Run bot and update output

Author: Bot

output.csv

@@ -79,7 +79,7 @@ https://www.biorxiv.org/content/10.1101/2025.07.25.666750v2#comment-6835983795,b
 https://www.biorxiv.org/content/10.64898/2026.01.29.702266v1#comment-6835723915,biorxivstage,0,"Dear Anna, My apologies, a typo slipped into the manuscript. A new version will be uploaded containing the revised DOI. This one should work: https://zenodo.org/records/17936657 Kind regards, Bart",2026-02-09T18:02:09,,Bart Van Puyvelde,10.64898/2026.01.29.702266,LFQ Benchmark Dataset - Generation Beta: Assessing Modern Proteomics Instruments and Acquisition Workflows with High-Throughput LC Gradients,"Bart Van Puyvelde, Robbe Devreese, Cristina Chiva, Eduard Sabidó, Sibylle Pfammatter, Christian Panse, Jeewan Babu Rijal, Charline Keller, Ihor Batruch, Patrick Pribil, Jean-Baptiste Vincendet, Frédéric Fontaine, Lars Lefever, Pedro Magalhães, Dieter Deforce, Paolo Nanni, Bart Ghesquière, Yasset Perez-Riverol, Lennart Martens, Christine Carapito, Robbin Bouwmeester, Maarten Dhaenens",2026-02-02
 https://www.biorxiv.org/content/10.1101/2023.07.26.550636v2#comment-6835643995,biorxivstage,0,"This article has been published in Nature Communications in December 2025. The published version has a different title, see citation below. Clowsley, A. H., Meletiou, A., Janicek, R., Bokhobza, A. F. E., Lučinskaitė, E., Bleuer, G., Jansen, I., Jones, P. P., Louch, W. E. & Soeller, C. MINFLUX microscopy resolves subunits of the cardiac ryanodine receptor and its 3D orientation in cells. Nat Commun 17, 1044 (2025).",2026-02-09T15:08:53,disqus_lM0EaqU2ko,Christian S,10.1101/2023.07.26.550636,Analysis of RyR2 distribution in HEK293 cells and mouse cardiac myocytes using 3D MINFLUX microscopy,"Alexander H Clowsley, Anna Meletiou, Radoslav Janicek, Alexandre F. E. Bokhobza, Evelina Lučinskaitė, Gabriele Bleuer, Isabelle Jansen, Peter P. Jones, William E. Louch, Christian Soeller",2025-05-23
 https://www.biorxiv.org/content/10.1101/2025.05.08.652602v1#comment-6835563488,biorxivstage,0,This paper has now been pubished here: https://doi.org/10.1002/nbm.70236,2026-02-09T11:16:44,holroydnatalie,"Holroyd, Natalie",10.1101/2025.05.08.652602,Real time evaluation of the liver microcirculation by whole organ machine perfusion within an MRI system,"Zainab L Rai, Natalie A Holroyd, Morenike Magbagbeola, Emre Doganay, Katie Doyle, Lucy Caselton, Agositino Stili, Danail Stoyanov, Simon Walker-Samuel, Brian R Davidson",2025-05-11
-http://www.biorxiv.org/content/early/2017/09/07/130633#comment-6835523240,biorxivstage,0,"I found some errors in the pseudocode on the paper. We've mistakenly swapped ev and fv; in the ""if (dir is DOWN)"" block and the corresponding ""else"" block, ""fv <- shift_right fv"" and ""ev <- shift_left ev"" don't make sense.",2026-02-09T07:55:14,masahirokasahara,Masahiro Kasahara,10.1101/130633,Acceleration of Nucleotide Semi-Global Alignment with Adaptive Banded Dynamic Programming,"Hajime Suzuki, Masahiro Kasahara",2017-09-07
+http://www.biorxiv.org/content/early/2017/09/07/130633#comment-6835523240,biorxivstage,0,"I found some errors in the pseudocode on the paper. We've mistakenly swapped ev and fv; in the ""if (dir is DOWN)"" block and the corresponding ""else"" block, ""fv <- shift_right fv"" and ""ev <- shift_left ev"" don't make sense.",2026-02-09T07:55:14,masahirokasahara,Masahiro Kasahara,,,,
 https://www.biorxiv.org/content/10.1101/2025.07.29.667052v2#comment-6835217682,biorxivstage,1,"Dear Misha, thank you very much for these insightful comments. We are currently working on the revision of the manuscript and are happy to incorporate your suggestions. We agree that “archaic” is the more appropriate term for extant proteins and will adjust the terminology accordingly. We also appreciate the suggestion to include melanopsins as an outgroup in Figure 2 and will consider this in the revision.",2026-02-08T16:01:44,pingkalairsenthilan,Pingkalai R. Senthilan,10.1101/2025.07.29.667052,"RHODOPSIN 7: An ancient non-retinal photoreceptor for contrast vision, darkness detection, and circadian regulation","Valentina Kirsch, Nils Reinhard, Heiko Hartlieb, Annika Mohr, Dirk Rieger, Peter Soba, Charlotte Helfrich-Förster, Pingkalai R. Senthilan",2025-11-13
 https://www.biorxiv.org/content/10.1101/2025.04.29.651129v1#comment-6834615707,biorxivstage,0,Now published in NAR [doi: 10.1093/nar/gkaf1061 / PMID 41182902],2026-02-06T23:36:39,disqus_KXdMXcuCHq,Michael Keogh,10.1101/2025.04.29.651129,Nucleosome context regulates chromatin reader preference,"Matthew R. Marunde, Irina K. Popova, Nathan W. Hall, Anup Vaidya, James R. Bone, Brandon A. Boone, Peter J. Brown, Ryan J. Ezell, Tessa M. Firestone, Harrison A. Fuchs, Elisa Gibson, Zachary B. Gillespie, Susan L. Gloor, Allison R. Hickman, Sarah A. Howard, Natalia Ledo Husby, Victoria T. Hsiung, Andrea L. Johnstone, Laiba F. Khan, Krzysztof Krajewski, Alexander S. Lee, Eileen T. McAnarney, Keith E. Maier, Danielle N. Maryanski, Kelsey E. Noll, Katherine Novitzky, Emily F. Patteson, Keli L. Rodriguez, Julio C. Sanchez, Luis F. Schachner, Catherine E. Smith, Lu Sun, Hailey F. Taylor, Rachel Watson, Hannah E. Willis, Catherine A. Musselman, Bryan J. Venters, Marcus A. Cheek, Matthew J. Meiners, Zu-Wen Sun, Neil L. Kelleher, Martis W. Cowles, Ellen N. Weinzapfel, Michael-Christopher Keogh, Jonathan M. Burg",2025-04-29
 https://www.biorxiv.org/content/10.64898/2026.01.30.702957v1#comment-6834388317,biorxivstage,2,"Thank you for taking time to read our manuscript. We would like to respond your comments here. 1.	We already showed in 2013 that Abs induce persistence by converting the whole population into persister cells without inducing death by pre-treating with rifampicin, tet, and CCCP (doi:10.1128/AAC.02135-12) so please add this to your paper. We vetted these persister cells 9 ways to show they are true persisters in later publication. This method has been used by over 60 groups to date in the persister field. Response: Thanks for pointing out. We totally agree that bacteriostatic antibiotics and drugs, by definition, can convert most of a bacterial population into persister cells without inducing death. Therefore, in this study we focus on bactericidal antibiotics, mostly used in time-kill assays, to examine and quantify persisters induced by lethal stresses. Broadly, your work agrees with our proposed drug-induced persistence spectrum (DIPS) model and a more general stress-induced-persistence-spectrum model. Your work will acknowledged in the Discussion. 2.	We were the first to show, using single cells, in 2018 (doi:10.1111/1462-2920.14093) that persister cells wake in minutes. Please update your line 85 text which is false as, we have shown and other groups corroborated, nearly all persister cells resuscitate within minutes of being introduced into fresh medium so they wake and multiply at the same growth rate of exponentially-growing cells within seconds. Response: Thank you for this clarification. We agree that most persister cells, once they wake, rapidly resume normal growth and proliferate at rates comparable to susceptible cells. Only a minority remain in a dormant state and constitute the pre-existing persisters, which are the persisters referred to in this context (line 85). We would like to clarify that “persister replication” in line 85 refers specifically to the rare events in which a persister cell divides to produce two persister cells, rather than to persister resuscitation and growth. We believe such events are rare and negligible relative to the contribution of pre-existing persisters. 3.	There is no credible evidence for ‘spontaneous’ persisters, only sloppy carryover from the inoculum. Response: Thank you for this comment. We agree that the vast majority of persisters, found in exponential-phase culture, originate from stationary-phase inocula and that carryover can contribute substantially to observed persister populations (when seed dilution factors are low, e.g, 100x). At the same time, we note that the existence of truly spontaneous persisters remains a theoretical possibility and has been suggested by several single-cell studies, although this remains a subject of debate. Such spontaneous persisters could arise from stochastic fluctuations or rare glitches in transcription, translation, metabolism, and/or asymmetric allocation during cell division, leading to unusual levels of ppGpp, toxins, or other effector proteins in a small subset of cells. If such events occur, we expect them to occur at extremely low frequencies. 4. Please replace your ref 23 single cell work of Van Melderen as the first single cell work.  the same conclusions was https://doi.org/10.1016/ j.isci.2019.100792 and doi:10.1111/1462-2920.14093. Response: Thank you for your suggestion. We agree that these studies are relevant and will be talked in our Discussion.",2026-02-06T15:01:25,yijiedeng,Yijie Deng,10.64898/2026.01.30.702957,Antibiotic exposure dynamically generates a substantial number of heterogeneous persisters along a spectrum of tolerance,"Yijie Deng, Douglas R. Beahm, Hannah E. Maurais, Kai Etheridge, Daniel Schultz, Rahul Sarpeshkar",2026-01-31