LightChainr · LightChainr · Aug 28, 2026 · Aug 28, 2026 · Aug 28, 2026
diff --git a/.zenodo.json b/.zenodo.json
@@ -1,21 +1,30 @@
 {
-  "title": "PathoNiche Resolver-Window: Analysis Code and Derived Data for Liver Fibrosis Regression Resistance",
+  "title": "Source data and analysis code for Stellate-cell retention progressively occupies liver scar and constricts repair interfaces",
   "upload_type": "software",
-  "publication_date": "2026-07-16",
-  "description": "Analysis-code snapshots, non-identifying aggregate clinical results, public-data-derived molecular and spatial results, and publication figures supporting the manuscript 'A resolver-window imbalance links stellate-cell scar occupation to liver fibrosis regression resistance.' The clinical component contains no participant-level records or identifiers. Large public raw datasets are referenced by accession and are not redistributed. Code is MIT licensed; author-owned documentation, figures, and derived tabular outputs are CC BY 4.0.",
+  "description": "Non-identifying aggregate clinical tables, public-data-derived molecular and spatial results, audit records, analysis-code snapshots, and revised publication figures supporting progressive stellate-cell occupation of liver scar and contraction of repair interfaces.",
   "creators": [
-    {"name": "Ying, Hongyu", "affiliation": "Shanghai Pudong Hospital, Fudan University Pudong Medical Center"},
+    {"name": "Ying, Hongyu", "affiliation": "Shanghai Pudong Hospital, Fudan University Pudong Medical Center", "orcid": "0009-0002-0072-3033"},
     {"name": "Zhang, Ze", "affiliation": "Shanghai Pudong Hospital, Fudan University Pudong Medical Center"},
     {"name": "Qiao, Chunping", "affiliation": "Shanghai Pudong Hospital, Fudan University Pudong Medical Center"},
-    {"name": "Dong, Chang", "affiliation": "Shanghai Pudong Hospital, Fudan University Pudong Medical Center"},
+    {"name": "Chang, Dong", "affiliation": "Shanghai Pudong Hospital, Fudan University Pudong Medical Center"},
     {"name": "Yu, Hong-wei", "affiliation": "Shanghai Pudong Hospital, Fudan University Pudong Medical Center"}
   ],
-  "keywords": ["liver fibrosis", "hepatic stellate cells", "spatial transcriptomics", "MASLD", "fibrosis regression", "resolver window", "single-cell transcriptomics", "transient elastography", "LINCS L1000", "reproducible research"],
-  "license": "MIT",
+  "keywords": [
+    "liver fibrosis",
+    "hepatic stellate cell",
+    "spatial transcriptomics",
+    "regression resistance",
+    "resolver window",
+    "MASLD"
+  ],
+  "license": "cc-by-4.0",
   "access_right": "open",
-  "version": "1.1.0",
+  "version": "2.1.0",
   "related_identifiers": [
-    {"identifier": "https://github.com/LightChainr/PathoNiche-ResolverWindow", "relation": "isSupplementTo", "scheme": "url"}
-  ],
-  "notes": "Dual-license release: MIT for code; CC BY 4.0 for author-owned documentation, figures, and derived tabular outputs. Supported by National Natural Science Foundation of China grant 82473682 and Project of Key Medical Specialty and Treatment Center of Pudong grant PWZxk2022-08."
+    {
+      "identifier": "https://github.com/LightChainr/PathoNiche-ResolverWindow",
+      "relation": "isSupplementTo",
+      "scheme": "url"
+    }
+  ]
 }
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,12 +1,33 @@
 # Changelog
 
-## 1.1.0 - 2026-07-16
-
-- Published the stable public research-companion release.
-- Added the Zenodo DOI `10.5281/zenodo.21388386` and GitHub repository URL.
-- Corrected machine-readable creator metadata for Chang Dong.
-- Added seven final main figures in PNG, PDF, and editable SVG formats to the archived release.
-- Added Supplementary Figures S1–S29 to the archived release.
-- Added figure-to-source mapping, data governance documentation, and deterministic release validation.
+## 2.1.0-rc1 - 2026-08-28
+
+- Rebuilt Figures 1, 2, 5, and 7 as editable, terminology-aligned SVG/PDF/PNG plates.
+- Added coordinate-only UQ biopsy reconstruction, six mapping scenarios, leave-one-array-out tests, and Supplementary Figure S30.
+- Added an evidence-coded 24-edge mechanism circuit with literature-established, project-supported, and candidate classes.
+- Added environment locks, clean Python validation, deterministic image rebuild comparisons, privacy checks, and exact release manifests.
+- Expanded the release to seven main figures and Supplementary Figures S1-S30.
+- Aligned manuscript methods, legends, panel provenance, data dictionary, workflow entry points, and release metadata.
+
+## 2.0.0-rc1 - 2026-08-27
+
+- Added a panel-level reproducibility audit and dated analysis chronology.
+- Added GSE306327 structure, UQ reconstruction, and complete drug-order scoring records.
+- Rebuilt Figures 3, 4, 6, and 7 to remove incompatible scales, pseudo-replicated stage trends, unestimated dynamical quantities, and treatment-order language that exceeded the computation.
+- Added a self-contained script and compact inputs for the four replacement panels.
+- Reframed the four predictions as the final analytical organization rather than prospective preregistration.
+- Declared biological and technical units for the clinical, mouse, pooled-library, Visium, CODEX, and LINCS analyses.
+
+## 1.1.0-rc1 - 2026-07-16
+
+- Aligned repository title and documentation with the JCTH-directed manuscript.
+- Added seven final main figures in PNG, PDF, and SVG formats.
+- Added Supplementary Figures S1-S29.
+- Added figure-to-source mapping and a public-release checklist.
+- Added a deterministic release validator and numerical-anchor audit.
 - Retained only aggregate proprietary clinical outputs and public-data-derived results.
-- Excluded manuscript drafts, ethics files, author contact files, clinical linkage material, credentials, raw public archives, and model weights.
+- Excluded manuscript drafts, AI-generated concept art, ethics files, author contact files, clinical linkage material, credentials, and raw public archives.
+
+## 1.0.0-rc1 - 2026-07-13
+
+- Initial privacy-screened source-data and code release candidate.
diff --git a/CITATION.bib b/CITATION.bib
diff --git a/CITATION.cff b/CITATION.cff
@@ -1,12 +1,9 @@
 cff-version: 1.2.0
-message: "Please cite this software release and the associated manuscript."
-title: "PathoNiche Resolver-Window: Analysis Code and Derived Data for Liver Fibrosis Regression Resistance"
+message: "Please cite the associated manuscript and this archived release."
+title: "Source data and analysis code for Stellate-cell retention progressively occupies liver scar and constricts repair interfaces"
 type: software
-version: 1.1.0
-date-released: 2026-07-16
-doi: 10.5281/zenodo.21388386
-url: "https://doi.org/10.5281/zenodo.21388386"
-repository-code: "https://github.com/LightChainr/PathoNiche-ResolverWindow"
+version: 2.1.0
+date-released: 2026-08-28
 authors:
   - family-names: Ying
     given-names: Hongyu
@@ -17,18 +14,22 @@ authors:
   - family-names: Qiao
     given-names: Chunping
     affiliation: "Shanghai Pudong Hospital, Fudan University Pudong Medical Center"
-  - family-names: Dong
-    given-names: Chang
+  - family-names: Chang
+    given-names: Dong
     affiliation: "Shanghai Pudong Hospital, Fudan University Pudong Medical Center"
   - family-names: Yu
     given-names: Hong-wei
     affiliation: "Shanghai Pudong Hospital, Fudan University Pudong Medical Center"
 keywords:
   - liver fibrosis
-  - hepatic stellate cells
+  - hepatic stellate cell
   - spatial transcriptomics
-  - fibrosis regression
+  - regression resistance
   - resolver window
   - MASLD
-  - reproducible research
-license: MIT
+license: CC-BY-4.0
+repository-code: "https://github.com/LightChainr/PathoNiche-ResolverWindow"
+identifiers:
+  - type: doi
+    value: "10.5281/zenodo.22138229"
+    description: "Version-specific archival DOI for release v2.1.0"
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -4,4 +4,4 @@ This repository is an archival research companion. Please use an issue for repro
 
 Do not submit participant-level clinical data, dates linked to individuals, identifiers, ethics documents, credentials, unpublished institutional files, or third-party raw data through issues or pull requests.
 
-Code contributions should preserve biological-unit handling, frozen module definitions, thresholds, and random seeds unless the change is explicitly labeled as a sensitivity analysis. Run the release validation workflow supplied in the Zenodo archive before proposing a change.
+Code contributions should preserve biological-unit handling, frozen module definitions, thresholds, and random seeds unless the change is explicitly labeled as a sensitivity analysis. Run `python scripts/validate_release.py` before proposing a change.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -4,4 +4,4 @@ This repository is an archival research companion. Please use an issue for repro

		Do not submit participant-level clinical data, dates linked to individuals, identifiers, ethics documents, credentials, unpublished institutional files, or third-party raw data through issues or pull requests.

		Code contributions should preserve biological-unit handling, frozen module definitions, thresholds, and random seeds unless the change is explicitly labeled as a sensitivity analysis. Run the release validation workflow supplied in the Zenodo archive before proposing a change.
		Code contributions should preserve biological-unit handling, frozen module definitions, thresholds, and random seeds unless the change is explicitly labeled as a sensitivity analysis. Run `python scripts/validate_release.py` before proposing a change.