{"id":"W4365459907","doi":"10.1101/2023.04.12.536611","title":"HIV reservoirs are dominated by genetically younger and clonally enriched proviruses","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":6,"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; National Institute of Neurological Disorders and Stroke; National Institute of Mental Health; National Institute of Diabetes and Digestive and Kidney Diseases; National Heart, Lung, and Blood Institute; Canadian Institutes of Health Research; National Institutes of Health; National Institute on Drug Abuse; Simon Fraser University; Michael Smith Health Research BC; Innovative Research Group Project of the National Natural Science Foundation of China","keywords":"Biology; Viremia; Genome; Viral evolution; Genetics; Virology; Viral quasispecies; Human immunodeficiency virus (HIV); Evolutionary 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002195613,0.0001278191,0.0001869754,0.000406323,0.0003027531,0.0005608628,0.0001959662,0.0002175338,0.001308383],"category_scores_gemma":[0.000536146,0.0001591254,0.0001451289,0.0002216988,0.0002399022,0.0004844732,0.0004082059,0.0003525946,0.0003041954],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001953406,"about_ca_system_score_gemma":0.0001567666,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009144281,"about_ca_topic_score_gemma":0.001277598,"domain_scores_codex":[0.9998862,0.00001308659,0.000006716153,0.00004349431,0.00002349329,0.00002713842],"domain_scores_gemma":[0.9997148,0.00005993984,0.0001115237,0.00003578168,0.00003458864,0.00004339285],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0003763146,0.00006778031,0.3711927,0.0000688892,0.00007017534,0.0005091762,0.001034296,0.00241924,0.5916085,0.001522451,0.0001715391,0.03095891],"study_design_scores_gemma":[0.00001468711,0.0005037483,0.9061389,0.00005107897,0.0001082624,0.003652744,0.0009612732,0.01093472,0.07019967,0.002126615,0.005256201,0.00005211498],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9978434,0.0002144374,0.001272648,0.00001066788,0.000001450501,0.000004783105,0.0001038266,0.00001901571,0.000529786],"genre_scores_gemma":[0.9984587,0.00007253079,0.0008961394,0.00001428314,0.000002916945,0.000003787281,0.0002010274,0.00001255959,0.0003379351],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001308383,"threshold_uncertainty_score":0.004376948,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01830081687894814,"score_gpt":0.2385058814915262,"score_spread":0.220205064612578,"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."}}