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Low-power wearable devices for disease diagnosis are used at anytime and anywhere. These are non-invasive and pain-free for the better quality of life. However, these devices are resource constrained in terms of memory and processing capability. Memory constraint allows these devices to store a limited number of patterns and processing constraint provides delayed response. It is a challenging task...
The estimation of heart rate variability (HRV) has become an increasingly popular and important tool for studying many disease pathologies in the past twenty years. This paper shows a Matlab software named KARDIA that is used for the analysis of cardiac interbeat interval (IBI). The graphic user interface of this Matlab software, KARDIA helps us to allow the study of phasic cardiac responses (PCRs)...
Abnormal regulation of signaling pathways is the key factor causing disease. For better understanding disease mechanisms, many methods have been proposed to identify the significantly differential pathways between diseases and normal individuals via microarray gene expression datasets. Unlike previous common analysis processes, which is focused on merging gene difference into difference of pathway...
Through the application of genetic algorithms (genetic algorithm, simplified as GA) and BP(Back Propation) neural network, I built a prediction model of roses diseases, in which I choose six indicators as the input of network, they are the minimum temperature, maximum temperature, average temperature, minimum humidity, maximum humidity, average humidity in the greenhouse, then I choose three diseases...
According to World Health Organization, Dengue is identified as one of the main pandemic viral disease in tropical and semi-tropical countries in the world. A lot of researches have divulged that the use of ovitraps has itself shown a simple and inexpensive alternative for monitoring and controlling Dengue vector, Aedes Aegypti, but generally the process of counting Dengue mosquito eggs in ovitraps...
Many important biological problems can be modeled as contagion diffusion processes over interaction networks. This paper shows how the EpiSimdemics interaction-based simulation system can be applied to the general contagion diffusion problem. Two specific problems, computational epidemiology and human immune system modeling, are given as examples. We then show how the graphics processing unit (GPU)...
Structural variation (SV) has been reported to be associated with numerous diseases such as cancer. With the advent of next generation sequencing (NGS) technologies, various types of SV can be potentially identified. We propose a model based clustering approach utilizing a set of features defined for each type of SV event. Our method, termed SVMiner, not only provides a probability score for each...
Whole-genome sequencing (WGS) allows direct interrogation of previously undetected uncommon or rare variants, which potentially contribute to the missing heritability of human diseases. However, cost of sequencing large numbers of samples limits its application in case control association studies. Here, theoretical and empirical design considerations for such sequencing studies, aimed at maximizing...
Summary form only given: Viruses have been implicated as the causative agents for a variety of cancers as well as diseases of the major physiological systems (e.g., nervous, respiratory, immune, reproductive, etc.), and viral infections have consistently ranked among the leading causes of death worldwide. Although viruses exhibit extreme biological diversity, plainly evidenced by the Baltimore classification...
The purpose of this NSF-Eager grant is to use high-throughput RNA sequencing of the transcriptome to assess the role of alternative splicing in the host-pathogen interaction between Arabidopsis thaliana and Pseudomonas syringae. Although previous studies have demonstrated that alternative splicing plays an important role for individual genes during this interaction, this whole-genome approach will...
In genome-wide case-control association studies, the genomic control factor, λ, is generally computed to estimate the inflation of chi-square statistics due to population heterogeneity. For a given estimated λ value, all chi-square values are then divided by λ before their associated significance level is computed. We hypothesize that in some studies λ may not be significantly larger than 1, in which...
The attachment of a glycosylphosphatidylinositol (GPI) is one of the most important posttranslational protein modifications and plays an important role in many vital reactions. It is well known that most GPI-anchored proteins (GPI-APs), such as receptors, nucleotidases, proteinases, immune antigens, and prion protein, are associated with serious human diseases. Consequently, the annotation of novel...
Improvements in automated urinalysis are largely requested by laboratory practice. Urine samples with noise and imbalance increase the difficulty of identifying and classifying urine-related diseases. For improving classification performance, this paper compared the effectiveness of several learning classifiers and proposed a hybrid sampling-based ensemble learning method. The experiments show that...
In this paper, we present a practical algorithm to deal with the data specific classification problem when there are datasets with different properties. We proposed to integrate error rate, missing values and expert judgment as factors for determining data specific pruning to form Expert Knowledge Based Pruning (EKBP). We conduct an extensive experimental study on openly available 40 real world datasets...
For years, we have researched epidemiology model suitable for Korea based on InfluSim model, to analyze the spread of pandemic influenza. However, there is a problem with InfluSim, because the demographic characteristics and the movement of population within the nation are not considered in the research. For this reason, it is improper to draw preparedness against widespread of pandemic influenza...
The aim of this study is to investigate the hemodynamic effect of the angulations in the left coronary bifurcation on subsequent development of coronary artery disease. Eight 3D left coronary artery models were generated based on the anatomical details and simulated for numerical analysis. The angulations at the left coronary bifurcation were simulated with angles ranging from 120°, 105°, 90°, 75°,...
In this paper we introduce the ODD protocol, proposed in ecology for easing the communication and replication of Individual Based Models (IBM). First, we use it to describe a realistic model in epidemiology, which deals with the local determinants of the propagation of the H5N1 virus. From this description we first point out the advantages of ODD. Then we focus on its weaknesses, the major ones being...
A tuberculosis model which incorporates chemo prophylaxis for latent infection and treatment for infectious infection is presented. The epidemic threshold known as the reproduction number is given, and the dynamics of the model is determined by the basic reproductive number. All solutions converge to the disease-free equilibrium when the basic reproduction number is less than or equal to one. When...
The VAST 2010 minichallenge 3 dataset scenario contains a set of genetic sequences from a hypothetical disease outbreak. We describe how we used AC, a plagiarism detection tool, to find the gene sequence similarity; and ManyNets, a network analysis tool, to trace back the gene-mutations and identify the characteristics of the sequences. Our analysis won the Innovative Tool Adaptation award.
There are various kinds of birds in the Qinghai Lake National Nature Reserve. In recent years, avian influenza breaks out in this region for several times. The biologists need to identify the species of birds after the discovery of infected birds. They can classify the birds according to the appearance by experience, or they can identify the birds according to the gene collected from the birds. But...
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