{"id":"W2020097327","doi":"10.1371/journal.pgen.1004295","title":"Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic","year":2014,"lang":"en","type":"article","venue":"PLoS Genetics","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":47,"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 Cancer Institute; Canadian Institutes of Health Research; Sanofi; Claude Leon Foundation; Michael Smith Health Research BC; Frederick National Laboratory for Cancer Research; Microsoft; Wellcome Trust; National Institute on Drug Abuse; Providence Health Care; National Institutes of Health; U.S. Department of Health and Human Services","keywords":"Biology; Population; Founder effect; Human leukocyte antigen; Genotype; Genetics; Viral evolution; Virology; Demography; Evolutionary biology; Haplotype; Gene; Genome; Antigen","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00005627224,0.0000715452,0.0001090825,0.00005202247,0.0001034739,0.000004547198,0.00004572996,0.00002467202,0.00004760072],"category_scores_gemma":[0.00007390002,0.00004797026,0.00003052991,0.00009485162,0.000053775,0.00001495378,0.00003168411,0.00006888346,0.0001887504],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003682758,"about_ca_system_score_gemma":0.00001873587,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009906715,"about_ca_topic_score_gemma":0.0002780047,"domain_scores_codex":[0.9994554,0.0001113274,0.0001209024,0.0001169106,0.00003627661,0.000159213],"domain_scores_gemma":[0.9996484,0.00009114255,0.00005882688,0.0001203751,0.0000530903,0.00002815283],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001392718,0.00005450849,0.8378451,0.00001074605,0.00017307,2.28103e-7,0.0003236887,0.002075845,0.1552243,0.00001238828,0.00007653843,0.004064335],"study_design_scores_gemma":[0.0003051162,0.0003110237,0.9900466,0.000003892637,0.0000230893,0.000004348124,0.00002661323,0.0004741804,0.008662261,0.000006050562,0.00009009542,0.00004674054],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9989762,0.0004182412,0.0001873791,0.0000974264,0.00002532647,0.0001862467,0.00007638676,0.000009507864,0.00002332068],"genre_scores_gemma":[0.9995089,0.00006241424,0.00007920559,0.0000173377,0.00002552703,0.00001431969,0.0001583907,0.000006908143,0.0001269617],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1522015,"threshold_uncertainty_score":0.2426067,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02361560930553152,"score_gpt":0.2589541856060829,"score_spread":0.2353385763005514,"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."}}