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https://www.readbyqxmd.com/read/28494999/modeling-and-control-of-operator-functional-state-in-a-unified-framework-of-fuzzy-inference-petri-nets
#1
Jian-Hua Zhang, Jia-Jun Xia, Jonathan M Garibaldi, Petros P Groumpos, Ru-Bin Wang
BACKGROUND AND OBJECTIVE: In human-machine (HM) hybrid control systems, human operator and machine cooperate to achieve the control objectives. To enhance the overall HM system performance, the discrete manual control task-load by the operator must be dynamically allocated in accordance with continuous-time fluctuation of psychophysiological functional status of the operator, so-called operator functional state (OFS). The behavior of the HM system is hybrid in nature due to the co-existence of discrete task-load (control) variable and continuous operator performance (system output) variable...
June 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28386100/petri-net-computational-modelling-of-langerhans-cell-interferon-regulatory-factor-network-predicts-their-role-in-t-cell-activation
#2
Marta E Polak, Chuin Ying Ung, Joanna Masapust, Tom C Freeman, Michael R Ardern-Jones
Langerhans cells (LCs) are able to orchestrate adaptive immune responses in the skin by interpreting the microenvironmental context in which they encounter foreign substances, but the regulatory basis for this has not been established. Utilising systems immunology approaches combining in silico modelling of a reconstructed gene regulatory network (GRN) with in vitro validation of the predictions, we sought to determine the mechanisms of regulation of immune responses in human primary LCs. The key role of Interferon regulatory factors (IRFs) as controllers of the human Langerhans cell response to epidermal cytokines was revealed by whole transcriptome analysis...
April 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28268829/arguing-effectiveness-of-biomedical-signal-acquisition-devices-using-colored-petri-nets-models-and-assurance-cases-in-gsn-an-ecg-case-study
#3
Alvaro Sobrinho, Paulo Cunha, Leandro Dias da Silva, Angelo Perkusich, Thiago Cordeiro, Jarbas Segundo
Reported cases of adverse events and product recalls expose limitations of biomedical signal acquisition devices. Approximately, ninety percent of the 1.210 recalls reported by the US Food and Drug Administration (FDA) between 2006 and 2011 were of class 2 devices such as Electrocardiography (ECG) devices. We show in this paper how manufacturers of biomedical signal acquisition devices can argue effectiveness of these devices using Colored Petri Nets (CPN) models and assurance cases in Goal Structuring Notation (GSN) by means of an ECG case study...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28253310/petri-net-based-approach-to-modeling-and-analysis-of-selected-aspects-of-the-molecular-regulation-of-angiogenesis
#4
Dorota Formanowicz, Marcin Radom, Piotr Zawierucha, Piotr Formanowicz
The functioning of both normal and pathological tissues depends on an adequate supply of oxygen through the blood vessels. A process called angiogenesis, in which new endothelial cells and smooth muscles interact with each other, forming new blood vessels either from the existing ones or from a primary vascular plexus, is particularly important and interesting, due to new therapeutic possibilities it offers. This is a multi-step and very complex process, so an accurate understanding of the underlying mechanisms is a significant task, especially in recent years, with the constantly increasing amount of new data that must be taken into account...
2017: PloS One
https://www.readbyqxmd.com/read/28227025/arguing-effectiveness-of-biomedical-signal-acquisition-devices-using-colored-petri-nets-models-and-assurance-cases-in-gsn-an-ecg-case-study
#5
Alvaro Sobrinho, Paulo Cunha, Leandro Dias da Silva, Angelo Perkusich, Thiago Cordeiro, Jarbas Segundo, Alvaro Sobrinho, Paulo Cunha, Leandro Dias da Silva, Angelo Perkusich, Thiago Cordeiro, Jarbas Segundo, Leandro Dias da Silva, Paulo Cunha, Alvaro Sobrinho, Angelo Perkusich, Jarbas Segundo, Thiago Cordeiro
Reported cases of adverse events and product recalls expose limitations of biomedical signal acquisition devices. Approximately, ninety percent of the 1.210 recalls reported by the US Food and Drug Administration (FDA) between 2006 and 2011 were of class 2 devices such as Electrocardiography (ECG) devices. We show in this paper how manufacturers of biomedical signal acquisition devices can argue effectiveness of these devices using Colored Petri Nets (CPN) models and assurance cases in Goal Structuring Notation (GSN) by means of an ECG case study...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28166885/a-colored-petri-nets-based-workload-evaluation-model-and-its-validation-through-multi-attribute-task-battery-ii
#6
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
https://www.readbyqxmd.com/read/28155706/a-methodological-approach-for-using-high-level-petri-nets-to-model-the-immune-system-response
#7
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
https://www.readbyqxmd.com/read/28113516/petri-net-siphon-analysis-and-graph-theoretic-measures-for-identifying-combination-therapies-in-cancer
#8
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/28092800/effect-of-venepuncture-process-design-on-efficiency-and-failure-rates-a-simulation-model-study-for-secondary-care
#9
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
https://www.readbyqxmd.com/read/28005249/runtime-verification-of-pacemaker-functionality-using-hierarchical-fuzzy-colored-petri-nets
#10
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
https://www.readbyqxmd.com/read/27906974/in-silico-knockout-studies-of-xenophagic-capturing-of-salmonella
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/27740493/petri-net-siphon-analysis-and-graph-theoretic-measures-for-identifying-combination-therapies-in-cancer
#16
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
#17
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
#18
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...
September 25, 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
#19
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
#20
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
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