{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38702721", "kind": "science-record", "revision": 4, "content_hash": "sha256:85f2db5ffb14ccc917723af425531d12097ad94f367caec6ad647b855e834ad1", "created_at": "2026-11-01T19:20:40Z", "updated_at": "2026-11-01T22:11:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of sepsis-associated mitochondrial genes through RNA and single-cell sequencing approaches.", "doi": "10.1186/s12920-024-01891-x", "pmid": "38702721", "authors": ["Shilin Li", "Xiang Li", "Sishi Jiang", "Chenglin Wang", "Yingchun Hu"], "journal": "BMC medical genomics", "year": 2024, "abstract": "BACKGROUND: Sepsis ranks among the most formidable clinical challenges, characterized by exorbitant treatment costs and substantial demands on healthcare resources. Mitochondrial dysfunction emerges as a pivotal risk factor in the pathogenesis of sepsis, underscoring the imperative to identify mitochondrial-related biomarkers. Such biomarkers are crucial for enhancing the accuracy of sepsis diagnostics and prognostication.\nMETHODS: In this study, adhering to the SEPSIS 3.0 criteria, we collected peripheral blood within 24 h of admission from 20 sepsis patients at the ICU of the Southwest Medical University Affiliated Hospital and 10 healthy volunteers as a control group for RNA-seq. The RNA-seq data were utilized to identify differentially expressed RNAs. Concurrently, mitochondrial-associated genes (MiAGs) were retrieved from the MitoCarta3.0 database. The differentially expressed genes were intersected with MiAGs. The intersected genes were then subjected to GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses and core genes were filtered using the PPI (Protein-Protein Interaction) network. Subsequently, relevant sepsis datasets (GSE65682, GSE28750, GSE54514, GSE67652, GSE69528, GSE95233) were downloaded from the GEO (Gene Expression Omnibus) database to perform bioinformatic validation of these core genes. Survival analysis was conducted to assess the prognostic value of the core genes, while ROC (Receiver Operating Characteristic) curves determined their diagnostic value, and a meta-analysis confirmed the accuracy of the RNA-seq data. Finally, we collected 5 blood samples (2 normal controls (NC); 2 sepsis; 1 SIRS (Systemic Inflammatory Response Syndrome), and used single-cell sequencing to assess the expression levels of the core genes in the different blood cell types.\nRESULTS: Integrating high-throughput sequencing with bioinformatics, this study identified two mitochondrial genes (COX7B, NDUFA4) closely linked with sepsis prognosis. Survival analysis demonstrated that patients with lower expression levels of COX7B and NDUFA4 exhibited a higher day survival rate over 28 days, inversely correlating with sepsis mortality. ROC curves highlighted the significant sensitivity and specificity of both genes, with AUC values of 0.985 for COX7B and 0.988 for NDUFA4, respectively. Meta-analysis indicated significant overexpression of COX7B and NDUFA4 in the sepsis group in contrast to the normal group (P < 0.01). Additionally, single-cell RNA sequencing revealed predominant expression of these core genes in monocytes-macrophages, T cells, and B cells.\nCONCLUSION: The mitochondrial-associated genes (MiAGs) COX7B and NDUFA4 are intimately linked with the prognosis of sepsis, offering potential guidance for research into the mechanisms underlying sepsis.", "claims": [{"id": "claim-method", "statement": "Data extraction and analysis were performed by Graphpad Prism 9.0, with the logrank test for statistical evaluation, setting p < 0.05 as the threshold for significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38702721", "locator": "sections[11] \"Survival analysis\" paragraph 2", "quote": "Data extraction and analysis were performed by Graphpad Prism 9.0, with the logrank test for statistical evaluation, setting p < 0.05 as the threshold for significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38702721", "locator": "sections[30] \"notes\" paragraph 1", "quote": "We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Patients with low expression of COX7B and NDUFA4 had higher 28-day survival rates than the high-expression group, with statistically significant differences (P < 0.05).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Patients with low expression of COX7B and NDUFA4 exhibited higher 28-day survival rates compared to the high-expression group, showing a negative correlation with the survival rate of sepsis patients, with statistically significant differences (P < 0.05) (Fig. 5A-B)."}, "evidence": [{"asset": "source:pmid:38702721", "locator": "sections[21] \"Discovery of mitochondrial genes associated with diagnosis and prognosis of sepsis\" paragraph 2", "quote": "Patients with low expression of COX7B and NDUFA4 exhibited higher 28-day survival rates compared to the high-expression group, showing a negative correlation with the survival rate of sepsis patients, with statistically significant differences (P < 0.05) (Fig. 5A-B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Patients with low expression of COX7B and NDUFA4 had higher 28-day survival rates than the high-expression group, with statistically significant differences (P < 0.05).", "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:38702721"], "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:GSE28750"], "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:GSE28750"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38702721", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-024-01891-x", "sha256": "sha256:b442363f6bd938419f2ae895784a22cae8d471d0c9b08817f3a21acf58577c63", "bytes": 38980, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12920-024-01891-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11067249", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE28750", "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=GSE28750", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28750", "version": null, "note": "We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM712478", "GSM712479", "GSM712480", "GSM712481", "GSM712482", "GSM712483", "GSM712484", "GSM712485", "GSM712486", "GSM712487", "GSM712488", "GSM712489", "GSM712490", "GSM712491", "GSM712492", "GSM712493", "GSM712494", "GSM712495", "GSM712496", "GSM712497", "GSM712498", "GSM712499", "GSM712500", "GSM712501", "GSM712502", "GSM712503", "GSM712504", "GSM712505", "GSM712506", "GSM712507", "GSM712508", "GSM712509", "GSM712510", "GSM712511", "GSM712512", "GSM712513", "GSM712514", "GSM712515", "GSM712516", "GSM712517", "GSM712518"], "sample_count": 41, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Development and Validation of a Novel Molecular Biomarker Diagnostic Test for the Early Detection of Sepsis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE54514", "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=GSE54514", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE54514", "version": null, "note": "We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1317896", "GSM1317897", "GSM1317898", "GSM1317899", "GSM1317900", "GSM1317901", "GSM1317902", "GSM1317903", "GSM1317904", "GSM1317905", "GSM1317906", "GSM1317907", "GSM1317908", "GSM1317909", "GSM1317910", "GSM1317911", "GSM1317912", "GSM1317913", "GSM1317914", "GSM1317915", "GSM1317916", "GSM1317917", "GSM1317918", "GSM1317919", "GSM1317920", "GSM1317921", "GSM1317922", "GSM1317923", "GSM1317924", "GSM1317925", "GSM1317926", "GSM1317927", "GSM1317928", "GSM1317929", "GSM1317930", "GSM1317931", "GSM1317932", "GSM1317933", "GSM1317934", "GSM1317935", "GSM1317936", "GSM1317937", "GSM1317938", "GSM1317939", "GSM1317940", "GSM1317941", "GSM1317942", "GSM1317943", "GSM1317944", "GSM1317945", "GSM1317946", "GSM1317947", "GSM1317948", "GSM1317949", "GSM1317950", "GSM1317951", "GSM1317952", "GSM1317953", "GSM1317954", "GSM1317955", "GSM1317956", "GSM1317957", "GSM1317958", "GSM1317959", "GSM1317960", "GSM1317961", "GSM1317962", "GSM1317963", "GSM1317964", "GSM1317965", "GSM1317966", "GSM1317967", "GSM1317968", "GSM1317969", "GSM1317970", "GSM1317971", "GSM1317972", "GSM1317973", "GSM1317974", "GSM1317975", "GSM1317976", "GSM1317977", "GSM1317978", "GSM1317979", "GSM1317980", "GSM1317981", "GSM1317982", "GSM1317983", "GSM1317984", "GSM1317985", "GSM1317986", "GSM1317987", "GSM1317988", "GSM1317989", "GSM1317990", "GSM1317991", "GSM1317992", "GSM1317993", "GSM1317994", "GSM1317995", "GSM1317996", "GSM1317997", "GSM1317998", "GSM1317999", "GSM1318000", "GSM1318001", "GSM1318002", "GSM1318003", "GSM1318004", "GSM1318005", "GSM1318006", "GSM1318007", "GSM1318008", "GSM1318009", "GSM1318010", "GSM1318011", "GSM1318012", "GSM1318013", "GSM1318014", "GSM1318015", "GSM1318016", "GSM1318017", "GSM1318018", "GSM1318019", "GSM1318020", "GSM1318021", "GSM1318022", "GSM1318023", "GSM1318024", "GSM1318025", "GSM1318026", "GSM1318027", "GSM1318028", "GSM1318029", "GSM1318030", "GSM1318031", "GSM1318032", "GSM1318033", "GSM1318034", "GSM1318035", "GSM1318036", "GSM1318037", "GSM1318038", "GSM1318039", "GSM1318040", "GSM1318041", "GSM1318042", "GSM1318043", "GSM1318044", "GSM1318045", "GSM1318046", "GSM1318047", "GSM1318048", "GSM1318049", "GSM1318050", "GSM1318051", "GSM1318052", "GSM1318053", "GSM1318054", "GSM1318055", "GSM1318056", "GSM1318057", "GSM1318058"], "sample_count": 163, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Whole blood transcriptome of survivors and nonsurvivors of sepsis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE65682", "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=GSE65682", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65682", "version": null, "note": "We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1602801", "GSM1602802", "GSM1602803", "GSM1602804", "GSM1602805", "GSM1602806", "GSM1602807", "GSM1602808", "GSM1602809", "GSM1602810", "GSM1602811", "GSM1602812", "GSM1602813", "GSM1602814", "GSM1602815", "GSM1602816", "GSM1602817", "GSM1602818", "GSM1602819", "GSM1602820", "GSM1602821", "GSM1602822", "GSM1602823", "GSM1602824", "GSM1602825", "GSM1602826", "GSM1602827", "GSM1602828", "GSM1602829", "GSM1602830", "GSM1602831", "GSM1602832", "GSM1602833", "GSM1602834", "GSM1602835", "GSM1602836", "GSM1602837", "GSM1602838", "GSM1602839", "GSM1602840", "GSM1602841", "GSM1602842", "GSM1602843", "GSM1602844", "GSM1602845", "GSM1602846", "GSM1602847", "GSM1602848", "GSM1602849", "GSM1602850", "GSM1602851", "GSM1602852", "GSM1602853", 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Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1652818", "GSM1652819", "GSM1652820", "GSM1652821", "GSM1652822", "GSM1652823", "GSM1652824", "GSM1652825", "GSM1652826", "GSM1652827", "GSM1652828", "GSM1652829", "GSM1652830", "GSM1652831", "GSM1652832", "GSM1652833", "GSM1652834", "GSM1652835", "GSM1652836", "GSM1652837", "GSM1652838", "GSM1652839", "GSM1652840", "GSM1652841"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "16699", "taxon": "Homo sapiens", "title": "Septic shock in advanced age: Transcriptome analysis reveals altered molecular signatures in neutrophil granulocytes", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE69528", "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=GSE69528", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE69528", "version": null, "note": "We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1702888", "GSM1702889", "GSM1702890", "GSM1702891", "GSM1702892", "GSM1702893", "GSM1702894", "GSM1702895", "GSM1702896", "GSM1702897", "GSM1702898", "GSM1702899", "GSM1702900", "GSM1702901", "GSM1702902", "GSM1702903", "GSM1702904", "GSM1702905", "GSM1702906", "GSM1702907", "GSM1702908", "GSM1702909", "GSM1702910", "GSM1702911", "GSM1702912", "GSM1702913", "GSM1702914", "GSM1702915", "GSM1702916", "GSM1702917", "GSM1702918", "GSM1702919", "GSM1702920", "GSM1702921", "GSM1702922", "GSM1702923", "GSM1702924", "GSM1702925", "GSM1702926", "GSM1702927", "GSM1702928", "GSM1702929", "GSM1702930", "GSM1702931", "GSM1702932", "GSM1702933", "GSM1702934", "GSM1702935", "GSM1702936", "GSM1702937", "GSM1702938", "GSM1702939", "GSM1702940", "GSM1702941", "GSM1702942", "GSM1702943", "GSM1702944", "GSM1702945", "GSM1702946", "GSM1702947", "GSM1702948", "GSM1702949", "GSM1702950", "GSM1702951", "GSM1702952", "GSM1702953", "GSM1702954", "GSM1702955", "GSM1702956", "GSM1702957", "GSM1702958", "GSM1702959", "GSM1702960", "GSM1702961", "GSM1702962", "GSM1702963", "GSM1702964", "GSM1702965", "GSM1702966", "GSM1702967", "GSM1702968", "GSM1702969", "GSM1702970", "GSM1702971", "GSM1702972", "GSM1702973", "GSM1702974", "GSM1702975", "GSM1702976", "GSM1702977", "GSM1702978", "GSM1702979", "GSM1702980", "GSM1702981", "GSM1702982", "GSM1702983", "GSM1702984", "GSM1702985", "GSM1702986", "GSM1702987", "GSM1702988", "GSM1702989", "GSM1702990", "GSM1702991", "GSM1702992", "GSM1702993", "GSM1702994", "GSM1702995", "GSM1702996", "GSM1702997", "GSM1702998", "GSM1702999", "GSM1703000", "GSM1703001", "GSM1703002", "GSM1703003", "GSM1703004", "GSM1703005", "GSM1703006", "GSM1703007", "GSM1703008", "GSM1703009", "GSM1703010", "GSM1703011", "GSM1703012", "GSM1703013", "GSM1703014", "GSM1703015", "GSM1703016", "GSM1703017", "GSM1703018", "GSM1703019", "GSM1703020", "GSM1703021", "GSM1703022", "GSM1703023", "GSM1703024", "GSM1703025"], "sample_count": 138, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "A Blood Transcriptional Diagnostic Assay for Septicemic Melioidosis", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE95233", "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=GSE95233", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE95233", "version": null, "note": "We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2500349", "GSM2500350", "GSM2500351", "GSM2500352", "GSM2500353", "GSM2500354", "GSM2500355", "GSM2500356", "GSM2500357", "GSM2500358", "GSM2500359", "GSM2500360", "GSM2500361", "GSM2500362", "GSM2500363", "GSM2500364", "GSM2500365", "GSM2500366", "GSM2500367", "GSM2500368", "GSM2500369", "GSM2500370", "GSM2500371", "GSM2500372", "GSM2500373", "GSM2500374", "GSM2500375", "GSM2500376", "GSM2500377", "GSM2500378", "GSM2500379", "GSM2500380", "GSM2500381", "GSM2500382", "GSM2500383", "GSM2500384", "GSM2500385", "GSM2500386", "GSM2500387", "GSM2500388", "GSM2500389", "GSM2500390", "GSM2500391", "GSM2500392", "GSM2500393", "GSM2500394", "GSM2500395", "GSM2500396", "GSM2500397", "GSM2500398", "GSM2500399", "GSM2500400", "GSM2500401", "GSM2500402", "GSM2500403", "GSM2500404", "GSM2500405", "GSM2500406", "GSM2500407", "GSM2500408", "GSM2500409", "GSM2500410", "GSM2500411", "GSM2500412", "GSM2500413", "GSM2500414", "GSM2500415", "GSM2500416", "GSM2500417", "GSM2500418", "GSM2500419", "GSM2500420", "GSM2500421", "GSM2500422", "GSM2500423", "GSM2500424", "GSM2500425", "GSM2500426", "GSM2500427", "GSM2500428", "GSM2500429", "GSM2500430", "GSM2500431", "GSM2500432", "GSM2500433", "GSM2500434", "GSM2500435", "GSM2500436", "GSM2500437", "GSM2500438", "GSM2500439", "GSM2500440", "GSM2500441", "GSM2500442", "GSM2500443", "GSM2500444", "GSM2500445", "GSM2500446", "GSM2500447", "GSM2500448", "GSM2500449", "GSM2500450", "GSM2500451", "GSM2500452", "GSM2500453", "GSM2500454", "GSM2500455", "GSM2500456", "GSM2500457", "GSM2500458", "GSM2500459", "GSM2500460", "GSM2500461", "GSM2500462", "GSM2500463", "GSM2500464", "GSM2500465", "GSM2500466", "GSM2500467", "GSM2500468", "GSM2500469", "GSM2500470", "GSM2500471", "GSM2500472"], "sample_count": 124, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Fractalkine receptor CX3CR1 and leukocyte Ig-like receptor B2 LILRB2 are prognostic biomarkers in septic shock", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE28750 not downloaded", "asset:data:geo:GSE28750 licence not read", "asset:data:geo:GSE54514 not downloaded", "asset:data:geo:GSE54514 licence not read", "asset:data:geo:GSE65682 not downloaded", "asset:data:geo:GSE65682 licence not read", "asset:data:geo:GSE67652 not downloaded", "asset:data:geo:GSE67652 licence not read", "asset:data:geo:GSE69528 not downloaded", "asset:data:geo:GSE69528 licence not read", "asset:data:geo:GSE95233 not downloaded", "asset:data:geo:GSE95233 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Data extraction and analysis were performed by Graphpad Prism 9.0, with the logrank test for statistical evaluation, setting p < 0.05 as the threshold for significance."}}, {"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": 0.7, "band": "medium", "quote": "PPI"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE65682", "GSE28750", "GSE54514", "GSE67652", "GSE69528", "GSE95233"], "resolved_accessions": ["GSE65682", "GSE28750", "GSE54514", "GSE67652", "GSE69528", "GSE95233"], "statements": ["We intend to share individual deidentified participant data. Peripheral blood RNA sequencing data from 20 patients with sepsis and 10 NC are available in the China National GeneBank DataBase (CNGBdb) and can be found below: https://db.cngb.org/, under the accession: CNP0002611, you can access it now and it’s valid forever. Our study used six datasets (GSE65682, GSE95233, GSE28750, GSE54514, GSE67652, and GSE69528), with all RNA sequencing data and clinical information coming from the GEO database."], "basis": "The paper names GSE65682, GSE28750, GSE54514, GSE67652, GSE69528, GSE95233 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:38702721", "data:geo:GSE28750"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE28750"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:17:37Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10310, "completion_tokens": 2398, "cached_tokens": 256}}, "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:38702721", "type": "paper", "label": "pmid:38702721"}, {"id": "source:pmid:38702721", "type": "manuscript", "label": "PMID 38702721 full text"}, {"id": "data:geo:GSE28750", "type": "dataset", "label": "GEO GSE28750"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38702721", "type": "paper", "label": "pmid:38702721"}, {"id": "source:pmid:38702721", "type": "manuscript", "label": "PMID 38702721 full text"}, {"id": "data:geo:GSE28750", "type": "dataset", "label": "GEO GSE28750"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38702721", "type": "extraction", "used": ["source:pmid:38702721"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE28750", "type": "accession_resolution", "used": ["data:geo:GSE28750"], "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:38702721", "parent_hash": "sha256:ba55174ee837e4405d079d28fd540a2ab081ff827738b025d961e3ce331c38c9", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE28750 licence not read", "asset:data:geo:GSE28750 not downloaded", "asset:data:geo:GSE54514 licence not read", "asset:data:geo:GSE54514 not downloaded", "asset:data:geo:GSE65682 licence not read", "asset:data:geo:GSE65682 not downloaded", "asset:data:geo:GSE67652 licence not read", "asset:data:geo:GSE67652 not downloaded", "asset:data:geo:GSE69528 licence not read", "asset:data:geo:GSE69528 not downloaded", "asset:data:geo:GSE95233 licence not read", "asset:data:geo:GSE95233 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["10 healthy volunteers as a control group for RNA-seq. The RNA-seq data were utilized to identify", "lunteers as a control group for RNA-seq. The RNA-seq data were utilized to identify differentiall", "meta-analysis confirmed the accuracy of the RNA-seq data. Finally, we collected 5 blood samples", "group (P < 0.01). Additionally, single-cell RNA sequencing revealed predominant expression of these cor"], "order_basis": "paper_text_order:745", "id": "assay:1"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["o the normal group (P < 0.01). Additionally, single-cell RNA sequencing revealed predominant expression of these cor"], "order_basis": "paper_text_order:2555", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Data extraction and analysis were performed by Graphpad Prism 9.0, with the logrank test for statistical evaluation, setting p < 0.05 as the threshold for significance."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T00:47:27+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}}}