{"id":"W2905622152","doi":"10.1111/mmi.14189","title":"Antigenic variation in the Lyme spirochete: detailed functional assessment of recombinational switching at <i>vlsE</i> in the JD1 strain of <i>Borrelia burgdorferi</i>","year":2018,"lang":"en","type":"article","venue":"Molecular Microbiology","topic":"Vector-borne infectious diseases","field":"Immunology and Microbiology","cited_by":18,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary","funders":"Canadian Institutes of Health Research; Génome Québec; McGill University","keywords":"Biology; Borrelia burgdorferi; Lyme disease; Antigenic variation; Genetics; Borrelia; Spirochaetaceae; Recombination; Gene conversion; Strain (injury); Gene; Inverted repeat; Virology; Genome; Antibody","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":[],"consensus_categories":[],"category_scores_codex":[0.0009984844,0.00021204,0.0003397405,0.0002049622,0.0001207595,0.000008463197,0.0004286896,0.0002814317,0.0003946621],"category_scores_gemma":[0.0001301119,0.0001519637,0.0001593406,0.000396909,0.0003441903,0.00005154066,0.0001039959,0.0003240921,0.00003788065],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001112541,"about_ca_system_score_gemma":0.0001695919,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001458464,"about_ca_topic_score_gemma":0.0003785435,"domain_scores_codex":[0.9973343,0.001286543,0.0006138738,0.0003657365,0.00005914462,0.0003403766],"domain_scores_gemma":[0.9987441,0.0003651123,0.0003337383,0.0004026443,0.000144419,0.000009936034],"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":[0.00009162791,0.0005296869,0.01874809,0.00001509859,0.0001190073,0.000006822027,0.000537854,0.00005823869,0.9763119,0.003076208,0.0003549368,0.0001505726],"study_design_scores_gemma":[0.003386388,0.0007841707,0.8320017,0.00004939034,0.0001140876,0.0004058904,0.0002620534,0.00003690869,0.1588759,0.001356362,0.002419584,0.0003075639],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9956617,0.0007137791,0.001548685,0.0004531248,0.0004952636,0.0004646987,0.0001100596,0.00001459081,0.0005380863],"genre_scores_gemma":[0.9983928,0.00001818153,0.00007737963,0.0009485401,0.00002674844,0.00005417447,0.0004419833,0.00001451799,0.00002563528],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8174359,"threshold_uncertainty_score":0.6196899,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008840684871936275,"score_gpt":0.2427310598666287,"score_spread":0.2338903749946924,"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."}}