Sparse departures from independence in two-way tables: a heteroscedasticity profile and detection boundary, an adaptive higher-criticism gate, and an assumption-lean exact anchor William J. Dwyer, MD, MPH, FAAP — Department of Mathematics and Statistics, University of Massachusetts Lowell. ORCID 0009-0004-0855-7222. Concept DOI (always resolves to the latest version): 10.5281/zenodo.21844797. Published v1.0.0:10.5281/zenodo.21844798. What this is The reproducibility deposit for a single combined manuscript on detecting sparse departures from independence in a two-way contingency table — the regime where dependence hides in a few cells rather than spreading across the table, so the omnibus chi-square is under-powered and a naive per-cell scan mis-calibrates. It is organized in three parts under one set of front/back matter, with a shared derivations supplement (D02): Part I — the heteroscedasticity profile and the detection boundary. The per-cell standardized deviations are heteroscedastic under the margin-conditional null; profiling that heteroscedasticity gives a closed-form detection boundary separating the sparsity/strength regimes where any test can succeed from those where none can. Part II — an adaptive higher-criticism gate. A higher-criticism statistic tuned to the margin-conditional cell law attains that boundary, with its exact null law and power characterized. Part III — an assumption-lean exact anchor and reporting apparatus. An exact margin-conditional calibration anchor and a routing rule, so a scan that mis-sizes under the asymptotic reference is replaced by one that holds its level: on a corpus of 5,543 real tables the asymptotic per-cell scan mis-sizes about two-thirds of them (mean realized size ≈ 0.33 against a 0.05 target) while the exact anchor holds near 0.01. What the deposit contains Combined manuscript (manuscripts/Dwyer_M02_Combined.{docx,pdf} + M02_Combined_Manuscript.md) and the three part-sources (manuscripts/parts/, provenance for the assembled combined text), plus the D02 derivations companion (derivations/). Verification and study code (code/) — the boundary, exact-anchor, and higher-criticism verification scripts and the power/size study drivers (numpy/scipy, fixed seeds); the docx builder (build_docx.py), the shared math-typography core (mseries_mathtype.py), the inline- and caption-math delimiters, the combined assembler (assemble_combined.py), and the audit gates (structure_audit.py, math_render_audit.py). Locked data (data/) — the study outputs (size/power, boundary, estimated-margins, efficiency) and the higher-replication "big box" runs, so every number regenerates. Figures (figures/), the novelty reviews (novelty_reviews/), the prior-art / adversarial / consistency audits (audits/), and the in-browser detector tools/honest_detection.html. All evaluation is simulation-based; the one empirical component is the public-corpus calibration scan, which uses only openly distributed contingency tables. Code is released under the MIT License; text, figures, and data under CC BY 4.0. How to cite Please cite this deposit if you use the package or the method. Citing the concept DOI references the work in general and always resolves to the latest version; cite a specific version DOI to point at an exact snapshot. Dwyer, W. J. (2026). Sparse departures from independence in two-way tables: a heteroscedasticity profile and detection boundary, an adaptive higher-criticism gate, and an assumption-lean exact anchor — reproducibility deposit [Software]. Zenodo. https://doi.org/10.5281/zenodo.21844797 BibTeX: bibtex @software{dwyer_m02_2026, author = {Dwyer, William J.}, title = {Sparse departures from independence in two-way tables: a heteroscedasticity profile and detection boundary, an adaptive higher-criticism gate, and an assumption-lean exact anchor --- reproducibility deposit}, year = {2026}, publisher = {Zenodo}, doi = {10.5281/zenodo.21844797}, url = {https://doi.org/10.5281/zenodo.21844797}, orcid = {0009-0004-0855-7222} } The DOI above is the concept DOI (resolves to the latest version); to cite a specific release use that version's DOI in place of it (e.g. 10.5281/zenodo.21844798 for v1.0.0). When the accompanying journal article appears, please cite it as the primary reference for the method and this deposit as the reproducibility archive. Version history v1.0.3 — deterministic recut (2026-08-30): the bundle is now cut with the shared mseries_deposit.write_deterministic_zip, so rebuilding the same content yields a byte-identical zip and a stable md5. Every manuscript, derivation, figure, dataset, code file, novelty review, and audit is byte-identical to v1.0.2 (all files SHA-256-matched except the three version-stamped ones). No number, theorem, table, figure, or dataset changed. Publishes as a New Version on concept 10.5281/zenodo.21844797 (build_m02_deposit.py; md5 8f2fa9f7e814ba807710480a7f60cb65, 112 files, 6,044,685 bytes). v1.0.2 — impact-first reframe (2026-08-23): the introduction and abstract reframed to lead with the applied motivation (sparse independence departures in genomics, network/text co-occurrence, pharmacovigilance, ecology, survey cross-tabulation) and the corpus calibration failure, before the detection-boundary theory. No number, theorem, figure, or dataset changed. v1.0.1 — published (2026-08-08): adds the Zenodo concept DOI to the manuscript Availability statement and CITATION.cff, and the widened Figure 8 top box. Content otherwise identical to v1.0.0. v1.0.0 ✅ 10.5281/zenodo.21844798 — first published deposit: the combined three-part manuscript, the D02 derivations, the verification and study code with fixed seeds and locked outputs, all figures, the in-browser detector, and the prior-art / adversarial / consistency audits. Provenance: every number traces to a named, deterministically-seeded script under code/; the combined manuscript is assembled by code/assemble_combined.py and built by code/build_docx.py. Related identifiers: T_root methodology 10.5281/zenodo.21522471; exact conditional engine 10.5281/zenodo.21831680.
William Dwyer· Zenodo (CERN European Organi...· 0 citations
Reproducibility package for the interval-estimate paper of the contingency-table effect-size arc, the companion to the point-estimate paper M0f. It regenerates every result behind the exact conditional confidence interval for phi^2 (and Cramer's V): the pre-registered Berger-Boos simulation (C1 passed, C2 and C3 failed) frozen before the run; the post-registration exact conditional (mid-p) interval that turns the two failures into a positive result; its characteristic-function / cosine (CF/COS) extension to larger and denser tables; the certified 2x2 coverage floor; the exact conditional median-unbiased point estimate (the fold) that resolves the residual; the shape-by-effect factorial decomposition of the small-effect coverage dip into its additive mechanisms (mid-p atom, estimand gap, discreteness residual); and the direct exact-coverage sweeps. Includes the manuscript and Additional File 1 (docx + pdf), all figures and their black-and-white-safe generators, the derivation companions, the pre-registration, a prior-art audit, the shared estimator/interval code with its exact dynamic-programming tail engines (verified to ~3e-15), and a null-coverage regression self-test. Every reported number regenerates under recorded seeds; runs are staged, resumable, and memory-capped. MIT License for code; CC BY 4.0 for documents and data.
William Dwyer· Zenodo (CERN European Organi...· 0 citations
This public reproducibility package accompanies the manuscript “Decision Robustness to Bibliographic Metadata Loss in Automated Research Evaluation: A Paired External Evaluation Study.” The study used a 1,031-record development benchmark and a frozen 1,240-record external evaluation set comprising 900 controls and 340 positives. The archive contains locked study configurations, source and freeze manifests, dataset hashes, non-identifying aggregate result tables, perturbation and analysis code, numerical-audit and supplementary-table code, the frozen rule-engine implementation, software environment specifications, and programmatically generated figures. The complete internal test suite passed 18 of 18 tests, the EV1 data gate passed all prespecified checks, and the manuscript and supplement were numerically consistent with the locked aggregate results. Record-level bibliographic metadata, labels, provenance fields, per-record predictions, adjudication materials, API caches, and LLM response caches are excluded pending licensing and reputational-safeguard review. The public package supports verification of the reported denominators, aggregate results, principal conclusions, and all six figures. A complete record-level refit requires separately governed assets identified by the hashes preserved in this archive.
Vu Minh Tue Phan, Gia Nhu Nguyen, van son Phan· Zenodo (CERN European Organi...· 0 citations
v.3.0.0 This release provides the reproducibility package supporting the manuscript: Sequence sensitivity varies across Implicit Association Tests and participant groups: a cross-domain analysis of Project Implicit archives Included cross-domain sequence-sensitivity analyses for 12 Project Implicit IAT domains in 2019; cross-year replication analyses for nine overlapping domains in 2021; subgroup heterogeneity analyses across demographic and archival groups; equal-sequence and sequence-allocation analyses; finite-sample resampling analyses; orientation and score-direction validation across all included domain-year datasets; final evidential audit and machine-readable audit tables; publication figures and compact manuscript-facing outputs. Main reproducibility additions analysis_cross_domain_sequence_sensitivity/ cross-domain and cross-year gamma estimates; subgroup gamma comparisons; allocation and standardization summaries; finite-sample results; final domain-year orientation validation; final subgroup heterogeneity magnitude summaries. Data Raw Project Implicit data and participant-level derived data are not redistributed. Public source archives and dataset-specific provenance are documented in the repository and supporting materials. License Analysis software is released under the MIT License. Source datasets remain governed by their original repository terms.
Felipe de Oliveira Matos, Marlos Andrade de Lima, Cristian Zanon et al.· Open MIND· 0 citations
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Your AI can say the test passed. Code Factory asks whether the test could ever have failed. Solo developers start with one local proof; teams bind the real diff, intent, independent checks, and receipts instead of trusting an agent's narrative. Version 0.45.1 adds a deterministic AppForge App Review evidence gate: 30 policy and release-risk checks bind the exact app build to required evidence, preserve unknowns, and keep final submission under named human control. The Graph Ops mission-control storyboard turns that review into a visible mission, tension, guidance, agency, transformation, and ready handoff. The workflow is designed to reduce avoidable App Review rework and waiting time; it does not guarantee approval or claim a measured rejection-rate reduction. Supplied local observations are not provider certification, payment settlement, production proof, security or compliance certification, or release authority. Dual licensed under MIT or Apache-2.0.
Richard Katz· Zenodo (CERN European Organi...· 0 citations
This repository contains the data, scripts, and processed outputs supporting the manuscript “Assessing boundary discontinuities in environmental protection systems in Cundinamarca, Colombia, using NDVI and spatial regression discontinuity”. The repository includes Google Earth Engine scripts used to generate annual Landsat-derived NDVI composites for 2015, 2017, 2022, and 2024; Stata do-files used to estimate annual spatial regression discontinuity models, difference-in-discontinuities models, placebo cutoff tests, density continuity tests, and manuscript figures; processed analytical datasets; statistical output tables; and figure files. The study evaluates localized boundary-level differences in vegetation condition across multiple environmental protection systems in Cundinamarca, Colombia, including protected areas registered in the National System of Protected Areas, Indigenous reserves, and Payment for Ecosystem Services schemes. The empirical approach uses institutional boundaries as geographic thresholds to compare NDVI values for pixels located immediately outside and inside protection systems. The repository is intended to support transparency and reproducibility of the analyses reported in the manuscript. Users should consult the README file and data dictionary for details on file structure, variable definitions, software requirements, and the recommended workflow for reproducing the results.
Andrés José Vergara Narváez, Tania Jiménez, Gastón Ballut-Dajud· Zenodo (CERN European Organi...· 0 citations
This paper establishes the observer as a physical node embedded in the causal graph and resolves the conceptual relation between General Relativity and Quantum Mechanics within the N.E.A. (Network Emergent Architecture) framework. The Mens Protocol defines the observer as a self-referential sampling operator, subject to the same finite bandwidth B=1 as every other node. The Stride-10 sampling window imposes a Nyquist limit on perceptual resolution. An SVD spectral audit reveals that over 95% of perceptual energy is concentrated in a single dominant mode across all tested lattice sizes — the topological origin of the subjective flow of time. This dominant mode is not a saturation plateau claim; the trend is monotonic and robust, with verification on larger lattices left as future numerical work. Three spatial dimensions are inherited from the d=3 efficiency plateau (H); the temporal dimension is inherited from the dominant singular mode of the directed sampling operator. Special and General Relativity are shown to be the geometry of bandwidth allocation on the causal graph (hardware). Motion is defined as the re-indexing of adjacency edges; the Pythagorean constraint f_int^2 + f_ext^2 = B^2 yields time dilation as an algebraic necessity. The 1/r gravitational potential is the Discrete Green's Function of the 3D graph Laplacian — a topological fingerprint of three-dimensional space. Quantum Mechanics describes the information-theoretic limits of observing that hardware with finite resources (software). The wavefunction arises as a beat envelope from aliased sampling, inheriting linearity from hardware unitarity. Measurement collapse is bandwidth hijacking. The uncertainty principle is the Nyquist limit, with a dimensionless uncertainty floor from the bandwidth constraint. Pauli exclusion is buffer-overflow protection with spin-±1/2 as time-division multiplexing. Entanglement is interpreted as a candidate topological trace on the 1D causal skeleton mandated by the Being Tax — a hypothesis, not yet a derivation. These two descriptions are not contradictory but are descriptively orthogonal, dynamically coupled layers of a single computational stack governed by the Pythagorean bandwidth constraint. The contradiction dissolves upon recognizing that physicists have been attempting to locate hardware bus specifications within software rendering algorithms. The observer's sampling rent is quantitatively denominated in Zhangyu (ZY): H_obs ≈ 1.0117 ZY as a preliminary numerical estimate. The hydrogen atom spectrum is reproduced on the discrete C8 lattice, converging to the continuum Schrödinger limit with 0.0024% deviation. ħ is demoted from fundamental status: ħ = Z × t_Tick, the product of bandwidth currency and the Tick. The preferred basis problem (OP-8), the first-principles derivation of the GR coefficient 2GM/c² (OP-O1), and Bell statistics for skeletal entanglement (OP-24) are honestly marked as open problems. The Born rule is identified as a maximum-entropy hypothesis, not yet a formal derivation from graph topology. A complete Scope and Logical Boundaries declaration is included, alongside extended classical references (Nyquist, Shannon, Born, Einstein, Bell).
Yu Zhang· Zenodo (CERN European Organi...· 0 citations
This repository contains the reproducibility package for the study “PGR-Guard: Cross-Layer Detection and Prevention of IT-to-OT Cyberattacks in Small Power-Generation Facilities.” The study introduces PGR-Guard, an applied cybersecurity framework designed to detect and interrupt multi-stage attack progression from information technology environments into operational technology and cyber-physical processes. The framework correlates five security layers: identity activity, network behavior, operational technology protocol activity, controller state, and physical-process context. The repository includes the synthetic/emulated dataset, Python source code, holdout evaluation results, confidence intervals, scenario-level detection results, ablation analysis, statistical significance tests, threshold-selection results, and publication figures used in the manuscript. The evaluation models ten representative attack scenarios, including password spraying, valid-account compromise, internal reconnaissance, IT-to-OT traversal, engineering workstation access, PLC discovery, unauthorized controller reads and writes, controller task modification, and operational disruption. The experiments compare PGR-Guard with signature-based intrusion detection, OT-only anomaly detection, and an independent multi-sensor baseline. On the separated holdout evaluation set, PGR-Guard achieved approximately 0.990 precision, 0.879 recall, 0.931 F1 score, 2.55-second mean time to detection, 97.8% attack interruption rate, and 99.7% Cyber-Physical Prevention Rate (CPPR). The package contains: reproduce_pgr_guard.py — end-to-end reproducibility script PGR_Guard_synthetic_trials.csv — trial-level synthetic/emulated dataset holdout performance and confidence-interval files attack-scenario detection results ablation-study results statistical significance analyses threshold-selection results publication figures data dictionary and software requirements Important data provenance note: the included dataset is generated from a controlled synthetic/emulated OT cybersecurity model. It does not contain telemetry from the 2026 UK power-generation cyber incident, a real utility, a physical power-generation facility, or a physical PLC testbed. The results should therefore be interpreted as controlled emulation results rather than real-world operational measurements. Fixed random seeds are included in the source code to support reproducibility. The repository is intended to support independent verification, extension, and comparison of cross-layer IT-to-OT cyberattack detection methods.
Halil Dursunoglu· Zenodo (CERN European Organi...· 0 citations
This dataset contains the underlying data and analysis files associated with the review article “One clip, many genomes: how genome state may shape the use of tandem HMG-box proteins in organellar nucleoids” by Mari Takusagawa and Yoshiki Nishimura. The deposited files support the phylogenetic and structure-based analyses presented in Figs. 2 and 3 of the article. The dataset includes: HMG-box amino-acid sequences, the MAFFT alignment, maximum-likelihood phylogenetic trees, IQ-TREE reports, and approximately unbiased (AU) test outputs underlying Fig. 2; numerical structural-similarity matrices, AlphaFold Database predicted-aligned-error matrices, and protein biophysical properties underlying Fig. 3; AlphaFold3 input specifications, predicted TFAM–DNA and HLP–DNA models, and associated confidence summaries; and the Python script and tabulated results used to estimate DNA bend angles from the predicted models. The TFAM and HLP modelling jobs used the same 30-bp DNA sequence. The bend-angle analysis fits principal axes to the outer thirds of the two DNA arms while excluding the bent apex. These computational models and analyses are provided to support inspection and reproducibility. AlphaFold3 model geometry is predictive and should not be interpreted as experimental evidence for HLP-mediated DNA bending or HBD1-mediated DNA bridging. No supplementary figures or supplementary tables are included in this deposit. A detailed description of the files, software versions and directory structure is provided in README.txt. The CC BY 4.0 licence applies to the authors’ original compilation, analyses and documentation. Third-party source data and prediction outputs remain subject to the terms of their respective providers.
Mari Takusagawa, Yoshiki Nishimura· Zenodo (CERN European Organi...· 0 citations
The purpose of this study is to determine whether Work-Life Balance, Family Supportive Supervisor Behavior (FSSB) significantly affect Employee Performance at the HokBen Store in Tangerang City. The sample in this study was 107 HokBen Store employees in Tangerang City. Data collected through a questionnaire with a Likert Scale processed using Microsoft 2016 Software and SPSS v.25 Software. The sampling technique used in this study is non probability Sampling using saturated sampling. The research method used is multiple linear regression. Data analysis techniques are used to test the Validity Test, Reliability Test, Descriptive Analysis Test, Classical Assumption Test, Normality Test, Heteroscedasticity Test, Multicollinearity Test, Correlation Coefficient Analysis Test, Simple Correlation Analysis Test, Multiple Linear Regression Analysis Test, Determination Coefficient Test, T Test, F Test The results of this study indicate that Work-Life Balance (X1) has a positive and significant effect on Employee Performance at the HokBen Store in Tangerang City. Family Supportive Supervisor Behavior (FSSB) (X2) has a positive and significant effect on Employee Performance (Y) at the HokBen Store in Tangerang City.
This dataset contains the underlying data and analysis files associated with the review article “One clip, many genomes: how genome state may shape the use of tandem HMG-box proteins in organellar nucleoids” by Mari Takusagawa and Yoshiki Nishimura. The deposited files support the phylogenetic and structure-based analyses presented in Figs. 2 and 3 of the article. The dataset includes: HMG-box amino-acid sequences, the MAFFT alignment, maximum-likelihood phylogenetic trees, IQ-TREE reports, and approximately unbiased (AU) test outputs underlying Fig. 2; numerical structural-similarity matrices, AlphaFold Database predicted-aligned-error matrices, and protein biophysical properties underlying Fig. 3; AlphaFold3 input specifications, predicted TFAM–DNA and HLP–DNA models, and associated confidence summaries; and the Python script and tabulated results used to estimate DNA bend angles from the predicted models. The TFAM and HLP modelling jobs used the same 30-bp DNA sequence. The bend-angle analysis fits principal axes to the outer thirds of the two DNA arms while excluding the bent apex. These computational models and analyses are provided to support inspection and reproducibility. AlphaFold3 model geometry is predictive and should not be interpreted as experimental evidence for HLP-mediated DNA bending or HBD1-mediated DNA bridging. No supplementary figures or supplementary tables are included in this deposit. A detailed description of the files, software versions and directory structure is provided in README.txt. The CC BY 4.0 licence applies to the authors’ original compilation, analyses and documentation. Third-party source data and prediction outputs remain subject to the terms of their respective providers.
Mari Takusagawa, Yoshiki Nishimura· Zenodo (CERN European Organi...· 0 citations
This repository contains the reproducibility package for the study “PGR-Guard: Cross-Layer Detection and Prevention of IT-to-OT Cyberattacks in Small Power-Generation Facilities.” The study introduces PGR-Guard, an applied cybersecurity framework designed to detect and interrupt multi-stage attack progression from information technology environments into operational technology and cyber-physical processes. The framework correlates five security layers: identity activity, network behavior, operational technology protocol activity, controller state, and physical-process context. The repository includes the synthetic/emulated dataset, Python source code, holdout evaluation results, confidence intervals, scenario-level detection results, ablation analysis, statistical significance tests, threshold-selection results, and publication figures used in the manuscript. The evaluation models ten representative attack scenarios, including password spraying, valid-account compromise, internal reconnaissance, IT-to-OT traversal, engineering workstation access, PLC discovery, unauthorized controller reads and writes, controller task modification, and operational disruption. The experiments compare PGR-Guard with signature-based intrusion detection, OT-only anomaly detection, and an independent multi-sensor baseline. On the separated holdout evaluation set, PGR-Guard achieved approximately 0.990 precision, 0.879 recall, 0.931 F1 score, 2.55-second mean time to detection, 97.8% attack interruption rate, and 99.7% Cyber-Physical Prevention Rate (CPPR). The package contains: reproduce_pgr_guard.py — end-to-end reproducibility script PGR_Guard_synthetic_trials.csv — trial-level synthetic/emulated dataset holdout performance and confidence-interval files attack-scenario detection results ablation-study results statistical significance analyses threshold-selection results publication figures data dictionary and software requirements Important data provenance note: the included dataset is generated from a controlled synthetic/emulated OT cybersecurity model. It does not contain telemetry from the 2026 UK power-generation cyber incident, a real utility, a physical power-generation facility, or a physical PLC testbed. The results should therefore be interpreted as controlled emulation results rather than real-world operational measurements. Fixed random seeds are included in the source code to support reproducibility. The repository is intended to support independent verification, extension, and comparison of cross-layer IT-to-OT cyberattack detection methods.
Halil Dursunoglu· Zenodo (CERN European Organi...· 0 citations
A USAF cadet and a Lincoln Laboratory researcher found AI chatbots can help nontechnical service members produce viable software applications for their unique problems.
