chore: daily update 2026-09-01
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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 9d4767c7, 2026-08-25, **5 new vault commits in the 2026-08-24T18:05Z → 2026-08-25T18:13Z 24-hour window — the SECOND consecutive single-day 5-paper LDR cluster: `089177a7` Tevonian 2026 Nat Commun vascularized liver MPS + `583859a8` Yang 2026 Stem Cell Res Ther cardiac organoid review + `9aa2af4c` Update Tevonian 2026 + Yang 2026 (CelVivo/Cellink/Mimetas/3Brain/FemtoBiomed product mapping retrofit + 净化 Robin mentions — the first post-publish vendor-mapping retrofit on the 2026-08-23/24/25 LDR cluster) + `5907cdfc` Shen 2026 Chin Med J vascularized organoids review + `9d4767c7` Zhai 2026 Sci Adv 3D skin pemphigus — combined with the 2026-08-23/24 5-paper burst, **10 papers in 48 hours = the largest sustained 2-day research output in Robin's vault activity log; the burst creates 3 new deep-read subfolders: `Vascularized-Organoids/` (Tevonian + Shen) + `Cardiac-Organoids/` (Yang) + `Skin-Organoids/` (Zhai)**; **vault HEAD unchanged at the 2026-08-30T18:06Z fetch** — 0 new vault commits for the 5th consecutive fetch since the 2026-08-24/25 burst, vault silent for the 5th consecutive fetch (5 calendar days stale); the carry-forward untracked-file set bumps: `Review/zhou2023_computer_vision_microfluidics.md` 18-day → 19-day (16 → 17 fetches silent), `celvivo_commercial/` + `templates/` 13-day → 14-day (confirmed one-off at the 2026-08-28 fetch, continuing to carry forward unchanged at the 2026-08-30 fetch), `deepread_40240593/` 6-day → 7-day (mtime unchanged across 6 fetches since creation — 6 consecutive silent fetches since the 2026-08-24/25 burst, working-folder pipeline hypothesis continues to weaken) and openwiki-wiki at /home/ldw/.openwiki/wiki (main branch, HEAD d56da3a, 2026-08-30, **2 new automated wiki commits in the 2026-08-29T18:10Z → 2026-08-30T18:06Z window: `7eed6ca` chore: daily update 2026-08-30 (2026-08-30 02:?? +0800; per `git show --stat 7eed6ca` the commit touched 13 files 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), then `d56da3a` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-30 — the **sixteenth** 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 + now `d56da3a` 2026-08-30) committed `sources/{nocodb,ragflow,seafile,wikijs}.md` re-touched by the sources-sync; the very next synthesis edits from the HN-1 2026-08-30T18:00Z + web-search-1 2026-08-30T18:0?Z + this git-repo-1 2026-08-30T18:06Z run re-touch the same files + 4 newly-dirty files (`sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` re-dirtied by the sources-sync) leaving the dirty count at 9 per the manifest `changedFiles` list — `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 8 at the 2026-08-29 fetch because `sources/openwiki-version-drift.md` re-touched by this run's synthesis edits + index.md re-touched by the 2026-08-30 daily update's CLI metadata update 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."
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title: "Git repo — evidence index (Obsidian vault + OpenWiki wiki, 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 `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."
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resource: "~/.openwiki/connectors/git-repo/config.json"
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tags: [git-repo, evidence, vault, openwiki-wiki, source, 2026-08-30, 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, tevonian-2026-vascularized-liver-mps, yang-2026-cardiac-organoid-review, shen-2026-vascularized-organoids-review, zhai-2026-3d-skin-pemphigus, second-consecutive-cluster, vascularized-organoids, cardiac-organoids, skin-organoids, vault-silent-5d, sixteenth-sources-sync, templates-celvivo-commercial-confirmed-one-off, deepread-40240593-six-silent-fetches]
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timestamp: 2026-08-30T18:06:00Z
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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]
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timestamp: 2026-08-31T18:09:00Z
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---
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# Git repo — evidence index (Obsidian vault + OpenWiki wiki)
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@@ -22,176 +22,204 @@ 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:**
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- `obsidian-vault` → `/home/ldw/workspace` (Robin Obsidian vault, on
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`main`, HEAD `9d4767c7034a59d8f3206756c2dfeb3f4339c2e0` as of
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2026-08-25 +0800 — **5 new vault commits** in the
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2026-08-24T18:05Z → 2026-08-25T18:13Z 24-hour window: the
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**2026-08-24/25 5-paper LDR cluster** (SECOND consecutive
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single-day 5-paper LDR burst) — `089177a7` Tevonian 2026 Nat Commun
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血管化肝 MPS deep read (PMID 41634021) + `583859a8` Yang 2026 Stem
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Cell Res Ther cardiac organoid review (PMID 41963991) + `9aa2af4c`
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Update Tevonian 2026 + Yang 2026 (CelVivo/Cellink/Mimetas/3Brain/
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FemtoBiomed product mapping retrofit + 净化 Robin mentions — the
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FIRST post-publish vendor-mapping retrofit on the 2026-08-23/24/25
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LDR cluster) + `5907cdfc` Shen 2026 Chin Med J vascularized
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organoids review (PMID 42268296) + `9d4767c7` Zhai 2026 Sci Adv 3D
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skin pemphigus (PMID 41512055). Combined with the 2026-08-23/24
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5-paper burst, **10 papers in 48 hours** = largest sustained 2-day
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research output in Robin's vault activity log. The cluster creates
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**3 new `04-Literature/Deep-Reads/` subfolders**: `Vascularized-Organoids/`
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(Tevonian + Shen) + `Cardiac-Organoids/` (Yang) + `Skin-Organoids/`
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(Zhai) — Robin expands the deep-read taxonomy from ~19 to ~22
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per-vendor / per-application-domain subfolders in a single day.
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The new `9aa2af4c` retrofit commit is the **first synthesis-grade
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post-publish LDR touch** on the 2026-08-23/24/25 cluster — the
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prior 5 papers (Ajongbolo + Kim + Tian + Aiello + CelVivo App Note)
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have NOT had this retrofit applied yet, only the new Tevonian + Yang
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pair get the retroactive 4-vendor mapping).
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`main`, HEAD `391e47131679ce9edf0f525236e78ebb13e0d232` as of
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2026-08-31 13:42 +0800 — **5 new vault commits** in the
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2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window: the
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**2026-08-31 brain-organoid infectious-disease + CelVivo
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ClinoStar/ClinoReactor 5-paper LDR cluster** (THIRD single-day
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5-paper LDR burst — the 2026-08-25 second cluster is now the
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THIRD-most-recent 5-paper cluster, vault bursts are now an
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established pattern at the cadence of ~2 per week) — `eb24ab72`
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Stewart 2023 Front Microbiol SARS-CoV-2 omicron BA.5/XBB
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neurotropic brain organoids (QIMR Berghofer Suhrbier/Rawle line)
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+ `030f31ed` Aiello 2025 EMBO reports reproducible brain organoids
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(CelVivo ApS is one author affiliation — first reproducibility
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benchmark with CelVivo as co-author) + `fad7e21e` Nguyen 2024 npj
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Viruses JEV G4 2022 Australia brain organoids (QIMR Berghofer
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Suhrbier/Rawle line) + `4fca0123` Miao 2025 Cell vascularized
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lung/gut organoids (CelVivo ClinoReactor) + `391e4713` Yan 2024
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Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids
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(QIMR Berghofer Suhrbier/Rawle line). 4 of 5 use brain organoids
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for viral neurotropism modeling (3 share the QIMR Berghofer
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Suhrbier/Rawle research line: Yan + Stewart + Nguyen) + 1 is a
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vascularized lung/gut paper (Miao) + 1 is the first reproducibility
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benchmark (Aiello, with CelVivo ApS co-author). **All 5 land in a
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new subfolder `obsidian-vault/04-Literature/Deep-Reads/CelVivo/`
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(capital V)** — Robin creates a **third** per-vendor CelVivo
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subfolder alongside the existing `04-Literature/Deep-Reads/Celvivo/`
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(143 papers, lower-case v) at the workspace root. **The 5-day
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vault silence from the 2026-08-25 burst ends at this fetch**.
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Combined with the 2026-08-23/24 + 2026-08-24/25 + 2026-08-31
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5-paper bursts, **15 LDR papers in 8 days** = 3 distinct
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single-day 5-paper bursts; the bursts create 4 new
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`04-Literature/Deep-Reads/` subfolders: `Vascularized-Organoids/`
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+ `Cardiac-Organoids/` + `Skin-Organoids/` (2026-08-25 burst) +
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`CelVivo/` (2026-08-31 burst) — Robin's deep-read taxonomy
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expands to ~23 per-vendor / per-application-domain subfolders).
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- `openwiki-wiki` → `/home/ldw/.openwiki/wiki` (the OpenWiki knowledge
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base itself, on `main`, HEAD `1003b92f3a1e43197ec8e21e7f69fd5db38316e7`
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as of 2026-08-25T +0800 — 2 new wiki-side commits in the
|
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2026-08-24T18:05Z → 2026-08-25T18:13Z 24-hour window: `3255613`
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chore: daily update 2026-08-25 + `1003b92` chore(sources): refresh
|
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NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-25) —
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the **eleventh** consecutive sources-sync re-applying the 2026-08-15
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count-data wipe pattern).
|
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base itself, on `main`, HEAD `9582deadda4681fe1481f9992905230ace7e5990`
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as of 2026-08-31T02:30 +0800 — 2 new wiki-side commits in the
|
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2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window: `c9e2770`
|
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chore: daily update 2026-08-31 + `9582dea` chore(sources): refresh
|
||||
NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-31) —
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the **seventeenth** consecutive sources-sync re-applying the
|
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2026-08-15 count-data wipe pattern).
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- **Auth:** local paths only — no remote, no credentials.
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- **Latest fetch:** `2026-08-30T18:06:00Z` (raw manifest
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`~/.openwiki/connectors/git-repo/raw/2026-08-30T18-06-??-???Z/manifest.json`).
|
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- **Latest fetch:** `2026-08-31T18:09:00Z` (raw manifest
|
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`~/.openwiki/connectors/git-repo/raw/2026-08-31T18-09-??-???Z/manifest.json`).
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- **Source config:** `~/.openwiki/connectors/git-repo/config.json`
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- **State:** `~/.openwiki/connectors/git-repo/state.json` records
|
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`latestIds` per repo; the 2026-08-30T18:06Z fetch observed vault HEAD
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**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 —
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**0 new vault commits** in the 24-hour window, **vault silent for
|
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the 5th consecutive fetch** since the 2026-08-24/25 SECOND 5-paper
|
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burst; the 2026-08-25 5-paper cluster is the most recent vault
|
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activity, 5 calendar days stale), and observed `openwiki-wiki`
|
||||
bumped from `37d1ba6d30b6c4fe43a1d357311e12c9084dd8dc` (2026-08-29T18:10Z fetch) to
|
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**`d56da3afddfced20a01fbecd9912fe3ec87a25b4`** (2 new automated wiki
|
||||
commits in the 24-hour window: `7eed6ca` chore: daily update
|
||||
2026-08-30 — single-connector raw data refresh (HN-1 + git-repo-1; web-search-1 skipped) — committed 13 files per
|
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`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 the
|
||||
working-tree dirty count from 8 → 5, then `d56da3a`
|
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chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts
|
||||
(sources-sync 2026-08-30, 2026-08-30T02:30 +0800 — the **sixteenth**
|
||||
`latestIds` per repo; the 2026-08-31T18:09Z fetch observed vault HEAD
|
||||
bumped from `9d4767c7034a59d8f3206756c2dfeb3f4339c2e0` (2026-08-30T18:06Z
|
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fetch — same as the 2026-08-29T18:10Z + 2026-08-28T18:09Z +
|
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2026-08-27T18:25Z + 2026-08-26T18:06Z + 2026-08-25T18:13Z fetches
|
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all observed `9d4767c7` — **0 new vault commits** in the prior 5
|
||||
fetches, **vault silent for the 5th consecutive fetch** since the
|
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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 + now
|
||||
`d56da3a` 2026-08-30; committed `sources/nocodb.md` +
|
||||
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 d56da3a`). The very next synthesis edits from
|
||||
the HN-1 2026-08-30T18:00Z + web-search-1 2026-08-30T18:0?Z (skipped)
|
||||
+ this git-repo-1 2026-08-30T18:06Z run re-touched the same files +
|
||||
the sources-sync `d56da3a` re-touched the 4 source-sync files —
|
||||
the dirty count at this fetch is **9 per the manifest
|
||||
`changedFiles` list**: `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 5**
|
||||
at the 2026-08-29T18:10Z fetch (post-`7eed6ca` baseline) because the sources-sync `d56da3a`
|
||||
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`).
|
||||
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 (2026-08-30)
|
||||
## obsidian-vault — working-tree status (2026-08-31)
|
||||
|
||||
- **Branch:** `main`
|
||||
- **HEAD:** `9d4767c7034a59d8f3206756c2dfeb3f4339c2e0` (vault HEAD
|
||||
**unchanged** from 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 — **0 new vault
|
||||
commits** in the 2026-08-29T18:10Z → 2026-08-30T18:06Z 24-hour
|
||||
window, **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 2026-08-24/25 cluster is the **SECOND
|
||||
consecutive single-day 5-paper LDR burst** — combined with the
|
||||
2026-08-23/24 5-paper burst (Ajongbolo + Kim + Tian + Aiello +
|
||||
CelVivo App Note), Robin has produced **10 LDR papers in 48
|
||||
hours**, the largest sustained 2-day research output in Robin's
|
||||
vault activity log. The cluster creates **3 NEW
|
||||
`04-Literature/Deep-Reads/` subfolders** — `Vascularized-Organoids/`
|
||||
(Tevonian + Shen) + `Cardiac-Organoids/` (Yang) + `Skin-Organoids/`
|
||||
(Zhai) — Robin expands the deep-read folder taxonomy from ~19 to
|
||||
~22 in a single day. Crucially, the cluster includes the FIRST
|
||||
post-publish vendor-mapping retrofit commit (`9aa2af4c`) which
|
||||
adds CelVivo / Cellink / Mimetas / 3Brain / FemtoBiomed product
|
||||
mapping + 净化 Robin mentions to the Tevonian + Yang files — the
|
||||
prior 5 papers (Ajongbolo + Kim + Tian + Aiello + CelVivo App Note)
|
||||
have NOT had this retrofit applied retroactively.
|
||||
- **mtime activity in window:** **0 new committed files** in the
|
||||
2026-08-29T18:10Z → 2026-08-30T18:06Z 24-hour window — vault is
|
||||
silent in this fetch for the 5th consecutive fetch since the 2026-08-24/25 burst; the 5-paper 2026-08-24/25 LDR cluster (4 new
|
||||
files + 1 retrofit commit) and the 5-paper 2026-08-23/24 LDR burst
|
||||
all carry forward unchanged from the prior fetches. The 3 NEW
|
||||
per-vendor / per-application-domain subfolders created in the
|
||||
2026-08-24/25 burst all remain at the same counts: `Tevonian_2026_Nat_Commun_Vascularized_Liver_MPS.md`
|
||||
+ `Yang_2026_Stem_Cell_Res_Ther_Cardiac_Organoid_Review.md` in
|
||||
`Vascularized-Organoids/` + `Cardiac-Organoids/` respectively +
|
||||
`Shen_2026_Chin_Med_J_Vascularized_Organoids_Review.md` second file
|
||||
in `Vascularized-Organoids/` + `Zhai_2026_Sci_Adv_3D_Skin_Pemphigus.md`
|
||||
in `Skin-Organoids/` — plus the Tevonian + Yang in-place `M`
|
||||
touches from the `9aa2af4c` retrofit commit. The 2026-08-23 + 2026-08-24
|
||||
LDR burst files (Ajongbolo + Kim + Tian + Aiello + CelVivo App Note
|
||||
+ `deepread_40240593/` pipeline workspace) all carry forward
|
||||
unchanged from the 2026-08-24T18:05Z fetch. The `celvivo_commercial/`
|
||||
+ `templates/` untracked dirs continue to carry forward (now
|
||||
**14-day carry-forward** at this fetch — was 13-day at the
|
||||
2026-08-29T18:10Z fetch, 12-day at the 2026-08-28T18:09Z fetch —
|
||||
**both entries confirmed one-off alongside the `Review/` subfolder
|
||||
at the 2026-08-28 fetch**; the 2026-08-30 fetch confirms the
|
||||
parallel one-off interpretation carrying forward unchanged; both
|
||||
should be demoted to stale / not recurring carry-forward notes on
|
||||
the next synthesis pass). The `Review/zhou2023_computer_vision_microfluidics.md`
|
||||
first-entry file is unchanged from the 2026-08-29T18:10Z fetch
|
||||
(mtime 2026-08-11, **19-day carry-forward** in the untracked set at
|
||||
this fetch — was 18-day at the 2026-08-29T18:10Z fetch; the
|
||||
- **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 — **17 fetches silent** at this fetch,
|
||||
was 16 fetches silent at the 2026-08-29T18:10Z fetch; the 2026-08-27
|
||||
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 2026-08-30 fetch (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** fetches — **6 fetches silent on directory mtime** at this
|
||||
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 2026-08-30 fetch (now **7-day carry-forward** — was 6-day at
|
||||
the 2026-08-29T18:10Z fetch, 5-day at the 2026-08-28T18:09Z fetch).
|
||||
- **Ahead of origin/main:** 30 commits new since 2026-08-03 fetch (+5
|
||||
from the prior 25-commit baseline at the 2026-08-24T18:05Z fetch —
|
||||
the 5 new commits land on top of the 25-commit carry-forward; **5 new
|
||||
commits land on top of the 25-commit carry-forward**, vault HEAD
|
||||
unchanged at the 2026-08-30T18:06Z fetch (vault silent for the 5th
|
||||
consecutive fetch since the 2026-08-24/25 5-paper burst; total
|
||||
remains 30 since 2026-08-03).
|
||||
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) — **19-day carry-forward** at this fetch (was 18-day
|
||||
at the 2026-08-29T18:10Z fetch); the structural signal continues to
|
||||
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
|
||||
**17 fetches silent** — was 16 fetches silent at the
|
||||
2026-08-29T18:10Z fetch; **the 2026-08-27 fetch already confirmed the
|
||||
**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 **14-day carry-forward** at this fetch — was 13-day
|
||||
at the 2026-08-29T18:10Z fetch — **the 2026-08-28 fetch already confirmed
|
||||
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 13-day
|
||||
threshold at this fetch; both should be demoted to stale / not
|
||||
recurring carry-forward notes on the next synthesis pass); the
|
||||
`deepread_40240593/` untracked pipeline workspace also continues to
|
||||
carry forward (now **7-day carry-forward** — was 6-day at the
|
||||
2026-08-29T18:10Z fetch, with mtime unchanged across 6 fetches
|
||||
since creation); no NEW untracked dirs at this fetch. The
|
||||
2026-08-30T18:06Z fetch confirms the parallel one-off interpretation
|
||||
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 (**7-day carry-forward** + **6 consecutive silent fetches**
|
||||
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):**
|
||||
|
||||
@@ -239,6 +267,11 @@ help locate things in the vault, not summarize their content.
|
||||
|
||||
| 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. |
|
||||
@@ -412,117 +445,121 @@ 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 (2026-08-30)
|
||||
## openwiki-wiki — working-tree status (2026-08-31)
|
||||
|
||||
- **Branch:** `main`
|
||||
- **HEAD:** `d56da3afddfced20a01fbecd9912fe3ec87a25b4` (the
|
||||
`chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-30)` commit). The 2026-08-30T18:06Z
|
||||
fetch observed wiki HEAD bumped from `37d1ba6d30b6c4fe43a1d357311e12c9084dd8dc` (2026-08-29T18:10Z
|
||||
fetch) to `d56da3a` — **2 new automated wiki commits** in the
|
||||
2026-08-29T18:10Z → 2026-08-30T18:06Z 24-hour window: (a) `7eed6ca`
|
||||
chore: daily update 2026-08-30 (2026-08-30 02:?? +0800, committed 13 files per `git show --stat
|
||||
7eed6ca` — including `.last-update.json` + `quickstart.md` +
|
||||
- **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/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 8 → 5 per the manifest `changedFiles` list at the 2026-08-30 fetch;
|
||||
(b) `d56da3a` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts
|
||||
(sources-sync 2026-08-30, 2026-08-30 02:30 +0800). The `d56da3a`
|
||||
`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 **sixteenth** consecutive time
|
||||
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 + now `d56da3a` 2026-08-30); the
|
||||
sources-sync committed 4 files per `git show --stat d56da3a` —
|
||||
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 2026-08-30T18:00Z +
|
||||
web-search-1 2026-08-30T18:0?Z + this git-repo-1
|
||||
2026-08-30T18:06Z run's synthesis edits re-touched the same files +
|
||||
the sources-sync `d56da3a` re-touched the 4 source-sync files (the
|
||||
same pattern as the 2026-08-28 + 2026-08-29 fetches). The combined effect is the
|
||||
working-tree dirty count bumped from 5 → 9 at this fetch because the
|
||||
sources-sync `d56da3a` re-touched the 4 source-sync files that the
|
||||
`7eed6ca` daily update had committed; `sources/openwiki-version-drift.md`
|
||||
re-touched by this run's synthesis edits (was previously committed by
|
||||
the 2026-08-28 `6024ac7` daily update but not by the 2026-08-29 + 2026-08-30
|
||||
daily updates, so it appears in the dirty set again); `index.md` re-touched by
|
||||
the CLI metadata update cycle.
|
||||
- **Working-tree state:** 9 modified files (uncommitted — pending
|
||||
next CLI orchestration). The 2026-08-30T18:06Z fetch observed the
|
||||
working tree at 9 uncommitted files (up from 8 at the
|
||||
2026-08-29T18:10Z fetch because the `d56da3a` sources-sync re-touched
|
||||
the 4 source-sync files + the `7eed6ca` daily update re-touched
|
||||
`.last-update.json` + this run's synthesis edits re-touched
|
||||
`sources/openwiki-version-drift.md` (the file was last committed by
|
||||
the 2026-08-28 `6024ac7` daily update but the 2026-08-29 + 2026-08-30
|
||||
daily updates re-dirtied it because the file is touched by the
|
||||
CLI metadata update cycle that runs alongside every daily update)
|
||||
+ `index.md` re-touched by the CLI metadata update cycle,
|
||||
even though the `7eed6ca` daily update had
|
||||
committed 13 of the prior dirty files per `git show --stat 7eed6ca`
|
||||
— including `commitments.md` was not in this set at the 2026-08-29
|
||||
fetch; the `7eed6ca` commit reduced the dirty count from 8 → 5).
|
||||
The 9 dirty files at this fetch per the manifest `changedFiles`
|
||||
`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 `7eed6ca` 2026-08-30
|
||||
`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 2026-08-29T18:00Z + 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 + the "Latest
|
||||
update — git-repo-1 (2026-08-29T18:10Z)" paragraph added by the
|
||||
2026-08-29 git-repo run; this git-repo-1 2026-08-30T18:06Z run
|
||||
adds the "Latest update — git-repo-1 (2026-08-30T18:06Z)" paragraph
|
||||
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
|
||||
`d56da3a` + the **sixteenth** consecutive sources-sync + the
|
||||
5-calendar-day-stale vault HEAD + the carry-forward bump to
|
||||
19/14/14/7-day + the parallel `templates/` + `celvivo_commercial/`
|
||||
`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 2026-08-30 fetch + the
|
||||
`deepread_40240593/` pipeline workspace at 6-day carry-forward with
|
||||
5 consecutive silent fetches since the 2026-08-24/25 burst.
|
||||
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 —
|
||||
2026-08-28 18:00 UTC" + "Latest update — 2026-08-29 18:00 UTC"
|
||||
sections from the prior HN-1 runs (Gemini-3.5-Transcribe 343 pts +
|
||||
NYT Anthropic blacklisting 318 pts + Reuters Anthropic blacklisting
|
||||
317 pts + Luanti DMCA 287 pts + GLM-5.3 open-weight 268 pts on the
|
||||
2026-08-28 pull + Cursor/SpaceX/OpenAI decision 736 pts +
|
||||
Debian "responsible use of generative AI" 400+401 pts + vphone-cli
|
||||
Virtual iPhone 351 pts + Iceland EU-vote 292 pts + LLM memory into
|
||||
program analysis 245 pts on the 2026-08-29 pull + the
|
||||
18th + 19th consecutive empty / noise Algolia lane streak notes +
|
||||
the strengthened open-weight-LLM cluster 10 items / ~2,954+ pts +
|
||||
AI-vendor-business-stack cluster 5 → 6 items / ~1,786+ pts →
|
||||
~2,522+ pts + the new AI-policy / copyright-DMCA lane adjacency
|
||||
~687 pts across 2 items in 2 pulls) — landed in uncommitted state
|
||||
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 **sixteenth**
|
||||
consecutive sources-sync `d56da3a` (2026-08-30 02:30 +0800); the
|
||||
+ `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
|
||||
`7eed6ca` 2026-08-30 daily update earlier in the window, then
|
||||
re-dirtied by the `d56da3a` sources-sync that landed later in
|
||||
the window — same pattern as the 2026-08-28 + 2026-08-29 fetches
|
||||
(5 → 8 → 9 dirty file re-bump after the sources-sync).
|
||||
`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 2026-08-29 + 2026-08-30 web-search-1 attempts (both skipped
|
||||
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 — 16th + 17th consecutive skips on the
|
||||
`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.
|
||||
- `sources/openwiki-version-drift.md` — auto-generated version-drift
|
||||
monitor (created in the 2026-08-17 daily update `5c70881`,
|
||||
last committed by the 2026-08-28 `6024ac7` daily update); the
|
||||
file re-appears as dirty at this fetch because the CLI metadata
|
||||
update cycle re-touches the file alongside every daily update
|
||||
(refresh of the timestamp).
|
||||
- `index.md` — directory index (auto-regenerated on every wiki
|
||||
commit cycle); re-dirtied by the CLI metadata update cycle that
|
||||
runs alongside the 2026-08-30 daily update.
|
||||
- `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`)
|
||||
@@ -536,6 +573,8 @@ on the same paper.
|
||||
|
||||
| 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" |
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||||
@@ -634,6 +673,8 @@ pipeline catches up.
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||||
|
||||
| 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`) |
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@@ -714,11 +755,12 @@ Markdown file counts per deep-read subfolder:
|
||||
| `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) |
|
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| `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)) |
|
||||
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||||
Total ≈ 1,217 deep-read notes on `main` (+4 new LDR files from the 2026-08-24/25 cluster on top of +5 from the 2026-08-23/24 single-shot LDR burst and +2 from the 2026-08-16 Quintard 2024 + Guo 2026 clusters; the 5th 2026-08-25 commit `9aa2af4c` is an in-place `M` touch on Tevonian + Yang files, not a new file). Robin's LDR cluster pattern is now **2 consecutive 5-commit windows** (2026-08-23/24 + 2026-08-24/25), totalling **11 commits / 9 new files** in 48 hours.
|
||||
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 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.
|
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`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.
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## Distributor map refresh (2026-08-07)
|
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@@ -779,6 +821,12 @@ fields still 待补).
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## Notable entities surfaced by the vault (structural hints only)
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- **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).
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- **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.
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- **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.
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- **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.
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- **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.
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- **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.
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- **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.
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- **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.
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- **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.
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@@ -879,6 +927,8 @@ fields still 待补).
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## Synthesis policy for this source
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- **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` → `9Line truncated
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- **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.
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- **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.
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Reference in new issue
Block a user