{"id":"W2157219992","doi":"10.1371/journal.ppat.1002106","title":"Detection of Inferred CCR5- and CXCR4-Using HIV-1 Variants and Evolutionary Intermediates Using Ultra-Deep Pyrosequencing","year":2011,"lang":"en","type":"article","venue":"PLoS Pathogens","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":60,"is_retracted":false,"has_abstract":true,"ca_institutions":"AIDS Vancouver","funders":"National Institute of Allergy and Infectious Diseases; Rijksinstituut voor Volksgezondheid en Milieu; Canadian Institutes of Health Research; Universiteit van Amsterdam; National Institutes of Health; Stichting Sanquin Bloedvoorziening; Small Business Innovation Research; GlaxoSmithKline","keywords":"Biology; V3 loop; CXCR4; Genetics; Phenotype; Computational biology; Human immunodeficiency virus (HIV); Transition (genetics); Gene; Virology; Peptide sequence; Chemokine; Receptor","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":[0.0006386039,0.0003197625,0.0004249257,0.0003895175,0.0002506416,0.0005713345,0.0003092097,0.0004660135,0.0004875768],"category_scores_gemma":[0.0009523574,0.0002152279,0.0004102092,0.0003412295,0.0002154587,0.0001990155,0.0003615075,0.0005847614,0.0002256824],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001767635,"about_ca_system_score_gemma":0.000150368,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008147377,"about_ca_topic_score_gemma":0.00178223,"domain_scores_codex":[0.999586,0.00008227632,0.00002329107,0.0001430023,0.0001044235,0.00006104451],"domain_scores_gemma":[0.9995603,0.0001862853,0.0001004714,0.00004396649,0.0000712984,0.00003770219],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0004169304,0.00008880822,0.04994915,0.0001161501,0.00007745843,0.0002715218,0.0004413728,0.003020331,0.9327123,0.0003208737,0.00013431,0.01245081],"study_design_scores_gemma":[0.00004086646,0.0009309315,0.4025061,0.00006433478,0.0002024767,0.002483951,0.0005683026,0.08961943,0.4982956,0.001369475,0.003830902,0.00008759607],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9810916,0.0003706578,0.01674954,0.00001995795,0.000008139045,0.00004058822,0.001099744,0.00008428582,0.0005354788],"genre_scores_gemma":[0.973265,0.0001240429,0.02465908,0.00005890659,0.000004874708,0.00004597825,0.001382489,0.00002596386,0.0004336979],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0008147377,"threshold_uncertainty_score":0.003377318,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04479428727955383,"score_gpt":0.2461303873434034,"score_spread":0.2013361000638496,"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."}}