Our Work

Minor Changes 40f1b85: Fixes from adopting utils and test-utils in the apps: bytes and fmtBytes print a sub-KB count exactly as given and send NaN to their top unit, as the apps' own formatters did (…

Minor Changes 40f1b85: Fixes from adopting utils and test-utils in the apps: bytes and fmtBytes print a sub-KB count exactly as given and send NaN to their top unit, as the apps' own formatters did (new exactBytes option on formatBytes); createChoiceStore and createFlagStore take an onError so an app keeps its own warning; bodyOf takes stripScripts; the shared Playwright preview runs with --strictPort, so a busy port fails instead of silently testing another app. Patch Changes @brain-bbqs/ember-client@0.1.1

This article develops a document-based, theoretically integrative sociological analysis of religious conversion in Burkina Faso, a country marked by deep religious plurality and an accelerating pace o…

This article develops a document-based, theoretically integrative sociological analysis of religious conversion in Burkina Faso, a country marked by deep religious plurality and an accelerating pace of affiliation change. It bases its analytical framework on the classical sociology of religion — Durkheim's account of collective effervescence and moral solidarity, Weber's theory of charismatic authority and theodicy, Simmel's distinction between religion as form and as content, and Troeltsch's church-sect-mysticism typology — and brings these tools into direct dialogue with Lewis Rambo's stage-model of conversion, Afrocentric frameworks developed by John Mbiti, Lamine Sanneh, and Ousmane Kane, Pierre Bourdieu's field theory, and Birgit Meyer's ethnography of West African Pentecostalism. Focusing on a thematically organized, qualitative synthesis of the historical, ethnographic, and demographic literature on Burkina Faso, the article identifies five interacting sociological drivers of conversion — economic precarity and health-seeking behaviour, the institutional capacity of competing religious networks, kinship and marriage pressure, forced displacement linked to the Sahel security crisis, and the persistent cosmological substrate of Mossi traditional religion — and shows how each is refracted through the historically specific configuration of the Burkinabè religious field. On this basis, the article proposes an original four-level model, Religious Capital under Structural Stress (RCSS), linking macro-historical, meso-institutional, micro-relational, and cosmological-symbolic dynamics of conversion, and formulates a set of testable propositions for future empirical research. The article concludes by discussing the methodological limits of document-based synthesis and the policy implications of treating conversion as a structurally conditioned rather than purely doctrinal phenomenon.

Trained models for CTadipo, a tool that measures adipose tissue depots in mice from microCT volumes.checkpoint_final.pth - nnU-Net (3d_lowres, ResEnc-M) segmenting outer body, abdominal wall and abdom…

Trained models for CTadipo, a tool that measures adipose tissue depots in mice from microCT volumes.checkpoint_final.pth - nnU-Net (3d_lowres, ResEnc-M) segmenting outer body, abdominal wall and abdominal cavity on a 0.15 mm isotropic grid. Fold 0 only, which is the configuration the published measurements used. Optimizer and grad-scaler state have been removed; the remaining weights were verified to produce bit-identical labels to the full training checkpoint.ctadipo_landmarks.zip - five cross-validation folds of the landmark model, which places five craniocaudal planes (lung apex, diaphragm, cranial and caudal kidney, bladder) used to divide fat into named depots.SHA-256: checkpoint_final.pth = 87c814c3e771ea0d65cf036c61155f4d301a0db17d252346490d921dcdafe80a; ctadipo_landmarks.zip = bd8dd09c6ca234d7f47df8df6dde158138769a06748f1efe9f4ffe81c3744985

This paper decomposes the final passage from IUT III Theorem 3.11 to Corollary 3.12 into an abstract interface designed for treatment in Lean 4. The logical core consists of three proof obligations: s…

This paper decomposes the final passage from IUT III Theorem 3.11 to Corollary 3.12 into an abstract interface designed for treatment in Lean 4. The logical core consists of three proof obligations: simultaneous intertwining on a post-sQ3/sQ4 comparable object, a Θ-side holomorphic-hull upper bound, and a fixed 1-column q-side normalization. Once these obligations are supplied, the inequality of Corollary 3.12 follows by a short order-theoretic argument. The paper matches this interface with source-level statements in IUT III and compares it with two points of uncertainty publicly identified in the Project LANA interim report of 17 July 2026. No claim is made that the concerns raised by Project LANA have been resolved; rather, they are reorganized as machine-checkable obligations. The abstract Lean prototype displayed here has been compilation-verified in an actual Lean/mathlib environment, while the implementation of O1-O3 using the actual IUT objects and maps remains outside the scope of this paper and is not yet complete.

YazSes is an open-source, offline voice-dictation daemon for Linux, macOS, and Windows. Hold a key, speak, release — speech is transcribed on-device with faster-whisper and typed into the focused appl…

YazSes is an open-source, offline voice-dictation daemon for Linux, macOS, and Windows. Hold a key, speak, release — speech is transcribed on-device with faster-whisper and typed into the focused application, with support for editor and terminal voice commands. No cloud dependency, no API key, no subscription.

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Mitoscope MitoScope is a scalable end-to-end workflow for long-read specific mtDNA and NUMT analysis. MitoScope integrates five key modules: 1) mtDNA selection, 2) variant calling and annotation, 3) a…

Mitoscope MitoScope is a scalable end-to-end workflow for long-read specific mtDNA and NUMT analysis. MitoScope integrates five key modules: 1) mtDNA selection, 2) variant calling and annotation, 3) assembly generation, 4) quality control, and 5) optional NUMT profiling. It is written using Nextflow and fully containerized using Singularity images. It can be run on either ONT or PacBio data and accepts raw sequencing data or aligned reads as input. mitoScope is currently in active development. Open an issue if you find a problem or have a suggestion. Table of Contents Installation Usage Outputs Installation Pre-requisites Nextflow Singularity Setup VERSION=0.5.0 wget https://github.com/czakarian/mitoscope/archive/refs/tags/v${VERSION}.tar.gz tar xvf v${VERSION}.tar.gz && rm v${VERSION}.tar.gz cd mitoscope-${VERSION}/ Usage nextflow run /path/to/mitoscope-${VERSION}/main.nf -params-file example_params.yaml Parameters Specifications The required -params-file argument accepts a yaml file with the following parameter specifications. See below or example_params.yaml for example. | name | description | |-----------------------|------------------------------------------------------------------------------- | | samplesheet | Path to a headerless csv file with 1) sample ids & 2) input file paths | | input_type | Input type (options are: 'bam', 'cram', 'fastq', 'fastq.gz'). | | is_aligned | Set to true if input is aligned, otherwise set to false. | | platform | Specify 'pb' for PacBio or 'ont' for ONT. | | outdir | Path to directory to output results. | | reference | Path to reference genome. | example_params.yaml samplesheet: "samples.csv" input_type: "bam" is_aligned: true platform: "pb" outdir: "/path/to/output/dir/result" reference: "/path/to/ref/for/cram/GRCH38.fa" Optional Parameters To call non-reference NUMT candidates, add numt_profiling: true to the yaml file. This functionality is turned off by default to otherwise reduce computational load and is only available for use with aligned input. To skip methylation related NUMT filtration and methylation calling add skip_methylation: true to the yaml file. This can be used to process long-read amplicon sequencing data or other long-read data that lacks methylation calls. Sample Manifest One of the required parameters in the yaml file is the path to a sample manifest (samplesheet). See below or example_sample_manifest.csv for example. samples.csv sample1,/path/to/sample1.bam sample2,/path/to/sample2.bam sample3,/path/to/sample3.bam sample4,/path/to/sample4.bam Outputs Mitoscope outputs a directory for each sample with the following subdirectories. | name | description | |----------------------|---------------------------------------------------------------- | | alignments/ | Bam files for retained mtDNA reads and discarded reads. | | assembly/ | Assembly output from meta-flye. | | methylation/ | Methylation calls from modkit/pb-CpG-tools. | | numts/ | Non-reference NUMT candidates. | | qc/ | QC metrics. | | variants/ | Variant calls (snv/indel, SV) | | logs/ | Log files. |

ClonoDynamics is a reproducible computational pipeline for noise-aware analysis of longitudinal T-cell receptor β (TCRβ) repertoire sequencing data with paired technical replicates. The soft…

ClonoDynamics is a reproducible computational pipeline for noise-aware analysis of longitudinal T-cell receptor β (TCRβ) repertoire sequencing data with paired technical replicates. The software implements replicate-resolved latent-state inference, longitudinal transition assembly, replicate-decoupled forward-dynamics analysis, cross-replicate fluctuation analysis, temporal-scaling estimation, pseudo-longitudinal technical-reference benchmarking, robustness analyses, and support-conditioned synthetic positive-control validation. This release corresponds to the frozen analysis code used for the associated ClonoDynamics manuscript and includes the production analysis modules, orchestration scripts, plotting code, methodological documentation, run manifest, and frozen Python environment. The pipeline is designed to separate technical measurement effects from reproducible longitudinal repertoire structure while preserving estimator-specific support and replicate information throughout the analysis. The associated reproducibility dataset, including processed clonotype tables, pseudo-longitudinal reference outputs, longitudinal analysis outputs, synthetic validation results, and Supplementary Data files, is available at https://doi.org/10.5281/zenodo.22925114. Raw sequencing data are available through NCBI BioProject PRJNA1457834 / SRA Study SRP694925. Version: v1.0.0-biorxivSource repository: https://github.com/ClonoDynamics/clonodynamics-pipeline

This dataset contains high-frequency dissolved oxygen (O₂) and temperature measurements from a shipboard incubation experiment conducted with mesopelagic seawater collected within the Southeast Pacifi…

This dataset contains high-frequency dissolved oxygen (O₂) and temperature measurements from a shipboard incubation experiment conducted with mesopelagic seawater collected within the Southeast Pacific oxygen minimum zone off central Chile during the DIZMO cruise in October 2025. The experiment investigated respiratory responses following the addition of fresh, diatom-derived particulate organic carbon (POC). Mesopelagic seawater was collected at 210 m depth at Station 8 (33.080° S, 72.860° W) and filtered through a 0.8-µm polycarbonate filter. Six experimental bottles received a pulse of diatom-derived POC, while unamended bottles served as controls. Dissolved O₂ was measured using optical sensor spots connected to a four-channel FireSting-O₂ meter (PyroScience). The dataset includes the high-frequency O₂ records for experimental Bottles 1–4 during the main monitoring period, as well as the shorter records obtained after the O₂ sensors were transferred to Bottles 5 and 6 and Control 1 at approximately 60 h of incubation. The Control 1 record is included for completeness but was not used to estimate a control O₂-consumption rate because no continuous O₂ record was available for the control over the incubation. Temperature records corresponding to both measurement periods are also provided. O₂ measurements were recorded at 10-s intervals, whereas temperature was recorded at 30-s intervals. Time in each file represents elapsed time from the beginning of the corresponding instrumental recording period. O₂ concentrations are reported in µmol kg⁻¹ and temperature in °C. Bottles 5 and 6 were not continuously monitored before sensor transfer. Consequently, their earlier O₂ trajectories used in the associated manuscript were reconstructed statistically and should not be interpreted as directly measured O₂ data. The files deposited here contain the instrumental observations rather than reconstructed O₂ trajectories. These data support the manuscript “Rapid mesopelagic respiration following a pulse of diatom-derived carbon in a Southeast Pacific oxygen minimum zone” by Díaz-Rosas et al., submission for consideration in Biogeosciences.