{"id":"W4411196291","doi":"10.1101/2025.06.07.658167","title":"Loss of B cell tolerance at the T2/T3a B cell transition is a convergent pathogenic mechanism in common variable immunodeficiency","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Immunodeficiency and Autoimmune Disorders","field":"Immunology and Microbiology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Sherbrooke","funders":"Pharming Technologies; American Academy of Allergy Asthma and Immunology; Howard Hughes Medical Institute","keywords":"Common variable immunodeficiency; Biology; B cell; Immunology; Autoimmunity; Cell biology; Immune system; Antibody","routes":{"ca_aff":true,"ca_fund":false,"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":[0.001053559,0.0006986689,0.001020209,0.0003101473,0.0004329657,0.00004234737,0.001234685,0.001046449,0.0005077074],"category_scores_gemma":[0.0000264373,0.0006549684,0.0003694589,0.0007946336,0.0003901621,0.0001045877,0.0006620603,0.001348667,0.0001545285],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002864717,"about_ca_system_score_gemma":0.0007321744,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005568421,"about_ca_topic_score_gemma":0.000004025017,"domain_scores_codex":[0.9961997,0.0005446963,0.001210082,0.001027672,0.0001621455,0.0008557434],"domain_scores_gemma":[0.9970544,0.0001426967,0.0007049146,0.001802587,0.0002773774,0.00001803055],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0001680604,0.0007322248,0.0002907462,0.0006940857,0.00009179744,0.00000930352,0.000388035,0.0007064062,0.9958478,0.0009957354,0.0000733939,0.000002441204],"study_design_scores_gemma":[0.001919563,0.00009155458,0.004267024,0.0005564833,0.0001958306,8.412555e-8,0.00007230922,0.000282926,0.9885699,0.00003520834,0.003275833,0.000733322],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9343196,0.05970173,0.0009963351,0.0001665936,0.002375055,0.001135629,0.001057421,0.000116107,0.0001315728],"genre_scores_gemma":[0.9971525,0.001893499,0.00009965237,0.0004266226,0.000007182704,0.0001577665,0.000007223288,0.00005633557,0.0001992361],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06283293,"threshold_uncertainty_score":0.9995902,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006052796025144652,"score_gpt":0.1912922983777979,"score_spread":0.1852395023526533,"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."}}