Analysis code and reproducibility archive for "A context-dependent DLD–lipoylation vulnerability in sepsis"
Year: 2026
Type: software
Abstract: Code, data and the submission snapshot for the manuscript "Tetrathiomolybdate attenuates copper-induced mitochondrial bioenergetic failure and organ injury in endotoxemic mice", submitted to Acta Pharmacologica Sinica. The model is LPS endotoxemia (intraperitoneal LPS 10 mg/kg); bench-recorded group labels in deposited raw files are retained verbatim and mapped to manuscript terminology in the change ledger (Addenda 5 and 8). The deposition contains: (1) a wetlab package with raw evidence (imaging, plate exports, qPCR, western blots with uncropped membranes, modeling records) and SHA-256 manifests; (2) code_and_logs with analysis scripts and run logs; (3) source_data_core tables linking every quantitative claim to deposited files; (4) the current Acta Pharmacologica Sinica submission snapshot — manuscript, cover letter, ARRIVE 2.0 checklist, supplementary methods, supplementary figures S1-S21 with uncropped immunoblot membranes, supplementary tables S1-S16, and the immutable preregistration of the si-DLD × TTM factorial prediction (the superseded Metabolism and Pharmacological Research snapshots remain accessible in versions v1.4.0–v1.4.10 under their own DOIs); (5) main figures 1-7 and the graphical abstract as submitted (300-dpi TIFF; the superseded four-figure renditions remain in versions v1.4.10–v1.4.11 under their own DOIs); (6) manifests and a versioned change ledger (CHANGELOG). The copper-DLD model: copper-induced ATP depletion in macrophages, gated by flux through DLD-containing complexes (DLD as a flux node / E3 hub, not a copper-binding site); organ protection by tetrathiomolybdate (TTM) in endotoxemic mice. Version history: v1.4.0-v1.4.2 accompanied a Metabolism submission (superseded). v1.4.3 (2026-10-07) regenerated the main immunoblot quantification (DLD induction 6.42-fold, TTM reversal 78.1%, ANOVA + Tukey), corrected the SuppFigS21 exposure summary and rebuilt the S10 forest. v1.4.4 added the Pharmacological Research snapshot. v1.4.5 synced the snapshots, added uncropped blots, and re-built Supplementary Fig. S14 as a single-page four-panel figure with dot-plot quantification (former bar charts superseded by deposited adjusted statistics; four-group membrane panel moved to Fig. 1I; DLD IHC and H&E panels removed as duplicates of Fig. 2D; panels re-lettered A-D). v1.4.6 fixed the author name (Huangwei Li → Huangwei Lin). v1.4.7 (2026-10-09) reworded one highlights bullet. v1.4.9 (2026-10-12) finalized Supplementary Fig. S14 at submission quality (membrane strips re-cropped from the author's re-exported composite; caption terminology corrected); completed the LPS model-terminology correction across the manuscript, supplementary methods, ARRIVE checklist, all four main figures, the graphical abstract and the supplementary-figure covers (bench-label mapping in CHANGELOG Addenda 5 and 8; public CLP datasets GSE342888/GSE313149 unchanged by design); aligned the author list and the co-first-author and corresponding-author annotations across the manuscript and all supplementary files; restored one Section 2.3 sentence (organ endpoints sampled 7.3-7.5 h after injection, per the deposited animal master list) that had regressed in the word-processor file; and replaced the western-blot display composite raw_WB_20260706/WB5_panel_ATP5A1-ATP5B.tif in the wetlab package by the author's re-export, with the superseded 2026-10-02 panel preserved inside the package under superseded/ with a notice (gray-value workbooks unchanged; all quantitative values identical in every version). v1.4.10 (2026-10-13) propagated two author-side image corrections into the snapshot: Figure 1 in the figures snapshot now carries the author's fix of the truncated panel I (immunoblot quantification), and page 16 of the uncropped immunoblot membranes PDF was re-spliced from the updated S14B ATP5A1 membrane-3 acquisition file. Docs, figures, wetlab and manifests packages were refreshed accordingly. Earlier superseded versions remain accessible under their own DOIs. All quantitative claims map to deposited source tables.Funding: NSFC 82660026; Hainan Provincial Natural Science Foundation 825RC864, 825RC856; Hainan Medical University XSTS2025168; Joint Program WSJK2026MS204. v1.4.11 delta (no quantitative value changed in any file): the manuscript was reshaped and resubmitted to Acta Pharmacologica Sinica; the Pharmacological Research snapshot (v1.4.3–v1.4.10) is superseded by an APS submission snapshot and remains accessible in version v1.4.10 under its own DOI. (1) APS_submission_snapshot_docs_v1.4.11.zip carries the text documents of the APS submission: the manuscript (new title; abstract rewritten; Springer Nature-style declarations; the Elsevier-only "Chemical compounds" section removed; all data, statistics and hedged wording unchanged), the cover letter, the ARRIVE 2.0 checklist, supplementary methods, supplementary tables S1–S16 (byte-identical to the file carried in v1.4.10, md5-verified) and the immutable preregistration (byte-identical). (2) The two large supplementary packages are deposited as separate files byte-identical to the Editorial Manager uploads: APS_Supplementary_Figures_S1-S21.zip (43-page PDF set; cover pages carry the new title and journal) and APS_Supplementary_Figure_Uncropped_Immunoblot_Membranes.zip (28-page PDF). (3) Main figures 1–4 are deposited as individual 300-dpi TIFFs md5-identical to the v1.4.10 renditions, and APS_Graphical_Abstract.tiff is a deterministic matplotlib redraw of the graphical abstract from the same audited copy on the same 3168×1344 @ 300 dpi canvas, superseding the generative-AI bitmap (Springer Nature policy on AI-generated images). The source-data core, wetlab, code-and-logs, CellSystems and manifests packages are byte-identical to v1.4.10. See CHANGELOG_v1.4.11.md for the full audit trail. v1.4.12 delta (no quantitative value changed in any file): the Acta Pharmacologica Sinica snapshot is refreshed to its final deposited state. (1) The four main-figure TIFFs carried by v1.4.11 (byte-identical to the superseded v1.4.10 renditions) are superseded by the seven main figures of the APS submission, APS_Figure_1.tiff – APS_Figure_7.tiff (300-dpi LZW RGB). Figures 1, 2, 4 and 7 carry 2026-10-15 layout refinements of the panel grid, label anchors and the internal composition of panels 2B (two-row WB-plus-quantification layout with a knockdown summary card) and 4F (four-column stress-test matrix); Figures 3, 5 and 6 are the corresponding final renditions; no data point, statistic or deposited value was altered. (2) APS_submission_snapshot_docs_v1.4.12.zip refreshes the text documents to the final Editorial Manager versions: the manuscript gains one caption clause (Figure 1F now states "n = 3 per group" for the fluorescence panel, replacing a footnote chip removed from the figure), and the cover letter, ARRIVE 2.0 checklist, supplementary methods and supplementary tables are the same-day final versions (the v1.4.11 docs zip had been staged earlier that day and carried predecessors of these five files). (3) APS_Supplementary_Figures_S1-S21.zip is refreshed to the final Editorial Manager upload and APS_Graphical_Abstract.tiff to the final deterministic redraw. (4) The uncropped-membrane package, the source-data core, wetlab, code-and-logs, CellSystems and manifests packages are byte-identical to v1.4.11. See CHANGELOG_v1.4.12.md for the full audit trail.
Institution: Hainan Medical University
Language: English
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W7204198548