{"id":"W3006983638","doi":"10.1128/mbio.02878-19","title":"Diversity and Complexity of the Large Surface Protein Family in the Compacted Genomes of Multiple<i>Pneumocystis</i>Species","year":2020,"lang":"en","type":"article","venue":"mBio","topic":"Pneumocystis jirovecii pneumonia detection and treatment","field":"Medicine","cited_by":20,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph","funders":"Office of Research Infrastructure Programs, National Institutes of Health; California National Primate Research Center; National Center for Research Resources; National Human Genome Research Institute; National Institute of Diabetes and Digestive and Kidney Diseases; Université de Lausanne; National Heart, Lung, and Blood Institute; National Cancer Institute; Institut National de la Recherche Agronomique; National Institute of Allergy and Infectious Diseases; Broad Institute; NIH Clinical Center; U.S. Department of Veterans Affairs; National Institutes of Health; U.S. Department of Health and Human Services","keywords":"Biology; Pneumocystis carinii; Pneumocystis pneumonia; Gene; Antigenic variation; Pneumocystis jirovecii; Phylogenetic tree; Phylogenetics; Genome; Immune system; Genetics; Evolutionary biology; Immunology; Human immunodeficiency virus (HIV)","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001857271,0.0001710894,0.0002015444,0.0005467406,0.0002798231,0.000560641,0.0001473947,0.0002629917,0.0007219834],"category_scores_gemma":[0.0004721243,0.0001006914,0.0001901725,0.0004081754,0.0003527204,0.0004823862,0.0004357917,0.000374994,0.0002567924],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002220754,"about_ca_system_score_gemma":0.0001864004,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007486248,"about_ca_topic_score_gemma":0.001065231,"domain_scores_codex":[0.9998084,0.00003305985,0.0000139237,0.00005848338,0.00004764424,0.00003853729],"domain_scores_gemma":[0.9997471,0.0000373762,0.00008469228,0.00003239126,0.00003772816,0.00006066964],"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":[0.0003386362,0.00003660138,0.06117295,0.0001397713,0.00005160717,0.0005683373,0.000604266,0.0004694275,0.9056116,0.00119633,0.000458875,0.02935151],"study_design_scores_gemma":[0.00002181375,0.0005529738,0.8634028,0.00015597,0.0001417041,0.007063,0.001728295,0.004715862,0.08143482,0.002855101,0.0378692,0.00005850053],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9934017,0.002174628,0.002399517,0.000283712,0.00002151445,0.000007033615,0.000271451,0.00003489213,0.001405442],"genre_scores_gemma":[0.9965279,0.0005499822,0.001886659,0.0001027329,0.00001912388,0.000007459545,0.0004261628,0.00001024933,0.0004697048],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0007486248,"threshold_uncertainty_score":0.002415299,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07494168810406597,"score_gpt":0.2417271238478498,"score_spread":0.1667854357437838,"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."}}