{"id":"W4384624948","doi":"10.1093/molbev/msad164","title":"Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses","year":2023,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research","keywords":"Biology; Phylogenetic tree; Primate; Phylogenetics; Most recent common ancestor; Lentivirus; Simian immunodeficiency virus; Infectivity; Virology; Evolutionary biology; Human immunodeficiency virus (HIV); Cell biology; Genetics; Virus; Gene; Viral disease","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0005287182,0.0002882915,0.000318804,0.001092167,0.0006835291,0.0007257593,0.0002943967,0.0003273923,0.0006477096],"category_scores_gemma":[0.001097209,0.0001997628,0.0002958457,0.0006130923,0.0003698893,0.000324477,0.0003844365,0.0006587816,0.0002883248],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004036668,"about_ca_system_score_gemma":0.0003477366,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001151763,"about_ca_topic_score_gemma":0.0009797086,"domain_scores_codex":[0.9998488,0.00005223135,0.000007691747,0.00004037304,0.00002678341,0.00002397843],"domain_scores_gemma":[0.9996766,0.00009745503,0.00005455784,0.0000510278,0.00005850038,0.00006182602],"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":[0.001237753,0.0001562926,0.1800499,0.0002747733,0.0002077152,0.00161663,0.002081811,0.03719623,0.7074242,0.009492634,0.0004460058,0.05981601],"study_design_scores_gemma":[0.00006042994,0.0006943226,0.5639012,0.0001512824,0.0003062307,0.004594565,0.001896245,0.3296086,0.06381225,0.009688049,0.02517588,0.0001109557],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9891976,0.0003475201,0.008833095,0.00004281234,0.000003367281,0.00001607604,0.0002904331,0.00003383926,0.001235303],"genre_scores_gemma":[0.991877,0.0003322189,0.00646132,0.00002061743,0.000007423555,0.00001252957,0.001000573,0.00003597921,0.0002523361],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001151763,"threshold_uncertainty_score":0.002928853,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01270606736594019,"score_gpt":0.247824276378508,"score_spread":0.2351182090125678,"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."}}