{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000104785,0.0001946115,0.0002249584,0.0005990994,0.0001818377,0.0003712881,0.0001332696,0.0003222623,0.0007867242],"category_scores_gemma":[0.0003806514,0.0001401355,0.0001618123,0.0005199584,0.0001984134,0.0002862814,0.0002403148,0.0003690216,0.000165642],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001753699,"about_ca_system_score_gemma":0.0002610049,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001003884,"about_ca_topic_score_gemma":0.001779537,"domain_scores_codex":[0.9999264,0.00001246932,0.000005000913,0.0000298568,0.00001109495,0.00001515907],"domain_scores_gemma":[0.9997886,0.00006849364,0.00006645434,0.00001780066,0.00002119076,0.00003741591],"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":[0.0004206814,0.00005614517,0.0551673,0.0004456483,0.00008039894,0.001446306,0.0009083413,0.001043771,0.8958005,0.001754112,0.0004452452,0.04243162],"study_design_scores_gemma":[0.00001543632,0.0002708387,0.9365258,0.0001591829,0.0001801712,0.002348449,0.0009658036,0.001595114,0.03209523,0.001952955,0.02386391,0.00002699778],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9851742,0.006891428,0.002963702,0.0003482346,0.00002024945,0.00001304476,0.002164972,0.00005045952,0.002373717],"genre_scores_gemma":[0.9911918,0.002712077,0.00295902,0.0001422618,0.00002733986,0.000007596479,0.002377308,0.00001289944,0.0005697613],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001003884,"threshold_uncertainty_score":0.002631843,"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."}}