{"id":"W4401517399","doi":"10.1080/19490976.2024.2379440","title":"Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the <i>Helicobacter pylori</i> Genome Project","year":2024,"lang":"en","type":"article","venue":"Gut Microbes","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias; Fondo Nacional de Desarrollo Científico y Tecnológico; National Institute on Minority Health and Health Disparities; U.S. National Library of Medicine; National Institute of Environmental Health Sciences; National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; National Cancer Institute; Horizon 2020; Comisión Nacional de Investigación Científica y Tecnológica; Ministry of Education; Universiti Malaya; Agencia Nacional de Investigación y Desarrollo; National Medical Research Council; Alberta Innovates; Fundação de Amparo à Pesquisa do Estado de São Paulo; Ministry of Science and Technology; Institut National Du Cancer; Ministry of Health, British Columbia; Conselho Nacional de Desenvolvimento Científico e Tecnológico; Ministero della Salute; ArcticNet; Fundação para a Ciência e a Tecnologia; Ministry of Higher Education; Bundesministerium für Bildung und Forschung; National Research Foundation; European Commission; Universidad de Costa Rica; National Cancer Center; National Institutes of Health; Health Research; U.S. Department of Veterans Affairs","keywords":"Prophage; Biology; Genome; Genetics; Helicobacter pylori; Gene; Genomics; Comparative genomics; Whole genome sequencing; Bacteriophage; Escherichia coli","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005138446,0.000405574,0.0004649047,0.001368275,0.0003649305,0.0008332848,0.0004105675,0.0003463379,0.00135692],"category_scores_gemma":[0.001545796,0.000173393,0.0008937296,0.001632777,0.0002913398,0.0005368118,0.0005176693,0.0004857805,0.0004461663],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004761508,"about_ca_system_score_gemma":0.0004968125,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004320436,"about_ca_topic_score_gemma":0.003316709,"domain_scores_codex":[0.999724,0.0000490114,0.00001585109,0.0001252289,0.00004510786,0.00004092233],"domain_scores_gemma":[0.9995698,0.0001929855,0.00007263235,0.00006183982,0.00006195032,0.00004068625],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001682269,0.0003197448,0.3981904,0.00305968,0.0007935775,0.001035498,0.001126516,0.1796203,0.231475,0.02200886,0.01504158,0.1456467],"study_design_scores_gemma":[0.00007805398,0.0003355647,0.3030729,0.0001887692,0.0005505226,0.0007792818,0.0005119762,0.6023716,0.02234872,0.03655483,0.03308615,0.0001215753],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9249344,0.004648703,0.03839961,0.0003900731,0.00003994539,0.00005573401,0.02612039,0.001072543,0.004338587],"genre_scores_gemma":[0.9258795,0.001914247,0.02254649,0.0001137163,0.0000284627,0.0001380214,0.04848811,0.0001803469,0.0007111445],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004320436,"threshold_uncertainty_score":0.008590579,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01814735249301469,"score_gpt":0.233516123395285,"score_spread":0.2153687709022704,"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."}}