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---
type: "Reference"
title: "Git repo — evidence index (Obsidian vault + OpenWiki wiki, 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 `391e4713`, 2026-08-31, **5 new vault commits in the 2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window ending the 5-day vault silence — the THIRD single-day 5-paper LDR cluster (Yan + Stewart + Nguyen + Aiello + Miao), all `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` deep-reads anchored on CelVivo ClinoStar/ClinoReactor: `eb24ab72` Stewart 2023 Front Microbiol SARS-CoV-2 omicron BA.5/XBB neurotropic brain organoids + `030f31ed` Aiello 2025 EMBO reports reproducible brain organoids (CelVivo ApS is one author affiliation) + `fad7e21e` Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids + `4fca0123` Miao 2025 Cell vascularized lung/gut organoids (CelVivo ClinoReactor) + `391e4713` Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids; 4 of 5 use brain organoids for viral neurotropism modeling (QIMR Berghofer Suhrbier/Rawle research line), 1 is the first reproducibility benchmark with CelVivo as co-author**, vault HEAD bumped `9d4767c7` → `391e4713`; **cluster ends the 5-day vault silence from the 2026-08-25 burst** (vault silent for the prior 5 fetches: 2026-08-26T18:06Z + 2026-08-27T18:25Z + 2026-08-28T18:09Z + 2026-08-29T18:10Z + 2026-08-30T18:06Z all observed HEAD = `9d4767c7`); carry-forward untracked-file set continues: `Review/zhou2023_computer_vision_microfluidics.md` 19-day → **20-day carry-forward** (17 → 18 fetches silent, stale carry-forward note per 2026-08-28 demotion), `celvivo_commercial/` + `templates/` 14-day → **15-day carry-forward** (both confirmed one-off alongside `Review/` at the 2026-08-28 fetch, carrying forward unchanged at the 2026-08-31 fetch), `deepread_40240593/` 7-day → **8-day carry-forward** (mtime unchanged across **7 consecutive silent fetches** since creation, working-folder pipeline hypothesis continues to weaken); and openwiki-wiki at /home/ldw/.openwiki/wiki (main branch, HEAD `9582dea`, 2026-08-31, **2 new automated wiki commits in the 2026-08-30T18:06Z → 2026-08-31T18:09Z window: `c9e2770` chore: daily update 2026-08-31 (2026-08-31 02:18 +0800; per `git show --stat c9e2770` the commit touched 15 files including `.last-update.json` + `index.md` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/nocodb.md` + `sources/openwiki-version-drift.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` + `sources/wikijs.md` + `themes/05-robin-research.md` + `themes/index.md`), then `9582dea` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-31 — the **seventeenth** 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 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + `502281f` 2026-08-27 + `c992dd6` 2026-08-28 + `37d1ba6` 2026-08-29 + `d56da3a` 2026-08-30 + now `9582dea` 2026-08-31) committed `sources/{nocodb,ragflow,seafile,wikijs}.md` re-touched by the sources-sync; the very next synthesis edits from the HN-1 2026-08-31T18:00Z + web-search-1 2026-08-31 (skipped) + this git-repo-1 2026-08-31T18:09Z run re-touch the same files + 4 newly-dirty files leaving the dirty count at **11 per the manifest `changedFiles` list** — `M .last-update.json` + `M quickstart.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` + `M themes.md` + `M themes/03-ai-agents.md` — up from 9 at the 2026-08-30 fetch because `themes.md` + `themes/03-ai-agents.md` re-touched by this turn's HN-1 Almanac row-refresh synthesis edits + `sources/literature.md` re-touched by the 2026-08-31 synthesis pass + the CLI metadata cycle**)**) 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, 2026-08-31, 2026-08-30, 2026-08-29, 2026-08-28, 2026-08-27, 2026-08-26, 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, yan-2024-tmem106b-sars-cov2-brain-organoid, stewart-2023-ba5-xbb-neurotropic-brain-organoid, nguyen-2024-jev-g4-australia-brain-organoid, aiello-2025-brain-organoid-reproducibility, miao-2025-vascularized-lung-gut-organoids, brain-organoid-virology-cluster, celvivo-clinoreactor-cluster, third-5paper-cluster, vault-silence-ended, seventeenth-sources-sync, templates-celvivo-commercial-confirmed-one-off, deepread-40240593-seven-silent-fetches]
timestamp: 2026-08-31T18:09:00Z
---
# Git repo — evidence index (Obsidian vault + OpenWiki wiki)
Compact manifest of the two local git repos configured under the
`git-repo` connector: Robin's Obsidian vault and the local OpenWiki
wiki. This page is a **navigation index** — content ingestion (paper
deep reads, sales scripts, customer files) happens via the Hermes skill
and RAGFlow, not here. Keep this page terse and structural; it should
help locate things in the vault, not summarize their content.
## Connector
- **Source instance:** `git-repo-1` (configured under
`~/.openwiki/connectors/git-repo/config.json`)
- **Configured repos:**
- `obsidian-vault` → `/home/ldw/workspace` (Robin Obsidian vault, on
`main`, HEAD `391e47131679ce9edf0f525236e78ebb13e0d232` as of
2026-08-31 13:42 +0800 — **5 new vault commits** in the
2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window: the
**2026-08-31 brain-organoid infectious-disease + CelVivo
ClinoStar/ClinoReactor 5-paper LDR cluster** (THIRD single-day
5-paper LDR burst — the 2026-08-25 second cluster is now the
THIRD-most-recent 5-paper cluster, vault bursts are now an
established pattern at the cadence of ~2 per week) — `eb24ab72`
Stewart 2023 Front Microbiol SARS-CoV-2 omicron BA.5/XBB
neurotropic brain organoids (QIMR Berghofer Suhrbier/Rawle line)
+ `030f31ed` Aiello 2025 EMBO reports reproducible brain organoids
(CelVivo ApS is one author affiliation — first reproducibility
benchmark with CelVivo as co-author) + `fad7e21e` Nguyen 2024 npj
Viruses JEV G4 2022 Australia brain organoids (QIMR Berghofer
Suhrbier/Rawle line) + `4fca0123` Miao 2025 Cell vascularized
lung/gut organoids (CelVivo ClinoReactor) + `391e4713` Yan 2024
Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids
(QIMR Berghofer Suhrbier/Rawle line). 4 of 5 use brain organoids
for viral neurotropism modeling (3 share the QIMR Berghofer
Suhrbier/Rawle research line: Yan + Stewart + Nguyen) + 1 is a
vascularized lung/gut paper (Miao) + 1 is the first reproducibility
benchmark (Aiello, with CelVivo ApS co-author). **All 5 land in a
new subfolder `obsidian-vault/04-Literature/Deep-Reads/CelVivo/`
(capital V)** — Robin creates a **third** per-vendor CelVivo
subfolder alongside the existing `04-Literature/Deep-Reads/Celvivo/`
(143 papers, lower-case v) at the workspace root. **The 5-day
vault silence from the 2026-08-25 burst ends at this fetch**.
Combined with the 2026-08-23/24 + 2026-08-24/25 + 2026-08-31
5-paper bursts, **15 LDR papers in 8 days** = 3 distinct
single-day 5-paper bursts; the bursts create 4 new
`04-Literature/Deep-Reads/` subfolders: `Vascularized-Organoids/`
+ `Cardiac-Organoids/` + `Skin-Organoids/` (2026-08-25 burst) +
`CelVivo/` (2026-08-31 burst) — Robin's deep-read taxonomy
expands to ~23 per-vendor / per-application-domain subfolders).
- `openwiki-wiki` → `/home/ldw/.openwiki/wiki` (the OpenWiki knowledge
base itself, on `main`, HEAD `9582deadda4681fe1481f9992905230ace7e5990`
as of 2026-08-31T02:30 +0800 — 2 new wiki-side commits in the
2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window: `c9e2770`
chore: daily update 2026-08-31 + `9582dea` chore(sources): refresh
NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-31) —
the **seventeenth** consecutive sources-sync re-applying the
2026-08-15 count-data wipe pattern).
- **Auth:** local paths only — no remote, no credentials.
- **Latest fetch:** `2026-08-31T18:09:00Z` (raw manifest
`~/.openwiki/connectors/git-repo/raw/2026-08-31T18-09-??-???Z/manifest.json`).
- **Source config:** `~/.openwiki/connectors/git-repo/config.json`
- **State:** `~/.openwiki/connectors/git-repo/state.json` records
`latestIds` per repo; the 2026-08-31T18:09Z fetch observed vault HEAD
bumped from `9d4767c7034a59d8f3206756c2dfeb3f4339c2e0` (2026-08-30T18:06Z
fetch — same as the 2026-08-29T18:10Z + 2026-08-28T18:09Z +
2026-08-27T18:25Z + 2026-08-26T18:06Z + 2026-08-25T18:13Z fetches
all observed `9d4767c7` — **0 new vault commits** in the prior 5
fetches, **vault silent for the 5th consecutive fetch** since the
2026-08-24/25 SECOND 5-paper burst; the 2026-08-25 5-paper cluster
was the most recent vault activity at the 2026-08-30T18:06Z fetch,
5 calendar days stale) to **`391e47131679ce9edf0f525236e78ebb13e0d232`** (5 new
vault commits in the 2026-08-30T18:06Z → 2026-08-31T18:09Z window:
`eb24ab72` + `030f31ed` + `fad7e21e` + `4fca0123` + `391e4713` — all
`obsidian-vault/04-Literature/Deep-Reads/CelVivo/` deep-reads; the
THIRD single-day 5-paper LDR burst; the cluster ends the 5-day
vault silence), and observed `openwiki-wiki` bumped from
`d56da3afddfced20a01fbecd9912fe3ec87a25b4` (2026-08-30T18:06Z fetch)
to **`9582deadda4681fe1481f9992905230ace7e5990`** (2 new automated
wiki commits in the 24-hour window: `c9e2770` chore: daily update
2026-08-31 (2026-08-31 02:18 +0800, committed 15 files per
`git show --stat c9e2770` — including `.last-update.json` +
`index.md` + `quickstart.md` + `sources/README.md` +
`sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` +
`sources/nocodb.md` + `sources/openwiki-version-drift.md` +
`sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` +
`sources/wikijs.md` + `themes/05-robin-research.md` + `themes/index.md`),
then `9582dea` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts
(sources-sync 2026-08-31, 2026-08-31T02:30 +0800 — the **seventeenth**
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 + `1003b92` 2026-08-25 + `ebb95c0`
2026-08-26 + `502281f` 2026-08-27 + `c992dd6` 2026-08-28 + `37d1ba6` 2026-08-29 + `d56da3a` 2026-08-30 + now
`9582dea` 2026-08-31; committed `sources/nocodb.md` +
`sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md`
per `git show --stat 9582dea`). The very next synthesis edits from
the HN-1 2026-08-31T18:00Z + web-search-1 2026-08-31 (skipped) + this
git-repo-1 2026-08-31T18:09Z run re-touched the same files +
the sources-sync `9582dea` re-touched the 4 source-sync files +
this turn's HN-1 Almanac synthesis wrote 3 NEW dirty files
(`sources/literature.md` + `themes.md` + `themes/03-ai-agents.md`) —
the dirty count at this fetch is **11 per the manifest
`changedFiles` list**: `M .last-update.json` + `M quickstart.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` + `M themes.md` + `M themes/03-ai-agents.md` —
**up from 9** at the 2026-08-30T18:06Z fetch because
`themes.md` + `themes/03-ai-agents.md` re-touched by this turn's
HN-1 Almanac 2026-08-31 row-refresh synthesis edits +
`sources/literature.md` re-touched by the 2026-08-31 synthesis
pass + the sources-sync `9582dea` re-touched the 4 source-sync
files that had been committed by the `c9e2770` daily update).
## obsidian-vault — working-tree status (2026-08-31)
- **Branch:** `main`
- **HEAD:** `391e47131679ce9edf0f525236e78ebb13e0d232` (vault HEAD
**bumped** from `9d4767c7034a59d8f3206756c2dfeb3f4339c2e0` (the
2026-08-30T18:06Z + 2026-08-29T18:10Z + 2026-08-28T18:09Z +
2026-08-27T18:25Z + 2026-08-26T18:06Z + 2026-08-25T18:13Z fetches
all observed HEAD = `9d4767c7`) — **5 new vault commits** in the
2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window, **ending the
5-day vault silence** since the 2026-08-24/25 SECOND 5-paper burst.
The cluster is the **THIRD single-day 5-paper LDR burst** in Robin's
vault activity log (2026-08-31 — Yan + Stewart + Nguyen + Aiello +
Miao) — combined with the prior 2026-08-23/24 (Ajongbolo + Kim +
Tian + Aiello + CelVivo App Note) + 2026-08-24/25 (Tevonian + Yang +
`9aa2af4c` retrofit + Shen + Zhai) bursts, Robin has produced
**15 LDR papers in 8 days** across 3 distinct single-day 5-paper
bursts, with the THIRD burst creating a **fourth** new
`04-Literature/Deep-Reads/` subfolder: `obsidian-vault/04-Literature/Deep-Reads/CelVivo/`
(capital V — alongside the existing `04-Literature/Deep-Reads/Celvivo/`
lower-case v at the workspace root) — Robin now has 4 new
per-vendor / per-application-domain subfolders opened in 8 days:
`Vascularized-Organoids/` + `Cardiac-Organoids/` + `Skin-Organoids/`
(2026-08-25 burst) + `CelVivo/` (2026-08-31 burst); the deep-read
folder taxonomy expands from ~22 to ~23 in the 2026-08-31 burst. The
burst is **not** a vendor-mapping retrofit commit — all 5 commits
are single-shot entries (no v2/v3 SOP rewrite cycles this cluster,
unlike the 2026-08-16 Quintard 4-commit + Guo 3-commit pattern).
- **mtime activity in window:** **5 new committed files** in the
2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window — the 5 new
files land in `obsidian-vault/04-Literature/Deep-Reads/CelVivo/`
(capital V), all single-shot entries:
`eb24ab72` (2026-08-31 13:05 +0800) `stewart-2023-ba5-xbb-neurotropic-brain-organoids.md`
+ `030f31ed` (2026-08-31 13:14 +0800)
`aiello-2025-brain-organoid-reproducibility.md` +
`fad7e21e` (2026-08-31 13:21 +0800)
`nguyen-2024-jev-g4-2022-australia-brain-organoids.md` +
`4fca0123` (2026-08-31 13:27 +0800)
`miao-2025-vascularized-lung-gut-organoids.md` +
`391e4713` (2026-08-31 13:42 +0800)
`yan-2024-tmem106b-sars-cov2-ace2-independent.md`. The 4 prior LDR
burst files (2026-08-23/24 + 2026-08-24/25) all carry forward
unchanged. The `celvivo_commercial/` + `templates/` untracked dirs
continue to carry forward (now **15-day carry-forward** at this
fetch — was 14-day at the 2026-08-30T18:06Z fetch, 13-day at the
2026-08-29T18:10Z fetch — **both entries confirmed one-off alongside
the `Review/` subfolder at the 2026-08-28 fetch**; the 2026-08-31
fetch confirms the parallel one-off interpretation carrying
forward unchanged). The `Review/zhou2023_computer_vision_microfluidics.md`
first-entry file is unchanged from the 2026-08-30T18:06Z fetch
(mtime 2026-08-11, **20-day carry-forward** in the untracked set at
this fetch — was 19-day at the 2026-08-30T18:06Z fetch; the
structural signal continues to weaken per the Notable-entity entry
on the `Review/` subfolder — **18 fetches silent** at this fetch,
was 17 fetches silent at the 2026-08-30T18:06Z fetch; the 2026-08-27
fetch already confirmed the 2026-08-26 watchlist-downgrade
consideration as a one-off and the entry is now a stale carry-forward
note). The `deepread_40240593/` untracked pipeline workspace mtime
is still **2026-08-24 16:31 +0800** at the 2026-08-31 fetch (mtime
unchanged across the 2026-08-25 + 2026-08-26 + 2026-08-27 + 2026-08-28 +
2026-08-29 + 2026-08-30 + **2026-08-31** fetches — **7 fetches silent on directory mtime** at this
fetch); the working-folder-pipeline hypothesis is further weakened
at the 2026-08-31 fetch (now **8-day carry-forward** — was 7-day at
the 2026-08-30T18:06Z fetch, 6-day at the 2026-08-29T18:10Z fetch).
- **Ahead of origin/main:** 35 commits new since 2026-08-03 fetch (+5
from the prior 30-commit baseline at the 2026-08-25T18:13Z fetch —
the 5 new commits land on top of the 30-commit carry-forward;
**5 new commits land on top of the 30-commit carry-forward**,
vault HEAD bumped `9d4767c7` → `391e4713` at the 2026-08-31T18:09Z
fetch; total 35 since 2026-08-03).
- **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) — **20-day carry-forward** at this fetch (was 19-day
at the 2026-08-30T18:06Z 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
**18 fetches silent** — was 17 fetches silent at the
2026-08-30T18:06Z fetch; **the 2026-08-27 fetch already confirmed the
one-off interpretation** per the 2026-08-26 watchlist-downgrade
consideration and the entry is now a stale carry-forward note). The
`celvivo_commercial/` + `templates/` untracked dirs continue to
carry forward (now **15-day carry-forward** at this fetch — was 14-day
at the 2026-08-30T18:06Z fetch — **the 2026-08-28 fetch already confirmed
the parallel `templates/` + `celvivo_commercial/` entries as one-off
alongside the `Review/` subfolder**, both reaching the 14-day
threshold at the 2026-08-30T18:06Z fetch; both remain demoted to
stale / not recurring carry-forward notes on the 2026-08-31 fetch);
the `deepread_40240593/` untracked pipeline workspace also
continues to carry forward (now **8-day carry-forward** — was 7-day
at the 2026-08-30T18:06Z fetch, with mtime unchanged across 7
fetches since creation); no NEW untracked dirs at this fetch. The
2026-08-31T18:09Z fetch confirms the parallel one-off interpretation
carrying forward unchanged for all 3 stale entries; the
`deepread_40240593/` pipeline workspace hypothesis continues to
weaken (**8-day carry-forward** + **7 consecutive silent fetches**
on directory mtime since the 2026-08-24/25 burst).
- **Working-tree status (raw manifest, abbreviated):**
| Status | Path |
| --- | --- |
| `A` (committed 2026-08-12, `e542c977`) | `04-Literature/Deep-Reads/Liver/2026-08-12_Liang_2026_SciRep_liver_organoid_fibrosis_platform.md` — **NEW external evidence** (Liang Y et al. Sci Rep 2026 DOI 10.1038/s41598-026-42990-2, PMID 41857098, 3 轨道 Hep-Orgs + Cho-Orgs + HSC, DAPT+Dex P1-P10 长程成熟, TGFβ 激活体外纤维化模型; Wiki.js Id=1716, NocoDB Id=770, SeaFile PDF + 7 真图) |
| `M` (committed 2026-08-12, `8699a154`) | same Liang 2026 file — page 946 9 项 SOP 重写版 (105+/122- lines) |
| `M` (committed 2026-08-12, `aacba7aa`) | same Liang 2026 file — frontmatter title 改中文 + 与正文 H1 一致 (1-line touch) |
| `M` (committed 2026-08-12, `297f106d`) | same Liang 2026 file — 修齐 page 934 标杆 (H1 去括号/元数据用bold/📄PDF文件名, 5+/4- lines) |
| `A` (committed 2026-08-16, `a4fa5a32`) | `obsidian-vault/Literature/Deep-Reads/Organoid/guo_2026_organoid_ethical_review.md` — **NEW external evidence** (Guo Z, Zhang N 2026 Front Cell Dev Biol DOI 10.3389/fcell.2026.1721946 — IRB / ethics systematic review; Wiki ID 1724, NocoDB Id 3298, 170 lines + 3 张真图; "与我们的产品" table lists CelVivo ClinoStar ⭐⭐⭐⭐ [临床转化类器官的伦理合规——7 大要点直接适用 IRB 申请] + Mimetas OrganoPlate ⭐⭐⭐⭐ [类器官 + 免疫细胞共培养伦理审查依据] + Emulate Organ-Chip ⭐⭐⭐; 3 commits `2e6f5989` → `00f824f2` → `a4fa5a32` = adds → -v2 修图床 → -v3 补 Fig 1) |
| `A` (committed 2026-08-16, `0fc8db24`) | `obsidian-vault/Literature/Deep-Reads/Organoid/quintard_2024_vasorganoid_chip.md` — **NEW external evidence** (Quintard C et al. 2024 Nat Commun DOI 10.1038/s41467-024-45710-4 — microfluidic platform for vascularized organoid chips; Wiki IDs 1719/1720/1722, NocoDB Id 3297; 4 commits `0fc8db24` → `290e9635` → `24c713de` → `4073abf4` = adds 189 lines → -v2 修图床/双 H1/落款 → -v3 Wiki.js 自带图床 6 张图 → -v4 转发语标题/落款加粗/删 3Brain; "与我们的产品" table lists Mimetas OrganoPlate ⭐⭐⭐⭐ [直接对标: Phaseguide 微流控技术用于血管化/肾/肠 organ-on-chip] + CelVivo ClinoStar ⭐⭐⭐ [类器官前段成熟期培养: BVO 在 hiPSC 分化到 day 15 需要悬浮旋转培养, ClinoStar 是该步骤的金标准; day 15 后才转入芯片, ClinoStar 是完整工作流的前置] + Emulate Organ-Chip ⭐⭐⭐) |
| `M` (committed 2026-08-10) | `04-Literature/Deep-Reads/Organoid/2026-07-29_Organoids_disease_modeling_treatment_2026_review.md` (Phase A batch frontmatter — `volume` / `pages` / `authors` array; also touched by `6b717aef` for related back-link) |
| `M` (committed 2026-08-10) | `CelVivo_精读报告_04_bioRxiv_PAH_Metabolomics.md` (Phase A batch frontmatter — `volume` / `pages` / `authors` array; also touched by `6b717aef`) |
| `M` (committed 2026-08-10) | `obsidian-vault/04-Literature/Deep-Reads/3Brain/shin-2024-thalamocortical-organoids-22q11ds.md` (Phase A batch frontmatter; also touched by `6b717aef`) |
| `M` (committed 2026-08-10) | `obsidian-vault/04-Literature/Deep-Reads/Cells/fernandez-vallone-2026-thsdc-brain-organoids.md` (Phase A batch frontmatter; also touched by `6b717aef`) |
| `M` (committed 2026-08-10) | `obsidian-vault/04-Literature/Deep-Reads/NBME-ShapeConformal/literature-liu-2026-nbme-shape-conformal-organoid.md` (Phase A batch frontmatter; also touched by `6b717aef`) |
| `M` (committed 2026-08-10) | `类器官综述_CMOS_HD_MEA_类器官电生理_2026-06-05.md` (Phase A batch frontmatter; also touched by `6b717aef`) |
| `M` (committed 2026-08-10) | `04-Literature/Deep-Reads/wang2024-org-on-chip.md` (方案 2 样品 — 6 frontmatter fields + 7 alt descriptions; also touched by `6b717aef`) |
| `A` (committed 2026-08-10) | `04-Literature/Deep-Reads/MOCs/MOC-类器官与3D培养.md` (方案 1 — **first MOC file**; 95 lines; 沙牛《AI 时代的 Obsidian 公开课》课时 1 pattern; `related:` already lists `[[MOC-3Brain-HD-MEA]]` as a forward link) |
| `??` (untracked) | `02-Clients/Agents/全国经销商地图-2026-0807.md` + 7 区域 `*2026-0807.md` files (8-07 distributor baseline refresh — see below) |
| `??` (untracked, **NEW 2026-08-17**) | `celvivo_commercial/1331651_20260630_131201.pdf` — **NEW** untracked directory; the 6-30 quote PDF Robin migrated into a new `celvivo_commercial/` folder; companion to the existing `05-Documents/Products/Celvivo/Industrial-Customers/` commercial-docs subtree |
| `??` (untracked, **NEW 2026-08-17**) | `templates/类器官IRB申请清单.md` — **NEW** untracked directory; the IRB application checklist derived from the Guo 2026 ethics-review deep-read (180 lines; 7 mandatory points [样本来源/知情同意/数据隐私/共培养主体性/3R 动物福利/跨境监管/长期保存与终止使用] + 5 customer Q&A + China vs International flow table + 10 attachments + 7 citations); Robin's **first customer-facing template** derived from a single deep-read — materializes the "Robin 业务定位: 类器官厂家给三甲医院 IRB 申请的标准模板 + Robin 客户培训材料核心" framing from the Guo 2026 deep-read |
| `??` (untracked) | `04-Literature/Deep-Reads/Brain/2026-08-06_Parfitt_GM_et_al_NatCommun_2024_DJ1_LOF_midbrain_organoid_PD.md` |
| `??` (untracked) | `Liu2026_NBME_shape_conformal_organoid.md` |
| `??` (untracked) | `Miao2025_Cell_v2.md` |
| `??` (untracked) | `Miao2025_Cell_vascularized_organoid.md` |
| `??` (untracked) | `Microbioreactor_2026_Rosero_FrontBioeng.md` |
| `??` (untracked) | `__pycache__/literature_deepread_v6.cpython-312.pyc` — **NEW** (2026-08-13) Python compiled cache file (build noise from running `literature_deepread_v6.py`, ignored) |
| `??` (untracked) | `dify精读进度-20260805.md` |
| `??` (untracked) | `literature_deepread_v6.py` |
| `??` (untracked) | `obsidian-vault/04-Literature/Deep-Reads/Review/zhou2023_computer_vision_microfluidics.md` — **NEW** (2026-08-13) **first entry in the new `Review/` subfolder** (Zhou 2023 computer vision + microfluidics — Robin deep-read in progress, untracked, future-commit candidate) |
| `??` (untracked) | `obsidian-vault/rustdesk-selfhosted-2026-08-05.md` |
| `??` (untracked) | `retinal_organoid_deep_read_2026-08-07.md` |
| `??` (untracked) | `文悦精读流水线.yml` + v2/v3/v4/v5-clean variants |
The 8 untracked `*2026-0807.md` files in `02-Clients/Agents/` are the
**2026-08-07 distributor baseline refresh** — see the "Distributor
map refresh (2026-08-07)" section below for synthesis. The 2 NEW
untracked files this fetch are: (a)
**`Review/zhou2023_computer_vision_microfluidics.md`** — first entry
in a new deep-read subfolder (see Notable-entity entry below);
(b) `__pycache__/...pyc` — build noise, ignored.
### Recent commits (latest first)
| Date | Hash | Note |
| --- | --- | --- |
| 2026-08-31 | `391e4713` | **deep-read: Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids (CelVivo)** — adds `obsidian-vault/04-Literature/Deep-Reads/CelVivo/yan-2024-tmem106b-sars-cov2-ace2-independent.md` (40 lines, single-shot LDR entry, Ollama audit 4/4 Fig 1-4 passed). **Yan K et al. Cell Reports 43:114921 (2024-11-26), DOI 10.1016/j.celrep.2024.114921** — QIMR Berghofer Medical Research Institute (Suhrbier + Rawle line; same affiliation as Stewart 2023 + Nguyen 2024 in this cluster); CRISPR 筛选 identifies TMEM106B / 硫酸乙酰肝素 / 内吞介导的 ACE2 非依赖 SARS-CoV-2 进入通路 (S-E484D escape mutant); 人源皮层脑类器官 (CelVivo ClinoStar) 中 MA1 strain 滴度 + 感染细胞数均高于 ancestral; K18-hACE2 小鼠中 MA1 疾病更重 + 生存率更低; **体内不成立**: 野生型 / Ifnar-/- 小鼠无增加神经侵袭, Ace2-/- 小鼠肺无法感染. **Fourth consecutive QIMR Berghofer Suhrbier/Rawle viral-neurotropism paper** this cluster (Yan + Stewart + Nguyen all share QIMR Berghofer affiliation + Suhrbier/Rawle corresponding-author signal); pairs with **Stewart 2023 BA.5/XBB** (also QIMR Berghofer, same brain organoid platform) for a viral-evolution × ACE2-independent-entry paired entry. Brain organoid application-domain |
| 2026-08-31 | `4fca0123` | **deep-read: Miao 2025 Cell vascularized lung/gut organoids (CelVivo ClinoReactor)** — adds `obsidian-vault/04-Literature/Deep-Reads/CelVivo/miao-2025-vascularized-lung-gut-organoids.md` (single-shot LDR entry, Ollama audit 7/7 Fig 1-7 passed, v1_full 8-08 精简版已升级完整版). **Miao Y, Pek NM, Tan C, Chen Y-W, Guo M*, Gu M* — Cell 188:1-19 (2025-08-07), DOI 10.1016/j.cell.2025.05.041** — 中胚层与内胚层共分化实现肺和肠道类器官的器官型血管化; **FOXF1 transcription-factor-driven co-differentiation of mesoderm + endoderm** enables organotypic vasculature in lung and gut organoids (single-cell + vascularization route in CelVivo ClinoReactor). **Distinct from the 2026-08-08 flywheel-sync Miao 2025 v2 deep-read** (`Miao2025_Cell_v2.md` at `/home/ldw/workspace/`, sourced from `/sources/literature-miao-2025-cell-vascularization-v2-deepread.md`); this is the canonical vault `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` version, carrying the v1_full complete body + Ollama audit + SeaFile PDF link. The 2026-08-08 v2 deep-read + this vault commit form a **paired community + vault copy** of the same paper. Vascularized organoid application-domain |
| 2026-08-31 | `fad7e21e` | **deep-read: Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids (CelVivo)** — adds `obsidian-vault/04-Literature/Deep-Reads/CelVivo/nguyen-2024-jev-g4-2022-australia-brain-organoids.md` (single-shot LDR entry, Ollama audit 8/8 Fig 1-8 passed). **Nguyen W, Gyawali N, Stewart R, Tang B, Cox AL, Yan K, Larcher T, Bishop CR, Wood N, Devine GJ, Suhrbier A, Rawle DJ — npj Viruses (Nature Portfolio) Article 25 (2024), DOI 10.1038/s44298-024-00025-5** — QIMR Berghofer Medical Research Institute + INRAE; **2022 澳大利亚爆发的日本脑炎病毒基因 4 型分离株特征研究** — JEV genotype 4 isolate from the 2022 Australian outbreak characterized in CelVivo brain organoids. **Third QIMR Berghofer Suhrbier/Rawle viral-neurotropism paper** this cluster (Yan + Stewart + Nguyen — all same affiliation, all viral neurotropism + CelVivo brain organoid platform). JEV is a mosquito-borne flavivirus with significant neurotropism; the 2022 Australian outbreak was the first JEV outbreak in the region, making this a clinically-relevant neurotropism characterization. Brain organoid + flavivirus application-domain |
| 2026-08-31 | `030f31ed` | **deep-read: Aiello 2025 EMBO reports reproducible brain organoids (CelVivo ClinoReactor)** — adds `obsidian-vault/04-Literature/Deep-Reads/CelVivo/aiello-2025-brain-organoid-reproducibility.md` (single-shot LDR entry, Ollama audit 6/6 Fig 1-6 passed). **Aiello G, Nemir M, Vidimova B, Ramel C, Viguie J, Ravera A, Wrzesinski K*, Bagni C* (corresponding) — EMBO reports Volume 26 (December 2025), pp 6209-6239, DOI 10.1038/s44319-025-00619-x** — 洛桑大学 + 罗马 Tor Vergata 大学 + 西北大学(南非) + **CelVivo ApS (丹麦) as author affiliation**; 通过受控流体动力学提高脑类器官的可重复性 — **first reproducibility benchmark with CelVivo ApS as co-author** (CelVivo is on the byline, not just an equipment reference); ClinoReactor-controlled brain organoid culture produces reproducible multi-batch + multi-iPSC-line outcomes via shear-stress control. **Distinct from the 2026-08-23 flywheel-sync `f2118a62` Aiello & Bagni 2025 biorxiv CFD deep-read** (`Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid.md` at `obsidian-vault/04-Literature/Deep-Reads/` root, the biorxiv preprint of this paper); this is the published-EMBO-reports vault commit, carrying the v1_full body + Ollama audit + SeaFile PDF link. The biorxiv + EMBO-reports pair = **single paper / two-deep-reads pattern** (one for the preprint, one for the published version). Brain organoid reproducibility application-domain |
| 2026-08-31 | `eb24ab72` | **deep-read: Stewart 2023 Front Microbiol BA.5/XBB neurotropic brain organoids (CelVivo)** — adds `obsidian-vault/04-Literature/Deep-Reads/CelVivo/stewart-2023-ba5-xbb-neurotropic-brain-organoids.md` (single-shot LDR entry, Ollama audit 6/6 Fig 1-6 passed). **Stewart R, Yan K, Ellis SA, Bishop CR, Dumenil T, Tang B, Nguyen W, Larcher T, Parry R, Sng JDJ, Khromykh AA, Sullivan RKP, Lor M, Meunier FA, Rawle DJ*, Suhrbier A* (corresponding) — Frontiers in Microbiology Volume 14, Article 1320856 (2023-11-23), DOI 10.3389/fmicb.2023.1320856** — QIMR Berghofer Medical Research Institute + University of Queensland; **SARS-CoV-2 omicron BA.5 和 XBB 变异株较 BA.1 具有增强的神经趋向性** — BA.5/XBB variants have increased neurotropic potential over BA.1 in K18-hACE2 mice and human brain organoids (CelVivo brain organoid platform). **Second QIMR Berghofer Suhrbier/Rawle viral-neurotropism paper** this cluster (Yan + Stewart + Nguyen all share QIMR Berghofer affiliation + Suhrbier/Rawle corresponding-author signal — three of five cluster papers share this single research line). Brain organoid + viral neurotropism application-domain |
| 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 |
| 2026-08-23 | `5f02489a` | **feat: Kim 2025 NatCommun 液态金属 3D MEA 精读** (Wiki.js 1744) — adds `obsidian-vault/04-Literature/Deep-Reads/Kim_2025_NatCommun_Liquid_Metal_3D_MEA.md` (13,567 bytes, single-shot entry) — **NEW 3D-MEA / electrophysiology evidence**: Kim E, Jeong E, Hong YM et al. (2025) Nat Commun DOI 10.1038/s41467-024-55752-3 — magnetically reshapable EGaIn (eutectic gallium-indium) liquid-metal 3D MEA pillar array via microfluidic direct-ink-writing; pillar height 25-310 µm linearly controlled by print speed (R²>0.95, n=12, SEM<5%); pillar diameter to 14 µm (single-neuron scale); parylene-C selective sidewall encapsulation (only tip conductive); hPSC cortical organoid 120-day maturation (dual-SMAD inhibition + FGF2/EGF + BDNF/NT3); 6-marker IHC (MAP2/GFAP/VGLUT1/SATB2/CTIP2) showing 6-layer cortical-like structure; Ni magnetic layer for magnetic reshaping; 64-channel MEA + SU spike + network synchronization; **third flexible-electronics / 3D-MEA paper this cycle** after Liu 2026 (NBME shape-conformal porous framework) + Sharma 2026 (60-channel MCS MEA retinal organoid) — direct 3Brain HD-MEA competitive pressure signal |
| 2026-08-23 | `ad4abcde` | **feat: Ajongbolo 2025 Cells 脑类器官综述精读** (Wiki.js 1743) — adds `obsidian-vault/04-Literature/Deep-Reads/Ajongbolo_2025_Cells_Brain_Organoids_Review.md` (11,367 bytes, single-shot entry) — **NEW brain-organoid review evidence**: Ajongbolo AO, Langhans SA (2025) Cells DOI 10.3390/cells14110842 — comprehensive brain-organoid + assembloid review covering (i) whole-brain vs region-specific vs complex systems (assembloid + OoC + tumoroid + transplant); (ii) 4-tier characterization (morphological / biochemical / functional / omics); (iii) disease modeling across neurodevelopmental (microcephaly / macrocephaly / ASD / Rett / fragile X / Timothy syndrome) + neurodegenerative (AD / PD / HD / ALS) + brain tumor (glioblastoma / medulloblastoma / AT/RT); (iv) drug discovery + HTS pathways; first brain-organoid review since the 2026-07-29 Organoids 2026 disease-modeling review; **mentions ClinoStar / orbital shaker reagent-supply chain** |
| 2026-08-16 | `a4fa5a32` | **literature: review 类 Guo 2026 -v3 补 Fig 1** — in-place update ID 1724, 3 张图全 |
| 2026-08-16 | `00f824f2` | **literature: review 类 Guo 2026 -v2 修图床** — in-place update ID 1724, 加 2 张 Wiki.js 自带图 |
| 2026-08-16 | `2e6f5989` | **literature: 精读 Guo 2026 Front Cell Dev Biol - 类器官伦理审查** (review 类, Wiki ID 1724, NocoDB Id 3298) — **NEW external evidence** (类器官研究 IRB / 伦理审查 7 大强制要点系统综述, 嘉兴市第一医院 + 嘉兴大学医学院视角) |
| 2026-08-16 | `4073abf4` | **literature: 精读 Quintard 2024 -v4** — 转发语标题/落款加粗/删3Brain |
| 2026-08-16 | `24c713de` | **literature: 精读 Quintard 2024 -v3 Wiki.js 自带图床** (ID 1722, 6 张图永久) |
| 2026-08-16 | `290e9635` | **literature: 精读 Quintard 2024 -v2 修图床/双 H1/落款** (Wiki ID 1720) |
| 2026-08-16 | `0fc8db24` | **literature: 精读 Quintard 2024 Nat Commun - 微流控血管化类器官芯片** (Wiki ID 1719, NocoDB Id 3297) — **NEW external evidence** (10 通道并行微流控 + hiPSC-BVO 30 天功能性灌注培养 + 跨类器官验证) |
| 2026-08-12 | `297f106d` | **literature: 修齐 page 934 标杆** — H1 去括号 / 元数据用 bold / 📄PDF 文件名 (Liang 2026 v3) |
| 2026-08-12 | `aacba7aa` | **literature: frontmatter title 改中文 + 与正文 H1 一致** (Liang 2026 v2) |
| 2026-08-12 | `8699a154` | **literature: Liang 2026 Sci Rep liver organoid fibrosis - page 946 9 项 SOP 重写版** (Liang 2026 v2; 105+/122- lines; core-question / research-model / 6-finding 3-stage tables / 6 SeaFile Fig / "与我们的产品" 4-star / 4-paper refs / 转发语 / 完整落款) |
| 2026-08-12 | `e542c977` | **literature: Liang 2026 Sci Rep liver organoid + fibrosis platform (Id=770 NocoDB)** — **NEW external evidence** (3 轨道 Hep/Cho/HSC + DAPT+Dex P1-P10 长程成熟 + TGFβ 激活 HSC 体外纤维化模型; 7/7 Ollama qwen2.5vl 视觉审核通过; SeaFile 7/7 公网 200 验真; 飞轮 PATCH comm Id=87 + product Id=10 + NocoDB PATCH 770) |
| 2026-08-10 | `d97b39ed` | **Phase A 批量：6 篇精读加 Front Matter 6 字段** (doi/journal/year/volume/pages/authors/pmid) — Organoids 2026 review + CelVivo PAH + Shin 2024 + Fernandez Vallone 2026 + Liu 2026 + 类器官综述_CMOS_HD_MEA |
| 2026-08-10 | `3b929c2f` | **wang2024 方案 2 样品：6 个 Front Matter 字段 + 7 张图加 alt 描述** — `wang2024-org-on-chip.md` |
| 2026-08-10 | `6b717aef` | **MOC 方案 1 样品：建 1 个 MOC + 7 篇加 Front Matter (related: 反链)** — first MOC `MOC-类器官与3D培养.md` created; 7 papers got `related:` back-link frontmatter |
| 2026-08-09 | `a14758b1` | 精读: Wang 2024 Theranostics 类器官-芯片综述 (7 张配图 + Wiki.js ID 1700) — first Organoid-on-Chip 综述 / 7 大主题板块 |
| 2026-08-08 | `d7df3830` | cells paper v2: 双 H1 + 5张真图 (xref) — Fernandez Vallone 2026 |
| 2026-08-08 | `6c16dc05` | 精读: Fernandez Vallone 2026 Cells hiPSC 脑类器官 THSDC |
| 2026-08-07 | `65fef021` | fix: v2 with SeaFile links — Microbioreactor 2026 |
| 2026-08-07 | `18bee69f` | feat: Microbioreactor design 2026 Front Bioeng Biotechnol Mini Review (PMID 42516424) |
| 2026-08-08 | `1614ccf9` | fix: v11 - forwarding per skill template (Liu 2026) |
| 2026-08-08 | `a7cfb8a4` | fix: final - per Research SOP strict + clean internal traces (Liu 2026) |
| 2026-08-08 | `d1e8c6dd` | fix: v5 - per Research SOP + page 946 benchmark (Liu 2026) |
| 2026-08-08 | `b7882b81` | fix: v4 - add forward message (Liu 2026) |
| 2026-08-08 | `84e93402` | fix: v3 - Fig 3 restored from page 6, audit table removed (Liu 2026) |
| 2026-08-08 | `a69ad9c4` | literature: liu 2026 NBME shape-conformal organoid |
| 2026-08-08 | `1c05eee7` | literature: miao 2025 cell organoid vascularization v2 |
| 2026-08-08 | `a0810433` | 精读: Sharma K 2026 Cell Stem Cell 视网膜类器官血管化RGC存活与功能成熟 |
| 2026-07-29 | `2341383e` | fix(hook4): 湖北行去掉 'Robin 8 月出差高发地' 残留 (Robin 真实出差意图) |
| 2026-07-29 | `aa8fd2bc` | fix(hook4): 改标题 '下次出差' → '按 xlsx 缺口', Robin 后续自规划出差路径 |
| 2026-07-29 | `4b237a82` | feat(hook): 4 个经销商管理 Hook 升级 |
| 2026-07-29 | `b9da34dc` | fix(literature): Organoids 2026 综述 - 按 literature-deep-read-review SOP 重写 |
| 2026-07-29 | `0cd44fa0` | feat(literature): 精读 Organoids for disease modeling and treatment 2026 综述 |
| 2026-07-28 | `642e3dc6` | feat(agent): 新增代理商技术同事董慧群档案 (推 CelVivo 产品) |
| 2026-07-28 | `2718e46d` | feat(literature): Parate 2020 SCRT — PEMF 增强 MSC 旁分泌功能促软骨再生 |
| 2026-07-28 | `032de92f` | feat: 精读 Lee 2025 Front Vet Sci 犬脂肪源 MSC 3D 球体 |
The **2026-08-16 cluster** is a **two-paper LDR cycle on the same day**
covering both an **organ-on-chip microfluidic platform paper** and an
**organoid ethical-review systematic-review paper**:
- **Quintard C et al. (2024) Nat Commun DOI 10.1038/s41467-024-45710-4**
— a microfluidic platform for vascularized organoids-on-chip. The
paper establishes: (i) 10-channel parallel microfluidic chip (COC
热压成型, U 型捕获位 300-800 µm 可调); (ii) fibrin + Matrigel hydrogel
with Landau-Levich-Bretherton 效应 → 100% 捕获效率 in 10 sec per
channel; (iii) hiPSC-derived blood vessel organoids (BVO, day 15)
+ GFP-HUVEC + 纤维细胞共培养 → 30 天功能性灌注培养; (iv) 壁剪切速率
27-2000 s⁻¹, mean 134-531 s⁻¹ (与人体毛细血管生理范围 50-1900 s⁻¹
完美匹配); (v) 层级化血管: 37 µm 上游动脉-静脉 + 8 µm BVO 毛细管.
The 4 commits are the same single file
`obsidian-vault/Literature/Deep-Reads/Organoid/quintard_2024_vasorganoid_chip.md`
walked through Robin's standard LDR cycle: (a) **`0fc8db24`** adds
the file (189 lines, single-pass entry); (b) **`290e9635`** rewrites
to -v2 修图床/双 H1/落款; (c) **`24c713de`** adds -v3 Wiki.js 自带
图床 6 张图 (永久); (d) **`4073abf4`** is the -v4 转发语标题/落款
加粗 + 删 3Brain 工具名硬门槛合规修正. The "与我们的产品" table on
the paper lists **Mimetas OrganoPlate ⭐⭐⭐⭐ (直接对标: Phaseguide
微流控技术)** + **CelVivo ClinoStar ⭐⭐⭐ (类器官前段成熟期培养:
BVO 在 hiPSC 分化到 day 15 需要悬浮旋转培养, ClinoStar 是该步骤
的金标准; day 15 后才转入芯片, ClinoStar 是完整工作流的前置)** +
**Emulate Organ-Chip ⭐⭐⭐**.
- **Guo Z, Zhang N (2026) Front Cell Dev Biol DOI 10.3389/fcell.2026.1721946**
— an IRB / ethical-review systematic-review paper for organoid
biomedical research. The paper establishes: (i) **7 大强制要点**
(样本来源合法性 / 捐赠者知情同意 [unlimited expansion / long-term
cryopreservation / inter-lab sharing / cross-border / future
unspecified research / commercial use / withdrawal mechanism] /
数据隐私与去标识化 / 共培养产物主体性评估 [Guo 2026 首次提出] /
动物福利 3R 原则 / 跨境监管合规 [中国 / 美国 / 欧盟 / 日本 / 韩国
对照表] / 长期保存与终止使用); (ii) **中国 IRB 实务视角 + 国际
ISSCR / GDPR / OHRP 双重参照** (作者团队 = 嘉兴市第一医院医学伦理
委员会 + 嘉兴大学医学院, 中国 IRB 实践者); (iii) **共培养产物
"新伦理实体" 框架** = 类器官 + 免疫细胞共培养 (CAR-T 培养) 不构成
"新生物体" 但构成 "新伦理实体", 需要独立审查. The 3 commits are
the same single file
`obsidian-vault/Literature/Deep-Reads/Organoid/guo_2026_organoid_ethical_review.md`
walked through Robin's standard LDR cycle: (a) **`2e6f5989`** adds
the file (170 lines, single-pass entry); (b) **`00f824f2`** -v2 修
图床 (加 2 张 Wiki.js 自带图); (c) **`a4fa5a32`** -v3 补 Fig 1
(3 张图全) — Fig 1 is the "类器官共培养模型" 概念图 (Robin 8-16
实战反思: 综述类概念图通常较小, 提取阈值要从 0KB 起步全收, 再按
caption 关联; 之前 >200KB 过滤漏了 Fig 1). The "与我们的产品"
table on the paper lists **CelVivo ClinoStar ⭐⭐⭐⭐ (临床转化类
器官的伦理合规——本文 7 大要点直接适用于 ClinoStar 客户 IRB 申请;
Robin 推广 ClinoStar 给三甲医院时, 可附带本框架作为增值)** +
**Mimetas OrganoPlate ⭐⭐⭐⭐ (类器官共培养芯片的伦理审查依据——
Mimetas 主打"类器官 + 免疫细胞共培养", 本文主题 B 的共培养伦理
框架直接适用)** + **Emulate Organ-Chip ⭐⭐⭐ (类器官 + 微流控
芯片的跨境监管参考)**.
The **2026-08-12 cluster** is a **single-paper LDR cycle** on
**Liang Y et al. (2026) Sci Rep DOI 10.1038/s41598-026-42990-2** — a
mouse liver organoid platform paper from 澳门科技大学 + 香港大学 that
establishes: (i) single-tissue 3-轨道 (Hep-Orgs + Cho-Orgs + HSC)
separation; (ii) DAPT (Notch 抑制) + Dexamethasone for P1-P10 长程
稳定成熟 (ALB / PAS / LDL / CYP all stable across 10 passages — single
DAPT only sustains P5); (iii) TGFβ 5-7 day activation of qHSC → aHSC
(Acta2 / Col1a1 上调); (iv) aHSC 共培养诱导 Hep-Orgs EMT
(Snail / Twist / Vimentin ↑; ALB / CK8 ↓; Lgr5 / EpCAM ↓; Ki67 ↓) =
体外肝纤维化模型. The 4 commits are the **same single file**
`04-Literature/Deep-Reads/Liver/2026-08-12_Liang_2026_SciRep_liver_organoid_fibrosis_platform.md`
walked through Robin's standard 3-stage SOP cycle: (a) **`e542c977`**
adds the file (186 lines, single-pass entry); (b) **`8699a154`** rewrites
the same file to the page 946 9 项 SOP 标杆 (105+/122- lines, adding
the 6 核心发现 三段式 tables + 6 SeaFile Fig + "与我们的产品" 4-star
table + 4-paper 参考文献 + 转发语 + 完整落款 + SeaFile PDF link); (c)
**`aacba7aa`** + **`297f106d`** are the **page 934 修齐** micro-revisions
(frontmatter title 改中文 / H1 去括号 / 元数据用 bold 单行 / 📄PDF
文件名 with actual filename) — the same alignment Robin applied across
the 2026-08-11 OVB-类器官 cycle. The "与我们的产品" 4-star table
on the paper lists CelVivo ClinoStar ⭐⭐⭐⭐ (P1-P10 长程扩增对应
旋转培养 30+ 天无剪切; HSC 静止态在模拟微重力下 7+ 天维持) +
CelVivo ClinoReactor ⭐⭐⭐⭐ (单组织 3 轨道分通道灌流; TGFβ 时间程序
精确切换) + CelVivo PhaseHolographic 成像 ⭐⭐⭐ + 3Brain HD-MEA ⭐⭐⭐
(肝-神经互作延伸).
**No new vault commits landed in the 2026-08-12T18:08Z →
2026-08-13T18:08Z window** — the vault HEAD is unchanged at
`297f106d`. The 2026-08-12 Liang 2026 cluster remains the most recent
committed vault activity. One new uncommitted file appeared in the
working tree this fetch:
`04-Literature/Deep-Reads/Review/zhou2023_computer_vision_microfluidics.md`
— the **first entry in a new `Review/` subfolder** (see the
Notable-entity section below).
**7 new vault commits landed in the 2026-08-15T18:07Z →
2026-08-17T18:09Z window** — the vault HEAD bumped from `297f106d`
to `a4fa5a32`. The two 2026-08-16 LDR cycles (Quintard 2024
microfluidic organ-on-chip + Guo 2026 organoid ethics systematic
review) are the **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. The 2026-08-16 cluster
replaces the 2026-08-12 Liang 2026 cluster as the most recent
committed vault activity. Two new untracked directories appeared in
the working tree this fetch: `celvivo_commercial/1331651_20260630_131201.pdf`
(the 6-30 quote PDF migrated into a new folder) + `templates/类器官IRB申请清单.md`
(the IRB application checklist derived from Guo 2026 — Robin's first
customer-facing sales ammunition template produced from a single
deep-read; see the Notable-entity section below for synthesis).
The **2026-08-10 cluster** is a **frontmatter-hygiene + MOC-discipline
sprint** rather than new external evidence: (a) **Phase A batch**
(`d97b39ed`) standardized 6 deep-read notes with the structured 6-field
frontmatter (doi / journal / year / **volume** / **pages** /
**authors** array / pmid) that the prior notes had been missing; (b)
**方案 2 样品** (`3b929c2f`) added 7 image alt descriptions on top of the
6-field frontmatter for `wang2024-org-on-chip.md`; (c) **MOC 方案 1
样品** (`6b717aef`) created Robin's first Map-of-Content file
(`04-Literature/Deep-Reads/MOCs/MOC-类器官与3D培养.md`, 95 lines, 沙牛《AI
时代的 Obsidian 公开课》课时 1 pattern) and added `related:` back-link
frontmatter to 7 papers. The MOC's own `related:` list already names
the next planned MOC — `[[MOC-3Brain-HD-MEA]]` — plus
`[[02-Clients/Agents/_known_associations]]` and
`[[02-Active-Deals/CellShot-TriArm-Demo-计划-v2-老师版-2026-07-20]]`,
so the MOC pattern is expected to extend.
The **2026-08-08 cluster** (prior manifest) was the literature
flywheel-sync output (Liu 2026, Miao 2025 v2, Sharma 2026) — already
indexed on [`/sources/literature.md`](/sources/literature.md). The
**2026-08-07 / 2026-08-08 micro-revisions** on Liu 2026 (`a69ad9c4` →
`1614ccf9`) are the 8-step SOP rewrite cycle (v3 → v11) Robin re-ran
on the same paper.
## openwiki-wiki — working-tree status (2026-08-31)
- **Branch:** `main`
- **HEAD:** `9582deadda4681fe1481f9992905230ace7e5990` (the
`chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-31)` commit). The 2026-08-31T18:09Z
fetch observed wiki HEAD bumped from `d56da3afddfced20a01fbecd9912fe3ec87a25b4` (2026-08-30T18:06Z
fetch) to `9582dea` — **2 new automated wiki commits** in the
2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window: (a) `c9e2770`
chore: daily update 2026-08-31 (2026-08-31 02:18 +0800, committed 15 files per `git show --stat
c9e2770` — including `.last-update.json` + `index.md` + `quickstart.md` +
`sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` +
`sources/index.md` + `sources/nocodb.md` + `sources/openwiki-version-drift.md` +
`sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` +
`sources/wikijs.md` + `themes/05-robin-research.md` + `themes/index.md` —
reducing the working-tree dirty count from 11 → 5 per the manifest `changedFiles` list at the 2026-08-31 fetch;
(b) `9582dea` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts
(sources-sync 2026-08-31, 2026-08-31 02:30 +0800). The `9582dea`
sources-sync re-applied the count-data wipe pattern on NocoDB /
SeaFile / Wiki.js / RAGFlow for the **seventeenth** consecutive time
(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 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + `502281f`
2026-08-27 + `c992dd6` 2026-08-28 + `37d1ba6` 2026-08-29 + `d56da3a` 2026-08-30 + now `9582dea` 2026-08-31); the
sources-sync committed 4 files per `git show --stat 9582dea` —
`sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` +
`sources/wikijs.md`. The very next HN-1 2026-08-31T18:00Z +
web-search-1 2026-08-31 (skipped) + this git-repo-1
2026-08-31T18:09Z run's synthesis edits re-touched the same files +
the sources-sync `9582dea` re-touched the 4 source-sync files (the
same pattern as the 2026-08-28 + 2026-08-29 + 2026-08-30 fetches).
The very next HN-1 2026-08-31 Almanac (YC S26) synthesis edits added 3 NEW
dirty files (`themes.md` + `themes/03-ai-agents.md` +
`sources/literature.md`) not previously touched by the
`c9e2770` daily update. The combined effect is the
working-tree dirty count bumped from 5 → 11 at this fetch because
the sources-sync `9582dea` re-touched the 4 source-sync files that
the `c9e2770` daily update had committed; the HN-1 Almanac
synthesis re-touched `themes.md` + `themes/03-ai-agents.md` (the
agent-memory-architecture row updated to mention Almanac as
shipped-product evidence) + `sources/literature.md` (Almanac
cross-reference added).
- **Working-tree state:** 11 modified files (uncommitted — pending
next CLI orchestration). The 2026-08-31T18:09Z fetch observed the
working tree at 11 uncommitted files (up from 9 at the
2026-08-30T18:06Z fetch because the `9582dea` sources-sync re-touched
the 4 source-sync files + the `c9e2770` daily update re-touched
`.last-update.json` + this run's HN-1 Almanac synthesis edits
re-touched `themes.md` + `themes/03-ai-agents.md` +
`sources/literature.md` + this git-repo-1 2026-08-31T18:09Z run's
synthesis edits re-touched `sources/git-repo.md` (this page) +
`quickstart.md` (the "Latest update" paragraph),
even though the `c9e2770` daily update had
committed 15 of the prior dirty files per `git show --stat c9e2770`
— including `commitments.md` was not in this set at the 2026-08-31
fetch; the `c9e2770` commit reduced the dirty count from 11 → 5).
The 11 dirty files at this fetch per the manifest `changedFiles`
list are:
- `.last-update.json` — CLI metadata, will be updated when this run's
`status: complete` lands (re-touched by `c9e2770` 2026-08-31
daily update after the previous metadata cycle).
- `quickstart.md` — contains the accumulated "Latest update"
paragraphs from the prior HN-1 2026-08-30T18:00Z + HN-1 2026-08-31T18:00Z
+ web-search-1 2026-08-30 (skipped) + web-search-1 2026-08-31
(skipped) + git-repo-1 2026-08-30T18:06Z runs + the "Latest
update — git-repo-1 (2026-08-30T18:06Z)" paragraph added by the
2026-08-30 git-repo run; this git-repo-1 2026-08-31T18:09Z run
adds the "Latest update — git-repo-1 (2026-08-31T18:09Z)" paragraph
and updates the Backlog git-repo entry to reflect the new wiki HEAD
`9582dea` + the **seventeenth** consecutive sources-sync + the
5-calendar-day-vault-silence-ended + the carry-forward bump to
20/15/15/8-day + the parallel `templates/` + `celvivo_commercial/`
confirmed-one-off alongside the `Review/` subfolder carrying
forward unchanged at the 2026-08-31 fetch + the
`deepread_40240593/` pipeline workspace at 7-day carry-forward with
6 consecutive silent fetches since the 2026-08-24/25 burst + the
new `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` subfolder
opened with 5 single-shot LDR entries in this fetch.
- `sources/hackernews.md` — accumulated "Latest update —
2026-08-30 18:00 UTC" + "Latest update — 2026-08-31 18:00 UTC"
sections from the prior HN-1 runs (the 2026-08-30 pull + the
2026-08-31 Almanac YC S26 pull — 21 pts + 22 cmts on item
`49511007`, surfaced via Algolia `organoid` + `3Brain`
substring-noise duplicate) — landed in uncommitted state
during the HN-1 runs.
- `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md`
+ `sources/wikijs.md` — count-data refresh from the **seventeenth**
consecutive sources-sync `9582dea` (2026-08-31 02:30 +0800); the
sources-sync re-applied the 2026-08-15 count-data wipe pattern on
all 4 source-sync files. These 4 files were committed by the
`c9e2770` 2026-08-31 daily update earlier in the window, then
re-dirtied by the `9582dea` sources-sync that landed later in
the window — same pattern as the 2026-08-28 + 2026-08-29 + 2026-08-30 fetches
(5 → 8 → 9 → 11 dirty file re-bump after the sources-sync + the
3 NEW HN-1 Almanac synthesis dirty files).
- `sources/literature.md` — NEW dirty file at this fetch (not in
the 2026-08-30 dirty set); the HN-1 Almanac 2026-08-31
synthesis pass added a cross-reference to the
`agent-memory-architecture` row's Almanac evidence in the
`/sources/literature.md` cross-reference section.
- `sources/web-search.md` — connector-skipped operational notes from
the 2026-08-30 + 2026-08-31 web-search-1 attempts (both skipped
because `web-search-1` is not enabled in the runtime registry and
`TAVILY_API_KEY` is empty — 17th + 18th consecutive skips on the
same code path); the file re-appears as dirty after the per-run
refresh of the operational-notes section.
- `themes.md` — NEW dirty file at this fetch (not in the 2026-08-30
dirty set); the HN-1 Almanac 2026-08-31 synthesis pass updated
the `agent-memory-architecture` row to add Almanac as
shipped-product evidence (Last seen 2026-08-13 → 2026-08-31;
Evidence count 16+ → 17+).
- `themes/03-ai-agents.md` — NEW dirty file at this fetch (not in
the 2026-08-30 dirty set); the HN-1 Almanac 2026-08-31
synthesis pass added the Almanac bullet to the "Adjacent
workflow signals (HN / Tavily)" section of the AI-agents theme.
- **Auth:** local path only — no remote, no credentials.
- **New file in this window:** none — the `sources/openwiki-version-drift.md`
auto-generated page (created in the 2026-08-17 daily update `5c70881`)
was committed by the `81ac94a` 2026-08-26 daily update + the
`6024ac7` 2026-08-28 daily update; the file re-appears as dirty after
this run because the very next synthesis edits re-touch the file
(refresh of the timestamp) — same pattern as prior daily updates.
- **Auth:** local path only — no remote, no credentials.
### Recent commits (latest first)
| Date | Hash | Note |
| --- | --- | --- |
| 2026-08-31 | `9582dea` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-31) — **count-data wipe re-applied** for the **seventeenth** 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` + 2026-08-25 `1003b92` + 2026-08-26 `ebb95c0` + 2026-08-27 `502281f` + 2026-08-28 `c992dd6` + 2026-08-29 `37d1ba6` + 2026-08-30 `d56da3a`); committed `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` per `git show --stat 9582dea`; see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-31 | `c9e2770` | chore: daily update 2026-08-31 (synthesis-layer edits accumulated from the prior HN-1 2026-08-30T18:00Z + HN-1 2026-08-31T18:00Z + web-search-1 2026-08-30 (skipped) + web-search-1 2026-08-31 (skipped) + git-repo-1 2026-08-30T18:06Z runs; per `git show --stat c9e2770` the commit touched 15 files from the prior dirty set including `.last-update.json` + `index.md` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/nocodb.md` + `sources/openwiki-version-drift.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` + `sources/wikijs.md` + `themes/05-robin-research.md` + `themes/index.md`; reducing uncommitted-file count from 11 → 5 at the 2026-08-31T18:09Z fetch) |
| 2026-08-30 | `d56da3a` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-30) — **count-data wipe re-applied** for the **sixteenth** 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` + 2026-08-25 `1003b92` + 2026-08-26 `ebb95c0` + 2026-08-27 `502281f` + 2026-08-28 `c992dd6` + 2026-08-29 `37d1ba6`); committed `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` per `git show --stat d56da3a`; see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-30 | `7eed6ca` | chore: daily update 2026-08-30 (synthesis-layer edits accumulated from the prior HN-1 2026-08-29T18:00Z + HN-1 2026-08-30T18:00Z + web-search-1 2026-08-29 (skipped) + web-search-1 2026-08-30 (skipped) + git-repo-1 2026-08-29T18:10Z runs; per `git show --stat 7eed6ca` the commit touched 13 files from the prior dirty set including `.last-update.json` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` + `sources/wikijs.md` + `themes/05-robin-research.md` + `themes/index.md`; reducing uncommitted-file count from 8 → 5 at the 2026-08-30T18:06Z fetch) |
| 2026-08-29 | `37d1ba6` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-29) — **count-data wipe re-applied** for the **fifteenth** 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` + 2026-08-25 `1003b92` + 2026-08-26 `ebb95c0` + 2026-08-27 `502281f` + 2026-08-28 `c992dd6`); committed `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` per `git show --stat 37d1ba6`; see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-29 | `ef0e144` | chore: daily update 2026-08-29 — `.last-update.json` only (re-touched after the `0f6a901` commit by the CLI metadata update) |
| 2026-08-29 | `0f6a901` | chore: daily update 2026-08-29 — 3-connector raw data refresh (HN-1 fully-zero + git-repo-1 vault-silent + web-search-1 skip) — committed 9 files per `git show --stat 0f6a901` — including `.last-update.json` + `index.md` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/web-search.md` + `themes/05-robin-research.md` + `themes/index.md`; reducing uncommitted-file count from 11 → 8 at the 2026-08-29T18:10Z fetch |
| 2026-08-28 | `6024ac7` | chore: daily update 2026-08-28 (synthesis-layer edits accumulated from the prior HN-1 2026-08-27T18:00Z + HN-1 2026-08-28T18:00Z + web-search-1 2026-08-27 (skipped) + web-search-1 2026-08-28 (skipped) + git-repo-1 2026-08-27T18:25Z runs; committed 16 files per `git show --stat 6024ac7` — including `.last-update.json` + `commitments.md` + `index.md` + `quickstart.md` + `sources/README.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` + `themes.md` + `themes/index.md` + `themes/05-robin-research.md`; reducing uncommitted-file count from 17 → 5 per the manifest `changedFiles` list at the 2026-08-28T18:09Z fetch) |
| 2026-08-28 | `c992dd6` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-28) — **count-data wipe re-applied** for the **fourteenth** 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` + 2026-08-25 `1003b92` + 2026-08-26 `ebb95c0` + 2026-08-27 `502281f`); see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-27 | `502281f` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-27) — **count-data wipe re-applied** for the **thirteenth** 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` + 2026-08-25 `1003b92` + 2026-08-26 `ebb95c0`); see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-27 | `f51ff7c` | chore: daily update 2026-08-27 (synthesis-layer edits accumulated from the prior HN-1 2026-08-26T18:00Z + HN-1 2026-08-27T18:00Z + web-search-1 2026-08-26 (skipped) + web-search-1 2026-08-27 (skipped) + git-repo-1 2026-08-26T18:06Z runs; committed 14 of the prior 17 dirty files per `git show --stat f51ff7c` — including `commitments.md` + `index.md` + `themes.md` + `themes/index.md` + `themes/05-robin-research.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/literature.md` + `sources/openwiki-version-drift.md` + `sources/web-search.md` + `sources/README.md` + `quickstart.md` + `.last-update.json`; reducing uncommitted-file count from 17 → 11) |
| 2026-08-26 | `ebb95c0` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-26) — **count-data wipe re-applied** for the **twelfth** 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` + 2026-08-25 `1003b92`); see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-26 | `81ac94a` | chore: daily update 2026-08-26 (synthesis-layer edits accumulated from the prior HN-1 2026-08-25T18:00Z + HN-1 2026-08-26T18:00Z + web-search-1 2026-08-25 (skipped) + git-repo-1 2026-08-25T18:13Z runs; committed 14 of the prior 17 dirty files per `git show --stat 81ac94a` — including `commitments.md` + `index.md` + `themes.md` + `themes/index.md` + `themes/05-robin-research.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/literature.md` + `sources/openwiki-version-drift.md` + `sources/web-search.md` + `sources/README.md` + `quickstart.md` + `.last-update.json`; reducing uncommitted-file count from 11 → 8) |
| 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" |
| 2026-08-23 | `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" |
| 2026-08-22 | `d8e2277` | chore: daily update 2026-08-22 (synthesis-layer edits accumulated from the prior HN-1 2026-08-22T18:00Z + web-search-1 2026-08-22 (skipped) + git-repo-1 2026-08-21T18:09Z runs) |
| 2026-08-21 | `f6c2576` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-21) — **count-data wipe re-applied** for the **seventh** 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`); see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-21 | `b6dc337` | chore: daily update 2026-08-21 (synthesis-layer edits accumulated from the prior HN-1 2026-08-21T18:00Z + web-search-1 2026-08-21 (skipped) + git-repo-1 2026-08-20T18:09Z runs; committed `sources/index.md` from the 2026-08-20 dirty set) |
| 2026-08-20 | `bd30339` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-20) — **count-data wipe re-applied** for the **sixth** consecutive sources-sync (after 2026-08-15 `2507925` + 2026-08-16 `997b648` + 2026-08-17 `be49285` + 2026-08-18 `1fc73ae` + 2026-08-19 `dcb53a2`); see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-20 | `a44f284` | chore: daily update 2026-08-20 (synthesis-layer edits accumulated from the prior HN-1 2026-08-20T18:00Z + web-search-1 2026-08-20 (skipped) + git-repo-1 2026-08-19T18:08Z runs) |
| 2026-08-19 | `dcb53a2` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-19) — **count-data wipe re-applied** for the **fifth** consecutive sources-sync (after 2026-08-15 `2507925` + 2026-08-16 `997b648` + 2026-08-17 `be49285` + 2026-08-18 `1fc73ae`); see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-19 | `7e904ec` | chore: daily update 2026-08-19 (synthesis-layer edits accumulated from the prior HN-1 2026-08-19T18:00Z + web-search-1 2026-08-19 + git-repo-1 2026-08-18T18:10Z runs + the prior `sources/openwiki-version-drift.md` carryover) |
| 2026-08-18 | `1fc73ae` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-18) — **count-data wipe re-applied** for the **fourth** consecutive sources-sync (after 2026-08-15 `2507925` + 2026-08-16 `997b648` + 2026-08-17 `be49285`); see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-18 | `8127797` | chore: daily update 2026-08-18 (synthesis-layer edits accumulated from the prior HN-1 2026-08-18T18:00Z + git-repo-1 2026-08-17T18:09Z runs + the new `sources/openwiki-version-drift.md` carryover) |
| 2026-08-17 | `be49285` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-17) |
| 2026-08-17 | `5c70881` | chore: daily update 2026-08-17 (added `sources/openwiki-version-drift.md` auto-generated page + refreshed HN-1 / web-search-1 / git-repo-1 sections) |
| 2026-08-16 | `997b648` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-16) |
| 2026-08-16 | `151d22b` | chore: daily update 2026-08-16 (committed `sources/index.md` from the 2026-08-15 dirty set; refreshed HN-1 / web-search-1 / git-repo-1 / themes/05-robin-research sections) |
| 2026-08-15 | `2507925` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-15) — **count-data wipe** (NocoDB 6614 → 0, Wiki.js 83 → 0, RAGFlow landing 200 → 000); see Notable-entity § "2026-08-15 sources-sync bug" |
| 2026-08-15 | `173b58c` | chore: daily update 2026-08-15 (added OKF frontmatter to nocodb.md / ragflow.md / seafile.md / wikijs.md) |
| 2026-08-14 | `6258717` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-14) |
| 2026-08-14 | `021e929` | chore: daily update 2026-08-14 |
| 2026-08-13 | `1737454` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-13) |
| 2026-08-13 | `8ddc6d9` | chore: daily update 2026-08-13 (commitment + quickstart + sources/literature + sources/web-search + themes/01-organoid-equipment + themes/05-robin-research from the HN-1 2026-08-13 synthesis pass) |
| 2026-08-12 | `c57ead4` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-12) |
| 2026-08-12 | `431ee6a` | chore: daily update 2026-08-12 |
| 2026-08-11 | `b64ae41` | lit: PMID 41536916 Bioactive Materials AIVOs 综述 (Wiki.js 1711) |
| 2026-08-11 | `523ee7f` | lit: PMID 41686639 Cell Reports TNBC DEO + ROCK (Wiki.js 1710) |
| 2026-08-11 | `9be4f55` | lit: PMID 41909700 Front Immunol 2026 类器官-小胶质细胞综述 (Wiki.js 1709) |
| 2026-08-11 | `cc69ece` | lit: PMID 42041571 v4 - 按 literature-deep-read-research 9 项强制格式 |
| 2026-08-11 | `b4bc8d9` | lit: PMID 42041571 修正 - 真实PDF + 10张真图链接 |
| 2026-08-11 | `12480ab` | lit: 修正 wiki_url 到真实内网地址 |
| 2026-08-11 | `cdc59c5` | lit: PMID 42041571 OVB-organoids vs cerebral organoids Cells 2026 |
| 2026-08-11 | `2bcde39` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-11) |
| 2026-08-11 | `7556e31` | chore: daily update 2026-08-11 |
| 2026-08-09 | `dde053a` | auto: 2026-08-09 Wang 2024 Theranostics OrgOC 综述精读入口 |
| 2026-08-09 | `3267338` | chore: daily update 2026-08-09 |
| 2026-08-09 | `06f60e1` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-09) |
| 2026-08-08 | `c94940c7` | feat: add Microbioreactor 2026 v4 (PMID 42516424, ID 1696) |
| 2026-08-08 | `7f65024` | feat: add Microbioreactor 2026 v3 (PMID 42516424) |
| 2026-08-08 | `ea4f14a` | feat: add Microbioreactor 2026 v2 (PMID 42516424) |
| 2026-08-08 | `a193e46` | feat: add Microbioreactor 2026 (PMID 42516424) deep-read entry |
| 2026-08-08 | `bf90a91` | fix: liu 2026 wiki link to main path |
| 2026-08-08 | `cf1dbe0` | fix: liu 2026 final link |
| 2026-08-08 | `26efd2f` | fix: liu 2026 v5 link |
| 2026-08-08 | `e18993a` | fix: liu 2026 v4 link |
| 2026-08-08 | `b206bd9` | fix: liu 2026 v3 link |
| 2026-08-08 | `c26dbdf` | fix: liu 2026 wiki link to v2 |
| 2026-08-08 | `703c3d4` | literature: liu 2026 NBME shape-conformal organoid |
| 2026-08-08 | `1b78735` | literature: miao 2025 cell v2 |
| 2026-08-08 | `5adc406` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-08) |
| 2026-08-08 | `037c5f3` | lit: add Sharma K 2026 Cell Stem Cell vRO retinal organoid (PMID 41529691) |
| 2026-08-07 | `9e80977` | feat(openwiki): complete data flywheel activation (2026-08-07) |
| 2026-08-07 | `45af5a4` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-07) |
| 2026-08-07 | `bcd4a4f` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-07) |
| 2026-08-07 | `0bbef0f` | feat(openwiki v0.3.1 --update): generate themes 4-5 + index.md + themes/ + sources/ index (2026-08-07) |
| 2026-08-07 | `285c53b` | feat(openwiki v0.3.1): add YAML frontmatter + install-id markers from initial init run (2026-08-07) |
| 2026-07-24 | `3102e96` | feat(sources): 全国 261 家经销商地图 (2026-07-24, 不含敏感信息) |
The wiki repo is the OpenWiki output itself — it persists across
update runs. **4 new wiki-side commits landed in the
2026-08-13T18:08Z → 2026-08-15T18:07Z window**: (a) `021e929`
(2026-08-14 +0800 02:18, `chore: daily update 2026-08-14`); (b)
`6258717` (2026-08-14 +0800 02:30, `chore(sources): refresh
NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-14)`);
(c) `173b58c` (2026-08-15 +0800 02:00, `chore: daily update 2026-08-15`
— added OKF frontmatter to nocodb.md / ragflow.md / seafile.md /
wikijs.md); (d) `2507925` (2026-08-15 +0800 02:31, `chore(sources):
refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync
2026-08-15)` — **count-data wipe** carried into the source pages; see
Notable-entity § "2026-08-15 sources-sync bug" below). Between these 4
commits, the wiki HEAD advanced from `1737454` (2026-08-13
sources-sync) to `2507925` (2026-08-15 sources-sync). The 6 wiki commits
from 2026-08-11 / 2026-08-12 (`7556e31` / `431ee6a` daily +
`2bcde39` / `c57ead4` sources-sync + the 6 lit-PMID commits on
2026-08-11 + `2bc03f3` / `06f60e1` / `5adc406` / `3267338` /
`dde053a` from the 2026-08-08 / 2026-08-09 cluster) are all already in
`2507925`'s ancestry. The **Liang 2026 wiki sync** has not yet landed
(the `/sources/literature.md` short row is in working tree only); the
next wiki commit should add a fuller Liang 2026 row when the synthesis
pipeline catches up.
### Summary of last 48 hours
| Window (UTC) | Vault | Wiki |
| --- | --- | --- |
| 2026-08-30T18:06:00Z → 2026-08-31T18:09:00Z | HEAD `9d4767c7` → **`391e47131679ce9edf0f525236e78ebb13e0d232`** (**5 new commits**, all on 2026-08-31 +0800 between 13:05 and 13:42, single-day cluster) — **breaks the 5-fetch vault silence streak** since the 2026-08-24/25 SECOND 5-paper burst, **5 calendar days of vault silence ended**; **the 2026-08-31 5-paper LDR cluster is the THIRD consecutive single-day 5-paper burst in 5 calendar days**, all CelVivo-anchored (Yan + Miao + Nguyen + Aiello + Stewart), all single-shot LDR entries in the **NEW `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` subfolder** (capital-V variant, distinct from the existing lowercase `04-Literature/Deep-Reads/Celvivo/` 143-file subfolder); the cluster creates **1 NEW `04-Literature/Deep-Reads/` subfolder** + adds 5 single-shot LDR files to it: `eb24ab72` Stewart 2023 Front Microbiol BA.5/XBB neurotropic brain organoids + `030f31ed` Aiello 2025 EMBO reports reproducible brain organoids (CelVivo ClinoReactor; **CelVivo ApS as co-author affiliation**) + `fad7e21e` Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids + `4fca0123` Miao 2025 Cell vascularized lung/gut organoids (CelVivo ClinoReactor; companion to the 2026-08-08 flywheel-sync Miao 2025 v2 deep-read) + `391e4713` Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids (CelVivo); 4 of 5 are brain organoids (Yan + Aiello + Nguyen + Stewart = QIMR Berghofer Suhrbier/Rawle viral-neurotropism line + CelVivo ApS co-authored reproducibility) + 1 vascularized lung/gut (Miao). All 5 land at `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` — Robin expands the per-vendor subfolder taxonomy from 1 (`Celvivo/` lowercase) → 2 (`Celvivo/` lowercase + `CelVivo/` capital) for **two parallel CelVivo-anchored canonical subfolders**; the carry-forward untracked-file set bumps: `Review/zhou2023_computer_vision_microfluidics.md` 19-day → **20-day carry-forward** (17 → **18 fetches silent**, stale carry-forward note) + `celvivo_commercial/` + `templates/` 14-day → **15-day carry-forward** (both confirmed one-off alongside the `Review/` subfolder, carrying forward unchanged at the 2026-08-31 fetch) + `deepread_40240593/` 7-day → **8-day carry-forward** (mtime unchanged across **7 consecutive silent fetches** since creation, working-folder-pipeline hypothesis further weakened at this fetch — **8th fetch silent on directory mtime**); no new untracked dirs at this fetch | HEAD `d56da3a` → `9582dea` (**2 new automated commits**: `c9e2770` chore: daily update 2026-08-31 (2026-08-31T02:18 +0800, committed 15 files per `git show --stat c9e2770` — including `.last-update.json` + `index.md` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/nocodb.md` + `sources/openwiki-version-drift.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` + `sources/wikijs.md` + `themes/05-robin-research.md` + `themes/index.md`; reducing uncommitted-file count from 11 → 5) + `9582dea` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-31, 2026-08-31T02:30 +0800, the **seventeenth** 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 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + `502281f` 2026-08-27 + `c992dd6` 2026-08-28 + `37d1ba6` 2026-08-29 + `d56da3a` 2026-08-30 + now `9582dea` 2026-08-31; committed `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` per `git show --stat 9582dea` — the same 4 source-sync files re-touched after the `c9e2770` commit had already cleared them, the same re-bump pattern as the 2026-08-28 + 2026-08-29 + 2026-08-30 fetches); the 11 dirty wiki files at this fetch per the manifest `changedFiles` list are `M .last-update.json` + `M quickstart.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` + `M themes.md` + `M themes/03-ai-agents.md` — up from the 9-dirty-file baseline at the 2026-08-30T18:06Z fetch because the `9582dea` sources-sync re-touched the 4 source-sync files that had been committed by the `c9e2770` daily update + the HN-1 2026-08-31 Almanac (YC S26) synthesis pass added 3 NEW dirty files (`sources/literature.md` + `themes.md` + `themes/03-ai-agents.md`) for the `agent-memory-architecture` row refresh) |
| --- | --- | --- |
| 2026-08-29T18:10:00Z → 2026-08-30T18:06:00Z | HEAD **unchanged** at `9d4767c7` (**0 new commits**, **0 new mtime changes** — **vault silent for the 5th consecutive fetch** since the 2026-08-24/25 SECOND 5-paper burst; the 2026-08-25 5-paper cluster remains the most recent vault activity, **5 calendar days stale**; the carry-forward untracked-file set bumps: `Review/zhou2023_computer_vision_microfluidics.md` 18-day → **19-day carry-forward** (16 → **17 fetches silent**, stale carry-forward note per the 2026-08-27 fetch confirming the 2026-08-26 watchlist-downgrade consideration as a one-off) + `celvivo_commercial/` + `templates/` 13-day → **14-day carry-forward** (**both confirmed one-off alongside the `Review/` subfolder at the 2026-08-28 fetch, carrying forward unchanged at the 2026-08-29 + 2026-08-30 fetches** — same duration at which the `Review/` entry was confirmed one-off) + `deepread_40240593/` 6-day → **7-day carry-forward** (mtime unchanged across **6 consecutive silent fetches** since creation, working-folder-pipeline hypothesis further weakened); no new untracked dirs) | HEAD `37d1ba6d` → `d56da3a` (**2 new automated commits**: `7eed6ca` chore: daily update 2026-08-30 (2026-08-30T02:?? +0800, committed 13 files per `git show --stat 7eed6ca` — including `.last-update.json` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` + `sources/wikijs.md` + `themes/05-robin-research.md` + `themes/index.md`; reducing uncommitted-file count from 8 → 5) + `d56da3a` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-30, 2026-08-30T02:30 +0800, the **sixteenth** 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 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + `502281f` 2026-08-27 + `c992dd6` 2026-08-28 + `37d1ba6` 2026-08-29 + now `d56da3a` 2026-08-30; committed `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` per `git show --stat d56da3a` — the same 4 source-sync files re-touched after the `7eed6ca` commit had already cleared them, the same re-bump pattern as the 2026-08-28 + 2026-08-29 fetches); the 9 dirty wiki files at this fetch per the manifest `changedFiles` list are `M .last-update.json` + `M index.md` + `M quickstart.md` + `M sources/hackernews.md` + `M sources/nocodb.md` + `M sources/openwiki-version-drift.md` + `M sources/ragflow.md` + `M sources/seafile.md` + `M sources/wikijs.md` — up from the 8-dirty-file baseline at the 2026-08-29T18:10Z fetch because the `d56da3a` sources-sync re-touched the 4 source-sync files that had been committed by the `7eed6ca` daily update + the CLI metadata cycle re-touched `sources/openwiki-version-drift.md` + `index.md`) |
| --- | --- | --- |
| 2026-08-28T18:09:00Z → 2026-08-29T18:10:00Z | HEAD **unchanged** at `9d4767c7` (**0 new commits**, **0 new mtime changes** — **vault silent for the 4th consecutive fetch** since the 2026-08-24/25 SECOND 5-paper burst; the 2026-08-25 5-paper cluster remains the most recent vault activity, **4 calendar days stale**; the carry-forward untracked-file set bumps: `Review/zhou2023_computer_vision_microfluidics.md` 17-day → **18-day carry-forward** (15 → **16 fetches silent**, stale carry-forward note per the 2026-08-27 fetch confirming the 2026-08-26 watchlist-downgrade consideration as a one-off) + `celvivo_commercial/` + `templates/` 12-day → **13-day carry-forward** (**the 2026-08-28 fetch confirmed the parallel `templates/` + `celvivo_commercial/` entries as one-off alongside the `Review/` subfolder** — both are confirmed one-off at the 2026-08-29 fetch, carrying forward unchanged; same duration at which the `Review/` entry was confirmed one-off) + `deepread_40240593/` 5-day → **6-day carry-forward** (mtime unchanged across **5 consecutive silent fetches** since creation, working-folder-pipeline hypothesis further weakened); no new untracked dirs) | HEAD `6024ac7` → `37d1ba6d` (**3 new automated commits**: `0f6a901` chore: daily update 2026-08-29 — 3-connector raw data refresh (HN-1 fully-zero + git-repo-1 vault-silent + web-search-1 skip) (2026-08-29T02:18 +0800, committed 9 files per `git show --stat 0f6a901` — including `.last-update.json` + `index.md` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/web-search.md` + `themes/05-robin-research.md` + `themes/index.md`; reducing uncommitted-file count from 11 → 8) + `ef0e144` chore: daily update 2026-08-29 (2026-08-29T02:30 +0800, touched `.last-update.json` only per `git show --stat ef0e144` — CLI metadata update after the `0f6a901` commit) + `37d1ba6` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-29, 2026-08-29T02:30 +0800, the **fifteenth** 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 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + `502281f` 2026-08-27 + `c992dd6` 2026-08-28 + now `37d1ba6` 2026-08-29; committed `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` per `git show --stat 37d1ba6` — the same 4 source-sync files re-touched after the `0f6a901` commit had already cleared them, the same re-bump pattern as the 2026-08-28 fetch); the 8 dirty wiki files at this fetch are `M .last-update.json` + `M quickstart.md` + `M sources/hackernews.md` + `M sources/nocodb.md` + `M sources/ragflow.md` + `M sources/seafile.md` + `M sources/web-search.md` + `M sources/wikijs.md`) |
| --- | --- | --- |
| 2026-08-27T18:25:00Z → 2026-08-28T18:09:00Z | HEAD **unchanged** at `9d4767c7` (**0 new commits**, **0 new mtime changes** — **vault silent for the 3rd consecutive fetch** since the 2026-08-24/25 SECOND 5-paper burst; the 2026-08-25 5-paper cluster remains the most recent vault activity, **3 calendar days stale**; the carry-forward untracked-file set bumps: `Review/zhou2023_computer_vision_microfluidics.md` 16-day → **17-day carry-forward** (14 → **15 fetches silent**, stale carry-forward note per the 2026-08-27 fetch confirming the 2026-08-26 watchlist-downgrade consideration as a one-off) + `celvivo_commercial/` + `templates/` 11-day → **12-day carry-forward** (**the 2026-08-28 fetch confirms the parallel `templates/` + `celvivo_commercial/` entries as one-off alongside the `Review/` subfolder** — both reach the 12-day threshold at this fetch, same duration at which the `Review/` entry was confirmed one-off) + `deepread_40240593/` 4-day → **5-day carry-forward** (mtime unchanged across 4 fetches since creation, working-folder-pipeline hypothesis further weakened); no new untracked dirs) | HEAD `502281f8` → `6024ac7` (**2 new automated commits**: `c992dd6` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-28, 2026-08-28T02:30 +0800, the **fourteenth** 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 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + `502281f` 2026-08-27 + now `c992dd6` 2026-08-28) + `6024ac7` chore: daily update 2026-08-28 (2026-08-28T02:42 +0800, committed 16 files per `git show --stat 6024ac7` — including `.last-update.json` + `commitments.md` + `index.md` + `quickstart.md` + `sources/README.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` + `themes.md` + `themes/index.md` + `themes/05-robin-research.md`; reducing uncommitted-file count from 17 → 5 per the manifest `changedFiles` list); the 5 dirty wiki files at this fetch are `M .last-update.json` + `M index.md` + `M quickstart.md` + `M sources/hackernews.md` + `M sources/web-search.md`) |
| --- | --- | --- |
| 2026-08-26T18:06:00Z → 2026-08-27T18:25:00Z | HEAD **unchanged** at `9d4767c7` (**0 new commits**, **0 new mtime changes** — **vault silent for the 2nd consecutive fetch** since the 2026-08-24/25 SECOND 5-paper burst; the 2026-08-25 5-paper cluster remains the most recent vault activity, **2 calendar days stale**; the carry-forward untracked-file set bumps: `Review/zhou2023_computer_vision_microfluidics.md` 15-day → **16-day carry-forward** (13 → **14 fetches silent**, **2026-08-27 fetch confirms the 2026-08-26 watchlist-downgrade consideration as a one-off**, entry should be demoted to a stale carry-forward note on the next synthesis pass) + `celvivo_commercial/` + `templates/` 10-day → **11-day carry-forward** + `deepread_40240593/` 3-day → **4-day carry-forward**; no new untracked dirs) | HEAD `ebb95c0` → `502281f` (**2 new automated commits**: `f51ff7c` chore: daily update 2026-08-27 (2026-08-27T02:13 +0800, committed 14 of the prior 17 dirty files per `git show --stat f51ff7c` — including `commitments.md` + `index.md` + `themes.md` + `themes/index.md` + `themes/05-robin-research.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/literature.md` + `sources/openwiki-version-drift.md` + `sources/web-search.md` + `sources/README.md` + `quickstart.md` + `.last-update.json`; reducing uncommitted-file count from 17 → 11) + `502281f` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-27, 2026-08-27T02:30 +0800, the **thirteenth** 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 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + now `502281f` 2026-08-27); 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/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` + `M themes/05-robin-research.md`) |
| --- | --- | --- |
| 2026-08-25T18:13:00Z → 2026-08-26T18:06:00Z | HEAD **unchanged** at `9d4767c7` (**0 new commits**, **0 new mtime changes** — **vault silent for the 1st consecutive fetch** since the 2026-08-24/25 SECOND 5-paper burst; the 2026-08-25 5-paper cluster remains the most recent vault activity, 1 calendar day stale; the carry-forward untracked-file set bumps: `Review/zhou2023_computer_vision_microfluidics.md` 14-day → **15-day carry-forward** (12 → **13 fetches silent**) + `celvivo_commercial/` + `templates/` 9-day → **10-day carry-forward** + `deepread_40240593/` 2-day → **3-day carry-forward**; no new untracked dirs) | HEAD `1003b92` → `ebb95c0a` (**2 new automated commits**: `81ac94a` chore: daily update 2026-08-26 (2026-08-26T02:23 +0800, committed 14 of the prior 17 dirty files per `git show --stat 81ac94a` — including `commitments.md` + `index.md` + `themes.md` + `themes/index.md` + `themes/05-robin-research.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/literature.md` + `sources/openwiki-version-drift.md` + `sources/web-search.md` + `sources/README.md` + `quickstart.md` + `.last-update.json`; reducing uncommitted-file count from 11 → 8) + `ebb95c0` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-26, 2026-08-26T02:30 +0800, the **twelfth** 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 + `1003b92` 2026-08-25 + now `ebb95c0` 2026-08-26); the manifest `changedFiles` shows 8 dirty wiki files this fetch — `M .last-update.json` + `M quickstart.md` + `M sources/README.md` + `M sources/hackernews.md` + `M sources/nocodb.md` + `M sources/ragflow.md` + `M sources/seafile.md` + `M sources/wikijs.md`) |
| --- | --- | --- |
| 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)) |
| 2026-08-19T18:08:24Z → 2026-08-20T18:09:15Z | HEAD **unchanged** at `a4fa5a32` (**0 new commits**, **0 new mtime changes** — vault is silent in this 24-hour window for the **4th consecutive fetch**; the 2026-08-16 Quintard 2024 + Guo 2026 cluster remains the most recent vault activity, **4 calendar days stale**) | HEAD `dcb53a2` → `bd30339` (**2 new automated commits**: `a44f284` chore: daily update 2026-08-20 + `bd30339` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-20, the **sixth** 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 + now `bd30339` 2026-08-20)) |
| 2026-08-18T18:10:12Z → 2026-08-19T18:08:24Z | HEAD **unchanged** at `a4fa5a32` (**0 new commits**, **0 new mtime changes** — vault is silent in this 24-hour window for the **3rd consecutive fetch**; the 2026-08-16 Quintard 2024 + Guo 2026 cluster remains the most recent vault activity, **3 calendar days stale**) | HEAD `1fc73ae` → `dcb53a2` (**2 new automated commits**: `7e904ec` chore: daily update 2026-08-19 + `dcb53a2` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-19, the **fifth** 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 + now `dcb53a2` 2026-08-19)) |
| 2026-08-20T18:09:15Z → 2026-08-21T18:09:00Z | HEAD **unchanged** at `a4fa5a32` (**0 new commits**, **0 new mtime changes** — vault is silent in this 24-hour window for the **5th consecutive fetch**; the 2026-08-16 Quintard 2024 + Guo 2026 cluster remains the most recent vault activity, **5 calendar days stale**) | HEAD `bd30339` → `f6c2576` (**2 new automated commits**: `b6dc337` chore: daily update 2026-08-21 + `f6c2576` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-21, the **seventh** 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 + now `f6c2576` 2026-08-21)) |
| 2026-08-21T18:09:00Z → 2026-08-22T18:13:00Z | HEAD **unchanged** at `a4fa5a32` (**0 new commits**, **0 new mtime changes** — vault is silent in this 24-hour window for the **6th consecutive fetch**; the 2026-08-16 Quintard 2024 + Guo 2026 cluster remains the most recent vault activity, **6 calendar days stale**) | HEAD `f6c2576` → `43d4548` (**2 new automated commits**: `d8e2277` chore: daily update 2026-08-22 + `43d4548` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-22, the **eighth** 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 + now `43d4548` 2026-08-22)) |
| 2026-08-22T18:13:00Z → 2026-08-23T18:11:00Z | HEAD **unchanged** at `a4fa5a32` (**0 new commits**, **0 new mtime changes** — vault is silent in this 24-hour window for the **7th consecutive fetch**; the 2026-08-16 Quintard 2024 + Guo 2026 cluster remains the most recent vault activity, **7 calendar days stale**) | HEAD `43d4548` → `a9568d8` (**2 new automated commits**: `8f8f767` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-23, the **ninth** 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 + now `8f8f767` 2026-08-23) + `a9568d8` chore: daily update 2026-08-23 (carried the synthesis-layer edits 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 7 of the prior 9 dirty files** — `sources/git-repo.md` + `sources/index.md` + `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` + `themes/05-robin-research.md` — reducing uncommitted-file count from 9 → 6; the very next synthesis edits from this git-repo-1 2026-08-23T18:11Z run re-touch the remaining 6 files + 1 newly dirty `sources/openwiki-version-drift.md`)) |
| **Net new external evidence** | **2 new paper deep-reads** (from the 2026-08-15T18:07Z → 2026-08-17T18:09Z window): Quintard 2024 Nat Commun microfluidic vascularized organoid chip + Guo 2026 Front Cell Dev Biol organoid ethics systematic review. **2 new untracked directories** (from the same window): `celvivo_commercial/1331651_20260630_131201.pdf` (the 6-30 quote PDF migrated into a new folder) + `templates/类器官IRB申请清单.md` (the IRB application checklist derived from Guo 2026 — Robin's first customer-facing sales ammunition template produced from a single deep-read). The `Review/zhou2023_computer_vision_microfluidics.md` first-entry-in-Review/-subfolder is still untracked, carrying forward from the 2026-08-13 fetch (**11-day carry-forward** at the 2026-08-22T18:13Z fetch — was 10-day at the 2026-08-21T18:09Z fetch — was 9-day at the 2026-08-20T18:09Z fetch). **No new vault evidence in the 2026-08-21T18:09Z → 2026-08-22T18:13Z 24-hour window** | **1 new wiki file** (from the 2026-08-17 daily update `5c70881`): `sources/openwiki-version-drift.md` (auto-generated OpenWiki version-drift monitor; v0.3.1 local → v0.3.3 npm latest as of 2026-08-15T20:00:03Z). **Wiki-side**: the 2026-08-22T18:13Z fetch observed wiki HEAD bump `f6c2576` → `43d4548` — 2 new automated wiki commits (`d8e2277` daily update 2026-08-22 + `43d4548` sources-sync 2026-08-22 — the **eighth** consecutive sources-sync re-applying the `2507925` 2026-08-15 count-data wipe pattern). Synthesis-layer edits accumulated across the prior HN-1 2026-08-13 + HN-1 2026-08-15 + HN-1 2026-08-16 + HN-1 2026-08-17 + HN-1 2026-08-18 + HN-1 2026-08-19 + HN-1 2026-08-20 + HN-1 2026-08-21 + HN-1 2026-08-22 + web-search-1 2026-08-15 + web-search-1 2026-08-17 + web-search-1 2026-08-18 + web-search-1 2026-08-19 + web-search-1 2026-08-20 (skipped) + web-search-1 2026-08-21 (skipped) + web-search-1 2026-08-22 (skipped) + git-repo-1 2026-08-13 + git-repo-1 2026-08-15 + git-repo-1 2026-08-17 + git-repo-1 2026-08-18 + git-repo-1 2026-08-19 + git-repo-1 2026-08-20 + git-repo-1 2026-08-21 + this git-repo-1 2026-08-22 runs are pending the next CLI commit cycle |
| Untracked → committed migrations | **Quintard 2024 file (4 commits)** + **Guo 2026 file (3 commits)** all moved from absent → committed on `main` (in the 2026-08-15T18:07Z → 2026-08-17T18:09Z window); **the 2 new untracked directories** are net-new in the same window. **None** in the 2026-08-17T18:09Z → 2026-08-18T18:10Z 24-hour window (vault silent) or the 2026-08-18T18:10Z → 2026-08-19T18:08Z 24-hour window (vault silent for the 3rd consecutive fetch) or the 2026-08-19T18:08Z → 2026-08-20T18:09Z 24-hour window (vault silent for the 4th consecutive fetch) or the 2026-08-20T18:09Z → 2026-08-21T18:09Z 24-hour window (vault silent for the 5th consecutive fetch) or the 2026-08-21T18:09Z → 2026-08-22T18:13Z 24-hour window (vault silent for the 6th consecutive fetch). | **2026-08-15T18:07Z → 2026-08-17T18:09Z window**: the `sources/index.md` from the 2026-08-15 dirty set was committed by the 2026-08-16 daily update `151d22b`; the remaining 9 dirty files are uncommitted synthesis edits accumulated across the prior HN-1 + web-search-1 + git-repo-1 runs. **2026-08-17T18:09Z → 2026-08-18T18:10Z window**: the `8127797` 2026-08-18 daily update committed a subset of the synthesis-layer edits from the prior HN-1 2026-08-18T18:00Z + git-repo-1 2026-08-17T18:09Z runs (touching `commitments.md` + `index.md` + `quickstart.md` + `sources/{README,git-repo,hackernews,index,literature,nocodb,ragflow,seafile,web-search,wikijs}.md` + `themes/{01-organoid-equipment,05-robin-research}.md` per `git show --stat 8127797`); the 9 dirty files re-appear in the working tree because the very next synthesis edits from this git-repo-1 2026-08-18T18:10Z run re-touch the same files. **2026-08-18T18:10Z → 2026-08-19T18:08Z window**: the `7e904ec` 2026-08-19 daily update committed a subset of the synthesis-layer edits from the prior HN-1 2026-08-19T18:00Z + web-search-1 2026-08-19 + git-repo-1 2026-08-18T18:10Z runs (touching `.last-update.json` + `quickstart.md` + `sources/{README,git-repo,hackernews,index,nocodb,ragflow,seafile,web-search,wikijs}.md` + `themes/05-robin-research.md` per `git show --stat 7e904ec`); the 10 dirty files (`.last-update.json` + `quickstart.md` + `sources/{README,hackernews,index,nocodb,ragflow,seafile,web-search,wikijs}.md`) re-appear in the working tree because the very next synthesis edits from this git-repo-1 2026-08-19T18:08Z run re-touch the same files. **2026-08-19T18:08Z → 2026-08-20T18:09Z window**: the `a44f284` 2026-08-20 daily update committed a subset of the synthesis-layer edits from the prior HN-1 2026-08-20T18:00Z + web-search-1 2026-08-20 (skipped) + git-repo-1 2026-08-19T18:08Z runs; the 10 dirty files re-appear in the working tree because the very next synthesis edits from this git-repo-1 2026-08-20T18:09Z run re-touch the same files. **2026-08-20T18:09Z → 2026-08-21T18:09Z window**: the `b6dc337` 2026-08-21 daily update committed a subset of the synthesis-layer edits from the prior HN-1 2026-08-21T18:00Z + web-search-1 2026-08-21 (skipped) + git-repo-1 2026-08-20T18:09Z runs; **`sources/index.md` was committed by `b6dc337`** (was re-appearing as dirty since 2026-08-16 daily update). The 9 dirty files (`.last-update.json` + `quickstart.md` + `sources/{README,hackernews,nocodb,ragflow,seafile,web-search,wikijs}.md`) re-appear in the working tree because the very next synthesis edits from this git-repo-1 2026-08-21T18:09Z run re-touch the same files. **2026-08-21T18:09Z → 2026-08-22T18:13Z window**: the `d8e2277` 2026-08-22 daily update committed a subset of the synthesis-layer edits from the prior HN-1 2026-08-22T18:00Z + web-search-1 2026-08-22 (skipped) + git-repo-1 2026-08-21T18:09Z runs; the 9 dirty files (`.last-update.json` + `quickstart.md` + `sources/{README,hackernews,nocodb,ragflow,seafile,web-search,wikijs}.md`) re-appear in the working tree because the very next synthesis edits from this git-repo-1 2026-08-22T18:13Z run re-touch the same files. The 9 dirty files are awaiting the next CLI commit cycle |
| **Operational issue carried over from prior runs** | n/a | **`2507925` 2026-08-15 sources-sync bug** + the 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` + 2026-08-25 `1003b92` + 2026-08-26 `ebb95c0` + 2026-08-27 `502281f` + 2026-08-28 `c992dd6` sources-syncs (which re-applied the same operational pattern as `2507925` — NocoDB / Wiki.js / RAGFlow count values stayed zero across all **14** sources-syncs). The on-disk `~/.openwiki/connectors/web-search/config.json` is unaffected — this is a wiki-side CRON issue with the auto-source-sync job, not a connector config issue. Recorded for traceability on `/sources/git-repo.md` Notable-entity § "2026-08-15 sources-sync bug" and on each affected `/sources/{nocodb,ragflow,seafile,wikijs}.md` page. The data is recoverable from `git show 8ddc6d9:sources/nocodb.md` etc. for any future recovery commit |
## Vault navigation index
The vault uses a numbered top-level layout. Scripts, caches, and `temp*`
working folders are excluded from this index.
| Dir | Purpose | Size hint |
| --- | --- | --- |
| `01-Active-Sales/` | Active sales pipeline files (board + per-account) | 6 .md |
| `02-Active-Deals/` | Deal-level active docs | 1 .md |
| `02-Clients/`, `02-Contacts/` | Client & contact records | sparse |
| `03-Product/` | Product briefs (e.g. 3Brain-Maxwell comparison) | 1 .md |
| `03-Resources/Agents/` | Distributor / agent profiles | a handful |
| `03-Resources/End-Customers/` | End-customer dossiers (3Brain MEA accounts, etc.) | 11+ .md |
| `03-Resources/ITX-24h-Host/` | Personal 24h Hermes-Agent / AI-workflow host build config (2026-07-31 untracked; not yet on `main`) | 1 .md |
| `04-Literature/` | Paper deep-reads + curated vendor PDFs | see breakdown |
| `05-Documents/Contracts/` | Signed/pending contracts (Celvivo subfolder) | — |
| `05-Documents/Products/` | Vendor-facing product docs (Celvivo/Industrial-Customers) | — |
| `05-Documents/{Proposals,Quotes,Visit-Plans}/` | Active commercial docs | — |
| `05-Products/` | In-house product briefs (MappingLab family) | 2 .md |
| `06-Sales/Competitors/` | Competitor tracking | — |
| `06-Sales/Configurations/` | Product configurations | — |
| `06-Sales/Content/{FAQ,Pain-Points,PPT-Scripts,Success-Stories,Training-Materials,推文模板}/` | Sales content library | — |
| `06-Sales/{Price-List,Product-Mapping,Recommendation-Engine}/` | Sales tooling | — |
| `99-Templates/` | Reusable Obsidian templates | 14 .md |
| `memory/` | Daily reports, weekly digests, `.dreams`, archive | 147 .md |
### `04-Literature/Deep-Reads/` breakdown
Markdown file counts per deep-read subfolder:
| Subfolder | .md count |
| --- | --- |
| `Organoid/` | 661 (+2 from 2026-08-16 — Quintard 2024 Nat Commun microfluidic vascularized organoid chip + Guo 2026 Front Cell Dev Biol organoid ethics systematic review) |
| `04-Literature/Deep-Reads/` root | +5 new files on 2026-08-23 single-shot LDR burst — CelVivo_Shear_Stress_AppNote_2026 + Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid + Tian_2025_NatCommun_Epicardium_mTOR + Kim_2025_NatCommun_Liquid_Metal_3D_MEA + Ajongbolo_2025_Cells_Brain_Organoids_Review (all in vault root, not in a per-vendor subfolder — this is a **non-standard pattern** vs the prior per-vendor subfolder discipline, see Notable-entity § "2026-08-23 root-level LDR burst") |
| `Celvivo/` | 142 |
| `3Brain/` | 136 |
| `Cellink/` | 129 |
| `Organoid-List/` | 51 |
| `Product-Reports/` | 38 |
| `Brain/` | 11 |
| `Brain-Tumor/` | 9 |
| `Cancer/` | 6 |
| `Liver/` | 6 |
| `Other/` | 6 |
| `RegenMed/` | 1 |
| `3Brain MEA/` | 3 |
| `Cardiac/` | 2 |
| `Kidney/` | 2 |
| `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; **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; **15-day carry-forward** at 2026-08-26 fetch, **13 fetches silent** — structural signal continues to weaken, subfolder is more likely one-off than recurring; **16-day carry-forward** at 2026-08-27 fetch, **14 fetches silent** — **2026-08-27 fetch confirms the 2026-08-26 watchlist-downgrade consideration as a one-off**, the entry should be demoted to a stale carry-forward note on the next synthesis pass; **17-day carry-forward** at 2026-08-28 fetch, **15 fetches silent** — **2026-08-28 fetch confirms the 2026-08-27 confirmation as a stale carry-forward note**; the entry should be **demoted to "stale / not recurring" carry-forward note** on the next synthesis pass alongside the parallel `templates/` + `celvivo_commercial/` confirmations; **18-day carry-forward** at 2026-08-29 fetch, **16 fetches silent** — carrying forward unchanged as a stale carry-forward note; **19-day carry-forward** at 2026-08-30 fetch, **17 fetches silent** — carrying forward unchanged as a stale carry-forward note) |
| `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; **10-day carry-forward** at 2026-08-26 fetch; **11-day carry-forward** at 2026-08-27 fetch — **approaching confirmed one-off interpretation alongside the `Review/` entry**; **12-day carry-forward** at 2026-08-28 fetch — **11 fetches silent** — **now confirmed one-off alongside the `Review/` + `celvivo_commercial/` entries** at the 2026-08-28 fetch; the entry should be demoted to a stale carry-forward note on the next synthesis pass; **13-day carry-forward** at 2026-08-29 fetch — **12 fetches silent** — carrying forward unchanged as a stale carry-forward note; **14-day carry-forward** at 2026-08-30 fetch — **13 fetches silent** — carrying forward unchanged as a stale carry-forward note) |
| `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; **10-day carry-forward** at 2026-08-26 fetch; **11-day carry-forward** at 2026-08-27 fetch — **approaching confirmed one-off interpretation alongside the `Review/` + `templates/` entries**; **12-day carry-forward** at 2026-08-28 fetch — **11 fetches silent** — **now confirmed one-off alongside the `Review/` + `templates/` entries** at the 2026-08-28 fetch; the entry should be demoted to a stale carry-forward note on the next synthesis pass; **13-day carry-forward** at 2026-08-29 fetch — **12 fetches silent** — carrying forward unchanged as a stale carry-forward note; **14-day carry-forward** at 2026-08-30 fetch — **13 fetches silent** — carrying forward unchanged as a stale carry-forward note) |
| `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) |
| `CelVivo/` (capital V, parallel to lowercase `Celvivo/`) | 5 (new as of 2026-08-31 — `stewart-2023-ba5-xbb-neurotropic-brain-organoids.md` + `aiello-2025-brain-organoid-reproducibility.md` + `nguyen-2024-jev-g4-2022-australia-brain-organoids.md` + `miao-2025-vascularized-lung-gut-organoids.md` + `yan-2024-tmem106b-sars-cov2-ace2-independent.md`; **all 5 single-shot LDR entries committed 2026-08-31 13:05-13:42 +0800**; 4 of 5 are brain organoid infectious-disease / reproducibility papers using CelVivo ClinoStar/ClinoReactor + 1 is vascularized lung/gut; the new capital-V subfolder sits at `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` parallel to the existing lowercase `04-Literature/Deep-Reads/Celvivo/` 143-file subfolder — Robin's first parallel-naming deep-read subfolder convention; subfolder semantics: QIMR Berghofer Suhrbier/Rawle viral-neurotropism brain-organoid line (Stewart + Nguyen + Yan) + CelVivo ApS co-authored reproducibility (Aiello) + vascularized lung/gut (Miao)) |
Total ≈ 1,222 deep-read notes on `main` (+5 new LDR files from the 2026-08-31 cluster on top of +4 from the 2026-08-24/25 cluster + +5 from the 2026-08-23/24 single-shot LDR burst + +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 **3 consecutive single-day 5-commit windows** (2026-08-23/24 + 2026-08-24/25 + **2026-08-31**), totalling **16 commits / 14 new files** in 8 calendar days (2026-08-23 → 2026-08-31).
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 2026-08-23/24 burst). The 2026-08-31 single-day 5-paper LDR burst (5 papers in `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` parallel capital-V subfolder) is the most recent committed deep-read cluster; the 2026-08-24/25 cluster (Vascularized-Organoids + Cardiac-Organoids + Skin-Organoids subfolders) remains the prior committed cluster; the 2026-08-23/24 single-shot LDR burst (5 papers at vault root) is the prior-prior committed cluster; the 2026-08-16 Quintard 2024 + Guo 2026 cluster remains the prior-prior-prior committed cluster; the 2026-08-07 / 2026-08-08 cluster (Microbioreactor + Cells) remains the prior-prior-prior-prior committed cluster. The 2026-08-31 cluster is **CelVivo-anchored exclusively** (all 5 papers use CelVivo ClinoStar/ClinoReactor; 1 paper — Aiello 2025 — has CelVivo ApS as a co-author affiliation), reinforcing the 4 of 5 from the 2026-08-23/24 cluster that were also CelVivo-aligned. 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.
## Distributor map refresh (2026-08-07)
Robin uploaded a refreshed `b7f52af896c1e3a9.xlsx` on 2026-08-07 11:11,
producing **8 new `*2026-0807.md` regional files** + a new
`全国经销商地图-2026-0807.md` index + a new **product-association
index** (`_known_associations.md`) + a new `_meta.json` reflecting the
259-dealer tally. The 2026-07-24 baseline (`*2026-0724.md` × 7 + index)
remains in the repo but is now stale.
What changed in the 2026-08-07 baseline vs the 2026-07-24 baseline:
| Dimension | 2026-07-24 (`_meta.json`) | 2026-08-07 (`全国经销商地图-2026-0807.md`) |
| --- | --- | --- |
| Total dealers | 261 (明细表口径) | 259 (公司数量汇总) |
| xlsx sha256 | `3afd448edcf3a9673848da0de2c554e6a4b22d7329b988695ca242c8bc8c10cf` | (re-uploaded with 8-04 同名 + 新增 2-3 家) |
| Region table | 华北 74 / 华东 68 / 华南 62 / 山东 25 / 湖北 19 / 西北 6 / 西南 7 | 华北 72 / 华东 68 / 华南 62 / 山东 25 / 湖北 19 / 西北 6 / 西南 7 |
| 华北 count | 74 | 72 (-2) |
| Hook 4 output | (none) | 4 dealer-management hooks + `_known_associations.md` |
The numeric 261 vs 259 difference is still rooted in the **华北 表 74 vs
汇总 72** discrepancy (two unnamed companies — 序号 63 / 67 — leave the
明细表 2 rows above the 汇总表); the 2026-08-07 baseline carries the
same data anomaly plus a new structural artifact: **济南成全生物科技
(曹沛起) is registered in both `华北-2026-0807.md` and `山东-2026-0807.md`
(legitimate cross-region duplicate)** — this is the only CelVivo
ClinoStar agent in the 259-dealer list and is the thread Robin should
follow to close the `agent-dong-huiqun-celvivo` open question.
### `_known_associations.md` (2026-08-07) — product → dealer mapping
The new index file `02-Clients/Agents/_known_associations.md` is the
canonical hook-4 output Robin needs to evaluate before the next
Chinese-region dealer visit. Key mappings surfaced (5 direct hits):
| Product line | 261-dealer表 命中 | 关联客户 / 商机 |
| --- | --- | --- |
| **CelVivo (ClinoStar / ClinoReactor)** | **济南成全生物科技有限公司 (曹沛起)** — registered in both 华北 + 山东 (cross-region, 2 次) | 董慧群关联 (待 Robin 确认是否同公司) |
| **FemtoBiomed (CellShot / PROLIVA)** | 0 direct hits (9X Bio / 汇佰生物 is the direct intermediate, not in the 261 dealer list) | TriArm Therapeutics (翁靖傑, 上海 CGT/CAR-T) — 128 万 Phase1 / 8-10 至 8-14 现场 demo |
| **3Brain (HD-MEA)** | 0 direct hits | — |
| **Cellink (BIO X)** | 0 direct hits | — |
| **西南医大 心研所 殴贤红** | 2 dealers: 成都百乐 (杨军, 钻石级 1亿, Bio-Rad / Sartorius / Oxford Nanopore / Cytek / Leica, 覆盖川渝黔藏) + 成都立德赛 (川渝云贵陕) | (待 Robin 决策) |
**Hook-4 questions** (Robin 优先补全, per `_known_associations.md`):
1. 董慧群 is which specific technical contact at 济南成全 — or is she at a
different CelVivo-代理?
2. 西南医大 殴贤红 → 成都百乐 vs 成都立德赛 — which dealer first?
3. 邓昊伦 (02-Contacts/) 蛇类神经方向 → 3Brain HD-MEA 拜访?
4. 261 dealer 表 has 0 3Brain / Cellink 代理 — is the dealer list
incomplete, or does Robin need to actively recruit those dealers?
Log these as a new commitment on `/commitments.md`
(`distributor-8-07-association-followup`) and as updates to
`/open-questions.md` (the `agent-dong-huiqun-celvivo` question now
**partially answered** — agency identified but personal contact
fields still 待补).
## Notable entities surfaced by the vault (structural hints only)
- **2026-08-31 cluster — THIRD consecutive single-day 5-paper LDR burst + NEW capital-V `CelVivo/` subfolder (vault HEAD `9d4767c7` → `391e4713`, 5 new vault commits)** — the 2026-08-31T18:09Z fetch observed the **THIRD consecutive single-day 5-paper LDR burst** at vault HEAD, ending a **5-calendar-day vault silence streak** since the 2026-08-24/25 cluster. **Combined with the prior 2026-08-23/24 (5 papers) + 2026-08-24/25 (5 papers) clusters, 15 LDR files in 8 calendar days (2026-08-23 → 2026-08-31), the largest sustained 8-day research output** in Robin's vault activity log; **all 3 clusters are CelVivo-anchored** (5/5 in 2026-08-23/24 + 4/5 in 2026-08-24/25 via the `9aa2af4c` retrofit + 5/5 in 2026-08-31). The 2026-08-31 cluster creates **1 NEW `04-Literature/Deep-Reads/` subfolder**: `CelVivo/` (capital-V) at `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` — Robin's **first parallel-naming deep-read subfolder convention** (parallel to the existing lowercase `04-Literature/Deep-Reads/Celvivo/` 142-file subfolder, total subfolder count goes from ~22 → ~23 in 8 days). The 5-commit cluster is (chronological, all on 2026-08-31 +0800 between 13:05 and 13:42): `eb24ab72` Stewart 2023 Front Microbiol BA.5/XBB neurotropic brain organoids → `030f31ed` Aiello 2025 EMBO reports reproducible brain organoids (CelVivo ApS co-author) → `fad7e21e` Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids → `4fca0123` Miao 2025 Cell vascularized lung/gut organoids → `391e4713` Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids. **Subfolder content mix**: 4 of 5 are brain organoids (the QIMR Berghofer Suhrbier/Rawle viral-neurotropism line + CelVivo ApS co-authored reproducibility) + 1 is vascularized lung/gut (Miao — companion to the 2026-08-08 flywheel-sync Miao 2025 v2 deep-read). The 2026-08-31 cluster did **NOT** receive the `9aa2af4c` vendor-mapping retrofit commit (no companion retrofit commit this cluster, unlike the 2026-08-24/25 cluster which had `9aa2af4c` as the 3rd of 5 commits). **Net-new external evidence** in this run (git-repo-1 2026-08-31). Synthesis routes into `/themes/01-organoid-equipment.md` (CelVivo ClinoStar/ClinoReactor evidence on brain + lung/gut infectious-disease models) + `/themes/05-robin-research.md` (vault-snapshot refresh + the 3rd 5-paper cluster + the parallel-naming convention) + `/sources/literature.md` (last-30-days table) + `/commitments.md` (5 new commitment rows for the 5 new papers). **Track on next fetch** whether (a) Robin produces deep-read synthesis pages for any of the 5 papers (none currently exist), (b) the 2026-08-31 cluster is retrofitted with the `9aa2af4c` 5-vendor mapping pattern (the absence of a retrofit commit this cluster may indicate the vendor mapping was applied at the original `git add` time, or that Robin has adopted a different convention), (c) more entries land in the new `CelVivo/` (capital-V) subfolder (currently 5 files; ≥3 was the threshold for "subfolder is in active use" but already at the threshold on first observation, indicating strong subfolder commitment), (d) the parallel capital-V vs lowercase `Celvivo/` subfolder naming convention is formalized in vault conventions (currently appears to be a convention shift without explicit documentation), (e) the working-folder `deepread_40240593/` pipeline finally gets committed or shows mtime movement at the 2026-08-31 fetch (**8th fetch silent on directory mtime**, hypothesis further weakened).
- **2026-08-31 Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids (CelVivo) (single-shot LDR entry `391e4713`, ~40 lines per `git show --stat 391e4713`)** — `obsidian-vault/04-Literature/Deep-Reads/CelVivo/yan-2024-tmem106b-sars-cov2-ace2-independent.md`. Yan K, Dumenil T, Stewart R, Bishop CR, Nguyen W, Suhrbier A*, Rawle DJ* (Cell Reports 43, 114921, 2024-11-26; DOI 10.1016/j.celrep.2024.114921; QIMR Berghofer Medical Research Institute; **`ollama_audit: 4/4 passed`**). The paper establishes: (i) **CRISPR screen identifies TMEM106B / heparan sulfate / endocytosis as ACE2-independent SARS-CoV-2 entry mediators** (S-E484D mutant bypassing ACE2 dependence); (ii) **human cortical brain organoids (CelVivo ClinoStar) show MA1 strain enhanced neurotropism** — higher titer + more infected cells vs ancestral variants; (iii) **K18-hACE2 mice show MA1 enhanced disease + lower survival**; (iv) **in vivo null result** — wild-type / Ifnar-/- mice do not show increased neuroinvasion; Ace2-/- mice cannot be infected via lung. Companion to **Stewart 2023** + **Nguyen 2024** in the same cluster — the 3 QIMR Berghofer Suhrbier/Rawle viral-neurotropism papers (all SARS-CoV-2 / JEV / brain organoid) form a 3-paper line validating the **CelVivo ClinoStar cortical brain organoid model for viral-neurotropism studies**. **Vendor-anchor mapping**: CelVivo ClinoStar ⭐⭐⭐⭐ (cortex brain organoid for neurotropic virus infection; 3-paper Suhrbier/Rawle line validates the platform for viral pathogenesis research). **Net-new external evidence** in this run (git-repo-1 2026-08-31). **Track on next fetch** whether Robin produces a deep-read synthesis page and whether the 3-paper Suhrbier/Rawle line folds into a single `suhrbier-rawle-celvivo-brain-organoid-virology-cluster` synthesis page.
- **2026-08-31 Miao 2025 Cell vascularized lung/gut organoids (CelVivo ClinoReactor) (single-shot LDR entry `4fca0123`)** — `obsidian-vault/04-Literature/Deep-Reads/CelVivo/miao-2025-vascularized-lung-gut-organoids.md`. Miao Y, Pek NM, Tan C, Chen Y-W, Guo M*, Gu M* (Cell 188, 1-19, 2025-08-07; DOI 10.1016/j.cell.2025.05.041; **`ollama_audit: 7/7 passed`** + 8-08 精简版已升级完整版). The paper establishes: **mesoderm-endoderm co-differentiation enables organotypic vascularization in lung + gut organoids** — a single-organoid protocol for hiPSC → lung + gut with embedded vasculature (rather than the prior 2-step "differentiate organoid then add vasculature"). **FoxF1** is identified as a key mesodermal TF driving vascular incorporation. Companion to the 2026-08-08 flywheel-sync `Miao2025_Cell_v2.md` deep-read (which was Robin's first deep-read of this paper); the 2026-08-31 re-read in the new `CelVivo/` capital-V subfolder is a **re-read with the CelVivo-anchored vendor perspective**. **Vendor-anchor mapping**: CelVivo ClinoReactor ⭐⭐⭐⭐⭐ (3-track lung/gut/vascular co-development requires low-shear suspension culture for the mesodermal-endodermal co-differentiation step; ClinoReactor is the canonical hardware). **Net-new external evidence** in this run. **Track on next fetch** whether Robin's existing Miao 2025 deep-read synthesis page at `/sources/literature-miao-2025-cell-vascularization-v2-deepread.md` gets a retrofitted vendor-mapping update referencing the 2026-08-31 re-read.
- **2026-08-31 Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids (CelVivo) (single-shot LDR entry `fad7e21e`)** — `obsidian-vault/04-Literature/Deep-Reads/CelVivo/nguyen-2024-jev-g4-2022-australia-brain-organoids.md`. Nguyen W, Gyawali N, Stewart R, Tang B, Cox AL, Yan K, Larcher T, Bishop CR, Wood N, Devine GJ, Suhrbier A, Rawle DJ (npj Viruses [Nature Portfolio], Article 25, 2024; DOI 10.1038/s44298-024-00025-5; QIMR Berghofer Medical Research Institute + INRAE; **`ollama_audit: 8/8 passed`**). The paper characterizes a **Japanese Encephalitis virus genotype 4 isolate from the 2022 Australian outbreak** — uses CelVivo ClinoStar brain organoids to validate the isolate's neurotropism in human cortical tissue (vs mouse models). **Flavivirus** family — companion to the SARS-CoV-2 / BA.5/XBB / TMEM106B cluster (Stewart + Yan) in establishing the **CelVivo ClinoStar brain organoid platform for neurotropic virus characterization**. **Vendor-anchor mapping**: CelVivo ClinoStar ⭐⭐⭐⭐. **Net-new external evidence** in this run. **Track on next fetch** whether Robin produces a deep-read synthesis page and whether the JEV-Australia outbreak context yields Australian academic / public-health customer entry material.
- **2026-08-31 Aiello 2025 EMBO reports reproducible brain organoids (CelVivo ClinoReactor; CelVivo ApS co-author) (single-shot LDR entry `030f31ed`)** — `obsidian-vault/04-Literature/Deep-Reads/CelVivo/aiello-2025-brain-organoid-reproducibility.md`. Aiello G, Nemir M, Vidimova B, Ramel C, Viguie J, Ravera A, Wrzesinski K*, Bagni C* (EMBO reports, Volume 26, December 2025, 6209-6239; DOI 10.1038/s44319-025-00619-x; 洛桑大学 + 罗马 Tor Vergata 大学 + 西北大学[南非] + **CelVivo ApS[丹麦] as co-author affiliation**; **`ollama_audit: 6/6 passed`**). The paper establishes: (i) **controlled fluid dynamics** through CelVivo ClinoReactor improves brain-organoid reproducibility (multi-batch + multi-iPSC line PCA shows CV < 15% vs static culture > 30%); (ii) **scRNA-seq OXPHOS profiling** validates metabolic maturation in ClinoReactor vs static; (iii) **multi-marker IHC** (SOX2/Nestin/PAX6 + DCX + TBR1/SATB2/MAP2) confirms cortical layer identity. This is the **first paper in the cluster where CelVivo ApS appears as a co-author affiliation** (vs the prior papers where CelVivo is just the bioreactor vendor) — significant credibility signal for the **CelVivo ClinoReactor as the canonical hardware for reproducible brain organoid culture**. Companion to the **2026-08-23 Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid** deep-read (Robin did a 2-deep-read cycle: biorxiv preprint version + EMBO reports final version, 8 days apart). **Vendor-anchor mapping**: CelVivo ClinoReactor ⭐⭐⭐⭐⭐ (CelVivo ApS is a co-author, validating the platform via academic-CelVivo collaboration). **Net-new external evidence** in this run. **Track on next fetch** whether Robin produces a deep-read synthesis page at `/sources/literature-aiello-2025-brain-organoid-reproducibility-deepread.md` and whether the 2026-08-23 Aiello deep-read synthesis page gets retrofitted to reference the 2026-08-31 EMBO reports final version.
- **2026-08-31 Stewart 2023 Front Microbiol BA.5/XBB neurotropic brain organoids (CelVivo) (single-shot LDR entry `eb24ab72`)** — `obsidian-vault/04-Literature/Deep-Reads/CelVivo/stewart-2023-ba5-xbb-neurotropic-brain-organoids.md`. Stewart R, Yan K, Ellis SA, Bishop CR, Dumenil T, Tang B, Nguyen W, Larcher T, Parry R, Sng JDJ, Khromykh AA, Sullivan RKP, Lor M, Meunier FA, Rawle DJ*, Suhrbier A* (Frontiers in Microbiology, Volume 14, Article 1320856, 2023-11-23; DOI 10.3389/fmicb.2023.1320856; QIMR Berghofer Medical Research Institute + University of Queensland; **`ollama_audit: 6/6 passed`**). The paper establishes: **SARS-CoV-2 omicron BA.5 + XBB variants have increased neurotropic potential over BA.1** — K18-hACE2 mice show enhanced brain infection + human brain organoids (CelVivo ClinoStar) confirm the BA.5/XBB enhancement in cortical tissue. Companion to **Yan 2024 TMEM106B** in the same QIMR Berghofer Suhrbier/Rawle viral-neurotropism line. **Vendor-anchor mapping**: CelVivo ClinoStar ⭐⭐⭐⭐. **Net-new external evidence** in this run. **Track on next fetch** whether Robin produces a deep-read synthesis page and whether the BA.5/XBB neurotropism data has implications for Robin's Chinese pharma R&D / CDMO customers working on SARS-CoV-2 long-COVID neurological complications.
- **2026-08-23 root-level LDR burst (5 papers, single-shot entries, vault HEAD bump `a4fa5a32` → `fb017e4f`)** — **largest single-day LDR cluster 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 files landed at `obsidian-vault/04-Literature/Deep-Reads/` **root** (not in a per-vendor subfolder) on 2026-08-23/24 between 07:50 +0800 and 16:39 +0800; **non-standard pattern** vs the prior per-vendor subfolder discipline (every prior LDR cluster since 2026-07-28 has sorted into `Organoid/` / `Celvivo/` / `3Brain/` / `Cells/` etc.). 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). Commit timestamps `2026-08-23` (Western time) + `2026-08-24` (UTC mtime): (a) **`ad4abcde` 2026-08-24 feat: Ajongbolo 2025 Cells 脑类器官综述精读 (Wiki.js 1743)** — `Ajongbolo_2025_Cells_Brain_Organoids_Review.md`, the canonical review paper of the cluster, 11,367 bytes; (b) **`5f02489a` 2026-08-24 feat: Kim 2025 NatCommun 液态金属 3D MEA 精读 (Wiki.js 1744)** — `Kim_2025_NatCommun_Liquid_Metal_3D_MEA.md`, 13,567 bytes, the **3D-MEA competitor paper** of the cluster; (c) **`40b357b8` 2026-08-24 feat: Tian 2025 NatCommun 心外膜 mTOR 精读 (Wiki.js 1745)** — `Tian_2025_NatCommun_Epicardium_mTOR.md`, 15,578 bytes, the **cardiac-epicardium paper** of the cluster; (d) **`f2118a62` 2026-08-24 feat: Aiello & Bagni 2025 biorxiv Rotating Chamber brain organoid 精读 (Wiki.js 1746)** — `Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid.md`, 11,731 bytes, the **CelVivo-KB-derived brain-organoid CFD paper** of the cluster; (e) **`fb017e4f` 2026-08-24 feat: CelVivo App Note 2026 shear stress ClinoStar vs orbital shaker (Wiki.js 1747)** — `CelVivo_Shear_Stress_AppNote_2026.md`, 10,145 bytes, the **vendor App Note** of the cluster. **3 of the 5 papers are CelVivo-aligned**: the App Note (direct CelVivo document) + Aiello (CelVivo KB-sourced) + Ajongbolo review (mentions ClinoStar in the synthesis). **1 is a 3D-MEA competitor**: Kim EGaIn magnetic-reshapable 3D MEA. **1 is a cardiac epicardium paper**: Tian mTOR. The cluster anchors **4 of 5 to Robin's 4 vendor product lines** (CelVivo=3, 3Brain-adjacent=1) plus 1 cardiac expansion. Synthesis routes into `/themes/01-organoid-equipment.md` (CelVivo evidence) + `/themes/05-robin-research.md` (vault-snapshot refresh + deep-reads breakdown) + `/sources/literature.md` (last-30-days table). **Net-new external evidence** in this run. **Track on next fetch** whether (a) more LDR files land in vault root (extending the root-level pattern) or migrate to per-vendor subfolders on next SOP revision, (b) the `deepread_40240593/` pipeline workspace gets committed (per the Notable-entity entry below), (c) the existing MOC pattern at `04-Literature/Deep-Reads/MOCs/MOC-类器官与3D培养.md` gets a 2026-08-23/24 LDR-cycle entry.
- **CelVivo App Note 2026 shear stress ClinoStar vs orbital shaker (2026-08-23, single-shot LDR entry `fb017e4f`, Wiki.js 1747)** — `obsidian-vault/04-Literature/Deep-Reads/CelVivo_Shear_Stress_AppNote_2026.md` (10,145 bytes). Stougaard Borgen Løschenkohl + Sedighi Frandsen, CelVivo Application Note 2026, sourced from RAGFlow CelVivo KB (1555e5b2..., Robin 8-24 上传). The note establishes **head-to-head comparison** of ClinoStar® vs orbital shaker for **3D 类器官/球体培养** (HepG2/C3A 15-day + embedded Caco-2 肠 + brain organoid). Core findings: (i) **low shear stress ClinoStar preserves cytoskeletal integrity** — phalloidin/DAPI 染色 shows ClinoStar F-actin 排列规则 + 形态紧凑 + 细胞间内聚性强 vs orbital shaker F-actin 散布 + 形态松散 + 内聚性下降 (4x + 20x dual magnification); (ii) **15-day standardized workflow** — same source cells (HepG2/C3A) + same pre-conditioning (SP5D 24孔球形板 Kugelmeiers, 1000 cells/aggregate) + same end-point assays (image + ATP + BCA + fluorescent staining + microscopy) + 3 bio-replicates per condition; (iii) **multi-model transferability** — embedded Caco-2 肠 + brain organoid both show ClinoStar advantage → vendor claim "low shear stress sensitive cell class (肝/肠/脑来源)" validated across 3 model systems. **Net-new external evidence** in this run (git-repo-1 2026-08-24). **Highest commercial-relevance paper of the cluster**: this is the **canonical CelVivo vs-orbital-shaker competitive-killer document** and is Robin's first **vendor App Note deep-read** (vs. 1 primary research paper + 1 review paper from prior clusters). **Track on next fetch** whether (a) Robin produces a deep-read synthesis page at `/sources/literature-celvivo-shear-stress-appnote-2026-deepread.md` mirroring the prior pattern, (b) the App Note is folded into `06-Sales/Content/Training-Materials/` (the existing CelVivo赋能培训 v1-v9 cluster could absorb the head-to-head comparison data as a new PPT module), (c) the App Note spawns a new sales commitment similar to the existing `celvivo-clinoreactor-thewell-bioscience-xeno-free` item.
- **Aiello & Bagni 2025 biorxiv Rotating Chamber brain organoid CFD (2026-08-23, single-shot LDR entry `f2118a62`, Wiki.js 1746)** — `obsidian-vault/04-Literature/Deep-Reads/Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid.md` (11,731 bytes). Aiello F, Bagni C et al., biorxiv preprint (the EMBO Reports submission version `Aiello_Bagni_EMBO R_050325`), 2026-08-24 Robin 从 CelVivo KB 找到的 PDF. The paper is **the first CFD-quantified Rotating Chamber (RC) low-shear-stress study** in Robin's deep-read set: (i) RC geometry: outer Ø 78.3 mm × H 24.2 mm, inner cavity Ø 37.7 mm × H 8.8 mm (reserved for organoid growth space); (ii) **COMSOL Multiphysics 6.2 CFD simulation shows cavity shear stress < 20 mPa** (extremely low vs. standard stirred/shaken systems) — **first quantitative number** on RC shear-stress field; (iii) **multi-density organoid shear-stress validation** — relative density 1010/1020/1030 vs medium 1000 confirms shear-stress uniformity across density range + 0-300 objects all experience stable low shear; (iv) **morphological consistency** — multi-batch + multi-cell-line brain organoid cultures show **CV < 15%** (vs static culture CV > 30%); (v) cortical cell type recapitulation (SOX2/Nestin/PAX6 + DCX + TBR1/SATB2/MAP2 multi-marker IHC) + scRNA-seq OXPHOS metabolic profiling. **Net-new external evidence** in this run. **Vendor-anchor mapping**: Aiello paper is **CelVivo ClinoStar-adjacent** (uses RC system which is the ClinoStar simplified geometry) + 3Brain HD-MEA-adjacent (cortical organoid electrophysiology read-out). The < 20 mPa quantitative claim is **direct ammunition** for the existing ClinoStar ⭐⭐⭐⭐ vendor-positioning pitch — no prior paper in Robin's deep-read set provides the **quantitative CFD number** for ClinoStar's low-shear-stress value proposition. **Track on next fetch** whether Robin produces a deep-read synthesis page; the deep-read pipeline currently does not carry an Aiello synthesis page.
- **Tian 2025 Nat Commun hiPSC epicardium mTOR maturation (2026-08-23, single-shot LDR entry `40b357b8`, Wiki.js 1745)** — `obsidian-vault/04-Literature/Deep-Reads/Tian_2025_NatCommun_Epicardium_mTOR.md` (15,578 bytes, the **largest** of the 5 new LDR files). Tian Y, Lucena-Cacace A, Tani K et al., Nat Commun 2025, DOI 10.1038/s41467-025-60934-8. The paper establishes: (i) **mTOR inhibition drives epicardium maturation** — Torin1 (dual mTORC1/2 inhibitor, 200 nM) on mouse E12 embryonic heart explants upregulates WT1 (mature epicardium marker) + downregulates EMT markers (SNAI1/2) + downregulates cell cycle (MKI67/PCNA) + downregulates mTOR pathway; bulk RNA-seq PCA shows 28.53% (PC1) + 36.01% (PC2) variance explained = significant transcriptome shift toward **adult** epicardium identity; (ii) **mTORC1/2 dual inhibition is critical** — Rapamycin (single mTORC1) alone is insufficient; mTORC2 is the key node; (iii) **hiPSC-derived epicardium maturation with Torin1** — qPCR validates mature markers (TJP1/WT1/TBX18/ALDH1A2/CDH18) up + EMT markers (SNAI1/SNAI2/CDH2/CDH1) down + proliferation markers (MKI67/PCNA/MCM2) down + fatty-acid metabolism maturation (PDK4/PPARGC1A/SIRT1/FASN/SREBF1); bulk RNA-seq with 379 DEGs; Torin1 vs adult epicardium GSE84085 heatmap confirms adult-like profile; YBX3 + MAFF identified as Torin1-specific TFs via Venn diagram + siRNA knockdown; (iv) **paracrine effect on cardiomyocyte maturation** — mature epicardium (Torin1-treated) co-cultured with hiPSC ventricular cardiomyocyte EBs for 10 days upregulates TNNI3 (adult cardiomyocyte marker) → epicardium-to-cardiomyocyte maturation cross-talk via paracrine signaling. **Net-new external evidence** in this run. **Application domain**: cardiac organoid regeneration; not directly anchored to CelVivo/3Brain/Cellink/Femtobiomed product lines (no vendor rating callouts in the deep-read) but **fits the broad cardiac application-domain bucket** that Robin's wiki scope covers. **Track on next fetch** whether (a) Robin produces a deep-read synthesis page, (b) the Tian paper routes into any commitment — there is no cardiac-specific commitment in `/commitments.md` yet.
- **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 → 2026-08-30, still uncommitted)** — `deepread_40240593/` is the **first** new untracked directory added at the 2026-08-24T18:05Z 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 (still 2026-08-30 at this fetch — directory mtime unchanged across the 2026-08-25 + 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + 2026-08-30 fetches, no pipeline activity since initial creation; **6 fetches silent on directory mtime** at this fetch). **Structural significance** (carried forward from 2026-08-24): (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 + the 2026-08-24/25 SECOND 5-paper burst means Robin is producing pipeline output faster than the manual commit cycle — **no commit despite a SECOND 5-paper burst landing at vault HEAD**. **Carry-forward status** (2026-08-30): untracked, **7-day carry-forward** (was 6-day at the 2026-08-29T18:10Z fetch, 5-day at the 2026-08-28T18:09Z fetch, 4-day at the 2026-08-27T18:25Z fetch, 3-day at the 2026-08-26T18:06Z fetch, 2-day at the 2026-08-25T18:13Z fetch, 1-day at the 2026-08-24T18:05Z fetch), future-commit candidate; **6 fetches silent on directory mtime** since the SECOND 5-paper burst landed. **Watchlist signal at the 2026-08-30 fetch**: the `deepread_40240593/` directory has not been committed despite the 2026-08-24/25 cluster producing 5 more committed LDR files, none of which appear to have routed through `deepread_<slug>/` working folders (the directory mtime is still 2026-08-24 16:31 +0800, unchanged since initial creation); the working-folder pipeline hypothesis has **further weakened evidence** at this fetch — if Robin had used the working folders for the 2026-08-24/25 burst, the directory mtime would have advanced to 2026-08-25 +0800; the absence of mtime movement in the 2026-08-25 + 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + 2026-08-30 fetches (**6 consecutive fetches silent on directory mtime**) suggests the working-folder pipeline may have been abandoned, formalized differently, or batched without intermediate commit. **Track on next fetch** whether (a) the directory is committed, (b) the directory mtime finally advances (which would re-strengthen the working-folder pipeline hypothesis), (c) the `deepread_<PMID>` vs `04-Literature/Deep-Reads/<slug>` separation is formalized in vault conventions, (d) Robin documents the working-folder pipeline somewhere (commit message / vault README / blog post). **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 2026-08-30, 19-day carry-forward, **one-off interpretation confirmed**, now a stale carry-forward note)** — `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 2026-08-30 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 + 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + 2026-08-30 fetches, **0 progress in the 2026-08-13 → 2026-08-30 408-hour window**, **17 consecutive fetches silent on the file**). **Watchlist signal demoted to "stale / not recurring" carry-forward note at the 2026-08-27 fetch, now confirmed at the 2026-08-28 fetch + 2026-08-29 fetch + 2026-08-30 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 2026-08-26 watchlist-downgrade consideration ("a 2026-08-27 fetch that lands the file as still-uncommitted would confirm the one-off interpretation"), the `Review/` subfolder at the 2026-08-30 fetch is **still single-entry, still untracked** — the structural signal is **confirmed as one-off**, **19-day carry-forward** with no commit, no follow-up paper landed in the subfolder across **17 consecutive fetches**, and 4 consecutive bursts of LDR activity (2026-08-23/24 + 2026-08-24/25 + 2026-08-23/24 + 2026-08-24/25) landing at the vault HEAD without routing any review-type paper to the `Review/` subfolder. The `Review/` subfolder entry is **now demoted to a "stale / not recurring" carry-forward note** rather than continuing as an active watchlist entry. No synthesis routes until the file is committed; if committed on a future fetch, the entry could be re-promoted to watchlist with the new mtime / commit evidence.
- **`templates/` subfolder — first entry (2026-08-16, NEW → 2026-08-30, still uncommitted, **one-off interpretation confirmed** at 2026-08-28 fetch alongside the `Review/` + `celvivo_commercial/` subfolders, carrying forward unchanged at 2026-08-29 + 2026-08-30 fetches)** — `templates/类器官IRB申请清单.md` (180 lines, mtime 2026-08-16, untracked) is the **first file in a new `templates/` directory** at the vault root. The file is Robin's **first customer-facing sales ammunition template produced from a single deep-read** (the Guo 2026 IRB ethics systematic review). Content: 7 mandatory IRB review points checklist (样本来源/知情同意/数据隐私/共培养主体性/3R 动物福利/跨境监管/长期保存与终止使用) + 5 customer Q&A ("类器官研究要不要 IRB 申请?" / "类器官共培养产品怎么申请 IRB?" / "类器官跨境研究怎么报?" / "3R 原则怎么写?" / "类器官 + 免疫细胞共培养 = CAR-T 体外培养, 算不算新生物体? 伦理上算什么?") + China vs International flow comparison table + 10-row 申请附件清单 + 7 references (Guo 2026 + ISSCR 2021 + OHRP 2016 + GDPR 2018 + China 2023 + China 2019 + Cambridge 2020). The template's `version: v1.0 (2026-08-16, Robin 8-16 实战沉淀)` and `Robin 业务定位: 类器官厂家给三甲医院 IRB 申请的标准模板 + Robin 客户培训材料核心` framing makes it explicit that this is the canonical "Robin 培训客户 IRB 申请" core material. **Structural significance** (carried forward from 2026-08-16): the `templates/` directory is new — none of the existing top-level folders (`01-Active-Sales/` / `02-Clients/` / `02-Active-Deals/` / `02-Contacts/` / `03-Product/` / `03-Resources/` / `04-Literature/` / `05-Documents/` / `06-Sales/` / `99-Templates/` / `memory/`) provides a vendor-agnostic customer-training-artifact slot at the vault root. The Obsidian vault already has `99-Templates/` for reusable Obsidian templates (note templates, daily-report templates — per `99-Templates/` size hint 14 .md), but the new `templates/` directory is **for customer-facing sales ammunition**, not Obsidian note templates — a different artifact type. The naming convention overlaps with `99-Templates/` and may need disambiguation; Robin's intent (per the file header) is for this `templates/` to be the **canonical customer-training artifact directory**, distinct from `99-Templates/` Obsidian-note templates. **Customer-entry scenarios** called out in the template: (a) 类器官厂家研发负责人 = IRB 申请准备, (b) Robin 客户开发 = 培训客户 IRB 申请核心材料, (c) 医院 IRB 委员会 = 类器官研究 IRB 审查标准参考, (d) 学术合作方 = 跨境合作时多国法规差异对照. **Carry-forward status** (2026-08-30): untracked, **14-day carry-forward** since first observation (was 13-day at the 2026-08-29T18:10Z fetch, 12-day at the 2026-08-28T18:09Z fetch, 11-day at the 2026-08-27T18:25Z fetch, 10-day at the 2026-08-26T18:06Z fetch, 9-day at the 2026-08-25T18:13Z fetch, 8-day at the 2026-08-24T18:05Z fetch, 7-day at the 2026-08-23T18:11Z fetch, 6-day at the 2026-08-22T18:13Z fetch, 5-day at the 2026-08-21T18:09Z fetch), future-commit candidate; **13 fetches silent since the directory first appeared** (first observed at the 2026-08-17T18:09Z fetch). The file mtime is still 2026-08-16 +0800 (unchanged since initial creation) — **no template authoring activity since the original 2026-08-16 creation**, despite 4 consecutive bursts of LDR activity (Quintard + Guo 2026-08-16 + the 2026-08-23 5-paper burst + the 2026-08-25 5-paper burst) that could have generated follow-up templates. **Watchlist signal demoted to "stale / not recurring" carry-forward note at the 2026-08-28 fetch**: the `templates/` directory has remained single-entry + uncommitted for **14 consecutive fetches** (same carry-forward duration at which the `Review/` entry was confirmed one-off) with no follow-up template landing despite multiple LDR bursts that could plausibly have generated sales ammunition templates — the entry is **confirmed as one-off alongside the `Review/` + `celvivo_commercial/` subfolders** at the 2026-08-28 fetch, and the 2026-08-29 + 2026-08-30 fetches confirm the carry-forward unchanged. **Track on next fetch** whether (a) Robin commits the file to `main`, (b) more templates land in the directory (extending the customer-training-artifact slot), (c) the `templates/` and `99-Templates/` naming overlap gets resolved (rename / docs / conventions), (d) any of the 4 prior LDR bursts produces a follow-up template (which would re-strengthen the sales-ammunition-pipeline hypothesis). Synthesis routes into `/themes/05-robin-research.md` (sales ammunition pipeline section).
- **`celvivo_commercial/` subfolder — first entry (2026-08-17, NEW → 2026-08-30, still uncommitted, **one-off interpretation confirmed** at 2026-08-28 fetch alongside the `Review/` + `templates/` subfolders, carrying forward unchanged at 2026-08-29 + 2026-08-30 fetches)** — `celvivo_commercial/1331651_20260630_131201.pdf` (56 KB PDF, mtime 2026-08-17, untracked) is the **first file in a new `celvivo_commercial/` directory** at the vault root. The PDF is the existing 6-30 quote PDF that Robin migrated into a new folder. The file is **a quote PDF**, not a synthesis target — the on-disk evidence is the existing 6-30 quote document that already exists in `05-Documents/Products/Celvivo/Industrial-Customers/` (per the 2026-08-15 synthesis-policy section above, "commercial docs (8 files: Exhibit 1 Price Book / Exhibit 3 SuperUser certification / Huibai demo discount agreement / 惠百 PO 盖章版 / Celvivo Distribution Agreement 2026 Huibai Bio / 1331651_20260630_131201 (6-30 quote) / Packing Slip Ordre 726_1 / Packing Slip Ordre 726_2)"). **Structural significance** (carried forward from 2026-08-17): the `celvivo_commercial/` directory is new — Robin has migrated the 6-30 quote out of wherever it was previously (presumably a working folder or `05-Documents/Products/Celvivo/` deep path) into a top-level dedicated directory. **The migration is unfinished** — only 1 file in the new directory; if Robin intends the directory to consolidate all 8 commercial docs from `05-Documents/Products/Celvivo/Industrial-Customers/`, the other 7 files (Exhibit 1 Price Book / Exhibit 3 SuperUser certification / Huibai demo discount agreement / 惠百 PO 盖章版 / Celvivo Distribution Agreement 2026 / Packing Slip Ordre 726_1 / Packing Slip Ordre 726_2) should eventually land here too. **No synthesis routes** until Robin commits the file or migrates more docs into the directory. Carry-forward status (2026-08-30): untracked, single-entry, **14-day carry-forward** since first observation (was 13-day at the 2026-08-29T18:10Z fetch, 12-day at the 2026-08-28T18:09Z fetch, 11-day at the 2026-08-27T18:25Z fetch, 10-day at the 2026-08-26T18:06Z fetch, 9-day at the 2026-08-25T18:13Z fetch, 8-day at the 2026-08-24T18:05Z fetch, 7-day at the 2026-08-23T18:11Z fetch, 6-day at the 2026-08-22T18:13Z fetch, 5-day at the 2026-08-21T18:09Z fetch); **13 fetches silent since the directory first appeared** (first observed at the 2026-08-17T18:09Z fetch). The file mtime is still 2026-08-17 +0800 (unchanged since initial creation) — **no commercial-doc migration activity since the original 2026-08-17 migration**, despite the 2026-08-25 SECOND 5-paper burst landing 5 more LDR commits in the vault (none of which involved commercial-doc migration). **Watchlist signal demoted to "stale / not recurring" carry-forward note at the 2026-08-28 fetch**: the `celvivo_commercial/` directory has remained single-entry + uncommitted for **14 consecutive fetches** (same carry-forward duration at which the `Review/` entry was confirmed one-off) with no follow-up commercial-doc migration despite 4 LDR bursts landing at vault HEAD; the entry is **confirmed as one-off alongside the `Review/` + `templates/` subfolders** at the 2026-08-28 fetch, and the 2026-08-29 + 2026-08-30 fetches confirm the carry-forward unchanged. Track on next fetch whether (a) the file gets committed, (b) more commercial docs migrate into the directory (which would re-strengthen the consolidation hypothesis), (c) the directory mtime finally advances.
- **2026-08-15 sources-sync bug — count-data wipe (operational)** — the `2507925e27b83b4f9d2e6f3b9c939d081a90f9f2` `chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-15)` commit at 2026-08-15 +0800 02:31 committed **empty count values** for NocoDB / Wiki.js / RAGFlow (SeaFile was already empty so the commit was a no-op there): (a) NocoDB: 6614 → **0** total records, with all 13 per-table counts (brain_organoid_literature / intestinal_organoid_literature / Celvivo_literature / cardiac_organoid_literature / cancer_organoid_literature / liver_organoid_literature / other_organoid_literature / kidney_organoid_literature / retinal_organoid_literature / Cellink_literature / organoid_literature_old / lung_organoid_literature / 3Brain_literature) cleared to empty cells; (b) SeaFile: libraries table unchanged (was empty in `1737454` already — a separate, older cron issue not introduced by `2507925`); (c) Wiki.js: 83 → **0** unique pages, ID range 22..1704 → **0..0**, Locale 分布 → empty, Top-level 路径分布 → empty; (d) RAGFlow: landing 200 → **000**, `/api/v1/health` 404 → **000**, `/api/v1/datasets` 401 → **000**. The header lines on each affected `/sources/{nocodb,ragflow,seafile,wikijs}.md` page still report `上次同步: 2026-08-14T18:30:42Z` (the prior successful sync timestamp), but the body count values are wiped. **Probable root cause**: the auto-source-sync CRON job ran but the underlying NocoDB / Wiki.js / RAGFlow API calls failed (likely the same operational issue already documented on `/sources/web-search.md` and `/sources/README.md` — runtime registry disagreement on `enabled: true` vs. disabled); the script committed the empty values instead of skipping the commit on failure. **Impact**: 3 source pages now show misleading zero/null values (NocoDB / Wiki.js / RAGFlow); Tavily / HN / git-repo synthesis is unaffected. **Recovery**: the wiped data is recoverable from the prior wiki commit (`git show 1737454:sources/nocodb.md` etc. will restore the pre-wipe state). This run restored the wiped data on all 3 affected pages (plus an operational note documenting the bug) so the wiki is internally consistent again. **Wiki-synthesis concern**: **none** — the synthesis layer (themes / commitments / open-questions / personal-logistics) is independent of the source-page counters. **Operational concern**: **yes** — the auto-source-sync job should (a) check connectivity before committing, (b) skip the commit on API failure rather than committing empty values, or (c) preserve the prior counter values when a fresh pull returns null/empty. Recorded for traceability here + on each affected `/sources/{nocodb,ragflow,seafile,wikijs}.md` page.
- **Liang 2026 liver organoid fibrosis platform (2026-08-12)** — `04-Literature/Deep-Reads/Liver/2026-08-12_Liang_2026_SciRep_liver_organoid_fibrosis_platform.md` (170 lines; `[[MOC-类器官与3D培养]]` already names this paper via `related:` back-link). The paper is **the net-new external evidence** this run (git-repo-1 2026-08-12) brought into the vault; see synthesis at `/themes/01-organoid-equipment.md` § CelVivo evidence (added 2026-08-12) and `/commitments.md` `liang-2026-celvivo-clinostar-positioning`. Single-paper LDR cycle: 4 commits (`e542c977` → `8699a154` → `aacba7aa` → `297f106d`) walked Robin's standard 3-stage SOP on the same file (186 lines → 105+/122- page 946 rewrite → page 934 修齐 micro-revisions). The 4-star "与我们的产品" table on the paper lists **CelVivo ClinoStar ⭐⭐⭐⭐** (P1-P10 长程扩增对应旋转培养 30+ 天无剪切; HSC 静止态在模拟微重力下 7+ 天维持) + **CelVivo ClinoReactor ⭐⭐⭐⭐** (单组织 3 轨道分通道灌流; TGFβ 时间程序精确切换) — **parallel CelVivo ClinoStar rating 5 to Miao 2025 v2's ClinoStar rating 5** from the 2026-08-08 flywheel-sync, but for liver organoid (long-term maturation + fibrosis modeling) rather than lung organoid (vascularization). 7 SeaFile Fig (Fig1-7) + 4-paper 参考文献 (Huch 2013 / Huch 2015 / Clevers 2016). Customer-entry: 药企临床前 (抗纤维化药筛) + 临床肝活检中心 (1-2 mg → 3 周药敏) + 学术 PI (2D vs 3D 旋转 efficiency). **MOC linkage**: the paper's `related:` field already names `[[MOC-类器官与3D培养]]` (the first MOC, created 2026-08-10) — confirming the MOC pattern is in active use on real deep-reads.
- **CelVivo industrial customers program** — a dedicated subfolder under
`05-Documents/Products/Celvivo/Industrial-Customers/` holds `CelVivo_中国工业
客户开发研究报告` (v1 + v2), `客户管线定位_1页图`, and `工业客户开发手册-v3`.
This is a self-contained CelVivo China commercial effort.
- **CelVivo sales training cluster** — `06-Sales/Content/Training-Materials/`
contains a `Robin稿生成通字稿` family (v3–v6), a `CelVivo赋能培训` PowerPoint
family (v1–v9, depth-flavored edits), and a `销售基础话术包` pair. Versions
progress from 基础 → 5大管线 → 深度版 → 终稿修正 → 销量仅看.
- **3Brain end-customer dossier set** — 11+ dossiers under
`03-Resources/End-Customers/` covering 神经所 (上海), 北京大学, 北京天坛医院,
浙大一附院, 中科院昆明动物所, 西南医科大学, 贵州医科大学, plus TCM accounts
at 云南中医药大学 and 天津创新中药.
- **CelVivo distributor technical contact (2026-07-28, partially resolved
2026-08-07)** — `02-Clients/Agents/董慧群.md` is the first profile under
the `02-Clients/Agents/` bucket (frontmatter `type: agent`, role:
代理商技术同事, products: CelVivo ClinoStar / ClinoReactor). The
2026-08-07 `_known_associations.md` index now identifies the CelVivo
dealer as **济南成全生物科技 (曹沛起)** — the only ClinoStar agent in
the 259-dealer list, registered in both 华北 + 山东. Robin still needs
to confirm: (a) is 董慧群 the same agency? (b) phone / WeChat / served
end-customers / opportunities. The agency-side gap is now closed.
- **ITX 24h host build (first observed 2026-07-31; still untracked)** —
`03-Resources/ITX-24h-Host/ITX_24h_Host_v18_Config_2026-07-31.md` is a
top-level bucket first observed between the 2026-07-30T18:13 fetch and the
2026-07-31T18:08 fetch; it remains untracked. Single file: Robin's personal
24h server build plan for hosting Hermes Agent + AI workflow stack — mATX +
i5-12400 + DDR4-2666 32G + 板载 Realtek 1Gb + Intel PRO/1000 GT 双网卡 NAS
隔离, ¥2,985.82, 10/11 parts arrived, planned hostnames/roles:
192.168.31.100 (主力机 SSH) vs 10.10.10.254 (RAGFlow / NAS RAGFlow API).
Workflow-tooling priority LOW (not vendor-anchored), so it does **not** earn a
`/themes.md` row, but the build remains a source-anchored personal-infra work
item and was promoted to `/commitments.md` as
`itx-24h-host-build-2026-q3` (Owner: me) for the post-assembly steps (Ubuntu
Server 22.04 install + 双网卡静态 IP + Hermes Agent install + 24h soak test).
- **Cells + 2026-08-08 cluster** — Fernandez Vallone 2026 Cells (hiPSC
brain organoids for THSDC chemical screening, NAMs platform) is the
first `04-Literature/Deep-Reads/Cells/` entry. New application domain
(toxicology + NAMs) compared to the prior Brain / Cancer / Liver
buckets. CelVivo + 3Brain application scenarios called out in tags.
- **Microbioreactor + 2026-08-07 cluster** — Rosero 2026 Front Bioeng
Biotechnol Microbioreactor design Mini Review is the first
`04-Literature/Deep-Reads/Microbioreactor/` entry. Cross-vendor
adjacent (CelVivo ClinoStar / Cellink BIO X / FemtoBiomed CellShot).
Landed in NocoDB `Robin_Picked_Papers` (PMID 42516424, Wiki.js ID
1696).
- **Parfitt 2024 Nat Commun (DJ1 LOF midbrain organoid + PD)** —
untracked file `04-Literature/Deep-Reads/Brain/2026-08-06_Parfitt_GM_et_al_NatCommun_2024_DJ1_LOF_midbrain_organoid_PD.md`
(15,972 bytes, mtime 2026-08-06). DJ1 LOF through astrocyte lysosomal
dysfunction → AGE → α-syn → DA neuron death; CelVivo + 3Brain
application scenarios in tags. Not yet on `main`; pending Robin
commit.
- **CellSweep** — referenced in the wiki goal focus areas; not surfaced as a
top-level vault folder in this run, so it likely lives under `Work/` or
`scripts/` (outside the navigation index).
- **Phase A metadata batch + first MOC (2026-08-10)** — Robin ran a
frontmatter-hygiene + MOC-discipline sprint on 2026-08-10:
(a) **`d97b39ed` Phase A 批量** standardized 6 deep-read notes with the
6-field frontmatter (doi / journal / year / **volume** / **pages** /
**authors** array / pmid) — `Organoids 2026 review` +
`CelVivo PAH Metabolomics` + `Shin 2024 thalamocortical organoids
22q11ds` + `Fernandez Vallone 2026 Cells THSDC` + `Liu 2026 NBME
shape-conformal organoid` + `类器官综述_CMOS_HD_MEA_类器官电生理_2026-06-05`;
(b) **`6b717aef` MOC 方案 1 样品** created the **first MOC** at
`04-Literature/Deep-Reads/MOCs/MOC-类器官与3D培养.md` (95 lines,
沙牛《AI 时代的 Obsidian 公开课》课时 1 pattern, `type: moc`) and added
`related:` back-link frontmatter to 7 papers; (c) **`3b929c2f` wang2024
方案 2 样品** added 7 image alt descriptions on top of the 6-field
frontmatter for `wang2024-org-on-chip.md`. The MOC's own `related:`
list already names `[[MOC-3Brain-HD-MEA]]` as the next planned MOC,
plus `[[02-Clients/Agents/_known_associations]]` and
`[[02-Active-Deals/CellShot-TriArm-Demo-计划-v2-老师版-2026-07-20]]`,
so the pattern is expected to extend. None of the changes add new
external evidence — the 6 papers already existed on `main`; this
commit set only normalizes their metadata and cross-references. The
MOC creation is the first durable structural artifact on the
knowledge-graph side and is worth tracking on the next git-repo
fetch.
## Synthesis policy for this source
- **This run (2026-08-31, git-repo-1 18:09Z):** **5 new vault commits** in the 2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window — vault HEAD bumped from `9d4767c7` (2026-08-30T18:06Z fetch) to `391e4713` (5 calendar days of vault silence ended; **THIRD consecutive single-day 5-paper LDR burst** after the 2026-08-23/24 + 2026-08-24/25 clusters, all CelVivo-anchored). **Net-new external evidence**: 5 new CelVivo-anchored brain-organoid infectious-disease + reproducibility LDR files (`eb24ab72` Stewart 2023 BA.5/XBB + `030f31ed` Aiello 2025 reproducible brain organoids [CelVivo ApS co-author] + `fad7e21e` Nguyen 2024 JEV G4 + `4fca0123` Miao 2025 vascularized lung/gut + `391e4713` Yan 2024 TMEM106B SARS-CoV-2 ACE2-independent) — **all 5 land in the NEW `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` subfolder** (capital-V, parallel to the existing lowercase `Celvivo/` 142-file subfolder; Robin's first parallel-naming deep-read subfolder convention); 4 of 5 are brain organoids (the QIMR Berghofer Suhrbier/Rawle viral-neurotropism line + CelVivo ApS co-authored reproducibility) + 1 vascularized lung/gut (Miao); **cluster does NOT receive the `9aa2af4c` post-publish vendor-mapping retrofit commit** (the 2026-08-24/25 cluster had `9aa2af4c` as the 3rd of 5 commits; the 2026-08-31 cluster does not have a comparable retrofit). The carry-forward untracked-file set bumps: `Review/zhou2023_computer_vision_microfluidics.md` **19-day → 20-day carry-forward** (**17 → 18 fetches silent**, stale carry-forward note) + `celvivo_commercial/` + `templates/` **14-day → 15-day carry-forward** (both confirmed one-off alongside the `Review/` subfolder, carrying forward unchanged at the 2026-08-31 fetch) + `deepread_40240593/` **7-day → 8-day carry-forward** (mtime unchanged across **7 consecutive silent fetches** since creation, working-folder-pipeline hypothesis further weakened at this fetch — **8th fetch silent on directory mtime**, no signs of pipeline activity despite 3 LDR clusters in 8 days). **Wiki-side**: **2 new automated wiki commits** landed in the 2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window — `c9e2770` chore: daily update 2026-08-31 (2026-08-31T02:18 +0800, committed 15 files per `git show --stat c9e2770` — including `.last-update.json` + `index.md` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/nocodb.md` + `sources/openwiki-version-drift.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` + `sources/wikijs.md` + `themes/05-robin-research.md` + `themes/index.md`; reducing uncommitted-file count from 11 → 5 per the manifest `changedFiles` list at the 2026-08-31T18:09Z fetch) + `9582dea` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-31, 2026-08-31T02:30 +0800, the **seventeenth** 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 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + `502281f` 2026-08-27 + `c992dd6` 2026-08-28 + `37d1ba6` 2026-08-29 + `d56da3a` 2026-08-30 + now `9582dea` 2026-08-31; per `git show --stat 9582dea` the commit touched `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` — the same 4 source-sync files that the `c9e2770` daily update had already cleared were re-touched by the sources-sync that landed later in the window; same re-bump pattern as the 2026-08-28 + 2026-08-29 + 2026-08-30 fetches). The manifest `changedFiles` shows **11 dirty wiki files** this fetch — `M .last-update.json` + `M quickstart.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` + `M themes.md` + `M themes/03-ai-agents.md` — up from the 9-dirty-file baseline at the 2026-08-30T18:06Z fetch because the `9582dea` sources-sync re-touched the 4 source-sync files that the `c9e2770` daily update had committed + the HN-1 2026-08-31 Almanac (YC S26) synthesis pass added 3 NEW dirty files (`sources/literature.md` + `themes.md` + `themes/03-ai-agents.md`) for the `agent-memory-architecture` row refresh. **Synthesis-layer impact**: vault delta is **material** — 5 new vault commits + 1 new subfolder + 5 new single-shot LDR files + 4 of 5 papers brain organoid infectious-disease / reproducibility + 1 vascularized lung/gut (Miao companion to the 2026-08-08 Miao v2 deep-read). Synthesis routes into: (a) `/sources/git-repo.md` (this page) — refreshed frontmatter (vault HEAD `9d4767c7` → `391e4713` + tags bumped to include the 2026-08-31 cluster + timestamp `2026-08-31T18:09:00Z`) + Connector section refreshed (vault HEAD + wiki HEAD `d56da3a` → `9582dea` + the **seventeenth** consecutive sources-sync note + the 11-dirty-file working tree state + the new `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` capital-V subfolder) + `obsidian-vault — working-tree status (2026-08-31)` section refreshed (5 new vault commits + 5 new file mtime changes + the new `CelVivo/` capital-V subfolder added to the breakdown + 0 new untracked dirs at this fetch + the carry-forward 20/15/8-day + the 8th fetch silent on `deepread_40240593/` directory mtime) + Recent-commits-for-vault table extended by 5 entries + Recent-commits-for-wiki table extended by 2 entries + Summary-of-last-48-hours table extended by 1 new window row (2026-08-30T18:06Z → 2026-08-31T18:09Z) + `04-Literature/Deep-Reads/` breakdown table extended by 1 new subfolder row (`CelVivo/` capital-V, 5 files) + Total ≈ 1,217 → **1,222** deep-read notes on `main` + Robin's LDR cluster pattern update from "2 consecutive 5-commit windows" → "**3 consecutive single-day 5-commit windows**" (2026-08-23/24 + 2026-08-24/25 + 2026-08-31) + 6 new entries to the Notable-entity section (cluster overview + Yan + Miao + Nguyen + Aiello + Stewart) + Synthesis-policy section refreshed (this run as "This run" + the previous 2026-08-30 0-vault-commit run demoted to "Previous run"); (b) `/themes/05-robin-research.md` — vault-snapshot metadata refreshed (fetch timestamp → `2026-08-31T18:09:00Z`, HEAD bumped `9d4767c7` → `391e4713`, the THIRD 5-paper LDR cluster noted + 1 new subfolder added to the breakdown + `celvivo_commercial/` + `templates/` 14-day → **15-day** + `Review/` 19-day → **20-day** + `deepread_40240593/` 7-day → **8-day**); (c) `/commitments.md` — 5 new commitment entries corresponding to the 5 new LDR papers (each with Owner: me + Source: git-repo-1 2026-08-31 + Status: open); (d) `/sources/literature.md` — 5 new rows to the "Last 30 days of deep reads" table under a new `2026-08-31` subsection; (e) `/quickstart.md` — added "Latest update — git-repo-1 (2026-08-31T18:09Z)" paragraph; updated the Backlog git-repo entry to reflect the new wiki HEAD `9582dea` + 2 new automated wiki commits + the carry-forward 11 uncommitted synthesis-layer edits + the **seventeenth** consecutive sources-sync note + the THIRD 5-paper LDR burst detail; (f) `/sources/README.md` — refreshed Active connectors Git repo row + Connector roll Git repo row to mention the 2026-08-31 18:09 UTC fetch + the **seventeenth** consecutive sources-sync + the 5 new vault commits + the new `CelVivo/` capital-V subfolder. **No `/themes.md` row added** — the existing `class-organoid-3d-bioprinting` row's evidence footprint is materially strengthened (3 of 5 papers vendor-aligned to CelVivo directly + 1 companion to Miao 2025 v2) 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. **No `/open-questions.md` row added** — none of the 5 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. Prior run (this section demoted): git-repo-1 2026-08-30T18:06Z.
- **This run (2026-08-30, git-repo-1 18:06Z):** **0 new vault commits** in the 2026-08-29T18:10Z → 2026-08-30T18:06Z 24-hour window — vault HEAD unchanged at `9d4767c7` (same as the 2026-08-29T18:10Z + 2026-08-28T18:09Z + 2026-08-27T18:25Z + 2026-08-26T18:06Z + 2026-08-25T18:13Z fetches); **vault silent for the 5th consecutive fetch** since the 2026-08-24/25 SECOND 5-paper burst, **5 calendar days stale**. **No new external evidence** in this run. The 2026-08-24/25 cluster remains the most recent committed vault activity (Tevonian + Yang + Shen + Zhai + the `9aa2af4c` retrofit). The carry-forward untracked-file set bumps: `Review/zhou2023_computer_vision_microfluidics.md` **18-day → 19-day carry-forward** (**16 → 17 fetches silent**, stale carry-forward note per the 2026-08-27 fetch confirming the 2026-08-26 watchlist-downgrade consideration as a one-off) + `celvivo_commercial/` + `templates/` **13-day → 14-day carry-forward** (**both confirmed one-off alongside the `Review/` subfolder at the 2026-08-28 fetch, carrying forward unchanged at the 2026-08-29 + 2026-08-30 fetches** — same duration at which the `Review/` entry was confirmed one-off) + `deepread_40240593/` **6-day → 7-day carry-forward** (mtime unchanged across **6 consecutive silent fetches** since creation, working-folder-pipeline hypothesis further weakened at this fetch). **Wiki-side**: **2 new automated wiki commits** landed in the 2026-08-29T18:10Z → 2026-08-30T18:06Z 24-hour window — `7eed6ca` chore: daily update 2026-08-30 (2026-08-30 02:?? +0800; per `git show --stat 7eed6ca` the commit touched 13 files from the prior dirty set including `.last-update.json` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` + `sources/wikijs.md` + `themes/05-robin-research.md` + `themes/index.md`; reducing uncommitted-file count from 8 → 5 per the manifest `changedFiles` list at the 2026-08-30T18:06Z fetch) + `d56da3a` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-30, 2026-08-30 02:30 +0800, the **sixteenth** 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 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + `502281f` 2026-08-27 + `c992dd6` 2026-08-28 + `37d1ba6` 2026-08-29 + now `d56da3a` 2026-08-30; per `git show --stat d56da3a` the commit touched `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` — the same 4 source-sync files that the `7eed6ca` daily update had already cleared were re-touched by the sources-sync that landed later in the window; same re-bump pattern as the 2026-08-28 + 2026-08-29 fetches). The manifest `changedFiles` shows **9 dirty wiki files** this fetch — `M .last-update.json` + `M index.md` + `M quickstart.md` + `M sources/hackernews.md` + `M sources/nocodb.md` + `M sources/openwiki-version-drift.md` + `M sources/ragflow.md` + `M sources/seafile.md` + `M sources/wikijs.md` — up from the 8-dirty-file baseline at the 2026-08-29T18:10Z fetch because the `d56da3a` sources-sync re-touched the 4 source-sync files that the `7eed6ca` daily update had committed + the CLI metadata cycle re-touched `sources/openwiki-version-drift.md` + `index.md`; the very next synthesis edits from the HN-1 + web-search-1 + git-repo-1 runs will re-touch these files. **Synthesis-layer impact**: **none** — vault delta is empty (no new commits, no new mtime changes) and the wiki delta is automated maintenance only; the synthesis layer (themes / commitments / open-questions / personal-logistics) is independent of the wiki-side automated maintenance commits. **No `/themes.md` row change, no `/commitments.md` row, no `/open-questions.md` row, no `/personal-logistics.md` item** at this fetch. The 3 of 4 carry-forward untracked directories that have now reached the `Review/` confirmation threshold (16+ day for `Review/`, 13+ day for `templates/` + `celvivo_commercial/`) are **all confirmed as one-off / stale / not recurring** at this fetch (same status as 2026-08-28 + 2026-08-29); on the next synthesis pass they should be **demoted from watchlist to stale carry-forward notes** in `/themes/05-robin-research.md` and the per-page working-tree status tables. The `deepread_40240593/` pipeline workspace at 7-day carry-forward + 6 consecutive silent fetches since the 2026-08-24/25 burst continues to weaken the working-folder pipeline hypothesis — on the next synthesis pass the entry should also be demoted from watchlist to stale carry-forward note. Prior run (this section demoted): git-repo-1 2026-08-29T18:10Z.
- **This run (2026-08-29, git-repo-1 18:10Z):** **0 new vault commits** in the 2026-08-28T18:09Z → 2026-08-29T18:10Z 24-hour window — vault HEAD unchanged at `9d4767c7` (same as the 2026-08-27T18:25Z + 2026-08-26T18:06Z + 2026-08-25T18:13Z fetches); **vault silent for the 4th consecutive fetch** since the 2026-08-24/25 SECOND 5-paper burst, **4 calendar days stale**. **No new external evidence** in this run. The 2026-08-24/25 cluster remains the most recent committed vault activity (Tevonian + Yang + Shen + Zhai + the `9aa2af4c` retrofit). The carry-forward untracked-file set bumps: `Review/zhou2023_computer_vision_microfluidics.md` **17-day → 18-day carry-forward** (**15 → 16 fetches silent**, stale carry-forward note per the 2026-08-27 fetch confirming the 2026-08-26 watchlist-downgrade consideration as a one-off) + `celvivo_commercial/` + `templates/` **12-day → 13-day carry-forward** (**the 2026-08-28 fetch confirmed the parallel `templates/` + `celvivo_commercial/` entries as one-off alongside the `Review/` subfolder** — both are confirmed one-off at the 2026-08-29 fetch, carrying forward unchanged; same duration at which the `Review/` entry was confirmed one-off) + `deepread_40240593/` **5-day → 6-day carry-forward** (mtime unchanged across **5 consecutive silent fetches** since creation, working-folder-pipeline hypothesis further weakened). **Wiki-side**: **3 new automated wiki commits** landed in the 2026-08-28T18:09Z → 2026-08-29T18:10Z 24-hour window — `0f6a901` chore: daily update 2026-08-29 — 3-connector raw data refresh (HN-1 fully-zero + git-repo-1 vault-silent + web-search-1 skip) (2026-08-29 02:18 +0800; per `git show --stat 0f6a901` the commit touched 9 files including `.last-update.json` + `index.md` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/web-search.md` + `themes/05-robin-research.md` + `themes/index.md`; reducing uncommitted-file count from 11 → 8) + `ef0e144` chore: daily update 2026-08-29 (2026-08-29 02:30 +0800; per `git show --stat ef0e144` the commit touched `.last-update.json` only — CLI metadata update after the `0f6a901` commit) + `37d1ba6` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-29, 2026-08-29 02:30 +0800, the **fifteenth** 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 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + `502281f` 2026-08-27 + `c992dd6` 2026-08-28 + now `37d1ba6` 2026-08-29; per `git show --stat 37d1ba6` the commit touched `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` — the same 4 source-sync files that the `0f6a901` daily update had already cleared were re-touched by the sources-sync that landed later in the window; same re-bump pattern as the 2026-08-28 fetch where the sources-sync re-touched 4 source-sync files that the daily update had cleared). The manifest `changedFiles` shows 8 dirty wiki files this fetch — `M .last-update.json` + `M quickstart.md` + `M sources/hackernews.md` + `M sources/nocodb.md` + `M sources/ragflow.md` + `M sources/seafile.md` + `M sources/web-search.md` + `M sources/wikijs.md` — the very next synthesis edits from the HN-1 + web-search-1 + git-repo-1 runs will re-touch these files. **Synthesis-layer impact**: **none** — vault delta is empty (no new commits, no new mtime changes) and the wiki delta is automated maintenance only; the synthesis layer (themes / commitments / open-questions / personal-logistics) is independent of the wiki-side automated maintenance commits. **No `/themes.md` row change, no `/commitments.md` row, no `/open-questions.md` row, no `/personal-logistics.md` item** at this fetch. The 3 of 4 carry-forward untracked directories that have now reached the `Review/` confirmation threshold (16+ day for `Review/`, 12+ day for `templates/` + `celvivo_commercial/`) are **all confirmed as one-off / stale / not recurring** at this fetch (same status as 2026-08-28); on the next synthesis pass they should be **demoted from watchlist to stale carry-forward notes** in `/themes/05-robin-research.md` and the per-page working-tree status tables. Prior run (this section demoted): git-repo-1 2026-08-28T18:09Z.
- **Previous run (2026-08-28, git-repo-1 18:09Z):** **0 new vault commits** in the 2026-08-27T18:25Z → 2026-08-28T18:09Z 24-hour window — vault HEAD unchanged at `9d4767c7` (same as the 2026-08-27T18:25Z + 2026-08-26T18:06Z + 2026-08-25T18:13Z fetches); **vault silent for the 3rd consecutive fetch** since the 2026-08-24/25 SECOND 5-paper burst, **3 calendar days stale**. **No new external evidence** in this run. The 2026-08-24/25 cluster remains the most recent committed vault activity (Tevonian + Yang + Shen + Zhai + the `9aa2af4c` retrofit). The carry-forward untracked-file set bumps: `Review/zhou2023_computer_vision_microfluidics.md` **16-day → 17-day carry-forward** (**14 → 15 fetches silent**, stale carry-forward note per the 2026-08-27 fetch confirming the 2026-08-26 watchlist-downgrade consideration as a one-off) + `celvivo_commercial/` + `templates/` **11-day → 12-day carry-forward** (**the 2026-08-28 fetch confirms the parallel `templates/` + `celvivo_commercial/` entries as one-off alongside the `Review/` subfolder** — both reach the 12-day threshold at this fetch, same duration at which the `Review/` entry was confirmed one-off; both should be demoted to stale / not recurring carry-forward notes on the next synthesis pass) + `deepread_40240593/` **4-day → 5-day carry-forward** (mtime unchanged across 4 fetches since creation, working-folder-pipeline hypothesis further weakened). **Wiki-side**: **2 new automated wiki commits** landed in the 2026-08-27T18:25Z → 2026-08-28T18:09Z 24-hour window — `c992dd6` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-28, 2026-08-28 02:30 +0800, the **fourteenth** 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 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + `502281f` 2026-08-27 + now `c992dd6` 2026-08-28) + `6024ac7` chore: daily update 2026-08-28 (2026-08-28 02:42 +0800; per `git show --stat 6024ac7` the commit touched 16 files including `.last-update.json` + `commitments.md` + `index.md` + `quickstart.md` + `sources/README.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` + `themes.md` + `themes/index.md` + `themes/05-robin-research.md`; reducing uncommitted-file count from 17 → 5 per the manifest `changedFiles` list at the 2026-08-28T18:09Z fetch). The manifest `changedFiles` shows 5 dirty wiki files this fetch — `M .last-update.json` + `M index.md` + `M quickstart.md` + `M sources/hackernews.md` + `M sources/web-search.md` — the very next synthesis edits from the HN-1 + web-search-1 + git-repo-1 runs will re-touch these files. **Synthesis-layer impact**: **none** — vault delta is empty (no new commits, no new mtime changes) and the wiki delta is automated maintenance only; the synthesis layer (themes / commitments / open-questions / personal-logistics) is independent of the wiki-side automated maintenance commits. **No `/themes.md` row change, no `/commitments.md` row, no `/open-questions.md` row, no `/personal-logistics.md` item** at this fetch. The 3 of 4 carry-forward untracked directories that have now reached the `Review/` confirmation threshold (16+ day for `Review/`, 12+ day for `templates/` + `celvivo_commercial/`) are **all confirmed as one-off / stale / not recurring** at this fetch; on the next synthesis pass they should be **demoted from watchlist to stale carry-forward notes** in `/themes/05-robin-research.md` and the per-page working-tree status tables. Prior run (this section demoted): git-repo-1 2026-08-27T18:25Z.
- **Previous run (2026-08-27, git-repo-1 18:25Z):** **0 new vault commits** in the 2026-08-26T18:06Z → 2026-08-27T18:25Z 24-hour window — vault HEAD unchanged at `9d4767c7` (same as the 2026-08-26T18:06Z + 2026-08-25T18:13Z fetches); **vault silent for the 2nd consecutive fetch** since the 2026-08-24/25 SECOND 5-paper burst, **2 calendar days stale**. **No new external evidence** in this run. The 2026-08-24/25 cluster remains the most recent committed vault activity (Tevonian + Yang + Shen + Zhai + the `9aa2af4c` retrofit). The carry-forward untracked-file set bumps: `Review/zhou2023_computer_vision_microfluidics.md` **15-day → 16-day carry-forward** (**13 → 14 fetches silent**, structural signal continuing to weaken — **the 2026-08-27 fetch confirms the 2026-08-26 watchlist-downgrade consideration as a one-off**, entry should be demoted to a stale carry-forward note on the next synthesis pass) + `celvivo_commercial/` + `templates/` **10-day → 11-day carry-forward** + `deepread_40240593/` **3-day → 4-day carry-forward**. **Wiki-side**: **2 new automated wiki commits** landed in the 2026-08-26T18:06Z → 2026-08-27T18:25Z 24-hour window — `f51ff7c` chore: daily update 2026-08-27 (2026-08-27 02:13 +0800; per `git show --stat f51ff7c` the commit touched 14 files from the prior dirty set including `.last-update.json` + `commitments.md` + `index.md` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/literature.md` + `sources/openwiki-version-drift.md` + `sources/web-search.md` + `themes.md` + `themes/index.md` + `themes/05-robin-research.md`; reducing uncommitted-file count from 17 → 11) + `502281f` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-27, 2026-08-27 02:30 +0800, the **thirteenth** 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 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + now `502281f` 2026-08-27). 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/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` + `M themes/05-robin-research.md` — the very next synthesis edits from the HN-1 + web-search-1 + git-repo-1 runs will re-touch these files. **Synthesis-layer impact**: **none** — vault delta is empty (no new commits, no new mtime changes) and the wiki delta is automated maintenance only; the synthesis layer (themes / commitments / open-questions / personal-logistics) is independent of the wiki-side automated maintenance commits. **No `/themes.md` row change, no `/commitments.md` row, no `/open-questions.md` row, no `/personal-logistics.md` item** at this fetch. Prior run (this section demoted): git-repo-1 2026-08-26T18:06Z.
- **Previous 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**
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
1745); (d) `f2118a62` Aiello & Bagni 2025 biorxiv Rotating Chamber
brain organoid CFD (Wiki.js 1746, CelVivo KB-derived); (e)
`fb017e4f` CelVivo App Note 2026 shear stress ClinoStar vs orbital
shaker (Wiki.js 1747). **All 5 files landed at
`obsidian-vault/04-Literature/Deep-Reads/` root** (not in a
per-vendor subfolder — non-standard pattern, see Notable-entity §
"2026-08-23 root-level LDR burst"). Vendor-anchor mapping: 3
CelVivo-aligned (App Note + Aiello + Ajongbolo review) + 1
3Brain-adjacent (Kim EGaIn 3D MEA) + 1 cardiac epicardium (Tian mTOR,
no vendor callouts). **1 new untracked directory** appeared in the
working tree this fetch — `deepread_40240593/` (7 subdirs: 5
PMID-named + 2 slug-named that exactly map to the Aiello + CelVivo
App Note papers; the new directory is Robin's LDR pipeline
intermediate-artifact workspace, see Notable-entity). The 2
prior untracked directories (`celvivo_commercial/` + `templates/`)
and the `Review/zhou2023_computer_vision_microfluidics.md` first-entry-in-Review/-subfolder carry forward unchanged from the
prior fetch (now **8-day carry-forward** for `celvivo_commercial/` +
`templates/`; **13-day carry-forward** + **11 fetches silent** for
the `Review/` file). Wiki-side: **2 new automated wiki commits**
landed in the 24-hour window — `9cc5e63` chore: daily update
2026-08-24 (2026-08-24 02:23 +0800) + `127c2dc` chore(sources):
refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync
2026-08-24, 2026-08-24 02:30 +0800) — advancing wiki HEAD from
`a9568d8` (2026-08-23T18:11Z fetch) to `127c2dc`. Both commits are
routine auto-orchestration: (a) the `9cc5e63` daily update carried
the synthesis-layer edits from the prior HN-1 2026-08-23T18:00Z +
web-search-1 2026-08-23 (skipped) + git-repo-1 2026-08-23T18:11Z
runs; the `9cc5e63` daily update 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 2026-08-23 dirty set; (b)
the `127c2dc` sources-sync re-applied the count-data wipe pattern
on NocoDB / SeaFile / Wiki.js / RAGFlow 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`).
**Net-new external evidence** in this run: **5 new paper deep-reads**
(1 vendor App Note + 4 primary research papers / 1 review / 1
preprint) — all committed to `main`. **Net-new working-tree
artifact**: `deepread_40240593/` pipeline-workspace directory
(1 new untracked dir). **New commitments** added on `/commitments.md`:
(a) `celvivo-app-note-2026-clinostar-vs-orbital-shaker-positioning`
(fold the head-to-head shear-stress comparison into the ClinoStar
sales narrative + into the existing CelVivo赋能培训 cluster); (b)
`aiello-2025-rc-cfd-clinostar-positioning` (the < 20 mPa quantitative
number is direct ClinoStar value-prop ammunition); (c)
`kim-2025-egain-3d-mea-vs-3brain-positioning` (next-gen HD-MEA
field consolidation: Liu 2026 Rogers Lab + Kim 2025 EGaIn + 3Brain
Accura-3D); (d) `ajongbolo-2025-brain-organoid-review-cluster`
(pair with the existing Organoids 2026 review to anchor
brain-organoid review lane); (e) `tian-2025-epicardium-mtor-cardiac-expansion`
(first cardiac-epicardium paper in deep-read set; no vendor
callouts). **New themes-row refresh candidate** for
`/themes.md` `class-organoid-3d-bioprinting` row: the 5-paper
burst is the largest single-day cluster since 2026-07-29 + breaks
the 7-fetch silence; 3 of the 5 papers directly reference CelVivo
ClinoStar or 3Brain, validating the recurring-signal evidence
footprint. **Track on next fetch** whether (a) the `deepread_40240593/`
directory gets committed (currently untracked, 1-day-old); (b) any
of the 5 new LDR files get a wiki-side synthesis page (none
currently in `/sources/literature-*` naming pattern). Wiki edits
this run: (a) `/sources/git-repo.md` (this page) — refreshed
frontmatter HEAD pointers (vault HEAD `a4fa5a32` → `fb017e4f`, wiki
HEAD `a9568d8` → `127c2dc`, tags + `2026-08-24`, timestamp →
`2026-08-24T18:05:00Z`), refreshed the Connector / State section
to the new `2026-08-24T18-05-31-919Z` raw manifest, refreshed the
obsidian-vault working-tree-status section to 2026-08-24 (5 new
vault commits, 1 new untracked dir `deepread_40240593/`,
`celvivo_commercial/` + `templates/` 7-day → 8-day carry-forward,
`Review/` 12-day → 13-day + **10 fetches silent** → **11 fetches
silent**), refreshed the openwiki-wiki working-tree-status section
to 2026-08-24 (2 new automated wiki commits + 8 uncommitted
synthesis-layer edits per the manifest `changedFiles` list), added
2 new entries at the top of the Recent-commits-for-vault table
(5 new vault commits) + 2 new entries at the top of the
Recent-commits-for-wiki table (`127c2dc` sources-sync 2026-08-24
+ `9cc5e63` daily update 2026-08-24), refreshed the
Summary-of-last-48-hours table to add the
2026-08-23T18:11Z → 2026-08-24T18:05Z window data (5 vault
commits / 2 wiki commits / operational row noting the **tenth**
consecutive sources-sync re-applying the count-data wipe pattern
+ the 5-paper LDR burst detail), refreshed the
`04-Literature/Deep-Reads/` breakdown table (added the root-level
5-file entry + bumped `Review/` 12 → 13-day + `celvivo_commercial/` +
`templates/` 7 → 8-day carry-forward + total 1,207 → 1,212), added 7
new entries to the Notable-entity section (the 2026-08-23
root-level LDR burst overview + 5 individual paper entries + the
`deepread_40240593/` pipeline workspace entry), refreshed the
Synthesis-policy section with this run's delta summary (the old
2026-08-23 "This run" was demoted to "Previous run (2026-08-23,
git-repo-1 18:11Z)" and the new "This run" reflects the 5-paper
LDR burst); (b) `/themes/05-robin-research.md` — vault-snapshot
metadata refreshed (fetch timestamp → `2026-08-24T18:05:00Z`,
raw-manifest path → the new `2026-08-24T18-05-31-919Z` manifest,
HEAD bumped `a4fa5a32` → `fb017e4f`, the 5-paper LDR burst noted
in the cluster section, the `04-Literature/Deep-Reads/` breakdown
table updated with the root-level 5-file entry + total 1,207 →
1,212, `celvivo_commercial/` + `templates/` 7-day → 8-day
carry-forward + `Review/` 12-day → 13-day + **10 fetches silent**
→ **11 fetches silent**); (c) `/commitments.md` — added 5 new
commitment entries corresponding to the 5 new LDR papers (each
with Owner: me + Source: git-repo-1 2026-08-24 + Status: open); (d)
`/sources/literature.md` — added 5 new rows to the "Last 30 days
of deep reads" table under a new `2026-08-23` subsection; (e)
`/quickstart.md` — added this "Latest update — git-repo-1
(2026-08-24T18:05Z)" paragraph; updated the Backlog git-repo entry
to reflect the new wiki HEAD `127c2dc` + 2 new automated wiki
commits + the carry-forward 8 uncommitted synthesis-layer edits
+ the **tenth** consecutive sources-sync note + the 5-paper LDR
burst detail; (f) `/sources/README.md` — refreshed Active
connectors Git repo row + Connector roll Git repo row to mention
the 2026-08-24 18:05 UTC fetch + the **tenth** consecutive
sources-sync. **No `/themes.md` row change** — the 5-paper LDR
burst strengthens the existing `class-organoid-3d-bioprinting`
evidence footprint (3 of 5 papers vendor-aligned to CelVivo +
3Brain) but does not warrant a new theme row at this fetch
(single-day burst, no recurrence yet); if a 2026-08-25 fetch
surfaces another deep-read cluster, that becomes the recurrence
trigger for a theme-row promotion.
- **Previous run (2026-08-23, git-repo-1 18:11Z):** **0 new vault commits**
in the 2026-08-22T18:13Z → 2026-08-23T18:11Z 24-hour window — the
vault HEAD is **unchanged at `a4fa5a32`** for the **7th consecutive
fetch** (the 2026-08-16 Quintard 2024 Nat Commun 4-commit LDR cycle
+ Guo 2026 Front Cell Dev Biol 3-commit LDR cycle remain the most
recent vault activity, **7 calendar days stale** at this fetch).
**0 new vault mtime changes** — the 2 untracked directories
(`celvivo_commercial/` + `templates/`) and the 23+ untracked files
from the 2026-08-17T18:09Z fetch carry forward unchanged. The
`Review/zhou2023_computer_vision_microfluidics.md` first-entry in the
new `Review/` subfolder is **12-day carry-forward** at this fetch
(uncommitted since 2026-08-11); the structural signal for `Review/`
continues to weaken per the Notable-entity entry (the subfolder has
been a single-entry watchlist since 2026-08-13, now **10 fetches
silent**). Wiki-side: **2 new automated wiki commits** landed in
the 24-hour window — `8f8f767` chore(sources): refresh
NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-23,
2026-08-23 02:30 +0800) + `a9568d8` chore: daily update 2026-08-23
(2026-08-23 02:29 +0800) — advancing wiki HEAD from `43d4548`
(2026-08-22T18:13Z fetch) to `a9568d8`. Both commits are routine
auto-orchestration: (a) the `a9568d8` daily update carried the
synthesis-layer edits 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; the `a9568d8` daily
update 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
2026-08-22 dirty set, reducing the uncommitted-file count from
9 → 6; (b) the `8f8f767` sources-sync re-applied the count-data
wipe pattern on NocoDB / SeaFile / Wiki.js / RAGFlow 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`).
**No new external evidence** in this run (vault silent), **no
new theme row**, **no new commitment row**, **no new open-question
row**, **no new personal-logistics item** — the synthesis layer
is unchanged. Wiki edits this run: (a) `/sources/git-repo.md` (this
page) — refreshed frontmatter HEAD pointers (vault HEAD unchanged at
`a4fa5a32`, wiki HEAD `43d4548` → `a9568d8`, tags + `2026-08-23`,
timestamp → `2026-08-23T18:11:00Z`), refreshed the Connector /
State section to the new `2026-08-23T18-11-34-883Z` raw manifest,
refreshed the obsidian-vault working-tree-status section to
2026-08-23 (0 new commits, 0 new mtime changes, untracked set
unchanged; `Review/` 11-day → 12-day + `templates/` + `celvivo_commercial/`
6-day → 7-day carry-forward), refreshed the openwiki-wiki
working-tree-status section to 2026-08-23 (2 new automated wiki
commits + 6 uncommitted synthesis-layer edits, down from 9 at the
2026-08-22T18:13Z fetch because `a9568d8` committed 7 of the prior
9 dirty files),
added 2 new entries at the top of the Recent-commits-for-wiki
table (`a9568d8` daily update 2026-08-23 + `8f8f767` sources-sync
2026-08-23), refreshed the Summary-of-last-48-hours table to add
the 2026-08-22T18:13Z → 2026-08-23T18:11Z window data (0 vault
commits / 2 wiki commits / operational row noting the **ninth**
consecutive sources-sync re-applying the count-data wipe pattern),
refreshed the Notable-entity `Review/` entry (11-day → 12-day carry-
forward, **9 fetches silent** → **10 fetches silent**) + bumped
`templates/` + `celvivo_commercial/` 6-day → 7-day + refreshed the
`04-Literature/Deep-Reads/` breakdown table, refreshed
the Synthesis-policy section with this run's delta summary;
(b) `/themes/05-robin-research.md` — vault-snapshot metadata
refreshed (fetch timestamp → `2026-08-23T18:11:00Z`, raw-manifest path
→ the new `2026-08-23T18-11-34-883Z` manifest); the vault HEAD
pointer stays `a4fa5a32` (unchanged across the 2026-08-17 +
2026-08-18 + 2026-08-19 + 2026-08-20 + 2026-08-21 + 2026-08-22 +
2026-08-23 fetches);
`Review/` 11-day → 12-day carry-forward; `Templates/` +
`CelVivo-commercial/` 6-day → 7-day; (c) `/quickstart.md` —
added the "Latest update — git-repo-1 (2026-08-23T18:11Z)"
paragraph; updated the Backlog git-repo entry to reflect the
new wiki HEAD `a9568d8` + 2 new automated wiki commits + 6
uncommitted synthesis-layer edits (down from 9 at the prior fetch
because `a9568d8` committed 7 of the prior 9 dirty files) +
the **ninth** consecutive sources-sync note; (d) `/sources/README.md`
— refreshed Active connectors Git repo row + Connector roll Git
repo row to mention the 2026-08-23 18:11 UTC fetch + the
**ninth** consecutive sources-sync. **No `/themes.md` row
change, no `/commitments.md` row, no `/open-questions.md` row,
no `/personal-logistics.md` item** — the vault delta is empty and
the wiki delta is automated maintenance only. The "vault is silent
on a 24-hour window" pattern continues to be normal cadence for
Robin's workflow (the 2026-08-13 + 2026-08-15 + 2026-08-18 +
2026-08-19 + 2026-08-20 + 2026-08-21 + 2026-08-22 fetches were also
0-new-vault-commits daily-cycle follow-ups; the 2026-08-23 fetch
makes it **8 consecutive 0-new-vault-commit fetches**). The synthesis
layer (themes / commitments / open-questions / personal-logistics) is
independent of the wiki-side automated maintenance commits.
- **Previous run (2026-08-22, git-repo-1 18:13Z):** **0 new vault commits**
in the 2026-08-21T18:09Z → 2026-08-22T18:13Z 24-hour window — the
vault HEAD is **unchanged at `a4fa5a32`** for the **6th consecutive
fetch** (the 2026-08-16 Quintard 2024 Nat Commun 4-commit LDR cycle
+ Guo 2026 Front Cell Dev Biol 3-commit LDR cycle remain the most
recent vault activity, **6 calendar days stale** at this fetch).
**0 new vault mtime changes** — the 2 untracked directories
(`celvivo_commercial/` + `templates/`) and the 23+ untracked files
from the 2026-08-17T18:09Z fetch carry forward unchanged. The
`Review/zhou2023_computer_vision_microfluidics.md` first-entry in the
new `Review/` subfolder is **11-day carry-forward** at this fetch
(uncommitted since 2026-08-11); the structural signal for `Review/`
continues to weaken per the Notable-entity entry (the subfolder has
been a single-entry watchlist since 2026-08-13, now **9 fetches
silent**). Wiki-side: **2 new automated wiki commits** landed in
the 24-hour window — `d8e2277` chore: daily update 2026-08-22
(2026-08-22 02:23 +0800) + `43d4548` chore(sources): refresh
NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-22,
2026-08-22 02:30 +0800) — advancing wiki HEAD from `f6c2576`
(2026-08-21T18:09Z fetch) to `43d4548`. Both commits are routine
auto-orchestration: (a) the `d8e2277` daily update carried the
synthesis-layer edits from the prior HN-1 2026-08-22T18:00Z +
web-search-1 2026-08-22 (skipped) + git-repo-1 2026-08-21T18:09Z
runs; (b) the `43d4548` sources-sync re-applied the count-data wipe
pattern on NocoDB / SeaFile / Wiki.js / RAGFlow 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`).
**No new external evidence** in this run (vault silent), **no
new theme row**, **no new commitment row**, **no new open-question
row**, **no new personal-logistics item** — the synthesis layer
is unchanged. Wiki edits this run: (a) `/sources/git-repo.md` (this
page) — refreshed frontmatter HEAD pointers (vault HEAD unchanged at
`a4fa5a32`, wiki HEAD `f6c2576` → `43d4548`, tags + `2026-08-22`,
timestamp → `2026-08-22T18:13:00Z`), refreshed the Connector /
State section to the new `2026-08-22T18-13-00-193Z` raw manifest,
refreshed the obsidian-vault working-tree-status section to
2026-08-22 (0 new commits, 0 new mtime changes, untracked set
unchanged; `Review/` 10-day → 11-day + `templates/` + `celvivo_commercial/`
5-day → 6-day carry-forward), refreshed the openwiki-wiki
working-tree-status section to 2026-08-22 (2 new automated wiki
commits + 9 uncommitted synthesis-layer edits, the same dirty
count as the 2026-08-21T18:09Z fetch),
added 2 new entries at the top of the Recent-commits-for-wiki
table (`43d4548` sources-sync 2026-08-22 + `d8e2277` daily update
2026-08-22), refreshed the Summary-of-last-48-hours table to add
the 2026-08-21T18:09Z → 2026-08-22T18:13Z window data (0 vault
commits / 2 wiki commits / operational row noting the **eighth**
consecutive sources-sync re-applying the count-data wipe pattern),
refreshed the Notable-entity `Review/` entry (10-day → 11-day carry-
forward, **8 fetches silent** → **9 fetches silent**) + bumped
`templates/` + `celvivo_commercial/` 5-day → 6-day, refreshed
the Synthesis-policy section with this run's delta summary;
(b) `/themes/05-robin-research.md` — vault-snapshot metadata
refreshed (fetch timestamp → `2026-08-22T18:13:00Z`, raw-manifest path
→ the new `2026-08-22T18-13-00-193Z` manifest); the vault HEAD
pointer stays `a4fa5a32` (unchanged across the 2026-08-17 +
2026-08-18 + 2026-08-19 + 2026-08-20 + 2026-08-21 + 2026-08-22 fetches);
`Review/` 10-day → 11-day carry-forward; `Templates/` +
`CelVivo-commercial/` 5-day → 6-day; (c) `/quickstart.md` —
added the "Latest update — git-repo-1 (2026-08-22T18:13Z)"
paragraph; updated the Backlog git-repo entry to reflect the
new wiki HEAD `43d4548` + 2 new automated wiki commits + 9
uncommitted synthesis-layer edits (same count as prior fetch) +
the **eighth** consecutive sources-sync note; (d) `/sources/README.md`
— refreshed Active connectors Git repo row + Connector roll Git
repo row to mention the 2026-08-22 18:13 UTC fetch + the
**eighth** consecutive sources-sync. **No `/themes.md` row
change, no `/commitments.md` row, no `/open-questions.md` row,
no `/personal-logistics.md` item** — the vault delta is empty and
the wiki delta is automated maintenance only. The "vault is silent
on a 24-hour window" pattern continues to be normal cadence for
Robin's workflow (the 2026-08-13 + 2026-08-15 + 2026-08-18 +
2026-08-19 + 2026-08-20 + 2026-08-21 fetches were also 0-new-vault-commits
daily-cycle follow-ups; the 2026-08-22 fetch makes it **7
consecutive 0-new-vault-commit fetches**). The synthesis layer
(themes / commitments / open-questions / personal-logistics) is
independent of the wiki-side automated maintenance commits.
- **Previous run (2026-08-21, git-repo-1 18:09Z):** **0 new vault commits**
in the 2026-08-20T18:09Z → 2026-08-21T18:09Z 24-hour window — the
vault HEAD is **unchanged at `a4fa5a32`** for the **5th consecutive
fetch** (the 2026-08-16 Quintard 2024 Nat Commun 4-commit LDR cycle
+ Guo 2026 Front Cell Dev Biol 3-commit LDR cycle remain the most
recent vault activity, **5 calendar days stale** at this fetch).
**0 new vault mtime changes** — the 2 untracked directories
(`celvivo_commercial/` + `templates/`) and the 23+ untracked files
from the 2026-08-17T18:09Z fetch carry forward unchanged. The
`Review/zhou2023_computer_vision_microfluidics.md` first-entry in the
new `Review/` subfolder is **10-day carry-forward** at this fetch
(uncommitted since 2026-08-11); the structural signal for `Review/`
continues to weaken per the Notable-entity entry (the subfolder has
been a single-entry watchlist since 2026-08-13, now **8 fetches
silent**). Wiki-side: **2 new automated wiki commits** landed in
the 24-hour window — `b6dc337` chore: daily update 2026-08-21
(2026-08-21 02:27 +0800) + `f6c2576` chore(sources): refresh
NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-21,
2026-08-21 02:30 +0800) — advancing wiki HEAD from `bd30339`
(2026-08-20T18:09Z fetch) to `f6c2576`. Both commits are routine
auto-orchestration: (a) the `b6dc337` daily update carried the
synthesis-layer edits from the prior HN-1 2026-08-21T18:00Z +
web-search-1 2026-08-21 (skipped) + git-repo-1 2026-08-20T18:09Z
runs; the `b6dc337` daily update committed `sources/index.md`
from the 2026-08-20 dirty set (reducing uncommitted-file count
from 10 → 9 at this fetch); (b) the `f6c2576` sources-sync
re-applied the count-data wipe pattern on NocoDB / SeaFile /
Wiki.js / RAGFlow for the **seventh** 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`).
**No new external evidence** in this run (vault silent), **no
new theme row**, **no new commitment row**, **no new open-question
row**, **no new personal-logistics item** — the synthesis layer
is unchanged. Wiki edits this run: (a) `/sources/git-repo.md` (this
page) — refreshed frontmatter HEAD pointers (vault HEAD unchanged at
`a4fa5a32`, wiki HEAD `dcb53a2` → `bd30339`, tags + `2026-08-20`,
timestamp → `2026-08-20T18:09:15Z`), refreshed the Connector /
State section to the new `2026-08-20T18-09-15-122Z` raw manifest,
refreshed the obsidian-vault working-tree-status section to
2026-08-20 (0 new commits, 0 new mtime changes, untracked set
unchanged; `Review/` 8-day → 9-day + `templates/` + `celvivo_commercial/`
3-day → 4-day carry-forward), refreshed the openwiki-wiki
working-tree-status section to 2026-08-20 (2 new automated wiki
commits + the carry-forward 10 uncommitted synthesis-layer edits),
added 2 new entries at the top of the Recent-commits-for-wiki
table (`bd30339` sources-sync 2026-08-20 + `a44f284` daily update
2026-08-20), refreshed the Summary-of-last-48-hours table to add
the 2026-08-19T18:08Z → 2026-08-20T18:09Z window data (0 vault
commits / 2 wiki commits / operational row noting the **sixth**
consecutive sources-sync re-applying the count-data wipe pattern),
refreshed the Notable-entity `Review/` entry (8-day → 9-day carry-
forward, **6 fetches silent** → **7 fetches silent**) + bumped
`templates/` + `celvivo_commercial/` 3-day → 4-day, refreshed
the Synthesis-policy section with this run's delta summary;
(b) `/themes/05-robin-research.md` — vault-snapshot metadata
refreshed (fetch timestamp → `2026-08-20T18:09:15Z`, raw-manifest path
→ the new `2026-08-20T18-09-15-122Z` manifest); the vault HEAD
pointer stays `a4fa5a32` (unchanged across the 2026-08-17 +
2026-08-18 + 2026-08-19 + 2026-08-20 fetches); `Review/`
8-day → 9-day carry-forward; `Templates/` + `CelVivo-commercial/`
3-day → 4-day; (c) `/quickstart.md` — added the "Latest update
— git-repo-1 (2026-08-20T18:09Z)" paragraph; updated the Backlog
git-repo entry to reflect the new wiki HEAD `bd30339` + 2 new
automated wiki commits + the carry-forward 10 uncommitted files +
the **sixth** consecutive sources-sync note; (d) `/sources/README.md`
— refreshed Active connectors Git repo row + Connector roll Git
repo row to mention the 2026-08-20 18:09 UTC fetch + the **sixth**
consecutive sources-sync. **No `/themes.md` row change, no
`/commitments.md` row, no `/open-questions.md` row, no
`/personal-logistics.md` item** — the vault delta is empty and the
wiki delta is automated maintenance only. The "vault is silent on
a 24-hour window" pattern continues to be normal cadence for Robin's
workflow (the 2026-08-13 + 2026-08-15 + 2026-08-18 + 2026-08-19
fetches were also 0-new-vault-commits daily-cycle follow-ups; the
2026-08-20 fetch makes it **5 consecutive 0-new-vault-commit
fetches**). The synthesis layer (themes / commitments /
open-questions / personal-logistics) is independent of the wiki-side
automated maintenance commits.
- **Previous run (2026-08-19, git-repo-1 18:08Z):** **0 new vault commits**
in the 2026-08-18T18:10Z → 2026-08-19T18:08Z 24-hour window — the
vault HEAD is **unchanged at `a4fa5a32`** for the **3rd consecutive
fetch** (the 2026-08-16 Quintard 2024 Nat Commun 4-commit LDR cycle
+ Guo 2026 Front Cell Dev Biol 3-commit LDR cycle remain the most
recent vault activity, **3 calendar days stale** at this fetch).
**0 new vault mtime changes** — the 2 untracked directories
(`celvivo_commercial/` + `templates/`) and the 23+ untracked files
from the 2026-08-17T18:09Z fetch carry forward unchanged. The
`Review/zhou2023_computer_vision_microfluidics.md` first-entry in the
new `Review/` subfolder is **8-day carry-forward** at this fetch
(uncommitted since 2026-08-11); the structural signal for `Review/`
continues to weaken per the Notable-entity entry (the subfolder has
been a single-entry watchlist since 2026-08-13, now **6 fetches
silent**). Wiki-side: **2 new automated wiki commits** landed in
the 24-hour window — `7e904ec` chore: daily update 2026-08-19
(2026-08-19 02:23 +0800) + `dcb53a2` chore(sources): refresh
NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-19,
2026-08-19 02:30 +0800) — advancing wiki HEAD from `1fc73ae`
(2026-08-18T18:10Z fetch) to `dcb53a2`. Both commits are routine
auto-orchestration: (a) the `7e904ec` daily update carried the
synthesis-layer edits from the prior HN-1 2026-08-19T18:00Z +
web-search-1 2026-08-19 + git-repo-1 2026-08-18T18:10Z runs
(touching `.last-update.json` + `quickstart.md` +
`sources/{README,git-repo,hackernews,index,nocodb,ragflow,seafile,web-search,wikijs}.md`
+ `themes/05-robin-research.md` per `git show --stat 7e904ec`);
(b) the `dcb53a2` sources-sync re-applied the count-data wipe
pattern on NocoDB / SeaFile / Wiki.js / RAGFlow for the **fifth**
consecutive sources-sync (after 2026-08-15 `2507925` + 2026-08-16
`997b648` + 2026-08-17 `be49285` + 2026-08-18 `1fc73ae`).
**No new external evidence** in this run (vault silent), **no
new theme row**, **no new commitment row**, **no new open-question
row**, **no new personal-logistics item** — the synthesis layer
is unchanged. Wiki edits this run: (a) `/sources/git-repo.md` (this
page) — refreshed frontmatter HEAD pointers (vault HEAD unchanged at
`a4fa5a32`, wiki HEAD `1fc73ae` → `dcb53a2`, tags + `2026-08-19`,
timestamp → `2026-08-19T18:08:24Z`), refreshed the Connector /
State section to the new `2026-08-19T18-08-24-164Z` raw manifest,
refreshed the obsidian-vault working-tree-status section to
2026-08-19 (0 new commits, 0 new mtime changes, untracked set
unchanged), refreshed the openwiki-wiki working-tree-status section
to 2026-08-19 (2 new automated wiki commits + the carry-forward 10
uncommitted synthesis-layer edits — `sources/index.md` re-appears
as dirty in the working tree at this fetch), added 2 new entries at
the top of the Recent-commits-for-wiki table (`dcb53a2` +
`7e904ec`), refreshed the Summary-of-last-48-hours table to add the
2026-08-18T18:10Z → 2026-08-19T18:08Z window data (0 vault commits /
2 wiki commits / operational row noting the **fifth** consecutive
sources-sync re-applying the count-data wipe pattern), refreshed
the Synthesis-policy section with this run's delta summary; (b)
`/themes/05-robin-research.md` — vault-snapshot metadata refreshed
(fetch timestamp → `2026-08-19T18:08:24Z`, raw-manifest path → the
new `2026-08-19T18-08-24-164Z` manifest); the vault HEAD pointer
stays `a4fa5a32` (unchanged across the 2026-08-17 + 2026-08-18 +
2026-08-19 fetches); (c) `/quickstart.md` — added the "Latest update
— git-repo-1 (2026-08-19T18:08Z)" paragraph; updated the Backlog
git-repo entry to reflect the new wiki HEAD `dcb53a2` + 2 new
automated wiki commits + the carry-forward 10 uncommitted files +
the **fifth** consecutive sources-sync note. **No `/themes.md` row
change, no `/commitments.md` row, no `/open-questions.md` row, no
`/personal-logistics.md` item** — the vault delta is empty and the
wiki delta is automated maintenance only. The "vault is silent on
a 24-hour window" pattern continues to be normal cadence for Robin's
workflow (the 2026-08-13 + 2026-08-15 + 2026-08-18 fetches were
also 0-new-vault-commits daily-cycle follow-ups; the 2026-08-19
fetch made it **4 consecutive 0-new-vault-commit fetches**).
The synthesis layer (themes / commitments / open-questions /
personal-logistics) is independent of the wiki-side automated
maintenance commits.
- **Previous run (2026-08-18, git-repo-1 18:10Z):** **0 new vault commits**
in the 2026-08-17T18:09Z → 2026-08-18T18:10Z 24-hour window — the
vault HEAD is **unchanged at `a4fa5a32`** (the 2026-08-16 Quintard
2024 Nat Commun 4-commit LDR cycle + Guo 2026 Front Cell Dev Biol
3-commit LDR cycle remain the most recent vault activity, 2 calendar
days stale at this fetch). **0 new vault mtime changes** — the 2
untracked directories (`celvivo_commercial/` + `templates/`) and the
23+ untracked files from the 2026-08-17T18:09Z fetch carry forward
unchanged. The `Review/zhou2023_computer_vision_microfluidics.md`
first-entry in the new `Review/` subfolder is **7-day carry-forward**
at this fetch (uncommitted since 2026-08-11); the structural signal
for `Review/` continues to weaken per the Notable-entity entry (the
subfolder has been a single-entry watchlist since 2026-08-13).
Wiki-side: **2 new automated wiki commits** landed in the 24-hour
window — `8127797` chore: daily update 2026-08-18 (2026-08-18
02:23 +0800) + `1fc73ae` chore(sources): refresh
NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-18,
2026-08-18 02:30 +0800) — advancing wiki HEAD from `be49285`
(2026-08-17T18:09Z fetch) to `1fc73ae`. Both commits are routine
auto-orchestration: (a) the `8127797` daily update carried the
synthesis-layer edits from the prior HN-1 2026-08-18T18:00Z run +
this git-repo-1 2026-08-17T18:09Z run (touching `commitments.md` +
`index.md` + `quickstart.md` + `sources/{README,git-repo,hackernews,index,literature,nocodb,ragflow,seafile,web-search,wikijs}.md`
+ `themes/{01-organoid-equipment,05-robin-research}.md` per
`git show --stat 8127797`); (b) the `1fc73ae` sources-sync
re-applied the count-data wipe pattern on NocoDB / SeaFile / Wiki.js
/ RAGFlow for the **fourth** consecutive sources-sync (after
2026-08-15 `2507925` + 2026-08-16 `997b648` + 2026-08-17 `be49285`).
**No new external evidence** in this run (vault silent), **no
new theme row**, **no new commitment row**, **no new open-question
row**, **no new personal-logistics item** — the synthesis layer
is unchanged. Wiki edits this run: (a) `/sources/git-repo.md` (this
page) — refreshed frontmatter HEAD pointers (vault HEAD unchanged at
`a4fa5a32`, wiki HEAD `be49285` → `1fc73ae`, tags + `2026-08-18`,
timestamp → `2026-08-18T18:10:12Z`), refreshed the Connector /
State section to the new `2026-08-18T18-10-12-916Z` raw manifest,
refreshed the obsidian-vault working-tree-status section to
2026-08-18 (0 new commits, 0 new mtime changes, untracked set
unchanged), refreshed the openwiki-wiki working-tree-status section
to 2026-08-18 (2 new automated wiki commits + the carry-forward 9
uncommitted synthesis-layer edits), added 2 new entries at the top
of the Recent-commits-for-wiki table (`1fc73ae` + `8127797`),
refreshed the Summary-of-last-48-hours table to add the
2026-08-17T18:09Z → 2026-08-18T18:10Z window data (0 vault commits /
2 wiki commits / operational row noting the **fourth** consecutive
sources-sync re-applying the count-data wipe pattern), refreshed
the Synthesis-policy section with this run's delta summary; (b)
`/themes/05-robin-research.md` — vault-snapshot metadata refreshed
(fetch timestamp → `2026-08-18T18:10:12Z`, raw-manifest path → the
new `2026-08-18T18-10-12-916Z` manifest); the vault HEAD pointer
stays `a4fa5a32` (unchanged across both 2026-08-17 and 2026-08-18
fetches); (c) `/quickstart.md` — added the "Latest update —
git-repo-1 (2026-08-18T18:10Z)" paragraph; updated the Backlog
git-repo entry to reflect the new wiki HEAD `1fc73ae` + 2 new
automated wiki commits + the carry-forward 9 uncommitted files +
the **fourth** consecutive sources-sync note. **No `/themes.md` row
change, no `/commitments.md` row, no `/open-questions.md` row, no
`/personal-logistics.md` item** — the vault delta is empty and the
wiki delta is automated maintenance only. The "vault is silent on
a 24-hour window" pattern continues to be normal cadence for Robin's
workflow (the 2026-08-13 fetch was also a 0-new-vault-commits
daily-cycle follow-up; the 2026-08-15 fetch was also a 0-new-vault-
commits daily-cycle follow-up). The synthesis layer (themes /
commitments / open-questions / personal-logistics) is independent
of the wiki-side automated maintenance commits.
- **Previous run (2026-08-17, git-repo-1 18:09Z):** **7 new vault commits**
landed in the 2026-08-15T18:07Z → 2026-08-17T18:09Z window — the vault
HEAD bumped from `297f106d` (the 2026-08-12 Liang 2026 cluster) to
`a4fa5a32` (the 2026-08-16 Quintard 2024 + Guo 2026 cluster). The
cluster breaks down as: (a) **Quintard 2024 Nat Commun 4-commit LDR
cycle** (`0fc8db24` adds 189 lines → `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) on `obsidian-vault/Literature/Deep-Reads/Organoid/quintard_2024_vasorganoid_chip.md`;
(b) **Guo 2026 Front Cell Dev Biol 3-commit LDR cycle** (`2e6f5989`
adds 170 lines → `00f824f2` -v2 修图床 (加 2 张 Wiki.js 自带图) →
`a4fa5a32` -v3 补 Fig 1) on
`obsidian-vault/Literature/Deep-Reads/Organoid/guo_2026_organoid_ethical_review.md`.
The 2026-08-16 cluster is **the 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, and **the first time a
review-type IRB / ethics systematic review (Guo 2026) was deep-read**
in any vault window. **2 new untracked directories** appeared in
the working tree this fetch: (a) `celvivo_commercial/1331651_20260630_131201.pdf`
(the 6-30 quote PDF migrated into a new folder); (b) `templates/类器官IRB申请清单.md`
(the IRB application checklist Robin produced from the Guo 2026
review — Robin's **first customer-facing sales ammunition template**
derived from a single deep-read). The 23 untracked working-tree
files from the 2026-08-13 fetch are unchanged at this fetch (the
`Review/zhou2023_computer_vision_microfluidics.md` first-entry-in-Review/-subfolder
is still untracked, now a **4-day carry-forward** with watchlist
signal weakening per the Notable-entity entry). Wiki-side: **4 new
wiki commits** landed (`151d22b` daily update 2026-08-16 +
`997b648` sources-sync 2026-08-16 + `5c70881` daily update 2026-08-17
(created the new `sources/openwiki-version-drift.md` auto-generated
page) + `be49285` sources-sync 2026-08-17), advancing HEAD from
`2507925` (2026-08-15) to `be49285` (2026-08-17). 9 dirty wiki files
in the working tree (`.last-update.json` + `quickstart.md` +
`sources/README.md` + `sources/hackernews.md` + `sources/nocodb.md`
+ `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md`
+ `sources/wikijs.md`) are **accumulated** synthesis-layer edits
from the prior HN-1 2026-08-15 + HN-1 2026-08-16 + HN-1 2026-08-17 +
web-search-1 2026-08-15 + web-search-1 2026-08-17 + git-repo-1
2026-08-15 runs that are pending the next CLI orchestration commit
(down from 10 dirty files at the 2026-08-15 fetch — `sources/index.md`
got committed in the `151d22b` 2026-08-16 daily update). One
**new wiki file** added in the window: `sources/openwiki-version-drift.md`
(auto-generated OpenWiki version drift monitor; reports `v0.3.1` local
→ `v0.3.3` npm latest as of 2026-08-15T20:00:03Z with a manual
`npm install -g openwiki@latest` action and a WARNING that v0.3.1 →
v0.4+ may have breaking changes; the page is informational, not a
synthesis target). **No `/commitments.md` row, no
`/open-questions.md` row, no `/personal-logistics.md` item**
added this run beyond the canonical synthesis pipeline — the
Quintard 2024 deep-read has no existing synthesis page yet (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`); the Guo 2026 IRB
review is the first ethics-side deep-read and the IRB checklist
template is the first customer-facing sales ammunition template,
both of which warrant a commitment + a synthesis page on a future
fetch. Wiki edits this run: (a) `/sources/git-repo.md` (this page)
— refreshed frontmatter HEAD pointers (vault HEAD `297f106d` →
`a4fa5a32`, wiki HEAD `2507925` → `be49285`, tags + `2026-08-17`,
timestamp → `2026-08-17T18:09:32Z`), refreshed the Connector / State
section to the new `2026-08-17T18-09-32-895Z` raw manifest, refreshed
the obsidian-vault working-tree-status section to 2026-08-17 (7 new
vault commits, 2 new untracked dirs, the `Review/zhou2023_computer_vision_microfluidics.md`
carries forward as still-untracked), refreshed the
Recent-commits-for-vault table to put the 7 new 2026-08-16 commits
on top of the 2026-08-12 cluster, refreshed the openwiki-wiki
working-tree-status section to 2026-08-17 (4 new wiki commits + 9
uncommitted synthesis-layer edits — `sources/index.md` got committed
in `151d22b`), refreshed the Recent-commits-for-wiki table to put
the 4 new 2026-08-16/2026-08-17 commits on top of the 2026-08-15
cluster, refreshed the Summary-of-last-48-hours table to add the
2026-08-15T18:07Z → 2026-08-17T18:09Z window data (7 vault commits /
4 wiki commits / 9 uncommitted wiki files / 1 new wiki file +
2 new untracked dirs + 4-day carry-forward on `Review/` subfolder),
refreshed the Notable-entity section to add (a) "Quintard 2024
microfluidic vascularized organoid chip" entry (with 4-star
Mimetas/CelVivo/Emulate mapping), (b) "Guo 2026 organoid ethics
systematic review" entry (with 4-star Mimetas/CelVivo/Emulate
mapping + IRB checklist template cross-link), (c) refreshed
"Review/ subfolder" entry with watchlist-trigger-met note, (d)
new "templates/ subfolder" entry (first customer-facing sales
ammunition template), (e) new "celvivo_commercial/ subfolder" entry
(the 6-30 quote PDF migration), refreshed the Synthesis-policy
section with this run's delta summary. **No `/themes.md` row change**
— the new external evidence routes into the existing
`class-organoid-3d-bioprinting` theme row (Quintard 2024 is
organ-on-chip adjacent to Robin's 4 application domains; Guo 2026
is IRB-side adjacent to the same row); the Robin-authored
IRB checklist template routes into the existing
`/themes/05-robin-research.md` "Sales ammunition pipeline" section
rather than a new theme row. **No `/open-questions.md` row, no
`/personal-logistics.md` item** — the IRB checklist is a
vendor-anchored customer-training artifact, not a memory-graph
uncertainty. (b) `/themes/05-robin-research.md` — vault-snapshot
metadata refreshed (fetch timestamp → `2026-08-17T18:09:32Z`,
raw-manifest path → the new `2026-08-17T18-09-32-895Z` manifest;
vault HEAD `297f106d` → `a4fa5a32`; untracked-dir set refreshed
with `celvivo_commercial/` + `templates/` entries; `04-Literature/Deep-Reads/Organoid/`
count `659` → `661` (Quintard + Guo); 30-day research output
table extended with the 2026-08-16 Quintard 2024 + Guo 2026 row;
by-vendor table extended with `Microfluidic / organ-on-chip
adjacent` and `Ethics / IRB` rows; Sales ammunition pipeline section
extended with the `templates/类器官IRB申请清单.md` IRB checklist
template). (c) `/themes/01-organoid-equipment.md` — Quintard 2024
added to CelVivo evidence anchors (CelVivo ClinoStar rating 3
upstream workflow step) and Guo 2026 added to the Regulatory /
China-specific context section (CelVivo ClinoStar rating 4 IRB
compliance ammunition; companion to the existing CDE classification
+ Order No. 818 items). (d) `/sources/literature.md` — Quintard 2024
+ Guo 2026 added to the 30-day deep-read index. (e) `/sources/README.md`
— git-repo last-updated refreshed from `2026-08-15 18:07 UTC` to
`2026-08-17 18:09 UTC`. (f) `/quickstart.md` — added the
"Latest update — git-repo-1 (2026-08-17T18:09Z)" paragraph. Wiki-side: **4 new wiki commits** landed (`021e929` daily
update 2026-08-14 + `6258717` sources-sync 2026-08-14 + `173b58c`
daily update 2026-08-15 + `2507925` sources-sync 2026-08-15),
advancing HEAD from `1737454` (2026-08-13) to `2507925` (2026-08-15).
**One operational issue** was surfaced by `2507925`: the 2026-08-15
sources-sync committed **empty count values** for NocoDB / SeaFile /
Wiki.js / RAGFlow (NocoDB 6614 → 0, Wiki.js 83 → 0, RAGFlow landing
200 → 000) — see Notable-entity § "2026-08-15 sources-sync bug"
below. 10 dirty wiki files in the working tree
(`.last-update.json` + `quickstart.md` + `sources/README.md` +
`sources/hackernews.md` + `sources/index.md` + `sources/nocodb.md` +
`sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md`
+ `sources/wikijs.md`) are **accumulated** synthesis-layer edits
from the prior HN-1 2026-08-13 + HN-1 2026-08-15 + web-search-1
2026-08-15 + this git-repo-1 2026-08-15 runs that are pending the
next CLI orchestration commit. Wiki edits this run: (a)
`/sources/git-repo.md` (this page) — refreshed frontmatter HEAD
pointers (vault HEAD unchanged, wiki HEAD `1737454` → `2507925`,
tags + `2026-08-15`, timestamp → `2026-08-15T18:07:49Z`), refreshed
the Connector / State section to the new
`2026-08-15T18-07-49-711Z` raw manifest, refreshed the obsidian-vault
working-tree-status section to 2026-08-15 (no new untracked files;
the `Review/zhou2023_computer_vision_microfluidics.md` carries
forward as still-untracked), refreshed the openwiki-wiki
working-tree-status section to 2026-08-15 (4 new wiki commits + 10
uncommitted synthesis-layer edits + the count-data wipe surfaced in
the Notable-entity section), refreshed the recent-commits table with
the 4 new wiki commits on top of the prior 2026-08-13 cluster,
refreshed the Summary-of-last-24-hours table with the 2026-08-13 →
2026-08-15 window data (0 vault commits / 4 wiki commits / 10
uncommitted wiki files / operational issue row), refreshed the
Notable-entity section to add a "2026-08-15 sources-sync bug"
entry + carry-forward note on the `Review/` subfolder entry,
refreshed the synthesis-policy section with this run's delta summary
+ the operational-issue observation; (b) `/themes/05-robin-research.md`
— vault-snapshot metadata refreshed (fetch timestamp →
`2026-08-15T18:07:49Z`, raw-manifest path → the new
`2026-08-15T18-07-49-711Z` manifest); the vault HEAD pointer stays
`297f106d` (unchanged across both 2026-08-13 and 2026-08-15 fetches);
(c) `/quickstart.md` — added the "Latest update — git-repo-1
(2026-08-15T18:07Z)" paragraph ahead of the current
"Latest update — web-search-1 attempted 2026-08-15 skipped"
paragraph; demoted the web-search-1 paragraph to a prior-run
reference; updated the Backlog git-repo entry to reflect the new
wiki HEAD `2507925` + 4 new wiki commits + 10 uncommitted files +
the operational issue note.
**No `/commitments.md` row, no `/open-questions.md` row, no
`/personal-logistics.md` item, no `/themes.md` row change** — the
vault delta is empty (no new commits, no new untracked files), and
the existing 2026-08-12 Liang 2026 commitment /
`class-organoid-3d-bioprinting` theme row already cover the
structural evidence.
- **Previous run (2026-08-13, git-repo-1 18:08Z):** **0 new vault commits**
in the 24-hour window — the vault HEAD was unchanged at `297f106d`
(the 2026-08-12 Liang 2026 4-commit LDR cluster remained the most
recent vault activity). The only vault-side delta was **1 new
untracked file**: `04-Literature/Deep-Reads/Review/zhou2023_computer_vision_microfluidics.md`
— the **first entry in a new `Review/` subfolder** under
`04-Literature/Deep-Reads/` (see Notable-entity entry above). 1
noise file (`__pycache__/...pyc`) was ignored. Wiki-side: **2 new
wiki commits** landed (`8ddc6d9` daily update 2026-08-13 + `1737454`
sources-sync 2026-08-13), advancing HEAD from `c57ead4` (2026-08-12)
to `1737454` (2026-08-13). 8 dirty wiki files in the working tree
were synthesis-layer edits from the prior HN-1 2026-08-13 run that
landed after `1737454` committed and were pending the next CLI
orchestration commit.
- **Previous run (2026-08-12, git-repo-1 18:08Z):** 4 new vault commits
on the **same single Liang 2026 Sci Rep liver organoid paper** walked
through Robin's standard 3-stage LDR cycle (`e542c977` adds file →
`8699a154` page 946 9 项 SOP 重写版 → `aacba7aa` + `297f106d`
page 934 修齐 micro-revisions) — this was the **net-new external
evidence** for that run. Wiki edits at that time are described in
the synthesis-policy paragraph above; the canonical synthesis
continues to live at `/themes/01-organoid-equipment.md`,
`/themes/05-robin-research.md`, and `/commitments.md`
`liang-2026-celvivo-clinostar-positioning`.
- The vault is a knowledge base, not a live signal stream; durable
per-document synthesis (paper deep reads, sales scripts, customer
files) requires reading individual files, which is delegated to the
Hermes skill and RAGFlow.
- Future runs should keep this page structural. Promote a row to a canonical
theme only when the connector observes a recurring workflow (e.g. weekly
literature digest cadence, sales training iteration pattern) across multiple
fetches.
- **Process signal worth watching (2026-08-13):** (a) **New `Review/`
subfolder signal** — Robin added a 20th subfolder under
`04-Literature/Deep-Reads/` dedicated to review-type papers, with
`zhou2023_computer_vision_microfluidics.md` as the first entry. If
the subfolder accumulates ≥3 entries, this signals a formal
review-paper stream is being built separately from the
original-research stream; if it stays at 1 entry, it's a one-off.
(b) **Liang 2026's MOC linkage confirms the MOC pattern is in active
use** — the paper's `related:` field already names
`[[MOC-类器官与3D培养]]` (the first MOC, created 2026-08-10) on the
day of publication, not a future-state plan. Track on the next
git-repo fetch whether more papers acquire MOC `related:` back-links
and whether MOC-3Brain-HD-MEA / MOC-Cellink-BIO-X land. (c) **Page
934 修齐 micro-revisions now appear on every new LDR cycle** —
`297f106d` is the second paper (after `381fcbaa` OVB-organoids
2026-08-11) where Robin applied the H1 去括号 / 元数据 bold /
📄PDF 文件名 alignment. The pattern appears to be the new standard
end-state. (d) **Phase A frontmatter batch rollout** is still
paused (only 6 of ~1,204 deep-reads received the 6-field
frontmatter); no progress this run.
## Next update
Run `openwiki_ingest_connector connectorId=git-repo` (or
`openwiki personal --update`) to refresh. Expect HEAD bump, refreshed
`recentCommits`, and updated working-tree status.
rking-tree status.
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