chore: daily update 2026-08-25
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@@ -1,10 +1,10 @@
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---
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type: "Reference"
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title: "Git repo — evidence index (Obsidian vault, Robin)"
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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 a4fa5a32, 2026-08-16, **0 new vault commits in the 2026-08-22T18:13Z → 2026-08-23T18:11Z 24-hour window — vault is silent for the 7th consecutive fetch after the 2026-08-16 Quintard + Guo cluster, 7 calendar days stale**) and openwiki-wiki at /home/ldw/.openwiki/wiki (main branch, HEAD a9568d8, 2026-08-23, **2 new automated wiki commits in the 2026-08-22T18:13Z → 2026-08-23T18:11Z window: `8f8f767` sources-sync 2026-08-23 + `a9568d8` daily update 2026-08-23 — the ninth consecutive sources-sync re-applying the 2026-08-15 count-data wipe pattern**). This page is a navigation index — content ingestion (paper deep reads, sales scripts, customer files) happens via the Hermes skill and RAGFlow, not here."
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description: "Compact manifest of Robin's Obsidian vault + the local OpenWiki wiki, ingested through the local git-repo connector. Two configured repos: obsidian-vault at /home/ldw/workspace (main branch, HEAD fb017e4f, 2026-08-23/24, **5 new vault commits in the 2026-08-23T18:11Z → 2026-08-24T18:05Z 24-hour window — the largest single-day LDR burst since the 2026-07-29 Parate / Lee / Hodge cluster: `ad4abcde` Ajongbolo 2025 Cells brain organoid review + `5f02489a` Kim 2025 Nat Commun EGaIn 3D MEA + `40b357b8` Tian 2025 Nat Commun hiPSC epicardium mTOR + `f2118a62` Aiello & Bagni 2025 biorxiv Rotating Chamber brain organoid CFD + `fb017e4f` CelVivo App Note 2026 ClinoStar vs orbital shaker — 3 CelVivo-aligned papers (App Note + Aiello + Ajongbolo mentions ClinoStar) + 1 3Brain-adjacent 3D-MEA competitor paper (Kim EGaIn) + 1 cardiac epicardium paper (Tian)**) and openwiki-wiki at /home/ldw/.openwiki/wiki (main branch, HEAD 127c2dc, 2026-08-24, **2 new automated wiki commits in the 2026-08-23T18:11Z → 2026-08-24T18:05Z window: `9cc5e63` daily update 2026-08-24 + `127c2dc` sources-sync 2026-08-24 — the tenth consecutive sources-sync re-applying the 2026-08-15 count-data wipe pattern**). This page is a navigation index — content ingestion (paper deep reads, sales scripts, customer files) happens via the Hermes skill and RAGFlow, not here."
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resource: "~/.openwiki/connectors/git-repo/config.json"
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tags: [git-repo, evidence, vault, openwiki-wiki, source, 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]
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timestamp: 2026-08-23T18:11:00Z
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tags: [git-repo, evidence, vault, openwiki-wiki, source, 2026-08-24, 2026-08-23, 2026-08-22, 2026-08-21, 2026-08-20, 2026-08-19, 2026-08-18, 2026-08-17, 2026-08-15, 2026-08-13, celvivo-app-note-2026, aiello-bagni-rc-cfd, tian-epicardium-mtor, kim-egain-3d-mea, ajongbolo-brain-organoid-review]
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timestamp: 2026-08-24T18:05:00Z
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---
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# Git repo — evidence index (Obsidian vault + OpenWiki wiki)
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@@ -22,112 +22,120 @@ help locate things in the vault, not summarize their content.
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`~/.openwiki/connectors/git-repo/config.json`)
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- **Configured repos:**
|
||||
- `obsidian-vault` → `/home/ldw/workspace` (Robin Obsidian vault, on
|
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`main`, HEAD `a4fa5a323d6dcabeb9eccad49e636ee6ba5f87a6` as of
|
||||
2026-08-16 +0800 — 7 new vault commits in the
|
||||
2026-08-15T18:07Z → 2026-08-17T18:09Z 48-hour window: the 2026-08-16
|
||||
**Quintard 2024 Nat Commun 4-commit LDR cycle** (`0fc8db24` adds
|
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file 189 lines → `290e9635` -v2 修图床/双 H1/落款 → `24c713de`
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||||
-v3 Wiki.js 自带图床 6 张图 → `4073abf4` -v4 转发语标题/落款加粗/删
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||||
3Brain) + the 2026-08-16 **Guo 2026 Front Cell Dev Biol 3-commit LDR
|
||||
cycle** (`2e6f5989` adds file 170 lines → `00f824f2` -v2 修图床 →
|
||||
`a4fa5a32` -v3 补 Fig 1) — the first time two new paper LDR cycles
|
||||
land within the same 48-hour window since the 2026-07-28 / 2026-07-29
|
||||
Parate / Lee / Hodge cluster. The 2026-08-12 Liang 2026 4-commit LDR
|
||||
cycle remains the prior baseline cluster).
|
||||
`main`, HEAD `fb017e4fb40f874e54fb2a92eff235abe1c487cb` as of
|
||||
2026-08-23/24 +0800 — **5 new vault commits** in the
|
||||
2026-08-23T18:11Z → 2026-08-24T18:05Z 24-hour window: the
|
||||
**2026-08-23/24 5-paper LDR burst** that broke the 7-day vault
|
||||
silence — `ad4abcde` Ajongbolo 2025 Cells brain organoid review +
|
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`5f02489a` Kim 2025 Nat Commun EGaIn 3D MEA + `40b357b8` Tian 2025
|
||||
Nat Commun hiPSC epicardium mTOR + `f2118a62` Aiello & Bagni 2025
|
||||
biorxiv Rotating Chamber brain organoid CFD + `fb017e4f` CelVivo
|
||||
App Note 2026 ClinoStar vs orbital shaker head-to-head. 3 CelVivo-
|
||||
aligned papers (App Note + Aiello + Ajongbolo mentions ClinoStar
|
||||
reagent supply chain) + 1 3Brain-adjacent 3D-MEA competitor paper
|
||||
(Kim EGaIn) + 1 cardiac epicardium paper (Tian); each commit is a
|
||||
single-shot entry (no v2/v3 SOP rewrite cycles this cluster — the
|
||||
page-934 / page-946 alignment work from the 2026-08-12 Liang 2026
|
||||
cluster is no longer in flight). **Largest single-day LDR burst
|
||||
since the 2026-07-29 Parate / Lee / Hodge cluster** — breaks the
|
||||
7-day vault silence streak that started after the 2026-08-16
|
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Quintard + Guo cluster).
|
||||
- `openwiki-wiki` → `/home/ldw/.openwiki/wiki` (the OpenWiki knowledge
|
||||
base itself, on `main`, HEAD `dcb53a2873d37b6396de682d658433c2ea85b376`
|
||||
as of 2026-08-19T +0800 — 8 new wiki-side commits across the
|
||||
2026-08-15T18:07Z → 2026-08-19T18:08Z window: `151d22b` daily
|
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update 2026-08-16 + `997b648` sources-sync 2026-08-16 + `5c70881`
|
||||
daily update 2026-08-17 + `be49285` sources-sync 2026-08-17 +
|
||||
`8127797` daily update 2026-08-18 + `1fc73ae` sources-sync
|
||||
2026-08-18 + `7e904ec` daily update 2026-08-19 + `dcb53a2`
|
||||
sources-sync 2026-08-19; the `5c70881` daily update also created
|
||||
the new `sources/openwiki-version-drift.md` auto-generated page;
|
||||
the 4 sources-syncs (`997b648` + `be49285` + `1fc73ae` + `dcb53a2`)
|
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all re-applied the `2507925` 2026-08-15 count-data wipe pattern).
|
||||
base itself, on `main`, HEAD `127c2dc60fb8398d02485313df25994e7e18c69f`
|
||||
as of 2026-08-24T +0800 — 2 new wiki-side commits in the
|
||||
2026-08-23T18:11Z → 2026-08-24T18:05Z 24-hour window: `9cc5e63`
|
||||
chore: daily update 2026-08-24 + `127c2dc` chore(sources): refresh
|
||||
NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-24) —
|
||||
the **tenth** consecutive sources-sync re-applying the 2026-08-15
|
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count-data wipe pattern).
|
||||
- **Auth:** local paths only — no remote, no credentials.
|
||||
- **Latest fetch:** `2026-08-23T18:11:00Z` (raw manifest
|
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`~/.openwiki/connectors/git-repo/raw/2026-08-23T18-11-34-883Z/manifest.json`).
|
||||
- **Latest fetch:** `2026-08-24T18:05:00Z` (raw manifest
|
||||
`~/.openwiki/connectors/git-repo/raw/2026-08-24T18-05-31-919Z/manifest.json`).
|
||||
- **Source config:** `~/.openwiki/connectors/git-repo/config.json`
|
||||
- **State:** `~/.openwiki/connectors/git-repo/state.json` records
|
||||
`latestIds` per repo; the 2026-08-23T18:11Z fetch observed vault HEAD
|
||||
unchanged at `a4fa5a32` (2026-08-16 — same as the 2026-08-17T18:09Z +
|
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`latestIds` per repo; the 2026-08-24T18:05Z fetch observed vault HEAD
|
||||
bumped from `a4fa5a32` (2026-08-16 — same as the 2026-08-17T18:09Z +
|
||||
2026-08-18T18:10Z + 2026-08-19T18:08Z + 2026-08-20T18:09Z +
|
||||
2026-08-21T18:09Z + 2026-08-22T18:13Z + 2026-08-23T18:11Z fetches;
|
||||
**0 new vault commits in the 24-hour window — vault is silent for
|
||||
the 7th consecutive fetch** after the 2026-08-16 Quintard + Guo
|
||||
cluster, **7 calendar days stale**), and observed `openwiki-wiki`
|
||||
bumped from `43d4548` (2026-08-22T18:13Z fetch) to `a9568d8`
|
||||
(2 new automated wiki commits in the 24-hour window: `8f8f767`
|
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sources-sync 2026-08-23 + `a9568d8` daily update 2026-08-23 — the
|
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**ninth** consecutive sources-sync re-applying the 2026-08-15
|
||||
2026-08-21T18:09Z + 2026-08-22T18:13Z + 2026-08-23T18:11Z fetches
|
||||
through 7 consecutive silent windows, **7 calendar days stale**) to
|
||||
`fb017e4f` (2026-08-23/24 — **5 new vault commits** in the 24-hour
|
||||
window, breaking the 7-day silence streak), and observed
|
||||
`openwiki-wiki` bumped from `a9568d8` (2026-08-23T18:11Z fetch) to
|
||||
`127c2dc` (2 new automated wiki commits in the 24-hour window:
|
||||
`9cc5e63` daily update 2026-08-24 + `127c2dc` sources-sync 2026-08-24
|
||||
— the **tenth** consecutive sources-sync re-applying the 2026-08-15
|
||||
count-data wipe pattern after `997b648` 2026-08-16 + `be49285`
|
||||
2026-08-17 + `1fc73ae` 2026-08-18 + `dcb53a2` 2026-08-19 + `bd30339`
|
||||
2026-08-20 + `f6c2576` 2026-08-21 + `43d4548` 2026-08-22 + now
|
||||
`8f8f767` 2026-08-23).
|
||||
2026-08-20 + `f6c2576` 2026-08-21 + `43d4548` 2026-08-22 + `8f8f767`
|
||||
2026-08-23 + now `127c2dc` 2026-08-24).
|
||||
|
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## obsidian-vault — working-tree status (2026-08-23)
|
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## obsidian-vault — working-tree status (2026-08-24)
|
||||
|
||||
- **Branch:** `main`
|
||||
- **HEAD:** `a4fa5a323d6dcabeb9eccad49e636ee6ba5f87a6` (vault HEAD
|
||||
**unchanged** at `a4fa5a32` across the 2026-08-23T18:11Z fetch —
|
||||
**0 new commits** in the 2026-08-22T18:13Z → 2026-08-23T18:11Z
|
||||
24-hour window; the vault is silent for the **7th consecutive
|
||||
fetch** after the 2026-08-17T18:09Z + 2026-08-18T18:10Z +
|
||||
2026-08-19T18:08Z + 2026-08-20T18:09Z + 2026-08-21T18:09Z +
|
||||
2026-08-22T18:13Z silent
|
||||
windows. 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 committed vault activity (vault HEAD last bumped on 2026-08-16,
|
||||
**7 calendar days before this fetch** — same state as the
|
||||
- **HEAD:** `fb017e4fb40f874e54fb2a92eff235abe1c487cb` (vault HEAD
|
||||
**bumped** from `a4fa5a32` (2026-08-16) → `fb017e4f` (2026-08-23/24)
|
||||
across the 2026-08-24T18:05Z fetch — **5 new commits** in the
|
||||
2026-08-23T18:11Z → 2026-08-24T18:05Z 24-hour window; the vault
|
||||
breaks the **7-fetch silent streak** that started after the
|
||||
2026-08-17T18:09Z + 2026-08-18T18:10Z + 2026-08-19T18:08Z +
|
||||
2026-08-20T18:09Z + 2026-08-21T18:09Z + 2026-08-22T18:13Z fetches).
|
||||
- **mtime activity in window:** **0 new mtime changes** in the
|
||||
2026-08-22T18:13Z → 2026-08-23T18:11Z 24-hour window. The 2
|
||||
2026-08-20T18:09Z + 2026-08-21T18:09Z + 2026-08-22T18:13Z +
|
||||
2026-08-23T18:11Z silent windows. The 2026-08-23/24 cluster is
|
||||
**the largest single-day LDR burst since the 2026-07-29 Parate /
|
||||
Lee / Hodge cluster** — 5 paper deep-reads added in <24h, all
|
||||
single-shot entry (no v2/v3 SOP rewrite cycles this cluster, vs the
|
||||
3-stage SOP cycle on the 2026-08-12 Liang 2026 cluster and the
|
||||
4-commit / 3-commit LDR cycles on the 2026-08-16 Quintard + Guo
|
||||
cluster). The 2026-08-16 Quintard 2024 Nat Commun + Guo 2026 Front
|
||||
Cell Dev Biol cluster has been replaced as the most recent committed
|
||||
vault activity after a **7-day stale period** (now stale 0 days).
|
||||
- **mtime activity in window:** **5 new committed files** in the
|
||||
2026-08-23T18:11Z → 2026-08-24T18:05Z 24-hour window — all 5 new
|
||||
paper LDR files at `obsidian-vault/04-Literature/Deep-Reads/` root
|
||||
(no subfolder) per the manifest paths `Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid.md`
|
||||
+ `Ajongbolo_2025_Cells_Brain_Organoids_Review.md` +
|
||||
`CelVivo_Shear_Stress_AppNote_2026.md` +
|
||||
`Kim_2025_NatCommun_Liquid_Metal_3D_MEA.md` +
|
||||
`Tian_2025_NatCommun_Epicardium_mTOR.md`. Commit order (mtime
|
||||
ascending): `ad4abcde` 2026-08-24 07:50 Ajongbolo review → `5f02489a`
|
||||
2026-08-24 08:05 Kim LM 3D MEA → `40b357b8` 2026-08-24 09:00 Tian
|
||||
epicardium mTOR → `f2118a62` 2026-08-24 16:23 Aiello RC brain
|
||||
organoid → `fb017e4f` 2026-08-24 16:39 CelVivo App Note 2026 — the
|
||||
burst spans the full 2026-08-24 day from 07:50 to 16:39 +0800. The 2
|
||||
untracked dirs from the 2026-08-17T18:09Z fetch are unchanged:
|
||||
`celvivo_commercial/` last touched 2026-08-17 15:04 +0800 (= 07:04
|
||||
UTC, **before** the 24h window) + `templates/` last touched
|
||||
2026-08-16 10:27 +0800 (= 02:27 UTC, well before the window). The
|
||||
`Review/zhou2023_computer_vision_microfluidics.md` first-entry
|
||||
file is unchanged from the 2026-08-17T18:09Z fetch (mtime
|
||||
2026-08-11, **12-day carry-forward** in the untracked set at this
|
||||
fetch — was 11-day at the 2026-08-22T18:13Z fetch; the structural
|
||||
signal continues to weaken per the Notable-entity entry on the
|
||||
`Review/` subfolder).
|
||||
- **Ahead of origin/main:** 20 commits new since 2026-08-03 fetch (unchanged from the 2026-08-17T18:09Z + 2026-08-18T18:10Z + 2026-08-19T18:08Z + 2026-08-20T18:09Z + 2026-08-21T18:09Z + 2026-08-22T18:13Z + 2026-08-23T18:11Z fetches — vault is silent in the 2026-08-22T18:13Z → 2026-08-23T18:11Z window).
|
||||
- **Dirty:** yes — the untracked file set is **unchanged** from the
|
||||
2026-08-17T18:09Z fetch (no new untracked files or directories
|
||||
appeared in the 2026-08-17T18:09Z → 2026-08-18T18:10Z 24-hour
|
||||
window, no new untracked files or directories appeared in the
|
||||
2026-08-18T18:10Z → 2026-08-19T18:08Z 24-hour window, no new
|
||||
untracked files or directories appeared in the 2026-08-19T18:08Z →
|
||||
2026-08-20T18:09Z 24-hour window, no new untracked files or
|
||||
directories appeared in the 2026-08-20T18:09Z → 2026-08-21T18:09Z
|
||||
24-hour window, no new untracked files or directories appeared in
|
||||
the 2026-08-21T18:09Z → 2026-08-22T18:13Z 24-hour window, and no
|
||||
new untracked files or directories appeared in the
|
||||
2026-08-22T18:13Z → 2026-08-23T18:11Z 24-hour window either).
|
||||
The 25+ untracked entries from the
|
||||
2026-08-17T18:09Z fetch carry forward unchanged: 8 ×
|
||||
`02-Clients/Agents/区域-2026-0807.md` distributor-rebuild files
|
||||
(per the 2026-08-07 Hermes hook 4 sweep) + 14 working-folder files
|
||||
(Parfitt 2024 DJ1 LOF midbrain + Liu2026 / Miao2025 v2 /
|
||||
Miao2025 vascularized / Microbioreactor 2026 /
|
||||
`__pycache__/literature_deepread_v6.cpython-312.pyc` /
|
||||
`dify精读进度-20260805.md` / `literature_deepread_v6.py` /
|
||||
`obsidian-vault/04-Literature/Deep-Reads/Review/zhou2023_computer_vision_microfluidics.md`
|
||||
/ `obsidian-vault/rustdesk-selfhosted-2026-08-05.md` /
|
||||
`retinal_organoid_deep_read_2026-08-07.md` / `文悦精读流水线.yml` +
|
||||
v2/v3/v4/v5-clean variants) + 2 new untracked working-tree
|
||||
directories from the 2026-08-17T18:09Z fetch (`celvivo_commercial/`
|
||||
+ `templates/`). The **`Review/zhou2023_computer_vision_microfluidics.md`
|
||||
first entry in the new `Review/` subfolder** is still **untracked**
|
||||
(Robin has not yet committed it) — **12-day carry-forward** at this
|
||||
fetch (was 11-day at the 2026-08-22T18:13Z 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 **10 fetches silent**).
|
||||
UTC) + `templates/` last touched 2026-08-16 10:27 +0800 (= 02:27
|
||||
UTC). The `Review/zhou2023_computer_vision_microfluidics.md`
|
||||
first-entry file is unchanged from the 2026-08-17T18:09Z fetch
|
||||
(mtime 2026-08-11, **13-day carry-forward** in the untracked set at
|
||||
this fetch — was 12-day at the 2026-08-23T18:11Z fetch; the
|
||||
structural signal continues to weaken per the Notable-entity entry
|
||||
on the `Review/` subfolder). **NEW this fetch**: 1 new untracked
|
||||
working dir `deepread_40240593/` (mtime 2026-08-24 16:31 +0800 = 08:31
|
||||
UTC, within the 24h window) — pipeline scratch workspace
|
||||
containing 7 PMID-specific subdirs (`deepread_40016200` /
|
||||
`deepread_40441268` / `deepread_40498018` / `deepread_40593704` /
|
||||
`deepread_41151577` + 2 named subdirs `deepread_brain_organoid_fluid`
|
||||
[Aiello paper] + `deepread_shear_stress_cs_os` [CelVivo App Note]).
|
||||
The 5 PMIDs are not currently on the vault `main` as deep-read files,
|
||||
suggesting the `deepread_40240593/` is the pipeline's pending-triage
|
||||
workspace for the 2026-08-24 batch.
|
||||
- **Ahead of origin/main:** 25 commits new since 2026-08-03 fetch (+5
|
||||
from the prior 20-commit baseline at the 2026-08-23T18:11Z fetch —
|
||||
the 5 new commits land on top of the 20-commit carry-forward).
|
||||
- **Dirty:** yes — the untracked file set is **partially changed**:
|
||||
the 8 × `02-Clients/Agents/区域-2026-0807.md` distributor-rebuild
|
||||
files + 14 working-folder files + 2 untracked dirs from the
|
||||
2026-08-17T18:09Z fetch carry forward unchanged, and the
|
||||
`Review/zhou2023_computer_vision_microfluidics.md` first-entry in the
|
||||
new `Review/` subfolder is still **untracked** (Robin has not yet
|
||||
committed it) — **13-day carry-forward** at this fetch (was 12-day
|
||||
at the 2026-08-23T18:11Z fetch); the structural signal continues to
|
||||
weaken per the Notable-entity entry on the `Review/` subfolder (the
|
||||
subfolder has been a single-entry watchlist since 2026-08-13, now
|
||||
**11 fetches silent**). **NEW this fetch**: 1 new untracked working
|
||||
directory `deepread_40240593/` (created 2026-08-24 16:31 +0800 =
|
||||
08:31 UTC, **0-day carry-forward** at this fetch — first observation,
|
||||
pipeline scratch workspace).
|
||||
- **Working-tree status (raw manifest, abbreviated):**
|
||||
|
||||
| Status | Path |
|
||||
@@ -174,6 +182,11 @@ help locate things in the vault, not summarize their content.
|
||||
|
||||
| Date | Hash | Note |
|
||||
| --- | --- | --- |
|
||||
| 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) |
|
||||
@@ -337,27 +350,26 @@ indexed on [`/sources/literature.md`](/sources/literature.md). The
|
||||
`1614ccf9`) are the 8-step SOP rewrite cycle (v3 → v11) Robin re-ran
|
||||
on the same paper.
|
||||
|
||||
## openwiki-wiki — working-tree status (2026-08-23)
|
||||
## openwiki-wiki — working-tree status (2026-08-24)
|
||||
|
||||
- **Branch:** `main`
|
||||
- **HEAD:** `a9568d8` (the
|
||||
`chore: daily update 2026-08-23` commit). The 2026-08-23T18:11Z
|
||||
fetch observed wiki HEAD bumped from `43d4548` (2026-08-22T18:13Z
|
||||
fetch) to `a9568d8` — **2 new automated wiki commits** in the
|
||||
2026-08-22T18:13Z → 2026-08-23T18:11Z 24-hour window: (a) `8f8f767`
|
||||
chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts
|
||||
(sources-sync 2026-08-23, 2026-08-23 02:30 +0800); (b) `a9568d8`
|
||||
chore: daily update 2026-08-23 (2026-08-23 02:29 +0800). Both
|
||||
commits are routine auto-orchestration — 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
|
||||
`8f8f767` sources-sync re-applied the count-data wipe pattern on
|
||||
NocoDB / SeaFile / Wiki.js / RAGFlow for the **ninth** 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 + now `8f8f767`
|
||||
2026-08-23).
|
||||
- **HEAD:** `127c2dc` (the
|
||||
`chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-24)` commit). The 2026-08-24T18:05Z
|
||||
fetch observed wiki HEAD bumped from `a9568d8` (2026-08-23T18:11Z
|
||||
fetch) to `127c2dc` — **2 new automated wiki commits** in the
|
||||
2026-08-23T18:11Z → 2026-08-24T18:05Z 24-hour window: (a) `9cc5e63`
|
||||
chore: daily update 2026-08-24 (2026-08-24 02:23 +0800); (b)
|
||||
`127c2dc` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts
|
||||
(sources-sync 2026-08-24, 2026-08-24 02:30 +0800). Both commits are
|
||||
routine auto-orchestration — 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 `127c2dc` sources-sync re-applied the count-data wipe
|
||||
pattern on NocoDB / SeaFile / Wiki.js / RAGFlow for the **tenth**
|
||||
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
|
||||
+ now `127c2dc` 2026-08-24).
|
||||
- **Working-tree state:** 6 modified files (uncommitted — pending
|
||||
next CLI orchestration). The 2026-08-23T18:11Z fetch observed the
|
||||
working tree at 6 uncommitted files (down from 9 at the
|
||||
@@ -449,6 +461,8 @@ on the same paper.
|
||||
|
||||
| Date | Hash | Note |
|
||||
| --- | --- | --- |
|
||||
| 2026-08-24 | `127c2dc` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-24) — **count-data wipe re-applied** for the **tenth** consecutive sources-sync (after 2026-08-15 `2507925` + 2026-08-16 `997b648` + 2026-08-17 `be49285` + 2026-08-18 `1fc73ae` + 2026-08-19 `dcb53a2` + 2026-08-20 `bd30339` + 2026-08-21 `f6c2576` + 2026-08-22 `43d4548` + 2026-08-23 `8f8f767`); see Notable-entity § "2026-08-15 sources-sync bug" |
|
||||
| 2026-08-24 | `9cc5e63` | chore: daily update 2026-08-24 (synthesis-layer edits accumulated from the prior HN-1 2026-08-23T18:00Z + web-search-1 2026-08-23 (skipped) + git-repo-1 2026-08-23T18:11Z runs; committed `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/openwiki-version-drift.md` + `sources/web-search.md` + `themes/05-robin-research.md` from the prior dirty set, reducing uncommitted-file count from 6 → 8 because the very next synthesis edits from this git-repo-1 2026-08-24T18:05Z run re-touch the same 6 files + add 2 newly dirty files `sources/literature.md` + `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` per the manifest `changedFiles` list) |
|
||||
| 2026-08-23 | `a9568d8` | chore: daily update 2026-08-23 (synthesis-layer edits accumulated from the prior HN-1 2026-08-22T18:00Z + web-search-1 2026-08-22 (skipped) + web-search-1 2026-08-23 (skipped) + git-repo-1 2026-08-22T18:13Z runs; committed `sources/git-repo.md` + `sources/index.md` + `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` + `themes/05-robin-research.md` from the prior dirty set, reducing uncommitted-file count from 9 → 6) |
|
||||
| 2026-08-23 | `8f8f767` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-23) — **count-data wipe re-applied** for the **ninth** consecutive sources-sync (after 2026-08-15 `2507925` + 2026-08-16 `997b648` + 2026-08-17 `be49285` + 2026-08-18 `1fc73ae` + 2026-08-19 `dcb53a2` + 2026-08-20 `bd30339` + 2026-08-21 `f6c2576` + 2026-08-22 `43d4548`); see Notable-entity § "2026-08-15 sources-sync bug" |
|
||||
| 2026-08-22 | `43d4548` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-22) — **count-data wipe re-applied** for the **eighth** consecutive sources-sync (after 2026-08-15 `2507925` + 2026-08-16 `997b648` + 2026-08-17 `be49285` + 2026-08-18 `1fc73ae` + 2026-08-19 `dcb53a2` + 2026-08-20 `bd30339` + 2026-08-21 `f6c2576`); see Notable-entity § "2026-08-15 sources-sync bug" |
|
||||
@@ -533,6 +547,7 @@ pipeline catches up.
|
||||
|
||||
| Window (UTC) | Vault | Wiki |
|
||||
| --- | --- | --- |
|
||||
| 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)) |
|
||||
@@ -577,6 +592,7 @@ 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 |
|
||||
@@ -594,14 +610,15 @@ Markdown file counts per deep-read subfolder:
|
||||
| `Retinal/` | 1 |
|
||||
| `Microbioreactor/` | 1 (new as of 2026-08-07 — Rosero 2026 Front Bioeng Biotechnol) |
|
||||
| `Cells/` | 1 (new as of 2026-08-08 — Fernandez Vallone 2026 Cells THSDC) |
|
||||
| `Review/` | 1 (new as of 2026-08-13 — Zhou 2023 computer vision + microfluidics, **untracked**, **10-day carry-forward** at 2026-08-21 fetch, **8 fetches silent** — structural signal continuing to weaken; **11-day carry-forward** at 2026-08-22 fetch, **9 fetches silent**; **12-day carry-forward** at 2026-08-23 fetch, **10 fetches silent**) |
|
||||
| `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 |
|
||||
| `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 |
|
||||
| `Review/` | 1 (new as of 2026-08-13 — Zhou 2023 computer vision + microfluidics, **untracked**, **10-day carry-forward** at 2026-08-21 fetch, **8 fetches silent** — structural signal continuing to weaken; **11-day carry-forward** at 2026-08-22 fetch, **9 fetches silent**; **12-day carry-forward** at 2026-08-23 fetch, **10 fetches silent**; **13-day carry-forward** at 2026-08-24 fetch, **11 fetches silent** — structural signal continues to weaken) |
|
||||
| `templates/` | 1 (new as of 2026-08-17 — `类器官IRB申请清单.md`, derived from the Guo 2026 ethics deep-read; Robin's first customer-facing template produced from a single deep-read, **untracked**, **5-day carry-forward** at 2026-08-21 fetch (was 4-day at 2026-08-20); **6-day carry-forward** at 2026-08-22 fetch; **7-day carry-forward** at 2026-08-23 fetch; **8-day carry-forward** at 2026-08-24 fetch) |
|
||||
| `celvivo_commercial/` | 1 (new as of 2026-08-17 — `1331651_20260630_131201.pdf`, the 6-30 quote PDF migrated into a new folder, **untracked**, **5-day carry-forward** at 2026-08-21 fetch (was 4-day at 2026-08-20); **6-day carry-forward** at 2026-08-22 fetch; **7-day carry-forward** at 2026-08-23 fetch; **8-day carry-forward** at 2026-08-24 fetch) |
|
||||
| `04-Literature/Deep-Reads/` root (5 new files) | 5 (new as of 2026-08-23/24 — single-shot LDR burst: `CelVivo_Shear_Stress_AppNote_2026.md` + `Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid.md` + `Tian_2025_NatCommun_Epicardium_mTOR.md` + `Kim_2025_NatCommun_Liquid_Metal_3D_MEA.md` + `Ajongbolo_2025_Cells_Brain_Organoids_Review.md` — all landed at the root of `04-Literature/Deep-Reads/` not in a per-vendor subfolder; **non-standard pattern** vs the prior per-vendor subfolder discipline, see Notable-entity § "2026-08-23 root-level LDR burst") |
|
||||
|
||||
Total ≈ 1,207 deep-read notes on `main` (+2 from the 2026-08-16 Quintard 2024 + Guo 2026 clusters).
|
||||
Total ≈ 1,212 deep-read notes on `main` (+5 from the 2026-08-23/24 single-shot LDR burst, on top of +2 from the 2026-08-16 Quintard 2024 + Guo 2026 clusters).
|
||||
Review/ zhou2023 computer vision + microfluidics, **untracked** — only
|
||||
counts once committed; +2 working-tree files in the new `templates/` +
|
||||
`celvivo_commercial/` directories, both untracked). The 2026-08-16 Quintard 2024 + Guo 2026 cluster is the most recent committed deep-read additions; the 2026-08-07 / 2026-08-08 cluster (Microbioreactor + Cells) remains the prior committed cluster. CelVivo, 3Brain, Cellink, and the broad `Organoid/` bucket cover Robin's product KB per the wiki goal focus areas (类器官培养与设备, 3D 生物打印). The new `templates/` folder signals Robin may be formalizing customer-facing deliverables (checklists / templates / sales scripts) as a separate vault subtree — the IRB application checklist is the first such artifact.
|
||||
`celvivo_commercial/` directories, both untracked; +1 working-tree directory `deepread_40240593/` (7 subdirs, 2026-08-24) carrying pipeline intermediate artifacts from the 5-paper burst). The 2026-08-23/24 single-shot LDR burst (5 papers at vault root) is the most recent committed deep-read cluster; the 2026-08-16 Quintard 2024 + Guo 2026 cluster remains the prior committed cluster; the 2026-08-07 / 2026-08-08 cluster (Microbioreactor + Cells) remains the prior-prior committed cluster. CelVivo, 3Brain, Cellink, and the broad `Organoid/` bucket cover Robin's product KB per the wiki goal focus areas (类器官培养与设备, 3D 生物打印). The new `templates/` folder signals Robin may be formalizing customer-facing deliverables (checklists / templates / sales scripts) as a separate vault subtree — the IRB application checklist is the first such artifact.
|
||||
|
||||
## Distributor map refresh (2026-08-07)
|
||||
|
||||
@@ -662,6 +679,13 @@ fields still 待补).
|
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|
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## Notable entities surfaced by the vault (structural hints only)
|
||||
|
||||
- **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 this fetch)** — `deepread_40240593/` is the **first** new untracked directory added this fetch, alongside the 5 root-level LDR files. The directory contains **7 subdirectories**: `deepread_40016200` + `deepread_40441268` + `deepread_40498018` + `deepread_40593704` + `deepread_41151577` + `deepread_brain_organoid_fluid` + `deepread_shear_stress_cs_os`. The directory is at the vault root (not in `04-Literature/`); the numeric-name pattern (`deepread_<PMID>`) suggests Robin's LDR pipeline is using these directories as **per-paper working folders** — the names include both PMIDs (40016200, 40441268, 40498018, 40593704, 41151577) and human-readable slugs (brain_organoid_fluid → maps to Aiello paper; shear_stress_cs_os → maps to CelVivo App Note). The directory mtime is 2026-08-24 16:31 +0800 (1-day-old at this fetch). **Structural significance**: (a) the `deepread_<PMID>` naming convention is **not** the prior `04-Literature/Deep-Reads/<vendor>/` convention — the new pattern is a **per-paper working-folder pattern** that holds pipeline intermediate artifacts (PDFs, image-extracts, qa-pass outputs, Ollama vision-audit intermediates, etc.) before final commit to `04-Literature/Deep-Reads/`. (b) The presence of 5 already-committed root-level LDR files (in `04-Literature/Deep-Reads/`) **plus** the 2 named `deepread_<slug>` folders (brain_organoid_fluid + shear_stress_cs_os) — which exactly map to 2 of the 5 committed papers — suggests Robin's pipeline writes the **committed LDR note** to `04-Literature/Deep-Reads/` and the **intermediate artifacts** to `deepread_40240593/deepread_<slug>/`; the other 5 PMID-named subdirs are pipeline intermediates for 5 other in-progress papers not yet on `main`. (c) The vault-root `deepread_40240593/` is **not yet committed** (carry-forward untracked); the 2026-08-23 7-paper burst means Robin is producing pipeline output faster than the manual commit cycle. **Carry-forward status** (2026-08-24): untracked, **1-day-old** at this fetch, future-commit candidate. **Track on next fetch** whether (a) the directory is committed, (b) more papers move through the pipeline, (c) the `deepread_<PMID>` vs `04-Literature/Deep-Reads/<slug>` separation is formalized in vault conventions. **No synthesis routes** until the directory is committed.
|
||||
- **Quintard 2024 Nat Commun microfluidic vascularized organoid chip (2026-08-16, 7 commits in 48-hour window)** — `obsidian-vault/Literature/Deep-Reads/Organoid/quintard_2024_vasorganoid_chip.md` (189 lines; 4-commit LDR cycle `0fc8db24` adds → `290e9635` -v2 修图床/双 H1/落款 → `24c713de` -v3 Wiki.js 自带图床 6 张图 → `4073abf4` -v4 转发语标题/落款加粗/删 3Brain; Wiki IDs 1719/1720/1722, NocoDB Id 3297). The paper is **the first microfluidic / organ-on-chip platform paper** Robin has deep-read in the 2026-08 window; the platform combines (i) 10-channel parallel microfluidic chips with U-shaped capture sites (300-800 µm adjustable), (ii) fibrin + Matrigel hydrogel layer deposition using Landau-Levich-Bretherton effect, (iii) ~10 s capture efficiency ~100%, (iv) dynamic perfusion 7-30 days with HUVEC + fibroblast co-culture + hiPSC-derived BVO + islet spheroid + lung organoid cross-validation, (v) hierarchical vasculature (37 µm upstream artery-vein + 8 µm BVO capillaries, matching physiological ranges 50-1900 s⁻¹). **Net-new external evidence** in this run (git-repo-1 2026-08-17). The 4-star "与我们的产品" table lists **Mimetas OrganoPlate ⭐⭐⭐⭐** (direct Phaseguide-based vascularized / kidney / intestine organ-on-chip competitor) + **CelVivo ClinoStar ⭐⭐⭐** (upstream workflow step: BVO differentiation day 0-15 needs rotating-wall suspension culture; ClinoStar is the canonical hardware for this stage; the paper's day 15 → chip-on-board handoff is the canonical CelVivo → organ-on-chip workflow) + **Emulate Organ-Chip ⭐⭐⭐** (Colon-Intestine-Liver platform companion). Synthesis routes into `/themes/05-robin-research.md` (新增 by-vendor entry) and `/sources/literature.md` (last-30-days deep-read table). Vendor-anchor mapping: CelVivo-adjacent (workflow upstream) + Mimetas OrganoPlate / Emulate Organ-Chip (organ-on-chip product lane that Robin's portfolio does not currently cover but represents a potential cross-sell if Robin's customers ask "where do I run my CelVivo-matured organoids in a vascularized microenvironment?"). Customer-entry: 药企临床前 (vascularized drug screening) + 微流控 organ-on-chip 平台集成商 (Mimetas / Emulate channel partners) + academic PI (vascular development / diabetes). **Track on next fetch** whether Robin publishes a `/sources/literature-quintard-2024-nat-commun-vasorganoid-chip-deepread.md` synthesis page; the deep-read pipeline currently only carries `liang-2026-celvivo-clinostar-positioning` + `miao-2025-celvivo-clinostar-positioning` + `liu-2026-hd-mea-roadmap-implication` + `sharma-2026-retinal-organoid-mea-cross-sell` — no Quintard synthesis page yet.
|
||||
- **Guo 2026 Front Cell Dev Biol organoid ethics systematic review (2026-08-16, 7 commits in 48-hour window)** — `obsidian-vault/Literature/Deep-Reads/Organoid/guo_2026_organoid_ethical_review.md` (170 lines + 3 真图; 3-commit LDR cycle `2e6f5989` adds → `00f824f2` -v2 修图床 (加 2 张 Wiki.js 自带图) → `a4fa5a32` -v3 补 Fig 1; Wiki ID 1724, NocoDB Id 3298). The paper is **the first organoid-research ethics / IRB systematic review** Robin has deep-read in any window — fills the methodological gap on the IRB-side that the prior clinical-translation evidence (CDE classification + Order No. 818) does not directly cover. The paper structures the IRB review framework as **7 mandatory points** (sample provenance + donor informed consent + data privacy & de-identification + co-culture agency + animal welfare 3R + cross-border regulation + long-term storage & termination); the cross-border table compares China (《人类遗传资源管理条例》+ 《涉及人的生命科学和医学研究伦理审查办法》2023), US (HIPAA + Common Rule + NIH GDS), EU (GDPR + Clinical Trials Regulation 536/2014), Japan, Korea. The 4-star "与我们的产品" table lists **CelVivo ClinoStar ⭐⭐⭐⭐** (clinical-translation IRB compliance — the 7 mandatory points directly apply to ClinoStar customer IRB submissions; **Robin 推广 ClinoStar 给三甲医院时, 可附带本框架作为增值**) + **Mimetas OrganoPlate ⭐⭐⭐⭐** (co-culture ethics — Mimetas 主营类器官 + 免疫细胞共培养, the co-culture agency framework from Guo 2026 point 4 directly applies) + **Emulate Organ-Chip ⭐⭐⭐** (organoid + microfluidic cross-border regulation reference). **Net-new external evidence** in this run (git-repo-1 2026-08-17). Robin translated the paper into a **customer-facing sales ammunition template** at `templates/类器官IRB申请清单.md` (180 lines; 7 mandatory points checklist + 5 customer Q&A + China vs International flow table + 10 attachments + 7 citations; v1.0 dated 2026-08-16, "Robin 8-16 实战沉淀") — see the templates/ entry in the next bullet. Customer-entry: 临床转化型医院 (class A tertiary hospitals running organoid IRB submissions) + 类器官厂家 Robin 培训客户 (the IRB checklist is the canonical "Robin 培训客户 IRB 申请" core material) + academic PI (cross-border collaboration IRB paperwork). **Track on next fetch** whether (a) the templates/ IRB checklist gets committed, (b) the Robin-author attribution in the template is recognized as a wiki-side customer-training artifact, (c) Robin produces a deep-read synthesis page at `/sources/literature-guo-2026-front-cell-dev-biol-organoid-ethics-deepread.md`, and (d) the IRB checklist routes into the existing CelVivo industrial-customers program (which currently lives at `05-Documents/Products/Celvivo/Industrial-Customers/`) as a standard customer-training artifact.
|
||||
- **Review/ subfolder — first entry (2026-08-13, still uncommitted at 2026-08-23, 12-day carry-forward, watchlist signal continuing to weaken)** — `obsidian-vault/04-Literature/Deep-Reads/Review/zhou2023_computer_vision_microfluidics.md` is the **first file in a new `Review/` subfolder** under `04-Literature/Deep-Reads/`. The file is **untracked** at the 2026-08-23 fetch (Robin has not yet committed it — same state as the 2026-08-13 + 2026-08-15 + 2026-08-17 + 2026-08-18 + 2026-08-19 + 2026-08-20 + 2026-08-21 + 2026-08-22 fetches, **0 progress in the 2026-08-13 → 2026-08-23 240-hour window**, **10 consecutive fetches silent on the file**). **Watchlist signal continuing to weaken at this fetch**: per the 2026-08-15 watchlist-trigger rubric ("if the file remains uncommitted at the next fetch (2026-08-17 or later), the structural signal weakens"), the `Review/` subfolder at the 2026-08-23 fetch is **still single-entry, still untracked** — the structural signal **continues to weaken** at this fetch (**12-day carry-forward** with no commit, no follow-up paper landed in the subfolder across **10 consecutive fetches**). The `Review/` subfolder is more likely to be a one-off than a recurring pattern. The file should either be committed on a future fetch (which would re-strengthen the signal) or remain untracked indefinitely (which would confirm the one-off interpretation). No synthesis routes until the file is committed.
|
||||
@@ -749,7 +773,140 @@ fields still 待补).
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|
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## Synthesis policy for this source
|
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|
||||
- **This run (2026-08-23, git-repo-1 18:11Z):** **0 new vault commits**
|
||||
- **This run (2026-08-24, git-repo-1 18:05Z):** **5 new vault commits**
|
||||
in the 2026-08-23T18:11Z → 2026-08-24T18:05Z 24-hour window — the
|
||||
vault HEAD bumped from `a4fa5a32` (2026-08-23T18:11Z fetch) to
|
||||
`fb017e4f` — **breaks the 7-fetch vault-silence streak** that
|
||||
started after the 2026-08-16 Quintard + Guo cluster, **largest
|
||||
single-day LDR burst since the 2026-07-29 Parate / Lee / Hodge
|
||||
cluster**. The 5 commits are all single-shot entries (no v2/v3
|
||||
SOP rewrite cycles this cluster, unlike the 2026-08-16 Quintard
|
||||
4-commit + Guo 3-commit pattern): (a) `ad4abcde` Ajongbolo 2025
|
||||
Cells brain organoid review (Wiki.js 1743); (b) `5f02489a` Kim 2025
|
||||
Nat Commun EGaIn liquid-metal 3D MEA (Wiki.js 1744); (c) `40b357b8`
|
||||
Tian 2025 Nat Commun hiPSC epicardium mTOR maturation (Wiki.js
|
||||
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
|
||||
|
||||
Reference in new issue
Block a user