{"id":"W4412972942","doi":"10.1128/mbio.00564-25","title":"Genomic epidemiology of <i>Histoplasma</i> in Africa","year":2025,"lang":"en","type":"article","venue":"mBio","topic":"Fungal Infections and Studies","field":"Medicine","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"National Institute of Environmental Health Sciences; National Institute of Allergy and Infectious Diseases; National Institute for Health and Care Research","keywords":"Biology; Lineage (genetic); Phylogenetic tree; Histoplasma; Evolutionary biology; Histoplasma capsulatum; Phylogenetics; Population; Genetics; Histoplasmosis; Gene; Medicine","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":[],"consensus_categories":[],"category_scores_codex":[0.0001552404,0.00003590222,0.0002112317,0.00008856437,0.00001695238,2.157943e-7,0.00001829259,0.00003588034,0.00002468074],"category_scores_gemma":[0.0001902538,0.00002961184,0.00003715512,0.0001319427,0.00004941288,0.000004767916,0.00002145168,0.00006720684,0.00001437805],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004187737,"about_ca_system_score_gemma":0.00002526199,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001425582,"about_ca_topic_score_gemma":0.00007269986,"domain_scores_codex":[0.9996364,0.00002219659,0.0001611628,0.0000759977,0.00001372473,0.00009051672],"domain_scores_gemma":[0.9997161,0.0001396189,0.00002116979,0.00009399939,0.0000174814,0.00001164581],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00003600539,0.00007996677,0.9759718,0.00005510272,0.00002773876,0.000004026612,0.0001494967,0.000007851097,0.004081392,0.004960351,0.01378828,0.000838031],"study_design_scores_gemma":[0.0005893564,0.0001209334,0.8852021,0.00006103644,0.00002750672,0.000005253145,0.00007431812,0.00006617072,0.0008746488,0.001430204,0.1115095,0.00003906051],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8546234,0.003470724,0.00008178285,0.001901179,0.0002193898,0.00009160847,0.000002464557,0.00001375252,0.1395957],"genre_scores_gemma":[0.9929906,0.0001079663,0.0003529419,0.0003350952,0.00001333475,0.000007875756,0.000001082151,0.000001850015,0.006189234],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1383672,"threshold_uncertainty_score":0.1207536,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04017962920091879,"score_gpt":0.306819895632472,"score_spread":0.2666402664315533,"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."}}