{"id":"W4393347780","doi":"10.1093/femsml/uqae005","title":"<i>Salmonella enterica</i> serovar Typhimurium ST313 sublineage 2.2 has emerged in Malawi with a characteristic gene expression signature and a fitness advantage","year":2024,"lang":"en","type":"article","venue":"microLife","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"Alliance for Accelerating Excellence in Science in Africa; African Academy of Sciences; Wellcome Trust","keywords":"Salmonella enterica; Serotype; Salmonella; Biology; Signature (topology); Gene; Microbiology; Gene expression; Virology; Genetics; Bacteria","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002807846,0.0002847514,0.0003886228,0.00003895974,0.0001085866,0.000124862,0.0002144321,0.0002034046,0.000206353],"category_scores_gemma":[0.00002764689,0.0001118593,0.00006900515,0.0003892133,0.0001142094,0.0001489689,0.0001199971,0.0003247762,0.00003220505],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002355018,"about_ca_system_score_gemma":0.00001428738,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009644898,"about_ca_topic_score_gemma":0.0001279063,"domain_scores_codex":[0.99827,0.0001760392,0.0003375782,0.0006357089,0.0001284644,0.0004522157],"domain_scores_gemma":[0.9994386,0.0002052028,0.00007796239,0.00009902662,0.00003449874,0.0001446731],"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":[0.0002159682,0.0000673792,0.04339842,0.00004695872,0.00001460297,0.0002091973,0.0001280501,0.000001822056,0.9524629,0.000008887344,0.001077594,0.002368259],"study_design_scores_gemma":[0.001360087,0.001117629,0.7168149,0.0007303344,0.0000909688,0.0006774504,0.001020332,0.0006635874,0.1687648,0.000235735,0.1070356,0.00148862],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9945492,0.002917778,0.0000333712,0.001702803,0.0002236452,0.0002434279,0.0001263142,0.0001204814,0.00008296572],"genre_scores_gemma":[0.9976801,0.0003808639,0.00018818,0.0008072823,0.0003288813,0.00003749439,0.0002132381,0.000005553817,0.0003584321],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.783698,"threshold_uncertainty_score":0.456149,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01717987338393548,"score_gpt":0.2250863640869866,"score_spread":0.2079064907030511,"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."}}