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Cancer of the pancreas is a highly lethal disease and has an extremely poor prognosis. Mathematical modelling and computer simulations have been proposed as important tool to predictor initiation and progression of cancer diseases, which are very important in cancer study. Among these studies, it is widely assumed that the gene mutation rate is unchanged, which is not realistic based on recently biological...
Before genotyping microarrays can be used, calling algorithms must first be calibrated with a control set. Calling algorithms that evaluate hybridization intensity data on the basis of individual markers are better able to compensate for sequence specific variations. However, they require that the control set includes samples sufficient to exercise every marker in all of its allelic states. Minimizing...
Genome-wide association studies have discovered many biologically important associations of genes with phenotypes. Typically, genome-wide association analyses formally test the association of each genetic feature (SNP, CNV, etc) with the phenotype of interest and summarize the results with multiplicity-adjusted p-values. However, very small p-values only provide evidence against the null hypothesis...
Improvements in melanoma diagnosis, treatment and prognosis are urgently warranted, given that it causes 3 out of 4 skin cancer deaths. A large amount of genomic and molecular data indicate that alterations occur at multiple scales in different stages of melanoma. Metabolic rewiring is a characteristic feature of progressive cancers that facilitates sustenance of tumors, and caters to the changing...
Alternative splicing (AS) produces multiple messenger RNAs by combining different regions of the precursor transcript to produce diversity in gene products. Under stress conditions, many genes produce transcripts that are not otherwise produced during normal conditions. Plant growth and development are extensively affected by environmental stresses. In this study, we combine Differentially Alternatively...
It is a grand challenge to reveal the causal effects of DNA variants in complex phenotypes. Although statistical techniques can establish correlations between genotypes and phenotypes in Genome-Wide Association Studies (GWAS), they often fail when the variant is rare. The emerging Network-based Association Studies aim to address this shortcoming in statistical analysis, but are mainly applied to coding...
Molecularly targeted therapies significantly contribute to the efforts of personalized approaches for cancer diagnosis and chemotherapeutic treatment. One of a critical step to identify target molecules is to determine the most representative features for different patient's sub-groups. Breast cancer, one of the most heterogeneous cancer has five main subtypes, so accurately identify gene signatures...
The use of Affective Computing in the medical domain is gaining momentum, but is challenged through requirements arising through the inherent processing of personal sensitive data, that will effect comprehensive analysis reproducibility. Reproducibility is a key element in good research practice and a key ingredient to comprehensively validate AC applications in a medical context. Various research...
We tested two techniques that can assist in the automatic extraction and analysis of laboratory mouse ultrasonic vocalizations. First, we substituted a Morlet-wavelet-based scalogram in place of the commonly used Fourier-based spectrogram. The frequencies in a scalogram are logarithmically scaled, which likely makes it better model a mouse's pitch perception based on the structure of its inner ear...
Frequent graph mining has received a lot of attention from the research community because of the increasing availability of graph data in several domains, including bioinformatics, social networks, and cyber security. On large graphs such as protein-protein interaction and gene coexpression networks, frequent subgraph mining algorithms take hours to finish. In this paper, we propose a parallel algorithm...
Bidomain or monodomain model has frequently been used to study electrical activities in the cardiac tissue. The finite difference method with second order accuracy is commonly used to approximate the spatial derivatives of the governing equations numerically. In this work, a higher order finite difference scheme has been implemented to solve the nonlinear monodomain equation. The unknown transmembrane...
In recent years, most breakthroughs in fields such as image and video processing were based on machine learning technologies that allow computers to recognize objects in images with nearly human precision. In some application domains, computers even surpassed human level performance. These breakthroughs result from an exponential increase of computational resources and digitization of society (massive...
The success of genome-wide association studies and the development of next generation sequencing technology have identified many disease-related common and rare variants. There have been several prediction models suggested using penalized regression or statistical learning methods. However, only a few prediction models are available which use both common and rare variants. The aim of our study is...
Protein-protein interaction extraction research can be widely applied to the field of life science research. However, most of the machine learning based methods focus on binary PPI relation extraction, which loses rich relationship type information that is critical to the PPIs study. The rule based open information extraction methods can extract the PPI triple (i.e. “protein1, interaction word, protein2”),...
Objective: To investigate the clinical efficacy of immersion of alternating cooling and heating Chinese medicine combined with acupuncture on treating shoulder-hand syndrome(SHS) after stroke Methods: 79 patients with post-stroke SHS in stage I were randomly divided into trial group(n=39) and control group(n=40). Both groups received routine treatment and rehabilitation treatment for 4 weeks. The...
OBJECTIVES: As a significant part of Traditional Chinese Medicine (TCM), acupoint positioning heavily depends on the acupuncturist's skills. Due to shortage of accurate acupoint detection system with favorable human-computer interactivity, a recognition and projection system for meridians and acupoints is proposed that is based on three-dimensional (3D) scanning. METHODS: First, a 3D human model is...
Of the examples of clonal competition for antigen among lymphocytes, the recently predicted “Memory anti-Naïve” phenomenon occurs when the challenging antigen is not identical to the priming, and will be consequently bound with lower avidity by preexisting memory cells. In this study we use computer modeling and a systematic schedule of viral injections to disentangle the complex relationship between...
A new modeling approach and conceptual framework to the immune system response and its dual role with respect to cancer is proposed based on Applied Category Theory. States of cells and pathogenes are structured as mathematical structures (categories), the interactions, at a given phase, between cells of the immune system and pathogenes, correspond to a pair of adjunctions (adjoint functors), the...
An effective yellow fever vaccine has been available since 1937. However, some issues regarding its use remain open, such as the minimum dose that can provide immunity against the disease. Mathematical-computational tools can be useful to assist the search for answers to some of these open issues. In this context, this study presents a simplified mathematical-computational model of the human immune...
While high-throughput single cell technologies enable in depth examination of specific cell subsets, these experiments lack the context of these subsets in other cell types and diseases. We compared novel dendritic and monocyte signatures from single cell RNAseq with bulk transcriptome of immune cells to show that the gene signatures for the novel cell subsets are also up-regulated in functionally...
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