Risk factors and predictors of urogenous sepsis after percutaneous nephrolithotomy for idiopathic calcium oxalate nephrolithiasis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37426597", "kind": "science-record", "revision": 4, "content_hash": "sha256:a53a2960c84924fabf9a3e8e129ecd86553f387bf869ddfd31baf526ad408ad0", "created_at": "2026-11-01T19:02:11Z", "updated_at": "2026-11-01T22:52:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Risk factors and predictors of urogenous sepsis after percutaneous nephrolithotomy for idiopathic calcium oxalate nephrolithiasis.", "doi": "10.21037/tau-23-219", "pmid": "37426597", "authors": ["Xinfeng Chen", "Siqi Li", "Chunmei Shi", "Wei Zhang", "Zhenmin Liu", "Jie Jiang", "Yong Zhang", "Zhan Chen", "Bing Zheng", "Hua Zhu"], "journal": "Translational andrology and urology", "year": 2023, "abstract": "Background: The aim of this study was to use bioinformatics approaches to screen and identify the key genes of idiopathic calcium oxalate nephrolithiasis, and explore its potential molecular mechanism.\nMethods: The GSE73680 kidney stone data set was downloaded from the Gene Expression Omnibus (GEO). R software (The R Foundation for Statistical Computing) was used to screen differentially expressed genes. GeneMANIA and Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) databases were used to analyze related genes interacting with crucial genes, and a protein-protein interaction (PPI) network was constructed. The differential genes were then subjected to the Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment analysis using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database. The clinical data of 156 patients who received percutaneous nephrolithotomy (PCNL) therapy at our facility between January 2013 and December 2017 were retrospectively analyzed. The various parameters associated with postoperative urogenous sepsis were identified using multivariable logistic regression analysis.\nResults: The study discovered one differentially expressed gene was nucleotide-binding oligomerization domain-containing protein 2 (NOD2). GO and KEGG analysis showed that NOD2 might affect the occurrence of idiopathic calcium oxalate kidney stones by affecting inflammation, receptor expression, immune environment, necrosis, apoptosis, and other pathways. The clinical parameter of patients who participated in the study, including preoperative urinary white blood cell (WBC) count, preoperative urinary nitrite, stone diameter, operation time, WBC count, and WBC D values, were statistically different between the systemic inflammatory response syndrome (SIRS) group and the urosepsis group. According to multivariate logistic regression analysis, the preoperative urine nitrite, calculus diameter, blood WBC, and NOD2 expression 3 hours after surgery were all independently associated with the urosepsis development.\nConclusions: Preoperative urinary nitrite positive status, postoperative WBC count ≥2.98×109/L 3 hours after operation, stone diameter >6 cm, and low expression of NOD2 in renal papillary tissue are more likely to cause the urinary source of idiopathic calcium oxalate nephrolithiasis after PCNL urogenous sepsis. These parameters also offer a viable treatment paradigm for the perioperative management of PCNL in treating idiopathic calcium oxalate kidney stones.", "claims": [{"id": "claim-method", "statement": "The R package “limma” (https://www.r-project.org/)was used to find the differentially expressed genes in the processed GSE73680 data set, with P<0.01 and |log2 fold change (FC)|>1 as the screening conditions.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37426597", "locator": "sections[5] \"Differentially expressed gene screening\" paragraph 2", "quote": "The R package “limma” (https://www.r-project.org/)was used to find the differentially expressed genes in the processed GSE73680 data set, with P<0.01 and |log2 fold change (FC)|>1 as the screening conditions."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Sharing Statement: Available at https://tau.amegroups.com/article/view/10.21037/tau-23-219/dss", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37426597", "locator": "sections[24] \"(untitled)\" paragraph 1", "quote": "Data Sharing Statement: Available at https://tau.amegroups.com/article/view/10.21037/tau-23-219/dss"}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified NOD2 as a differentially expressed gene and found that preoperative urinary nitrite, calculus diameter, 3-hour postoperative blood WBC count, and NOD2 expression were independently associated with postoperative urosepsis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37426597", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The study discovered one differentially expressed gene was nucleotide-binding oligomerization domain-containing protein 2 (NOD2)."}, {"asset": "source:pmid:37426597", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "According to multivariate logistic regression analysis, the preoperative urine nitrite, calculus diameter, blood WBC, and NOD2 expression 3 hours after surgery were all independently associated with the urosepsis development."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified NOD2 as a differentially expressed gene and found that preoperative urinary nitrite, calculus diameter, 3-hour postoperative blood WBC count, and NOD2 expression were independently associated with postoperative urosepsis.", "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:37426597"], "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. 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