{"id":"W2019700487","doi":"10.1371/journal.pcbi.1002484","title":"Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA","year":2012,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"DNA and Nucleic Acid Chemistry","field":"Biochemistry, Genetics and Molecular Biology","cited_by":37,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"National Human Genome Research Institute; National Institutes of Health; National Science Foundation","keywords":"DNA supercoil; DNA; Base pair; Transition (genetics); Sequence (biology); Physics; DNA sequencing; Biology; Biophysics; Crystallography; Genetics; Gene; Chemistry; DNA replication","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001454731,0.00008487198,0.0001894822,0.0001004802,0.00002922286,0.000003054686,0.0000949743,0.0001230423,0.0003294379],"category_scores_gemma":[0.000066452,0.00008116569,0.0001024825,0.0001928769,0.0002520104,0.000004561275,0.00003663902,0.00006808079,0.000006342182],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000101522,"about_ca_system_score_gemma":0.00003527417,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001300044,"about_ca_topic_score_gemma":0.000001590076,"domain_scores_codex":[0.9992648,0.00006133859,0.0002784732,0.0001301954,0.00008400868,0.0001812116],"domain_scores_gemma":[0.9996526,0.00007460259,0.00005124132,0.00008644441,0.00007449748,0.00006067047],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00009816723,0.0005078015,0.128366,0.00002239122,0.0007370542,4.751371e-7,0.0003420945,0.004291884,0.6065085,0.258774,0.00005663759,0.0002949715],"study_design_scores_gemma":[0.003897744,0.000533531,0.4499772,0.00005339878,0.001169266,0.00007126,0.001064382,0.1756099,0.3451207,0.01919372,0.00201564,0.001293265],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9926521,0.00009488028,0.003657596,0.0002360185,0.00002669877,0.00004773465,0.0001178076,0.000006362107,0.003160774],"genre_scores_gemma":[0.9955003,0.000004540171,0.0019242,0.0002044967,0.00007437845,0.000007969467,0.002275663,0.000005131008,0.000003282704],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3216112,"threshold_uncertainty_score":0.3607115,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009238756316140897,"score_gpt":0.2548516088633662,"score_spread":0.2456128525472253,"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."}}