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petri net

Behnam Behinaein, Karen Rudie, Waheed Sangrar
Epidermal Growth Factor Receptor (EGFR) signaling to the Ras-MAPK pathway is implicated in the development and progression of cancer and is a major focus of targeted combination therapies. Physiochemical models have been used for identifying and testing the signal-inhibiting potential of targeted therapies, however, their application to larger multi-pathway networks is limited by the availability of experimentally-determined rate and concentration parameters. An alternate strategy for identifying and evaluating drug-targetable nodes is proposed...
October 3, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
George Milis, Panayiotis Kolios, Gaby Van Melick, Toni Staykova, Ira Helsloot, Georgios Ellinas, Christos Panayiotou, Marios Polycarpou
The medical emergency response comprises a domain with complex processes, encompassing multiple heterogeneous entities, from organisations involved in the response to human actors to key information sources. Due to the heterogeneity of the entities and the complexity of the domain, it is important to fully understand the individual processes in which the components are involved and their inter-operations, before attempting to design any technological tool for coordination and decision support. This work starts with the gluing together and visualisation of the interactions of involved entities into a conceptual model, along the identified five workspaces of emergency response...
September 2016: Healthcare Technology Letters
Feng Zhang, Yuetong Xu, Jarong Chou
The service of sensor device in Emerging Sensor Networks (ESNs) is the extension of traditional Web services. Through the sensor network, the service of sensor device can communicate directly with the entity in the geographic environment, and even impact the geographic entity directly. The interaction between the sensor device in ESNs and geographic environment is very complex, and the interaction modeling is a challenging problem. This paper proposed a novel Petri Nets-based modeling method for the interaction between the sensor device and the geographic environment...
2016: Sensors
Scott L Collins, Laura M Ladwig, Matthew D Petrie, Sydney K Jones, John M Mulhouse, James R Thibault, William T Pockman
Global environmental change is altering temperature, precipitation patterns, resource availability, and disturbance regimes. Theory predicts that ecological presses will interact with pulse events to alter ecosystem structure and function. In 2006, we established a long-term, multifactor global change experiment to determine the interactive effects of nighttime warming, increased atmospheric nitrogen (N) deposition, and increased winter precipitation on plant community structure and aboveground net primary production (ANPP) in a northern Chihuahuan Desert grassland...
September 9, 2016: Global Change Biology
Carlos A Rovetto, Tomás J Concepción, Elia Esther Cano
Prevention and avoidance of deadlocks in sensor networks that use the wormhole routing algorithm is an active research domain. There are diverse control policies that will address this problem being our approach a new method. In this paper we present a virtual control policy for the new specialized Petri net subclass called Binary Ordered Resources Petri Net (BORPN). Essentially, it is an ordinary class constructed from various state machines that share unitary resources in a complex form, which allows branching and joining of processes...
2016: Sensors
Judith Somekh, Mor Peleg, Alal Eran, Itay Koren, Ariel Feiglin, Alik Demishtein, Ruth Shiloh, Monika Heiner, Sek Won Kong, Zvulun Elazar, Isaac Kohane
We propose a model-driven methodology aimed to shed light on complex disorders. Our approach enables exploring shared etiologies of comorbid diseases at the molecular pathway level. The method, Comparative Comorbidities Simulation (CCS), uses stochastic Petri net simulation for examining the phenotypic effects of perturbation of a network known to be involved in comorbidities to predict new roles for mutations in comorbid conditions. To demonstrate the utility of our novel methodology, we investigated the molecular convergence of autism spectrum disorder (ASD) and inflammatory bowel disease (IBD) on the autophagy pathway...
August 10, 2016: Journal of Biomedical Informatics
Mani Mehraei, Rza Bashirov, Şükrü Tüzmen
Recent molecular studies provide important clues into treatment of [Formula: see text]-thalassemia, sickle-cell anaemia and other [Formula: see text]-globin disorders revealing that increased production of fetal hemoglobin, that is normally suppressed in adulthood, can ameliorate the severity of these diseases. In this paper, we present a novel approach for drug prediction for [Formula: see text]-globin disorders. Our approach is centered upon quantitative modeling of interactions in human fetal-to-adult hemoglobin switch network using hybrid functional Petri nets...
June 21, 2016: Journal of Bioinformatics and Computational Biology
Diogo Almeida, Vasco Azevedo, Artur Silva, Jan Baumbach
Systems biology plays a central role for biological network analysis in the post-genomic era. Cytoscape is the standard bioinformatics tool offering the community an extensible platform for computational analysis of the emerging cellular network together with experimental omics data sets. However, only few apps/plugins/tools are available for simulating network dynamics in Cytoscape 3. Many approaches of varying complexity exist but none of them have been integrated into Cytoscape as app/plugin yet. Here, we introduce PetriScape, the first Petri net simulator for Cytoscape...
2016: Journal of Integrative Bioinformatics
Niloofar Nickaeen, Shiva Moein, Zarifeh Heidary, Jafar Ghaisari
BACKGROUND: Mathematical modeling of biological systems is an attractive way for studying complex biological systems and their behaviors. Petri Nets, due to their ability to model systems with various levels of qualitative information, have been wildly used in modeling biological systems in which enough qualitative data may not be at disposal. These nets have been used to answer questions regarding the dynamics of different cell behaviors including the translation process. In one stage of the translation process, the RNA sequence may be degraded...
2016: Advanced Biomedical Research
Lei Niu, Fenghui Ren, Minjie Zhang, Quan Bai
Concurrent multiple negotiation (CMN) provides a mechanism for an agent to simultaneously conduct more than one negotiation. There may exist different interdependency relationships among these negotiations and these interdependency relationships can impact the outcomes of these negotiations. The outcomes of these concurrent negotiations contribute together for the agent to achieve an overall negotiation goal. Handling a CMN while considering interdependency relationships among multiple negotiations is a challenging research problem...
June 21, 2016: IEEE Transactions on Cybernetics
Annika Jacobsen, Nika Heijmans, Folkert Verkaar, Martine J Smit, Jaap Heringa, Renée van Amerongen, K Anton Feenstra
The Wnt/β-catenin signaling pathway is important for multiple developmental processes and tissue maintenance in adults. Consequently, deregulated signaling is involved in a range of human diseases including cancer and developmental defects. A better understanding of the intricate regulatory mechanism and effect of physiological (active) and pathophysiological (hyperactive) WNT signaling is important for predicting treatment response and developing novel therapies. The constitutively expressed CTNNB1 (commonly and hereafter referred to as β-catenin) is degraded by a destruction complex, composed of amongst others AXIN1 and GSK3...
2016: PloS One
Jelili Oyelade, Itunuoluwa Isewon, Solomon Rotimi, Ifeoluwa Okunoren
Malaria is one of the deadly diseases, which affects a large number of the world's population. The Plasmodium falciparum parasite during erythrocyte stages produces its energy mainly through anaerobic glycolysis, with pyruvate being converted into lactate. The glycolysis metabolism in P. falci-parum is one of the important metabolic pathways of the parasite because the parasite is entirely dependent on it for energy. Also, several glycolytic enzymes have been proposed as drug targets. Petri nets (PNs) have been recognized as one of the important models for representing biological pathways...
2016: Bioinformatics and Biology Insights
Aditya Khamparia, Babita Pandey
Vulnerabilities at various levels are main cause of security risks in e-learning system. This paper presents a modified threat driven modeling framework, to identify the threats after risk assessment which requires mitigation and how to mitigate those threats. To model those threat mitigations aspects oriented stochastic petri nets are used. This paper included security metrics based on vulnerabilities present in e-learning system. The Common Vulnerability Scoring System designed to provide a normalized method for rating vulnerabilities which will be used as basis in metric definitions and calculations...
2016: SpringerPlus
Michael A Boemo, Alexandra E Lucas, Andrew J Turberfield, Luca Cardelli
Simple computation can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be described as a stochastic Petri net. The system can be verified by mapping the Petri net onto a continuous-time Markov chain, which can also be used to find an optimal design for the circuit. This theoretical machinery can be applied to create software that automatically designs a DNA circuit, linking an abstract propositional formula to a physical DNA computation system that is capable of evaluating it...
August 19, 2016: ACS Synthetic Biology
Colette E Jackson, Caroline Haig, Paul Welsh, Jonathan R Dalzell, Ioannis K Tsorlalis, Alex McConnachie, David Preiss, Stefan D Anker, Naveed Sattar, Mark C Petrie, Roy S Gardner, John J V McMurray
AIMS: In recent years there has been an increase in the number of biomarkers in heart failure (HF). The clinical role for these novel biomarkers in combination is not clear. METHODS AND RESULTS: The following novel biomarkers were measured from 628 patients recently hospitalized with decompensated HF; mid-regional pro-adrenomedullin (MR-proADM), mid-regional pro-atrial natriuretic peptide (MR-proANP), copeptin, high-sensitivity cardiac troponin T (hs-cTnT), ST2, galectin-3, cystatin C, combined free light chains (cFLC) and high sensitivity C-reactive protein (hsCRP)...
April 25, 2016: European Journal of Heart Failure
Hsiu-Sen Chiang, Shun-Chi Pao
Alzheimer's disease is a degenerative brain disease that results in cardinal memory deterioration and significant cognitive impairments. The early treatment of Alzheimer's disease can significantly reduce deterioration. Early diagnosis is difficult, and early symptoms are frequently overlooked. While much of the literature focuses on disease detection, the use of electroencephalography (EEG) in Alzheimer's diagnosis has received relatively little attention. This study combines the fuzzy and associative Petri net methodologies to develop a model for the effective and objective detection of Alzheimer's disease...
May 2016: Journal of Medical Systems
Jiwei Huang, Yeping Zhu, Bo Cheng, Chuang Lin, Junliang Chen
With the growing popularity of complex dynamic activities in manufacturing processes, traceability of the entire life of every product has drawn significant attention especially for food, clinical materials, and similar items. This paper studies the traceability issue in cyber-physical manufacturing systems from a theoretical viewpoint. Petri net models are generalized for formulating dynamic manufacturing processes, based on which a detailed approach for enabling traceability analysis is presented. Models as well as algorithms are carefully designed, which can trace back the lifecycle of a possibly contaminated item...
2016: Sensors
H N Su, Y Y Xu, X Wang, K Q Zhang, G H Li
A total of 11 bacterial strains were assayed for bacteria-induced trap formation in the nematode-trapping fungus Arthrobotrys oligospora YMF1·01883 with two-compartmented Petri dish. These strains were identified on the basis of their 16S rRNA gene sequences. Volatile organic compounds (VOCs) of eight isolates were extracted using solid-phase micro-extraction (SPME) and their structures were identified based on gas chromatography-mass spectrometry (GC-MS). At the same time, all isolates were used for quantitative measurement of ammonia by the indophenol blue method...
April 2016: Letters in Applied Microbiology
Fei Liu, Monika Heiner, Ming Yang
Stochastic Petri nets (SPNs) have been widely used to model randomness which is an inherent feature of biological systems. However, for many biological systems, some kinetic parameters may be uncertain due to incomplete, vague or missing kinetic data (often called fuzzy uncertainty), or naturally vary, e.g., between different individuals, experimental conditions, etc. (often called variability), which has prevented a wider application of SPNs that require accurate parameters. Considering the strength of fuzzy sets to deal with uncertain information, we apply a specific type of stochastic Petri nets, fuzzy stochastic Petri nets (FSPNs), to model and analyze biological systems with uncertain kinetic parameters...
2016: PloS One
Misbah Razzaq, Jamil Ahmad
Internet worms are analogous to biological viruses since they can infect a host and have the ability to propagate through a chosen medium. To prevent the spread of a worm or to grasp how to regulate a prevailing worm, compartmental models are commonly used as a means to examine and understand the patterns and mechanisms of a worm spread. However, one of the greatest challenge is to produce methods to verify and validate the behavioural properties of a compartmental model. This is why in this study we suggest a framework based on Petri Nets and Model Checking through which we can meticulously examine and validate these models...
2015: PloS One
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