Analysis-code snapshots, non-identifying aggregate clinical results, public-data-derived molecular and spatial results, and publication figures supporting the manuscript “Persistent stellate-cell programs form larger connected scar regions with fewer repair interfaces in advanced human liver fibrosis.”
Submission-aligned release: v1.2.0
Repository: https://github.com/LightChainr/PathoNiche-ResolverWindow
Archived release: https://doi.org/10.5281/zenodo.22138229
The repository supports five principal findings:
- HSC-retention coupling to the scar field strengthens across human fibrosis stages.
- HSC-dominant regions enlarge and become more spatially connected as fibrosis advances.
- Interfaces between HSC-dominant tissue and endothelial/macrophage repair-associated regions contract with fibrosis stage.
- Injury withdrawal produces an incomplete molecular return toward the control state.
- Multi-omic and perturbation analyses nominate regulators and treatment-sequence experiments for direct testing.
The clinical component contains only non-identifying aggregate tables from an 8,142-patient index cohort and a 772-patient longitudinal elastography cohort. No participant-level clinical record is distributed.
The versioned research companion, including analysis-code snapshots, derived aggregate outputs, documentation, sensitivity results, and publication figures, is archived on Zenodo:
Qiao C, Ying H, Bu L, Xiong W. Persistent HSC Scar Topology: Analysis Code and Derived Data for Human Liver Fibrosis. Version 1.2.0. Zenodo; 2026. https://doi.org/10.5281/zenodo.22138229
The GitHub repository provides the public development and issue-tracking location. The Zenodo record is the archival citation for the submission-aligned release.
| Level | Contents | Publicly runnable |
|---|---|---|
| A | Verification of key reported numerical results | Yes, from the archived release |
| B | Inspection of derived UQ, mouse, LINCS, and aggregate clinical results | Yes, from included files |
| C | Full reconstruction of public molecular and spatial analyses | Yes, after obtaining the public raw data listed in the archive |
| D | Patient-level clinical and flow analyses | No; these require institutional approval and governed source data |
Excluded material includes participant-level records, dates linked to individuals, direct or transformed clinical identifiers, linkage keys, ethics documents, author contact files, credentials, raw third-party sequencing or imaging archives, model weights, and manuscript drafts.
- Original analysis code: MIT License.
- Author-owned documentation, figures, and derived tabular outputs: Creative Commons Attribution 4.0 International.
- Third-party source datasets remain governed by their original terms and citation requirements.
Machine-readable citation metadata are provided in CITATION.cff and CITATION.bib.