{"id":"W4388405615","doi":"10.1016/j.ebiom.2023.104867","title":"Tracking coreceptor switch of the transmitted/founder HIV-1 identifies co-evolution of HIV-1 antigenicity, coreceptor usage and CD4 subset targeting: the RV217 acute infection cohort study","year":2023,"lang":"en","type":"article","venue":"EBioMedicine","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":11,"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; U.S. Army; U.S. Department of Defense; Gilead Sciences; ViiV Healthcare; Henry M. Jackson Foundation; National Institutes of Health; U.S. Department of Health and Human Services","keywords":"Biology; Virology; Antigenicity; Virus; Viral evolution; Mutagenesis; Mutation; Neutralization; Deep sequencing; Genetics; Genome; Gene; Antibody","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":[0.0007395461,0.000405402,0.0003913448,0.0003769862,0.0006373012,0.0007677843,0.0005378841,0.0004358015,0.0009379078],"category_scores_gemma":[0.0007504899,0.0002702449,0.0005624898,0.000250979,0.000277058,0.0003721551,0.0006554445,0.0006253121,0.0004047864],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003428187,"about_ca_system_score_gemma":0.0003071123,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002216931,"about_ca_topic_score_gemma":0.003392362,"domain_scores_codex":[0.9995604,0.00007880726,0.00002558314,0.0001681675,0.00007042704,0.0000965725],"domain_scores_gemma":[0.9993753,0.00006174276,0.0001203962,0.0001749624,0.0001089588,0.0001586336],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0005947918,0.0001151016,0.9900713,0.000014758,0.000119389,0.0003397033,0.0002403567,0.00007260417,0.005168604,0.00005381239,0.0003560469,0.002853544],"study_design_scores_gemma":[0.00003061584,0.001022003,0.993722,0.00001200345,0.0001328227,0.001781902,0.0004321942,0.0004943578,0.001395005,0.0000561274,0.0009084431,0.00001240813],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9993173,0.00005227308,0.0001195333,0.00000905216,0.000003118156,0.0000147832,0.0003499392,0.000003627301,0.0001304775],"genre_scores_gemma":[0.9982765,0.00004820407,0.0002046475,0.00001770366,0.000007998073,0.00002000855,0.001179234,0.000008308237,0.0002373957],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002216931,"threshold_uncertainty_score":0.004408062,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01730107431342323,"score_gpt":0.2900066144217049,"score_spread":0.2727055401082817,"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."}}