{"id":"W4408106136","doi":"10.1101/2025.03.03.641190","title":"Early pandemic HIV-1 integration site preferences differ across anatomical reservoirs","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta; University of Calgary; Western University","funders":"","keywords":"Pandemic; Human immunodeficiency virus (HIV); Coronavirus disease 2019 (COVID-19); Geography; Virology; Biology; Medicine; Infectious disease (medical specialty); Internal medicine","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":[0.0001269034,0.0001204476,0.0001653304,0.000398654,0.0001526829,0.0004835217,0.00009452452,0.0002240715,0.001693756],"category_scores_gemma":[0.0002357334,0.0001299949,0.0001060978,0.0002439449,0.0001743785,0.0001530576,0.0002519267,0.0002351612,0.0004200756],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007579113,"about_ca_system_score_gemma":0.00006202062,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005752125,"about_ca_topic_score_gemma":0.0007670661,"domain_scores_codex":[0.999911,0.00001120472,0.000005708232,0.00003237578,0.00001757084,0.00002222279],"domain_scores_gemma":[0.9998612,0.00003505126,0.00004202755,0.0000153839,0.00002033233,0.00002586086],"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":[0.0002242366,0.00001325467,0.03737837,0.00003358689,0.00001843394,0.00007001918,0.0001194117,0.00007898051,0.9585615,0.0000551649,0.00004152941,0.0034055],"study_design_scores_gemma":[0.000008314642,0.0002257293,0.8123806,0.00001385298,0.00003842357,0.001443364,0.0005001157,0.001170084,0.182684,0.0002456899,0.001279379,0.00001045656],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9976242,0.00037744,0.001095761,0.00001310199,0.00000218924,0.00000510828,0.0003417136,0.00001288846,0.0005277054],"genre_scores_gemma":[0.9976031,0.0001653228,0.001133458,0.00002283208,0.00000306043,0.000006206317,0.0005319589,0.00001143786,0.0005225518],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001693756,"threshold_uncertainty_score":0.005666196,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02164272187656457,"score_gpt":0.269525400854267,"score_spread":0.2478826789777024,"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."}}