{"id":"W3120120538","doi":"10.1093/ve/veaa104","title":"Quantifying the clonality and dynamics of the within-host HIV-1 latent reservoir","year":2020,"lang":"en","type":"article","venue":"Virus Evolution","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University","funders":"National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research; NHLBI Division of Intramural Research; National Institutes of Health; Division of Intramural Research, National Institute of Allergy and Infectious Diseases","keywords":"Provirus; Phylogenetic tree; Biology; Population; Evolutionary biology; Viral quasispecies; Mechanism (biology); Virology; Long terminal repeat; Virus; Genetics; Genome; Demography; 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":[0.0002121444,0.00007175268,0.00009924854,0.00001330712,0.0002226024,0.000007438657,0.0001519199,0.00007045286,0.00005701272],"category_scores_gemma":[0.0001147477,0.00003712777,0.00004893709,0.0001236246,0.0002806803,0.00003565998,0.0001414422,0.0002060932,0.0001406117],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00006119831,"about_ca_system_score_gemma":0.00005191063,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008176561,"about_ca_topic_score_gemma":0.001131712,"domain_scores_codex":[0.999255,0.0002514912,0.0001480772,0.0001413706,0.00004921222,0.0001548203],"domain_scores_gemma":[0.9996055,0.00007383412,0.00007218941,0.0001882431,0.00004148449,0.00001871651],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0009280842,0.000230049,0.5427233,0.0001043989,0.0004803273,0.000004960554,0.003338127,0.0001468127,0.4090777,0.03679087,0.005050106,0.001125226],"study_design_scores_gemma":[0.00140186,0.000269776,0.9610404,0.00004198674,0.00007487483,0.00002091846,0.0005790807,0.001635947,0.02697471,0.0005548071,0.007275469,0.0001301623],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9902128,0.001972587,0.0001846719,0.006843702,0.0001198983,0.0002291939,0.0002395593,0.00001795644,0.0001796265],"genre_scores_gemma":[0.9995669,0.00006076685,0.00001746579,0.00008417832,0.00001236629,0.000008669597,0.00005147392,0.000004678325,0.0001934985],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4183171,"threshold_uncertainty_score":0.1807326,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04583544182490924,"score_gpt":0.2784308553263778,"score_spread":0.2325954135014686,"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."}}