213 lines
20 KiB
Markdown
213 lines
20 KiB
Markdown
---
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type: "Reference"
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title: "Literature Deep-Reads — cross-agent deep-read index"
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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."
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tags: [literature, deep-read, flywheel, celvivo, 3brain, cellink, femtobiomed]
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---
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# Literature Deep-Reads — cross-agent deep-read index
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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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## Last 30 days of deep reads (mtime descending)
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### 2026-08-09
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| DOI | Vendor | Application | Title (short) | Vault path |
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| --- | --- | --- | --- | --- |
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| `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` |
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### 2026-08-08 (4 papers — flywheel-sync completed today)
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| DOI | Vendor | Application | Title (short) | Vault path |
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| --- | --- | --- | --- | --- |
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| `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/`) |
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| `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/`) |
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| `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) |
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| `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/`) |
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### 2026-08-08 (Fernandez Vallone 2026 — untracked, deep-read commit `6c16dc05` + `d7df3830`)
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| DOI | Vendor | Application | Title (short) | Vault path |
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| --- | --- | --- | --- | --- |
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| `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` |
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### 2026-08-06 (Parfitt 2024 Nat Commun — untracked deep-read, hiPSC midbrain organoid DJ1 LOF PD model)
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| DOI | Vendor | Application | Title (short) | Vault path |
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| --- | --- | --- | --- | --- |
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| `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` |
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### 2026-07-29
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| DOI | Vendor | Application | Title (short) | Vault path |
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| --- | --- | --- | --- | --- |
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| `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` |
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### 2026-07-28
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| DOI | Vendor | Application | Title (short) | Vault path |
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| --- | --- | --- | --- | --- |
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| `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` |
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| `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` |
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### 2026-07-17
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| DOI / slug | Vendor | Application | Title (short) | Vault path |
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| --- | --- | --- | --- | --- |
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| `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` |
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| `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` |
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| `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` |
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| `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` |
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### 2026-07-05
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| DOI | Vendor | Application | Title (short) | Vault path |
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| --- | --- | --- | --- | --- |
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| `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` |
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### 2026-06-25 (2 papers)
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| DOI | Vendor | Application | Title (short) | Vault path |
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| --- | --- | --- | --- | --- |
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| `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` |
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| `10.1016_j.stemcr.2025.102646_v2` | CelVivo | Generic | Same as v1, rewritten | `Celvivo/10.1016_j.stemcr.2025.102646_v2.md` |
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### 2026-06-24 (2 papers)
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| DOI | Vendor | Application | Title (short) | Vault path |
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| --- | --- | --- | --- | --- |
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| `10.1021_acsomega.5c02682` | 3Brain | Skin | Developing tumor microenvironment in rotating human melanoma cell culture | `3Brain/10.1021_acsomega.5c02682.md` |
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| `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` |
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### 2026-06-23 (2 papers)
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| DOI | Vendor | Application | Title (short) | Vault path |
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| --- | --- | --- | --- | --- |
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| `10.1002_jbm4.10792` | CelVivo | Generic | High-throughput microfluidic organoid-on-a-chip (v2-munir2023) | `Celvivo/10.1002_jbm4.10792-v2-munir2023.md` |
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| `10.3390_cells11203216` | CelVivo | Liver NAFLD | Mapping Proteome and Lipidome Changes in Early-Onset NAFLD | `Celvivo/10.3390_cells11203216.md` |
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## Vendor statistics (mtime 2026-06-16 → 2026-08-08)
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| Vendor | 30-day deep-read count | Most recent | New this run (2026-08-08) |
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| --- | ---: | --- | --- |
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| **CelVivo** | 5 | 2026-07-05 | — |
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| **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) |
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| **Cellink** | 1 | 2026-07-27 | — |
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| **CelVivo + 3Brain cross** | 1 | 2026-07-27 | Miao 2025 v2 (CelVivo ClinoStar rating 5, HD-MEA rating 4) |
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| **Cellink + 3Brain cross** | 0 | — | Liu 2026 (3D bioprinting microlattice rating 5) |
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| **Across all 4 vendors** (Microbioreactor review) | 1 | 2026-08-08 | Rosero 2026 Front Bioeng Biotechnol (CAR-T / mAb / iPSC / organoid — 4 applications) |
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| **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) |
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| **Brain organoid + PD model** | 1 | 2026-08-06 | Parfitt 2024 Nat Commun (DJ1 LOF midbrain organoid PD model, untracked) |
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| **Ronawk Bio-Block** (KB 0 hit) | 1 | 2026-07-28 | — |
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## 4-week MSC long-term-culture keyword hits (cumulative)
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- `Bio-Block Ronawk 3D culture mesenchymal` (2026-07-28 added, **not KB-validated**; 4-week window vs 2D/spheroid/Matrigel platform comparison)
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- `Hodge Mellott Bio-Block 3D culture` (2026-07-28 added, **not KB-validated**; same Ronawk team USC Kansas)
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## ClinoReactor keyword hits (cumulative)
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- `Planimetry measurements of spheroids in a ClinoReactor using FIJI` (2026-04-01 added, **not yet deep-read**)
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## Flywheel-sync pipeline (today, 2026-08-08)
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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:
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| Paper | NocoDB destination | Wiki.js URL | Wiki Id |
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| --- | --- | --- | ---: |
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| 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 |
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| Miao 2025 Cell v2 | `Organoid_Literature` table (row 93) | https://wiki.biokingdom.top/zh/literature/miao-2025-cell-organoid-vascularization-v2 | 1681 |
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| 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 |
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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).
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## Cross-reference with other OpenWiki sources
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| Source | Look here for |
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| --- | --- |
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| **This page** (`/sources/literature.md`) | Deep-read notes index + flywheel-sync pipeline status |
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| [`/sources/hackernews.md`](/sources/hackernews.md) | External public discussion |
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| [`/sources/git-repo.md`](/sources/git-repo.md) | Vault overall structure |
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| [`/commitments.md`](/commitments.md) | Robin's task commitments |
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| [`/themes.md`](/themes.md) | Cross-source synthesis |
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| [`/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) |
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| [`/themes/02-bioprinting.md`](/themes/02-bioprinting.md) | Cellink + 3D bioprinting synthesis (with Liu 2026 microlattice evidence anchor) |
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## Trigger queries (for MiniMax code)
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- "What CelVivo papers has Robin deep-read recently?" → read this page's CelVivo rows + `/themes/01-organoid-equipment.md` CelVivo section
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- "Latest ClinoReactor research" → read this page's ClinoReactor keyword hits + Miao 2025 v2 (vascularization cross-reference)
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- "What new papers in the past week?" → read this page's "Last 30 days" section, top 3 rows
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- "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)
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- "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)
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- "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)
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## 8-07 vault mtime additions (working-tree deep-reads — not yet on `main`)
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> 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`.
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| Path | Status | Note |
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| --- | --- | --- |
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| `Liu2026_NBME_shape_conformal_organoid.md` | untracked @ `/home/ldw/workspace/` | canonical 2026-08-08 paper; v2-v11 已经 commit `1614ccf9` to `main` |
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| `Miao2025_Cell_v2.md` | untracked @ `/home/ldw/workspace/` | canonical 2026-08-08 paper; v2 已 commit `1c05eee7` to `main` |
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| `Miao2025_Cell_vascularized_organoid.md` | untracked @ `/home/ldw/workspace/` | 出处未明 working copy |
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| `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` |
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| `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) |
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| `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`) |
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| `retinal_organoid_deep_read_2026-08-07.md` | untracked @ `/home/ldw/workspace/` | Sharma 2026 working copy |
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| `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`) |
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| `dify精读进度-20260805.md` | untracked @ `/home/ldw/workspace/` | Dify 文档精读进度追踪 |
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| `literature_deepread_v6.py` + `__pycache__/` | untracked @ `/home/ldw/workspace/` | LDR pipeline v6 脚本 (脚本源) |
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| `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) |
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## 8-07 _known_associations.md 接续
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> 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。
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## Maintenance
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- **Manual trigger:** notify Robin "update literature index"
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- **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.
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- **Path:** `~/.openwiki/wiki/sources/literature.md` (synced to Gitea)
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### 2026-08-11 - PMID 42041571
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- **Title**: Multiscale Comparative Analyses of OVB-Organoids and Cerebral Organoids
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- **Authors**: Yang J, Zhang X, Li S, Gao Z
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- **Journal**: Cells 2026, 15(8), 703 (MDPI, IF ~5.1, CC-BY OA)
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- **DOI**: 10.3390/cells15080703
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- **Wiki.js**: [ID 1708](http://10.10.10.254:3000/zh/organoid/ovb-cerebral-organoid-multiscale-2026)
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- **NocoDB Id**: 1103
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- **PDF**: [cells_15_00703.pdf](https://fb.biokingdom.top/f/582d1f055f6e4365a924/?raw=1) + 10 张真实配图(xref extract)
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- **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
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- **Business relevance**: OVB-organoids + 3Brain MEA = 眼-脑协同发育研究完整解决方案
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- **Tags**: OVB-organoids, cerebral-organoids, brain-development, retinal-organoid, FOXG1, VSX2
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### 2026-08-11 - PMID 41909700
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- **Title**: Organoid-microglia system for modeling the immune microenvironment of the brain and retina
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- **Authors**: Yu J, Tang B, Gu Z, Wang G, Liu A
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- **Journal**: Frontiers in Immunology 2026, 17:1747589
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- **DOI**: 10.3389/fimmu.2026.1747589
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- **Wiki.js**: [ID 1709](http://10.10.10.254:3000/zh/organoid/yu-2026-organoid-microglia-front-immunol)
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- **NocoDB Id**: 715
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- **PDF**: [yu_2026_organoid_microglia.pdf](https://fb.biokingdom.top/f/4537d08bf4d14c6db0bc/?dl=1) + 4 张真图
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- **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
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- **Business relevance**: 3Brain MEA + CelVivo ClinoStar + Femtobiomed CellShot + Cellink BIO X 4 大产品线全交叉
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- **Tags**: 类器官, 小胶质细胞, 神经免疫, 脑-视网膜, 共培养
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### 2026-08-11 - PMID 41686639
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|
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- **Title**: High-throughput engineered tumor organoids reveal ROCK signaling as an immunotherapeutic target in triple-negative breast cancer
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- **Authors**: Zhou X, Zhu Y, Nicolas G, Wang Z, Lobie P, Ma S
|
||
- **Journal**: Cell Reports 2026, 45:116987
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||
- **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)
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- **NocoDB Id**: 3296
|
||
- **PDF**: [zhou_2026_cell_reports_rock_tnbc.pdf](https://fb.biokingdom.top/f/bbe6f494811047c2bba0/?dl=1) + 6 张真图
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- **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%)
|
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- **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)
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- **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
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