Robin/openwiki-wiki
1
0 Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
0442735a59eda432a8b1f14f0ad9fddda8bc2738
openwiki-wiki/sources/literature.md
T

55 KiB
Raw Blame History

type, title, openwiki_generated
type title openwiki_generated
Reference Literature Deep-Reads — cross-agent deep-read index true

Zhu 2025 Adv Sci - 类器官 + 个体化 CAR-γδ T cocktail 治疗异质性 GBM (2026-09-28)

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, brain-organoid ALI oxygen engineering, HGSC ovarian cancer precision medicine). Backed by the Obsidian vault 04-Literature/Deep-Reads/ and the flywheel-sync pipeline; synthesis pages are linked per paper. The 2026-09-11 fetch added 2 new entries after the vault silence streak was broken at 2026-09-10 (Tomas 2026 HGSC + Vijakumaran 2026 brain-organoid ALI oxygen engineering, the latter being the first v4 Flywheel auto-sink pipeline entry); the prior 2026-08-31 CelVivo cluster remains the most-recent vault activity for 11 calendar days before the 2026-09-10 / 2026-09-11 resumption." tags: [literature, deep-read, flywheel, celvivo, 3brain, cellink, femtobiomed, tevonian-2026-vascularized-liver-mps, yang-2026-cardiac-organoid-review, shen-2026-vascularized-organoids-review, zhai-2026-3d-skin-pemphigus, yan-2024-tmem106b-sars-cov2-brain-organoid, stewart-2023-ba5-xbb-neurotropic-brain-organoid, nguyen-2024-jev-g4-australia-brain-organoid, aiello-2025-brain-organoid-reproducibility, miao-2025-vascularized-lung-gut-organoids, pasca-2025-nature-assembloid, microgravity-reproductive-review-2026, tomas-2026-hgsoc-parpi-spheroid-organoid, vijakumaran-2026-brain-organoid-ali-oxygen-engineering, 2026-09-11, 2026-09-10, 2026-08-31, 2026-08-27, 2026-08-25, 2026-08-24, 2026-08-23, vascularized-organoids, cardiac-organoids, skin-organoids, brain-organoid-virology-cluster, third-5paper-burst, celvivo-capital-v-parallel-subfolder, flywheel-v4-auto-sink, vault-silence-broken, vault-resumed-after-11d, post-celvivo-burst-cluster-resumption] timestamp: 2026-09-11T18:14:00Z

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)

2026-09-12 (colorectal neuroendocrine-neoplasm PDO+PDOX BRAF/MEK — non-vendor, PMC gold OA)

DOI Vendor Application Title (short) Vault path
10.1210/jendso/bvag196 none — 0 product mentions (Matrigel static) Rare colorectal NEN: 3 PDO lines (37.5%), WES/RNA-seq fidelity, BRAF-mutant BRAF/MEK combo Chen et al 2026 J Endocr Soc bvag196 (PMID 42694446; PMC13538959; Wiki 1790) — combo IC50 dabrafenib 3.766→0.505µM; PDOX TGI 66.27% (P=.021) obsidian-vault/04-Literature/Deep-Reads/chen-2026-crc-neuroendocrine-neoplasm-organoid-braf.md

2026-09-11 (Vijakumaran 2026 brain-organoid ALI oxygen engineering — first v4 Flywheel auto-sink pipeline entry)

DOI / slug Vendor Application Title (short) Vault path
vijakumaran2026-brain-organoid-ali-oxygen-engineering TBD — vendor callout pending (path is Literature/Deep-Reads/Organoid/, suggesting Robin classified it under brain-organoid culture-technique domain; NocoDB Id=3029; vendor mapping pending Tavily verification) Brain organoid air-liquid interface (ALI) oxygen engineering Vijakumaran 2026 Air-liquid interface-centered oxygen engineering in human brain organoids (NocoDB Id=3029; Wiki ID TBD; first paper routed through the v4 Flywheel auto-sink pipeline per the 09bec367 commit message 飞轮 v4 自动 sink) — air-liquid interface (ALI) culture technique applied to human brain organoids to control oxygen exposure for neural maturation; the ALI-centered oxygen engineering pattern is structurally adjacent to CelVivo ClinoReactor (long-term stable oxygen-controlled organoid culture) + 3Brain HD-MEA (downstream functional validation via electrophysiology) + Mimetas OrganoPlate (ALI culture is the canonical Mimetas OrganoPlate use case for airway / lung / intestinal epithelia, now applied to brain organoid) — vendor-mapping step pending obsidian-vault/Literature/Deep-Reads/Organoid/vijakumaran2026-brain-organoid-ali-oxygen-engineering.md

2026-09-10 (HGSC ovarian-cancer PDO combination-therapy deep-read — non-vendor, PMC gold OA — vault commit landed 2026-09-10)

DOI Vendor Application Title (short) Vault path
10.1080/15384047.2025.2611602 none — 0 product mentions (spheroid = ULA static plate; organoid = Cultrex BME; no bioreactor/spinner) HGSC patient-ascites iOvCa lines (n=6) as spheroids + organoids; carboplatin ± olaparib/niraparib direct vs sequential Tomas EJ, Davis J, Ramos Valdes Y, Shepherd TG (2026) Evaluating carboplatin and PARP inhibitor combination efficacy using high-grade serous carcinoma spheroids and organoids (Cancer Biol Ther 27(1):2611602; Western University; PMID 41520277; PMC12795296 gold OA; Wiki.js 1787; vault commit 1fd63019 2026-09-10 — first vault commit since the 2026-08-31 CelVivo cluster) — direct combination did NOT exceed carboplatin alone (no additivity/synergy); only exception = BRCA1-mutant iOvCa195 organoids benefit when PARPi given FIRST; niraparib more potent than olaparib except iOvCa256 (27.16 vs 18.09 µM); RAD51 foci functional HRD validation. Key "honest negative" for clinical-trial sequencing of PARPi-before-chemo in HRD patients obsidian-vault/04-Literature/Deep-Reads/tomas-2026-hgsoc-carboplatin-parpi-spheroid-organoid.md

2026-08-31 (5-paper CelVivo-anchored single-shot LDR burst — NEW CelVivo/ capital-V subfolder)

DOI Vendor Application Title (short) Vault path
10.3389/fmicb.2023.1320856 CelVivo ClinoStar (direct platform) SARS-CoV-2 omicron BA.5/XBB neurotropic brain organoids (K18-hACE2 mice + human brain organoids) Stewart R, Yan K, Ellis SA et al. (2023) SARS-CoV-2 omicron BA.5 and XBB variants have increased neurotropic potential over BA.1 in K18-hACE2 mice and human brain organoids (Front Microbiol 14:1320856; QIMR Berghofer Medical Research Institute + University of Queensland; first file in NEW CelVivo/ capital-V subfolder) — BA.5/XBB variants have increased neurotropic potential vs BA.1; MA1 infection cell count higher in human brain organoids (CelVivo ClinoStar); companion to Yan 2024 + Nguyen 2024 in the QIMR Berghofer Suhrbier/Rawle viral-neurotropism brain-organoid trio obsidian-vault/04-Literature/Deep-Reads/CelVivo/stewart-2023-ba5-xbb-neurotropic-brain-organoids.md
10.1038/s44319-025-00619-x CelVivo ClinoStar/ClinoReactor ⭐⭐⭐⭐⭐ (CelVivo ApS is a co-author) Brain organoid reproducibility via controlled fluid dynamics Aiello G, Nemir M, Vidimova B, Ramel C, Viguie J, Ravera A, Wrzesinski K*, Bagni C* et al. (2025) Increased reproducibility of brain organoids through controlled fluid dynamics (EMBO reports 26:6209-6239; 洛桑大学 + 罗马 Tor Vergata 大学 + 西北大学 (南非) + CelVivo ApS (丹麦) co-author; second file in NEW CelVivo/ capital-V subfolder) — CV <15% morphological consistency vs static culture CV >30% across multi-batch + multi-iPSC-line brain organoid cultures + scRNA-seq OXPHOS metabolic profiling + cortical cell type recapitulation (SOX2/Nestin/PAX6 + DCX + TBR1/SATB2/MAP2 multi-marker IHC). The CelVivo ApS co-author affiliation is the first direct CelVivo-platform co-authored deep-read in Robin's set obsidian-vault/04-Literature/Deep-Reads/CelVivo/aiello-2025-brain-organoid-reproducibility.md
10.1038/s44298-024-00025-5 CelVivo ClinoStar (direct platform) Japanese Encephalitis virus genotype 4 isolate characterization (2022 Australian outbreak) + brain organoids Nguyen W, Gyawali N, Stewart R, Tang B, Cox AL, Yan K, Larcher T, Bishop CR, Wood N, Devine GJ, Suhrbier A, Rawle DJ (2024) Characterisation of a Japanese Encephalitis virus genotype 4 isolate from the 2022 Australian outbreak (npj Viruses 25; QIMR Berghofer + INRAE; third file in NEW CelVivo/ capital-V subfolder) — JEV G4 isolate from 2022 Australian outbreak; brain organoid CelVivo ClinoStar + mouse model; extends the QIMR Berghofer Suhrbier/Rawle viral-neurotropism brain-organoid line into the flavivirus (JEV) application domain. JEV is endemic in 东南亚 + 中国南方 + 西太平洋 — directly relevant to Chinese infectious-disease R&D customer base obsidian-vault/04-Literature/Deep-Reads/CelVivo/nguyen-2024-jev-g4-2022-australia-brain-organoids.md
10.1016/j.cell.2025.05.041 CelVivo ClinoReactor ⭐⭐⭐⭐⭐ (direct platform validation as co-differentiation + vascularization standard) Co-development mesoderm+endoderm for organotypic vascularization in lung and gut organoids Miao Y, Pek NM, Tan C, Chen Y-W, Guo M*, Gu M* (2025) Co-development of mesoderm and endoderm enables organotypic vascularization in lung and gut organoids (Cell 188:1-19; 8-08 精简版已升级完整版; fourth file in NEW CelVivo/ capital-V subfolder) — companion to the 2026-08-08 flywheel-sync Miao 2025 v2 deep-read (/home/ldw/workspace/Miao2025_Cell_v2.md); the Cell published version extends the v2 deep-read with the canonical CelVivo ClinoReactor co-differentiation mesoderm+endoderm platform + scRNA-seq single-cell profiling of FOXF1 endothelial-mesenchymal transition obsidian-vault/04-Literature/Deep-Reads/CelVivo/miao-2025-vascularized-lung-gut-organoids.md
10.1016/j.celrep.2024.114921 CelVivo ClinoStar (direct platform) TMEM106B-mediated SARS-CoV-2 ACE2-independent brain organoid infection Yan K, Dumenil T, Stewart R, Bishop CR, Nguyen W, Suhrbier A*, Rawle DJ* (2024) TMEM106B-mediated SARS-CoV-2 infection allows for robust ACE2-independent infection in vitro but not in vivo (Cell Reports 43:114921; QIMR Berghofer Medical Research Institute; fifth file in NEW CelVivo/ capital-V subfolder) — CRISPR 筛选鉴定 TMEM106B / 硫酸乙酰肝素 / 内吞介导 ACE2 非依赖进入 in human cortical brain organoids (CelVivo ClinoStar); MA1 神经毒力更强 in vitro (滴度更高 / 感染细胞更多) + K18-hACE2 小鼠疾病更重 / 生存率更低; in vivo 不成立: wild-type / Ifnar-/- 小鼠无增加神经侵袭 + Ace2-/- 小鼠肺无法感染. Companion to Stewart 2023 + Nguyen 2024 in the QIMR Berghofer Suhrbier/Rawle viral-neurotropism trio obsidian-vault/04-Literature/Deep-Reads/CelVivo/yan-2024-tmem106b-sars-cov2-ace2-independent.md

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 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
  • "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 § "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
  • 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

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
  • NocoDB Id: 715
  • PDF: yu_2026_organoid_microglia.pdf + 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
  • NocoDB Id: 3296
  • PDF: zhou_2026_cell_reports_rock_tnbc.pdf + 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
  • NocoDB Id: 502
  • PDF: bai_2026_bioactmat_aivos.pdf + 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

2026-08-25

Tevonian 2026 Nat Commun 血管化肝 MPS (PMID 41634021)

  • DOI: 10.1038/s41467-025-68031-6
  • Path: literature/tevonian-2026-nat-commun-vascularized-liver-mps
  • Wiki ID: 1749
  • 关键发现: PDMS+fibrin+原代肝+HUVEC 血管化肝 MPS, 14天 IR 建模, 单核细胞浸润增强
  • Robin 业务对接: MASLD/NASH 体外建模 + 个性化药筛 + 血管化类器官平台

Yang 2026 Stem Cell Res Ther cardiac organoid review (PMID 41963991)

  • DOI: 10.1186/s13287-026-04996-5
  • Path: literature/yang-2026-stem-cell-res-ther-cardiac-organoid-review
  • Wiki ID: 1750
  • 关键发现: 复旦 + InnoStar 综述从化学定义 hiPSC 到自组织心脏类器官的完整路径, 涵盖 FGF/PI3K/Wnt/BMP/Activin/RA 五大信号通路 + 三种 3D 培养策略
  • Robin 业务对接: 心脏药物毒性测试 + hiPSC 衍生心脏类器官服务 + 心血管疾病建模

Shen 2026 Chin Med J vascularized organoids review (PMID 42268296)

  • DOI: 10.1097/CM9.0000000000004136
  • Path: literature/shen-2026-cmj-vascularized-organoids
  • Wiki ID: 1751
  • 关键发现: 华西医院综述血管化类器官 4 大策略(共培养 + 转录因子诱导 + 微流控 + 生物材料支架) + 12 维对比 + 三大未来方向
  • Robin 业务对接: 血管化类器官服务 + 多层血管网络平台 + 个性化精准医疗

Zhai 2026 Sci Adv 3D skin pemphigus (PMID 41512055)

  • DOI: 10.1126/sciadv.adz5003
  • Path: literature/zhai-2026-sciadv-3d-skin-pemphigus
  • Wiki ID: 1752
  • 关键发现: 3D 打印 + 自组织多层血管化皮肤模型, 建模天疱疮自身免疫 + EGFR 靶向治疗 + ML 辅助药筛
  • Robin 业务对接: 皮肤自身免疫病药筛 + 3D 打印客户 + 精准医疗应用

2026-08-31 (5-paper CelVivo-anchored single-shot LDR burst — NEW CelVivo/ capital-V parallel subfolder)

Stewart 2023 Front Microbiol BA.5/XBB neurotropic brain organoids (PMID 37984455)

  • DOI: 10.3389/fmicb.2023.1320856
  • Path: obsidian-vault/04-Literature/Deep-Reads/CelVivo/stewart-2023-ba5-xbb-neurotropic-brain-organoids.md
  • QIMR Berghofer Medical Research Institute + University of Queensland
  • 关键发现: SARS-CoV-2 omicron BA.5 + XBB variants have increased neurotropic potential over BA.1 in K18-hACE2 mice + human brain organoids (CelVivo ClinoStar); MA1 infection cell count higher in brain organoids
  • Robin 业务对接: 病毒神经嗜性 + 变异株 screening + 抗病毒药筛

Aiello 2025 EMBO reports brain organoid reproducibility (PMID 40976390)

  • DOI: 10.1038/s44319-025-00619-x
  • Path: obsidian-vault/04-Literature/Deep-Reads/CelVivo/aiello-2025-brain-organoid-reproducibility.md
  • 洛桑大学 + 罗马 Tor Vergata 大学 + 西北大学 (南非) + CelVivo ApS (丹麦) co-author
  • 关键发现: 受控流体动力学提高脑类器官可重复性 — CV <15% morphological consistency vs static culture CV >30% across multi-batch + multi-iPSC-line brain organoid cultures; cortical cell type recapitulation (SOX2/Nestin/PAX6 + DCX + TBR1/SATB2/MAP2 multi-marker IHC) + scRNA-seq OXPHOS metabolic profiling
  • Robin 业务对接: 脑类器官可重复性金标准 + 三甲医院 / 中国脑科学客户 + CDMO brain organoid manufacturing benchmark + multi-iPSC-line cross-validation reference

Nguyen 2024 npj Viruses JEV G4 2022 Australia brain organoids (PMID 39384709)

  • DOI: 10.1038/s44298-024-00025-5
  • Path: obsidian-vault/04-Literature/Deep-Reads/CelVivo/nguyen-2024-jev-g4-2022-australia-brain-organoids.md
  • QIMR Berghofer Medical Research Institute + INRAE
  • 关键发现: 2022 澳大利亚爆发的日本脑炎病毒基因 4 型分离株特征研究 — JEV G4 isolate characterization using human brain organoids (CelVivo ClinoStar) + mouse model
  • Robin 业务对接: 虫媒病毒 (JEV / Zika / dengue) 神经嗜性研究 + 疫苗开发 + 抗病毒药筛 + 东南亚 + 中国南方 + 西太平洋 客户对接

Miao 2025 Cell vascularized lung/gut organoids v1 published version (PMID 40713703)

  • DOI: 10.1016/j.cell.2025.05.041
  • Path: obsidian-vault/04-Literature/Deep-Reads/CelVivo/miao-2025-vascularized-lung-gut-organoids.md
  • 关键发现: 中胚层与内胚层共分化实现肺和肠道类器官的器官型血管化 — companion to the 2026-08-08 flywheel-sync Miao 2025 v2 deep-read; Cell published version extends the v2 deep-read with the canonical CelVivo ClinoReactor co-differentiation mesoderm+endoderm platform + scRNA-seq single-cell profiling of FOXF1 endothelial-mesenchymal transition
  • Robin 业务对接: lung organoid + gut organoid + 血管化 + 呼吸道病毒 / 肠道病毒感染模型 + 中国肺纤维化 / IBD pharma R&D positioning

Yan 2024 Cell Reports TMEM106B SARS-CoV-2 ACE2-independent brain organoids (PMID 39576284)

  • DOI: 10.1016/j.celrep.2024.114921
  • Path: obsidian-vault/04-Literature/Deep-Reads/CelVivo/yan-2024-tmem106b-sars-cov2-ace2-independent.md
  • QIMR Berghofer Medical Research Institute
  • 关键发现: TMEM106B 介导的 SARS-CoV-2 感染：体外强效 ACE2 非依赖感染但体内不成立 — CRISPR 筛选鉴定 TMEM106B/硫酸乙酰肝素/内吞介导 ACE2 非依赖进入 in human cortical brain organoids (CelVivo ClinoStar); MA1 神经毒力更强 in vitro; in vivo 不成立
  • Robin 业务对接: viral entry mechanism + 抗病毒药筛 + brain organoid platform validation

https://fb.biokingdom.top/api/v4/file/content/m99qHL/0/pasca...

  • Title: Human assembloid model of the ascending neural sensory pathway
  • Authors: Ji-il Kim, Kent Imaizumi, Ovidiu Jurjut, Kevin W. Kelley, Dong Wang, Mayuri V. Thete, Zuzana Hudacova, Neal D. Amin, Rebecca J. Levy, Gregory Scherrer, Sergiu P. Pasca
  • Venue: Nature (5 June 2025)
  • DOI: 10.1038/s41586-025-08808-3
  • PMID: 40205039 | PMC: PMC12137141
  • Wiki.js: https://wiki.biokingdom.top/literature/pasca-2025-nature-hasa-assembloid (ID 1758)
  • NocoDB Brain 表: Id=104
  • PDF: https://fb.biokingdom.top/api/v4/file/content/m99qHL/0/pasca-2025-assembloid-20260827.pdf
  • Citations: 99 (Nature 主刊 4 个月)
  • Business match: CelVivo ClinoStar ⭐⭐⭐⭐⭐ + 3Brain BioCAM X ⭐⭐⭐⭐⭐ + Mimetas OrganoPlate ⭐⭐⭐⭐ + Cellink BIO X ⭐⭐⭐⭐ + Femtobiomed CellShot ⭐⭐⭐
  • Method: First 4-part assembloid (hSeO/hdSpO/hDiO/hCO) from hiPS cells, scRNA-seq (54K cells), rabies tracing, calcium imaging, MEA extracellular recording. SCN9A/NaV1.7 KO reproduces CIP (Congenital Insensitivity to Pain).
  • Date added: 2026-08-27

iScience 2026 - Microgravity Reproductive Review

  • Title: A systematic review of microgravity on reproductive systems: Implications for space biology and human health

  • Authors: C.-F.L., C.-Y.C., P.-T.L., Y.-C.H. (corresponding)

  • Venue: iScience (13 Jan 2026)

  • DOI: 10.1016/j.isci.2026.114663

  • PMID: 41675042 | PMC: PMC12886544

  • Wiki.js: https://wiki.biokingdom.top/literature/microgravity-reproductive-review-2026 (ID 1759)

  • NocoDB Brain 表: Id=105

  • PDF Status: 5 路径 + S2 + Europe PMC 镜像全失败 (Robin 8-26 撞坑诚实停手);RAGFlow 解析文本 82546B 可下

  • Method: First cross-paradigm review (spaceflight + SMG + animal + human). 7 mechanisms (oxidative stress / DNA damage / cell signaling / cytoskeleton / mitochondria / EV / epigenetics). Countermeasures: AG / antioxidants / cryopreservation / RNAi.

  • Date added: 2026-08-27

  • Stewart 2023 Front Microbiol 14:1320856 — SARS-CoV-2 omicron BA.5/XBB 较 BA.1 神经趋向性增强（K18-hACE2 小鼠 + CelVivo ClinoStar 培养的人源皮层脑类器官）。BA.5 感染类器官滴度高 1-2 log、RNA 高 25 倍，神经元为主要靶细胞，脑内细胞因子风暴主导。DOI: 10.3389/fmicb.2023.1320856 | Wiki: https://wiki.biokingdom.top/literature/stewart-2023-sarscov2-ba5-xbb-neurotropic-brain-organoids

  • Aiello 2025 EMBO reports 26:6209-6239 — 通过受控流体动力学提高脑类器官可重复性：CelVivo ClinoReactor 垂直旋转培养降低流体剪切力(fFSS)，90天形态+10参数PCA显示跨批次/跨细胞系变异显著降低，17,738单细胞重现完整皮层细胞类型，OXPHOS代谢接近胎儿脑。CelVivo员工为共同作者。DOI: 10.1038/s44319-025-00619-x | Wiki: https://wiki.biokingdom.top/literature/aiello-2025-brain-organoid-reproducibility-rotating-chamber

  • Nguyen 2024 npj Viruses Article 25 — 2022 澳大利亚 JEV 基因 4 型爆发株 JEVNSW/22 特征研究：三小鼠模型 (C57BL/6J/Irf7-/-/Ifnar-/-) 毒力低于 G2/G3 且对 I 型 IFN 敏感；人源皮层脑类器官 (CelVivo Clinostar 培养) 所有 JEV/MVEV 均致细胞病变感染；IMOJEV 疫苗可交叉中和。DOI: 10.1038/s44298-024-00025-5 | Wiki: https://wiki.biokingdom.top/literature/nguyen-2024-jev-genotype4-2022-australia-brain-organoids

  • Miao 2025 Cell 188:1-19 — 中胚层-内胚层共分化 + CelVivo ClinoReactor 无 ECM 大规模培养 (约2000类器官/反应器) 实现肺/肠类器官器官型血管化：单细胞证实 aCap/gCap 毛细血管内皮 + 器官型间充质，体内移植重建人源血管网络，FOXF1/ACD 疾病模型。DOI: 10.1016/j.cell.2025.05.041 | Wiki: https://wiki.biokingdom.top/literature/miao-2025-vascularized-lung-gut-organoids-cell

  • Yan 2024 Cell Reports 43:114921 — TMEM106B 介导 SARS-CoV-2MA1 (S-E484D) ACE2 非依赖进入：CRISPR 筛选锁定 TMEM106B/硫酸乙酰肝素/内吞；人源皮层脑类器官 (CelVivo ClinoStar 培养) 中神经毒力增强，但小鼠体内 ACE2 仍必需 (Ace2-/- 肺无法感染)。DOI: 10.1016/j.celrep.2024.114921 | Wiki: https://wiki.biokingdom.top/literature/yan-2024-tmem106b-sars-cov2-ace2-independent-brain-organoids

  • Wang 2026 Cell Proliferation - Liver Organoids: From Disease Modelling to Regenerative Medicine

Scordamaglia 2025 J Transl Med - TNBC IL-1β / IGF1 / Celvivo ClinoReactor

Reference in new issue View Git Blame Copy Permalink