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https://www.readbyqxmd.com/read/27906974/in-silico-knockout-studies-of-xenophagic-capturing-of-salmonella
#1
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
https://www.readbyqxmd.com/read/27881934/modeling-biological-gradient-formation-combining-partial-differential-equations-and-petri-nets
#2
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
https://www.readbyqxmd.com/read/27819158/diagnostic-and-prognostic-significance-of-neurofilament-light-chain-nf-l-but-not-progranulin-and-s100b-in-the-course-of-amyotrophic-lateral-sclerosis-data-from-the-german-mnd-net
#3
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
https://www.readbyqxmd.com/read/27781158/formal-modeling-and-analysis-of-er-%C3%AE-associated-biological-regulatory-network-in-breast-cancer
#4
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
https://www.readbyqxmd.com/read/27769750/predicting-changes-of-reaction-networks-with-partial-kinetic-information
#5
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 16, 2016: Bio Systems
https://www.readbyqxmd.com/read/27740493/petri-net-siphon-analysis-and-graph-theoretic-measures-for-identifying-combination-therapies-in-cancer
#6
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
https://www.readbyqxmd.com/read/27733927/integrated-modelling-of-medical-emergency-response-process-for-improved-coordination-and-decision-support
#7
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
https://www.readbyqxmd.com/read/27681730/a-novel-petri-nets-based-modeling-method-for-the-interaction-between-the-sensor-and-the-geographic-environment-in-emerging-sensor-networks
#8
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
https://www.readbyqxmd.com/read/27612326/press-pulse-interactions-effects-of-warming-n-deposition-altered-winter-precipitation-and-fire-on-desert-grassland-community-structure-and-dynamics
#9
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
https://www.readbyqxmd.com/read/27548170/virtual-control-policy-for-binary-ordered-resources-petri-net-class
#10
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
https://www.readbyqxmd.com/read/27522000/a-model-driven-methodology-for-exploring-complex-disease-comorbidities-applied-to-autism-spectrum-disorder-and-inflammatory-bowel-disease
#11
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
https://www.readbyqxmd.com/read/27431020/target-based-drug-discovery-for-formula-see-text-globin-disorders-drug-target-prediction-using-quantitative-modeling-with-hybrid-functional-petri-nets
#12
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
https://www.readbyqxmd.com/read/27402693/petriscape-a-plugin-for-discrete-petri-net-simulations-in-cytoscape
#13
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
https://www.readbyqxmd.com/read/27376039/colored-petri-net-modeling-of-small-interfering-rna-mediated-messenger-rna-degradation
#14
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
https://www.readbyqxmd.com/read/27337734/a-concurrent-multiple-negotiation-protocol-based-on-colored-petri-nets
#15
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
https://www.readbyqxmd.com/read/27218469/construction-and-experimental-validation-of-a-petri-net-model-of-wnt-%C3%AE-catenin-signaling
#16
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
https://www.readbyqxmd.com/read/27199550/modeling-of-the-glycolysis-pathway-in-plasmodium-falciparum-using-petri-nets
#17
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
https://www.readbyqxmd.com/read/27119050/threat-driven-modeling-framework-using-petri-nets-for-e-learning-system
#18
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
https://www.readbyqxmd.com/read/27114350/the-formal-language-and-design-principles-of-autonomous-dna-walker-circuits
#19
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
https://www.readbyqxmd.com/read/27114189/the-incremental-prognostic-and-clinical-value-of-multiple-novel-biomarkers-in-heart-failure
#20
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)...
December 2016: European Journal of Heart Failure
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