{"id":"W4407355947","doi":"10.1186/s40168-025-02028-7","title":"The intestinal microbiome and metabolome discern disease severity in cytotoxic T-lymphocyte-associated protein 4 deficiency","year":2025,"lang":"en","type":"article","venue":"Microbiome","topic":"Immunodeficiency and Autoimmune Disorders","field":"Immunology and Microbiology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity; Université de Montréal; Montreal Clinical Research Institute","funders":"NHLBI Division of Intramural Research; National Institute of Allergy and Infectious Diseases; National Human Genome Research Institute; Canadian Institutes of Health Research; Bundesministerium für Bildung und Forschung; Institut de Recherche Clinique De Montréal; Tokyo Medical and Dental University; Università degli Studi di Brescia; Medizinische Fakultät der Albert-Ludwigs-Universität Freiburg; Universitätsklinikum Regensburg; Sungkyunkwan University; Albert-Ludwigs-Universität Freiburg; National Institutes of Health; Deutsche Forschungsgemeinschaft; Université de Liège; Wilhelm Sander-Stiftung","keywords":"Metabolome; Microbiome; Immunology; Biology; Immune dysregulation; Dysbiosis; Immune system; Common variable immunodeficiency; Disease; Immunodeficiency; Medical microbiology; Cytotoxic T cell; Metabolomics; Gut flora; Medicine; Internal medicine; Genetics; Bioinformatics; Antibody","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0007269616,0.0003942692,0.0004342328,0.0003542605,0.0009074836,0.0001120081,0.0006633046,0.0002337417,0.00006341695],"category_scores_gemma":[0.0003736924,0.0003044284,0.0001492564,0.001109496,0.001114281,0.0001488429,0.0004095662,0.0004692871,0.000158798],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002208045,"about_ca_system_score_gemma":0.0003038718,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004234626,"about_ca_topic_score_gemma":0.0000829304,"domain_scores_codex":[0.9974257,0.000392711,0.0006230044,0.0006128924,0.00004350648,0.0009021905],"domain_scores_gemma":[0.9989864,0.0001743547,0.000229139,0.0005152458,0.00007650235,0.0000183312],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0002793129,0.0004500483,0.002106523,0.00005720841,0.00007327827,0.00001031381,0.0003057774,0.000002167093,0.9862115,0.000980044,0.0001905024,0.009333303],"study_design_scores_gemma":[0.0141762,0.0003001461,0.5093865,0.00136291,0.0003378408,0.0001545175,0.00239705,0.00008507778,0.3038912,0.005130786,0.1604515,0.00232616],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9198349,0.07724275,0.000039633,0.001035529,0.000490659,0.0007530762,0.0001034264,0.0001137399,0.0003863137],"genre_scores_gemma":[0.9926333,0.0002208082,0.0000152979,0.0002149555,0.000001699682,0.0001120342,0.000153958,0.00002230266,0.006625576],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6823203,"threshold_uncertainty_score":0.9999408,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.004495753309750517,"score_gpt":0.2143984244110372,"score_spread":0.2099026711012867,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}