{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31676851", "kind": "science-record", "revision": 7, "content_hash": "sha256:00a0aa759d4d8d3dc0a226b18ee30ab6e8d232babed74aac1c46e5e698e2d4aa", "created_at": "2026-11-01T15:40:51Z", "updated_at": "2026-11-01T22:00:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic changes in the milk of water buffaloes (Bubalus bubalis) with subclinical mastitis due to intramammary infection by Staphylococcus aureus and by non-aureus staphylococci.", "doi": "10.1038/s41598-019-52063-2", "pmid": "31676851", "authors": ["Salvatore Pisanu", "Carla Cacciotto", "Daniela Pagnozzi", "Giulia Maria Grazia Puggioni", "Sergio Uzzau", "Paolo Ciaramella", "Jacopo Guccione", "Martina Penati", "Claudia Pollera", "Paolo Moroni", "Valerio Bronzo", "Maria Filippa Addis"], "journal": "Scientific reports", "year": 2019, "abstract": "Subclinical mastitis by Staphylococcus aureus (SAU) and by non-aureus staphylococci (NAS) is a major issue in the water buffalo. To understand its impact on milk, 6 quarter samples with >3,000,000 cells/mL (3 SAU-positive and 3 NAS-positive) and 6 culture-negative quarter samples with <50,000 cells/mL were investigated by shotgun proteomics and label-free quantitation. A total of 1530 proteins were identified, of which 152 were significantly changed. SAU was more impacting, with 162 vs 127 differential proteins and higher abundance changes (P < 0.0005). The 119 increased proteins had mostly structural (n = 43, 28.29%) or innate immune defence functions (n = 39, 25.66%) and included vimentin, cathelicidins, histones, S100 and neutrophil granule proteins, haptoglobin, and lysozyme. The 33 decreased proteins were mainly involved in lipid metabolism (n = 13, 59.10%) and included butyrophilin, xanthine dehydrogenase/oxidase, and lipid biosynthetic enzymes. The same biological processes were significantly affected also upon STRING analysis. Cathelicidins were the most increased family, as confirmed by western immunoblotting, with a stronger reactivity in SAU mastitis. S100A8 and haptoglobin were also validated by western immunoblotting. In conclusion, we generated a detailed buffalo milk protein dataset and defined the changes occurring in SAU and NAS mastitis, with potential for improving detection (ProteomeXchange identifier PXD012355).", "claims": [{"id": "claim-method", "statement": "The Wilcoxon test62 was performed to demonstrate a statistically significant differences between SAU/Neg and NAS/Neg Rsc, by using the MedCalc Statistical Software version 18.9 (MedCalc Software bvba, Ostend, Belgium; http://www.medcalc.org; 2018).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31676851", "locator": "sections[19] \"Proteomic data analysis\" paragraph 2", "quote": "The Wilcoxon test62 was performed to demonstrate a statistically significant differences between SAU/Neg and NAS/Neg Rsc, by using the MedCalc Statistical Software version 18.9 (MedCalc Software bvba, Ostend, Belgium; http://www.medcalc.org; 2018)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data have been deposited to the ProteomeXchange with identifier PXD012355.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31676851", "locator": "sections[24] \"Data availability\" paragraph 2", "quote": "The data have been deposited to the ProteomeXchange with identifier PXD012355."}], "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:31676851"], "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:PXD012355"], "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:group_comparison_wilcoxon", "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:PXD012355"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31676851", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-019-52063-2", "sha256": "sha256:9c84a5074ca6b71d1bcf22e17dd543dc5ad39ee577e08aed058bb393425a15e5", "bytes": 51514, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-019-52063-2", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6825138", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD012355", "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=PXD012355", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD012355", "version": null, "note": "The data have been deposited to the ProteomeXchange with identifier PXD012355.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data have been deposited to the ProteomeXchange with identifier PXD012355.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomic changes in the milk of water buffalo (Bubalus bubalis) with intramammary infection by Staphylococcus aureus and by non-aureus staphylococciProteomic changes in the milk of water buffalo (Bubalus bubalis) with intramammary infection by Staphylococcus aureus and by non-aureus staphylococci", "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:31676851:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4ee0cf8f71af1d337684ae52f021f6d3dd5743011e1042233e8fefb18104ea14", "bytes": 717, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Sample groups, milk samples, and their characteristics.", "structure": {"pmcid": "PMC6825138", "section_index": 3, "section_title": "Animals and milk samples", "row_count": 15, "column_count": 3}, "table": {"label": "Table 1", "caption": "Sample groups, milk samples, and their characteristics.", "rows": [["Sample group", "SCCa (cells/mL × 103)", "Bacteriology"], ["Positive", "Mean value 5545 (CMTb + 3)", ""], ["1", "4091", "Staphylococcus aureus"], ["2", "3782", "Staphylococcus aureus"], ["3", "8440", "Staphylococcus aureus"], ["4", ">10000", "Non-aureus staphylococci"], ["5", "4035", "Non-aureus staphylococci"], ["6", "2924", "Non-aureus staphylococci"], ["Negative", "Mean value 23.5 (CMT Neg)", ""], ["7", "46", "Negative"], ["8", "37", "Negative"], ["9", "30", "Negative"], ["10", "14", "Negative"], ["11", "8", "Negative"], ["12", "6", "Negative"]], "row_count": 15, "column_count": 3, "numeric_cells": 27, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:31676851:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:544d15f6dcc2caa71902063080795530c3b90b589add61a45ad1aacf1fcd1fb5", "bytes": 459, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#Tab2", "version": null, "note": "Summary of differential proteomic results.", "structure": {"pmcid": "PMC6825138", "section_index": 5, "section_title": "Shotgun proteomics and differential analysis", "row_count": 4, "column_count": 6}, "table": {"label": "Table 2", "caption": "Summary of differential proteomic results.", "rows": [["", "Eligible for comparison*", "Changed**", "Differential***1.5 ≤ RSC ≤ −1.5", "Increased***RSC ≥ 1.5", "Decreased***RSC ≤ −1.5"], ["Posa/negb", "1034", "302", "152", "119", "33"], ["SAUc/neg", "1025", "268", "162", "128", "34"], ["NASd/neg", "940", "202", "127", "108", "19"]], "row_count": 4, "column_count": 6, "numeric_cells": 18, "header_rows": 1, "locator": "section[5]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:31676851:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bbc9aaef2c7814b61f2766db0d84ccce77bf944fa0db2a84172aa4320de14282", "bytes": 12311, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#Tab3", "version": null, "note": "Significantly differential proteins in Staphylococcus-positive milk with RSC ≥ 1.5 or RSC ≤ −1.5.", "structure": {"pmcid": "PMC6825138", "section_index": 5, "section_title": "Shotgun proteomics and differential analysis", "row_count": 182, "column_count": 6}, "table": {"label": "Table 3", "caption": "Significantly differential proteins in Staphylococcus-positive milk with RSC ≥ 1.5 or RSC ≤ −1.5.", "rows": [["Accession", "Description", "RSCPos/Neg", "RSCSAU/Neg", "RSCNAS/Neg", "Generalfunction"], ["P48616", "Vimentin*", "4.78", "4.96", "4.58", "S"], ["A0A0A7NSG7", "Cathelicidin 4*", "4.75", "4.72", "4.78", "I"], ["Q1JPB0", "Leukocyte elastase inhibitor*", "4.09", "4.17", "4", "I"], ["X5I0G0", "Cathelicidin 1*", "4.04", "4.1", "3.98", "I"], ["C8CF42", "Probactenecin 7*", "3.91", "4.02", "3.78", "I"], ["P46193", "Annexin A1", "3.86", "4.02", "3.67", "I"], ["P52176", "Matrix metalloproteinase-9*", "3.8", "3.93", "3.66", "I"], ["P54228", "Cathelicidin 6*", "3.67", "3.72", "3.62", "I"], ["A0A0A7V3V9", "Cathelicidin 2*", "3.64", "3.74", "3.52", "I"], ["E1AHZ7", "Protein S100A8*", "3.52", "3.54", "3.51", "I"], ["Q92176", "Coronin-1A*", "3.51", "3.51", "3.51", "I"], ["A5D7D1", "Alpha-actinin-4", "3.48", "3.63", "3.31", "S"], ["P62803", "Histone H4*", "3.47", "3.67", "3.24", "S"], ["Q2KJD0", "Tubulin beta-5 chain", "3.45", "3.63", "3.25", "S"], ["Q0VCM4", "Glycogen phosphorylase", "3.42", "3.43", "3.42", "CM"], ["Q3MHM5", "Tubulin beta-4B chain", "3.37", "3.49", "3.23", "S"], ["Q3T149", "Heat shock protein beta-1*", "3.33", "3.39", "3.26", "PD"], ["Q27991", "Myosin-10*", "3.31", "3.28", "3.34", "S"], ["L0L830", "Cathelicidin 7*", "3.26", "3.37", "3.15", "I"], ["P40673", "High mobility group protein B2*", "3.25", "3.43", "3.04", "I"], ["Q5MAR3", "Integrin beta*", "3.22", "3.48", "2.9", "I"], ["Q0VCW4", "L-serine dehydratase/L-threonine deaminase*", "3.09", "3.16", "3.01", "AM"], ["P55052", "Fatty acid-binding protein, epidermal*", "3.08", "3.08", "3.08", "LM"], ["P02253", "Histone H1.2*", "3.08", "3.06", "3.11", "S"], ["F6MFD5", "Peptidoglycan-recognition protein", "3.08", "3.26", "2.86", "I"], ["P62808", "Histone H2B type 1", "3.04", "3.04", "3.04", "S"], ["Q9TU25", "Ras-related C3 botulinum toxin substrate 2", "2.97", "2.99", "2.95", "I"], ["Q9TU03", "Rho GDP-dissociation inhibitor 2*", "2.97", "3.13", "2.79", "S"], ["Q2TBL6", "Transaldolase*", "2.96", "3.05", "2.86", "CM"], ["V9LY96", "Cathelicidin 5*", "2.95", "3.05", "2.84", "I"], ["Q2HJ86", "Tubulin alpha-1D chain", "2.95", "3.11", "2.76", "S"], ["Q3SWX7", "Annexin A3*", "2.86", "3.04", "2.65", "I"], ["Q3B7N2", "Alpha-actinin-1", "2.85", "3.01", "2.68", "S"], ["Q5E9F5", "Transgelin-2*", "2.85", "2.83", "2.86", "S"], ["Q3SYV4", "Adenylyl cyclase-associated protein 1", "2.84", "2.78", "2.9", "S"], ["Q2KJH4", "WD repeat-containing protein 1*", "2.81", "2.63", "2.97", "S"], ["P68432", "Histone H3.1*", "2.79", "2.91", "2.66", "S"], ["A7E3Q8", "Plastin-3*", "2.79", "2.86", "2.7", "S"], ["P81948", "Tubulin alpha-4A chain", "2.74", "2.93", "2.51", "S"], ["Q3MHR7", "Actin-related protein 2/3 complex subunit 2*", "2.68", "2.61", "2.75", "S"], ["A7MB62", "Actin-related protein 2", "2.62", "2.6", "2.64", "S"], ["Q5E9B1", "L-lactate dehydrogenase B chain", "2.61", "2.69", "2.52", "CM"], ["M1JVB9", "Haptoglobin", "2.59", "2.68", "2.49", "I"], ["A0A0C5AGQ3", "Lysozyme*", "2.59", "2.64", "2.55", "I"], ["Q6B855", "Transketolase", "2.59", "2.65", "2.54", "CM"], ["P02584", "Profilin-1", "2.58", "2.6", "2.56", "S"], ["Q5E956", "Triosephosphate isomerase", "2.53", "2.56", "2.49", "S"], ["P10103", "High mobility group protein B1", "2.52", "2.73", "2.28", "I"], ["A2I7N1", "Serpin A3-5", "2.52", "2.67", "2.35", "PD"], ["Q3ZBD7", "Glucose-6-phosphate isomerase", "2.5", "2.59", "2.4", "CM"], ["P0C0S9", "Histone H2A type 1", "2.5", "2.54", "2.45", "S"], ["Q3T0P6", "Phosphoglycerate kinase 1", "2.5", "2.53", "2.47", "CM"], ["P19858", "L-lactate dehydrogenase A chain", "2.48", "2.43", "2.52", "CM"], ["Q3T114", "Ribonuclease UK114*", "2.47", "2.4", "2.53", "CP"], ["Q32LE5", "Isoaspartyl peptidase/L-asparaginase*", "2.46", "2.34", "2.58", "CP"], ["P30922", "Chitinase-3-like protein 1", "2.45", "2.32", "2.57", "I"], ["Q2HJ60", "Heterogeneous nuclear ribonucleoproteins A2/B1*", "2.39", "2.66", "2.06", "NM"], ["A5A4L2", "Histone H2B*,a", "2.38", "2.59", "", "I"], ["P79136", "F-actin-capping protein subunit beta", "2.32", "2.41", "2.23", "S"], ["P61157", "Actin-related protein 3", "2.31", "2.27", "2.35", "S"], ["Q5KR47", "Tropomyosin alpha-3 chain", "2.31", "2.37", "2.24", "S"], ["P09867", "Heterogeneous nuclear ribonucleoprotein A1*", "2.3", "2.45", "2.14", "S"], ["A4IF97", "Myosin regulatory light chain 12B*", "2.27", "2.39", "2.14", "S"], ["A3KMV5", "Ubiquitin-like modifier-activating enzyme 1*", "2.26", "2.57", "1.87", "PD"], ["Q2HJ57", "Coactosin-like protein*", "2.22", "2.24", "2.21", "I"], ["Q58CQ2", "Actin-related protein 2/3 complex subunit 1B*", "2.2", "2.22", "2.18", "S"], ["G3N131", "Histone H1.1*", "2.19", "", "", "S"], ["P49951", "Clathrin heavy chain 1*", "2.08", "2.22", "1.92", "S"], ["A5D7A0", "EF-hand domain-containing protein D2*", "2.08", "2.2", "1.95", "S"], ["Q2TA49", "Vasodilator-stimulated phosphoprotein", "2.06", "2.42", "1.58", "S"], ["Q3ZC84", "Cytosolic non-specific dipeptidase", "2.05", "2.18", "1.91", "OM"], ["P10096", "Glyceraldehyde-3-phosphate dehydrogenase", "2.05", "2.14", "1.97", "CM"], ["P60661", "Myosin light polypeptide 6", "2.02", "2.15", "1.87", "S"], ["Q3T0D0", "Heterogeneous nuclear ribonucleoprotein K*", "2.01", "2.08", "1.94", "NM"], ["P33433", "Histidine-rich glycoproteina", "2.01", "2.52", "", "I"], ["Q4U5R3", "Proteasome activator complex subunit 1", "2.01", "2.07", "1.96", "PD"], ["Q32PI5", "Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform", "1.98", "2.29", "1.59", "S"], ["Q56JZ9", "Glia maturation factor gamma*", "1.97", "2.02", "1.92", "S"], ["Q0VCX1", "Complement C1s subcomponent*", "1.96", "2.24", "1.62", "I"], ["Q3SZH7", "Leukotriene A-4 hydrolase*", "1.96", "1.91", "2.02", "I"], ["P31081", "60 kDa heat shock protein, mitochondrial*", "1.95", "2.12", "1.76", "I"], ["Q32LP0", "Fermitin family homolog 3*", "1.94", "2.15", "1.69", "I"], ["D2U6Q0", "Serum amyloid A protein*", "1.93", "1.86", "2", "I"], ["P62326", "Thymosin beta-4*", "1.91", "2.03", "1.78", "I"], ["P13752", "BOLA class I histocompatibility antigen, alpha chain BL3-6*", "1.9", "2.08", "1.7", "I"], ["Q2KJI3", "Protein FAM49B*", "1.89", "1.87", "1.92", "I"], ["Q762I5", "Resistin*", "1.89", "1.92", "1.85", "LM"], ["Q76LV2", "Heat shock protein HSP 90-alpha", "1.88", "2.06", "1.68", "PD"], ["Q3SZ54", "Eukaryotic initiation factor 4A-I", "1.85", "1.82", "1.88", "GE"], ["Q3MHL4", "Adenosylhomocysteinase", "1.83", "1.82", "1.84", "AM"], ["P80724", "Brain acid soluble protein 1*", "1.82", "1.61", "2", "GE"], ["P60712", "Actin, cytoplasmic 1", "1.8", "2.01", "1.57", "S"], ["J9Q6V1", "Glutathione peroxidase*", "1.8", "2.05", "1.5", "OM"], ["P55859", "Purine nucleoside phosphorylase*", "1.78", "1.51", "2", "NM"], ["Q9XSJ4", "Alpha-enolase", "1.77", "1.8", "1.75", "CM"], ["Q27970", "Calpain-1 catalytic subunita", "1.77", "2.13", "", "PD"], ["Q865V6", "Macrophage-capping protein*", "1.76", "1.65", "1.86", "S"], ["Q9GMB8", "Serine–tRNA ligase, cytoplasmica", "1.74", "2.02", "", "AM"], ["Q9BGI1", "Peroxiredoxin-5, mitochondrial", "1.73", "1.92", "1.52", "OM"], ["P51122", "Acidic leucine-rich nuclear phosphoprotein 32 family member Aa", "", "1.72", "", "CT"], ["Q148J6", "Actin-related protein 2/3 complex subunit 4*", "1.7", "1.71", "1.69", "S"], ["A4FUA8", "F-actin-capping protein subunit alpha-1*", "1.68", "1.63", "1.73", "S"], ["P06868", "Plasminogen", "1.68", "1.77", "1.58", "C"], ["P07589", "Fibronectin", "1.67", "", "", "I"], ["P13753", "BOLA class I histocompatibility antigen, alpha chain BL3-7*,a", "1.65", "1.96", "", "I"], ["O46522", "Cytochrome b-245 heavy chaina", "1.64", "2", "", "I"], ["Q3SZI4", "14-3-3 protein theta", "1.62", "1.69", "1.55", "GE"], ["A6H742", "Plastin-1*", "1.62", "1.54", "1.69", "S"], ["D2U6Z5", "Ceruloplasminb", "1.61", "", "1.75", "IM"], ["Q3T035", "Actin-related protein 2/3 complex subunit 3*,a", "1.57", "1.71", "", "S"], ["P20000", "Aldehyde dehydrogenase, mitochondrial*,a", "1.57", "1.71", "", "CM"], ["P01030", "Complement C4b", "1.57", "", "1.72", "I"], ["P0C0S4", "Histone H2A.Za", "1.56", "1.66", "", "S"], ["Q27996", "Lysozyme C, tracheal isozyme", "1.56", "1.51", "1.61", "I"], ["Q5E9B7", "Chloride intracellular channel protein 1", "1.55", "1.52", "1.57", "C"], ["P68138", "Actin, alpha skeletal musclea", "1.54", "1.72", "", "S"], ["X2IZ01", "Signal transducer and activator of transcriptiona", "1.54", "1.59", "", "I"], ["Q3ZBT1", "Transitional endoplasmic reticulum ATPasea", "1.54", "1.68", "", "CT"], ["Q2HJG5", "Vacuolar protein sorting-associated protein 35a", "1.54", "1.84", "", "I"], ["O97680", "Thioredoxina", "1.53", "1.79", "", "OM"], ["P19483", "ATP synthase subunit alpha, mitochondrialb", "", "", "1.52", "CT"], ["P02676", "Fibrinogen beta chaina", "", "1.79", "", "C"], ["P02672", "Fibrinogen alpha chaina", "", "1.83", "", "I"], ["Q5E9R3", "EH domain-containing protein 1a", "", "1.78", "", "CaM"], ["P00829", "ATP synthase subunit beta, mitochondriala", "", "1.66", "", "OM"], ["P81644", "Apolipoprotein A-IIa", "", "1.64", "", "LM"], ["Q3B7M5", "LIM and SH3 domain protein 1a", "", "1.61", "", "S"], ["A6H7G2", "Drebrin-like proteina", "", "1.58", "", "I"], ["Q3ZBH0", "T-complex protein 1 subunit betaa", "", "1.57", "", "PD"], ["Q3MHL7", "T-complex protein 1 subunit zetaa", "", "1.52", "", "PD"], ["Q7SIH1", "Alpha-2-macroglobulina", "", "1.52", "", "I"], ["P27214", "Annexin A11a", "", "1.52", "", "S"], ["Q3SZV7", "Hemopexina", "", "1.5", "", "IM"], ["P11116", "Galectin-1b", "", "", "1.61", "I"], ["P35466", "Protein S100-A4b", "", "", "1.6", "I"], ["O02675", "Dihydropyrimidinase-related protein 2*,b", "", "", "1.51", "S"], ["Q3T054", "GTP-binding nuclear protein Ranb", "", "", "1.61", "CT"], ["Q3T0D7", "GTP-binding protein SAR1a", "−1.51", "", "", "CT"], ["Q71SP7", "Fatty acid synthasea", "−1.52", "−1.8", "", "LM"], ["P02638", "Protein S100-B", "−1.53", "", "", "I"], ["P10790", "Fatty acid-binding protein, hearta", "", "−1.53", "", "LM"], ["M9WP41", "BTN1A1a", "", "−1.57", "", "S"], ["Q17QE5", "Calcium and integrin-binding protein 1a", "−1.56", "−1.85", "", "I"], ["Q9N0T1", "Stanniocalcin-1a", "−1.57", "−1.9", "", "CaM"], ["A0A0C5GDU2", "Myostatina", "", "−1.59", "", "S"], ["Q6RUS0", "Butyrophilinb", "−1.6", "", "−1.75", "LM"], ["G1AQP3", "Xanthine dehydrogenase/oxidasea", "−1.61", "−1.81", "", "LM"], ["E9NV81", "ATP-binding cassette sub-family G (WHITE) member 2a", "−1.62", "−1.95", "", "LM"], ["Q05927", "5′-nucleotidaseb", "−1.65", "", "−1.88", "NM"], ["M4QG36", "Insulin induced protein 1a", "−1.65", "−1.88", "", "S"], ["O77588", "Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1a", "−1.68", "−2.19", "", "S"], ["A5PK13", "Volume-regulated anion channel subunit LRRC8C", "−1.68", "", "", "LM"], ["Q2KIY5", "Putative phospholipase B-like 2a", "−1.69", "−2.24", "", "LM"], ["P81127", "Gamma-soluble NSF attachment protein", "−1.71", "", "", "CT"], ["Q58CY6", "Prostamide/prostaglandin F synthaseb", "−1.73", "", "−1.83", "LM"], ["Q06805", "Tyrosine-protein kinase receptor Tie-1", "−1.73", "", "", "A"], ["P37980", "Inorganic pyrophosphatase", "−1.74", "−1.99", "−1.53", "LM"], ["Q3T0Q2", "Transmembrane protein 59", "−1.75", "−1.87", "−1.63", "CT"], ["Q3SYV1", "Transmembrane protein 263", "−1.77", "", "", "CT"], ["Q3SYS6", "Calcineurin B homologous protein 1", "−1.81", "−1.87", "−1.75", "CaM"], ["Q58DD4", "Syndecan-2a", "−1.81", "−2.13", "", "S"], ["D3K0R6", "Plasma membrane calcium-transporting ATPase 4", "−1.93", "−2.04", "−1.82", "CaM"], ["C1KGU3", "Solute carrier family 11 member 2", "−1.93", "−2.02", "−1.85", "CT"], ["Q5GJ77", "Glycerol-3-phosphate acyltransferase 1, mitochondrial", "−2.01", "−2.13", "−1.91", "LM"], ["A0A088F8E5", "Acyl-CoA synthetase short-chain family member 2", "−2.08", "−2.19", "−1.97", "LM"], ["P08239", "Guanine nucleotide-binding protein G(o) 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"Ras-related protein Rab-5Aa", "", "−2.11", "", "CT"], ["A6QR11", "Protein kinase C-binding protein NELL2a", "", "−2.37", "", "CaM"], ["Q5E9B5", "Actin, gamma-enteric smooth muscleb", "", "", "−3.76", "S"]], "row_count": 182, "column_count": 6, "numeric_cells": 653, "header_rows": 1, "locator": "section[5]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:31676851:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4ee0cf8f71af1d337684ae52f021f6d3dd5743011e1042233e8fefb18104ea14", "bytes": 717, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Sample groups, milk samples, and their characteristics.", "structure": {"pmcid": "PMC6825138", "section_index": 14, "section_title": "Animals and milk samples", "row_count": 15, "column_count": 3}, "table": {"label": "Table 1", "caption": "Sample groups, milk samples, and their characteristics.", "rows": [["Sample group", "SCCa (cells/mL × 103)", "Bacteriology"], ["Positive", "Mean value 5545 (CMTb + 3)", ""], ["1", "4091", "Staphylococcus aureus"], ["2", "3782", "Staphylococcus aureus"], ["3", "8440", "Staphylococcus aureus"], ["4", ">10000", "Non-aureus staphylococci"], ["5", "4035", "Non-aureus staphylococci"], ["6", "2924", "Non-aureus staphylococci"], ["Negative", "Mean value 23.5 (CMT Neg)", ""], ["7", "46", "Negative"], ["8", "37", "Negative"], ["9", "30", "Negative"], ["10", "14", "Negative"], ["11", "8", "Negative"], ["12", "6", "Negative"]], "row_count": 15, "column_count": 3, "numeric_cells": 27, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}], "gaps": ["asset:data:geo:PXD012355 not downloaded", "asset:data:geo:PXD012355 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Wilcoxon test62 was performed to demonstrate a statistically significant differences between SAU/Neg and NAS/Neg Rsc, by using the MedCalc Statistical Software version 18.9 (MedCalc Software bvba, Ostend, Belgium; http://www.medcalc.org; 2018)."}}], "targets": [], "gaps": ["method.group_comparison_wilcoxon"]}, "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": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["PXD012355"], "resolved_accessions": ["PXD012355"], "statements": ["The data have been deposited to the ProteomeXchange with identifier PXD012355."], "basis": "The paper names PXD012355 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:31676851", "data:geo:PXD012355", "asset:table:pmid:31676851:1", "asset:table:pmid:31676851:2", "asset:table:pmid:31676851:3", "asset:table:pmid:31676851:4"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD012355"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:17:01Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 39922, "completion_tokens": 1391, "cached_tokens": 13321}}, "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:31676851", "type": "paper", "label": "pmid:31676851"}, {"id": "source:pmid:31676851", "type": "manuscript", "label": "PMID 31676851 full text"}, {"id": "data:geo:PXD012355", "type": "dataset", "label": "GEO PXD012355"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31676851", "type": "paper", "label": "pmid:31676851"}, {"id": "source:pmid:31676851", "type": "manuscript", "label": "PMID 31676851 full text"}, {"id": "data:geo:PXD012355", "type": "dataset", "label": "GEO PXD012355"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31676851", "type": "extraction", "used": ["source:pmid:31676851"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD012355", "type": "accession_resolution", "used": ["data:geo:PXD012355"], "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:31676851", "parent_hash": "sha256:3381c6de3a50859fb07fe93db45576614c99146b1c37b0a894fcb7bd591a926f", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD012355 licence not read", "asset:data:geo:PXD012355 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["st increased family, as confirmed by western immunoblotting, with a stronger reactivity in SAU mastitis.", "d haptoglobin were also validated by western immunoblotting. In conclusion, we generated a detailed buff"], "order_basis": "paper_text_order:1257", "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": ["The Wilcoxon test62 was performed to demonstrate a statistically significant differences between SAU/Neg and NAS/Neg Rsc, by using the MedCalc Statistical Software version 18.9 (MedCalc Software bvba, Ostend, Belgium; http://www.medcalc.org; 2018)."], "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":"2026-11-04T01:48:31+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}}}