{"id":"W2989492122","doi":"10.3390/v11111012","title":"HIV-1 Envelope Glycoprotein Amino Acids Signatures Associated with Clade B Transmitted/Founder and Recent Viruses","year":2019,"lang":"en","type":"article","venue":"Viruses","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":7,"is_retracted":false,"has_abstract":true,"ca_institutions":"Centre Hospitalier de l’Université de Montréal; Institut National de Santé Publique du Québec; Université de Montréal","funders":"Islamic Development Bank; Fonds de Recherche du Québec - Santé; Université du Québec en Outaouais; Institut National de Santé Publique du Québec; Université de Montréal; Université de Sherbrooke","keywords":"Glycoprotein; Clade; Virology; Human immunodeficiency virus (HIV); Biology; Founder effect; Viral envelope; Amino acid; Genetics; Phylogenetics; Gene; Haplotype; Allele","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":["insufficient_payload"],"category_scores_codex":[0.0001160468,0.0002742448,0.0003374254,0.0001244695,0.000186243,0.00004627286,0.0001695666,0.000295422,0.002406901],"category_scores_gemma":[0.00007203788,0.0001902105,0.00004582965,0.0001906838,0.0002707571,0.0001620238,0.00005222042,0.0003858426,0.001747298],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007762996,"about_ca_system_score_gemma":0.0001233457,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001569222,"about_ca_topic_score_gemma":0.0001524986,"domain_scores_codex":[0.9984832,0.0002400391,0.0002034895,0.0004256097,0.00009762104,0.0005500139],"domain_scores_gemma":[0.9992768,0.0002451612,0.00007465295,0.0002686003,0.00007285496,0.00006190706],"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":[0.002041491,0.0007834885,0.2226768,0.00004900614,0.002072361,0.00007776629,0.0008577612,0.000007746396,0.7472475,0.0006192905,0.008191673,0.01537514],"study_design_scores_gemma":[0.006925034,0.001539023,0.251891,0.0001572741,0.000115553,0.00003697513,0.0002314576,8.386e-7,0.317797,0.0001890924,0.4205638,0.0005529515],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9900305,0.006713274,0.00003841341,0.0003279072,0.0001276034,0.0006520225,0.000291947,0.000132981,0.001685387],"genre_scores_gemma":[0.9952502,0.0006905436,0.00005986485,0.0009117897,0.00001646134,0.00006988415,0.0002808613,0.0000266806,0.002693716],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4294505,"threshold_uncertainty_score":0.9990299,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02146174127464493,"score_gpt":0.2568359173864108,"score_spread":0.2353741761117658,"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."}}