{"id":"W4353060534","doi":"10.3390/ddc2010012","title":"Optimizing Protein Production in Therapeutic Phages against a Bacterial Pathogen, Mycobacterium abscessus","year":2023,"lang":"en","type":"article","venue":"Drugs and Drug Candidates","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Translation (biology); Gene; Genetics; Codon usage bias; Bacteriophage; Start codon; Stop codon; Phage therapy; Genome; Computational biology; Messenger RNA; Escherichia coli","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":[],"consensus_categories":[],"category_scores_codex":[0.0002220318,0.0001676111,0.0001600972,0.00008763676,0.000162716,0.0001241069,0.0001046431,0.00004870788,0.0004198377],"category_scores_gemma":[0.00001564015,0.0001485153,0.00003901274,0.0003354248,0.00009381823,0.0003886534,0.000143962,0.0001291112,0.0002284138],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009026438,"about_ca_system_score_gemma":0.00001188505,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000568675,"about_ca_topic_score_gemma":0.0004300888,"domain_scores_codex":[0.998926,0.00005822067,0.0002111199,0.0003844753,0.00009775752,0.000322364],"domain_scores_gemma":[0.9996656,0.0000198666,0.0000725127,0.0001640334,0.000007134204,0.00007091559],"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":[0.0000426861,0.00003827209,0.0009098165,0.00001778841,0.000007913065,0.00001118151,0.002299968,0.00006236998,0.9845734,0.000007225324,0.0005118519,0.01151754],"study_design_scores_gemma":[0.002570042,0.0001580775,0.1674109,0.0004230303,0.00007369355,0.00004968882,0.006668541,0.001370531,0.6717492,0.0006040547,0.1472467,0.001675618],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9970979,0.00007805106,0.000004604561,0.0007720703,0.0004277579,0.0003586377,0.00003973504,0.00009538505,0.001125857],"genre_scores_gemma":[0.9970895,0.0001388279,0.0001143434,0.00008261692,0.0001284096,0.00007540554,0.000088843,0.0000217018,0.002260365],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3128242,"threshold_uncertainty_score":0.605628,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007070976741720812,"score_gpt":0.2256209737134503,"score_spread":0.2185499969717295,"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."}}