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petri net

Peng Wang, Weining Fang, Beiyuan Guo
This paper proposed a colored petri nets based workload evaluation model. A formal interpretation of workload was firstly introduced based on the process that reflection of petri nets components to task. A petri net based description of Multiple Resources theory was given by comprehending it from a new angle. A new application of VACP rating scales named V/A-C-P unit, and the definition of colored transitions were proposed to build a model of task process. The calculation of workload mainly has the following four steps: determine token's initial position and values; calculate the weight of directed arcs on the basis of the rules proposed; calculate workload from different transitions, and correct the influence of repetitive behaviors...
April 2017: Applied Ergonomics
Marzio Pennisi, Salvatore Cavalieri, Santo Motta, Francesco Pappalardo
BACKGROUND: Mathematical and computational models showed to be a very important support tool for the comprehension of the immune system response against pathogens. Models and simulations allowed to study the immune system behavior, to test biological hypotheses about diseases and infection dynamics, and to improve and optimize novel and existing drugs and vaccines. Continuous models, mainly based on differential equations, usually allow to qualitatively study the system but lack in description; conversely discrete models, such as agent based models and cellular automata, permit to describe in detail entities properties at the cost of losing most qualitative analyses...
December 22, 2016: BMC Bioinformatics
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
Sean Reed, Rasa Remenyte-Prescott, Ben Rees
BACKGROUND: Healthcare aims to deliver good patient outcomes. For many clinical procedures there are multiple alternative task sequences that can be performed. These deviations can influence procedure reliability, efficiency of usage of hospital resources and risk to staff and patient safety. Venepuncture is one of the most common invasive procedures in healthcare. Literature of clinical practice shows evidence of wide variability in the procedure order and the duration of each step, which can depend on attributes, such as patient health, sampling method and staff skills...
December 29, 2016: International Journal of Nursing Studies
Negar Majma, Seyed Morteza Babamir, Amirhassan Monadjemi
Today, implanted medical devices are increasingly used for many patients and in case of diverse health problems. However, several runtime problems and errors are reported by the relevant organizations, even resulting in patient death. One of those devices is the pacemaker. The pacemaker is a device helping the patient to regulate the heartbeat by connecting to the cardiac vessels. This device is directed by its software, so any failure in this software causes a serious malfunction. Therefore, this study aims to a better way to monitor the device's software behavior to decrease the failure risk...
February 2017: Journal of Medical Systems
Jennifer Scheidel, Leonie Amstein, Jörg Ackermann, Ivan Dikic, Ina Koch
The degradation of cytosol-invading pathogens by autophagy, a process known as xenophagy, is an important mechanism of the innate immune system. Inside the host, Salmonella Typhimurium invades epithelial cells and resides within a specialized intracellular compartment, the Salmonella-containing vacuole. A fraction of these bacteria does not persist inside the vacuole and enters the host cytosol. Salmonella Typhimurium that invades the host cytosol becomes a target of the autophagy machinery for degradation...
December 2016: PLoS Computational Biology
Laura M F Bertens, Jetty Kleijn, Sander C Hille, Monika Heiner, Maciej Koutny, Fons J Verbeek
Both Petri nets and differential equations are important modeling tools for biological processes. In this paper we demonstrate how these two modeling techniques can be combined to describe biological gradient formation. Parameters derived from partial differential equation describing the process of gradient formation are incorporated in an abstract Petri net model. The quantitative aspects of the resulting model are validated through a case study of gradient formation in the fruit fly.
2016: Natural Computing
Petra Steinacker, André Huss, Benjamin Mayer, Torsten Grehl, Julian Grosskreutz, Guntram Borck, Jens Kuhle, Dorothée Lulé, Thomas Meyer, Patrick Oeckl, Susanne Petri, Jochen Weishaupt, Albert C Ludolph, Markus Otto
There is a need for diagnostic, prognostic, and monitoring blood biomarkers for ALS. We aimed to analyse and compare proposed candidate markers for disease progression in the course of ALS. Blood samples were taken from 125 ALS patients, including nine patients with C9orf72 or SOD1 mutation, at regular intervals of six months. ALS patients were characterized by the ALS functional rating scale (ALSFRS-R) and the Edinburgh Cognitive and Behavioural ALS Screen (ECAS). We quantified neurofilament light chain (NF-L), S100B, and progranulin (PGRN) and analysed it in relation to disease progression...
November 5, 2016: Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration
Samra Khalid, Rumeza Hanif, Samar H K Tareen, Amnah Siddiqa, Zurah Bibi, Jamil Ahmad
BACKGROUND: Breast cancer (BC) is one of the leading cause of death among females worldwide. The increasing incidence of BC is due to various genetic and environmental changes which lead to the disruption of cellular signaling network(s). It is a complex disease in which several interlinking signaling cascades play a crucial role in establishing a complex regulatory network. The logical modeling approach of René Thomas has been applied to analyze the behavior of estrogen receptor-alpha (ER-α) associated Biological Regulatory Network (BRN) for a small part of complex events that leads to BC metastasis...
2016: PeerJ
Joachim Niehren, Cristian Versari, Mathias John, François Coutte, Philippe Jacques
We wish to predict changes of reaction networks with partial kinetic information that lead to target changes of their steady states. The changes may be either increases or decreases of influxes, reaction knockouts, or multiple changes of these two kinds. Our prime applications are knockout prediction tasks for metabolic and regulation networks. In a first step, we propose a formal modeling language for reaction networks with partial kinetic information. The modeling language has a graphical syntax reminiscent to Petri nets...
November 2016: Bio Systems
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...
October 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...
June 4, 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
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