biogenesis in V. cholerae and other vibrio species as well as in the other genera where this protein is found.\n" + "http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1004433&representation=PDF" ] }, - "file_hashes": [ + "fulltext_xml": { + "value": [ + "http://www.plosgenetics.org/article/article/asset?id=10.1371/journal.pgen.1004433.XML" + ] + }, + "supplementary_file": { + "value": [ + + ] + }, + "figures_image": { + "value": [ + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004433.g001", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004433.g002", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004433.g003", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004433.g004", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004433.g005", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004433.g006", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004433.g007", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004433.g008", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pgen.1004433.g009" + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_sizes": [ { - "fulltext.pdf": "890d664254554ae5142d7a8e0d10633e" + "fulltext.html": 186398 }, { - "fulltext.xml": "078a5543dd025d13f966e683187b85fd" + "fulltext.pdf": 6212531 + }, + { + "fulltext.xml": 11134 } ] }, "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0098781": { - "fulltext_pdf": { + "publisher": { "value": [ - "http://dx.plos.org/10.1371/journal.pone.0098781.pdf" + ] }, - "fulltext_html": { + "journal_name": { "value": [ - + "PLOS ONE" ] }, - "fulltext_xml": { + "journal_issn": { "value": [ - "/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0098781&representation=XML" + "1932-6203" ] }, "title": { @@ -330,16 +1137,47 @@ "Foldscope: Origami-Based Paper Microscope" ] }, - "author": { + "keywords": { + "value": [ + + ] + }, + "author_name": { "value": [ "James S. Cybulski", "James Clements", "Manu Prakash" ] }, - "date": { + "author_institution": { + "value": [ + + ] + }, + "editor_name": { + "value": [ + + ] + }, + "date_published": { + "value": [ + [ + " June 18, 2014" + ] + ] + }, + "date_accepted": { + "value": [ + [ + "May 7, 2014" + ] + ] + }, + "date_submitted": { "value": [ - "2014/6/18" + [ + "January 25, 2014" + ] ] }, "doi": { @@ -362,47 +1200,198 @@ "e98781" ] }, - "description": { + "abstract": { "value": [ - "PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world." + ] }, - "abstract": { + "abstract_html": { + "value": [ + "

              Abstract

              Here we describe an ultra-low-cost origami-based approach for large-scale manufacturing of microscopes, specifically demonstrating brightfield, darkfield, and fluorescence microscopes. Merging principles of optical design with origami enables high-volume fabrication of microscopes from 2D media. Flexure mechanisms created via folding enable a flat compact design. Structural loops in folded paper provide kinematic constraints as a means for passive self-alignment. This light, rugged instrument can survive harsh field conditions while providing a diversity of imaging capabilities, thus serving wide-ranging applications for cost-effective, portable microscopes in science and education.

              \n" + ] + }, + "abstract_text": { + "value": [ + + ] + }, + "introduction_html": { + "value": [ + + ] + }, + "methods_html": { "value": [ - "AbstractHere we describe an ultra-low-cost origami-based approach for large-scale manufacturing of microscopes, specifically demonstrating brightfield, darkfield, and fluorescence microscopes. Merging principles of optical design with origami enables high-volume fabrication of microscopes from 2D media. Flexure mechanisms created via folding enable a flat compact design. Structural loops in folded paper provide kinematic constraints as a means for passive self-alignment. This light, rugged instrument can survive harsh field conditions while providing a diversity of imaging capabilities, thus serving wide-ranging applications for cost-effective, portable microscopes in science and education.\n" + + ] + }, + "results_html": { + "value": [ + + ] + }, + "discussion_html": { + "value": [ + + ] + }, + "author_contrib_html": { + "value": [ + "Conceived and designed the experiments: JSC MP. Performed the experiments: JSC JC MP. Analyzed the data: JSC JC MP. Wrote the paper: JSC MP." + ] + }, + "references_html": { + "value": [ + "1.\n Keller E, Goldman R (2006) Light Microscopy. Woodbury, NY: Cold Spring Harbor Laboratory Press. p. 8.
                ", + "2.\n Whitesides GM (2011) The Frugal Way. The Economist - The World in 2012 ", + "3.\n Rothemund PW (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440: 297–302.\n doi:\n 10.1038/nature04586 ", + "4.\n Hyde RA (1999) Eyeglass, a large-aperture space telescope. Appl Opt 38(19): 4198–4212.\n doi:\n 10.1364/ao.38.004198 ", + "5.\n Hoover AM, Fearing RS (2008) Fast scale prototyping for folded millirobots. IEEE International Conference on Robotics and Automation 5: 886–892.\n doi:\n 10.1109/robot.2008.4543317 ", + "6.\n Whitney JP, Sreetharan PS, Ma KY, Wood RJ (2011) Pop-up book MEMS. J Micromech Microeng 21(115021): 1–7.\n doi:\n 10.1088/0960-1317/21/11/115021 ", + "7.\n Sreetharan PS, Whitney JP, Strauss MD, Wood RJ (2012) Monolithic fabrication of millimeter-scale machines. J Micromech Microeng 22(055027): 1–6.\n doi:\n 10.1088/0960-1317/22/5/055027 ", + "8.\n Porter JR (1976) Antony van Leeuwenhoek: tercentenary of his discovery of bacteria. Bacteriol 40: 260–269. ", + "9.\n McArthur M, Lang R (2012) Folding paper: The infinite possibilities of Origami. Washington, DC: International Arts & Artists. 96 p.
                  ", + "10.\n Demaine ED, O'Rourke J (2007) Geometric Folding Algorithms: Linkages, Origami, Polyhedra. Cambridge, MA: Cambridge Univ Press. 472 p.
                    ", + "11.\n Myer JH (1969) Optigami - A Tool for Optical System Design. Appl Opt 8: 260–260. ", + "12.\n Cerda E, Mahadevan L (2005) Confined developable elastic surfaces: cylinders, cones and the Elastica. Proc R Soc A 461: 671–700.\n doi:\n 10.1098/rspa.2004.1371 ", + "13.\n Slocum AH (1992) Precision Machine Design. Englewood Cliffs, NJ: Prentice Hall. 750 p.
                      ", + "14.\n Doushkina V, Fleming E (2009) Optical and mechanical design advantages using polymer optics. Advances in Optomechanics 74: 24–31.\n doi:\n 10.1117/12.832319 ", + "15.\n Lee C-C, Hsiao S-Y, Fang W (2009) Formation and integration of a ball lens utilizing two-phase liquid technology. IEEE 22nd International Conference on Micro Electro Mechanical Systems: pp. 172–175.
                        ", + "16.\n Jeong K-H, Liu GL, Chronis N, Lee LP (2004) Tunable microdoublet lens array integrated with microfluidic network. Optics Express 12(11): 2494–2500.\n doi:\n 10.1364/opex.12.002494 ", + "17.\n Goldberg O (1980) Köhler illumination. The Microscope 28: 15–22. ", + "18.\n Brady S, Willard C (1998) Microscopic Explorations. UC Berkeley: Lawrence Hall of Science. pp. 20–21.
                          ", + "19.\n Cox CA, Carpenter JR (1989) Improving attitudes toward teaching science and reducing science anxiety through increasing confidence in science ability in inservice elementary school teachers. Journal of Elementary Science Education 1(2): 14–34.\n doi:\n 10.1007/bf03173020 ", + "20.\n Bredderman T (1983) The effects of activity-based science on student outcomes: A quantitative synthesis. Review of Education Research 53: 499–518.\n doi:\n 10.3102/00346543053004499 ", + "21.\n Bower JM (1996) Scientists and science education reform: myths, methods, and madness. National Academies of Science Resources for Involving Scientists in Education. Available: http://www.nas.edu/rise/backg2a.htm. Accessed: 1 May 2014.
                            ", + "22.\n Kremer M, Brannen C, Glennerster R (2013) The Challenge of Education and Learning in the Developing World. Science 340(6130): 297–300.\n doi:\n 10.1126/science.1235350 ", + "23.\n O'Neill I (2011) Supernova Discovered by 10-Year-Old. Discovery News. Available: http://news.discovery.com/space/astronom​y/supernova-discovered-by-10-year-old.ht​m. Accessed: 2014 May 1.
                              ", + "24.\n Garcia LS (2007) Diagnostic medical parasitology, 5th ed. Washington, DC: ASM Press, 142–180.
                                ", + "25.\n Baron EJ, Miller JM, Weinstein MP, Richter SS, Gilligan PH, et al. (2013) A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2013 Recommendations by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM). Clinical Infectious Diseases 57(4): e22–e121 doi:10.1093/cid/cit278. ", + "26.\n Smith ZJ, Chu K, Espenson AR, Rahimzadeh M, Gryshuk A, et al. (2011) Cell-Phone-Based Platform for Biomedical Device Development and Education Applications. PLOS ONE 6(3): e17150 doi:10.1371/journal.pone.0017150. ", + "27.\n Breslauer DN, Maamari RN, Switz NA, Lam WA, Fletcher DA (2009) Mobile phone based clinical microscopy for global health applications. PLOS ONE 4(7): e6320 doi:10.1371/journal.pone.0006320. ", + "28.\n Zhu H, Isikman SO, Mudanyali O, Greenbaum A, Ozcan A (2013) Optical imaging techniques for point-of-care diagnostics. Lab Chip 13: 51–67.\n doi:\n 10.1039/c2lc40864c ", + "29.\n Bogoch II, Andrews JR, Speich B, Utzinger J, Ame SM, et al. (2013) Mobile Phone Microscopy for the Diagnosis of Soil-Transmitted Helminth Infections: A Proof-of-Concept Study. Am J Trop Med Hyg 88(4): 626–629.\n doi:\n 10.4269/ajtmh.12-0742 ", + "30.\n Martinez AW, Phillips ST, Whitesides GM (2010) Diagnostics for the Developing World: Microfluidic Paper-Based Analytical Devices. Anal Chem 82(1): 3–10.\n doi:\n 10.1021/ac9013989 ", + "31.\n Kikuchi K, Morikawa T, Shimada J, Sakurai K (1981) Cladded radially inhomogeneous sphere lenses. Appl Opt 20(3): 388–394.\n doi:\n 10.1364/ao.20.000388 ", + "32.\n Koike Y, Kanemitsu A, Shioda Y, Nihei E, Ohtsuka Y (1994) Spherical gradient-index polymer lens with low spherical aberration. Appl Opt 33(16): 3394–3400.\n doi:\n 10.1364/ao.33.003394 " + ] + }, + "figures_html": { + "value": [ + "
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                                Figure 1. Foldscope design, components and usage.

                                (A) CAD layout of Foldscope paper components on an A4 sheet. (B) Schematic of an assembled Foldscope illustrating panning, and (C) cross-sectional view illustrating flexure-based focusing. (D) Foldscope components and tools used in the assembly, including Foldscope paper components, ball lens, button-cell battery, surface-mounted LED, switch, copper tape and polymeric filters. (E) Different modalities assembled from colored paper stock. (F) Novice users demonstrating the technique for using the Foldscope. (G) Demonstration of the field-rugged design, such as stomping under foot.

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                                doi:10.1371/journal.pone.0098781.g001

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                                Table 1. Bill of Materials.

                                doi:10.1371/journal.pone.0098781.t001

                                ", + "\n Download:\n ", + "
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                                Table 2. Foldscope Analytical Model Parameter Summary Table.

                                doi:10.1371/journal.pone.0098781.t002

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                                Figure 2. Foldscope imaging modalities.

                                (A) Brightfield Foldscope image of a monolayer of 1 µm polystyrene microspheres (Polysciences 07310-15) using a 1,450X lens. (B) Fluorescent Foldscope image of 2 µm polyfluorescent microspheres (Polysciences 19508-2) using a 1,140X lens with Roscolux gel filters #19 and #80. (C) 2X2 lens-array Brightfield Foldscope image of Giemsa-stained thin blood smear using 1,450X lenses. (D) 140X Darkfield Foldscope images of 6 µm polystyrene microspheres (Polysciences 15714-5), using a 140X lens for the darkfield condenser. Darkfield condenser aperture shown in inset has 1.5 mm inner diameter and 4.0 mm outer diameter. (E–H) Schematic cross-sections of Brightfield, Fluorescence, Lens-Array, and Darkfield Foldscope configurations, showing the respective arrangements of ball lenses, filters, and LEDs. See table 2 for ball lenses used for specific magnifications.

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                                doi:10.1371/journal.pone.0098781.g002

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                                Figure 3. Manufacturing innovations for lens- and specimen- mounting.

                                (A) Fabrication, mounting, and characterization of capillary-encapsulation process for lens-mounted apertures. X and Y error bars for all measurements are 2.5 µm. (B) Reel of polystyrene carrier tape with custom pockets and punched holes for mounting over 2,000 ball lenses with optimal apertures. The first ten pockets include mounted ball lenses. Inset shows sectioned view from CAD model of carrier tape mounted lenses. Note the aperture is the punched hole shown on the bottom side of the ball lens. This tape is 16 mm wide and is designed for 2.4 mm ball lenses (aperture diameter is 0.7 mm). (C) Top: Paper microscope slide shown next to standard glass slide with coverslip, both with wet mount algae specimens. Bottom: Schematic of paper microscope slide, showing specimen containment cavity formed between upper tape and lower tape in middle of slide.

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                                doi:10.1371/journal.pone.0098781.g003

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                                Figure 4. Analytical, numerical, and empirical characterization of Foldscope.

                                (A,B) Analytical “design curves” for normalized optimal aperture radius (nOAR) and optimal resolution (RES) versus magnification (MAG) over index of refraction (range 1.33–1.91) and ball lens radius (range 40–1200 µm). (C) Comparison of analytical (3D surface) and numerical (plotted as points) results for RES versus index of refraction and ball lens radius. (D) Modulus of the Optical Transfer Function (MTF) over the optimal field of view for a 300 µm sapphire lens with optimal aperture. (E,F) Image of USAF 1951 resolution target taken with 430X ball lens, including an enlarged caption of Group 9, and an intensity profile plot along path denoted by green line in image caption. This demonstrates resolvability for Group 9, Element 4 corresponding to 724 Line Pairs/mm or 1.38 µm resolution. (G,H) Image of USAF 1951 resolution target taken with 140X ball lens, including an enlarged caption of Group 8, and an intensity profile plot along path denoted by green line in image caption. This demonstrates resolvability for Group 8, Element 6 corresponding to 456 Line Pairs/mm or 2.19 µm resolution. The data was taken using GUPPY Pro 503C scientific camera, with 2592×1944 pixels and pixel size 2.2×2.2 µm2.

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                                doi:10.1371/journal.pone.0098781.g004

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                                Figure 5. Mosaic of Foldscope Images.

                                Bright field images of (A) Giardia lamblia (2,180X), (B) Leishmania donovani (1,450X), (C) Trypanosoma cruzi (1,450X), (D) gram-negative Escherichia coli (1,450X), (E) gram-positive Bacillus cereus (1,450X), (F) Schistosoma haematobium (140X), and (G) Dirofilaria immitis (140X). Unstained (H) leg muscles and (I) tarsi of an unidentified ladybug (genus Coccinella). (J) Unstained leg muscles (fixed in formaldehyde) of an unidentified red ant (genus Solenopsis). An LED diffuser (Roscolux #111) was added for (A) and an LED condenser (2.4 mm borosilicate ball lens) was used for (C). Images (H–J) were taken by novice user using a self-made Foldscope (140X). See table 2 for ball lenses used for specific magnifications. White scale bar: 5 µm; black scale bar: 100 µm.

                                \n

                                doi:10.1371/journal.pone.0098781.g005

                                ", + "\n Download:\n " + ] + }, + "tables_html": { + "value": [ + "
                                \"thumbnail\"
                                Figure 1. Foldscope design, components and usage.

                                (A) CAD layout of Foldscope paper components on an A4 sheet. (B) Schematic of an assembled Foldscope illustrating panning, and (C) cross-sectional view illustrating flexure-based focusing. (D) Foldscope components and tools used in the assembly, including Foldscope paper components, ball lens, button-cell battery, surface-mounted LED, switch, copper tape and polymeric filters. (E) Different modalities assembled from colored paper stock. (F) Novice users demonstrating the technique for using the Foldscope. (G) Demonstration of the field-rugged design, such as stomping under foot.

                                \n

                                doi:10.1371/journal.pone.0098781.g001

                                ", + "\n Download:\n ", + "
                                \"thumbnail\"
                                Table 1. Bill of Materials.

                                doi:10.1371/journal.pone.0098781.t001

                                ", + "\n Download:\n ", + "
                                \"thumbnail\"
                                Table 2. Foldscope Analytical Model Parameter Summary Table.

                                doi:10.1371/journal.pone.0098781.t002

                                ", + "\n Download:\n ", + "
                                \"thumbnail\"
                                Figure 2. Foldscope imaging modalities.

                                (A) Brightfield Foldscope image of a monolayer of 1 µm polystyrene microspheres (Polysciences 07310-15) using a 1,450X lens. (B) Fluorescent Foldscope image of 2 µm polyfluorescent microspheres (Polysciences 19508-2) using a 1,140X lens with Roscolux gel filters #19 and #80. (C) 2X2 lens-array Brightfield Foldscope image of Giemsa-stained thin blood smear using 1,450X lenses. (D) 140X Darkfield Foldscope images of 6 µm polystyrene microspheres (Polysciences 15714-5), using a 140X lens for the darkfield condenser. Darkfield condenser aperture shown in inset has 1.5 mm inner diameter and 4.0 mm outer diameter. (E–H) Schematic cross-sections of Brightfield, Fluorescence, Lens-Array, and Darkfield Foldscope configurations, showing the respective arrangements of ball lenses, filters, and LEDs. See table 2 for ball lenses used for specific magnifications.

                                \n

                                doi:10.1371/journal.pone.0098781.g002

                                ", + "\n Download:\n ", + "
                                \"thumbnail\"
                                Figure 3. Manufacturing innovations for lens- and specimen- mounting.

                                (A) Fabrication, mounting, and characterization of capillary-encapsulation process for lens-mounted apertures. X and Y error bars for all measurements are 2.5 µm. (B) Reel of polystyrene carrier tape with custom pockets and punched holes for mounting over 2,000 ball lenses with optimal apertures. The first ten pockets include mounted ball lenses. Inset shows sectioned view from CAD model of carrier tape mounted lenses. Note the aperture is the punched hole shown on the bottom side of the ball lens. This tape is 16 mm wide and is designed for 2.4 mm ball lenses (aperture diameter is 0.7 mm). (C) Top: Paper microscope slide shown next to standard glass slide with coverslip, both with wet mount algae specimens. Bottom: Schematic of paper microscope slide, showing specimen containment cavity formed between upper tape and lower tape in middle of slide.

                                \n

                                doi:10.1371/journal.pone.0098781.g003

                                ", + "\n Download:\n ", + "
                                \"thumbnail\"
                                Figure 4. Analytical, numerical, and empirical characterization of Foldscope.

                                (A,B) Analytical “design curves” for normalized optimal aperture radius (nOAR) and optimal resolution (RES) versus magnification (MAG) over index of refraction (range 1.33–1.91) and ball lens radius (range 40–1200 µm). (C) Comparison of analytical (3D surface) and numerical (plotted as points) results for RES versus index of refraction and ball lens radius. (D) Modulus of the Optical Transfer Function (MTF) over the optimal field of view for a 300 µm sapphire lens with optimal aperture. (E,F) Image of USAF 1951 resolution target taken with 430X ball lens, including an enlarged caption of Group 9, and an intensity profile plot along path denoted by green line in image caption. This demonstrates resolvability for Group 9, Element 4 corresponding to 724 Line Pairs/mm or 1.38 µm resolution. (G,H) Image of USAF 1951 resolution target taken with 140X ball lens, including an enlarged caption of Group 8, and an intensity profile plot along path denoted by green line in image caption. This demonstrates resolvability for Group 8, Element 6 corresponding to 456 Line Pairs/mm or 2.19 µm resolution. The data was taken using GUPPY Pro 503C scientific camera, with 2592×1944 pixels and pixel size 2.2×2.2 µm2.

                                \n

                                doi:10.1371/journal.pone.0098781.g004

                                ", + "\n Download:\n ", + "
                                \"thumbnail\"
                                Figure 5. Mosaic of Foldscope Images.

                                Bright field images of (A) Giardia lamblia (2,180X), (B) Leishmania donovani (1,450X), (C) Trypanosoma cruzi (1,450X), (D) gram-negative Escherichia coli (1,450X), (E) gram-positive Bacillus cereus (1,450X), (F) Schistosoma haematobium (140X), and (G) Dirofilaria immitis (140X). Unstained (H) leg muscles and (I) tarsi of an unidentified ladybug (genus Coccinella). (J) Unstained leg muscles (fixed in formaldehyde) of an unidentified red ant (genus Solenopsis). An LED diffuser (Roscolux #111) was added for (A) and an LED condenser (2.4 mm borosilicate ball lens) was used for (C). Images (H–J) were taken by novice user using a self-made Foldscope (140X). See table 2 for ball lenses used for specific magnifications. White scale bar: 5 µm; black scale bar: 100 µm.

                                \n

                                doi:10.1371/journal.pone.0098781.g005

                                ", + "\n Download:\n " + ] + }, + "fulltext_html": { + "value": [ + "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098781" + ] + }, + "fulltext_pdf": { + "value": [ + "http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0098781&representation=PDF" + ] + }, + "fulltext_xml": { + "value": [ + "http://www.plosone.org/article/article/asset?id=10.1371/journal.pone.0098781.XML" + ] + }, + "supplementary_file": { + "value": [ + + ] + }, + "figures_image": { + "value": [ + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0098781.g001", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0098781.t001", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0098781.t002", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0098781.g002", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0098781.g003", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0098781.g004", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0098781.g005" ] }, - "file_hashes": [ + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_sizes": [ { - "fulltext.pdf": "5dfa35bcba2f631b40673c498c62f64b" + "fulltext.html": 149726 }, { - "fulltext.xml": "49e918d4fee77f96ff9f1d49615f3785" + "fulltext.pdf": 13012549 + }, + { + "fulltext.xml": 12542 } ] }, "http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099348": { - "fulltext_pdf": { + "publisher": { "value": [ - "http://dx.plos.org/10.1371/journal.pone.0099348.pdf" + ] }, - "fulltext_html": { + "journal_name": { "value": [ - + "PLOS ONE" ] }, - "fulltext_xml": { + "journal_issn": { "value": [ - "/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0099348&representation=XML" + "1932-6203" ] }, "title": { "value": [ - "Co-Infection of Blacklegged Ticks with Babesia microti and Borrelia burgdorferi Is Higher than Expected and Acquired from Small Mammal Hosts" + "Co-Infection of Blacklegged Ticks with Babesia microti and Borrelia burgdorferi Is Higher than Expected and Acquired from Small Mammal Hosts" ] }, - "author": { + "keywords": { + "value": [ + + ] + }, + "author_name": { "value": [ "Michelle H. Hersh", "Richard S. Ostfeld", @@ -415,9 +1404,35 @@ "Felicia Keesing" ] }, - "date": { + "author_institution": { + "value": [ + + ] + }, + "editor_name": { "value": [ - "2014/6/18" + + ] + }, + "date_published": { + "value": [ + [ + " June 18, 2014" + ] + ] + }, + "date_accepted": { + "value": [ + [ + "May 13, 2014" + ] + ] + }, + "date_submitted": { + "value": [ + [ + "February 13, 2014" + ] ] }, "doi": { @@ -440,22 +1455,187 @@ "e99348" ] }, - "description": { + "abstract": { "value": [ - "PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world." + ] }, - "abstract": { + "abstract_html": { + "value": [ + "

                                Abstract

                                Humans in the northeastern and midwestern United States are at increasing risk of acquiring tickborne diseases – not only Lyme disease, but also two emerging diseases, human granulocytic anaplasmosis and human babesiosis. Co-infection with two or more of these pathogens can increase the severity of health impacts. The risk of co-infection is intensified by the ecology of these three diseases because all three pathogens (Borrelia burgdorferi, Anaplasma phagocytophilum, and Babesia microti) are transmitted by the same vector, blacklegged ticks (Ixodes scapularis), and are carried by many of the same reservoir hosts. The risk of exposure to multiple pathogens from a single tick bite and the sources of co-infected ticks are not well understood. In this study, we quantify the risk of co-infection by measuring infection prevalence in 4,368 questing nymphs throughout an endemic region for all three diseases (Dutchess County, NY) to determine if co-infections occur at frequencies other than predicted by independent assortment of pathogens. Further, we identify sources of co-infection by quantifying rates of co-infection on 3,275 larval ticks fed on known hosts. We find significant deviations of levels of co-infection in questing nymphs, most notably 83% more co-infection with Babesia microti and Borrelia burgdorferi than predicted by chance alone. Further, this pattern of increased co-infection was observed in larval ticks that fed on small mammal hosts, but not on meso-mammal, sciurid, or avian hosts. Co-infections involving A. phagocytophilum were less common, and fewer co-infections of A. phagocytophilum and B. microti than predicted by chance were observed in both questing nymphs and larvae fed on small mammals. Medical practitioners should be aware of the elevated risk of B. microti/B. burgdorferi co-infection.

                                \n" + ] + }, + "abstract_text": { + "value": [ + + ] + }, + "introduction_html": { + "value": [ + + ] + }, + "methods_html": { + "value": [ + + ] + }, + "results_html": { + "value": [ + + ] + }, + "discussion_html": { + "value": [ + + ] + }, + "author_contrib_html": { + "value": [ + "Conceived and designed the experiments: RSO MT JLB MEK KL KAS FK. Performed the experiments: MHH DJM JLB MEK KL KAS. Analyzed the data: MHH. Contributed reagents/materials/analysis tools: MHH DJM MT FK. Wrote the paper: MHH RSO DJM MT FK." + ] + }, + "references_html": { + "value": [ + "1.\n Dahlgren F, Mandel E, Krebs J, Massung R, McQuiston J (2011) Increasing incidence of Ehrlichia chaffeensis and Anaplasma phagocytophilum in the United States, 2000–2007. Am J Trop Med Hyg 85: 124–131 doi:10.4269/ajtmh.2011.10-0613. ", + "2.\n Krause P, McKay K, Gadbaw J, Christianson D, Closter L, et al. (2003) Increasing health burden of human babesiosis in endemic sites. Am J Trop Med Hyg 68: 431–436 doi:not available. ", + "3.\n Joseph JT, Roy SS, Shams N, Visintainer P, Nadelman RB, et al. (2011) Babesiosis in Lower Hudson Valley, New York, USA. Emerg Infect Dis 17: 843–847 doi:10.3201/eid1705.101334. ", + "4.\n Diuk-Wasser MA, Liu Y, Steeves TK, Folsom-O'Keefe C, Dardick K, et al. (2014) Monitoring human babesiosis emergence through vector surveillance, New England, USA. Emerg Infect Dis 20: 225–231 doi:dx.doi.org/10.3201/eid2002.130644. ", + "5.\n Ostfeld RS (2010) Lyme disease: the ecology of a complex system. New York, NY, USA: Oxford University Press. 232 p.
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                                      ", + "28.\n Ostfeld RS, LoGiudice K (2003) Community disassembly, biodiversity loss, and the erosion of an ecosystem service. Ecology 84: 1421–1427 doi:10.1890/02-3125. ", + "29.\n Keesing F, Brunner J, Duerr S, Killilea M, LoGiudice K, et al. (2009) Hosts as ecological traps for the vector of Lyme disease. Proc Biol Sci 276: 3911–3919 doi:10.1098/rspb.2009.1159. ", + "30.\n Keesing F, Belden LK, Daszak P, Dobson A, Harvell CD, et al. (2010) Impacts of biodiversity on the emergence and transmission of infectious diseases. Nature 468: 647–652 doi:10.1038/nature09575. ", + "31.\n Courtney JW, Kostelnik LM, Zeidner NS, Massung RF (2004) Multiplex real-time PCR for detection of Anaplasma phagocytophilum and Borrelia burgdorferi. J Clin Microbiol 42: 3164–3168 doi:10.1128/jcm.42.7.3164-3168.2004. ", + "32.\n Chihara LM, Hesterberg TC (2011) Mathematical Statistics with Resampling and R. Hoboken, NJ, USA: John Wiley & Sons. 440 p.
                                        ", + "33.\n Schulze TL, Jordan RA, Healy SP, Roegner VE (2013) Detection of Babesia microti and Borrelia burgdorferi in host-seeking Ixodes scapularis (Acari: Ixodidae) in Monmouth County, New Jersey. J Med Entomol 50: 379–383 doi:10.1603/ME12088. ", + "34.\n Brunner JL, Ostfeld RS (2008) Multiple causes of variable tick burdens on small-mammal hosts. Ecology 89: 2259–2272 doi:10.1890/07-0665.1. ", + "35.\n Nieto NC, Foley JE (2009) Meta-analysis of coinfection and coexposure with Borrelia burgdorferi and Anaplasma phagocytophilum in humans, domestic animals, wildlife, and Ixodes ricinus-complex Ticks. Vector Borne Zoonotic Dis 9: 93–101 doi:10.1089/vbz.2008.0072. ", + "36.\n Civitello DJ, Rynkiewicz E, Clay K (2010) Meta-analysis of co-infections in ticks. Isr J Ecol Evol 56: 417–431 doi:10.1560/ijee.56.3-4.417. ", + "37.\n Levin ML, Nicholson WL, Massung RF, Sumner JW, Fish D (2002) Comparison of the reservoir competence of medium-sized mammals and Peromyscus leucopus for Anaplasma phagocytophilum in Connecticut. Vector Borne Zoonotic Dis 2: 125–136 doi:10.1089/15303660260613693. ", + "38.\n Piesman J, Mather TN, Telford SR, Spielman A (1986) Concurrent Borrelia burgdorferi and Babesia microti infection in nymphal Ixodes dammini. J Clin Microbiol 24: 446–447 doi:not available. ", + "39.\n Swanson KI, Norris DE (2007) Co-circulating microorganisms in questing Ixodes scapularis nymphs in Maryland. J Vector Ecol 32: 243–251 doi:[];10.3376/1081-1710(2007)32[243:cmiqis]2.0​.co;2. ", + "40.\n Schauber EM, Gertz SJ, Maple WT, Ostfeld RS (1998) Coinfection of blacklegged ticks (Acari:Ixodidae) in Dutchess County, New York, with the agents of Lyme disease and human granulocytic ehrlichiosis. J Med Entomol 35: 901–903 doi:not available. ", + "41.\n Varde S, Beckley J, Schwartz I (1998) Prevalence of tick-borne pathogens in Ixodes scapularis in a rural New Jersey county. Emerg Infect Dis 4: 97–99 doi:10.3201/eid0401.980113. ", + "42.\n Walk ST, Xu G, Stull JW, Rich SM (2009) Correlation between tick density and pathogen endemicity, New Hampshire. Emerg Infect Dis 15: 585–587 doi:10.3201/eid1504.080940. ", + "43.\n Tokarz R, Jain K, Bennett A, Briese T, Lipkin WI (2010) Assessment of polymicrobial infections in ticks in New York state. Vector Borne Zoonotic Dis 10: 217–221 doi:10.1089/vbz.2009.0036. ", + "44.\n Steiner FE, Pinger RR, Vann CN, Grindle N, Civitello D, et al. (2008) Infection and co-infection rates of Anaplasma phagocytophilum variants, Babesia spp., Borrelia burgdorferi, and the rickettsial endosymbiont in Ixodes scapularis (Acari: Ixodidae) from sites in Indiana, Maine, Pennsylvania, and Wisconsin. J Med Entomol 45: 289–297 doi:[];10.1603/0022-2585(2008)45[289:IACROA]2.0​.CO;2. ", + "45.\n Levi T, Kilpatrick AM, Mangel M, Wilmers CC (2012) Deer, predators, and the emergence of Lyme disease. Proc Natl Acad Sci USA 109: 10942–10947 doi:10.1073/pnas.1204536109. ", + "46.\n Ostfeld RS, Keesing F (2012) Effects of host diversity on infectious disease. Annu Rev Ecol Evol Syst 43: 157–182 doi:10.1146/annurev-ecolsys-102710-145022. " + ] + }, + "figures_html": { + "value": [ + "
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                                        Figure 1. Mean levels of co-infection prevalence of Anaplasma phagocytophilum, Babesia microti, and Borrelia burgdorferi in questing Ixodes scapularis nymphs, by site.

                                        Mean levels of co-infection with Anaplasma phagocytophilum (Ap), Babesia microti (Bm), and Borrelia burgdorferi (Bb) in questing nymphal Ixodes scapularis ticks by site, 2011–2012. Each category represents mean overall prevalence as opposed to the prevalence of each specific infection type – for example, the “Ap” bar represents not just single infections but also ticks co-infected with Ap and either or both of the other two pathogens. Error bars represent standard error. For individual years see Figure S2.

                                        \n

                                        doi:10.1371/journal.pone.0099348.g001

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                                        Figure 2. Log (base 2) of the observed: expected ratio of questing Ixodes scapularis nymphs.

                                        Log (base 2) of observed: expected ratio of each infection status of questing Ixodes scapularis ticks sampled at 161 sites across Dutchess County, NY, USA. The magnitude and direction of the log ratios illustrates the extent to which the observed levels of co-infection differed from expected levels of co-infection due to random assortment of pathogens. Pathogens sampled include Anaplasma phagocytophilum (Ap), Babesia microti (Bm), and Borrelia burgdorferi (Bb). Expected infection frequencies are based on 100,000 random permutations of infection frequencies for each pathogen.

                                        \n

                                        doi:10.1371/journal.pone.0099348.g002

                                        ", + "\n Download:\n ", + "
                                        \"thumbnail\"
                                        Table 1. Predictions of infection prevalence in questing Ixodes scapularis nymphal ticks using a permutation analysis assuming independent assortment of all three pathogens, and deviations of observed data from those predictions.

                                        doi:10.1371/journal.pone.0099348.t001

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                                        \"thumbnail\"
                                        Figure 3. Co-infection prevalence of Anaplasma phagocytophilum, Babesia microti, and Borrelia burgdorferi in wildlife host species groups.

                                        Mean co-infection prevalence for Anaplasma phagocytophilum (Ap), Babesia microti (Bm), and Borrelia burgdorferi (Bb) of host-collected Ixodes scapularis ticks fed on (A) small mammal, (B) meso-mammal, (C) sciurid, and (D) bird host species. Each category represents the mean prevalence of each specific co-infection type as opposed to overall prevalence. Error bars show standard error. Note that no co-infections were observed in D. carolinensis.

                                        \n

                                        doi:10.1371/journal.pone.0099348.g003

                                        ", + "\n Download:\n ", + "
                                        \"thumbnail\"
                                        Table 2. Predictions of infection prevalence in host-collected ticks fed on small mammals using a permutation analysis assuming independent assortment of all three pathogens, and deviations of observed data from those predictions.

                                        doi:10.1371/journal.pone.0099348.t002

                                        ", + "\n Download:\n ", + "
                                        \"thumbnail\"
                                        Table 3. Predictions of infection prevalence in host-collected ticks fed on meso-mammals using a permutation analysis assuming independent assortment of all three pathogens, and deviations of observed data from those predictions.

                                        doi:10.1371/journal.pone.0099348.t003

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                                        \"thumbnail\"
                                        Table 4. Predictions of infection prevalence in host-collected ticks fed on sciurids using a permutation analysis assuming independent assortment of all three pathogens, and deviations of observed data from those predictions.

                                        doi:10.1371/journal.pone.0099348.t004

                                        ", + "\n Download:\n ", + "
                                        \"thumbnail\"
                                        Table 5. Predictions of infection prevalence in host-collected ticks fed on birds using a permutation analysis assuming independent assortment of all three pathogens, and deviations of observed data from those predictions.

                                        doi:10.1371/journal.pone.0099348.t005

                                        ", + "\n Download:\n " + ] + }, + "tables_html": { + "value": [ + "
                                        \"thumbnail\"
                                        Figure 1. Mean levels of co-infection prevalence of Anaplasma phagocytophilum, Babesia microti, and Borrelia burgdorferi in questing Ixodes scapularis nymphs, by site.

                                        Mean levels of co-infection with Anaplasma phagocytophilum (Ap), Babesia microti (Bm), and Borrelia burgdorferi (Bb) in questing nymphal Ixodes scapularis ticks by site, 2011–2012. Each category represents mean overall prevalence as opposed to the prevalence of each specific infection type – for example, the “Ap” bar represents not just single infections but also ticks co-infected with Ap and either or both of the other two pathogens. Error bars represent standard error. For individual years see Figure S2.

                                        \n

                                        doi:10.1371/journal.pone.0099348.g001

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                                        \"thumbnail\"
                                        Figure 2. Log (base 2) of the observed: expected ratio of questing Ixodes scapularis nymphs.

                                        Log (base 2) of observed: expected ratio of each infection status of questing Ixodes scapularis ticks sampled at 161 sites across Dutchess County, NY, USA. The magnitude and direction of the log ratios illustrates the extent to which the observed levels of co-infection differed from expected levels of co-infection due to random assortment of pathogens. Pathogens sampled include Anaplasma phagocytophilum (Ap), Babesia microti (Bm), and Borrelia burgdorferi (Bb). Expected infection frequencies are based on 100,000 random permutations of infection frequencies for each pathogen.

                                        \n

                                        doi:10.1371/journal.pone.0099348.g002

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                                        \"thumbnail\"
                                        Table 1. Predictions of infection prevalence in questing Ixodes scapularis nymphal ticks using a permutation analysis assuming independent assortment of all three pathogens, and deviations of observed data from those predictions.

                                        doi:10.1371/journal.pone.0099348.t001

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                                        \"thumbnail\"
                                        Figure 3. Co-infection prevalence of Anaplasma phagocytophilum, Babesia microti, and Borrelia burgdorferi in wildlife host species groups.

                                        Mean co-infection prevalence for Anaplasma phagocytophilum (Ap), Babesia microti (Bm), and Borrelia burgdorferi (Bb) of host-collected Ixodes scapularis ticks fed on (A) small mammal, (B) meso-mammal, (C) sciurid, and (D) bird host species. Each category represents the mean prevalence of each specific co-infection type as opposed to overall prevalence. Error bars show standard error. Note that no co-infections were observed in D. carolinensis.

                                        \n

                                        doi:10.1371/journal.pone.0099348.g003

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                                        Table 2. Predictions of infection prevalence in host-collected ticks fed on small mammals using a permutation analysis assuming independent assortment of all three pathogens, and deviations of observed data from those predictions.

                                        doi:10.1371/journal.pone.0099348.t002

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                                        Table 3. Predictions of infection prevalence in host-collected ticks fed on meso-mammals using a permutation analysis assuming independent assortment of all three pathogens, and deviations of observed data from those predictions.

                                        doi:10.1371/journal.pone.0099348.t003

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                                        Table 4. Predictions of infection prevalence in host-collected ticks fed on sciurids using a permutation analysis assuming independent assortment of all three pathogens, and deviations of observed data from those predictions.

                                        doi:10.1371/journal.pone.0099348.t004

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                                        Table 5. Predictions of infection prevalence in host-collected ticks fed on birds using a permutation analysis assuming independent assortment of all three pathogens, and deviations of observed data from those predictions.

                                        doi:10.1371/journal.pone.0099348.t005

                                        ", + "\n Download:\n " + ] + }, + "fulltext_html": { + "value": [ + "http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099348" + ] + }, + "fulltext_pdf": { "value": [ - "AbstractHumans in the northeastern and midwestern United States are at increasing risk of acquiring tickborne diseases – not only Lyme disease, but also two emerging diseases, human granulocytic anaplasmosis and human babesiosis. Co-infection with two or more of these pathogens can increase the severity of health impacts. The risk of co-infection is intensified by the ecology of these three diseases because all three pathogens (Borrelia burgdorferi, Anaplasma phagocytophilum, and Babesia microti) are transmitted by the same vector, blacklegged ticks (Ixodes scapularis), and are carried by many of the same reservoir hosts. The risk of exposure to multiple pathogens from a single tick bite and the sources of co-infected ticks are not well understood. In this study, we quantify the risk of co-infection by measuring infection prevalence in 4,368 questing nymphs throughout an endemic region for all three diseases (Dutchess County, NY) to determine if co-infections occur at frequencies other than predicted by independent assortment of pathogens. Further, we identify sources of co-infection by quantifying rates of co-infection on 3,275 larval ticks fed on known hosts. We find significant deviations of levels of co-infection in questing nymphs, most notably 83% more co-infection with Babesia microti and Borrelia burgdorferi than predicted by chance alone. Further, this pattern of increased co-infection was observed in larval ticks that fed on small mammal hosts, but not on meso-mammal, sciurid, or avian hosts. Co-infections involving A. phagocytophilum were less common, and fewer co-infections of A. phagocytophilum and B. microti than predicted by chance were observed in both questing nymphs and larvae fed on small mammals. Medical practitioners should be aware of the elevated risk of B. microti/B. burgdorferi co-infection.\n" + "http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0099348&representation=PDF" ] }, - "file_hashes": [ + "fulltext_xml": { + "value": [ + "http://www.plosone.org/article/article/asset?id=10.1371/journal.pone.0099348.XML" + ] + }, + "supplementary_file": { + "value": [ + + ] + }, + "figures_image": { + "value": [ + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0099348.g001", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0099348.g002", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0099348.t001", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0099348.g003", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0099348.t002", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0099348.t003", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0099348.t004", + "article/figure/image?size=large&id=info:doi/10.1371/journal.pone.0099348.t005" + ] + }, + "license": { + "value": [ + + ] + }, + "copyright": { + "value": [ + + ] + }, + "file_sizes": [ + { + "fulltext.html": 178485 + }, { - "fulltext.pdf": "71ff4b0cd5933789dbb0a38d756c6193" + "fulltext.pdf": 354297 }, { - "fulltext.xml": "b8506c6bdd446151410a270ea4fde031" + "fulltext.xml": 12542 } ] } diff --git a/test/test_all.rb b/test/test_all.rb index bc7c2f9..172f6da 100755 --- a/test/test_all.rb +++ b/test/test_all.rb @@ -19,7 +19,7 @@ def coverage(scraperjsonpath, results) # calculate coverage elements.each do |element| # calculate coverage for this line - if results.detect { |result| result.is_a? Hash && result.key? element } + if results.detect { |result| result.is_a?(Hash) && result.key?(element) } coverage << 1 else coverage << 0 @@ -67,20 +67,21 @@ def coverage(scraperjsonpath, results) results = JSON.load(File.open 'results.json') files = Dir['*'] files = files.keep_if { |f| f != 'results.json' }.map{ |f| f.strip } - file_hashes = [] + file_sizes = [] files.each do |f| - file_hashes << { f => Digest::MD5.file(f).hexdigest } + file_sizes << { f => File.size(f) } end - results['file_hashes'] = file_hashes + results['file_sizes'] = file_sizes end coverage_files << coverage(scraper, results) # compare results to expected expected.each do |hash| key = hash.keys.first - next if key == 'file_hashes' exp_val = hash[key] exist = results.detect { |result| result.key? key } - match = results.detect { |result| result[key] == exp_val } + match = results.detect do |result| + result.key?(key) && result[key] == exp_val + end if exist && match puts "PASS: #{key}" passed += 1 From 83c9d92c413fe8d555c37161a37574112433c940 Mon Sep 17 00:00:00 2001 From: CHJ Hartgerink Date: Tue, 22 Sep 2015 15:48:29 +0200 Subject: [PATCH 143/154] Rename psychscience scraper to sage scraper --- scrapers/{psychologicalscience.json => sage.json} | 2 +- test/{psychologicalscience.json => sage.json} | 0 test/{psychologicalscience_test_urls.txt => sage_test_urls.txt} | 0 3 files changed, 1 insertion(+), 1 deletion(-) rename scrapers/{psychologicalscience.json => sage.json} (98%) rename test/{psychologicalscience.json => sage.json} (100%) rename test/{psychologicalscience_test_urls.txt => sage_test_urls.txt} (100%) diff --git a/scrapers/psychologicalscience.json b/scrapers/sage.json similarity index 98% rename from scrapers/psychologicalscience.json rename to scrapers/sage.json index 663638c..eaf5dc8 100644 --- a/scrapers/psychologicalscience.json +++ b/scrapers/sage.json @@ -1,5 +1,5 @@ { - "url": "pss\\.sagepub\\.com", + "url": ".*\\.sagepub\\.com", "elements": { "publisher": { "selector": "//meta[@name='DC.Publisher']", diff --git a/test/psychologicalscience.json b/test/sage.json similarity index 100% rename from test/psychologicalscience.json rename to test/sage.json diff --git a/test/psychologicalscience_test_urls.txt b/test/sage_test_urls.txt similarity index 100% rename from test/psychologicalscience_test_urls.txt rename to test/sage_test_urls.txt From 2cc51db230cfbfa1b8f9bd521111eb590bf556de Mon Sep 17 00:00:00 2001 From: CHJ Hartgerink Date: Thu, 1 Oct 2015 08:59:48 +0200 Subject: [PATCH 144/154] Minor update sage --- scrapers/sage.json | 64 ++++++++++++---------------------------------- 1 file changed, 16 insertions(+), 48 deletions(-) diff --git a/scrapers/sage.json b/scrapers/sage.json index eaf5dc8..ea632b9 100644 --- a/scrapers/sage.json +++ b/scrapers/sage.json @@ -32,10 +32,15 @@ }, "title": { - "selector": "//meta[@name='DC.Title']", + "selector": "//meta[@name='citation_title']", "attribute": "content" }, + "keywords": { + "selector": "//ul[contains(@class, 'kwd-group')]", + "attribute": "text" + }, + "author_name": { "selector": "//meta[@name='citation_author']", "attribute": "content" @@ -45,22 +50,12 @@ "selector": "//meta[@name='citation_author_institution']", "attribute": "content" }, - + "date_published": { "selector": "//*[@id='slugline']/cite/span[1]", - "attribute": "html" - }, - - "date_accepted": { - "selector": "//*[contains(@class, 'accepted')]", "attribute": "text" }, - "date_submitted": { - "selector": "//*[contains(@class, 'received')]", - "attribute": "html" - }, - "doi": { "selector": "//meta[@name='citation_doi']", "attribute": "content" @@ -93,43 +88,16 @@ }, "abstract_html": { - "selector": "//*[@id='abstract-1']", - "attribute": "html" - }, - - "methods_html": { - "selector": "//*[@id='sec-1']", - "attribute": "html" - }, - - "results_html": { - "selector": "//*[@id='sec-5']", - "attribute": "html" - }, - - "discussion_html": { - "selector": "//*[@id='sec-6']", - "attribute": "html" - }, - - "conclusions_html": { - "selector": "//*[@id='sec-7']", - "attribute": "html" - }, - - "author_contrib_html": { - "selector": "//*[@id='fn-1']", - "attribute": "html" + "selector": "//meta[@name='citation_abstract_html_url']", + "attribute": "content", + "download": { + "rename": "abstract.html" + } }, - + "competing_interests_html": { - "selector": "//*[contains(@class, 'conflict')]", - "attribute": "html" - }, - - "references_html": { - "selector": "//*[@id='ref-list-1']", - "attribute": "html" + "selector": "//*[contains(@class, 'fn-conflict')]", + "attribute": "text" } } -} \ No newline at end of file +} \ No newline at end of file From 63491340e76db5334ca768f61ee9df95e1c12ae4 Mon Sep 17 00:00:00 2001 From: CHJ Hartgerink Date: Fri, 2 Oct 2015 08:47:18 +0200 Subject: [PATCH 145/154] Update test links sage --- test/sage.json | 1283 --------------------------------------- test/sage_test_urls.txt | 18 +- 2 files changed, 10 insertions(+), 1291 deletions(-) delete mode 100644 test/sage.json diff --git a/test/sage.json b/test/sage.json deleted file mode 100644 index c8d09f6..0000000 --- a/test/sage.json +++ /dev/null @@ -1,1283 +0,0 @@ -{ - "http://pss.sagepub.com/content/26/4/363.full": { - "publisher": { - "value": [ - "SAGE Publications" - ] - }, - "journal_name": { - "value": [ - "Psychological Science" - ] - }, - "journal_issn": { - "value": [ - "0956-7976", - "1467-9280" - ] - }, - "volume": { - "value": [ - "26" - ] - }, - "issue": { - "value": [ - "4" - ] - }, - "firstpage": { - "value": [ - "363" - ] - }, - "title": { - "value": [ - "Sadness Shifts to Anxiety Over Time and Distance From the National Tragedy in Newtown, Connecticut" - ] - }, - "author_name": { - "value": [ - "Bruce Doré", - "Leonard Ort", - "Ofir Braverman", - "Kevin N. Ochsner" - ] - }, - "author_institution": { - "value": [ - "Columbia University", - "Columbia University", - "Columbia University", - "Columbia University" - ] - }, - "date_published": { - "value": [ - "\n \t April 2015 \n " - ] - }, - "date_accepted": { - "value": [ - "Accepted July 11, 2014.\n ", - "Accepted " - ] - }, - "date_submitted": { - "value": [ - "Received March 26, 2014.\n ", - "Received " - ] - }, - "doi": { - "value": [ - "10.1177/0956797614562218" - ] - }, - "pmid": { - "value": [ - "25767209" - ] - }, - "copyright": { - "value": [ - "© The Author(s) 2015" - ] - }, - "fulltext_html": { - "value": [ - "http://pss.sagepub.com/content/26/4/363.full" - ] - }, - "fulltext_pdf": { - "value": [ - "http://pss.sagepub.com/content/26/4/363.full.pdf" - ] - }, - "abstract_html": { - "value": [ - "\n \n

                                        Abstract

                                        \n \n

                                        How do increasing temporal and spatial distance affect the emotions people feel and express in response to tragic events?\n Standard views suggest that emotional intensity should decrease but are silent on changes in emotional quality. Using a large\n Twitter data set, we identified temporal and spatial patterns in use of emotional and cognitive words in tweets about the\n Sandy Hook Elementary School shooting. Although use of sadness words decreased with time and spatial distance, use of anxiety\n words showed the opposite pattern and was associated with concurrent increases in language reflecting causal thinking. In\n a follow-up experiment, we found that thinking about abstract causes (as opposed to concrete details) of this event similarly\n evoked decreased sadness but increased anxiety, which was associated with perceptions that a similar event might occur in\n the future. These data challenge current theories of emotional reactivity and identify time, space, and abstract causal thinking\n as factors that elicit categorical shifts in emotional responses to tragedy.\n

                                        \n \n " - ] - }, - "methods_html": { - "value": [ - "\n \n \n

                                        Study 1: Using Twitter to Track Responses to the Newtown Shooting Over Time and Space

                                        \n \n

                                        We gathered tweets (brief public messages posted to twitter.com) containing the keywords “Newtown” or “Sandy Hook” for nearly 6 months following the tragedy, sampling over three discrete\n time periods: December 14 through December 21, 2012; January 27 through March 3, 2013; and April 26 through May 30, 2013 (see\n Fig. 1a). Tweets were accessed via calls to the Twitter Streaming Application Programming Interface (API; Twitter, 2013). All study procedures were approved by the Columbia University Institutional Review Board.\n

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                                        Fig. 1. \n \n

                                        Distribution of the final sample of tweets containing the keywords “Newtown” or “Sandy Hook” across (a) time and (b) space.\n This sample excluded all instances of retweeted content, tweets in which less than 60% of the words were in the English dictionary,\n multiple tweets from a single user, tweets from different users that contained identical content, and tweets from users whose\n geographic location was not available in their profiles.\n

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                                        Data cleaning

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                                        All tweets were downloaded in real time as they were published to the Streaming API (for details, see the Supplemental Material\n available online). Inspection of the resulting data set revealed that some of the tweets we had sampled were duplicates, were\n spam, or had non-English content. We attempted to filter this content in order to focus our analyses on tweets with original,\n English-language content from individual users. We excluded all instances of retweeted content, tweets in which less than\n 60% of the words were in the English dictionary, multiple tweets from a single user, and tweets from different users that\n contained identical content (see the Supplemental Material for more details on these exclusions).\n

                                        \n \n

                                        In order to estimate the proportion of tweets in the cleaned data set that were issued by personal rather than news media\n accounts, we had four raters code a random sample of 1,000 tweets as having been posted by an individual person or by a news\n media organization (an “unclear/other” option was also available), on the basis of the name of the account and the content\n of the tweet. Tweets were coded in groups of 200 at a time, and each tweet was coded by two raters. These judgments showed\n good levels of average absolute agreement (93%; Krippendorff’s α = .66). They indicated that the majority of tweets in the\n cleaned data set had been posted by individuals (82%) and a minority had been posted by news media organizations (5%; see\n Table S1 in the Supplemental Material for further description of this sample of tweets).\n

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                                        Variables of interest

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                                        Predictor variables

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                                        Each message from Twitter was time-stamped, which allowed us to quantify temporal distance from the tragedy (in seconds).\n To quantify spatial distance, we constrained our analyses to users whose location field in their Twitter profile made it possible\n to locate them to a U.S. city or state (e.g., “New York City,” “Arcata, California,” “Colorado,” or “Florida panhandle”).\n This left us with a data set of 43,548 tweets (see Fig. 1b for their geographic distribution). We used an open-source geocoding database to convert this location information to approximate\n latitude and longitude coordinates (OpenStreetMap Contributors, 2013) and conducted subsequent manual checks to flag and correct or remove geocoding errors and ambiguities (see the Supplemental\n Material). To validate these geocoded coordinates, we compared them against captured GPS location data, which were available\n for approximately 0.6% of our sample, and found that the two types of location data agreed within 200 miles for 92% of tweets\n with both types of data available. Finally, for each tweet, we calculated the geometric distance from Sandy Hook, Connecticut,\n using the Haversine formula (Sinnott, 1984). We used this measure in our analyses of spatial distance.\n

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                                        Outcome variables

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                                        We derived several outcome variables of psychological relevance on a tweet-by-tweet basis. For an index of the societal-level\n expression of thoughts related to this tragedy across time and space, we estimated tragedy-related tweet volume for each tweet\n in our data set. Specifically, we determined the per-second rate of publication of tragedy-related tweets at the moment the\n tweet was published. We refer to this variable as the tweet-per-second rate. We next quantified the emotional and cognitive content of the tweets using Linguistic Inquiry and Word Count (LIWC), a prominent\n lexicon and software package that computes frequencies of words reflective of particular psychological states (Pennebaker, Chung, Ireland, Gonzales, & Booth, 2007). The LIWC dictionary includes multiple word categories that have been validated against human judgments of texts’ psychological\n content. We focused on three broad classes of content. First, we considered present-tense verbs and first-person pronouns,\n which indicate attention to one’s self and one’s present temporal context and thus reflect a sense of psychological immediacy\n (Tausczik & Pennebaker, 2010). Second, we considered affect words, which are reflective of experience and expression of emotional states in general (Kahn, Tobin, Massey, & Anderson, 2007), as well as sadness words, anxiety words, and anger words, categories that reflect particular kinds of negative emotion\n (Tausczik & Pennebaker, 2010; Tov, Ng, Lin, & Qiu, 2013). Third, we looked at words that reflect attention to causal processes, which in the context of traumatic events are known\n to mark a relatively complex and abstract style of thought focused on creating causal explanations (Boals & Klein, 2005; Tausczik & Pennebaker, 2010).\n

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                                        Analyses

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                                        We used regression models to quantify independent effects of time (rescaled for interpretation as number of months) and approximate\n distance (rescaled for interpretation as thousands of miles) on tweet features; rescalings were conducted via multiplication\n by a conversion factor. We simultaneously included covariates of no interest to model effects of total tweet word count, county-level\n population density (U.S. Census Bureau, 2013), local politics (i.e., percentage of the popular vote Mitt Romney received in the 2012 presidential election, at county\n and state levels; Rogers & Cage, 2013), and linear, quadratic, and cubic effects of time of day. These covariates allowed us to statistically account for potential\n third variables that may have obscured or driven relationships between remoteness and use of particular word categories. For\n example, the total-word-count covariate allowed us to account for the possibility that time and spatial distance led to changes\n in the overall number of words used. The local-politics and population-density covariates allowed us to account for the possibility\n that social and political qualities of Twitter users’ local environments were related to distance from Newtown and also predictive\n of word use. The time-of-day covariates allowed us to account for circadian changes in word use.\n

                                        \n \n

                                        We tested exponential decay of tragedy-related tweet volume by taking the natural log transform of the tweets-per-second index\n and entering this transformed variable into an ordinary least squares model. Because the raw LIWC word-count variables followed\n overdispersed count distributions (i.e., with variance greater than the mean), we fit these data with negative binomial regression\n models (see Hilbe, 2011).\n

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                                        Results

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                                        Average word counts

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                                        To characterize the affective content of the tweets in our data set, we computed word-count averages for the LIWC emotion\n categories, collapsing across time and distance. On average, the tweets in our data set had a total of 14.89 words (SE = 0.03) and 0.97 affect words (SE = 0.005). Within specific negative-emotion categories, the mean number of words was 0.16 for sadness words (SE = 0.002), 0.05 for anxiety words (SE = 0.001), and 0.26 for anger words (SE = 0.003).\n

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                                        Effects on expression, immediacy, and overall affect

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                                        As predicted by both the nonspecific distance hypothesis (which posits that remoteness has general effects on emotion) and\n the construal-level hypothesis (which posits that remoteness leads to more abstract forms of representation), we found that\n the passage of time led to an exponential decrease in tweet-per-second rate, b = −1.27, 95% confidence interval (CI) = [−1.28, −1.26], p < .001, and linear decreases in number of first-person pronouns, b = −0.062, 95% CI = [−0.082, −0.043], p < .001; present-tense verbs, b = −0.069, 95% CI = [−0.079, −0.059], p < .001; and affect words overall, b = −0.073, 95% CI = [−0.082, −0.064], p < .001. Increasing spatial distance brought about an independent and corresponding pattern, evoking an exponential decrease\n in the tweet-per-second rate, b = −0.040, 95% CI = [−0.056, −0.022], p < .001, as well as linear decreases in use of first-person pronouns, b = −0.049, 95% CI = [−0.081, −0.017], p < .005; present-tense verbs, b = −0.022, 95% CI = [−0.038, −0.006], p < .01; and affect words overall, b = −0.033, 95% CI = [−0.047, −0.020], p < .001. In summary, we observed time- and distance-related changes in word use suggesting decreases in posting of tragedy-related\n content, expression of psychological immediacy, and expression of emotion.\n

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                                        Effects on sadness, anxiety, and causal thought

                                        \n \n

                                        Next, we considered changes in use of sadness, anxiety, and causality words, for which the construal-level hypothesis makes\n unique predictions. As predicted by this hypothesis, increasing time led to a decrease in use of sadness words, b = −0.377, 95% CI = [−0.405, −0.349], p < .001; an increase in use of anxiety words, b = 0.116, 95% CI = [0.079, 0.152], p < .001; and an increase in use of causality words, b = 0.021, 95% CI = [0.004, 0.038], p < .05 (see the graphs in Fig. 2). Similarly, increasing spatial distance brought about a decrease in use of sadness words, b = −0.057, 95% CI = [−0.091, −0.022], p < .001, and increases in use of anxiety words, b = 0.105, 95% CI = [0.044, 0.166], p < .001, and causality words, b = 0.050, 95% CI = [0.023, 0.077], p < .001. Follow-up analyses suggested that temporal patterns in word use were still evident when analyses were limited to\n sampling waves of equal duration (see the Supplemental Material).\n

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                                        Fig. 2. \n \n

                                        Results from Study 1: mean number of (a) sadness, (b) anxiety, and (c) causality words per tweet in tweets collected during\n the three sampling periods between December 14, 2012, and May 30, 2013. Effects of spatial distance are illustrated in the\n maps, which were derived from a series of three-dimensional spatial regression models; mean frequencies are indicated by color\n (and greater precision of the model’s predictions is represented by greater opacity). Effects of temporal distance are illustrated\n in the graphs, in which mean frequencies are plotted as a function of time since the Newtown shooting (aggregated in 24-hr\n bins); error bars represent 95% confidence intervals.\n

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                                        Moreover, a path model (with time and distance as predictors, number of causality words as a mediator, number of anxiety words\n as the outcome, and total tweet word count as a covariate) revealed that the increase in use of anxiety words with increasing\n time and spatial distance was partially mediated by an associated increase in use of causality words, indirect effect of time\n = 0.006, 95% CI = [0.003, 0.009], p < .001; indirect effect of spatial distance = 0.005, 95% CI = [0.000, 0.009], p < .05. An analogous path model with use of sadness words as the outcome indicated that number of causality words did not\n significantly mediate either the effect of time on use of sadness words, indirect effect = −0.0006, 95% CI = [−0.002, 0.0004],\n p = .24, or the effect of spatial distance on use of sadness words, indirect effect = −0.002, 95% CI = [−0.004, 0.001], p = .23. These two path models were implemented via the gsem (generalized structural equation modeling) command in Stata 13,\n with family set to “negative binomial.” Significance of indirect paths was assessed with the nlcom command (which computes\n delta-method standard errors; StataCorp, 2013).\n

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                                        \n \n

                                        Effects on anger

                                        \n \n

                                        For comparison purposes, we also investigated effects of time and spatial distance on anger, an emotion previously identified\n as a key component of the societal-level reaction to violent tragedy (e.g., Lerner, Gonzalez, Small, & Fischhoff, 2003). We found that use of anger words did not change significantly across time, b = −0.01, 95% CI = [−0.03, 0.01], p = .37, but did increase significantly with increasing spatial distance, b = 0.10, 95% CI = [0.07, 0.13], p < .001. (For additional information about the magnitude of the effects of time and spatial distance, see Tables S2 and S3\n in the Supplemental Material.)\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Mapping patterns of use of sadness, anxiety, and causality words

                                        \n \n

                                        To more thoroughly model and visualize patterns of word use across space, we ran a series of three-dimensional spatial regression\n models. In each model, a smooth surface was fitted to the observed data to predict a tweet feature (y) across the continental United States as a function of latitude (x\n 1) and longitude (x\n 2). To define these surfaces, we implemented a penalized thin-plate regression spline method using the bam function within the mgcv package in R (Wood, 2003). The mapped surfaces (see Fig. 2) represent levels of word use with variations in color and model precision (i.e., the inverse of prediction standard error,\n determined in part by data density) with variations in opacity. As expected, these mapped models are consistent with the linear\n regression analyses reported earlier (which collapsed latitude and longitude into a single distance dimension), but they provide\n more information about the spatial patterns of change in use of sadness, anxiety, and causality words.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Word-level analyses

                                        \n \n

                                        To characterize the nature of these relationships at the level of individual words, we correlated time (in seconds) and approximate\n distance (in miles) with frequencies of each of the words in the LIWC sadness, anxiety, and causality categories. Table 1 summarizes the results of these analyses by showing, for each category, the five words whose usage was most strongly associated\n with spatial distance and the five words whose usage was most strongly associated with the passage of time. We corrected for\n multiple comparisons within word category using the false-discovery-rate procedure (Benjamini & Hochberg, 1995). (For additional information about word-level patterns in use of affective words, see Fig. S1 in the Supplemental Material.)\n

                                        \n \n
                                        \n
                                        \n \n
                                        \n
                                        Table 1. \n \n

                                        Individual Sadness, Anxiety, and Causality Words Most Strongly Associated With Increasing Time and Spatial Distance From the\n Newtown Tragedy\n

                                        \n \n
                                        \n
                                        \n
                                        \n \n
                                        \n \n
                                        \n \n " - ] - }, - "results_html": { - "value": [ - "\n \n

                                        Outcome variables

                                        \n \n

                                        We derived several outcome variables of psychological relevance on a tweet-by-tweet basis. For an index of the societal-level\n expression of thoughts related to this tragedy across time and space, we estimated tragedy-related tweet volume for each tweet\n in our data set. Specifically, we determined the per-second rate of publication of tragedy-related tweets at the moment the\n tweet was published. We refer to this variable as the tweet-per-second rate. We next quantified the emotional and cognitive content of the tweets using Linguistic Inquiry and Word Count (LIWC), a prominent\n lexicon and software package that computes frequencies of words reflective of particular psychological states (Pennebaker, Chung, Ireland, Gonzales, & Booth, 2007). The LIWC dictionary includes multiple word categories that have been validated against human judgments of texts’ psychological\n content. We focused on three broad classes of content. First, we considered present-tense verbs and first-person pronouns,\n which indicate attention to one’s self and one’s present temporal context and thus reflect a sense of psychological immediacy\n (Tausczik & Pennebaker, 2010). Second, we considered affect words, which are reflective of experience and expression of emotional states in general (Kahn, Tobin, Massey, & Anderson, 2007), as well as sadness words, anxiety words, and anger words, categories that reflect particular kinds of negative emotion\n (Tausczik & Pennebaker, 2010; Tov, Ng, Lin, & Qiu, 2013). Third, we looked at words that reflect attention to causal processes, which in the context of traumatic events are known\n to mark a relatively complex and abstract style of thought focused on creating causal explanations (Boals & Klein, 2005; Tausczik & Pennebaker, 2010).\n

                                        \n \n " - ] - }, - "discussion_html": { - "value": [ - "\n \n

                                        Analyses

                                        \n \n

                                        We used regression models to quantify independent effects of time (rescaled for interpretation as number of months) and approximate\n distance (rescaled for interpretation as thousands of miles) on tweet features; rescalings were conducted via multiplication\n by a conversion factor. We simultaneously included covariates of no interest to model effects of total tweet word count, county-level\n population density (U.S. Census Bureau, 2013), local politics (i.e., percentage of the popular vote Mitt Romney received in the 2012 presidential election, at county\n and state levels; Rogers & Cage, 2013), and linear, quadratic, and cubic effects of time of day. These covariates allowed us to statistically account for potential\n third variables that may have obscured or driven relationships between remoteness and use of particular word categories. For\n example, the total-word-count covariate allowed us to account for the possibility that time and spatial distance led to changes\n in the overall number of words used. The local-politics and population-density covariates allowed us to account for the possibility\n that social and political qualities of Twitter users’ local environments were related to distance from Newtown and also predictive\n of word use. The time-of-day covariates allowed us to account for circadian changes in word use.\n

                                        \n \n

                                        We tested exponential decay of tragedy-related tweet volume by taking the natural log transform of the tweets-per-second index\n and entering this transformed variable into an ordinary least squares model. Because the raw LIWC word-count variables followed\n overdispersed count distributions (i.e., with variance greater than the mean), we fit these data with negative binomial regression\n models (see Hilbe, 2011).\n

                                        \n \n " - ] - }, - "conclusions_html": { - "value": [ - "\n \n

                                        Results

                                        \n \n
                                        \n \n

                                        Average word counts

                                        \n \n

                                        To characterize the affective content of the tweets in our data set, we computed word-count averages for the LIWC emotion\n categories, collapsing across time and distance. On average, the tweets in our data set had a total of 14.89 words (SE = 0.03) and 0.97 affect words (SE = 0.005). Within specific negative-emotion categories, the mean number of words was 0.16 for sadness words (SE = 0.002), 0.05 for anxiety words (SE = 0.001), and 0.26 for anger words (SE = 0.003).\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Effects on expression, immediacy, and overall affect

                                        \n \n

                                        As predicted by both the nonspecific distance hypothesis (which posits that remoteness has general effects on emotion) and\n the construal-level hypothesis (which posits that remoteness leads to more abstract forms of representation), we found that\n the passage of time led to an exponential decrease in tweet-per-second rate, b = −1.27, 95% confidence interval (CI) = [−1.28, −1.26], p < .001, and linear decreases in number of first-person pronouns, b = −0.062, 95% CI = [−0.082, −0.043], p < .001; present-tense verbs, b = −0.069, 95% CI = [−0.079, −0.059], p < .001; and affect words overall, b = −0.073, 95% CI = [−0.082, −0.064], p < .001. Increasing spatial distance brought about an independent and corresponding pattern, evoking an exponential decrease\n in the tweet-per-second rate, b = −0.040, 95% CI = [−0.056, −0.022], p < .001, as well as linear decreases in use of first-person pronouns, b = −0.049, 95% CI = [−0.081, −0.017], p < .005; present-tense verbs, b = −0.022, 95% CI = [−0.038, −0.006], p < .01; and affect words overall, b = −0.033, 95% CI = [−0.047, −0.020], p < .001. In summary, we observed time- and distance-related changes in word use suggesting decreases in posting of tragedy-related\n content, expression of psychological immediacy, and expression of emotion.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Effects on sadness, anxiety, and causal thought

                                        \n \n

                                        Next, we considered changes in use of sadness, anxiety, and causality words, for which the construal-level hypothesis makes\n unique predictions. As predicted by this hypothesis, increasing time led to a decrease in use of sadness words, b = −0.377, 95% CI = [−0.405, −0.349], p < .001; an increase in use of anxiety words, b = 0.116, 95% CI = [0.079, 0.152], p < .001; and an increase in use of causality words, b = 0.021, 95% CI = [0.004, 0.038], p < .05 (see the graphs in Fig. 2). Similarly, increasing spatial distance brought about a decrease in use of sadness words, b = −0.057, 95% CI = [−0.091, −0.022], p < .001, and increases in use of anxiety words, b = 0.105, 95% CI = [0.044, 0.166], p < .001, and causality words, b = 0.050, 95% CI = [0.023, 0.077], p < .001. Follow-up analyses suggested that temporal patterns in word use were still evident when analyses were limited to\n sampling waves of equal duration (see the Supplemental Material).\n

                                        \n \n
                                        \n
                                        \"Fig.
                                        View larger version:\n \n
                                        \n
                                        \n
                                        Fig. 2. \n \n

                                        Results from Study 1: mean number of (a) sadness, (b) anxiety, and (c) causality words per tweet in tweets collected during\n the three sampling periods between December 14, 2012, and May 30, 2013. Effects of spatial distance are illustrated in the\n maps, which were derived from a series of three-dimensional spatial regression models; mean frequencies are indicated by color\n (and greater precision of the model’s predictions is represented by greater opacity). Effects of temporal distance are illustrated\n in the graphs, in which mean frequencies are plotted as a function of time since the Newtown shooting (aggregated in 24-hr\n bins); error bars represent 95% confidence intervals.\n

                                        \n \n
                                        \n
                                        \n
                                        \n \n

                                        Moreover, a path model (with time and distance as predictors, number of causality words as a mediator, number of anxiety words\n as the outcome, and total tweet word count as a covariate) revealed that the increase in use of anxiety words with increasing\n time and spatial distance was partially mediated by an associated increase in use of causality words, indirect effect of time\n = 0.006, 95% CI = [0.003, 0.009], p < .001; indirect effect of spatial distance = 0.005, 95% CI = [0.000, 0.009], p < .05. An analogous path model with use of sadness words as the outcome indicated that number of causality words did not\n significantly mediate either the effect of time on use of sadness words, indirect effect = −0.0006, 95% CI = [−0.002, 0.0004],\n p = .24, or the effect of spatial distance on use of sadness words, indirect effect = −0.002, 95% CI = [−0.004, 0.001], p = .23. These two path models were implemented via the gsem (generalized structural equation modeling) command in Stata 13,\n with family set to “negative binomial.” Significance of indirect paths was assessed with the nlcom command (which computes\n delta-method standard errors; StataCorp, 2013).\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Effects on anger

                                        \n \n

                                        For comparison purposes, we also investigated effects of time and spatial distance on anger, an emotion previously identified\n as a key component of the societal-level reaction to violent tragedy (e.g., Lerner, Gonzalez, Small, & Fischhoff, 2003). We found that use of anger words did not change significantly across time, b = −0.01, 95% CI = [−0.03, 0.01], p = .37, but did increase significantly with increasing spatial distance, b = 0.10, 95% CI = [0.07, 0.13], p < .001. (For additional information about the magnitude of the effects of time and spatial distance, see Tables S2 and S3\n in the Supplemental Material.)\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Mapping patterns of use of sadness, anxiety, and causality words

                                        \n \n

                                        To more thoroughly model and visualize patterns of word use across space, we ran a series of three-dimensional spatial regression\n models. In each model, a smooth surface was fitted to the observed data to predict a tweet feature (y) across the continental United States as a function of latitude (x\n 1) and longitude (x\n 2). To define these surfaces, we implemented a penalized thin-plate regression spline method using the bam function within the mgcv package in R (Wood, 2003). The mapped surfaces (see Fig. 2) represent levels of word use with variations in color and model precision (i.e., the inverse of prediction standard error,\n determined in part by data density) with variations in opacity. As expected, these mapped models are consistent with the linear\n regression analyses reported earlier (which collapsed latitude and longitude into a single distance dimension), but they provide\n more information about the spatial patterns of change in use of sadness, anxiety, and causality words.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Word-level analyses

                                        \n \n

                                        To characterize the nature of these relationships at the level of individual words, we correlated time (in seconds) and approximate\n distance (in miles) with frequencies of each of the words in the LIWC sadness, anxiety, and causality categories. Table 1 summarizes the results of these analyses by showing, for each category, the five words whose usage was most strongly associated\n with spatial distance and the five words whose usage was most strongly associated with the passage of time. We corrected for\n multiple comparisons within word category using the false-discovery-rate procedure (Benjamini & Hochberg, 1995). (For additional information about word-level patterns in use of affective words, see Fig. S1 in the Supplemental Material.)\n

                                        \n \n
                                        \n
                                        \n \n
                                        \n
                                        Table 1. \n \n

                                        Individual Sadness, Anxiety, and Causality Words Most Strongly Associated With Increasing Time and Spatial Distance From the\n Newtown Tragedy\n

                                        \n \n
                                        \n
                                        \n
                                        \n \n
                                        \n \n " - ] - }, - "author_contrib_html": { - "value": [ - "\n \n \n

                                        Author Contributions B. Doré and K. N. Ochsner designed the research. B. Doré, L. Ort, and O. Braverman collected and managed the data. B. Doré\n analyzed and visualized the data. B. Doré wrote the manuscript, and K. N. Ochsner provided critical revisions.\n

                                        \n \n " - ] - }, - "competing_interests_html": { - "value": [ - "\n \n \n

                                        Declaration of Conflicting Interests The authors declared that they had no conflicts of interest with respect to their authorship or the publication of this article.\n

                                        \n \n " - ] - }, - "references_html": { - "value": [ - "\n \n

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                                        \n " - ] - }, - "file_hashes": [ - { - "fulltext.html": "6ed6cd9e0c522dad65896595b42d4af9" - }, - { - "fulltext.pdf": "37da58bf1a2074a2b89eb444dee0ddd4" - } - ] - }, - "http://pss.sagepub.com/content/26/4/385.full": { - "publisher": { - "value": [ - "SAGE Publications" - ] - }, - "journal_name": { - "value": [ - "Psychological Science" - ] - }, - "journal_issn": { - "value": [ - "0956-7976", - "1467-9280" - ] - }, - "volume": { - "value": [ - "26" - ] - }, - "issue": { - "value": [ - "4" - ] - }, - "firstpage": { - "value": [ - "385" - ] - }, - "title": { - "value": [ - "Bogus Visual Feedback Alters Onset of Movement-Evoked Pain in People With Neck Pain" - ] - }, - "author_name": { - "value": [ - "Daniel S. Harvie", - "Markus Broecker", - "Ross T. Smith", - "Ann Meulders", - "Victoria J. Madden", - "G. Lorimer Moseley" - ] - }, - "author_institution": { - "value": [ - "\n 1Sansom Institute for Health Research, University of South Australia", - "\n 2School of Information Technology and Mathematical Science, University of South Australia", - "\n 2School of Information Technology and Mathematical Science, University of South Australia", - "\n 3Research Group on Health Psychology, University of Leuven", - "\n 1Sansom Institute for Health Research, University of South Australia", - "\n 1Sansom Institute for Health Research, University of South Australia" - ] - }, - "date_published": { - "value": [ - "\n \t April 2015 \n " - ] - }, - "date_accepted": { - "value": [ - "Accepted November 18, 2014.\n ", - "Accepted " - ] - }, - "date_submitted": { - "value": [ - "Received July 15, 2014.\n ", - "Received " - ] - }, - "doi": { - "value": [ - "10.1177/0956797614563339" - ] - }, - "pmid": { - "value": [ - "25691362" - ] - }, - "copyright": { - "value": [ - "© The Author(s) 2015" - ] - }, - "fulltext_html": { - "value": [ - "http://pss.sagepub.com/content/26/4/385.full" - ] - }, - "fulltext_pdf": { - "value": [ - "http://pss.sagepub.com/content/26/4/385.full.pdf" - ] - }, - "abstract_html": { - "value": [ - "\n \n

                                        Abstract

                                        \n \n

                                        Pain is a protective perceptual response shaped by contextual, psychological, and sensory inputs that suggest danger to the\n body. Sensory cues suggesting that a body part is moving toward a painful position may credibly signal the threat and thereby\n modulate pain. In this experiment, we used virtual reality to investigate whether manipulating visual proprioceptive cues\n could alter movement-evoked pain in 24 people with neck pain. We hypothesized that pain would occur at a lesser degree of\n head rotation when visual feedback overstated true rotation and at a greater degree of rotation when visual feedback understated\n true rotation. Our hypothesis was clearly supported: When vision overstated the amount of rotation, pain occurred at 7% less\n rotation than under conditions of accurate visual feedback, and when vision understated rotation, pain occurred at 6% greater\n rotation than under conditions of accurate visual feedback. We concluded that visual-proprioceptive information modulated\n the threshold for movement-evoked pain, which suggests that stimuli that become associated with pain can themselves trigger\n pain.\n

                                        \n \n " - ] - }, - "methods_html": { - "value": [ - "\n \n \n

                                        Method

                                        \n \n
                                        \n \n

                                        Participants

                                        \n \n

                                        Twenty-four individuals (6 men, 18 women; mean age = 45 years, SD = 15) volunteered to participate in this study. Sample size was determined a priori to enable detection of a small- to medium-sized\n effect (ηp\n 2 = .04) with 80% power, conservatively assuming a 60% correlation among repeated measures. The average duration of complaint\n was 11 years (SD = 11; range: 2 months to 45 years), and the participants’ pain conditions resulted primarily from posture, tension, or repeated\n strain (n = 9); whiplash (n = 7); degeneration (n = 5); trauma (n = 2); and scoliosis (n = 1). Participants were mildly to moderately disabled (Neck Pain Disability Index score = 29%, SD = 13%). Participants were recruited through local physiotherapy clinics and were reimbursed AU$20 for their participation.\n Participants were excluded if they had pain-free neck rotation, were unable to tolerate repeated rotation to the position\n at which they experienced the onset of pain, had severely impaired vision, or were under the age of 18. Participants were\n also excluded if a physiotherapist had identified significant neurological impairments, such as sensory or motor deficits\n and easily provoked, constant, or progressive upper-limb dysesthesia. The protocol was approved by the Human Research Ethics\n Committee of the University of South Australia (Protocol Number 31537).\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Stimulus material and apparatus

                                        \n \n

                                        A virtual-reality (VR) technique known as redirected walking modulates visual-proprioceptive feedback by tracking real-world movement and then feeding this back into the virtual environment\n in an understated or overstated form. Rotation gain (the factor by which real rotation is translated to virtual rotation) can be manipulated such that virtual and physical rotation\n differ. This process creates the illusion of either more or less movement than is actually happening. Within certain limits,\n participants remain unaware of the manipulation (Steinicke, Bruder, Jerald, Frenz, & Lappe, 2008). We used a VR head-mounted display (HMD) designed for immersive VR environments (Oculus Rift; Oculus VR, Irvine, CA). The\n HMD shown in Figure 1 displayed a virtual world and recorded head movement using internal gyroscopes. Customized software was used to map each\n of six scenes to the virtual template and apply the selected rotation gains. The six scenes included four outdoor scenes (a\n park, a mountain, a countryside, and church grounds) and two indoor scenes (a dining room and a living room).\n

                                        \n \n
                                        \n
                                        \"Fig.
                                        View larger version:\n \n
                                        \n
                                        \n
                                        Fig. 1. \n \n

                                        Virtual reality equipment. Participants sat in supportive chairs that prevented trunk movement (i.e., a seat belt around their\n shoulders) and wore headphones and head-mounted displays. A 360° (cylindrical) virtual template accommodated six virtual scenes.\n

                                        \n \n
                                        \n
                                        \n
                                        \n \n
                                        \n \n
                                        \n \n

                                        Experimental design

                                        \n \n

                                        We used a within-subjects, randomized, double-blinded, repeated-measures design. The distance from center position to the\n left or right position at which participants experienced the onset of pain (i.e., the pain-free range of motion) was quantified in three conditions. Virtual rotation was (a) 20% less than actual physical rotation (rotation gain = 0.8),\n (b) equal to actual physical rotation (rotation gain = 1), or (c) 20% greater than actual physical rotation (rotation gain\n = 1.2). The order of the three conditions was counterbalanced across participants, which created six possible orders in which\n conditions could be presented. Four participants were randomly assigned to each order. Participants were blinded to the experimental\n manipulation and study purpose, and the files relating to the three VR conditions were coded, thereby blinding the experimenter\n to the order of conditions. The measurement of neck rotation was automated, and data were extracted only after collection\n was completed.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Measurement

                                        \n \n

                                        Pain-free range of motion for axial neck rotation was measured in degrees. Because participants stopped at the onset of pain\n in each trial, the distance from center position to the left or right position at which participants experienced the onset\n of pain was defined as the peak rotation for each trial. This measure was extracted from each automated trial output by a\n blinded assessor.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Protocol

                                        \n \n

                                        To prevent changes in postural alignment and to isolate neck movement, we asked participants to sit in a supportive chair,\n and their torsos were fixed in place by a seat belt at the level of the shoulders (see Fig. 1). A laser pointer was affixed to the HMD; the dot it produced was used to mark the starting position on the wall as a physical\n reference point for zeroing of the gyroscopes between measures and conditions. Participants wore headphones that emitted white\n noise to counter any incidental noise that might inform head orientation and disrupt the illusion.\n

                                        \n \n

                                        For each of the three conditions, participants were asked to rotate their heads slowly to the left and to stop at the onset\n of pain. They then returned their heads to the center, at which point the next trial was loaded, and the task was repeated\n on the right side. Each condition consisted of six measures of left rotation and six measures of right rotation. After each\n condition, participants were asked to rate the average pain intensity experienced for each rotation direction. This allowed\n for subsequent assessment of any overall differences in pain intensity between conditions. Pain was rated on an 11-point numerical\n scale (0 = no pain, 10 = the worst imaginable pain). To minimize the possibility that subjects would become aware of the different rotation settings and thus directly compare\n them, we used a 3-min interval between conditions. In addition, the six different VR scenes acted as a distraction from the\n actual study purpose and reduced the risk of participants’ anchoring their rotation to a previous visual cue within a VR scene.\n To assess blinding, at the end of the experiment we asked participants whether they noticed anything different between the\n three conditions.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Manipulation Check 1: setting boundaries for altered visual-proprioceptive feedback

                                        \n \n

                                        To blind participants to this manipulation, we based the upper and lower limits of the rotation gain on the results of a pilot\n study. During this pilot study, an independent cohort of 9 healthy participants (7 men, 2 women; mean age = 32 years, SD = 12) were presented with a range of rotation-gain settings and asked to rotate their heads. They were to indicate when a\n difference between real and virtual rotation occurred by rating the observed rotation as slower than, equal to, or faster\n than the true physical rotation. We aimed to determine the rotation gain at which participants were more likely to judge the\n virtual and real rotation to be equal than they were to judge them to be different. As shown in Figure 2, the rotation gains that corresponded to these points were 0.72 and 1.18. As a result, our experimental gain settings were\n chosen to fall between 0.8 and 1.2, and additional controls were implemented to ensure that participants in the main study\n remained blinded.\n

                                        \n \n
                                        \n
                                        \"Fig.
                                        View larger version:\n \n
                                        \n
                                        \n
                                        Fig. 2. \n \n

                                        Results from the pilot study. The graph shows the percentage of rotations rated as slower than, equal to, or faster than the\n true physical rotation as a function of rotation gain. The double-headed arrow indicates the range of rotation-gain settings\n at which virtual movement speeds were more often perceived as equal to, rather than faster or slower than, real-world movement\n speeds.\n

                                        \n \n
                                        \n
                                        \n
                                        \n \n
                                        \n \n
                                        \n \n

                                        Manipulation Check 2: reliability and validity of measurement

                                        \n \n

                                        The reliability of the gyroscopic measurement of rotation was tested by attaching the HMD to a mechanical (goniometric) arm\n and testing its ability to repeatedly and accurately measure three set angles (20°, 40°, and 60°). Initial observation of\n repeated measures revealed that the measurement was highly precise over a small number of trials, but error gradually increased\n as the number of trials increased. Therefore, a protocol was developed that required the virtual compass to be zeroed every\n five trials. To further prevent accumulation of error, we refreshed the program between conditions. This protocol enabled\n rotation as measured by the HMD to be correlated with actual rotation, r = .994, and produced a high degree of precision in the HDM’s measurements of rotations of 20° (M = 19.8°, SD = 0.8), 40° (M = 39.6°, SD = 0.3), and 60° (M = 59.1°, SD = 2.5).\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Data extraction and statistical-analysis overview

                                        \n \n

                                        To test our main hypothesis (i.e., that visual information that overstates or understates true rotation can affect movement-evoked\n pain), we compared pain-free range of motion across the three conditions. We used repeated measures analysis of variance (ANOVA)\n with Bonferroni-corrected pairwise comparisons. To account for between-subject differences in range of motion, we transformed\n data for each participant to a proportion of the average range of motion demonstrated in the neutral condition. Alpha was\n set at p < .05, and we used Cohen’s guidelines (Cohen, 1988) to interpret the effect sizes ηp\n 2 (.01 = small, .059 = medium, and .138 = large) and Cohen’s d (0.2 = small, 0.5 = medium, and 0.8 = large). As a manipulation check, each participant’s average movement-evoked pain for\n each condition was normalized to a proportion of their average across conditions. Normalized pain ratings were then compared\n among conditions using repeated measures ANOVA.\n

                                        \n \n
                                        \n \n " - ] - }, - "results_html": { - "value": [ - "\n \n

                                        Measurement

                                        \n \n

                                        Pain-free range of motion for axial neck rotation was measured in degrees. Because participants stopped at the onset of pain\n in each trial, the distance from center position to the left or right position at which participants experienced the onset\n of pain was defined as the peak rotation for each trial. This measure was extracted from each automated trial output by a\n blinded assessor.\n

                                        \n \n " - ] - }, - "discussion_html": { - "value": [ - "\n \n

                                        Protocol

                                        \n \n

                                        To prevent changes in postural alignment and to isolate neck movement, we asked participants to sit in a supportive chair,\n and their torsos were fixed in place by a seat belt at the level of the shoulders (see Fig. 1). A laser pointer was affixed to the HMD; the dot it produced was used to mark the starting position on the wall as a physical\n reference point for zeroing of the gyroscopes between measures and conditions. Participants wore headphones that emitted white\n noise to counter any incidental noise that might inform head orientation and disrupt the illusion.\n

                                        \n \n

                                        For each of the three conditions, participants were asked to rotate their heads slowly to the left and to stop at the onset\n of pain. They then returned their heads to the center, at which point the next trial was loaded, and the task was repeated\n on the right side. Each condition consisted of six measures of left rotation and six measures of right rotation. After each\n condition, participants were asked to rate the average pain intensity experienced for each rotation direction. This allowed\n for subsequent assessment of any overall differences in pain intensity between conditions. Pain was rated on an 11-point numerical\n scale (0 = no pain, 10 = the worst imaginable pain). To minimize the possibility that subjects would become aware of the different rotation settings and thus directly compare\n them, we used a 3-min interval between conditions. In addition, the six different VR scenes acted as a distraction from the\n actual study purpose and reduced the risk of participants’ anchoring their rotation to a previous visual cue within a VR scene.\n To assess blinding, at the end of the experiment we asked participants whether they noticed anything different between the\n three conditions.\n

                                        \n \n " - ] - }, - "conclusions_html": { - "value": [ - "\n \n

                                        Manipulation Check 1: setting boundaries for altered visual-proprioceptive feedback

                                        \n \n

                                        To blind participants to this manipulation, we based the upper and lower limits of the rotation gain on the results of a pilot\n study. During this pilot study, an independent cohort of 9 healthy participants (7 men, 2 women; mean age = 32 years, SD = 12) were presented with a range of rotation-gain settings and asked to rotate their heads. They were to indicate when a\n difference between real and virtual rotation occurred by rating the observed rotation as slower than, equal to, or faster\n than the true physical rotation. We aimed to determine the rotation gain at which participants were more likely to judge the\n virtual and real rotation to be equal than they were to judge them to be different. As shown in Figure 2, the rotation gains that corresponded to these points were 0.72 and 1.18. As a result, our experimental gain settings were\n chosen to fall between 0.8 and 1.2, and additional controls were implemented to ensure that participants in the main study\n remained blinded.\n

                                        \n \n
                                        \n
                                        \"Fig.
                                        View larger version:\n \n
                                        \n
                                        \n
                                        Fig. 2. \n \n

                                        Results from the pilot study. The graph shows the percentage of rotations rated as slower than, equal to, or faster than the\n true physical rotation as a function of rotation gain. The double-headed arrow indicates the range of rotation-gain settings\n at which virtual movement speeds were more often perceived as equal to, rather than faster or slower than, real-world movement\n speeds.\n

                                        \n \n
                                        \n
                                        \n
                                        \n \n " - ] - }, - "author_contrib_html": { - "value": [ - "\n \n \n

                                        Author Contributions D. S. Harvie and G. L. Moseley developed the study concept; contributed to design, data analysis, and interpretation; and\n helped write the manuscript. D. S. Harvie collected the data. V. J. Madden contributed to study design and helped write the\n manuscript. M. Broecker and R. T. Smith contributed to study design and provided technical expertise for the virtual reality\n setup. A. Meulders contributed to interpretation and helped write the manuscript. All authors approved the final version of\n the manuscript for submission.\n

                                        \n \n " - ] - }, - "competing_interests_html": { - "value": [ - "\n \n \n

                                        Declaration of Conflicting Interests The authors declared that they had no conflicts of interest with respect to their authorship or the publication of this article.\n

                                        \n \n " - ] - }, - "references_html": { - "value": [ - "\n \n

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                                        \n " - ] - }, - "file_hashes": [ - { - "fulltext.html": "3fa5cf143b97ce4fbe0d7653c516dc8c" - }, - { - "fulltext.pdf": "69c828e0a026fa897671b55a40e4e657" - } - ] - }, - "http://pss.sagepub.com/content/26/4/424.full": { - "publisher": { - "value": [ - "SAGE Publications" - ] - }, - "journal_name": { - "value": [ - "Psychological Science" - ] - }, - "journal_issn": { - "value": [ - "0956-7976", - "1467-9280" - ] - }, - "volume": { - "value": [ - "26" - ] - }, - "issue": { - "value": [ - "4" - ] - }, - "firstpage": { - "value": [ - "424" - ] - }, - "title": { - "value": [ - "Chinese Kindergartners Learn to Read Characters Analytically" - ] - }, - "author_name": { - "value": [ - "Li Yin", - "Catherine McBride" - ] - }, - "author_institution": { - "value": [ - "\n 1Tsinghua University", - "\n 2The Chinese University of Hong Kong" - ] - }, - "date_published": { - "value": [ - "\n \t April 2015 \n " - ] - }, - "date_accepted": { - "value": [ - "Accepted December 13, 2014.\n ", - "Accepted " - ] - }, - "date_submitted": { - "value": [ - "Received March 27, 2014.\n ", - "Received " - ] - }, - "doi": { - "value": [ - "10.1177/0956797614567203" - ] - }, - "pmid": { - "value": [ - "25711130" - ] - }, - "copyright": { - "value": [ - "© The Author(s) 2015" - ] - }, - "fulltext_html": { - "value": [ - "http://pss.sagepub.com/content/26/4/424.full" - ] - }, - "fulltext_pdf": { - "value": [ - "http://pss.sagepub.com/content/26/4/424.full.pdf" - ] - }, - "abstract_html": { - "value": [ - "\n \n

                                        Abstract

                                        \n \n

                                        Do Chinese children implicitly extract information from Chinese print before they are formally taught to read? We examined\n Chinese kindergartners’ sensitivity to regularities in Chinese characters and the relationship between such sensitivity and\n later literacy ability. Eighty-five kindergartners from Beijing were given a character-learning task and assessed on word\n reading and word writing twice within a 1-year interval. Sensitivity to the structural and phonetic regularities in Chinese\n appeared in 4-year-olds, and sensitivity to the positions of radicals in Chinese characters emerged in 5-year-olds. Such sensitivities\n explained unique variance in Chinese word reading and writing 1 year later, with age and nonverbal IQ statistically controlled.\n Young children detected regularities in written Chinese before they received formal instruction in it, which underscores both\n the importance of early statistical learning for literacy development and the analytic properties of Chinese print.\n

                                        \n \n " - ] - }, - "methods_html": { - "value": [ - "\n \n \n

                                        Method

                                        \n \n
                                        \n \n

                                        Participants

                                        \n \n

                                        Eighty-five native Chinese-speaking children (46 boys, 39 girls) from a public kindergarten in Beijing participated at Time\n 1. Forty-two children were from second-year kindergarten (K2; range = 4 years,1 month to 5 years, 2 months; mean age = 4 years,\n 7 months; SD = 3.0 months), and 43 children were from third-year kindergarten (K3; range = 5 years, 1 month to 6 years, 2 months; mean\n age = 5 years, 5 months; SD = 4.1 months). The kindergarten follows the governmental guidelines for preschool education in China. Children are not formally\n taught to read and write at school. Teachers read aloud to children often, and children have the opportunity to look at books\n on their own. They see characters on walls, food packages, product labels, and furniture, and in many other locations. Teachers\n identify characters for children if they ask but do not provide systematic instruction on how to read and write. One year\n later, 73 of the children were tested again for reading and writing at Time 2; 12 additional children who were tested at Time\n 1 were excluded from the study because contact information was unavailable for them at Time 2.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Measures

                                        \n \n
                                        \n \n

                                        Character-learning task

                                        \n \n

                                        In the character-learning task, children were taught to pronounce novel characters (written stimuli) that were based on three\n orthographic conditions (random strokes, noncharacter, and pseudocharacter) and two phonetic-cue conditions (available and\n not available). In the random-strokes condition, the stimuli contained real strokes, but they were not always organized into\n radicals, and they were in arbitrary positions (e.g., “\"Graphic\"”). In the noncharacter condition, the stimuli contained real radicals in illegal positions (e.g., “\"Graphic\"”). In the pseudocharacter condition, the stimuli contained real radicals in legal positions (e.g., “\"Graphic\"”).\n

                                        \n \n

                                        Six sets of stimuli, each consisting of five items, were constructed. In three sets, there were phonetic cues in the pseudocharacter\n and noncharacter conditions, that is, the pronunciation of the whole stimulus was the same as the pronunciation of the phonetic\n radical contained in the stimulus (e.g., the whole-stimulus pronunciation was “yang” for “\"Graphic\"” and “\"Graphic\",” where the real phonetic radical “\"Graphic\"” is also pronounced “yang”). In the other three sets, there were no phonetic cues. The radicals used to construct the pseudocharacters\n and noncharacters were taken from characters familiar to children of this age range, as judged by the schoolteachers, and\n the pronunciations were taken from vocabulary familiar to children. Visual complexity (indexed by the number of strokes) was\n balanced across conditions. Table 1 shows sample stimuli and pronunciations (shown in pinyin, a phonological coding system in which Chinese characters are transcribed in Roman alphabet letters and lexical tones).\n

                                        \n \n
                                        \n
                                        \n \n
                                        \n
                                        Table 1. \n \n

                                        Sample Written Stimuli and Pronunciations Used in the Character-Learning Task

                                        \n \n
                                        \n
                                        \n
                                        \n \n

                                        The character-learning task consisted of a demonstration phase and up to eight learning trials. The experimenters began by\n saying that they would play a character-learning game with the child and that the characters to be learned were unfamiliar,\n but the child should try his or her best to learn. In the demonstration phase, the experimenter showed the child a card displaying\n the character and pronounced it aloud, running his or her fingers under the character. The experimenter then asked the child\n to follow by saying, “This character is read . . . ,” prompting the child to pronounce the character. The procedure was repeated\n for all five stimuli in each set, and the order of demonstration was randomized for each child. Once all five stimuli had\n been introduced, the first learning trial began: The experimenter showed the child one of the cards and asked the child to\n give the pronunciation of the character to which it corresponded. The experimenter praised the child if he or she named the\n character correctly and provided the correct answer if the child named it incorrectly or did not remember. This process was\n repeated for each of the five characters, and the order of learning was randomized for each child. Learning trials continued\n until the child achieved the criterion of responding correctly to all five items on two consecutive trials.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Chinese word reading

                                        \n \n

                                        Children were asked to read aloud 50 Chinese single-character words presented in order of increasing difficulty (Lin et al., 2010). Testing was discontinued when children failed to read 10 characters consecutively. One point was given for each correctly\n read item. The maximum score was 50. The internal consistency for this task was .96 at Time 1 and .91 at Time 2.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Chinese word writing

                                        \n \n

                                        Children were asked to write 10 Chinese words (Wang, McBride-Chang, & Chan, 2014): 3 single-character words and 7 two-character words, totaling 17 characters. All words were orally familiar to children.\n The experimenter read each word twice, putting it in a sentence each time, and then asked the children to try their best to\n write the target word. One point was given for each correctly written character, and the maximum score was 17. The internal\n consistency for this task was .82 at Time 1 and .86 at Time 2.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Nonverbal IQ

                                        \n \n

                                        Sets A and B of Raven’s Standard Progressive Matrices (Raven, Court, & Raven, 1996) were used to measure children’s nonverbal IQ at Time 1 only. The maximum score was 24 points.\n

                                        \n \n
                                        \n \n
                                        \n \n
                                        \n \n

                                        Procedure

                                        \n \n

                                        Testing took place in the middle of the school year. Tasks were administered by trained graduates with degrees in psychology\n or linguistics. At Time 1, each child participated in four sessions, each on separate days over a 3-week period, and was tested\n individually in a quiet room. In Sessions 1 to 3, children took completed each of the three orthographic conditions (with\n and without phonetic cues). The order of conditions was balanced across children, and a different stimulus set was used for\n each orthographic condition. In Session 4, children completed the measures of Chinese word reading, Chinese word spelling,\n and nonverbal IQ, with the order of testing balanced across children. At Time 2, children were tested on Chinese word reading\n and Chinese word writing again.\n

                                        \n \n
                                        \n \n " - ] - }, - "results_html": { - "value": [ - "\n \n

                                        Chinese word reading

                                        \n \n

                                        Children were asked to read aloud 50 Chinese single-character words presented in order of increasing difficulty (Lin et al., 2010). Testing was discontinued when children failed to read 10 characters consecutively. One point was given for each correctly\n read item. The maximum score was 50. The internal consistency for this task was .96 at Time 1 and .91 at Time 2.\n

                                        \n \n " - ] - }, - "discussion_html": { - "value": [ - "\n \n

                                        Chinese word writing

                                        \n \n

                                        Children were asked to write 10 Chinese words (Wang, McBride-Chang, & Chan, 2014): 3 single-character words and 7 two-character words, totaling 17 characters. All words were orally familiar to children.\n The experimenter read each word twice, putting it in a sentence each time, and then asked the children to try their best to\n write the target word. One point was given for each correctly written character, and the maximum score was 17. The internal\n consistency for this task was .82 at Time 1 and .86 at Time 2.\n

                                        \n \n " - ] - }, - "conclusions_html": { - "value": [ - "\n \n

                                        Nonverbal IQ

                                        \n \n

                                        Sets A and B of Raven’s Standard Progressive Matrices (Raven, Court, & Raven, 1996) were used to measure children’s nonverbal IQ at Time 1 only. The maximum score was 24 points.\n

                                        \n \n " - ] - }, - "author_contrib_html": { - "value": [ - "\n \n \n

                                        Author Contributions C. McBride developed the study concept. Both authors contributed to the study design and analyzed and interpreted the data.\n Testing and data collection were performed by L. Yin. L. Yin drafted the manuscript, and C. McBride provided critical revisions.\n Both authors approved the final version of the manuscript for submission.\n

                                        \n \n " - ] - }, - "competing_interests_html": { - "value": [ - "\n \n \n

                                        Declaration of Conflicting Interests The authors declared that they had no conflicts of interest with respect to their authorship or the publication of this article.\n

                                        \n \n " - ] - }, - "references_html": { - "value": [ - "\n \n

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                                        \n " - ] - }, - "file_hashes": [ - { - "fulltext.html": "d4451899b787c5885232af23887f0c03" - }, - { - "fulltext.pdf": "820715e6e58a9a98af8e7ee0fe96a9bf" - } - ] - }, - "http://pss.sagepub.com/content/26/4/456.full": { - "publisher": { - "value": [ - "SAGE Publications" - ] - }, - "journal_name": { - "value": [ - "Psychological Science" - ] - }, - "journal_issn": { - "value": [ - "0956-7976", - "1467-9280" - ] - }, - "volume": { - "value": [ - "26" - ] - }, - "issue": { - "value": [ - "4" - ] - }, - "firstpage": { - "value": [ - "456" - ] - }, - "title": { - "value": [ - "Improving Vision Among Older Adults" - ] - }, - "author_name": { - "value": [ - "Denton J. DeLoss", - "Takeo Watanabe", - "George J. Andersen" - ] - }, - "author_institution": { - "value": [ - "\n 1University of California, Riverside", - "\n 2Brown University", - "\n 1University of California, Riverside" - ] - }, - "date_published": { - "value": [ - "\n \t April 2015 \n " - ] - }, - "date_accepted": { - "value": [ - "Accepted December 17, 2014.\n ", - "Accepted " - ] - }, - "date_submitted": { - "value": [ - "Received August 31, 2014.\n ", - "Received " - ] - }, - "doi": { - "value": [ - "10.1177/0956797614567510" - ] - }, - "pmid": { - "value": [ - "25749697" - ] - }, - "copyright": { - "value": [ - "© The Author(s) 2015" - ] - }, - "fulltext_html": { - "value": [ - "http://pss.sagepub.com/content/26/4/456.full" - ] - }, - "fulltext_pdf": { - "value": [ - "http://pss.sagepub.com/content/26/4/456.full.pdf" - ] - }, - "abstract_html": { - "value": [ - "\n \n

                                        Abstract

                                        \n \n

                                        A major problem for the rapidly growing population of older adults (age 65 and over) is age-related declines in vision, which\n have been associated with increased risk of falls and vehicle crashes. Research suggests that this increased risk is associated\n with declines in contrast sensitivity and visual acuity. We examined whether a perceptual-learning task could be used to improve\n age-related declines in contrast sensitivity. Older and younger adults were trained over 7 days using a forced-choice orientation-discrimination\n task with stimuli that varied in contrast with multiple levels of additive noise. Older adults performed as well after training\n as did college-age younger adults prior to training. Improvements transferred to performance for an untrained stimulus orientation\n and were not associated with changes in retinal illuminance. Improvements in far acuity in younger adults and in near acuity\n in older adults were also found. These findings indicate that behavioral interventions can greatly improve visual performance\n for older adults.\n

                                        \n \n " - ] - }, - "methods_html": { - "value": [ - "\n \n \n

                                        Method

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                                        Subjects

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                                        Sixteen younger adults (mean age = 22.43 years, SD = 1.16) from the University of California, Riverside (8 male and 8 female) and 16 older adults (mean age = 71.23 years, SD = 5.85) from the surrounding community (8 male and 8 female) participated in the study. The sample size was determined on\n the basis of pilot studies and previous research demonstrating an effect of training in older and younger adults (Andersen et al., 2010; Bower & Andersen, 2012; Bower et al., 2013; DeLoss et al., 2014). All subjects were compensated for their participation at a rate of $10 per hour. Older individuals received an additional\n $5 per hour to cover transportation costs to the campus. The sample size for each age group was comparable with sample sizes\n in other studies investigating the effects of perceptual learning. Subjects were naive to the purpose of the study, and all\n had normal or corrected-to-normal visual acuity.\n

                                        \n \n

                                        All subjects were screened using an array of cognitive and perceptual tests. This procedure ensured that the older group did\n not exhibit any early or atypical cognitive decline (e.g., Alzheimer’s disease) that could influence the results of the study.\n Demographic information for the subjects is presented in Table 1. One-way analyses of variance revealed that prior to training, there were significant differences between the two age groups\n in acuity and on the Matrix Reasoning subtest of the third edition of the Wechsler Adult Intelligence Scale (Wechsler, 1997; Fs ≤ 2.5, ps > .05). While the older group’s performance was significantly different from that of the younger group on Matrix Reasoning,\n their score was well above the age norm found in previous research (Ardila, 2007). Subjects were also screened for eye disease and neurological disorders.\n

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                                        Table 1. \n \n

                                        Demographic Information and Results From Cognitive and Perceptual Tests Administered Prior to the Start of the Study

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                                        Apparatus

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                                        Stimuli were presented on a 21-in. CRT monitor (Viewsonic P225F) at a resolution of 1,024 × 768 pixels; the monitor had a\n refresh rate of 100 Hz (noninterlaced) and a mean luminance value of 53.82 cd/m2. Stimuli were generated on a Dell Vostro 430 PC equipped with an Intel Core i5 750 processor using the Windows XP (Service\n Pack 3) operating system. A GeForce GTS 240 graphics card (NVIDIA, Santa Clara, CA) was used along with a Bits++ system (Cambridge\n Research Systems, Rochester, Kent, United Kingdom) to achieve 14-bit gray scale (16,384 gray-scale levels). Custom experimental\n software was written in MATLAB (The MathWorks, Natick, MA); Psychophysics Toolbox extensions were also utilized (Brainard, 1997; Pelli, 1997). The monitor was calibrated using a ColorCal2 colorimeter (Cambridge Research Systems). Gamma correction was performed through\n linearization of the color lookup table.\n

                                        \n \n

                                        Pupil size was measured on testing days using an EyeLink 1000 Tower Mount (SR Research, Ottawa, Ontario, Canada); subjects’\n head position was also stabilized with this device. Subjects’ far acuity was measured using the 2000 Series Revised ETDRS\n Chart 2 (Precision Vision, La Salle, IL) at a distance of 3 m. Subjects’ near acuity was measured using the 2000 series New\n ETDRS Chart 3 at a distance of 40 cm. Contrast sensitivity was measured using the Pelli-Robson Contrast Sensitivity Chart\n (Precision Vision).\n

                                        \n \n
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                                        Stimuli and procedure

                                        \n \n

                                        The experiment consisted of 1.5 hr per day of testing and training over 7 days. Subjects were required to complete the study\n within 3 weeks of their first testing session. Stimuli were viewed binocularly on a monitor at a distance of 94 cm. Corrective\n lenses normally worn by the subjects were allowed during the experiment. All stimuli were viewed through a plano-convex glass\n collimation lens (45.7 cm diameter) with a 19% magnification factor to minimize any age-related differences in accommodative\n focus. The size of the stimuli was corrected to account for this magnification factor. The experiment was run in a darkened\n room; the only light source was the monitor. Stimuli were Gabor patches presented at 1.5 cycles per degree of visual angle\n (0.65° standard deviation of the Gaussian mask), and the phase of the Gabor was randomized ±180° on each trial.\n

                                        \n \n
                                        \n \n

                                        Familiarization task

                                        \n \n

                                        On the first day of the study, before the experiment began, all subjects were given a 30-trial practice session to familiarize\n them with the task. These practice trials were presented without Gaussian noise. Subjects completed 15 trials in which the\n Gabor patch appeared in a standard orientation 45° clockwise off vertical and 15 trials in which the Gabor patch had a standard\n orientation 45° counterclockwise off vertical. At the beginning of each trial, subjects saw a fixation point in the center\n of the display for 1,600 ms. This fixation point alternated between black and white every 400 ms, to attract attention (Betts, Taylor, Sekuler, & Bennett, 2005). A Gabor patch then appeared at one of the two standard orientations for 100 ms. A second fixation point then appeared for\n 1,200 ms, alternating between black and white every 300 ms, followed by the target stimulus for 100 ms. During this phase,\n the target was rotated either 25° clockwise or 25° counterclockwise away from the standard orientation. After the target disappeared,\n the screen assumed a uniform midgray value indicating that the subject should judge whether the target stimulus was rotated\n clockwise or counterclockwise compared with the standard orientation (Fig. 1). Responses were made using the left and right arrow keys on the keyboard. Audio feedback was provided on each trial to indicate\n whether the subject was correct. Subjects were then prompted to “press any key to continue” to begin the next trial. During\n the familiarization task, subjects were instructed to get at least one trial incorrect to familiarize themselves with the\n corresponding auditory feedback.\n

                                        \n \n
                                        \n
                                        \"Fig.
                                        View larger version:\n \n
                                        \n
                                        \n
                                        Fig. 1. \n \n

                                        Example of the task used in the study. In each trial, subjects saw a Gabor patch at one of two standard orientations—25° clockwise\n (shown here) or 25° counterclockwise for training and testing trials, 45° clockwise or 45° counterclockwise for familiarization\n trials. After this Gabor patch disappeared, subjects saw a second stimulus and had to judge whether it was rotated clockwise\n or counterclockwise in comparison with the standard orientation (the examples shown here are rotated 15° clockwise and counterclockwise\n off the standard orientation, respectively).\n

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                                        Testing

                                        \n \n

                                        Orientation-discrimination thresholds were tested during the first and last days (Days 1 and 7) of the experiment. During\n testing, the Gabor patches were embedded in additive Gaussian noise in four of the five testing blocks. The first block consisted\n of a no-noise condition with the standard deviation of the additive Gaussian noise set to zero; the standard deviation of\n the Gaussian distribution was then increased by 0.084375 in each successive block to a maximum of 0.3375 in Block 5.\n

                                        \n \n

                                        Standard stimulus orientations were either clockwise 25° or counterclockwise 25° off vertical (see Fig. 2 for an example of the stimuli). The testing order of these standard orientations was counterbalanced across subjects. These\n two orientations were chosen on the basis of previous research demonstrating that improvements in orientation sensitivity\n begin to degrade when the stimulus is rotated approximately 40° away from the trained orientation (Matthews, Liu, & Qian, 2001). These two specific standard orientations were chosen because they are 50° offset from one another.\n

                                        \n \n
                                        \n
                                        \"Fig.
                                        View larger version:\n \n
                                        \n
                                        \n
                                        Fig. 2. \n \n

                                        Example of contrast and noise levels used in the experiment. Gabor patches are displayed at 75% contrast in the top row and\n at 25% contrast in the bottom row. Stimuli were presented in five blocks (examples shown from left to right). There was no\n noise in the first block, but starting with the second block, stimuli were presented in Gaussian noise, with the noise level\n increasing in each subsequent block.\n

                                        \n \n
                                        \n
                                        \n
                                        \n \n

                                        During Days 1 and 7, pretraining Michelson contrast thresholds for the trained and untrained standard orientations were assessed\n at five noise levels using the QUEST procedure (Watson & Pelli, 1983). QUEST was initialized with a criterion level of 0.75 (β = 1.4, δ = 0.025, γ = 0.5). On testing days, the estimated contrast\n values for QUEST for each successive noise level were 10%, 15%, 20%, 25%, and 30%, with a standard deviation of 5%. Subjects\n completed 60 trials at each noise level during testing. All stimuli were viewed through a circular annulus with a radius of\n 8 degrees of visual angle that was placed against the surface of the monitor. The annulus removed any edge cues that may have\n been used in the orientation-discrimination task. The background between trials and during interstimulus intervals consisted\n of the midgray value of the monitor (for no-noise blocks) or additive Gaussian noise with the mean set at the midgray level\n of the monitor and a standard deviation that matched the additive Gaussian noise (for blocks with external noise).\n

                                        \n \n

                                        Trials progressed in the same fashion as in the familiarization task. The orientation offset was fixed at 15° on all test\n trials. Posttraining thresholds for the trained and untrained orientations were measured on Day 7 using the same procedure\n as on Day 1. Pupil size was also measured on each trial during testing days to derive retinal-illuminance values.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Training

                                        \n \n

                                        Training occurred on Days 2 through 6 using the same stimuli and a similar procedure as in the testing phase, with the key\n difference being that subjects were trained on only one standard orientation instead of the two they saw on testing days.\n During training, all subjects completed five blocks, one at each noise level. There were 150 trials per block, and subjects\n were allowed to take a short break after each block. During each training day, the QUEST procedure was run using the same\n parameters as during the testing days, but with one modification. The contrast threshold estimate for QUEST for each subject\n used the threshold derived on the previous day of testing or training as the initial estimate. Subsequent trials used the\n current threshold, taking into account each trial during the training sessions. Using this method, subjects were constantly\n trained at their threshold (75% correct) during each training day. This allowed training to be constantly optimized for any\n improvement that occurred between or within testing or training sessions. All subjects received 750 training trials per day,\n for a total of 3,750 training trials over the course of the experiment.\n

                                        \n \n
                                        \n \n
                                        \n \n " - ] - }, - "results_html": { - "value": [ - "\n \n

                                        Familiarization task

                                        \n \n

                                        On the first day of the study, before the experiment began, all subjects were given a 30-trial practice session to familiarize\n them with the task. These practice trials were presented without Gaussian noise. Subjects completed 15 trials in which the\n Gabor patch appeared in a standard orientation 45° clockwise off vertical and 15 trials in which the Gabor patch had a standard\n orientation 45° counterclockwise off vertical. At the beginning of each trial, subjects saw a fixation point in the center\n of the display for 1,600 ms. This fixation point alternated between black and white every 400 ms, to attract attention (Betts, Taylor, Sekuler, & Bennett, 2005). A Gabor patch then appeared at one of the two standard orientations for 100 ms. A second fixation point then appeared for\n 1,200 ms, alternating between black and white every 300 ms, followed by the target stimulus for 100 ms. During this phase,\n the target was rotated either 25° clockwise or 25° counterclockwise away from the standard orientation. After the target disappeared,\n the screen assumed a uniform midgray value indicating that the subject should judge whether the target stimulus was rotated\n clockwise or counterclockwise compared with the standard orientation (Fig. 1). Responses were made using the left and right arrow keys on the keyboard. Audio feedback was provided on each trial to indicate\n whether the subject was correct. Subjects were then prompted to “press any key to continue” to begin the next trial. During\n the familiarization task, subjects were instructed to get at least one trial incorrect to familiarize themselves with the\n corresponding auditory feedback.\n

                                        \n \n
                                        \n
                                        \"Fig.
                                        View larger version:\n \n
                                        \n
                                        \n
                                        Fig. 1. \n \n

                                        Example of the task used in the study. In each trial, subjects saw a Gabor patch at one of two standard orientations—25° clockwise\n (shown here) or 25° counterclockwise for training and testing trials, 45° clockwise or 45° counterclockwise for familiarization\n trials. After this Gabor patch disappeared, subjects saw a second stimulus and had to judge whether it was rotated clockwise\n or counterclockwise in comparison with the standard orientation (the examples shown here are rotated 15° clockwise and counterclockwise\n off the standard orientation, respectively).\n

                                        \n \n
                                        \n
                                        \n
                                        \n \n " - ] - }, - "discussion_html": { - "value": [ - "\n \n

                                        Testing

                                        \n \n

                                        Orientation-discrimination thresholds were tested during the first and last days (Days 1 and 7) of the experiment. During\n testing, the Gabor patches were embedded in additive Gaussian noise in four of the five testing blocks. The first block consisted\n of a no-noise condition with the standard deviation of the additive Gaussian noise set to zero; the standard deviation of\n the Gaussian distribution was then increased by 0.084375 in each successive block to a maximum of 0.3375 in Block 5.\n

                                        \n \n

                                        Standard stimulus orientations were either clockwise 25° or counterclockwise 25° off vertical (see Fig. 2 for an example of the stimuli). The testing order of these standard orientations was counterbalanced across subjects. These\n two orientations were chosen on the basis of previous research demonstrating that improvements in orientation sensitivity\n begin to degrade when the stimulus is rotated approximately 40° away from the trained orientation (Matthews, Liu, & Qian, 2001). These two specific standard orientations were chosen because they are 50° offset from one another.\n

                                        \n \n
                                        \n
                                        \"Fig.
                                        View larger version:\n \n
                                        \n
                                        \n
                                        Fig. 2. \n \n

                                        Example of contrast and noise levels used in the experiment. Gabor patches are displayed at 75% contrast in the top row and\n at 25% contrast in the bottom row. Stimuli were presented in five blocks (examples shown from left to right). There was no\n noise in the first block, but starting with the second block, stimuli were presented in Gaussian noise, with the noise level\n increasing in each subsequent block.\n

                                        \n \n
                                        \n
                                        \n
                                        \n \n

                                        During Days 1 and 7, pretraining Michelson contrast thresholds for the trained and untrained standard orientations were assessed\n at five noise levels using the QUEST procedure (Watson & Pelli, 1983). QUEST was initialized with a criterion level of 0.75 (β = 1.4, δ = 0.025, γ = 0.5). On testing days, the estimated contrast\n values for QUEST for each successive noise level were 10%, 15%, 20%, 25%, and 30%, with a standard deviation of 5%. Subjects\n completed 60 trials at each noise level during testing. All stimuli were viewed through a circular annulus with a radius of\n 8 degrees of visual angle that was placed against the surface of the monitor. The annulus removed any edge cues that may have\n been used in the orientation-discrimination task. The background between trials and during interstimulus intervals consisted\n of the midgray value of the monitor (for no-noise blocks) or additive Gaussian noise with the mean set at the midgray level\n of the monitor and a standard deviation that matched the additive Gaussian noise (for blocks with external noise).\n

                                        \n \n

                                        Trials progressed in the same fashion as in the familiarization task. The orientation offset was fixed at 15° on all test\n trials. Posttraining thresholds for the trained and untrained orientations were measured on Day 7 using the same procedure\n as on Day 1. Pupil size was also measured on each trial during testing days to derive retinal-illuminance values.\n

                                        \n \n " - ] - }, - "conclusions_html": { - "value": [ - "\n \n

                                        Training

                                        \n \n

                                        Training occurred on Days 2 through 6 using the same stimuli and a similar procedure as in the testing phase, with the key\n difference being that subjects were trained on only one standard orientation instead of the two they saw on testing days.\n During training, all subjects completed five blocks, one at each noise level. There were 150 trials per block, and subjects\n were allowed to take a short break after each block. During each training day, the QUEST procedure was run using the same\n parameters as during the testing days, but with one modification. The contrast threshold estimate for QUEST for each subject\n used the threshold derived on the previous day of testing or training as the initial estimate. Subsequent trials used the\n current threshold, taking into account each trial during the training sessions. Using this method, subjects were constantly\n trained at their threshold (75% correct) during each training day. This allowed training to be constantly optimized for any\n improvement that occurred between or within testing or training sessions. All subjects received 750 training trials per day,\n for a total of 3,750 training trials over the course of the experiment.\n

                                        \n \n " - ] - }, - "author_contrib_html": { - "value": [ - "\n \n \n

                                        Author Contributions All authors contributed to the design of the study. Data were collected by D. J. DeLoss and analyzed by D. J. DeLoss and\n G. J. Andersen. D. J. DeLoss drafted the manuscript. G. J. Andersen and D. J. DeLoss provided revisions. All authors approved\n the final manuscript.\n

                                        \n \n " - ] - }, - "competing_interests_html": { - "value": [ - "\n \n \n

                                        Declaration of Conflicting Interests The authors declared that they had no conflicts of interest with respect to their authorship or the publication of this article.\n

                                        \n \n " - ] - }, - "references_html": { - "value": [ - "\n \n

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                                        90. \n
                                        \n " - ] - }, - "file_hashes": [ - { - "fulltext.html": "8dba5cddc4478a8192d1a82fb8d3fe19" - }, - { - "fulltext.pdf": "a5b3005e8626bc1ed65f61da553c274c" - } - ] - }, - "http://pss.sagepub.com/content/26/4/499.full": { - "publisher": { - "value": [ - "SAGE Publications" - ] - }, - "journal_name": { - "value": [ - "Psychological Science" - ] - }, - "journal_issn": { - "value": [ - "0956-7976", - "1467-9280" - ] - }, - "volume": { - "value": [ - "26" - ] - }, - "issue": { - "value": [ - "4" - ] - }, - "firstpage": { - "value": [ - "499" - ] - }, - "title": { - "value": [ - "Young Children Show the Bystander Effect in Helping Situations" - ] - }, - "author_name": { - "value": [ - "Maria Plötner", - "Harriet Over", - "Malinda Carpenter", - "Michael Tomasello" - ] - }, - "author_institution": { - "value": [ - "\n 1Department of Developmental and Comparative Psychology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany", - "\n 2Department of Psychology, University of York", - "\n 1Department of Developmental and Comparative Psychology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany", - "\n 3School of Psychology & Neuroscience, University of St Andrews", - "\n 1Department of Developmental and Comparative Psychology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany" - ] - }, - "date_published": { - "value": [ - "\n \t April 2015 \n " - ] - }, - "date_accepted": { - "value": [ - "Accepted January 6, 2015.\n ", - "Accepted " - ] - }, - "date_submitted": { - "value": [ - "Received April 15, 2014.\n ", - "Received " - ] - }, - "doi": { - "value": [ - "10.1177/0956797615569579" - ] - }, - "pmid": { - "value": [ - "25792132" - ] - }, - "copyright": { - "value": [ - "© The Author(s) 2015" - ] - }, - "fulltext_html": { - "value": [ - "http://pss.sagepub.com/content/26/4/499.full" - ] - }, - "fulltext_pdf": { - "value": [ - "http://pss.sagepub.com/content/26/4/499.full.pdf" - ] - }, - "abstract_html": { - "value": [ - "\n \n

                                        Abstract

                                        \n \n

                                        Much research in social psychology has shown that otherwise helpful people often fail to help when bystanders are present.\n Research in developmental psychology has shown that even very young children help and that the presence of others can actually\n increase helping in some cases. In the current study, in contrast, 5-year-old children helped an experimenter at very high\n levels when they were alone but helped significantly less often in the presence of bystanders who were potentially available\n to help. In another condition designed to elucidate the mechanism underlying the effect, children’s helping was not reduced\n when bystanders were present but confined behind a barrier and thus unable to help (a condition that has not been run in previous\n studies with adults). Young children thus show the bystander effect, and it is due not to social referencing or shyness to\n act in front of others but, rather, to a sense of a diffusion of responsibility.\n

                                        \n \n " - ] - }, - "methods_html": { - "value": [ - "\n \n \n

                                        Method

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                                        Participants

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                                        Participants were sixty 5-year-olds (mean age: 5 years 7 months; age range: 5 years 0 months–5 years 11 months). The sample\n size was specified prior to data collection, based on typical sample sizes in this field. In each condition, half of the participants\n were female and half were male. Children were recruited through a database of parents who had agreed to participate in studies\n on child development. Children were randomly assigned to one of the three conditions. A total of 12 peer confederates (mean\n age: 5 years 10 months; age range: 4 years 11 months–6 years 11 months) were assigned to mixed-sex dyads on the basis of their\n availability to participate in testing and their reliability as confederates. These children were bystanders in the bystander\n and the bystander-unavailable conditions and were always strangers to the participant.\n

                                        \n \n

                                        Four additional children were invited but not tested because they refused to participate. An additional 14 participants were\n tested but excluded from analyses for video-camera error (n = 1), experimenter error (n = 3), or confederate error (n = 10). Confederate error was coded if confederates deviated from their instructions in significant ways: if they gave hints\n to a participant that they knew what was going to happen next (n = 3), if they revealed that they had participated before (n = 4), if a participant noticed them looking toward him or her on more than two occasions during the test phase (n = 1), or if they talked excessively (n = 2). Interrater reliability on the decision to exclude participants because of confederate error was assessed for 12 randomly\n selected cases (including 6 of the 10 confederate errors) by a coder who was naive to the hypotheses of the study (κ = .83).\n The few disagreements were resolved by discussion.\n

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                                        Setup and materials

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                                        Testing was conducted in a room containing four child-sized tables and chairs, one for the experimenter and three for the\n participant and the two bystanders. The children’s tables stood next to each other (at a distance of 130 cm) in the back of\n the room, facing the experimenter’s table, and were separated by 135 cm × 80 cm barriers (which were opaque up to a height\n of 70 cm, i.e., approximately the shoulder height of the seated children). From the participant’s sitting position, both bystanders\n were equally visible in the bystander and the bystander-unavailable conditions (see Fig. 1). There was a pile of paper towels on the floor between children’s tables and the experimenter’s table (175 cm from each\n of the children’s tables). Other materials were a set of 10 different pictures for coloring, colored pencils, a 300 cm × 80\n cm cardboard wall, a cup of green paint, and a cup containing colored water and paintbrushes.\n

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                                        \"Fig.
                                        View larger version:\n \n
                                        \n
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                                        Fig. 1. \n \n

                                        A re-creation of the experimental setup in the alone condition (a), the bystander condition (b), and the bystander-unavailable\n condition (c). The participant is seated on the left in each picture.\n

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                                        \n \n

                                        Procedure

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                                        Introduction

                                        \n \n

                                        Participants were told that they were going to color a picture. In the alone condition, participants were led to the testing\n room, where they were asked to choose a picture to color. In the bystander and bystander-unavailable conditions, participants\n met the two confederates in front of the testing room. They were introduced by name and said to be participating as well.\n All children and the experimenter then entered the testing room and chose a picture. Participants always were asked (seemingly\n randomly) to choose first, and then the confederates each chose different pictures.\n

                                        \n \n
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                                        Familiarization phase

                                        \n \n

                                        In all conditions, the experimenter then noticed a puddle of water in the middle of the room, which she wiped up with some\n paper towels. She put the leftover paper towels on the floor, saying that she was doing so “in case something needs to be\n wiped up later.”\n

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                                        Manipulation phase

                                        \n \n

                                        The children were asked to sit down to color. The experimenter then said that while the children colored their pictures, she\n would paint her cardboard wall and, to do that more easily, she would place it in a certain way. In the bystander condition,\n she put it to the side (against the right wall of the room). In the bystander-unavailable condition, she attached the cardboard\n wall to the barriers separating the two tables on the right, such that the two confederates were fenced in and unable to leave\n their compartments (see Fig. 1c). In this condition, the experimenter then commented on the wall with apparent surprise, saying, “Oh, I’ve just realized,\n now you two can’t get out of here. Well, you are fenced in now, briefly, but don’t worry, you can get out as soon as we’re\n finished here.” In the alone condition, the wall was put to the side (as in the bystander condition) for half of the participants\n and was attached to the barriers (as in the bystander-unavailable condition) for the other half. In all conditions, the participants\n were able to move freely. After this, all children were given pencils and were asked to start coloring while the experimenter\n painted her cardboard wall. After approximately a minute, the experimenter then said she needed to clean her paintbrushes\n and sat down at her table with the cup of water and the paintbrushes.\n

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                                        Test phase

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                                        After approximately half a minute, the experimenter “accidentally” knocked over the cup and spilled colored water all over\n her table. She tried to hold back the water with her forearms to prevent it from spilling onto the floor. During the first\n 15 s after spilling the water, the experimenter looked down at the water, said “Oops,” and groaned. She repeated this two\n more times. After those 15 s, if participants had not yet helped, she said, “My cup has fallen over.” After 30 s, the experimenter\n said, “The water is about to drip onto the floor.” After 45 s, she said “I need something to wipe it up” while looking back\n and forth between the water and the paper towels on the floor. After 60 s, she said, “I need the paper towels there,” looking\n at the paper towels, which were out of her reach. She then looked for the first time at the children, starting with the participant\n on the left and then moving her gaze to the right to each of the bystanders (or, in the alone condition, toward the empty\n tables), and did so twice. After 75 s, she said, “Could somebody give me the paper towels there?” while looking at the children\n again as described above. After 90 s, if the participant still had not brought her some paper towels, she appeared to realize\n that there were paper towels behind her that she could reach easily and used them to clean up the water herself.\n

                                        \n \n

                                        Confederates had been instructed to be friendly throughout the study but not to talk, and especially to give no hints about\n being confederates of the experimenter, about having participated in the study before, or about what would happen later. In\n the test phase, they were instructed to look at the experimenter neutrally from time to time but to continue drawing, and\n not to look at the participant. Details about the coding and analyses of confederates’ behavior to check that it was equivalent\n in the two bystander conditions can be found in the Supplemental Material available online. Confederates were told that they\n were just playacting for the sake of the study and that normally one should help in these situations.\n

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                                        Interview

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                                        We also interviewed participants after the main test phase was complete. This interview was based on the first four steps\n of Darley and Latané’s (1970) five-step model and also included a manipulation check. An assistant with whom participants had interacted briefly prior\n to the experiment interviewed them alone. She expressed her regret that she had missed the children’s drawing session, and\n to measure whether the children had noticed the accident, she asked what had happened and, in particular, whether there was\n anything that had happened to the experimenter (Step 1). To measure whether children had understood that the experimenter\n needed help, she asked whether the experimenter had really needed help in the situation (Step 2). To measure who children\n thought was responsible for helping, she asked whose job it was to help in the situation and how participants knew who should\n help (Step 3). To measure whether children knew appropriate means for helping, she asked if participants had known how to\n help the experimenter (Step 4). Finally, as a manipulation check to see whether the cardboard wall was a convincing barrier\n for participants in the bystander-unavailable condition, she asked if anybody else could have helped in the situation.\n

                                        \n \n

                                        At the very end of the test session, after the interview, the assistant emphasized to participants who had helped that it\n was good to help and to participants who had not helped that generally helping is good, but it was probably OK not to help\n in this case, since the experimenter was able to help herself eventually. Participants in the bystander condition were told\n that the bystanders had probably not helped because they had not noticed that the experimenter needed help.\n

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                                        Coding and reliability

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                                        \n \n

                                        Coding of helping

                                        \n \n

                                        For the helping situation, the main measure was whether participants did or did not help the experimenter by bringing her\n at least one paper towel within the 90-s response phase. In addition, we coded how quickly participants helped, using a 7-point\n scale that indicated the phase in which children had helped (phases corresponded to each 15-s step described above, during\n which the experimenter made her need for help increasingly more explicit). Children received a score of 1 if they helped spontaneously\n in the first part of the test phase, a score of 2 if they helped in the second part of the test phase, and so on up to the\n sixth and final part of the test phase; if they did not help, they were not included in the analyses on latency to help.\n

                                        \n \n
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                                        Coding of social referencing

                                        \n \n

                                        For the bystander and bystander-unavailable conditions, we also took a measure of social referencing by coding how often participants\n looked toward the bystanders. The number of looks was divided by the helping phase to correct for the time it took children\n to help. This resulted in a mean number of looks per helping phase for each child.\n

                                        \n \n
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                                        Coding of the interview

                                        \n \n

                                        For Step 1, we coded for whether participants mentioned the water-spilling incident or not. For Step 2, we coded for whether\n participants answered “[experimenter’s name] needed help” or “[experimenter’s name] did not need help.” For Step 3, we asked\n children whose job it had been to help and coded for whether they said “mine” (vs. “everybody’s,” “nobody’s,” or another answer);\n we also asked how they knew who should help and coded for whether they said “because I had to do it” (vs. “everybody could\n do it,” “nobody could do it,” or another answer). For Step 4, we coded for whether children answered “I knew how to help”\n or “I did not know how to help.” Finally, for the manipulation check, we coded for whether children mentioned the cardboard\n wall as a reason why nobody else could have helped.\n

                                        \n \n
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                                        Reliability

                                        \n \n

                                        Videos of the helping situation and the interview were coded by the first author. Reliability coding for the full sample by\n a naive coder who was unaware of the hypotheses of the study revealed perfect agreement on whether or not children helped\n (κ = 1) and the phase in which children helped (rs\n = 1; no difference between coders, Mann-Whitney U test, p = 1) and excellent agreement on the number of times participants looked toward the bystanders (r = .95; no difference between coders, Mann-Whitney U test, p = .65) and the interview responses (all κs > .82). Disagreements were resolved through discussion.\n

                                        \n \n
                                        \n \n
                                        \n \n " - ] - }, - "results_html": { - "value": [ - "\n \n

                                        Introduction

                                        \n \n

                                        Participants were told that they were going to color a picture. In the alone condition, participants were led to the testing\n room, where they were asked to choose a picture to color. In the bystander and bystander-unavailable conditions, participants\n met the two confederates in front of the testing room. They were introduced by name and said to be participating as well.\n All children and the experimenter then entered the testing room and chose a picture. Participants always were asked (seemingly\n randomly) to choose first, and then the confederates each chose different pictures.\n

                                        \n \n " - ] - }, - "discussion_html": { - "value": [ - "\n \n

                                        Familiarization phase

                                        \n \n

                                        In all conditions, the experimenter then noticed a puddle of water in the middle of the room, which she wiped up with some\n paper towels. She put the leftover paper towels on the floor, saying that she was doing so “in case something needs to be\n wiped up later.”\n

                                        \n \n " - ] - }, - "conclusions_html": { - "value": [ - "\n \n

                                        Manipulation phase

                                        \n \n

                                        The children were asked to sit down to color. The experimenter then said that while the children colored their pictures, she\n would paint her cardboard wall and, to do that more easily, she would place it in a certain way. In the bystander condition,\n she put it to the side (against the right wall of the room). In the bystander-unavailable condition, she attached the cardboard\n wall to the barriers separating the two tables on the right, such that the two confederates were fenced in and unable to leave\n their compartments (see Fig. 1c). In this condition, the experimenter then commented on the wall with apparent surprise, saying, “Oh, I’ve just realized,\n now you two can’t get out of here. Well, you are fenced in now, briefly, but don’t worry, you can get out as soon as we’re\n finished here.” In the alone condition, the wall was put to the side (as in the bystander condition) for half of the participants\n and was attached to the barriers (as in the bystander-unavailable condition) for the other half. In all conditions, the participants\n were able to move freely. After this, all children were given pencils and were asked to start coloring while the experimenter\n painted her cardboard wall. After approximately a minute, the experimenter then said she needed to clean her paintbrushes\n and sat down at her table with the cup of water and the paintbrushes.\n

                                        \n \n " - ] - }, - "author_contrib_html": { - "value": [ - "\n \n \n

                                        Author Contributions All authors contributed to the idea of the study and its design. Testing and data collection were performed by M. Plötner.\n M. Plötner analyzed the data under the supervision of H. Over, M. Carpenter, and M. Tomasello. M. Plötner drafted the manuscript,\n and H. Over, M. Carpenter, and M. Tomasello provided critical revisions. All authors approved the final version of the manuscript\n for submission.\n

                                        \n \n " - ] - }, - "competing_interests_html": { - "value": [ - "\n \n \n

                                        Declaration of Conflicting Interests The authors declared that they had no conflicts of interest with respect to their authorship or the publication of this article.\n

                                        \n \n " - ] - }, - "references_html": { - "value": [ - "\n \n

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                                        \n " - ] - }, - "file_hashes": [ - { - "fulltext.html": "6f62b7b7bf8a69a60da33876a5a7aa07" - }, - { - "fulltext.pdf": "59a92b6aa0247154202a982f6d5ec379" - } - ] - }, - "http://pss.sagepub.com/content/17/8/670.full": { - "publisher": { - "value": [ - "SAGE Publications" - ] - }, - "journal_name": { - "value": [ - "Psychological Science" - ] - }, - "journal_issn": { - "value": [ - "0956-7976", - "1467-9280" - ] - }, - "volume": { - "value": [ - "17" - ] - }, - "issue": { - "value": [ - "8" - ] - }, - "firstpage": { - "value": [ - "670" - ] - }, - "title": { - "value": [ - "Naps Promote Abstraction in Language-Learning Infants" - ] - }, - "author_name": { - "value": [ - "Rebecca L. Gómez", - "Richard R. Bootzin", - "Lynn Nadel" - ] - }, - "author_institution": { - "value": [ - - ] - }, - "date_published": { - "value": [ - "\n \t August 2006 \n " - ] - }, - "date_accepted": { - "value": [ - "Accepted November 8, 2005.\n ", - "Accepted " - ] - }, - "date_submitted": { - "value": [ - "Received September 26, 2005.\n ", - "Received " - ] - }, - "doi": { - "value": [ - "10.1111/j.1467-9280.2006.01764.x" - ] - }, - "pmid": { - "value": [ - "16913948" - ] - }, - "copyright": { - "value": [ - "© 2006 Association for Psychological Science" - ] - }, - "fulltext_html": { - "value": [ - "http://pss.sagepub.com/content/17/8/670.full" - ] - }, - "fulltext_pdf": { - "value": [ - "http://pss.sagepub.com/content/17/8/670.full.pdf" - ] - }, - "abstract_html": { - "value": [ - "\n \n

                                        Abstract

                                        \n \n

                                        Infants engage in an extraordinary amount of learning during their waking hours even though much of their day is consumed\n by sleep. What role does sleep play in infant learning? Fifteen-month-olds were familiarized with an artificial language 4\n hr prior to a lab visit. Learning the language involved relating initial and final words in auditory strings by remembering\n the exact word dependencies or by remembering an abstract relation between initial and final words. One group napped during\n the interval between familiarization and test. Another group did not nap. Infants who napped appeared to remember a more abstract\n relation, one they could apply to stimuli that were similar but not identical to those from familiarization. Infants who did\n not nap showed a memory effect. Naps appear to promote a qualitative change in memory, one involving greater flexibility in\n learning.\n

                                        \n \n " - ] - }, - "methods_html": { - "value": [ - "\n \n \n

                                        METHOD

                                        \n \n \n

                                        Participants

                                        \n \n

                                        Forty-eight healthy 15-month-olds were recruited from the Tucson area and were randomly assigned to nap, no-nap, and nap-control\n conditions. Infants in the no-nap condition were not deprived of sleep, but were scheduled at times that were not expected\n to coincide with the usual time of their nap, whereas infants in the nap condition were scheduled such that their usual naptime\n would occur between exposure and test. The nap-control condition was included to eliminate the possibility that performance\n in the nap condition was due to one-trial learning (we describe the rationale fully in the Results section). These infants\n also napped between exposure and test, but unlike the other groups, they were exposed to a language with only a small set\n of elements used in the medial position. There were 8 males and 8 females in each condition. Fifteen additional infants were\n tested, but were withdrawn from consideration for various reasons. In several cases, infants were excluded from the analyses\n because their napping was inconsistent with their condition assignment. A nap was defined as 30 min or more of uninterrupted\n sleep in the 4-hr interval between familiarization and test. One infant in the nap-control group who did not meet this criterion\n was excluded, as were 8 infants in the no-nap group who exceeded it. Additionally, infants were excluded if they slept during\n familiarization (1 infant in the nap condition), a parent interfered with the test procedure (1 infant in the nap condition),\n they cried during the test procedure (3 infants in the no-nap condition), or they dozed during the test procedure (1 infant\n in the nap-control condition). Infants in the three groups were tested at similar times of day (see Table 1).\n

                                        \n \n
                                        \n
                                        \n \n
                                        \n
                                        TABLE 1 \n

                                        Mean Looking Times (in Seconds)

                                        \n
                                        \n
                                        \n
                                        \n \n \n \n

                                        Materials

                                        \n \n

                                        Strings in the artificial language took the form pel-X-jic and vot-X-rud in Version A, and pel-X-rud and vot-X-jic in Version B. X elements for the experimental conditions were wadim, kicey, puser, fengle, coomo, loga, gople, taspu, hiftam, deecha, vamey, skiger, benez, gensim, feenam, laeljeen, chila, roosa, plizet, balip, malsig, suleb, nilbo, and wiffle. For the control condition, the X elements were wadim, kicey, and puser. Half of the infants in each condition were familiarized with Version A, and half with Version B.\n

                                        \n \n \n

                                        Familiarization Stimuli

                                        \n \n

                                        A female speaker recorded sample strings. Word tokens from the recorded strings were used to construct Version A and B strings\n (using the same tokens in both versions eliminates random differences in the pronunciation of words or strings in the two\n versions, so that the nonadjacent dependencies are the only source of difference). Strings were separated by 1,000-ms pauses.\n Infants in the nap and no-nap groups were familiarized with high variability (24 X items) and heard each of the 48 strings of their training language 5 times during familiarization. Infants in the nap-control\n group were familiarized with low variability (3 X items) and heard each of the 6 strings of their training language 40 times. Thus, all three groups heard each of the two\n nonadjacent word dependencies 120 times.\n

                                        \n \n \n \n

                                        Test Stimuli

                                        \n \n

                                        Six strings in each version of the language (the subset of strings used in the nap-control condition) were test items in all\n three conditions. Thus, infants in all groups were tested on the same materials. Four test sets were created—the Version A\n strings and Version B strings, each presented in two random orders. Each test set was presented four times (once in each of\n four test blocks), for a total of 16 trials (i.e., a trial consisted of the presentation of a test set). Test sets were 17\n s in duration.\n

                                        \n \n \n \n \n

                                        Procedure

                                        \n \n

                                        An experimenter visited each infant's home 4 hr prior to testing. She attached a Minimitter® Actiwatch with a memory chip to the infant's ankle in order to record body movements. Actigraphy has proven an accurate tool\n for monitoring infants' sleep behavior (Acebo et al., 2005; Gnidovec, Neubauer, & Zidar, 2002; Sadeh, Acebo, Seifer, Aytur, & Carskadon, 1995). As an extra check on accuracy, caregivers kept a log of their infant's activity, noting periods of sleep and externally\n produced motion. A small number of discrepancies between actigraph and log data (fewer than 9% of cases) were resolved by\n detailed comparison of the actigraph data and notes in the logs.\n

                                        \n \n

                                        Familiarization, which took place in the infant's home, lasted 15 min. During this time, the experimenter played quietly with\n the infant while the language played from a tape recorder in the periphery of the area where they were playing.\n

                                        \n \n

                                        Each infant was tested 4 hr later in the laboratory using the head-turn preference procedure (Kemler Nelson et al., 1995). The infant was seated on the caregiver's lap in an enclosed test booth. A center light, directly in front of the infant,\n was used to obtain his or her attention at the beginning of a trial. Two side lights, mounted directly underneath audio speakers\n on the infant's left and right, were used to draw the infant's attention to the speaker that would emit the stimulus on a\n given trial. Side of presentation was determined randomly, with familiar and unfamiliar test trials played from each side.\n

                                        \n \n

                                        An observer outside the booth monitored the infant's looking behavior using a computer program. The program initiated test\n trials in random order and recorded direction and duration of head-turn responses.\n

                                        \n \n

                                        Each of the 16 test trials began with the center light blinking. Once the infant fixated, the light was extinguished, initiating\n blinking of a side light. When the infant made a head turn of at least 30° in the direction of the blinking side light, the\n sample began to play, continuing until its completion or until the infant failed to maintain the minimum 30° head turn for\n 2 consecutive seconds (signaling the infant's loss of attention). The dependent measure was the amount of time the infant\n oriented toward the test stimulus.\n

                                        \n \n \n " - ] - }, - "results_html": { - "value": [ - - ] - }, - "discussion_html": { - "value": [ - - ] - }, - "conclusions_html": { - "value": [ - "\n \n \n

                                        RESULTS

                                        \n \n

                                        There were no differences in looking time as a function of gender or language version, so means were combined over these variables\n (see Table 1).\n

                                        \n \n \n

                                        Nap Condition

                                        \n \n

                                        The first postsleep trial set the direction of preference for the remaining trials. Mean looking-time difference between trials\n consistent with and inconsistent with the first test trial differed significantly from zero, t(15) = 5.15, p = .0001, prep = .996, d = 1.29 (14 of 16 infants showed this pattern).1 This difference was significant whether the first trial was familiar, M = 1.62 s, t(8) = 2.76, p = .024, prep = .923, d = 0.69, or unfamiliar, M = 2.84 s, t(6) = 5.45, p = .002, prep = .984, d = 1.36. In contrast, the difference between looking time to familiar strings and looking time to unfamiliar strings did not\n differ significantly from zero, t(15) < 1.\n

                                        \n \n \n \n

                                        No-Nap Condition

                                        \n \n

                                        The no-nap group showed the opposite pattern of effects, looking significantly longer to familiar than to unfamiliar strings,\n t(15) = 2.52, p = .024, prep = .923, d = 0.63, but exhibiting no pattern of preference based on the first test trial. The looking-time difference between trials\n consistent with and inconsistent with the first test trial did not deviate significantly from zero, t(15) = 1.13, p = .278, prep = .655, d = 0.28 (only 9 of 16 infants followed this pattern). The significant preference for familiar over unfamiliar strings is a\n replication of the effect reported when there is no delay between familiarization and test (Gómez & Maye, 2005) and is impressive given that familiarization occurred 4 hr earlier.\n

                                        \n \n \n \n

                                        Nap Versus No-Nap Conditions

                                        \n \n

                                        The looking-time difference between trials consistent with and inconsistent with the first test trial was significantly greater\n for the nap than for the no-nap condition, t(30) = 2.14, p = .04, prep = .894, d = 0.38, suggesting that sleep had an effect that was not found after the delay. The preference for familiar over unfamiliar\n strings was not significantly greater in the no-nap than in the nap condition, t(30) = 1.82, p = .079, prep = .838, d = 0.32.\n

                                        \n \n \n \n

                                        Nap-Control Condition

                                        \n \n

                                        Initial experience may have familiarized infants with general characteristics of the language (such as vocabulary) so that\n one-trial learning might take place. We needed a control group of infants who had equivalent prior experience and rest, but\n who were unlikely to have learned the nonadjacent dependency. The control group napped after exposure to a low-variability\n version of the language (middle element drawn from a set of three possible words) that does not promote learning of the nonadjacent\n dependency (Gómez, 2002). If performance in the nap group resulted from one-trial learning, the same pattern of effects would be found in the nap-control\n group. However, these infants did not show a pattern of preference based on the first trial, t(15) = 0.827, p = .421, prep = .553, d = 0.21. The nap group significantly outperformed the nap-control group on this measure, t(30) = 3.59, p = .001, prep = .985, d = 0.63.\n

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                                        \n " - ] - }, - "file_hashes": [ - { - "fulltext.html": "16c4af33baed897a4ea2dc007bb78699" - }, - { - "fulltext.pdf": "a230cfda91a0f386b7d59692249159be" - } - ] - }, - "http://pss.sagepub.com/content/17/8/660.full": { - "publisher": { - "value": [ - "SAGE Publications" - ] - }, - "journal_name": { - "value": [ - "Psychological Science" - ] - }, - "journal_issn": { - "value": [ - "0956-7976", - "1467-9280" - ] - }, - "volume": { - "value": [ - "17" - ] - }, - "issue": { - "value": [ - "8" - ] - }, - "firstpage": { - "value": [ - "660" - ] - }, - "title": { - "value": [ - "How Do I Love Thee? Let Me Count the Words" - ] - }, - "author_name": { - "value": [ - "Richard B. Slatcher", - "James W. Pennebaker" - ] - }, - "author_institution": { - "value": [ - - ] - }, - "date_published": { - "value": [ - "\n \t August 2006 \n " - ] - }, - "date_accepted": { - "value": [ - "Accepted December 21, 2005.\n ", - "Accepted " - ] - }, - "date_submitted": { - "value": [ - "Received June 16, 2005.\n ", - "Received " - ] - }, - "doi": { - "value": [ - "10.1111/j.1467-9280.2006.01762.x" - ] - }, - "pmid": { - "value": [ - "16913946" - ] - }, - "copyright": { - "value": [ - "© 2006 Association for Psychological Science" - ] - }, - "fulltext_html": { - "value": [ - "http://pss.sagepub.com/content/17/8/660.full" - ] - }, - "fulltext_pdf": { - "value": [ - "http://pss.sagepub.com/content/17/8/660.full.pdf" - ] - }, - "abstract_html": { - "value": [ - "\n \n

                                        Abstract

                                        \n \n

                                        Writing about emotional experiences is associated with a host of positive outcomes. This study extended the expressive-writing\n paradigm to the realm of romantic relationships to examine the social effects of writing. For 3 consecutive days, one person\n from each of 86 dating couples either wrote about his or her deepest thoughts and feelings about the relationship or wrote\n about his or her daily activities. In the days before and after writing, instant messages were collected from the couples.\n Participants who wrote about their relationship were significantly more likely to still be dating their romantic partners\n 3 months later. Linguistic analyses of the instant messages revealed that participants and their partners used significantly\n more positive and negative emotion words in the days following the expressive-writing manipulation if the participants had\n written about their relationship than if they had written about their daily activities. Increases in positive emotion words\n partially mediated the relation between expressive writing and relationship stability.\n

                                        \n \n " - ] - }, - "methods_html": { - "value": [ - "\n \n \n

                                        METHOD

                                        \n \n \n

                                        Participants

                                        \n \n

                                        Eighty-six undergraduate psychology students (55 women, 31 men; mean age = 18.7, SD = 1.0) and their partners (31 women, 55 men; mean age = 19.3, SD = 1.6) were recruited on the basis that they were in a committed heterosexual romantic relationship and that they engaged\n in IM conversation with each other every day. The couples had been dating an average of 1.31 years (SD = 1.06).\n

                                        \n \n \n \n

                                        Procedure

                                        \n \n

                                        One member of each couple participated in the writing phase of the study. An experimenter met with participants individually\n or in small groups of 2 to 5 to give them an overview of the study. They were told that its purpose was to quantify the types\n of words that people use in writing and everyday interactions.\n

                                        \n \n

                                        Participants were instructed to forward to a secure e-mail address all daily IM conversations between themselves and their\n partners during the 10 days of the study. Considerable effort was taken during the introductory session to reassure participants\n that their messages would be completely confidential.\n

                                        \n \n

                                        Questionnaires assessing demographic information, relationship status, and relationship satisfaction were completed by participants\n and their partners on-line from home on the first day of the study. Satisfaction was measured using the Relationship Assessment\n Scale (RAS; Hendrick, 1988). The RAS consists of seven items, such as “In general, how satisfied are you with your relationship?” Ratings are made on\n a 7-point Likert scale.\n

                                        \n \n

                                        Participants were randomly assigned to the experimental (n = 44) or control (n = 42) writing condition and were instructed to set aside 20 min per day on the fourth, fifth, and sixth days of the study\n for completion of the on-line writing exercises. Participants in the experimental condition were instructed to write about\n their deepest thoughts and feelings about their current romantic relationship, “to really let go and explore your very deepest\n emotions and thoughts about your relationship.” Those in the control condition were instructed to write in detail about their\n daily activities—a standard control condition for expressive-writing studies. The purpose of the writing assignments was left\n intentionally vague to reduce the possibility of demand characteristics; participants were told that the writing assignments\n would be used to assess basic word use.\n

                                        \n \n

                                        Three months later, participants completed a brief on-line questionnaire that assessed relationship status and satisfaction.

                                        \n \n \n \n

                                        Linguistic Analysis

                                        \n \n

                                        The IM conversations were analyzed using the Linguistic Inquiry and Word Count program (LIWC; Pennebaker, Francis, & Booth, 2001). All conversations from couples in both conditions were spell-checked prior to being submitted to LIWC. They were converted\n to text files, categorized by speaker (participant or partner), and subcategorized according to whether they dated from before\n or after the writing manipulation, resulting in a total of four separate IM text files per couple.\n

                                        \n \n \n " - ] - }, - "results_html": { - "value": [ - "\n \n \n

                                        RESULTS

                                        \n \n \n

                                        Relationship Stability and Language Use

                                        \n \n

                                        Expressive writing was significantly related to the long-term stability of relationships, odds ratio = 3.09, prep = .95, Cohen's d = 0.54. Thirty-four participants (77%) in the experimental condition were still dating their partners at the 3-month follow-up\n mark, compared with 22 participants (52%) in the control condition. There were no significant differences in baseline relationship\n satisfaction between the conditions (experimental M = 6.21, SD = 0.63; control M = 6.01, SD = 0.66), nor was condition related to satisfaction at the 3-month follow-up (experimental M = 5.87, SD = 1.50; control M = 5.94, SD = 0.94). Note that the follow-up satisfaction measures are difficult to interpret because they were available only for couples\n still in their relationships.\n

                                        \n \n

                                        Hierarchical linear modeling (HLM; Raudenbush & Bryk, 2002) was employed to analyze changes in use of emotion words within couples' IM conversations as a function of experimental condition.\n Initial analyses focused on the effects of expressive writing on positive emotion words in couples' conversations. Level 1\n (individual-level) predictors were baseline use of positive emotion words and speaker (participant or partner). Only baseline\n use of positive emotion words was a significant Level 1 predictor, β1 = .51, prep > .99, d = 1.19. Level 2 (couple-level) predictors were gender of the participant, experimental condition, and a Gender × Condition\n interaction term. Only experimental condition was a significant Level 2 predictor, γ01 = .51, prep = .93, d = 0.46. Couples in the expressive-writing condition were more likely than those in the control condition to increase their\n use of positive emotion words with their romantic partners in the days following the manipulation. Additionally, participants\n and partners in the experimental condition increased their use of positive emotion words at similar rates as they communicated\n with each other via IM, even though only the participants were involved in the expressive-writing manipulation.\n

                                        \n \n

                                        Next, the effect of expressive writing on negative emotion words was analyzed. Level 1 predictors were baseline use of negative\n emotion words, as well as the speaker variable. Only baseline use of negative emotion words was a significant Level 1 predictor,\n β1 = .28, prep = .98, d = 0.46. Level 2 predictors were gender of the participant, experimental condition, and a Gender × Condition interaction term.\n Significant Level 2 predictors were experimental condition, γ01 = .54, prep = .98, d = 0.64, and the Gender × Condition interaction, γ02 = .52, prep = .97, d = 0.61. Compared with control couples, couples in the expressive-writing condition were more likely to increase their use\n of negative emotion words with their romantic partners in the days following the writing manipulation. This effect was moderated\n by the gender of the person in each couple who took part in the writing manipulation. Specifically, couples in which the male\n wrote about the relationship increased their use of negative emotion words significantly compared with control couples, whereas\n couples in which the female wrote about the relationship did not change in their use of negative emotion words compared with\n control couples.1

                                        \n \n \n \n

                                        Mediation Effects of Changes in Use of Emotion Words

                                        \n \n

                                        A strength of this design is that it allowed us to explore the degree to which measures of language may reflect the social\n psychological processes underlying the effects of expressive writing. Two sets of mediation analyses were conducted—one with\n positive emotion words as the potential mediator, the other with negative emotion words as the potential mediator. In both\n cases, the outcome measure was relationship stability at the 3-month follow-up. Means and standard deviations for couples'\n use of emotion words in their IM conversations are shown in Table 1.\n

                                        \n \n
                                        \n
                                        \n \n
                                        \n
                                        TABLE 1 \n

                                        Couples' Use of Emotion Words in Instant Messages as a Function of Time and Condition

                                        \n
                                        \n
                                        \n
                                        \n \n \n

                                        Positive Emotion Words

                                        \n \n

                                        Experimental condition and use of positive emotion words before and after the writing manipulation were entered in separate\n steps into a logistic regression in which relationship stability was the dependent variable. Higher levels of postwriting\n positive emotion words were associated with higher levels of couple stability, odds ratio = 3.04, prep = .99, d = 0.95. After controlling for changes in positive emotion words, the effects of experimental condition on relationship stability\n were no longer significant, suggesting possible mediation. The results of a Sobel z test (Sobel, 1982) supported this analysis (z = 2.00, prep = .92). Thus, the salutary effects of writing about one's relationship were at least partially mediated by increases in use\n of positive emotion words in daily IM conversations.\n

                                        \n \n \n \n

                                        Negative Emotion Words

                                        \n \n

                                        No relationship was found between increases in negative emotion words and couple stability (prep < .50). This also was the case in a separate analysis for just those couples in which the male was the participant. The effects\n of expressive writing on stability therefore were not mediated by changes in use of negative emotion words.\n

                                        \n \n \n \n " - ] - }, - "discussion_html": { - "value": [ - - ] - }, - "conclusions_html": { - "value": [ - - ] - }, - "author_contrib_html": { - "value": [ - - ] - }, - "competing_interests_html": { - "value": [ - - ] - }, - "references_html": { - "value": [ - "\n \n

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                                        Abstract

                                        \n \n

                                        This study was designed to determine whether the characteristics of the neighborhood environment are related to the substitution\n of physical activity for sedentary behavior among youth. Fifty-eight 8- to 15-year-old youth were studied in a within-subjects\n crossover design with three phases: baseline, increased sedentary behavior, and decreased sedentary behavior. The relations\n between changes in physical activity and design, diversity, and density attributes of the neighborhood environment were determined\n using random coefficient models. Compared with girls, boys showed greater increases in physical activity when sedentary behaviors\n were reduced and greater decreases in physical activity when sedentary behaviors were increased. Greater access to parks was\n associated with greater physical activity when sedentary behaviors were reduced.\n

                                        \n \n " - ] - }, - "methods_html": { - "value": [ - "\n \n \n

                                        METHOD

                                        \n \n \n

                                        Participants

                                        \n \n

                                        Participants were fifty-eight 8- to 15-year-old youth recruited from the Buffalo-Niagara Falls Metropolitan Area, which is\n home to more than 1 million people. To be included, youth had to report engaging in 15 to 25 hr per week of targeted sedentary\n activities (watching television or videos, playing video games, or using a computer for recreation). Additional inclusion\n criteria were having no dietary, physical-activity, or medical restrictions and not experiencing systematic changes in factors\n that could influence energy intake or energy expenditure during the 9 weeks of the study (e.g., starting a newspaper route\n or beginning summer camp). Sixty percent of the population in the Buffalo-Niagara Falls Metropolitan Area resides in single-family\n detached housing; 40% lives in other housing types, including condominiums, multi-unit houses, and apartments. The city of\n Buffalo and its inner-ring suburbs offer a compact built environment, whereas newer outer-ring suburbs have larger lot sizes\n and lower housing density.\n

                                        \n \n

                                        The characteristics of the youth in this sample are summarized in Table 1 (see also Epstein, Roemmich, Paluch, & Raynor, 2005). Fifty-one (87.9%) of the participants were White, 4 (6.9%) were Black, 2 (3.4%) were Hispanic, and 1 (1.7%) reported “other”\n ethnicity. Parents of boys reported more pieces of exercise equipment in the home than did parents of girls (2.3 ± 1.8 vs.\n 1.1 ± 1.1, p = .006), and boys were more active than girls (518.9 ± 193.6 vs. 401.2 ± 182.5 accelerometer counts/min, p = .021).\n

                                        \n \n
                                        \n
                                        \n \n
                                        \n
                                        TABLE 1 \n

                                        Characteristics of the Participants

                                        \n
                                        \n
                                        \n
                                        \n \n

                                        The consent form was approved by the institutional review board of the University at Buffalo School of Medicine and Biomedical\n Sciences. Written assent to participate was obtained from each child and adolescent, and written consent was obtained from\n their parents.\n

                                        \n \n \n \n

                                        Design and Procedure

                                        \n \n

                                        Families participated in a 9-week experiment, with a 3-week baseline, a 3-week phase in which sedentary behavior was increased,\n and a 3-week phase in which sedentary behavior was decreased. Order of the experimental phases was counterbalanced across\n families. Participants were asked to maintain their usual pattern of sedentary behavior, physical activity, and energy intake\n during baseline. During the experimental phases, the goal was a 25% to 50% increase or decrease from baseline in self-reported\n targeted sedentary behaviors (watching television and videos, playing video games, and using computers for recreation). Families\n could earn up to $475 for adherence to the protocol, and incentives were provided for recording sedentary behaviors and making\n recommended changes in targeted sedentary behaviors. No incentives were earned for changes in physical activity. Families\n attended three meetings, one for each phase of the study, at which we determined whether or not they had met their goals and\n completed all the required measurements. At these meetings, the families also were informed about their next phase and received\n help solving any problems related to the study. Three cohorts began the study in the summer, and two began it during the school\n year. The methods of this study are reported in greater detail elsewhere (Epstein, Roemmich, Paluch, & Raynor, 2005).\n

                                        \n \n \n \n

                                        Measurement

                                        \n \n \n

                                        Sedentary Behavior

                                        \n \n

                                        During 3 baseline days, the youth recorded in a habit book the time and duration of targeted sedentary behaviors (watching\n television or a video, playing video games, and using a computer for recreation). In addition, each family member, including\n the participating youth, recorded his or her television and computer use in a log that was attached to the device, and every\n television and computer was attached to a Brultech event logger (EL-100; Brultech Research, Inc., Port Colborne, Ontario,\n Canada) that recorded whether the appliance was turned on or off on a minute-by-minute basis. Family logs and the Brultech\n event logger were used during the baseline period to develop reliability data on the children's records. There was 90.6% agreement\n (κ = .72) between the youths' habit books and log recordings and 91.8% agreement (κ = .67) between the total time recorded\n on family logs and Brultech devices.\n

                                        \n \n

                                        The participating youth continued to record their targeted sedentary behavior daily throughout the study. Reported minutes\n of sedentary behavior on the 2 weekdays and 1 weekend day that activity data were collected (see the next paragraph) were\n used as the measure of targeted sedentary behavior. Parents reported the number of televisions, computers, and pieces of exercise\n equipment in the home.\n

                                        \n \n \n \n

                                        Physical Activity

                                        \n \n

                                        A unidirectional accelerometer, the Model 7164 Actigraph (formerly CSA; Health One Technology, Fort Walton Beach, FL), validated\n as a measure of physical activity in children (Ekelund et al., 2001; Janz, 1994; Janz, Witt, & Mahoney, 1995), was used to measure physical activity on 2 weekdays and 1 weekend day during the last week of each phase. Participants\n recorded when the Actigraph was put on and removed (e.g., for showering and swimming) on the Previous Day Physical Activity\n Recall (PD-PAR) form (Weston, Petosa, & Pate, 1997).\n

                                        \n \n

                                        Activity counts generated by the Actigraph were recorded in 1-min epochs over the day. The activity counts served as the primary\n dependent measure for the statistical analyses. In addition to activity counts, the number of minutes of moderate to vigorous\n physical activity (MVPA) was estimated. MVPA is defined as activity expenditure that is equal to or greater than 3 METS. One\n MET is equivalent to resting metabolic rate, and METS, measured in milliliters of oxygen consumed per kilogram of body mass\n per minute, are multiples of resting metabolic rate. Estimated activity energy expenditure was based on accelerometer counts\n (Puyau, Adolph, Vohra, & Butte, 2002), and resting metabolic rate was estimated on the basis of age, gender, and weight (Firouzbakhsh et al., 1993). METS values were calculated as follows: (activity energy expenditure + resting metabolic rate)/resting metabolic rate.\n Minutes when this value was greater than or equal to 3 were included as minutes of MVPA. Objective activity data were not\n available for 2 participants in one phase because of equipment malfunction. Their activity counts were estimated using the\n intercept and beta coefficient for the regression model relating Actigraph accelerometer counts and METS (based on PD-PAR\n self-reported activities).\n

                                        \n \n \n \n

                                        Body Mass Index

                                        \n \n

                                        Body mass index (BMI) was calculated from height and weight (kg/m2), with height measured using a stadiometer (Seca, Columbia, MD) and weight measured using a balance-beam scale (Healthometer,\n Bridgeview, IL) calibrated daily. Standardized z-BMI values were calculated by the following formula: (BMI − 50th percentile\n BMI)/SD of BMI, using the 50th-percentile BMI for the child's age and sex (Kuczmarski et al., 2002).\n

                                        \n \n \n \n

                                        Characteristics of the Neighborhood Environment

                                        \n \n

                                        A geographic information system (GIS) measured attributes of the neighborhood environment within a 0.5-mile radius around\n each child's residence using ArcGIS 8 and ArcView 3.3 (network analyst) software (ESRI, 2004). Each child's address was matched (geo-coded) to a unique parcel of land in a land-parcel data layer of either Erie or Niagara\n County in New York State. The attribute table accompanying the data layer was used to identify the type of housing (e.g.,\n single-family, two-family, garden apartment, or public housing project) in which the child lived. Variables related to housing\n density and age of housing in the block where a child's house was located were derived from block-group data from the 2000\n U.S. Census (retrieved from the Census Bureau's American FactFinder Web site, http://factfinder.census.gov, on December 13, 2005).\n

                                        \n \n

                                        On the basis of previous theoretical and conceptual work, we chose to focus on 4 of 67 neighborhood-environment variables\n for which we had data. These variables reflect density, diversity, and design of the neighborhood environment (Table 2; Ewing, 2005). Density, which is a measure of the compactness of an environment or the degree to which residences are located close to\n each other, was calculated as the number of housing units per residential acre. Design of the neighborhood environment includes,\n among other things, the degree to which the layout of the neighborhood facilitates connectivity through its transportation\n network. Design was assessed using a connectivity measure defined as the number of intersections divided by the length of\n the street network in feet. Finally, diversity in land use, the mix of land uses available in a neighborhood, was assessed\n by the percentage of residential parcels (i.e., number of residential parcels as a percentage of the total number of parcels\n accessible by the street network) and by the amount of park area accessible by the street network.\n

                                        \n \n
                                        \n
                                        \n \n
                                        \n
                                        TABLE 2 \n

                                        Neighborhood-Environment Variables

                                        \n
                                        \n
                                        \n
                                        \n \n \n \n \n

                                        Analytic Plan

                                        \n \n

                                        We used analysis of variance to test differences in characteristics of the neighborhood environment by sex (boys vs. girls).\n Separate random coefficient models were built to predict activity changes from baseline in each of the experimental phases\n (i.e., decreasing sedentary behaviors and increasing sedentary behaviors), because previous studies have shown asymmetry in\n how decreasing and increasing sedentary behavior influence physical activity (Epstein, Roemmich, Paluch, & Raynor, 2005). We developed random coefficient models with daily accelerometer measures of physical activity as the dependent variable,\n with time-varying minutes of sedentary behavior and time-invariant age, sex, socioeconomic status, z-BMI, and built-environment\n variables as predictors. The models included a random intercept, with the predictors set as fixed effects. Random coefficient\n models were implemented using natural logs of the measures of activity and sedentary behavior to provide estimates of elasticity—the\n relation between proportional change in sedentary behaviors and proportional change in physical activity. Negative elasticity\n coefficients (e.g., as sedentary behavior decreases, physical activity increases) represent substitution of physical activity\n for sedentary behaviors. Initial models included interactions among the between-subjects variables and interactions between\n sedentary-behavior change and the between-subjects variables. The final models included only significant predictors.\n

                                        \n \n

                                        After the model to predict accelerometer counts was developed, a random regression model to predict minutes of MVPA was developed\n for the study sample using accelerometer counts, targeted sedentary behavior, age, sex, park area within 0.5 mile of the family's\n home, and the interaction of targeted sedentary behavior and sex as predictors.\n

                                        \n \n

                                        Both traditional probability levels and prep, the probability of replicating the results (Killeen, 2005), are reported. To measure effect sizes, we calculated r2 for the relation between the predictors and physical activity in univariate regression models and converted this value to\n d using the formula \"Formula\"\"Graphic\" (Rosnow & Rosenthal, 1996). Analyses were conducted using SYSTAT software (2004).\n

                                        \n \n \n " - ] - }, - "results_html": { - "value": [ - - ] - }, - "discussion_html": { - "value": [ - - ] - }, - "conclusions_html": { - "value": [ - - ] - }, - "author_contrib_html": { - "value": [ - - ] - }, - "competing_interests_html": { - "value": [ - - ] - }, - "references_html": { - "value": [ - "\n \n

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                                        \n " - ] - }, - "file_hashes": [ - { - "fulltext.html": "4287086772b5f8c208b09e3f7aebb7f3" - }, - { - "fulltext.pdf": "bf30f304a49a461f2f1e4a22cfb8d5fb" - } - ] - }, - "http://pss.sagepub.com/content/17/12/1021.full": { - "publisher": { - "value": [ - "SAGE Publications" - ] - }, - "journal_name": { - "value": [ - "Psychological Science" - ] - }, - "journal_issn": { - "value": [ - "0956-7976", - "1467-9280" - ] - }, - "volume": { - "value": [ - "17" - ] - }, - "issue": { - "value": [ - "12" - ] - }, - "firstpage": { - "value": [ - "1021" - ] - }, - "title": { - "value": [ - "The Time Course of Orthographic and Phonological Code Activation" - ] - }, - "author_name": { - "value": [ - "Jonathan Grainger", - "Kristi Kiyonaga", - "Phillip J. Holcomb" - ] - }, - "author_institution": { - "value": [ - - ] - }, - "date_published": { - "value": [ - "\n \t December 2006 \n " - ] - }, - "date_accepted": { - "value": [ - "Accepted May 3, 2006.\n ", - "Accepted " - ] - }, - "date_submitted": { - "value": [ - "Received December 9, 2005.\n ", - "Received " - ] - }, - "doi": { - "value": [ - "10.1111/j.1467-9280.2006.01821.x" - ] - }, - "pmid": { - "value": [ - "17201781" - ] - }, - "copyright": { - "value": [ - "© 2006 Association for Psychological Science" - ] - }, - "fulltext_html": { - "value": [ - "http://pss.sagepub.com/content/17/12/1021.full" - ] - }, - "fulltext_pdf": { - "value": [ - "http://pss.sagepub.com/content/17/12/1021.full.pdf" - ] - }, - "abstract_html": { - "value": [ - "\n \n

                                        Abstract

                                        \n \n

                                        The present study used event-related potentials (ERPs) to examine the time course of orthographic and phonological priming\n in the masked priming paradigm. Participants monitored visual target words for occasional animal names, and ERPs to nonanimal\n critical items were recorded. These critical items were preceded by different types of primes: Orthographic priming was examined\n using transposed-letter (TL) primes (e.g., barin-BRAIN) and their controls (e.g., bosin-BRAIN); phonological priming was examined\n using pseudohomophone primes (e.g., brane-BRAIN) and their controls (e.g., brant-BRAIN). Both manipulations modulated the\n N250 ERP component, which is hypothesized to reflect sublexical processing during visual word recognition. Orthographic (TL)\n priming and phonological (pseudohomophone) priming were found to have distinct topographical distributions and different timing,\n with orthographic effects arising earlier than phonological effects.\n

                                        \n \n " - ] - }, - "methods_html": { - "value": [ - "\n \n \n

                                        METHOD

                                        \n \n
                                        \n \n

                                        Subjects

                                        \n \n

                                        Twenty volunteers (14 female; mean age = 20, SD = 1.71) from Tufts University were paid $25 to participate in this experiment. All reported being right-handed native speakers\n of English with normal or corrected-to-normal vision.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Stimuli

                                        \n \n

                                        The critical stimuli for this experiment were formed from 332 five-letter words and their respective five-letter pseudohomophones.\n Fifteen subjects (who did not participate in the main experiment) rated each word-pseudohomophone pair for phonological similarity\n on a scale from 1 (low) to 7 (high), and the 200 most similar pairs were selected as stimuli for the main experiment (mean rating = 6.52, range = 4.75–7, SD = 0.57).\n

                                        \n \n

                                        Each of the 200 target words was paired with four prime stimuli: the pseudohomophone that was pretested (e.g., brane-BRAIN), a pseudohomophone control prime (e.g., brant-BRAIN), a TL prime (e.g., barin-BRAIN), and a TL control prime (e.g., bosin-BRAIN). Control primes for pseudohomophones were formed by replacing one letter of the pseudohomophone that did not overlap with\n the target word (e.g., the e in brane became a t in brant); the pseudohomophone primes and pseudohomophone control primes were therefore matched in terms of the number of letters\n shared by prime and target and the position of the shared letters. Control primes for TL primes had two different letters\n replacing the transposed letters. For purposes of counterbalancing, each participant was tested with one of four lists of\n prime-target pairings; each list included all four priming conditions, with each target word appearing only once. Thus, each\n target word was tested in all four priming conditions across different participants.\n

                                        \n \n

                                        Sixty noncritical trials were intermixed with the 200 critical trials. Thirty of the noncritical trials contained an animal\n name in the prime position and a filler word in the target position (e.g., horse-TABLE), and 30 contained an animal name in the target position and an unrelated pseudohomophone, TL, or corresponding control prime\n in the prime position (e.g., trane-HORSE, trian-HORSE, troun-HORSE). Each of 30 animal names was used once as a prime and once as a target in each list. The animal names served as probe items\n in a go/no-go semantic categorization task in which participants were instructed to rapidly press a button whenever they detected\n an animal name. Subjects were told to read all other words passively (i.e., critical stimuli did not require an overt response).\n The trials on which animal names were in the prime position provided a measure of prime awareness during the course of the\n experiment. A practice session was administered before the main experiment to familiarize the subjects with the procedure.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Procedure

                                        \n \n

                                        Visual stimuli were presented on a 19-in. monitor set to a refresh rate of 60 Hz (which allows 16.67-ms resolution of stimulus\n control) and located 143 cm in front of the participant. Stimuli were displayed at high contrast as white letters (Arial font)\n on a black background (letter matrix was 30 pixels tall × 15 pixels wide). Each trial began with the termination of a fixation\n stimulus in the middle of the screen. After 500 ms, a forward mask of seven pound signs (#######) was presented for a duration\n of 500 ms. This forward mask was replaced at the same location on the screen by a five-letter prime, presented in lowercase\n letters for 50 ms. The prime was immediately replaced by a backward mask of seven random consonants (e.g., CFTRPQB). The backward\n mask remained on the screen for one retrace interval (16.67 ms) and was immediately replaced by the visual target, presented\n in uppercase letters for a duration of 500 ms. All target words were followed by a 1,000-ms black screen, which was replaced\n by a 2,000-ms fixation stimulus marking the end of the trial. The next trial followed a 500-ms blank screen. Subjects were\n asked to blink and move their eyes only when the fixation stimulus appeared on the screen.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Electroencephalogram Recording

                                        \n \n

                                        Participants were seated in a comfortable chair in a sound-attenuated darkened room. The electroencephalogram (EEG) was recorded\n from 29 active tin electrodes held in place on the scalp by an elastic cap (Electrode-Cap International, Eaton, OH). Additional\n electrodes were attached below the left eye (to monitor for vertical eye movement or blinks), to the right of the right eye\n (to monitor for horizontal eye movements), over the left mastoid bone (reference), and over the right mastoid bone (recorded\n actively to monitor for differential mastoid activity). All EEG electrode impedances were maintained below 5 kΩ (impedance\n for eye electrodes was less than 10 kΩ). The EEG was amplified by an SA Bioamplifier with a band pass of 0.01 to 40 Hz, and\n the EEG was continuously sampled at a rate of 200 Hz throughout the experiment.\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Data Analysis

                                        \n \n

                                        Averaged ERPs were formed off-line from trials free of ocular and muscular artifact (less than 5% of trials). Separate waveforms\n were calculated by averaging compound-stimulus ERPs (i.e., the EEG time-locked to a point 100 ms before prime onset and lasting\n until 900 ms after target onset) for each of the four priming conditions. In order to carefully quantify the time course of\n the ERP effects, we measured mean amplitudes in three contiguous windows after target onset: 150 through 250 ms, 250 through\n 350 ms, and 350 through 550 ms. Repeated measures analyses of variance (ANOVAs) with within-participants factors of prime\n type (pseudohomophone vs. TL) and repetition (repeated vs. control) were used to analyze the ERP data. The Geisser and Greenhouse (1959) correction was applied to all repeated measures with more than one degree of freedom (corrected p values are reported). Three anterior (FP1, FPz, FP2), three middle (C3, Cz, C4), and three posterior (P3, Pz, P4) electrode\n sites were chosen for analysis; these sites provided ANOVA factors of laterality (left vs. center vs. right) and front-to-back\n extent (anterior vs. middle vs. posterior).\n

                                        \n \n
                                        \n \n " - ] - }, - "results_html": { - "value": [ - "\n \n

                                        Electroencephalogram Recording

                                        \n \n

                                        Participants were seated in a comfortable chair in a sound-attenuated darkened room. The electroencephalogram (EEG) was recorded\n from 29 active tin electrodes held in place on the scalp by an elastic cap (Electrode-Cap International, Eaton, OH). Additional\n electrodes were attached below the left eye (to monitor for vertical eye movement or blinks), to the right of the right eye\n (to monitor for horizontal eye movements), over the left mastoid bone (reference), and over the right mastoid bone (recorded\n actively to monitor for differential mastoid activity). All EEG electrode impedances were maintained below 5 kΩ (impedance\n for eye electrodes was less than 10 kΩ). The EEG was amplified by an SA Bioamplifier with a band pass of 0.01 to 40 Hz, and\n the EEG was continuously sampled at a rate of 200 Hz throughout the experiment.\n

                                        \n \n " - ] - }, - "discussion_html": { - "value": [ - "\n \n

                                        Data Analysis

                                        \n \n

                                        Averaged ERPs were formed off-line from trials free of ocular and muscular artifact (less than 5% of trials). Separate waveforms\n were calculated by averaging compound-stimulus ERPs (i.e., the EEG time-locked to a point 100 ms before prime onset and lasting\n until 900 ms after target onset) for each of the four priming conditions. In order to carefully quantify the time course of\n the ERP effects, we measured mean amplitudes in three contiguous windows after target onset: 150 through 250 ms, 250 through\n 350 ms, and 350 through 550 ms. Repeated measures analyses of variance (ANOVAs) with within-participants factors of prime\n type (pseudohomophone vs. TL) and repetition (repeated vs. control) were used to analyze the ERP data. The Geisser and Greenhouse (1959) correction was applied to all repeated measures with more than one degree of freedom (corrected p values are reported). Three anterior (FP1, FPz, FP2), three middle (C3, Cz, C4), and three posterior (P3, Pz, P4) electrode\n sites were chosen for analysis; these sites provided ANOVA factors of laterality (left vs. center vs. right) and front-to-back\n extent (anterior vs. middle vs. posterior).\n

                                        \n \n " - ] - }, - "conclusions_html": { - "value": [ - "\n \n \n

                                        RESULTS

                                        \n \n

                                        ERPs for the pseudohomophone-, TL-, and control-prime conditions are plotted separately in Figures 1a and 1b for the nine electrodes used in the analyses presented here. Figure 2 presents the voltage maps (formed from all 29 scalp sites) for pseudohomophone and TL priming effects in each of the three\n analysis windows.\n

                                        \n \n
                                        \n
                                        \"Fig.
                                        View larger version:\n \n
                                        \n
                                        \n
                                        Fig. 1. \n

                                        Event-related potentials time-locked to target onset in the pseudohomophone (a) and transposed-letter (b) conditions, plotted\n with the waveforms for their respective control conditions.\n

                                        \n
                                        \n
                                        \n
                                        \n \n
                                        \n
                                        \"Fig.
                                        View larger version:\n \n
                                        \n
                                        \n
                                        Fig. 2. \n

                                        Voltage maps of the pseudohomophone (a) and transposed-letter (b) priming effects. Each effect was calculated by subtracting\n event-related potentials (ERPs) to the target in the priming condition from ERPs to the target in the control condition.\n

                                        \n
                                        \n
                                        \n
                                        \n \n
                                        \n \n

                                        150- to 250-Ms Target Epoch

                                        \n \n

                                        As can be seen in Figures 1 and 2, between about 150 and 250 ms, targets following TL primes showed an early priming effect over the more posterior electrode\n sites, but targets following pseudohomophone primes showed little evidence of a priming effect. ANOVA results were consistent\n with this observation: There was a significant interaction among prime type, repetition, anterior-posterior extent, and laterality,\n F(4, 76) = 4.59, p = .01, η2 = .195. Follow-up analyses confirmed that in the TL condition, there was a significant priming effect at posterior sites,\n F(1, 19) = 4.69, p = .043, η2 = .198, and a marginal effect at the middle sites, F(1, 19) = 3.41, p = .08, η2 = .152, but no effect at anterior sites (F < 1). There was no significant effect of priming for pseudohomophones at any location in this epoch (Fs < 1).\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        250- to 350-Ms Target Epoch

                                        \n \n

                                        As can be seen in Figures 1 and 2, between 250 and 350 ms, it was targets following pseudohomophone primes that showed priming effects, whereas targets following\n TL primes showed little to no priming. This observation was supported by a significant interaction of prime type, repetition,\n laterality, and anterior-posterior extent, F(4, 76) = 3.24, p = .045, η2 = .146. Follow-up analyses demonstrated that whereas pseudohomophones showed a significant priming effect, F(1, 19) = 4.77, p = .042, η2 = .201, TL primes did not (F < 1). Moreover, the pseudohomophone effect was significant at anterior sites, F(1, 19) = 5.97, p = .025, η2 = .239, but was not reliable at middle or more posterior sites (ps < .1).\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        350- to 550-Ms Target Epoch

                                        \n \n

                                        Examination of Figures 1 and 2 reveals that the third interval contained the bulk of the activity resembling the classic N400 component. This observation\n was confirmed by the presence of a large main effect of repetition, F(1, 19) = 7.78, p = .012, η2 = .291. Follow-up analyses indicated that priming effects were significant for pseudohomophones across the scalp. The effect\n of pseudohomophone priming was significant, F(1, 19) = 7.20, p = .015, η2 = .275, and remained significant in analyses of anterior sites, F(1, 19) = 7.24, p = .014, η2 = .276; middle sites, F(1, 19) = 5.31, p = .033, η2 = .218; and posterior sites, F(1, 19) = 5.89, p = .025, η2 = .237. In contrast, there was no significant TL priming (ps < .12).\n

                                        \n \n
                                        \n \n
                                        \n \n

                                        Time Course of Priming

                                        \n \n

                                        To better understand the time course of the effects, we also binned successive 50-ms epochs between 150 and 500 ms for the\n TL and pseudohomophone primes and their respective controls, and ran separate ANOVAs on each 50-ms epoch. The results are\n reported in Table 1 separately for anterior, middle, and posterior electrode sites. During the N250 epoch, TL priming began approximately 50\n ms earlier (200–250 ms vs. 250–300 ms) than pseudohomophone priming, and the scalp distribution of these earliest effects\n was posteriorly oriented for TL priming and anteriorly oriented for pseudohomophone priming. During the N400 epoch, it was\n pseudohomophone priming that started earlier (300–350 ms vs. 450–500 ms), and pseudohomophone priming was generally more robust\n than TL priming, although in this case the scalp distribution was similar for the two types of priming.\n

                                        \n \n
                                        \n
                                        \n \n
                                        \n
                                        TABLE 1 \n

                                        Time Course of Priming Effects: Results of Tests of Significance for Three Anterior-Posterior Rows of Electrodes

                                        \n
                                        \n
                                        \n
                                        \n \n
                                        \n \n
                                        \n \n

                                        Behavioral Data

                                        \n \n

                                        Participants detected 91.3% (SD = 6.1) of animal probes in the target position and 2% (SD = 3.3) of animal probes in the prime position within a window from 200 to 1,200 ms after probe onset.\n

                                        \n \n
                                        \n \n " - ] - }, - "author_contrib_html": { - "value": [ - - ] - }, - "competing_interests_html": { - "value": [ - - ] - }, - "references_html": { - "value": [ - "\n \n

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+http://psi.sagepub.com/content/8/1/1.full +http://pwq.sagepub.com/content/28/2/136.full +http://psr.sagepub.com/content/19/2/148.full +http://psp.sagepub.com/content/39/3/279.full +http://pec.sagepub.com/content/44/6/613.full +http://top.sagepub.com/content/39/1/24.full \ No newline at end of file From bc8399759a08d80eff730bf3c6cd4c7b692d1105 Mon Sep 17 00:00:00 2001 From: CHJ Hartgerink Date: Fri, 2 Oct 2015 09:26:03 +0200 Subject: [PATCH 146/154] Add springer test urls --- test/springer_test_urls.txt | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 test/springer_test_urls.txt diff --git a/test/springer_test_urls.txt b/test/springer_test_urls.txt new file mode 100644 index 0000000..ee49441 --- /dev/null +++ b/test/springer_test_urls.txt @@ -0,0 +1,10 @@ +http://link.springer.com/article/10.1007/s10802-011-9571-x +http://link.springer.com/article/10.1023/B%3AIJSM.0000008709.11196.19 +http://link.springer.com/article/10.1007/BF01786044 +http://link.springer.com/article/10.1007/s10567-008-0035-y +http://link.springer.com/article/10.1007/BF00709379 +http://link.springer.com/article/10.1007/s10566-006-9010-2 +http://link.springer.com/article/10.1007/s10560-013-0312-6 +http://link.springer.com/article/10.1007/BF01014524 +http://link.springer.com/article/10.1007/s10900-015-0023-3 +http://link.springer.com/article/10.1007/BF02578420 \ No newline at end of file From 93f52875908156039b18b1d6828211d6232e98c8 Mon Sep 17 00:00:00 2001 From: CHJ Hartgerink Date: Fri, 2 Oct 2015 09:29:25 +0200 Subject: [PATCH 147/154] Add taylorfrancis test urls --- test/taylorfrancis_test_urls.txt | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 test/taylorfrancis_test_urls.txt diff --git a/test/taylorfrancis_test_urls.txt b/test/taylorfrancis_test_urls.txt new file mode 100644 index 0000000..dcf0ce7 --- /dev/null +++ b/test/taylorfrancis_test_urls.txt @@ -0,0 +1,10 @@ +http://www.tandfonline.com/doi/full/10.1080/17470911003708032 +http://www.tandfonline.com/doi/full/10.1080/17586801.2014.893862 +http://www.tandfonline.com/doi/full/10.1080/13506285.2013.823140 +http://www.tandfonline.com/doi/full/10.1080/15298868.2015.1036918 +http://www.tandfonline.com/doi/full/10.1080/10463280701489053 +http://www.tandfonline.com/doi/full/10.1080/09602010701748644 +http://www.tandfonline.com/doi/full/10.1080/1357650X.2013.783045 +http://www.tandfonline.com/doi/full/10.1080/02699930903132496 +http://www.tandfonline.com/doi/full/10.1080/13554794.2011.556128 +http://www.tandfonline.com/doi/full/10.1080/13825585.2013.795514 \ No newline at end of file From 066890b25d4c1f8618746861dc820bd5e3651dd7 Mon Sep 17 00:00:00 2001 From: CHJ Hartgerink Date: Fri, 2 Oct 2015 09:32:14 +0200 Subject: [PATCH 148/154] Add wiley test urls --- test/wiley_test_urls.txt | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 test/wiley_test_urls.txt diff --git a/test/wiley_test_urls.txt b/test/wiley_test_urls.txt new file mode 100644 index 0000000..5e95948 --- /dev/null +++ b/test/wiley_test_urls.txt @@ -0,0 +1,10 @@ +http://onlinelibrary.wiley.com/doi/10.1002/smi.2536/full +http://onlinelibrary.wiley.com/doi/10.1002/icd.1868/full +http://onlinelibrary.wiley.com/doi/10.1002/icd.1876/full +http://onlinelibrary.wiley.com/doi/10.1002/mhw.30026/full +http://onlinelibrary.wiley.com/doi/10.1002/cbl.30034/full +http://onlinelibrary.wiley.com/doi/10.1002/cpu.30048/full +http://onlinelibrary.wiley.com/doi/10.1111/ajsp.12077/full +http://onlinelibrary.wiley.com/doi/10.1111/desc.12177/full +http://onlinelibrary.wiley.com/doi/10.1111/jopy.12079/full +http://onlinelibrary.wiley.com/doi/10.1111/anzs.12067/full From 4f3617949a09b34362656067a2c78308b81da3c8 Mon Sep 17 00:00:00 2001 From: CHJ Hartgerink Date: Fri, 2 Oct 2015 09:45:17 +0200 Subject: [PATCH 149/154] Add APA test urls --- test/apa_test_urls.txt | 10 ++++++++++ test/elsevier_test_urls.txt | 10 ++++++++++ 2 files changed, 20 insertions(+) create mode 100644 test/apa_test_urls.txt create mode 100644 test/elsevier_test_urls.txt diff --git a/test/apa_test_urls.txt b/test/apa_test_urls.txt new file mode 100644 index 0000000..d29e2fc --- /dev/null +++ b/test/apa_test_urls.txt @@ -0,0 +1,10 @@ +http://web.b.ebscohost.com/ehost/viewarticle?data=dGJyMPPp44rp2%2fdV0%2bnjisfk5Ie46bNQrqazS7ek63nn5Kx95uXxjL6vrUqzpbBIr6ueTLioslKvqJ5oy5zyit%2fk8Xnh6ueH7N%2fiVbCmsEyuqq9JtKykhN%2fk5VXj5KR84LPufOac8nnls79mpNfsVbCmr0yrqbRPrqurSK6npH7t6Ot58rPmjOvixI3q4tJ99uoA&hid=106 +http://web.b.ebscohost.com/ehost/viewarticle?data=dGJyMPPp44rp2%2fdV0%2bnjisfk5Ie46bNQrqazS7ek63nn5Kx95uXxjL6vrUq1pbBIr6ueSa6ws0m4q7c4zsOkjPDX7Ivf2fKB7eTnfLujr0%2b3rrdPsq%2b1TqTi34bls%2bOGpNrgVe7a5j7y1%2bVVv8SkeeyzsEivq6tJsa%2b0Taumrkmk3O2K69fyVebq64TE6%2bqE0tv2jAAA&hid=116 +http://web.b.ebscohost.com/ehost/viewarticle?data=dGJyMPPp44rp2%2fdV0%2bnjisfk5Ie46bNQrqazS7ek63nn5Kx95uXxjL6nrkevpbBIr6ueT7iprlKurJ5oy5zyit%2fk8Xnh6ueH7N%2fiVbSot0uxrLNOtJzqeezdu33snOJ6u%2bbigKTq33%2b7t8w%2b3%2bS7Sq6ns0WvqK5Ns6OuSLKc5Ifw49%2bMu97yheq884TqyuOQ8gAA&hid=125 +http://web.b.ebscohost.com/ehost/viewarticle?data=dGJyMPPp44rp2%2fdV0%2bnjisfk5Ie46bNQrqazS7ek63nn5Kx95uXxjL6vrUq1pbBIr6ueUbintlKuq55oy5zyit%2fk8Xnh6ueH7N%2fiVbKrr0y0rbJJsZzqeezdu33snOJ6u%2bbigKTq33%2b7t8w%2b3%2bS7Sq6ns0WvqLJKsqOuSK%2bc5Ifw49%2bMu97yheq884TqyuOQ8gAA&hid=128 +http://web.a.ebscohost.com/ehost/viewarticle?data=dGJyMPPp44rp2%2fdV0%2bnjisfk5Ie46bNQrqazS7ek63nn5Kx95uXxjL6vrUuupbBIr6ueUbinsFKyp55Zy5zyit%2fk8Xnh6ueH7N%2fiVauntUq2rK5Nrq%2byPurX7H%2b72%2bw%2b4ti7iOLepIzf3btZzJzfhruorkmyo7FNsKmzRa6mrz7k5fCF3%2bq7gPLj6l7z4ups4%2b7y&hid=4214 +http://web.b.ebscohost.com/ehost/viewarticle?data=dGJyMPPp44rp2%2fdV0%2bnjisfk5Ie46bNQrqazS7ek63nn5Kx95uXxjL6vrUqzpbBIr6ueSbCwr0m4prQ4zsOkjPDX7Ivf2fKB7eTnfLutrkqwqLNMtqekhN%2fk5VXj5KR84LPufOac8nnls79mpNfsVa%2bvt06rqa9JtqyrSK6npH7t6Ot58rPmjOvixI3q4tJ99uoA&hid=116 +http://web.a.ebscohost.com/ehost/viewarticle?data=dGJyMPPp44rp2%2fdV0%2bnjisfk5Ie46bNQrqazS7ek63nn5Kx95uXxjL6vrUqzpbBIr6ueSrimtVKvp55oy5zyit%2fk8Xnh6ueH7N%2fiVbKvsFCuq69MsJzqeezdu33snOJ6u%2bbigKTq33%2b7t8w%2b3%2bS7Sq6ns0Wvr69RsKOuSK%2bc5Ifw49%2bMu97yheq884TqyuOQ8gAA&hid=4209 +http://web.b.ebscohost.com/ehost/viewarticle?data=dGJyMPPp44rp2%2fdV0%2bnjisfk5Ie46bNQrqazS7ek63nn5Kx95uXxjL6vrUuupbBIr6ueTbintVKvpp5Zy5zyit%2fk8Xnh6ueH7N%2fiVaustUi2p7VMsqikhN%2fk5VXj5KR84LPufOac8nnls79mpNfsVbCmr02rprdLsKerSK6npH7t6Ot58rPmjOvixI3q4tJ99uoA&hid=110 +http://web.a.ebscohost.com/ehost/viewarticle?data=dGJyMPPp44rp2%2fdV0%2bnjisfk5Ie46bNQrqazS7ek63nn5Kx95uXxjL6vrUqzpbBIr6ueTLimr1Kuqp5oy5zyit%2fk8Xnh6ueH7N%2fiVbWtrkmxrbVPpOLfhuWz44ak2uBV7trmPvLX5VW%2fxKR57LOwSK%2brq0izrLFMq6auSaTc7Yrr1%2fJV5urrhMTr6oTS2%2faM&hid=4112 +http://web.a.ebscohost.com/ehost/viewarticle?data=dGJyMPPp44rp2%2fdV0%2bnjisfk5Ie46bNQrqazS7ek63nn5Kx95uXxjL6vrUqzpbBIr6ueTLimr1Kuqp5oy5zyit%2fk8Xnh6ueH7N%2fiVbWtrkmxrbVPpOLfhuWz44ak2uBV7trmPvLX5VW%2fxKR57LOwSK%2brq0mxq7VPq6auSaTc7Yrr1%2fJV5urrhMTr6oTS2%2faM&hid=4112 \ No newline at end of file diff --git a/test/elsevier_test_urls.txt b/test/elsevier_test_urls.txt new file mode 100644 index 0000000..6b41c73 --- /dev/null +++ b/test/elsevier_test_urls.txt @@ -0,0 +1,10 @@ +http://www.sciencedirect.com/science/article/pii/S1353113103001093 +http://www.sciencedirect.com/science/article/pii/S123028131500029X +http://www.sciencedirect.com/science/article/pii/S1155170404974721 +http://www.sciencedirect.com/science/article/pii/S1162908804000787 +http://www.sciencedirect.com/science/article/pii/S115813600600096X +http://www.sciencedirect.com/science/article/pii/S1132055912700662 +http://www.sciencedirect.com/science/article/pii/S1138207408700265 +http://www.sciencedirect.com/science/article/pii/S1098214099802069 +http://www.sciencedirect.com/science/article/pii/S1364661397890547 +http://www.sciencedirect.com/science/article/pii/S1499404606600973 \ No newline at end of file From b18640320a3b972c7a539ee2f800d8a0829df1b5 Mon Sep 17 00:00:00 2001 From: CHJ Hartgerink Date: Fri, 2 Oct 2015 10:54:59 +0200 Subject: [PATCH 150/154] First run at wiley scraper (fails figure download and pdf download) --- scrapers/wiley.json | 89 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 scrapers/wiley.json diff --git a/scrapers/wiley.json b/scrapers/wiley.json new file mode 100644 index 0000000..579aab5 --- /dev/null +++ b/scrapers/wiley.json @@ -0,0 +1,89 @@ +{ + "url": "onlinelibrary\\.wiley\\.com/doi/.*/.*/full", + "elements": { + "publisher": { + "selector": "//meta[contains(@name, 'publisher')]", + "attribute": "content" + }, + + "journal_name": { + "selector": "//meta[contains(@name, 'citation_journal_title')]", + "attribute": "content" + }, + + "journal_issn": { + "selector": "//meta[contains(@name, 'citation_issn')]", + "attribute": "content" + }, + + "volume": { + "selector": "//meta[contains(@name, 'citation_volume')]", + "attribute": "content" + }, + + "issue": { + "selector": "//meta[contains(@name, 'citation_issue')]", + "attribute": "content" + }, + + "firstpage": { + "selector": "//meta[contains(@name, 'citation_firstpage')]", + "attribute": "content" + }, + + "title": { + "selector": "//meta[contains(@name, 'citation_title')]", + "attribute": "content" + }, + + "author_name": { + "selector": "//meta[contains(@name, 'citation_author')]", + "attribute": "content" + }, + + "author_institution": { + "selector": "//meta[contains(@name, 'citation_author_institution')]", + "attribute": "content" + }, + + "date_published": { + "selector": "//meta[contains(@name, 'citation_publication_date')]", + "attribute": "text" + }, + + "doi": { + "selector": "//meta[contains(@name, 'citation_doi')]", + "attribute": "content" + }, + + "fulltext_html": { + "selector": "//meta[contains(@name, 'citation_fulltext_html_url')]", + "attribute": "content", + "download": { + "rename": "fulltext.html" + } + }, + + "fulltext_pdf": { + "selector": "//meta[contains(@name, 'citation_pdf_url')]", + "attribute": "content", + "download": { + "rename": "fulltext.pdf" + } + }, + + "abstract_html": { + "selector": "//meta[contains(@name, 'citation_abstract_html_url')]", + "attribute": "href", + "download": { + "rename": "abstract.html" + }, + + "figures_image": { + "selector": "//*[@id='desc12177-fig-0001_img']", + "attribute": "src", + "download": true + } + } + } +} \ No newline at end of file From a215a420e821c972db0cf07f601340cdcde5091f Mon Sep 17 00:00:00 2001 From: CHJ Hartgerink Date: Mon, 26 Oct 2015 11:21:28 +0100 Subject: [PATCH 151/154] Add elsevier, wiley, springer, sage; init apa --- scrapers/apa.json | 103 +++++++++++++++++++++++++++++++++++++++++ scrapers/elsevier.json | 21 +++++++++ scrapers/springer.json | 83 +++++++++++++++++++++++++++++++++ scrapers/wiley.json | 42 +++++++++++------ 4 files changed, 235 insertions(+), 14 deletions(-) create mode 100644 scrapers/apa.json create mode 100644 scrapers/elsevier.json create mode 100644 scrapers/springer.json diff --git a/scrapers/apa.json b/scrapers/apa.json new file mode 100644 index 0000000..18f12f8 --- /dev/null +++ b/scrapers/apa.json @@ -0,0 +1,103 @@ + { + "url": "web.a.ebscohost.com", + "elements": { + "publisher": { + "selector": "//meta[@name='DC.Publisher']", + "attribute": "content" + }, + + "journal_name": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" + }, + + "journal_issn": { + "selector": "//meta[@name='citation_issn']", + "attribute": "content" + }, + + "volume": { + "selector": "//meta[@name='citation_volume']", + "attribute": "content" + }, + + "issue": { + "selector": "//meta[@name='citation_issue']", + "attribute": "content" + }, + + "firstpage": { + "selector": "//meta[@name='citation_firstpage']", + "attribute": "content" + }, + + "title": { + "selector": "//title", + "attribute": "content" + }, + + "keywords": { + "selector": "//ul[contains(@class, 'kwd-group')]", + "attribute": "text" + }, + + "author_name": { + "selector": "//meta[@name='citation_author']", + "attribute": "content" + }, + + "author_institution": { + "selector": "//meta[@name='citation_author_institution']", + "attribute": "content" + }, + + "date_published": { + "selector": "//*[@id='slugline']/cite/span[1]", + "attribute": "text" + }, + + "doi": { + "selector": "//meta[@name='citation_doi']", + "attribute": "content" + }, + + "pmid": { + "selector": "//meta[@name='citation_pmid']", + "attribute": "content" + }, + + "copyright": { + "selector": "//*[@id='copyright-statement-1']", + "attribute": "html" + }, + + "fulltext_html": { + "selector": "//meta[@name='citation_fulltext_html_url']", + "attribute": "content", + "download": { + "rename": "fulltext.html" + } + }, + + "fulltext_pdf": { + "selector": "//meta[@name='citation_pdf_url']", + "attribute": "content", + "download": { + "rename": "fulltext.pdf" + } + }, + + "abstract_html": { + "selector": "//meta[@name='citation_abstract_html_url']", + "attribute": "content", + "download": { + "rename": "abstract.html" + } + }, + + "competing_interests_html": { + "selector": "//*[contains(@class, 'fn-conflict')]", + "attribute": "text" + } + } +} \ No newline at end of file diff --git a/scrapers/elsevier.json b/scrapers/elsevier.json new file mode 100644 index 0000000..d886fae --- /dev/null +++ b/scrapers/elsevier.json @@ -0,0 +1,21 @@ +{ + "url": "sciencedirect\\.com", + "elements": { + "fulltext_html": { + "selector": "//link[contains(@rel, 'canonical')]", + "attribute": "href", + "download": { + "rename": "fulltext.html" + } + }, + + "fulltext_pdf": { + "selector": "//*[contains(@id, 'pdfLink')]", + "attribute": "href", + "download": { + "rename": "fulltext.pdf" + } + } + } +} + diff --git a/scrapers/springer.json b/scrapers/springer.json new file mode 100644 index 0000000..ac59ee2 --- /dev/null +++ b/scrapers/springer.json @@ -0,0 +1,83 @@ + { + "url": "link.springer.com", + "elements": { + "publisher": { + "selector": "//meta[@name='citation_publisher']", + "attribute": "content" + }, + + "journal_name": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" + }, + + "journal_issn": { + "selector": "//meta[@name='citation_issn']", + "attribute": "content" + }, + + "volume": { + "selector": "//meta[@name='citation_volume']", + "attribute": "content" + }, + + "issue": { + "selector": "//meta[@name='citation_issue']", + "attribute": "content" + }, + + "firstpage": { + "selector": "//meta[@name='citation_firstpage']", + "attribute": "content" + }, + + "title": { + "selector": "//meta[@name='citation_title']", + "attribute": "content" + }, + + "author_name": { + "selector": "//meta[@name='citation_author']", + "attribute": "content" + }, + + "author_institution": { + "selector": "//meta[@name='citation_author_institution']", + "attribute": "content" + }, + + "date_published": { + "selector": "//meta[@name='citation_cover_date']", + "attribute": "text" + }, + + "doi": { + "selector": "//meta[@name='citation_doi']", + "attribute": "content" + }, + + "fulltext_html": { + "selector": "//meta[@name='citation_fulltext_html_url']", + "attribute": "content", + "download": { + "rename": "fulltext.html" + } + }, + + "fulltext_pdf": { + "selector": "//meta[@name='citation_pdf_url']", + "attribute": "content", + "download": { + "rename": "fulltext.pdf" + } + }, + + "abstract_html": { + "selector": "//meta[@name='citation_abstract_html_url']", + "attribute": "content", + "download": { + "rename": "abstract.html" + } + } + } +} \ No newline at end of file diff --git a/scrapers/wiley.json b/scrapers/wiley.json index 579aab5..7face2c 100644 --- a/scrapers/wiley.json +++ b/scrapers/wiley.json @@ -1,5 +1,13 @@ { - "url": "onlinelibrary\\.wiley\\.com/doi/.*/.*/full", + "url": "onlinelibrary.wiley.com", + + "followables": { + "pdf_container": { + "selector": "//meta[contains(@name, 'citation_pdf_url')]", + "attribute": "content" + } + }, + "elements": { "publisher": { "selector": "//meta[contains(@name, 'publisher')]", @@ -36,6 +44,11 @@ "attribute": "content" }, + "keywords": { + "selector": "//meta[contains(@name, 'citation_keywords')]", + "attribute": "content" + }, + "author_name": { "selector": "//meta[contains(@name, 'citation_author')]", "attribute": "content" @@ -48,7 +61,7 @@ "date_published": { "selector": "//meta[contains(@name, 'citation_publication_date')]", - "attribute": "text" + "attribute": "content" }, "doi": { @@ -64,26 +77,27 @@ } }, - "fulltext_pdf": { - "selector": "//meta[contains(@name, 'citation_pdf_url')]", + "abstract_html": { + "selector": "//meta[contains(@name, 'citation_abstract_html_url')]", "attribute": "content", "download": { - "rename": "fulltext.pdf" + "rename": "abstract.html" } }, - "abstract_html": { - "selector": "//meta[contains(@name, 'citation_abstract_html_url')]", + "figures_image": { + "selector": "//*[contains(@id, '-fig-')]/a[contains(@class, 'figZoom')]", "attribute": "href", - "download": { - "rename": "abstract.html" - }, + "download": true + }, - "figures_image": { - "selector": "//*[@id='desc12177-fig-0001_img']", + "fulltext_pdf": { + "selector": "//*[@id='pdfDocument']", "attribute": "src", - "download": true - } + "follow": "pdf_container", + "download": { + "rename": "fulltext.pdf" + } } } } \ No newline at end of file From 9d36fa4c37045cca9ac29aa2cce58995a1935e32 Mon Sep 17 00:00:00 2001 From: Chris Hartgerink Date: Fri, 30 Oct 2015 12:50:17 +0100 Subject: [PATCH 152/154] minor changes to elsevier and springer, while testing --- scrapers/elsevier.json | 4 ++++ scrapers/springer.json | 4 ++-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/scrapers/elsevier.json b/scrapers/elsevier.json index d886fae..717584e 100644 --- a/scrapers/elsevier.json +++ b/scrapers/elsevier.json @@ -1,6 +1,10 @@ { "url": "sciencedirect\\.com", "elements": { + "title": { + "selector": "//title", + "attribute": "content" + }, "fulltext_html": { "selector": "//link[contains(@rel, 'canonical')]", "attribute": "href", diff --git a/scrapers/springer.json b/scrapers/springer.json index ac59ee2..8d6f687 100644 --- a/scrapers/springer.json +++ b/scrapers/springer.json @@ -57,7 +57,7 @@ }, "fulltext_html": { - "selector": "//meta[@name='citation_fulltext_html_url']", + "selector": "//meta[contains(@name, 'fulltext_html']", "attribute": "content", "download": { "rename": "fulltext.html" @@ -80,4 +80,4 @@ } } } -} \ No newline at end of file +} From 7e861d15e53bdd42f287a1ed9526a8a319d829f8 Mon Sep 17 00:00:00 2001 From: CHJ Hartgerink Date: Thu, 14 Apr 2016 07:02:32 +0200 Subject: [PATCH 153/154] Add TaylorFrancis scraper --- scrapers/taylorfrancis.json | 66 +++++++++++++++++++++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 scrapers/taylorfrancis.json diff --git a/scrapers/taylorfrancis.json b/scrapers/taylorfrancis.json new file mode 100644 index 0000000..5f40991 --- /dev/null +++ b/scrapers/taylorfrancis.json @@ -0,0 +1,66 @@ +{ + "url": "tandfonline.com", + "elements": { + "publisher": { + "selector": "//meta[@name='dc.Publisher']", + "attribute": "content" + }, + + "journal_name": { + "selector": "//meta[@name='citation_journal_title']", + "attribute": "content" + }, + + "volume": { + "selector": "//*[@id='unit2']/div[1]/div/div/table/tbody/tr/td[1]/h3/a[1]", + "attribute": "content" + }, + + "issue": { + "selector": "//*[@id='unit2']/div[1]/div/div/table/tbody/tr/td[1]/h3/a[2]", + "attribute": "content" + }, + + "title": { + "selector": "//meta[@name='dc.Title']", + "attribute": "content" + }, + + "keywords": { + "selector": "//meta[@name='dc.Subject']", + "attribute": "text" + }, + + "author_name": { + "selector": "//meta[@name='dc.Creator']", + "attribute": "content" + }, + + "date_published": { + "selector": "//meta[@name='dc.Date']", + "attribute": "text" + }, + + "doi": { + "selector": "//meta[@scheme='doi']", + "attribute": "content" + }, + + "fulltext_html": { + "selector": "//meta[@name='dc.Source']", + "attribute": "content", + "download": { + "rename": "fulltext.html" + } + }, + + "fulltext_pdf": { + "selector": "//a[text()='PDF']", + "attribute": "content", + "download": { + "rename": "fulltext.pdf" + } + } + + } +} \ No newline at end of file From 187b323612e1b95f6174171c512efbcc661c4a6c Mon Sep 17 00:00:00 2001 From: Chris Hartgerink Date: Thu, 14 Apr 2016 08:07:20 +0200 Subject: [PATCH 154/154] Minor updates to springer and taylorfrancis definitions --- scrapers/springer.json | 2 +- scrapers/taylorfrancis.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/scrapers/springer.json b/scrapers/springer.json index 8d6f687..d7747c3 100644 --- a/scrapers/springer.json +++ b/scrapers/springer.json @@ -57,7 +57,7 @@ }, "fulltext_html": { - "selector": "//meta[contains(@name, 'fulltext_html']", + "selector": "//meta[contains(@name, 'fulltext_html')]", "attribute": "content", "download": { "rename": "fulltext.html" diff --git a/scrapers/taylorfrancis.json b/scrapers/taylorfrancis.json index 5f40991..4bf2abc 100644 --- a/scrapers/taylorfrancis.json +++ b/scrapers/taylorfrancis.json @@ -56,7 +56,7 @@ "fulltext_pdf": { "selector": "//a[text()='PDF']", - "attribute": "content", + "attribute": "href", "download": { "rename": "fulltext.pdf" }