{"id":"W4413409304","doi":"10.1101/2025.08.13.670189","title":"The interplay between glucose and aromatic compound regulation by two IclR-type transcription factors, LigR1 and LigR2, in <i>Pseudomonas putida</i> KT2440","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Microbial Metabolic Engineering and Bioproduction","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"","keywords":"Pseudomonas putida; Transcription factor; Transcription (linguistics); Chemistry; Biology; Biochemistry; Gene; Philosophy","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":[0.0001480632,0.0004310822,0.0002888735,0.0002108388,0.0001442479,0.0004181961,0.0002021753,0.000242459,0.0006017476],"category_scores_gemma":[0.0001810098,0.0001744638,0.0002369082,0.0001267142,0.0002557366,0.0001393116,0.0002599657,0.0003878571,0.0004152738],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005571253,"about_ca_system_score_gemma":0.0001919528,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001541824,"about_ca_topic_score_gemma":0.001295717,"domain_scores_codex":[0.9997696,0.00003773776,0.00001484566,0.00006743509,0.00005440817,0.00005588902],"domain_scores_gemma":[0.9998604,0.0000365518,0.00003901557,0.00001640686,0.00001600606,0.0000316679],"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":[0.00008095473,0.00001845882,0.0004822822,0.00001191047,0.000002171638,0.00003706321,0.00001889565,0.00006075998,0.9986304,0.00002834903,0.00001760615,0.0006111302],"study_design_scores_gemma":[0.00002094133,0.000276599,0.02664942,0.00000708456,0.00001962485,0.0002785457,0.0001857187,0.004982028,0.9663913,0.00006216059,0.001103968,0.00002262131],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9977041,0.0002785905,0.001072775,0.00005227682,0.000008420475,0.000009137088,0.0002510623,0.00009181186,0.0005317729],"genre_scores_gemma":[0.9973245,0.00007216664,0.000993926,0.00004261768,0.000004416338,0.00001586921,0.0004642823,0.00002322043,0.001059056],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001541824,"threshold_uncertainty_score":0.004042268,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006466873027107742,"score_gpt":0.2219698590367405,"score_spread":0.2155029860096328,"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."}}