{"id":"W4404235320","doi":"10.1093/ve/veae094","title":"A simple phylogenetic approach to analyze hypermutated HIV proviruses reveals insights into their dynamics and persistence during antiretroviral therapy","year":2024,"lang":"en","type":"article","venue":"Virus Evolution","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; AIDS Vancouver; Simon Fraser University","funders":"National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research; National Institutes of Health","keywords":"Phylogenetic tree; Biology; Genetics; Genome; Viral quasispecies; Viral evolution; Somatic hypermutation; Phylogenetics; Virology; Evolutionary biology; Computational biology; Gene","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001005063,0.0002050265,0.00021604,0.0002775502,0.0003122527,0.00005669251,0.0001324399,0.0001346681,0.00002618387],"category_scores_gemma":[0.0000268531,0.0001513913,0.00007406973,0.0004008633,0.0001657413,0.0001135454,0.00008106267,0.000183984,0.000342448],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002833144,"about_ca_system_score_gemma":0.00007757498,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004248418,"about_ca_topic_score_gemma":0.0001432702,"domain_scores_codex":[0.9987143,0.000184892,0.0001879775,0.0004811455,0.00005589745,0.0003757757],"domain_scores_gemma":[0.9995909,0.00004640133,0.00002863954,0.0002276089,0.00004723273,0.00005916611],"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":[0.0002637474,0.0001930482,0.01998564,0.00008769669,0.0003352413,0.00001546352,0.002091573,0.00003863482,0.9666331,0.0004933383,0.0002478251,0.009614726],"study_design_scores_gemma":[0.005269784,0.003777519,0.7066485,0.0002986113,0.0002292213,0.0003477705,0.00369589,0.01185087,0.2546887,0.002519856,0.009080722,0.001592528],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9754196,0.02244633,0.0009189342,0.00004962187,0.00007686646,0.0005033084,0.0001290503,0.000127114,0.000329199],"genre_scores_gemma":[0.9981724,0.0006333296,0.00009614218,0.00002541509,0.0000264495,0.00008844351,0.0002798832,0.00002167134,0.0006562454],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7119443,"threshold_uncertainty_score":0.6173558,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01739318415385983,"score_gpt":0.2481759150794828,"score_spread":0.230782730925623,"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."}}