{"id":"W3133637501","doi":"10.1038/s42003-021-01799-7","title":"Genomic insights into the host specific adaptation of the Pneumocystis genus","year":2021,"lang":"en","type":"article","venue":"Communications Biology","topic":"Pneumocystis jirovecii pneumonia detection and treatment","field":"Medicine","cited_by":40,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of Allergy and Infectious Diseases; National Heart, Lung, and Blood Institute; NIH Clinical Center; U.S. Department of Health and Human Services; National Institutes of Health; Canadian Institute for Advanced Research; U.S. Department of Veterans Affairs","keywords":"Biology; Pneumocystis jirovecii; Genome; Phylogenetics; Host adaptation; Pneumocystis pneumonia; Adaptation (eye); Pneumocystis carinii; Evolutionary biology; Host (biology); Genetics; Virology; Gene; Human immunodeficiency virus (HIV)","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00008692311,0.0001053928,0.000191209,0.00004349072,0.0003740801,0.000009609099,0.0004579992,0.00008367269,0.00004202494],"category_scores_gemma":[0.000103973,0.00006129073,0.0001222886,0.0003663303,0.0004256403,0.00002023915,0.000353442,0.0002272698,0.00006588372],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000111491,"about_ca_system_score_gemma":0.0001626451,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001083812,"about_ca_topic_score_gemma":0.0005800997,"domain_scores_codex":[0.9989868,0.00035819,0.0002961288,0.0001722103,0.00007434949,0.0001122849],"domain_scores_gemma":[0.9971231,0.0002719715,0.0001468634,0.002235199,0.0001818931,0.00004099709],"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":[0.00004205552,0.00043323,0.01768946,0.00001702177,0.0002203227,0.000006927627,0.003181564,0.00002771837,0.9047505,0.02414342,0.0001147731,0.049373],"study_design_scores_gemma":[0.0009698044,0.0001692093,0.5140269,0.00004653137,0.0001471788,0.0002725379,0.001313978,0.001091458,0.02288891,0.001364422,0.4575826,0.0001264735],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.961336,0.01908422,0.0003866683,0.01472144,0.0003296269,0.0003977922,0.000010477,0.00003806806,0.003695709],"genre_scores_gemma":[0.9927316,0.005361069,0.001023783,0.0003569752,0.00003681485,0.00006291507,0.00006103962,0.00001160003,0.0003542333],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8818616,"threshold_uncertainty_score":0.287716,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0423281803228782,"score_gpt":0.2867847559450807,"score_spread":0.2444565756222025,"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."}}