{"id":"W2157437937","doi":"10.1128/jcm.01502-14","title":"Using Crude Whole-Genome Assemblies of Neisseria gonorrhoeae as a Platform for Strain Analysis: Clonal Spread of Gonorrhea Infection in Saskatchewan, Canada","year":2014,"lang":"en","type":"article","venue":"Journal of Clinical Microbiology","topic":"Reproductive tract infections research","field":"Immunology and Microbiology","cited_by":20,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan","funders":"U.S. Public Health Service","keywords":"Neisseria gonorrhoeae; Biology; Gonorrhea; Neisseria meningitidis; Single-nucleotide polymorphism; Housekeeping gene; Population; Genome; Genetics; Whole genome sequencing; Phenotype; SNP array; Penicillin; Neisseriaceae; Microbiology; Multilocus sequence typing; Genotype; Virology; Gene; Antibiotics; Bacteria; Medicine","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":true,"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":[0.0007343307,0.0005781755,0.0004808463,0.001464307,0.001259746,0.001156123,0.0007084481,0.0003412334,0.001005814],"category_scores_gemma":[0.002719934,0.0003264993,0.0005040087,0.003550887,0.0003145915,0.0002537247,0.0007893746,0.0005889048,0.0003397545],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.005279466,"about_ca_system_score_gemma":0.01310512,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.8956155,"about_ca_topic_score_gemma":0.9704954,"domain_scores_codex":[0.9995139,0.00005042289,0.00003233935,0.0001516368,0.0001491599,0.0001026604],"domain_scores_gemma":[0.9987613,0.0002133228,0.00009353278,0.0001360925,0.0006583732,0.0001373099],"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":[0.0008415981,0.0001464129,0.3937722,0.0004409671,0.00163889,0.001109072,0.00414452,0.02748585,0.4470995,0.002632514,0.00646824,0.1142201],"study_design_scores_gemma":[0.00005399652,0.0000742795,0.930863,0.00006314411,0.0002749625,0.0002072104,0.001776216,0.02539857,0.01966281,0.0007139107,0.02082443,0.00008745631],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9453818,0.0005424887,0.02323692,0.0001656597,0.00002048013,0.0002526016,0.0261878,0.0003390223,0.003873217],"genre_scores_gemma":[0.8570219,0.001019972,0.07324355,0.0001815345,0.000006312773,0.0002653493,0.06376655,0.000257446,0.004237444],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1043845,"threshold_uncertainty_score":0.2099984,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06391507429190457,"score_gpt":0.3884684744849333,"score_spread":0.3245534001930288,"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."}}