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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|
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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.
|
||||
|
||||
- **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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+21
-5
@@ -2,8 +2,8 @@
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type: "Reference"
|
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title: "Hacker News — evidence index"
|
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description: "Compact evidence trail for the Hacker News connector (hackernews-1, Robin-curated life-sciences + AI workflow). Synthesis lives on /themes.md, /commitments.md, etc.; this page only records ingestion coverage and notable items."
|
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tags: [hackernews, evidence-index, 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, 2026-08-16, 2026-08-15, 2026-08-13, 2026-08-12, 2026-08-10]
|
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timestamp: 2026-08-30T18:00:39Z
|
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tags: [hackernews, evidence-index, 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, 2026-08-16, 2026-08-15, 2026-08-13, 2026-08-12, 2026-08-10]
|
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timestamp: 2026-08-31T18:00:32Z
|
||||
---
|
||||
|
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# Hacker News — evidence index
|
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@@ -16,10 +16,26 @@ Compact evidence trail for the Hacker News connector (`hackernews-1`, Robin-cura
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- **Backend:** public HN feeds (`top`, `new`) + Algolia HN search queries
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- **Auth:** none — public feeds
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- **Window:** last 24 hours
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- **Latest fetch:** `2026-08-30T18:00:39Z` (LLM-agent topic set: `organoid`, `CelVivo`, `3Brain`, `Cellink`, `openwiki`, `deepagents` — 6 queries; the source-specific instruction "Track organoid / CelVivo / 3Brain / Cellink / openwiki / AI agent stories" is the active query set; prior 2026-08-29 18:00, 2026-08-28 18:00, 2026-08-27 18:00, 2026-08-26 18:00, 2026-08-25 18:00, 2026-08-24 18:00, 2026-08-23 18:00, 2026-08-22 18:00, 2026-08-21 18:00, 2026-08-20 18:00, 2026-08-19 18:00, 2026-08-18 18:00, 2026-08-17 18:00, 2026-08-16 18:00, 2026-08-15 18:00, 2026-08-13 18:00, 2026-08-12 18:00, 2026-08-10 18:00, 2026-08-08 18:00, 2026-08-08 03:15, 2026-08-07 12:29, 2026-08-03 18:00, 2026-08-02 18:00, 2026-08-01 18:00, 2026-07-31 18:00, 2026-07-30 18:00, 2026-07-29 18:00, 2026-07-28 18:00, 2026-07-27 18:00, 2026-07-26 18:16 and 18:00 pulls also documented below)
|
||||
- **Raw dumps:** `~/.openwiki/connectors/hackernews/raw/2026-08-30T18-00-02-250Z/hackernews-results.json` (current — **twentieth pull since 2026-08-07; fully-zero Algolia lane on all 6 queries** (`organoid` / `CelVivo` / `3Brain` / `Cellink` / `openwiki` / `deepagents` each returned `nbHits=null / hits=0`) — **third consecutive fully-zero Algolia lane pull bookending the 2026-08-22 + 2026-08-27 substring-noise-only pulls**, with no substring-noise false positives on the vendor queries (clean zero across the board, distinct from the 2026-08-22 + 2026-08-27 substring-noise-only pulls); **eighth fully-zero Algolia lane in nine consecutive pulls** (after 2026-08-22 + 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 — **the longest empty/noise Algolia lane streak of the entire 2026-08-07 streak to date**, confirming the empty-pulls-on-vendor-queries cadence is normal under the 6-query LLM-agent topic set, not an outage, no config-side intervention needed); **27 unique top+best items** (top 19 + best 12 - 4 overlap: `49492632` Tencent Hy4 + `49494520` Bug Blindness + `49497063` Brits private messages + `49494301` Rise and Fall of Agent Civilizations; the 27-item dedup count is a +13 jump from the 2026-08-29 pull's 14 unique items — the **largest single-day dedup increase of the 2026-08-07 streak**, driven by a more populated 24-hour window with `top` resolving 19/30 IDs and `best` resolving 12/30 IDs — the highest combined-resolution pair of the streak to date, with `best` 12/30 = **highest `best` resolution since the 2026-08-15 16/30 and 2026-08-12 14/30 pulls**); no in-scope vendor / customer / application-domain / named-stack signal — strongest adjacent items are **the Tencent Hy4 preview `49492632`** (364 pts top, 229 cmts, by `shenli3514` 2026-08-30, https://www.tencent.com/tencent-releases-and-open-sources-tencent-hy4-preview/ — Tencent blog; **highest-engagement Tencent AI model item of the 2026-08-07 streak** and **11th entry in the open-weight-LLM cluster**, joining the 2026-08-21 DeepSeek V4 Flash vision + 2026-08-19 Unsloth Dynamic 3.0 GGUFs + 2026-08-23 GLM-5.3 vs Anthropic/OpenAI essay + 2026-08-23 Qwen 3.8 27B reverse-engineering test + 2026-08-25 Qwen 3.8-Flash-Next "releasing tomorrow" + 2026-08-26 GLM-5.3-Flash + 2026-08-26 Qwen3.8-Flash-Next actual release + 2026-08-26 Z.ai Ox Alpha confirmation + 2026-08-27 Small Models Have Arrived + 2026-08-28 GLM-5.3 is now open-weight cluster entries; **direct open-weight-LLM cross-walk to the `MiniMax-m3` row's open-weight comparison anchor** — adjacent-not-promoted per scope because Tencent is not on Robin's named stack — Hermes / MiniMax-M3+H3 / OpenWiki / RAGFlow / NocoDB / SeaFile / Codex CLI are the named agents), **the Claude Session URL appended to commits `49498201`** (116 pts top, 143 cmts, by `sparsesignal` 2026-08-30, https://github.com/anthropics/claude-code/issues/66504 — GitHub Anthropic claude-code issue; **named-stack-adjacent by Claude Code / Codex CLI competitor framing** because Codex CLI is on Robin's named coding-agent stack but this is about Claude Code, not Codex CLI — adjacent-not-promoted per scope because the issue is upstream Claude Code default-behavior context, not a Codex CLI change Robin acts on), **the "Rise and Fall of Agent Civilizations" `49494301`** (177 pts best, 103 cmts, by `consumer451` 2026-08-30, https://www.dwarkesh.com/p/openai-huggingface — Dwarkesh Patel interview / essay on OpenAI + Hugging Face + agent-civilizations framing; **agent-civilizations-adjacent item** by Dwarkesh's "Rise and Fall of Agent Civilizations" framing — adjacent-not-promoted per scope because the post is a Dwarkesh essay / interview, not a canonical Hermes / MiniMax / OpenWiki artifact, though the agent-civilizations framing directly cross-walks to the `hermes-agent-v0-19-quicksilver` row's agent-as-primary-compute-substrate narrative), **the "No AI Fridays" `49498095`** (240 pts best, 157 cmts, by `xendo` 2026-08-30, https://noaifridays.com/ — noaifridays.com AI-workplace-policy movement; **AI-workplace-policy-adjacent item** — adjacent-not-promoted per scope because AI-workplace policy is upstream context, not on Robin's named stack), **the Haiku R1/beta6 `49499867`** (92 pts top, 20 cmts, by `metrofun` 2026-08-30, https://www.haiku-os.org/news/2026-08-26_haiku_r1_beta6 — Haiku OS; **off-scope per scope** because Haiku is an OS project, not in Robin's 4 application domains and not on Robin's named stack), **the "Bug Blindness" `49494520`** (347 pts top, 226 cmts, by `davidmckenna` 2026-08-30, https://danluu.com/bug-blind/ — Dan Luu essay on bug blindness; **off-scope per scope** because essay-style content is not in Robin's 4 application domains and not on Robin's named stack), **the "Brits private messages stay private" `49497063`** (306 pts best, 242 cmts, by `defrost` 2026-08-30, https://www.theregister.com/... — The Register; **off-scope per scope** becauseLine truncated
|
||||
- **Latest fetch:** `2026-08-31T18:00:32Z` (LLM-agent topic set: `organoid`, `CelVivo`, `3Brain`, `Cellink`, `openwiki`, `deepagents` — 6 queries; the source-specific instruction "Track organoid / CelVivo / 3Brain / Cellink / openwiki / AI agent stories" is the active query set; prior 2026-08-29 18:00, 2026-08-28 18:00, 2026-08-27 18:00, 2026-08-26 18:00, 2026-08-25 18:00, 2026-08-24 18:00, 2026-08-23 18:00, 2026-08-22 18:00, 2026-08-21 18:00, 2026-08-20 18:00, 2026-08-19 18:00, 2026-08-18 18:00, 2026-08-17 18:00, 2026-08-16 18:00, 2026-08-15 18:00, 2026-08-13 18:00, 2026-08-12 18:00, 2026-08-10 18:00, 2026-08-08 18:00, 2026-08-08 03:15, 2026-08-07 12:29, 2026-08-03 18:00, 2026-08-02 18:00, 2026-08-01 18:00, 2026-07-31 18:00, 2026-07-30 18:00, 2026-07-29 18:00, 2026-07-28 18:00, 2026-07-27 18:00, 2026-07-26 18:16 and 18:00 pulls also documented below)
|
||||
- **Raw dumps:** `~/.openwiki/connectors/hackernews/raw/2026-08-31T18-00-02-091Z/hackernews-results.json` (current — **twenty-first pull since 2026-08-07; connector anomaly: nbHits-positive-but-items-zero on 3 of 6 queries** (`organoid` returned `nbHits=4 / items=0`; `3Brain` returned `nbHits=6 / items=0`; `Cellink` returned `nbHits=1 / items=0` — Algolia substring-noise hits materialized as `hits` in the raw response object but were not promoted to the connector-level `items` field, distinct from the prior 2026-08-22 + 2026-08-27 substring-noise-only pulls which had material items like `49394827` OzBrain 72 pts; `CelVivo` + `openwiki` + `deepagents` returned clean zero on both `nbHits` and `items`); the only substantive HN item surfacing on this pull is **`49511007` "Launch HN: Almanac (YC S26) – AI that knows your company"** (21 pts top+best + 22 cmts, by `kushagrchitkar` 2026-08-31, https://usealmanac.com/ — YC S26 launch) — **first HN item since the 2026-07-16 `langchain-ai/openwiki` row anchor to land a direct architectural match on the wikis-as-agent-memory-substrate pattern that the `agent-memory-architecture` row documents**; see 2026-08-31 18:00 UTC entry below) · `~/.openwiki/connectors/hackernews/raw/2026-08-28T18-00-01-954Z/hackernews-results.json` (prior — **eighteenth pull since 2026-08-07; fully-zero Algolia lane on all 6 queries** (`organoid` / `CelVivo` / `3Brain` / `Cellink` / `openwiki` / `deepagents` each returned `nbHits=null / hits=0`) — **fifth consecutive fully-zero Algolia lane pull bookending the 2026-08-22 + 2026-08-27 substring-noise-only pulls**; **fifth consecutive fully-zero pull of the 2026-08-07 streak** (after 2026-08-21 + 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26), confirming the empty-pulls-on-vendor-queries cadence is normal under the 6-query LLM-agent topic set, not an outage, no config-side intervention needed; **31 unique top+best items** (top 29 + best 7 - 5 overlap: 49477600, 49478340, 49475079, 49479878, 49473522), no in-scope vendor / customer / application-domain / named-stack signal — strongest adjacent items are **the Google Gemini-3.5-Transcribe `49468818`** (343 pts best — Google blog; **highest-engagement best-feed item of the pull**; named-stack-adjacent via Gemini / M3 closed-weight cross-walk), **the Anthropic blacklisting ruling NYT `49473522` + Reuters `49477055` (318 + 317 = 635 pts combined)** (highest-engagement AI-vendor-business-stack signal of the streak; cross-walks to the 2026-08-24 FT Anthropic 738 pts + 2026-08-25 WFH-security-strike 89 pts + 2026-08-27 OpenAI HF-incident blog 324 pts — the 4-item AI-vendor-business-stack cluster now totals ~1,697+ pts across 4 items in 5 pulls), **the Luanti DMCA-tracer AI copyright notice `49475079`** (287 pts top+best — **first AI policy / copyright DMCA signal in the 2026-08-07 streak**; the luanti project was removed from Google Play after a baseless AI copyright notice from a tracer-AI tool, surfacing the AI-policy / copyright-DMCA lane as a new adjacency), and **the GLM-5.3 is now open-weight `49479878`** (268 pts top+best — **10th open-weight-LLM cluster entry**; confirms the GLM-5.3 open-weight release foreshadowed by the 2026-08-26 GLM-5.3-Flash 530 pts + the 2026-08-23 GLM-5.3 vs Anthropic/OpenAI 141 pts + the 2026-08-23 GLM-5.3 tablet experiment 268 pts + the 2026-08-26 Z.ai Ox Alpha 391 pts — the open-weight-LLM cluster now totals ~2,954+ pts across 10 items in 8 pulls over 11 days, the strongest sustained engagement cluster of the streak); see 2026-08-28 18:00 UTC entry below) · `~/.openwiki/connectors/hackernews/raw/2026-08-27T18-00-02-889Z/hackernews-results.json` (prior — **seventeenth pull since 2026-08-07; first non-fully-zero Algolia lane since 2026-08-22**: 10 substring-noise hits on `organoid` (all `organiz-` collisions: organizational knowledge graph / Backprompter / Vertex archiver / KnotQ calendar / LinkedIn / etc.), 0 hits on `CelVivo`, 9 substring-noise hits on `3Brain` (all `brain` collisions: Tell HN AI killing brain / Braindump / Vibe-Coded Brain / AI-assisted brain surgery / roller coaster brain injury / brain preservation / neurosurgeons / brain aging), 4 substring-noise hits on `Cellink` (all `clink`/`helsinki`/`calling` collisions: ThunderPhone Voice AI / SaaS in India / Voice Calling / C++ stream Clink), 0 hits on `openwiki`, **1 thematic hit on `deepagents`** — `49461911` "LangChain-AI/deepagents: agent harness" (1 pt, 0 cmts, by `OutOfHere` 2026-08-27, https://github.com/langchain-ai/deepagents) — **first positive `deepagents` Algolia hit since the query was added to the LLM-agent topic set**; 32 unique top+best items, no in-scope vendor / customer / application-domain / named-stack signal — strongest adjacent items are **the Nvidia-Hugging Face acquisition `49458161`** (1719 pts, 802 cmts — highest-engagement item on the pull, top+best — major open-weight-LLM infrastructure consolidation event; **adjacent-not-promoted** per Line truncated
|
||||
|
||||
## Latest update — 2026-08-30 18:00 UTC
|
||||
## Latest update — 2026-08-31 18:00 UTC
|
||||
|
||||
- **Coverage:** 2 feeds (`top`, `best`), 6 search queries (the same simplified LLM-agent topic set from the source-specific instruction "Track organoid / CelVivo / 3Brain / Cellink / openwiki / AI agent stories": `organoid`, `CelVivo`, `3Brain`, `Cellink`, `openwiki`, `deepagents`). `top` feed had 30 IDs (~19 resolved), `best` feed had 30 IDs (~12 resolved); deduplication gave **29 unique items across both feeds** (low single-digit overlap, on par with the prior 2026-08-30 pull's 27 unique). The 6-query lane returned a **new connector anomaly**: `organoid` returned `nbHits=4 / items=0`, `3Brain` returned `nbHits=6 / items=0`, `Cellink` returned `nbHits=1 / items=0` — Algolia substring-noise hits materialized as `hits` in the raw response object but were not promoted to the connector-level `items` field, distinct from the prior 2026-08-22 + 2026-08-27 substring-noise-only pulls which had material items like `49394827` OzBrain 72 pts; `CelVivo` + `openwiki` + `deepagents` returned clean zero on both `nbHits` and `items`. The connector completed normally at `fetchedAt: 2026-08-31T18:00:32.102Z` (24-hour window). The Algolia substring-noise / items=0 anomaly is the **first of its kind in the 2026-08-07 streak** — prior noise-only pulls (2026-08-22 + 2026-08-27) had material items in the noise lane, and prior fully-zero pulls (2026-08-21 + 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26 + 2026-08-28 + 2026-08-29 + 2026-08-30) had `nbHits=null / hits=0`. Future agents reading the 2026-08-31 raw data should not treat the Algolia lane as fully-zero — the `nbHits > 0` substring-noise false positives surfaced as `hits` in `queryResults[i].response.hits` and were visible to the agent, but the connector's top-level `items` field reported 0. This is a connector-side materialization gap, not a content gap. Tavily (web-search) remains the productive lane for vendor news.
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- **Life-science lane:** **zero vendor-anchored hits across all four named vendor queries, but the Algolia substring-noise hits are visible in the raw response and are flagged for traceability.** `organoid` returned 4 substring-noise hits (all on the `organiz-` stem: **`49511126` Revue — Review large code changes in your terminal** + **`49509142` Decispher — persistent engineering context and memory for coding agents** + **`49501845` Invovanta — Invoicing and business management for freelancers** + **`49511007` Almanac — AI that knows your company**); `3Brain` returned 6 substring-noise hits (all on the substring `brain`: **`49511007` Almanac** + **`49511544` Rta-Smriti — local-first project memory for coding agents** + **`49503121` Music Sparks Story-Like Brain Activity** + **`49502891` Could a Computer Scientist Build a Brain?** + **`49502826` Hide the Mac menu bar or clock, dynamically synced w focus (DND)** + **`49501858` From doomscrolling to nomophobia: new digital-age conditions reshaping brains**); `Cellink` returned 1 substring-noise hit via typo tolerance on `telling` (`49504798` Just finished building a security audit tool). None of these substring-noise hits refer to biological organoids / 3Brain HD-MEA / Cellink BIO X. A title/URL regex sweep across the 29 unique top+best items also turned up **zero organoid / 3D-bioprinting / CelVivo / 3Brain / Cellink / ClinoStar / ClinoReactor / MEA / spheroid / organ-on-chip items**. The "no material HN footprint for the 4 vendor lines" finding continues to hold — this is the **twenty-first pull since 2026-08-07** (after the 2026-08-08 03:15 + 2026-08-08 18:00 + 2026-08-13 + 2026-08-15 + 2026-08-16 + 2026-08-18 + 2026-08-19 + 2026-08-21 + 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26 + 2026-08-28 + 2026-08-29 + 2026-08-30 fully-zero pulls + the 2026-08-10 + 2026-08-12 + 2026-08-17 + 2026-08-20 + 2026-08-22 + 2026-08-27 substring-noise-only pulls + the 2026-08-31 nbHits-positive-but-items-zero pull; the 2026-08-31 pull is a **new anomaly type** — neither fully-zero (the Algolia response did report `nbHits > 0` for 3 queries) nor substring-noise-with-material-items like the prior noise-only pulls). The Tavily (web-search) lane remains the productive lane for vendor news; the HN lane's stable role is now "high-engagement inference-lane / agent-stack adjacents + low-engagement application-domain watchlist items + low-engagement self-hosted-agentic-substrate cluster essays + occasional substring-noise false positives on the vendor queries (now with a connector-side materialization gap on the 2026-08-31 pull)" rather than vendor-direct signals.
|
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|
||||
- **Workflow lane:** **zero positive `openwiki` brand hits; zero positive `deepagents` hits; one direct architectural match on the wikis-as-agent-memory-substrate pattern.** `openwiki` returned clean `nbHits=0 / hits=0` — so the `openwiki-brand` watchlist row on `/themes.md` stays at Last seen 2026-07-16. `deepagents` returned clean `nbHits=0 / hits=0` — the fourth fully-zero `deepagents` lane in a row (after the 2026-08-28 + 2026-08-29 + 2026-08-30 fully-zero pulls), continuing to confirm the 2026-08-27 first-positive `deepagents` Algolia hit (LangChain deepagents `49461911` at 1 pt) stood as a single-event thematic signal. The 29 unique top+best items include **one direct architectural match on the wikis-as-agent-memory-substrate pattern** — **`49511007` "Launch HN: Almanac (YC S26) – AI that knows your company"** (21 pts top+best + 22 cmts, by `kushagrchitkar` 2026-08-31, https://usealmanac.com/ — YC S26 launch) — **first HN item since the 2026-07-16 `langchain-ai/openwiki` row anchor to land a direct architectural match on the wikis-as-agent-memory-substrate pattern that the `agent-memory-architecture` row documents**; the submitter text explicitly builds "The 'brain' of this agent is wikis. We pull in information from your connected sources, and start organizing this information in two wikis. A personal one, for you, which understands who you are, what your preferences are, the people in your life, and the things going on in your life. The second wiki is a company wiki, which includes what the company is, what you're working on, what the roadmap is, and what the blockers of the company are" — operationalizing the same Karpathy LLM Wiki + Google OKF + MCP + shared-agent-memory substrate pattern that the `agent-memory-architecture` row documents, with cross-source connectors (Gmail, Calendar, Granola, PostHog) mirroring the OpenWiki 7-connector cron pipeline; pre-compiled knowledge layer with explicit upfront-compute investment in memory + long-horizon tasks tracked in an "ongoing projects" section + proactive background-worker suggesting automations. The 29 unique top+best items also include **the highest-engagement top-feed item** (`49511856` "I turned my security cameras into an automatic bird identification system" 66 pts top + 27 cmts, by `speckx` 2026-08-31, https://jasontucker.blog/... — **off-scope per scope** because wildlife-identification is not in Robin's 4 application domains and not on Robin's named stack), **the highest-engagement best-feed item** (`49510514` "Playa Phone" 248 pts best + 108 cmts, by `cutoff` 2026-08-31 — **off-scope per scope** because Burning Man hardware is not in Robin's 4 application domains and not on Robin's named stack). Per the brief: low-engagement items stay watchlist by default; only high-engagement + directly-relevant items earn promotion. The Almanac item matches existing topics (`agent-memory-architecture` row) + corroborates existing sources (Karpathy LLM Wiki + OKF + MCP + Verginglabs + MCP Memory + mooreds + Moorcheh + Open Knowledge Format pattern), qualifying for the corroboration-criterion promotion even at moderate 21-pt + 22-cmt engagement. **Promoted**: the `agent-memory-architecture` row on `/themes.md` gets a Last-seen refresh from 2026-08-13 to 2026-08-31 + Evidence count 16+ → 17+, with the Almanac item added as the new refresh anchor.
|
||||
|
||||
- **Synthesis result:** **one theme-row refresh, no commitment row, no open-question row, no personal-logistics item.** The `class-organoid-3d-bioprinting` row on `/themes.md` stays at Last seen 2026-08-20 (no organoid / 3D-bioprinting / CelVivo / 3Brain / Cellink thematic item — the 29 unique feed items include zero application-domain matches; the 2026-08-31 pull's 4 substring-noise hits on `organoid` + 6 on `3Brain` + 1 on `Cellink` are all on unrelated substrings; the prior 2026-08-20 refresh from the `49366519` Nature organoid-time-passage paper + `49373812` Science Alert write-up carries forward unchanged). The **`agent-memory-architecture` row gets a Last-seen refresh from 2026-08-13 → 2026-08-31** + Evidence count `16+` → `17+` + a new Evidence cell entry for `49511007` Almanac (21 pts + 22 cmts; **first shipped-product evidence of the wikis-as-agent-memory-substrate pattern** — every prior source on the row (Karpathy LLM Wiki + OKF + MCP + MCP Memory `49286073` 46 pts + Moorcheh.ai + verginglabs.com `49156055` 2 pts + mooreds shared-memory public AI + Verginglabs markdown-wiki + LLM-Wiki-v2 + pi-llm-wiki + MinIO AIStor Memory + arXiv 2607.24759v1 + Exabase M-1 BEAM benchmark + akitaonrails/ai-memory + Matt_D "I accidentally turned LLM memory into program analysis" `49485416` 245 pts 2026-08-29 + OzBrain `49394827` 72 pts 2026-08-22) is either a substrate-pattern essay, an open-source library, or a research write-up — Almanac is the first YC S26 launch that operationalizes the pattern as a hosted product with personal + company wikis; the row was already `source-backed` at Last seen 2026-08-13 — the new refresh keeps `source-backed` confidence and adds the Almanac evidence anchor). The `MiniMax-m3` row stays at Last seen 2026-08-03 (no MiniMax model release; the 29 unique feed items include zero MiniMax-M3 + zero MiniMax-H3 items; the `open-weight-LLM cluster` and `AI-vendor-business-stack cluster` and `AI-policy / copyright-DMCA lane` and `self-hosted-agentic-substrate cluster` all carry forward unchanged from the 2026-08-30 pull — the 2026-08-31 pull does not surface any open-weight LLM vendor / vendor-business / AI-policy / substrate-essay item to qualify as a new cluster entry). The `hermes-agent-v0-19-quicksilver` row stays at Last seen 2026-08-03 (no Hermes Agent release; **no new entry in the self-hosted-agentic-substrate cluster on this pull** — the 7-entry / 792-pts / 0.50-entries-per-day / 14-day cluster from the 2026-08-27 LangChain deepagents entry carries forward unchanged; the 2026-08-31 pull does not surface any agent-harness / agent-substrate canonical artifact that would qualify as a new cluster entry, though `49511007` Almanac operationalizes the same wikis-as-agent-memory-substrate pattern as a hosted product rather than a canonical substrate artifact). The `openwiki-brand` watchlist row stays at Last seen 2026-07-16 (no positive `openwiki` hits — clean zero across both feed sweep and Algolia lane; the 2026-07-16 `langchain-ai/openwiki` HN item at 96 pts is the canonical row anchor, and the 2026-08-31 pull adds zero evidence to that anchor — `49511007` Almanac is NOT a positive `openwiki` brand hit even though it operationalizes the same architectural pattern, because the brand is `Almanac` not `openwiki`). The `china-cde-cell-gene-therapy-rules-2026` and `china-order-no-818-clinical-translation` watchlist rows stay at Last seen 2026-07-24 / 2026-07-28 (no China regulatory items on this pull). The **open-weight-LLM cluster** stays at **~3,318+ pts across 11 items in 9 pulls over 12 days** — no new entry on the 2026-08-31 pull; the **AI-vendor-business-stack cluster** stays at **~2,522+ pts across 6 items in 6 pulls over 6 days** — no new entry on the 2026-08-31 pull; the **AI-policy / copyright-DMCA lane** stays at **~687 pts across 2 items in 2 pulls over 2 days** — no new entry on the 2026-08-31 pull; the **self-hosted-agentic-substrate cluster** stays at **7 entries / 792 pts / 0.50 entries/day over 14 days** — no new entry on the 2026-08-31 pull; the **agent-memory-architecture theme row** is now refreshed at Last seen 2026-08-31 with 17+ distinct sources (Almanac is the 17th source and the first shipped-product evidence of the pattern). **Key call**:
|
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|
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- **`49511007` Almanac (YC S26) – AI that knows your company** is the **first shipped-product evidence on the `agent-memory-architecture` theme row** by virtue of (a) the **21-pt top+best + 22-cmt engagement** — moderate engagement, below the 100-pt vendor-release refresh bar but above the 46-pt MCP Memory refresh anchor from the 2026-08-13 pull; the **22-cmt comment thread** is a substantive discussion of the architectural pattern, not a passive upvote stream; (b) the **usealmanac.com source** is the canonical Almanac product site — the canonical source for Almanac releases; (c) the **"AI that knows your company" framing** is a YC S26 launch from a 3-founder team (Kushagra Chitrao, IIT Kharagpur → Harvard; Rohan, IIT Delhi → Harvard; Divit, BITS Pilani Hyderabad; all 11-year friends from IIT-JEE prep; the Harvard capstone thesis became the pre-compilation layer that Almanac builds on) explicitly operationalizing the **wikis-as-agent-memory-substrate pattern**: "The 'brain' of this agent is wikis. We pull in information from your connected sources, and start organizing this information in two wikis. A personal one, for you, which understands who you are, what your preferences are, the people in your life, and the things going on in your life. The second wiki is a company wiki, which includes what the company is, what you're working on, what the roadmap is, and what the blockers of the company are. Your agent ultimately has access to these two wikis and the original accounts, which invoke the feeling of 'it just knows you.'" — every element of the Karpathy LLM Wiki + OKF + MCP substrate pattern is present (personal + company wikis = structured memory substrate; Gmail + Calendar + Granola + PostHog connectors = cross-source ingestion; pre-compiled knowledge layer = explicit upfront-compute investment in memory; long-horizon tasks tracked in an "ongoing projects" section = memory atom versioning; proactive background-worker suggesting automations = agentic activation of the memory substrate); (d) the **direct cross-walk to the `agent-memory-architecture` row** strengthens the row from 16+ distinct sources to **17+ distinct sources** with the first shipped-product evidence — every prior source was either a substrate-pattern essay (verginglabs.com markdown-wiki-outscored-every-AI-agent-memory-product 2 pts), an open-source library (MCP Memory using OKF 46 pts + LLM-Wiki-v2 + pi-llm-wiki + MinIO AIStor Memory + arXiv 2607.24759v1 + akitaonrails/ai-memory + Matt_D "I accidentally turned LLM memory into program analysis" 245 pts 2026-08-29 + OzBrain 72 pts 2026-08-22 + LangChain deepagents 1 pt 2026-08-27 + Knowl 1 pt 2026-08-22), a research write-up (akitaonrails/ai-memory docs/research-karpathy-llm-wiki.md), or a benchmark (Exabase M-1 BEAM 76.9%/75.0%/68.0% at 100K/1M/10M tokens); Almanac is the first YC S26 launch that operationalizes the pattern as a hosted product with personal + company wikis + cross-source connectors + proactive agents; (e) any future HN item at higher engagement combining wikis-as-agent-memory-substrate + concrete Hermes / MiniMax / OpenWiki / MCP-canonical artifact delivery becomes the first corroborating event for an `agent-memory-architecture-row-annex-almanac-shipped-product` annex. **Promoted**: the `agent-memory-architecture` row on `/themes.md` gets a Last-seen refresh from 2026-08-13 to 2026-08-31 + Evidence count 16+ → 17+ with the Almanac item added as the new refresh anchor; the existing row description already cites the Karpathy LLM Wiki + OKF + MCP + 16+ distinct sources — the Almanac refresh adds the first shipped-product evidence to the row's evidence footprint without changing the row's structural framing.
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- **This is the twenty-first pull since 2026-08-07** (after the 2026-08-08 03:15 + 2026-08-08 18:00 + 2026-08-13 + 2026-08-15 + 2026-08-16 + 2026-08-18 + 2026-08-19 + 2026-08-21 + 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26 + 2026-08-28 + 2026-08-29 + 2026-08-30 fully-zero pulls + the 2026-08-10 + 2026-08-12 + 2026-08-17 + 2026-08-20 + 2026-08-22 + 2026-08-27 substring-noise-only pulls + the 2026-08-31 nbHits-positive-but-items-zero pull; the 2026-08-31 pull is a **new anomaly type** — neither fully-zero (the Algolia response did report `nbHits > 0` for 3 queries) nor substring-noise-with-material-items like the prior noise-only pulls — the connector's top-level `items` field reports 0 even though `queryResults[i].response.hits` is populated). The pattern confirms that the empty-pulls-on-vendor-queries cadence is normal under the 6-query LLM-agent topic set; the substring-noise-only / fully-zero / nbHits-positive-but-items-zero Algolia lane is the expected normal state, with occasional thematic hits surfacing on the workflow queries (e.g., the 2026-08-22 `49394827` OzBrain 72 pts on `3Brain` substring-noise + the 2026-08-22 `49400587` Brain Organoids 1 pt on `3Brain` substring-noise + the 2026-08-17 `49331423` Copilot Autofix 1 pt on substring-noise + the 2026-08-27 `49461911` LangChain deepagents 1 pt on `deepagents` substring-noise — 4 thematic Algolia hits across the 19 prior pulls, with zero thematic Algolia hits on the 2026-08-30 + 2026-08-31 pulls). The 2026-08-31 pull surfaces the **first item-level match on the wikis-as-agent-memory-substrate pattern since the 2026-07-16 `langchain-ai/openwiki` row anchor** — `49511007` Almanac at 21 pts top+best + 22 cmts is now the row's primary refresh anchor. The Tavily (web-search) lane remains the productive lane for vendor news; the HN lane's stable role is now "high-engagement inference-lane / agent-stack adjacents (... + Tencent Hy4 + Claude Session URL appended to commits + Dwarkesh 'Rise and Fall of Agent Civilizations' + No AI Fridays + Haiku R1/beta6 + **Almanac (YC S26) — first shipped-product wikis-as-agent-memory-substrate evidence**) + low-engagement application-domain watchlist items (organoid / neuroscience / Wired features / clinical-research papers) + low-engagement self-hosted-agentic-substrate cluster essays (DeepSeek Harness + machine0 + OneCLI + self-hosted factory + Munder Difflin + What Is a Harness? + LangChain deepagents)" rather than vendor-direct signals.
|
||||
|
||||
### Flag-for-traceability: Almanac (YC S26) – AI that knows your company (21 pts top+best + 22 cmts, first shipped-product evidence on the `agent-memory-architecture` theme row, first item-level match on the wikis-as-agent-memory-substrate pattern since the 2026-07-16 `langchain-ai/openwiki` row anchor, direct cross-walk to `agent-memory-architecture` row's Karpathy LLM Wiki + Google OKF + MCP substrate pattern) — promoted to `agent-memory-architecture` row Last-seen refresh from 2026-08-13 to 2026-08-31
|
||||
|
||||
## Update — 2026-08-30 18:00 UTC
|
||||
|
||||
- **Coverage:** 2 feeds (`top`, `best`), 6 search queries (the same simplified LLM-agent topic set from the source-specific instruction "Track organoid / CelVivo / 3Brain / Cellink / openwiki / AI agent stories": `organoid`, `CelVivo`, `3Brain`, `Cellink`, `openwiki`, `deepagents`). `top` feed had 30 IDs (19 resolved items — a notably higher top-feed resolution than the 2026-08-29 pull's 13/30), `best` feed had 30 IDs (12 resolved items — **highest `best` resolution of the 2026-08-07 streak since the 2026-08-15 16/30 and 2026-08-12 14/30 pulls**); deduplication gave **27 unique items across both feeds** (4 overlap between top and best — `49492632` Tencent Hy4 + `49494520` Bug Blindness + `49497063` Brits private messages + `49494301` Rise and Fall of Agent Civilizations; the +27-item count is a +13 jump from the 2026-08-29 pull's 14 unique items — the **largest single-day dedup increase of the 2026-08-07 streak**, driven by a more populated 24-hour window on 2026-08-30 than on 2026-08-29). The 6-query lane returned **a fully-zero Algolia lane on all 6 queries** — `organoid` returned 0 hits (`nbHits=null / hits=0`), `CelVivo` returned 0 hits, `3Brain` returned 0 hits, `Cellink` returned 0 hits, `openwiki` returned 0 hits, `deepagents` returned 0 hits (clean zero across the board, no substring-noise collisions — same shape as the 2026-08-28 + 2026-08-29 fully-zero pulls, distinct from the 2026-08-22 + 2026-08-27 substring-noise-only pulls); the connector completed normally at `fetchedAt: 2026-08-30T18:00:39.438Z` (24-hour window). The fully-zero Algolia lane is the **8th consecutive fully-zero pull of the 2026-08-07 streak** (after 2026-08-21 + 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26 + 2026-08-28 + 2026-08-29 — seven fully-zero pulls bookending the 2026-08-22 + 2026-08-27 substring-noise-only pulls) and **the 8th fully-zero / noise-only Algolia lane in 9 consecutive pulls** (after 2026-08-22 + 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + 2026-08-30 — **the longest empty/noise Algolia lane streak of the entire 2026-08-07 streak to date**), confirming that the empty-pulls-on-vendor-queries cadence is normal under the 6-query LLM-agent topic set, not an outage, no config-side intervention needed. The Tavily (web-search) lane remains the productive lane for vendor news.
|
||||
|
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+1
-1
@@ -4,7 +4,7 @@
|
||||
- [Agents 代理商档案索引 — 跨 agent CRM 同步](agents.md) - Cross-agent index of the Obsidian vault 02-Clients/Agents/* profiles (which agents Robin is actively working with, mapped by vendor product line). Base identity only — sensitive fields (phone / WeChat / email / end-customer list / opportunity value) live only in the private vault. Updated 2026-08-07 with _known_associations.md product-line → agent → end-customer mapping.
|
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- [全国经销商地图 (2026-08-07 时点)](distributors-china-2026.md) - Compact index of Robin's 2026-08-07 China distributor baseline (259 dealers across 7 regions, replacing 261 in the 2026-07-24 baseline) plus the new product-association index _known_associations.md. Surfaces CelVivo ClinoStar → 济南成全 + FemtoBiomed CellShot → 9X Bio → TriArm Therapeutics chain. Routes pricing-sensitive fields to the private Obsidian vault per /sources/agents.md privacy rule.
|
||||
- [飞书邮箱 (Robin customer mailbox)](feishu-mail.md) - Planned cross-agent mailbox sync target for Robin's Feishu (飞书) mailbox (imap.feishu.cn:993 / imap.larksuite.com:993) — would let MiniMax code / Hermes recall 'what did Robin last discuss with customer X' from email metadata + summaries. Not yet provisioned — IMAP credentials + update script + crontab still pending Robin setup; this page documents the planned configuration and the sync policy that will be applied once provisioned.
|
||||
- [Git repo — evidence index (Obsidian vault, Robin)](git-repo.md) - 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.
|
||||
- [Git repo — evidence index (Obsidian vault + OpenWiki wiki, Robin)](git-repo.md) - 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.
|
||||
- [Hacker News — evidence index](hackernews.md) - Compact evidence trail for the Hacker News connector (hackernews-1, Robin-curated life-sciences + AI workflow). Synthesis lives on /themes.md, /commitments.md, etc.; this page only records ingestion coverage and notable items.
|
||||
- [文献精读 Master Template (Robin 7-27 实战版, "真适合浏览" 1 文件)](ldr-report-template.md) - Master template for Robin's literature-deep-read (LDR) pipeline — consolidates 4 literature skills (`literature-deep-read` / `research` / `review` / `curation-for-sales`) into a single 8-rule + 3-trigger + 5-section "真适合浏览" report format. Synthesized from 4-27 SOP范本 + 7-27 实战 lessons (Tasevska / Raji / Bosnjakovic). Triggers "精读吧" / "发 wikijs" / "入库" / "A" / Id/DOI/PMID/PDF signals into 4-step精简 or 8-step完整 flows. PDF全文必传 + PyMuPDF xref去重 + 9项强制 + SeaFile hostname `fb.biokingdom.top` + NocoDB v1 JSON + 3张真图 + `journal-year-topic` 报告路径.
|
||||
- [Bosnjakovic 2025 PAH 3D 球体代谢组学: 跟 CelVivo ClinoStar dynamic culture 关系 (Bosnjakovic 2025 bioRxiv)](literature-cel-bosnjakovic-2025-pah-deepread.md) - Deep-read synthesis of Bosnjakovic A et al. 2025 bioRxiv preprint (DOI 10.1101/2025.07.10.663939v1, 2025-07-10) — 21-day mature HepG2 3D spheroids with graded non-cytotoxic BaP + BBF (PAH代表物) exposure for metabolomics biomarker discovery. Robin's connection: 3D spheroid protocol maps directly onto CelVivo ClinoStar dynamic culture; supports PAH exposure metabolomics positioning for hepatotoxicity / NAFLD modeling applications. 精读 2026-07-27.
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|
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+57
-1
@@ -2,7 +2,7 @@
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||||
type: "Reference"
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||||
title: "Literature Deep-Reads — cross-agent deep-read index"
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||||
description: "Cross-agent index of Robin's literature deep-reads across the 4 vendor product lines (CelVivo / 3Brain / Cellink / Femtobiomed) and adjacent application domains (organoid IRB / ethics, vascularized organoids, microfluidic / organ-on-chip). Backed by the Obsidian vault 04-Literature/Deep-Reads/ and the flywheel-sync pipeline; synthesis pages are linked per paper."
|
||||
tags: [literature, deep-read, flywheel, celvivo, 3brain, cellink, femtobiomed, tevonian-2026-vascularized-liver-mps, yang-2026-cardiac-organoid-review, shen-2026-vascularized-organoids-review, zhai-2026-3d-skin-pemphigus, pasca-2025-nature-assembloid, microgravity-reproductive-review-2026, 2026-08-27, 2026-08-25, 2026-08-24, 2026-08-23, vascularized-organoids, cardiac-organoids, skin-organoids, second-5paper-burst]
|
||||
tags: [literature, deep-read, flywheel, celvivo, 3brain, cellink, femtobiomed, tevonian-2026-vascularized-liver-mps, yang-2026-cardiac-organoid-review, shen-2026-vascularized-organoids-review, zhai-2026-3d-skin-pemphigus, 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, pasca-2025-nature-assembloid, microgravity-reproductive-review-2026, 2026-08-31, 2026-08-27, 2026-08-25, 2026-08-24, 2026-08-23, vascularized-organoids, cardiac-organoids, skin-organoids, brain-organoid-virology-cluster, third-5paper-burst, celvivo-capital-v-parallel-subfolder]
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||||
timestamp: 2026-08-27T18:25:00Z
|
||||
---
|
||||
|
||||
@@ -14,6 +14,16 @@ timestamp: 2026-08-27T18:25:00Z
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||||
|
||||
## Last 30 days of deep reads (mtime descending)
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||||
|
||||
### 2026-08-31 (5-paper CelVivo-anchored single-shot LDR burst — NEW `CelVivo/` capital-V subfolder)
|
||||
|
||||
| DOI | Vendor | Application | Title (short) | Vault path |
|
||||
| --- | --- | --- | --- | --- |
|
||||
| `10.3389/fmicb.2023.1320856` | **CelVivo ClinoStar** (direct platform) | SARS-CoV-2 omicron BA.5/XBB neurotropic brain organoids (K18-hACE2 mice + human brain organoids) | Stewart R, Yan K, Ellis SA et al. (2023) **SARS-CoV-2 omicron BA.5 and XBB variants have increased neurotropic potential over BA.1 in K18-hACE2 mice and human brain organoids** (Front Microbiol 14:1320856; QIMR Berghofer Medical Research Institute + University of Queensland; first file in NEW `CelVivo/` capital-V subfolder) — BA.5/XBB variants have increased neurotropic potential vs BA.1; MA1 infection cell count higher in human brain organoids (CelVivo ClinoStar); companion to Yan 2024 + Nguyen 2024 in the QIMR Berghofer Suhrbier/Rawle viral-neurotropism brain-organoid trio | `obsidian-vault/04-Literature/Deep-Reads/CelVivo/stewart-2023-ba5-xbb-neurotropic-brain-organoids.md` |
|
||||
| `10.1038/s44319-025-00619-x` | **CelVivo ClinoStar/ClinoReactor** ⭐⭐⭐⭐⭐ (CelVivo ApS is a co-author) | Brain organoid reproducibility via controlled fluid dynamics | Aiello G, Nemir M, Vidimova B, Ramel C, Viguie J, Ravera A, Wrzesinski K*, Bagni C* et al. (2025) **Increased reproducibility of brain organoids through controlled fluid dynamics** (EMBO reports 26:6209-6239; 洛桑大学 + 罗马 Tor Vergata 大学 + 西北大学 (南非) + **CelVivo ApS (丹麦) co-author**; second file in NEW `CelVivo/` capital-V subfolder) — **CV <15% morphological consistency** vs static culture CV >30% across multi-batch + multi-iPSC-line brain organoid cultures + scRNA-seq OXPHOS metabolic profiling + cortical cell type recapitulation (SOX2/Nestin/PAX6 + DCX + TBR1/SATB2/MAP2 multi-marker IHC). The CelVivo ApS co-author affiliation is the **first direct CelVivo-platform co-authored deep-read** in Robin's set | `obsidian-vault/04-Literature/Deep-Reads/CelVivo/aiello-2025-brain-organoid-reproducibility.md` |
|
||||
| `10.1038/s44298-024-00025-5` | **CelVivo ClinoStar** (direct platform) | Japanese Encephalitis virus genotype 4 isolate characterization (2022 Australian outbreak) + brain organoids | Nguyen W, Gyawali N, Stewart R, Tang B, Cox AL, Yan K, Larcher T, Bishop CR, Wood N, Devine GJ, Suhrbier A, Rawle DJ (2024) **Characterisation of a Japanese Encephalitis virus genotype 4 isolate from the 2022 Australian outbreak** (npj Viruses 25; QIMR Berghofer + INRAE; third file in NEW `CelVivo/` capital-V subfolder) — JEV G4 isolate from 2022 Australian outbreak; brain organoid CelVivo ClinoStar + mouse model; extends the QIMR Berghofer Suhrbier/Rawle viral-neurotropism brain-organoid line into the flavivirus (JEV) application domain. JEV is endemic in 东南亚 + 中国南方 + 西太平洋 — directly relevant to Chinese infectious-disease R&D customer base | `obsidian-vault/04-Literature/Deep-Reads/CelVivo/nguyen-2024-jev-g4-2022-australia-brain-organoids.md` |
|
||||
| `10.1016/j.cell.2025.05.041` | **CelVivo ClinoReactor** ⭐⭐⭐⭐⭐ (direct platform validation as co-differentiation + vascularization standard) | Co-development mesoderm+endoderm for organotypic vascularization in lung and gut organoids | Miao Y, Pek NM, Tan C, Chen Y-W, Guo M*, Gu M* (2025) **Co-development of mesoderm and endoderm enables organotypic vascularization in lung and gut organoids** (Cell 188:1-19; 8-08 精简版已升级完整版; fourth file in NEW `CelVivo/` capital-V subfolder) — companion to the 2026-08-08 flywheel-sync Miao 2025 v2 deep-read (`/home/ldw/workspace/Miao2025_Cell_v2.md`); the **Cell published version** extends the v2 deep-read with the canonical CelVivo ClinoReactor co-differentiation mesoderm+endoderm platform + scRNA-seq single-cell profiling of FOXF1 endothelial-mesenchymal transition | `obsidian-vault/04-Literature/Deep-Reads/CelVivo/miao-2025-vascularized-lung-gut-organoids.md` |
|
||||
| `10.1016/j.celrep.2024.114921` | **CelVivo ClinoStar** (direct platform) | TMEM106B-mediated SARS-CoV-2 ACE2-independent brain organoid infection | Yan K, Dumenil T, Stewart R, Bishop CR, Nguyen W, Suhrbier A*, Rawle DJ* (2024) **TMEM106B-mediated SARS-CoV-2 infection allows for robust ACE2-independent infection in vitro but not in vivo** (Cell Reports 43:114921; QIMR Berghofer Medical Research Institute; fifth file in NEW `CelVivo/` capital-V subfolder) — CRISPR 筛选鉴定 **TMEM106B / 硫酸乙酰肝素 / 内吞介导 ACE2 非依赖进入** in human cortical brain organoids (CelVivo ClinoStar); MA1 神经毒力更强 in vitro (滴度更高 / 感染细胞更多) + K18-hACE2 小鼠疾病更重 / 生存率更低; **in vivo 不成立**: wild-type / Ifnar-/- 小鼠无增加神经侵袭 + Ace2-/- 小鼠肺无法感染. Companion to Stewart 2023 + Nguyen 2024 in the QIMR Berghofer Suhrbier/Rawle viral-neurotropism trio | `obsidian-vault/04-Literature/Deep-Reads/CelVivo/yan-2024-tmem106b-sars-cov2-ace2-independent.md` |
|
||||
|
||||
### 2026-08-23 (5-paper single-shot LDR burst — vault root, non-standard pattern)
|
||||
|
||||
| DOI / slug | Vendor | Application | Title (short) | Vault path |
|
||||
@@ -337,6 +347,42 @@ The `Robin_Picked_Papers` table is **new as of today** — created per Robin's 2
|
||||
- **关键发现**: 3D 打印 + 自组织多层血管化皮肤模型, 建模天疱疮自身免疫 + EGFR 靶向治疗 + ML 辅助药筛
|
||||
- **Robin 业务对接**: 皮肤自身免疫病药筛 + 3D 打印客户 + 精准医疗应用
|
||||
|
||||
## 2026-08-31 (5-paper CelVivo-anchored single-shot LDR burst — NEW `CelVivo/` capital-V parallel subfolder)
|
||||
|
||||
## Stewart 2023 Front Microbiol BA.5/XBB neurotropic brain organoids (PMID 37984455)
|
||||
- **DOI**: 10.3389/fmicb.2023.1320856
|
||||
- **Path**: `obsidian-vault/04-Literature/Deep-Reads/CelVivo/stewart-2023-ba5-xbb-neurotropic-brain-organoids.md`
|
||||
- **QIMR Berghofer Medical Research Institute** + University of Queensland
|
||||
- **关键发现**: SARS-CoV-2 omicron BA.5 + XBB variants have **increased neurotropic potential over BA.1** in K18-hACE2 mice + human brain organoids (CelVivo ClinoStar); MA1 infection cell count higher in brain organoids
|
||||
- **Robin 业务对接**: 病毒神经嗜性 + 变异株 screening + 抗病毒药筛
|
||||
|
||||
## Aiello 2025 EMBO reports brain organoid reproducibility (PMID 40976390)
|
||||
- **DOI**: 10.1038/s44319-025-00619-x
|
||||
- **Path**: `obsidian-vault/04-Literature/Deep-Reads/CelVivo/aiello-2025-brain-organoid-reproducibility.md`
|
||||
- **洛桑大学** + 罗马 Tor Vergata 大学 + 西北大学 (南非) + **CelVivo ApS (丹麦) co-author**
|
||||
- **关键发现**: 受控流体动力学提高脑类器官可重复性 — **CV <15% morphological consistency** vs static culture CV >30% across multi-batch + multi-iPSC-line brain organoid cultures; cortical cell type recapitulation (SOX2/Nestin/PAX6 + DCX + TBR1/SATB2/MAP2 multi-marker IHC) + scRNA-seq OXPHOS metabolic profiling
|
||||
- **Robin 业务对接**: 脑类器官可重复性金标准 + 三甲医院 / 中国脑科学客户 + CDMO brain organoid manufacturing benchmark + multi-iPSC-line cross-validation reference
|
||||
|
||||
## Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids (PMID 39384709)
|
||||
- **DOI**: 10.1038/s44298-024-00025-5
|
||||
- **Path**: `obsidian-vault/04-Literature/Deep-Reads/CelVivo/nguyen-2024-jev-g4-2022-australia-brain-organoids.md`
|
||||
- **QIMR Berghofer Medical Research Institute** + INRAE
|
||||
- **关键发现**: 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 G4 isolate characterization using human brain organoids (CelVivo ClinoStar) + mouse model
|
||||
- **Robin 业务对接**: 虫媒病毒 (JEV / Zika / dengue) 神经嗜性研究 + 疫苗开发 + 抗病毒药筛 + 东南亚 + 中国南方 + 西太平洋 客户对接
|
||||
|
||||
## Miao 2025 Cell vascularized lung/gut organoids v1 published version (PMID 40713703)
|
||||
- **DOI**: 10.1016/j.cell.2025.05.041
|
||||
- **Path**: `obsidian-vault/04-Literature/Deep-Reads/CelVivo/miao-2025-vascularized-lung-gut-organoids.md`
|
||||
- **关键发现**: 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 — companion to the 2026-08-08 flywheel-sync Miao 2025 v2 deep-read; **Cell published version** extends the v2 deep-read with the canonical CelVivo ClinoReactor co-differentiation mesoderm+endoderm platform + scRNA-seq single-cell profiling of FOXF1 endothelial-mesenchymal transition
|
||||
- **Robin 业务对接**: lung organoid + gut organoid + 血管化 + 呼吸道病毒 / 肠道病毒感染模型 + 中国肺纤维化 / IBD pharma R&D positioning
|
||||
|
||||
## Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids (PMID 39576284)
|
||||
- **DOI**: 10.1016/j.celrep.2024.114921
|
||||
- **Path**: `obsidian-vault/04-Literature/Deep-Reads/CelVivo/yan-2024-tmem106b-sars-cov2-ace2-independent.md`
|
||||
- **QIMR Berghofer Medical Research Institute**
|
||||
- **关键发现**: TMEM106B 介导的 SARS-CoV-2 感染：体外强效 ACE2 非依赖感染但体内不成立 — CRISPR 筛选鉴定 TMEM106B/硫酸乙酰肝素/内吞介导 ACE2 非依赖进入 in human cortical brain organoids (CelVivo ClinoStar); MA1 神经毒力更强 in vitro; in vivo 不成立
|
||||
- **Robin 业务对接**: viral entry mechanism + 抗病毒药筛 + brain organoid platform validation
|
||||
|
||||
## https://fb.biokingdom.top/api/v4/file/content/m99qHL/0/pasca...
|
||||
|
||||
- **Title**: Human assembloid model of the ascending neural sensory pathway
|
||||
@@ -364,3 +410,13 @@ The `Robin_Picked_Papers` table is **new as of today** — created per Robin's 2
|
||||
- **PDF Status**: 5 路径 + S2 + Europe PMC 镜像全失败 (Robin 8-26 撞坑诚实停手);RAGFlow 解析文本 82546B 可下
|
||||
- **Method**: First cross-paradigm review (spaceflight + SMG + animal + human). 7 mechanisms (oxidative stress / DNA damage / cell signaling / cytoskeleton / mitochondria / EV / epigenetics). Countermeasures: AG / antioxidants / cryopreservation / RNAi.
|
||||
- **Date added**: 2026-08-27
|
||||
|
||||
- **Stewart 2023 Front Microbiol 14:1320856** — SARS-CoV-2 omicron BA.5/XBB 较 BA.1 神经趋向性增强（K18-hACE2 小鼠 + CelVivo ClinoStar 培养的人源皮层脑类器官）。BA.5 感染类器官滴度高 1-2 log、RNA 高 25 倍，神经元为主要靶细胞，脑内细胞因子风暴主导。DOI: 10.3389/fmicb.2023.1320856 | Wiki: https://wiki.biokingdom.top/literature/stewart-2023-sarscov2-ba5-xbb-neurotropic-brain-organoids
|
||||
|
||||
- **Aiello 2025 EMBO reports 26:6209-6239** — 通过受控流体动力学提高脑类器官可重复性：CelVivo ClinoReactor 垂直旋转培养降低流体剪切力(fFSS)，90天形态+10参数PCA显示跨批次/跨细胞系变异显著降低，17,738单细胞重现完整皮层细胞类型，OXPHOS代谢接近胎儿脑。CelVivo员工为共同作者。DOI: 10.1038/s44319-025-00619-x | Wiki: https://wiki.biokingdom.top/literature/aiello-2025-brain-organoid-reproducibility-rotating-chamber
|
||||
|
||||
- **Nguyen 2024 npj Viruses Article 25** — 2022 澳大利亚 JEV 基因 4 型爆发株 JEVNSW/22 特征研究：三小鼠模型 (C57BL/6J/Irf7-/-/Ifnar-/-) 毒力低于 G2/G3 且对 I 型 IFN 敏感；人源皮层脑类器官 (CelVivo Clinostar 培养) 所有 JEV/MVEV 均致细胞病变感染；IMOJEV 疫苗可交叉中和。DOI: 10.1038/s44298-024-00025-5 | Wiki: https://wiki.biokingdom.top/literature/nguyen-2024-jev-genotype4-2022-australia-brain-organoids
|
||||
|
||||
- **Miao 2025 Cell 188:1-19** — 中胚层-内胚层共分化 + CelVivo ClinoReactor 无 ECM 大规模培养 (约2000类器官/反应器) 实现肺/肠类器官器官型血管化：单细胞证实 aCap/gCap 毛细血管内皮 + 器官型间充质，体内移植重建人源血管网络，FOXF1/ACD 疾病模型。DOI: 10.1016/j.cell.2025.05.041 | Wiki: https://wiki.biokingdom.top/literature/miao-2025-vascularized-lung-gut-organoids-cell
|
||||
|
||||
- **Yan 2024 Cell Reports 43:114921** — TMEM106B 介导 SARS-CoV-2MA1 (S-E484D) ACE2 非依赖进入：CRISPR 筛选锁定 TMEM106B/硫酸乙酰肝素/内吞；人源皮层脑类器官 (CelVivo ClinoStar 培养) 中神经毒力增强，但小鼠体内 ACE2 仍必需 (Ace2-/- 肺无法感染)。DOI: 10.1016/j.celrep.2024.114921 | Wiki: https://wiki.biokingdom.top/literature/yan-2024-tmem106b-sars-cov2-ace2-independent-brain-organoids
|
||||
@@ -1,3 +1,9 @@
|
||||
---
|
||||
type: "Reference"
|
||||
title: "NocoDB 文献库索引 — 跨 agent 数据层"
|
||||
openwiki_generated: true
|
||||
---
|
||||
|
||||
# NocoDB 文献库索引 — 跨 agent 数据层
|
||||
|
||||
> 数据源: NocoDB 13 个文献库 + 2 个公司库 (实时,每次 OpenWiki cron 跑时更新)
|
||||
|
||||
@@ -1,3 +1,9 @@
|
||||
---
|
||||
type: "Reference"
|
||||
title: "RAGFlow 全文检索索引 (Robin KB system)"
|
||||
openwiki_generated: true
|
||||
---
|
||||
|
||||
# RAGFlow 全文检索索引 (Robin KB system)
|
||||
|
||||
> 数据源: RAGFlow (http://10.10.10.254:9980/) 14 个 KB 全文检索结果
|
||||
|
||||
@@ -1,3 +1,9 @@
|
||||
---
|
||||
type: "Reference"
|
||||
title: "SeaFile 大文件存储索引"
|
||||
openwiki_generated: true
|
||||
---
|
||||
|
||||
# SeaFile 大文件存储索引
|
||||
|
||||
> 数据源: SeaFile (http://10.10.10.254:9898/) 共 N 个资料库
|
||||
|
||||
+13
-5
@@ -2,13 +2,21 @@
|
||||
type: "Reference"
|
||||
title: "Web Search Evidence"
|
||||
description: "Compact, source-backed evidence and ingestion coverage for the web-search-1 Tavily lane tracking CelVivo, 3Brain, Cellink, and related organoid news."
|
||||
tags: [source, web-search, tavily, celvivo, 3brain, cellink, organoids, 2026-08-12, 2026-08-15, 2026-08-16, 2026-08-17, 2026-08-18, 2026-08-19, 2026-08-20, 2026-08-21, 2026-08-22, 2026-08-23, 2026-08-24, 2026-08-25, 2026-08-27, 2026-08-28, 2026-08-29]
|
||||
timestamp: 2026-08-29T18:09:00Z
|
||||
tags: [source, web-search, tavily, celvivo, 3brain, cellink, organoids, 2026-08-12, 2026-08-15, 2026-08-16, 2026-08-17, 2026-08-18, 2026-08-19, 2026-08-20, 2026-08-21, 2026-08-22, 2026-08-23, 2026-08-24, 2026-08-25, 2026-08-27, 2026-08-28, 2026-08-29, 2026-08-30, 2026-08-31]
|
||||
timestamp: 2026-08-31T18:06:00Z
|
||||
---
|
||||
|
||||
# Web Search Evidence
|
||||
|
||||
> Connector: `web-search-1` (Tavily). This page records compact, relevant evidence from Tavily pulls; search results are discovery leads, not vendor-confirmed announcements. Latest successful pull: 2026-08-03 18:08 UTC. The 2026-08-08, 2026-08-10, 2026-08-12, 2026-08-15, 2026-08-17, 2026-08-18, 2026-08-19, 2026-08-20, 2026-08-21, 2026-08-22, 2026-08-23, 2026-08-24, 2026-08-25, 2026-08-27, 2026-08-28, 2026-08-29, and 2026-08-30 update attempts were skipped because the connector is disabled and `TAVILY_API_KEY` is not present; no new 24-hour evidence was available on any of these seventeen runs.
|
||||
> Connector: `web-search-1` (Tavily). This page records compact, relevant evidence from Tavily pulls; search results are discovery leads, not vendor-confirmed announcements. Latest successful pull: 2026-08-03 18:08 UTC. The 2026-08-08, 2026-08-10, 2026-08-12, 2026-08-15, 2026-08-17, 2026-08-18, 2026-08-19, 2026-08-20, 2026-08-21, 2026-08-22, 2026-08-23, 2026-08-24, 2026-08-25, 2026-08-27, 2026-08-28, 2026-08-29, 2026-08-30, and 2026-08-31 update attempts were skipped because the connector is disabled and `TAVILY_API_KEY` is not present; no new 24-hour evidence was available on any of these eighteen runs.
|
||||
|
||||
## 2026-08-31 attempted update — skipped
|
||||
|
||||
- **Status:** skipped. `web-search-1` is not enabled; the connector reports that `enabled=true` must be set in `~/.openwiki/connectors/web-search/config.json`.
|
||||
- **Authentication:** `TAVILY_API_KEY` is not present, so no Tavily request was made.
|
||||
- **Coverage:** no raw data files were written for this attempted 24-hour window. No web-search evidence of any kind landed in the 24-hour window. No new CelVivo, 3Brain, Cellink, or organoid findings were available for synthesis; the latest successful pull remains 2026-08-03 18:08 UTC.
|
||||
- **Synthesis:** no changes were made to `/themes.md`, `/commitments.md`, `/open-questions.md`, or `/personal-logistics.md` from this source attempt.
|
||||
- **Operational note (cross-check):** the on-disk `~/.openwiki/connectors/web-search/config.json` does show `enabled: true` plus 6 Chinese-language queries (`CelVivo ClinoStar ClinoReactor 类器官培养新进展`, `3Brain HD-MEA 高密度微电极阵列 电生理`, `Cellink BIO X 3D生物打印 类器官`, `Femtobiomed CellShot 流式电转 精准医疗`, `类器官 vendor 2026年新发布`, `MiniMax M3 智能体 Hermes`). The agent runtime still reports the connector as disabled, so there is a discrepancy between disk config and runtime registry. This is an operational concern (connector enable / auth / re-registration), not a wiki-synthesis concern, and is recorded here for traceability rather than triggering wiki edits. The 2026-08-08, 2026-08-10, 2026-08-12, 2026-08-15, 2026-08-17, 2026-08-18, 2026-08-19, 2026-08-20, 2026-08-21, 2026-08-22, 2026-08-23, 2026-08-24, 2026-08-25, 2026-08-27, 2026-08-28, 2026-08-29, and 2026-08-30 runs hit the same blocker; this is the **eighteenth consecutive skip on the same code path**. To resolve: set `TAVILY_API_KEY` in the OpenWiki runtime environment and ensure the runtime registry refreshes the connector's enabled state.
|
||||
|
||||
## 2026-08-30 attempted update — skipped
|
||||
|
||||
@@ -16,7 +24,7 @@ timestamp: 2026-08-29T18:09:00Z
|
||||
- **Authentication:** `TAVILY_API_KEY` is not present, so no Tavily request was made.
|
||||
- **Coverage:** no raw data files were written for this attempted 24-hour window. The nightly searxng-fallback slot for the 24-hour window (`~/.openwiki/connectors/web-search/raw/2026-08-29T18-35-04-searxng-fallback/`, written at 2026-08-30 02:35 by the nightly searxng-fallback job) is empty on disk (confirmed — only `.` and `..` entries) — no web-search evidence of any kind landed in the 24-hour window. No new CelVivo, 3Brain, Cellink, or organoid findings were available for synthesis; the latest successful pull remains 2026-08-03 18:08 UTC.
|
||||
- **Synthesis:** no changes were made to `/themes.md`, `/commitments.md`, `/open-questions.md`, or `/personal-logistics.md` from this source attempt.
|
||||
- **Operational note (cross-check):** the on-disk `~/.openwiki/connectors/web-search/config.json` does show `enabled: true` plus 6 Chinese-language queries (`CelVivo ClinoStar ClinoReactor 类器官培养新进展`, `3Brain HD-MEA 高密度微电极阵列 电生理`, `Cellink BIO X 3D生物打印 类器官`, `Femtobiomed CellShot 流式电转 精准医疗`, `类器官 vendor 2026年新发布`, `MiniMax M3 智能体 Hermes`). The agent runtime still reports the connector as disabled, so there is a discrepancy between disk config and runtime registry. This is an operational concern (connector enable / auth / re-registration), not a wiki-synthesis concern, and is recorded here for traceability rather than triggering wiki edits. The 2026-08-08, 2026-08-10, 2026-08-12, 2026-08-15, 2026-08-17, 2026-08-18, 2026-08-19, 2026-08-20, 2026-08-21, 2026-08-22, 2026-08-23, 2026-08-24, 2026-08-25, 2026-08-27, 2026-08-28, and 2026-08-29 runs hit the same blocker; this is the **seventeenth consecutive skip on the same code path**. To resolve: set `TAVILY_API_KEY` in the OpenWiki runtime environment and ensure the runtime registry refreshes the connector's enabled state.
|
||||
- **Operational note (cross-check):** the on-disk `~/.openwiki/connectors/web-search/config.json` does show `enabled: true` plus 6 Chinese-language queries (`CelVivo ClinoStar ClinoReactor 类器官培养新进展`, `3Brain HD-MEA 高密度微电极阵列 电生理`, `Cellink BIO X 3D生物打印 类器官`, `Femtobiomed CellShot 流式电转 精准医疗`, `类器官 vendor 2026年新发布`, `MiniMax M3 智能体 Hermes`). The agent runtime still reports the connector as disabled, so there is a discrepancy between disk config and runtime registry. This is an operational concern (connector enable / auth / re-registration), not a wiki-synthesis concern, and is recorded here for traceability rather than triggering wiki edits. The 2026-08-08, 2026-08-10, 2026-08-12, 2026-08-15, 2026-08-17, 2026-08-18, 2026-08-19, 2026-08-20, 2026-08-21, 2026-08-22, 2026-08-23, 2026-08-24, 2026-08-25, 2026-08-27, 2026-08-28, and 2026-08-29 runs hit the same blocker; the 2026-08-31 run hit the same blocker too. This was the **seventeenth consecutive skip on the same code path at the time of the 2026-08-30 attempt** (and the eighteenth skip including the 2026-08-31 follow-up). To resolve: set `TAVILY_API_KEY` in the OpenWiki runtime environment and ensure the runtime registry refreshes the connector's enabled state.
|
||||
|
||||
## 2026-08-29 attempted update — skipped
|
||||
|
||||
@@ -600,7 +608,7 @@ Every query in the 10-query lane returned the same structured error (no answer t
|
||||
- Pull 10: fetched 2026-08-02T18:07:53Z — raw `~/.openwiki/connectors/web-search/raw/2026-08-02T18-06-12-521Z/web-search-results.json` — **all 10 queries returned `"error": "fetch failed"`; no usable evidence**
|
||||
- Pull 11: fetched 2026-08-03T18:08:50Z — raw `~/.openwiki/connectors/web-search/raw/2026-08-03T18-07-31-803Z/web-search-results.json` — **first successful pull after the 3-day outage streak; Tavily back online; see section below**
|
||||
- Pull 12: attempted 2026-08-10T18:35Z — **skipped** (connector reported disabled; `TAVILY_API_KEY` not present; no raw files written; no synthesis update)
|
||||
- 2026-08-12 / 2026-08-15 / 2026-08-17 / 2026-08-18 / 2026-08-19 / 2026-08-20 / 2026-08-21 / 2026-08-22 / 2026-08-23 / 2026-08-24 / 2026-08-25 / 2026-08-27 / 2026-08-28 / 2026-08-29 / 2026-08-30 update attempts: all **skipped** on the same code path (connector reported disabled; `TAVILY_API_KEY` not present; no raw files written; no synthesis update; seventeenth consecutive skip including 2026-08-30); see individual sections above for per-day operational notes
|
||||
- 2026-08-12 / 2026-08-15 / 2026-08-17 / 2026-08-18 / 2026-08-19 / 2026-08-20 / 2026-08-21 / 2026-08-22 / 2026-08-23 / 2026-08-24 / 2026-08-25 / 2026-08-27 / 2026-08-28 / 2026-08-29 / 2026-08-30 / 2026-08-31 update attempts: all **skipped** on the same code path (connector reported disabled; `TAVILY_API_KEY` not present; no raw files written; no synthesis update; eighteenth consecutive skip including 2026-08-31); see individual sections above for per-day operational notes
|
||||
- Queries: pulls 1, 2, 4, 5, 6, 7, 8, 9, 10, 11 = 10 queries each; pull 3 = 6 queries (vendor-anchored only)
|
||||
- Instance: `web-search-1`
|
||||
|
||||
|
||||
@@ -1,3 +1,9 @@
|
||||
---
|
||||
type: "Reference"
|
||||
title: "Wiki.js 索引 — 跨 agent 文档发布层"
|
||||
openwiki_generated: true
|
||||
---
|
||||
|
||||
# Wiki.js 索引 — 跨 agent 文档发布层
|
||||
|
||||
> 数据源: Wiki.js (http://10.10.10.254:3000/graphql) Biokingdom 实例
|
||||
|
||||
Reference in new issue
Block a user