{"id":"W2527201338","doi":"10.21769/bioprotoc.1270","title":"Design of a Transcription-based Secretion Activity Reporter (TSAR) for the Type III Secretion Apparatus of Shigella flexneri and Uses Thereof","year":2014,"lang":"en","type":"article","venue":"BIO-PROTOCOL","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Canadian Institutes of Health Research; Howard Hughes Medical Institute","keywords":"Shigella flexneri; Secretion; Shigella; Green fluorescent protein; Cell biology; Microbiology; Effector; Type three secretion system; Biology; Vacuole; Flow cytometry; Bacteria; Virulence; Cytoplasm; Salmonella; Molecular biology; Escherichia coli; Biochemistry; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006449565,0.0001309478,0.0001781352,0.00002770656,0.00009046597,0.00001438951,0.000111411,0.0001209616,0.0000120281],"category_scores_gemma":[0.0002093357,0.00008988404,0.00007070479,0.00009155018,0.0002065889,0.000005335966,0.00003261426,0.00005258313,3.327912e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000009035609,"about_ca_system_score_gemma":0.0001057437,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004610027,"about_ca_topic_score_gemma":0.00002476322,"domain_scores_codex":[0.999041,0.0001810625,0.0002220262,0.0002415828,0.0001538008,0.000160555],"domain_scores_gemma":[0.9990824,0.0001022748,0.0002005672,0.0003150592,0.0002645084,0.00003522428],"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":[0.00247029,0.00008121002,0.0007942452,0.000258863,0.00006021826,1.123229e-7,0.00004320997,0.00009576592,0.9942837,0.00003054898,0.0003794531,0.001502404],"study_design_scores_gemma":[0.002200201,0.002078481,0.004442092,0.00004700623,0.00003470302,0.000001279984,0.00004400152,0.008613385,0.9448051,0.00009477222,0.0374779,0.0001610935],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"protocol","genre_gemma":"empirical","genre_scores_codex":[0.2186767,0.00004775107,0.2802283,0.0002322065,0.00007758629,0.5000931,0.00002854954,0.00002556452,0.0005902057],"genre_scores_gemma":[0.7346524,0.000006064743,0.0009327173,0.00003067078,0.00006610826,0.2641754,0.000009076869,0.00001383457,0.0001137536],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.5159758,"threshold_uncertainty_score":0.3665364,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04580683177604532,"score_gpt":0.3345449190814376,"score_spread":0.2887380873053923,"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."}}