{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33238539", "kind": "science-record", "revision": 8, "content_hash": "sha256:ac21908d7422dc63109c4e3b7bdd8c6a47c8b7924f3ff84cf22c874d37d1d548", "created_at": "2026-11-01T15:41:17Z", "updated_at": "2026-11-01T22:45:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Effects of Excess Manganese on the Xylem Sap Protein Profile of Tomato (Solanum lycopersicum) as Revealed by Shotgun Proteomic Analysis.", "doi": "10.3390/ijms21228863", "pmid": "33238539", "authors": ["Laura Ceballos-Laita", "Elain Gutierrez-Carbonell", "Daisuke Takahashi", "Andrew Lonsdale", "Anunciación Abadía", "Monika S Doblin", "Antony Bacic", "Matsuo Uemura", "Javier Abadía", "Ana Flor López-Millán"], "journal": "International journal of molecular sciences", "year": 2020, "abstract": "Metal toxicity is a common problem in crop species worldwide. Some metals are naturally toxic, whereas others such as manganese (Mn) are essential micro-nutrients for plant growth but can become toxic when in excess. Changes in the composition of the xylem sap, which is the main pathway for ion transport within the plant, is therefore vital to understanding the plant's response(s) to metal toxicity. In this study we have assessed the effects of exposure of tomato roots to excess Mn on the protein profile of the xylem sap, using a shotgun proteomics approach. Plants were grown in nutrient solution using 4.6 and 300 µM MnCl2 as control and excess Mn treatments, respectively. This approach yielded 668 proteins reliably identified and quantified. Excess Mn caused statistically significant (at p ≤ 0.05) and biologically relevant changes in relative abundance (≥2-fold increases or ≥50% decreases) in 322 proteins, with 82% of them predicted to be secretory using three different prediction tools, with more decreasing than increasing (181 and 82, respectively), suggesting that this metal stress causes an overall deactivation of metabolic pathways. Processes most affected by excess Mn were in the oxido-reductase, polysaccharide and protein metabolism classes. Excess Mn induced changes in hydrolases and peroxidases involved in cell wall degradation and lignin formation, respectively, consistent with the existence of alterations in the cell wall. Protein turnover was also affected, as indicated by the decrease in proteolytic enzymes and protein synthesis-related proteins. Excess Mn modified the redox environment of the xylem sap, with changes in the abundance of oxido-reductase and defense protein classes indicating a stress scenario. Finally, results indicate that excess Mn decreased the amounts of proteins associated with several signaling pathways, including fasciclin-like arabinogalactan-proteins and lipids, as well as proteases, which may be involved in the release of signaling peptides and protein maturation. The comparison of the proteins changing in abundance in xylem sap and roots indicate the existence of tissue-specific and systemic responses to excess Mn. Data are available via ProteomeXchange with identifier PXD021973.", "claims": [{"id": "claim-method", "statement": "Only changes with a p ≤ 0.05 (ANOVA) and a ratio (fold change) ≥2 or ≤0.5 were considered as statistically significant and biologically relevant, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33238539", "locator": "sections[21] \"4.5. Label Free Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)\" paragraph 5", "quote": "Only changes with a p ≤ 0.05 (ANOVA) and a ratio (fold change) ≥2 or ≤0.5 were considered as statistically significant and biologically relevant, respectively."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD021973.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33238539", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD021973."}], "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:33238539"], "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:PXD021973"], "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:PXD021973"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33238539", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms21228863", "sha256": "sha256:b6d668adebac3a1d4eeb5e7416f416c2e8268fd2fec2d76f97e4e61e09d5111c", "bytes": 91874, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms21228863", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7700171", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD021973", "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=PXD021973", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD021973", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD021973.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD021973.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Xylem sap shotgun proteomics from Mn-excess tomato plants", "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:33238539:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:da25833e04745e67a9342ed09d433e4ce92d89a8d5eaf3007d568d092934706c", "bytes": 1048, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#ijms-21-08863-t001", "version": null, "note": "Exudation rates, protein yields, leaf transpiration rates and Mn, Fe, Zn and Cu concentrations in the xylem sap of Solanum lycopersicum plants grown in control and excess Mn conditions for 8 days. Data are means ± SE (n = 6 for collection parameters and n = 4 for micronutrient concentrations). Statistically significant differences were calculated with the Student’s t-test: * p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001).", "structure": {"pmcid": "PMC7700171", "section_index": 3, "section_title": "2.1. Xylem Sap Collection and Mineral Composition", "row_count": 9, "column_count": 3}, "table": {"label": "Table 1", "caption": "Exudation rates, protein yields, leaf transpiration rates and Mn, Fe, Zn and Cu concentrations in the xylem sap of Solanum lycopersicum plants grown in control and excess Mn conditions for 8 days. Data are means ± SE (n = 6 for collection parameters and n = 4 for micronutrient concentrations). Statistically significant differences were calculated with the Student’s t-test: * p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001).", "rows": [["Collection Parameters", "Control", "Excess Mn"], ["Exudation rate (mL g−1 DW h−1)", "0.56 ± 0.11", "0.52 ± 0.21"], ["Protein yield (ng protein µL−1 xylem)", "9.0 ± 3.4", "27.0 ± 12.5 *"], ["Leaf transpiration rate (mmol H2O m−2 s−1)", "10.9 ± 0.5", "5.2 ± 0.1 ***"], ["Micronutrient concentrations (µM)"], ["Mn", "6.5 ± 0.8", "385.7 ± 16.1 ***"], ["Fe", "47.8 ± 12.5", "15.7 ± 2.5 **"], ["Zn", "9.5 ± 1.3", "8.0 ± 0.9 *"], ["Cu", "3.6 ± 0.8", "3.1 ± 0.5"]], "row_count": 9, "column_count": 3, "numeric_cells": 17, "header_rows": 1, "locator": "section[3]/table-wrap[1]#ijms-21-08863-t001"}}, {"id": "asset:table:pmid:33238539:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9e0eb0f6fdb84c87a0f562462b36c9d0be7a8ba76e26cecd967e9d8ac5d395b2", "bytes": 3571, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#ijms-21-08863-t002", "version": null, "note": "List of proteins contributing to component 1 in the PCA. Standardized component scores were obtained in the PCA analysis of the differential proteins (ANOVA, p ≤ 0.05). Accession and description correspond to identifier and name in the ITAG3.2 database, respectively. Fold-changes (Fold +Mn/Control) were calculated by dividing the mean of normalized abundances (obtained with Progenesis QI v.2.5.1) in plants affected by excess Mn by that of control plants. The single protein with an asterisk after the ITAG database identifier was not included in Table S3 because it was out of the biological threshold range.", "structure": {"pmcid": "PMC7700171", "section_index": 4, "section_title": "2.2. Proteins Detected, Class Annotation and PCA Analysis", "row_count": 37, "column_count": 5}, "table": {"label": "Table 2", "caption": "List of proteins contributing to component 1 in the PCA. Standardized component scores were obtained in the PCA analysis of the differential proteins (ANOVA, p ≤ 0.05). Accession and description correspond to identifier and name in the ITAG3.2 database, respectively. Fold-changes (Fold +Mn/Control) were calculated by dividing the mean of normalized abundances (obtained with Progenesis QI v.2.5.1) in plants affected by excess Mn by that of control plants. The single protein with an asterisk after the ITAG database identifier was not included in Table S3 because it was out of the biological threshold range.", "rows": [["Accession", "Comp. 1 Score", "Comp. 2 Score", "Description", "Fold +Mn/Control"], ["Polysaccharide metabolism (9 proteins)"], ["Solyc01g104950.3.1", "0.001", "0.013", "LEXYL2 (GH3)", "0.5"], ["Solyc12g056960.2.1", "−0.002", "−0.061", "glucan endo-1,3-β-d-glucosidase (GH17)", "4.0"], ["Solyc10g079860.2.1", "−0.008", "−0.034", "glucan endo-1,3-β-d-glucosidase (GH17)", "51.6"], ["Solyc01g008620.3.1", "−0.024", "0.169", "glucan endo-1,3-β-glucosidase (GH17)", "233.6"], ["Solyc01g059965.1.1", "−0.492", "−2.371", "glucan endo-1,3- β-glucosidase (GH17)", "188.7"], ["Solyc02g086700.3.1", "−0.001", "−0.018", "glucan endo-1,3-β-glucosidase-like (GH17)", "48.8"], ["Solyc05g050130.3.1", "−0.001", "0.002", "acidic endochitinase (GH18)", "18.3"], ["Solyc10g055800.2.1", "−0.004", "−0.041", "endochitinase (GH19)", "51.1"], ["Solyc02g082920.3.1", "−0.001", "0.005", "chitinase (GH19)", "91.3"], ["Protein metabolism (5 proteins)"], ["Solyc04g078110.1.1", "0.002", "0.014", "serine protease SBT1 (MEROPS peptidase family S8)", "0.5"], ["Solyc06g074850.3.1", "0.001", "0.006", "carboxypeptidase (MEROPS peptidase family S10)", "0.3"], ["Solyc08g067100.2.1", "0.024", "0.047", "eukaryotic aspartyl protease family protein (MEROPS peptidase family A1)", "0.5"], ["Solyc08g079870.3.1", "−0.011", "0.072", "Subtilisin (MEROPS peptidase family S8)", "74.3"], ["Solyc08g079900.3.1", "−0.390", "3.028", "subtilisin-like protease (MEROPS peptidase family S8)", "57.1"], ["Oxido-reductases (5 proteins)"], ["Solyc06g076630.3.1", "0.007", "0.093", "peroxidase", "0.3"], ["Solyc12g094620.2.1", "0.015", "0.247", "catalase", "0.2"], ["Solyc01g105070.3.1", "−0.012", "−0.205", "LECEVI16G peroxidase precursor", "14.1"], ["Solyc06g005940.3.1", "−0.001", "−0.001", "protein disulfide-isomerase-like", "11.5"], ["Solyc09g009390.3.1", "−0.001", "−0.004", "monodehydroascorbate reductase", "2.2"], ["Defense (5 proteins)"], ["Solyc01g097240.3.1", "−0.003", "0.011", "pathogenesis-related protein PR-4", "153.6"], ["Solyc00g174340.2.1", "−0.001", "0.003", "pathogenesis-related protein PR-1", "27.2"], ["Solyc09g090980.3.1", "0.003", "−0.024", "major allergen Mal d 1", "25.7"], ["Solyc12g005720.1.1", "−0.001", "−0.012", "cysteine-rich receptor-like kinase protein", "9.8"], ["Solyc09g091000.3.1", "0.003", "−0.016", "major allergen d 1", "54.3"], ["Lipid metabolism (2 proteins)"], ["Solyc03g079880.3.1", "0.003", "0.043", "protease inhibitor/seed storage/lipid transfer family protein", "0.4"], ["Solyc08g067500.1.1", "0.002", "0.030", "non-specific lipid-transfer protein", "0.2"], ["Carbohydrate metabolism (1 protein)"], ["Solyc06g073190.3.1 *", "0.003", "0.66", "fructokinase-2", "0.7"], ["Miscellaneous (2 proteins)"], ["Solyc01g111170.3.1", "0.002", "0.032", "diageotropica/Peptidyl-prolyl cis-trans isomerase", "0.2"], ["Solyc08g074682.1.1", "0.001", "−0.015", "polyphenol oxidase precursor", "22.3"]], "row_count": 37, "column_count": 5, "numeric_cells": 140, "header_rows": 1, "locator": "section[4]/table-wrap[1]#ijms-21-08863-t002"}}, {"id": "asset:table:pmid:33238539:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e44d25093fd6229fd9338481d218476cb061ad319f2896f0bc2ae2055757e423", "bytes": 6744, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#ijms-21-08863-t003", "version": null, "note": "Xylem sap proteins showing large changes in abundance (>25-fold increases or 90% decreases) among the total 263 secretory proteins affected by excess Mn (ANOVA, p ≤ 0.05 and fold-change ≥2 or ≤0.5). Accession ITAG3.2 and UniProt indicates the database entry. Abundance changes (change +Mn/Control) were calculated by dividing the mean of normalized abundances (obtained with Progenesis QI v.2.5.1) in plants affected by excess Mn by that in control plants. Description includes the protein name according to the ITAG3.2 and UniProt databases. The column Category indicates the classification (CPS, UPS or sUPS), and the column Prediction tool indicates the algorithms providing true values (SignalP, TargetP, SecretomeP, LSP and SPL). Detailed information about functional classification, identification and quantification is given in Tables S3 and S4.", "structure": {"pmcid": "PMC7700171", "section_index": 6, "section_title": "2.4. Protein Species Decreasing in Abundance", "row_count": 61, "column_count": 7}, "table": {"label": "Table 3", "caption": "Xylem sap proteins showing large changes in abundance (>25-fold increases or 90% decreases) among the total 263 secretory proteins affected by excess Mn (ANOVA, p ≤ 0.05 and fold-change ≥2 or ≤0.5). Accession ITAG3.2 and UniProt indicates the database entry. Abundance changes (change +Mn/Control) were calculated by dividing the mean of normalized abundances (obtained with Progenesis QI v.2.5.1) in plants affected by excess Mn by that in control plants. Description includes the protein name according to the ITAG3.2 and UniProt databases. The column Category indicates the classification (CPS, UPS or sUPS), and the column Prediction tool indicates the algorithms providing true values (SignalP, TargetP, SecretomeP, LSP and SPL). Detailed information about functional classification, identification and quantification is given in Tables S3 and S4.", "rows": [["#", "AccessionITAG3.2", "AccessionUniProt", "Change+Mn/Control", "Description", "Category", "Prediction Tool"], ["Polysaccharide metabolism (13 proteins)"], ["1", "Solyc09g092170.2.1", "A0A3Q7IA20", "0.1", "β-galactosidase STBG2 (GH35)", "CPS", "TarP, SecP"], ["2", "Solyc07g062210.3.1", "A0A3Q7HE74", "0.1", "protein trichome birefringence-like 41", "CPS", "SigP, TarP, SecP"], ["3", "Solyc04g016470.3.1", "A0A3Q7GST1", "111.6", "glucan endo-1,3-β-D-glucosidase (GH17)", "CPS", "TarP, SecP"], ["4", "Solyc10g079860.2.1", "A0A3Q7IKF2", "51.6", "glucan endo-1,3-β-D-glucosidase (GH17)", "CPS", "SigP, TarP, SecP"], ["5", "Solyc01g008620.3.1", "A0A3Q7E938", "233.6", "glucan endo-1,3-β-glucosidase (GH17)", "CPS", "SigP, TarP, SecP"], ["6", "Solyc01g059965.1.1", "Q01413", "188.7", "glucan endo-1,3-β-glucosidase (GH17)", "CPS", "SigP, TarP, SecP"], ["7", "Solyc02g086700.3.1", "A0A3Q7FVX4", "48.8", "glucan endo-1,3-β-glucosidase-like (GH17)", "CPS", "TarP, SecP"], ["8", "Solyc07g005100.3.1", "A0A3Q7H377", "30.4", "Chitinase/lysozyme (GH18)", "CPS", "SigP, TarP, SecP"], ["9", "Solyc10g055800.2.1", "A0A3Q7IHS3", "51.1", "endochitinase (GH19)", "CPS", "SigP, TarP, SecP"], ["10", "Solyc10g055810.2.1", "Q05538", "80.9", "basic 30 kDa endochitinase (GH19)", "CPS", "SigP, TarP, SecP"], ["11", "Solyc02g082920.3.1", "Q05539", "91.3", "acidic extracellular 26 kD chitinase (GH19)", "CPS", "SigP, TarP, SecP"], ["12", "Solyc10g055820.2.1", "A0A3Q7IIQ3", "44.4", "endochitinase (GH19)", "CPS", "SigP, TarP, SecP"], ["13", "Solyc11g005480.2.1", "A0A3Q7IP30", "26.1", "citrate-binding protein-like", "CPS", "SigP, TarP, SecP"], ["Protein metabolism (12 proteins)"], ["14", "Solyc00g005000.3.1", "A0A494G8A2", "0.1", "eukaryotic aspartyl protease family protein", "CPS", "SigP, TarP, SecP"], ["15", "Solyc07g064590.3.1", "A0A3Q7HFD0", "0.1", "inducible plastid-lipid associated protein", "UPS", "LSP, SecP"], ["16", "Solyc06g008170.3.1", "K4CUW3", "0.1", "50S ribosomal protein L14", "sUPS", "SecP"], ["17", "Solyc09g066430.3.1", "A0A3Q7J0J5", "0.1", "60S ribosomal protein L14", "sUPS", "SecP"], ["18", "Solyc08g079870.3.1", "-", "74.3", "subtilisin (MEROPS S8, clan SB)", "CPS", "SigP, TarP, SecP"], ["19", "Solyc08g079900.3.1", "-", "57.1", "subtilisin-like protease (MEROPS S8, clan SB)", "CPS", "SigP, TarP, SecP"], ["20", "Solyc06g008620.1.1", "A0A3Q7GN27", "31.7", "tolB protein-like protein (MEROPS S9)", "UPS", "SPL, SecP"], ["21", "Solyc01g087850.2.1", "O82777", "31.0", "serine protease SBT3 (MEROPS I13, clan IG)", "CPS", "SigP, TarP, SecP"], ["22", "Solyc03g020010.1.1", "O48625", "93.3", "Miraculin (MEROPS I13, clan IG)", "CPS", "SigP, TarP, SecP"], ["23", "Solyc03g019690.1.1", "A0A3Q7FGU5", "37.8", "kunitz-type protease inhibitor (MEROPS I13, clan IG)", "CPS", "SigP, TarP, SecP"], ["24", "Solyc03g098740.1.1", "A0A3Q7FNG4", "208.5", "kunitz trypsin inhibitor (MEROPS I3, clan IC)", "CPS", "SigP, TarP, SecP"], ["25", "Solyc08g080630.3.1", "A0A3Q7IQ00", "31.8", "ethylene-responsive proteinase inhibitor 1 (MEROPS I3, clan IC)", "CPS", "SigP, TarP, SecP"], ["Oxido-reductases (6 proteins)"], ["26", "Solyc06g005160.3.1", "Q3I5C4", "0.1", "Ascorbate peroxidase", "UPS", "LSP"], ["27", "Solyc04g074740.3.1", "A0A3Q7G526", "0.0", "blue copper protein-like", "CPS", "SigP, TarP, SecP"], ["28", "Solyc08g066740.3.1", "A0A3Q7HR33", "0.1", "early nodulin-like protein 1-like", "CPS", "SigP, TarP, SecP"], ["29", "Solyc08g028690.3.1", "A0A3Q7HMQ9", "0.0", "NAD(P)-binding Rossmann-fold superfamily protein", "UPS", "LSP, SPL, SecP"], ["30", "Solyc03g006700.3.1", "A0A3Q7FFR5", "28.7", "peroxidase (AtPrx52)", "CPS", "SigP, TarP, SecP"], ["31", "Solyc04g071890.3.1", "-", "71.6", "peroxidase", "CPS", "TarP, SecP"], ["Defense (5 proteins)"], ["32", "Solyc01g097240.3.1", "P32045", "153.6", "pathogenesis-related protein PR-4", "CPS", "SigP, TarP, SecP"], ["33", "Solyc00g174340.2.1", "A0A494GA45", "27.2", "pathogenesis-related protein 1", "CPS", "SigP, TarP, SecP"], ["34", "Solyc01g106620.2.1", "B2LW68", "61.8", "pathogenesis-related protein 1", "CPS", "SigP, TarP, SecP"], ["35", "Solyc07g005380.3.1", "A0A3Q7H2K6", "37.7", "pathogenesis-related PR-10-related/norcoclaurine synthase-like protein", "UPS", "SPL, SecP"], ["36", "Solyc09g090980.3.1", "-", "25.7", "major allergen Mal d 1", "UPS", "SPL"], ["Carbohydrate metabolism (4 proteins)"], ["37", "Solyc01g094200.3.1", "A0A3Q7EKQ6", "0.1", "malic enzyme", "UPS", "LSP, SecP"], ["38", "Solyc01g101040.3.1", "A0A3Q7EPC2", "0.1", "ATP-citrate synthase", "UPS", "LSP"], ["39", "Solyc01g058390.3.1", "A0A3Q7EEN4", "0.1", "galactokinase", "sUPS", "SecP"], ["40", "Solyc02g088690.3.1", "A0A3Q7F9B8", "0.1", "UDP-glucose 6-dehydrogenase family protein", "UPS", "LSP, SecP"], ["Signaling/regulation (5 proteins)"], ["41", "Solyc02g063090.3.1", "A0A3Q7FJZ3", "0.1", "T-complex protein 1 subunit zeta 1", "UPS", "LSP"], ["42", "Solyc05g056310.3.1", "A0A3Q7GLM4", "0.1", "T-complex protein 1 subunit gamma", "UPS", "LSP"], ["43", "Solyc01g086920.3.1", "A0A3Q7F2I5", "0.0", "leucine-rich repeat receptor-like protein kinase family", "CPS", "SigP, TarP, SecP"], ["44", "Solyc10g050110.1.1", "A0A3Q7IFT3", "0.1", "leucine-rich repeat receptor-like protein kinase family", "CPS", "SigP, TarP, SecP"], ["45", "Solyc08g082820.3.1", "A0A3Q7HX02", "31.3", "tomato BiP (binding protein)/grp78 (HSP70)", "CPS", "SigP, TarP, SecP"], ["Lipid metabolism (1 protein)"], ["46", "Solyc01g107990.3.1", "A0A3Q7FCU3", "0.1", "PI-PLC X domain-containing protein", "CPS", "SigP, TarP, SecP"], ["Miscellaneous (4 proteins)"], ["47", "Solyc03g115630.3.1", "A0A3Q7FR13", "0.1", "carbamoyl-phosphate synthase", "UPS", "LSP, SPL, SecP"], ["48", "Solyc06g005360.3.1", "A0A3Q7GNQ9", "0.1", "actin-depolymerizing factor family protein", "sUPS", "SecP"], ["49", "Solyc07g064160.3.1", "A0A3Q7HFB9", "0.1", "thiamine thiazole synthase", "sUP", "SecP"], ["50", "Solyc10g049970.2.1", "A0A3Q7IFZ6", "24.9", "kynurenine formamidase", "CPS", "SigP, TarP, SecP"], ["Unknown function (1 protein)"], ["51", "Solyc06g035920.3.1", "A0A3Q7GU06", "0.1", "remorin", "sUPS", "SecP"]], "row_count": 61, "column_count": 7, "numeric_cells": 213, "header_rows": 1, "locator": "section[6]/table-wrap[1]#ijms-21-08863-t003"}}, {"id": "asset:table:pmid:33238539:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5404389272315c674074ac505549da21eb2d2b2aa09a5de68f96016c0aa860b2", "bytes": 4038, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#ijms-21-08863-t004", "version": null, "note": "Comparison of the changes in the xylem and root protein profiles. List of proteins showing statistically significant (ANOVA, p ≤ 0.05) and biologically relevant (fold ≥ 2 or ≤ 0.5) changes in abundance in both root and xylem sap proteomes when tomato plants grown in excess Mn were compared to controls. The column Category indicates the classification (CPS, UPS or sUPS), and the column Prediction tool indicates the algorithms providing true values (SignalP, TargetP, SecretomeP, LSP and SPL). Proteins changing in abundance in roots as a result of excess Mn were described in [42].", "structure": {"pmcid": "PMC7700171", "section_index": 8, "section_title": "2.6. Comparison of Changes Observed in the Xylem and Root Protein Profiles in Response to Excess Mn", "row_count": 35, "column_count": 7}, "table": {"label": "Table 4", "caption": "Comparison of the changes in the xylem and root protein profiles. List of proteins showing statistically significant (ANOVA, p ≤ 0.05) and biologically relevant (fold ≥ 2 or ≤ 0.5) changes in abundance in both root and xylem sap proteomes when tomato plants grown in excess Mn were compared to controls. The column Category indicates the classification (CPS, UPS or sUPS), and the column Prediction tool indicates the algorithms providing true values (SignalP, TargetP, SecretomeP, LSP and SPL). Proteins changing in abundance in roots as a result of excess Mn were described in [42].", "rows": [["", "", "", "Xylem sap", "Root"], ["", "Category", "Prediction Tool", "Fold +Mn/Control", "Fold +Mn/Control"], ["Proteins decreasing in both proteomes (16 proteins)"], ["Polysaccharide metabolism", "Solyc01g104950.3.1", "β -D-xylosidase 2 precursor (LEXYL2)", "CPS", "SigP, TarP, SecP", "0.5", "0.4"], ["Solyc05g012070.3.1", "UDP-glucose:protein transglucosylase-like protein", "UPS", "SPL", "0.2", "0.5"], ["Protein metabolism", "Solyc02g068740.3.1", "glycine cleavage system H family protein (MEROPS peptidase family C1)", "CPS", "SecP", "0.3", "0.5"], ["Solyc12g008630.2.1", "mitochondrial-processing peptidase subunit α-like (MEROPS peptidase family M16)", "UPS", "LSP, SecP", "0.4", "0.3"], ["Solyc02g081700.1.1", "proteasome subunit α type (MEROPS peptidase family T1A)", "UPS", "LSP, SecP", "0.5", "0.4"], ["Solyc06g073310.3.1", "60S ribosomal protein l9", "sUPS", "SecP", "0.5", "0.5"], ["Oxido-reductases", "Solyc06g005160.3.1", "ascorbate peroxidase", "UPS", "LSP", "0.1", "0.2"], ["Solyc01g107590.3.1", "cinnamyl alcohol dehydrogenase", "UPS", "LSP", "0.2", "0.3"], ["Amino acid metabolism", "Solyc02g080810.3.1", "aminomethyltransferase", "UPS", "LSP, SecP", "0.4", "0.5"], ["Solyc01g080280.3.1 *", "glutamine synthetase", "lnS", "LSP", "0.4", "0.5"], ["Carbohydrate metabolism", "Solyc08g080140.3.1", "3,5-epimerase/4-reductase", "sUPS", "SecP", "0.3", "0.2"], ["Signaling/regulation", "Solyc06g065520.3.1", "T-complex protein 1 subunit eta", "UPS", "LSP", "0.3", "0.2"], ["Miscellaneous", "Solyc02g087300.1.1", "transducin/WD40 repeat-like superfamily protein", "UPS", "SPL, SecP", "0.4", "0.5"], ["Solyc01g006280.3.1", "formate-tetrahydrofolate ligase", "UPS", "LSP, SPL", "0.4", "0.3"], ["Solyc01g109660.2.1", "meloidogyne-induced giant cell protein DB275 (glycine-rich RNA-binding protein)", "lnS", "None", "0.3", "0.5"], ["Solyc12g098150.2.1", "Aldo/keto reductase", "lnS", "None", "0.2", "0.5"], ["Proteins increasing in both proteomes (12 proteins)"], ["Polysaccharide metabolism", "Solyc01g059965.1.1", "β-1,3-glucanase (GH17)", "CPS", "SigP, TarP, SecP", "188.7", "8.3"], ["Solyc07g005100.3.1", "chitinase/lysozyme (GH18)", "CPS", "SigP, TarP, SecP", "30.4", "3.4"], ["Solyc10g055800.2.1", "chitinase (GH19)", "CPS", "SigP, TarP, SecP", "51.1", "3.6"], ["Solyc10g055810.2.1", "chitinase Z15140 (GH19)", "CPS", "SigP, TarP, SecP", "80.9", "4.9"], ["Solyc10g055820.2.1", "chitinase (GH19)", "CPS", "SigP, TarP, SecP", "44.4", "9.5"], ["Protein metabolism", "Solyc03g019690.1.1", "Kunitz-type protease inhibitor (MEROPS I3, clan IC)", "CPS", "SigP, TarP, SecP", "37.8", "105.3"], ["Oxido-reductases", "Solyc03g006700.3.1", "peroxidase", "CPS", "SigP, TarP, SecP", "28.7", "8.4"], ["Defense", "Solyc01g097240.3.1", "pathogenesis-related protein PR-4", "CPS", "SigP, TarP, SecP", "153.6", "12.2"], ["Solyc01g106620.2.1", "pathogenesis-related protein 1", "CPS", "SigP, TarP, SecP", "61.8", "4.3"], ["Solyc09g091000.3.1", "Major allergen d 1", "lnS", "None", "54.3", "10.5"], ["Miscellaneous", "Solyc10g049970.2.1", "kynurenine formamidase", "CPS", "SigP, TarP, SecP", "24.9", "32.6"], ["Solyc09g090430.3.1", "cyanate hydratase", "lnS", "None", "3.4", "2.4"], ["Proteins with opposite responses in root and xylem sap proteomes (2 proteins)"], ["Lipid metabolism", "Solyc12g017460.1.1", "GDSL esterase/lipase At1g28590-like", "CPS", "SigP, TarP, SecP", "13.5", "0.5"], ["Signaling/regulation", "Solyc01g106210.3.1", "heat shock protein 70", "UPS", "LSP", "3.4", "0.4"]], "row_count": 35, "column_count": 7, "numeric_cells": 110, "header_rows": 2, "locator": "section[8]/table-wrap[1]#ijms-21-08863-t004"}}], "gaps": ["asset:data:geo:PXD021973 not downloaded", "asset:data:geo:PXD021973 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Only changes with a p ≤ 0.05 (ANOVA) and a ratio (fold change) ≥2 or ≤0.5 were considered as statistically significant and biologically relevant, respectively."}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "PCA"}}], "targets": [], "gaps": []}, "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": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["PXD021973"], "resolved_accessions": ["PXD021973"], "statements": ["Data are available via ProteomeXchange with identifier PXD021973."], "basis": "The paper names PXD021973 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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:33238539", "data:geo:PXD021973", "asset:table:pmid:33238539:1", "asset:table:pmid:33238539:2", "asset:table:pmid:33238539:3", "asset:table:pmid:33238539:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD021973"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:33Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 73939, "completion_tokens": 1610, "cached_tokens": 528}}, "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:33238539", "type": "paper", "label": "pmid:33238539"}, {"id": "source:pmid:33238539", "type": "manuscript", "label": "PMID 33238539 full text"}, {"id": "data:geo:PXD021973", "type": "dataset", "label": "GEO PXD021973"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33238539", "type": "paper", "label": "pmid:33238539"}, {"id": "source:pmid:33238539", "type": "manuscript", "label": "PMID 33238539 full text"}, {"id": "data:geo:PXD021973", "type": "dataset", "label": "GEO PXD021973"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33238539", "type": "extraction", "used": ["source:pmid:33238539"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD021973", "type": "accession_resolution", "used": ["data:geo:PXD021973"], "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:33238539", "parent_hash": "sha256:ba283dd2c14767f037f130a9e7156fdef94a5af0125fe050c3e7ba5897ce85ea", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD021973 licence not read", "asset:data:geo:PXD021973 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Only changes with a p ≤ 0.05 (ANOVA) and a ratio (fold change) ≥2 or ≤0.5 were considered as statistically significant and biologically relevant, respectively."], "order_basis": "analysis_only", "id": "assay:1"}]},"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":"2026-11-04T03:32:52+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}}}