Graphlet Degree Distribution Sensibility in Petri Net-Based Models of Biological Systems.

Graphlet Degree Distribution Agreement (GDDA) is a comparison metric created for graphlets. Unfortunately, it has been reported and confirmed that it has an issue with the stability of result values in low-density graphs. Recently, graphlets have been modified for comparison of Petri net-based models of biological systems.

The Interplay Between Carotid Intima-Media Thickness and Selected Serum Biomarkers in Various Stages of Chronic Kidney Disease.

: Chronic kidney disease (CKD), the most common cause of which is hypertension and diabetes, is a recognized risk factor for cardiovascular disease (CVD). This study investigated the association between selected serum biomarkers in the context of intima-media thickness (IMT) changes, a common predictor of subsequent cardiovascular (CV) events. : A total of 251 individuals were enrolled in the study, divided into groups based on the severity of CKD, the presence of CVD, and healthy controls.

Exploring relationship between hypercholesterolemia and instability of atherosclerotic plaque - An approach based on a matrix population model.

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 plaque formation and is linked to atherosclerosis on many levels, i.

Comparison by partition-Finding Petri nets similarity on the basis of subnets.

Petri nets are used for modeling in many scientific areas. The existence of a large number of models gives a possibility for their comparison in search of desired or undesired characteristic structures. Unfortunately, there are only few comparison methods dedicated for Petri nets, and a search for new efficient approaches is still ongoing.

Algorithms for evaluation of minimal cut sets.

Objective: We propose a way to enhance the evaluation of minimal cut sets (MCSs) in biological systems modeled by Petri nets, by providing criteria and methodology for determining their optimality in disabling specific processes without affecting critical system components.

Methods: This study concerns Petri nets to model biological systems and utilizes two primary approaches for MCS evaluation. First is the analyzing impact on t-invariants to identify structural dependencies.

Key Therapeutic Targets to Treat Hyperglycemia-Induced Atherosclerosis Analyzed Using a Petri Net-Based Model.

Chronic superphysiological glucose concentration is a hallmark of diabetes mellitus (DM) and a cause of damage to many types of cells. Atherosclerosis coexists with glucose metabolism disturbances, constituting a significant problem and exacerbating its complications. Atherosclerosis in DM is accelerated, so it is vital to slow its progression.

Searching for significant reactions and subprocesses in models of biological systems based on Petri nets.

The primary aim of this research was to propose algorithms enabling the identification of significant reactions and subprocesses within models of biological systems constructed using classical Petri nets. These solutions allow to performance of two analysis methods: an importance analysis for identifying individual reactions critical to the functioning of the model and an occurrence analysis for finding essential subprocesses. To demonstrate the utility of these methods, analyses of an example model have been performed.

Is It Feasible to Predict Cardiovascular Risk among Healthy Vegans, Lacto-/Ovo-Vegetarians, Pescatarians, and Omnivores under Forty?

Guidelines for cardiovascular (CV) risk assessment among young adults are uncertain. Researchers are still looking for new tools for earlier diagnosis of cardiovascular diseases (CVD), the leading cause of mortality in the modern world. This study aimed to assess whether CV risk estimation is possible in groups of healthy individuals under the age of 40 on different dietary patterns (vegans-VEGAN ( = 48), lacto-/ovo-vegetarians-VEGE ( = 49), pescatarians-PESCA ( = 23), and omnivores-OMN ( = 35)) during the pandemic period.

Dietary Habits and Lifestyle, Including Cardiovascular Risk among Vegetarians and Omnivores during the COVID-19 Pandemic in the Polish Population.

Background: This study assessed how two food groups—omnivores (OMN) and vegetarians (VEGE)—differ in lifestyle changes, including dietary habits during the COVID-19 pandemic. Materials: A total of 861 persons participated in the survey and were divided into two groups: persons following a mixed diet (n = 489) and vegetarians, including vegans (n = 372). The mean age shows no significant differences.

Graphlets in comparison of Petri net-based models of biological systems.

Capability to compare biological models is a crucial step needed in an analysis of complex organisms. Petri nets as a popular modelling technique, needs a possibility to determine the degree of structural similarities (e.g.

Nutritional Status and Habits among People on Vegan, Lacto/Ovo-Vegetarian, Pescatarian and Traditional Diets.

Background: This study assessed the possible dependencies between nutritional habits and body composition among subjects with different dietary habits. Materials: A total of 196 healthy (aged 18−50 yrs) participants were enrolled in the study and divided into 4 groups according to their diet: vegans-VEGAN (n = 53), lacto/ovo-vegetarians—VEGE (n = 52), pescatarians-PESCA (n = 28), and omnivores-OMN (n = 43). Methods: The Food Frequency Questionnaire (FFQ) was used, and body composition was assessed on the In-Body120 analyzer.

On anti-occurrence of subsets of transitions in Petri net-based models of complex biological systems.

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 expressive power.

Chronic Kidney Disease as a Cardiovascular Disorder-Tonometry Data Analyses.

Tonometry is commonly used to provide efficient and good diagnostics for cardiovascular disease (CVD). There are many advantages of this method, including low cost, non-invasiveness and little time to perform. In this study, the effort was undertaken to check whether tonometry data hides valuable information associated with different stages of chronic kidney disease (CKD) and end-stage renal disease (ESRD) treatment.

Comparing Petri net-based models of biological systems using Holmes.

Motivation: The first and necessary step in systems approach to study biological phenomena is building a formal model. One of the possibilities is to construct a model based on Petri nets. They have an intuitive graphical representation on one hand, and on the other, can be analyzed using formal mathematical methods.

Control of Cholesterol Metabolism Using a Systems Approach.

Cholesterol is an essential component of mammalian cells and is involved in many fundamental physiological processes; hence, its homeostasis in the body is tightly controlled, and any disturbance has serious consequences. Disruption of the cellular metabolism of cholesterol, accompanied by inflammation and oxidative stress, promotes the formation of atherosclerotic plaques and, consequently, is one of the leading causes of death in the Western world. Therefore, new drugs to regulate disturbed cholesterol metabolism are used and developed, which help to control cholesterol homeostasis but still do not entirely cure atherosclerosis.

The Mutual Contribution of 3-NT, IL-18, Albumin, and Phosphate Foreshadows Death of Hemodialyzed Patients in a 2-Year Follow-Up.

Patients with chronic kidney disease (CKD), especially those who are hemodialyzed (HD), are at significantly high risk of contracting cardiovascular disease and having increased mortality. This study aimed to find potential death predictors, the measurement of which may reflect increased mortality in HD patients, and then combine the most promising ones in frames of a simple death risk assessment model. For this purpose, HD patients (n=71) with acute myocardial infarction in the last year (HD group) and healthy people (control group) as a comparative group (n=32) were included in the study.

Interrelations between Iron and Vitamin A-Studied Using Systems Approach.

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.

Petri nets and ODEs as complementary methods for comprehensive analysis on an example of the ATM-p53-NF-[Formula: see text]B signaling pathways.

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 properties of these systems, but also help in specific tasks, such as search for drug molecular targets or treatment protocols.

The Crosstalk between SARS-CoV-2 Infection and the RAA System in Essential Hypertension-Analyses Using Systems Approach.

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 study, we have modeled the selected processes in a patient with essential hypertension and chronic kidney disease (CKD) suffering from COVID-19, emphasizing the function of the renin-angiotensin-aldosterone (RAA) system.

A Stochastic Petri Net-Based Model of the Involvement of Interleukin 18 in Atherosclerosis.

Interleukin 18 (IL-18) is a proinflammatory and proatherogenic cytokine with pleiotropic properties, which is involved in T and NK cell maturation and the synthesis of other inflammatory cytokines and cell adhesion molecules. It plays a significant role in orchestrating the cytokine cascade, accelerates atherosclerosis and influences plaque vulnerability. To investigate the influence of IL-18 cytokine on atherosclerosis development, a stochastic Petri net model was built and then analyzed.

Selected Atherosclerosis-Related Diseases May Differentially Affect the Relationship between Plasma Advanced Glycation End Products, Receptor sRAGE, and Uric Acid.

Our study aimed to identify the relationship between advanced glycation end products (AGEs), soluble receptor for advanced glycation end products (sRAGE), the AGEs/sRAGE, and uric acid (UA) levels in selected atherosclerosis diseases, i.e., abdominal aortic aneurysms (AAA), aortoiliac occlusive disease (AIOD), and chronic kidney disease (CKD), resulting from apparent differences in oxidative stress intensity.

A Role of Inflammation and Immunity in Essential Hypertension-Modeled and Analyzed Using Petri Nets.

Recent studies have shown that the innate and adaptive immune system, together with low-grade inflammation, may play an important role in essential hypertension. In this work, to verify the importance of selected factors for the development of essential hypertension, we created a Petri net-based model and analyzed it. The analysis was based mainly on t-invariants, knockouts of selected fragments of the net and its simulations.

Petri net-based model of the human DNA base excision repair pathway.

Cellular DNA is daily exposed to several damaging agents causing a plethora of DNA lesions. As a first aid to restore DNA integrity, several enzymes got specialized in damage recognition and lesion removal during the process called base excision repair (BER). A large number of DNA damage types and several different readers of nucleic acids lesions during BER pathway as well as two sub-pathways were considered in the definition of a model using the Petri net framework.

Systems Approach to Study Associations between OxLDL and Abdominal Aortic Aneurysms.

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, individual factors can act independently or synergistically with atherosclerosis.

Advanced Oxidation Protein Products and Carbonylated Proteins Levels in Endovascular and Open Repair of an Abdominal Aortic Aneurysm: The Effect of Pre-, Intra-, and Postoperative Treatment.

Background: In recent years, a rapid increase in studies focusing on the role of oxidative stress in the pathogenesis of an abdominal aortic aneurysm (AAA) has been observed. Oxidative modifications of proteins are infrequently evaluated in reference to AAA.

Objectives: The intensity of oxidative protein modifications, presented as advanced oxidation protein products (AOPP) and carbonylated proteins (C=O), in AAA patients qualified for surgery was estimated.