{"id":"W4406486707","doi":"10.1101/2025.01.14.633004","title":"An artifact of recombinatorial cloning challenges established beliefs of plasmid co-transformation, selection, and maintenance","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Enzyme Production and Characterization","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Brandon University; Children's Hospital Research Institute of Manitoba; CancerCare Manitoba","funders":"","keywords":"Cloning (programming); Artifact (error); Transformation (genetics); Plasmid; Selection (genetic algorithm); Computational biology; Computer science; Biology; Biotechnology; Genetics; Artificial intelligence; DNA; Gene; Programming language","routes":{"ca_aff":true,"ca_fund":false,"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":[0.01918587,0.000923973,0.001340285,0.001022848,0.001421164,0.003813115,0.002059814,0.001133015,0.001755167],"category_scores_gemma":[0.02729994,0.0005894256,0.00048222,0.001036133,0.00542443,0.00341803,0.003106938,0.005553389,0.002386704],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001168361,"about_ca_system_score_gemma":0.00124405,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004231913,"about_ca_topic_score_gemma":0.0003897071,"domain_scores_codex":[0.9803998,0.006730828,0.00169715,0.002029171,0.00856547,0.000577593],"domain_scores_gemma":[0.9748981,0.008869676,0.003032873,0.009873752,0.00265986,0.0006656909],"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":[0.0006878317,0.0004071119,0.007581487,0.001151975,0.0001441989,0.001856993,0.002760104,0.0004969062,0.8252805,0.08120553,0.005492589,0.07293472],"study_design_scores_gemma":[0.00003904614,0.0005790141,0.003768987,0.0002713678,0.000144247,0.008060075,0.0007084844,0.002661741,0.879515,0.03467759,0.06948572,0.00008869592],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1867121,0.003597877,0.778638,0.01377273,0.00135423,0.0004490342,0.0006322766,0.00356361,0.0112802],"genre_scores_gemma":[0.6819745,0.004515428,0.2921667,0.003802008,0.0003864491,0.0004673993,0.00166369,0.002318098,0.01270567],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.01918587,"threshold_uncertainty_score":0.1014658,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008914654987540079,"score_gpt":0.2301306258564874,"score_spread":0.2212159708689473,"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."}}