{"id":"W4409826757","doi":"10.1101/2025.04.24.650125","title":"Harnessing Coding Sequence Cleavage: Theophylline Aptazymes as Portable Gene Regulators in Bacteria","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Bacterial Genetics and Biotechnology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institut National de la Recherche Scientifique","funders":"Fonds de recherche du Québec – Nature et technologies; Natural Sciences and Engineering Research Council of Canada; Mitacs","keywords":"Theophylline; Bacteria; Coding region; Cleavage (geology); Gene; Coding (social sciences); Chemistry; Computational biology; Biology; Genetics; Pharmacology; Mathematics","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":[0.0001912768,0.000266532,0.0001697372,0.0001165272,0.0001037451,0.0003504747,0.0002914898,0.0004129455,0.001161308],"category_scores_gemma":[0.0001506925,0.0001237264,0.0001515521,0.0001011857,0.000228303,0.0002137077,0.0002791841,0.0005100445,0.0006234997],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003115596,"about_ca_system_score_gemma":0.000124597,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003406681,"about_ca_topic_score_gemma":0.0003144869,"domain_scores_codex":[0.9998711,0.00002381134,0.000009072885,0.00003168437,0.00004467991,0.00001962837],"domain_scores_gemma":[0.9999422,0.00001377512,0.0000158554,0.000008959229,0.000007469678,0.00001166938],"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":[0.00001719072,0.000009232046,0.00003210234,0.0000244208,0.000001739582,0.000022252,0.000007639458,0.0001525245,0.9975529,0.0004978406,0.00006087604,0.00162122],"study_design_scores_gemma":[0.000007067442,0.00006973492,0.0001461889,0.000002454304,0.000002909381,0.0000521812,0.00000370075,0.0008940608,0.9959248,0.00008502954,0.002807852,0.000003870087],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8488548,0.003428404,0.1327543,0.0006855059,0.0002446325,0.0001750726,0.0006514359,0.001577097,0.01162867],"genre_scores_gemma":[0.9534659,0.001086178,0.03785568,0.0001307718,0.00001697084,0.00007873166,0.0002319569,0.00008286216,0.007051076],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001161308,"threshold_uncertainty_score":0.003884971,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01137015860411594,"score_gpt":0.2314311949666054,"score_spread":0.2200610363624895,"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."}}