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Code, retained outputs, protocols, verification package and Supporting Information accompanying the article “Reading an Unchanged AUROC: Invariance, Insensitivity and Infeasibility in Distance-B…

Code, retained outputs, protocols, verification package and Supporting Information accompanying the article “Reading an Unchanged AUROC: Invariance, Insensitivity and Infeasibility in Distance-Based Out-of-Distribution Detection” (prepared for submission to Expert Systems). Contents: the flatresaudit Python package (three checks: ranking reach and realized reordering from image-level scores, separating low-reach responses from empirical protection at the tested dose; pre-data feasibility of corrected permutation inference; mean-shift projection, with construction-target status left to a separate provenance review); the full analysis pipeline (73 scripts) and every retained output; a verification script that checks 376 reported numbers; a map from every table and figure to its script, input, output and reproducibility level; the Supporting Information (proofs S1.1–S1.9, Tables S1–S10, LaTeX source and PDF); the internal protocols (none filed with a third-party registry) with a protocol registry of dates and SHA-256 hashes, the deviation and correction logs and a provenance record; split metadata, data-access terms and tested environments. The audit diagnoses a detector’s scores and rankings; it does not certify clinical safety. The planted-ground-truth validation, including its confirmatory test and the comparison with confidence-interval and equivalence readings, is reproducible end-to-end from this archive (byte-identical outputs under the pinned versions). The dermatology study is verifiable from retained outputs and partially re-executable: images, the PanDerm checkpoint, embeddings, adapter weights, per-example scores, and two unpublished upstream modules are not included. Derived statistics and identifiers remain subject to the source datasets’ terms (DATA_LICENSE.md). The revised main Results include the retained five- versus ten-seed calibration comparison. The multiway bootstrap intervals are exploratory and unadjusted. Adapter-external evaluation does not establish backbone-pretraining disjointness: image-, lesion-, and patient-level overlap with PanDerm pretraining has not been independently verified. The ISIC near-duplicate screen does not inspect the complete pretraining corpus. MIT applies to author-written code and documentation. Third-party derived data remain subject to the original providers’ terms in DATA_LICENSE.md; the record license does not relicense third-party data.

FASTA peptide verification and protein-group annotation for APB2 results.

Semantic source catalogues and column resolution for APB results.

Rules-driven conversion of quantitative proteomics software output to AnnData, with search-parameter parsing and storage-neutral result tooling.

Typed peptide-to-protein matching and parsimonious protein inference.

Streaming protein records and config-driven Polars FASTA frames.

Foundational Note 03 established the static–dynamic architecture of first bifurcation: the undivided whole is structurally static, the two branches are static when considered in themse…

Foundational Note 03 established the static–dynamic architecture of first bifurcation: the undivided whole is structurally static, the two branches are static when considered in themselves, and primitive motion resides in the persistent shared interface as continuous relational change. Foundational Note 05 supplied an arithmetic–topological realisation of the same architecture through the Pontryagin pair Aval ∼=⨁︂p∈PZ, ˆ︁ Aval ∼=Π︂p∈PU(1), where the discrete valuation lattice supports no non-constant continuous path, while the compact character interface supports continuous phase evolution. The present note therefore does not ask again where motion resides. It asks the next question: how can relational phase motion support a metric readout without presupposing spacetime and without identifying internal phase coordinates directly with physical spacetime coordinates? The answer is developed in four steps. First, primitive motion is represented by an unparametrised phase history on the character interface; the auxiliary path parameter is not identified with time. Second, the ordinary logarithm is characterised, up to an overall calibration, as the continuous multiplicative-to-additive readout on positive scale. Third, every finite prime sector carries a unique translation-invariant diagonal metric whose channelscale is ℓ∗ log p: gF = ℓ2∗Σ︂p∈F(log p)2ϑp ⊗ ϑp, where ϑp = −iz−1 p dzp is the Maurer–Cartan one-form on the p-th circle. The full infinite interface is handled by a finite-log-length admissibility condition rather than by an unjustified infinite-dimensional Riemannian metric. Fourth, a bounded finite-rank readout map produces a genuine finite-dimensional quotient metric. Macroscopic dimension is therefore determined by the rank of the physical readout, not by the number of prime channels. The Euler product is treated separately and rigorously. For s > 1, ζ(s) =Σ︂n≥1e−s log n =Π︂p(1 − p−s) is the convergent partition function of the logarithmic branch functional E∗ log n, and μs(n) = n−s/ζ(s) is a genuine probability measure. This multiplicative-layer normalisation is kept strictly distinct from any additive-layer zeta regularisation of divergent series. The note derives a positive metric precursor and its finite-rank readout. It does not derive a physical clock, a Lorentzian spacetime, a universal causal speed, or equations of motion. Those require the additional bundle, central-sign, QGT, and Hamiltonian structures of FBT0B, FBT01A, FBT01E, FBT06A, and Paper–Ξ.

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. VERSION 1.1 (5 October 2026). Corrections to the analysis script only; no data and no result changed. (1) The script's header comments, command-line help text and log banner no longer describe the analysis as pre-registered, consistent with the manuscript: the study was not prospectively registered. (2) The script now treats the template-only sheets 00_README_AR and 99_Example_Row as optional, and writes the qPCR not-detected counts with text keys, so that it runs directly on the deposited workbook. The script was re-run on the deposited workbook with the same package versions (Python 3.11, numpy 2.4.4, pandas 3.0.2, scipy 1.17.1, statsmodels 0.15.0, pingouin 0.7.0); every numerical result in stats_full.json is identical to version 1.0. analysis_log.txt and stats_full.json in this version are the outputs of that re-run. 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 openly available, consistent with the data-availability statement of the manuscript.

The agribusiness system is suitable to be used as a development strategy. To formulate an appropriate pattern of agribusiness system for development, we need to understand the stage of adoption of the…

The agribusiness system is suitable to be used as a development strategy. To formulate an appropriate pattern of agribusiness system for development, we need to understand the stage of adoption of the community. This is very important to help policy makers formulate an appropriate society coaching patterns, which matches the socio-cultural of the region. This study aims to determine the stage of community adoption of the agribusiness system and the percentage of people who are at each stage of adoption. The study also examines the differences in adoption stage of society based on their differences in farming experience. The study will formulate a society coaching pattern that is in accordance with social conditions and the stage of community adoption stage. The results shown that the adoption stage of people in Hulu Sungai Selatan Regency is majority at the assessment or evaluation stage. The research also found that a longer farming experience tend to lead to a higher adoption stage. A more appropriate society coaching patterns includes a package of policies to: eliminate obstructing factors, develop driving factors, promote group pioneering and design agribusiness of community interest. published by the International Journal of Biosciences | IJB  

This dataset contains depth-normalized soil profile data from 128 profiles sampled to 500 cm depth in northeastern China. It supports the analyses in the manuscript “Carbon–Iron–Text…

This dataset contains depth-normalized soil profile data from 128 profiles sampled to 500 cm depth in northeastern China. It supports the analyses in the manuscript “Carbon–Iron–Texture Coupling Efficiency as a Diagnostic Indicator of Anomalous Deep SOC Retention.” Each profile was normalized into six standardized depth increments: H1 (0–50 cm), H2 (50–100 cm), H3 (100–200 cm), H4 (200–300 cm), H5 (300–400 cm), and H6 (400–500 cm). The Excel file contains one sheet with the following variables for each profile and depth increment: Profile ID: unique soil profile identifier depth (cm): normalized depth interval SOC (g/kg): soil organic carbon concentration clay content (<0.002 mm; %): clay fraction silt content (0.002–0.05 mm; %): silt fraction Fe₂O₃ (%): total iron oxide content measured by XRF CaO (%): calcium oxide content (clay + silt)(%): fine particle fraction FTI: Iron–Texture Index, calculated as Fe₂O₃ × (clay + silt) CE (10⁻²): Carbon–Iron–Texture Coupling Efficiency, calculated as SOC / FTI The dataset was used to compare anomalous and normal deep SOC profiles, to compute FTI and CE, and to evaluate the diagnostic performance of CE. Profiles with FTI = 0 were excluded from CE-based analyses because CE is undefined when the denominator is zero. This dataset is intended for reproducing the statistical analyses and figures in the associated manuscript.