18 KiB
18 KiB
type, title, description, tags
| type | title | description | tags | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Reference | Literature Deep-Reads — cross-agent deep-read index | 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. |
|
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.jsonlfor 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 completedflywheel_indexon 3 papers (Sharma 2026 Cell Stem Cell, Miao 2025 Cell v2, Liu 2026 Nat Biomed Eng) — see the new entries below.
Last 30 days of deep reads (mtime descending)
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 |
External public discussion |
/sources/git-repo.md |
Vault overall structure |
/commitments.md |
Robin's task commitments |
/themes.md |
Cross-source synthesis |
/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 |
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.mdCelVivo 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 - "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 (commit4b237a82) 的输出。这页 index 是新引入的 cross-product mapping — connector 证据已在/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 readssection is updated by mtime census, and the## Flywheel-sync pipelinesection is updated by inspecting theflywheel_completed_atfield. - 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
- NocoDB Id: 1103
- PDF: cells_15_00703.pdf + 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