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Zhou P, Ye L, Li S. Liver Fibrosis Scores as Predictors of Blood-Culture-Positive and Sepsis in Patients with Klebsiella pneumoniae Liver Abscess. Infect Drug Resist 2024; 17:3037-3045. [PMID: 39050840 PMCID: PMC11268646 DOI: 10.2147/idr.s470255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
Objective Klebsiella pneumoniae liver abscess (KPLA) is an invasive infectious disease with a considerable prevalence and complications. This study aimed to determine the predicted value of aspartate aminotransferase-to-platelet ratio index (APRI) and fibrosis-4 index (FIB-4) for positive blood cultures and sepsis in patients with KPLA. Methods We evaluated 248 consecutive participants diagnosed with KPLA. Demographic characteristics, clinical features, and laboratory test results of the participants were recorded. Multivariate logistic regression analysis was performed to identify the risk factors. Receiver operating characteristic (ROC) analyses were conducted to evaluate the discriminatory ability of APRI and FIB-4. Results 30.2% (75 of 248) KPLA patients presented with positive blood cultures, and 70 (28.2%) developed sepsis. Among the positive blood culture and sepsis groups, the APRI and FIB-4 showed statistically significant increases. Multivariate analysis showed that APRI (odds ratio [OR] = 1.190, 95% confidence interval [CI] 1.051-1.347, p = 0.006) and FIB-4 (OR = 1.110, 95% CI 1.046-1.179, p = 0.001) were independent prognostic factors for positive blood cultures. Both APRI (OR = 1.505, 95% CI 1.149-1.988, p = 0.004) and FIB-4 (OR = 1.187, 95% CI 1.054-1.336, p = 0.005) were independent risk factors for sepsis. The area under the ROC curve (AUC) of APRI and FIB-4 for predicting positive blood cultures of KPLA was 0.783 and 0.766, respectively. APRI had an AUC of 0.801, with a sensitivity and specificity of 71.4% and 81.5%, respectively, for predicting sepsis in patients with KPLA, and the prediction performance of APRI was better than that of FIB-4 (AUC = 0.798). Conclusion In our study, APRI and FIB-4 are effective methods for predicting KPLA patients with positive blood cultures and sepsis.
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Affiliation(s)
- Peng Zhou
- Department of Pharmacy, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of China
| | - Lingling Ye
- Department of Science and Education, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Taizhou, Zhejiang, People’s Republic of China
| | - Shixiao Li
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, People’s Republic of China
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2
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Yi X, Jin D, Huang S, Xie Z, Zheng M, Zhou F, Jin Y. Association between lactate-to-albumin ratio and 28-days all-cause mortality in patients with sepsis-associated liver injury: a retrospective cohort study. BMC Infect Dis 2024; 24:65. [PMID: 38195421 PMCID: PMC10775525 DOI: 10.1186/s12879-024-08978-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 01/02/2024] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND The mortality rate of sepsis-associated liver injury (SALI) is relatively high, but there is currently no authoritative prognostic criterion for the outcome of SALI. Meanwhile, lactate-to-albumin ratio (LAR) has been confirmed to be associated with mortality rates in conditions such as sepsis, heart failure, and respiratory failure. However, there is a scarcity of research reporting on the association between LAR and SALI. This study aimed to elucidate the association between LAR and the 28-day mortality rate of SALI. METHODS In this retrospective cohort study, data were obtained from the Medical Information Mart for Intensive Care IV (v2.2). Adult patients with SALI were admitted to the intensive care unit in this study. The LAR level at admission was included, and the primary aim was to assess the relationship between the LAR and 28-day all-cause mortality. RESULTS A total of 341 patients with SALI (SALI) were screened. They were divided into a survival group (241) and a non-survival group (100), and the 28-day mortality rate was 29.3%. Multivariable Cox regression analysis revealed that for every 1-unit increase in LAR, the 28-day mortality risk for SALI patients increased by 21%, with an HR of 1.21 (95% CI 1.11 ~ 1.31, p < 0.001). CONCLUSIONS This study indicates that in patients with SALI, a higher LAR is associated with an increased risk of all-cause mortality within 28 days of admission. This suggests that LAR may serve as an independent risk factor for adverse outcomes in SALI patients.
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Affiliation(s)
- Xiaona Yi
- Department of Critical Care Medicine, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China
| | - Dongcai Jin
- Department of Critical Care Medicine, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China
| | - Shanshan Huang
- Department of Critical Care Medicine, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China
| | - Zhenye Xie
- Department of Critical Care Medicine, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China
| | - Meixia Zheng
- Department of Critical Care Medicine, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China
| | - Fen Zhou
- Department of Critical Care Medicine, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China
| | - Yuhong Jin
- Department of Critical Care Medicine, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, China.
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3
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He S, Han Q, Wang X, Zhang X, Li N, Liu Z. Aspartate aminotransferase to platelet ratio at admission can predict the prognosis of patients with hemorrhagic fever with renal syndrome. J Med Virol 2023; 95:e29126. [PMID: 37786231 DOI: 10.1002/jmv.29126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/30/2023] [Accepted: 09/05/2023] [Indexed: 10/04/2023]
Abstract
Early indicators are needed to predict the prognosis of patients with hemorrhagic fever with renal syndrome (HFRS). Aspartate aminotransferase to platelet ratio index (APRI) has been shown to be related to mortality risk of patients with various diseases. This study evaluated the prognostic value of APRI and other inflammatory scores in HFRS patients. Data of hospitalized HFRS patients from a tertiary hospital in northwest China were collected and the inflammatory scores such as APRI and neutrophil to lymphocyte count ratio (NLR) were calculated at the day of patient admission. Independent factors related to the survival of patients were determined by multivariate logistic regression. Receiver operating characteristic curve was used to analyze the predictive value, and area under the curve (AUC) and 95% confidence interval (CI) were calculated for quantification. Of the 317 HFRS patients included in study, 15 patients died. Age (OR: 1.10, 95% CI: 1.04-1.16, p = 0.001), NLR (OR: 1.11, 95% CI: 1.02-1.19, p = 0.01), and APRI (OR: 1.06, 95% CI: 1.03-1.10, p = 0.001) were quantitative objective factors independently associated with the survival of patients. APRI had an AUC of 0.95 (95% CI: 0.91-1.00, p < 0.001) for predicting the prognosis of patients, with a sensitivity of 93.3% and a specificity of 86.8%. The performance of APRI was better than that of age or NLR. Patients with an APRI ≥ 6.15 had significantly decreased survival compared with those with an APRI < 6.15. In conclusion, this simple index APRI calculated at admission can serve as a biomarker to identify HFRS patients at risk of poor prognosis.
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Affiliation(s)
- Shan He
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Postgraduate Department, Xi'an Medical University, Xi'an, Shaanxi, China
| | - Qunying Han
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaoyun Wang
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaoge Zhang
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Na Li
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhengwen Liu
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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Development of a nomogram for predicting 90-day mortality in patients with sepsis-associated liver injury. Sci Rep 2023; 13:3662. [PMID: 36871054 PMCID: PMC9985651 DOI: 10.1038/s41598-023-30235-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
The high mortality rate in sepsis patients is related to sepsis-associated liver injury (SALI). We sought to develop an accurate forecasting nomogram to estimate individual 90-day mortality in SALI patients. Data from 34,329 patients were extracted from the public Medical Information Mart for Intensive Care (MIMIC-IV) database. SALI was defined by total bilirubin (TBIL) > 2 mg/dL and the occurrence of an international normalized ratio (INR) > 1.5 in the presence of sepsis. Logistic regression analysis was performed to establish a prediction model called the nomogram based on the training set (n = 727), which was subsequently subjected to internal validation. Multivariate logistic regression analysis showed that SALI was an independent risk factor for mortality in patients with sepsis. The Kaplan‒Meier curves for 90-day survival were different between the SALI and non-SALI groups after propensity score matching (PSM) (log rank: P < 0.001 versus P = 0.038), regardless of PSM balance. The nomogram demonstrated better discrimination than the sequential organ failure assessment (SOFA) score, logistic organ dysfunction system (LODS) score, simplified acute physiology II (SAPS II) score, and Albumin-Bilirubin (ALBI) score in the training and validation sets, with areas under the receiver operating characteristic curve (AUROC) of 0.778 (95% CI 0.730-0.799, P < 0.001) and 0.804 (95% CI 0.713-0.820, P < 0.001), respectively. The calibration plot showed that the nomogram was sufficiently successful to predict the probability of 90-day mortality in both groups. The DCA of the nomogram demonstrated a higher net benefit regarding clinical usefulness than SOFA, LODS, SAPSII, and ALBI scores in the two groups. The nomogram performs exceptionally well in predicting the 90-day mortality rate in SALI patients, which can be used to assess the prognosis of patients with SALI and may assist in guiding clinical practice to enhance patient outcomes.
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Miao H, Cui Z, Guo Z, Chen Q, Su W, Sun Y, Sun M, Ma X, Ding R. IDENTIFICATION OF SUBPHENOTYPES OF SEPSIS-ASSOCIATED LIVER DYSFUNCTION USING CLUSTER ANALYSIS. Shock 2023; 59:368-374. [PMID: 36562264 DOI: 10.1097/shk.0000000000002068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
ABSTRACT Objectives: We attempted to identify and validate the subphenotypes of sepsis-associated liver dysfunction (SALD) using routine clinical information. Design: This article is a retrospective observational cohort study. Setting: We used the Medical Information Mart for Intensive Care IV database and the eICU Collaborative Research Database. Patients: We included adult patients (age ≥18 years) who developed SALD within the first 48 hours of intensive care unit (ICU) admission. We excluded patients who died or were discharged from the ICU within the first 48 hours of admission. Patients with abnormal liver function before ICU admission were also excluded. Measurements and Main Results: Patients in the MIMIC-IV 1.0 database served as a derivation cohort. Patients in the eICU database were used as validation cohort. We identified four subphenotypes of SALD (subphenotype α, β, γ, δ) using K-means cluster analysis in 5234 patients in derivation cohort. The baseline characteristics and clinical outcomes were compared between the phenotypes using one-way analysis of variance/Kruskal-Wallis test and the χ 2 test. Moreover, we used line charts to illustrate the trend of liver function parameters over 14 days after ICU admission. Subphenotype α (n = 1,055) was the most severe cluster, characterized by shock with multiple organ dysfunction (MODS) group. Subphenotype β (n = 1,179) had the highest median bilirubin level and the highest proportion of patients with underlying liver disease and coexisting coagulopathy (increased bilirubin group). Subphenotype γ (n = 1,661) was the cluster with the highest mean age and had the highest proportion of patients with chronic kidney disease (aged group). Subphenotype δ (n = 1,683) had the lowest 28-day and in-hospital mortality (mild group). The characteristics of clusters in the validation cohort were similar to those in the derivation cohort. In addition, we were surprised to find that GGT levels in subphenotype δ were significantly higher than in other subphenotypes, showing a different pattern from bilirubin. Conclusions: We identified four subphenotypes of SALD that presented with different clinical features and outcomes. These results can provide a valuable reference for understanding the clinical characteristics and associated outcomes to improve the management of patients with SALD in the ICU.
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Affiliation(s)
- He Miao
- Department of Intensive Care Unit, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Zhigang Cui
- School of Nursing, China Medical University, Shenyang, Liaoning Province, China
| | - Zhaotian Guo
- Department of Intensive Care Unit, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Qianhui Chen
- Department of Intensive Care Unit, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Wantin Su
- Department of Intensive Care Unit, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Yongqiang Sun
- Neusoft Corporation, Shenyang, Liaoning Province, China
| | - Mu Sun
- Neusoft Corporation, Shenyang, Liaoning Province, China
| | - Xiaochun Ma
- Department of Intensive Care Unit, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Renyu Ding
- Department of Intensive Care Unit, The First Hospital of China Medical University, Shenyang, Liaoning Province, China
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Xie T, Xin Q, Cao X, Chen R, Ren H, Liu C, Zhang J. Clinical characteristics and construction of a predictive model for patients with sepsis related liver injury. Clin Chim Acta 2022; 537:80-86. [DOI: 10.1016/j.cca.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/25/2022] [Accepted: 10/07/2022] [Indexed: 11/03/2022]
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7
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Matouk AI, El-Daly M, Habib HA, Senousy S, Naguib Abdel Hafez SM, Kasem AW, Almalki WH, Alzahrani A, Alshehri A, Ahmed ASF. Protective effects of menthol against sepsis-induced hepatic injury: Role of mediators of hepatic inflammation, apoptosis, and regeneration. Front Pharmacol 2022; 13:952337. [PMID: 36120368 PMCID: PMC9476320 DOI: 10.3389/fphar.2022.952337] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 11/22/2022] Open
Abstract
Liver dysfunction in sepsis is a major complication that amplifies multiple organ failure and increases the risk of death. Inflammation and oxidative stress are the main mediators in the pathophysiology of sepsis. Therefore, we investigated the role of menthol, a natural antioxidant, against sepsis-induced liver injury in female Wistar rats. Sepsis was induced by cecal ligation and puncture (CLP). Menthol (100 mg/kg) was given intragastric 2 h after CLP. Blood samples and liver tissues were collected 24 h after surgery. Menthol significantly (p < 0.05) attenuated the sepsis-induced elevation in serum liver enzymes and improved the hepatic histopathological changes. Menthol treatment significantly (p < 0.05) decreased hepatic levels of tumor necrosis factor-alpha, malondialdehyde, total nitrite, and cleaved caspase-3. It restored the hepatic levels of superoxide dismutase and reduced glutathione. Additionally, menthol significantly (p < 0.05) increased hepatic levels of B-cell lymphoma 2 (Bcl-2); an anti-apoptotic factor, and proliferating cell nuclear antigen (PCNA), a biomarker of regeneration and survival. Our results showed the therapeutic potential of menthol against liver injury induced by sepsis.
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Affiliation(s)
- Asmaa I. Matouk
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Minia University, Minya, Egypt
| | - Mahmoud El-Daly
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Minia University, Minya, Egypt
| | - Heba A. Habib
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Minia University, Minya, Egypt
| | - Shaymaa Senousy
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Minia University, Minya, Egypt
| | | | - AlShaimaa W. Kasem
- Department of Histology and Cell Biology, Faculty of Medicine, Minia University, Minya, Egypt
| | - Waleed Hassan Almalki
- Department of Pharmacology and Toxicology, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Abdulaziz Alzahrani
- Department of Pharmacology and Toxicology, College of Clinical Pharmacy, AlBaha University, Al Bahah, Saudi Arabia
| | - Ahmed Alshehri
- Department of Pharmacology and Toxicology, College of Clinical Pharmacy, AlBaha University, Al Bahah, Saudi Arabia
| | - Al-Shaimaa F. Ahmed
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Minia University, Minya, Egypt
- *Correspondence: Al-Shaimaa F. Ahmed,
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Incidence, predictors and outcome of sepsis-associated liver injury in children: a prospective observational study. Eur J Pediatr 2022; 181:1699-1707. [PMID: 35020050 PMCID: PMC8753337 DOI: 10.1007/s00431-022-04374-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 01/17/2023]
Abstract
Sepsis-associated liver injury (SALI) occurs as a result of the systemic and microcirculatory changes that happen because of sepsis. Its prognostic significance in the paediatric population is unclear. We enrolled all children < 19 years, admitted between July, 2020 and July, 2021 to the paediatric unit (ward or intensive care unit) with a diagnosis of sepsis for this study. Clinical and biochemical parameters of children with sepsis who developed SALI were compared with those without SALI to determine the risk factors of SALI and its impact on in-hospital mortality. A total of 127 children, median age 72 (1-204) months, 74 males were included. SALI developed in 45 (31.3%) at a median 1 (1-13) days after the diagnosis of sepsis. The SALI pattern was cholestatic in 18 (40%), hepatocellular in 17 (37.7%) and hypoxic hepatitis in 10 (22.3%). Paediatric sequential organ failure assessment (pSOFA) was an independent predictor of SALI - OR 1.17 (95% CI 1.067-1.302), p = 0.001. A pSOFA score of > 9.5 predicted the development of SALI with 66.7% sensitivity and 77.1% specificity. SALI was an independent predictor of mortality in children with sepsis - OR 1.9 (95% CI 1.3-3.4), p = 0.01. Conclusions: SALI develops in 45 (31.3%) with sepsis. A higher pSOFA score is associated with SALI. Children who develop SALI have a ~ twofold higher risk of mortality than those without SALI. What is Known: • During the process of sepsis, the liver plays a role by scavenging bacteria and producing inflammatory mediators. However, at times the liver itself becomes a target of the dysregulated inflammatory response. This is known as sepsis-associated liver injury (SALI). • The incidence of sepsis-associated liver injury and its prognostic significance in children is not known.. What is New: • SALI develops in one-third children with sepsis and is associated with a higher pSOFA score. • Children who develop SALI have a higher risk of mortality.
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TLR4-NLRP3-GSDMD-Mediated Pyroptosis Plays an Important Role in Aggravated Liver Injury of CD38 -/- Sepsis Mice. J Immunol Res 2021; 2021:6687555. [PMID: 33860064 PMCID: PMC8026301 DOI: 10.1155/2021/6687555] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/21/2021] [Accepted: 03/05/2021] [Indexed: 02/08/2023] Open
Abstract
Clinically, severe bacterial infection can cause septicemia and multiple organ dysfunction syndrome, especially liver injury. CD38 is closely related to many inflammatory pathways, but its role in liver injury caused by bacterial infection remains unclear. The purpose of this study is to discuss the specific role of CD38 in bacterial liver injury. Eight-week-old male C57BL/6 mice (WT, CD38−/− and CD38−/−TLR4mut) were used and stimulated with Escherichia coli (ATCC25922) or PBS, intraperitoneally. After 3 hours of bacterial stimulation, serum was collected to detect ALT and AST concentration, and liver tissue was harvested for hematoxylin and eosin staining and bacterial culture. The mRNA expressions of TLR4, NLRP3, IL-1β, IL-18, and GSDMD were quantitatively determined by RT-qPCR. The expressions of TLR4, MyD88, TRIF, NF-κB p65, NLRP3, GSDMD, and cytokines were detected by Western blot. The expression and localization of ERK1/2 were detected by immunohistochemistry and Western blot. The results showed that bacterial stimulation could upregulate the expression of inflammatory cytokines, leading to hepatic dysfunction. Moreover, bacterial stimulation of CD38-deficient mice can aggravate the inflammatory response, the expressions of TLR4, NF-κB, and ERK1/2 were significantly increased, and the biomarkers related to pyroptosis also manifested more obvious pyroptosis. However, TLR4 mutation significantly alleviated inflammation and pyroptosis in the liver caused by bacteria, on the basis of CD38 deficiency. Overall, CD38 knockout exacerbates bacteria-induced liver damage through TLR4-NLRP3-GSDMD-mediated pyroptosis.
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10
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Shakur AH, Huang S, Qian X, Chang X. SURVFIT: Doubly sparse rule learning for survival data. J Biomed Inform 2021; 117:103691. [PMID: 33610882 DOI: 10.1016/j.jbi.2021.103691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 12/16/2020] [Accepted: 01/12/2021] [Indexed: 10/22/2022]
Abstract
Survival data analysis has been leveraged in medical research to study disease morbidity and mortality, and to discover significant bio-markers affecting them. A crucial objective in studying high dimensional medical data is the development of inherently interpretable models that can efficiently capture sparse underlying signals while retaining a high predictive accuracy. Recently developed rule ensemble models have been shown to effectively accomplish this objective; however, they are computationally expensive when applied to survival data and do not account for sparsity in the number of variables included in the generated rules. To address these gaps, we present SURVFIT, a "doubly sparse" rule extraction formulation for survival data. This doubly sparse method can induce sparsity both in the number of rules and in the number of variables involved in the rules. Our method has the computational efficiency needed to realistically solve the problem of rule-extraction from survival data if we consider both rule sparsity and variable sparsity, by adopting a quadratic loss function with an overlapping group regularization. Further, a systematic rule evaluation framework that includes statistical testing, decomposition analysis and sensitivity analysis is provided. We demonstrate the utility of SURVFIT via experiments carried out on a synthetic dataset and a sepsis survival dataset from MIMIC-III.
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Affiliation(s)
- Ameer Hamza Shakur
- Industrial and Systems Engineering, University of Washington, Seattle, United States.
| | - Shuai Huang
- Industrial and Systems Engineering, University of Washington, Seattle, United States.
| | - Xiaoning Qian
- Electrical and Computer Engineering, Texas A&M University, United States.
| | - Xiangyu Chang
- School of Management, Xi'an Jiaotong University, China.
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11
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Sun X, Dai Y, Tan G, Liu Y, Li N. Integration Analysis of m 6A-SNPs and eQTLs Associated With Sepsis Reveals Platelet Degranulation and Staphylococcus aureus Infection are Mediated by m 6A mRNA Methylation. Front Genet 2020; 11:7. [PMID: 32174955 PMCID: PMC7054457 DOI: 10.3389/fgene.2020.00007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/06/2020] [Indexed: 12/22/2022] Open
Abstract
Sepsis is a major threat with high mortality rate for critically ill patients. Response to pathogen infection by the host immune system is a key biological process involved in the onset and development of sepsis. Heterogeneous host genome variation, especially single nucleotide polymorphisms (SNPs), has long been suggested to contribute to differences in disease progression. However, the function of SNPs located in non-coding regions remains to be elucidated. Recently, m6A mRNA modification levels were revealed to differ at SNPs. As m6A is a crucial regulator of gene expression, these SNPs might control genes by changing the m6A level on mRNA. To investigate the potential role of m6A SNPs in sepsis, we integrated m6A-SNP and expression quantitative trait loci (eQTLs) data. Analysis revealed 15,720 m6A-cis-eQTLs and 381 m6A-trans-eQTLs associated with sepsis. We identified 1321 genes as locations of m6A-cis-eQTLs. These were enriched in platelet degranulation and Staphylococcus aureus infection pathways, which are vital for the pathophysiological process of sepsis. We conclude that m6A modification of mRNA plays a very important role in sepsis, with m6A-cis-eQTLs potentially having the most effect on individual variation in sepsis progression.
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Affiliation(s)
- Xuri Sun
- Department of Critical Care Medicine, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China.,Respiratory Medicine Center of Fujian Province, Quanzhou, China
| | - Yishuang Dai
- Department of Outpatient operating room, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Guoliang Tan
- Department of Critical Care Medicine, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China.,Respiratory Medicine Center of Fujian Province, Quanzhou, China
| | - Yuqi Liu
- Department of Critical Care Medicine, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China.,Respiratory Medicine Center of Fujian Province, Quanzhou, China
| | - Neng Li
- Department of Pathogenic Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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