Characterizing the Behavior of Mutated Proteins with EMCAP: the Energy Minimization Curve Analysis Pipeline

2021 ◽  
Author(s):  
Matthew Lee ◽  
Bodi Van Roy ◽  
Filip Jagodzinski
Keyword(s):  
Energy Minimization ◽  
Curve Analysis ◽  
Analysis Pipeline

Which Data to Meta-Analyze, and How?

2019 ◽  
Vol 227 (1) ◽  
pp. 64-82 ◽  
Author(s):  
Martin Voracek ◽  
Michael Kossmeier ◽  
Ulrich S. Tran
Keyword(s):  
Empirical Research ◽  
Meta Analysis ◽  
Curve Analysis ◽  
Research Progress ◽  
Primary Data ◽  
Statistical Procedures ◽  
Graphical Displays ◽  
Primary Data Analysis ◽  
Meta Analyses ◽  
Data Analytic

Abstract. Which data to analyze, and how, are fundamental questions of all empirical research. As there are always numerous flexibilities in data-analytic decisions (a “garden of forking paths”), this poses perennial problems to all empirical research. Specification-curve analysis and multiverse analysis have recently been proposed as solutions to these issues. Building on the structural analogies between primary data analysis and meta-analysis, we transform and adapt these approaches to the meta-analytic level, in tandem with combinatorial meta-analysis. We explain the rationale of this idea, suggest descriptive and inferential statistical procedures, as well as graphical displays, provide code for meta-analytic practitioners to generate and use these, and present a fully worked real example from digit ratio (2D:4D) research, totaling 1,592 meta-analytic specifications. Specification-curve and multiverse meta-analysis holds promise to resolve conflicting meta-analyses, contested evidence, controversial empirical literatures, and polarized research, and to mitigate the associated detrimental effects of these phenomena on research progress.

Two Candidate Approaches o Text Sequencing: An Addendum to “The Diachrony Debate: A Tutorial on Methods”

2018 ◽  
Vol 26 (2) ◽  
Author(s):  
Dean A. Forbes
Keyword(s):  
Computational Biology ◽  
Middle English ◽  
Diagnostic Tool ◽  
Reliable Method ◽  
Biblical Hebrew ◽  
Quantitative Comparison ◽  
Curve Analysis ◽  
Single Feature ◽  
S Curve ◽  
Temporal Ordering

In a recent essay published in this journal, I illustrated the limitations one may encounter when sequencing texts temporally using s-curve analysis. I also introduced seriation, a more reliable method for temporal ordering much used in both archaeology and computational biology. Lacking independently ordered Biblical Hebrew (BH) data to assess the potential power of seriation in the context of diachronic studies, I used classic Middle English data originally compiled by Ellegård. In this addendum, I reintroduce and extend s-curve analysis, applying it to one rather noisy feature of Middle English. My results support Holmstedt’s assertion that s-curve analysis can be a useful diagnostic tool in diachronic studies. Upon quantitative comparison, however, the five-feature seriation results derived in my former paper are found to be seven times more accurate than the single-feature s-curve results presented here. 

Serum miR-21 and miR-26a Levels Negatively Correlate with Severity of Cirrhosis in Patients with Chronic Hepatitis B

MicroRNA ◽  
2018 ◽  
Vol 8 (1) ◽  
pp. 86-92 ◽  
Author(s):  
Shili Jiang ◽  
Wei Jiang ◽  
Ying Xu ◽  
Xiaoning Wang ◽  
Yongping Mu ◽  
...  
Keyword(s):  
Chronic Hepatitis ◽  
Hepatitis B ◽  
Chronic Hepatitis B ◽  
Operating Characteristic ◽  
Characteristic Curve ◽  
Curve Analysis ◽  
Pugh Class ◽  
Operating Characteristic Curve ◽  
Class C ◽  
Circulating Levels

Background and Objective: Accurately evaluating the severity of liver cirrhosis is essential for clinical decision making and disease management. This study aimed to evaluate the value of circulating levels of microRNA (miR)-26a and miR-21 as novel noninvasive biomarkers in detecting severity of cirrhosis in patients with chronic hepatitis B. </P><P> Methods: Thirty patients with clinically diagnosed chronic hepatitis B-related cirrhosis and 30 healthy individuals were selected. The serum levels of miR-26a and miR-21 were quantified by qRT-PCR. Receiver operating characteristic curve analysis was performed to evaluate the sensitivity and specificity of the miRNAs for detecting the severity of cirrhosis. Results: Serum miR-26a and miR-21 levels were found to be significantly downregulated in patients with severe cirrhosis scored at Child-Pugh class C in comparison to healthy controls (miR-26a p<0.01, and miR-21 p<0.001, respectively). The circulating miR-26a and miR-21 levels in patients were positively correlated with serum albumin concentration but negatively correlated with serum total bilirubin concentration and prothrombin time. Receiver operating characteristic curve analysis revealed that both serum miR-26a and miR-21 levels were associated with a high diagnostic accuracy for patients with cirrhosis scored at Child-Pugh class C (miR-26a Cut-off fold change at ≤0.4, Sensitivity: 84.62%, Specificity: 89.36%, P<0.0001; miR-21 Cut-off fold change at ≤0.6, Sensitivity: 84.62%, Specificity: 78.72%, P<0.0001). Our results indicate that the circulating levels of miR-26a and miR-21 are closely related to the extent of liver decompensation, and the decreased levels are capable of discriminating patients with cirrhosis at Child-Pugh class C from the whole cirrhosis cases.

Comments on the Antonow and interfacial interaction rules

1990 ◽  
Vol 55 (5) ◽  
pp. 1143-1148 ◽  
Author(s):  
Jan Kloubek
Keyword(s):  
Free Energy ◽  
Energy Minimization ◽  
Interfacial Interaction ◽  
Aliphatic Hydrocarbon ◽  
Theoretical Base ◽  
Water Interface ◽  
Free Energy Minimization ◽  
Interaction Rule

Results presented for the aliphatic hydrocarbon-water interface show that the recent hypothesis of the free energy minimization called interfacial interaction rule, which was suggested as a theoretical base of the Antonow rule, cannot be generally valid.

A validated novel preoperative index to predict the extent of intraperitoneal contamination in patients with acute abdominal pathology: A cohort study

2019 ◽  
Vol 30 (7-8) ◽  
pp. 221-228
Author(s):  
Shahab Hajibandeh ◽  
Shahin Hajibandeh ◽  
Nicholas Hobbs ◽  
Jigar Shah ◽  
Matthew Harris ◽  
...  
Keyword(s):  
Receiver Operating Characteristic Curve ◽  
Receiver Operating Characteristic ◽  
Operating Characteristic ◽  
Validation Cohort ◽  
Characteristic Curve ◽  
Curve Analysis ◽  
Emergency Laparotomy ◽  
Contamination Index ◽  
Operating Characteristic Curve ◽  
Receiver Operating

Aims To investigate whether an intraperitoneal contamination index (ICI) derived from combined preoperative levels of C-reactive protein, lactate, neutrophils, lymphocytes and albumin could predict the extent of intraperitoneal contamination in patients with acute abdominal pathology. Methods Patients aged over 18 who underwent emergency laparotomy for acute abdominal pathology between January 2014 and October 2018 were randomly divided into primary and validation cohorts. The proposed intraperitoneal contamination index was calculated for each patient in each cohort. Receiver operating characteristic curve analysis was performed to determine discrimination of the index and cut-off values of preoperative intraperitoneal contamination index that could predict the extent of intraperitoneal contamination. Results Overall, 468 patients were included in this study; 234 in the primary cohort and 234 in the validation cohort. The analyses identified intraperitoneal contamination index of 24.77 and 24.32 as cut-off values for purulent contamination in the primary cohort (area under the curve (AUC): 0.73, P < 0.0001; sensitivity: 84%, specificity: 60%) and validation cohort (AUC: 0.83, P < 0.0001; sensitivity: 91%, specificity: 69%), respectively. Receiver operating characteristic curve analysis also identified intraperitoneal contamination index of 33.70 and 33.41 as cut-off values for feculent contamination in the primary cohort (AUC: 0.78, P < 0.0001; sensitivity: 87%, specificity: 64%) and validation cohort (AUC: 0.79, P < 0.0001; sensitivity: 86%, specificity: 73%), respectively. Conclusions As a predictive measure which is derived purely from biomarkers, intraperitoneal contamination index may be accurate enough to predict the extent of intraperitoneal contamination in patients with acute abdominal pathology and to facilitate decision-making together with clinical and radiological findings.

scholarly journals Scoring system development and validation for prediction choledocholithiasis before open cholecystectomy

2015 ◽  
Vol 143 (11-12) ◽  
pp. 681-687 ◽  
Author(s):  
Tomislav Pejovic ◽  
Miroslav Stojadinovic
Keyword(s):  
Bile Duct ◽  
Clinical Utility ◽  
Clinical Decision Making ◽  
Prediction Models ◽  
Open Cholecystectomy ◽  
Univariate Analysis ◽  
Curve Analysis ◽  
Decision Curve Analysis ◽  
Scoring Model ◽  
Validation Set

Introduction. Accurate precholecystectomy detection of concurrent asymptomatic common bile duct stones (CBDS) is key in the clinical decision-making process. The standard preoperative methods used to diagnose these patients are often not accurate enough. Objective. The aim of the study was to develop a scoring model that would predict CBDS before open cholecystectomy. Methods. We retrospectively collected preoperative (demographic, biochemical, ultrasonographic) and intraoperative (intraoperative cholangiography) data for 313 patients at the department of General Surgery at Gornji Milanovac from 2004 to 2007. The patients were divided into a derivation (213) and a validation set (100). Univariate and multivariate regression analysis was used to determine independent predictors of CBDS. These predictors were used to develop scoring model. Various measures for the assessment of risk prediction models were determined, such as predictive ability, accuracy, the area under the receiver operating characteristic curve (AUC), calibration and clinical utility using decision curve analysis. Results. In a univariate analysis, seven risk factors displayed significant correlation with CBDS. Total bilirubin, alkaline phosphatase and bile duct dilation were identified as independent predictors of choledocholithiasis. The resultant total possible score in the derivation set ranged from 7.6 to 27.9. Scoring model shows good discriminatory ability in the derivation and validation set (AUC 94.3 and 89.9%, respectively), excellent accuracy (95.5%), satisfactory calibration in the derivation set, similar Brier scores and clinical utility in decision curve analysis. Conclusion. Developed scoring model might successfully estimate the presence of choledocholithiasis in patients planned for elective open cholecystectomy.

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