{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26453029", "kind": "science-record", "revision": 6, "content_hash": "sha256:29150767728bf9747dc908a8e9ad1b668319d475cdc4e0c9c1cc830cf973ff7a", "created_at": "2026-11-01T15:40:11Z", "updated_at": "2026-11-01T21:20:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A.", "doi": "10.1186/s12866-015-0532-3", "pmid": "26453029", "authors": ["Jennifer M H Geddes", "Daniel Croll", "Mélissa Caza", "Nikolay Stoynov", "Leonard J Foster", "James W Kronstad"], "journal": "BMC microbiology", "year": 2015, "abstract": "BACKGROUND: The pathogenic yeast Cryptococcus neoformans causes life-threatening meningoencephalitis in individuals suffering from HIV/AIDS. The cyclic-AMP/protein kinase A (PKA) signal transduction pathway regulates the production of extracellular virulence factors in C. neoformans, but the influence of the pathway on the secretome has not been investigated. In this study, we performed quantitative proteomics using galactose-inducible and glucose-repressible expression of the PKA1 gene encoding the catalytic subunit of PKA to identify regulated proteins in the secretome.\nMETHODS: The proteins in the supernatants of cultures of C. neoformans were precipitated and identified using liquid chromatography-coupled tandem mass spectrometry. We also employed multiple reaction monitoring in a targeted approach to identify fungal proteins in samples from macrophages after phagocytosis of C. neoformans cells, as well as from the blood and bronchoalveolar fluid of infected mice.\nRESULTS: We identified 61 secreted proteins and found that changes in PKA1 expression influenced the extracellular abundance of five proteins, including the Cig1 and Aph1 proteins with known roles in virulence. We also observed a change in the secretome profile upon induction of Pka1 from proteins primarily involved in catabolic and metabolic processes to an expanded set that included proteins for translational regulation and the response to stress. We further characterized the secretome data using enrichment analysis and by predicting conventional versus non-conventional secretion. Targeted proteomics of the Pka1-regulated proteins allowed us to identify the secreted proteins in lysates of phagocytic cells containing C. neoformans, and in samples from infected mice. This analysis also revealed that modulation of PKA1 expression influences the intracellular survival of cryptococcal cells upon phagocytosis.\nCONCLUSIONS: Overall, we found that the cAMP/PKA pathway regulates specific components of the secretome including proteins that affect the virulence of C. neoformans. The detection of secreted cryptococcal proteins from infected phagocytic cells and tissue samples suggests their potential utility as biomarkers of infection. The proteomics data are available via ProteomeXchange with identifiers PXD002731 and PASS00736.", "claims": [{"id": "claim-method", "statement": "For the comparative analysis of the end-point samples, the statistical significance of the fold changes of the identified secreted proteins present under both Pka1-repressed and Pka1-induced conditions was evaluated using a Student’s t-test (p-value < 0.05). To confirm the statistically significant Pka1-regulated proteins identified from the end-point analysis, a multiple-hypothesis testing correction was performed on the secretome data using the Benjamini and Hochberg method with a false discovery rate of 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26453029", "locator": "sections[21] \"Protein identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and mass spectrometry data analysis\" paragraph 4", "quote": "For the comparative analysis of the end-point samples, the statistical significance of the fold changes of the identified secreted proteins present under both Pka1-repressed and Pka1-induced conditions was evaluated using a Student’s t-test (p-value < 0.05). To confirm the statistically significant Pka1-regulated proteins identified from the end-point analysis, a multiple-hypothesis testing correction was performed on the secretome data using the Benjamini and Hochberg method with a false discovery rate of 0.05."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:26453029"], "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:PXD002731"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "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:PXD002731"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26453029", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12866-015-0532-3", "sha256": "sha256:96cdc6571f643ba9e54d82009842e0a5a02e9291b117145bb969786700715ec5", "bytes": 104821, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12866-015-0532-3", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4600298", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD002731", "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=PXD002731", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD002731", "version": null, "note": "Availability of supporting dataThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [93] via the PRIDE partner repository [94] with the dataset identifier PXD002731 and the PASSEL partner repository with the dataset identifier PASS00736.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Availability of supporting dataThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [93] via the PRIDE partner repository [94] with the dataset identifier PXD002731 and the PASSEL partner repository with the dataset identifier PASS00736.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A", "resolution_checked_at": "2026-11-01T15:39:58Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26453029:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:127d70052fd2c771b7d78823f0d7788a4b70107d568ec94dbfcfc8355c082dcb", "bytes": 2513, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Proteins identified in the secretome of C. neoformans collected at 16, 48, 72, and 120 hpi grown in Pka1-repressed (glucose-containing medium) and Pka1-induced (galactose-containing medium) conditions", "structure": {"pmcid": "PMC4600298", "section_index": 3, "section_title": "Control of PKA1 expression results in a change of the protein secretion profile", "row_count": 32, "column_count": 8}, "table": {"label": "Table 1", "caption": "Proteins identified in the secretome of C. neoformans collected at 16, 48, 72, and 120 hpi grown in Pka1-repressed (glucose-containing medium) and Pka1-induced (galactose-containing medium) conditions", "rows": [["GO categoriesa", "Accession number", "Protein Name", "", "Fold changeb*", "Std. 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Dev."], ["Carbohydrate catabolic process"], ["", "CNAG_02189", "α-Amylase", "0.777", "0.019"], ["GTP catabolic process"], ["", "CNAG_06125", "Translation elongation factor 1 α", "2.062", "2.181"], ["Carbohydrate metabolic process"], ["", "CNAG_02860", "Endo-1,3(4)-β-glucanase", "0.947", "0.583"], ["", "CNAG_06501", "1,3-β-glucanosyltransferase", "0.968", "0.100"], ["", "CNAG_05799", "Chitin deacetylase", "1.439", "0.775"], ["", "CNAG_06291", "Deacetylase", "1.464", "0.778"], ["", "CNAG_01239", "Chitin deacetylase", "2.014", "0.584"], ["Cellular carbohydrate metabolic process"], ["", "CNAG_03225", "Malate dehydrogenase", "0.472", "0.546"], ["Pentose-phosphate pathway"], ["", "CNAG_07561", "Phosphogluconate dehydrogenase", ">10", ">10"], ["Protein ubiquitination"], ["", "CNAG_01920", "Polyubiquitin", "1.261", "0.396"], ["ATP hydrolysis coupled proton transport"], ["", "CNAG_05918", "F0F1 ATP synthase subunit β", "0.451", "0.249"], ["", "CNAG_05750", "ATPase α subunit", "0.604", "0.387"], ["Transmembrane transport"], ["", "CNAG_06101", "Eukaryotic ADP/ATP carrier", "7.524", "9.753"], ["Methionine biosynthetic process"], ["", "CNAG_01890", "5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase", "0.778", "0.327"], ["Dephosphorylation"], ["", "CNAG_02944", "Acid phosphatase", "1.862", "0.083"], ["Glycolysis"], ["", "CNAG_03072", "Phosphopyruvate hydratase", "3.093", "3.377"], ["Oxidation-reduction process"], ["", "CNAG_01019", "Cu/Zn superoxide dismutase", "0.302", "0.161"], ["", "CNAG_03465", "Laccase", "0.718", "0.668"], ["Proteolysis"], ["", "CNAG_00919", "Carboxypeptidase D", "4.664", "5.261"], ["Response to stress"], ["", "CNAG_01727", "Hsc70-4", "1.883", "2.094"], ["Translation"], ["", "CNAG_06095", "Ribosomal protein L13", "0.147", "0.057"], ["Unknown/Unclassified"], ["", "CNAG_01653", "Cytokine-inducing glycoprotein", "0.134", "0.158"], ["", "CNAG_00407", "Glyoxal oxidase", "0.719", "0.230"], ["", "CNAG_04291", "Glycosyl-hydrolase", "0.583", "0.287"], ["", "CNAG_02030", "Glyoxal oxidase", "0.513", "0.109"], ["", "CNAG_06267", "Rds1 protein", "3.409", "0.106"], ["Hypothetical"], ["", "CNAG_05312", "Conserved hypothetical protein", "0.341", "0.100"], ["", "CNAG_03007", "Conserved hypothetical protein", "0.518", "0.649"], ["", "CNAG_01562", "Conserved hypothetical protein", "0.942", "0.194"], ["", "CNAG_05893", "Conserved hypothetical protein", "0.991", "0.487"], ["", "CNAG_01047", "Conserved hypothetical protein", "6.714", "6.494"], ["", "CNAG_00588", "Conserved hypothetical protein", ">10", ">10"], ["", "CNAG_03223", "Conserved hypothetical protein", ">10", ">10"], ["", "CNAG_00586", "Conserved hypothetical protein", ">10", ">10"]], "row_count": 52, "column_count": 5, "numeric_cells": 108, "header_rows": 1, "locator": "section[4]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:26453029:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:61fe43962faf342ccbe12440603ddaedca31f9ad7223ef07187b7bc19dcc281f", "bytes": 1924, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[2]#Tab3", "version": null, "note": "Proteins identified in the secretome of C. neoformans collected at 96 hpi from cells grown in Pka1-induced (galactose-containing medium) conditions", "structure": {"pmcid": "PMC4600298", "section_index": 4, "section_title": "Identification of secreted proteins regulated by Pka1", "row_count": 33, "column_count": 5}, "table": {"label": "Table 3", "caption": "Proteins identified in the secretome of C. neoformans collected at 96 hpi from cells grown in Pka1-induced (galactose-containing medium) conditions", "rows": [["GO categoriesa", "Accession number", "Protein name", "Fold changeb", "Std. Dev."], ["Carbohydrate catabolic process", "", ""], ["", "CNAG_02189", "α-Amylase", "1.061", "0.080"], ["GTP catabolic process", "", ""], ["", "CNAG_06125", "Translation elongation factor 1 α", "0.462", "0.555"], ["Carbohydrate metabolic process", "", ""], ["", "CNAG_04245", "Chitinase", "0.621", "0.562"], ["", "CNAG_06501", "1,3-β-glucanosyltransferase", "1.101", "0.140"], ["", "CNAG_01239", "Chitin deacetylase", "2.659", "1.996"], ["", "CNAG_02860", "Endo-1,3(4)-β-glucanase", "3.210", "1.665"], ["Protein ubiquitination", "", ""], ["", "CNAG_01920", "Polyubiquitin", "0.509", "0.501"], ["ATP hydrolysis coupled proton transport", "", ""], ["", "CNAG_05750", "ATPase α subunit", "1.785", "1.765"], ["Dephosphorylation", "", ""], ["", "CNAG_02944", "Acid phosphatase", "0.233", "0.061"], ["Oxidation-reduction process", "", ""], ["", "CNAG_01019", "Cu/Zn superoxide dismutase", "0.350", "0.142"], ["", "CNAG_03465", "Laccase", "1.000", "0.107"], ["Proteolysis", "", ""], ["", "CNAG_00919", "Carboxypeptidase D", "5.770", "3.708"], ["Response to stress", "", ""], ["", "CNAG_01750", "Chaperone", ">10", ">10"], ["Unknown/Unclassified", "", ""], ["", "CNAG_04291", "Glycosyl-hydrolase", "0.989", "0.959"], ["", "CNAG_00407", "Glyoxal oxidase", "1.209", "0.648"], ["", "CNAG_06267", "Rds1 protein", "2.834", "0.518"], ["", "CNAG_01653", "Cytokine-inducing glycoprotein", "2.951", "2.753"], ["", "CNAG_04753", "Lactonohydrolase", ">10", ">10"], ["Hypothetical", "", ""], ["", "CNAG_06109", "Conserved hypothetical protein", "0.463", "0.431"], ["", "CNAG_05893", "Conserved hypothetical protein", "1.062", "0.307"], ["", "CNAG_05312", "Conserved hypothetical protein", "3.737", "2.342"]], "row_count": 33, "column_count": 5, "numeric_cells": 66, "header_rows": 1, "locator": "section[4]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:26453029:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:256ba98575043afac369413565760d51c58955ef5dcd626c10123f5143ef08c4", "bytes": 5718, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#Tab4", "version": null, "note": "Bioinformatic analysis of identified and quantified proteins in the secretome of C. neoformans under Pka1-repressed and Pka1-induced conditions", "structure": {"pmcid": "PMC4600298", "section_index": 6, "section_title": "A bioinformatic analysis of the secretome predicts modes of secretion", "row_count": 83, "column_count": 6}, "table": {"label": "Table 4", "caption": "Bioinformatic analysis of identified and quantified proteins in the secretome of C. neoformans under Pka1-repressed and Pka1-induced conditions", "rows": [["GO categoriesa", "Accession number", "Protein name", "Signal peptideb (position)", "GPI anchorc (position)", "Sample preparation"], ["Carbohydrate catabolic process", "", "", ""], ["", "CNAG_02189", "α-Amylase", "Yes (21/22)", "Yes (C-26)", "EtOH, TCA/acetone"], ["GTP catabolic process", "", "", ""], ["", "CNAG_06125", "Translation elongation factor 1 α", "No", "No", "EtOH, TCA/acetone"], ["", "CNAG_06840", "Translation elongation factor 2", "No", "No", "TCA/acetone"], ["Carbohydrate metabolic process", "", "", ""], ["", "CNAG_00799", "Cellulase", "Yes (22/23)", "No", "TCA/acetone"], ["", "CNAG_01239", "Chitin deacetylase", "Yes (18/19)", "Yes (C-28)", "EtOH, TCA/acetone"], ["", "CNAG_02860", "Endo-1,3(4)-β-glucanase", "Yes (22/23)", "No", "EtOH"], ["", "CNAG_04245", "Chitinase", "Yes (21/22)", "No", "EtOH, TCA/acetone"], ["", "CNAG_05799", "Chitin deacetylase", "Yes (18/19)", "Yes (C-28)", "EtOH"], ["", "CNAG_06291", "Deacetylase", "Yes (19/20)", "No", "EtOH, TCA/acetone"], ["", "CNAG_06313", "Phosphoglucomutase", "No", "No", "TCA/acetone"], ["", "CNAG_06501", "1,3-β-glucanosyltransferase", "Yes (20/21)", "Yes (C-6)", "EtOH, TCA/acetone"], ["Cellular carbohydrate metabolic process", "", "", ""], ["", "CNAG_03225", "Malate dehydrogenase", "No", "No", "EtOH, TCA/acetone"], ["Trehalose metabolic process", "", "", ""], ["", "CNAG_03525", "Trehalase", "Yes (18/19)", "No", "TCA/acetone"], ["Glyoxylate metabolic process", "", "", ""], ["", "CNAG_01137", "Aconitase", "No", "No", "TCA/acetone"], ["Pentose-phosphate pathway", "", "", ""], ["", "CNAG_01984", "Transaldolase", "No", "No", "TCA/acetone"], ["", "CNAG_07561", "Phosphogluconate dehydrogenase", "No", "No", "EtOH"], ["Protein ubiquitination", "", "", ""], ["", "CNAG_01920", "Polyubiquitin", "No", "No", "EtOH"], ["ATP hydrolysis coupled proton transport", "", "", ""], ["", "CNAG_05750", "ATPase α subunit", "No", "No", "EtOH, TCA/acetone"], ["", "CNAG_05918", "F0F1 ATP synthase subunit β", "No", "No", "EtOH"], ["Transmembrane transport", "", "", ""], ["", "CNAG_02974", "Voltage-dependent ion-selective channel", "No", "No", "TCA/acetone"], ["", "CNAG_06101", "Eukaryotic ADP/ATP carrier", "No", "Yes (C-25)", "EtOH, TCA/acetone"], ["Methionine biosynthetic process", "", "", ""], ["", "CNAG_01890", "5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase", "No", "No", "EtOH"], ["Dephosphorylation", "", "", ""], ["", "CNAG_02944", "Acid phosphatase", "Yes (16/17)", "No", "EtOH, TCA/acetone"], ["Glycolysis", "", "", ""], ["", "CNAG_03072", "Phosphopyruvate hydratase", "No", "No", "EtOH, TCA/acetone"], ["", "CNAG_06699", "Glyceraldehyde-3-phosphate dehydrogenase", "No", "No", "TCA/acetone"], ["Oxidation-reduction process", "", "", ""], ["", "CNAG_01019", "Cu/Zn superoxide dismutase", "No", "No", "EtOH"], ["", "CNAG_03465", "Laccase", "Yes (20/21)", "No", "EtOH, TCA/acetone"], ["Proteolysis", "", "", ""], ["", "CNAG_00581", "Endopeptidase", "Yes (19/20)", "No", "TCA/acetone"], ["", "CNAG_00919", "Carboxypeptidase D", "Yes (21/22)", "No", "EtOH, TCA/acetone"], ["Response to stress", "", "", ""], ["", "CNAG_00334", "Heat shock protein", "No", "No", "TCA/acetone"], ["", "CNAG_01727", "Hsc70-4", "No", "No", "EtOH"], ["", "CNAG_01750", "Chaperone", "No", "No", "EtOH, TCA/acetone"], ["", "CNAG_06150", "Heat-shock protein 90", "No", "No", "TCA/acetone"], ["Translation", "", "", ""], ["", "CNAG_04021", "60S ribosomal protein L26", "No", "No", "TCA/acetone"], ["", "CNAG_04114", "40S ribosomal protein S0", "No", "No", "TCA/acetone"], ["", "CNAG_06095", "Ribosomal protein L13", "No", "No", "EtOH"], ["", "CNAG_06605", "Ribosomal protein S2", "No", "No", "TCA/acetone"], ["Regulation of transcription", "", "", ""], ["", "CNAG_00483", "Actin", "No", "No", "TCA/acetone"], ["Nucleosome assembly", "", "", ""], ["", "CNAG_06746", "Histone h2b", "No", "No", "TCA/acetone"], ["Unknown/Unclassified", "", "", ""], ["", "CNAG_00407", "Glyoxal oxidase", "Yes (16/17)", "Yes (C-27)", "EtOH, TCA/acetone"], ["", "CNAG_00776", "Immunoreactive mannoprotein MP88", "Yes (22/23)", "Yes (C-30)", "TCA/acetone"], ["", "CNAG_01653", "Cytokine-inducing glycoprotein", "Yes (19/20)", "No", "EtOH"], ["", "CNAG_02030", "Glyoxal oxidase", "Yes (21/22)", "Yes (C-32)", "EtOH, TCA/acetone"], ["", "CNAG_02850", "Glucan endo-1,3-α-glucosidase agn1", "Yes (21/22)", "Yes (C-26)", "TCA/acetone"], ["", "CNAG_02864", "Predicted protein", "Yes (16/17)", "No", "TCA/acetone"], ["", "CNAG_02943", "Cytoplasmic protein", "No", "No", "TCA/acetone"], ["", "CNAG_04291", "Glycosyl-hydrolase", "Yes (17/18)", "Yes (C-31)", "EtOH"], ["", "CNAG_04753", "Lactonohydrolase", "No", "No", "EtOH, TCA/acetone"], ["", "CNAG_06267", "Rds1 protein", "Yes (20/21)", "Yes", "EtOH, TCA/acetone"], ["Hypothetical", "", "", ""], ["", "CNAG_00586", "Conserved hypothetical protein", "Yes (23/24)", "No", "EtOH, TCA/acetone"], ["", "CNAG_00587", "Conserved hypothetical protein", "Yes (19/20)", "No", "TCA/acetone"], ["", "CNAG_00588", "Conserved hypothetical protein", "Yes (16/17)", "No", "EtOH"], ["", "CNAG_01047", "Conserved hypothetical protein", "Yes (19/20)", "No", "EtOH, TCA/acetone"], ["", "CNAG_01562", "Conserved hypothetical protein", "Yes (18/19)", "No", "EtOH"], ["", "CNAG_03007", "Conserved hypothetical protein", "No", "No", "EtOH"], ["", "CNAG_03223", "Conserved hypothetical protein", "Yes (19/20)", "Yes (C-18)", "EtOH"], ["", "CNAG_03492", "Conserved hypothetical protein", "Yes (19/20)", "No", "TCA/acetone"], ["", "CNAG_05312", "Conserved hypothetical protein", "Yes (19/20)", "Yes (C-19)", "EtOH, TCA/acetone"], ["", "CNAG_05595", "Conserved hypothetical protein", "Yes (18/19)", "Yes (C-29)", "TCA/acetone"], ["", "CNAG_05893", "Conserved hypothetical protein", "Yes (16/17)", "Yes (C-13)", "EtOH, TCA/acetone"], ["", "CNAG_06109", "Conserved hypothetical protein", "No", "No", "EtOH"]], "row_count": 83, "column_count": 6, "numeric_cells": 119, "header_rows": 1, "locator": "section[6]/table-wrap[1]#Tab4"}}], "gaps": ["asset:data:geo:PXD002731 not downloaded", "asset:data:geo:PXD002731 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Benjamini-Hochberg-corrected Student’s t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For the comparative analysis of the end-point samples, the statistical significance of the fold changes of the identified secreted proteins present under both Pka1-repressed and Pka1-induced conditions was evaluated using a Student’s t-test (p-value < 0.05). To confirm the statistically significant Pka1-regulated proteins identified from the end-point analysis, a multiple-hypothesis testing correction was performed on the secretome data using the Benjamini and Hochberg method with a false discovery rate of 0.05."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Benjamini-Hochberg-corrected Student’s t-test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["PXD002731"], "resolved_accessions": ["PXD002731"], "statements": ["Availability of supporting dataThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [93] via the PRIDE partner repository [94] with the dataset identifier PXD002731 and the PASSEL partner repository with the dataset identifier PASS00736."], "basis": "The paper names PXD002731 in ProteomeXchange Consortium via the PRIDE partner repository and the PASSEL 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:26453029", "data:geo:PXD002731", "asset:table:pmid:26453029:1", "asset:table:pmid:26453029:2", "asset:table:pmid:26453029:3", "asset:table:pmid:26453029:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD002731"]}, "gaps": ["method:not_determinable"]}, "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:26453029", "type": "paper", "label": "pmid:26453029"}, {"id": "source:pmid:26453029", "type": "manuscript", "label": "PMID 26453029 full text"}, {"id": "data:geo:PXD002731", "type": "dataset", "label": "GEO PXD002731"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26453029", "type": "paper", "label": "pmid:26453029"}, {"id": "source:pmid:26453029", "type": "manuscript", "label": "PMID 26453029 full text"}, {"id": "data:geo:PXD002731", "type": "dataset", "label": "GEO PXD002731"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26453029", "type": "extraction", "used": ["source:pmid:26453029"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD002731", "type": "accession_resolution", "used": ["data:geo:PXD002731"], "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:26453029", "parent_hash": "sha256:05bcf45421ee90aa5c517190de184286996e630fc339b54b04a9ed2cba17fbea", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD002731 licence not read", "asset:data:geo:PXD002731 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": ["d using liquid chromatography-coupled tandem mass spectrometry. We also employed multiple reaction monitori", "ed. In this study, we performed quantitative proteomics using galactose-inducible and glucose-repres", "versus non-conventional secretion. Targeted proteomics of the Pka1-regulated proteins allowed us to", "tial utility as biomarkers of infection. The proteomics data are available via ProteomeXchange with"], "order_basis": "paper_text_order:515", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["sions (1.0 x 107 cells) was performed. Three mice were selected for the analysis based on establish", "ptococcosis [34–37]. At 48 hpi, the infected mice were euthanized by CO2 inhalation and 1 ml of BAL", "ng (MRM) sample collection from macrophages, mouse bronchoalveolar lavage, and mouse blood The", "crophages, mouse bronchoalveolar lavage, and mouse blood The survival rates of the WT, pka1Δ mu"], "order_basis": "paper_text_order:3901", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["riefly, cells of the J774A.1 macrophage-like cell line were grown to 80 % confluence in Dulbecco’s Modified Ea"], "order_basis": "paper_text_order:4165", "id": "assay:3"}]},"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":"2026-11-04T02:59:18+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}}}