{"id":"W4410631609","doi":"10.1371/journal.ppat.1013177","title":"Transmitted/founder (T/F) HIV-1 derived from sexual contact exhibits greater transmission fitness in human cervical tissue than T/F HIV-1 from blood-to-blood contact: Unique glycan profiles on T/F envelopes associated with transmission phenotypes","year":2025,"lang":"en","type":"article","venue":"PLoS Pathogens","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta; Western University","funders":"Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases; Institute of Infection and Immunity; National Institute of Allergy and Infectious Diseases; Canada Research Chairs","keywords":"Transmission (telecommunications); Virology; Biology; Ex vivo; Sexual transmission; Immunology; Virus; Human immunodeficiency virus (HIV); Genetics; In vivo; Microbicide","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":["metaepi_narrow","insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0001813064,0.0007226381,0.001026536,0.0003881176,0.0004488729,0.00006844617,0.0004596222,0.0007114463,0.00153106],"category_scores_gemma":[0.00004520873,0.0005454646,0.0001338585,0.0004330933,0.0001437284,0.0001292383,0.0000527449,0.0007996553,0.0002612499],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001638684,"about_ca_system_score_gemma":0.0002872732,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001468728,"about_ca_topic_score_gemma":0.00145027,"domain_scores_codex":[0.9958847,0.0009872548,0.0006579595,0.001223185,0.0002382067,0.001008688],"domain_scores_gemma":[0.9984408,0.0005551605,0.0001189973,0.0005156626,0.000136101,0.0002332857],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.002233944,0.002894405,0.07824476,0.00005920009,0.001933874,0.0005341657,0.004441831,0.000007550262,0.9059765,0.00007364346,0.000138237,0.003461865],"study_design_scores_gemma":[0.01120696,0.001726486,0.3197973,0.001098745,0.0006901079,0.000005533241,0.0003805522,0.000008919144,0.6636522,0.0001451424,0.0007174678,0.0005705282],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9908453,0.0006790012,0.001207461,0.00120006,0.00006293075,0.001710064,0.003464227,0.0002159169,0.0006150982],"genre_scores_gemma":[0.9898358,0.00005112484,0.0003658597,0.0002681278,0.00003427935,0.0003372305,0.007520516,0.0000814757,0.001505608],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2423243,"threshold_uncertainty_score":0.9996997,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0175478107391937,"score_gpt":0.2486302239048722,"score_spread":0.2310824131656785,"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."}}