{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25216269", "kind": "science-record", "revision": 7, "content_hash": "sha256:8dcb64d32a75848acdedb762d6241a8855f6c66f908652fee2fa7097129b9609", "created_at": "2026-11-01T15:40:06Z", "updated_at": "2026-11-01T21:58:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579.", "doi": "10.1371/journal.pone.0107354", "pmid": "25216269", "authors": ["Sabrina Laouami", "Géremy Clair", "Jean Armengaud", "Catherine Duport"], "journal": "PloS one", "year": 2014, "abstract": "The facultative anaerobe, Bacillus cereus, causes diarrheal diseases in humans. Its ability to deal with oxygen availability is recognized to be critical for pathogenesis. The B. cereus genome comprises a gene encoding a protein with high similarities to the redox regulator, Rex, which is a central regulator of anaerobic metabolism in Bacillus subtilis and other Gram-positive bacteria. Here, we showed that B. cereus rex is monocistronic and down-regulated in the absence of oxygen. The protein encoded by rex is an authentic Rex transcriptional factor since its DNA binding activity depends on the NADH/NAD+ ratio. Rex deletion compromised the ability of B. cereus to cope with external oxidative stress under anaerobiosis while increasing B. cereus resistance against such stress under aerobiosis. The deletion of rex affects anaerobic fermentative and aerobic respiratory metabolism of B. cereus by decreasing and increasing, respectively, the carbon flux through the NADH-recycling lactate pathway. We compared both the cellular proteome and exoproteome of the wild-type and Δrex cells using a high throughput shotgun label-free quantitation approach and identified proteins that are under control of Rex-mediated regulation. Proteomics data have been deposited to the ProteomeXchange with identifier PXD000886. The data suggest that Rex regulates both the cross-talk between metabolic pathways that produce NADH and NADPH and toxinogenesis, especially in oxic conditions.", "claims": [{"id": "claim-method", "statement": "MS/MS spectral counts were compared with the TFold method using the PatternLab software program 2.0.0.13 [33] using a p-value cut-off set at 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25216269", "locator": "sections[10] \"Proteomic sample preparation and nanoLC-MS/MS analysis of tryptic peptides\" paragraph 2", "quote": "MS/MS spectral counts were compared with the TFold method using the PatternLab software program 2.0.0.13 [33] using a p-value cut-off set at 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The authors confirm that all data underlying the findings are fully available without restriction. Our MS/MS data are deposited on the PRIDE repository database http://www.ebi.ac.uk/pride/; Username: reviewer73547@ebi.ac.uk; Password: 0EbXtIq9.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25216269", "locator": "sections[33] \"Data Availability\" paragraph 2", "quote": "The authors confirm that all data underlying the findings are fully available without restriction. Our MS/MS data are deposited on the PRIDE repository database http://www.ebi.ac.uk/pride/; Username: reviewer73547@ebi.ac.uk; Password: 0EbXtIq9."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:25216269"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD000856"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD000856"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:25216269", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0107354", "sha256": "sha256:d265c5aeeba5f3c77faf306e975e293c09f2b0a8dd2f7ff8cb0954269fa204f8", "bytes": 67443, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0107354", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4162614", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD000856", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD000856", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD000856", "version": null, "note": "The authors confirm that all data underlying the findings are fully available without restriction. Our MS/MS data are deposited on the PRIDE repository database http://www.ebi.ac.uk/pride/; Username: reviewer73547@ebi.ac.uk; Password: 0EbXtIq9.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The authors confirm that all data underlying the findings are fully available without restriction. Our MS/MS data are deposited on the PRIDE repository database http://www.ebi.ac.uk/pride/; Username: reviewer73547@ebi.ac.uk; Password: 0EbXtIq9.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Bacillus cereus proteomics -  Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:25216269:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f8870cb63bf817bb9217abe01d2f430980a3bf371768cb510003450dc616f46e", "bytes": 1282, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#pone-0107354-t001", "version": null, "note": "Results from controlled batch cultures of Δrex mutant and its parent strain, B. cereus ATCC 14579a.", "structure": {"pmcid": "PMC4162614", "section_index": 14, "section_title": "Rex regulates glucose catabolism in B. cereus", "row_count": 15, "column_count": 5}, "table": {"label": "Table 1", "caption": "Results from controlled batch cultures of Δrex mutant and its parent strain, B. cereus ATCC 14579a.", "rows": [["", "Anaerobic fermentative growth", "Aerobic respiratory growth"], ["", "WTb", "Δrex", "WTb", "Δrex"], ["Maximal specific growth rate (µmax) (h−1)", "0.84±0.04", "0.90±0.02*", "1.22±0.11", "1.41±0.04*"], ["Final biomass (g.liter−1)", "0.78±0.01", "0.83±0.06", "2.38±0.12", "2.31±0.12"], ["Yglucose (g of cells. mol of glucose−1)", "26±1", "28±1", "79±1", "77±1"], ["Maximal specific glucose consumption(mmol.g−1.h−1)", "32±2", "32±2", "15±1", "18±2"], ["Yields of end products (mol.mol glucose−1)c", "", "", "", ""], ["Lactate (Y lactate)", "1.33±0.01", "1.25±0.02*", "0.05±0.02", "0.40±0.01*"], ["Acetate (Yacetate)", "0.32±0.01", "0.36±0.01*", "1.05±0.01", "0.69±0.03*"], ["Formate (Yformate)", "0.23±0.01", "0.27±0.01*", "0.01±0.01", "0.01±0.01"], ["Ethanol (Yethanol)", "0.13±0.01", "0.18±0.01*", "NZd", "NZ"], ["Succinate (Ysuccinate)", "0.01±0.01", "0.01±0.01", "0.05±0.01", "0.04±0.01"], ["Ethanol versus Acetate", "0.40", "0.50*", "", ""], ["ATP yielde", "2.10", "2.15", "NDf", "ND"], ["NADH recoveredg", "1.2", "1.2", "ND", "ND"]], "row_count": 15, "column_count": 5, "numeric_cells": 45, "header_rows": 2, "locator": "section[14]/table-wrap[1]#pone-0107354-t001"}}, {"id": "asset:table:pmid:25216269:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3a1e693b2f36181107ee6dd24faa408bbede346d710ccda9c03ea25cd0217c03", "bytes": 5702, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[24]/table-wrap[1]#pone-0107354-t002", "version": null, "note": "Cellular abundance level changes of cell membrane, transport, stress response, transcriptional regulation, virulence and phage-related proteins in Δrex mutant relative to wild-type under anaerobiosis and aerobiosis.", "structure": {"pmcid": "PMC4162614", "section_index": 24, "section_title": "(iii) Impact of Rex on other relevant cellular pathways", "row_count": 59, "column_count": 8}, "table": {"label": "Table 2", "caption": "Cellular abundance level changes of cell membrane, transport, stress response, transcriptional regulation, virulence and phage-related proteins in Δrex mutant relative to wild-type under anaerobiosis and aerobiosis.", "rows": [["", "", "", "", "Abundance level change and significance"], ["", "", "", "", "Anaerobiosis", "Aerobiosis"], ["Accession no (NP)", "Proteinname", "Gene number", "Functionnal annotation", "log2(fold-change)a", "p-value", "log2(fold-change)", "p-value"], ["", "", "", "Cell wall, membrane and cell surface proteins", "", "", "", ""], ["NP_833630.1", "-", "BC_3910", "N-acetylglucosaminyl transferase", "1,561", "0,018", "−1,515", "0,197"], ["NP_835080.1", "TagA", "BC_5419", "N-acetyl-beta-D-mannosaminyltransferase", "1,263", "0,042", "−0,377", "0,382"], ["NP_832677.1", "-", "BC_2929", "Peptidoglycan N-acetylglucosamine deacetylase", "0,832", "0,019", "0,799", "0,183"], ["NP_835088.1", "-", "BC_5427", "Cell wall biosynthesis glycosyltransferase", "−1,120", "0,046", "−0,889", "0,070"], ["NP_834932.1", "AmsK", "BC_5269", "Amylovoran biosynthesis AmsK", "−0,713", "0,112", "1,595", "0,001"], ["NP_834404.1", "-", "BC_4698", "Choline kinase", "0,949", "0,032", "0,214", "0,199"], ["NP_834827.1", "Lgt", "BC_5163", "Prolipoprotein diacylglyceryl transferase", "1,007", "0,012", "−0,811", "0,004"], ["NP_834936.1", "-", "BC_5273", "UDP-bacillosamine synthetase", "1,322", "0,033", "0,632", "0,110"], ["NP_835093.1", "-", "BC_5432", "Bactoprenol glucosyl transferase", "−1,218", "0,032", "0,536", "0,306"], ["NP_835019.1", "-", "BC_5358", "Collagen adhesion protein", "0,918", "0,088", "1,170", "0,045"], ["NP_830682.1", "-", "BC_0896", "S-layer protein", "−0,234", "0,180", "−0,286", "0,017"], ["", "", "", "Transport-related proteins", "", "", "", ""], ["NP_829996.1", "SecE", "BC_0115", "Preprotein translocase subunit", "−0,971", "0,044", "0,411", "0,252"], ["NP_834447.1", "-", "BC_4743", "ABC transporter ATP-binding protein", "1,561", "0,018", "−0,029", "0,485"], ["NP_834539.1", "-", "BC_4839", "ABC transporter ATP-binding protein", "1,585", "0,031", "0,856", "0,115"], ["NP_830141.1", "Uup", "BC_0290", "ABC transporter ATP-binding protein", "0,151", "0,382", "0,705", "0,045"], ["NP_830187.1", "-", "BC_0348", "Methionine ABC transporter", "−1,690", "0,004", "2,160", "0,064"], ["NP_830967.1", "OppD", "BC_1182", "Oligopeptide transport ATP-binding protein", "0,651", "0,002", "−0,044", "0,421"], ["NP_830660.1", "-", "BC_0874", "Arginine ABC transporter ATP-binding protein", "−0,396", "0,349", "−1,218", "0,024"], ["NP_832817.1", "CutC", "BC_3071", "Copper tansport", "0,903", "0,007", "−0,358", "0,341"], ["NP_830432.1", "-", "BC_0615", "Di-/tripeptide transporter", "−0,837", "0,047", "0,422", "0,232"], ["NP_830429.1", "-", "BC_0612", "L-lactate permease", "0,748", "0,026", "−0,644", "0,261"], ["", "", "", "Stress response-related proteins", "", "", "", ""], ["NP_831381.1", "-", "BC_1603", "Cold shock protein", "−1,120", "0,037", "−0,474", "0,277"], ["NP_830286.1", "TelA", "BC_0447", "Tellurite resistance protein", "0,084", "0,432", "0,840", "0,008"], ["NP_833675.1", "-", "BC_3956", "GTP-binding protein TypA/BipA", "0,310", "0,049", "0,043", "0,419"], ["NP_833972.1", "-", "BC_4258", "Hydroxyacylglutathione hydrolase", "0,824", "0,028", "−0,578", "0,213"], ["NP_833576.1", "-", "BC_3855", "Alkaline-shock protein", "0,014", "0,488", "0,740", "0,026"], ["NP_834187.1", "OhrA", "BC_4475", "Organic hydroxyperoxide protein A", "0,189", "0,340", "2,029", "0,015"], ["NP_829959.1", "Hsp15", "BC_0062", "Heat shock protein 15", "0,799", "0,082", "1,667", "0,007"], ["NP_830216.1", "AhpC", "BC_0377", "Alkyl hydroperoxide reductase C22", "−0,136", "0,426", "−1,029", "0,007"], ["NP_830941.1", "KatE", "BC_1155", "Catalase", "1,111", "0,014", "−0,074", "0,466"], ["NP_834345.1", "-", "BC_4639", "Thiol peroxidase", "−0,044", "0,463", "−0,737", "0,034"], ["", "", "", "Transcriptional Regulation", "", "", "", ""], ["NP_833888.1", "ArgR2", "BC_4174", "Arginine biosynthesis repressor", "1,511", "0,030", "1,269", "0,079"], ["NP_833771.1", "-", "BC_4053", "Transcriptional regulator, GntR family", "0,895", "0,019", "0,227", "0,399"], ["NP_833799.1", "-", "BC_4081", "MarR family transcriptional regulator", "0,029", "0,464", "1,903", "0,001"], ["NP_834861.1", "-", "BC_5197", "MarR family transcriptional regulator", "0,345", "0,029", "0,604", "0,123"], ["NP_832113.1", "-", "BC_2351", "MerR family transcriptional regulator", "0,485", "0,276", "1,170", "0,045"], ["NP_830532.1", "TenA", "BC_0742", "Transcriptional activator", "0,791", "0,046", "−0,621", "0,193"], ["NP_834137.1", "-", "BC_4425", "Transcriptional regulator", "0,632", "0,044", "−1,029", "0,051"], ["NP_831310.1", "-", "BC_1531", "Transcriptional regulatory protein", "−0,029", "0,471", "1,480", "0,004"], ["NP_831256.1", "ResD", "BC_1477", "Transcriptional regulatory protein", "0,356", "0,008", "−0,599", "0,119"], ["NP_830596.1", "-", "BC_0806", "BigG family transcription antiterminator", "0,485", "0,276", "1,922", "0,000"], ["", "", "", "Virulence-related proteins", "", "", "", ""], ["NP_834769.1", "HlyI", "BC_5101", "Hemolysin I", "−0,152", "0,438", "2,611", "0,001"], ["NP_832488.1", "Npr2", "BC_2735", "Bacillolysin", "−1,089", "0,193", "−2,120", "0,013"], ["NP_833332.1", "HhoA", "BC_3600", "Protease", "0,485", "0,098", "−1,690", "0,026"], ["NP_831147.1", "-", "BC_1366", "SSEB protein", "1,163", "0,036", "1,269", "0,055"], ["", "", "", "Phage-related proteins", "", "", "", ""], ["NP_831667.1", "-", "BC_1894", "Phage protein", "3,023", "0,014", "−1,358", "0,286"], ["NP_831632.1", "-", "BC_1859", "Phage protein", "2,526", "0,039", "−0,644", "0,261"], ["NP_831635.1", "-", "BC_1862", "Phage protein", "1,714", "0,027", "−0,761", "0,302"], ["NP_831673.1", "-", "BC_1901", "Phage protein", "1,727", "0,012", "−1,889", "0,205"], ["NP_831676.1", "-", "BC_1904", "Phage protein", "1,975", "0,038", "−0,515", "0,367"]], "row_count": 59, "column_count": 8, "numeric_cells": 303, "header_rows": 3, "locator": "section[24]/table-wrap[1]#pone-0107354-t002"}}, {"id": "asset:table:pmid:25216269:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ee151df068088bd167cfbe8a3c4c50e9d7a1f592671429e6954a837157b66620", "bytes": 1533, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[26]/table-wrap[1]#pone-0107354-t003", "version": null, "note": "Changes in mRNA and protein abundance of toxins and putative toxins induced by Δrex mutation under anaerobic and aerobic growth conditions#.", "structure": {"pmcid": "PMC4162614", "section_index": 26, "section_title": "(i) Focus on toxin-related proteins", "row_count": 18, "column_count": 8}, "table": {"label": "Table 3", "caption": "Changes in mRNA and protein abundance of toxins and putative toxins induced by Δrex mutation under anaerobic and aerobic growth conditions#.", "rows": [["Protein name", "", "Log2(fold-change) in B. cereus Δrex vs wild-typea"], ["", "Gene", "Anaerobiosis", "Aerobiosis"], ["", "", "mRNA", "Protein", "mRNA", "Protein"], ["", "", "", "cellular", "extracellular", "s", "cellular", "extracellular"], ["CytK", "BC_1110", "NS", "NSa", "NS", "NS", "NS", "1,72 ( p = 0.001)"], ["EntA", "BC_5239", "NS", "NS", "0,29 ( p = 0.035)", "NS", "NS", "0,53 ( p = 0.001)"], ["EntB", "BC_2952", "NS", "NS", "NS", "NS", "NS", "NS"], ["EntC", "BC_0813", "NS", "NS", "0,37 ( p = 0.042)", "−1,29 (p<0.05)", "NS", "0,75 ( p = 0.002)"], ["EntFM", "BC_1953", "NS", "NS", "NS", "−1,49 (p<0.05)", "NS", "0,68 ( p = 0.000)"], ["HblB", "BC_3102", "NS", "NS", "NS", "NS", "NS", "1,38 ( p = 0.001)"], ["HblB'", "BC_3101", "NS", "NS", "NS", "NS", "NS", "1,28 ( p = 0.002)"], ["HblL1", "BC_3103", "NS", "NS", "0,32 ( p = 0.039)", "NS", "NS", "1,09 ( p = 0.006)"], ["HblL2", "BC_3104", "NS", "NS", "NS", "NS", "NS", "1,29 ( p = 0.000)"], ["HlyI", "BC_5101", "NS", "NS", "NS", "NS", "2,61( p = 0.001)", "NS"], ["HlyII", "BC_3523", "NS", "NS", "NS", "NS", "NS", "2,45 ( p = 0.000)"], ["NheA", "BC_1809", "NS", "NS", "0,47 ( p = 0.003)", "NS", "NS", "1,35 ( p = 0.002)"], ["NheB", "BC_1810", "NS", "NS", "0,42 ( p = 0.008)", "NS", "NS", "1,34 ( p = 0.001)"], ["NheC", "BC_1811", "NS", "NS", "0,83 ( p = 0.001)", "NS", "NS", "1,70 ( p = 0.001)"]], "row_count": 18, "column_count": 8, "numeric_cells": 35, "header_rows": 4, "locator": "section[26]/table-wrap[1]#pone-0107354-t003"}}, {"id": "asset:table:pmid:25216269:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5a344c45944a2d9a7f557431e73f7dc239a66b3eed572277f57e63e4602ccad8", "bytes": 8358, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[27]/table-wrap[1]#pone-0107354-t004", "version": null, "note": "Changes in protein abundances in Δrex exoproteome compared to wild-type exoproteome under anaerobiosis and aerobiosis.", "structure": {"pmcid": "PMC4162614", "section_index": 27, "section_title": "(ii) Other predicted extracellular proteins", "row_count": 88, "column_count": 10}, "table": {"label": "Table 4", "caption": "Changes in protein abundances in Δrex exoproteome compared to wild-type exoproteome under anaerobiosis and aerobiosis.", "rows": [["", "", "", "", "", "", "Log2 fold-change and significancea"], ["Proteinname", "Gene", "Accession no. (NP)", "Functional annotation", "TM domain", "Export Signal peptide", "Anaerobiosis", "Aerobiosis"], ["", "", "", "", "", "", "log2-fold-change", "p-value", "log2-fold-change", "p-value"], ["Degradative enzymes and adhesins", "", "", "", "", "", ""], ["ColC", "BC_0556", "NP_830373", "Collagenase", "N", "Y", "0,4", "0,03", "1,9", "0,00"], ["NprB", "BC_5351", "NP_835012", "Bacillolysin", "N", "Y", "0,67", "0,00", "1,97", "0,00"], ["NprP2", "BC_2735", "NP_832488", "Bacillolysin", "N", "Y", "1,58", "0,00", "2,6", "0,01"], ["HhoA", "BC_3600", "NP_833332", "Protease", "N", "Y", "0,176", "0,241", "0,6", "0,03"], ["Tgc", "BC_1991", "NP_831760", "Putative murein endopeptidase", "N", "Y", "0,45", "0,01", "1,71", "0,00"], ["PlcB", "BC_0670", "NP_830483", "phospholipase C", "N", "Y", "0,6", "0,00", "2,25", "0,00"], ["PlcA", "BC_3761", "NP_833485", "Phosphatidylinositol phosphodiesterase", "N", "Y", "0,48", "0,02", "2,55", "0,00"], ["InhA2", "BC_0666", "NP_830479", "Immune inhibitor A precursor", "N", "Y", "1,59", "0,01", "3,43", "0,00"], ["PgdA", "BC_2929", "NP_832677", "Peptidoglycan deacetylase", "N", "Y", "0,585", "0,055", "0,87", "0,04"], ["Sph", "BC_0671", "NP_830484", "Sphingomyelin phosphodiesterase", "N", "Y", "0,82", "0,03", "2,82", "0,00"], ["Flagella components", "", "", "", "", "", ""], ["FlaA", "BC_1659", "NP_831436", "Flagellin", "N", "N", "0,516", "0,117", "0,6", "0,02"], ["FlgK", "BC_1636", "NP_831414", "Flagellar hook-associated protein", "N", "N", "0,96", "0,01", "1,04", "0,05"], ["FlgL", "BC_1637", "NP_831415", "Flagellar hook-associated protein", "N", "N", "0,78", "0,04", "1,28", "0,00"], ["FliD", "BC_1638", "NP_831416", "Flagellar capping protein", "N", "N", "0,526", "0,063", "1,22", "0,00"], ["FlgB", "BC_1641", "NP_831419", "Flagellar basal body rod protein", "N", "N", "0,111", "0,411", "0,9", "0,01"], ["Cell wall and membrane-related proteins", "", "", "", "", "", ""], ["FtsI", "BC_4270", "NP_833984", "Penicillin-binding protein", "Y", "N", "0,189", "0,145", "1,73", "0,02"], ["YvgJ1", "BC_2932", "NP_832680", "Phosphoglycerol transferase", "Y", "N", "−0,03", "0,462", "1,25", "0,03"], ["YvgJ2", "BC_5232", "NP_834895", "phosphoglycerol transferase", "Y", "N", "−0,03", "0,463", "0,71", "0,00"], ["CwlD", "BC_5196", "NP_834860", "N-acetylmuramoyl-L-alanine amidase", "N", "Y", "0,485", "0,022", "0,67", "0,00"], ["CwlB", "BC_0902", "NP_830688", "N-acetylmuramoyl-L-alanine amidase", "N", "Y", "1,091", "0,187", "−1,1", "0,04"], ["Metabolism", "", "", "", "", "", ""], ["Eno", "BC_5135", "NP_834803", "Phosphopyruvate hydratase", "N", "N", "−1,2", "0,01", "−0,12", "0,385"], ["PfkA", "BC_4600", "NP_834306", "6-Phosphofructokinase", "N", "N", "−0,9", "0,04", "−0,18", "0,377"], ["PykA", "BC_4599", "NP_834305", "Pyruvate kinase", "N", "N", "−0,15", "0,429", "−4,6", "0,01"], ["Pgi", "BC_4898", "NP_834571", "Glucose-6-phosphate isomerase", "N", "N", "−1", "0,04", "0,014", "0,493"], ["AtpA", "BC_3230", "NP_832971", "F0F1 ATP synthase subunit alpha", "N", "Y", "−0,03", "0,448", "1,75", "0,00"], ["GapA", "BC_5140", "NP_834805", "Glyceraldehyde-3-phosphate dehydrogenase", "N", "N", "−0,62", "0,144", "−2,9", "0,00"], ["PtA", "BC_5387", "NP_835048", "Phosphotransacetylase", "N", "N", "−1,6", "0,01", "−2,1", "0,03"], ["GapN", "BC_0868", "NP_830654", "NADP-dependent glyceraldehyde-3-phosphate dehydrogenase", "N", "N", "−3,6", "0,00", "−1,32", "0,054"], ["FbA", "BC_5335", "NP_834997", "Fructose-bisphosphate aldolase", "N", "N", "−0,76", "0,298", "−3,6", "0,03"], ["Hpr", "BC_4049", "NP_833767", "Phosphocarrier protein HPr", "N", "N", "−2,4", "0,03", "−1,18", "0,079"], ["Bdh", "BC_0868", "NP_830481", "(R,R)-butanediol dehydrogenase", "N", "N", "−3,32", "0,06", "−3,6", "0,02"], ["PtsA", "BC_4048", "NP_833766", "Phosphotransferase", "N", "N", "−2,12", "0,058", "−3,2", "0,00"], ["SfcA", "BC_4604", "NP_834310", "NAD-dependent malic enzyme", "N", "N", "−0,86", "0,187", "−1,6", "0,04"], ["GlmM", "BC_0188", "NP_830056", "Phosphoglucosamine mutase", "N", "N", "−1,32", "0,058", "−3,8", "0,00"], ["GdhA", "BC_4162", "NP_833877", "Leucine dehydrogenase", "N", "N", "−1,8", "0,04", "−2,4", "0,081"], ["-", "BC_4366", "NP_834078", "Cystathionine beta-lyase", "N", "N", "0,151", "0,447", "−2", "0,03"], ["AdsS", "BC_5468", "NP_835123", "Adenylosuccinate synthetase", "N", "N", "−1,8", "0,04", "−1,15", "0,202"], ["-", "BC_3799", "NP_833521", "Aspartate-semialdehyde dehydrogenase", "N", "N", "−2,56", "0,079", "−3,2", "0,01"], ["ThiG", "BC_0749", "NP_830539", "Thiazole synthase", "N", "N", "ND", "ND", "−2,2", "0,01"], ["-", "BC_0071", "NP_829966", "Phosphoribosyltransferase", "N", "N", "−0,23", "0,425", "−3,5", "0,00"], ["DeoD", "BC_1463", "NP_831242", "Purine nucleoside phosphorylase", "N", "N", "−2,6", "0,02", "−1,06", "0,185"], ["-", "BC_0015", "NP_829919", "Pyridoxine biosynthesis protein", "N", "N", "−1,8", "0,01", "−3,6", "0,00"], ["-", "BC_3981", "NP_833700", "tetrahydrodipicolinate -acetyltransferase", "N", "N", "ND", "ND", "−3,3", "0,00"], ["MoaB", "BC_4758", "NP_834462", "Molybdenum cofactor", "N", "N", "−0,94", "0,187", "−2,3", "0,02"], ["FrvB", "BC_4571", "NP_834277", "Deblocking aminopeptidase", "N", "N", "−3,2", "0,00", "−0,92", "0,215"], ["PepT", "BC_4143", "NP_833858", "Peptidase T", "N", "N", "−1,6", "0,04", "−1,94", "0,061"], ["Stress-related proteins", "", "", "", "", "", ""], ["AhpC", "BC_0377", "NP_830216", "Alkyl hydroperoxide reductase C22", "N", "N", "−0,94", "0,154", "−2,2", "0,00"], ["GrpE", "BC_4313", "NP_834025", "Chaperon", "N", "N", "−1,4", "0,04", "−0,38", "0,335"], ["GroEL", "BC_0295", "NP_830146", "Chaperon", "N", "N", "−0,69", "0,214", "−2,3", "0,01"], ["Dps2", "BC_5044", "NP_834714", "Non-specific DNA-binding protein", "N", "N", "−2,4", "0,00", "−1", "0,165"], ["Dps1", "BC_2011", "NP_831779", "Non-specific DNA-binding protein", "N", "N", "−1", "0,04", "0", "0,499"], ["Sod", "BC_5445", "NP_835106", "Superoxide dismutase [Mn]", "N", "N", "−2,4", "0,03", "−0,92", "0,226"], ["AhpF", "BC_0376", "NP_830215", "Alkyl hydroperoxide reductase subunit F", "N", "N", "ND", "ND", "−2,4", "0,02"], ["TerD", "BC_0443", "NP_830282", "tellurium resistance protein", "N", "N", "−2,7", "0,00", "−0,97", "0,064"], ["Translation", "", "", "", "", "", ""], ["RpsF", "BC_5476", "NP_835129", "30 S ribosomal protein S6", "N", "N", "−2,3", "0,01", "−2,32", "0,073"], ["RpsG", "BC_0126", "NP_830007", "30 S ribosomal protein S7", "N", "N", "0,566", "0,2", "−1,8", "0,01"], ["RpsH", "BC_0145", "NP_830025", "30 S ribosomal protein S8", "N", "N", "1,709", "0,059", "−1,8", "0,00"], ["RpsJ", "BC_0130", "NP_830010", "30 S ribosomal protein S10", "N", "N", "ND", "ND", "−2,7", "0,01"], ["RplJ", "BC_0119", "NP_830000", "50 S ribosomal protein L10", "N", "N", "−0,58", "0,16", "−4,3", "0,00"], ["RplK", "BC_5075", "NP_834743", "50 S ribosomal protein L11", "N", "N", "−0,94", "0,187", "−2,4", "0,02"], ["RplL", "BC_0120", "NP_830001", "50 S ribosomal protein L7/L12", "N", "N", "−1,7", "0,03", "−1,1", "0,03"], ["RpsT", "BC_4320", "NP_834032", "30 S ribosomal protein S20", "N", "N", "ND", "ND", "−2", "0,03"], ["RplX", "BC_0142", "NP_830022", "50 S ribosomal protein L24", "N", "N", "−2,2", "0,03", "−0,79", "0,154"], ["RpmD", "BC_0149", "NP_830029", "50 S ribosomal protein L30", "N", "N", "−1,03", "0,095", "−2,4", "0,02"], ["Frr", "BC_3822", "NP_833543", "Ribosome recycling factor", "N", "N", "−1,6", "0,04", "−0,23", "0,405"], ["RaiA", "BC_5190", "NP_834854", "SSU ribosomal protein S30P", "N", "N", "−2,3", "0,04", "−2,6", "0,02"], ["EftS", "BC_3824", "NP_833545", "Elongation factor Ts", "N", "N", "1,263", "0,204", "−3,1", "0,01"], ["Transcriptional Regulation", "", "", "", "", "", ""], ["AbrB", "BC_0042", "NP_829939", "Transcription state regulator", "N", "N", "−1,15", "0,082", "−3,3", "0,00"], ["CodY", "BC_3826", "NP_833547", "Transcriptional repressor", "N", "N", "ND", "ND", "−2,6", "0,02"], ["-", "BC_3728", "NP_833453", "DNA-binding protein HU", "N", "N", "−0,23", "0,422", "−2,5", "0,00"], ["Other", "", "", "", "", "", ""], ["-", "BC_1984", "NP_831667", "Phage protein", "N", "N", "3,113", "0,134", "4,77", "0,01"], ["-", "BC_1012", "NP_830798", "unknown", "N", "N", "−0,81", "0,291", "−3,5", "0,00"], ["-", "BC_5360", "NP_835021", "unknown", "Y", "Y", "0,299", "0,134", "2,38", "0,00"], ["-", "BC_0002", "NP_829890", "unknown", "N", "N", "−4,1", "0,00", "−3,1", "0,01"], ["-", "BC_2077", "NP_831845", "unknown", "N", "N", "−4,6", "0,00", "−0,01", "0,477"], ["-", "BC_4062", "NP_833780", "unknown", "Y", "N", "0,31", "0,363", "0,9", "0,01"], ["-", "BC_2705", "NP_832458", "unknown", "N", "N", "−1,89", "0,084", "−3,6", "0,00"]], "row_count": 88, "column_count": 10, "numeric_cells": 466, "header_rows": 3, "locator": "section[27]/table-wrap[1]#pone-0107354-t004"}}], "gaps": ["asset:data:geo:PXD000856 not downloaded", "asset:data:geo:PXD000856 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "MS/MS spectral counts were compared with the TFold method using the PatternLab software program 2.0.0.13 [33] using a p-value cut-off set at 0.05."}}], "targets": [], "gaps": ["method.student_t"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD000856", "DOI 10.6019/PXD000856"], "resolved_accessions": ["PXD000856"], "statements": ["The authors confirm that all data underlying the findings are fully available without restriction. Our MS/MS data are deposited on the PRIDE repository database http://www.ebi.ac.uk/pride/; Username: reviewer73547@ebi.ac.uk; Password: 0EbXtIq9."], "basis": "The paper names PXD000856 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:25216269", "data:geo:PXD000856", "asset:table:pmid:25216269:1", "asset:table:pmid:25216269:2", "asset:table:pmid:25216269:3", "asset:table:pmid:25216269:4"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD000856"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 0, "usage": {}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:25216269", "type": "paper", "label": "pmid:25216269"}, {"id": "source:pmid:25216269", "type": "manuscript", "label": "PMID 25216269 full text"}, {"id": "data:geo:PXD000856", "type": "dataset", "label": "GEO PXD000856"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:25216269", "type": "paper", "label": "pmid:25216269"}, {"id": "source:pmid:25216269", "type": "manuscript", "label": "PMID 25216269 full text"}, {"id": "data:geo:PXD000856", "type": "dataset", "label": "GEO PXD000856"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-25216269", "type": "extraction", "used": ["source:pmid:25216269"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD000856", "type": "accession_resolution", "used": ["data:geo:PXD000856"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:25216269", "parent_hash": "sha256:8cd47d981b240e22ee55c10eeb8a4be33f5eb64d171c0a3524a4d93fea2a6654", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD000856 licence not read", "asset:data:geo:PXD000856 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Proteomic evidences for rex regulation of metabolism i", "re under control of Rex-mediated regulation. Proteomics data have been deposited to the ProteomeXcha", "Materials and Methods Proteomic sample preparation and nanoLC-MS/MS analysis", "t-off were considered. The mass spectrometry proteomics data have been deposited to the ProteomeXcha"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["MS/MS spectral counts were compared with the TFold method using the PatternLab software program 2.0.0.13 [33] using a p-value cut-off set at 0.05."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:50:36+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}