{"id":"W4388728133","doi":"10.1128/mbio.02417-23","title":"HIV reservoirs are dominated by genetically younger and clonally enriched proviruses","year":2023,"lang":"en","type":"article","venue":"mBio","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":18,"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","keywords":"Human immunodeficiency virus (HIV); Biology; Virology; Computational biology; Genetics","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":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0001525854,0.0001264897,0.0001678879,0.00008086282,0.0001532404,0.00002483439,0.0001328071,0.0001520764,0.000468951],"category_scores_gemma":[0.0001080154,0.00009930737,0.00003608033,0.0001774815,0.0002089732,0.00004467445,0.0001266036,0.0001608658,0.005794277],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002386661,"about_ca_system_score_gemma":0.00004251473,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000773292,"about_ca_topic_score_gemma":0.00004023057,"domain_scores_codex":[0.9989793,0.0001285924,0.0001371686,0.0002833657,0.00004758952,0.0004239272],"domain_scores_gemma":[0.9995512,0.0001173583,0.00003208111,0.0001950373,0.00005286189,0.00005145428],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0002801683,0.0001568718,0.02996461,0.00002299276,0.000250509,0.00009895473,0.0001890688,2.757408e-7,0.6777735,0.0001149261,0.2867451,0.004403072],"study_design_scores_gemma":[0.005028305,0.0005811873,0.4063888,0.00003265951,0.00006556797,0.00005271357,0.0003912069,0.000007239468,0.1054717,0.0003560842,0.4812264,0.0003981536],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.991693,0.003565694,0.000009223046,0.002505785,0.0000855139,0.000283811,0.0003074463,0.0001380507,0.001411439],"genre_scores_gemma":[0.9687705,0.000428767,0.00004382092,0.000146649,0.00001324573,0.00007683454,0.0006880314,0.00001696504,0.02981516],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5723017,"threshold_uncertainty_score":0.9949798,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01556131438024395,"score_gpt":0.2590805768340903,"score_spread":0.2435192624538464,"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."}}