The immune-inflammation factor is associated with diabetic nephropathy: evidence from NHANES 2013-2018 and GEO database.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39085362", "kind": "science-record", "revision": 3, "content_hash": "sha256:2440a53a4a7ca04fcc8a158752ae05d610e05eb76b4cb2e5ed380c243d839802", "created_at": "2026-11-01T20:29:09Z", "updated_at": "2026-11-01T22:12:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The immune-inflammation factor is associated with diabetic nephropathy: evidence from NHANES 2013-2018 and GEO database.", "doi": "10.1038/s41598-024-68347-1", "pmid": "39085362", "authors": ["Yan Wang", "Shu-Yan Zhao", "Yong-Chun Wang", "Jia Xu", "Jie Wang"], "journal": "Scientific reports", "year": 2024, "abstract": "Diabetic nephropathy (DN) is a common secondary kidney disease. Immune and inflammatory responses play an influential role in the development of DN. This study aims to explore the role and mechanisms of immune- and inflammatory-related factors in DN. Participants from the NHANES 2013-2018 were included to evaluate the association between the SII and DN. Considering the skewed distribution of SII, log SII was used for subsequent analysis. Then, the DEGs were extracted from the GSE96804 dataset by the \"limma\" package of R, which were further screened out genes in the key module based on WGCNA. The intersection genes between DEGs and key module genes were the key genes for the following mechanism exploration. The CyTargetlinker plug-in of Cytoscape software was used to construct the drug-genes network. Molecular docking was used to calculate the binding affinity between potential drugs and the hub genes. Among the 8236 participants from NHANES 2013-2018, Log SII was significantly associated with DN (p < 0.05). DEG and WGCNA revealed 30 DN-related genes, which mainly regulated immune- and inflammation pathways, and the NOD-like receptor signaling pathway was the core pathway highly involved in the DN occurrence. Moreover, NAIP, ZFP36, and DUSP1 were identified as hub genes in DN progression and there was a strong binding interaction between resveratrol and DUSP1.In conclusion, immune inflammation plays an influential role in the occurrence and development of DN. SII is an effective diagnostic marker for DN and resveratrol might have potential value in treating DN.", "claims": [{"id": "claim-method", "statement": "The non-linear association between logSII and DN was investigated using the restricted cubic spline (RCS) analysis. Then, three generalized linear models were used to further evaluate the correlation between SII and DN.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39085362", "locator": "sections[17] \"Statistical analysis\" paragraph 2", "quote": "The non-linear association between logSII and DN was investigated using the restricted cubic spline (RCS) analysis. Then, three generalized linear models were used to further evaluate the correlation between SII and DN."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data and material supporting the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39085362", "locator": "sections[32] \"Data availability\" paragraph 2", "quote": "The data and material supporting the findings of this study are available from the corresponding author upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Higher log SII was independently associated with diabetic nephropathy.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "When all the covariates were adjusted in model 3, logSII was an independent predictor for DN (P < 0.05)."}, "evidence": [{"asset": "source:pmid:39085362", "locator": "sections[21] \"The association between Log SII and DN\" paragraph 4", "quote": "When all the covariates were adjusted in model 3, logSII was an independent predictor for DN (P < 0.05)."}, {"asset": "source:pmid:39085362", "locator": "sections[21] \"The association between Log SII and DN\" paragraph 4", "quote": "PAF analysis showed that 23.41% (16.18%-30.64%) of DN cases could be attributed to the increase in LogSII level (Table 3)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Higher log SII was independently associated with diabetic nephropathy.", "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:39085362"], "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:GSE137301"], "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:GSE137301"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39085362", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-024-68347-1", "sha256": "sha256:8b812231baa1e02aae288c9784ca6970a8fde5cf49de33b25131dd127d9a7cee", "bytes": 39266, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-024-68347-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11291652", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE137301", "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=GSE137301", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE137301", "version": null, "note": "The data and material supporting the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data and material supporting the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4074949", "GSM4074950", "GSM4074951", "GSM4074952", "GSM4074953", "GSM4074954", "GSM4074955", "GSM4074956", "GSM4074957", "GSM4074958", "GSM4074959", "GSM4074960", "GSM4074961", "GSM4074962", "GSM4074963", "GSM4074964", "GSM4074965", "GSM4074966", "GSM4074967", "GSM4074968", "GSM4074969", "GSM4074970", "GSM4074971", "GSM4074972", "GSM4074973", "GSM4074974"], "sample_count": 26, "group_sizes": null, "group_sizes_basis": null, "platform": "23159", "taxon": "Homo sapiens", "title": "Human Regulatory T cells from Umbilical Cord Blood Display Increased Repertoire Diversity and Lineage Stability Relative to Adult Peripheral Blood", "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:GSE137902", "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=GSE137902", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE137902", "version": null, "note": "The data and material supporting the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data and material supporting the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4092744", "GSM4092745", "GSM4092746", "GSM4092747", "GSM4092748", "GSM4092749", "GSM4092750", "GSM4092751", "GSM4092752", "GSM4092753", "GSM4092754", "GSM4092755", "GSM4092756", "GSM4092757", "GSM4092758"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "13667", "taxon": "Homo sapiens", "title": "Expression data from isolated endothelial cells from glioblastoma and normal brain cultured as monolayer on gelatin and on Matrigel", "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:GSE30528", "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=GSE30528", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30528", "version": null, "note": "The data and material supporting the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data and material supporting the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM756992", "GSM756993", "GSM756994", "GSM756995", "GSM756996", "GSM756997", "GSM756998", "GSM756999", "GSM757000", "GSM757001", "GSM757002", "GSM757003", "GSM757004", "GSM757005", "GSM757006", "GSM757007", "GSM757008", "GSM757009", "GSM757010", "GSM757011", "GSM757012", "GSM757013"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Transcriptome Analysis of Human Diabetic Kidney Disease (DKD Glomeruli vs. Control Glomeruli)", "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:GSE30529", "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=GSE30529", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30529", "version": null, "note": "The data and material supporting the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data and material supporting the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM757014", "GSM757015", "GSM757016", "GSM757017", "GSM757018", "GSM757019", "GSM757020", "GSM757021", "GSM757022", "GSM757023", "GSM757024", "GSM757025", "GSM757026", "GSM757027", "GSM757028", "GSM757029", "GSM757030", "GSM757031", "GSM757032", "GSM757033", "GSM757034", "GSM757035"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Transcriptome Analysis of Human Diabetic Kidney Disease (DKD Tubuli vs. Control Tubuli)", "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:GSE96804", "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=GSE96804", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE96804", "version": null, "note": "The data and material supporting the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data and material supporting the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2544275", "GSM2544276", "GSM2544277", "GSM2544278", "GSM2544279", "GSM2544280", "GSM2544281", "GSM2544282", "GSM2544283", "GSM2544284", "GSM2544285", "GSM2544286", "GSM2544287", "GSM2544288", "GSM2544289", "GSM2544290", "GSM2544291", "GSM2544292", "GSM2544293", "GSM2544294", "GSM2544295", "GSM2544296", "GSM2544297", "GSM2544298", "GSM2544299", "GSM2544300", "GSM2544301", "GSM2544302", "GSM2544303", "GSM2544304", "GSM2544305", "GSM2544306", "GSM2544307", "GSM2544308", "GSM2544309", "GSM2544310", "GSM2544311", "GSM2544312", "GSM2544313", "GSM2544314", "GSM2544315", "GSM2544316", "GSM2544317", "GSM2544318", "GSM2544319", "GSM2544320", "GSM2544321", "GSM2544322", "GSM2544323", "GSM2544324", "GSM2544325", "GSM2544326", "GSM2544327", "GSM2544328", "GSM2544329", "GSM2544330", "GSM2544331", "GSM2544332", "GSM2544333", "GSM2544334", "GSM2544335"], "sample_count": 61, "group_sizes": null, "group_sizes_basis": null, "platform": "17586", "taxon": "Homo sapiens", "title": "Exon Level Expression Profiling of Diabetic Nephropathy", "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:GSE137301 not downloaded", "asset:data:geo:GSE137301 licence not read", "asset:data:geo:GSE137902 not downloaded", "asset:data:geo:GSE137902 licence not read", "asset:data:geo:GSE30528 not downloaded", "asset:data:geo:GSE30528 licence not read", "asset:data:geo:GSE30529 not downloaded", "asset:data:geo:GSE30529 licence not read", "asset:data:geo:GSE96804 not downloaded", "asset:data:geo:GSE96804 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": "Principal Component Analysis"}}, {"id": "method-2", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-3", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi-square"}}, {"id": "method-4", "family": null, "specific": null, "label": "Restricted cubic spline analysis and three generalized linear models", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The non-linear association between logSII and DN was investigated using the restricted cubic spline (RCS) analysis. Then, three generalized linear models were used to further evaluate the correlation between SII and DN."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "chi_square_test", "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": ["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": ["pca_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca."}, "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": ["GSE96804", "GSE30528", "GSE30529", "GSE137902", "GSE137301"], "resolved_accessions": ["GSE96804", "GSE30528", "GSE30529", "GSE137902", "GSE137301"], "statements": ["The data and material supporting the findings of this study are available from the corresponding author upon request."], "basis": "The paper names GSE96804, GSE30528, GSE30529, GSE137902, GSE137301 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pca_fit"], "assets": ["source:pmid:39085362", "data:geo:GSE137301"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE137301"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:26:02Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12039, "completion_tokens": 2715, "cached_tokens": 0}}, "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:39085362", "type": "paper", "label": "pmid:39085362"}, {"id": "source:pmid:39085362", "type": "manuscript", "label": "PMID 39085362 full text"}, {"id": "data:geo:GSE137301", "type": "dataset", "label": "GEO GSE137301"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39085362", "type": "paper", "label": "pmid:39085362"}, {"id": "source:pmid:39085362", "type": "manuscript", "label": "PMID 39085362 full text"}, {"id": "data:geo:GSE137301", "type": "dataset", "label": "GEO GSE137301"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39085362", "type": "extraction", "used": ["source:pmid:39085362"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE137301", "type": "accession_resolution", "used": ["data:geo:GSE137301"], "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:39085362", "parent_hash": "sha256:81a0f88301cc7ee48529b8ae899dfa08a47bf06d6c333f80445e849afc75e37f", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE137301 licence not read", "asset:data:geo:GSE137301 not downloaded", "asset:data:geo:GSE137902 licence not read", "asset:data:geo:GSE137902 not downloaded", "asset:data:geo:GSE30528 licence not read", "asset:data:geo:GSE30528 not downloaded", "asset:data:geo:GSE30529 licence not read", "asset:data:geo:GSE30529 not downloaded", "asset:data:geo:GSE96804 licence not read", "asset:data:geo:GSE96804 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Principal Component Analysis"], "order_basis": "analysis_only", "id": "assay:1"}]}