openwiki-wiki/sources/literature.md

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-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: 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.

Last 30 days of deep reads (mtime descending)

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)
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 1694)	Microbioreactor_2026_Rosero_FrontBioeng.md (in /home/ldw/workspace/)

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)
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.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

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)