{"id":"W4317715921","doi":"10.1101/2023.01.21.525033","title":"Tracking coreceptor switch of the transmitted/founder HIV-1 identifies co-evolution of HIV-1 antigenicity, coreceptor usage and CD4 subset targeting","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"Centre Hospitalier de l’Université de Montréal","funders":"U.S. Army Medical Research and Development Command; National Institute of Allergy and Infectious Diseases; National Institutes of Health; U.S. Army; U.S. Department of Defense; Gilead Sciences; ViiV Healthcare; Henry M. Jackson Foundation","keywords":"Tropism; Biology; Virology; Antigenicity; Tissue tropism; Human immunodeficiency virus (HIV); CXCR4; Mutation; Virus; Immune system; Genetics; Gene; Antigen; Chemokine","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0002117214,0.0001144037,0.000116179,0.0002422702,0.0001414934,0.0003385139,0.0001350668,0.000205671,0.001076609],"category_scores_gemma":[0.0002596024,0.0000873177,0.0001108872,0.0001414974,0.0001374452,0.0001271315,0.000167434,0.0003702758,0.0002059033],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001524138,"about_ca_system_score_gemma":0.00007554695,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006241829,"about_ca_topic_score_gemma":0.0005833977,"domain_scores_codex":[0.9999247,0.00001344952,0.000003238949,0.00002331047,0.00001604305,0.0000193027],"domain_scores_gemma":[0.999858,0.00003638675,0.00003614986,0.00002313039,0.00001869223,0.00002762775],"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":[0.0005740169,0.0001374872,0.1973183,0.00003531086,0.00004577236,0.0004701669,0.0002530756,0.0006641776,0.7845168,0.000510495,0.0004346577,0.01503987],"study_design_scores_gemma":[0.00002148197,0.0007961394,0.7143756,0.00001446425,0.00005664233,0.003596219,0.000377876,0.01079344,0.2672568,0.0004721866,0.002224242,0.0000150123],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9988362,0.0001022666,0.0006218963,0.00001652544,0.00000325402,0.000003007411,0.0001056953,0.0000106723,0.0003003929],"genre_scores_gemma":[0.9984659,0.00004694913,0.0008352926,0.00001599322,0.000003198227,0.000003615612,0.000157547,0.000005138889,0.0004665192],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001076609,"threshold_uncertainty_score":0.003601611,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02179971468559046,"score_gpt":0.2464627735348825,"score_spread":0.224663058849292,"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."}}