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Publications
Publications (18)
Background: Cardiovascular diseases have long been studied to identify their causal
factors and counteract them effectively. Atherosclerosis, an inflammatory process of the blood vessel wall, is a common cardiovascular disease. Among the many well-known risk factors, hypercholesterolemia is undoubtedly a significant condition for atherosclerotic pl...
Background and Objective
In the last two decades there can be observed a rapid development of systems biology. The basis of systems methods is a formal model of an analyzed system. It can be created in a language of some branch of mathematics and recently Petri net-based biological models seem to be especially promising since they have a great expr...
A deficiency of vitamin A (VAD) and iron is the most common nutritional problem affecting people worldwide. Given the scale of the problem, the interactions between vitamin A and iron levels are widely studied. However, the exact mechanism of the impact of vitamin A on the regulation of iron metabolism remains unclear. An extremely significant issu...
Intracellular processes are cascades of biochemical reactions, triggered in response to various types of stimuli. Mathematical models describing their dynamics have become increasingly popular in recent years, as tools supporting experimental work in analysis of pathways and regulatory networks. Not only do they provide insights into general proper...
We present an approach to discriminate SARS-CoV-2 virus types based on their RNA sequence descriptions avoiding a sequence alignment. For that purpose, sequences are preprocessed by feature extraction and the resulting feature vectors are analyzed by prototype-based classification to remain interpretable. In particular, we propose to use variants o...
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the coronavirus disease of 2019 (COVID-19) pandemic, has affected and continues to affect millions of people across the world. Patients with essential arterial hypertension and renal complications are at particular risk of the fatal course of this infection. In our st...
The ability to diagnose acid-base imbalances correctly is essential for physicians and other healthcare workers. Despite its importance, it is often considered too complex and confusing. Although most people dealing with arterial blood gases (ABGs) do not usually have problems with acid-base disorder assessment, such an analysis is also carried out...
Motivation
Viruses are the most abundant biological entities and constitute a large reservoir of genetic diversity. In recent years, knowledge about them has increased significantly as a result of dynamic development in life sciences and rapid technological progress. This knowledge is scattered across various data repositories, making a comprehensi...
We present an approach to investigate SARS-CoV-2 virus sequences based
on alignment-free methods for RNA sequence comparison. In particular,
we verify a given clustering result for the GISAID data set, which
was obtained analyzing the molecular differences in coronavirus populations
by phylogenetic trees. For this purpose, we use alignment-free
dis...
The most plausible hypothesis for explaining the origins of life on earth is the RNA world hypothesis supported by a growing number of research results from various scientific areas. Frequently, the existence of a hypothetical species on earth is supposed, with a base RNA sequence probably dissimilar from any known genomes today. It is hard to dist...
Living organisms, as well as their functional blocks, are complex systems. From this follows that for their deep understanding it is necessary to use systems methods for their analysis. The basis for such an analysis is a precise mathematical model. It seems that models expressed as Petri nets are especially promising in the area of modeling and an...
Although abdominal aortic aneurysm (AAA) is a common vascular disease and is associated with high mortality, the full pathogenesis of AAA remains unknown to researchers. Abdominal aortic aneurysms and atherosclerosis are strongly related. Currently, it is more often suggested that development of AAA is not a result of atherosclerosis, however, indi...
Regulation of gene expression is one of the most important problems analyzed in systems biology. It involves, among other, interactions of mRNA with miRNA-a small (21-25 nt) single-stranded non-coding RNA molecule. Its main function is post-transcriptional regulation of gene expression leading to gene silencing. It is achieved either by inhibition...
Many factors, such as endothelial dysfunction, inflammation and hemostatic disturbances, affect formation and progression of atherosclerotic plaque. In our study, we have focused on hemostatic disturbances with particular emphasis on the extrinsic pathways of coagulation. Thrombin is a main enzyme of coagulation and it is engaged in many different...
Interleukin 18 (IL-18) is one of the pro-inflammatory cytokines expressed by macrophages, suggesting that it plays important physiological and immunological functions, among the others: stimulation of natural killers (NKs) and T cells to interferon gamma (IFN- γ ) synthesis. IL-18 was originally identified as interferon gamma inducing factor and no...
The effect of cigarette smoking on endothelial damage and atherosclerosis development – modeled and analyzed using Petri nets
KAJA CHMIELEWSKA, DOROTA FORMANOWICZ and PIOTR FORMANOWICZ
Atherosclerosis as one of the crucial causes of cardiovascular diseases (CVD) is the leading reason of death worldwide. One of the contributing factors to this phe...