---
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]
---

# Literature Deep-Reads — cross-agent deep-read index

> 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: 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.

## Last 30 days of deep reads (mtime descending)

### 2026-08-23 (5-paper single-shot LDR burst — vault root, non-standard pattern)

| DOI / slug | Vendor | Application | Title (short) | Vault path |
| --- | --- | --- | --- | --- |
| `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` |
| `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` |
| `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` |
| `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` |
| `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` |

### 2026-08-16 (Quintard 2024 + Guo 2026 — 2 papers on the same day)

| DOI | Vendor | Application | Title (short) | Vault path |
| --- | --- | --- | --- | --- |
| `10.1038/s41467-024-45710-4` | CelVivo (ClinoStar rating 3 upstream) + Mimetas OrganoPlate (rating 4 direct) + Emulate Organ-Chip (rating 3) | Microfluidic platform for vascularized organoids | Quintard C et al. (2024) A microfluidic platform integrating functional vascularized organoids-on-chip (Nat Commun; 10 通道并行微流控芯片 + U 型捕获位 + 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) — Wiki.js IDs 1719/1720/1722, NocoDB Id 3297; 4-commit LDR cycle 2026-08-16 (`0fc8db24` → `290e9635` → `24c713de` → `4073abf4`); last commit deleted the 3Brain reference per the SOP "硬门槛合规修正" cleanup rule | `obsidian-vault/Literature/Deep-Reads/Organoid/quintard_2024_vasorganoid_chip.md` |
| `10.3389/fcell.2026.1721946` | CelVivo (ClinoStar rating 4 clinical-translation IRB) + Mimetas OrganoPlate (rating 4 co-culture ethics) + Emulate Organ-Chip (rating 3) | Organoid research IRB / ethics systematic review | Guo Z & Zhang N (2026) Ethical review key considerations for organoid applications in biomedical research—a systematic review (Front Cell Dev Biol; 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] + 5 国对照 [中国《人类遗传资源管理条例》+《涉及人的生命科学和医学研究伦理审查办法》2023 / 美国 HIPAA + Common Rule + NIH GDS / 欧盟 GDPR + Clinical Trials Regulation 536/2014 / 日本 / 韩国]) — Wiki.js ID 1724, NocoDB Id 3298; 3-commit LDR cycle 2026-08-16 (`2e6f5989` → `00f824f2` → `a4fa5a32`); Robin translated the paper into a customer-facing IRB application checklist template at `templates/类器官IRB申请清单.md` v1.0 (180 lines; 7 mandatory points + 5 customer Q&A + China vs International flow + 10 attachments + 7 citations) | `obsidian-vault/Literature/Deep-Reads/Organoid/guo_2026_organoid_ethical_review.md` |

### 2026-08-09

| DOI | Vendor | Application | Title (short) | Vault path |
| --- | --- | --- | --- | --- |
| `10.7150/thno.90492` | Microfluidic chip system + 类器官培养试剂 + 高内涵成像 + 单细胞与空间组学 (4 类共性硬件) | Organoid-on-Chip 综述 / 类器官 + 器官芯片协同平台 / 血管化、疾病建模、精准医学 | Wang H, Ning X, Zhao F, Zhao H, Li D. (2024) Human organoids-on-chips for biomedical research and applications (Theranostics 14(2):788-818, PMID 38169573; 7 图覆盖 7 大主题板块: OOCs/HOs/OrgOCs 架构 + 器官发育/血管化/免疫/器官通讯/疾病建模/精准医学; PMCID PMC10758054) — NocoDB row 3295 in `Organoid_Literature`, Wiki.js ID 1700 (v2 - grp:3 ghost page 累加) | `04-Literature/Deep-Reads/wang2024-org-on-chip.md` |

### 2026-08-08 (4 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) |
| `10.3389/fbioe.2026.1854988` | CelVivo (ClinoStar adjacent) + Cellink (BIO X adjacent) + FemtoBiomed (CellShot adjacent) | Microbioreactor design for eukaryotic cell-based biomedical applications | Rosero G et al. (2026) Microbioreactor design for eukaryotic cell-based biomedical applications (Front Bioeng Biotechnol, Mini Review; 6x productivity vs T-flask; organoid size 140% vs static control; 4 applications: CAR-T / mAb / iPSC / organoid) — NocoDB: `Robin_Picked_Papers` (PMID 42516424, Wiki.js ID 1696) | `Microbioreactor_2026_Rosero_FrontBioeng.md` (in `/home/ldw/workspace/`) |

### 2026-08-08 (Fernandez Vallone 2026 — untracked, deep-read commit `6c16dc05` + `d7df3830`)

| DOI | Vendor | Application | Title (short) | Vault path |
| --- | --- | --- | --- | --- |
| `10.3390/cells15110963` | CelVivo (ClinoStar adjacent) + 3Brain (HD-MEA adjacent) | hiPSC brain organoid Thyroid Hormone System Disrupting Chemicals (THSDC) platform | Fernandez Vallone V et al. (2026) Comparative Evaluation of hiPSC-Derived Brain Organoids as Platforms for Assessing Thyroid Hormone System Disrupting Chemicals (Cells 15:963, PMID 42274556; COs vs NSCOs; LC-MS/MS T3代谢; qRT-PCR HR/KLF9/DIO3/SEMA3C; HCA; THSDC = iopanoic acid + silychristin) — NocoDB row 3263 in `Robin_Picked_Papers`, Wiki.js Id 1698, v2 (5 张真图 + 双 H1) | `obsidian-vault/04-Literature/Deep-Reads/Cells/fernandez-vallone-2026-thsdc-brain-organoids.md` |

### 2026-08-06 (Parfitt 2024 Nat Commun — untracked deep-read, hiPSC midbrain organoid DJ1 LOF PD model)

| DOI | Vendor | Application | Title (short) | Vault path |
| --- | --- | --- | --- | --- |
| `10.1038/s41467-024-44732-2` | CelVivo (ClinoStar adjacent) + 3Brain (HD-MEA adjacent) | DJ1 LOF / midbrain organoid / Parkinson disease model | Parfitt GM et al. (2024) DJ1 缺失破坏星形胶质溶酶体蛋白降解，引发中脑类器官蛋白稳态崩溃（Nat Commun 15:1071, PMID 38200091; DJ1 KO + L166P 突变 iPSC hMIDOs; 星形胶质 α-synuclein 旁分泌毒性放大 DA 神经元死亡) | `04-Literature/Deep-Reads/Brain/2026-08-06_Parfitt_GM_et_al_NatCommun_2024_DJ1_LOF_midbrain_organoid_PD.md` |

### 2026-07-29

| 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 | 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 / 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 | 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 papers)

| 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` |

### 2026-06-24 (2 papers)

| 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` |

### 2026-06-23 (2 papers)

| 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` |

## Vendor statistics (mtime 2026-06-16 → 2026-08-08)

| 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) |
| **Across all 4 vendors** (Microbioreactor review) | 1 | 2026-08-08 | Rosero 2026 Front Bioeng Biotechnol (CAR-T / mAb / iPSC / organoid — 4 applications) |
| **Brain organoid + THSDC** (NAMs adjacent) | 1 | 2026-08-08 | Fernandez Vallone 2026 Cells (hiPSC brain organoid THSDC platform, v2 5 张真图 + 双 H1; Wiki.js Id 1698) |
| **Brain organoid + PD model** | 1 | 2026-08-06 | Parfitt 2024 Nat Commun (DJ1 LOF midbrain organoid PD model, untracked) |
| **Ronawk Bio-Block** (KB 0 hit) | 1 | 2026-07-28 | — |

## 4-week MSC long-term-culture keyword hits (cumulative)

- `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)

## ClinoReactor keyword hits (cumulative)

- `Planimetry measurements of spheroids in a ClinoReactor using FIJI` (2026-04-01 added, **not yet deep-read**)

## Flywheel-sync pipeline (today, 2026-08-08)

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:

| 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 |

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).

## Cross-reference with other OpenWiki sources

| 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)
- "Fernandez Vallone 2026 hiPSC brain organoid THSDC — what is it?" → deep-read at `obsidian-vault/04-Literature/Deep-Reads/Cells/fernandez-vallone-2026-thsdc-brain-organoids.md` (Wiki.js Id 1698, NocoDB row 3263, v2 with 5 张真图 + 双 H1)
- "Parfitt 2024 DJ1 LOF midbrain organoid PD model — what is it?" → deep-read at `04-Literature/Deep-Reads/Brain/2026-08-06_Parfitt_GM_et_al_NatCommun_2024_DJ1_LOF_midbrain_organoid_PD.md` (Nat Commun 15:1071, PMID 38200091)

## 8-07 vault mtime additions (working-tree deep-reads — not yet on `main`)

> Observed in the 2026-08-08 git-repo connector pull as **untracked files in the working tree**. These are working-tree deep-reads that the next LDR commits will fold onto `main`.

| Path | Status | Note |
| --- | --- | --- |
| `Liu2026_NBME_shape_conformal_organoid.md` | untracked @ `/home/ldw/workspace/` | canonical 2026-08-08 paper; v2-v11 已经 commit `1614ccf9` to `main` |
| `Miao2025_Cell_v2.md` | untracked @ `/home/ldw/workspace/` | canonical 2026-08-08 paper; v2 已 commit `1c05eee7` to `main` |
| `Miao2025_Cell_vascularized_organoid.md` | untracked @ `/home/ldw/workspace/` | 出处未明 working copy |
| `Microbioreactor_2026_Rosero_FrontBioeng.md` | untracked @ `/home/ldw/workspace/` | 2026-08-08 论文 working copy; v2 with SeaFile links 已 commit `65fef021` to `main` |
| `04-Literature/Deep-Reads/Brain/2026-08-06_Parfitt_GM_et_al_NatCommun_2024_DJ1_LOF_midbrain_organoid_PD.md` | untracked (2026-08-06) | DJ1 LOF midbrain organoid PD model (Parfitt 2024 Nat Commun) |
| `obsidian-vault/04-Literature/Deep-Reads/Cells/fernandez-vallone-2026-thsdc-brain-organoids.md` | untracked (2026-08-08) | Fernandez Vallone 2026 Cells hiPSC 脑类器官 THSDC (commits `6c16dc05` + `d7df3830`) |
| `retinal_organoid_deep_read_2026-08-07.md` | untracked @ `/home/ldw/workspace/` | Sharma 2026 working copy |
| `rustdesk-selfhosted-2026-08-05.md` | untracked @ `/home/ldw/workspace/obsidian-vault/` | 独立的 RustDesk 自建部署笔记 (related to `/sources/rustdesk-sop.md`) |
| `dify精读进度-20260805.md` | untracked @ `/home/ldw/workspace/` | Dify 文档精读进度追踪 |
| `literature_deepread_v6.py` + `__pycache__/` | untracked @ `/home/ldw/workspace/` | LDR pipeline v6 脚本 (脚本源) |
| `文悦精读流程线.yml` v1-v5-clean | untracked @ `/home/ldw/workspace/` | Dify 精读流程线 workflow YAML (5 版迭代) |

## 8-07 _known_associations.md 接续

> 2026-08-07 added Obsidian vault `02-Clients/Agents/_known_associations.md` 是 4 个经销商管理 Hook 升级 (commit `4b237a82`) 的输出。这页 index 是新引入的 cross-product mapping — connector 证据已在 [`/sources/distributors-china-2026.md`](/sources/distributors-china-2026.md) § "8-07 新增：_known_associations.md 索引" 索引。

## 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)
### 2026-08-11 - PMID 42041571

- **Title**: Multiscale Comparative Analyses of OVB-Organoids and Cerebral Organoids
- **Authors**: Yang J, Zhang X, Li S, Gao Z
- **Journal**: Cells 2026, 15(8), 703 (MDPI, IF ~5.1, CC-BY OA)
- **DOI**: 10.3390/cells15080703
- **Wiki.js**: [ID 1708](http://10.10.10.254:3000/zh/organoid/ovb-cerebral-organoid-multiscale-2026)
- **NocoDB Id**: 1103
- **PDF**: [cells_15_00703.pdf](https://fb.biokingdom.top/f/582d1f055f6e4365a924/?raw=1) + 10 张真实配图(xref extract)
- **Key finding**: Cells 2026 重磅 - OVB-organoids vs Cerebral 多尺度对比(中国军事医学科学院); Day 30 FOXG1+53.86% + VSX2+4.18%; TEM 突触+髓鞘; 1625 上调 + 2924 下调 DEGs; CHRNB2 6.5 倍差异; KEGG 富集到神经突触功能 vs 免疫炎症代谢
- **Business relevance**: OVB-organoids + 3Brain MEA = 眼-脑协同发育研究完整解决方案
- **Tags**: OVB-organoids, cerebral-organoids, brain-development, retinal-organoid, FOXG1, VSX2

### 2026-08-11 - PMID 41909700

- **Title**: Organoid-microglia system for modeling the immune microenvironment of the brain and retina
- **Authors**: Yu J, Tang B, Gu Z, Wang G, Liu A
- **Journal**: Frontiers in Immunology 2026, 17:1747589
- **DOI**: 10.3389/fimmu.2026.1747589
- **Wiki.js**: [ID 1709](http://10.10.10.254:3000/zh/organoid/yu-2026-organoid-microglia-front-immunol)
- **NocoDB Id**: 715
- **PDF**: [yu_2026_organoid_microglia.pdf](https://fb.biokingdom.top/f/4537d08bf4d14c6db0bc/?dl=1) + 4 张真图
- **Key finding**: 类器官-小胶质细胞共培养 3 大策略 + 6 大应用 (AD/ASD/视网膜/药筛/CRISPR/OoC); 神经-免疫体外模型空白填补
- **Business relevance**: 3Brain MEA + CelVivo ClinoStar + Femtobiomed CellShot + Cellink BIO X 4 大产品线全交叉
- **Tags**: 类器官, 小胶质细胞, 神经免疫, 脑-视网膜, 共培养

### 2026-08-11 - PMID 41686639

- **Title**: High-throughput engineered tumor organoids reveal ROCK signaling as an immunotherapeutic target in triple-negative breast cancer
- **Authors**: Zhou X, Zhu Y, Nicolas G, Wang Z, Lobie P, Ma S
- **Journal**: Cell Reports 2026, 45:116987
- **DOI**: 10.1016/j.celrep.2026.116987
- **Wiki.js**: [ID 1710](http://10.10.10.254:3000/zh/organoid/zhou-2026-deo-rock-tnbc-cell-reports)
- **NocoDB Id**: 3296
- **PDF**: [zhou_2026_cell_reports_rock_tnbc.pdf](https://fb.biokingdom.top/f/bbe6f494811047c2bba0/?dl=1) + 6 张真图
- **Key finding**: DEO 平台保留 TNBC 患者内源 TIL;ROCK 通路激动剂戊酸(PA)维持 TIL + 协同 anti-PD-1 解除 BLIS 亚型免疫抑制(联合治疗肿瘤抑制率 ~70%)
- **Business relevance**: 4 大产品线全交叉 (CelVivo ClinoStar 培养/3Brain MEA 评估/Femtobiomed CellShot 基因编辑/Cellink BIO X 制造)
- **Tags**: 肿瘤类器官, 三阴乳腺癌, ROCK信号, TIL, anti-PD-1, 戊酸, 马少华, BLIS亚型

### 2026-08-11 - PMID 41536916

- **Title**: Artificial Intelligence Virtual Organoids (AIVOs)
- **Authors**: Bai L, Su J
- **Journal**: Bioactive Materials 2026 (IF 18.2)
- **DOI**: 10.1016/j.bioactmat.2025.12.030
- **Type**: Review
- **Wiki.js**: [ID 1711](http://10.10.10.254:3000/zh/organoid/bai-2026-aivos-bioactmat)
- **NocoDB Id**: 502
- **PDF**: [bai_2026_bioactmat_aivos.pdf](https://fb.biokingdom.top/f/59c6a647037346a28197/?dl=1) + 6 张真图
- **Key finding**: AI Virtual Organoids (AIVOs) = 物理类器官 + AI 数字孪生; 数据-模型-交互三层架构; 6 大临床应用方向
- **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
- **Tags**: 综述, 类器官, 人工智能, 虚拟器官, 数字孪生, 多组学, Bioactive-Materials-2026
| 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 |

## 2026-08-24 - Ajongbolo & Langhans 2025 Cells (PMID 40498018)
- **DOI**: 10.3390/cells14110842 | **JIF**: 7.0 (Cells MDPI)
- **Wiki.js**: https://wiki.biokingdom.top/literature/ajongbolo-2025-cells-brain-organoids-review (ID 1743)
- **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
- **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
- **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
- **PDF**: NAS SMB fallback (8-18 坑 12 命中第 2 次, Cloudreve share 返 200 但公网 404)

## 8-24 精读报告永久格式规则 (Robin 拍板)
1. **不写本地副本路径** — 报告末尾 PDF 行后不再加 NAS SMB 路径
2. **转发语加 "转发语:" 前缀** — 末尾 `> **转发语:**` 起头,不裸 `>`
3. 这 2 条永久生效, 未来精读报告 + patch 必守

## 2026-08-24 - Kim et al. 2025 Nat Commun (PMID 40016200)
- **DOI**: 10.1038/s41467-024-55752-3 | **JIF**: 16.6 (Nat Commun)
- **Wiki.js**: https://wiki.biokingdom.top/literature/kim-2025-natcommun-liquid-metal-3d-mea (ID 1744)
- **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
- **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
- **配图**: 6 张 (Fig 1-6, ADOPT 6/6) — Wiki.js /u 公网
- **PDF**: NAS SMB fallback (8-18 坑 12 第 3 次命中,Nature 系 frp/share-handler 系统性 bug)
- **PDF 直链可用**: https://www.nature.com/articles/s41467-024-55752-3.pdf (Nature 子刊 PDF 公开访问)

## 8-24 精读配图永久规则 (Robin 拍板)
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
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
3. **Springer Nature 系双栏全宽 Figure** — caption 在图下方, 整页渲染到 caption_y - 15
4. **视觉审核 panel 数 ≥ 原文 caption 声明** — 是判 ADOPT 的硬阈值
5. 这 4 条永久生效, 未来精读 + patch 必守

## 8-24 v2 二次反馈: Springer Nature PDF 嵌入图只含部分 panel
- 根因: PDF 嵌入图 xref 只含 raster 部分, 部分 panel 是矢量绘制 (PDF vector, 无 xref)
- 修法: 每个 Figure 走"完整 page 渲染" — 从 page 顶部 (y=33 article header 后) 到 caption_y - 15
- 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
- 这条永久生效, 未来精读 + patch 必守

## 2026-08-24 - Tian et al. 2025 Nat Commun (PMID 40593704)
- **DOI**: 10.1038/s41467-025-60934-8 | **JIF**: 16.6 (Nat Commun)
- **Wiki.js**: https://wiki.biokingdom.top/literature/tian-2025-natcommun-epicardium-mtor (ID 1745)
- **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
- **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
- **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)
- **PDF**: NAS SMB fallback (8-18 坑 12 第 4 次命中)

## 2026-08-24 - Aiello & Bagni biorxiv preprint (CelVivo KB 来源)
- **Title**: Design and validation of a low-shear Rotating Chamber system for brain organoid culture
- **Source**: RAGFlow CelVivo KB (1555e5b2... 170 docs), Brain_Organoid_Fluid_biorxiv.pdf (14MB, 49 chunks)
- **Wiki.js**: https://wiki.biokingdom.top/literature/aiello-bagni-2025-biorxiv-rotating-chamber-brain-organoid (ID 1746)
- **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
- **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)
- **PDF**: NAS SMB fallback

## 2026-08-24 - CelVivo App Note shear stress (CelVivo KB 来源)
- **Title**: Influence of shear stress on long-term 3D construct performance: Comparison of orbital shaker and ClinoStar system
- **Source**: RAGFlow CelVivo KB (1555e5b2... 170 docs), Shear_Stress_OS_CelVivo_appnote.pdf (1.4MB, 11 chunks)
- **Wiki.js**: https://wiki.biokingdom.top/literature/celvivo-appnote-shear-stress-2026 (ID 1747)
- **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
- **配图**: 5 张 (Fig 1-5, MiniMax 限流未审) — v4 智能拼接 (xref bbox + caption 段)
- **PDF**: NAS SMB fallback