{"id":"W4401521586","doi":"10.1038/s41564-024-01769-9","title":"Staphylococcus aureus adapts to exploit collagen-derived proline during chronic infection","year":2024,"lang":"en","type":"article","venue":"Nature Microbiology","topic":"Antimicrobial Resistance in Staphylococcus","field":"Medicine","cited_by":26,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary","funders":"National Heart, Lung, and Blood Institute; Alberta Innovates; National Cancer Institute; National Science Foundation; National Institutes of Health; Yale University; National Center for Research Resources; International Microbiome Centre, University of Calgary","keywords":"Staphylococcus aureus; Microbiology; Chronic infection; Biology; Virulence; Pathogenesis; Proline; Downregulation and upregulation; Staphylococcal infections; Immunology; Bacteria; Amino acid; Gene; Biochemistry; Immune system","routes":{"ca_aff":true,"ca_fund":true,"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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0002008484,0.0004237651,0.0006067042,0.0005313071,0.0001545127,0.00005510824,0.0001876037,0.0009775045,0.0003571009],"category_scores_gemma":[0.0001861826,0.0003710382,0.0002438614,0.0009291588,0.0001549874,0.00009246051,0.0001601759,0.001052164,0.0005631763],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008615308,"about_ca_system_score_gemma":0.0004807643,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003340824,"about_ca_topic_score_gemma":0.0003904099,"domain_scores_codex":[0.9976485,0.00008481602,0.0004592133,0.0009230065,0.0001174765,0.0007670307],"domain_scores_gemma":[0.9988583,0.00008383449,0.00007827999,0.0005270573,0.0002379215,0.0002145946],"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":[0.0005553689,0.00007558823,0.0006192701,0.0005125388,0.0002050234,0.0003734746,0.0001970274,0.00003958619,0.9768471,0.0001311114,0.01881882,0.001625057],"study_design_scores_gemma":[0.001350707,0.0006840045,0.008190255,0.0007041695,0.0001469548,0.0003894117,0.00002928131,0.00003082186,0.6400973,0.00003698327,0.3478523,0.0004878394],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9825196,0.009619858,0.00065461,0.002393578,0.001825587,0.001575175,0.0001431387,0.000574292,0.0006941161],"genre_scores_gemma":[0.9935366,0.0002938913,0.000882006,0.001105071,0.001416232,0.0001104535,0.0001635581,0.00009795952,0.002394218],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3367498,"threshold_uncertainty_score":0.9998742,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008378345406600167,"score_gpt":0.2817642547606661,"score_spread":0.273385909354066,"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."}}