{"id":"W4313544669","doi":"10.1073/pnas.2217111120","title":"Similar evolutionary trajectories in an environmental <i>Cryptococcus neoformans</i> isolate after human and murine infection","year":2023,"lang":"en","type":"article","venue":"Proceedings of the National Academy of Sciences","topic":"Fungal Infections and Studies","field":"Medicine","cited_by":21,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases; National Heart, Lung, and Blood Institute; U.S. Department of Health and Human Services; National Institutes of Health; National Institute of Allergy and Infectious Diseases; Broad Institute; National Institute of Neurological Disorders and Stroke; Canadian Institute for Advanced Research","keywords":"Biology; Virulence; Cryptococcus neoformans; Frameshift mutation; Gene; Nonsynonymous substitution; Phenotype; Genetics; Genome; Microbiology; Whole genome sequencing; Strain (injury); Virology","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":[0.000414156,0.00006960153,0.0001164284,0.0002231675,0.0002063571,0.000008465015,0.00006624966,0.00004866706,0.00001401078],"category_scores_gemma":[0.00004819124,0.00004784871,0.00003576189,0.0005239774,0.0005454766,0.0004140008,0.00007790926,0.0001209153,0.000001071181],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003902347,"about_ca_system_score_gemma":0.000008285815,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001361975,"about_ca_topic_score_gemma":8.338211e-7,"domain_scores_codex":[0.9991519,0.00000360398,0.0001999791,0.0001484384,0.0003843357,0.0001116877],"domain_scores_gemma":[0.9998149,0.00002579171,0.0000888856,0.000005472069,0.00004032318,0.00002458545],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00003167621,0.0000737802,0.7966881,0.00006694505,0.00001019986,2.905771e-8,0.000386685,0.00003405031,0.2010762,0.001330564,0.0001810938,0.0001206806],"study_design_scores_gemma":[0.0002221278,0.0001759677,0.984606,0.00005776467,0.00001066692,0.000009469025,0.0001828301,0.0005912221,0.008712102,0.005158764,0.0002248004,0.00004828432],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9979951,0.0000914469,1.022199e-7,0.0007907326,0.00001468761,0.0001761875,0.00001043509,0.00001600999,0.0009053191],"genre_scores_gemma":[0.9995044,0.0001297447,0.00008784476,0.00009557264,0.0000568217,0.00002962938,4.371999e-7,0.000002946085,0.00009258251],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1923641,"threshold_uncertainty_score":0.2009831,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03117297753673661,"score_gpt":0.3074213349624646,"score_spread":0.276248357425728,"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."}}