paper-scaffold: provenance-checked Typst manuscripts that are safe for AI agents to edit
September, 2026 • Software
Garrett, Patrick T.
paper-scaffold is a Typst manuscript scaffold in which every number in the prose is read by id from a declaration file written by the analysis, with a checksum, a record of the code and data behind it…
paper-scaffold is a Typst manuscript scaffold in which every number in the prose is read by id from a declaration file written by the analysis, with a checksum, a record of the code and data behind it, and guards on what the prose assumes about it. A static gate reports stale figures, tables and builds without re-running the analysis, and checks prose rules, word limits and journal profiles. Word export goes through pandoc with native equations. An edit guard lets a wording pass drop a number but never invent one, and a set of packaged agent skills audits claims and methods against the code that computes them.
Supplementary data and analysis code for: Enteric serotonin and the 5-HT3 gut-to-brain axis in chronic environmental heat stress — a loss-of-function and gain-of-function study in rats
September, 2026 • Dataset
Elbeeh, Mohamed E.
Supplementary data and analysis code for the manuscript "Enteric serotonin and the 5-HT3 gut-to-brain axis in chronic environmental heat stress: a loss-of-function and gain-of-function study in rats" …
Supplementary data and analysis code for the manuscript "Enteric serotonin and the 5-HT3 gut-to-brain axis in chronic environmental heat stress: a loss-of-function and gain-of-function study in rats" by Mohamed E. Elbeeh (Department of Biology, Jamoum University College, Umm Al-Qura University, 21955 Makkah, Saudi Arabia).
STUDY. Wistar rats underwent a 14-day chronic environmental heat-stress protocol under thermoneutral or heat conditions. The loss-of-function arm received the 5-HT3 receptor antagonist ondansetron (1 mg/kg/day orally); the gain-of-function arm received intracolonic serotonin (0.5 mL of a 1e-5 M solution per day) under thermoneutral conditions. Vehicle, drug-only, glutamine positive-control arms and a confirmatory female cohort were included (101 animals in total). The primary endpoint was in-vivo intestinal permeability measured as plasma 4-kDa FITC-dextran. Secondary endpoints covered barrier and translocation markers, colonic and hippocampal cytokines, redox and oxidative-stress measures, regional monoamines by HPLC, qPCR gene expression, ex-vivo colonic contractility, and a behavioural battery.
CONTENTS.
DataTemplate_heat_5HT3_gutbrain_FILLED.xlsx: the complete structured source workbook (animal log, exposure and welfare records, every endpoint sheet, and the reagent, ELISA-kit and qPCR-primer metadata sheets).
analysis_heat_5HT3_gutbrain.py: the analysis script that generates every value reported in the manuscript.
stats_full.json: the full machine-readable statistical output (group summaries, effect sizes with bootstrap confidence intervals, family-wise Sidak and Holm corrected p-values, and Benjamini-Hochberg FDR values within endpoint families).
analysis_log.txt: the execution log of the analysis run.
Supplementary_S8_Individual_animal_data.xlsx: individual animal-level values for all endpoints (101 animals, 68 endpoints).
REPRODUCIBILITY. Running the script on the workbook regenerates the complete statistical output; no value in the manuscript was entered by hand. The study was not prospectively registered; the full analysis plan is described in the Methods section of the manuscript.
ETHICS. Approved by the Biomedical Research Ethics Committee, Umm Al-Qura University (approval no. HAPO-02-K-012-2023-03-1709, March 2023). Reported in accordance with ARRIVE 2.0.
ACCESS. The files in this record are restricted. Access is granted on reasonable request to the depositor for non-commercial academic use, consistent with the data-availability statement of the manuscript.
IMPSY v1.2.1
Patch release that makes IMPSY easier to install alongside other packages.
Fixes
websockets 13 to 17 are now allowed (#120). IMPSY capped websockets below 14 for no particular reason, so…
IMPSY v1.2.1
Patch release that makes IMPSY easier to install alongside other packages.
Fixes
websockets 13 to 17 are now allowed (#120). IMPSY capped websockets below 14 for no particular reason, so installing it downgraded websockets and broke other packages that need a newer version, e.g., Colab's preinstalled tools. A new test connects a real WebSocket client to check input and output still work.
Colab notebook
The training notebook now installs the ALSA headers before pip install impsy (#118). Colab has moved to Python 3.13, and python-rtmidi has no Python 3.13 wheel for Linux yet, so pip has to build it from source (see #117). The notebook is loaded from GitHub, so this fix already applies to the "Open in Colab" link.
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