{"id":"W4391170116","doi":"10.3390/antibiotics13020112","title":"The Role of Prophage ϕSa3 in the Adaption of Staphylococcus aureus ST398 Sublineages from Human to Animal Hosts","year":2024,"lang":"en","type":"article","venue":"Antibiotics","topic":"Antimicrobial Resistance in Staphylococcus","field":"Medicine","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary; Alberta Health Services","funders":"Alberta Health Services","keywords":"Clade; Prophage; Phylogenetic tree; Biology; Phylogenetics; Lineage (genetic); Evolutionary biology; Genetics; Gene; Bacteriophage; Escherichia coli","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004725544,0.0001706811,0.0003119856,0.0001413126,0.00007990628,0.00005236271,0.0003212408,0.000109645,0.00001743167],"category_scores_gemma":[0.0001764282,0.0001016666,0.0001249178,0.0005960896,0.0001929371,0.00006058652,0.00007609178,0.000295456,0.00001628343],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004347083,"about_ca_system_score_gemma":0.000120628,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003925108,"about_ca_topic_score_gemma":0.0005158592,"domain_scores_codex":[0.9984571,0.00008508946,0.0005130274,0.0002670641,0.0004023892,0.000275317],"domain_scores_gemma":[0.9988595,0.0002952494,0.0001167552,0.0005289863,0.0001482682,0.0000512325],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0002831693,0.0001987787,0.02750407,0.0001572203,0.00007701673,0.00007029593,0.001495302,0.0000103903,0.9598433,0.00597751,0.001687838,0.002695153],"study_design_scores_gemma":[0.0005568624,0.001043695,0.3153007,0.000939584,0.0001653081,0.000003078396,0.0031492,0.0004703687,0.6682105,0.0007015185,0.009253876,0.0002053218],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9943174,0.002826734,0.00009605876,0.0008765385,0.0001177849,0.0007291674,0.000119495,0.00003269546,0.000884094],"genre_scores_gemma":[0.9988664,0.0001699977,0.0004877116,0.0001016391,0.000174068,0.000001044179,0.00002244797,0.00002971368,0.0001470074],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2916327,"threshold_uncertainty_score":0.4145842,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01312972446037648,"score_gpt":0.2967054667221209,"score_spread":0.2835757422617444,"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."}}