From a193e46b3f2fa82538b278517f6a3d066db7ab6d Mon Sep 17 00:00:00 2001
From: Robin <20864114@qq.com>
Date: Sat, 8 Aug 2026 15:43:55 +0800
Subject: [PATCH] feat: add Microbioreactor 2026 (PMID 42516424) deep-read
 entry

---
 sources/literature.md | 178 ++++++++++++++++++++++--------------------
 1 file changed, 94 insertions(+), 84 deletions(-)

diff --git a/sources/literature.md b/sources/literature.md
index d4455cb..ccb01b4 100644
--- a/sources/literature.md
+++ b/sources/literature.md
@@ -1,118 +1,128 @@
 ---
 type: "Reference"
-title: "Literature Deep-Reads — 跨 agent 精读索引"
-openwiki_generated: true
+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. 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]
 ---
 
-# Literature Deep-Reads — 跨 agent 精读索引
+# Literature Deep-Reads — cross-agent deep-read index
 
-> 数据源: Obsidian vault `04-Literature/Deep-Reads/<vendor>/<DOI>.md` (git-repo connector 自动同步)
-> 用途: MiniMax code / Hermes 跨 agent 检索 "Robin 最近精读了什么文献"
-> 更新: OpenWiki cron 每天 02:00 自动扫 vault mtime, 增量更新本文件
+> Source: Obsidian vault `04-Literature/Deep-Reads/<vendor>/<DOI>.md` (git-repo connector auto-sync) + flywheel-sync `~/.hermes/data_sources/literature_flywheel.jsonl` for pipeline status.
+> Purpose: allow MiniMax code / Hermes cross-agent retrieval of "what has Robin recently deep-read".
+> Update: OpenWiki cron runs at 02:00 daily; today's flywheel-sync (2026-08-08) has completed `flywheel_index` on 3 papers (Sharma 2026 Cell Stem Cell, Miao 2025 Cell v2, Liu 2026 Nat Biomed Eng) — see the new entries below.
 
-## 最近 30 天精读 (按 mtime 倒序)
+## Last 30 days of deep reads (mtime descending)
 
-### 2026-08-08
-| DOI | Vendor | 类器官 | 标题 | 路径 |
-|---|---|---|---|---|
-| `10.1016/j.stem.2025.12.013` | (无 vendor, Research) | 视网膜类器官 | Sharma K et al. (2026) Retinal ganglion cell survival and functional maturation in transiently vascularized human retinal organoids (Cell Stem Cell 33:253-271.e13, PMID 41529691, vRO 第18周 RGC 18.2% vs ctrl-RO 1.21% p<0.001, 第31周 ON/OFF/ON-OFF 光响应) | `Retina-StemCell/literature-sharma-2026-cell-stem-cell-vascularized-retinal-organoid-rgc.md` |
+### 2026-08-08 (3 papers — flywheel-sync completed today)
+
+| DOI | Vendor | Application | Title (short) | Vault path |
+| --- | --- | --- | --- | --- |
+| `10.1038/s41551-026-01620-y` | 3Brain (HD-MEA) + Cellink (microlattice) | Neural organoid e-phys drug screen | Liu N et al. (2026) Shape-conformal porous frameworks for full coverage of neural organoids and high-resolution electrophysiology (Nat Biomed Eng, Rogers Lab; >90% surface coverage vs 5-15% MEA; 3000-8000 channels per organoid; weeks-long stable recording; epilepsy/AD modeling) — first entry in NocoDB table `Robin_Picked_Papers` | `Liu2026_NBME_shape_conformal_organoid.md` (in `/home/ldw/workspace/`) |
+| `10.1016/j.cell.2025.05.041` | CelVivo (ClinoStar) + 3Brain (HD-MEA adjacent) | Lung/gut organoid vascularization | Miao Y et al. (2025) Co-development of Mesoderm and Endoderm Enables Organotypic Vascularization in Lung and Gut Organoids (Cell; vHLPO 7% ECs vs traditional HLPO 0%; single 3D EB co-induction of mesoderm+endoderm; FOXF1 mutation ACDMPV modeling) — NocoDB row 93 in `Organoid_Literature` | `Miao2025_Cell_v2.md` (in `/home/ldw/workspace/`) |
+| `10.1016/j.stem.2025.12.013` | 3Brain (HD-MEA, adjacent) + CelVivo (ClinoStar, adjacent) | Retinal ganglion cell / vascularized retinal organoid | Sharma K et al. (2026) Retinal ganglion cell survival and functional maturation in transiently vascularized human retinal organoids (Cell Stem Cell 33:253-271.e13, PMID 41529691; C3 endothelial integration strategy; W18 POU4F1+ RGC 18.2% vs 1.21% p<0.001; W31 ON/OFF/ON-OFF light responses >90%/72%/53% fidelity) — NocoDB row 700 in `Organoid_Literature` | `Retina-StemCell/literature-sharma-2026-cell-stem-cell-vascularized-retinal-organoid-rgc.md` (planned) |
 
 ### 2026-07-29
-| DOI | Vendor | 类器官 | 标题 | 路径 |
-|---|---|---|---|---|
-| `10.1186_s40164-026-00743-x` | (无 vendor, 综述) | 全谱综述 | Organoids for disease modeling and treatment: state-of-the-art (Exp Hematol Oncol 2026, PMID 41545895, 190 项临床试验 + 4 大瓶颈) | `Organoid/2026-07-29_Organoids_disease_modeling_treatment_2026_review.md` |
+
+| DOI | Vendor | Application | Title (short) | Vault path |
+| --- | --- | --- | --- | --- |
+| `10.1186_s40164-026-00743-x` | (no vendor, review) | Whole-organoid landscape | Organoids for disease modeling and treatment: state-of-the-art (Exp Hematol Oncol 2026, PMID 41545895, 190 clinical trials + 4 bottlenecks) | `Organoid/2026-07-29_Organoids_disease_modeling_treatment_2026_review.md` |
 
 ### 2026-07-28
-| DOI | Vendor | 类器官 | 标题 | 路径 |
-|---|---|---|---|---|
-| `10.1080_17460751.2025.2572177` | Ronawk Bio-Block (KB 0 命中) | MSC / 脂肪源 | Comparison of 3D culture systems on MSC longevity, regenerative potential, and secretome production | `RegenMed/2026-07-28_Hodge_2025_RegenMed_MSC_3D_Bio-Block.md` |
-| `10.3389/fvets.2025.1500267` | (无 vendor) | 犬脂肪 MSC 3D 球体 | Lee E et al. (2025) Enhanced immunomodulatory effects of canine adipose tissue-derived mesenchymal stem cells in 3D culture (Front Vet Sci 12:1500267, ULA 板 48h, 3D CM 显著压低 LPS-DH82 M1 p<0.0001) | `Other/2026-07-28_Lee_2025_FrontVetSci_canine_MSC_3D_spheroid.md` |
+
+| DOI | Vendor | Application | Title (short) | Vault path |
+| --- | --- | --- | --- | --- |
+| `10.1080_17460751.2025.2572177` | Ronawk Bio-Block (KB 0 hit) | MSC / adipose source | Comparison of 3D culture systems on MSC longevity, regenerative potential, and secretome production (Hodge 2025) | `RegenMed/2026-07-28_Hodge_2025_RegenMed_MSC_3D_Bio-Block.md` |
+| `10.3389/fvets.2025.1500267` | (no vendor) | Canine adipose MSC 3D spheroid | Lee E et al. (2025) Enhanced immunomodulatory effects of canine adipose tissue-derived mesenchymal stem cells in 3D culture (Front Vet Sci 12:1500267, ULA plate 48h, 3D CM significantly suppresses LPS-DH82 M1 p<0.0001) | `Other/2026-07-28_Lee_2025_FrontVetSci_canine_MSC_3D_spheroid.md` |
 
 ### 2026-07-17
-| DOI | Vendor | 类器官 | 标题 | 路径 |
-|---|---|---|---|---|
-| `260528_appnote` | CelVivo | 通用 | Influence of shear stress on long-term 3D construct performance: Comparison of orbital shaker and ClinoStar system (vs 竞品杀手文档) | `Celvivo/260528_CS_versus_OS_appnote_2026-07-17.md` |
-| `111_appnote` | CelVivo | 球体量化 | Planimetry measurements of spheroids in a ClinoReactor using FIJI - Application Note | `Celvivo/111_Planimetry_ClinoReactor_FIJI_2026-07-17.md` |
-| `Raji_2026_hMOs` | 3Brain | 多巴胺 / 中脑类器官 | Engineering functional ventral midbrain dopaminergic neurons in human organoids (hMOs + 3Brain HD-MEA) | `3Brain/Raji_2026_hMOs_dopaminergic_3Brain_MEA_2026-07-27.md` |
-| `Tasevska_2025_HCTZ` | Cellink | 缓释药片 | 3D printed extended-release hydrochlorothiazide tablets (SSE 工艺, BIO X 适用) | `Cellink/Tasevska_2025_HCTZ_3D_printed_extended_release_2026-07-27.md` |
+
+| DOI / slug | Vendor | Application | Title (short) | Vault path |
+| --- | --- | --- | --- | --- |
+| `260528_appnote` | CelVivo | Generic | Influence of shear stress on long-term 3D construct performance: Comparison of orbital shaker and ClinoStar system (vs-competitor killer document) | `Celvivo/260528_CS_versus_OS_appnote_2026-07-17.md` |
+| `111_appnote` | CelVivo | Spheroid quantification | Planimetry measurements of spheroids in a ClinoReactor using FIJI — Application Note | `Celvivo/111_Planimetry_ClinoReactor_FIJI_2026-07-17.md` |
+| `Raji_2026_hMOs` | 3Brain | Dopaminergic / midbrain organoid | Engineering functional ventral midbrain dopaminergic neurons in human organoids (hMOs + 3Brain HD-MEA) | `3Brain/Raji_2026_hMOs_dopaminergic_3Brain_MEA_2026-07-27.md` |
+| `Tasevska_2025_HCTZ` | Cellink | Extended-release tablet | 3D printed extended-release hydrochlorothiazide tablets (SSE process, BIO X compatible) | `Cellink/Tasevska_2025_HCTZ_3D_printed_extended_release_2026-07-27.md` |
 
 ### 2026-07-05
-| DOI | Vendor | 类器官 | 标题 | 路径 |
-|---|---|---|---|---|
+
+| DOI | Vendor | Application | Title (short) | Vault path |
+| --- | --- | --- | --- | --- |
 | `10.1002_btpr.2528` | CelVivo | Spheroid dissociation | Novel fluid shear-based dissociation device for improved single cell dissociation of spheroids | `Celvivo/10.1002_btpr.2528.md` |
 
-### 2026-06-25 (2 篇)
-| DOI | Vendor | 类器官 | 标题 | 路径 |
-|---|---|---|---|---|
-| `10.1016_j.stemcr.2025.102646` (v1) | CelVivo | 通用 | High-throughput human microfluidic organoid-on-a-chip platform | `Celvivo/10.1016_j.stemcr.2025.102646.md` |
-| `10.1016_j.stemcr.2025.102646_v2` | CelVivo | 通用 | 同上 v2 (重写) | `Celvivo/10.1016_j.stemcr.2025.102646_v2.md` |
+### 2026-06-25 (2 papers)
 
-### 2026-06-24 (2 篇)
-| DOI | Vendor | 类器官 | 标题 | 路径 |
-|---|---|---|---|---|
-| `10.1021_acsomega.5c02682` | 3Brain | 皮肤 | Developing tumor microenvironment in rotating human melanoma cell culture | `3Brain/10.1021_acsomega.5c02682.md` |
-| `10.1016_j.xpro.2025.103923` | CelVivo | 肺 | Protocol for the Establishment and Characterization of Lung Tumoroids | `Celvivo/10.1016_j.xpro.2025.103923.md` |
+| DOI | Vendor | Application | Title (short) | Vault path |
+| --- | --- | --- | --- | --- |
+| `10.1016_j.stemcr.2025.102646` (v1) | CelVivo | Generic | High-throughput human microfluidic organoid-on-a-chip platform | `Celvivo/10.1016_j.stemcr.2025.102646.md` |
+| `10.1016_j.stemcr.2025.102646_v2` | CelVivo | Generic | Same as v1, rewritten | `Celvivo/10.1016_j.stemcr.2025.102646_v2.md` |
 
-### 2026-06-23 (2 篇)
-| DOI | Vendor | 类器官 | 标题 | 路径 |
-|---|---|---|---|---|
-| `10.1002_jbm4.10792` | CelVivo | 通用 | High-throughput microfluidic organoid-on-a-chip (v2-munir2023) | `Celvivo/10.1002_jbm4.10792-v2-munir2023.md` |
-| `10.3390_cells11203216` | CelVivo | 肝 NAFLD | Mapping Proteome and Lipidome Changes in Early-Onset NAFLD | `Celvivo/10.3390_cells11203216.md` |
+### 2026-06-24 (2 papers)
 
-## 按 Vendor 统计 (mtime 2026-06-16 → 2026-07-28)
+| DOI | Vendor | Application | Title (short) | Vault path |
+| --- | --- | --- | --- | --- |
+| `10.1021_acsomega.5c02682` | 3Brain | Skin | Developing tumor microenvironment in rotating human melanoma cell culture | `3Brain/10.1021_acsomega.5c02682.md` |
+| `10.1016_j.xpro.2025.103923` | CelVivo | Lung | Protocol for the Establishment and Characterization of Lung Tumoroids | `Celvivo/10.1016_j.xpro.2025.103923.md` |
 
-| Vendor | 30 天精读数 | 最近一篇 |
-|---|---|---|
-| **CelVivo** | 5 篇 | 2026-07-05 |
-| **3Brain** | 1 篇 | 2026-06-24 |
-| **Cellink** | 1 篇 | 2026-07-27 |
-| **Ronawk Bio-Block** (KB 0 命中) | 1 篇 | 2026-07-28 |
+### 2026-06-23 (2 papers)
 
-## 4 周 MSC 长期培养关键词命中 (累计)
+| DOI | Vendor | Application | Title (short) | Vault path |
+| --- | --- | --- | --- | --- |
+| `10.1002_jbm4.10792` | CelVivo | Generic | High-throughput microfluidic organoid-on-a-chip (v2-munir2023) | `Celvivo/10.1002_jbm4.10792-v2-munir2023.md` |
+| `10.3390_cells11203216` | CelVivo | Liver NAFLD | Mapping Proteome and Lipidome Changes in Early-Onset NAFLD | `Celvivo/10.3390_cells11203216.md` |
 
-- `Bio-Block Ronawk 3D culture mesenchymal` (2026-07-28 入库, **未 KB 验证**; 4 周时窗 vs 2D/球体/Matrigel 平台对比)
-- `Hodge Mellott Bio-Block 3D culture` (2026-07-28 入库, **未 KB 验证**; 同上 Ronawk 团队 USC Kansas)
+## Vendor statistics (mtime 2026-06-16 → 2026-08-08)
 
-## ClinoReactor 关键词命中 (累计)
+| Vendor | 30-day deep-read count | Most recent | New this run (2026-08-08) |
+| --- | ---: | --- | --- |
+| **CelVivo** | 5 | 2026-07-05 | — |
+| **3Brain** | 1 (+ Liu 2026 + Sharma 2026 as adjacent) | 2026-06-24 (canonical) / 2026-08-08 (Liu / Sharma as HD-MEA-adjacent) | Liu 2026 (HD-MEA rating 5), Sharma 2026 (HD-MEA rating 4) |
+| **Cellink** | 1 | 2026-07-27 | — |
+| **CelVivo + 3Brain cross** | 1 | 2026-07-27 | Miao 2025 v2 (CelVivo ClinoStar rating 5, HD-MEA rating 4) |
+| **Cellink + 3Brain cross** | 0 | — | Liu 2026 (3D bioprinting microlattice rating 5) |
+| **Ronawk Bio-Block** (KB 0 hit) | 1 | 2026-07-28 | — |
 
-- `Planimetry measurements of spheroids in a ClinoReactor using FIJI` (2026-04-01 入库, **未精读**)
+## 4-week MSC long-term-culture keyword hits (cumulative)
 
-## 跟 OpenWiki 其他源的关系
+- `Bio-Block Ronawk 3D culture mesenchymal` (2026-07-28 added, **not KB-validated**; 4-week window vs 2D/spheroid/Matrigel platform comparison)
+- `Hodge Mellott Bio-Block 3D culture` (2026-07-28 added, **not KB-validated**; same Ronawk team USC Kansas)
 
-| 源 | 看什么 |
-|---|---|
-| **本文件** (literature.md) | 精读笔记 (本文件) |
-| `sources/hackernews.md` | 外部公开讨论 |
-| `sources/git-repo.md` | vault 整体结构 |
-| `commitments.md` | Robin 任务承诺 |
-| `themes.md` | 跨源主题综合 |
+## ClinoReactor keyword hits (cumulative)
 
-## 触发查询示例 (MiniMax code 用)
+- `Planimetry measurements of spheroids in a ClinoReactor using FIJI` (2026-04-01 added, **not yet deep-read**)
 
-- "Robin 最近精读了哪些 CelVivo 文献" → 读本文件 CelVivo 段
-- "ClinoReactor 相关最新研究" → 读本文件 ClinoReactor 段 + ClinoReactor 关键词命中
-- "近一周有什么新文献" → 读本文件 "最近 7 天" 段
+## Flywheel-sync pipeline (today, 2026-08-08)
 
-## 维护方式
+The `~/.hermes/data_sources/literature_flywheel.jsonl` records each paper's 8-step pipeline status (`type_judgment` → `pdf_full_text` → `image_extract` → `ollama_audit` → `seafile_upload` → `report_written` → `wiki_published` → `nocodb_patched` → `obsidian_pushed` → `openwiki_pushed` → `flywheel_index`). Today's `flywheel_index` completions:
 
-- **手动触发**: 通知 Robin "更新 literature 索引"
-- **自动**: OpenWiki cron 每天 02:00 跑 git-repo connector, 写本文件
-- **路径**: `~/.openwiki/wiki/sources/literature.md` (同步推 Gitea)
-### 2026-07-28
-| DOI | Vendor | 类器官 | 标题 | 路径 |
-|---|---|---|---|---|
-| `10.1080_17460751.2025.2572177` | Ronawk Bio-Block (KB 0 命中) | MSC / 脂肪源 | Comparison of 3D culture systems on MSC longevity (Hodge 2025) | `RegenMed/10.1080_17460751.2025.2572177.md` |
-| `10.1186_s13287-018-1085-9` | KB: CelVivo+Cellink 命中 | MSC / 3D 漂浮 | Type I collagen deposition ameliorates YAP/TAZ (Komatsu 2018) | `Cellink/10.1186_s13287-018-1085-9.md` |
-| `10.3389_fvets.2025.1500267` | KB: 0 命中 | MSC 犬源 | Enhanced immunomodulation of canine MSC 3D (Lee 2025) | `Other/10.3389_fvets.2025.1500267.md` |
-| `10.1186_s13287-020-1566-5` | KB: CelVivo+Cellink 命中 | MSC / PEMF / 软骨 | PEMF potentiate MSC paracrine cartilage (Parate 2020) | `Other/10.1186_s13287-020-1566-5.md` |
+| Paper | NocoDB destination | Wiki.js URL | Wiki Id |
+| --- | --- | --- | ---: |
+| Liu 2026 Nat Biomed Eng | **new table `Robin_Picked_Papers`** (created 2026-08-08, table_id `mbjo0wb56qv1qly`, row_id 1) | https://wiki.biokingdom.top/zh/literature/liu-2026-nbme-shape-conformal-organoid | 1692 |
+| Miao 2025 Cell v2 | `Organoid_Literature` table (row 93) | https://wiki.biokingdom.top/zh/literature/miao-2025-cell-organoid-vascularization-v2 | 1681 |
+| Sharma 2026 Cell Stem Cell | `Organoid_Literature` table (row 700) | http://10.10.10.254:3000/zh/literature/sharma-2026-cell-stem-cell-vascularized-retinal-organoid-rgc | 1678 |
 
-### 2026-08-04 (ITX 端 hermes test)
-| DOI | Vendor | 类器官 | 标题 | 路径 |
-|---|---|---|---|---|
-| `10.1038_s41586-026-assembloids-periportal` | Nature 650, 438-449 | Liver / Assembloid | Human assembloids recapitulate periportal liver (Yuan 2026) | `Organoid/10.1038_s41586-026-assembloids-periportal.md` |
+The `Robin_Picked_Papers` table is **new as of today** — created per Robin's 2026-08-08 instruction to capture papers Robin hand-picks / provides outside the regular PubMed triage. Liu 2026 is the first entry. This is **separate** from the existing `Organoid_Literature` table (which Miao 2025 v2 + Sharma 2026 landed in).
 
-### 2026-08-08
-| 10.1016/j.cell.2025.05.041 | Miao 2025 Cell - 共分化中胚层-内胚层实现类器官血管化 | Cell | 2025 | https://wiki.biokingdom.top/zh/literature/miao-2025-cell-organoid-vascularization-v2 |
+## Cross-reference with other OpenWiki sources
 
-### 2026-08-08
-| 10.1038/s41551-026-01620-y | Liu 2026 Nat Biomed Eng - Shape-conformal porous frameworks for neural organoids + HD-MEA electrophysiology | Nature Biomedical Engineering | 2026 | https://wiki.biokingdom.top/zh/literature/liu-2026-nbme-shape-conformal-organoid |
+| Source | Look here for |
+| --- | --- |
+| **This page** (`/sources/literature.md`) | Deep-read notes index + flywheel-sync pipeline status |
+| [`/sources/hackernews.md`](/sources/hackernews.md) | External public discussion |
+| [`/sources/git-repo.md`](/sources/git-repo.md) | Vault overall structure |
+| [`/commitments.md`](/commitments.md) | Robin's task commitments |
+| [`/themes.md`](/themes.md) | Cross-source synthesis |
+| [`/themes/01-organoid-equipment.md`](/themes/01-organoid-equipment.md) | CelVivo + 3Brain vendor synthesis (with HD-MEA + ClinoStar evidence anchors for Liu 2026 / Miao 2025 v2 / Sharma 2026) |
+| [`/themes/02-bioprinting.md`](/themes/02-bioprinting.md) | Cellink + 3D bioprinting synthesis (with Liu 2026 microlattice evidence anchor) |
+
+## Trigger queries (for MiniMax code)
+
+- "What CelVivo papers has Robin deep-read recently?" → read this page's CelVivo rows + `/themes/01-organoid-equipment.md` CelVivo section
+- "Latest ClinoReactor research" → read this page's ClinoReactor keyword hits + Miao 2025 v2 (vascularization cross-reference)
+- "What new papers in the past week?" → read this page's "Last 30 days" section, top 3 rows
+- "Liu 2026 shape-conformal neural organoid HD-MEA — what is it?" → [`/sources/literature-liu-2026-nbme-shape-conformal-organoid-deepread.md`](/sources/literature-liu-2026-nbme-shape-conformal-organoid-deepread.md)
+
+## Maintenance
+
+- **Manual trigger:** notify Robin "update literature index"
+- **Automatic:** OpenWiki cron 02:00 daily runs the git-repo connector + observes the flywheel-sync jsonl; the `## Last 30 days of deep reads` section is updated by mtime census, and the `## Flywheel-sync pipeline` section is updated by inspecting the `flywheel_completed_at` field.
+- **Path:** `~/.openwiki/wiki/sources/literature.md` (synced to Gitea)
\ No newline at end of file