{"id":"W4220654560","doi":"10.1101/2022.03.10.483817","title":"<i>Rickettsia typhi</i> peptidoglycan mapping with data-dependent tandem mass spectrometry","year":2022,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Vector-borne infectious diseases","field":"Immunology and Microbiology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"Genome British Columbia; University of Victoria","funders":"National Institute of Allergy and Infectious Diseases; Genome British Columbia; National Institutes of Health; University of Victoria; Genome Canada","keywords":"Peptidoglycan; Biology; Microbiology; Glycan; Typhus; Cell envelope; Rickettsia prowazekii; Rickettsia; Cell wall; Biochemistry; Virology; Glycoprotein; Escherichia coli; Virus","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003825059,0.0008189483,0.0003497797,0.0009946589,0.0003684001,0.000413349,0.0003944429,0.00046541,0.001809253],"category_scores_gemma":[0.0005772637,0.0001774172,0.0003008139,0.0005229934,0.000199346,0.0003465204,0.0003690752,0.0004934145,0.001316701],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002405206,"about_ca_system_score_gemma":0.0003957991,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008414772,"about_ca_topic_score_gemma":0.001380518,"domain_scores_codex":[0.9997236,0.00003946213,0.00002996206,0.00008131562,0.00008553844,0.00004011443],"domain_scores_gemma":[0.9997947,0.00002882771,0.00004618321,0.00002200207,0.00008225591,0.00002613956],"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":[0.00009539438,0.00001942388,0.0008943441,0.0001360549,0.00002443569,0.000228298,0.00002653983,0.0001006768,0.9923441,0.0001172034,0.0007652507,0.005248312],"study_design_scores_gemma":[0.00001931877,0.0001506538,0.01617039,0.00003875601,0.00004134994,0.001915029,0.0001131873,0.006674112,0.9579318,0.0002723433,0.01662548,0.00004754699],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8666949,0.006736983,0.09011452,0.001055456,0.0003737571,0.0003962343,0.01861871,0.004405834,0.01160365],"genre_scores_gemma":[0.7745827,0.003492023,0.1926041,0.000685301,0.00008756144,0.0003176947,0.02086959,0.0004277669,0.006933325],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001809253,"threshold_uncertainty_score":0.006052494,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01862786640439026,"score_gpt":0.2229908583787439,"score_spread":0.2043629919743536,"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."}}