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type: "Reference"
title: "Literature Deep-Reads — cross-agent deep-read index"
description: "Cross-agent index of Robin's literature deep-reads across the 4 vendor product lines (CelVivo / 3Brain / Cellink / Femtobiomed) and adjacent application domains (organoid IRB / ethics, vascularized organoids, microfluidic / organ-on-chip). Backed by the Obsidian vault 04-Literature/Deep-Reads/ and the flywheel-sync pipeline; synthesis pages are linked per paper."
tags: [literature, deep-read, flywheel, celvivo, 3brain, cellink, femtobiomed, tevonian-2026-vascularized-liver-mps, yang-2026-cardiac-organoid-review, shen-2026-vascularized-organoids-review, zhai-2026-3d-skin-pemphigus, pasca-2025-nature-assembloid, microgravity-reproductive-review-2026, 2026-08-27, 2026-08-25, 2026-08-24, 2026-08-23, vascularized-organoids, cardiac-organoids, skin-organoids, second-5paper-burst]
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, 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]
timestamp: 2026-08-27T18:25:00Z
---
@@ -14,6 +14,16 @@ timestamp: 2026-08-27T18:25:00Z
## Last 30 days of deep reads (mtime descending)
### 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 |
@@ -337,6 +347,42 @@ The `Robin_Picked_Papers` table is **new as of today** — created per Robin's 2
- **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
@@ -364,3 +410,13 @@ The `Robin_Picked_Papers` table is **new as of today** — created per Robin's 2
- **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