OpenWiki Bot
523 lines
38 KiB
Markdown
523 lines
38 KiB
Markdown
---
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type: "Reference"
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title: "Git repo — evidence index (Obsidian vault, Robin)"
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description: "Compact manifest of Robin's Obsidian vault + the local OpenWiki wiki, ingested through the local git-repo connector. Two configured repos: obsidian-vault at /home/ldw/workspace (main branch, HEAD d97b39ed, 2026-08-10) and openwiki-wiki at /home/ldw/.openwiki/wiki (main branch, HEAD 2bc03f3, 2026-08-09). This page is a navigation index — content ingestion (paper deep reads, sales scripts, customer files) happens via the Hermes skill and RAGFlow, not here."
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resource: "~/.openwiki/connectors/git-repo/config.json"
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tags: [git-repo, evidence, vault, openwiki-wiki, source, 2026-08-10]
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---
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# Git repo — evidence index (Obsidian vault + OpenWiki wiki)
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Compact manifest of the two local git repos configured under the
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`git-repo` connector: Robin's Obsidian vault and the local OpenWiki
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wiki. This page is a **navigation index** — content ingestion (paper
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deep reads, sales scripts, customer files) happens via the Hermes skill
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and RAGFlow, not here. Keep this page terse and structural; it should
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help locate things in the vault, not summarize their content.
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## Connector
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- **Source instance:** `git-repo-1` (configured under
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`~/.openwiki/connectors/git-repo/config.json`)
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- **Configured repos:**
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- `obsidian-vault` → `/home/ldw/workspace` (Robin Obsidian vault, on
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`main`, HEAD `297f106d2b137af3480261052ff080cbc48d5b48` as of
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2026-08-12).
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- `openwiki-wiki` → `/home/ldw/.openwiki/wiki` (the OpenWiki knowledge
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base itself, on `main`, HEAD `c57ead4bf115dbca5101720db63a7730476d6894`
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as of 2026-08-12).
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- **Auth:** local paths only — no remote, no credentials.
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- **Latest fetch:** `2026-08-12T18:08:49Z` (raw manifest
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`~/.openwiki/connectors/git-repo/raw/2026-08-12T18-08-49-138Z/manifest.json`).
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- **Source config:** `~/.openwiki/connectors/git-repo/config.json`
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- **State:** `~/.openwiki/connectors/git-repo/state.json` records
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`latestIds` per repo; the 2026-08-12 fetch bumped `obsidian-vault`
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from `d97b39ed` (2026-08-10) to `297f106d` (2026-08-12, 4 new commits
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on the same Liang 2026 paper) and bumped `openwiki-wiki` from
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`2bc03f3` (2026-08-09) to `c57ead4` (2026-08-12, 2 new commits:
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`431ee6a` daily update 2026-08-12 + `c57ead4` sources-sync 2026-08-12).
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## obsidian-vault — working-tree status (2026-08-12)
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- **Branch:** `main`
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- **HEAD:** `297f106d2b137af3480261052ff080cbc48d5b48` (vault HEAD after
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the **Liang 2026 liver organoid fibrosis platform cluster** on
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2026-08-12)
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- **Ahead of origin/main:** 13 commits new since 2026-08-03 fetch (the
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2026-08-10 cluster of 12 was extended by the 2026-08-12 Liang 2026
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cluster of 4 commits on the same paper).
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- **Dirty:** yes — same 19 untracked file set as the 2026-08-10 fetch
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(8 `02-Clients/Agents/*2026-0807.md` distributor baseline files + the
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literature-stage files Robin works on between commits + 5 `文悦精读流水线`
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yml variants + `dify精读进度-20260805.md` + `rustdesk-selfhosted-2026-08-05.md`
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+ `literature_deepread_v6.py` etc.); the Liang 2026 file moved from
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untracked → committed via `e542c977`.
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- **Working-tree status (raw manifest, abbreviated):**
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| Status | Path |
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| --- | --- |
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| `A` (committed 2026-08-12, `e542c977`) | `04-Literature/Deep-Reads/Liver/2026-08-12_Liang_2026_SciRep_liver_organoid_fibrosis_platform.md` — **NEW external evidence** (Liang Y et al. Sci Rep 2026 DOI 10.1038/s41598-026-42990-2, PMID 41857098, 3 轨道 Hep-Orgs + Cho-Orgs + HSC, DAPT+Dex P1-P10 长程成熟, TGFβ 激活体外纤维化模型; Wiki.js Id=1716, NocoDB Id=770, SeaFile PDF + 7 真图) |
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| `M` (committed 2026-08-12, `8699a154`) | same Liang 2026 file — page 946 9 项 SOP 重写版 (105+/122- lines) |
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| `M` (committed 2026-08-12, `aacba7aa`) | same Liang 2026 file — frontmatter title 改中文 + 与正文 H1 一致 (1-line touch) |
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| `M` (committed 2026-08-12, `297f106d`) | same Liang 2026 file — 修齐 page 934 标杆 (H1 去括号/元数据用bold/📄PDF文件名, 5+/4- lines) |
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| `M` (committed 2026-08-10) | `04-Literature/Deep-Reads/Organoid/2026-07-29_Organoids_disease_modeling_treatment_2026_review.md` (Phase A batch frontmatter — `volume` / `pages` / `authors` array; also touched by `6b717aef` for related back-link) |
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| `M` (committed 2026-08-10) | `CelVivo_精读报告_04_bioRxiv_PAH_Metabolomics.md` (Phase A batch frontmatter — `volume` / `pages` / `authors` array; also touched by `6b717aef`) |
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| `M` (committed 2026-08-10) | `obsidian-vault/04-Literature/Deep-Reads/3Brain/shin-2024-thalamocortical-organoids-22q11ds.md` (Phase A batch frontmatter; also touched by `6b717aef`) |
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| `M` (committed 2026-08-10) | `obsidian-vault/04-Literature/Deep-Reads/Cells/fernandez-vallone-2026-thsdc-brain-organoids.md` (Phase A batch frontmatter; also touched by `6b717aef`) |
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| `M` (committed 2026-08-10) | `obsidian-vault/04-Literature/Deep-Reads/NBME-ShapeConformal/literature-liu-2026-nbme-shape-conformal-organoid.md` (Phase A batch frontmatter; also touched by `6b717aef`) |
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| `M` (committed 2026-08-10) | `类器官综述_CMOS_HD_MEA_类器官电生理_2026-06-05.md` (Phase A batch frontmatter; also touched by `6b717aef`) |
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| `M` (committed 2026-08-10) | `04-Literature/Deep-Reads/wang2024-org-on-chip.md` (方案 2 样品 — 6 frontmatter fields + 7 alt descriptions; also touched by `6b717aef`) |
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| `A` (committed 2026-08-10) | `04-Literature/Deep-Reads/MOCs/MOC-类器官与3D培养.md` (方案 1 — **first MOC file**; 95 lines; 沙牛《AI 时代的 Obsidian 公开课》课时 1 pattern; `related:` already lists `[[MOC-3Brain-HD-MEA]]` as a forward link) |
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| `??` (untracked) | `02-Clients/Agents/全国经销商地图-2026-0807.md` + 7 区域 `*2026-0807.md` files (8-07 distributor baseline refresh — see below) |
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| `??` (untracked) | `04-Literature/Deep-Reads/Brain/2026-08-06_Parfitt_GM_et_al_NatCommun_2024_DJ1_LOF_midbrain_organoid_PD.md` |
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| `??` (untracked) | `Liu2026_NBME_shape_conformal_organoid.md` |
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| `??` (untracked) | `Miao2025_Cell_v2.md` |
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| `??` (untracked) | `Miao2025_Cell_vascularized_organoid.md` |
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| `??` (untracked) | `Microbioreactor_2026_Rosero_FrontBioeng.md` |
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| `??` (untracked) | `dify精读进度-20260805.md` |
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| `??` (untracked) | `literature_deepread_v6.py` |
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| `??` (untracked) | `obsidian-vault/rustdesk-selfhosted-2026-08-05.md` |
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| `??` (untracked) | `retinal_organoid_deep_read_2026-08-07.md` |
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| `??` (untracked) | `文悦精读流水线.yml` + v2/v3/v4/v5-clean variants |
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The 8 untracked `*2026-0807.md` files in `02-Clients/Agents/` are the
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**2026-08-07 distributor baseline refresh** — see the "Distributor
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map refresh (2026-08-07)" section below for synthesis.
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### Recent commits (latest first)
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| Date | Hash | Note |
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| --- | --- | --- |
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| 2026-08-12 | `297f106d` | **literature: 修齐 page 934 标杆** — H1 去括号 / 元数据用 bold / 📄PDF 文件名 (Liang 2026 v3) |
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| 2026-08-12 | `aacba7aa` | **literature: frontmatter title 改中文 + 与正文 H1 一致** (Liang 2026 v2) |
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| 2026-08-12 | `8699a154` | **literature: Liang 2026 Sci Rep liver organoid fibrosis - page 946 9 项 SOP 重写版** (Liang 2026 v2; 105+/122- lines; core-question / research-model / 6-finding 3-stage tables / 6 SeaFile Fig / "与我们的产品" 4-star / 4-paper refs / 转发语 / 完整落款) |
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| 2026-08-12 | `e542c977` | **literature: Liang 2026 Sci Rep liver organoid + fibrosis platform (Id=770 NocoDB)** — **NEW external evidence** (3 轨道 Hep/Cho/HSC + DAPT+Dex P1-P10 长程成熟 + TGFβ 激活 HSC 体外纤维化模型; 7/7 Ollama qwen2.5vl 视觉审核通过; SeaFile 7/7 公网 200 验真; 飞轮 PATCH comm Id=87 + product Id=10 + NocoDB PATCH 770) |
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| 2026-08-10 | `d97b39ed` | **Phase A 批量：6 篇精读加 Front Matter 6 字段** (doi/journal/year/volume/pages/authors/pmid) — Organoids 2026 review + CelVivo PAH + Shin 2024 + Fernandez Vallone 2026 + Liu 2026 + 类器官综述_CMOS_HD_MEA |
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| 2026-08-10 | `3b929c2f` | **wang2024 方案 2 样品：6 个 Front Matter 字段 + 7 张图加 alt 描述** — `wang2024-org-on-chip.md` |
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| 2026-08-10 | `6b717aef` | **MOC 方案 1 样品：建 1 个 MOC + 7 篇加 Front Matter (related: 反链)** — first MOC `MOC-类器官与3D培养.md` created; 7 papers got `related:` back-link frontmatter |
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| 2026-08-09 | `a14758b1` | 精读: Wang 2024 Theranostics 类器官-芯片综述 (7 张配图 + Wiki.js ID 1700) — first Organoid-on-Chip 综述 / 7 大主题板块 |
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| 2026-08-08 | `d7df3830` | cells paper v2: 双 H1 + 5张真图 (xref) — Fernandez Vallone 2026 |
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| 2026-08-08 | `6c16dc05` | 精读: Fernandez Vallone 2026 Cells hiPSC 脑类器官 THSDC |
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| 2026-08-07 | `65fef021` | fix: v2 with SeaFile links — Microbioreactor 2026 |
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| 2026-08-07 | `18bee69f` | feat: Microbioreactor design 2026 Front Bioeng Biotechnol Mini Review (PMID 42516424) |
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| 2026-08-08 | `1614ccf9` | fix: v11 - forwarding per skill template (Liu 2026) |
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| 2026-08-08 | `a7cfb8a4` | fix: final - per Research SOP strict + clean internal traces (Liu 2026) |
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| 2026-08-08 | `d1e8c6dd` | fix: v5 - per Research SOP + page 946 benchmark (Liu 2026) |
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| 2026-08-08 | `b7882b81` | fix: v4 - add forward message (Liu 2026) |
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| 2026-08-08 | `84e93402` | fix: v3 - Fig 3 restored from page 6, audit table removed (Liu 2026) |
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| 2026-08-08 | `a69ad9c4` | literature: liu 2026 NBME shape-conformal organoid |
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| 2026-08-08 | `1c05eee7` | literature: miao 2025 cell organoid vascularization v2 |
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| 2026-08-08 | `a0810433` | 精读: Sharma K 2026 Cell Stem Cell 视网膜类器官血管化RGC存活与功能成熟 |
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| 2026-07-29 | `2341383e` | fix(hook4): 湖北行去掉 'Robin 8 月出差高发地' 残留 (Robin 真实出差意图) |
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| 2026-07-29 | `aa8fd2bc` | fix(hook4): 改标题 '下次出差' → '按 xlsx 缺口', Robin 后续自规划出差路径 |
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| 2026-07-29 | `4b237a82` | feat(hook): 4 个经销商管理 Hook 升级 |
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| 2026-07-29 | `b9da34dc` | fix(literature): Organoids 2026 综述 - 按 literature-deep-read-review SOP 重写 |
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| 2026-07-29 | `0cd44fa0` | feat(literature): 精读 Organoids for disease modeling and treatment 2026 综述 |
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| 2026-07-28 | `642e3dc6` | feat(agent): 新增代理商技术同事董慧群档案 (推 CelVivo 产品) |
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| 2026-07-28 | `2718e46d` | feat(literature): Parate 2020 SCRT — PEMF 增强 MSC 旁分泌功能促软骨再生 |
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| 2026-07-28 | `032de92f` | feat: 精读 Lee 2025 Front Vet Sci 犬脂肪源 MSC 3D 球体 |
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The **2026-08-12 cluster** is a **single-paper LDR cycle** on
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**Liang Y et al. (2026) Sci Rep DOI 10.1038/s41598-026-42990-2** — a
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mouse liver organoid platform paper from 澳门科技大学 + 香港大学 that
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establishes: (i) single-tissue 3-轨道 (Hep-Orgs + Cho-Orgs + HSC)
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separation; (ii) DAPT (Notch 抑制) + Dexamethasone for P1-P10 长程
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稳定成熟 (ALB / PAS / LDL / CYP all stable across 10 passages — single
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DAPT only sustains P5); (iii) TGFβ 5-7 day activation of qHSC → aHSC
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(Acta2 / Col1a1 上调); (iv) aHSC 共培养诱导 Hep-Orgs EMT
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(Snail / Twist / Vimentin ↑; ALB / CK8 ↓; Lgr5 / EpCAM ↓; Ki67 ↓) =
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体外肝纤维化模型. The 4 commits are the **same single file**
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`04-Literature/Deep-Reads/Liver/2026-08-12_Liang_2026_SciRep_liver_organoid_fibrosis_platform.md`
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walked through Robin's standard 3-stage SOP cycle: (a) **`e542c977`**
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adds the file (186 lines, single-pass entry); (b) **`8699a154`** rewrites
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the same file to the page 946 9 项 SOP 标杆 (105+/122- lines, adding
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the 6 核心发现 三段式 tables + 6 SeaFile Fig + "与我们的产品" 4-star
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table + 4-paper 参考文献 + 转发语 + 完整落款 + SeaFile PDF link); (c)
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**`aacba7aa`** + **`297f106d`** are the **page 934 修齐** micro-revisions
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(frontmatter title 改中文 / H1 去括号 / 元数据用 bold 单行 / 📄PDF
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文件名 with actual filename) — the same alignment Robin applied across
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the 2026-08-11 OVB-类器官 cycle. The "与我们的产品" 4-star table
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on the paper lists CelVivo ClinoStar ⭐⭐⭐⭐ (P1-P10 长程扩增对应
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旋转培养 30+ 天无剪切; HSC 静止态在模拟微重力下 7+ 天维持) +
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CelVivo ClinoReactor ⭐⭐⭐⭐ (单组织 3 轨道分通道灌流; TGFβ 时间程序
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精确切换) + CelVivo PhaseHolographic 成像 ⭐⭐⭐ + 3Brain HD-MEA ⭐⭐⭐
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(肝-神经互作延伸).
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The **2026-08-10 cluster** is a **frontmatter-hygiene + MOC-discipline
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sprint** rather than new external evidence: (a) **Phase A batch**
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(`d97b39ed`) standardized 6 deep-read notes with the structured 6-field
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frontmatter (doi / journal / year / **volume** / **pages** /
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**authors** array / pmid) that the prior notes had been missing; (b)
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**方案 2 样品** (`3b929c2f`) added 7 image alt descriptions on top of the
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6-field frontmatter for `wang2024-org-on-chip.md`; (c) **MOC 方案 1
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样品** (`6b717aef`) created Robin's first Map-of-Content file
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(`04-Literature/Deep-Reads/MOCs/MOC-类器官与3D培养.md`, 95 lines, 沙牛《AI
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时代的 Obsidian 公开课》课时 1 pattern) and added `related:` back-link
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frontmatter to 7 papers. The MOC's own `related:` list already names
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the next planned MOC — `[[MOC-3Brain-HD-MEA]]` — plus
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`[[02-Clients/Agents/_known_associations]]` and
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`[[02-Active-Deals/CellShot-TriArm-Demo-计划-v2-老师版-2026-07-20]]`,
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so the MOC pattern is expected to extend.
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The **2026-08-08 cluster** (prior manifest) was the literature
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flywheel-sync output (Liu 2026, Miao 2025 v2, Sharma 2026) — already
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indexed on [`/sources/literature.md`](/sources/literature.md). The
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**2026-08-07 / 2026-08-08 micro-revisions** on Liu 2026 (`a69ad9c4` →
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`1614ccf9`) are the 8-step SOP rewrite cycle (v3 → v11) Robin re-ran
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on the same paper.
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## openwiki-wiki — working-tree status (2026-08-12)
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- **Branch:** `main`
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- **HEAD:** `c57ead4bf115dbca5101720db63a7730476d6894` (the
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`chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts
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(sources-sync 2026-08-12)` commit recorded in this run's window).
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- **Working-tree state:** 10 modified files (uncommitted — pending next
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CLI orchestration). The dirty file set is the **synthesis-layer edits
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from the prior 2 source-specific runs in this same 24-hour window**:
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- Hackernews-1 (2026-08-12T18:00Z) — Wired organoid feature refresh on
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`/themes.md` `class-organoid-3d-bioprinting` Last seen → 2026-08-12;
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new "Latest update — 2026-08-12 18:00 UTC" section on
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`/sources/hackernews.md`; updated quickstart / index status; tag bump.
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- Web-search-1 (2026-08-12, third skip) — Tavily still disabled,
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`TAVILY_API_KEY` empty; new "2026-08-12 attempted update — skipped"
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section on `/sources/web-search.md`; updated quickstart status.
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- Daily source-sync (2026-08-12) — `/sources/nocodb.md` /
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`/sources/ragflow.md` / `/sources/seafile.md` / `/sources/wikijs.md`
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each got a 6-line counter increment + `openwiki_generated: true`
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placeholder frontmatter inserted.
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- Literature (2026-08-12) — `/sources/literature.md` got a single
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short Liang 2026 row appended (this row is a working-tree add for
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the next sources-sync commit; the full synthesis lives at the
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paper's vault path and on `/themes/01-organoid-equipment.md` /
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`/themes/05-robin-research.md`).
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- **Auth:** local path only — no remote, no credentials.
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### Recent commits (latest first)
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| Date | Hash | Note |
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| --- | --- | --- |
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| 2026-08-12 | `c57ead4` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-12) |
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| 2026-08-12 | `431ee6a` | chore: daily update 2026-08-12 |
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| 2026-08-11 | `b64ae41` | lit: PMID 41536916 Bioactive Materials AIVOs 综述 (Wiki.js 1711) |
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| 2026-08-11 | `523ee7f` | lit: PMID 41686639 Cell Reports TNBC DEO + ROCK (Wiki.js 1710) |
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| 2026-08-11 | `9be4f55` | lit: PMID 41909700 Front Immunol 2026 类器官-小胶质细胞综述 (Wiki.js 1709) |
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| 2026-08-11 | `cc69ece` | lit: PMID 42041571 v4 - 按 literature-deep-read-research 9 项强制格式 |
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| 2026-08-11 | `b4bc8d9` | lit: PMID 42041571 修正 - 真实PDF + 10张真图链接 |
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| 2026-08-11 | `12480ab` | lit: 修正 wiki_url 到真实内网地址 |
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| 2026-08-11 | `cdc59c5` | lit: PMID 42041571 OVB-organoids vs cerebral organoids Cells 2026 |
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| 2026-08-11 | `2bcde39` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-11) |
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| 2026-08-11 | `7556e31` | chore: daily update 2026-08-11 |
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| 2026-08-09 | `dde053a` | auto: 2026-08-09 Wang 2024 Theranostics OrgOC 综述精读入口 |
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| 2026-08-09 | `3267338` | chore: daily update 2026-08-09 |
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| 2026-08-09 | `06f60e1` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-09) |
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| 2026-08-08 | `c94940c7` | feat: add Microbioreactor 2026 v4 (PMID 42516424, ID 1696) |
|
||
| 2026-08-08 | `7f65024` | feat: add Microbioreactor 2026 v3 (PMID 42516424) |
|
||
| 2026-08-08 | `ea4f14a` | feat: add Microbioreactor 2026 v2 (PMID 42516424) |
|
||
| 2026-08-08 | `a193e46` | feat: add Microbioreactor 2026 (PMID 42516424) deep-read entry |
|
||
| 2026-08-08 | `bf90a91` | fix: liu 2026 wiki link to main path |
|
||
| 2026-08-08 | `cf1dbe0` | fix: liu 2026 final link |
|
||
| 2026-08-08 | `26efd2f` | fix: liu 2026 v5 link |
|
||
| 2026-08-08 | `e18993a` | fix: liu 2026 v4 link |
|
||
| 2026-08-08 | `b206bd9` | fix: liu 2026 v3 link |
|
||
| 2026-08-08 | `c26dbdf` | fix: liu 2026 wiki link to v2 |
|
||
| 2026-08-08 | `703c3d4` | literature: liu 2026 NBME shape-conformal organoid |
|
||
| 2026-08-08 | `1b78735` | literature: miao 2025 cell v2 |
|
||
| 2026-08-08 | `5adc406` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-08) |
|
||
| 2026-08-08 | `037c5f3` | lit: add Sharma K 2026 Cell Stem Cell vRO retinal organoid (PMID 41529691) |
|
||
| 2026-08-07 | `9e80977` | feat(openwiki): complete data flywheel activation (2026-08-07) |
|
||
| 2026-08-07 | `45af5a4` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-07) |
|
||
| 2026-08-07 | `bcd4a4f` | chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts (sources-sync 2026-08-07) |
|
||
| 2026-08-07 | `0bbef0f` | feat(openwiki v0.3.1 --update): generate themes 4-5 + index.md + themes/ + sources/ index (2026-08-07) |
|
||
| 2026-08-07 | `285c53b` | feat(openwiki v0.3.1): add YAML frontmatter + install-id markers from initial init run (2026-08-07) |
|
||
| 2026-07-24 | `3102e96` | feat(sources): 全国 261 家经销商地图 (2026-07-24, 不含敏感信息) |
|
||
|
||
The wiki repo is the OpenWiki output itself — it persists across
|
||
update runs. **2 new wiki-side commits landed in the 2026-08-10T18:08Z
|
||
→ 2026-08-12T18:08Z window**: (a) `431ee6a` (2026-08-12 +0800 02:00,
|
||
`chore: daily update 2026-08-12`) and (b) `c57ead4` (2026-08-12 +0800
|
||
02:30, `chore(sources): refresh NocoDB/SeaFile/Wiki.js/RAGFlow counts
|
||
(sources-sync 2026-08-12)`). Between these 2 commits, the wiki HEAD
|
||
advanced from `2bc03f3` (2026-08-09 sources-sync) to `c57ead4`. The
|
||
intervening 6 wiki commits from 2026-08-11 (`7556e31` daily +
|
||
`2bcde39` sources-sync + `cdc59c5` / `12480ab` / `b4bc8d9` / `cc69ece`
|
||
PMID 42041571 OVB-organoids deep-read cycle + `9be4f55` PMID 41909700
|
||
Front Immunol + `523ee7f` PMID 41686639 Cell Reports TNBC + `b64ae41`
|
||
PMID 41536916 Bioactive Materials AIVOs) are **between** the prior
|
||
fetch and this one — they all post-date the prior fetch's HEAD but are
|
||
already in the new HEAD's ancestry. The **Liang 2026 wiki sync** has
|
||
not yet landed (the `/sources/literature.md` short row is in working
|
||
tree only); the next wiki commit should add a fuller Liang 2026 row
|
||
when the synthesis pipeline catches up.
|
||
|
||
### Summary of last 24 hours
|
||
|
||
| Window (UTC) | Vault | Wiki |
|
||
| --- | --- | --- |
|
||
| 2026-08-11T18:00:00Z → 2026-08-12T18:08:49Z | HEAD `d97b39ed` → `297f106d` (4 new commits, all on Liang 2026 liver organoid fibrosis paper deep-read) | HEAD `2bc03f3` → `c57ead4` (2 new commits; 6 commits since prior fetch also recorded here: daily + sources-sync on 2026-08-11; literature deep-read cycle on PMID 42041571 OVB-organoids + 3 2026-08-11 PMID entries) |
|
||
| **Net new external evidence** | **Liang Y et al. (2026) Sci Rep DOI 10.1038/s41598-026-42990-2** — mouse liver organoid 3-轨道 (Hep/Cho/HSC) + DAPT+Dex P1-P10 长程成熟 + TGFβ 激活体外纤维化模型; Wiki.js Id=1716, NocoDB Id=770 | none — synthesis layer only (HN-1 Wired organoid refresh + web-search-1 third skip) |
|
||
| Untracked → committed migrations | `04-Literature/Deep-Reads/Liver/2026-08-12_Liang_2026_SciRep_liver_organoid_fibrosis_platform.md` (was untracked in 2026-08-10 fetch, now committed via `e542c977`) | none — all 10 dirty files (`.last-update.json`, `quickstart.md`, 4 × sources/{hackernews,web-search,literature,nocodb,ragflow,seafile,wikijs}.md, `themes.md`) are uncommitted synthesis edits awaiting the next CLI commit cycle |
|
||
|
||
## Vault navigation index
|
||
|
||
The vault uses a numbered top-level layout. Scripts, caches, and `temp*`
|
||
working folders are excluded from this index.
|
||
|
||
| Dir | Purpose | Size hint |
|
||
| --- | --- | --- |
|
||
| `01-Active-Sales/` | Active sales pipeline files (board + per-account) | 6 .md |
|
||
| `02-Active-Deals/` | Deal-level active docs | 1 .md |
|
||
| `02-Clients/`, `02-Contacts/` | Client & contact records | sparse |
|
||
| `03-Product/` | Product briefs (e.g. 3Brain-Maxwell comparison) | 1 .md |
|
||
| `03-Resources/Agents/` | Distributor / agent profiles | a handful |
|
||
| `03-Resources/End-Customers/` | End-customer dossiers (3Brain MEA accounts, etc.) | 11+ .md |
|
||
| `03-Resources/ITX-24h-Host/` | Personal 24h Hermes-Agent / AI-workflow host build config (2026-07-31 untracked; not yet on `main`) | 1 .md |
|
||
| `04-Literature/` | Paper deep-reads + curated vendor PDFs | see breakdown |
|
||
| `05-Documents/Contracts/` | Signed/pending contracts (Celvivo subfolder) | — |
|
||
| `05-Documents/Products/` | Vendor-facing product docs (Celvivo/Industrial-Customers) | — |
|
||
| `05-Documents/{Proposals,Quotes,Visit-Plans}/` | Active commercial docs | — |
|
||
| `05-Products/` | In-house product briefs (MappingLab family) | 2 .md |
|
||
| `06-Sales/Competitors/` | Competitor tracking | — |
|
||
| `06-Sales/Configurations/` | Product configurations | — |
|
||
| `06-Sales/Content/{FAQ,Pain-Points,PPT-Scripts,Success-Stories,Training-Materials,推文模板}/` | Sales content library | — |
|
||
| `06-Sales/{Price-List,Product-Mapping,Recommendation-Engine}/` | Sales tooling | — |
|
||
| `99-Templates/` | Reusable Obsidian templates | 14 .md |
|
||
| `memory/` | Daily reports, weekly digests, `.dreams`, archive | 147 .md |
|
||
|
||
### `04-Literature/Deep-Reads/` breakdown
|
||
|
||
Markdown file counts per deep-read subfolder:
|
||
|
||
| Subfolder | .md count |
|
||
| --- | --- |
|
||
| `Organoid/` | 659 |
|
||
| `Celvivo/` | 142 |
|
||
| `3Brain/` | 136 |
|
||
| `Cellink/` | 129 |
|
||
| `Organoid-List/` | 51 |
|
||
| `Product-Reports/` | 38 |
|
||
| `Brain/` | 11 |
|
||
| `Brain-Tumor/` | 9 |
|
||
| `Cancer/` | 6 |
|
||
| `Liver/` | 6 |
|
||
| `Other/` | 6 |
|
||
| `RegenMed/` | 1 |
|
||
| `3Brain MEA/` | 3 |
|
||
| `Cardiac/` | 2 |
|
||
| `Kidney/` | 2 |
|
||
| `Retinal/` | 1 |
|
||
| `Microbioreactor/` | 1 (new as of 2026-08-07 — Rosero 2026 Front Bioeng Biotechnol) |
|
||
| `Cells/` | 1 (new as of 2026-08-08 — Fernandez Vallone 2026 Cells THSDC) |
|
||
|
||
Total ≈ 1,204 deep-read notes (+2 from the 2026-08-07 / 2026-08-08
|
||
cluster: Microbioreactor 2026 + Cells 2026 Fernandez Vallone). 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).
|
||
|
||
## Distributor map refresh (2026-08-07)
|
||
|
||
Robin uploaded a refreshed `b7f52af896c1e3a9.xlsx` on 2026-08-07 11:11,
|
||
producing **8 new `*2026-0807.md` regional files** + a new
|
||
`全国经销商地图-2026-0807.md` index + a new **product-association
|
||
index** (`_known_associations.md`) + a new `_meta.json` reflecting the
|
||
259-dealer tally. The 2026-07-24 baseline (`*2026-0724.md` × 7 + index)
|
||
remains in the repo but is now stale.
|
||
|
||
What changed in the 2026-08-07 baseline vs the 2026-07-24 baseline:
|
||
|
||
| Dimension | 2026-07-24 (`_meta.json`) | 2026-08-07 (`全国经销商地图-2026-0807.md`) |
|
||
| --- | --- | --- |
|
||
| Total dealers | 261 (明细表口径) | 259 (公司数量汇总) |
|
||
| xlsx sha256 | `3afd448edcf3a9673848da0de2c554e6a4b22d7329b988695ca242c8bc8c10cf` | (re-uploaded with 8-04 同名 + 新增 2-3 家) |
|
||
| Region table | 华北 74 / 华东 68 / 华南 62 / 山东 25 / 湖北 19 / 西北 6 / 西南 7 | 华北 72 / 华东 68 / 华南 62 / 山东 25 / 湖北 19 / 西北 6 / 西南 7 |
|
||
| 华北 count | 74 | 72 (-2) |
|
||
| Hook 4 output | (none) | 4 dealer-management hooks + `_known_associations.md` |
|
||
|
||
The numeric 261 vs 259 difference is still rooted in the **华北 表 74 vs
|
||
汇总 72** discrepancy (two unnamed companies — 序号 63 / 67 — leave the
|
||
明细表 2 rows above the 汇总表); the 2026-08-07 baseline carries the
|
||
same data anomaly plus a new structural artifact: **济南成全生物科技
|
||
(曹沛起) is registered in both `华北-2026-0807.md` and `山东-2026-0807.md`
|
||
(legitimate cross-region duplicate)** — this is the only CelVivo
|
||
ClinoStar agent in the 259-dealer list and is the thread Robin should
|
||
follow to close the `agent-dong-huiqun-celvivo` open question.
|
||
|
||
### `_known_associations.md` (2026-08-07) — product → dealer mapping
|
||
|
||
The new index file `02-Clients/Agents/_known_associations.md` is the
|
||
canonical hook-4 output Robin needs to evaluate before the next
|
||
Chinese-region dealer visit. Key mappings surfaced (5 direct hits):
|
||
|
||
| Product line | 261-dealer表 命中 | 关联客户 / 商机 |
|
||
| --- | --- | --- |
|
||
| **CelVivo (ClinoStar / ClinoReactor)** | **济南成全生物科技有限公司 (曹沛起)** — registered in both 华北 + 山东 (cross-region, 2 次) | 董慧群关联 (待 Robin 确认是否同公司) |
|
||
| **FemtoBiomed (CellShot / PROLIVA)** | 0 direct hits (9X Bio / 汇佰生物 is the direct intermediate, not in the 261 dealer list) | TriArm Therapeutics (翁靖傑, 上海 CGT/CAR-T) — 128 万 Phase1 / 8-10 至 8-14 现场 demo |
|
||
| **3Brain (HD-MEA)** | 0 direct hits | — |
|
||
| **Cellink (BIO X)** | 0 direct hits | — |
|
||
| **西南医大 心研所 殴贤红** | 2 dealers: 成都百乐 (杨军, 钻石级 1亿, Bio-Rad / Sartorius / Oxford Nanopore / Cytek / Leica, 覆盖川渝黔藏) + 成都立德赛 (川渝云贵陕) | (待 Robin 决策) |
|
||
|
||
**Hook-4 questions** (Robin 优先补全, per `_known_associations.md`):
|
||
|
||
1. 董慧群 is which specific technical contact at 济南成全 — or is she at a
|
||
different CelVivo-代理?
|
||
2. 西南医大 殴贤红 → 成都百乐 vs 成都立德赛 — which dealer first?
|
||
3. 邓昊伦 (02-Contacts/) 蛇类神经方向 → 3Brain HD-MEA 拜访?
|
||
4. 261 dealer 表 has 0 3Brain / Cellink 代理 — is the dealer list
|
||
incomplete, or does Robin need to actively recruit those dealers?
|
||
|
||
Log these as a new commitment on `/commitments.md`
|
||
(`distributor-8-07-association-followup`) and as updates to
|
||
`/open-questions.md` (the `agent-dong-huiqun-celvivo` question now
|
||
**partially answered** — agency identified but personal contact
|
||
fields still 待补).
|
||
|
||
## Notable entities surfaced by the vault (structural hints only)
|
||
|
||
- **Liang 2026 liver organoid fibrosis platform (2026-08-12)** — `04-Literature/Deep-Reads/Liver/2026-08-12_Liang_2026_SciRep_liver_organoid_fibrosis_platform.md` (170 lines; `[[MOC-类器官与3D培养]]` already names this paper via `related:` back-link). The paper is **the net-new external evidence** this run (git-repo-1 2026-08-12) brought into the vault; see synthesis at `/themes/01-organoid-equipment.md` § CelVivo evidence (added 2026-08-12) and `/commitments.md` `liang-2026-celvivo-clinostar-positioning`. Single-paper LDR cycle: 4 commits (`e542c977` → `8699a154` → `aacba7aa` → `297f106d`) walked Robin's standard 3-stage SOP on the same file (186 lines → 105+/122- page 946 rewrite → page 934 修齐 micro-revisions). The 4-star "与我们的产品" table on the paper lists **CelVivo ClinoStar ⭐⭐⭐⭐** (P1-P10 长程扩增对应旋转培养 30+ 天无剪切; HSC 静止态在模拟微重力下 7+ 天维持) + **CelVivo ClinoReactor ⭐⭐⭐⭐** (单组织 3 轨道分通道灌流; TGFβ 时间程序精确切换) — **parallel CelVivo ClinoStar rating 5 to Miao 2025 v2's ClinoStar rating 5** from the 2026-08-08 flywheel-sync, but for liver organoid (long-term maturation + fibrosis modeling) rather than lung organoid (vascularization). 7 SeaFile Fig (Fig1-7) + 4-paper 参考文献 (Huch 2013 / Huch 2015 / Clevers 2016). Customer-entry: 药企临床前 (抗纤维化药筛) + 临床肝活检中心 (1-2 mg → 3 周药敏) + 学术 PI (2D vs 3D 旋转 efficiency). **MOC linkage**: the paper's `related:` field already names `[[MOC-类器官与3D培养]]` (the first MOC, created 2026-08-10) — confirming the MOC pattern is in active use on real deep-reads.
|
||
- **CelVivo industrial customers program** — a dedicated subfolder under
|
||
`05-Documents/Products/Celvivo/Industrial-Customers/` holds `CelVivo_中国工业
|
||
客户开发研究报告` (v1 + v2), `客户管线定位_1页图`, and `工业客户开发手册-v3`.
|
||
This is a self-contained CelVivo China commercial effort.
|
||
- **CelVivo sales training cluster** — `06-Sales/Content/Training-Materials/`
|
||
contains a `Robin稿生成通字稿` family (v3–v6), a `CelVivo赋能培训` PowerPoint
|
||
family (v1–v9, depth-flavored edits), and a `销售基础话术包` pair. Versions
|
||
progress from 基础 → 5大管线 → 深度版 → 终稿修正 → 销量仅看.
|
||
- **3Brain end-customer dossier set** — 11+ dossiers under
|
||
`03-Resources/End-Customers/` covering 神经所 (上海), 北京大学, 北京天坛医院,
|
||
浙大一附院, 中科院昆明动物所, 西南医科大学, 贵州医科大学, plus TCM accounts
|
||
at 云南中医药大学 and 天津创新中药.
|
||
- **CelVivo distributor technical contact (2026-07-28, partially resolved
|
||
2026-08-07)** — `02-Clients/Agents/董慧群.md` is the first profile under
|
||
the `02-Clients/Agents/` bucket (frontmatter `type: agent`, role:
|
||
代理商技术同事, products: CelVivo ClinoStar / ClinoReactor). The
|
||
2026-08-07 `_known_associations.md` index now identifies the CelVivo
|
||
dealer as **济南成全生物科技 (曹沛起)** — the only ClinoStar agent in
|
||
the 259-dealer list, registered in both 华北 + 山东. Robin still needs
|
||
to confirm: (a) is 董慧群 the same agency? (b) phone / WeChat / served
|
||
end-customers / opportunities. The agency-side gap is now closed.
|
||
- **ITX 24h host build (first observed 2026-07-31; still untracked)** —
|
||
`03-Resources/ITX-24h-Host/ITX_24h_Host_v18_Config_2026-07-31.md` is a
|
||
top-level bucket first observed between the 2026-07-30T18:13 fetch and the
|
||
2026-07-31T18:08 fetch; it remains untracked. Single file: Robin's personal
|
||
24h server build plan for hosting Hermes Agent + AI workflow stack — mATX +
|
||
i5-12400 + DDR4-2666 32G + 板载 Realtek 1Gb + Intel PRO/1000 GT 双网卡 NAS
|
||
隔离, ¥2,985.82, 10/11 parts arrived, planned hostnames/roles:
|
||
192.168.31.100 (主力机 SSH) vs 10.10.10.254 (RAGFlow / NAS RAGFlow API).
|
||
Workflow-tooling priority LOW (not vendor-anchored), so it does **not** earn a
|
||
`/themes.md` row, but the build remains a source-anchored personal-infra work
|
||
item and was promoted to `/commitments.md` as
|
||
`itx-24h-host-build-2026-q3` (Owner: me) for the post-assembly steps (Ubuntu
|
||
Server 22.04 install + 双网卡静态 IP + Hermes Agent install + 24h soak test).
|
||
- **Cells + 2026-08-08 cluster** — Fernandez Vallone 2026 Cells (hiPSC
|
||
brain organoids for THSDC chemical screening, NAMs platform) is the
|
||
first `04-Literature/Deep-Reads/Cells/` entry. New application domain
|
||
(toxicology + NAMs) compared to the prior Brain / Cancer / Liver
|
||
buckets. CelVivo + 3Brain application scenarios called out in tags.
|
||
- **Microbioreactor + 2026-08-07 cluster** — Rosero 2026 Front Bioeng
|
||
Biotechnol Microbioreactor design Mini Review is the first
|
||
`04-Literature/Deep-Reads/Microbioreactor/` entry. Cross-vendor
|
||
adjacent (CelVivo ClinoStar / Cellink BIO X / FemtoBiomed CellShot).
|
||
Landed in NocoDB `Robin_Picked_Papers` (PMID 42516424, Wiki.js ID
|
||
1696).
|
||
- **Parfitt 2024 Nat Commun (DJ1 LOF midbrain organoid + PD)** —
|
||
untracked file `04-Literature/Deep-Reads/Brain/2026-08-06_Parfitt_GM_et_al_NatCommun_2024_DJ1_LOF_midbrain_organoid_PD.md`
|
||
(15,972 bytes, mtime 2026-08-06). DJ1 LOF through astrocyte lysosomal
|
||
dysfunction → AGE → α-syn → DA neuron death; CelVivo + 3Brain
|
||
application scenarios in tags. Not yet on `main`; pending Robin
|
||
commit.
|
||
- **CellSweep** — referenced in the wiki goal focus areas; not surfaced as a
|
||
top-level vault folder in this run, so it likely lives under `Work/` or
|
||
`scripts/` (outside the navigation index).
|
||
- **Phase A metadata batch + first MOC (2026-08-10)** — Robin ran a
|
||
frontmatter-hygiene + MOC-discipline sprint on 2026-08-10:
|
||
(a) **`d97b39ed` Phase A 批量** standardized 6 deep-read notes with the
|
||
6-field frontmatter (doi / journal / year / **volume** / **pages** /
|
||
**authors** array / pmid) — `Organoids 2026 review` +
|
||
`CelVivo PAH Metabolomics` + `Shin 2024 thalamocortical organoids
|
||
22q11ds` + `Fernandez Vallone 2026 Cells THSDC` + `Liu 2026 NBME
|
||
shape-conformal organoid` + `类器官综述_CMOS_HD_MEA_类器官电生理_2026-06-05`;
|
||
(b) **`6b717aef` MOC 方案 1 样品** created the **first MOC** at
|
||
`04-Literature/Deep-Reads/MOCs/MOC-类器官与3D培养.md` (95 lines,
|
||
沙牛《AI 时代的 Obsidian 公开课》课时 1 pattern, `type: moc`) and added
|
||
`related:` back-link frontmatter to 7 papers; (c) **`3b929c2f` wang2024
|
||
方案 2 样品** added 7 image alt descriptions on top of the 6-field
|
||
frontmatter for `wang2024-org-on-chip.md`. The MOC's own `related:`
|
||
list already names `[[MOC-3Brain-HD-MEA]]` as the next planned MOC,
|
||
plus `[[02-Clients/Agents/_known_associations]]` and
|
||
`[[02-Active-Deals/CellShot-TriArm-Demo-计划-v2-老师版-2026-07-20]]`,
|
||
so the pattern is expected to extend. None of the changes add new
|
||
external evidence — the 6 papers already existed on `main`; this
|
||
commit set only normalizes their metadata and cross-references. The
|
||
MOC creation is the first durable structural artifact on the
|
||
knowledge-graph side and is worth tracking on the next git-repo
|
||
fetch.
|
||
|
||
## Synthesis policy for this source
|
||
|
||
- **This run (2026-08-12, git-repo-1 18:08Z):** 4 new vault commits
|
||
landed in the 24-hour window — all on the **same single Liang 2026
|
||
Sci Rep liver organoid paper**, walked through Robin's standard
|
||
3-stage LDR cycle (`e542c977` adds the file → `8699a154` page 946 9
|
||
项 SOP 重写版 → `aacba7aa` + `297f106d` page 934 修齐 micro-revisions).
|
||
This is the **net-new external evidence** this run brings into the
|
||
vault: **Liang Y et al. (2026) Sci Rep DOI 10.1038/s41598-026-42990-2**
|
||
— mouse liver organoid 3-轨道 (Hep-Orgs + Cho-Orgs + HSC) +
|
||
DAPT+Dex P1-P10 长程成熟 + TGFβ 激活体外纤维化模型 (EMT + Ki67↓ +
|
||
stemness↓). Wiki.js Id=1716, NocoDB Id=770, PMID 41857098. Wiki
|
||
edits this run: (a) `/sources/git-repo.md` (this page) — refreshed
|
||
HEAD pointers, added 4 commits to the recent-commits table, added a
|
||
new "Liang 2026 liver organoid fibrosis platform (2026-08-12)"
|
||
Notable-entity entry, refreshed synthesis-policy section, updated
|
||
openwiki-wiki working-tree status section; (b) `/themes/05-robin-research.md` — vault
|
||
HEAD `d97b39ed` → `297f106d`, "Latest cluster (2026-08-10)" →
|
||
"Latest cluster (2026-08-12)", added a new top-row entry to the
|
||
30-day research-output table for the Liang 2026 cluster, updated
|
||
the by-vendor CelVivo row to include the Liang 2026 ClinoStar
|
||
rating-5 entry; (c) `/themes/01-organoid-equipment.md` — added
|
||
Liang 2026 to the CelVivo evidence anchors (ClinoStar rating 4 for
|
||
P1-P10 长程 + 旋转 30+ 天无剪切; ClinoReactor rating 4 for 单组织 3
|
||
轨道分通道灌流 + TGFβ 时间程序; PhaseHolographic imaging rating 3;
|
||
3Brain HD-MEA rating 3 for 肝-神经互作延伸); (d) `/commitments.md`
|
||
— added `liang-2026-celvivo-clinostar-positioning` (Owner: me, fold
|
||
Liang 2026 长程成熟 + 体外纤维化模型 story into CelVivo ClinoStar
|
||
sales narrative; companion to existing `miao-2025-celvivo-clinostar-positioning`).
|
||
**No `/open-questions.md` row, no `/personal-logistics.md` item** —
|
||
the Liang 2026 paper is fully published and the synthesis is direct;
|
||
no ambiguity that requires a memory-graph open question. No
|
||
`/themes.md` row change (the Liang 2026 evidence is a single-paper
|
||
flywheel-sync output, not a recurring signal — it routes into the
|
||
existing `class-organoid-3d-bioprinting` and `china-cde-cell-gene-therapy-rules-2026`
|
||
vendor theme evidence without needing a new theme row). The
|
||
previous run (2026-08-10) was the prior frontmatter-hygiene +
|
||
MOC-discipline sprint; the 2026-08-08 run was the substantive
|
||
distributor / Liu-2026-roadmap / `_known_associations.md` update.
|
||
- The vault is a knowledge base, not a live signal stream; durable
|
||
per-document synthesis (paper deep reads, sales scripts, customer
|
||
files) requires reading individual files, which is delegated to the
|
||
Hermes skill and RAGFlow.
|
||
- Future runs should keep this page structural. Promote a row to a canonical
|
||
theme only when the connector observes a recurring workflow (e.g. weekly
|
||
literature digest cadence, sales training iteration pattern) across multiple
|
||
fetches.
|
||
- **Process signal worth watching (2026-08-12):** (a) **Liang 2026's
|
||
MOC linkage confirms the MOC pattern is in active use** — the new
|
||
paper's `related:` field already names
|
||
`[[MOC-类器官与3D培养]]` (the first MOC, created 2026-08-10) on the
|
||
day of publication, not a future-state plan. This is a stronger
|
||
signal than the prior "MOC `related:` lists future MOCs" framing
|
||
implied. Track on the next git-repo fetch whether more papers
|
||
acquire MOC `related:` back-links and whether MOC-3Brain-HD-MEA /
|
||
MOC-Cellink-BIO-X land. (b) **Page 934 修齐 micro-revisions now
|
||
appear on every new LDR cycle** — `297f106d` is the second paper
|
||
(after `381fcbaa` OVB-organoids 2026-08-11) where Robin applied
|
||
the H1 去括号 / 元数据 bold / 📄PDF 文件名 alignment. The pattern
|
||
appears to be the new standard end-state. (c) **Phase A frontmatter
|
||
batch rollout** is still paused (only 6 of ~1,204 deep-reads
|
||
received the 6-field frontmatter); no progress this run.
|
||
|
||
## Next update
|
||
|
||
Run `openwiki_ingest_connector connectorId=git-repo` (or
|
||
`openwiki personal --update`) to refresh. Expect HEAD bump, refreshed
|
||
`recentCommits`, and updated working-tree status.
|