{"id":"W2895933668","doi":"10.1099/mgen.0.000227","title":"Genomic epidemiology of clinical Campylobacter spp. at a single health trust site","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":25,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Biotechnology and Biological Sciences Research Council; Medical Research Council; Public Health England; Trent University; Nottingham Trent University","keywords":"Campylobacteriosis; Campylobacter; Typing; Biology; Locus (genetics); Multilocus sequence typing; Genetics; Epidemiology; Single-nucleotide polymorphism; Lineage (genetic); Population; Whole genome sequencing; SNP; Genome; Medicine; Environmental health; Genotype; Gene; Pathology; Bacteria","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":["insufficient_payload"],"category_scores_codex":[0.002274511,0.0002734452,0.001132807,0.00002173749,0.0002324521,0.000007723182,0.0004539246,0.0003774609,0.001108715],"category_scores_gemma":[0.0003144937,0.0001289397,0.0004034396,0.0001784506,0.0006253787,0.00004218935,0.0003618395,0.0002174817,0.0008817351],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001908194,"about_ca_system_score_gemma":0.00005533517,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001268274,"about_ca_topic_score_gemma":0.003861943,"domain_scores_codex":[0.9958869,0.0008996336,0.001657664,0.0007013325,0.00005940107,0.0007951242],"domain_scores_gemma":[0.9976305,0.0009016917,0.0008632799,0.0002156627,0.0001058223,0.0002830763],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0002268289,0.0001260971,0.4945047,0.000007542826,0.00002725495,0.000001363921,0.0001017635,0.000001829778,0.4835684,0.00005865045,0.008324031,0.0130515],"study_design_scores_gemma":[0.0002980351,0.001016275,0.7017843,0.00000914196,0.00001600866,0.00004824543,0.00003256559,0.00002009923,0.002465703,0.0001824142,0.2938957,0.0002315373],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9955081,0.0004434793,0.00002177608,0.00182064,0.001009769,0.0002748935,0.0002686365,0.0000518545,0.0006008141],"genre_scores_gemma":[0.9885986,0.0001692974,0.001358738,0.006439378,0.002427769,0.00000395647,0.0002640723,0.000004905577,0.0007333083],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4811027,"threshold_uncertainty_score":0.9998962,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1012030663882651,"score_gpt":0.324264546388623,"score_spread":0.2230614800003579,"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."}}