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---
type: "Reference"
title: "Git repo — evidence index (Obsidian vault, Robin)"
description: "Compact manifest of Robin's Obsidian vault + the local OpenWiki wiki, ingested through the local git-repo connector. Two configured repos: obsidian-vault at /home/ldw/workspace (main branch, HEAD fb017e4f, 2026-08-23/24, **5 new vault commits in the 2026-08-23T18:11Z → 2026-08-24T18:05Z 24-hour window — the largest single-day LDR burst since the 2026-07-29 Parate / Lee / Hodge cluster: `ad4abcde` Ajongbolo 2025 Cells brain organoid review + `5f02489a` Kim 2025 Nat Commun EGaIn 3D MEA + `40b357b8` Tian 2025 Nat Commun hiPSC epicardium mTOR + `f2118a62` Aiello & Bagni 2025 biorxiv Rotating Chamber brain organoid CFD + `fb017e4f` CelVivo App Note 2026 ClinoStar vs orbital shaker — 3 CelVivo-aligned papers (App Note + Aiello + Ajongbolo mentions ClinoStar) + 1 3Brain-adjacent 3D-MEA competitor paper (Kim EGaIn) + 1 cardiac epicardium paper (Tian)**) and openwiki-wiki at /home/ldw/.openwiki/wiki (main branch, HEAD 127c2dc, 2026-08-24, **2 new automated wiki commits in the 2026-08-23T18:11Z → 2026-08-24T18:05Z window: `9cc5e63` daily update 2026-08-24 + `127c2dc` sources-sync 2026-08-24 — the tenth consecutive sources-sync re-applying the 2026-08-15 count-data wipe pattern**). This page is a navigation index — content ingestion (paper deep reads, sales scripts, customer files) happens via the Hermes skill and RAGFlow, not here."
description: "Compact manifest of Robin's Obsidian vault + the local OpenWiki wiki, ingested through the local git-repo connector. Two configured repos: obsidian-vault at /home/ldw/workspace (main branch, HEAD 9d4767c7, 2026-08-25, **5 new vault commits in the 2026-08-24T18:05Z → 2026-08-25T18:13Z 24-hour window — the SECOND consecutive single-day 5-paper LDR cluster: `089177a7` Tevonian 2026 Nat Commun vascularized liver MPS + `583859a8` Yang 2026 Stem Cell Res Ther cardiac organoid review + `9aa2af4c` Update Tevonian 2026 + Yang 2026 (CelVivo/Cellink/Mimetas/3Brain/FemtoBiomed product mapping retrofit + 净化 Robin mentions — the first post-publish vendor-mapping retrofit on the 2026-08-23/24/25 LDR cluster) + `5907cdfc` Shen 2026 Chin Med J vascularized organoids review + `9d4767c7` Zhai 2026 Sci Adv 3D skin pemphigus — combined with the 2026-08-23/24 5-paper burst, **10 papers in 48 hours = the largest sustained 2-day research output in Robin's vault activity log; the burst creates 3 new deep-read subfolders: `Vascularized-Organoids/` (Tevonian + Shen) + `Cardiac-Organoids/` (Yang) + `Skin-Organoids/` (Zhai)**) and openwiki-wiki at /home/ldw/.openwiki/wiki (main branch, HEAD 1003b92, 2026-08-25, **2 new automated wiki commits in the 2026-08-24T18:05Z → 2026-08-25T18:13Z window: `3255613` daily update 2026-08-25 + `1003b92` sources-sync 2026-08-25 — the eleventh consecutive sources-sync re-applying the 2026-08-15 count-data wipe pattern**). This page is a navigation index — content ingestion (paper deep reads, sales scripts, customer files) happens via the Hermes skill and RAGFlow, not here."
resource: "~/.openwiki/connectors/git-repo/config.json"
tags: [git-repo, evidence, vault, openwiki-wiki, source, 2026-08-24, 2026-08-23, 2026-08-22, 2026-08-21, 2026-08-20, 2026-08-19, 2026-08-18, 2026-08-17, 2026-08-15, 2026-08-13, celvivo-app-note-2026, aiello-bagni-rc-cfd, tian-epicardium-mtor, kim-egain-3d-mea, ajongbolo-brain-organoid-review]
timestamp: 2026-08-24T18:05:00Z
tags: [git-repo, evidence, vault, openwiki-wiki, source, 2026-08-25, 2026-08-24, 2026-08-23, 2026-08-22, 2026-08-21, 2026-08-20, 2026-08-19, 2026-08-18, 2026-08-17, 2026-08-15, 2026-08-13, tevonian-2026-vascularized-liver-mps, yang-2026-cardiac-organoid-review, shen-2026-vascularized-organoids-review, zhai-2026-3d-skin-pemphigus, second-consecutive-cluster, vascularized-organoids, cardiac-organoids, skin-organoids]
timestamp: 2026-08-25T18:13:00Z
---
# Git repo — evidence index (Obsidian vault + OpenWiki wiki)
@@ -22,120 +22,129 @@ help locate things in the vault, not summarize their content.
`~/.openwiki/connectors/git-repo/config.json`)
- **Configured repos:**
- `obsidian-vault` → `/home/ldw/workspace` (Robin Obsidian vault, on
`main`, HEAD `fb017e4fb40f874e54fb2a92eff235abe1c487cb` as of
2026-08-23/24 +0800 — **5 new vault commits** in the
2026-08-23T18:11Z → 2026-08-24T18:05Z 24-hour window: the
**2026-08-23/24 5-paper LDR burst** that broke the 7-day vault
silence — `ad4abcde` Ajongbolo 2025 Cells brain organoid review +
`5f02489a` Kim 2025 Nat Commun EGaIn 3D MEA + `40b357b8` Tian 2025
Nat Commun hiPSC epicardium mTOR + `f2118a62` Aiello & Bagni 2025
biorxiv Rotating Chamber brain organoid CFD + `fb017e4f` CelVivo
App Note 2026 ClinoStar vs orbital shaker head-to-head. 3 CelVivo-
aligned papers (App Note + Aiello + Ajongbolo mentions ClinoStar
reagent supply chain) + 1 3Brain-adjacent 3D-MEA competitor paper
(Kim EGaIn) + 1 cardiac epicardium paper (Tian); each commit is a
single-shot entry (no v2/v3 SOP rewrite cycles this cluster — the
page-934 / page-946 alignment work from the 2026-08-12 Liang 2026
cluster is no longer in flight). **Largest single-day LDR burst
since the 2026-07-29 Parate / Lee / Hodge cluster** — breaks the
7-day vault silence streak that started after the 2026-08-16
Quintard + Guo cluster).
`main`, HEAD `9d4767c7034a59d8f3206756c2dfeb3f4339c2e0` as of
2026-08-25 +0800 — **5 new vault commits** in the
2026-08-24T18:05Z → 2026-08-25T18:13Z 24-hour window: the
**2026-08-24/25 5-paper LDR cluster** (SECOND consecutive
single-day 5-paper LDR burst) — `089177a7` Tevonian 2026 Nat Commun
血管化肝 MPS deep read (PMID 41634021) + `583859a8` Yang 2026 Stem
Cell Res Ther cardiac organoid review (PMID 41963991) + `9aa2af4c`
Update Tevonian 2026 + Yang 2026 (CelVivo/Cellink/Mimetas/3Brain/
FemtoBiomed product mapping retrofit + 净化 Robin mentions — the
FIRST post-publish vendor-mapping retrofit on the 2026-08-23/24/25
LDR cluster) + `5907cdfc` Shen 2026 Chin Med J vascularized
organoids review (PMID 42268296) + `9d4767c7` Zhai 2026 Sci Adv 3D
skin pemphigus (PMID 41512055). Combined with the 2026-08-23/24
5-paper burst, **10 papers in 48 hours** = largest sustained 2-day
research output in Robin's vault activity log. The cluster creates
**3 new `04-Literature/Deep-Reads/` subfolders**: `Vascularized-Organoids/`
(Tevonian + Shen) + `Cardiac-Organoids/` (Yang) + `Skin-Organoids/`
(Zhai) — Robin expands the deep-read taxonomy from ~19 to ~22
per-vendor / per-application-domain subfolders in a single day.
The new `9aa2af4c` retrofit commit is the **first synthesis-grade
post-publish LDR touch** on the 2026-08-23/24/25 cluster — the
prior 5 papers (Ajongbolo + Kim + Tian + Aiello + CelVivo App Note)
have NOT had this retrofit applied yet, only the new Tevonian + Yang
pair get the retroactive 4-vendor mapping).
- `openwiki-wiki` → `/home/ldw/.openwiki/wiki` (the OpenWiki knowledge
base itself, on `main`, HEAD `127c2dc60fb8398d02485313df25994e7e18c69f`
as of 2026-08-24T +0800 — 2 new wiki-side commits in the
2026-08-23T18:11Z → 2026-08-24T18:05Z 24-hour window: `9cc5e63`
chore: daily update 2026-08-24 + `127c2dc` chore(sources): refresh
NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-24) —
the **tenth** consecutive sources-sync re-applying the 2026-08-15
base itself, on `main`, HEAD `1003b92f3a1e43197ec8e21e7f69fd5db38316e7`
as of 2026-08-25T +0800 — 2 new wiki-side commits in the
2026-08-24T18:05Z → 2026-08-25T18:13Z 24-hour window: `3255613`
chore: daily update 2026-08-25 + `1003b92` chore(sources): refresh
NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-25) —
the **eleventh** consecutive sources-sync re-applying the 2026-08-15
count-data wipe pattern).
- **Auth:** local paths only — no remote, no credentials.
- **Latest fetch:** `2026-08-24T18:05:00Z` (raw manifest
`~/.openwiki/connectors/git-repo/raw/2026-08-24T18-05-31-919Z/manifest.json`).
- **Latest fetch:** `2026-08-25T18:13:00Z` (raw manifest
`~/.openwiki/connectors/git-repo/raw/2026-08-25T18-13-42-494Z/manifest.json`).
- **Source config:** `~/.openwiki/connectors/git-repo/config.json`
- **State:** `~/.openwiki/connectors/git-repo/state.json` records
`latestIds` per repo; the 2026-08-24T18:05Z fetch observed vault HEAD
bumped from `a4fa5a32` (2026-08-16 — same as the 2026-08-17T18:09Z +
2026-08-18T18:10Z + 2026-08-19T18:08Z + 2026-08-20T18:09Z +
2026-08-21T18:09Z + 2026-08-22T18:13Z + 2026-08-23T18:11Z fetches
through 7 consecutive silent windows, **7 calendar days stale**) to
`fb017e4f` (2026-08-23/24 — **5 new vault commits** in the 24-hour
window, breaking the 7-day silence streak), and observed
`openwiki-wiki` bumped from `a9568d8` (2026-08-23T18:11Z fetch) to
`127c2dc` (2 new automated wiki commits in the 24-hour window:
`9cc5e63` daily update 2026-08-24 + `127c2dc` sources-sync 2026-08-24
— the **tenth** consecutive sources-sync re-applying the 2026-08-15
count-data wipe pattern after `997b648` 2026-08-16 + `be49285`
2026-08-17 + `1fc73ae` 2026-08-18 + `dcb53a2` 2026-08-19 + `bd30339`
2026-08-20 + `f6c2576` 2026-08-21 + `43d4548` 2026-08-22 + `8f8f767`
2026-08-23 + now `127c2dc` 2026-08-24).
`latestIds` per repo; the 2026-08-25T18:13Z fetch observed vault HEAD
bumped from `fb017e4f` (2026-08-23/24, the prior 5-paper burst
landed at the 2026-08-24T18:05Z fetch) to
`9d4767c7` (2026-08-25 — **5 new vault commits** in the 24-hour
window, the SECOND consecutive single-day 5-paper LDR cluster), and
observed `openwiki-wiki` bumped from `127c2dc` (2026-08-24T18:05Z
fetch) to `1003b92` (2 new automated wiki commits in the 24-hour
window: `3255613` chore: daily update 2026-08-25 (2026-08-25T02:23
+0800; committed 17 files from the prior dirty set per `git show
--stat 3255613`) + `1003b92` chore(sources): refresh
NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-25,
2026-08-25T02:30 +0800 — the **eleventh** consecutive sources-sync
re-applying the 2026-08-15 count-data wipe pattern after `2507925`
2026-08-15 + `997b648` 2026-08-16 + `be49285` 2026-08-17 + `1fc73ae`
2026-08-18 + `dcb53a2` 2026-08-19 + `bd30339` 2026-08-20 + `f6c2576`
2026-08-21 + `43d4548` 2026-08-22 + `8f8f767` 2026-08-23 + `127c2dc`
2026-08-24 + now `1003b92` 2026-08-25).
## obsidian-vault — working-tree status (2026-08-24)
## obsidian-vault — working-tree status (2026-08-25)
- **Branch:** `main`
- **HEAD:** `fb017e4fb40f874e54fb2a92eff235abe1c487cb` (vault HEAD
**bumped** from `a4fa5a32` (2026-08-16) → `fb017e4f` (2026-08-23/24)
across the 2026-08-24T18:05Z fetch — **5 new commits** in the
2026-08-23T18:11Z → 2026-08-24T18:05Z 24-hour window; the vault
breaks the **7-fetch silent streak** that started after the
2026-08-17T18:09Z + 2026-08-18T18:10Z + 2026-08-19T18:08Z +
2026-08-20T18:09Z + 2026-08-21T18:09Z + 2026-08-22T18:13Z +
2026-08-23T18:11Z silent windows. The 2026-08-23/24 cluster is
**the largest single-day LDR burst since the 2026-07-29 Parate /
Lee / Hodge cluster** — 5 paper deep-reads added in <24h, all
single-shot entry (no v2/v3 SOP rewrite cycles this cluster, vs the
3-stage SOP cycle on the 2026-08-12 Liang 2026 cluster and the
4-commit / 3-commit LDR cycles on the 2026-08-16 Quintard + Guo
cluster). The 2026-08-16 Quintard 2024 Nat Commun + Guo 2026 Front
Cell Dev Biol cluster has been replaced as the most recent committed
vault activity after a **7-day stale period** (now stale 0 days).
- **HEAD:** `9d4767c7034a59d8f3206756c2dfeb3f4339c2e0` (vault HEAD
**bumped** from `fb017e4f` (2026-08-23/24, the prior 5-paper burst)
→ `9d4767c7` (2026-08-25) across the 2026-08-25T18:13Z fetch —
**5 new commits** in the 2026-08-24T18:05Z → 2026-08-25T18:13Z
24-hour window. The 2026-08-24/25 cluster is the **SECOND
consecutive single-day 5-paper LDR burst** — combined with the
2026-08-23/24 5-paper burst (Ajongbolo + Kim + Tian + Aiello +
CelVivo App Note), Robin has produced **10 LDR papers in 48
hours**, the largest sustained 2-day research output in Robin's
vault activity log. The cluster creates **3 NEW
`04-Literature/Deep-Reads/` subfolders** — `Vascularized-Organoids/`
(Tevonian + Shen) + `Cardiac-Organoids/` (Yang) + `Skin-Organoids/`
(Zhai) — Robin expands the deep-read folder taxonomy from ~19 to
~22 in a single day. Crucially, the cluster includes the FIRST
post-publish vendor-mapping retrofit commit (`9aa2af4c`) which
adds CelVivo / Cellink / Mimetas / 3Brain / FemtoBiomed product
mapping + 净化 Robin mentions to the Tevonian + Yang files — the
prior 5 papers (Ajongbolo + Kim + Tian + Aiello + CelVivo App Note)
have NOT had this retrofit applied retroactively.
- **mtime activity in window:** **5 new committed files** in the
2026-08-23T18:11Z → 2026-08-24T18:05Z 24-hour window — all 5 new
paper LDR files at `obsidian-vault/04-Literature/Deep-Reads/` root
(no subfolder) per the manifest paths `Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid.md`
+ `Ajongbolo_2025_Cells_Brain_Organoids_Review.md` +
`CelVivo_Shear_Stress_AppNote_2026.md` +
`Kim_2025_NatCommun_Liquid_Metal_3D_MEA.md` +
`Tian_2025_NatCommun_Epicardium_mTOR.md`. Commit order (mtime
ascending): `ad4abcde` 2026-08-24 07:50 Ajongbolo review → `5f02489a`
2026-08-24 08:05 Kim LM 3D MEA → `40b357b8` 2026-08-24 09:00 Tian
epicardium mTOR → `f2118a62` 2026-08-24 16:23 Aiello RC brain
organoid → `fb017e4f` 2026-08-24 16:39 CelVivo App Note 2026 — the
burst spans the full 2026-08-24 day from 07:50 to 16:39 +0800. The 2
untracked dirs from the 2026-08-17T18:09Z fetch are unchanged:
`celvivo_commercial/` last touched 2026-08-17 15:04 +0800 (= 07:04
UTC) + `templates/` last touched 2026-08-16 10:27 +0800 (= 02:27
UTC). The `Review/zhou2023_computer_vision_microfluidics.md`
first-entry file is unchanged from the 2026-08-17T18:09Z fetch
(mtime 2026-08-11, **13-day carry-forward** in the untracked set at
this fetch — was 12-day at the 2026-08-23T18:11Z fetch; the
2026-08-24T18:05Z → 2026-08-25T18:13Z 24-hour window — all 5 land
at per-vendor / per-application-domain subfolders (different pattern
from the prior 5-paper cluster which all landed at the
`04-Literature/Deep-Reads/` root). Manifest paths confirm 3 NEW
subfolders: `Tevonian_2026_Nat_Commun_Vascularized_Liver_MPS.md`
+ `Yang_2026_Stem_Cell_Res_Ther_Cardiac_Organoid_Review.md` +
`Shen_2026_Chin_Med_J_Vascularized_Organoids_Review.md` +
`Zhai_2026_Sci_Adv_3D_Skin_Pemphigus.md` — plus the
Tevonian + Yang in-place `M` touches from the `9aa2af4c` retrofit
commit. Chronological commit order (mtime ascending per manifest):
`089177a7` 2026-08-25 Tevonian 2026 vascularized liver MPS →
`583859a8` 2026-08-25 Yang 2026 cardiac organoid review →
`9aa2af4c` 2026-08-25 Tevonian + Yang product-mapping retrofit →
`5907cdfc` 2026-08-25 Shen 2026 vascularized organoids review →
`9d4767c7` 2026-08-25 Zhai 2026 3D skin pemphigus. The 2026-08-23
+ 2026-08-24 LDR burst files (Ajongbolo + Kim + Tian + Aiello +
CelVivo App Note + `deepread_40240593/` pipeline workspace) all
carry forward unchanged from the 2026-08-24T18:05Z fetch. The
`celvivo_commercial/` + `templates/` untracked dirs continue to
carry forward (now **9-day carry-forward** at this fetch — was
8-day at the 2026-08-24T18:05Z fetch). The `Review/zhou2023_computer_vision_microfluidics.md`
first-entry file is unchanged from the 2026-08-24T18:05Z fetch
(mtime 2026-08-11, **14-day carry-forward** in the untracked set at
this fetch — was 13-day at the 2026-08-24T18:05Z fetch; the
structural signal continues to weaken per the Notable-entity entry
on the `Review/` subfolder). **NEW this fetch**: 1 new untracked
working dir `deepread_40240593/` (mtime 2026-08-24 16:31 +0800 = 08:31
UTC, within the 24h window) — pipeline scratch workspace
containing 7 PMID-specific subdirs (`deepread_40016200` /
`deepread_40441268` / `deepread_40498018` / `deepread_40593704` /
`deepread_41151577` + 2 named subdirs `deepread_brain_organoid_fluid`
[Aiello paper] + `deepread_shear_stress_cs_os` [CelVivo App Note]).
The 5 PMIDs are not currently on the vault `main` as deep-read files,
suggesting the `deepread_40240593/` is the pipeline's pending-triage
workspace for the 2026-08-24 batch.
- **Ahead of origin/main:** 25 commits new since 2026-08-03 fetch (+5
from the prior 20-commit baseline at the 2026-08-23T18:11Z fetch —
the 5 new commits land on top of the 20-commit carry-forward).
on the `Review/` subfolder).
- **Ahead of origin/main:** 30 commits new since 2026-08-03 fetch (+5
from the prior 25-commit baseline at the 2026-08-24T18:05Z fetch —
the 5 new commits land on top of the 25-commit carry-forward).
- **Dirty:** yes — the untracked file set is **partially changed**:
the 8 × `02-Clients/Agents/区域-2026-0807.md` distributor-rebuild
files + 14 working-folder files + 2 untracked dirs from the
2026-08-17T18:09Z fetch carry forward unchanged, and the
`Review/zhou2023_computer_vision_microfluidics.md` first-entry in the
new `Review/` subfolder is still **untracked** (Robin has not yet
committed it) — **13-day carry-forward** at this fetch (was 12-day
at the 2026-08-23T18:11Z fetch); the structural signal continues to
committed it) — **14-day carry-forward** at this fetch (was 13-day
at the 2026-08-24T18:05Z fetch); the structural signal continues to
weaken per the Notable-entity entry on the `Review/` subfolder (the
subfolder has been a single-entry watchlist since 2026-08-13, now
**11 fetches silent**). **NEW this fetch**: 1 new untracked working
directory `deepread_40240593/` (created 2026-08-24 16:31 +0800 =
08:31 UTC, **0-day carry-forward** at this fetch — first observation,
pipeline scratch workspace).
**12 fetches silent**). The `celvivo_commercial/` + `templates/`
untracked dirs continue to carry forward (now **9-day carry-forward**
at this fetch — was 8-day at the 2026-08-24T18:05Z fetch); the
`deepread_40240593/` untracked pipeline workspace also continues to
carry forward (now **2-day carry-forward** — was 1-day at the
2026-08-24T18:05Z fetch); no NEW untracked dirs at this fetch.
- **Working-tree status (raw manifest, abbreviated):**
| Status | Path |
@@ -182,6 +191,11 @@ help locate things in the vault, not summarize their content.
| Date | Hash | Note |
| --- | --- | --- |
| 2026-08-25 | `9d4767c7` | **feat: Zhai 2026 Sci Adv 3D skin pemphigus** (PMID 41512055) — adds `obsidian-vault/04-Literature/Deep-Reads/Skin-Organoids/Zhai_2026_Sci_Adv_3D_Skin_Pemphigus.md` — **FIRST file in the new `Skin-Organoids/` subfolder**, single-shot LDR entry. Zhai T et al. Sci Adv 2026 — 3D skin organoid + pemphigus disease-modeling application domain; **net-new application domain (autoimmune dermatology + 3D skin)** to Robin's deep-read set, distinct from cancer organoid (cancer) / brain organoid (Raji 2026 etc.) / vascularized organoid (Tevonian + Shen in this cluster) / cardiac organoid (Yang in this cluster) / liver organoid (Liang 2026) / brain-tumor organoid buckets. Vendor anchor mapping: TBD on the wiki-side synthesis page; skin organoid is adjacent to CelVivo ClinoReactor (long-term 3D skin culture) but no vendor callouts confirmed in the manifest entry. Future implication: skin organoid is a candidate workflow for the Robin CelVivo industrial-customers program (cosmetic + dermatology pharma R&D). |
| 2026-08-25 | `5907cdfc` | **feat: Shen 2026 Chin Med J vascularized organoids review** (PMID 42268296) — adds `obsidian-vault/04-Literature/Deep-Reads/Vascularized-Organoids/Shen_2026_Chin_Med_J_Vascularized_Organoids_Review.md` — **FIRST review-type file in the new `Vascularized-Organoids/` subfolder**, single-shot LDR entry. Shen Y et al. Chin Med J 2026 — vascularized organoid systematic review (peer-reviewed Chinese-language journal); companion to the Tevonian 2026 vascularized liver MPS deep-read in the same cluster. Vendor anchor mapping: TBD on the wiki-side synthesis page; vascularized organoid literature is CelVivo ClinoStar-adjacent (long-term stable vascular maturation) + Mimetas OrganoPlate-adjacent (organ-on-chip for vascularized microenvironment) + Cellink BIO X-adjacent (decellularized scaffold for vascularization). |
| 2026-08-25 | `9aa2af4c` | **Update Tevonian 2026 + Yang 2026: add CelVivo/Cellink/Mimetas/3Brain/Femtobiomed product mapping + 净化 Robin mentions** — `M` touches `obsidian-vault/04-Literature/Deep-Reads/Cardiac-Organoids/Yang_2026_Stem_Cell_Res_Ther_Cardiac_Organoid_Review.md` + `M` touches `obsidian-vault/04-Literature/Deep-Reads/Vascularized-Organoids/Tevonian_2026_Nat_Commun_Vascularized_Liver_MPS.md` — **FIRST post-publish vendor-mapping retrofit commit in Robin's LDR pipeline**; the prior 5-paper 2026-08-23/24 cluster (Ajongbolo + Kim + Tian + Aiello + CelVivo App Note) did NOT have this retrofit applied retroactively; only the new Tevonian + Yang pair get the retroactive 5-vendor mapping (CelVivo + Cellink + Mimetas + 3Brain + Femtobiomed) plus 净化 Robin mentions. **Robin's LDR SOP iteration**: the 5-vendor product-mapping table is now a standard post-publish step for new LDR commits. The 净化 Robin mentions specifically removes any direct attribution strings ("Robin"s, "Robin 8-XX 实战沉淀" patterns, etc.) that might leak into the production deep-read narrative. |
| 2026-08-25 | `583859a8` | **feat: Yang 2026 Stem Cell Res Ther cardiac organoid review** (PMID 41963991) — adds `obsidian-vault/04-Literature/Deep-Reads/Cardiac-Organoids/Yang_2026_Stem_Cell_Res_Ther_Cardiac_Organoid_Review.md` — **FIRST file in the new `Cardiac-Organoids/` subfolder**, single-shot LDR entry. Yang L et al. Stem Cell Res Ther 2026 — cardiac organoid review (companion to Tian 2025 Nat Commun cardiac epicardium mTOR paper from the prior 5-paper cluster). The new `Cardiac-Organoids/` subfolder joins the existing `Cardiac/` subfolder (2 prior papers) — Robin has expanded the cardiac application-domain treatment from a sparse 2-paper bucket to a dedicated subfolder. Vendor anchor mapping: TBD; the `9aa2af4c` retrofit commit updated the file with the 5-vendor mapping (CelVivo + Cellink + Mimetas + 3Brain + Femtobiomed). |
| 2026-08-25 | `089177a7` | **feat: Tevonian 2026 Nat Commun 血管化肝 MPS deep read** (PMID 41634021) — adds `obsidian-vault/04-Literature/Deep-Reads/Vascularized-Organoids/Tevonian_2026_Nat_Commun_Vascularized_Liver_MPS.md` — **FIRST file in the new `Vascularized-Organoids/` subfolder**, single-shot LDR entry. Tevonian et al. (2026) Nat Commun — vascularized liver MPS (microphysiological system) deep read. Companion to the existing `Liver/` subfolder entries (Liang 2026 fibrosis platform etc.) — this adds the vascularization dimension to the liver organoid application-domain bucket. Vendor anchor mapping: TBD; the `9aa2af4c` retrofit commit updated the file with the 5-vendor mapping (CelVivo + Cellink + Mimetas + 3Brain + Femtobiomed). |
| 2026-08-23 | `fb017e4f` | **feat: CelVivo App Note 2026 shear stress ClinoStar vs orbital shaker** (Wiki.js 1747) — adds `obsidian-vault/04-Literature/Deep-Reads/CelVivo_Shear_Stress_AppNote_2026.md` (10,145 bytes, single-shot entry) — **NEW vendor-anchored CelVivo evidence**: Stougaard Borgen Løschenkohl, Sedighi Frandsen (CelVivo App Note 2026) head-to-head ClinoStar® vs orbital shaker, 15-day HepG2/C3A + embedded Caco-2 + brain organoid; F-actin + DAPI staining shows ClinoStar preserves cytoskeleton integrity vs orbital shaker structural decay; ATP + BCA + 3 biological replicates per condition; SP5D 24-well ball-plate 1000 cells/aggregate pre-conditioning; ClinoReactor® vessel (CelVivo 10004-12) in ClinoStar® system (30003) vs ULA 6-well + Steinberg SBS-LVS-100 shaker; low-shear fFSS confirmation |
| 2026-08-23 | `f2118a62` | **feat: Aiello & Bagni 2025 biorxiv Rotating Chamber brain organoid 精读** (Wiki.js 1746) — adds `obsidian-vault/04-Literature/Deep-Reads/Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid.md` (11,731 bytes, single-shot entry) — **NEW CelVivo-aligned evidence**: EMBO Reports 投稿版 (Aiello_Bagni_EMBO R_050325) — COMSOL Multiphysics 6.2 CFD quantification of Rotating Chamber (RC) shear stress field; chamber geometry 78.3 mm × 24.2 mm (outer) / 37.7 mm × 8.8 mm (inner); **shear stress < 20 mPa confirmed** (vs qualitative "low-shear" only previously); 0-300 objects per chamber all stable low-shear across densities 1010/1020/1030; multi-batch + multi-iPSC line brain organoid morphology PCA (CV <15% vs static >30%); scRNA-seq OXPHOS profiling; SOX2/Nestin/PAX6 + DCX + TBR1/SATB2/MAP2 multi-marker IHC; first **quantitative** confirmation of CelVivo RC low-shear claim |
| 2026-08-23 | `40b357b8` | **feat: Tian 2025 NatCommun 心外膜 mTOR 精读** (Wiki.js 1745) — adds `obsidian-vault/04-Literature/Deep-Reads/Tian_2025_NatCommun_Epicardium_mTOR.md` (15,578 bytes, single-shot entry) — **NEW cardiac organoid evidence**: Tian Y, Lucena-Cacace A, Tani K et al. (2025) Nat Commun DOI 10.1038/s41467-025-60934-8 — Torin1 (dual mTORC1/2 inhibitor, 200 nM) drives hiPSC epicardium maturation from embryonic to adult phenotype; qHSC→aHSC EMT reactivation pathway; bulk RNA-seq 379 DEGs; PCA explains 28.53% PC1 + 36.01% PC2 variance; co-culture hiPSC epicardium + ventricular cardiomyocyte EB → TNNI3 upregulation (paracrine maturation); mTORC1/2 dual inhibition is critical (Rapamycin alone insufficient); YBX3 + MAFF TF candidates via siRNA knockdown; first cardiac epicardium paper since MOC 心肌 maturation track started |
@@ -461,8 +475,9 @@ on the same paper.
| Date | Hash | Note |
| --- | --- | --- |
| 2026-08-25 | `1003b92` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-25) — **count-data wipe re-applied** for the **eleventh** consecutive sources-sync (after 2026-08-15 `2507925` + 2026-08-16 `997b648` + 2026-08-17 `be49285` + 2026-08-18 `1fc73ae` + 2026-08-19 `dcb53a2` + 2026-08-20 `bd30339` + 2026-08-21 `f6c2576` + 2026-08-22 `43d4548` + 2026-08-23 `8f8f767` + 2026-08-24 `127c2dc`); see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-25 | `3255613` | chore: daily update 2026-08-25 (synthesis-layer edits accumulated from the prior HN-1 2026-08-25T18:00Z + web-search-1 2026-08-25 (skipped) + git-repo-1 2026-08-25T18:13Z runs; committed 17 files from the prior dirty set per `git show --stat 3255613` — including `commitments.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/literature.md` + `sources/nocodb.md` + `sources/openwiki-version-drift.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` + `sources/wikijs.md` + `index.md` + `quickstart.md` + `sources/README.md` + `themes.md` + `themes/05-robin-research.md` + `themes/index.md`; the very next synthesis edits from the git-repo-1 2026-08-25T18:13Z run re-touch the same files + add 2 newly dirty files per the manifest `changedFiles` list) |
| 2026-08-24 | `127c2dc` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-24) — **count-data wipe re-applied** for the **tenth** consecutive sources-sync (after 2026-08-15 `2507925` + 2026-08-16 `997b648` + 2026-08-17 `be49285` + 2026-08-18 `1fc73ae` + 2026-08-19 `dcb53a2` + 2026-08-20 `bd30339` + 2026-08-21 `f6c2576` + 2026-08-22 `43d4548` + 2026-08-23 `8f8f767`); see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-24 | `9cc5e63` | chore: daily update 2026-08-24 (synthesis-layer edits accumulated from the prior HN-1 2026-08-23T18:00Z + web-search-1 2026-08-23 (skipped) + git-repo-1 2026-08-23T18:11Z runs; committed `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/openwiki-version-drift.md` + `sources/web-search.md` + `themes/05-robin-research.md` from the prior dirty set, reducing uncommitted-file count from 6 → 8 because the very next synthesis edits from this git-repo-1 2026-08-24T18:05Z run re-touch the same 6 files + add 2 newly dirty files `sources/literature.md` + `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` per the manifest `changedFiles` list) |
| 2026-08-23 | `a9568d8` | chore: daily update 2026-08-23 (synthesis-layer edits accumulated from the prior HN-1 2026-08-22T18:00Z + web-search-1 2026-08-22 (skipped) + web-search-1 2026-08-23 (skipped) + git-repo-1 2026-08-22T18:13Z runs; committed `sources/git-repo.md` + `sources/index.md` + `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` + `themes/05-robin-research.md` from the prior dirty set, reducing uncommitted-file count from 9 → 6) |
| 2026-08-23 | `8f8f767` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-23) — **count-data wipe re-applied** for the **ninth** consecutive sources-sync (after 2026-08-15 `2507925` + 2026-08-16 `997b648` + 2026-08-17 `be49285` + 2026-08-18 `1fc73ae` + 2026-08-19 `dcb53a2` + 2026-08-20 `bd30339` + 2026-08-21 `f6c2576` + 2026-08-22 `43d4548`); see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-22 | `43d4548` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-22) — **count-data wipe re-applied** for the **eighth** consecutive sources-sync (after 2026-08-15 `2507925` + 2026-08-16 `997b648` + 2026-08-17 `be49285` + 2026-08-18 `1fc73ae` + 2026-08-19 `dcb53a2` + 2026-08-20 `bd30339` + 2026-08-21 `f6c2576`); see Notable-entity § "2026-08-15 sources-sync bug" |
@@ -547,6 +562,7 @@ pipeline catches up.
| Window (UTC) | Vault | Wiki |
| --- | --- | --- |
| 2026-08-24T18:05:00Z → 2026-08-25T18:13:00Z | HEAD `fb017e4f` → `9d4767c7` (**5 new commits**: `089177a7` Tevonian 2026 Nat Commun 血管化肝 MPS + `583859a8` Yang 2026 Stem Cell Res Ther cardiac organoid review + `9aa2af4c` Tevonian + Yang product-mapping retrofit + `5907cdfc` Shen 2026 Chin Med J vascularized organoids review + `9d4767c7` Zhai 2026 Sci Adv 3D skin pemphigus — **SECOND consecutive single-day 5-paper LDR burst**; combined with the 2026-08-23/24 5-paper burst, **10 LDR papers in 48 hours** = largest sustained 2-day research output in Robin's vault activity log; the cluster creates **3 new `04-Literature/Deep-Reads/` subfolders**: `Vascularized-Organoids/` (Tevonian + Shen) + `Cardiac-Organoids/` (Yang) + `Skin-Organoids/` (Zhai), expanding Robin's per-vendor / per-application-domain subfolder taxonomy from ~19 to ~22; the cluster includes the **first post-publish vendor-mapping retrofit commit** (`9aa2af4c`) — adding CelVivo/Cellink/Mimetas/3Brain/Femtobiomed product mapping + 净化 Robin mentions to Tevonian + Yang retroactively) | HEAD `127c2dc` → `1003b92` (**2 new automated commits**: `3255613` chore: daily update 2026-08-25 + `1003b92` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-25, the **eleventh** consecutive sources-sync re-applying the `2507925` 2026-08-15 count-data wipe pattern after `997b648` 2026-08-16 + `be49285` 2026-08-17 + `1fc73ae` 2026-08-18 + `dcb53a2` 2026-08-19 + `bd30339` 2026-08-20 + `f6c2576` 2026-08-21 + `43d4548` 2026-08-22 + `8f8f767` 2026-08-23 + `127c2dc` 2026-08-24 + now `1003b92` 2026-08-25); the `3255613` daily update committed 17 files per `git show --stat 3255613` (including `commitments.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/literature.md` + `sources/nocodb.md` + `sources/openwiki-version-drift.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` + `sources/wikijs.md` + `index.md` + `quickstart.md` + `sources/README.md` + `themes.md` + `themes/05-robin-research.md` + `themes/index.md`); the manifest `changedFiles` shows 11 dirty wiki files this fetch — `M .last-update.json` + `M index.md` + `M quickstart.md` + `M sources/README.md` + `M sources/git-repo.md` + `M sources/hackernews.md` + `M sources/literature.md` + `M sources/nocodb.md` + `M sources/ragflow.md` + `M sources/seafile.md` + `M sources/web-search.md` + `M sources/wikijs.md`) |
| 2026-08-23T18:11:00Z → 2026-08-24T18:05:00Z | HEAD `a4fa5a32` → `fb017e4f` (**5 new commits**: `ad4abcde` Ajongbolo 2025 Cells brain organoid review + `5f02489a` Kim 2025 Nat Commun EGaIn 3D MEA + `40b357b8` Tian 2025 Nat Commun hiPSC epicardium mTOR + `f2118a62` Aiello & Bagni 2025 biorxiv Rotating Chamber brain organoid CFD + `fb017e4f` CelVivo App Note 2026 ClinoStar vs orbital shaker head-to-head — **largest single-day LDR burst since the 2026-07-29 Parate / Lee / Hodge cluster**, breaks the **7-fetch vault silence streak** that started after the 2026-08-16 Quintard + Guo cluster; all 5 are single-shot entries at `obsidian-vault/04-Literature/Deep-Reads/` root (no v2/v3 SOP rewrite cycles this cluster); commit timestamps 07:50 → 16:39 +0800 across the 2026-08-24 day) | HEAD `a9568d8` → `127c2dc` (**2 new automated commits**: `9cc5e63` chore: daily update 2026-08-24 + `127c2dc` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-24, the **tenth** consecutive sources-sync re-applying the `2507925` 2026-08-15 count-data wipe pattern after `997b648` 2026-08-16 + `be49285` 2026-08-17 + `1fc73ae` 2026-08-18 + `dcb53a2` 2026-08-19 + `bd30339` 2026-08-20 + `f6c2576` 2026-08-21 + `43d4548` 2026-08-22 + `8f8f767` 2026-08-23 + now `127c2dc` 2026-08-24) + the prior `a9568d8` 2026-08-23 daily update was committed in this fetch's prior daily update cycle before the 5-paper burst landed; `9cc5e63` committed `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/openwiki-version-drift.md` + `sources/web-search.md` + `themes/05-robin-research.md` from the prior dirty set; the manifest `changedFiles` shows 8 dirty files this fetch — `M .last-update.json` + `M sources/hackernews.md` + `M sources/literature.md` + `M sources/nocodb.md` + `M sources/ragflow.md` + `M sources/seafile.md` + `M sources/web-search.md` + `M sources/wikijs.md`) |
| 2026-08-15T18:07:49Z → 2026-08-17T18:09:32Z | HEAD `297f106d` → `a4fa5a32` (**7 new commits**: `0fc8db24` + `290e9635` + `24c713de` + `4073abf4` Quintard 2024 Nat Commun microfluidic vascularized organoid chip 4-commit LDR cycle + `2e6f5989` + `00f824f2` + `a4fa5a32` Guo 2026 Front Cell Dev Biol organoid ethics systematic review 3-commit LDR cycle — **first time since the 2026-07-28 / 2026-07-29 Parate / Lee / Hodge cluster that two new paper deep-reads landed on `main` in the same 48-hour window**) | HEAD `2507925` → `be49285` (**4 new commits**: `151d22b` daily update 2026-08-16 + `997b648` sources-sync 2026-08-16 + `5c70881` daily update 2026-08-17 + `be49285` sources-sync 2026-08-17) |
| 2026-08-17T18:09:32Z → 2026-08-18T18:10:12Z | HEAD **unchanged** at `a4fa5a32` (**0 new commits**, **0 new mtime changes** — vault is silent in this 24-hour window; the 2026-08-16 Quintard 2024 + Guo 2026 cluster remains the most recent vault activity) | HEAD `be49285` → `1fc73ae` (**2 new automated commits**: `8127797` chore: daily update 2026-08-18 + `1fc73ae` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-18, the **fourth** consecutive sources-sync re-applying the `2507925` 2026-08-15 count-data wipe pattern)) |
@@ -610,12 +626,14 @@ Markdown file counts per deep-read subfolder:
| `Retinal/` | 1 |
| `Microbioreactor/` | 1 (new as of 2026-08-07 — Rosero 2026 Front Bioeng Biotechnol) |
| `Cells/` | 1 (new as of 2026-08-08 — Fernandez Vallone 2026 Cells THSDC) |
| `Review/` | 1 (new as of 2026-08-13 — Zhou 2023 computer vision + microfluidics, **untracked**, **10-day carry-forward** at 2026-08-21 fetch, **8 fetches silent** — structural signal continuing to weaken; **11-day carry-forward** at 2026-08-22 fetch, **9 fetches silent**; **12-day carry-forward** at 2026-08-23 fetch, **10 fetches silent**; **13-day carry-forward** at 2026-08-24 fetch, **11 fetches silent** — structural signal continues to weaken) |
| `templates/` | 1 (new as of 2026-08-17 — `类器官IRB申请清单.md`, derived from the Guo 2026 ethics deep-read; Robin's first customer-facing template produced from a single deep-read, **untracked**, **5-day carry-forward** at 2026-08-21 fetch (was 4-day at 2026-08-20); **6-day carry-forward** at 2026-08-22 fetch; **7-day carry-forward** at 2026-08-23 fetch; **8-day carry-forward** at 2026-08-24 fetch) |
| `celvivo_commercial/` | 1 (new as of 2026-08-17 — `1331651_20260630_131201.pdf`, the 6-30 quote PDF migrated into a new folder, **untracked**, **5-day carry-forward** at 2026-08-21 fetch (was 4-day at 2026-08-20); **6-day carry-forward** at 2026-08-22 fetch; **7-day carry-forward** at 2026-08-23 fetch; **8-day carry-forward** at 2026-08-24 fetch) |
| `04-Literature/Deep-Reads/` root (5 new files) | 5 (new as of 2026-08-23/24 — single-shot LDR burst: `CelVivo_Shear_Stress_AppNote_2026.md` + `Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid.md` + `Tian_2025_NatCommun_Epicardium_mTOR.md` + `Kim_2025_NatCommun_Liquid_Metal_3D_MEA.md` + `Ajongbolo_2025_Cells_Brain_Organoids_Review.md` — all landed at the root of `04-Literature/Deep-Reads/` not in a per-vendor subfolder; **non-standard pattern** vs the prior per-vendor subfolder discipline, see Notable-entity § "2026-08-23 root-level LDR burst") |
| `Review/` | 1 (new as of 2026-08-13 — Zhou 2023 computer vision + microfluidics, **untracked**, **10-day carry-forward** at 2026-08-21 fetch, **8 fetches silent** — structural signal continuing to weaken; **11-day carry-forward** at 2026-08-22 fetch, **9 fetches silent**; **12-day carry-forward** at 2026-08-23 fetch, **10 fetches silent**; **13-day carry-forward** at 2026-08-24 fetch, **11 fetches silent** — structural signal continues to weaken; **14-day carry-forward** at 2026-08-25 fetch, **12 fetches silent** — structural signal continues to weaken, subfolder is more likely one-off than recurring) |
| `templates/` | 1 (new as of 2026-08-17 — `类器官IRB申请清单.md`, derived from the Guo 2026 ethics deep-read; Robin's first customer-facing template produced from a single deep-read, **untracked**, **5-day carry-forward** at 2026-08-21 fetch (was 4-day at 2026-08-20); **6-day carry-forward** at 2026-08-22 fetch; **7-day carry-forward** at 2026-08-23 fetch; **8-day carry-forward** at 2026-08-24 fetch; **9-day carry-forward** at 2026-08-25 fetch) |
| `celvivo_commercial/` | 1 (new as of 2026-08-17 — `1331651_20260630_131201.pdf`, the 6-30 quote PDF migrated into a new folder, **untracked**, **5-day carry-forward** at 2026-08-21 fetch (was 4-day at 2026-08-20); **6-day carry-forward** at 2026-08-22 fetch; **7-day carry-forward** at 2026-08-23 fetch; **8-day carry-forward** at 2026-08-24 fetch; **9-day carry-forward** at 2026-08-25 fetch) |
| `Vascularized-Organoids/` | 2 (new as of 2026-08-25 — `Tevonian_2026_Nat_Commun_Vascularized_Liver_MPS.md` + `Shen_2026_Chin_Med_J_Vascularized_Organoids_Review.md`; the prior per-vendor subfolder discipline returns after the 2026-08-23/24 root-level burst; subfolder semantics: vascularized organoid application-domain cluster) |
| `Cardiac-Organoids/` | 1 (new as of 2026-08-25 — `Yang_2026_Stem_Cell_Res_Ther_Cardiac_Organoid_Review.md`; expanded from the prior 2-file `Cardiac/` subfolder into a dedicated Cardiac-Organoids subfolder — companion application-domain to the existing 2-paper Cardiac bucket) |
| `Skin-Organoids/` | 1 (new as of 2026-08-25 — `Zhai_2026_Sci_Adv_3D_Skin_Pemphigus.md`; **net-new application domain (autoimmune dermatology + 3D skin)** to Robin's deep-read set; companion to the existing Cardiac / Brain / Liver / Vascularized-Organoids / Cancer / Kidney / Retinal application-domain subfolders) |
Total ≈ 1,212 deep-read notes on `main` (+5 from the 2026-08-23/24 single-shot LDR burst, on top of +2 from the 2026-08-16 Quintard 2024 + Guo 2026 clusters).
Total ≈ 1,217 deep-read notes on `main` (+4 new LDR files from the 2026-08-24/25 cluster on top of +5 from the 2026-08-23/24 single-shot LDR burst and +2 from the 2026-08-16 Quintard 2024 + Guo 2026 clusters; the 5th 2026-08-25 commit `9aa2af4c` is an in-place `M` touch on Tevonian + Yang files, not a new file). Robin's LDR cluster pattern is now **2 consecutive 5-commit windows** (2026-08-23/24 + 2026-08-24/25), totalling **11 commits / 9 new files** in 48 hours.
Review/ zhou2023 computer vision + microfluidics, **untracked** — only
counts once committed; +2 working-tree files in the new `templates/` +
`celvivo_commercial/` directories, both untracked; +1 working-tree directory `deepread_40240593/` (7 subdirs, 2026-08-24) carrying pipeline intermediate artifacts from the 5-paper burst). The 2026-08-23/24 single-shot LDR burst (5 papers at vault root) is the most recent committed deep-read cluster; the 2026-08-16 Quintard 2024 + Guo 2026 cluster remains the prior committed cluster; the 2026-08-07 / 2026-08-08 cluster (Microbioreactor + Cells) remains the prior-prior committed cluster. CelVivo, 3Brain, Cellink, and the broad `Organoid/` bucket cover Robin's product KB per the wiki goal focus areas (类器官培养与设备, 3D 生物打印). The new `templates/` folder signals Robin may be formalizing customer-facing deliverables (checklists / templates / sales scripts) as a separate vault subtree — the IRB application checklist is the first such artifact.
@@ -686,6 +704,12 @@ fields still 待补).
- **Kim 2025 Nat Commun EGaIn liquid-metal 3D MEA (2026-08-23, single-shot LDR entry `5f02489a`, Wiki.js 1744)** — `obsidian-vault/04-Literature/Deep-Reads/Kim_2025_NatCommun_Liquid_Metal_3D_MEA.md` (13,567 bytes). Kim E, Jeong E, Hong YM et al., Nat Commun 2025, DOI 10.1038/s41467-024-55752-3. The paper establishes: (i) **EGaIn (eutectic gallium-indium) 3D pillar MEA** — microfluidic direct-ink-writing fabrication with **pillar height 25-310 μm controllable by printing speed** (R² > 0.95, n=12 datapoints), **pillar diameter down to 14 μm** (single-neuron scale), parylene-C selective encapsulation with only pillar tip exposed as electrode; (ii) **magnetically reshapable** — Ni magnetic layer on pillar exterior + external magnetic field drives pillar bending → 3D MEA shape conforms to different organoid sizes/shapes (no fabrication re-spin needed); (iii) **hPSC cortical organoid maturation timeline** — Dorsomorphin + SB-431542 (dual-SMAD) → FGF2/EGF expansion → BDNF/NT3 maturation at 15/30/45/60/120 days; 30d SOX2+/TUJ1+ early neuronal; 60d SOX2↓ + TUJ1↑↑; 120d 6-marker co-expression (MAP2/GFAP/VGLUT1/SATB2/CTIP2) = cortical 6-layer-like structure; (iv) **biocompatible integration** — 4-month organoid seeded on 3D MEA, co-cultured 14 days; live/dead + qPCR (PAX6/Nestin/TUJ1) + IHC (Nestin/TUJ1/SOX2/MAP2/GFAP) all confirm biocompatibility; (v) **single-unit spike + network synchronization recording** — 64-channel MEA acquisition + SU spike detection + synchronization score + network graph analysis across 1/2/4/6 month organoid maturation. **Net-new external evidence** in this run. **Vendor-anchor mapping**: **3Brain HD-MEA competitor / adjacent paper** — Kim's EGaIn 3D MEA is a next-generation flexible 3D MEA approach that is **adjacent to but not directly competing with** 3Brain's rigid Accura-3D chip (3Brain uses 4096-electrode planar CMOS, Kim uses 3D pillar EGaIn with magnetic reshape). The Liu 2026 NBME shape-conformal framework from the 2026-08-08 cluster is a third next-gen HD-MEA approach — **3 distinct next-gen HD-MEA approaches now in Robin's deep-read set**: Liu 2026 Rogers Lab flexible-electronics framework (3000-8000 ch, >90% surface coverage) + Kim 2025 EGaIn 3D pillar (25-310 μm height, magnetic reshape) + Kim's pillar biocompatibility with cortical organoid (1/2/4/6-month maturation timeline). **Track on next fetch** whether (a) Robin produces a deep-read synthesis page at `/sources/literature-kim-2025-nat-commun-liquid-metal-3d-mea-deepread.md`, (b) the Kim paper routes into the existing `liu-2026-hd-mea-roadmap-implication` commitment as a corroborating evidence point (the "next-gen HD-MEA field" consolidation narrative now has 3 distinct data points), (c) the Kim paper pairs with Liu 2026 to anchor a new `liu-kim-2025-2026-next-gen-hd-mea-roadmap` consolidation synthesis page.
- **Ajongbolo 2025 Cells brain organoid review (2026-08-23, single-shot LDR entry `ad4abcde`, Wiki.js 1743)** — `obsidian-vault/04-Literature/Deep-Reads/Ajongbolo_2025_Cells_Brain_Organoids_Review.md` (11,367 bytes). Ajongbolo AO, Langhans SA, Cells 2025, DOI 10.3390/cells14110842. The paper is the **canonical brain organoid + assembloid review** for Robin's deep-read set: (i) **3-tier brain-organoid taxonomy** — whole-brain organoid (Lancaster 2013 archetype, multi-brain-region identity, unguided spontaneous differentiation) → region-specific organoid (前脑/中脑/小脑/下丘脑 with patterning-factor-guided TF markers FOXG1 / OTX2 / EN1/EN2 / GBX2 / FGF8 / SHH) → complex organoid systems (assembloid multi-region fusion / OoC vascularization-perfusion / tumoroid tumor modeling / xenograft immunodeficient-mouse intracranial transplant); (ii) **4-class characterization methodology** — morphological (IF + confocal) + biochemical (qPCR/Western/bulk RNA-seq) + functional (MEA / patch clamp / calcium imaging) + omics (scRNA-seq / spatial transcriptomics / mass spec) = standardized decision tree for any new brain-organoid line publication; (iii) **disease-modeling real-world boundaries** — neurodevelopmental (microcephaly / macrocephaly / ASD / Rett / Fragile X / Timothy syndrome) + neurodegenerative (AD / PD / HD / ALS) + brain-tumor (glioblastoma / medulloblastoma / AT/RT); (iv) **drug-discovery pipeline standardization** — 96-well + microfluidic chip + automated imaging + AI phenotype recognition → emerging HTS platform. **Net-new external evidence** in this run. **Vendor-anchor mapping**: **CelVivo ClinoStar-adjacent** (long-term stable brain organoid culture) + 3Brain HD-MEA-adjacent (functional electrophysiology read-out via MEA in the 4-class characterization). **Cross-vendor**: Ajongbolo review is the **first comprehensive brain-organoid review** in Robin's deep-read set since the 2026-07-29 Organoids 2026 review (`10.1186_s40164-026-00743-x`) — pairs with that review to give Robin a **review-paper anchor for the brain-organoid lane**. **Track on next fetch** whether (a) Robin produces a deep-read synthesis page at `/sources/literature-ajongbolo-2025-cells-brain-organoids-review-deepread.md`, (b) the review routes into `/themes/05-robin-research.md` as a "review-paper cluster" entry alongside the Organoids 2026 review.
- **`deepread_40240593/` pipeline workspace (2026-08-24, NEW this fetch)** — `deepread_40240593/` is the **first** new untracked directory added this fetch, alongside the 5 root-level LDR files. The directory contains **7 subdirectories**: `deepread_40016200` + `deepread_40441268` + `deepread_40498018` + `deepread_40593704` + `deepread_41151577` + `deepread_brain_organoid_fluid` + `deepread_shear_stress_cs_os`. The directory is at the vault root (not in `04-Literature/`); the numeric-name pattern (`deepread_<PMID>`) suggests Robin's LDR pipeline is using these directories as **per-paper working folders** — the names include both PMIDs (40016200, 40441268, 40498018, 40593704, 41151577) and human-readable slugs (brain_organoid_fluid → maps to Aiello paper; shear_stress_cs_os → maps to CelVivo App Note). The directory mtime is 2026-08-24 16:31 +0800 (1-day-old at this fetch). **Structural significance**: (a) the `deepread_<PMID>` naming convention is **not** the prior `04-Literature/Deep-Reads/<vendor>/` convention — the new pattern is a **per-paper working-folder pattern** that holds pipeline intermediate artifacts (PDFs, image-extracts, qa-pass outputs, Ollama vision-audit intermediates, etc.) before final commit to `04-Literature/Deep-Reads/`. (b) The presence of 5 already-committed root-level LDR files (in `04-Literature/Deep-Reads/`) **plus** the 2 named `deepread_<slug>` folders (brain_organoid_fluid + shear_stress_cs_os) — which exactly map to 2 of the 5 committed papers — suggests Robin's pipeline writes the **committed LDR note** to `04-Literature/Deep-Reads/` and the **intermediate artifacts** to `deepread_40240593/deepread_<slug>/`; the other 5 PMID-named subdirs are pipeline intermediates for 5 other in-progress papers not yet on `main`. (c) The vault-root `deepread_40240593/` is **not yet committed** (carry-forward untracked); the 2026-08-23 7-paper burst means Robin is producing pipeline output faster than the manual commit cycle. **Carry-forward status** (2026-08-24): untracked, **1-day-old** at this fetch, future-commit candidate. **Track on next fetch** whether (a) the directory is committed, (b) more papers move through the pipeline, (c) the `deepread_<PMID>` vs `04-Literature/Deep-Reads/<slug>` separation is formalized in vault conventions. **No synthesis routes** until the directory is committed.
- **2026-08-24/25 cluster — SECOND consecutive single-day 5-paper LDR burst (vault HEAD `fb017e4f` → `9d4767c7`, 5 new vault commits)** — the 2026-08-25T18:13Z fetch observed a **SECOND consecutive single-day 5-paper LDR burst** at vault HEAD. Combined with the 2026-08-23/24 5-paper burst, **10 LDR files in 48 hours**, the largest sustained 2-day research output in Robin's vault activity log; the cluster creates **3 NEW `04-Literature/Deep-Reads/` subfolders**: `Vascularized-Organoids/` (Tevonian + Shen) + `Cardiac-Organoids/` (Yang) + `Skin-Organoids/` (Zhai) — Robin expands the deep-read folder taxonomy from ~19 to ~22 in a single day, **returning to the per-vendor / per-application-domain subfolder discipline** after the 2026-08-23/24 5-paper vault-root burst (the only LDR cluster that landed at the root of `04-Literature/Deep-Reads/` rather than in a subfolder). The 5-commit cluster is (chronological): `089177a7` Tevonian 2026 Nat Commun 血管化肝 MPS deep read (PMID 41634021) → `583859a8` Yang 2026 Stem Cell Res Ther cardiac organoid review (PMID 41963991) → `9aa2af4c` Update Tevonian 2026 + Yang 2026 (CelVivo/Cellink/Mimetas/3Brain/Femtobiomed product mapping retrofit + 净化 Robin mentions — **FIRST post-publish vendor-mapping retrofit commit in Robin's LDR pipeline**) → `5907cdfc` Shen 2026 Chin Med J vascularized organoids review (PMID 42268296) → `9d4767c7` Zhai 2026 Sci Adv 3D skin pemphigus (PMID 41512055). Vendor anchor mapping (via `9aa2af4c` retrofit): 4-vendor (CelVivo / Cellink / Mimetas / 3Brain / Femtobiomed) product mapping applied retroactively to Tevonian + Yang files. **Net-new external evidence** in this run. Synthesis routes into `/themes/01-organoid-equipment.md` (vascularized liver MPS + cardiac organoid review + autoimmune dermatology adjacency — likely the first significant expansion of Robin's coverage outside the canonical 4 application domains), `/themes/05-robin-research.md` (vault-snapshot refresh + the 2.5x expansion of subfolder taxonomy), `/sources/literature.md` (last-30-days table), `/commitments.md` (4 new commitment rows), `/themes.md` (potential `class-organoid-3d-bioprinting` evidence footprint strengthening — 4 of 5 papers are tissue-organoid deep-reads; if the 2026-08-25 burst recurs, the theme row may need a deeper evidence-footprint refresh). **Track on next fetch** whether (a) more per-vendor / per-application-domain subfolders land (extending the post-root-burst return to subfolder discipline), (b) the `9aa2af4c` retrofit pattern is applied to the prior 5 papers from the 2026-08-23/24 cluster (currently only Tevonian + Yang got the retrofit), (c) the `Vascularized-Organoids/` + `Cardiac-Organoids/` + `Skin-Organoids/` subfolders accumulate additional entries (≥3 total entries per subfolder is the threshold for "subfolder is in active use"), (d) the `deepread_40240593/` pipeline workspace directory finally gets committed.
- **Tevonian 2026 Nat Commun 血管化肝 MPS (2026-08-25, single-shot LDR entry `089177a7`, PMID 41634021)** — `obsidian-vault/04-Literature/Deep-Reads/Vascularized-Organoids/Tevonian_2026_Nat_Commun_Vascularized_Liver_MPS.md`. Tevonian et al. (2026) Nat Commun — **first vascularized liver MPS (microphysiological system) paper** in Robin's deep-read set. Vendor anchor mapping (via `9aa2af4c` retrofit): the retrofit commit added the **5-vendor product mapping table** (CelVivo + Cellink + Mimetas + 3Brain + Femtobiomed) to the file; the deep-read likely ranks Mimetas OrganoPlate for the multi-channel vascularized MPS architecture (OrganoPlate is the canonical microphysiological system for vascularized liver tissue) + CelVivo ClinoReactor for upstream hepatocyte maturation (Hep-Orgs source) + Cellink BIO X for the decellularized liver scaffold matrix. Companion to the existing **Liang 2026** liver organoid entry (ClinoStar ⭐⭐⭐⭐ for P1-P10 long-term maturation + ClinoReactor ⭐⭐⭐⭐ for 3-track HEP/CHO/HSC perfusion). **Application domain**: vascularized liver — extends the existing `Liver/` subfolder's (6 papers) fibrotic disease modeling story with a vascularization dimension. **Net-new external evidence** in this run (git-repo-1 2026-08-25). Synthesis routes into `/themes/01-organoid-equipment.md` (vascularized liver vendor mapping) + `/commitments.md` (new commitment entry once Robin produces a synthesis page). **Track on next fetch** whether (a) Robin produces a deep-read synthesis page at `/sources/literature-tevonian-2026-nat-commun-vascularized-liver-mps-deepread.md`, (b) the retrofitted 5-vendor mapping tables yield specific ROI for the active CelVivo / Cellink / Mimetas / 3Brain / Femtobiomed Chinese pharma R&D / CDMO account targeting, (c) the Tevonian paper pairs with Shen 2026 to anchor a `vascularized-organoid` review-paper cluster that the existing Subfolder lacks.
- **Yang 2026 Stem Cell Res Ther cardiac organoid review (2026-08-25, single-shot LDR entry `583859a8`, PMID 41963991)** — `obsidian-vault/04-Literature/Deep-Reads/Cardiac-Organoids/Yang_2026_Stem_Cell_Res_Ther_Cardiac_Organoid_Review.md`. Yang L et al. (2026) Stem Cell Res Ther — **first comprehensive cardiac organoid review** in Robin's deep-read set. Vendor anchor mapping (via `9aa2af4c` retrofit): the retrofit commit added the **5-vendor product mapping table** to the file. Companion to **Tian 2025 Nat Commun** (the cardiac epicardium mTOR paper from the 2026-08-23 burst) which established the actual mechanistic depth; Yang 2026 is the canonical review that contextualizes Tian alongside the prior cardiac organoid literature (hPSC cardiac organoid generation methods, maturation protocols, disease modeling applications, regenerative medicine routes). **Application domain**: cardiac organoid — Robin expands from the prior 2-paper `Cardiac/` subfolder to a dedicated `Cardiac-Organoids/` subfolder; this is the first time Robin has opened a new subfolder explicitly for an application-domain cluster (prior new subfolders have been for review types or vendor types). **Net-new external evidence** in this run (git-repo-1 2026-08-25). Synthesis routes into `/themes/01-organoid-equipment.md` (cardiac organoid vendor mapping) + `/commitments.md` (new commitment entry) + `/sources/literature.md` (last-30-days table). **Track on next fetch** whether (a) Robin produces a synthesis page at `/sources/literature-yang-2026-stem-cell-res-ther-cardiac-organoid-review-deepread.md`, (b) the cardiac-organoid commitment folds Tian + Yang as a paired mechanistic + review cluster, (c) the Cardiac-Organoids subfolder accumulates ≥3 entries.
- **Shen 2026 Chin Med J vascularized organoids review (2026-08-25, single-shot LDR entry `5907cdfc`, PMID 42268296)** — `obsidian-vault/04-Literature/Deep-Reads/Vascularized-Organoids/Shen_2026_Chin_Med_J_Vascularized_Organoids_Review.md`. Shen Y et al. Chin Med J 2026 — **Chinese-language peer-reviewed vascularized organoid systematic review**; companion to **Tevonian 2026** in the same cluster. Vendor anchor mapping: TBD; the deep-read is in the Chinese-language journal 中华医学杂志 (English edition) which makes it a credential **Chinese-hospital-academic** source for Robin's active Chinese pharma R&D / CDMO customer base. **Application domain**: vascularized organoid — adds a 2-paper cluster to the new `Vascularized-Organoids/` subfolder. The Shen 2026 review is the **review-paper anchor** for the new subfolder (review-type) and the Tevonian 2026 primary research paper is the **research-paper anchor** (primary-type). **Net-new external evidence** in this run. **Track on next fetch** whether Robin produces a deep-read synthesis page and whether the Chinese-language source yields any CelVivo-specific IRB or vascularization positioning material.
- **Zhai 2026 Sci Adv 3D skin pemphigus (2026-08-25, single-shot LDR entry `9d4767c7`, PMID 41512055)** — `obsidian-vault/04-Literature/Deep-Reads/Skin-Organoids/Zhai_2026_Sci_Adv_3D_Skin_Pemphigus.md`. Zhai T et al. Sci Adv 2026 — **first 3D-skin organoid disease-modeling paper** in Robin's deep-read set; **net-new application domain** (autoimmune dermatology + 3D skin) that Robin's existing ~22 deep-read subfolders do not cover. Vendor anchor mapping: TBD; the deep-read does not have the `9aa2af4c` retrofit 5-vendor mapping (the retrofit was applied only to Tevonian + Yang); skin organoid is a candidate workflow for **CelVivo ClinoReactor** (long-term 3D skin culture — similar to the existing liver, brain, lung, retinal organoid applications) but the Sci Adv paper's specific ClinoReactor / ClinoStar callouts are not in the manifest entry. **Application domain**: 3D skin organoid + autoimmune dermatology (pemphigus) — distinct from the existing Cancer / Brain / Liver / Vascularized-Organoids / Cardiac-Organoids / Kidney / Retinal / Brain-Tumor application-domain subfolders. **Net-new external evidence** in this run. Synthesis routes into `/themes/01-organoid-equipment.md` (autoimmune dermatology adjacency to the vascularized-organoid cluster) + `/commitments.md` (new commitment entry). **Track on next fetch** whether (a) Robin produces a deep-read synthesis page, (b) the Skin-Organoids subfolder accumulates ≥3 entries to confirm a recurring application-domain pattern, (c) the Zhai paper yields Chinese cosmetic / dermatology pharma R&D positioning material that the active CRM portfolio could absorb.
- **`9aa2af4c` post-publish vendor-mapping retrofit commit (2026-08-25, NEW SOP step in Robin's LDR pipeline)** — `9aa2af4c` is a non-paper-content commit that touches the Tevonian 2026 + Yang 2026 files in-place to add the **5-vendor product mapping table** (CelVivo / Cellink / Mimetas / 3Brain / Femtobiomed) plus **净化 Robin mentions** (sanitization of any "Robin" / "Robin 8-XX 实战沉淀" attribution strings that might leak into the production deep-read narrative). The commit is the **first post-publish vendor-mapping retrofit** in Robin's LDR pipeline; the prior 5-paper 2026-08-23/24 cluster (Ajongbolo + Kim + Tian + Aiello + CelVivo App Note) did NOT receive the retrofit — only the new Tevonian + Yang pair got the retroactive 5-vendor mapping. The retrofit is **methodologically significant**: it indicates Robin's LDR workflow is now adding a **post-publish vendor-mapping step** to the standard 8-step SOP (the 8 铁律 + 3 trigger modes + 5-section report pattern at `/sources/ldr-report-template.md`). The prior 8-step SOP does not include a vendor-mapping retrofit step — Robin has effectively iterated to a 9-step SOP for the new Tevonian + Yang pair. The retrofit's 净化 Robin mentions specifically addresses the "客户-facing deep-read 净化" concern flagged in the prior synthesis policy — Robin's deep-reads are increasingly being routed into customer conversations (the Guo 2026 IRB checklist template is the canonical example) and any Robin attribution in the body could break the "vendor-anchored customer-facing artifact" framing. **Track on next fetch** whether (a) the `9aa2af4c` retrofit pattern is applied retroactively to the prior 5 papers (Ajongbolo + Kim + Tian + Aiello + CelVivo App Note) — if Robin retro-fits the vendor mapping, the existing `class-organoid-3d-bioprinting` theme evidence footprint strengthens materially; if not, the retrofit might be an LDR-pipeline ad-hoc patch rather than a recurring pattern; (b) the `9aa2af4c` retrofit becomes a standard LDR step (replacing the existing 8-step SOP iteration pattern); (c) the LDR SOP iteration is documented at `/sources/ldr-report-template.md` and `/sources/2026-07-27-4-27-sop-vs-implementation.md`.
- **Quintard 2024 Nat Commun microfluidic vascularized organoid chip (2026-08-16, 7 commits in 48-hour window)** — `obsidian-vault/Literature/Deep-Reads/Organoid/quintard_2024_vasorganoid_chip.md` (189 lines; 4-commit LDR cycle `0fc8db24` adds → `290e9635` -v2 修图床/双 H1/落款 → `24c713de` -v3 Wiki.js 自带图床 6 张图 → `4073abf4` -v4 转发语标题/落款加粗/删 3Brain; Wiki IDs 1719/1720/1722, NocoDB Id 3297). The paper is **the first microfluidic / organ-on-chip platform paper** Robin has deep-read in the 2026-08 window; the platform combines (i) 10-channel parallel microfluidic chips with U-shaped capture sites (300-800 µm adjustable), (ii) fibrin + Matrigel hydrogel layer deposition using Landau-Levich-Bretherton effect, (iii) ~10 s capture efficiency ~100%, (iv) dynamic perfusion 7-30 days with HUVEC + fibroblast co-culture + hiPSC-derived BVO + islet spheroid + lung organoid cross-validation, (v) hierarchical vasculature (37 µm upstream artery-vein + 8 µm BVO capillaries, matching physiological ranges 50-1900 s⁻¹). **Net-new external evidence** in this run (git-repo-1 2026-08-17). The 4-star "与我们的产品" table lists **Mimetas OrganoPlate ⭐⭐⭐⭐** (direct Phaseguide-based vascularized / kidney / intestine organ-on-chip competitor) + **CelVivo ClinoStar ⭐⭐⭐** (upstream workflow step: BVO differentiation day 0-15 needs rotating-wall suspension culture; ClinoStar is the canonical hardware for this stage; the paper's day 15 → chip-on-board handoff is the canonical CelVivo → organ-on-chip workflow) + **Emulate Organ-Chip ⭐⭐⭐** (Colon-Intestine-Liver platform companion). Synthesis routes into `/themes/05-robin-research.md` (新增 by-vendor entry) and `/sources/literature.md` (last-30-days deep-read table). Vendor-anchor mapping: CelVivo-adjacent (workflow upstream) + Mimetas OrganoPlate / Emulate Organ-Chip (organ-on-chip product lane that Robin's portfolio does not currently cover but represents a potential cross-sell if Robin's customers ask "where do I run my CelVivo-matured organoids in a vascularized microenvironment?"). Customer-entry: 药企临床前 (vascularized drug screening) + 微流控 organ-on-chip 平台集成商 (Mimetas / Emulate channel partners) + academic PI (vascular development / diabetes). **Track on next fetch** whether Robin publishes a `/sources/literature-quintard-2024-nat-commun-vasorganoid-chip-deepread.md` synthesis page; the deep-read pipeline currently only carries `liang-2026-celvivo-clinostar-positioning` + `miao-2025-celvivo-clinostar-positioning` + `liu-2026-hd-mea-roadmap-implication` + `sharma-2026-retinal-organoid-mea-cross-sell` — no Quintard synthesis page yet.
- **Guo 2026 Front Cell Dev Biol organoid ethics systematic review (2026-08-16, 7 commits in 48-hour window)** — `obsidian-vault/Literature/Deep-Reads/Organoid/guo_2026_organoid_ethical_review.md` (170 lines + 3 真图; 3-commit LDR cycle `2e6f5989` adds → `00f824f2` -v2 修图床 (加 2 张 Wiki.js 自带图) → `a4fa5a32` -v3 补 Fig 1; Wiki ID 1724, NocoDB Id 3298). The paper is **the first organoid-research ethics / IRB systematic review** Robin has deep-read in any window — fills the methodological gap on the IRB-side that the prior clinical-translation evidence (CDE classification + Order No. 818) does not directly cover. The paper structures the IRB review framework as **7 mandatory points** (sample provenance + donor informed consent + data privacy & de-identification + co-culture agency + animal welfare 3R + cross-border regulation + long-term storage & termination); the cross-border table compares China (《人类遗传资源管理条例》+ 《涉及人的生命科学和医学研究伦理审查办法》2023), US (HIPAA + Common Rule + NIH GDS), EU (GDPR + Clinical Trials Regulation 536/2014), Japan, Korea. The 4-star "与我们的产品" table lists **CelVivo ClinoStar ⭐⭐⭐⭐** (clinical-translation IRB compliance — the 7 mandatory points directly apply to ClinoStar customer IRB submissions; **Robin 推广 ClinoStar 给三甲医院时, 可附带本框架作为增值**) + **Mimetas OrganoPlate ⭐⭐⭐⭐** (co-culture ethics — Mimetas 主营类器官 + 免疫细胞共培养, the co-culture agency framework from Guo 2026 point 4 directly applies) + **Emulate Organ-Chip ⭐⭐⭐** (organoid + microfluidic cross-border regulation reference). **Net-new external evidence** in this run (git-repo-1 2026-08-17). Robin translated the paper into a **customer-facing sales ammunition template** at `templates/类器官IRB申请清单.md` (180 lines; 7 mandatory points checklist + 5 customer Q&A + China vs International flow table + 10 attachments + 7 citations; v1.0 dated 2026-08-16, "Robin 8-16 实战沉淀") — see the templates/ entry in the next bullet. Customer-entry: 临床转化型医院 (class A tertiary hospitals running organoid IRB submissions) + 类器官厂家 Robin 培训客户 (the IRB checklist is the canonical "Robin 培训客户 IRB 申请" core material) + academic PI (cross-border collaboration IRB paperwork). **Track on next fetch** whether (a) the templates/ IRB checklist gets committed, (b) the Robin-author attribution in the template is recognized as a wiki-side customer-training artifact, (c) Robin produces a deep-read synthesis page at `/sources/literature-guo-2026-front-cell-dev-biol-organoid-ethics-deepread.md`, and (d) the IRB checklist routes into the existing CelVivo industrial-customers program (which currently lives at `05-Documents/Products/Celvivo/Industrial-Customers/`) as a standard customer-training artifact.
- **Review/ subfolder — first entry (2026-08-13, still uncommitted at 2026-08-23, 12-day carry-forward, watchlist signal continuing to weaken)** — `obsidian-vault/04-Literature/Deep-Reads/Review/zhou2023_computer_vision_microfluidics.md` is the **first file in a new `Review/` subfolder** under `04-Literature/Deep-Reads/`. The file is **untracked** at the 2026-08-23 fetch (Robin has not yet committed it — same state as the 2026-08-13 + 2026-08-15 + 2026-08-17 + 2026-08-18 + 2026-08-19 + 2026-08-20 + 2026-08-21 + 2026-08-22 fetches, **0 progress in the 2026-08-13 → 2026-08-23 240-hour window**, **10 consecutive fetches silent on the file**). **Watchlist signal continuing to weaken at this fetch**: per the 2026-08-15 watchlist-trigger rubric ("if the file remains uncommitted at the next fetch (2026-08-17 or later), the structural signal weakens"), the `Review/` subfolder at the 2026-08-23 fetch is **still single-entry, still untracked** — the structural signal **continues to weaken** at this fetch (**12-day carry-forward** with no commit, no follow-up paper landed in the subfolder across **10 consecutive fetches**). The `Review/` subfolder is more likely to be a one-off than a recurring pattern. The file should either be committed on a future fetch (which would re-strengthen the signal) or remain untracked indefinitely (which would confirm the one-off interpretation). No synthesis routes until the file is committed.
@@ -773,15 +797,168 @@ fields still 待补).
## Synthesis policy for this source
- **This run (2026-08-25, git-repo-1 18:13Z):** **5 new vault commits**
in the 2026-08-24T18:05Z → 2026-08-25T18:13Z 24-hour window — the
vault HEAD bumped from `fb017e4f` (2026-08-24T18:05Z fetch) to
`9d4767c7` (2026-08-25T18:13Z fetch) — **SECOND consecutive single-day
5-paper LDR burst** at vault HEAD. Combined with the 2026-08-23/24 5-paper
burst, **10 LDR files in 48 hours**, the largest sustained 2-day
research output in Robin's vault activity log. The 2026-08-25 cluster
returns to the per-vendor / per-application-domain subfolder discipline
(Tevonian → `Vascularized-Organoids/` + Shen → `Vascularized-Organoids/` +
Yang → `Cardiac-Organoids/` + Zhai → `Skin-Organoids/`), creating **3 NEW
subfolders** in `04-Literature/Deep-Reads/` (one less than the 5 papers,
because Tevonian + Shen share the `Vascularized-Organoids/` subfolder).
The 5 commits are (a) `089177a7` Tevonian 2026 Nat Commun 血管化肝 MPS
deep read (PMID 41634021) — first vascularized liver MPS paper +
first file in the new `Vascularized-Organoids/` subfolder; (b) `583859a8`
Yang 2026 Stem Cell Res Ther cardiac organoid review (PMID 41963991) —
first comprehensive cardiac organoid review + first file in the new
`Cardiac-Organoids/` subfolder; (c) `9aa2af4c` post-publish vendor-mapping
retrofit commit on Tevonian + Yang files — FIRST post-publish
vendor-mapping retrofit in Robin's LDR pipeline (adds CelVivo / Cellink /
Mimetas / 3Brain / Femtobiomed 5-vendor mapping + 净化 Robin mentions);
(d) `5907cdfc` Shen 2026 Chin Med J vascularized organoids review
(PMID 42268296) — Chinese-language peer-reviewed vascularized organoid
systematic review + second file in the new `Vascularized-Organoids/`
subfolder; (e) `9d4767c7` Zhai 2026 Sci Adv 3D skin pemphigus
(PMID 41512055) — first 3D skin organoid disease-modeling paper +
first file in the new `Skin-Organoids/` subfolder (NEW application
domain — autoimmune dermatology + 3D skin). The 2026-08-24/25 cluster
differs from the prior 2026-08-23/24 cluster in three ways: (i) all 5
files landed in **per-application-domain subfolders** rather than at the
`04-Literature/Deep-Reads/` root (return to standard subfolder discipline
after the 2026-08-23/24 root-level non-standard pattern); (ii) the cluster
includes a **non-paper-content retrofit commit** (`9aa2af4c`) which
reflects a new SOP step not present in the prior 8 铁律 + 3 trigger
modes pattern; (iii) the cluster's application-domain coverage **expands
into autoimmune dermatology** (Zhai skin) which is the first new
application-domain subfolder Robin has opened since the 2026-08-13 Review
subfolder was added (and even then, Review is type-based, not
application-domain-based). Vendor anchor mapping via the `9aa2af4c`
retrofit: 5-vendor product mapping applied retroactively to Tevonian +
Yang; the prior 5-paper 2026-08-23/24 cluster (Ajongbolo + Kim + Tian +
Aiello + CelVivo App Note) did NOT receive retroactive retrofit — Tevonian
+ Yang are the first LDR files to use the new post-publish vendor-mapping
step. **Net-new external evidence** in this run (4 paper deep-reads + 1
retrofit commit) — CelVivo/Cellink/Mimetas/3Brain/Femtobiomed product
mapping table is the net-new contribution. **Wiki-side**: **2 new
automated wiki commits** landed in the 2026-08-24T18:05Z →
2026-08-25T18:13Z 24-hour window — `3255613` chore: daily update 2026-08-25
(2026-08-25 02:23 +0800; per `git show --stat 3255613` the commit touched
17 files including `commitments.md` + `sources/git-repo.md` +
`sources/hackernews.md` + `sources/index.md` + `sources/literature.md` +
`sources/nocodb.md` + `sources/openwiki-version-drift.md` +
`sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` +
`sources/wikijs.md` + `index.md` + `quickstart.md` + `sources/README.md`
+ `themes.md` + `themes/05-robin-research.md` + `themes/index.md`) +
`1003b92` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts
(sources-sync 2026-08-25, 2026-08-25 02:30 +0800 — the **eleventh**
consecutive sources-sync re-applying the `2507925` 2026-08-15 count-data
wipe pattern after `997b648` 2026-08-16 + `be49285` 2026-08-17 + `1fc73ae`
2026-08-18 + `dcb53a2` 2026-08-19 + `bd30339` 2026-08-20 + `f6c2576`
2026-08-21 + `43d4548` 2026-08-22 + `8f8f767` 2026-08-23 + `127c2dc`
2026-08-24 + now `1003b92` 2026-08-25). Both commits are routine
auto-orchestration: (a) the `3255613` daily update carried the
synthesis-layer edits from the prior HN-1 2026-08-25T18:00Z +
web-search-1 2026-08-25 (skipped) + git-repo-1 2026-08-24T18:05Z runs;
the `3255613` daily update committed 17 of the prior dirty files; (b)
the `1003b92` sources-sync re-applied the count-data wipe pattern on
NocoDB / SeaFile / Wiki.js / RAGFlow for the **eleventh** consecutive
sources-sync. The manifest `changedFiles` shows 11 dirty wiki files this
fetch — `M .last-update.json` + `M index.md` + `M quickstart.md` + `M
sources/README.md` + `M sources/git-repo.md` + `M sources/hackernews.md`
+ `M sources/literature.md` + `M sources/nocodb.md` + `M sources/ragflow.md`
+ `M sources/seafile.md` + `M sources/web-search.md` + `M sources/wikijs.md`.
**Net-new external evidence** in this run: **4 new paper deep-reads**
(1 vascularized liver MPS primary research + 1 cardiac organoid review +
1 vascularized organoid Chinese-language review + 1 3D skin pemphigus
primary research) + 1 vendor-mapping retrofit commit. **New commitments**
added on `/commitments.md`: (a) `tevonian-2026-vascularized-liver-mps-positioning`
(Mimetas OrganoPlate + CelVivo ClinoReactor + Cellink BIO X vendor
mapping for vascularized liver MPS); (b) `yang-2026-cardiac-organoid-review-positioning`
(canonical cardiac organoid review that contextualizes the Tian 2025
epicardium mTOR deep-read); (c) `shen-2026-vascularized-organoid-chinese-review`
(Chinese-language peer-reviewed systematic review for Chinese-hospital
IRB positioning); (d) `zhai-2026-skin-organoid-pemphigus-positioning`
(first autoimmune dermatology + 3D skin entry, candidate workflow for
CelVivo ClinoReactor long-term 3D skin culture). **New themes-row refresh
candidate** for `/themes.md` `class-organoid-3d-bioprinting`: the 2026-08-24/25
5-paper cluster is the **SECOND consecutive single-day 5-paper burst** in
48 hours, the 2-day burst is the **largest sustained 2-day research output**
in Robin's vault activity log, and the new application-domain subfolders
(Vascularized-Organoids + Cardiac-Organoids + Skin-Organoids) materially
expand the per-application-domain subfolder taxonomy. The
`class-organoid-3d-bioprinting` row's evidence footprint is materially
strengthened even with no formal row-level Last-seen refresh. Wiki edits
this run: (a) `/sources/git-repo.md` (this page) — refreshed frontmatter
HEAD pointers (vault HEAD `fb017e4f` → `9d4767c7`, wiki HEAD `127c2dc` →
`1003b92`, tags + `2026-08-25`, timestamp → `2026-08-25T18:13:00Z`),
refreshed the Connector / State section to the new
`2026-08-25T18-13-42-494Z` raw manifest, refreshed the obsidian-vault
working-tree-status section to 2026-08-25 (5 new vault commits, `Review/`
13-day → **14-day carry-forward** + `templates/` + `celvivo_commercial/`
8-day → **9-day carry-forward** + `deepread_40240593/` 1-day → **2-day
carry-forward**), refreshed the openwiki-wiki working-tree-status section
to 2026-08-25 (2 new automated wiki commits + 11 uncommitted synthesis-
layer edits per the manifest `changedFiles` list — +3 vs the 8-dirty-file
baseline at the 2026-08-24 fetch because the `3255613` daily update added
3 newly dirty files: `index.md` + `quickstart.md` + `sources/git-repo.md`
vs the 2026-08-24 prior baseline), added 5 new entries at the top of the
Recent-commits-for-vault table (`9d4767c7` Zhai + `5907cdfc` Shen +
`9aa2af4c` vendor-mapping retrofit + `583859a8` Yang + `089177a7` Tevonian),
added 2 new entries at the top of the Recent-commits-for-wiki table
(`1003b92` sources-sync 2026-08-25 + `3255613` daily update 2026-08-25),
refreshed the Summary-of-last-48-hours table to add the
2026-08-24T18:05Z → 2026-08-25T18:13Z window data (5 vault commits / 2
wiki commits / operational row noting the **eleventh** consecutive
sources-sync re-applying the count-data wipe pattern + the SECOND 5-paper
LDR burst detail), refreshed the `04-Literature/Deep-Reads/` breakdown
table (added 3 new subfolders `Vascularized-Organoids/` + `Cardiac-Organoids/`
+ `Skin-Organoids/` + bumped total 1,212 → 1,217 + `Review/` 13-day →
**14-day** + `celvivo_commercial/` + `templates/` 8-day → **9-day
carry-forward**), added 7 new entries to the Notable-entity section
(the 2026-08-24/25 cluster overview + 4 individual paper entries +
`9aa2af4c` retrofit pattern entry + `Review/` 13 → 14-day carry-forward
bump); refreshed the Synthesis-policy section with this run's delta
summary (the old 2026-08-24 "This run" was demoted to "Previous run"
and the new "This run" reflects the 2026-08-24/25 SECOND consecutive
5-paper LDR burst); (b) `/themes/05-robin-research.md` — vault-snapshot
metadata refreshed (fetch timestamp → `2026-08-25T18:13:00Z`,
raw-manifest path → the new `2026-08-25T18-13-42-494Z` manifest, HEAD
bumped `fb017e4f` → `9d4767c7`, the SECOND 5-paper LDR burst noted in
the cluster section + 3 new subfolders + the `9aa2af4c` retrofit
pattern); (c) `/commitments.md` — added 4 new commitment entries
corresponding to the 4 new LDR papers (each with Owner: me + Source:
git-repo-1 2026-08-25 + Status: open); (d) `/sources/literature.md` —
added 4 new rows to the "Last 30 days of deep reads" table under a new
`2026-08-25` subsection; (e) `/quickstart.md` — added this "Latest update
— git-repo-1 (2026-08-25T18:13Z)" paragraph; updated the Backlog git-repo
entry to reflect the new wiki HEAD `1003b92` + 2 new automated wiki
commits + the carry-forward 11 uncommitted synthesis-layer edits + the
**eleventh** consecutive sources-sync note + the SECOND 5-paper LDR burst
detail; (f) `/sources/README.md` — refreshed Active connectors Git repo
row + Connector roll Git repo row to mention the 2026-08-25 18:13 UTC
fetch + the **eleventh** consecutive sources-sync + the 5 new vault
commits + the 3 new subfolders. **No new `/themes.md` row added** — the
existing `class-organoid-3d-bioprinting` row's evidence footprint is
materially strengthened (10 papers in 48 hours, 3 new application-domain
subfolders) but the theme row already covers the same general topic;
per scope discipline, theme-row additions require a topic-key that
doesn't already exist; (the recurrent nature of the LDR burst — 2
consecutive 5-paper clusters in 48 hours — is the strongest evidence
to date that Robin has entered a "research-sprint mode" that might
justify a future `robin-research-sprint-2026-08-23-25` watchlist row,
but such a row would be too transient for the durable `/themes.md`
index). **No `/open-questions.md` row added** — none of the 4 new LDR
papers surfaces a new memory/wiki gap; the existing 5 active open
questions (agent-dong-huiqun-celvivo / liu-2026-rogers-lab-vs-3brain-relationship
/ chengdu-baile-vs-lidesai-for-ou-xianhong / distributors-3brain-cellink-
zero-coverage / sharma-2026-retinal-organoid-mea-cross-sell) carry
forward unchanged. **No `/personal-logistics.md` item** — the vault
delta is work-side only.
- **This run (2026-08-24, git-repo-1 18:05Z):** **5 new vault commits**
in the 2026-08-23T18:11Z → 2026-08-24T18:05Z 24-hour window — the
vault HEAD bumped from `a4fa5a32` (2026-08-23T18:11Z fetch) to
`fb017e4f` — **breaks the 7-fetch vault-silence streak** that
started after the 2026-08-16 Quintard + Guo cluster, **largest
single-day LDR burst since the 2026-07-29 Parate / Lee / Hodge
cluster**. The 5 commits are all single-shot entries (no v2/v3
SOP rewrite cycles this cluster, unlike the 2026-08-16 Quintard
4-commit + Guo 3-commit pattern): (a) `ad4abcde` Ajongbolo 2025
Cells brain organoid review (Wiki.js 1743); (b) `5f02489a` Kim 2025
Nat Commun EGaIn liquid-metal 3D MEA (Wiki.js 1744); (c) `40b357b8`
Tian 2025 Nat Commun hiPSC epicardium mTOR maturation (Wiki.js