scholarly journals Septicemic Melioidosis Detection Using Support Vector Machine with Five Immune Cell Types

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Ke Xu ◽  
Fang Lian ◽  
Yunfan Quan ◽  
Jun Liu ◽  
Li Yin ◽  
...  

Melioidosis, caused by Burkholderia pseudomallei (B. pseudomallei), predominantly occurs in the tropical regions. Of various types of melioidosis, septicemic melioidosis is the most lethal one with a mortality rate of 40%. Early detection of the disease is paramount for the better chances of cure. In this study, we developed a novel approach for septicemic melioidosis detection, using a machine learning technique—support vector machine (SVM). Several SVM models were built, and 19 features characterized by the corresponding immune cell types were generated by Cell type Identification Estimating Relative Subsets Of RNA Transcripts (CIBERSORT). Using these features, we trained a binomial SVM model on the training set and evaluated it on the independent testing set. Our findings indicated that this model performed well with means of sensitivity and specificity up to 0.962 and 0.979, respectively. Meanwhile, the receiver operating characteristic (ROC) curve analysis gave area under curves (AUCs) ranging from 0.952 to 1.000. Furthermore, we found that a concise SVM model, built upon a combination of CD8+ T cells, resting CD4+ memory T cells, monocytes, M2 macrophages, and activated mast cells, worked perfectly on the detection of septicemic melioidosis. Our data showed that its mean of sensitivity was up to 0.976 while that of specificity up to 0.993. In addition, the ROC curve analysis gave AUC close to 1.000. Taken together, this SVM model is a robust classification tool and may serve as a complementary diagnostic technique to septicemic melioidosis.

2021 ◽  
Author(s):  
Zhijian Wang ◽  
Xuenuo Chen ◽  
Zheng Jiang

Abstract Background: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with a dismal prognosis according to updated statistics. At present, there are many deficiencies in targeted therapy for liver cancer. The solute carrier family 17 member 2 (SLC17A2) has not been studied in liver cancer, therefore, we evaluate the role of SLC17A2 in HCC by bioinformatics analysis.Methods: The expression level of SLC17A2 in HCC, the clinicopathological data were analyzed based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database, the SLC17A2 protein expression was validated by immunohistochemical staining. Besides, the Kaplan–Meier plotter database and receiver operating characteristic (ROC) curve analysis were used to explore the prognostic significance. The biological analyses of SLC17A2 were performed using the gene set enrichment analysis (GSEA). Finally, Tumor Immune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis (GEPIA) databases were used to explore the relationship between immune cell infiltration, immune cell markers and SLC17A2 in HCC.Results: The multivariate Cox regression analysis showed that SLC17A2 expression was low in HCC (P < 0.05), and closely related to the clinical stage of HCC. Besides, SLC17A2 had certain prognostic and diagnostic value in HCC according to ROC curve analysis. Further biological analyses showed that SLC17A2 can regulate fatty acid metabolism, amino acid metabolism and cytochrome P450-related metabolism and is closely related to the peroxisome pathway. Notably, we found that SLC17A2 expression was positively correlated with the infiltration levels of CD4 + T cells, naive CD8+ T cells, naive B cells, negatively associated with the levels of regulatory T cells and closely correlated with most immune cell markers in HCC.Conclusion: SLC17A2 expression is low in HCC and correlates with immune infiltration; thus, it could serve as an independent prognostic factor for HCC.


2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1313.2-1313
Author(s):  
R. Shumnalieva ◽  
D. Kachakova ◽  
T. Velikova ◽  
R. Kaneva ◽  
Z. Kolarov ◽  
...  

Background:Interleukin 17 (IL-17) is a proinflammatory cytokine, which overproduction promotes the autoimmune reaction in rheumatoid arthritis (RA). Posttranscriptional regulation of IL-17 by specific microRNAs (miRNAs) is of great interest in the recent years. 146a was associated with IL-17 expression in IL-17 producing T-cells in the synovium when miR-155 enhanced Treg and Th17 cells differentiation and IL-17A production by directly targeting the suppressor of cytokine signaling (SOCS) 1 [1, 2]. It has been shown that IL-17 production in lymphocytes or its function could be regulated by miR-223 by targeting Roquin ubiquitin ligase or its receptors [3].Objectives:To examine a possible correlation between systemic and local concentrations of IL-17A and systemic and local miR-146a, miR-155 and miR-223 expression in RA patients.Methods:Expression levels of three miRNAs were determined in matched peripheral blood (PB) and synovial fluid (SF) samples of RA patients by relative quantitation method 2-ΔΔCt. As reference control for normalization RNU6B gene was used. Concentrations of IL-17A were compared between matched serum and SF samples from 20 RA patients by Human IL-17A ELISA kit (Gene probe, Diaclone, France). Healthy donors were used as controls.Results:miR-146a, miR-155 and miR-223 showed overexpression in RA SF when compared to HCs SF (in 70.83%, p=0.007; in 79.17%, p=1.63x10-4and in 79.17%, p=1.64x10-3, respectively). The ROC curve analysis showed diagnostic accuracy for miR-146a in SF with AUC=0.769, p=0.006, AUC for SF miR-155 was 0.858, p=2.3x10-4and AUC for SF miR-223 was 0.841 p=4.6x10-4. SF levels of miR-146a and miR-155 were overexpressed in 52.17% and in 76.09% of the RA patients compared to its systemic levels. SF miR-223 was underexpressed in 58.7% of the patients compared to its systemic levels. Levels of IL-17A were higher in RA SF compared to serum (8.645 pg/ml versus 0.315 pg/ml, p=0.012). ROC curve analysis for SF IL-17A showed area under the curve (AUC) = 0.885, p<0.000.Conclusion:The difference between the systemic and local concentration of IL-17A and miRNAs expression shows that the inflammatory disease process leads to their altered expression with a possible role of these molecules in the disease pathogenesis. The higher local levels of miR-155, miR-146 and IL-17A confirm the data about the possible role of these miRNAs in regulating IL-17A production. The opposite changes of IL-17A and miR-223 systemic and local levels confirm the data about the possible role of miR-223 in regulating IL-17 function. Further analysis with larger sets is needed to confirm these results.References:[1]Niimoto T, Nakasa T, Ishikawa M, Okuhara A, Izumi B, Deie M, et al. MicroRNA-146a expresses in interleukin-17 producing T cells in rheumatoid arthritis patients. BMC Musculoskelet Disord. 2010; 11:209.[2]Yao R, Ma YL, Liang W, Li HH, Ma ZJ, Yu X. et al. MicroRNA-155 modulates Treg and Th17 cells differentiation and Th17 cell function by targeting SOCS1. PLoS ONE 2012; 7(10):e46082.[3]Schaefer J, Nakra N, Montufar-Solis D, Vigneswaran N, Klein J. Role for miR-223 and Roquin in IL-10 mediated regulation of IL-17. J Immunol. 2013; 190 (1 Supplement) 171.9.Acknowledgments:The study was supported by Grant 14-D/2012, Grant 60/2013 and Grant 61/2015 from Medical University-Sofia, BulgariaDisclosure of Interests:None declared


2018 ◽  
Vol 1 (1) ◽  
pp. 120-130 ◽  
Author(s):  
Chunxiang Qian ◽  
Wence Kang ◽  
Hao Ling ◽  
Hua Dong ◽  
Chengyao Liang ◽  
...  

Support Vector Machine (SVM) model optimized by K-Fold cross-validation was built to predict and evaluate the degradation of concrete strength in a complicated marine environment. Meanwhile, several mathematical models, such as Artificial Neural Network (ANN) and Decision Tree (DT), were also built and compared with SVM to determine which one could make the most accurate predictions. The material factors and environmental factors that influence the results were considered. The materials factors mainly involved the original concrete strength, the amount of cement replaced by fly ash and slag. The environmental factors consisted of the concentration of Mg2+, SO42-, Cl-, temperature and exposing time. It was concluded from the prediction results that the optimized SVM model appeared to perform better than other models in predicting the concrete strength. Based on SVM model, a simulation method of variables limitation was used to determine the sensitivity of various factors and the influence degree of these factors on the degradation of concrete strength.


2021 ◽  
Vol 28 (Supplement_1) ◽  
Author(s):  
M Santos ◽  
S Paula ◽  
I Almeida ◽  
H Santos ◽  
H Miranda ◽  
...  

Abstract Funding Acknowledgements Type of funding sources: None. Introduction Patients (P) with acute heart failure (AHF) are a heterogeneous population. Risk stratification at admission may help predict in-hospital complications and needs. The Get With The Guidelines Heart Failure score (GWTG-HF) predicts in-hospital mortality (M) of P admitted with AHF. ACTION ICU score is validated to estimate the risk of complications requiring ICU care in non-ST elevation acute coronary syndromes. Objective To validate ACTION-ICU score in AHF and to compare ACTION-ICU to GWTG-HF as predictors of in-hospital M (IHM), early M [1-month mortality (1mM)] and 1-month readmission (1mRA), using real-life data. Methods Based on a single-center retrospective study, data collected from P admitted in the Cardiology department with AHF between 2010 and 2017. P without data on previous cardiovascular history or uncompleted clinical data were excluded. Statistical analysis used chi-square, non-parametric tests, logistic regression analysis and ROC curve analysis. Results Among the 300 P admitted with AHF included, mean age was 67.4 ± 12.6 years old and 72.7% were male. Systolic blood pressure (SBP) was 131.2 ± 37.0mmHg, glomerular filtration rate (GFR) was 57.1 ± 23.5ml/min. 35.3% were admitted in Killip-Kimball class (KKC) 4. ACTION-ICU score was 10.4 ± 2.3 and GWTG-HF was 41.7 ± 9.6. Inotropes’ usage was necessary in 32.7% of the P, 11.3% of the P needed non-invasive ventilation (NIV), 8% needed invasive ventilation (IV). IHM rate was 5% and 1mM was 8%. 6.3% of the P were readmitted 1 month after discharge. Older age (p &lt; 0.001), lower SBP (p = 0,035) and need of inotropes (p &lt; 0.001) were predictors of IHM in our population. As expected, patients presenting in KKC 4 had higher IHM (OR 8.13, p &lt; 0.001). Older age (OR 1.06, p = 0.002, CI 1.02-1.10), lower SBP (OR 1.01, p = 0.05, CI 1.00-1.02) and lower left ventricle ejection fraction (LVEF) (OR 1.06, p &lt; 0.001, CI 1.03-1.09) were predictors of need of NIV. None of the variables were predictive of IV. LVEF (OR 0.924, p &lt; 0.001, CI 0.899-0.949), lower SBP (OR 0.80, p &lt; 0.001, CI 0.971-0.988), higher urea (OR 1.01, p &lt; 0.001, CI 1.005-1.018) and lower sodium (OR 0.92, p = 0.002, CI 0.873-0.971) were predictors of inotropes’ usage. Logistic regression showed that GWTG-HF predicted IHM (OR 1.12, p &lt; 0.001, CI 1.05-1.19), 1mM (OR 1.10, p = 1.10, CI 1.04-1.16) and inotropes’s usage (OR 1.06, p &lt; 0.001, CI 1.03-1.10), however it was not predictive of 1mRA, need of IV or NIV. Similarly, ACTION-ICU predicted IHM (OR 1.51, p = 0.02, CI 1.158-1.977), 1mM (OR 1.45, p = 0.002, CI 1.15-1.81) and inotropes’ usage (OR 1.22, p = 0.002, CI 1.08-1.39), but not 1mRA, the need of IV or NIV. ROC curve analysis revealed that GWTG-HF score performed better than ACTION-ICU regarding IHM (AUC 0.774, CI 0.46-0-90 vs AUC 0.731, CI 0.59-0.88) and 1mM (AUC 0.727, CI 0.60-0.85 vs AUC 0.707, CI 0.58-0.84). Conclusion In our population, both scores were able to predict IHM, 1mM and inotropes’s usage.


2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yuichiro Shimoyama ◽  
Osamu Umegaki ◽  
Noriko Kadono ◽  
Toshiaki Minami

Abstract Objective Sepsis is a major cause of mortality for critically ill patients. This study aimed to determine whether presepsin values can predict mortality in patients with sepsis. Results Receiver operating characteristic (ROC) curve analysis, Log-rank test, and multivariate analysis identified presepsin values and Prognostic Nutritional Index as predictors of mortality in sepsis patients. Presepsin value on Day 1 was a predictor of early mortality, i.e., death within 7 days of ICU admission; ROC curve analysis revealed an AUC of 0.84, sensitivity of 89%, and specificity of 77%; and multivariate analysis showed an OR of 1.0007, with a 95%CI of 1.0001–1.0013 (p = 0.0320).


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jiajia Liu ◽  
Xiaoyi Tian ◽  
Yan Wang ◽  
Xixiong Kang ◽  
Wenqi Song

Abstract Background The cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) is widely considered as a pivotal immune checkpoint molecule to suppress antitumor immunity. However, the significance of soluble CTLA-4 (sCTLA-4) remains unclear in the patients with brain glioma. Here we aimed to investigate the significance of serum sCTLA-4 levels as a noninvasive biomarker for diagnosis and evaluation of the prognosis in glioma patients. Methods In this study, the levels of sCTLA-4 in serum from 50 patients diagnosed with different grade gliomas including preoperative and postoperative, and 50 healthy individuals were measured by an enzyme-linked immunosorbent assay (ELISA). And then ROC curve analysis and survival analyses were performed to explore the clinical significance of sCTLA-4. Results Serum sCTLA-4 levels were significantly increased in patients with glioma compared to that of healthy individuals, and which was also positively correlated with the tumor grade. ROC curve analysis showed that the best cutoff value for sCTLA-4 for glioma is 112.1 pg/ml, as well as the sensitivity and specificity with 82.0 and 78.0%, respectively, and a cut-off value of 220.43 pg/ml was best distinguished in patients between low-grade glioma group and high-grade glioma group with sensitivity 73.1% and specificity 79.2%. Survival analysis revealed that the patients with high sCTLA-4 levels (> 189.64 pg/ml) had shorter progression-free survival (PFS) compared to those with low sCTLA-4 levels (≤189.64 pg/ml). In the univariate analysis, elder, high-grade tumor, high sCTLA-4 levels and high Ki-67 index were significantly associated with shorter PFS. In the multivariate analysis, sCTLA-4 levels and tumor grade remained an independent prognostic factor. Conclusion These findings indicated that serum sCTLA-4 levels play a critical role in the pathogenesis and development of glioma, which might become a valuable predictive biomarker for supplementary diagnosis and evaluation of the progress and prognosis in glioma.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaohua Ban ◽  
Xinping Shen ◽  
Huijun Hu ◽  
Rong Zhang ◽  
Chuanmiao Xie ◽  
...  

Abstract Background To determine the predictive CT imaging features for diagnosis in patients with primary pulmonary mucoepidermoid carcinomas (PMECs). Materials and methods CT imaging features of 37 patients with primary PMECs, 76 with squamous cell carcinomas (SCCs) and 78 with adenocarcinomas were retrospectively reviewed. The difference of CT features among the PMECs, SCCs and adenocarcinomas was analyzed using univariate analysis, followed by multinomial logistic regression and receiver operating characteristic (ROC) curve analysis. Results CT imaging features including tumor size, location, margin, shape, necrosis and degree of enhancement were significant different among the PMECs, SCCs and adenocarcinomas, as determined by univariate analysis (P < 0.05). Only lesion location, shape, margin and degree of enhancement remained independent factors in multinomial logistic regression analysis. ROC curve analysis showed that the area under curve of the obtained multinomial logistic regression model was 0.805 (95%CI: 0.704–0.906). Conclusion The prediction model derived from location, margin, shape and degree of enhancement can be used for preoperative diagnosis of PMECs.


2019 ◽  
Vol 11 ◽  
pp. 1759720X1988555 ◽  
Author(s):  
Wanlong Wu ◽  
Jun Ma ◽  
Yuhong Zhou ◽  
Chao Tang ◽  
Feng Zhao ◽  
...  

Background: Infection remains a major cause of morbidity and mortality in patients with systemic lupus erythematosus (SLE). This study aimed to establish a clinical prediction model for the 3-month all-cause mortality of invasive infection events in patients with SLE in the emergency department. Methods: SLE patients complicated with invasive infection admitted into the emergency department were included in this study. Patient’s demographic, clinical, and laboratory characteristics on admission were retrospectively collected as baseline data and compared between the deceased and the survivors. Independent predictors were identified by multivariable logistic regression analysis. A prediction model for all-cause mortality was established and evaluated by receiver operating characteristic (ROC) curve analysis. Results: A total of 130 eligible patients were collected with a cumulative 38.5% 3-month mortality. Lymphocyte count <800/ul, urea >7.6mmol/l, maximum prednisone dose in the past ⩾60 mg/d, quick Sequential Organ Failure Assessment (qSOFA) score, and age at baseline were independent predictors for all-cause mortality (LUPHAS). In contrast, a history of hydroxychloroquine use was protective. In a combined, odds ratio-weighted LUPHAS scoring system (score 3–22), patients were categorized to three groups: low-risk (score 3–9), medium-risk (score 10–15), and high-risk (score 16–22), with mortalities of 4.9% (2/41), 45.9% (28/61), and 78.3% (18/23) respectively. ROC curve analysis indicated that a LUPHAS score could effectively predict all-cause mortality [area under the curve (AUC) = 0.86, CI 95% 0.79–0.92]. In addition, LUPHAS score performed better than the qSOFA score alone (AUC = 0.69, CI 95% 0.59–0.78), or CURB-65 score (AUC = 0.69, CI 95% 0.59–0.80) in the subgroup of lung infections ( n = 108). Conclusions: Based on a large emergency cohort of lupus patients complicated with invasive infection, the LUPHAS score was established to predict the short-term all-cause mortality, which could be a promising applicable tool for risk stratification in clinical practice.


2014 ◽  
Vol 5 (3) ◽  
pp. 30-34 ◽  
Author(s):  
Balkishan Sharma ◽  
Ravikant Jain

Objective: The clinical diagnostic tests are generally used to identify the presence of a disease. The cutoff value of a diagnostic test should be chosen to maximize the advantage that accrues from testing a population of human and others. When a diagnostic test is to be used in a clinical condition, there may be an opportunity to improve the test by changing the cutoff value. To enhance the accuracy of diagnosis is to develop new tests by using a proper statistical technique with optimum sensitivity and specificity. Method: Mean±2SD method, Logistic Regression Analysis, Receivers Operating Characteristics (ROC) curve analysis and Discriminant Analysis (DA) have been discussed with their respective applications. Results: The study highlighted some important methods to determine the cutoff points for a diagnostic test. The traditional method is to identify the cut-off values is Mean±2SD method. Logistic Regression Analysis, Receivers Operating Characteristics (ROC) curve analysis and Discriminant Analysis (DA) have been proved to be beneficial statistical tools for determination of cut-off points.Conclusion: There may be an opportunity to improve the test by changing the cut-off value with the help of a correctly identified statistical technique in a clinical condition when a diagnostic test is to be used. The traditional method is to identify the cut-off values is Mean ± 2SD method. It was evidenced in certain conditions that logistic regression is found to be a good predictor and the validity of the same can be confirmed by identifying the area under the ROC curve. Abbreviations: ROC-Receiver operating characteristics and DA-Discriminant Analysis. Asian Journal of Medical Science, Volume-5(3) 2014: 30-34 http://dx.doi.org/10.3126/ajms.v5i3.9296      


2012 ◽  
Vol 2012 ◽  
pp. 1-10
Author(s):  
Pijush Samui

The main objective of site characterization is the prediction of in situ soil properties at any half-space point at a site based on limited tests. In this study, the Support Vector Machine (SVM) has been used to develop a three dimensional site characterization model for Bangalore, India based on large amount of Standard Penetration Test. SVM is a novel type of learning machine based on statistical learning theory, uses regression technique by introducing ε-insensitive loss function. The database consists of 766 boreholes, with more than 2700 field SPT values () spread over 220 sq km area of Bangalore. The model is applied for corrected () values. The three input variables (, , and , where , , and are the coordinates of the Bangalore) were used for the SVM model. The output of SVM was the data. The results presented in this paper clearly highlight that the SVM is a robust tool for site characterization. In this study, a sensitivity analysis of SVM parameters (σ, , and ε) has been also presented.


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