chore: daily update 2026-08-25
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@@ -9,10 +9,20 @@ tags: [literature, deep-read, flywheel, celvivo, 3brain, cellink, femtobiomed]
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> 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.
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> Purpose: allow MiniMax code / Hermes cross-agent retrieval of "what has Robin recently deep-read".
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> 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.
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> Update: git-repo-1 2026-08-24 18:05 UTC — **5-paper root-level LDR burst** (CelVivo App Note + Aiello + Tian + Kim + Ajongbolo) — the largest single-day cluster since 2026-07-29; all 5 files landed at `04-Literature/Deep-Reads/` root (non-standard pattern vs the prior per-vendor subfolder discipline). Previous flywheel-sync (2026-08-08) completed `flywheel_index` on 3 papers (Sharma 2026 Cell Stem Cell, Miao 2025 Cell v2, Liu 2026 Nat Biomed Eng) — see entries below.
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## Last 30 days of deep reads (mtime descending)
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### 2026-08-23 (5-paper single-shot LDR burst — vault root, non-standard pattern)
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| DOI / slug | Vendor | Application | Title (short) | Vault path |
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| --- | --- | --- | --- | --- |
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| `CelVivo_AppNote_2026` | **CelVivo (ClinoStar vs Orbital Shaker direct comparison)** | Low shear stress + cytoskeletal integrity for 3D constructs (HepG2/C3A 15d + embedded Caco-2 + brain organoid) | Stougaard Borgen Løschenkohl + Sedighi Frandsen, **CelVivo Application Note 2026** (sourced from RAGFlow CelVivo KB 1555e5b2, Robin 8-24 上传; Wiki.js 1747) — head-to-head **ClinoStar vs orbital shaker** comparison: ClinoStar preserves F-actin organization + cytoskeletal integrity + tight cellular cohesion vs orbital shaker's dispersed F-actin + loose morphology + reduced cohesion (phalloidin/DAPI dual-magnification 4x + 20x); 15-day standardized workflow with 3 bio-replicates; multi-model transferability across HepG2/C3A + embedded Caco-2 + brain organoid. **Canonical ClinoStar vs-orbital-shaker competitive-killer document**; Robin's first vendor App Note deep-read | `obsidian-vault/04-Literature/Deep-Reads/CelVivo_Shear_Stress_AppNote_2026.md` |
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| `biorxiv_Aiello_Bagni_2025_RC_CFD` | **CelVivo (ClinoStar-adjacent — RC = ClinoStar simplified geometry)** + 3Brain (cortical organoid e-phys, adjacent) | CFD-quantified low shear stress Rotating Chamber for brain organoid | Aiello F, Bagni C et al. (2025) **biorxiv preprint** (the EMBO Reports submission version `Aiello_Bagni_EMBO R_050325`, Robin 8-24 从 CelVivo KB 找到的 PDF; Wiki.js 1746) — **first CFD-quantified Rotating Chamber (RC) study**: cavity geometry Ø 37.7 mm × H 8.8 mm; **COMSOL Multiphysics 6.2 shows cavity shear stress < 20 mPa** (extremely low); multi-density 1010/1020/1030 vs medium 1000 confirms shear-stress uniformity; morphological CV < 15% vs static culture CV > 30% across batches + cell lines; cortical cell type recapitulation (SOX2/Nestin/PAX6 + DCX + TBR1/SATB2/MAP2 multi-marker IHC) + scRNA-seq OXPHOS metabolic profiling. **The < 20 mPa quantitative number is direct ammunition** for the existing ClinoStar vendor-positioning pitch | `obsidian-vault/04-Literature/Deep-Reads/Aiello_Bagni_2025_biorxiv_Brain_Organoid_Fluid.md` |
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| `10.1038/s41467-025-60934-8` | (no vendor callout — cardiac application-domain) | hiPSC epicardium mTOR-driven maturation + paracrine cardiomyocyte cross-talk | Tian Y, Lucena-Cacace A, Tani K et al. (2025) **Generation of mature epicardium derived from human-induced pluripotent stem cells via inhibition of mechanistic target of rapamycin** (Nat Commun; Wiki.js 1745) — **Torin1 (dual mTORC1/2 inhibitor, 200 nM) drives hiPSC epicardium maturation**: mature markers (TJP1/WT1/TBX18/ALDH1A2/CDH18) up + EMT markers (SNAI1/SNAI2/CDH2/CDH1) down + proliferation markers (MKI67/PCNA/MCM2) down + fatty-acid metabolism maturation (PDK4/PPARGC1A/SIRT1/FASN/SREBF1); 379 DEGs; adult-like profile vs GSE84085; YBX3 + MAFF identified as Torin1-specific TFs; **paracrine TNNI3 upregulation in hiPSC ventricular cardiomyocyte EBs co-cultured for 10 days**. **First cardiac-epicardium paper in Robin's deep-read set** | `obsidian-vault/04-Literature/Deep-Reads/Tian_2025_NatCommun_Epicardium_mTOR.md` |
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| `10.1038/s41467-024-55752-3` | **3Brain (HD-MEA competitor / adjacent paper — 3rd next-gen HD-MEA approach)** | EGaIn liquid-metal 3D MEA + magnetically reshapable + cortical organoid electrophysiology | Kim E, Jeong E, Hong YM et al. (2025) **Magnetically reshapable 3D multi-electrode arrays of liquid metals for electrophysiological analysis** (Nat Commun; Wiki.js 1744) — microfluidic direct-ink-writing EGaIn 3D pillar MEA with **pillar height 25-310 μm (R² > 0.95, n=12)** + **pillar diameter 14 μm** (single-neuron scale) + parylene-C selective encapsulation; **Ni magnetic layer for magnetic reshape** → shape conforms to different organoid sizes; hPSC cortical organoid maturation 15/30/45/60/120 days → 6-marker co-expression (MAP2/GFAP/VGLUT1/SATB2/CTIP2) = cortical 6-layer-like structure; biocompatible 4-month organoid + 3D MEA co-culture 14d; 64-channel MEA single-unit spike + network synchronization. **3 distinct next-gen HD-MEA approaches now in Robin's deep-read set**: Liu 2026 Rogers Lab flexible-electronics framework + Kim 2025 EGaIn 3D pillar + 3Brain Accura-3D rigid CMOS | `obsidian-vault/04-Literature/Deep-Reads/Kim_2025_NatCommun_Liquid_Metal_3D_MEA.md` |
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| `10.3390/cells14110842` | **CelVivo (ClinoStar-adjacent) + 3Brain (HD-MEA-adjacent)** | Brain organoid + assembloid review (disease modeling + drug discovery) | Ajongbolo AO, Langhans SA (2025) **Brain Organoids and Assembloids—From Disease Modeling to Drug Discovery** (Cells; Wiki.js 1743) — **canonical brain organoid + assembloid review**: 3-tier taxonomy (whole-brain → region-specific → complex systems); 4-class characterization methodology (morphological + biochemical + functional + omics); disease-modeling boundaries (neurodevelopmental / neurodegenerative / brain-tumor); drug-discovery HTS pipeline (96-well + microfluidic + automated imaging + AI phenotype). **First comprehensive brain-organoid review** in Robin's deep-read set since the 2026-07-29 Organoids 2026 review — pairs with that review to anchor the brain-organoid review lane | `obsidian-vault/04-Literature/Deep-Reads/Ajongbolo_2025_Cells_Brain_Organoids_Review.md` |
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### 2026-08-16 (Quintard 2024 + Guo 2026 — 2 papers on the same day)
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| DOI | Vendor | Application | Title (short) | Vault path |
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@@ -232,3 +242,62 @@ The `Robin_Picked_Papers` table is **new as of today** — created per Robin's 2
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- **Business relevance**: 4 大产品线 (CelVivo ClinoStar / 3Brain MEA / Femtobiomed CellShot / Cellink BIO X) 全部可对接 AIVOs 平台 = 完整 湿+干 实验方案
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- **Tags**: 综述, 类器官, 人工智能, 虚拟器官, 数字孪生, 多组学, Bioactive-Materials-2026
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| 10.1038/s41598-026-42990-2 | Sci Rep 2026 | Liver | Liang 2026 小鼠肝类器官成熟+纤维化建模平台 | obsidian-vault/04-Literature/Deep-Reads/Liver/2026-08-12_Liang_2026_SciRep_liver_organoid_fibrosis_platform.md |
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## 2026-08-24 - Ajongbolo & Langhans 2025 Cells (PMID 40498018)
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- **DOI**: 10.3390/cells14110842 | **JIF**: 7.0 (Cells MDPI)
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- **Wiki.js**: https://wiki.biokingdom.top/literature/ajongbolo-2025-cells-brain-organoids-review (ID 1743)
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- **主题**: 脑类器官 + assembloid + 类器官芯片 + tumoroid 四大范式综述;神经发育/神经退行/脑肿瘤建模与高通量药物筛选
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- **关键发现**: 综述把脑类器官从分散成果整合成标准化决策树;神经发育建模最成熟(复现率 70%+),脑肿瘤个性化最高
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- **配图**: 2 张 (Fig 1 分类树 + Fig 2 表征方法分类) — Wiki.js /u 公网, ADOPT 2/2
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- **PDF**: NAS SMB fallback (8-18 坑 12 命中第 2 次, Cloudreve share 返 200 但公网 404)
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## 8-24 精读报告永久格式规则 (Robin 拍板)
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1. **不写本地副本路径** — 报告末尾 PDF 行后不再加 NAS SMB 路径
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2. **转发语加 "转发语:" 前缀** — 末尾 `> **转发语:**` 起头,不裸 `>`
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3. 这 2 条永久生效, 未来精读报告 + patch 必守
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## 2026-08-24 - Kim et al. 2025 Nat Commun (PMID 40016200)
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- **DOI**: 10.1038/s41467-024-55752-3 | **JIF**: 16.6 (Nat Commun)
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- **Wiki.js**: https://wiki.biokingdom.top/literature/kim-2025-natcommun-liquid-metal-3d-mea (ID 1744)
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- **主题**: 液态金属(EGaIn)3D pillar MEA + 磁可重塑 + 皮层类器官内部 SU 电生理记录 + 6 月成熟度量化
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- **关键发现**: 首次实现类器官**内部**单单元电生理记录 + 噪声 13 μV + 6 月成熟(spike rate↑, burst duration↑, p<0.05);磁场驱动 pillar 重塑 20 循环稳定
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- **配图**: 6 张 (Fig 1-6, ADOPT 6/6) — Wiki.js /u 公网
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- **PDF**: NAS SMB fallback (8-18 坑 12 第 3 次命中,Nature 系 frp/share-handler 系统性 bug)
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- **PDF 直链可用**: https://www.nature.com/articles/s41467-024-55752-3.pdf (Nature 子刊 PDF 公开访问)
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## 8-24 精读配图永久规则 (Robin 拍板)
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1. **多 panel 复合图必须整页渲染** — caption_y 裁剪到 caption 上方, 覆盖 panel 字母
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2. **嵌入大图 xref 仅用于单 panel 纯图像图** — 嵌入图本身不含文字标注
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3. **Springer Nature 系双栏全宽 Figure** — caption 在图下方, 整页渲染到 caption_y - 15
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4. **视觉审核 panel 数 ≥ 原文 caption 声明** — 是判 ADOPT 的硬阈值
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5. 这 4 条永久生效, 未来精读 + patch 必守
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## 8-24 v2 二次反馈: Springer Nature PDF 嵌入图只含部分 panel
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- 根因: PDF 嵌入图 xref 只含 raster 部分, 部分 panel 是矢量绘制 (PDF vector, 无 xref)
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- 修法: 每个 Figure 走"完整 page 渲染" — 从 page 顶部 (y=33 article header 后) 到 caption_y - 15
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- 实战: Kim 2025 Fig 5 嵌入图 xref 212 只含 f-j 网络图, 完整 Fig 5 还有 a-e SU trace + 柱状图 (5 个矢量绘制 panel)。Fig 5 v4: 228/50 ADOPT, 10/10 panels 全在
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- 这条永久生效, 未来精读 + patch 必守
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## 2026-08-24 - Tian et al. 2025 Nat Commun (PMID 40593704)
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- **DOI**: 10.1038/s41467-025-60934-8 | **JIF**: 16.6 (Nat Commun)
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- **Wiki.js**: https://wiki.biokingdom.top/literature/tian-2025-natcommun-epicardium-mtor (ID 1745)
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- **主题**: mTORC1/2 双抑制 (Torin1) 驱动 hiPSC 心外膜成熟, YBX3/MAFF TF 轴 + 3D 类器官 + 心肌旁分泌共培养
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- **关键发现**: 379 DEGs; 心外膜转录组从胎儿表型推到成体; mTORC2 是关键节点; 心外膜旁分泌 IGF2/FN1 推动心肌 TNNI3 成熟
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- **配图**: 7 张 (Fig 1-7, 4/7 ADOPT Fig 4-7, Fig 1-3 待限流补审) — v5 智能渲染 (含跨页拼接)
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- **PDF**: NAS SMB fallback (8-18 坑 12 第 4 次命中)
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## 2026-08-24 - Aiello & Bagni biorxiv preprint (CelVivo KB 来源)
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- **Title**: Design and validation of a low-shear Rotating Chamber system for brain organoid culture
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- **Source**: RAGFlow CelVivo KB (1555e5b2... 170 docs), Brain_Organoid_Fluid_biorxiv.pdf (14MB, 49 chunks)
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- **Wiki.js**: https://wiki.biokingdom.top/literature/aiello-bagni-2025-biorxiv-rotating-chamber-brain-organoid (ID 1746)
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- **主题**: CelVivo ClinoStar 旋转腔 COMSOL CFD 量化 (<20 mPa 剪切力) + 跨细胞系/批次形态变异系数 <15% + 完整皮层细胞类型与代谢成熟
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- **配图**: 5 张 (Fig 1-5, MiniMax 限流未审) — v3 拼接 (figure 在 page 40-44, caption 在 page 32-35, 跨页布局)
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- **PDF**: NAS SMB fallback
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## 2026-08-24 - CelVivo App Note shear stress (CelVivo KB 来源)
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- **Title**: Influence of shear stress on long-term 3D construct performance: Comparison of orbital shaker and ClinoStar system
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- **Source**: RAGFlow CelVivo KB (1555e5b2... 170 docs), Shear_Stress_OS_CelVivo_appnote.pdf (1.4MB, 11 chunks)
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- **Wiki.js**: https://wiki.biokingdom.top/literature/celvivo-appnote-shear-stress-2026 (ID 1747)
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- **主题**: CelVivo 官方 App Note — ClinoStar vs Orbital Shaker head-to-head 对比 HepG2/C3A + Caco-2 + 脑 organoid 三模型, 证明低剪切力优势跨细胞模型可复现
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- **配图**: 5 张 (Fig 1-5, MiniMax 限流未审) — v4 智能拼接 (xref bbox + caption 段)
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- **PDF**: NAS SMB fallback
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