chore: daily update 2026-09-01

.last-update.json

@@ -1,5 +1,5 @@
 {
-  "updatedAt": "2026-08-30T18:18:56.213Z",
+  "updatedAt": "2026-08-31T18:24:33.209Z",
   "command": "update",
   "model": "MiniMax-M3",
   "status": "complete",

commitments.md

@@ -2,8 +2,8 @@
 type: "Reference"
 title: "Commitments"
 description: "Active work tasks, follow-ups, approvals, and scheduled items extracted from sources (web-search, git-repo, literature flywheel-sync, etc.). Personal errands live in /personal-logistics.md instead."
-tags: [commitments, work, follow-ups, distributors-2026-08-07-refresh, dong-huiqun-ji-nan-chengquan-link, liang-2026-celvivo-clinostar-positioning, guo-2026-organoid-irb-checklist-rollout, celvivo-app-note-2026-clinostar-vs-orbital-shaker-positioning, aiello-2025-rc-cfd-clinostar-positioning, kim-2025-egain-3d-mea-vs-3brain-positioning, ajongbolo-2025-brain-organoid-review-cluster, tian-2025-epicardium-mtor-cardiac-expansion, tevonian-2026-vascularized-liver-mps-positioning, yang-2026-cardiac-organoid-review-positioning, shen-2026-vascularized-organoid-chinese-review, zhai-2026-skin-organoid-pemphigus-positioning, 2026-08-25]
-timestamp: 2026-08-25T18:13:00Z
+tags: [commitments, work, follow-ups, distributors-2026-08-07-refresh, dong-huiqun-ji-nan-chengquan-link, liang-2026-celvivo-clinostar-positioning, guo-2026-organoid-irb-checklist-rollout, celvivo-app-note-2026-clinostar-vs-orbital-shaker-positioning, aiello-2025-rc-cfd-clinostar-positioning, kim-2025-egain-3d-mea-vs-3brain-positioning, ajongbolo-2025-brain-organoid-review-cluster, tian-2025-epicardium-mtor-cardiac-expansion, tevonian-2026-vascularized-liver-mps-positioning, yang-2026-cardiac-organoid-review-positioning, shen-2026-vascularized-organoid-chinese-review, zhai-2026-skin-organoid-pemphigus-positioning, stewart-2023-ba5-xbb-neurotropic-brain-organoid, aiello-2025-brain-organoid-reproducibility-celvivo, nguyen-2024-jev-g4-australia-brain-organoid, miao-2025-vascularized-lung-gut-celvivo, yan-2024-tmem106b-sars-cov2-brain-organoid, 2026-08-31, 2026-08-25]
+timestamp: 2026-08-31T18:09:00Z
 ---
 
 # Commitments
@@ -187,6 +187,41 @@ Concrete work tasks, follow-ups, approvals, and scheduled items extracted from G
 - Status: open
 - Notes: **First 3D-skin organoid disease-modeling paper** in Robin's deep-read set; **net-new application domain** (autoimmune dermatology + 3D skin) that Robin's existing ~22 deep-read subfolders do not cover. Uses **3D 打印 + 自组织多层血管化皮肤模型** to model 天疱疮 (pemphigus) autoimmune disease + EGFR 靶向治疗 + ML 辅助药筛. **Vendor anchor mapping**: TBD — Zhai paper does NOT have the `9aa2af4c` retrofit 5-vendor mapping (only Tevonian + Yang got the retrofit). Skin organoid is a candidate workflow for **CelVivo ClinoReactor** (long-term 3D skin culture — similar to the existing liver, brain, lung, retinal organoid applications) but the Sci Adv paper's specific ClinoReactor / ClinoStar callouts are not in the manifest entry. **Application domain**: 3D skin organoid + autoimmune dermatology (pemphigus) — distinct from the existing Cancer / Brain / Liver / Vascularized-Organoids / Cardiac-Organoids / Kidney / Retinal / Brain-Tumor application-domain subfolders. **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. Follow-ups: (a) add a wiki-side deep-read synthesis page at `/sources/literature-zhai-2026-sciadv-3d-skin-pemphigus-deepread.md`; (b) verify whether the Skin-Organoids subfolder accumulates ≥3 entries to confirm a recurring application-domain pattern; (c) check whether the Zhai paper yields Chinese cosmetic / dermatology pharma R&D positioning material that the active CRM portfolio could absorb.
 
+### stewart-2023-ba5-xbb-neurotropic-brain-organoid: Stewart 2023 Front Microbiol BA.5/XBB neurotropic brain organoid CelVivo viral-pathology positioning
+- Owner: me
+- Source: git-repo-1 2026-08-31 — vault commit `eb24ab72` (Stewart R et al. Front Microbiol 2023 SARS-CoV-2 omicron BA.5/XBB neurotropic brain organoids, DOI 10.3389/fmicb.2023.1320856; vault path `obsidian-vault/04-Literature/Deep-Reads/CelVivo/stewart-2023-ba5-xbb-neurotropic-brain-organoids.md`, **first file in NEW `CelVivo/` (capital-V) parallel subfolder** at `obsidian-vault/04-Literature/Deep-Reads/CelVivo/`; QIMR Berghofer Medical Research Institute + University of Queensland)
+- Due: unscheduled
+- Status: open
+- Notes: **First file in NEW `CelVivo/` (capital-V) parallel subfolder** — Robin's first parallel-naming deep-read subfolder convention (parallel to existing lowercase `Celvivo/` 142-file subfolder). BA.5/XBB variants have increased neurotropic potential vs BA.1 in K18-hACE2 mice + human brain organoids. **Vendor anchor mapping**: CelVivo ClinoStar (direct platform) — the paper uses CelVivo ClinoStar brain organoid platform for the SARS-CoV-2 BA.5/XBB infection model; supports Robin's CelVivo ClinoStar ⭐⭐⭐⭐⭐ positioning for brain organoid viral-pathology applications (脑类器官病毒感染 + 神经嗜性研究). Companion to the Yan 2024 + Nguyen 2024 brain-organoid infectious-disease papers from the same 2026-08-31 cluster — all 3 are QIMR Berghofer Suhrbier/Rawle viral-neurotropism line. Follow-ups: (a) add a wiki-side deep-read synthesis page at `/sources/literature-stewart-2023-front-microbiol-ba5-xbb-neurotropic-brain-organoids-deepread.md`; (b) bundle Stewart + Yan + Nguyen as the QIMR Berghofer Suhrbier/Rawle viral-neurotropism brain-organoid trio on `/themes/05-robin-research.md`; (c) verify whether the Stewart paper yields Chinese pharma R&D / CDMO viral-pathology positioning material (COVID-19 长期后遗症 + 神经嗜性变异株 screening).
+
+### aiello-2025-brain-organoid-reproducibility-celvivo: Aiello 2025 EMBO reports brain organoid reproducibility — CelVivo ApS co-authored platform standard
+- Owner: me
+- Source: git-repo-1 2026-08-31 — vault commit `030f31ed` (Aiello G, Nemir M, Vidimova B et al. EMBO reports 2025 Increased reproducibility of brain organoids through controlled fluid dynamics, DOI 10.1038/s44319-025-00619-x; vault path `obsidian-vault/04-Literature/Deep-Reads/CelVivo/aiello-2025-brain-organoid-reproducibility.md`; **CelVivo ApS (丹麦) is a co-author affiliation** + 洛桑大学 + 罗马 Tor Vergata 大学 + 西北大学(南非))
+- Due: unscheduled
+- Status: open
+- Notes: **CelVivo ApS is a co-author affiliation** — first Robin deep-read paper with CelVivo ApS as a direct co-author (vs prior papers that mention CelVivo ClinoStar/ClinoReactor but CelVivo ApS is not on the author list). The paper establishes that **controlled fluid dynamics (ClinoStar/ClinoReactor) produces CV <15% morphological consistency** vs static culture CV >30% across multi-batch + multi-iPSC-line brain organoid cultures + SOX2/Nestin/PAX6 + DCX + TBR1/SATB2/MAP2 multi-marker IHC recapitulation + scRNA-seq OXPHOS metabolic profiling. **Vendor anchor mapping**: **CelVivo ClinoStar ⭐⭐⭐⭐⭐** (direct platform validation as a reproducibility-benchmarking standard; the paper IS the canonical ClinoStar/ClinoReactor platform standard for any Chinese brain organoid customer) + 3Brain HD-MEA-adjacent (cortical organoid electrophysiology read-out). **Robin 业务对接**: brain organoid reproducibility standard for 三甲医院 / 中国脑科学客户 + CDMO brain organoid manufacturing benchmark + multi-iPSC-line cross-validation reference. Follow-ups: (a) add a wiki-side deep-read synthesis page at `/sources/literature-aiello-2025-embo-reports-brain-organoid-reproducibility-deepread.md`; (b) cross-link Aiello with the existing `aiello-bagni-2025-rc-cfd-clinostar-positioning` commitment from the 2026-08-23/24 cluster (same authors + same paper, but the 2026-08-23/24 entry was a biorxiv preprint and the 2026-08-31 entry is the EMBO reports published version — pair as pre-print + published); (c) cross-link Aiello with the existing `class-organoid-3d-bioprinting` theme row at `/themes.md` as the brain-organoid reproducibility reference.
+
+### nguyen-2024-jev-g4-australia-brain-organoid: Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoid viral-pathology positioning
+- Owner: me
+- Source: git-repo-1 2026-08-31 — vault commit `fad7e21e` (Nguyen W et al. npj Viruses 2024 Characterisation of a Japanese Encephalitis virus genotype 4 isolate from the 2022 Australian outbreak, DOI 10.1038/s44298-024-00025-5; vault path `obsidian-vault/04-Literature/Deep-Reads/CelVivo/nguyen-2024-jev-g4-2022-australia-brain-organoids.md`; QIMR Berghofer Medical Research Institute + INRAE)
+- Due: unscheduled
+- Status: open
+- Notes: **JEV genotype 4 isolate characterization** using human brain organoids (CelVivo ClinoStar) + mouse model. The paper extends the QIMR Berghofer Suhrbier/Rawle viral-neurotropism brain-organoid line into the flavivirus (JEV) application domain — distinct from the SARS-CoV-2 BA.5/XBB (Stewart 2023) + TMEM106B SARS-CoV-2 (Yan 2024) papers in the same cluster. **Vendor anchor mapping**: CelVivo ClinoStar (direct platform) — supports Robin's CelVivo ClinoStar ⭐⭐⭐⭐ positioning for brain organoid viral-pathology applications in flavivirus / JEV research (Japanese encephalitis is endemic in 东南亚 + 中国南方 + 西太平洋 — directly relevant to Chinese infectious-disease R&D customer base). **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. Follow-ups: (a) add a wiki-side deep-read synthesis page at `/sources/literature-nguyen-2024-npj-viruses-jev-g4-brain-organoids-deepread.md`; (b) bundle Nguyen with Stewart + Yan as the QIMR Berghofer Suhrbier/Rawle viral-neurotropism brain-organoid trio on `/themes/05-robin-research.md`; (c) verify whether the JEV/flavivirus application domain yields Chinese pharma R&D / CDMO positioning material (active CRM profile set is mostly CelVivo / 3Brain neural-organoid focused — no flavivirus customer dossier surfaced yet).
+
+### miao-2025-vascularized-lung-gut-celvivo: Miao 2025 Cell vascularized lung/gut organoids — CelVivo ClinoReactor co-differentiation platform
+- Owner: me
+- Source: git-repo-1 2026-08-31 — vault commit `4fca0123` (Miao Y et al. Cell 2025 Co-development of mesoderm and endoderm enables organotypic vascularization in lung and gut organoids, DOI 10.1016/j.cell.2025.05.041; vault path `obsidian-vault/04-Literature/Deep-Reads/CelVivo/miao-2025-vascularized-lung-gut-organoids.md`)
+- Due: unscheduled
+- Status: open
+- Notes: **Miao 2025 v1 (Cell published version, 8-08 精简版已升级完整版)** — companion to the 2026-08-08 flywheel-sync Miao 2025 v2 deep-read that already exists in Robin's vault as `/home/ldw/workspace/Miao2025_Cell_v2.md`. The Cell published version (this commit) extends the v2 deep-read with the canonical CelVivo ClinoReactor co-differentiation mesoderm+endoderm platform for **organotypic vascularization in lung and gut organoids**. **Vendor anchor mapping**: **CelVivo ClinoReactor ⭐⭐⭐⭐⭐** (direct platform validation as the co-differentiation + vascularization standard; the paper IS the canonical ClinoReactor lung/gut vascularization standard) + scRNA-seq single-cell profiling of FOXF1 endothelial-mesenchymal transition. **Robin 业务对接**: lung organoid + gut organoid + vascularization + 呼吸道病毒 / 肠道病毒感染模型 + 中国肺纤维化 / IBD pharma R&D positioning. Follow-ups: (a) add a wiki-side deep-read synthesis page at `/sources/literature-miao-2025-cell-vascularized-lung-gut-organoids-celvivo-deepread.md` (separate from the existing `/sources/literature-miao-2025-cell-vascularization-v2-deepread.md` which is the 2026-08-08 flywheel-sync synthesis); (b) cross-link Miao 2025 v1 (this commit, in `CelVivo/` capital-V subfolder) with Miao 2025 v2 (the 2026-08-08 flywheel-sync, in vault root) on `/sources/literature.md`; (c) verify whether the lung/gut vascularization application domain yields Chinese pharma R&D positioning material for respiratory / IBD CDMO accounts.
+
+### yan-2024-tmem106b-sars-cov2-brain-organoid: Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoid viral-entry positioning
+- Owner: me
+- Source: git-repo-1 2026-08-31 — vault commit `391e4713` (Yan K, Dumenil T, Stewart R et al. Cell Reports 2024 TMEM106B-mediated SARS-CoV-2 infection allows for robust ACE2-independent infection in vitro but not in vivo, DOI 10.1016/j.celrep.2024.114921; vault path `obsidian-vault/04-Literature/Deep-Reads/CelVivo/yan-2024-tmem106b-sars-cov2-ace2-independent.md`; QIMR Berghofer Medical Research Institute)
+- Due: unscheduled
+- Status: open
+- Notes: **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) — establishes a novel ACE2-independent SARS-CoV-2 viral entry pathway. **In vitro vs in vivo discrepancy** — MA1 has stronger neurotropism in vitro brain organoids but does not increase neuroinvasion in wild-type / Ifnar-/- mice; Ace2-/- mice cannot be infected via lung. **Vendor anchor mapping**: CelVivo ClinoStar (direct platform) — supports Robin's CelVivo ClinoStar ⭐⭐⭐⭐ positioning for brain organoid viral-entry-mechanism research (SARS-CoV-2 TMEM106B / 硫酸乙酰肝素 / 内吞介导). Companion to Stewart 2023 (BA.5/XBB) + Nguyen 2024 (JEV G4) in the QIMR Berghofer Suhrbier/Rawle viral-neurotropism trio. **Robin 业务对接**: viral entry mechanism + 抗病毒药筛 + brain organoid platform validation. Follow-ups: (a) add a wiki-side deep-read synthesis page at `/sources/literature-yan-2024-cell-reports-tmem106b-sars-cov2-brain-organoids-deepread.md`; (b) bundle Yan with Stewart + Nguyen as the QIMR Berghofer Suhrbier/Rawle viral-neurotropism brain-organoid trio on `/themes/05-robin-research.md`; (c) verify whether the TMEM106B / 硫酸乙酰肝素 viral-entry-mechanism research yields Chinese pharma R&D / CDMO positioning material for ACE2-independent antiviral drug screening.
+
 <!--
 Structure for new entries:
 

index.md

@@ -8,7 +8,7 @@ okf_version: "0.1"
 - [2026-07-16 工具链打通战报](memory-2026-07-16-tools-final.md) - After-action report on Robin's 2026-07-16 end-to-end toolchain integration: OpenWiki + Gitea + NocoDB + RAGFlow + Wiki.js + MiniMax code all wired together and working in production. Snapshot of the pre-flywheel-sync state — pre-dates the 2026-07-26 HN + Tavily launches and the 2026-07-29 Tavily cluster / 2026-08-08 literature flywheel-sync milestones.
 - [Open Questions](open-questions.md) - Active, Answered, and Stale unresolved questions about Robin's memory, recurring routines, people, projects, and wiki quality. Source-document TODOs and product questions live on their source pages instead.
 - [Personal Logistics](personal-logistics.md) - Personal errands, appointments, pickups, travel, household/life-admin deadlines, and other non-work logistics. Work commitments live in /commitments.md.
-- [Robin's Local Knowledge Base](quickstart.md) - OpenWiki entrypoint and orientation — Robin's personal knowledge base with 5 synthesis themes (organoid equipment, bioprinting, AI agents, local LLM, personal research), navigation map, current connector status, and backlog. The 2026-08-28 18:09 UTC git-repo-1 fetch observed **vault HEAD unchanged** at `9d4767c7` (**0 new vault commits** for the 3rd consecutive fetch since the 2026-08-24/25 burst, 3 calendar days stale); wiki HEAD bumped `502281f8` → `6024ac7` via 2 automated wiki commits (`c992dd6` sources-sync 2026-08-28 — the **fourteenth** consecutive sources-sync re-applying the count-data wipe pattern + `6024ac7` 16-file daily update 2026-08-28 reducing dirty count 17 → 5); the 4 carry-forward untracked directories bumped carry-forward at the 2026-08-28 fetch: `Review/zhou2023_computer_vision_microfluidics.md` 16 → 17-day (**one-off interpretation confirmed at 2026-08-28 fetch**, entry should be demoted to stale / not recurring carry-forward note on next synthesis pass), `celvivo_commercial/` + `templates/` 11 → 12-day (**now confirmed one-off alongside the `Review/` entry**), `deepread_40240593/` 4 → 5-day (working-folder pipeline hypothesis continuing to weaken — 4 consecutive silent fetches since the 2026-08-24/25 burst) — synthesis layer unchanged because vault produced no new external evidence. The 2026-08-27 18:00 UTC hackernews-1 fetch is the **seventeenth pull since 2026-08-07**, surfacing **the first non-fully-zero / non-clean-zero Algolia lane since the 2026-08-22 noise-only pull** — `organoid` 10 substring-noise hits + `3Brain` 9 substring-noise hits + `Cellink` 4 substring-noise hits + **`deepagents` 1 thematic hit** (`49461911` LangChain-AI/deepagents agent-harness repo, 1 pt); `CelVivo` + `openwiki` returned 0 hits; 32 unique top+best items. Five adjacents worth flagging for traceability, none promoting a `/themes.md` row — `49458161` Nvidia agrees to acquire Hugging Face for $13B (1719 pts, 802 cmts, **highest-engagement item of the entire 2026-08-07 streak to date**, the largest AI-infrastructure consolidation event of the streak) + `49458418` CEO fired developers to make room for AI. Developers create open source AI CEO (890 pts, 608 cmts, SenteLabsAI/OpenExecutive) + `49454314` The Hugging Face incident and the road ahead (324 pts, 417 cmts, OpenAI blog, highest comment-vs-upvote ratio on the pull at 1.29, direct corollary to the Nvidia-HF acquisition) + `49466917` Small Models Have Arrived (135 pts, 46 cmts, local-LLM cross-walk to the `MiniMax-m3` row) + `49461911` LangChain-AI/deepagents agent harness (1 pt, 0 cmts, **7th entry in the now 14-day self-hosted-agentic-substrate cluster**, ends the cooling-density pattern of the past 3 pulls 2026-08-24 + 2026-08-25 + 2026-08-26; cluster engagement now 792 pts across 7 items in 14 days; cluster density now 0.50 entries/day; strongest cluster diversity of the streak — independent vendors + personal-blog essays + definitional essays + canonical open-source LLM framework). The 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26 fully-zero Algolia lanes are four consecutive fully-zero pulls bookended with the 2026-08-22 + 2026-08-27 substring-noise-only pulls — **four fully-zero Algolia lanes in four consecutive pulls bookended by substring-noise-only Algolia lanes**, the longest fully-zero streak of the 2026-08-07 streak to date; Tavily (web-search) remains the productive lane for vendor news; the open-weight-LLM cluster now totals 9 items / 2,686+ pts across 7 pulls over 10 days — the strongest sustained engagement cluster in the 2026-08-07 streak. The 2026-08-28 18:00 UTC hackernews-1 fetch is the **eighteenth pull since 2026-08-07**, surfacing **a fully-zero Algolia lane on all 6 queries** (no substring-noise false positives either — distinct from the 2026-08-22 + 2026-08-27 substring-noise-only pulls) — the **fifth consecutive fully-zero Algolia lane pull bookending the 2026-08-22 + 2026-08-27 substring-noise-only pulls**, the longest fully-zero streak of the 2026-08-07 streak to date (five fully-zero lanes in six consecutive pulls bookended by substring-noise-only Algolia lanes); 31 unique top+best items. Five adjacents worth flagging for traceability, none promoting a `/themes.md` row — `49468818` Gemini-3.5-Transcribe (343 pts best, **highest-engagement best-feed item of the pull**, **highest-engagement Google AI model item of the 2026-08-07 streak**, closed-weight competitor to MiniMax-M3) + `49473522` NYT "Judge rules Trump administration's blacklisting of Anthropic was illegal" (318 pts top+best, NYT-side coverage of the federal-court AI-vendor-government ruling) + `49477055` Reuters companion (317 pts best, NYT+Reuters multi-source confirmation, **highest combined-engagement AI-vendor-business-stack signal of the 2026-08-07 streak** at 635 pts combined; cluster now ~1,786+ pts across 5 items in 5 pulls over 5 days) + `49475079` Luanti removed froLine truncated
+- [Robin's Local Knowledge Base](quickstart.md) - OpenWiki entrypoint and orientation — Robin's personal knowledge base with 5 synthesis themes (organoid equipment, bioprinting, AI agents, local LLM, personal research), navigation map, current connector status, and backlog. The 2026-08-28 18:09 UTC git-repo-1 fetch observed **vault HEAD unchanged** at `9d4767c7` (**0 new vault commits** for the 3rd consecutive fetch since the 2026-08-24/25 burst, 3 calendar days stale); wiki HEAD bumped `502281f8` → `6024ac7` via 2 automated wiki commits (`c992dd6` sources-sync 2026-08-28 — the **fourteenth** consecutive sources-sync re-applying the count-data wipe pattern + `6024ac7` 16-file daily update 2026-08-28 reducing dirty count 17 → 5); the 4 carry-forward untracked directories bumped carry-forward at the 2026-08-28 fetch: `Review/zhou2023_computer_vision_microfluidics.md` 16 → 17-day (**one-off interpretation confirmed at 2026-08-28 fetch**, entry should be demoted to stale / not recurring carry-forward note on next synthesis pass), `celvivo_commercial/` + `templates/` 11 → 12-day (**now confirmed one-off alongside the `Review/` entry**), `deepread_40240593/` 4 → 5-day (working-folder pipeline hypothesis continuing to weaken — 4 consecutive silent fetches since the 2026-08-24/25 burst) — synthesis layer unchanged because vault produced no new external evidence. The 2026-08-27 18:00 UTC hackernews-1 fetch is the **seventeenth pull since 2026-08-07**, surfacing **the first non-fully-zero / non-clean-zero Algolia lane since the 2026-08-22 noise-only pull** — `organoid` 10 substring-noise hits + `3Brain` 9 substring-noise hits + `Cellink` 4 substring-noise hits + **`deepagents` 1 thematic hit** (`49461911` LangChain-AI/deepagents agent-harness repo, 1 pt); `CelVivo` + `openwiki` returned 0 hits; 32 unique top+best items. Five adjacents worth flagging for traceability, none promoting a `/themes.md` row — `49458161` Nvidia agrees to acquire Hugging Face for $13B (1719 pts, 802 cmts, **highest-engagement item of the entire 2026-08-07 streak to date**, the largest AI-infrastructure consolidation event of the streak) + `49458418` CEO fired developers to make room for AI. Developers create open source AI CEO (890 pts, 608 cmts, SenteLabsAI/OpenExecutive) + `49454314` The Hugging Face incident and the road ahead (324 pts, 417 cmts, OpenAI blog, highest comment-vs-upvote ratio on the pull at 1.29, direct corollary to the Nvidia-HF acquisition) + `49466917` Small Models Have Arrived (135 pts, 46 cmts, local-LLM cross-walk to the `MiniMax-m3` row) + `49461911` LangChain-AI/deepagents agent harness (1 pt, 0 cmts, **7th entry in the now 14-day self-hosted-agentic-substrate cluster**, ends the cooling-density pattern of the past 3 pulls 2026-08-24 + 2026-08-25 + 2026-08-26; cluster engagement now 792 pts across 7 items in 14 days; cluster density now 0.50 entries/day; strongest cluster diversity of the streak — independent vendors + personal-blog essays + definitional essays + canonical open-source LLM framework). The 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26 fully-zero Algolia lanes are four consecutive fully-zero pulls bookended with the 2026-08-22 + 2026-08-27 substring-noise-only pulls — **four fully-zero Algolia lanes in four consecutive pulls bookended by substring-noise-only Algolia lanes**, the longest fully-zero streak of the 2026-08-07 streak to date; Tavily (web-search) remains the productive lane for vendor news; the open-weight-LLM cluster now totals 9 items / 2,686+ pts across 7 pulls over 10 days — the strongest sustained engagement cluster in the 2026-08-07 streak. The 2026-08-28 18:00 UTC hackernews-1 fetch is the **eighteenth pull since 2026-08-07**, surfacing **a fully-zero Algolia lane on all 6 queries** (no substring-noise false positives either — distinct from the 2026-08-22 + 2026-08-27 substring-noise-only pulls) — the **fifth consecutive fully-zero Algolia lane pull bookending the 2026-08-22 + 2026-08-27 substring-noise-only pulls**, the longest fully-zero streak of the 2026-08-07 streak to date (five fully-zero lanes in six consecutive pulls bookended by substring-noise-only Algolia lanes); 31 unique top+best items. Five adjacents worth flagging for traceability, none promoting a `/themes.md` row — `49468818` Gemini-3.5-Transcribe (343 pts best, **highest-engagement best-feed item of the pull**, **highest-engagement Google AI model item of the 2026-08-07 streak**, closed-weight competitor to MiniMax-M3) + `49473522` NYT "Judge rules Trump administration's blacklisting of Anthropic was illegal" (318 pts top+best, NYT-side coverage of the federal-court AI-vendor-government ruling) + `49477055` Reuters companion (317 pts best, NYT+Reuters multi-source confirmation, **highest combined-engagement AI-vendor-business-stack signal of the 2026-08-07 streak** at 635 pts combined; cluster now ~1,786+ pts across 5 items in 5 pulls over 5 days) + `49475079` Luanti removed froLine truncated
 
 - [OpenWiki 现状 + 操作手册 (2026-07-27)](README-ACTIVATION.md) - Activation status + operations manual for Robin's local OpenWiki knowledge base as of 2026-07-27. Documents 4 active connectors (HN + git-repo + Tavily + RAGFlow) and the per-source sync scripts (HN top+best feeds, Tavily web-search with TAVILY_API_KEY, git-repo Obsidian vault at /home/ldw/workspace, RAGFlow full-text retrieval at 10.10.10.254:9980). Captures the on-disk Gitea commit + push pattern.
 - [Themes](themes.md) - Recurring topics, signals, and trends observed across Robin's sources. Index of theme rows with confidence labels and source citations; details live on the linked source and synthesis pages.

quickstart.md

@@ -2,9 +2,9 @@
 type: "Reference"
 title: "Robin's Local Knowledge Base"
 description: >
-  OpenWiki entrypoint and orientation — Robin's personal knowledge base with 5 synthesis themes (organoid equipment, bioprinting, AI agents, local LLM, personal research), navigation map, current connector status, and backlog. The 2026-08-28 18:09 UTC git-repo-1 fetch observed **vault HEAD unchanged** at `9d4767c7` (**0 new vault commits** for the 3rd consecutive fetch since the 2026-08-24/25 burst, 3 calendar days stale); wiki HEAD bumped `502281f8` → `6024ac7` via 2 automated wiki commits (`c992dd6` sources-sync 2026-08-28 — the **fourteenth** consecutive sources-sync re-applying the count-data wipe pattern + `6024ac7` 16-file daily update 2026-08-28 reducing dirty count 17 → 5); the 4 carry-forward untracked directories bumped carry-forward at the 2026-08-28 fetch: `Review/zhou2023_computer_vision_microfluidics.md` 16 → 17-day (**one-off interpretation confirmed at 2026-08-28 fetch**, entry should be demoted to stale / not recurring carry-forward note on next synthesis pass), `celvivo_commercial/` + `templates/` 11 → 12-day (**now confirmed one-off alongside the `Review/` entry**), `deepread_40240593/` 4 → 5-day (working-folder pipeline hypothesis continuing to weaken — 4 consecutive silent fetches since the 2026-08-24/25 burst) — synthesis layer unchanged because vault produced no new external evidence. The 2026-08-27 18:00 UTC hackernews-1 fetch is the **seventeenth pull since 2026-08-07**, surfacing **the first non-fully-zero / non-clean-zero Algolia lane since the 2026-08-22 noise-only pull** — `organoid` 10 substring-noise hits + `3Brain` 9 substring-noise hits + `Cellink` 4 substring-noise hits + **`deepagents` 1 thematic hit** (`49461911` LangChain-AI/deepagents agent-harness repo, 1 pt); `CelVivo` + `openwiki` returned 0 hits; 32 unique top+best items. Five adjacents worth flagging for traceability, none promoting a `/themes.md` row — `49458161` Nvidia agrees to acquire Hugging Face for $13B (1719 pts, 802 cmts, **highest-engagement item of the entire 2026-08-07 streak to date**, the largest AI-infrastructure consolidation event of the streak) + `49458418` CEO fired developers to make room for AI. Developers create open source AI CEO (890 pts, 608 cmts, SenteLabsAI/OpenExecutive) + `49454314` The Hugging Face incident and the road ahead (324 pts, 417 cmts, OpenAI blog, highest comment-vs-upvote ratio on the pull at 1.29, direct corollary to the Nvidia-HF acquisition) + `49466917` Small Models Have Arrived (135 pts, 46 cmts, local-LLM cross-walk to the `MiniMax-m3` row) + `49461911` LangChain-AI/deepagents agent harness (1 pt, 0 cmts, **7th entry in the now 14-day self-hosted-agentic-substrate cluster**, ends the cooling-density pattern of the past 3 pulls 2026-08-24 + 2026-08-25 + 2026-08-26; cluster engagement now 792 pts across 7 items in 14 days; cluster density now 0.50 entries/day; strongest cluster diversity of the streak — independent vendors + personal-blog essays + definitional essays + canonical open-source LLM framework). The 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26 fully-zero Algolia lanes are four consecutive fully-zero pulls bookended with the 2026-08-22 + 2026-08-27 substring-noise-only pulls — **four fully-zero Algolia lanes in four consecutive pulls bookended by substring-noise-only Algolia lanes**, the longest fully-zero streak of the 2026-08-07 streak to date; Tavily (web-search) remains the productive lane for vendor news; the open-weight-LLM cluster now totals 9 items / 2,686+ pts across 7 pulls over 10 days — the strongest sustained engagement cluster in the 2026-08-07 streak. The 2026-08-28 18:00 UTC hackernews-1 fetch is the **eighteenth pull since 2026-08-07**, surfacing **a fully-zero Algolia lane on all 6 queries** (no substring-noise false positives either — distinct from the 2026-08-22 + 2026-08-27 substring-noise-only pulls) — the **fifth consecutive fully-zero Algolia lane pull bookending the 2026-08-22 + 2026-08-27 substring-noise-only pulls**, the longest fully-zero streak of the 2026-08-07 streak to date (five fully-zero lanes in six consecutive pulls bookended by substring-noise-only Algolia lanes); 31 unique top+best items. Five adjacents worth flagging for traceability, none promoting a `/themes.md` row — `49468818` Gemini-3.5-Transcribe (343 pts best, **highest-engagement best-feed item of the pull**, **highest-engagement Google AI model item of the 2026-08-07 streak**, closed-weight competitor to MiniMax-M3) + `49473522` NYT "Judge rules Trump administration's blacklisting of Anthropic was illegal" (318 pts top+best, NYT-side coverage of the federal-court AI-vendor-government ruling) + `49477055` Reuters companion (317 pts best, NYT+Reuters multi-source confirmation, **highest combined-engagement AI-vendor-business-stack signal of the 2026-08-07 streak** at 635 pts combined; cluster now ~1,786+ pts across 5 items in 5 pulls over 5 days) + `49475079` Luanti removed from Google Play due to baseless AI copyright noticLine truncated
-tags: [quickstart, navigation, openwiki, status, 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, vault-silent-4d, fourteenth-sources-sync, fifteenth-sources-sync, twentieth-hn-pull, nineteenth-hn-pull, sixteenth-websearch-skip, templates-celvivo-commercial-confirmed-one-off, tencent-hy4-adjacent]
-timestamp: 2026-08-30T18:00:39Z
+  OpenWiki entrypoint and orientation — Robin's personal knowledge base with 5 synthesis themes (organoid equipment, bioprinting, AI agents, local LLM, personal research), navigation map, current connector status, and backlog. The 2026-08-28 18:09 UTC git-repo-1 fetch observed **vault HEAD unchanged** at `9d4767c7` (**0 new vault commits** for the 3rd consecutive fetch since the 2026-08-24/25 burst, 3 calendar days stale); wiki HEAD bumped `502281f8` → `6024ac7` via 2 automated wiki commits (`c992dd6` sources-sync 2026-08-28 — the **fourteenth** consecutive sources-sync re-applying the count-data wipe pattern + `6024ac7` 16-file daily update 2026-08-28 reducing dirty count 17 → 5); the 4 carry-forward untracked directories bumped carry-forward at the 2026-08-28 fetch: `Review/zhou2023_computer_vision_microfluidics.md` 16 → 17-day (**one-off interpretation confirmed at 2026-08-28 fetch**, entry should be demoted to stale / not recurring carry-forward note on next synthesis pass), `celvivo_commercial/` + `templates/` 11 → 12-day (**now confirmed one-off alongside the `Review/` entry**), `deepread_40240593/` 4 → 5-day (working-folder pipeline hypothesis continuing to weaken — 4 consecutive silent fetches since the 2026-08-24/25 burst) — synthesis layer unchanged because vault produced no new external evidence. The 2026-08-27 18:00 UTC hackernews-1 fetch is the **seventeenth pull since 2026-08-07**, surfacing **the first non-fully-zero / non-clean-zero Algolia lane since the 2026-08-22 noise-only pull** — `organoid` 10 substring-noise hits + `3Brain` 9 substring-noise hits + `Cellink` 4 substring-noise hits + **`deepagents` 1 thematic hit** (`49461911` LangChain-AI/deepagents agent-harness repo, 1 pt); `CelVivo` + `openwiki` returned 0 hits; 32 unique top+best items. Five adjacents worth flagging for traceability, none promoting a `/themes.md` row — `49458161` Nvidia agrees to acquire Hugging Face for $13B (1719 pts, 802 cmts, **highest-engagement item of the entire 2026-08-07 streak to date**, the largest AI-infrastructure consolidation event of the streak) + `49458418` CEO fired developers to make room for AI. Developers create open source AI CEO (890 pts, 608 cmts, SenteLabsAI/OpenExecutive) + `49454314` The Hugging Face incident and the road ahead (324 pts, 417 cmts, OpenAI blog, highest comment-vs-upvote ratio on the pull at 1.29, direct corollary to the Nvidia-HF acquisition) + `49466917` Small Models Have Arrived (135 pts, 46 cmts, local-LLM cross-walk to the `MiniMax-m3` row) + `49461911` LangChain-AI/deepagents agent harness (1 pt, 0 cmts, **7th entry in the now 14-day self-hosted-agentic-substrate cluster**, ends the cooling-density pattern of the past 3 pulls 2026-08-24 + 2026-08-25 + 2026-08-26; cluster engagement now 792 pts across 7 items in 14 days; cluster density now 0.50 entries/day; strongest cluster diversity of the streak — independent vendors + personal-blog essays + definitional essays + canonical open-source LLM framework). The 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26 fully-zero Algolia lanes are four consecutive fully-zero pulls bookended with the 2026-08-22 + 2026-08-27 substring-noise-only pulls — **four fully-zero Algolia lanes in four consecutive pulls bookended by substring-noise-only Algolia lanes**, the longest fully-zero streak of the 2026-08-07 streak to date; Tavily (web-search) remains the productive lane for vendor news; the open-weight-LLM cluster now totals 9 items / 2,686+ pts across 7 pulls over 10 days — the strongest sustained engagement cluster in the 2026-08-07 streak. The 2026-08-28 18:00 UTC hackernews-1 fetch is the **eighteenth pull since 2026-08-07**, surfacing **a fully-zero Algolia lane on all 6 queries** (no substring-noise false positives either — distinct from the 2026-08-22 + 2026-08-27 substring-noise-only pulls) — the **fifth consecutive fully-zero Algolia lane pull bookending the 2026-08-22 + 2026-08-27 substring-noise-only pulls**, the longest fully-zero streak of the 2026-08-07 streak to date (five fully-zero lanes in six consecutive pulls bookended by substring-noise-only Algolia lanes); 31 unique top+best items. Five adjacents worth flagging for traceability, none promoting a `/themes.md` row — `49468818` Gemini-3.5-Transcribe (343 pts best, **highest-engagement best-feed item of the pull**, **highest-engagement Google AI model item of the 2026-08-07 streak**, closed-weight competitor to MiniMax-M3) + `49473522` NYT "Judge rules Trump administration's blacklisting of Anthropic was illegal" (318 pts top+best, NYT-side coverage of the federal-court AI-vendor-government ruling) + `49477055` Reuters companion (317 pts best, NYT+Reuters multi-source confirmation, **highest combined-engagement AI-vendor-business-stack signal of the 2026-08-07 streak** at 635 pts combined; cluster now ~1,786+ pts across 5 items in 5 pulls over 5 days) + `49475079` Luanti removed from Google Play due to baseless AI copyright noticLine truncated
+tags: [quickstart, navigation, openwiki, status, 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, vault-silent-4d, fourteenth-sources-sync, fifteenth-sources-sync, twentieth-hn-pull, twenty-first-hn-pull, nineteenth-hn-pull, sixteenth-websearch-skip, templates-celvivo-commercial-confirmed-one-off, tencent-hy4-adjacent, almanac-yc-s26-wikis-as-agent-memory]
+timestamp: 2026-08-31T18:00:32Z
 ---
 
 # Robin's Local Knowledge Base
@@ -35,7 +35,7 @@ timestamp: 2026-08-30T18:00:39Z
 
 ## Current status
 
-- **Wiki state:** initialized — Hacker News, the local Obsidian vault, and Tavily web search are active and feeding `/sources/hackernews.md`, `/sources/git-repo.md`, `/sources/web-search.md`, and `/themes.md`. All 5 synthesis themes (`/themes/01-organoid-equipment.md`, `/themes/02-bioprinting.md`, `/themes/03-ai-agents.md`, `/themes/04-local-llm.md`, `/themes/05-robin-research.md`) are now generated; the 2026-08-17 daily update created `/sources/openwiki-version-drift.md` (auto-generated OpenWiki version-drift monitor); the 2026-08-25 daily update committed 17 files from the prior dirty set (the largest single daily update in Robin's OpenWiki activity log), including the synthesis-layer edits from the prior HN-1 2026-08-25T18:00Z + web-search-1 2026-08-25 (skipped) + git-repo-1 2026-08-24T18:05Z runs; the wiki HEAD bumped to `1003b92` (sources-sync 2026-08-25, the **eleventh** consecutive sources-sync re-applying the `2507925` 2026-08-15 count-data wipe pattern after `997b648` 2026-08-16 + `be49285` 2026-08-17 + `1fc73ae` 2026-08-18 + `dcb53a2` 2026-08-19 + `bd30339` 2026-08-20 + `f6c2576` 2026-08-21 + `43d4548` 2026-08-22 + `8f8f767` 2026-08-23 + `127c2dc` 2026-08-24 + now `1003b92` 2026-08-25). The 11 uncommitted synthesis-layer edits re-appear in the working tree because the very next synthesis edits from this git-repo-1 2026-08-25T18:13Z run re-touch the same files. The 2026-08-26 daily update (`81ac94a`, 2026-08-26T02:23 +0800) committed 14 of the prior 17 dirty files (reducing the dirty count from 11 → 8); the wiki HEAD then bumped to `ebb95c0a` via the 2026-08-26 sources-sync (`ebb95c0`, the **twelfth** consecutive sources-sync re-applying the count-data wipe pattern); the 2026-08-26T18:06Z git-repo-1 fetch (vault HEAD unchanged at `9d4767c7`, **0 new vault commits** — vault silent for the 1st consecutive fetch since the 2026-08-24/25 burst) re-touches the same synthesis-layer files leaving the dirty count at 8. The 2026-08-27 daily update (`f51ff7c`, 2026-08-27T02:13 +0800) committed 14 of the prior 17 dirty files (reducing the dirty count from 17 → 11, +3 vs the 8-dirty-file baseline at the 2026-08-26 fetch because the very next synthesis edits from the HN-1 2026-08-27 + web-search-1 2026-08-27 (skipped) + git-repo-1 2026-08-27 runs re-touched the same files + bumped the dirty count to 11 again); the wiki HEAD then bumped to `502281f86483a4226af6b0c2d1c28cdc5f1d1143` via the 2026-08-27 sources-sync (`502281f`, the **thirteenth** consecutive sources-sync re-applying the count-data wipe pattern); the 2026-08-27T18:25Z git-repo-1 fetch (vault HEAD unchanged at `9d4767c7`, **0 new vault commits** — vault silent for the 2nd consecutive fetch since the 2026-08-24/25 burst, **2 calendar days stale**) re-touches the same synthesis-layer files leaving the dirty count at 11 — see the "Latest update — git-repo-1 (2026-08-27T18:25Z)" paragraph above for the full 2026-08-27 fetch delta. The 4 carry-forward untracked directories (Review/zhou2023_computer_vision_microfluidics.md + celvivo_commercial/ + templates/ + deepread_40240593/) bumped carry-forward at the 2026-08-27 fetch — `Review/` 15 → **16-day** (**one-off interpretation confirmed at 2026-08-27 fetch**, entry should be demoted to stale / not recurring carry-forward note on the next synthesis pass), `celvivo_commercial/` + `templates/` 10 → **11-day** (approaching the same confirmed-one-off interpretation alongside the `Review/` subfolder), `deepread_40240593/` 3 → **4-day**. **2026-08-25 18:13 UTC update** . The 2026-08-28 daily update (`6024ac7`, 2026-08-28T02:42 +0800) committed 16 of the prior 17 dirty files (reducing the dirty count from 17 → 5, the largest cleanup in several cycles); the wiki HEAD then bumped to `6024ac74387c76ffca58ef4af5e155396aa13c0c` via the 2026-08-28 sources-sync (`c992dd6`, the **fourteenth** consecutive sources-sync re-applying the 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 + now `c992dd6` 2026-08-28); the 2026-08-28T18:09Z git-repo-1 fetch (vault HEAD unchanged at `9d4767c7`, **0 new vault commits** — vault silent for the 3rd consecutive fetch since the 2026-08-24/25 burst, **3 calendar days stale**) re-touches the same synthesis-layer files leaving the dirty count at 5 — see the "Latest update — git-repo-1 (2026-08-28T18:09Z)" paragraph above for the full 2026-08-28 fetch delta. The 2026-08-30 daily update (`7eed6ca`, 2026-08-30T02:?? +0800 — **single-connector raw-data refresh** combining the HN-1 2026-08-30T18:00Z fully-zero pull + git-repo-1 2026-08-30T18:06Z vault-silent fetch + web-search-1 2026-08-30 (skipped) at the 2026-08-30 fetch) committed 13 files (`.last-update.json` + `quickstart.md` + `sources/RLine truncated
+- **Wiki state:** initialized — Hacker News, the local Obsidian vault, and Tavily web search are active and feeding `/sources/hackernews.md`, `/sources/git-repo.md`, `/sources/web-search.md`, and `/themes.md`. All 5 synthesis themes (`/themes/01-organoid-equipment.md`, `/themes/02-bioprinting.md`, `/themes/03-ai-agents.md`, `/themes/04-local-llm.md`, `/themes/05-robin-research.md`) are now generated; the 2026-08-17 daily update created `/sources/openwiki-version-drift.md` (auto-generated OpenWiki version-drift monitor); the 2026-08-25 daily update committed 17 files from the prior dirty set (the largest single daily update in Robin's OpenWiki activity log), including the synthesis-layer edits from the prior HN-1 2026-08-25T18:00Z + web-search-1 2026-08-25 (skipped) + git-repo-1 2026-08-24T18:05Z runs; the wiki HEAD bumped to `1003b92` (sources-sync 2026-08-25, the **eleventh** consecutive sources-sync re-applying the `2507925` 2026-08-15 count-data wipe pattern after `997b648` 2026-08-16 + `be49285` 2026-08-17 + `1fc73ae` 2026-08-18 + `dcb53a2` 2026-08-19 + `bd30339` 2026-08-20 + `f6c2576` 2026-08-21 + `43d4548` 2026-08-22 + `8f8f767` 2026-08-23 + `127c2dc` 2026-08-24 + now `1003b92` 2026-08-25). The 11 uncommitted synthesis-layer edits re-appear in the working tree because the very next synthesis edits from this git-repo-1 2026-08-25T18:13Z run re-touch the same files. The 2026-08-26 daily update (`81ac94a`, 2026-08-26T02:23 +0800) committed 14 of the prior 17 dirty files (reducing the dirty count from 11 → 8); the wiki HEAD then bumped to `ebb95c0a` via the 2026-08-26 sources-sync (`ebb95c0`, the **twelfth** consecutive sources-sync re-applying the count-data wipe pattern); the 2026-08-26T18:06Z git-repo-1 fetch (vault HEAD unchanged at `9d4767c7`, **0 new vault commits** — vault silent for the 1st consecutive fetch since the 2026-08-24/25 burst) re-touches the same synthesis-layer files leaving the dirty count at 8. The 2026-08-27 daily update (`f51ff7c`, 2026-08-27T02:13 +0800) committed 14 of the prior 17 dirty files (reducing the dirty count from 17 → 11, +3 vs the 8-dirty-file baseline at the 2026-08-26 fetch because the very next synthesis edits from the HN-1 2026-08-27 + web-search-1 2026-08-27 (skipped) + git-repo-1 2026-08-27 runs re-touched the same files + bumped the dirty count to 11 again); the wiki HEAD then bumped to `502281f86483a4226af6b0c2d1c28cdc5f1d1143` via the 2026-08-27 sources-sync (`502281f`, the **thirteenth** consecutive sources-sync re-applying the count-data wipe pattern); the 2026-08-27T18:25Z git-repo-1 fetch (vault HEAD unchanged at `9d4767c7`, **0 new vault commits** — vault silent for the 2nd consecutive fetch since the 2026-08-24/25 burst, **2 calendar days stale**) re-touches the same synthesis-layer files leaving the dirty count at 11 — see the "Latest update — git-repo-1 (2026-08-27T18:25Z)" paragraph above for the full 2026-08-27 fetch delta. The 4 carry-forward untracked directories (Review/zhou2023_computer_vision_microfluidics.md + celvivo_commercial/ + templates/ + deepread_40240593/) bumped carry-forward at the 2026-08-27 fetch — `Review/` 15 → **16-day** (**one-off interpretation confirmed at 2026-08-27 fetch**, entry should be demoted to stale / not recurring carry-forward note on the next synthesis pass), `celvivo_commercial/` + `templates/` 10 → **11-day** (approaching the same confirmed-one-off interpretation alongside the `Review/` subfolder), `deepread_40240593/` 3 → **4-day**. **2026-08-25 18:13 UTC update** . The 2026-08-28 daily update (`6024ac7`, 2026-08-28T02:42 +0800) committed 16 of the prior 17 dirty files (reducing the dirty count from 17 → 5, the largest cleanup in several cycles); the wiki HEAD then bumped to `6024ac74387c76ffca58ef4af5e155396aa13c0c` via the 2026-08-28 sources-sync (`c992dd6`, the **fourteenth** consecutive sources-sync re-applying the 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 + now `c992dd6` 2026-08-28); the 2026-08-28T18:09Z git-repo-1 fetch (vault HEAD unchanged at `9d4767c7`, **0 new vault commits** — vault silent for the 3rd consecutive fetch since the 2026-08-24/25 burst, **3 calendar days stale**) re-touches the same synthesis-layer files leaving the dirty count at 5 — see the "Latest update — git-repo-1 (2026-08-28T18:09Z)" paragraph above for the full 2026-08-28 fetch delta. The 2026-08-30 daily update (`7eed6ca`, 2026-08-30T02:?? +0800 — **single-connector raw-data refresh** combining the HN-1 2026-08-30T18:00Z fully-zero pull + git-repo-1 2026-08-30T18:06Z vault-silent fetch + web-search-1 2026-08-30 (skipped) at the 2026-08-30 fetch) committed 13 files (`.last-update.json` + `quickstart.md` + `sources/RLine truncated
 - **Connectors:** Hacker News, git-repo, and web search active. 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 web-search update attempts were skipped because the connector is not enabled and `TAVILY_API_KEY` is empty (16 consecutive skips on the same code path; per-day operational notes are in [`/sources/web-search.md`](/sources/web-search.md)); the latest successful Tavily pull remains 2026-08-03 18:08 UTC. Gmail, Slack, Notion, and X are not yet configured — see "Adding sources" below.
 
 **Latest update — git-repo-1 (2026-08-27T18:25Z).** One source-specific update run for `git-repo-1` (Obsidian vault + OpenWiki wiki) per the source-specific instruction "Track vault + OpenWiki wiki mtime + commits (Robin 8-07 added)". Fresh connector ingest ran via `openwiki_ingest_connector connectorId=git-repo` and wrote manifest at `~/.openwiki/connectors/git-repo/raw/2026-08-27T18-25-58-335Z/manifest.json`. **Vault HEAD unchanged** at `9d4767c7034a59d8f3206756c2dfeb3f4339c2e0` (same as the 2026-08-26T18:06Z + 2026-08-25T18:13Z fetches) — **0 new vault commits** in the 2026-08-26T18:06Z → 2026-08-27T18:25Z 24-hour window; the 2026-08-24/25 SECOND consecutive single-day 5-paper LDR burst (Tevonian + Yang + `9aa2af4c` retrofit + Shen + Zhai) remains the most recent committed vault activity. **Vault silent for the 2nd consecutive fetch** since the 2026-08-24/25 burst, **2 calendar days stale**. **No new vault mtime changes** — the 4 untracked vault directories / files from the 2026-08-26 fetch carry forward with bumped carry-forward counts: `Review/zhou2023_computer_vision_microfluidics.md` **15-day → 16-day carry-forward** (**13 → 14 fetches silent**, **structural signal now confirmed as one-off at the 2026-08-27 fetch per the 2026-08-26 watchlist-downgrade consideration**; entry should be demoted to a "stale / not recurring" carry-forward note on the next synthesis pass) + `celvivo_commercial/` + `templates/` **10-day → 11-day carry-forward** (each remaining single-entry + uncommitted, no follow-up content in either directory despite 4 LDR bursts landing at vault HEAD; both directories are now **approaching the confirmed one-off interpretation** alongside the `Review/` subfolder) + `deepread_40240593/` pipeline workspace **3-day → 4-day carry-forward** (the directory mtime is still 2026-08-24 16:31 +0800, unchanged since initial creation; the absence of mtime movement across the 2026-08-25 + 2026-08-26 + 2026-08-27 fetches suggests the working-folder pipeline may have been abandoned, formalized differently, or batched without intermediate commit). **Wiki HEAD** bumped from `ebb95c0a85b85e5abb8d11463cfa8b855c504e5f` (2026-08-26T18:06Z fetch) to **`502281f86483a4226af6b0c2d1c28cdc5f1d1143`** (2026-08-27T02:30 +0800, the 2026-08-27 sources-sync); **2 new automated wiki commits** in the 24-hour window: `f51ff7c` chore: daily update 2026-08-27 (2026-08-27T02:13 +0800 — per `git show --stat f51ff7c` the commit touched 14 files from the prior dirty set including `.last-update.json` + `commitments.md` + `index.md` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/literature.md` + `sources/openwiki-version-drift.md` + `sources/web-search.md` + `themes.md` + `themes/index.md` + `themes/05-robin-research.md`; reducing uncommitted-file count from 17 → 11) + `502281f` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-27, 2026-08-27T02:30 +0800 — the **thirteenth** consecutive sources-sync re-applying the `2507925` 2026-08-15 count-data wipe pattern after `997b648` 2026-08-16 + `be49285` 2026-08-17 + `1fc73ae` 2026-08-18 + `dcb53a2` 2026-08-19 + `bd30339` 2026-08-20 + `f6c2576` 2026-08-21 + `43d4548` 2026-08-22 + `8f8f767` 2026-08-23 + `127c2dc` 2026-08-24 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + now `502281f` 2026-08-27). **11 uncommitted wiki files** in working tree per the manifest `changedFiles` list (`M .last-update.json` + `M index.md` + `M quickstart.md` + `M sources/README.md` + `M sources/hackernews.md` + `M sources/literature.md` + `M sources/nocodb.md` + `M sources/ragflow.md` + `M sources/seafile.md` + `M sources/web-search.md` + `M sources/wikijs.md` + `M themes/05-robin-research.md`) — the very next synthesis edits from the HN-1 2026-08-27 + web-search-1 2026-08-27 (skipped) + git-repo-1 2026-08-27 runs re-touch the same 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. Wiki edits this run: (a) `/sources/git-repo.md` — refreshed the obsidian-vault working-tree-status section to 2026-08-27 (0 new commits, 0 new mtime changes, the 4 untracked set bumps: `Review/` 15 → **16-day** + **one-off interpretation confirmed at 2026-08-27 fetch** + `celvivo_commercial/` + `templates/` 10 → **11-day** + `deepread_40240593/` 3 → **4-day**), refreshed the openwiki-wiki working-tree-status section to 2026-08-27 (2 new automated wiki commits + the carry-forward 11 uncommitted synthesis-layer edits), refreshed the Notable-entity section for the 4 untracked directories (the `Review/` subfolder entry updated to **demote the entry to a "stale / not recurring" carry-forward note** per the 2026-08-27 fetch confirming the 2026-08-26 watchLine truncated
@@ -44,6 +44,10 @@ timestamp: 2026-08-30T18:00:39Z
 
 **Latest update — git-repo-1 (2026-08-28T18:09Z).** One source-specific update run for `git-repo-1` (Obsidian vault + OpenWiki wiki) per the source-specific instruction "Track vault + OpenWiki wiki mtime + commits (Robin 8-07 added)". Fresh connector ingest ran via `openwiki_ingest_connector connectorId=git-repo` and wrote manifest at `~/.openwiki/connectors/git-repo/raw/2026-08-28T18-09-49-822Z/manifest.json`. **Vault HEAD unchanged** at `9d4767c7034a59d8f3206756c2dfeb3f4339c2e0` (same as the 2026-08-27T18:25Z + 2026-08-26T18:06Z + 2026-08-25T18:13Z fetches) — **0 new vault commits** in the 2026-08-27T18:25Z → 2026-08-28T18:09Z 24-hour window; the 2026-08-24/25 SECOND consecutive single-day 5-paper LDR burst (Tevonian + Yang + `9aa2af4c` retrofit + Shen + Zhai) remains the most recent committed vault activity. **Vault silent for the 3rd consecutive fetch** since the 2026-08-24/25 burst, **3 calendar days stale**. **No new vault mtime changes** — the 4 untracked vault directories / files from the 2026-08-27 fetch carry forward with bumped carry-forward counts: `Review/zhou2023_computer_vision_microfluidics.md` **16-day → 17-day carry-forward** (**14 → 15 fetches silent**, **2026-08-28 fetch confirms the 2026-08-27 one-off confirmation** and the entry should be **demoted to a "stale / not recurring" carry-forward note** on the next synthesis pass alongside the parallel `templates/` + `celvivo_commercial/` confirmations) + `celvivo_commercial/` **11-day → 12-day carry-forward** + `templates/` **11-day → 12-day carry-forward** (both now **confirmed one-off alongside the `Review/` entry** at the 2026-08-28 fetch) + `deepread_40240593/` **4-day → 5-day carry-forward** (the directory mtime is still 2026-08-24 16:31 +0800, unchanged since initial creation; the absence of mtime movement across the 2026-08-25 + 2026-08-26 + 2026-08-27 + 2026-08-28 fetches — now **4 consecutive silent fetches** since the 2026-08-24/25 burst — suggests the working-folder pipeline hypothesis has continued to weaken; the entry should be downgraded to a stale carry-forward note on the next synthesis pass alongside the other 3 entries). **Wiki HEAD** bumped from `502281f86483a4226af6b0c2d1c28cdc5f1d1143` (2026-08-27T18:25Z fetch) to **`6024ac74387c76ffca58ef4af5e155396aa13c0c`** (2026-08-28T02:42 +0800, the 2026-08-28 daily update); **2 new automated wiki commits** in the 2026-08-27T18:25Z → 2026-08-28T18:09Z 24-hour window: (a) `c992dd6` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-28, 2026-08-28T02:30 +0800 — the **fourteenth** consecutive sources-sync re-applying the `2507925` 2026-08-15 count-data wipe pattern after `997b648` 2026-08-16 + `be49285` 2026-08-17 + `1fc73ae` 2026-08-18 + `dcb53a2` 2026-08-19 + `bd30339` 2026-08-20 + `f6c2576` 2026-08-21 + `43d4548` 2026-08-22 + `8f8f767` 2026-08-23 + `127c2dc` 2026-08-24 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + `502281f` 2026-08-27 + now `c992dd6` 2026-08-28) + (b) `6024ac7` chore: daily update 2026-08-28 (2026-08-28T02:42 +0800; per `git show --stat 6024ac7` the commit touched 16 files from the prior dirty set including `.last-update.json` + `commitments.md` + `index.md` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/literature.md` + `sources/nocodb.md` + `sources/openwiki-version-drift.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` + `sources/wikijs.md` + `themes.md` + `themes/05-robin-research.md` + `themes/index.md`; reducing uncommitted-file count from 17 → 5). **5 uncommitted wiki files** in working tree per the manifest `changedFiles` list (`M .last-update.json` + `M index.md` + `M quickstart.md` + `M sources/hackernews.md` + `M sources/web-search.md`) — significantly down from the 11-dirty-file baseline at the 2026-08-27T18:25Z fetch (the `6024ac7` daily update was the largest cleanup of the dirty-file carry-forward in several cycles). **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. Wiki edits this run: (a) `/sources/git-repo.md` — refreshed the obsidian-vault working-tree-status section to 2026-08-28 (0 new commits, 0 new mtime changes, the 4 untracked set bumps: `Review/` 16 → **17-day** + `celvivo_commercial/` 11 → **12-day** + `templates/` 11 → **12-day** + `deepread_40240593/` 4 → **5-day**), refreshed the openwiki-wiki working-tree-status section to 2026-08-28 (2 new automated wiki commits + the carry-forward 5 uncommitted synthesis-layer edits), refreshed the Notable-entity section for the 4 untracked directories (the `Review/` subfolder entry updated to **demote the entry to a "stale / not recurring" carry-forward note** per the 2026-08-28 fetLine truncated
 
+**Latest update — git-repo-1 (2026-08-31T18:09Z).** One source-specific update run for `git-repo-1` (Obsidian vault + OpenWiki wiki) per the source-specific instruction "Track vault + OpenWiki wiki mtime + commits (Robin 8-07 added)". Fresh connector ingest ran via `openwiki_ingest_connector connectorId=git-repo` and wrote manifest at `~/.openwiki/connectors/git-repo/raw/2026-08-31T18-09-XX-XXXZ/manifest.json`. **Vault HEAD bumped** from `9d4767c7034a59d8f3206756c2dfeb3f4339c2e0` (same as 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`) to **`391e47131679ce9edf0f525236e78ebb13e0d232`** — **5 new vault commits** in the 2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window, **ending the 5-calendar-day vault silence streak** since the 2026-08-24/25 SECOND 5-paper burst. The cluster is the **THIRD consecutive 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's **first parallel-naming deep-read subfolder convention** (the existing lowercase `Celvivo/` subfolder has 142 files; the new capital-V subfolder adds 5 files); 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). **5 new vault commits** (all on 2026-08-31 +0800 between 13:05 and 13:42, all single-shot entries landing at `obsidian-vault/04-Literature/Deep-Reads/CelVivo/`): (a) **`eb24ab72`** 2026-08-31 13:05 +0800 **deep-read: Stewart 2023 Front Microbiol BA.5/XBB neurotropic brain organoids (CelVivo)** — `stewart-2023-ba5-xbb-neurotropic-brain-organoids.md`, single-shot 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* (Front Microbiol 14:1320856, 2023-11-23, DOI 10.3389/fmicb.2023.1320856, QIMR Berghofer + University of Queensland); (b) **`030f31ed`** 2026-08-31 13:14 +0800 **deep-read: Aiello 2025 EMBO reports reproducible brain organoids (CelVivo ClinoReactor)** — `aiello-2025-brain-organoid-reproducibility.md`, single-shot 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* (EMBO reports 26:6209-6239, December 2025, 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) co-author**) — **first direct CelVivo ApS co-authored deep-read in Robin's set**, CV <15% morphological consistency vs static culture CV >30%; (c) **`fad7e21e`** 2026-08-31 13:21 +0800 **deep-read: Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids (CelVivo)** — `nguyen-2024-jev-g4-2022-australia-brain-organoids.md`, single-shot 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 Article 25, 2024, DOI 10.1038/s44298-024-00025-5, QIMR Berghofer + INRAE); (d) **`4fca0123`** 2026-08-31 13:27 +0800 **deep-read: Miao 2025 Cell vascularized lung/gut organoids (CelVivo ClinoReactor)** — `miao-2025-vascularized-lung-gut-organoids.md`, single-shot 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) — companion to the 2026-08-08 flywheel-sync v2 deep-read; (e) **`391e4713`** 2026-08-31 13:42 +0800 **deep-read: Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids (CelVivo)** — `yan-2024-tmem106b-sars-cov2-ace2-independent.md`, single-shot entry, Ollama audit 4/4 Fig 1-4 passed. 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). **Subfolder content mix**: 4 of 5 are brain organoid infectious-disease / reproducibility papers using CelVivo ClinoStar/ClinoReLine truncated
+
+**Latest update — hackernews-1 (2026-08-31T18:00Z).** One source-specific update run for `hackernews-1` (Hacker News — LLM-agent topic set) per the source-specific instruction "Track organoid / CelVivo / 3Brain / Cellink / openwiki / AI agent stories". Fresh connector ingest ran via `openwiki_ingest_connector connectorId=hackernews` and wrote raw data at `~/.openwiki/connectors/hackernews/raw/2026-08-31T18-00-02-091Z/hackernews-results.json`. 2 feeds (`top` 30 IDs / ~19 resolved + `best` 30 IDs / ~12 resolved) → **29 unique items across both feeds** (low single-digit overlap, on par with the 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`. This is the **twenty-first pull since 2026-08-07** (after 20 prior pulls — 15 fully-zero + 5 substring-noise-only — bookended by the 2026-08-22 + 2026-08-27 + 2026-08-31 nbHits-positive-but-items-zero pulls) and the **first pull of the 2026-08-07 streak with the `nbHits > 0 / items = 0` anomaly** — 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. Future agents reading the 2026-08-31 raw data should not treat the Algolia lane as fully-zero — the substring-noise false positives are visible in `queryResults[i].response.hits` even though the connector's top-level `items` field reports 0. **One substantive AI-agent item surfacing**: **`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 shipped-product evidence on the `agent-memory-architecture` theme row**; 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 ... 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 + OKF frontmatter + `/commitments.md` long-horizon tracking + `~/.openwiki/wiki` local markdown substrate; surfaced via Algolia `organoid` + `3Brain` substring-noise duplicate (the word "brain" appears 4+ times in the launch text). **One theme-row promotion**: the **`agent-memory-architecture` row on `/themes.md` gets a Last-seen refresh from 2026-08-13 → 2026-08-31** + Evidence count `16+` → `17+` with the Almanac item added as the new refresh anchor (Almanac is the first YC S26 launch that operationalizes the wikis-as-agent-memory-substrate pattern as a hosted product with personal + company wikis; every prior source on the row is either a substrate-pattern essay, an open-source library, a research write-up, or a benchmark — Almanac is the first shipped-product evidence; row confidence stays `source-backed`). See [`/themes.md`](/themes.md) `agent-memory-architecture` row + [`/themes/03-ai-agents.md`](/themes/03-ai-agents.md) "Adjacent workflow signals" section for the canonical competitive-parallel framing. **Important cluster findings** (carry forward + extend): the **open-weight-LLM cluster** (11 items / ~3,318+ pts across 9 pulls / 12 days) — no new entry on the 2026-08-31 pull; the **AI-vendor-business-stack cluster** (6 items / ~2,522+ pts across 6 pulls / 6 days) — no new entry; the **AI-policy / copyright-DMCA / governance lane** (2 items / ~687 pts across 2 pulls / 2 days) — no new entry; the **self-hosted-agentic-substrate cluster** (7 entries / 792 pts / 0.50 entries/day over 14 days) — no new entry; 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). Wiki edits this run: (a) `/sources/hackernews.md` — added new "Latest update — 2026-08-31 18:00 UTC" section ahead of the 2026-08-30 entry; demoted 2026-08-30 from "Latest" to a regular "Update" section; updated Connector section with the new raw dump path (`2026-08-31T18-00-02-091Z/hackernews-results.json`) + the new latest-fetch timestamp (`2026-08-31T18:00:32Z`) + the `nbHits > 0 / items = 0` anomaly note; added a "FlLine truncated
+
 **Latest update — hackernews-1 (2026-08-30T18:00Z).** One source-specific update run for `hackernews-1` (Hacker News — LLM-agent topic set) per the source-specific instruction "Track organoid / CelVivo / 3Brain / Cellink / openwiki / AI agent stories". Fresh connector ingest ran via `openwiki_ingest_connector connectorId=hackernews` and wrote raw data at `~/.openwiki/connectors/hackernews/raw/2026-08-30T18-00-02-250Z/hackernews-results.json`. 2 feeds (`top` 30 IDs / 19 resolved + `best` 30 IDs / 12 resolved) → **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 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` 19/30 and `best` 12/30 = **highest `best` resolution of the 2026-08-07 streak since the 2026-08-15 16/30 and 2026-08-12 14/30 pulls**). 6 search queries returned **a fully-zero Algolia lane on all 6 queries** — `organoid` 0 hits + `CelVivo` 0 hits + `3Brain` 0 hits + `Cellink` 0 hits + `openwiki` 0 hits + `deepagents` 0 hits (clean zero across the board, no substring-noise false positives — 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). This is the **twentieth 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 2026-08-30 pull is the **8th fully-zero Algolia lane in 9 consecutive pulls** — 2026-08-22 substring-noise-only + 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26 + 2026-08-27 substring-noise-only + 2026-08-28 + 2026-08-29 + 2026-08-30 fully-zero — **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). Tavily (web-search) remains the productive lane for vendor news. **Five adjacents worth flagging for traceability, none promoting a `/themes.md` row** — **`49492632` "Hy4 preview"** (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 379 + 2026-08-19 Unsloth Dynamic 3.0 GGUFs 314 + 2026-08-23 GLM-5.3 vs Anthropic/OpenAI 141 + 2026-08-23 Qwen 3.8 27B 234 + 2026-08-25 Qwen 3.8-Flash-Next "releasing tomorrow" 244 + 2026-08-26 GLM-5.3-Flash 530 + 2026-08-26 Qwen3.8-Flash-Next release 441 + 2026-08-26 Z.ai Ox Alpha 391 + 2026-08-27 Small Models Have Arrived 135 + 2026-08-28 GLM-5.3 is now open-weight 268 — the **open-weight-LLM cluster now totals ~3,318+ pts across 11 items in 9 pulls over 12 days**, the **strongest sustained engagement cluster of the entire 2026-08-07 streak**; **direct open-weight-LLM cross-walk to the `MiniMax-m3` row's open-weight comparison anchor** — adjacent-not-promoted per scope because Tencent / Hy4 is not on Robin's named stack — Hermes / MiniMax-M3+H3 / OpenWiki / RAGFlow / NocoDB / SeaFile / Codex CLI are the named agents. **`49498201` "Claude Session URL appended to commit messages and PR descriptions by default"** (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-coding-agent framing**; Codex CLI is on Robin's named coding-agent stack but the issue is about Claude Code (Anthropic's coding agent), not Codex CLI (OpenAI's coding agent); **adjacent-not-promoted** per scope because the issue is upstream Claude Code default-behavior context, not a Codex CLI change Robin acts on; the 1.23 comment-vs-upvote ratio (143 cmts / 116 pts) is the highest of the pull, indicating an active Claude Code community comment thread about the default-behavior change. **`49494301` "The Rise and Fall of Agent Civilizations"** (177 pts best + 103 cmts, by `consumer451` 2026-08-30, https://www.dwarkesh.com/p/openai-huggingface — Dwarkesh Patel essay / interview) — **strongest agent-substrate essay adjacency of the 2026-08-07 streak since the 2026-08-23 "What Is a Harness?" entry**; the "Rise and Fall of Agent Civilizations" framing directly speaks to the agent-as-primary-compute-substrate narrative that `hermes-agent-v0-19-quicksilver` documents; **Line truncated
 
 **Latest update — git-repo-1 (2026-08-30T18:06Z).** One source-specific update run for `git-repo-1` (Obsidian vault + OpenWiki wiki) per the source-specific instruction "Track vault + OpenWiki wiki mtime + commits (Robin 8-07 added)". Fresh connector ingest ran via `openwiki_ingest_connector connectorId=git-repo` and wrote manifest at `~/.openwiki/connectors/git-repo/raw/2026-08-30T18-06-24-410Z/manifest.json`. **Vault HEAD unchanged** at `9d4767c7034a59d8f3206756c2dfeb3f4339c2e0` (same as the 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; the 2026-08-24/25 SECOND consecutive single-day 5-paper LDR burst (Tevonian + Yang + `9aa2af4c` retrofit + Shen + Zhai) remains the most recent committed vault activity. **Vault silent for the 5th consecutive fetch** since the 2026-08-24/25 burst, **5 calendar days stale**. **No new vault mtime changes** — the 4 untracked vault directories / files from the 2026-08-29 fetch carry forward with bumped carry-forward counts: `Review/zhou2023_computer_vision_microfluidics.md` **18-day → 19-day carry-forward** (**16 → 17 fetches silent**, **the 2026-08-27 fetch already confirmed the 2026-08-26 watchlist-downgrade consideration as a one-off**, carrying forward unchanged at the 2026-08-28 + 2026-08-29 + 2026-08-30 fetches) + `celvivo_commercial/` **13-day → 14-day carry-forward** + `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) + `deepread_40240593/` **6-day → 7-day carry-forward** (the directory mtime is still 2026-08-24 16:31 +0800, unchanged since initial creation; the absence of mtime movement across the 2026-08-25 + 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + **2026-08-30** fetches — now **6 consecutive silent fetches** since the 2026-08-24/25 burst — suggests the working-folder pipeline hypothesis has continued to weaken; the entry should be downgraded to a stale carry-forward note on the next synthesis pass alongside the other 3 entries). **Wiki HEAD** bumped from `37d1ba6d30b6c4fe43a1d357311e12c9084dd8dc` (2026-08-29T18:10Z fetch) to **`d56da3afddfced20a01fbecd9912fe3ec87a25b4`** (2026-08-30T02:?? +0800, the 2026-08-30 daily update + sources-sync); **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 (2026-08-30T02:?? +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) + (b) `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; per `git show --stat d56da3a` the commit re-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 very next synthesis edits from the HN-1 + web-search-1 + git-repo-1 runs will re-touch the re-dirtied files). **9 uncommitted wiki files** in working tree 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 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`. **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. WikiLine truncated
@@ -156,7 +160,7 @@ Deferred until Robin configures connectors or asks for specific documentation:
 - **X / Twitter evidence index** — `/sources/x.md` (no X connector configured yet)
 - **Hacker News evidence index** — `/sources/hackernews.md` (active; last refreshed 2026-08-28 18:00 UTC — source-specific LLM-agent topic set (`organoid`, `CelVivo`, `3Brain`, `Cellink`, `openwiki`, `deepagents`); **eighteenth pull since 2026-08-07**, the **fifth consecutive fully-zero Algolia lane pull bookending the 2026-08-22 + 2026-08-27 substring-noise-only pulls** — `organoid` 0 hits + `CelVivo` 0 + `3Brain` 0 + `Cellink` 0 + `openwiki` 0 + `deepagents` 0 (clean zero across the board, no substring-noise collisions — distinct from the 2026-08-22 + 2026-08-27 substring-noise-only pulls; the 2026-08-28 pull is the **first fully-zero pull since 2026-08-26 with no substring-noise false positives on the vendor queries**); the 2026-08-23 + 2026-08-24 + 2026-08-25 + 2026-08-26 + 2026-08-28 are five fully-zero Algolia lanes bookending the 2026-08-22 + 2026-08-27 substring-noise-only pulls — **five fully-zero Algolia lanes in six consecutive pulls bookended by substring-noise-only Algolia lanes**, the longest fully-zero streak of the 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; Tavily (web-search) remains the productive lane for vendor news; 31 unique top+best items (top 29 + best 7 - 5 overlap); **five named-stack-adjacent items flagged for traceability this pull, none promoting a `/themes.md` row**: **`49468818` "Gemini-3.5-Transcribe"** (343 pts best, by `k9294` 2026-08-28, https://blog.google/innovation-and-ai/models-and-research/gemini-models/gemini-3.5-transcribe/ — Google blog) — **highest-engagement best-feed item of the pull** and **highest-engagement Google AI model item of the 2026-08-07 streak to date**; the **direct Gemini / M3 closed-weight cross-walk to the `MiniMax-m3` row** (Gemini is a closed-weight competitor to MiniMax-M3, not on Robin's named stack — Hermes / MiniMax-M3+H3 / OpenWiki / RAGFlow / NocoDB / SeaFile / Codex CLI are the named agents); **adjacent-not-promoted** per scope — Google Gemini is a closed-weight competitor, not on Robin's named stack; **`49473522` "Judge rules Trump administration's blacklisting of Anthropic was illegal"** (318 pts top+best, by `jbegley` 2026-08-28, https://www.nytimes.com/2026/08/27/technology/anthropic-government-blacklisting-ruling.html — New York Times) — **second-highest-engagement item on the pull** and the **direct AI-vendor-government ruling signal** (NYT-side coverage); cross-walked with the 317-pt Reuters companion `49477055` — the **highest combined-engagement AI-vendor-business-stack signal of the 2026-08-07 streak** (635 pts NYT + Reuters combined); the **AI-vendor-business-stack cluster** now totals **~1,786+ pts across 5 items in 5 pulls over 5 days** (FT Anthropic 738 + WFH-security-strike 89 + OpenAI HF-incident blog 324 + NYT Anthropic-blacklisting 318 + Reuters Anthropic-blacklisting 317); **adjacent-not-promoted** per scope — AI-vendor-government rulings are upstream AI-vendor regulatory context; **`49477055` "Pentagon's blacklisting of Anthropic was unlawful, US judge rules"** (317 pts best, by `softwaredoug` 2026-08-28, https://www.reuters.com/legal/government/us-judge-blocks-pentagons-anthropic-blacklisting-2026-08-28/ — Reuters) — **third-highest-engagement item on the pull** and the **Reuters companion to the NYT Anthropic-blacklisting ruling**; the multi-source NYT + Reuters pair at 635 pts combined provides multi-source journalistic confirmation; **adjacent-not-promoted** per scope — Reuters AI-vendor-government coverage is upstream AI-vendor regulatory context; **`49475079` "Luanti removed from Google Play due to baseless AI copyright notice"** (287 pts top+best, by `miniBill` 2026-08-28, https://blog.luanti.org/2026/08/27/luanti-dmca-tracer-ai/ — Luanti blog) — **fourth-highest top-feed engagement on the pull** and **the first AI-policy / copyright-DMCA signal in the 2026-08-07 streak** — the open-source Luanti game engine was struck from Google Play by a DMCA notice citing AI-generated content; **adjacent-not-promoted** per scope — AI-policy / copyright-DMCA items are upstream AI-policy context; **`49479878` "GLM-5.3 is now open-weight"** (268 pts top+best, by `jeudesprits` 2026-08-28, https://twitter.com/Zai_org/status/2093354097122455713 — Z.ai Twitter) — **fifth-highest top-feed engagement on the pull** and the **10th entry in the open-weight-LLM cluster**; **direct open-weight-LLM cross-walk to the `MiniMax-m3` row's open-weight comparison anchor** (DeepSeek V4 Flash / GLM / Qwen / Llama — GLM-5.3 is one of the canonical open-weight comparison anchors); **adjacent-not-promoted** per scope — Z.ai / GLM-5.3 is not on Robin's named stack; **important cluster findings** (carry forward + extend): the **self-hosted-agentic-substrate cluster** (DeepSeek Harness 2026-08-13 + machine0 2026-08-18 + OneCLI 2026-08-19 + self-hosted agentic softwarLine truncated
 - **Web search evidence index** — `/sources/web-search.md` (active; last successful pull 2026-08-03 18:08 UTC — first pull after the 3-day outage streak; CELLINK × Volumetric new Lumen X + 3Brain Utrecht Summer School + CelVivo ClinoStar 2 / Thailand Lab 2026 surfaced, see source page; 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, and 2026-08-27 update attempts skipped — connector not enabled in runtime registry, `TAVILY_API_KEY` missing; disk config shows `enabled: true` + 6 Chinese queries but the runtime registry disagrees — operational concern, not a wiki-synthesis concern; **fourteenth consecutive skip on the same code path** including 2026-08-27)
-- **Git repo evidence index** — `/sources/git-repo.md` (active; last refreshed 2026-08-30 18:06 UTC — covers Robin's Obsidian vault (HEAD `9d4767c7` 2026-08-25, the 2026-08-24/25 SECOND 5-paper LDR burst remains the most recent committed vault activity at **5 calendar days stale** after 5 consecutive silent fetches since the 2026-08-24/25 burst; the 2026-08-30T18:06Z fetch is documented in the "Latest update" section at the top — **vault HEAD unchanged** at `9d4767c7` because the 2026-08-30 fetch observed **0 new vault commits** (vault silent for the 5th consecutive fetch since the 2026-08-24/25 burst); the 4 untracked directories carry forward with bumped carry-forward counts: `Review/zhou2023_computer_vision_microfluidics.md` 18 → **19-day** (**one-off interpretation confirmed at 2026-08-28 fetch** per the 2026-08-27 one-off confirmation; **17 fetches silent** on the file), `celvivo_commercial/` 13 → **14-day** + `templates/` 13 → **14-day** (**confirmed one-off alongside the `Review/` entry** at the 2026-08-28 fetch; carrying forward unchanged at 2026-08-29 + 2026-08-30 fetches; **13 fetches silent** on each), `deepread_40240593/` 6 → **7-day** (**6 consecutive silent fetches** since the 2026-08-24/25 burst, working-folder pipeline hypothesis continuing to weaken) + OpenWiki wiki (HEAD `d56da3afddfced20a01fbecd9912fe3ec87a25b4` 2026-08-30; the wiki HEAD bumped from `37d1ba6d30b6c4fe43a1d357311e12c9084dd8dc` to `d56da3a` via 2 automated commits (`7eed6ca` chore: daily update 2026-08-30, 2026-08-30T02:?? +0800 — committed 13 of the prior 8 dirty files per `git show --stat 7eed6ca` reducing uncommitted-file count from 8 → 5, then `d56da3a` sources-sync 2026-08-30, 2026-08-30T02:30 +0800 — the **sixteenth** consecutive sources-sync re-applying the count-data wipe pattern; per `git show --stat d56da3a` the commit re-touched `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` — the same 4 source-sync files the `7eed6ca` daily update had cleared, so the dirty-file count re-bumped to **9** at the 2026-08-30T18:06Z fetch); the prior 3 wiki commits at the 2026-08-29T18:10Z fetch were `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`, reducing uncommitted-file count from 11 → 8) + `ef0e144` chore: daily update 2026-08-29 (touched `.last-update.json` only) + `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); the prior 2 wiki commits at the 2026-08-28T18:09Z fetch were `c992dd6` sources-sync 2026-08-28, 2026-08-28T02:30 +0800 — the **fourteenth** consecutive sources-sync + `6024ac7` chore: daily update 2026-08-28, 2026-08-28T02:42 +0800 — committed 16 of the prior 17 dirty files per `git show --stat 6024ac7`, reducing uncommitted-file count from 17 → 5, the largest cleanup in several cycles); **30 vault commits since 2026-08-03 fetch** (5 new commits at the 2026-08-24/25 burst + 0 commits at the 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + 2026-08-30 silent fetches; total remains 30 since 2026-08-03); wiki-side carries **9 uncommitted synthesis-layer edits** (+1 vs the 5-dirty-file baseline at the 2026-08-28T18:09Z fetch because the `d56da3a` sources-sync re-touched the 4 source-sync files that the `7eed6ca` daily update had cleared + the CLI metadata cycle re-touched `sources/openwiki-version-drift.md` + `index.md`; the very next synthesis edits re-touch the same files); **operational issue carries forward** — the `2507925` 2026-08-15 sources-sync count-data wipe (NocoDB 6614 → 0 records, Wiki.js 83 → 0 unique pages, RAGFlow landing 200 → 000) is now re-applied across **16 sources-syncs** (`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); the on-disk source configs are unaffected; data is recoverable from `git show 1737454:sources/nocodb.md` etc. — recorded for traceability on `/sources/git-repo.md` Notable-entity § "2026-08-15 sources-sync bug" and on each affected `/sources/{nocodb,ragflow,seafile,wikijs}.md` page; the synthesis layer (themes / commitments / open-questions / personal-logistics) is independent of the source-page counters and is not affected; **the 2026-08-24/25 10-paper LDR burst across 48 hours strengthens the `class-organoid-3d-bioprinting` theme-row evidence footprint** (3 new application-domain subfolders Vascularized-Organoids + Cardiac-Organoids + Skin-Organoids, plus the `9aa2af4c` reLine truncated
+- **Git repo evidence index** — `/sources/git-repo.md` (active; last refreshed 2026-08-31 18:09 UTC — covers Robin's Obsidian vault (HEAD `391e47131679ce9edf0f525236e78ebb13e0d232` 2026-08-31, the 2026-08-31 **THIRD consecutive single-day 5-paper LDR burst** is the most recent committed vault activity, **ending the 5-calendar-day vault silence streak** since the 2026-08-24/25 SECOND 5-paper burst; the 2026-08-31T18:09Z fetch is documented in the "Latest update" section at the top — **vault HEAD bumped** from `9d4767c7` to **`391e4713`** because the 2026-08-31 fetch observed **5 new vault commits** (the **THIRD consecutive single-day 5-paper LDR burst** anchored on CelVivo platform — `eb24ab72` Stewart 2023 Front Microbiol BA.5/XBB neurotropic brain organoids + `030f31ed` Aiello 2025 EMBO reports reproducible brain organoids (first direct CelVivo ApS co-authored deep-read) + `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 — all landing at the **NEW `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` capital-V parallel subfolder** — Robin's **first parallel-naming deep-read subfolder convention** parallel to the existing lowercase `Celvivo/` 142-file subfolder; combined with the prior 2026-08-23/24 + 2026-08-24/25 bursts Robin has produced **15 LDR papers in 8 calendar days** across 3 distinct single-day 5-paper bursts; the **QIMR Berghofer Suhrbier/Rawle trio** (Stewart 2023 + Nguyen 2024 + Yan 2024) anchors the CelVivo ClinoStar brain-organoid viral-neurotropism line with 3 distinct virus families); the 4 untracked directories carry forward with bumped carry-forward counts: `Review/zhou2023_computer_vision_microfluidics.md` 19 → **20-day** (**one-off interpretation confirmed at 2026-08-28 fetch** per the 2026-08-27 one-off confirmation; **18 fetches silent** on the file), `celvivo_commercial/` 14 → **15-day** + `templates/` 14 → **15-day** (**confirmed one-off alongside the `Review/` entry** at the 2026-08-28 fetch; carrying forward unchanged at 2026-08-29 + 2026-08-30 + 2026-08-31 fetches; **14 fetches silent** on each), `deepread_40240593/` 7 → **8-day** (**7 consecutive silent fetches** since the 2026-08-24/25 burst, working-folder pipeline hypothesis continuing to weaken) + OpenWiki wiki (HEAD `9582deadda4681fe1481f9992905230ace7e5990` 2026-08-31; the wiki HEAD bumped from `d56da3afddfced20a01fbecd9912fe3ec87a25b4` to `9582dea` via 2 automated commits (`c9e2770` chore: daily update 2026-08-31, 2026-08-31T02:18 +0800 — committed 15 files per `git show --stat c9e2770` reducing uncommitted-file count from 11 → 5, then `9582dea` sources-sync 2026-08-31, 2026-08-31T02:30 +0800 — the **seventeenth** consecutive sources-sync re-applying the count-data wipe pattern; per `git show --stat 9582dea` the commit re-touched `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` — the same 4 source-sync files the `c9e2770` daily update had cleared, so the dirty-file count re-bumped to **11** at the 2026-08-31T18:09Z fetch); the prior 2 wiki commits at the 2026-08-30T18:06Z fetch were `7eed6ca` chore: daily update 2026-08-30, 2026-08-30T02:?? +0800 — committed 13 of the prior 8 dirty files per `git show --stat 7eed6ca` reducing uncommitted-file count from 8 → 5, then `d56da3a` sources-sync 2026-08-30, 2026-08-30T02:30 +0800 — the **sixteenth** consecutive sources-sync re-applying the count-data wipe pattern; per `git show --stat d56da3a` the commit re-touched the same 4 source-sync files that the `7eed6ca` daily update had cleared, re-bumping the dirty-file count to **9** at the 2026-08-30T18:06Z fetch); the prior 3 wiki commits at the 2026-08-29T18:10Z fetch were `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`, reducing uncommitted-file count from 11 → 8) + `ef0e144` chore: daily update 2026-08-29 (touched `.last-update.json` only) + `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); the prior 2 wiki commits at the 2026-08-28T18:09Z fetch were `c992dd6` sources-sync 2026-08-28, 2026-08-28T02:30 +0800 — the **fourteenth** consecutive sources-sync + `6024ac7` chore: daily update 2026-08-28, 2026-08-28T02:42 +0800 — committed 16 of the prior 17 dirty files per `git show --stat 6024ac7`, reducing uncommitted-file count from 17 → 5, the largest cleanup in several cycles); **35 vault commits since 2026-08-03 fetch** (5 new commits at the 2026-08-24/25 burst + 0 commits at the 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + 2026-08-30 silent Line truncated
 - **Project / people / company pages** — only created when durable entities emerge from ingested data
 
 These are intentionally blank until there is real evidence to put in them. Populating them with placeholders would dilute the synthesis layer. the synthesis layer.

sources/git-repo.md

@@ -1,10 +1,10 @@
 ---
 type: "Reference"
-title: "Git repo — evidence index (Obsidian vault, Robin)"
-description: "Compact manifest of Robin's Obsidian vault + the local OpenWiki wiki, ingested through the local git-repo connector. Two configured repos: obsidian-vault at /home/ldw/workspace (main branch, HEAD 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."
+title: "Git repo — evidence index (Obsidian vault + OpenWiki wiki, Robin)"
+description: "Compact manifest of Robin's Obsidian vault + the local OpenWiki wiki, ingested through the local git-repo connector. Two configured repos: obsidian-vault at /home/ldw/workspace (main branch, HEAD `391e4713`, 2026-08-31, **5 new vault commits in the 2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window ending the 5-day vault silence — the THIRD single-day 5-paper LDR cluster (Yan + Stewart + Nguyen + Aiello + Miao), all `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` deep-reads anchored on CelVivo ClinoStar/ClinoReactor: `eb24ab72` Stewart 2023 Front Microbiol SARS-CoV-2 omicron BA.5/XBB neurotropic brain organoids + `030f31ed` Aiello 2025 EMBO reports reproducible brain organoids (CelVivo ApS is one author affiliation) + `fad7e21e` Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids + `4fca0123` Miao 2025 Cell vascularized lung/gut organoids (CelVivo ClinoReactor) + `391e4713` Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids; 4 of 5 use brain organoids for viral neurotropism modeling (QIMR Berghofer Suhrbier/Rawle research line), 1 is the first reproducibility benchmark with CelVivo as co-author**, vault HEAD bumped `9d4767c7` → `391e4713`; **cluster ends the 5-day vault silence from the 2026-08-25 burst** (vault silent for the prior 5 fetches: 2026-08-26T18:06Z + 2026-08-27T18:25Z + 2026-08-28T18:09Z + 2026-08-29T18:10Z + 2026-08-30T18:06Z all observed HEAD = `9d4767c7`); carry-forward untracked-file set continues: `Review/zhou2023_computer_vision_microfluidics.md` 19-day → **20-day carry-forward** (17 → 18 fetches silent, stale carry-forward note per 2026-08-28 demotion), `celvivo_commercial/` + `templates/` 14-day → **15-day carry-forward** (both confirmed one-off alongside `Review/` at the 2026-08-28 fetch, carrying forward unchanged at the 2026-08-31 fetch), `deepread_40240593/` 7-day → **8-day carry-forward** (mtime unchanged across **7 consecutive silent fetches** since creation, working-folder pipeline hypothesis continues to weaken); and openwiki-wiki at /home/ldw/.openwiki/wiki (main branch, HEAD `9582dea`, 2026-08-31, **2 new automated wiki commits in the 2026-08-30T18:06Z → 2026-08-31T18:09Z window: `c9e2770` chore: daily update 2026-08-31 (2026-08-31 02:18 +0800; per `git show --stat c9e2770` the commit touched 15 files including `.last-update.json` + `index.md` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/nocodb.md` + `sources/openwiki-version-drift.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` + `sources/wikijs.md` + `themes/05-robin-research.md` + `themes/index.md`), then `9582dea` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-31 — the **seventeenth** consecutive sources-sync re-applying the 2026-08-15 count-data wipe pattern after `2507925` 2026-08-15 + `997b648` 2026-08-16 + `be49285` 2026-08-17 + `1fc73ae` 2026-08-18 + `dcb53a2` 2026-08-19 + `bd30339` 2026-08-20 + `f6c2576` 2026-08-21 + `43d4548` 2026-08-22 + `8f8f767` 2026-08-23 + `127c2dc` 2026-08-24 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + `502281f` 2026-08-27 + `c992dd6` 2026-08-28 + `37d1ba6` 2026-08-29 + `d56da3a` 2026-08-30 + now `9582dea` 2026-08-31) committed `sources/{nocodb,ragflow,seafile,wikijs}.md` re-touched by the sources-sync; the very next synthesis edits from the HN-1 2026-08-31T18:00Z + web-search-1 2026-08-31 (skipped) + this git-repo-1 2026-08-31T18:09Z run re-touch the same files + 4 newly-dirty files leaving the dirty count at **11 per the manifest `changedFiles` list** — `M .last-update.json` + `M quickstart.md` + `M sources/hackernews.md` + `M sources/literature.md` + `M sources/nocodb.md` + `M sources/ragflow.md` + `M sources/seafile.md` + `M sources/web-search.md` + `M sources/wikijs.md` + `M themes.md` + `M themes/03-ai-agents.md` — up from 9 at the 2026-08-30 fetch because `themes.md` + `themes/03-ai-agents.md` re-touched by this turn's HN-1 Almanac row-refresh synthesis edits + `sources/literature.md` re-touched by the 2026-08-31 synthesis pass + the CLI metadata cycle**)**) This page is a navigation index — content ingestion (paper deep reads, sales scripts, customer files) happens via the Hermes skill and RAGFlow, not here."
 resource: "~/.openwiki/connectors/git-repo/config.json"
-tags: [git-repo, evidence, vault, openwiki-wiki, source, 2026-08-30, 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]
-timestamp: 2026-08-30T18:06:00Z
+tags: [git-repo, evidence, vault, openwiki-wiki, source, 2026-08-31, 2026-08-30, 2026-08-29, 2026-08-28, 2026-08-27, 2026-08-26, 2026-08-25, 2026-08-24, 2026-08-23, 2026-08-22, 2026-08-21, 2026-08-20, 2026-08-19, 2026-08-18, 2026-08-17, 2026-08-15, 2026-08-13, yan-2024-tmem106b-sars-cov2-brain-organoid, stewart-2023-ba5-xbb-neurotropic-brain-organoid, nguyen-2024-jev-g4-australia-brain-organoid, aiello-2025-brain-organoid-reproducibility, miao-2025-vascularized-lung-gut-organoids, brain-organoid-virology-cluster, celvivo-clinoreactor-cluster, third-5paper-cluster, vault-silence-ended, seventeenth-sources-sync, templates-celvivo-commercial-confirmed-one-off, deepread-40240593-seven-silent-fetches]
+timestamp: 2026-08-31T18:09:00Z
 ---
 
 # Git repo — evidence index (Obsidian vault + OpenWiki wiki)
@@ -22,176 +22,204 @@ help locate things in the vault, not summarize their content.
   `~/.openwiki/connectors/git-repo/config.json`)
 - **Configured repos:**
   - `obsidian-vault` → `/home/ldw/workspace` (Robin Obsidian vault, on
-    `main`, HEAD `9d4767c7034a59d8f3206756c2dfeb3f4339c2e0` as of
-    2026-08-25 +0800 — **5 new vault commits** in the
-    2026-08-24T18:05Z → 2026-08-25T18:13Z 24-hour window: the
-    **2026-08-24/25 5-paper LDR cluster** (SECOND consecutive
-    single-day 5-paper LDR burst) — `089177a7` Tevonian 2026 Nat Commun
-    血管化肝 MPS deep read (PMID 41634021) + `583859a8` Yang 2026 Stem
-    Cell Res Ther cardiac organoid review (PMID 41963991) + `9aa2af4c`
-    Update Tevonian 2026 + Yang 2026 (CelVivo/Cellink/Mimetas/3Brain/
-    FemtoBiomed product mapping retrofit + 净化 Robin mentions — the
-    FIRST post-publish vendor-mapping retrofit on the 2026-08-23/24/25
-    LDR cluster) + `5907cdfc` Shen 2026 Chin Med J vascularized
-    organoids review (PMID 42268296) + `9d4767c7` Zhai 2026 Sci Adv 3D
-    skin pemphigus (PMID 41512055). Combined with the 2026-08-23/24
-    5-paper burst, **10 papers in 48 hours** = largest sustained 2-day
-    research output in Robin's vault activity log. The cluster creates
-    **3 new `04-Literature/Deep-Reads/` subfolders**: `Vascularized-Organoids/`
-    (Tevonian + Shen) + `Cardiac-Organoids/` (Yang) + `Skin-Organoids/`
-    (Zhai) — Robin expands the deep-read taxonomy from ~19 to ~22
-    per-vendor / per-application-domain subfolders in a single day.
-    The new `9aa2af4c` retrofit commit is the **first synthesis-grade
-    post-publish LDR touch** on the 2026-08-23/24/25 cluster — the
-    prior 5 papers (Ajongbolo + Kim + Tian + Aiello + CelVivo App Note)
-    have NOT had this retrofit applied yet, only the new Tevonian + Yang
-    pair get the retroactive 4-vendor mapping).
+    `main`, HEAD `391e47131679ce9edf0f525236e78ebb13e0d232` as of
+    2026-08-31 13:42 +0800 — **5 new vault commits** in the
+    2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window: the
+    **2026-08-31 brain-organoid infectious-disease + CelVivo
+    ClinoStar/ClinoReactor 5-paper LDR cluster** (THIRD single-day
+    5-paper LDR burst — the 2026-08-25 second cluster is now the
+    THIRD-most-recent 5-paper cluster, vault bursts are now an
+    established pattern at the cadence of ~2 per week) — `eb24ab72`
+    Stewart 2023 Front Microbiol SARS-CoV-2 omicron BA.5/XBB
+    neurotropic brain organoids (QIMR Berghofer Suhrbier/Rawle line)
+    + `030f31ed` Aiello 2025 EMBO reports reproducible brain organoids
+    (CelVivo ApS is one author affiliation — first reproducibility
+    benchmark with CelVivo as co-author) + `fad7e21e` Nguyen 2024 npj
+    Viruses JEV G4 2022 Australia brain organoids (QIMR Berghofer
+    Suhrbier/Rawle line) + `4fca0123` Miao 2025 Cell vascularized
+    lung/gut organoids (CelVivo ClinoReactor) + `391e4713` Yan 2024
+    Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids
+    (QIMR Berghofer Suhrbier/Rawle line). 4 of 5 use brain organoids
+    for viral neurotropism modeling (3 share the QIMR Berghofer
+    Suhrbier/Rawle research line: Yan + Stewart + Nguyen) + 1 is a
+    vascularized lung/gut paper (Miao) + 1 is the first reproducibility
+    benchmark (Aiello, with CelVivo ApS co-author). **All 5 land in a
+    new subfolder `obsidian-vault/04-Literature/Deep-Reads/CelVivo/`
+    (capital V)** — Robin creates a **third** per-vendor CelVivo
+    subfolder alongside the existing `04-Literature/Deep-Reads/Celvivo/`
+    (143 papers, lower-case v) at the workspace root. **The 5-day
+    vault silence from the 2026-08-25 burst ends at this fetch**.
+    Combined with the 2026-08-23/24 + 2026-08-24/25 + 2026-08-31
+    5-paper bursts, **15 LDR papers in 8 days** = 3 distinct
+    single-day 5-paper bursts; the bursts create 4 new
+    `04-Literature/Deep-Reads/` subfolders: `Vascularized-Organoids/`
+    + `Cardiac-Organoids/` + `Skin-Organoids/` (2026-08-25 burst) +
+    `CelVivo/` (2026-08-31 burst) — Robin's deep-read taxonomy
+    expands to ~23 per-vendor / per-application-domain subfolders).
   - `openwiki-wiki` → `/home/ldw/.openwiki/wiki` (the OpenWiki knowledge
-    base itself, on `main`, HEAD `1003b92f3a1e43197ec8e21e7f69fd5db38316e7`
-    as of 2026-08-25T +0800 — 2 new wiki-side commits in the
-    2026-08-24T18:05Z → 2026-08-25T18:13Z 24-hour window: `3255613`
-    chore: daily update 2026-08-25 + `1003b92` chore(sources): refresh
-    NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-25) —
-    the **eleventh** consecutive sources-sync re-applying the 2026-08-15
-    count-data wipe pattern).
+    base itself, on `main`, HEAD `9582deadda4681fe1481f9992905230ace7e5990`
+    as of 2026-08-31T02:30 +0800 — 2 new wiki-side commits in the
+    2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window: `c9e2770`
+    chore: daily update 2026-08-31 + `9582dea` chore(sources): refresh
+    NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-31) —
+    the **seventeenth** consecutive sources-sync re-applying the
+    2026-08-15 count-data wipe pattern).
 - **Auth:** local paths only — no remote, no credentials.
-- **Latest fetch:** `2026-08-30T18:06:00Z` (raw manifest
-  `~/.openwiki/connectors/git-repo/raw/2026-08-30T18-06-??-???Z/manifest.json`).
+- **Latest fetch:** `2026-08-31T18:09:00Z` (raw manifest
+  `~/.openwiki/connectors/git-repo/raw/2026-08-31T18-09-??-???Z/manifest.json`).
 - **Source config:** `~/.openwiki/connectors/git-repo/config.json`
 - **State:** `~/.openwiki/connectors/git-repo/state.json` records
-  `latestIds` per repo; the 2026-08-30T18:06Z fetch observed 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 —
-  **0 new vault commits** in the 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 is the most recent vault
-  activity, 5 calendar days stale), and observed `openwiki-wiki`
-  bumped from `37d1ba6d30b6c4fe43a1d357311e12c9084dd8dc` (2026-08-29T18:10Z fetch) to
-  **`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
-  `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`
-  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
+  fetch — same as the 2026-08-29T18:10Z + 2026-08-28T18:09Z +
+  2026-08-27T18:25Z + 2026-08-26T18:06Z + 2026-08-25T18:13Z fetches
+  all observed `9d4767c7` — **0 new vault commits** in the prior 5
+  fetches, **vault silent for the 5th consecutive fetch** since the
+  2026-08-24/25 SECOND 5-paper burst; the 2026-08-25 5-paper cluster
+  was the most recent vault activity at the 2026-08-30T18:06Z fetch,
+  5 calendar days stale) to **`391e47131679ce9edf0f525236e78ebb13e0d232`** (5 new
+  vault commits in the 2026-08-30T18:06Z → 2026-08-31T18:09Z window:
+  `eb24ab72` + `030f31ed` + `fad7e21e` + `4fca0123` + `391e4713` — all
+  `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` deep-reads; the
+  THIRD single-day 5-paper LDR burst; the cluster ends the 5-day
+  vault silence), and observed `openwiki-wiki` bumped from
+  `d56da3afddfced20a01fbecd9912fe3ec87a25b4` (2026-08-30T18:06Z fetch)
+  to **`9582deadda4681fe1481f9992905230ace7e5990`** (2 new automated
+  wiki commits in the 24-hour window: `c9e2770` chore: daily update
+  2026-08-31 (2026-08-31 02:18 +0800, committed 15 files per
+  `git show --stat c9e2770` — including `.last-update.json` +
+  `index.md` + `quickstart.md` + `sources/README.md` +
+  `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` +
+  `sources/nocodb.md` + `sources/openwiki-version-drift.md` +
+  `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` +
+  `sources/wikijs.md` + `themes/05-robin-research.md` + `themes/index.md`),
+  then `9582dea` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts
+  (sources-sync 2026-08-31, 2026-08-31T02:30 +0800 — the **seventeenth**
   consecutive sources-sync re-applying the 2026-08-15 count-data wipe
   pattern after `2507925` 2026-08-15 + `997b648` 2026-08-16 + `be49285`
   2026-08-17 + `1fc73ae` 2026-08-18 + `dcb53a2` 2026-08-19 + `bd30339`
   2026-08-20 + `f6c2576` 2026-08-21 + `43d4548` 2026-08-22 + `8f8f767`
   2026-08-23 + `127c2dc` 2026-08-24 + `1003b92` 2026-08-25 + `ebb95c0`
-  2026-08-26 + `502281f` 2026-08-27 + `c992dd6` 2026-08-28 + `37d1ba6` 2026-08-29 + 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" |
@@ -634,6 +673,8 @@ pipeline catches up.
 
 | 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) |
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 | 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`) |
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 | 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`) |
@@ -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) |
 | `Skin-Organoids/` | 1 (new as of 2026-08-25 — `Zhai_2026_Sci_Adv_3D_Skin_Pemphigus.md`; **net-new application domain (autoimmune dermatology + 3D skin)** to Robin's deep-read set; companion to the existing Cardiac / Brain / Liver / Vascularized-Organoids / Cancer / Kidney / Retinal application-domain subfolders) |
+| `CelVivo/` (capital V, parallel to lowercase `Celvivo/`) | 5 (new as of 2026-08-31 — `stewart-2023-ba5-xbb-neurotropic-brain-organoids.md` + `aiello-2025-brain-organoid-reproducibility.md` + `nguyen-2024-jev-g4-2022-australia-brain-organoids.md` + `miao-2025-vascularized-lung-gut-organoids.md` + `yan-2024-tmem106b-sars-cov2-ace2-independent.md`; **all 5 single-shot LDR entries committed 2026-08-31 13:05-13:42 +0800**; 4 of 5 are brain organoid infectious-disease / reproducibility papers using CelVivo ClinoStar/ClinoReactor + 1 is vascularized lung/gut; the new capital-V subfolder sits at `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` parallel to the existing lowercase `04-Literature/Deep-Reads/Celvivo/` 143-file subfolder — Robin's first parallel-naming deep-read subfolder convention; subfolder semantics: QIMR Berghofer Suhrbier/Rawle viral-neurotropism brain-organoid line (Stewart + Nguyen + Yan) + CelVivo ApS co-authored reproducibility (Aiello) + vascularized lung/gut (Miao)) |
 
-Total ≈ 1,217 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.
+`celvivo_commercial/` directories, both untracked; +1 working-tree directory `deepread_40240593/` (7 subdirs, 2026-08-24) carrying pipeline intermediate artifacts from the 2026-08-23/24 burst). The 2026-08-31 single-day 5-paper LDR burst (5 papers in `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` parallel capital-V subfolder) is the most recent committed deep-read cluster; the 2026-08-24/25 cluster (Vascularized-Organoids + Cardiac-Organoids + Skin-Organoids subfolders) remains the prior committed cluster; the 2026-08-23/24 single-shot LDR burst (5 papers at vault root) is the prior-prior committed cluster; the 2026-08-16 Quintard 2024 + Guo 2026 cluster remains the prior-prior-prior committed cluster; the 2026-08-07 / 2026-08-08 cluster (Microbioreactor + Cells) remains the prior-prior-prior-prior committed cluster. The 2026-08-31 cluster is **CelVivo-anchored exclusively** (all 5 papers use CelVivo ClinoStar/ClinoReactor; 1 paper — Aiello 2025 — has CelVivo ApS as a co-author affiliation), reinforcing the 4 of 5 from the 2026-08-23/24 cluster that were also CelVivo-aligned. CelVivo, 3Brain, Cellink, and the broad `Organoid/` bucket cover Robin's product KB per the wiki goal focus areas (类器官培养与设备, 3D 生物打印). The new `templates/` folder signals Robin may be formalizing customer-facing deliverables (checklists / templates / sales scripts) as a separate vault subtree — the IRB application checklist is the first such artifact.
 
 ## Distributor map refresh (2026-08-07)
 
@@ -779,6 +821,12 @@ fields still 待补).
 
 ## Notable entities surfaced by the vault (structural hints only)
 
+- **2026-08-31 cluster — THIRD consecutive single-day 5-paper LDR burst + NEW capital-V `CelVivo/` subfolder (vault HEAD `9d4767c7` → `391e4713`, 5 new vault commits)** — the 2026-08-31T18:09Z fetch observed the **THIRD consecutive single-day 5-paper LDR burst** at vault HEAD, ending a **5-calendar-day vault silence streak** since the 2026-08-24/25 cluster. **Combined with the prior 2026-08-23/24 (5 papers) + 2026-08-24/25 (5 papers) clusters, 15 LDR files in 8 calendar days (2026-08-23 → 2026-08-31), the largest sustained 8-day research output** in Robin's vault activity log; **all 3 clusters are CelVivo-anchored** (5/5 in 2026-08-23/24 + 4/5 in 2026-08-24/25 via the `9aa2af4c` retrofit + 5/5 in 2026-08-31). The 2026-08-31 cluster creates **1 NEW `04-Literature/Deep-Reads/` subfolder**: `CelVivo/` (capital-V) at `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` — Robin's **first parallel-naming deep-read subfolder convention** (parallel to the existing lowercase `04-Literature/Deep-Reads/Celvivo/` 142-file subfolder, total subfolder count goes from ~22 → ~23 in 8 days). The 5-commit cluster is (chronological, all on 2026-08-31 +0800 between 13:05 and 13:42): `eb24ab72` Stewart 2023 Front Microbiol BA.5/XBB neurotropic brain organoids → `030f31ed` Aiello 2025 EMBO reports reproducible brain organoids (CelVivo ApS co-author) → `fad7e21e` Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids → `4fca0123` Miao 2025 Cell vascularized lung/gut organoids → `391e4713` Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids. **Subfolder content mix**: 4 of 5 are brain organoids (the QIMR Berghofer Suhrbier/Rawle viral-neurotropism line + CelVivo ApS co-authored reproducibility) + 1 is vascularized lung/gut (Miao — companion to the 2026-08-08 flywheel-sync Miao 2025 v2 deep-read). The 2026-08-31 cluster did **NOT** receive the `9aa2af4c` vendor-mapping retrofit commit (no companion retrofit commit this cluster, unlike the 2026-08-24/25 cluster which had `9aa2af4c` as the 3rd of 5 commits). **Net-new external evidence** in this run (git-repo-1 2026-08-31). Synthesis routes into `/themes/01-organoid-equipment.md` (CelVivo ClinoStar/ClinoReactor evidence on brain + lung/gut infectious-disease models) + `/themes/05-robin-research.md` (vault-snapshot refresh + the 3rd 5-paper cluster + the parallel-naming convention) + `/sources/literature.md` (last-30-days table) + `/commitments.md` (5 new commitment rows for the 5 new papers). **Track on next fetch** whether (a) Robin produces deep-read synthesis pages for any of the 5 papers (none currently exist), (b) the 2026-08-31 cluster is retrofitted with the `9aa2af4c` 5-vendor mapping pattern (the absence of a retrofit commit this cluster may indicate the vendor mapping was applied at the original `git add` time, or that Robin has adopted a different convention), (c) more entries land in the new `CelVivo/` (capital-V) subfolder (currently 5 files; ≥3 was the threshold for "subfolder is in active use" but already at the threshold on first observation, indicating strong subfolder commitment), (d) the parallel capital-V vs lowercase `Celvivo/` subfolder naming convention is formalized in vault conventions (currently appears to be a convention shift without explicit documentation), (e) the working-folder `deepread_40240593/` pipeline finally gets committed or shows mtime movement at the 2026-08-31 fetch (**8th fetch silent on directory mtime**, hypothesis further weakened).
+- **2026-08-31 Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids (CelVivo) (single-shot LDR entry `391e4713`, ~40 lines per `git show --stat 391e4713`)** — `obsidian-vault/04-Literature/Deep-Reads/CelVivo/yan-2024-tmem106b-sars-cov2-ace2-independent.md`. Yan K, Dumenil T, Stewart R, Bishop CR, Nguyen W, Suhrbier A*, Rawle DJ* (Cell Reports 43, 114921, 2024-11-26; DOI 10.1016/j.celrep.2024.114921; QIMR Berghofer Medical Research Institute; **`ollama_audit: 4/4 passed`**). The paper establishes: (i) **CRISPR screen identifies TMEM106B / heparan sulfate / endocytosis as ACE2-independent SARS-CoV-2 entry mediators** (S-E484D mutant bypassing ACE2 dependence); (ii) **human cortical brain organoids (CelVivo ClinoStar) show MA1 strain enhanced neurotropism** — higher titer + more infected cells vs ancestral variants; (iii) **K18-hACE2 mice show MA1 enhanced disease + lower survival**; (iv) **in vivo null result** — wild-type / Ifnar-/- mice do not show increased neuroinvasion; Ace2-/- mice cannot be infected via lung. Companion to **Stewart 2023** + **Nguyen 2024** in the same cluster — the 3 QIMR Berghofer Suhrbier/Rawle viral-neurotropism papers (all SARS-CoV-2 / JEV / brain organoid) form a 3-paper line validating the **CelVivo ClinoStar cortical brain organoid model for viral-neurotropism studies**. **Vendor-anchor mapping**: CelVivo ClinoStar ⭐⭐⭐⭐ (cortex brain organoid for neurotropic virus infection; 3-paper Suhrbier/Rawle line validates the platform for viral pathogenesis research). **Net-new external evidence** in this run (git-repo-1 2026-08-31). **Track on next fetch** whether Robin produces a deep-read synthesis page and whether the 3-paper Suhrbier/Rawle line folds into a single `suhrbier-rawle-celvivo-brain-organoid-virology-cluster` synthesis page.
+- **2026-08-31 Miao 2025 Cell vascularized lung/gut organoids (CelVivo ClinoReactor) (single-shot LDR entry `4fca0123`)** — `obsidian-vault/04-Literature/Deep-Reads/CelVivo/miao-2025-vascularized-lung-gut-organoids.md`. Miao Y, Pek NM, Tan C, Chen Y-W, Guo M*, Gu M* (Cell 188, 1-19, 2025-08-07; DOI 10.1016/j.cell.2025.05.041; **`ollama_audit: 7/7 passed`** + 8-08 精简版已升级完整版). The paper establishes: **mesoderm-endoderm co-differentiation enables organotypic vascularization in lung + gut organoids** — a single-organoid protocol for hiPSC → lung + gut with embedded vasculature (rather than the prior 2-step "differentiate organoid then add vasculature"). **FoxF1** is identified as a key mesodermal TF driving vascular incorporation. Companion to the 2026-08-08 flywheel-sync `Miao2025_Cell_v2.md` deep-read (which was Robin's first deep-read of this paper); the 2026-08-31 re-read in the new `CelVivo/` capital-V subfolder is a **re-read with the CelVivo-anchored vendor perspective**. **Vendor-anchor mapping**: CelVivo ClinoReactor ⭐⭐⭐⭐⭐ (3-track lung/gut/vascular co-development requires low-shear suspension culture for the mesodermal-endodermal co-differentiation step; ClinoReactor is the canonical hardware). **Net-new external evidence** in this run. **Track on next fetch** whether Robin's existing Miao 2025 deep-read synthesis page at `/sources/literature-miao-2025-cell-vascularization-v2-deepread.md` gets a retrofitted vendor-mapping update referencing the 2026-08-31 re-read.
+- **2026-08-31 Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids (CelVivo) (single-shot LDR entry `fad7e21e`)** — `obsidian-vault/04-Literature/Deep-Reads/CelVivo/nguyen-2024-jev-g4-2022-australia-brain-organoids.md`. Nguyen W, Gyawali N, Stewart R, Tang B, Cox AL, Yan K, Larcher T, Bishop CR, Wood N, Devine GJ, Suhrbier A, Rawle DJ (npj Viruses [Nature Portfolio], Article 25, 2024; DOI 10.1038/s44298-024-00025-5; QIMR Berghofer Medical Research Institute + INRAE; **`ollama_audit: 8/8 passed`**). The paper characterizes a **Japanese Encephalitis virus genotype 4 isolate from the 2022 Australian outbreak** — uses CelVivo ClinoStar brain organoids to validate the isolate's neurotropism in human cortical tissue (vs mouse models). **Flavivirus** family — companion to the SARS-CoV-2 / BA.5/XBB / TMEM106B cluster (Stewart + Yan) in establishing the **CelVivo ClinoStar brain organoid platform for neurotropic virus characterization**. **Vendor-anchor mapping**: CelVivo ClinoStar ⭐⭐⭐⭐. **Net-new external evidence** in this run. **Track on next fetch** whether Robin produces a deep-read synthesis page and whether the JEV-Australia outbreak context yields Australian academic / public-health customer entry material.
+- **2026-08-31 Aiello 2025 EMBO reports reproducible brain organoids (CelVivo ClinoReactor; CelVivo ApS co-author) (single-shot LDR entry `030f31ed`)** — `obsidian-vault/04-Literature/Deep-Reads/CelVivo/aiello-2025-brain-organoid-reproducibility.md`. Aiello G, Nemir M, Vidimova B, Ramel C, Viguie J, Ravera A, Wrzesinski K*, Bagni C* (EMBO reports, Volume 26, December 2025, 6209-6239; DOI 10.1038/s44319-025-00619-x; 洛桑大学 + 罗马 Tor Vergata 大学 + 西北大学[南非] + **CelVivo ApS[丹麦] as co-author affiliation**; **`ollama_audit: 6/6 passed`**). The paper establishes: (i) **controlled fluid dynamics** through CelVivo ClinoReactor improves brain-organoid reproducibility (multi-batch + multi-iPSC line PCA shows CV < 15% vs static culture > 30%); (ii) **scRNA-seq OXPHOS profiling** validates metabolic maturation in ClinoReactor vs static; (iii) **multi-marker IHC** (SOX2/Nestin/PAX6 + DCX + TBR1/SATB2/MAP2) confirms cortical layer identity. This is the **first paper in the cluster where CelVivo ApS appears as a co-author affiliation** (vs the prior papers where CelVivo is just the bioreactor vendor) — significant credibility signal for the **CelVivo ClinoReactor as the canonical hardware for reproducible brain organoid culture**. Companion to the **2026-08-23 Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid** deep-read (Robin did a 2-deep-read cycle: biorxiv preprint version + EMBO reports final version, 8 days apart). **Vendor-anchor mapping**: CelVivo ClinoReactor ⭐⭐⭐⭐⭐ (CelVivo ApS is a co-author, validating the platform via academic-CelVivo collaboration). **Net-new external evidence** in this run. **Track on next fetch** whether Robin produces a deep-read synthesis page at `/sources/literature-aiello-2025-brain-organoid-reproducibility-deepread.md` and whether the 2026-08-23 Aiello deep-read synthesis page gets retrofitted to reference the 2026-08-31 EMBO reports final version.
+- **2026-08-31 Stewart 2023 Front Microbiol BA.5/XBB neurotropic brain organoids (CelVivo) (single-shot LDR entry `eb24ab72`)** — `obsidian-vault/04-Literature/Deep-Reads/CelVivo/stewart-2023-ba5-xbb-neurotropic-brain-organoids.md`. Stewart R, Yan K, Ellis SA, Bishop CR, Dumenil T, Tang B, Nguyen W, Larcher T, Parry R, Sng JDJ, Khromykh AA, Sullivan RKP, Lor M, Meunier FA, Rawle DJ*, Suhrbier A* (Frontiers in Microbiology, Volume 14, Article 1320856, 2023-11-23; DOI 10.3389/fmicb.2023.1320856; QIMR Berghofer Medical Research Institute + University of Queensland; **`ollama_audit: 6/6 passed`**). The paper establishes: **SARS-CoV-2 omicron BA.5 + XBB variants have increased neurotropic potential over BA.1** — K18-hACE2 mice show enhanced brain infection + human brain organoids (CelVivo ClinoStar) confirm the BA.5/XBB enhancement in cortical tissue. Companion to **Yan 2024 TMEM106B** in the same QIMR Berghofer Suhrbier/Rawle viral-neurotropism line. **Vendor-anchor mapping**: CelVivo ClinoStar ⭐⭐⭐⭐. **Net-new external evidence** in this run. **Track on next fetch** whether Robin produces a deep-read synthesis page and whether the BA.5/XBB neurotropism data has implications for Robin's Chinese pharma R&D / CDMO customers working on SARS-CoV-2 long-COVID neurological complications.
 - **2026-08-23 root-level LDR burst (5 papers, single-shot entries, vault HEAD bump `a4fa5a32` → `fb017e4f`)** — **largest single-day LDR cluster since the 2026-07-29 Parate / Lee / Hodge cluster**; breaks the **7-fetch vault-silence streak** that started after the 2026-08-16 Quintard + Guo cluster; all 5 files landed at `obsidian-vault/04-Literature/Deep-Reads/` **root** (not in a per-vendor subfolder) on 2026-08-23/24 between 07:50 +0800 and 16:39 +0800; **non-standard pattern** vs the prior per-vendor subfolder discipline (every prior LDR cluster since 2026-07-28 has sorted into `Organoid/` / `Celvivo/` / `3Brain/` / `Cells/` etc.). The 5 commits are all single-shot entries (no v2/v3 SOP rewrite cycles this cluster, unlike the 2026-08-16 Quintard 4-commit + Guo 3-commit pattern). Commit timestamps `2026-08-23` (Western time) + `2026-08-24` (UTC mtime): (a) **`ad4abcde` 2026-08-24 feat: Ajongbolo 2025 Cells 脑类器官综述精读 (Wiki.js 1743)** — `Ajongbolo_2025_Cells_Brain_Organoids_Review.md`, the canonical review paper of the cluster, 11,367 bytes; (b) **`5f02489a` 2026-08-24 feat: Kim 2025 NatCommun 液态金属 3D MEA 精读 (Wiki.js 1744)** — `Kim_2025_NatCommun_Liquid_Metal_3D_MEA.md`, 13,567 bytes, the **3D-MEA competitor paper** of the cluster; (c) **`40b357b8` 2026-08-24 feat: Tian 2025 NatCommun 心外膜 mTOR 精读 (Wiki.js 1745)** — `Tian_2025_NatCommun_Epicardium_mTOR.md`, 15,578 bytes, the **cardiac-epicardium paper** of the cluster; (d) **`f2118a62` 2026-08-24 feat: Aiello & Bagni 2025 biorxiv Rotating Chamber brain organoid 精读 (Wiki.js 1746)** — `Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid.md`, 11,731 bytes, the **CelVivo-KB-derived brain-organoid CFD paper** of the cluster; (e) **`fb017e4f` 2026-08-24 feat: CelVivo App Note 2026 shear stress ClinoStar vs orbital shaker (Wiki.js 1747)** — `CelVivo_Shear_Stress_AppNote_2026.md`, 10,145 bytes, the **vendor App Note** of the cluster. **3 of the 5 papers are CelVivo-aligned**: the App Note (direct CelVivo document) + Aiello (CelVivo KB-sourced) + Ajongbolo review (mentions ClinoStar in the synthesis). **1 is a 3D-MEA competitor**: Kim EGaIn magnetic-reshapable 3D MEA. **1 is a cardiac epicardium paper**: Tian mTOR. The cluster anchors **4 of 5 to Robin's 4 vendor product lines** (CelVivo=3, 3Brain-adjacent=1) plus 1 cardiac expansion. Synthesis routes into `/themes/01-organoid-equipment.md` (CelVivo evidence) + `/themes/05-robin-research.md` (vault-snapshot refresh + deep-reads breakdown) + `/sources/literature.md` (last-30-days table). **Net-new external evidence** in this run. **Track on next fetch** whether (a) more LDR files land in vault root (extending the root-level pattern) or migrate to per-vendor subfolders on next SOP revision, (b) the `deepread_40240593/` pipeline workspace gets committed (per the Notable-entity entry below), (c) the existing MOC pattern at `04-Literature/Deep-Reads/MOCs/MOC-类器官与3D培养.md` gets a 2026-08-23/24 LDR-cycle entry.
 - **CelVivo App Note 2026 shear stress ClinoStar vs orbital shaker (2026-08-23, single-shot LDR entry `fb017e4f`, Wiki.js 1747)** — `obsidian-vault/04-Literature/Deep-Reads/CelVivo_Shear_Stress_AppNote_2026.md` (10,145 bytes). Stougaard Borgen Løschenkohl + Sedighi Frandsen, CelVivo Application Note 2026, sourced from RAGFlow CelVivo KB (1555e5b2..., Robin 8-24 上传). The note establishes **head-to-head comparison** of ClinoStar® vs orbital shaker for **3D 类器官/球体培养** (HepG2/C3A 15-day + embedded Caco-2 肠 + brain organoid). Core findings: (i) **low shear stress ClinoStar preserves cytoskeletal integrity** — phalloidin/DAPI 染色 shows ClinoStar F-actin 排列规则 + 形态紧凑 + 细胞间内聚性强 vs orbital shaker F-actin 散布 + 形态松散 + 内聚性下降 (4x + 20x dual magnification); (ii) **15-day standardized workflow** — same source cells (HepG2/C3A) + same pre-conditioning (SP5D 24孔球形板 Kugelmeiers, 1000 cells/aggregate) + same end-point assays (image + ATP + BCA + fluorescent staining + microscopy) + 3 bio-replicates per condition; (iii) **multi-model transferability** — embedded Caco-2 肠 + brain organoid both show ClinoStar advantage → vendor claim "low shear stress sensitive cell class (肝/肠/脑来源)" validated across 3 model systems. **Net-new external evidence** in this run (git-repo-1 2026-08-24). **Highest commercial-relevance paper of the cluster**: this is the **canonical CelVivo vs-orbital-shaker competitive-killer document** and is Robin's first **vendor App Note deep-read** (vs. 1 primary research paper + 1 review paper from prior clusters). **Track on next fetch** whether (a) Robin produces a deep-read synthesis page at `/sources/literature-celvivo-shear-stress-appnote-2026-deepread.md` mirroring the prior pattern, (b) the App Note is folded into `06-Sales/Content/Training-Materials/` (the existing CelVivo赋能培训 v1-v9 cluster could absorb the head-to-head comparison data as a new PPT module), (c) the App Note spawns a new sales commitment similar to the existing `celvivo-clinoreactor-thewell-bioscience-xeno-free` item.
 - **Aiello & Bagni 2025 biorxiv Rotating Chamber brain organoid CFD (2026-08-23, single-shot LDR entry `f2118a62`, Wiki.js 1746)** — `obsidian-vault/04-Literature/Deep-Reads/Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid.md` (11,731 bytes). Aiello F, Bagni C et al., biorxiv preprint (the EMBO Reports submission version `Aiello_Bagni_EMBO R_050325`), 2026-08-24 Robin 从 CelVivo KB 找到的 PDF. The paper is **the first CFD-quantified Rotating Chamber (RC) low-shear-stress study** in Robin's deep-read set: (i) RC geometry: outer Ø 78.3 mm × H 24.2 mm, inner cavity Ø 37.7 mm × H 8.8 mm (reserved for organoid growth space); (ii) **COMSOL Multiphysics 6.2 CFD simulation shows cavity shear stress < 20 mPa** (extremely low vs. standard stirred/shaken systems) — **first quantitative number** on RC shear-stress field; (iii) **multi-density organoid shear-stress validation** — relative density 1010/1020/1030 vs medium 1000 confirms shear-stress uniformity across density range + 0-300 objects all experience stable low shear; (iv) **morphological consistency** — multi-batch + multi-cell-line brain organoid cultures show **CV < 15%** (vs static culture CV > 30%); (v) cortical cell type recapitulation (SOX2/Nestin/PAX6 + DCX + TBR1/SATB2/MAP2 multi-marker IHC) + scRNA-seq OXPHOS metabolic profiling. **Net-new external evidence** in this run. **Vendor-anchor mapping**: Aiello paper is **CelVivo ClinoStar-adjacent** (uses RC system which is the ClinoStar simplified geometry) + 3Brain HD-MEA-adjacent (cortical organoid electrophysiology read-out). The < 20 mPa quantitative claim is **direct ammunition** for the existing ClinoStar ⭐⭐⭐⭐ vendor-positioning pitch — no prior paper in Robin's deep-read set provides the **quantitative CFD number** for ClinoStar's low-shear-stress value proposition. **Track on next fetch** whether Robin produces a deep-read synthesis page; the deep-read pipeline currently does not carry an Aiello synthesis page.
@@ -879,6 +927,8 @@ fields still 待补).
 
 ## Synthesis policy for this source
 
+- **This run (2026-08-31, git-repo-1 18:09Z):** **5 new vault commits** in the 2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window — vault HEAD bumped from `9d4767c7` (2026-08-30T18:06Z fetch) to `391e4713` (5 calendar days of vault silence ended; **THIRD consecutive single-day 5-paper LDR burst** after the 2026-08-23/24 + 2026-08-24/25 clusters, all CelVivo-anchored). **Net-new external evidence**: 5 new CelVivo-anchored brain-organoid infectious-disease + reproducibility LDR files (`eb24ab72` Stewart 2023 BA.5/XBB + `030f31ed` Aiello 2025 reproducible brain organoids [CelVivo ApS co-author] + `fad7e21e` Nguyen 2024 JEV G4 + `4fca0123` Miao 2025 vascularized lung/gut + `391e4713` Yan 2024 TMEM106B SARS-CoV-2 ACE2-independent) — **all 5 land in the NEW `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` subfolder** (capital-V, parallel to the existing lowercase `Celvivo/` 142-file subfolder; Robin's first parallel-naming deep-read subfolder convention); 4 of 5 are brain organoids (the QIMR Berghofer Suhrbier/Rawle viral-neurotropism line + CelVivo ApS co-authored reproducibility) + 1 vascularized lung/gut (Miao); **cluster does NOT receive the `9aa2af4c` post-publish vendor-mapping retrofit commit** (the 2026-08-24/25 cluster had `9aa2af4c` as the 3rd of 5 commits; the 2026-08-31 cluster does not have a comparable retrofit). The carry-forward untracked-file set bumps: `Review/zhou2023_computer_vision_microfluidics.md` **19-day → 20-day carry-forward** (**17 → 18 fetches silent**, stale carry-forward note) + `celvivo_commercial/` + `templates/` **14-day → 15-day carry-forward** (both confirmed one-off alongside the `Review/` subfolder, carrying forward unchanged at the 2026-08-31 fetch) + `deepread_40240593/` **7-day → 8-day carry-forward** (mtime unchanged across **7 consecutive silent fetches** since creation, working-folder-pipeline hypothesis further weakened at this fetch — **8th fetch silent on directory mtime**, no signs of pipeline activity despite 3 LDR clusters in 8 days). **Wiki-side**: **2 new automated wiki commits** landed in the 2026-08-30T18:06Z → 2026-08-31T18:09Z 24-hour window — `c9e2770` chore: daily update 2026-08-31 (2026-08-31T02:18 +0800, committed 15 files per `git show --stat c9e2770` — including `.last-update.json` + `index.md` + `quickstart.md` + `sources/README.md` + `sources/git-repo.md` + `sources/hackernews.md` + `sources/index.md` + `sources/nocodb.md` + `sources/openwiki-version-drift.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/web-search.md` + `sources/wikijs.md` + `themes/05-robin-research.md` + `themes/index.md`; reducing uncommitted-file count from 11 → 5 per the manifest `changedFiles` list at the 2026-08-31T18:09Z fetch) + `9582dea` chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-31, 2026-08-31T02:30 +0800, the **seventeenth** consecutive sources-sync re-applying the `2507925` 2026-08-15 count-data wipe pattern after `997b648` 2026-08-16 + `be49285` 2026-08-17 + `1fc73ae` 2026-08-18 + `dcb53a2` 2026-08-19 + `bd30339` 2026-08-20 + `f6c2576` 2026-08-21 + `43d4548` 2026-08-22 + `8f8f767` 2026-08-23 + `127c2dc` 2026-08-24 + `1003b92` 2026-08-25 + `ebb95c0` 2026-08-26 + `502281f` 2026-08-27 + `c992dd6` 2026-08-28 + `37d1ba6` 2026-08-29 + `d56da3a` 2026-08-30 + now `9582dea` 2026-08-31; per `git show --stat 9582dea` the commit touched `sources/nocodb.md` + `sources/ragflow.md` + `sources/seafile.md` + `sources/wikijs.md` — the same 4 source-sync files that the `c9e2770` daily update had already cleared were re-touched by the sources-sync that landed later in the window; same re-bump pattern as the 2026-08-28 + 2026-08-29 + 2026-08-30 fetches). The manifest `changedFiles` shows **11 dirty wiki files** this fetch — `M .last-update.json` + `M quickstart.md` + `M sources/hackernews.md` + `M sources/literature.md` + `M sources/nocodb.md` + `M sources/ragflow.md` + `M sources/seafile.md` + `M sources/web-search.md` + `M sources/wikijs.md` + `M themes.md` + `M themes/03-ai-agents.md` — up from the 9-dirty-file baseline at the 2026-08-30T18:06Z fetch because the `9582dea` sources-sync re-touched the 4 source-sync files that the `c9e2770` daily update had committed + the HN-1 2026-08-31 Almanac (YC S26) synthesis pass added 3 NEW dirty files (`sources/literature.md` + `themes.md` + `themes/03-ai-agents.md`) for the `agent-memory-architecture` row refresh. **Synthesis-layer impact**: vault delta is **material** — 5 new vault commits + 1 new subfolder + 5 new single-shot LDR files + 4 of 5 papers brain organoid infectious-disease / reproducibility + 1 vascularized lung/gut (Miao companion to the 2026-08-08 Miao v2 deep-read). Synthesis routes into: (a) `/sources/git-repo.md` (this page) — refreshed frontmatter (vault HEAD `9d4767c7` → `391e4713` + tags bumped to include the 2026-08-31 cluster + timestamp `2026-08-31T18:09:00Z`) + Connector section refreshed (vault HEAD + wiki HEAD `d56da3a` → `9Line truncated
+
 - **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.

sources/hackernews.md

@@ -2,8 +2,8 @@
 type: "Reference"
 title: "Hacker News — evidence index"
 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."
-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]
-timestamp: 2026-08-30T18:00:39Z
+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]
+timestamp: 2026-08-31T18:00:32Z
 ---
 
 # Hacker News — evidence index
@@ -16,10 +16,26 @@ Compact evidence trail for the Hacker News connector (`hackernews-1`, Robin-cura
 - **Backend:** public HN feeds (`top`, `new`) + Algolia HN search queries
 - **Auth:** none — public feeds
 - **Window:** last 24 hours
-- **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.
+
+- **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.
+
+- **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**:
+
+  - **`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.
+
+  - **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.
 

sources/index.md

@@ -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.
 - [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.

sources/literature.md

@@ -2,7 +2,7 @@
 type: "Reference"
 title: "Literature Deep-Reads — cross-agent deep-read index"
 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]
 timestamp: 2026-08-27T18:25:00Z
 ---
 
@@ -14,6 +14,16 @@ timestamp: 2026-08-27T18:25:00Z
 
 ## Last 30 days of deep reads (mtime descending)
 
+### 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

sources/nocodb.md

@@ -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)

sources/ragflow.md

@@ -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

sources/seafile.md

@@ -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

sources/web-search.md

@@ -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`
 

sources/wikijs.md

@@ -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

themes.md

@@ -19,7 +19,7 @@ Index kept narrow by design: only themes that map to Robin's actual work (life-s
 | `MiniMax-m3` | MiniMax-M3 (1M context multimodal) HuggingFace model card + Twitter launch; the daily-driver inference provider behind every OpenWiki run and most of Robin's agent work; haimaker.ai July 2026 third-party eval ranks models for Hermes Agent usage; MyClaw.ai 2026-07-29 confirms M3 + M2.7 are the operational models for both OpenClaw and Hermes, with M3 supporting multimodal (image, video, music, speech, web search); pull 11 (2026-08-03) adds **unsloth/MiniMax-M3-GGUF** (HuggingFace 2026-08-01) confirming quantized local-LLM run path + **benchlm.ai "DeepSeek V4 Flash vs MiniMax M3: Benchmarks & Cost"** (2026-08-01) reframing M3 as "1M context window at $0.30…"; this 2026-08-03 HN pull surfaces the **MiniMax-H3 launch cluster** (item `49155629` 167pts top-feed ComfyUI Day-0 support with open weights + native audio + 2K video; item `49150583` 8pts "MiniMax-H3 weights are up" on HuggingFace model card; item `49150861` 2pts "Run MiniMax-H3 Locally with SGLang Diffusion on 2× RTX 5090s or 1× RTX Pro 6000" via LMSYS Twitter) — three distinct primary sources on the same day confirming H3 as the next frontier model release after M3 | 2026-07-16 | 2026-08-03 | source-backed | hackernews, web-search | 8+ | active | [HN: M3 model cluster + H3 launch cluster 2026-08-03](/sources/hackernews.md); [Tavily: Hermes Agent best-models eval](/sources/web-search.md); [Tavily: MyClaw OpenClaw vs MiniMax Agent 2026-07-29](/sources/web-search.md#2026-07-29-1803-pull); [Tavily: unsloth/MiniMax-M3-GGUF + BenchLM M3 vs DeepSeek V4 Flash 2026-08-03](/sources/web-search.md#2026-08-03-1808-pull) |
 | `hermes-agent-v0-19-quicksilver` | Hermes Agent v0.19 "Quicksilver" release (2026-07-25): first-token delay 4.3s → 0.9s, profile routing, live subagent, delivery ledger, 1Password/Bitwarden integration; relevant to Robin's daily-driver stack; MCP 2026-07-28 revision finalization (not backward-compatible) is a related protocol-layer signal; `configuration.md` (2026-07-26) documents the iteration-budget behavior change (April 2026: removed premature 70%/90% warnings, now single wrap-up at 500/500 with grace call) and `features/api-server.md` (2026-07-27) documents new `/v1/runs/{run_id}/stop` + `/approval` endpoints with MiniMax-M3 as the documented default model; pull 7 (2026-07-30) re-anchors `api-server.md` with a new per-profile `API_SERVER_KEY` breaking-change warning and a runs API for long-form sessions, and adds a third-party Hermes Atlas "State of Hermes Agent — July 2026" report; this 2026-08-03 HN pull surfaces **Hermes Agent v0.20.0** (item `49159200`, NousResearch GitHub releases tag `v2026.8.3`, 1pt on HN day-of — the next major version after v0.19 Quicksilver); pull 11 (2026-08-03) adds a **Hermes Agent 0.19.1 GitHub bug report** (NousResearch issues/77000, 2026-08-02, score 0.790, "gpt-5.6-luna + opencode-go") confirming patch-version activity on the v0.19.x track between the v0.19 Quicksilver release and the v0.20.0 release; Tavily answer text on the Hermes/M3 lane was partially fabricated ("release date of June 1, 2026") and should be ignored — the underlying GitHub issue URL is the credible signal | 2026-07-25 | 2026-08-03 | source-backed | hackernews, web-search | 10 | active | [Tavily: Hermes v0.19 Quicksilver + MCP revision 2026-07-27](/sources/web-search.md); [Tavily: hermes-agent configuration.md + api-server.md + MyClaw 2026-07-29](/sources/web-search.md#2026-07-29-1803-pull); [Tavily: api-server.md API_SERVER_KEY break + Hermes Atlas state report 2026-07-30](/sources/web-search.md#2026-07-30-1804-pull); [Tavily: Hermes Agent 0.19.1 GitHub bug report 2026-08-03](/sources/web-search.md#2026-08-03-1808-pull); [HN: Hermes Agent v0.20.0 release 2026-08-03](/sources/hackernews.md) |
 | `openwiki-brand` | `langchain-ai/openwiki` (96 pts) — same product family as Robin's OpenWiki; high-engagement on HN | 2026-07-16 | 2026-07-16 | source-backed | hackernews | 1 (+ 2 adjacent wrappers) | watchlist | [HN: openwiki cluster](/sources/hackernews.md#openwiki-brand-signal) |
-| `agent-memory-architecture` | Shared agent-memory architecture using Karpathy's LLM Wiki + Google's Open Knowledge Format (OKF) + MCP — let "every Local AI share ONE permanent memory"; this 2026-07-29 Tavily pull adds four more corroborated sources (Hackernoon Moorcheh.ai "Agent Memory Has a Lock-In Problem. Open Formats Are How We Fix It." with diffability / reviewability / auditability framing; Towards Data Science "Usage-Reinforced Decay Engine for AI Agent Memory" using Ebbinghaus forgetting curve; The Register / MinIO AIStor Memory for long-running multi-step workflows; HPCwire Exabase M-1 BEAM benchmark numbers 76.9% / 75.0% / 68.0% at 100K/1M/10M tokens) on top of the prior HN + Tavily sources; the Hackernoon piece is the strongest OpenWiki-aligning source yet; pull 7 (2026-07-30) adds arXiv 2607.24759v1 "A Templated Substrate for Heterogeneous Collaborative" + rohitg00 LLM Wiki v2 (extending Karpathy's LLM Wiki pattern with lessons from building agentmemory) + Pi `@zosmaai/pi-llm-wiki` package + MinIO AIStor Memory (HPCwire 2026-07-29 + SiliconANGLE 2026-07-30); pull 11 (2026-08-03) adds **akitaonrails/ai-memory `docs/research-karpathy-llm-wiki.md`** (GitHub 2026-07-28, score 0.601) — a third-party research write-up of the Karpathy LLM Wiki pattern — bringing the cluster to 15+ distinct sources; **2026-08-13 HN pull** adds item `49286073` "Show HN: MCP Memory – Fast Agent Memory Using Google's OKF and SQLite FTS5" (46 pts, 22 cmts, github.com/fellowgeek/mcp-memory) — **the first HN item since the 2026-07-16 `langchain-ai/openwiki` brand signal to explicitly name Google's OKF frontmatter** (the same schema OpenWiki uses at `/index.md` frontmatter `okf_version: "0.1"` and across every concept page's per-page frontmatter), paired with an MCP-server delivery channel that touches the 2026-07-28 MCP-protocol revision watchlist already feeding [`hermes-agent-v0-19-quicksilver`](/sources/hackernews.md) Evidence cell — direct corroboration of the OKF+memory schema pattern rather than a new theme | 2026-07-26 | 2026-08-13 | source-backed | hackernews, web-search | 16+ | active | [HN: 49059959, 49059889, 49060215](/sources/hackernews.md); [HN: MCP Memory using Google's OKF 2026-08-13](/sources/hackernews.md#agent-memory-architecture-refreshed-this-run); [Tavily: LLM Wiki + OKF cluster 2026-07-28](/sources/web-search.md); [Tavily: Moorcheh.ai + TDS + MinIO + Exabase cluster 2026-07-29](/sources/web-search.md#2026-07-29-1803-pull); [Tavily: arXiv 2607.24759v1 + LLM Wiki v2 + Pi pi-llm-wiki + MinIO AIStor 2026-07-30](/sources/web-search.md#2026-07-30-1804-pull); [Tavily: akitaonrails/ai-memory research write-up 2026-08-03](/sources/web-search.md#2026-08-03-1808-pull) |
+| `agent-memory-architecture` | Shared agent-memory architecture using Karpathy's LLM Wiki + Google's Open Knowledge Format (OKF) + MCP — let "every Local AI share ONE permanent memory"; this 2026-07-29 Tavily pull adds four more corroborated sources (Hackernoon Moorcheh.ai "Agent Memory Has a Lock-In Problem. Open Formats Are How We Fix It." with diffability / reviewability / auditability framing; Towards Data Science "Usage-Reinforced Decay Engine for AI Agent Memory" using Ebbinghaus forgetting curve; The Register / MinIO AIStor Memory for long-running multi-step workflows; HPCwire Exabase M-1 BEAM benchmark numbers 76.9% / 75.0% / 68.0% at 100K/1M/10M tokens) on top of the prior HN + Tavily sources; the Hackernoon piece is the strongest OpenWiki-aligning source yet; pull 7 (2026-07-30) adds arXiv 2607.24759v1 "A Templated Substrate for Heterogeneous Collaborative" + rohitg00 LLM Wiki v2 (extending Karpathy's LLM Wiki pattern with lessons from building agentmemory) + Pi `@zosmaai/pi-llm-wiki` package + MinIO AIStor Memory (HPCwire 2026-07-29 + SiliconANGLE 2026-07-30); pull 11 (2026-08-03) adds **akitaonrails/ai-memory `docs/research-karpathy-llm-wiki.md`** (GitHub 2026-07-28, score 0.601) — a third-party research write-up of the Karpathy LLM Wiki pattern — bringing the cluster to 15+ distinct sources; **2026-08-13 HN pull** adds item `49286073` "Show HN: MCP Memory – Fast Agent Memory Using Google's OKF and SQLite FTS5" (46 pts, 22 cmts, github.com/fellowgeek/mcp-memory) — **the first HN item since the 2026-07-16 `langchain-ai/openwiki` brand signal to explicitly name Google's OKF frontmatter** (the same schema OpenWiki uses at `/index.md` frontmatter `okf_version: "0.1"` and across every concept page's per-page frontmatter), paired with an MCP-server delivery channel that touches the 2026-07-28 MCP-protocol revision watchlist already feeding [`hermes-agent-v0-19-quicksilver`](/sources/hackernews.md) Evidence cell — direct corroboration of the OKF+memory schema pattern rather than a new theme; **2026-08-31 HN pull** adds item `49511007` "Launch HN: Almanac (YC S26) – AI that knows your company" (21 pts top+best + 22 cmts, https://usealmanac.com/ — YC S26 launch) — **first shipped-product evidence of the wikis-as-agent-memory-substrate pattern** (every prior source on the row is either a substrate-pattern essay, an open-source library, a research write-up, or a benchmark; Almanac is the first YC S26 launch that operationalizes the pattern as a hosted product with personal + company wikis + cross-source connectors (Gmail, Calendar, Granola, PostHog) + pre-compiled knowledge layer + long-horizon task tracking + proactive background-worker agents — the same architectural pattern as OpenWiki's 7-connector cron pipeline + OKF frontmatter + `/commitments.md` long-horizon tracking + `~/.openwiki/wiki` local markdown substrate); surfaced via Algolia `organoid` + `3Brain` substring-noise duplicate (the word "brain" appears 4+ times in the launch text). Refresh anchor: 2026-08-13 → 2026-08-31; Evidence count 16+ → 17+; row confidence stays `source-backed` (the row was already corroborated by 16+ sources before the Almanac refresh; the new refresh adds shipped-product evidence without changing the row's structural framing) | 2026-07-26 | 2026-08-31 | source-backed | hackernews, web-search | 17+ | active | [HN: 49059959, 49059889, 49060215](/sources/hackernews.md); [HN: MCP Memory using Google's OKF 2026-08-13](/sources/hackernews.md#agent-memory-architecture-refreshed-this-run); [HN: Almanac (YC S26) – AI that knows your company 2026-08-31](/sources/hackernews.md#latest-update--2026-08-31-1800-utc); [Tavily: LLM Wiki + OKF cluster 2026-07-28](/sources/web-search.md); [Tavily: Moorcheh.ai + TDS + MinIO + Exabase cluster 2026-07-29](/sources/web-search.md#2026-07-29-1803-pull); [Tavily: arXiv 2607.24759v1 + LLM Wiki v2 + Pi pi-llm-wiki + MinIO AIStor 2026-07-30](/sources/web-search.md#2026-07-30-1804-pull); [Tavily: akitaonrails/ai-memory research write-up 2026-08-03](/sources/web-search.md#2026-08-03-1808-pull) |
 
 ## Notes
 

themes/03-ai-agents.md

@@ -117,7 +117,8 @@ The architecture shows three agent surfaces sharing the OpenWiki memory substrat
 
 ## Adjacent workflow signals (HN / Tavily)
 
-- **`agent-memory-architecture` theme row** on [`/themes.md`](/themes.md) — clusters Karpathy LLM Wiki + Google OKF + MCP + verginglabs.com "A Markdown wiki outscored every AI agent memory product we benchmarked" (HN `49156055`, 2 pts, watchlist). 15+ distinct sources on the shared-agent-memory pattern. OpenWiki aligns with this lane (Open Knowledge Format front-matter is the structural backbone).
+- **`agent-memory-architecture` theme row** on [`/themes.md`](/themes.md) — clusters Karpathy LLM Wiki + Google OKF + MCP + verginglabs.com "A Markdown wiki outscored every AI agent memory product we benchmarked" (HN `49156055`, 2 pts, watchlist). 17+ distinct sources on the shared-agent-memory pattern. OpenWiki aligns with this lane (Open Knowledge Format front-matter is the structural backbone).
+- **`Almanac (YC S26) – AI that knows your company`** — Launch HN `49511007` 2026-08-31 (21 pts + 22 cmts, https://usealmanac.com/). **First shipped-product evidence on the `agent-memory-architecture` row**: builds personal + company wikis as the agent's primary memory substrate, pulls from Gmail / Calendar / Granola / PostHog, runs a pre-compiled knowledge layer, tracks long-horizon tasks in an "ongoing projects" section, and activates proactive background workers. Founders are IIT-EE + Harvard grads (Kushagra / Rohan / Divit); the Harvard capstone thesis became the pre-compilation layer. Architecturally parallel to OpenWiki (local markdown wiki + 7-connector cron pipeline + `/commitments.md` long-horizon tracking + OKF frontmatter), but as a hosted SaaS product rather than a local-first knowledge base. Surfaced via the 2026-08-31 Algolia `organoid` + `3Brain` substring-noise duplicate. Promoted: `agent-memory-architecture` row Last seen 2026-08-13 → 2026-08-31; Evidence count 16+ → 17+. **Not on Robin's named stack** — Almanac is a hosted SaaS competitor to OpenWiki, not a tool Robin uses. Track as a competitive-parallel signal; do not adopt unless the cross-source connector model proves compelling.
 - **Tavily / Hermes / MiniMax-M3 lane** — Tavily answer text on this lane is **partially fabricated** (e.g. Tavily claimed a "release date of June 1, 2026" for Hermes v0.19 Quicksilver; the actual release is 2026-07-25 per Nous Research). Trust underlying URLs + GitHub release tags; ignore Tavily answer text.
 
 ## Cross-cutting relationships

themes/05-robin-research.md

@@ -1,8 +1,8 @@
 ---
 type: "Reference"
 title: "Theme 5 · Robin's personal research (vendor deep reads + sales ammunition + CRM)"
-description: "Synthesis page for Robin's personal research portfolio — Obsidian vault + literature deep-read pipeline + sales ammunition + China distributor map + active CRM profiles + work-rhythm snapshots. Output routes into vendor themes 01 (organoid-equipment) and 02 (bioprinting). The 2026-08-23/24 fetch surfaced the largest single-day LDR burst since 2026-07-29 — 5 papers committed to main + new `deepread_40240593/` pipeline workspace directory. The 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + 2026-08-30 fetches observed vault HEAD unchanged at `9d4767c7` (vault silent for the 1st + 2nd + 3rd + 4th + 5th consecutive fetches since the 2026-08-24/25 SECOND 5-paper LDR burst, **5 calendar days stale**) with the 4 carry-forward untracked directories (Review + templates + celvivo_commercial + deepread_40240593) bumping their carry-forward counts to 19/14/14/7 days — the `Review/` + `templates/` + `celvivo_commercial/` entries are **confirmed one-off** at the 2026-08-28 fetch (carrying forward unchanged at 2026-08-29 + 2026-08-30) and all 3 entries should be demoted to stale / not recurring carry-forward notes on the next synthesis pass."
-tags: [theme, research, vault, deep-read, sales, crm, life-sciences, 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, celvivo-app-note-2026, aiello-bagni-rc-cfd, tian-epicardium-mtor, kim-egain-3d-mea, ajongbolo-brain-organoid-review, tevonian-2026-vascularized-liver-mps, yang-2026-cardiac-organoid-review, shen-2026-vascularized-organoids-review, zhai-2026-3d-skin-pemphigus, vascularized-organoids, cardiac-organoids, skin-organoids, vault-silent-5d, sixteenth-sources-sync, review-templates-celvivo-commercial-confirmed-one-off, deepread-40240593-six-silent-fetches]
+description: "Synthesis page for Robin's personal research portfolio — Obsidian vault + literature deep-read pipeline + sales ammunition + China distributor map + active CRM profiles + work-rhythm snapshots. Output routes into vendor themes 01 (organoid-equipment) and 02 (bioprinting). The 2026-08-23/24 fetch surfaced the largest single-day LDR burst since 2026-07-29 — 5 papers committed to main + new `deepread_40240593/` pipeline workspace directory. The 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + 2026-08-30 fetches observed vault HEAD unchanged at `9d4767c7` (vault silent for the 1st + 2nd + 3rd + 4th + 5th consecutive fetches since the 2026-08-24/25 SECOND 5-paper LDR burst, 5 calendar days stale). The 2026-08-31 fetch observed vault HEAD bumped `9d4767c7` → `391e4713` — **THIRD consecutive single-day 5-paper LDR burst** (Stewart + Aiello + Nguyen + Miao + Yan, all CelVivo-anchored, all in the NEW `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` capital-V subfolder — Robin's first parallel-naming deep-read subfolder convention), ending the 5-day vault silence; combined with the 2026-08-23/24 + 2026-08-24/25 clusters, **15 LDR files in 8 calendar days = the largest sustained 8-day research output** in Robin's vault activity log. The 4 carry-forward untracked directories (Review + templates + celvivo_commercial + deepread_40240593) bump their carry-forward counts to 20/15/15/8 days — the `Review/` + `templates/` + `celvivo_commercial/` entries are **confirmed one-off** at the 2026-08-28 fetch (carrying forward unchanged at 2026-08-29 + 2026-08-30 + 2026-08-31) and all 3 entries should be demoted to stale / not recurring carry-forward notes on the next synthesis pass."
+tags: [theme, research, vault, deep-read, sales, crm, life-sciences, 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, celvivo-app-note-2026, aiello-bagni-rc-cfd, tian-epicardium-mtor, kim-egain-3d-mea, ajongbolo-brain-organoid-review, 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, brain-organoid-virology-cluster, celvivo-clinoreactor-cluster, vascularized-organoids, cardiac-organoids, skin-organoids, celvivo-capital-v-parallel-subfolder, vault-silence-ended, third-5paper-cluster, seventeenth-sources-sync, review-templates-celvivo-commercial-confirmed-one-off, deepread-40240593-seven-silent-fetches]
 timestamp: 2026-08-30T18:06:00Z
 ---
 
@@ -51,19 +51,19 @@ The diagram shows Robin's research substrate: a single Obsidian vault with 8 buc
 
 ## Knowledge substrate: Obsidian vault
 
-Snapshot from [`/sources/git-repo.md`](/sources/git-repo.md) (last fetch 2026-08-30T18:06:00Z):
+Snapshot from [`/sources/git-repo.md`](/sources/git-repo.md) (last fetch 2026-08-31T18:09:00Z):
 
 | Field | Value |
 | --- | --- |
 | Repo path | `/home/ldw/workspace` |
 | Branch | `main` |
-| HEAD | `9d4767c7034a59d8f3206756c2dfeb3f4339c2e0` (**unchanged** at the 2026-08-30T18:06Z fetch — **0 new vault commits** for the 5th consecutive fetch since the 2026-08-25T18:13Z fetch; the 2026-08-25 SECOND 5-paper LDR burst remains the most recent committed vault activity, 5 calendar days stale; combined with the 2026-08-23/24 burst, **10 LDR files in 48 hours** remains the largest sustained 2-day research output in Robin's vault activity log) |
-| 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; total remains 30 since 2026-08-03) |
+| HEAD | `391e47131679ce9edf0f525236e78ebb13e0d232` (vault HEAD bumped from `9d4767c7` at the 2026-08-30T18:06Z fetch — **5 new vault commits** at the 2026-08-31T18:09Z fetch, ending the **5-calendar-day vault silence streak** since the 2026-08-24/25 SECOND 5-paper burst; **THIRD consecutive single-day 5-paper LDR burst** at 2026-08-31, all CelVivo-anchored; combined with the 2026-08-23/24 + 2026-08-24/25 clusters, **15 LDR files in 8 calendar days** = the largest sustained 8-day research output in Robin's vault activity log; all 3 clusters are CelVivo-anchored) |
+| Ahead of origin/main | 35 commits new since 2026-08-03 fetch (+5 from the prior 30-commit baseline at the 2026-08-30T18:06Z fetch; +5 total since 2026-08-03) |
 | Auth | local path only — no remote, no credentials |
-| Working-tree state | dirty (23 untracked files + 4 untracked directories — `celvivo_commercial/1331651_20260630_131201.pdf` + `templates/类器官IRB申请清单.md` + `deepread_40240593/` (7 subdirs, **7-day carry-forward** at 2026-08-30, was 6-day at 2026-08-29, **6 consecutive silent fetches** since the 2026-08-24/25 burst — working-folder pipeline hypothesis continuing to weaken) + `Review/zhou2023_computer_vision_microfluidics.md` (**19-day carry-forward** at the 2026-08-30T18:06Z fetch, **17 fetches silent**, **one-off interpretation confirmed at 2026-08-28 fetch** per the 2026-08-27 fetch confirmation, carrying forward unchanged at the 2026-08-29 + 2026-08-30 fetches; the `celvivo_commercial/` + `templates/` entries are also **confirmed one-off alongside the `Review/` entry** at the 2026-08-28 fetch, both at **14-day carry-forward** + **13 fetches silent** at the 2026-08-30 fetch; all 3 entries should be **demoted to "stale / not recurring" carry-forward notes** on the next synthesis pass)) |
-| Raw manifest | `~/.openwiki/connectors/git-repo/raw/2026-08-30T18-06-24-410Z/manifest.json` |
-| **Latest cluster (2026-08-24/25, replacing the 2026-08-23/24 root-level burst)** | **5-paper LDR burst** (`089177a7` Tevonian 2026 Nat Commun 血管化肝 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 — **FIRST post-publish vendor-mapping retrofit commit in Robin's LDR pipeline**) → `5907cdfc` Shen 2026 Chin Med J vascularized organoids review → `9d4767c7` Zhai 2026 Sci Adv 3D skin pemphigus) — all 5 files landed in **per-application-domain subfolders** (Tevonian + Shen → `Vascularized-Organoids/` + Yang → `Cardiac-Organoids/` + Zhai → `Skin-Organoids/`) returning to the standard subfolder discipline after the 2026-08-23/24 root-level non-standard pattern; the cluster creates **3 NEW `04-Literature/Deep-Reads/` subfolders**; all 5 single-shot entries plus 1 in-place `M` retrofit commit. Vendor mapping: 4 of 5 papers vendor-anchored to 5-vendor mapping (CelVivo / Cellink / Mimetas / 3Brain / FemtoBiomed) applied retroactively via `9aa2af4c`; the 2026-08-24/25 cluster was the **SECOND consecutive single-day 5-paper LDR burst** — combined with the 2026-08-23/24 burst, **10 LDR files in 48 hours** |
-| **Latest uncommitted artifacts (2026-08-13 → 2026-08-30, multi-file, unchanged across the 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + 2026-08-30 fetches)** | `04-Literature/Deep-Reads/Review/zhou2023_computer_vision_microfluidics.md` (carry-forward untracked from 2026-08-13, now at **19-day carry-forward** at the 2026-08-30 fetch — file mtime `2026-08-11 16:31:54 +0800` so mtime-based carry-forward is 19 days; first-observation-date-based carry-forward is 17 days; **structural signal confirmed as one-off** per `/sources/git-repo.md` Notable-entity entry — 17 consecutive fetches silent on the file; the entry should be demoted to a stale / not recurring carry-forward note on the next synthesis pass) + **2 prior untracked directories added at the 2026-08-17 fetch**, still-uncommitted at the 2026-08-30 fetch (**14-day carry-forward** each — was 13-day at the 2026-08-29 fetch, 12-day at the 2026-08-28 fetch, 11-day at the 2026-08-27 fetch, 10-day at the 2026-08-26 fetch): `celvivo_commercial/1331651_20260630_131201.pdf` (6-30 quote PDF migrated into new folder; **confirmed one-off at 2026-08-28 fetch** carrying forward unchanged at 2026-08-29 + 2026-08-30) + `templates/类器官IRB申请清单.md` (180-line IRB application checklist derived from Guo 2026; Robin's first customer-facing template produced from a single deep-read — see the new Templates subtree below; **confirmed one-off at 2026-08-28 fetch** carrying forward unchanged at 2026-08-29 + 2026-08-30) + **1 new untracked directory added at the 2026-08-24 fetch** — `deepread_40240593/` (7 subdirs: 5 PMID-named `deepread_<PMID>/` + 2 slug-named `deepread_brain_organoid_fluid/` + `deepread_shear_stress_cs_os/` that exactly map to the Aiello + CelVivo App Note papers; the new directory is Robin's LDR pipeline intermediate-artifact workspace, see `/sources/git-repo.md` Notable-entity § "deepread_40240593/ pipeline workspace"; **7-day carry-forward** at 2026-08-30, directory mtime unchanged since 2026-08-24 16:31 +0800, the working-folder pipeline hypothesis continues to weaken — the absence of mtime movement across the 2026-08-25 + 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + 2026-08-30 fetches (6 consecutive silent fetches) suggests the pipeline may have been abandoned, formalized differently, or batched without intermediate commit) |
+| Working-tree state | dirty (28 untracked files + 4 untracked directories — `celvivo_commercial/1331651_20260630_131201.pdf` + `templates/类器官IRB申请清单.md` + `deepread_40240593/` (7 subdirs, **8-day carry-forward** at 2026-08-31, was 7-day at 2026-08-30, **7 consecutive silent fetches** since the 2026-08-24/25 burst — working-folder pipeline hypothesis continuing to weaken; the 2026-08-31 burst did NOT route through `deepread_<slug>/` working folders, the directory mtime is still 2026-08-24 16:31 +0800 — **8 fetches silent on directory mtime**) + `Review/zhou2023_computer_vision_microfluidics.md` (**20-day carry-forward** at the 2026-08-31T18:09Z fetch, **18 fetches silent**, **one-off interpretation confirmed at 2026-08-28 fetch** per the 2026-08-27 fetch confirmation, carrying forward unchanged at the 2026-08-29 + 2026-08-30 + 2026-08-31 fetches; the `celvivo_commercial/` + `templates/` entries are also **confirmed one-off alongside the `Review/` entry** at the 2026-08-28 fetch, both at **15-day carry-forward** + **14 fetches silent** at the 2026-08-31 fetch; all 3 entries should be **demoted to "stale / not recurring" carry-forward notes** on the next synthesis pass)) |
+| Raw manifest | `~/.openwiki/connectors/git-repo/raw/2026-08-31T18-09-??-???Z/manifest.json` |
+| **Latest cluster (2026-08-31, replacing the 2026-08-24/25 cluster)** | **THIRD consecutive single-day 5-paper LDR burst** (`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 co-author affiliation) → `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) — **all 5 files landed in the NEW `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` subfolder (capital-V, parallel to the existing lowercase `04-Literature/Deep-Reads/Celvivo/` 142-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); 4 of 5 are brain organoids + 1 is vascularized lung/gut (Miao companion to the 2026-08-08 Miao 2025 v2 deep-read); the cluster did NOT receive the `9aa2af4c` vendor-mapping retrofit commit (no companion retrofit commit this cluster); **net-new external evidence** in this run; subfolder taxonomy from ~22 → ~23 in 8 calendar days. Combined with the 2026-08-23/24 + 2026-08-24/25 bursts = **15 LDR files in 8 calendar days** |
+| **Latest uncommitted artifacts (2026-08-13 → 2026-08-31, multi-file, unchanged across the 2026-08-26 → 2026-08-31 fetches)** | `04-Literature/Deep-Reads/Review/zhou2023_computer_vision_microfluidics.md` (carry-forward untracked from 2026-08-13, now at **20-day carry-forward** at the 2026-08-31 fetch — file mtime `2026-08-11 16:31:54 +0800` so mtime-based carry-forward is 20 days; first-observation-date-based carry-forward is 18 days; **structural signal confirmed as one-off** per `/sources/git-repo.md` Notable-entity entry — 18 consecutive fetches silent on the file; the entry should be demoted to a stale / not recurring carry-forward note on the next synthesis pass) + **2 prior untracked directories added at the 2026-08-17 fetch**, still-uncommitted at the 2026-08-31 fetch (**15-day carry-forward** each — was 14-day at the 2026-08-30 fetch, 13-day at the 2026-08-29 fetch, 12-day at the 2026-08-28 fetch, 11-day at the 2026-08-27 fetch, 10-day at the 2026-08-26 fetch): `celvivo_commercial/1331651_20260630_131201.pdf` (6-30 quote PDF migrated into new folder; **confirmed one-off at 2026-08-28 fetch** carrying forward unchanged at 2026-08-29 + 2026-08-30 + 2026-08-31) + `templates/类器官IRB申请清单.md` (180-line IRB application checklist derived from Guo 2026; Robin's first customer-facing template produced from a single deep-read — see the new Templates subtree below; **confirmed one-off at 2026-08-28 fetch** carrying forward unchanged at 2026-08-29 + 2026-08-30 + 2026-08-31) + **1 new untracked directory added at the 2026-08-24 fetch** — `deepread_40240593/` (7 subdirs: 5 PMID-named `deepread_<PMID>/` + 2 slug-named `deepread_brain_organoid_fluid/` + `deepread_shear_stress_cs_os/` that exactly map to the Aiello + CelVivo App Note papers; the new directory is Robin's LDR pipeline intermediate-artifact workspace, see `/sources/git-repo.md` Notable-entity § "deepread_40240593/ pipeline workspace"; **8-day carry-forward** at 2026-08-31, directory mtime unchanged since 2026-08-24 16:31 +0800, the working-folder pipeline hypothesis continues to weaken — the absence of mtime movement across the 2026-08-25 + 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + 2026-08-30 + **2026-08-31** fetches (7 consecutive silent fetches, plus the 2026-08-31 burst did NOT route through `deepread_<slug>/` working folders, **8 fetches silent on directory mtime**) suggests the pipeline may have been abandoned, formalized differently, or batched without intermediate commit) |
 
 ### Vault navigation index (top-level folders)
 
@@ -102,6 +102,7 @@ Snapshot from [`/sources/git-repo.md`](/sources/git-repo.md) (last fetch 2026-08
 | `Vascularized-Organoids/` | 2 (NEW 2026-08-25 subfolder — Tevonian + Shen vascularized liver MPS / organoid review) | vascularized organoid (Tevonian primary + Shen review) |
 | `Cardiac-Organoids/` | 1 (NEW 2026-08-25 subfolder — Yang cardiac organoid review) | cardiac organoid |
 | `Skin-Organoids/` | 1 (NEW 2026-08-25 subfolder — Zhai 3D skin pemphigus) | autoimmune dermatology + 3D skin (net-new application domain) |
+| `CelVivo/` (capital-V, parallel to lowercase `Celvivo/`) | 5 (NEW 2026-08-31 subfolder — `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 organoids** for viral-neurotropism modeling (QIMR Berghofer Suhrbier/Rawle research line) + **1 is vascularized lung/gut** (Miao); Robin's first parallel-naming deep-read subfolder convention; subfolder sits at `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` parallel to lowercase `04-Literature/Deep-Reads/Celvivo/`; first LDR cluster **exclusively CelVivo-anchored** since the 2026-08-23/24 + 2026-08-24/25 clusters were partially vendor-distributed) | CelVivo ClinoStar / ClinoReactor brain organoid infectious-disease + reproducibility |
 | `Brain/` | 11 | brain organoid focus |
 | `Brain-Tumor/` | 9 | brain tumor organoid |
 | `Cancer/` | 6 | cancer organoid |
@@ -118,7 +119,7 @@ Snapshot from [`/sources/git-repo.md`](/sources/git-repo.md) (last fetch 2026-08
 | `Templates/` | 1 | `类器官IRB申请清单.md` v1.0 (2026-08-16, derived from Guo 2026 ethics deep-read, **untracked**; first customer-facing template produced from a single deep-read; **5-day carry-forward** at 2026-08-21 fetch — was 4-day at 2026-08-20; **6-day carry-forward** at 2026-08-22 fetch; **7-day carry-forward** at 2026-08-23 fetch; **8-day carry-forward** at 2026-08-24 fetch; **9-day carry-forward** at 2026-08-25 fetch; **10-day carry-forward** at 2026-08-26 fetch; **11-day carry-forward** at 2026-08-27 fetch — **approaching confirmed one-off interpretation alongside the `Review/` entry**; **12-day carry-forward** at 2026-08-28 fetch — **11 fetches silent** — **now confirmed one-off alongside the `Review/` + `CelVivo-commercial/` entries** at the 2026-08-28 fetch; **13-day carry-forward** at 2026-08-29 fetch — **12 fetches silent** — carries forward unchanged at the 2026-08-29 fetch, the 2026-08-28 confirmation still standing; **14-day carry-forward** at 2026-08-30 fetch — **13 fetches silent** — carries forward unchanged at the 2026-08-30 fetch, the 2026-08-28 confirmation still standing; entry should be demoted to a stale carry-forward note on the next synthesis pass) |
 | `CelVivo-commercial/` | 1 | `1331651_20260630_131201.pdf` (2026-06-30 quote PDF migrated into new folder 2026-08-17, **untracked**; **5-day carry-forward** at 2026-08-21 fetch — was 4-day at 2026-08-20; **6-day carry-forward** at 2026-08-22 fetch; **7-day carry-forward** at 2026-08-23 fetch; **8-day carry-forward** at 2026-08-24 fetch; **9-day carry-forward** at 2026-08-25 fetch; **10-day carry-forward** at 2026-08-26 fetch; **11-day carry-forward** at 2026-08-27 fetch — **approaching confirmed one-off interpretation alongside the `Review/` + `Templates/` entries**; **12-day carry-forward** at 2026-08-28 fetch — **11 fetches silent** — **now confirmed one-off alongside the `Review/` + `Templates/` entries** at the 2026-08-28 fetch; **13-day carry-forward** at 2026-08-29 fetch — **12 fetches silent** — carries forward unchanged at the 2026-08-29 fetch, the 2026-08-28 confirmation still standing; **14-day carry-forward** at 2026-08-30 fetch — **13 fetches silent** — carries forward unchanged at the 2026-08-30 fetch, the 2026-08-28 confirmation still standing; entry should be demoted to a stale carry-forward note on the next synthesis pass) |
 
-Total ≈ 1,206 deep-read notes on `main` + **1 untracked entry in the new `Review/` subfolder** (`zhou2023_computer_vision_microfluidics.md`, 2026-08-13 — first review-type subfolder; future-commit candidate) + **2 new untracked directories** (`templates/类器官IRB申请清单.md` + `celvivo_commercial/1331651_20260630_131201.pdf`, 2026-08-17). The 4 vendor subfolders (Celvivo / 3Brain / Cellink / Organoid) cover the canonical product KB per the wiki goal focus areas. 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.
+Total ≈ 1,211 deep-read notes on `main` (+5 new LDR files from the 2026-08-31 CelVivo-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). The 4 vendor subfolders (Celvivo / 3Brain / Cellink / Organoid) cover the canonical product KB per the wiki goal focus areas. 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. The 2026-08-31 cluster creates the **NEW `CelVivo/` (capital-V) parallel subfolder** — Robin's first parallel-naming deep-read subfolder convention.
 
 ## Literature deep-read (LDR) pipeline
 
@@ -198,6 +199,7 @@ From [`/sources/literature.md`](/sources/literature.md) last sync, broken out by
 | --- | --- | --- | --- |
 | 2026-08-16 | **Quintard 2024 Nat Commun + Guo 2026 Front Cell Dev Biol 7-commit LDR cluster** (commits `0fc8db24` + `290e9635` + `24c713de` + `4073abf4` Quintard + `2e6f5989` + `00f824f2` + `a4fa5a32` Guo) | **CelVivo adjacent + Mimetas OrganoPlate ⭐⭐⭐⭐ + Emulate Organ-Chip ⭐⭐⭐** (Quintard) / **CelVivo ClinoStar ⭐⭐⭐⭐ + Mimetas OrganoPlate ⭐⭐⭐⭐ + Emulate Organ-Chip ⭐⭐⭐** (Guo) | Quintard C et al. (2024) A microfluidic platform integrating functional vascularized organoids-on-chip (Nat Commun DOI 10.1038/s41467-024-45710-4, Wiki ID 1719/1720/1722, NocoDB Id 3297; 10 通道并行微流控 + hiPSC-BVO 30 天功能性灌注培养 + 跨类器官验证 [间充质球体 / BVO / 胰岛球体 / 肺类器官]; 血管层级化 37 µm 上游动脉-静脉 + 8 µm BVO 毛细管, 壁剪切 27-2000 s⁻¹, 完美匹配人体毛细血管生理范围 50-1900 s⁻¹) + Guo Z & Zhang N (2026) Ethical review key considerations for organoid applications in biomedical research—a systematic review (Front Cell Dev Biol DOI 10.3389/fcell.2026.1721946, Wiki ID 1724, NocoDB Id 3298; 嘉兴市第一医院 + 嘉兴大学医学院视角; 类器官研究 IRB / 伦理审查 7 大强制要点系统综述 [样本来源/知情同意/数据隐私/共培养主体性/3R 动物福利/跨境监管/长期保存与终止使用] + 中国《人类遗传资源管理条例》+ 国际 ISSCR/GDPR/HIPAA 多国对照表). **Robin translated Guo 2026 into a customer-facing IRB application checklist template** (`templates/类器官IRB申请清单.md` v1.0 180 lines) — first customer-facing template produced from a single deep-read. |
 | 2026-08-25 | **SECOND consecutive single-day 5-paper LDR burst** (commits `089177a7` Tevonian + `583859a8` Yang + `9aa2af4c` vendor-mapping retrofit + `5907cdfc` Shen + `9d4767c7` Zhai) | **5-vendor product mapping retrofit on Tevonian + Yang** (CelVivo ClinoStar/ClinoReactor + Cellink BIO X + Mimetas OrganoPlate + 3Brain HD-MEA + FemtoBiomed CellShot) | **Tevonian 2026 Nat Commun vascularized liver MPS** (PMID 41634021, Wiki.js 1749; PDMS+fibrin+原代肝+HUVEC vascularized liver MPS, 14天 IR modeling, 单核细胞 infiltration enhancement; **first file in new Vascularized-Organoids/ subfolder**) + **Yang 2026 Stem Cell Res Ther cardiac organoid review** (PMID 41963991, Wiki.js 1750; 复旦 + InnoStar comprehensive review of hPSC cardiac organoid generation methods (FGF/PI3K/Wnt/BMP/Activin/RA 五大信号通路) + maturation protocols + disease modeling + regenerative medicine; **first file in new Cardiac-Organoids/ subfolder** — first new subfolder explicitly for an application-domain cluster) + **post-publish vendor-mapping retrofit commit `9aa2af4c`** on Tevonian + Yang (adds 5-vendor mapping table + 净化 Robin mentions; **first post-publish vendor-mapping retrofit step in Robin's LDR pipeline**, iterates the 8-step SOP to a 9-step SOP) + **Shen 2026 Chin Med J vascularized organoids review** (PMID 42268296, Wiki.js 1751; 华西医院 Chinese-language peer-reviewed systematic review of vascularized organoids 4 大策略 (共培养 + 转录因子诱导 + 微流控 + 生物材料支架) + 12 维对比 + 三大未来方向; second file in Vascularized-Organoids/ subfolder) + **Zhai 2026 Sci Adv 3D skin pemphigus** (PMID 41512055, Wiki.js 1752; 3D 打印 + 自组织 multilayer vascularized skin model for 天疱疮 autoimmune disease modeling + EGFR-targeted therapy + ML-assisted drug screening; **first file in new Skin-Organoids/ subfolder** — **net-new application domain** autoimmune dermatology + 3D skin). **3 NEW `04-Literature/Deep-Reads/` subfolders** created in a single day: `Vascularized-Organoids/` + `Cardiac-Organoids/` + `Skin-Organoids/` (Robin expands the deep-read folder taxonomy from ~19 → ~22, returning to per-vendor / per-application-domain subfolder discipline after the 2026-08-23/24 root-level non-standard pattern). **Combined with the 2026-08-23/24 5-paper burst = 10 LDR files in 48 hours = the largest sustained 2-day research output** in Robin's vault activity log. |
+| 2026-08-31 | **THIRD consecutive single-day 5-paper LDR burst** (commits `eb24ab72` Stewart + `030f31ed` Aiello + `fad7e21e` Nguyen + `4fca0123` Miao + `391e4713` Yan) — **all 5 exclusively CelVivo-anchored** (QIMR Berghofer Suhrbier/Rawle viral-neurotropism line + CelVivo ApS co-authored reproducibility + vascularized lung/gut) | **CelVivo ClinoStar / ClinoReactor** (direct platform validation across 4 brain organoid infectious-disease papers + 1 vascularized lung/gut paper; 1 paper — Aiello 2025 — has CelVivo ApS as a co-author affiliation, validating the ClinoStar/ClinoReactor platform as a reproducibility-benchmarking standard) | **Stewart 2023 Front Microbiol SARS-CoV-2 omicron BA.5/XBB neurotropic brain organoids** (DOI 10.3389/fmicb.2023.1320856; QIMR Berghofer Medical Research Institute + University of Queensland; K18-hACE2 mice + human brain organoids; MA1 infection cell count higher; **first file in new `CelVivo/` capital-V subfolder**) + **Aiello 2025 EMBO reports reproducible brain organoids** (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) co-author**; controlled fluid dynamics brain organoid reproducibility; CV <15% multi-batch + multi-cell-line) + **Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids** (DOI 10.1038/s44298-024-00025-5; QIMR Berghofer + INRAE; JEV genotype 4 isolate characterization) + **Miao 2025 Cell vascularized lung/gut organoids** (DOI 10.1016/j.cell.2025.05.041; co-differentiation mesoderm+endoderm for organotypic vascularization; **companion to the 2026-08-08 flywheel-sync Miao 2025 v2 deep-read**) + **Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids** (DOI 10.1016/j.celrep.2024.114921; QIMR Berghofer; CRISPR 筛选鉴定 TMEM106B/硫酸乙酰肝素/内吞介导 ACE2 非依赖进入; 人源皮层脑类器官 CelVivo ClinoStar; MA1 神经毒力更强 in vitro but in vivo not consistent). **5 papers all single-shot LDR entries** (no v2/v3 SOP rewrite cycles this cluster); cluster does **NOT receive the `9aa2af4c` post-publish vendor-mapping retrofit commit** (no companion retrofit this cluster, unlike the 2026-08-24/25 cluster which had `9aa2af4c` as the 3rd of 5 commits). **1 NEW `04-Literature/Deep-Reads/` subfolder created**: `CelVivo/` (capital-V, parallel to existing lowercase `Celvivo/` subfolder) at `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` — **Robin's first parallel-naming deep-read subfolder convention** (subfolder taxonomy from ~22 → ~23 in 8 calendar days). **Combined with 2026-08-23/24 + 2026-08-24/25 = 15 LDR files in 8 calendar days = the largest sustained 8-day research output** in Robin's vault activity log. Ends the 5-day vault silence streak from the 2026-08-24/25 burst. |
 | 2026-08-24 | **First 5-paper LDR burst in 24-hour window** (commits `ad4abcde` Ajongbolo + `5f02489a` Kim + `40b357b8` Tian + `f2118a62` Aiello + `fb017e4f` CelVivo App Note) | **CelVivo-aligned (3) + 3Brain-adjacent (1) + cardiac-epicardium (1)** | Ajongbolo 2025 Cells brain organoid review (PMID DOI 10.3390/cells14110842, Wiki.js 1743; canonical brain organoid + assembloid review with 3-tier taxonomy + 4-class characterization methodology) + Kim 2025 Nat Commun EGaIn liquid-metal 3D MEA (DOI 10.1038/s41467-024-55752-3, Wiki.js 1744; 25-310 µm pillar height, 14 µm diameter, magnetically reshapeable; 3Brain HD-MEA adjacent) + Tian 2025 Nat Commun hiPSC epicardium mTOR maturation (DOI 10.1038/s41467-025-60934-8, Wiki.js 1745; Torin1 dual mTORC1/2 inhibition drives mature epicardium via YBX3/MAFF TFs) + Aiello & Bagni 2025 biorxiv Rotating Chamber brain organoid CFD (Wiki.js 1746; COMSOL CFD < 20 mPa cavity shear stress, cross-organoid-line morphological CV < 15%) + CelVivo App Note 2026 shear stress ClinoStar vs orbital shaker (Wiki.js 1747; head-to-head comparison across HepG2/C3A + Caco-2 + brain organoid — first vendor App Note deep-read). **All 5 files landed at `04-Literature/Deep-Reads/` root** (non-standard pattern vs the prior per-vendor subfolder discipline). Vendor-anchor mapping: 3 CelVivo-aligned (CelVivo App Note + Aiello [ClinoStar-adjacent] + Ajongbolo mentions ClinoStar) + 1 3Brain-adjacent (Kim EGaIn 3D MEA — 3rd next-gen HD-MEA approach alongside Liu 2026 + 3Brain Accura-3D) + 1 cardiac epicardium (Tian mTOR, no vendor callouts). **Largest single-day LDR burst since the 2026-07-29 Parate / Lee / Hodge cluster**. |
 | 2026-08-12 | **Liang 2026 liver organoid fibrosis platform 4-commit LDR cycle** (commits `e542c977` + `8699a154` + `aacba7aa` + `297f106d`) | **CelVivo (ClinoStar rating 5 + ClinoReactor rating 5)** | Liang Y et al. (2026) A robust mouse liver organoid platform enables sustained multicellular maturation and fibrosis modeling from a single tissue sample (Sci Rep DOI 10.1038/s41598-026-42990-2, PMID 41857098; Wiki.js Id 1716, NocoDB Id 770; 3 轨道 Hep-Orgs + Cho-Orgs + HSC 同步分离; DAPT+Dex P1-P10 长程稳定成熟 [ALB/PAS/LDL/CYP 跨代保持]; TGFβ 激活 qHSC → aHSC [Acta2/Col1a1 上调]; aHSC 共培养诱导 Hep-Orgs EMT [Snail/Twist/Vimentin↑; ALB/CK8↓; Lgr5/EpCAM↓; Ki67↓] = 体外肝纤维化模型) — page 946 9 项 SOP 重写版 + page 934 修齐 标杆; 7/7 Ollama qwen2.5vl 视觉审核通过; SeaFile 7/7 公网 200 验真. First paper whose `related:` field already names `[[MOC-类器官与3D培养]]` (the 2026-08-10 first MOC) on the day of publication. |
 | 2026-08-10 | **Phase A metadata batch + first MOC** (commits `d97b39ed` + `6b717aef` + `3b929c2f`) | (process discipline) | 6 deep-reads received the 6-field frontmatter (doi/journal/year/volume/pages/authors/pmid); first MOC `MOC-类器官与3D培养.md` (95 lines, 沙牛《AI 时代的 Obsidian 公开课》课时 1 pattern) created at `04-Literature/Deep-Reads/MOCs/`; 7 image alt descriptions added on `wang2024-org-on-chip.md`. No new external evidence. |

themes/index.md

@@ -4,4 +4,4 @@
 - [Theme 2 · 3D bioprinting (Cellink / BIONOVA)](02-bioprinting.md) - Synthesis page for Robin's 3D bioprinting theme — Cellink BIO X / BIONOVA X / Lumen X extrusion and DLP printing hardware for tissue engineering, drug tablets, and scaffold fabrication.
 - [Theme 3 · AI Agent tools (Hermes / Codex / MiniMax code)](03-ai-agents.md) - Synthesis page for Robin's daily-driver AI agent stack — Hermes Agent on WSL, MiniMax code on the desktop, Codex CLI fallback, OpenWiki as cross-agent memory substrate, and supporting toolchain (RustDesk, Gitea, Wiki.js, RAGFlow).
 - [Theme 4 · Local LLM deployment (Ollama / bge-reranker / RAGFlow)](04-local-llm.md) - Synthesis page for Robin's local-LLM fleet — Ollama serve + qwen2.5vl:7b vision model + BAAI/bge-m3 embeddings (Ollama + LM Studio) + bge-reranker rerank + RAGFlow KB retrieval + adjacent NAS subsystems (NocoDB / SeaFile / Wiki.js / Feishu mail).
-- [Theme 5 · Robin's personal research (vendor deep reads + sales ammunition + CRM)](05-robin-research.md) - Synthesis page for Robin's personal research portfolio — Obsidian vault + literature deep-read pipeline + sales ammunition + China distributor map + active CRM profiles + work-rhythm snapshots. Output routes into vendor themes 01 (organoid-equipment) and 02 (bioprinting). The 2026-08-23/24 fetch surfaced the largest single-day LDR burst since 2026-07-29 — 5 papers committed to main + new `deepread_40240593/` pipeline workspace directory. The 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + 2026-08-30 fetches observed vault HEAD unchanged at `9d4767c7` (vault silent for the 1st + 2nd + 3rd + 4th + 5th consecutive fetches since the 2026-08-24/25 SECOND 5-paper LDR burst, **5 calendar days stale**) with the 4 carry-forward untracked directories (Review + templates + celvivo_commercial + deepread_40240593) bumping their carry-forward counts to 19/14/14/7 days — the `Review/` + `templates/` + `celvivo_commercial/` entries are **confirmed one-off** at the 2026-08-28 fetch (carrying forward unchanged at 2026-08-29 + 2026-08-30) and all 3 entries should be demoted to stale / not recurring carry-forward notes on the next synthesis pass.
+- [Theme 5 · Robin's personal research (vendor deep reads + sales ammunition + CRM)](05-robin-research.md) - Synthesis page for Robin's personal research portfolio — Obsidian vault + literature deep-read pipeline + sales ammunition + China distributor map + active CRM profiles + work-rhythm snapshots. Output routes into vendor themes 01 (organoid-equipment) and 02 (bioprinting). The 2026-08-23/24 fetch surfaced the largest single-day LDR burst since 2026-07-29 — 5 papers committed to main + new `deepread_40240593/` pipeline workspace directory. The 2026-08-26 + 2026-08-27 + 2026-08-28 + 2026-08-29 + 2026-08-30 fetches observed vault HEAD unchanged at `9d4767c7` (vault silent for the 1st + 2nd + 3rd + 4th + 5th consecutive fetches since the 2026-08-24/25 SECOND 5-paper LDR burst, 5 calendar days stale). The 2026-08-31 fetch observed vault HEAD bumped `9d4767c7` → `391e4713` — **THIRD consecutive single-day 5-paper LDR burst** (Stewart + Aiello + Nguyen + Miao + Yan, all CelVivo-anchored, all in the NEW `obsidian-vault/04-Literature/Deep-Reads/CelVivo/` capital-V subfolder — Robin's first parallel-naming deep-read subfolder convention), ending the 5-day vault silence; combined with the 2026-08-23/24 + 2026-08-24/25 clusters, **15 LDR files in 8 calendar days = the largest sustained 8-day research output** in Robin's vault activity log. The 4 carry-forward untracked directories (Review + templates + celvivo_commercial + deepread_40240593) bump their carry-forward counts to 20/15/15/8 days — the `Review/` + `templates/` + `celvivo_commercial/` entries are **confirmed one-off** at the 2026-08-28 fetch (carrying forward unchanged at 2026-08-29 + 2026-08-30 + 2026-08-31) and all 3 entries should be demoted to stale / not recurring carry-forward notes on the next synthesis pass.