{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32374750", "kind": "science-record", "revision": 7, "content_hash": "sha256:857fbcfc8a551d424725f01ac06b3ed67abe58ea20e7baebe05faae7943c37ba", "created_at": "2026-11-01T15:41:00Z", "updated_at": "2026-11-01T22:01:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparison of a human neuronal model proteome upon Japanese encephalitis or West Nile Virus infection and potential role of mosquito saliva in neuropathogenesis.", "doi": "10.1371/journal.pone.0232585", "pmid": "32374750", "authors": ["Benoit Besson", "Justine Basset", "Sandrine Gatellier", "Hélène Chabrolles", "Thibault Chaze", "Véronique Hourdel", "Mariette Matondo", "Nathalie Pardigon", "Valérie Choumet"], "journal": "PloS one", "year": 2020, "abstract": "Neurotropic flavivirus Japanese encephalitis virus (JEV) and West Nile virus (WNV) are amongst the leading causes of encephalitis. Using label-free quantitative proteomics, we identified proteins differentially expressed upon JEV (gp-3, RP9) or WNV (IS98) infection of human neuroblastoma cells. Data are available via ProteomeXchange with identifier PXD016805. Both viruses were associated with the up-regulation of immune response (IFIT1/3/5, ISG15, OAS, STAT1, IRF9) and the down-regulation of SSBP2 and PAM, involved in gene expression and in neuropeptide amidation respectively. Proteins associated to membranes, involved in extracellular matrix organization and collagen metabolism represented major clusters down-regulated by JEV and WNV. Moreover, transcription regulation and mRNA processing clusters were also heavily regulated by both viruses. The proteome of neuroblastoma cells infected by JEV or WNV was significantly modulated in the presence of mosquito saliva, but distinct patterns were associated to each virus. Mosquito saliva favored modulation of proteins associated with gene regulation in JEV infected neuroblastoma cells while modulation of proteins associated with protein maturation, signal transduction and ion transporters was found in WNV infected neuroblastoma cells.", "claims": [{"id": "claim-method", "statement": "Statistical analysis of label free data was performed using the MS-Stat package on R environment [29].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32374750", "locator": "sections[7] \"Statistical analysis of label free MS data\" paragraph 2", "quote": "Statistical analysis of label free data was performed using the MS-Stat package on R environment [29]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All relevant data are within the manuscript and its Supporting Information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32374750", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "All relevant data are within the manuscript and its Supporting Information files."}], "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:32374750"], "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:PXD016805"], "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:PXD016805"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32374750", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0232585", "sha256": "sha256:e35ead43302cf58cb65504b196b143a3e8b043becfb61c89a57e42cbbd470ab3", "bytes": 59967, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0232585", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7202638", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD016805", "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=PXD016805", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD016805", "version": null, "note": "All relevant data are within the manuscript and its Supporting Information files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All relevant data are within the manuscript and its Supporting Information files.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Comparison of the Human Neuronal Proteome upon Japanese Encephalitis or West Nile Virus Infection and potential role of mosquito saliva in neuropathogenesis", "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:32374750:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:53b53adc1f432713174e8b0a0bc60e65a3ebf7c3a8068f00e0eadb8e3cbd7b1b", "bytes": 4131, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#pone.0232585.t001", "version": null, "note": "Top 10 up-regulated proteins during JEV and/or WNV infection.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells compared to the Mock. For complete list, see S1 Table.", "structure": {"pmcid": "PMC7202638", "section_index": 12, "section_title": "Identification of differentially expressed proteins following JEV or WNV infection", "row_count": 31, "column_count": 8}, "table": {"label": "Table 1", "caption": "Top 10 up-regulated proteins during JEV and/or WNV infection.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells compared to the Mock. For complete list, see S1 Table.", "rows": [["Effect", "Uniprot #", "GeneID #", "Gene symbol", "Name", "Clusters", "JEV/Mock FC (pValue)", "WNV/Mock FC (pValue)"], ["Up-regulated during JEV infection", "P32886", "1489713", "N/A", "JEV genomic polyprotein", "", "65.95 (0.00E+00)", ""], ["Q5EBM0-4", "129607", "CMPK2", "UMP-CMP kinase 2, mitochondrial", "Nucleotide-binding", "3.82 (3.25E-02)", ""], ["O60664", "10226", "PLIN3", "Perilipin-3", "Cell-cell adhesion", "1.82 (1.81E-06)", ""], ["P11047", "3915", "LAMC1", "Laminin subunit gamma-1", "Collagen metabolism, EGF-like domain, Extracellular matrix org., Glycoprotein", "1.80 (5.28E-06)", ""], ["Q9BXJ9", "80155", "NAA15", "N-alpha-acetyltransferase 15, NatA auxiliary subunit", "Tetratricopeptide repeat, Transcription regulation", "1.78 (1.80E-02)", ""], ["O00622", "3491", "CYR61", "Protein CYR61", "Glycoprotein, Nucleotide-binding", "1.76 (1.82E-02)", ""], ["Q9Y520-4", "23215", "PRRC2C", "Protein PRRC2C", "", "1.76 (1.16E-02)", ""], ["Q9Y3Z3", "25939", "SAMHD1", "Deoxynucleoside triphosphate triphosphohydrolase SAMHD1", "Innate immunity", "1.74 (1.58E-05)", ""], ["F8VVL1", "8562", "DENR", "Density-regulated protein", "", "1.66 (2.90E-02)", ""], ["Q9UNF0-2", "11252", "PACSIN2", "Protein kinase C and casein kinase substrate in neurons protein 2", "Cell-cell adhesion", "1.66 (2.26E-02)", ""], ["Up-regulated during both JEV and WNV infection", "P09914", "3434", "IFIT1", "Interferon-induced protein with tetratricopeptide repeats 1", "Innate immunity, Tetratricopeptide repeat", "13.60 (1.34E-13)", "7.838 (2.36E-09)"], ["O14879", "3437", "IFIT3", "Interferon-induced protein with tetratricopeptide repeats 3", "Innate immunity, Tetratricopeptide repeat", "12.31 (0.00E+00)", "6.944 (3.20E-13)"], ["P05161", "9636", "ISG15", "Ubiquitin-like protein ISG15", "Anchored protein, Innate immunity", "9.08 (7.93E-09)", "4.59 (4.85E-05)"], ["Q9Y6K5", "4940", "OAS3", "2'-5'-oligoadenylate synthase 3", "Innate immunity, Nucleotide-binding, Transmembrane protein", "5.32 (0.00E+00)", "3.17 (0.00E+00)"], ["P42224", "6772", "STAT1", "Signal transducer and activator of transcription 1-alpha/beta", "Cell-cell adhesion, Innate immunity, Transcription regulation", "3.96 (0.00E+00)", "2.49 (0.00E+00)"], ["Q9BQE5", "23780", "APOL2", "Apolipoprotein L2", "Transmembrane protein", "3.04 (9.67E-04)", "2.13 (4.43E-02)"], ["Q13325", "24138", "IFIT5", "Interferon-induced protein with tetratricopeptide repeats 5", "Innate immunity, Tetratricopeptide repeat, Transmembrane protein", "2.98 (5.96E-11)", "1.93 (6.50E-05)"], ["Q8WUP2-3", "54751", "FBLIM1", "Filamin-binding LIM protein 1", "", "2.96 (4.13E-02)", "2.94 (4.26E-02)"], ["Q5K651", "54809", "SAMD9", "Sterile alpha motif domain-containing protein 9", "2.61 (9.24E-05)", "2.11 (4.97E-04)"], ["Q9NUQ6-2", "26010", "SPATS2L", "SPATS2-like protein", "", "2.47 (2.95E-09)", "2.02 (2.37E-06)"], ["Up-regulated during WNV infection", "P06935", "912267", "N/A", "WNV genomic polyprotein", "", "", "271.78 (3.88E-04)"], ["Q6GMV3", "391356", "PTRHD1", "Putative peptidyl-tRNA hydrolase PTRHD1", "", "4.22 (3.58E-02)"], ["Q5QNY5", "5824", "PEX19", "Peroxisomal biogenesis factor 19", "Transmembrane", "", "3.35 (1.43E-03)"], ["Q96C90", "26472", "PP1R14B", "Protein phosphatase 1 regulatory subunit 14B", "", "2.21 (1.43E-02)"], ["P0DMV8/9", "3303", "HSPA1A", "Heat shock 70 kDa protein 1A", "Cell-cell adhesion, Nucleotide-binding", "2.03 (4.86E-11)"], ["Q9Y6G9", "51143", "YNC1LI1", "Cytoplasmic dynein 1 light intermediate chain 1", "Nucleotide-binding", "", "2.01 (2.58E-02)"], ["Q8TDX7", "140609", "NEK7", "Serine/threonine-protein kinase Nek7", "Kinase, Nucleotide-binding", "1.99 (8.66E-03)"], ["Q9BUF5", "84617", "TUBB6", "Tubulin beta-6 chain", "Nucleotide-binding", "", "1.96 (2.40E-02)"], ["O95817", "9531", "BAG3", "BAG family molecular chaperone regulator 3", "Cell-cell adhesion", "", "1.96 (6.14E-03)"], ["O00592-2", "5420", "PODXL", "Podocalyxin", "Glycoprotein, Transmembrane", "1.77 (1.43E-02)"]], "row_count": 31, "column_count": 8, "numeric_cells": 115, "header_rows": 1, "locator": "section[12]/table-wrap[1]#pone.0232585.t001"}}, {"id": "asset:table:pmid:32374750:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3c8b10ec08c1673efd3255b77dc5b095e8cab8db459cc4e4156b3344319afa75", "bytes": 4295, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#pone.0232585.t002", "version": null, "note": "Top 10 down-regulated proteins during JEV and/or WNV infection.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells compared to the Mock. For complete list, see S2 Table.", "structure": {"pmcid": "PMC7202638", "section_index": 12, "section_title": "Identification of differentially expressed proteins following JEV or WNV infection", "row_count": 31, "column_count": 8}, "table": {"label": "Table 2", "caption": "Top 10 down-regulated proteins during JEV and/or WNV infection.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells compared to the Mock. For complete list, see S2 Table.", "rows": [["Effect", "Uniprot #", "GeneID #", "Gene symbol", "Name", "Clusters", "JEV/Mock FC (pValue)", "WNV/Mock FC (pValue)"], ["Down-regulated during JEV infection", "Q99797", "4285", "MIPEP", "Mitochondrial intermediate peptidase", "Metalloprotease", "7.84 (1.53E-03)", ""], ["P21810", "633", "BGN", "Biglycan", "Extracellular matrix org., Glycoprotein, Leucine-rich repeat", "3.21 (4.36E-02)", ""], ["Q8WZ42-5", "7273", "TTN", "Titin", "Immunoglobulin domain, Nucleotide-binding, Tetratricopeptide repeat", "3.12 (2.25E-02)", ""], ["O14657", "27348", "TOR1B", "Torsin-1B", "Glycoprotein, Nucleotide-binding", "3.09 (6.62E-03)", ""], ["P55083", "4239", "MFAP4", "Microfibril-associated glycoprotein 4", "Extracellular matrix org., Glycoprotein", "2.95 (6.07E-03)", ""], ["O75063", "9917", "FAM20B", "Glycosaminoglycan xylosylkinase", "Glycoprotein, Nucleotide-binding, Transmembrane protein", "2.70 (3.24E-02)", ""], ["Q9P032", "29078", "NDUFAF4", "NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 4", "", "2.37 (2.00E-02)", ""], ["Q13641", "7162", "TPBG", "Trophoblast glycoprotein", "Glycoprotein, Leucine-rich repeat, Transmembrane protein", "2.36 (4.55E-02)", ""], ["Q86UV5-2", "84196", "USP48", "Ubiquitin carboxyl-terminal hydrolase 48", "", "2.24 (3.92E-02)", ""], ["P63218", "2787", "GNG5", "Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-5", "Anchored protein, Collagen metabolism", "2.22 (4.35E-02)", ""], ["Down-regulated during both JEV and WNV infection", "P81877-2", "23635", "SSBP2", "Single-stranded DNA-binding protein 2", "", "26.22 (2.60E-02)", "15,05 (3.46E-02)"], ["P19021-2", "5066", "PAM", "Peptidyl-glycine alpha-amidating monooxygenase", "Glycoprotein, Transmembrane protein", "5.05 (3.74E-02)", "9,23 (2.02E-02)"], ["P02452", "1277", "COL1A1", "Collagen alpha-1(I) chain", "Extracellular matrix org., Collagen metabolism, Glycoprotein, Transmembrane protein", "4.65 (0.00E+00)", "2,96 (0.00E+00)"], ["P08123", "1278", "COL1A2", "Collagen alpha-2(I) chain", "Extracellular matrix org., Collagen metabolism, Glycoprotein", "4.29 (0.00E+00)", "2,16 (5.21E-09)"], ["P02461", "1281", "COL3A1", "Collagen alpha-1(III) chain", "Extracellular matrix org., Collagen metabolism, Glycoprotein", "4.28 (0.00E+00)", "2,16 (1.89E-11)"], ["Q9H3M7", "10628", "TXNIP", "Thioredoxin-interacting protein", "Transcription regulation", "4.13 (1.20E-04)", "4,98 (1.82E-04)"], ["Q96CG8", "115908", "CTHRC1", "Collagen triple helix repeat-containing protein 1", "Extracellular matrix org., Collagen metabolism, Glycoprotein", "3.98 (0.00E+00)", "2,54 (0.00E+00)"], ["O95864", "9415", "FADS2", "Fatty acid desaturase 2", "Transmembrane protein", "3.41 (1.60E-12)", "3,36 (3.20E-11)"], ["Q15113", "5118", "PCOLCE", "Procollagen C-endopeptidase enhancer 1", "Extracellular matrix org., Collagen metabolism, Glycoprotein", "3.35 (0.00E+00)", "1,81 (3.60E-08)"], ["C9JEZ4", "10602", "CDC42EP3", "Cdc42 effector protein 3", "Transmembrane protein", "3.09 (8.20E-05)", "2,26 (1.88E-02)"], ["Down-regulated during WNV infection", "P33908", "4121", "MAN1A1", "Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA", "Glycoprotein, Transmembrane", "", "4.52 (4.01E-02)"], ["B4DWB0", "80224", "NUBPL", "Iron-sulfur protein NUBPL", "Glycoprotein, Nucleotide-binding", "", "4.30 (3.39E-02)"], ["Q8N129", "245812", "CNPY4", "Protein canopy homolog 4", "Glycoprotein", "", "3.65 (2.81E-02)"], ["H3BQR0", "10073", "SNUPN", "Snurportin-1", "", "", "3.10 (4.33E-02)"], ["Q16706", "4124", "MAN2A1", "Alpha-mannosidase 2", "Glycoprotein, Transmembrane", "", "2.98 (3.58E-02)"], ["Q9Y294", "25842", "ASF1A", "Histone chaperone ASF1A", "Transcription regulation", "", "2.93 (4.58E-02)"], ["Q9NRX1", "56902", "PNO1", "RNA-binding protein PNO1", "", "", "2.70 (4.97E-03)"], ["P07711", "1514", "CTSL", "Cathepsin L1", "Collagen metabolism, Glycoprotein, Lysosome", "", "2.63 (4.66E-02)"], ["P38571-2", "3988", "LIPA", "Lysosomal acid lipase/cholesteryl ester hydrolase", "Glycoprotein, Lysosome", "", "2.58 (1.19E-02)"], ["O00754-2", "4125", "MAN2B1", "Lysosomal alpha-mannosidase", "Glycoprotein, Lysosome", "", "2.53 (6.58E-03)"]], "row_count": 31, "column_count": 8, "numeric_cells": 115, "header_rows": 1, "locator": "section[12]/table-wrap[2]#pone.0232585.t002"}}, {"id": "asset:table:pmid:32374750:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:049af42cb7cffc470bd8f2359c9f456a537b01ff0d39fd4ed04971c878e60ea2", "bytes": 1268, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#pone.0232585.t003", "version": null, "note": "Effect of SGE on non infected human neuroblastoma cells.", "structure": {"pmcid": "PMC7202638", "section_index": 14, "section_title": "Role of mosquito saliva in a neuron model of infection", "row_count": 13, "column_count": 7}, "table": {"label": "Table 3", "caption": "Effect of SGE on non infected human neuroblastoma cells.", "rows": [["Effect", "Uniprot #", "GeneID #", "Gene symbol", "Name", "Fold change (adjusted pValue)", ""], ["Up-regulated in presence of SGE", "O95218-2", "9406", "ZRANB2", "zinc finger RANBP2-type containing 2", "3.04 (2,33E-03)", ""], ["Down-regulated in presence of SGE", "Q5QNY5", "5824", "PEX19", "peroxisomal biogenesis factor 19", "2.45 (3,45E-02)", ""], ["E9PJ95", "29099", "COMMD9", "COMM domain containing 9", "2.08 (1,87E-02)", ""], ["E7EQI7", "9897", "KIAA0196", "KIAA0196", "2.04 (1,77E-02)", ""], ["Q9NRG7-2", "56948", "SDR39U1", "short chain dehydrogenase/reductase family 39U member 1", "1.91 (1,49E-02)", ""], ["Q66K74", "55201", "MAP1S", "microtubule associated protein 1S", "1.79 (1,49E-02)", ""], ["O43592", "11260", "XPOT", "exportin for tRNA", "1.79 (2,33E-03)", "*"], ["Q9BZH6", "55717", "WDR11", "WD repeat domain 11", "1.68 (1,87E-02)", "*"], ["O60443", "1687", "DFNA5", "deafness associated tumor suppressor", "1.58 (1,65E-02)", ""], ["Q9HAV4", "57510", "XPO5", "exportin 5", "1.56 (5,53E-03)", "*"], ["O95373", "10527", "IPO7", "importin 7", "1.51 (1,58E-02)", "*"], ["* involved in nuclear transport", ""]], "row_count": 13, "column_count": 7, "numeric_cells": 42, "header_rows": 1, "locator": "section[14]/table-wrap[1]#pone.0232585.t003"}}, {"id": "asset:table:pmid:32374750:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e1c8a8539d7bd1cc25642a98d503a95590c949a89f3f872230dea79bb4a51bf0", "bytes": 2485, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#pone.0232585.t004", "version": null, "note": "Top 10 proteins up-regulated by SGE in JEV and/or WNV infected cells.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells treated or not with SGE. For complete list, see S5 Table.", "structure": {"pmcid": "PMC7202638", "section_index": 14, "section_title": "Role of mosquito saliva in a neuron model of infection", "row_count": 23, "column_count": 7}, "table": {"label": "Table 4", "caption": "Top 10 proteins up-regulated by SGE in JEV and/or WNV infected cells.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells treated or not with SGE. For complete list, see S5 Table.", "rows": [["Effect", "Protein #", "Gene ID #", "Gene", "Gene name", "JEV infected FC (adj. pValue)", "WNV infected FC (adj. pValue)"], ["Up-regulated proteins during JEV infection", "Q15388", "9804", "TOMM20", "translocase of outer mitochondrial membrane 20", "3.52 (1,94E-02)", ""], ["P16403", "3006", "HIST1H1C", "histone cluster 1 H1 family member c", "2.28 (2,48E-02)", ""], ["P07305", "3005", "H1F0", "H1 histone family member 0", "1.96 (7,76E-05)", ""], ["P53999", "10923", "SUB1", "SUB1 homolog transcriptional regulator", "1.92 (1,93E-02)", ""], ["Q5TAQ0", "84300", "UQCC2", "ubiquinol-cytochrome c reductase complex assembly factor 2", "1.85 (4,01E-02)", ""], ["Q9NR30", "9188", "DDX21", "DExD-box helicase 21", "1.70 (3,02E-09)", ""], ["P11387", "7150", "TOP1", "topoisomerase DNA I", "1.64 (1,27E-03)", ""], ["O15446", "10849", "CD3EAP", "CD3e molecule associated protein", "1.60 (2,48E-02)", ""], ["Q9UIG0-2", "9031", "BAZ1B", "bromodomain adjacent to zinc finger domain 1B", "1.59 (1,85E-03)", ""], ["P11388", "7153", "TOP2A", "topoisomerase DNA II alpha", "1.57 (2,48E-02)", ""], ["Up-regulated proteins during JEV and WNV infection", "Q9BZF1-3", "114882", "OSBPL8", "oxysterol binding protein like 8", "1.57 (1,65E-04)", "1.55 (2,83E-05)"], ["P16401", "3009", "HIST1H1B", "histone cluster 1 H1 family member b", "2.01 (1,98E-06)", "1.50 (2,85E-03)"], ["Up-regulated proteins during WNV infection", "P60468", "10952", "SEC61B", "Sec61 translocon beta subunit", "", "7.71 (1,61E-07)"], ["H0YI58", "51290", "ERGIC2", "ERGIC and golgi 2", "", "3.90 (1,23E-02)"], ["Q9P0L0", "9218", "VAPA", "VAMP associated protein A", "", "3.78 (8,72E-04)"], ["P07099", "2052", "EPHX1", "epoxide hydrolase 1", "", "2.18 (5,44E-08)"], ["O15427", "9123", "SLC16A3", "solute carrier family 16 member 3", "", "2.10 (4,83E-02)"], ["Q13619", "8451", "CUL4A", "cullin 4A", "", "2.09 (3,11E-02)"], ["O00264", "10857", "PGRMC1", "progesterone receptor membrane component 1", "", "2.04 (2,72E-03)"], ["Q9BT22", "56052", "ALG1", "ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase", "2.01 (1,08E-02)"], ["P04844", "6185", "RPN2", "ribophorin II", "", "1.98 (1,66E-06)"], ["Q9HC07", "55858", "TMEM165", "transmembrane protein 165", "", "1.97 (2,59E-02)"]], "row_count": 23, "column_count": 7, "numeric_cells": 86, "header_rows": 1, "locator": "section[14]/table-wrap[2]#pone.0232585.t004"}}, {"id": "asset:table:pmid:32374750:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9aa0116fde97ae86f6af37dbb11c38d16b287369b3393109022957cfb65e1beb", "bytes": 2757, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[3]#pone.0232585.t005", "version": null, "note": "Top 10 proteins down-regulated by SGE in JEV and/or WNV infected cells.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells treated or not with SGE. For complete list, see S6 Table.", "structure": {"pmcid": "PMC7202638", "section_index": 14, "section_title": "Role of mosquito saliva in a neuron model of infection", "row_count": 26, "column_count": 7}, "table": {"label": "Table 5", "caption": "Top 10 proteins down-regulated by SGE in JEV and/or WNV infected cells.Proteins are sorted according to the fold change in the JEV- (or secondly in WNV-) infected cells treated or not with SGE. For complete list, see S6 Table.", "rows": [["Effect", "Uniprot #", "GeneID #", "Gene symbol", "Name", "JEV infected FC (adj. pValue)", "WNV infected FC (adj. pValue)"], ["Down-regulated proteins during JEV infection", "Q99797", "4285", "MIPEP", "mitochondrial intermediate peptidase", "4.61 (3,06E-02)", ""], ["Q9Y6W5-2", "10163", "WASF2", "WAS protein family member 2", "3.67 (4,08E-05)", ""], ["E7ESU0", "10869", "USP19", "ubiquitin specific peptidase 19", "3.24 (4,61E-02)", ""], ["Q9BZX2", "7371", "UCK2", "uridine-cytidine kinase 2", "2.58 (1,85E-03)", ""], ["O95400", "10421", "CD2BP2", "CD2 cytoplasmic tail binding protein 2", "1.82 (1,53E-02)", ""], ["P00338", "3939", "LDHA", "lactate dehydrogenase A", "1.77 (2,33E-02)", ""], ["Q9Y316", "51072", "MEMO1", "mediator of cell motility 1", "1.75 (2,34E-03)", ""], ["Q9H3M7", "10628", "TXNIP", "thioredoxin interacting protein", "1.74 (3,06E-02)", ""], ["Q9NRG7-2", "56948", "SDR39U1", "short chain dehydrogenase/reductase family 39U member 1", "1.69 (2,48E-02)", ""], ["Q9NPQ8-4", "60626", "RIC8A", "RIC8 guanine nucleotide exchange factor A", "1.66 (3,29E-02)", ""], ["Down-regulated proteins during JEV and WNV infection", "R4GN98", "6277", "S100A6", "S100 calcium binding protein A6", "2.73 (1,22E-02)", "2.78 (1,49E-02)"], ["F8VZJ2", "4666", "NACA", "nascent polypeptide-associated complex alpha subunit", "1.80 (1,94E-02)", "2.15 (1,88E-03)"], ["Q15056-2", "7458", "EIF4H", "eukaryotic translation initiation factor 4H", "1.78 (1,80E-02)", "2.05 (1,60E-03)"], ["E9PGT6", "10920", "COPS8", "COP9 signalosome subunit 8", "1.67 (9,82E-03)", "2.22 (1,93E-04)"], ["P09382", "3956", "LGALS1", "galectin 1", "1.66 (7,22E-03)", "1.98 (2,36E-04)"], ["Down-regulated proteins during WNV infection", "Q9P0S9", "51522", "TMEM14C", "transmembrane protein 14C", "", "4.12 (1,10E-02)"], ["Q9NRX1", "56902", "PNO1", "partner of NOB1 homolog", "", "3.03 (1,23E-02)"], ["P61758", "7411", "VBP1", "VHL binding protein 1", "", "2.69 (1,93E-06)"], ["P49366", "1725", "DHPS", "deoxyhypusine synthase", "", "2.56 (1,36E-02)"], ["Q99497", "11315", "PARK7", "Parkinsonism associated deglycase", "", "2.49 (1,32E-07)"], ["Q04837", "6742", "SSBP1", "single stranded DNA binding protein 1", "", "2.14 (8,85E-05)"], ["O00499-9", "274", "BIN1", "bridging integrator 1", "", "2.06 (2,90E-02)"], ["O00743", "5537", "PPP6C", "protein phosphatase 6 catalytic subunit", "", "1.85 (2,85E-03)"], ["Q9Y3B8", "25996", "REXO2", "RNA exonuclease 2", "", "1.73 (1,36E-02)"], ["P46777", "6125", "RPL5", "ribosomal protein L5", "", "1.60 (2,73E-02)"]], "row_count": 26, "column_count": 7, "numeric_cells": 92, "header_rows": 1, "locator": "section[14]/table-wrap[3]#pone.0232585.t005"}}], "gaps": ["asset:data:geo:PXD016805 not downloaded", "asset:data:geo:PXD016805 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "dendrogram"}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "PPI"}}, {"id": "method-3", "family": null, "specific": null, "label": "MS-Stat package on R environment", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Statistical analysis of label free data was performed using the MS-Stat package on R environment [29]."}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["hierarchical_cluster"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: hierarchical."}, "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": ["PXD016805"], "resolved_accessions": ["PXD016805"], "statements": ["All relevant data are within the manuscript and its Supporting Information files."], "basis": "The paper names PXD016805 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": ["hierarchical_cluster"], "assets": ["source:pmid:32374750", "data:geo:PXD016805", "asset:table:pmid:32374750:1", "asset:table:pmid:32374750:2", "asset:table:pmid:32374750:3", "asset:table:pmid:32374750:4", "asset:table:pmid:32374750:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD016805"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:19:36Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 46400, "completion_tokens": 608, "cached_tokens": 784}}, "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:32374750", "type": "paper", "label": "pmid:32374750"}, {"id": "source:pmid:32374750", "type": "manuscript", "label": "PMID 32374750 full text"}, {"id": "data:geo:PXD016805", "type": "dataset", "label": "GEO PXD016805"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32374750", "type": "paper", "label": "pmid:32374750"}, {"id": "source:pmid:32374750", "type": "manuscript", "label": "PMID 32374750 full text"}, {"id": "data:geo:PXD016805", "type": "dataset", "label": "GEO PXD016805"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32374750", "type": "extraction", "used": ["source:pmid:32374750"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD016805", "type": "accession_resolution", "used": ["data:geo:PXD016805"], "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:32374750", "parent_hash": "sha256:c4f0f13efd5a107f146b6d1c76e1e117fbc8cf5f30658706dfeb28cd63676828", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD016805 licence not read", "asset:data:geo:PXD016805 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": ["encephalitis. Using label-free quantitative proteomics, we identified proteins differentially expre", "of the infection in the samples processed by mass spectrometry.(PDF)Click here for additional data file. S3", "terials S1 FigHierarchical clustering of the LC-MS/MS data.The dendrogram was obtained in Perseus"], "order_basis": "paper_text_order:279", "id": "assay:1"}, {"role": "analysis", "definition_id": "clustering", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["hierarchical_cluster"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["dendrogram"], "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":"2026-11-04T01:22:03+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}}}