{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00005934217,0.0002349512,0.000180448,0.0002058847,0.0003053643,0.0003977588,0.00009135503,0.0002085925,0.000608333],"category_scores_gemma":[0.0001066259,0.0001336974,0.0002341863,0.0003250163,0.0001910919,0.0001124308,0.0002506124,0.0003725727,0.000171912],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000292142,"about_ca_system_score_gemma":0.0001824993,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004711332,"about_ca_topic_score_gemma":0.0075983,"domain_scores_codex":[0.9999089,0.000006803361,0.00000441651,0.00002952293,0.00001204654,0.00003833774],"domain_scores_gemma":[0.9999048,0.00001150062,0.00004088896,0.000009396383,0.00001345931,0.00001998707],"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":[0.0002148874,0.0000164451,0.016577,0.00005464178,0.00001173608,0.0001601073,0.0001916472,0.00004565566,0.9812869,0.00003670985,0.00009722103,0.001307113],"study_design_scores_gemma":[0.00001171212,0.0003444588,0.908859,0.00003106199,0.00004268112,0.0008279015,0.0007556314,0.0005301365,0.08358154,0.00005242153,0.004950223,0.00001329443],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9984611,0.0002122776,0.0001662335,0.000021546,0.000003378758,0.000009249082,0.0009143577,0.000007202801,0.0002045644],"genre_scores_gemma":[0.9950895,0.0002297793,0.0005398869,0.00009425108,0.000005434415,0.0000187141,0.003108456,0.000009522209,0.0009043967],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004711332,"threshold_uncertainty_score":0.009367824,"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."}}