Association of Lower Extremity Vascular Disease, Coronary Artery, and Carotid Artery Atherosclerosis in Patients with Type 2 Diabetes MellitusRead the full article
Computational and Mathematical Methods in Medicine publishes research and review articles focused on the application of mathematics to problems arising from the biomedical sciences.
Chief Editor, David Winkler's research focuses on dissecting the quantitative structure-activity method and rebuilding it with modern mathematical and AI methods, and adapting evolutionary methods to design of bioactive molecules and materials for diagnostics, therapeutics, and regeneration.
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Comparing the Prognostic Value of Stress Myocardial Perfusion Imaging by Conventional and Cadmium-Zinc Telluride Single-Photon Emission Computed Tomography through a Machine Learning Approach
We compared the prognostic value of myocardial perfusion imaging (MPI) by conventional- (C-) single-photon emission computed tomography (SPECT) and cadmium-zinc-telluride- (CZT-) SPECT in a cohort of patients with suspected or known coronary artery disease (CAD) using machine learning (ML) algorithms. A total of 453 consecutive patients underwent stress MPI by both C-SPECT and CZT-SPECT. The outcome was a composite end point of all-cause death, cardiac death, nonfatal myocardial infarction, or coronary revascularization procedures whichever occurred first. ML analysis performed through the implementation of random forest (RF) and -nearest neighbors (KNN) algorithms proved that CZT-SPECT has greater accuracy than C-SPECT in detecting CAD. For both algorithms, the sensitivity of CZT-SPECT (96% for RF and 60% for KNN) was greater than that of C-SPECT (88% for RF and 53% for KNN). A preliminary univariate analysis was performed through Mann-Whitney tests separately on the features of each camera in order to understand which ones could distinguish patients who will experience an adverse event from those who will not. Then, a machine learning analysis was performed by using Matlab (v. 2019b). Tree, KNN, support vector machine (SVM), Naïve Bayes, and RF were implemented twice: first, the analysis was performed on the as-is dataset; then, since the dataset was imbalanced (patients experiencing an adverse event were lower than the others), the analysis was performed again after balancing the classes through the Synthetic Minority Oversampling Technique. According to KNN and SVM with and without balancing the classes, the accuracy ( value = 0.02 and value = 0.01) and recall ( value = 0.001 and value = 0.03) of the CZT-SPECT were greater than those obtained by C-SPECT in a statistically significant way. ML approach showed that although the prognostic value of stress MPI by C-SPECT and CZT-SPECT is comparable, CZT-SPECT seems to have higher accuracy and recall.
Mathematical Modelling of COVID-19 Transmission in Kenya: A Model with Reinfection Transmission Mechanism
In this study we propose a Coronavirus Disease 2019 (COVID-19) mathematical model that stratifies infectious subpopulations into: infectious asymptomatic individuals, symptomatic infectious individuals who manifest mild symptoms and symptomatic individuals with severe symptoms. In light of the recent revelation that reinfection by COVID-19 is possible, the proposed model attempt to investigate how reinfection with COVID-19 will alter the future dynamics of the recent unfolding pandemic. Fitting the mathematical model on the Kenya COVID-19 dataset, model parameter values were obtained and used to conduct numerical simulations. Numerical results suggest that reinfection of recovered individuals who have lost their protective immunity will create a large pool of asymptomatic infectious individuals which will ultimately increase symptomatic individuals with mild symptoms and symptomatic individuals with severe symptoms (critically ill) needing urgent medical attention. The model suggests that reinfection with COVID-19 will lead to an increase in cumulative reported deaths. Comparison of the impact of non pharmaceutical interventions on curbing COVID19 proliferation suggests that wearing face masks profoundly reduce COVID-19 prevalence than maintaining social/physical distance. Further, numerical findings reveal that increasing detection rate of asymptomatic cases via contact tracing, testing and isolating them can drastically reduce COVID-19 surge, in particular individuals who are critically ill and require admission into intensive care.
A Deep Learning Approach for Predicting Antigenic Variation of Influenza A H3N2
Modeling antigenic variation in influenza (flu) virus A H3N2 using amino acid sequences is a promising approach for improving the prediction accuracy of immune efficacy of vaccines and increasing the efficiency of vaccine screening. Antigenic drift and antigenic jump/shift, which arise from the accumulation of mutations with small or moderate effects and from a major, abrupt change with large effects on the surface antigen hemagglutinin (HA), respectively, are two types of antigenic variation that facilitate immune evasion of flu virus A and make it challenging to predict the antigenic properties of new viral strains. Despite considerable progress in modeling antigenic variation based on the amino acid sequences, few studies focus on the deep learning framework which could be most suitable to be applied to this task. Here, we propose a novel deep learning approach that incorporates a convolutional neural network (CNN) and bidirectional long-short-term memory (BLSTM) neural network to predict antigenic variation. In this approach, CNN extracts the complex local contexts of amino acids while the BLSTM neural network captures the long-distance sequence information. When compared to the existing methods, our deep learning approach achieves the overall highest prediction performance on the validation dataset, and more encouragingly, it achieves prediction agreements of 99.20% and 96.46% for the strains in the forthcoming year and in the next two years included in an existing set of chronological amino acid sequences, respectively. These results indicate that our deep learning approach is promising to be applied to antigenic variation prediction of flu virus A H3N2.
Development and Validation of Prediction Model for High Ovarian Response in In Vitro Fertilization-Embryo Transfer: A Longitudinal Study
Objective. To develop and validate a prediction model for high ovarian response in in vitro fertilization-embryo transfer (IVF-ET) cycles. Methods. Totally, 480 eligible outpatients with infertility who underwent IVF-ET were selected and randomly divided into the training set for developing the prediction model and the testing set for validating the model. Univariate and multivariate logistic regressions were carried out to explore the predictive factors of high ovarian response, and then, the prediction model was constructed. Nomogram was plotted for visualizing the model. Area under the receiver-operating characteristic (ROC) curve, Hosmer-Lemeshow test and calibration curve were used to evaluate the performance of the prediction model. Results. Antral follicle count (AFC), anti-Müllerian hormone (AMH) at menstrual cycle day 3 (MC3), and progesterone (P) level on human chorionic gonadotropin (HCG) day were identified as the independent predictors of high ovarian response. The value of area under the curve (AUC) for our multivariate model reached 0.958 (95% CI: 0.936-0.981) with the sensitivity of 0.916 (95% CI: 0.863-0.953) and the specificity of 0.911 (95% CI: 0.858-0.949), suggesting the good discrimination of the prediction model. The Hosmer-Lemeshow test and the calibration curve both suggested model’s good calibration. Conclusion. The developed prediction model had good discrimination and accuracy via internal validation, which could help clinicians efficiently identify patients with high ovarian response, thereby improving the pregnancy rates and clinical outcomes in IVF-ET cycles. However, the conclusion needs to be confirmed by more related studies.
Genetic Algorithm in Data Mining of Colorectal Images
There is currently no effective analytical method in colorectal image analysis, which leads to certain errors in colorectal image analysis. In order to improve the accuracy of colorectal imaging detection, this study used a genetic algorithm as the data mining algorithm and combined it with image processing technology to perform image analysis. At the same time, combined with the actual requirements of image detection, the gray theory model is used as the basic theory of image processing, and the image detection prediction model is constructed to predict the data. In addition, in order to study the effectiveness of the algorithm, the experiment is carried out to analyze the validity of the data of the study, and the predicted value is compared with the actual value. The research shows that the proposed algorithm has certain accuracy and can provide theoretical reference for subsequent related research.
Construction and Evaluation of a Tumor Mutation Burden-Related Prognostic Signature for Thyroid Carcinoma
Thyroid carcinoma is a type of prevalent cancer. Its prognostic evaluation depends on clinicopathological features. However, such conventional methods are deficient. Based on mRNA, single nucleotide variants (SNV), and clinical information of thyroid carcinoma from The Cancer Genome Atlas (TCGA) database, this study statistically analyzed mutational signature of patients with this disease. Missense mutation and SNV are the most common variant classification and variant type, respectively. Next, tumor mutation burden (TMB) of sample was calculated. Survival status of high/low TMB groups was analyzed, as well as the relationship between TMB and clinicopathological features. Results revealed that patients with high TMB had poor survival status, and TMB was related to several clinicopathological features. Through analysis on DEGs in high/low TMB groups, 381 DEGs were obtained. They were found to be mainly enriched in muscle tissue development through enrichment analysis. Then, through Cox regression analysis, a 5-gene prognostic signature was established, which was then evaluated through survival curves and receiver operation characteristic (ROC) curves. The result showed that the signature was able to effectively predict patient’s prognosis and to serve as an independent prognostic risk factor. Finally, through Gene Set Enrichment Analysis (GSEA) on high/low-risk groups, DEGs were found to be mainly enriched in signaling pathways related to DNA repair. Overall, based on the TCGA-THCA dataset, we constructed a 5-gene prognostic signature through a trail of bioinformatics analysis.