Merge remote-tracking branch 'origin/main'

Author: wong-ziyi

source/content/.obsidian/app.json

@@ -8,5 +8,12 @@
     "Dry/Nucleic Acid/index",
     "Wet/Nucleic Acid/index",
     "Wet/Reagents/index"
-  ]
+  ],
+  "pdfExportSettings": {
+    "includeName": true,
+    "pageSize": "A3",
+    "landscape": false,
+    "margin": "2",
+    "downscalePercent": 40
+  }
 }

source/content/.obsidian/workspace.json

@@ -20,8 +20,23 @@
               "icon": "lucide-file",
               "title": "BRAP"
             }
+          },
+          {
+            "id": "d85828b1ab4c9728",
+            "type": "leaf",
+            "state": {
+              "type": "markdown",
+              "state": {
+                "file": "conflict-files-obsidian-git.md",
+                "mode": "source",
+                "source": false
+              },
+              "icon": "lucide-file",
+              "title": "conflict-files-obsidian-git"
+            }
           }
-        ]
+        ],
+        "currentTab": 1
       }
     ],
     "direction": "vertical"
@@ -142,13 +157,13 @@
             "state": {
               "type": "outline",
               "state": {
-                "file": "BSGOU-System/RNA-seq Tool Kits/BRAP.md",
+                "file": "conflict-files-obsidian-git.md",
                 "followCursor": false,
                 "showSearch": false,
                 "searchQuery": ""
               },
               "icon": "lucide-list",
-              "title": "Outline of BRAP"
+              "title": "Outline of conflict-files-obsidian-git"
             }
           }
         ],
@@ -169,16 +184,30 @@
       "obsidian-git:Open Git source control": false
     }
   },
-  "active": "438080deb723bad3",
+  "active": "d85828b1ab4c9728",
   "lastOpenFiles": [
+    "BSGOU-System/RNA-seq Tool Kits/BRAP.md",
+    "conflict-files-obsidian-git.md",
+    "BSGOU-System/Journal Club/index.md",
+    "BSGOU-System/Journal Club/The One Mutation That Let Us Speak?.md",
+    "BSGOU-System/Journal Club/PTSD Brain Fog Is Real—and It’s Complicated.md",
+    "BSGOU-System/Journal Club/JC000022.md",
+    "BSGOU-System/Journal Club/JC000020.md",
+    "BSGOU-System/Journal Club/JC000019.md",
+    "BSGOU-System/Journal Club/JC000018.md",
+    "BSGOU-System/Journal Club/JC000017.md",
+    "BSGOU-System/Journal Club/JC000015.md",
+    "BSGOU-System/Journal Club/JC000016.md",
+    "BSGOU-System/Journal Club/JC000014.md",
+    "BSGOU-System/Journal Club/JC000013.md",
+    "BSGOU-System/Journal Club/Is Inflammaging Really Universal? This Study Says Nope.md",
+    "BSGOU-System/Journal Club",
     "BSGOU-System/RNA-seq Tool Kits/DeVlog/20250729-fenA-processx_convert-theme.md",
     "BSGOU-System/RNA-seq Tool Kits/DeVlog/index.md",
     "BSGOU-System/RNA-seq Tool Kits/index.md",
     "BSGOU-System/RNA-seq Tool Kits/DeVlog",
-    "BSGOU-System/RNA-seq Tool Kits/BRAP.md",
     "BSGOU-System/RNA-seq Tool Kits/GREP1.md",
     "Dry/Software Engineering/BAM file Cheat Sheet - Linux OS.md",
-    "conflict-files-obsidian-git.md",
     "Dry/Software Engineering/CARLIN Lineage Analysis on Stereo-seq.md",
     "Wet/Nucleic Acid/in situ hybridization.md",
     "BSGOU-System/index.md",
@@ -187,28 +216,14 @@
     "Dry/Software Engineering/Extract Tissue CIDs from Stereo-seq.md",
     "Dry/Software Engineering/FASTQ Cheat Sheet - Linux OS.md",
     "Dry/Software Engineering/TikZ.md",
-    "Dry/Nucleic Acid/Spatial Transcriptomics.md",
-    "Wet/Reagents/index.md",
     "Wet/Reagents",
-    "Dry/Software Engineering/CARLIN Lineage Analysis from Stereo-seq Data.md",
-    "index.md",
-    "Wet/Nucleic Acid/index.md",
-    "Wet/index.md",
-    "ShinyApps in BSGOU-choice/ShinyGO.md",
-    "ShinyApps in BSGOU-choice/index.md",
-    "ShinyApps in BSGOU-choice/iDEP.md",
-    "ShinyApps in BSGOU-choice/Heatmapper.md",
-    "Dry/index.md",
-    "Dry/Software Engineering/index.md",
-    "Dry/Nucleic Acid/index.md",
     "00.Images/Workflow-of-CID-mapping.png",
     "00.Images",
     "ShinyApps in BSGOU-choice",
     "Pasted image 20250603224626.png",
     "IGV_BAM_Screenshot.png",
     "Wet/Nucleic Acid",
     "Dry/Nucleic Acid",
-    "Dry/Software Engineering",
-    "Dry"
+    "Dry/Software Engineering"
   ]
 }

source/content/BSGOU-System/Journal Club/Is Inflammaging Really Universal? This Study Says Nope.md

@@ -0,0 +1,75 @@
+---
+title: Is Inflammaging Really Universal? This Study Says Nope.
+draft: false
+tags:
+  - Inflammation
+  - Immunity
+  - Aging
+  - Lifestyle
+---
+# Reference:
+[https://pubmed.ncbi.nlm.nih.gov/40588649/](https://pubmed.ncbi.nlm.nih.gov/40588649/)
+
+### Summary
+
+Franck et al. (2025) challenge the prevailing assumption of universal "inflammaging"—a chronic, systemic, low-grade inflammation associated with aging—by comparing biomarkers across diverse global populations. The study analyzed blood samples from five rural and urban populations in Bolivia, Ghana, and the U.S., including the Tsimane and Moseten Amerindians. Surprisingly, some groups showed little or no age-related increase in inflammatory markers such as CRP and IL-6, suggesting inflammaging is not a universal biological outcome of aging. The findings argue for a more nuanced understanding that incorporates evolutionary, ecological, and lifestyle contexts into aging research.
+
+### Key Points:
+
+1. **Inflammaging** is widely believed to be a universal aging hallmark, but this study disputes that.
+2. Researchers measured inflammatory biomarkers (CRP, IL-6, TNF-α, IL-10) across five distinct populations.
+3. The Tsimane and Moseten showed no or weak age-related increases in CRP and IL-6.
+4. U.S. and urban Ghanaian populations had strong age-related increases in inflammatory markers.
+5. Results suggest that lifestyle and ecological context mediate age-related immune changes.
+6. Calls for reconsideration of "universal" biological aging theories.
+
+# Logic Flow
+
+```mermaid
+flowchart TB
+    subgraph "🧠 Introduction"
+        A1["Aging often associated with chronic inflammation ('inflammaging')"]
+        A2["Assumed to be a universal biological process"]
+        A3["Is inflammaging consistent across all human populations?"]
+        A1 --> A2 --> A3
+    end
+
+    subgraph "🎯 Research Question"
+        B1["Does the relationship between age and inflammation vary across populations?"]
+        A3 --> B1
+    end
+
+    subgraph "🧪 Study Design"
+        C1["Populations studied:<br>• Tsimane<br>• Moseten<br>• Urban Ghana<br>• Rural Ghana<br>• U.S. (NHANES)"]
+        C2["Biomarkers measured:<br>• CRP<br>• IL-6<br>• TNF-α<br>• IL-10"]
+        C3["Cross-sectional analysis of adults aged 18–90+"]
+        B1 --> C1 --> C2 --> C3
+    end
+
+    subgraph "📊 Results: Age-Biomarker Patterns"
+        D1["Tsimane & Moseten:<br>• Weak/no age-related increase in CRP/IL-6"]
+        D2["Urban Ghana & U.S.:<br>• Strong age-related increase in CRP/IL-6"]
+        D3["Rural Ghana:<br>• Mixed patterns depending on biomarker"]
+        C3 --> D1
+        C3 --> D2
+        C3 --> D3
+    end
+
+    subgraph "🔍 Interpretation"
+        E1["Inflammaging is not biologically inevitable"]
+        E2["Ecological and lifestyle factors shape immune aging"]
+        D1 --> E1
+        D2 --> E2
+        D3 --> E2
+    end
+
+    subgraph "🏁 Conclusion"
+        F1["Reframe aging research to include:<br>• Ecological diversity<br>• Evolutionary context"]
+        F2["Question universality of biological aging hallmarks"]
+        E1 --> F1
+        E2 --> F1 --> F2
+    end
+
+```
+
+

source/content/BSGOU-System/Journal Club/JC000013.md

@@ -0,0 +1,84 @@
+---
+title: Can a Low-Carb Diet Reverse Diabetes—in Real Life?
+draft: true
+tags:
+  - Diabetes
+  - Lifestyle
+---
+# Reference:
+[https://pubmed.ncbi.nlm.nih.gov/33521540/](https://pubmed.ncbi.nlm.nih.gov/33521540/)
+
+# Summary
+
+Unwin et al. (2020) conducted a six-year service evaluation in a UK general practice setting to assess the impact of a lower carbohydrate diet on patients with Type 2 diabetes (T2D) and prediabetes. A total of 199 patients participated, receiving individualized and group-based dietary counseling. Key outcomes included significant reductions in weight, HbA1c, blood pressure, and lipid profiles. Notably, 46% of T2D patients achieved drug-free remission and 93% of prediabetic patients normalized their HbA1c. The study also reported considerable reductions in diabetes medication prescriptions and associated healthcare costs. These real-world results support the viability of incorporating low-carb dietary advice into routine primary care.
+
+# Key Points:
+
+1. A six-year evaluation of low-carb dietary intervention in UK primary care (n=199).
+2. Significant improvements in HbA1c, weight, blood pressure, and lipid profiles.
+3. 46% of T2D patients achieved drug-free remission.
+4. 93% of prediabetic patients reverted to normal HbA1c levels.
+5. Medication prescribing and costs significantly reduced.
+6. Outcomes were consistent across age and disease duration subgroups.
+
+# Logic Flow
+
+```mermaid
+flowchart TB
+
+    subgraph "📌 Background & Motivation"
+        A1["Rising prevalence of T2D in UK & globally"]
+        A2["Low-carb diets supported by some guidelines but need real-world evaluation"]
+        A3["Objective: Assess low-carb intervention on glycaemic and metabolic outcomes"]
+        A1 --> A2 --> A3
+    end
+
+    subgraph "🧪 Study Design"
+        B1["Setting: Norwood GP, UK (2013–2019)"]
+        B2["Population: 128 T2D & 71 prediabetes patients"]
+        B3["Intervention: Lower-carb diet advice via 1:1 and group sessions"]
+        B4["Metrics: HbA1c, weight, BP, lipids, prescribing"]
+        A3 --> B1 --> B2 --> B3 --> B4
+    end
+
+    subgraph "📊 Results: Type 2 Diabetes"
+        C1["↓ HbA1c: 65.5 → 48 mmol/mol (p<0.001)"]
+        C2["↓ Weight: 99.7 → 91.4 kg (p<0.001)"]
+        C3["46% drug-free remission"]
+        C4["↓ BP & improved lipid profile"]
+        B4 --> C1 --> C2 --> C3 --> C4
+    end
+
+    subgraph "🟢 Results: Prediabetes"
+        D1["↓ HbA1c: 44 → 39 mmol/mol"]
+        D2["↓ Weight: 90.6 → 82.2 kg"]
+        D3["93% achieved normal HbA1c"]
+        D4["Similar trends in BP & lipids"]
+        B4 --> D1 --> D2 --> D3 --> D4
+    end
+
+    subgraph "🔍 Subgroup Analysis"
+        E1["Patients >65 yrs & T2D >6 yrs: similar improvements"]
+        E2["Higher baseline HbA1c → greater improvement"]
+        E3["Weak correlation between weight loss and HbA1c drop"]
+        C4 --> E1 --> E2 --> E3
+    end
+
+    subgraph "💰 Prescribing & Cost Impact"
+        F1["↓ Medication use (e.g., gliclazide, metformin)"]
+        F2["↓ Antidiabetic drug costs: £50,885/year savings"]
+        F3["Avoided starting meds in most prediabetics"]
+        E3 --> F1 --> F2 --> F3
+    end
+
+    subgraph "🏁 Conclusion"
+        G1["Low-carb diet feasible in routine primary care"]
+        G2["Leads to clinical & financial improvements"]
+        G3["Supports patient hope & empowerment"]
+        D4 --> G1
+        F3 --> G1 --> G2 --> G3
+    end
+
+```
+
+

source/content/BSGOU-System/Journal Club/JC000014.md

@@ -0,0 +1,74 @@
+---
+title: "Stem Cells vs. Type 1 Diabetes: A Game-Changer?"
+draft: true
+tags:
+  - Diabetes
+  - Lifestyle
+  - Cell
+  - Therapy
+---
+# Reference:
+[https://pubmed.ncbi.nlm.nih.gov/40544428/](https://pubmed.ncbi.nlm.nih.gov/40544428/)
+
+# **Summary**
+
+Reichman et al. (2025) conducted a Phase 1–2 study to evaluate **zimislecel (VX-880)**, an allogeneic, stem cell–derived islet-cell therapy designed to restore insulin production in individuals with type 1 diabetes (T1D). Participants with long-standing T1D and impaired awareness of hypoglycemia received either half or full doses of zimislecel via portal vein infusion, combined with immunosuppressive therapy. The study demonstrated that a single full dose could restore islet function, with 83% of participants achieving insulin independence, all achieving freedom from severe hypoglycemic events, and marked improvements in glycemic control. Most adverse events were manageable and linked to immunosuppression. These findings suggest that zimislecel may offer a viable, scalable beta-cell replacement therapy, supporting further investigation.
+
+---
+
+# **Key Points**
+
+1. Zimislecel is a fully differentiated, allogeneic stem cell–derived islet therapy.
+2. Phase 1–2 trial involved 14 participants with type 1 diabetes; 12 received a full dose.
+3. 100% of full-dose recipients achieved freedom from severe hypoglycemic events.
+4. 83% became insulin independent by day 365.
+5. C-peptide production confirmed islet engraftment and function.
+6. Adverse events were primarily due to immunosuppressive treatment.
+
+# Logic Flow
+
+```mermaid
+flowchart TB
+
+  subgraph "🧪 Study Design"
+    A1["Type 1 diabetes patients<br>with impaired hypoglycemia awareness"]
+    A2["Phase 1–2 trial of zimislecel (VX-880)"]
+    A3["Part A: Half dose (0.4×10⁹ cells)<br>Part B & C: Full dose (0.8×10⁹ cells)"]
+    A4["Single infusion via portal vein"]
+    A5["Glucocorticoid-free immunosuppression"]
+  end
+
+
+  subgraph "📏 Endpoints"
+    B1["Primary (Part A): Safety"]
+    B2["Primary (Part C):<br>Freedom from severe hypoglycemia<br>+ HbA1c <7% or ΔHbA1c ≥1%"]
+    B3["Secondary:<br>Insulin independence, islet function (C-peptide), glucose control"]
+  end
+
+
+  subgraph "📊 Results"
+    C1["14 patients analyzed:<br>2 Half dose, 12 Full dose"]
+    C2["All: Baseline C-peptide undetectable"]
+    C3["All: Post-infusion C-peptide detectable (Engraftment)"]
+    C4["12/12 full-dose: No severe hypoglycemia,<br>HbA1c <7% sustained"]
+    C5["10/12 full-dose: Insulin independence at day 365"]
+    C6["Improved time in glucose range:<br>49.5% ➝ 93.3%"]
+    C7["Adverse events:<br>mostly mild/moderate, mainly from immunosuppressants"]
+    C8["2 deaths (unrelated to zimislecel directly)"]
+  end
+
+
+  subgraph "🔬 Conclusions"
+    D1["Zimislecel restored endogenous insulin production"]
+    D2["Supports beta-cell replacement via stem-cell–derived islets"]
+    D3["Justifies larger, longer-term studies"]
+  end
+
+
+  A1 --> A2 --> A3 --> A4 --> A5 --> B1
+  B1 --> C1 --> C2 --> C3 --> C4 --> C5 --> C6 --> C7 --> C8 --> D1
+  D1 --> D2 --> D3
+  B2 --> C4
+  B3 --> C5
+
+```