{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004836257,0.0001179292,0.0001679576,0.0003866575,0.0004541579,0.0005024617,0.0002434981,0.0002236783,0.0005804733],"category_scores_gemma":[0.001184192,0.0001129945,0.0001011008,0.0004551974,0.0004397474,0.0002791987,0.0003834612,0.0002901907,0.00008702544],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00053176,"about_ca_system_score_gemma":0.0002803708,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01584828,"about_ca_topic_score_gemma":0.03180498,"domain_scores_codex":[0.9997458,0.00008630782,0.0000109135,0.00006704675,0.00004364563,0.00004627714],"domain_scores_gemma":[0.9996537,0.00008003369,0.00008894613,0.00004607578,0.00007369457,0.00005762846],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0003404711,0.00004029539,0.9623758,0.00002145764,0.00008228714,0.0002591406,0.001173846,0.0009895315,0.0247243,0.0002243197,0.00009874692,0.009669843],"study_design_scores_gemma":[0.000001318234,0.00002182055,0.998625,0.000002449716,0.00001083631,0.0001182107,0.0003876382,0.0003158876,0.0003238088,0.00003392751,0.0001560188,0.000003087707],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.999687,0.00003934442,0.00001955113,0.00000697769,3.638191e-7,8.004147e-7,0.00002521453,5.482619e-7,0.0002202007],"genre_scores_gemma":[0.9997116,0.00005895704,0.00005244313,0.000008085033,0.000001497353,0.00000137453,0.00008264653,0.000001155774,0.00008210159],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01584828,"threshold_uncertainty_score":0.03151208,"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."}}