Discrete Deterministic and Stochastic Petri Nets

NASA Technical Reports Server (NTRS)

Zijal, Robert; Ciardo, Gianfranco

1996-01-01

Petri nets augmented with timing specifications gained a wide acceptance in the area of performance and reliability evaluation of complex systems exhibiting concurrency, synchronization, and conflicts. The state space of time-extended Petri nets is mapped onto its basic underlying stochastic process, which can be shown to be Markovian under the assumption of exponentially distributed firing times. The integration of exponentially and non-exponentially distributed timing is still one of the major problems for the analysis and was first attacked for continuous time Petri nets at the cost of structural or analytical restrictions. We propose a discrete deterministic and stochastic Petri net (DDSPN) formalism with no imposed structural or analytical restrictions where transitions can fire either in zero time or according to arbitrary firing times that can be represented as the time to absorption in a finite absorbing discrete time Markov chain (DTMC). Exponentially distributed firing times are then approximated arbitrarily well by geometric distributions. Deterministic firing times are a special case of the geometric distribution. The underlying stochastic process of a DDSPN is then also a DTMC, from which the transient and stationary solution can be obtained by standard techniques. A comprehensive algorithm and some state space reduction techniques for the analysis of DDSPNs are presented comprising the automatic detection of conflicts and confusions, which removes a major obstacle for the analysis of discrete time models.

Colored Petri net modeling and simulation of signal transduction pathways.

PubMed

Lee, Dong-Yup; Zimmer, Ralf; Lee, Sang Yup; Park, Sunwon

2006-03-01

Presented herein is a methodology for quantitatively analyzing the complex signaling network by resorting to colored Petri nets (CPN). The mathematical as well as Petri net models for two basic reaction types were established, followed by the extension to a large signal transduction system stimulated by epidermal growth factor (EGF) in an application study. The CPN models based on the Petri net representation and the conservation and kinetic equations were used to examine the dynamic behavior of the EGF signaling pathway. The usefulness of Petri nets is demonstrated for the quantitative analysis of the signal transduction pathway. Moreover, the trade-offs between modeling capability and simulation efficiency of this pathway are explored, suggesting that the Petri net model can be invaluable in the initial stage of building a dynamic model.

Teaching Petri Nets Using P3

ERIC Educational Resources Information Center

Gasevic, Dragan; Devedzic, Vladan

2004-01-01

This paper presents Petri net software tool P3 that is developed for training purposes of the Architecture and organization of computers (AOC) course. The P3 has the following features: graphical modeling interface, interactive simulation by single and parallel (with previous conflict resolution) transition firing, two well-known Petri net…

A Petri net controller for distributed hierarchical systems. Thesis

NASA Technical Reports Server (NTRS)

Peck, Joseph E.

1991-01-01

The solutions to a wide variety of problems are often best organized as a distributed hierarchical system. These systems can be graphically and mathematically modeled through the use of Petri nets, which can easily represent synchronous, asynchronous, and concurrent operations. This thesis presents a controller implementation based on Petri nets and a design methodology for the interconnection of distributed Petri nets. Two case studies are presented in which the controller operates a physical system, the Center for Intelligent Robotic Systems for Space Exploration Dual Arm Robotic Testbed.

Ontology based standardization of Petri net modeling for signaling pathways.

PubMed

Takai-Igarashi, Takako

2005-01-01

Taking account of the great availability of Petri nets in modeling and analyzing large complicated signaling networks, semantics of Petri nets is in need of systematization for the purpose of consistency and reusability of the models. This paper reports on standardization of units of Petri nets on the basis of an ontology that gives an intrinsic definition to the process of signaling in signaling pathways.

Ontology based standardization of petri net modeling for signaling pathways.

PubMed

Takai-Igarashi, Takako

2011-01-01

Taking account of the great availability of Petri nets in modeling and analyzing large complicated signaling networks, semantics of Petri nets is in need of systematization for the purpose of consistency and reusability of the models. This paper reports on standardization of units of Petri nets on the basis of an ontology that gives an intrinsic definition to the process of signaling in signaling pathways.

Petri net based model of the body iron homeostasis.

PubMed

Formanowicz, Dorota; Sackmann, Andrea; Formanowicz, Piotr; Błazewicz, Jacek

2007-10-01

The body iron homeostasis is a not fully understood complex process. Despite the fact that some components of this process have been described in the literature, the complete model of the whole process has not been proposed. In this paper a Petri net based model of the body iron homeostasis is presented. Recently, Petri nets have been used for describing and analyzing various biological processes since they allow modeling the system under consideration very precisely. The main result presented in the paper is twofold, i.e., an informal description of the main part of the whole iron homeostasis process is described, and then it is also formulated in the formal language of Petri net theory. This model allows for a possible simulation of the process, since Petri net theory provides a lot of established analysis techniques.

Snoopy--a unifying Petri net framework to investigate biomolecular networks.

PubMed

Rohr, Christian; Marwan, Wolfgang; Heiner, Monika

2010-04-01

To investigate biomolecular networks, Snoopy provides a unifying Petri net framework comprising a family of related Petri net classes. Models can be hierarchically structured, allowing for the mastering of larger networks. To move easily between the qualitative, stochastic and continuous modelling paradigms, models can be converted into each other. We get models sharing structure, but specialized by their kinetic information. The analysis and iterative reverse engineering of biomolecular networks is supported by the simultaneous use of several Petri net classes, while the graphical user interface adapts dynamically to the active one. Built-in animation and simulation are complemented by exports to various analysis tools. Snoopy facilitates the addition of new Petri net classes thanks to its generic design. Our tool with Petri net samples is available free of charge for non-commercial use at http://www-dssz.informatik.tu-cottbus.de/snoopy.html; supported operating systems: Mac OS X, Windows and Linux (selected distributions).

Parallel firing strategy on Petri nets: A review

NASA Astrophysics Data System (ADS)

Mavlankulov, Gairatzhan; Turaev, Sherzod; Zhumabaeva, Laula; Zhukabayeva, Tamara

2015-05-01

In this paper we review the recent results related on Petri net controlled grammars and the close related topics. Though the theme of regulated grammars is one of the classic topics in formal language theory, a Petri net controlled grammar is still interesting subject for the investigation for many reasons. This type of grammars can successfully be used in modeling new problems emerging in manufacturing systems, systems biology and other areas. Moreover, the graphically illustrability, the ability to represent both a grammar and its control in one structure, and the possibility to unify different regulated rewritings make this formalization attractive for the study. We also summarize the obtained results and propose a new conception such as parallel firing strategy on Petri Nets.

A Petri Net Approach Based Elementary Siphons Supervisor for Flexible Manufacturing Systems

NASA Astrophysics Data System (ADS)

Abdul-Hussin, Mowafak Hassan

2015-05-01

This paper presents an approach to constructing a class of an S3PR net for modeling, simulation and control of processes occurring in the flexible manufacturing system (FMS) used based elementary siphons of a Petri net. Siphons are very important to the analysis and control of deadlocks of FMS that is significant objectives of siphons. Petri net models in the efficiency structure analysis, and utilization of the FMSs when different policy can be implemented lead to the deadlock prevention. We are representing an effective deadlock-free policy of a special class of Petri nets called S3PR. Simulation of Petri net structural analysis and reachability graph analysis is used for analysis and control of Petri nets. Petri nets contain been successfully as one of the most powerful tools for modelling of FMS, where Using structural analysis, we show that liveness of such systems can be attributed to the absence of under marked siphons.

Petri nets SM-cover-based on heuristic coloring algorithm

NASA Astrophysics Data System (ADS)

Tkacz, Jacek; Doligalski, Michał

2015-09-01

In the paper, coloring heuristic algorithm of interpreted Petri nets is presented. Coloring is used to determine the State Machines (SM) subnets. The present algorithm reduces the Petri net in order to reduce the computational complexity and finds one of its possible State Machines cover. The proposed algorithm uses elements of interpretation of Petri nets. The obtained result may not be the best, but it is sufficient for use in rapid prototyping of logic controllers. Found SM-cover will be also used in the development of algorithms for decomposition, and modular synthesis and implementation of parallel logic controllers. Correctness developed heuristic algorithm was verified using Gentzen formal reasoning system.

Modified Petri net model sensitivity to workload manipulations

NASA Technical Reports Server (NTRS)

White, S. A.; Mackinnon, D. P.; Lyman, J.

1986-01-01

Modified Petri Nets (MPNs) are investigated as a workload modeling tool. The results of an exploratory study of the sensitivity of MPNs to work load manipulations in a dual task are described. Petri nets have been used to represent systems with asynchronous, concurrent and parallel activities (Peterson, 1981). These characteristics led some researchers to suggest the use of Petri nets in workload modeling where concurrent and parallel activities are common. Petri nets are represented by places and transitions. In the workload application, places represent operator activities and transitions represent events. MPNs have been used to formally represent task events and activities of a human operator in a man-machine system. Some descriptive applications demonstrate the usefulness of MPNs in the formal representation of systems. It is the general hypothesis herein that in addition to descriptive applications, MPNs may be useful for workload estimation and prediction. The results are reported of the first of a series of experiments designed to develop and test a MPN system of workload estimation and prediction. This first experiment is a screening test of MPN model general sensitivity to changes in workload. Positive results from this experiment will justify the more complicated analyses and techniques necessary for developing a workload prediction system.

Utilization Elementary Siphons of Petri Net to Solved Deadlocks in Flexible Manufacturing Systems

NASA Astrophysics Data System (ADS)

Abdul-Hussin, Mowafak Hassan

2015-07-01

This article presents an approach to the constructing a class structural analysis of Petri nets, where elementary siphons are mainly used in the development of a deadlock control policy of flexible manufacturing systems (FMSs), that has been exploited successfully for the design of supervisors of some supervisory control problems. Deadlock-free operation of FMSs is significant objectives of siphons in the Petri net. The structure analysis of Petri net models has efficiency in control of FMSs, however different policy can be implemented for the deadlock prevention. Petri nets models based deadlock prevention for FMS's has gained considerable interest in the development of control theory and methods for design, controlling, operation, and performance evaluation depending of the special class of Petri nets called S3PR. Both structural analysis and reachability tree analysis is used for the purposes analysis, simulation and control of Petri nets. In our ex-perimental approach based to siphon is able to resolve the problem of deadlock occurred to Petri nets that are illustrated with an FMS.

Petri Nets - A Mathematical Formalism to Analyze Chemical Reaction Networks.

PubMed

Koch, Ina

2010-12-17

In this review we introduce and discuss Petri nets - a mathematical formalism to describe and analyze chemical reaction networks. Petri nets were developed to describe concurrency in general systems. We find most applications to technical and financial systems, but since about twenty years also in systems biology to model biochemical systems. This review aims to give a short informal introduction to the basic formalism illustrated by a chemical example, and to discuss possible applications to the analysis of chemical reaction networks, including cheminformatics. We give a short overview about qualitative as well as quantitative modeling Petri net techniques useful in systems biology, summarizing the state-of-the-art in that field and providing the main literature references. Finally, we discuss advantages and limitations of Petri nets and give an outlook to further development. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fault Diagnosis System of Wind Turbine Generator Based on Petri Net

NASA Astrophysics Data System (ADS)

Zhang, Han

Petri net is an important tool for discrete event dynamic systems modeling and analysis. And it has great ability to handle concurrent phenomena and non-deterministic phenomena. Currently Petri nets used in wind turbine fault diagnosis have not participated in the actual system. This article will combine the existing fuzzy Petri net algorithms; build wind turbine control system simulation based on Siemens S7-1200 PLC, while making matlab gui interface for migration of the system to different platforms.

Fluid Stochastic Petri Nets: Theory, Applications, and Solution

NASA Technical Reports Server (NTRS)

Horton, Graham; Kulkarni, Vidyadhar G.; Nicol, David M.; Trivedi, Kishor S.

1996-01-01

In this paper we introduce a new class of stochastic Petri nets in which one or more places can hold fluid rather than discrete tokens. We define a class of fluid stochastic Petri nets in such a way that the discrete and continuous portions may affect each other. Following this definition we provide equations for their transient and steady-state behavior. We present several examples showing the utility of the construct in communication network modeling and reliability analysis, and discuss important special cases. We then discuss numerical methods for computing the transient behavior of such nets. Finally, some numerical examples are presented.

Discrete-time Markovian stochastic Petri nets

NASA Technical Reports Server (NTRS)

Ciardo, Gianfranco

1995-01-01

We revisit and extend the original definition of discrete-time stochastic Petri nets, by allowing the firing times to have a 'defective discrete phase distribution'. We show that this formalism still corresponds to an underlying discrete-time Markov chain. The structure of the state for this process describes both the marking of the Petri net and the phase of the firing time for each transition, resulting in a large state space. We then modify the well-known power method to perform a transient analysis even when the state space is infinite, subject to the condition that only a finite number of states can be reached in a finite amount of time. Since the memory requirements might still be excessive, we suggest a bounding technique based on truncation.

Multi-variants synthesis of Petri nets for FPGA devices

NASA Astrophysics Data System (ADS)

Bukowiec, Arkadiusz; Doligalski, Michał

2015-09-01

There is presented new method of synthesis of application specific logic controllers for FPGA devices. The specification of control algorithm is made with use of control interpreted Petri net (PT type). It allows specifying parallel processes in easy way. The Petri net is decomposed into state-machine type subnets. In this case, each subnet represents one parallel process. For this purpose there are applied algorithms of coloring of Petri nets. There are presented two approaches of such decomposition: with doublers of macroplaces or with one global wait place. Next, subnets are implemented into two-level logic circuit of the controller. The levels of logic circuit are obtained as a result of its architectural decomposition. The first level combinational circuit is responsible for generation of next places and second level decoder is responsible for generation output symbols. There are worked out two variants of such circuits: with one shared operational memory or with many flexible distributed memories as a decoder. Variants of Petri net decomposition and structures of logic circuits can be combined together without any restrictions. It leads to existence of four variants of multi-variants synthesis.

BioNetSim: a Petri net-based modeling tool for simulations of biochemical processes.

PubMed

Gao, Junhui; Li, Li; Wu, Xiaolin; Wei, Dong-Qing

2012-03-01

BioNetSim, a Petri net-based software for modeling and simulating biochemistry processes, is developed, whose design and implement are presented in this paper, including logic construction, real-time access to KEGG (Kyoto Encyclopedia of Genes and Genomes), and BioModel database. Furthermore, glycolysis is simulated as an example of its application. BioNetSim is a helpful tool for researchers to download data, model biological network, and simulate complicated biochemistry processes. Gene regulatory networks, metabolic pathways, signaling pathways, and kinetics of cell interaction are all available in BioNetSim, which makes modeling more efficient and effective. Similar to other Petri net-based softwares, BioNetSim does well in graphic application and mathematic construction. Moreover, it shows several powerful predominances. (1) It creates models in database. (2) It realizes the real-time access to KEGG and BioModel and transfers data to Petri net. (3) It provides qualitative analysis, such as computation of constants. (4) It generates graphs for tracing the concentration of every molecule during the simulation processes.

Learning Petri net models of non-linear gene interactions.

PubMed

Mayo, Michael

2005-10-01

Understanding how an individual's genetic make-up influences their risk of disease is a problem of paramount importance. Although machine-learning techniques are able to uncover the relationships between genotype and disease, the problem of automatically building the best biochemical model or "explanation" of the relationship has received less attention. In this paper, I describe a method based on random hill climbing that automatically builds Petri net models of non-linear (or multi-factorial) disease-causing gene-gene interactions. Petri nets are a suitable formalism for this problem, because they are used to model concurrent, dynamic processes analogous to biochemical reaction networks. I show that this method is routinely able to identify perfect Petri net models for three disease-causing gene-gene interactions recently reported in the literature.

Modeling of water treatment plant using timed continuous Petri nets

NASA Astrophysics Data System (ADS)

Nurul Fuady Adhalia, H.; Subiono, Adzkiya, Dieky

2017-08-01

Petri nets represent graphically certain conditions and rules. In this paper, we construct a model of the Water Treatment Plant (WTP) using timed continuous Petri nets. Specifically, we consider that (1) the water pump always active and (2) the water source is always available. After obtaining the model, the flow through the transitions and token conservation laws are calculated.

Model-based occluded object recognition using Petri nets

NASA Astrophysics Data System (ADS)

Zhou, Chuan; Hura, Gurdeep S.

1998-09-01

This paper discusses the use of Petri nets to model the process of the object matching between an image and a model under different 2D geometric transformations. This transformation finds its applications in sensor-based robot control, flexible manufacturing system and industrial inspection, etc. A description approach for object structure is presented by its topological structure relation called Point-Line Relation Structure (PLRS). It has been shown how Petri nets can be used to model the matching process, and an optimal or near optimal matching can be obtained by tracking the reachability graph of the net. The experiment result shows that object can be successfully identified and located under 2D transformation such as translations, rotations, scale changes and distortions due to object occluded partially.

Quantitative petri net model of gene regulated metabolic networks in the cell.

PubMed

Chen, Ming; Hofestädt, Ralf

2011-01-01

A method to exploit hybrid Petri nets (HPN) for quantitatively modeling and simulating gene regulated metabolic networks is demonstrated. A global kinetic modeling strategy and Petri net modeling algorithm are applied to perform the bioprocess functioning and model analysis. With the model, the interrelations between pathway analysis and metabolic control mechanism are outlined. Diagrammatical results of the dynamics of metabolites are simulated and observed by implementing a HPN tool, Visual Object Net ++. An explanation of the observed behavior of the urea cycle is proposed to indicate possibilities for metabolic engineering and medical care. Finally, the perspective of Petri nets on modeling and simulation of metabolic networks is discussed.

Petri net modeling of high-order genetic systems using grammatical evolution.

PubMed

Moore, Jason H; Hahn, Lance W

2003-11-01

Understanding how DNA sequence variations impact human health through a hierarchy of biochemical and physiological systems is expected to improve the diagnosis, prevention, and treatment of common, complex human diseases. We have previously developed a hierarchical dynamic systems approach based on Petri nets for generating biochemical network models that are consistent with genetic models of disease susceptibility. This modeling approach uses an evolutionary computation approach called grammatical evolution as a search strategy for optimal Petri net models. We have previously demonstrated that this approach routinely identifies biochemical network models that are consistent with a variety of genetic models in which disease susceptibility is determined by nonlinear interactions between two DNA sequence variations. In the present study, we evaluate whether the Petri net approach is capable of identifying biochemical networks that are consistent with disease susceptibility due to higher order nonlinear interactions between three DNA sequence variations. The results indicate that our model-building approach is capable of routinely identifying good, but not perfect, Petri net models. Ideas for improving the algorithm for this high-dimensional problem are presented.

Fuzzy Petri nets to model vision system decisions within a flexible manufacturing system

NASA Astrophysics Data System (ADS)

Hanna, Moheb M.; Buck, A. A.; Smith, R.

1994-10-01

The paper presents a Petri net approach to modelling, monitoring and control of the behavior of an FMS cell. The FMS cell described comprises a pick and place robot, vision system, CNC-milling machine and 3 conveyors. The work illustrates how the block diagrams in a hierarchical structure can be used to describe events at different levels of abstraction. It focuses on Fuzzy Petri nets (Fuzzy logic with Petri nets) including an artificial neural network (Fuzzy Neural Petri nets) to model and control vision system decisions and robot sequences within an FMS cell. This methodology can be used as a graphical modelling tool to monitor and control the imprecise, vague and uncertain situations, and determine the quality of the output product of an FMS cell.

Gradient-based controllers for timed continuous Petri nets

NASA Astrophysics Data System (ADS)

Lefebvre, Dimitri; Leclercq, Edouard; Druaux, Fabrice; Thomas, Philippe

2015-07-01

This paper is about control design for timed continuous Petri nets that are described as piecewise affine systems. In this context, the marking vector is considered as the state space vector, weighted marking of place subsets are defined as the model outputs and the model inputs correspond to multiplicative control actions that slow down the firing rate of some controllable transitions. Structural and functional sensitivity of the outputs with respect to the inputs are discussed in terms of Petri nets. Then, gradient-based controllers (GBC) are developed in order to adapt the control actions of the controllable transitions according to desired trajectories of the outputs.

Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets.

PubMed

Formanowicz, Dorota; Kozak, Adam; Głowacki, Tomasz; Radom, Marcin; Formanowicz, Piotr

2013-12-01

Systems biology approach to investigate biological phenomena seems to be very promising because it is capable to capture one of the fundamental properties of living organisms, i.e. their inherent complexity. It allows for analysis biological entities as complex systems of interacting objects. The first and necessary step of such an analysis is building a precise model of the studied biological system. This model is expressed in the language of some branch of mathematics, as for example, differential equations. During the last two decades the theory of Petri nets has appeared to be very well suited for building models of biological systems. The structure of these nets reflects the structure of interacting biological molecules and processes. Moreover, on one hand, Petri nets have intuitive graphical representation being very helpful in understanding the structure of the system and on the other hand, there is a lot of mathematical methods and software tools supporting an analysis of the properties of the nets. In this paper a Petri net based model of the hemojuvelin-hepcidin axis involved in the maintenance of the human body iron homeostasis is presented. The analysis based mainly on T-invariants of the model properties has been made and some biological conclusions have been drawn. Copyright © 2013 Elsevier Inc. All rights reserved.

Algebraic properties of automata associated to Petri nets and applications to computation in biological systems.

PubMed

Egri-Nagy, Attila; Nehaniv, Chrystopher L

2008-01-01

Biochemical and genetic regulatory networks are often modeled by Petri nets. We study the algebraic structure of the computations carried out by Petri nets from the viewpoint of algebraic automata theory. Petri nets comprise a formalized graphical modeling language, often used to describe computation occurring within biochemical and genetic regulatory networks, but the semantics may be interpreted in different ways in the realm of automata. Therefore, there are several different ways to turn a Petri net into a state-transition automaton. Here, we systematically investigate different conversion methods and describe cases where they may yield radically different algebraic structures. We focus on the existence of group components of the corresponding transformation semigroups, as these reflect symmetries of the computation occurring within the biological system under study. Results are illustrated by applications to the Petri net modelling of intermediary metabolism. Petri nets with inhibition are shown to be computationally rich, regardless of the particular interpretation method. Along these lines we provide a mathematical argument suggesting a reason for the apparent all-pervasiveness of inhibitory connections in living systems.

Decentralised control of continuous Petri nets

NASA Astrophysics Data System (ADS)

Wang, Liewei; Wang, Xu

2017-05-01

This paper focuses on decentralised control of systems modelled by continuous Petri nets, in which a target marking control problem is discussed. In some previous works, an efficient ON/OFF strategy-based minimum-time controller was developed. Nevertheless, the convergence is only proved for subclasses like Choice-Free nets. For a general net, the pre-conditions of applying the ON/OFF strategy are not given; therefore, the application scope of the method is unclear. In this work, we provide two sufficient conditions of applying the ON/OFF strategy-based controller to general nets. Furthermore, an extended algorithm for general nets is proposed, in which control laws are computed based on some limited information, without knowing the detailed structure of subsystems.

Application of growing nested Petri nets for modeling robotic systems operating under risk

NASA Astrophysics Data System (ADS)

Sorokin, E. V.; Senkov, A. V.

2017-10-01

The paper studies the peculiarities of modeling robotic systems engaged in mining. Existing modeling mechanisms are considered, which are based on nested Petri nets, and a new formalism of growing Petri nets is presented that allows modeling robotic systems operating under risk. Modeling is provided both for the regular operation mode and for non-standard modes in which individual elements of the system can perform uncharacteristic functions. The example shows growing Petri nets that are used for modeling extraction of flat coal seams by a robotic system consisting of several different-type autonomous robots.

Simulation of a Petri net-based model of the terpenoid biosynthesis pathway.

PubMed

Hawari, Aliah Hazmah; Mohamed-Hussein, Zeti-Azura

2010-02-09

The development and simulation of dynamic models of terpenoid biosynthesis has yielded a systems perspective that provides new insights into how the structure of this biochemical pathway affects compound synthesis. These insights may eventually help identify reactions that could be experimentally manipulated to amplify terpenoid production. In this study, a dynamic model of the terpenoid biosynthesis pathway was constructed based on the Hybrid Functional Petri Net (HFPN) technique. This technique is a fusion of three other extended Petri net techniques, namely Hybrid Petri Net (HPN), Dynamic Petri Net (HDN) and Functional Petri Net (FPN). The biological data needed to construct the terpenoid metabolic model were gathered from the literature and from biological databases. These data were used as building blocks to create an HFPNe model and to generate parameters that govern the global behaviour of the model. The dynamic model was simulated and validated against known experimental data obtained from extensive literature searches. The model successfully simulated metabolite concentration changes over time (pt) and the observations correlated with known data. Interactions between the intermediates that affect the production of terpenes could be observed through the introduction of inhibitors that established feedback loops within and crosstalk between the pathways. Although this metabolic model is only preliminary, it will provide a platform for analysing various high-throughput data, and it should lead to a more holistic understanding of terpenoid biosynthesis.

Biopathways representation and simulation on hybrid functional petri net.

PubMed

Matsuno, Hiroshi; Tanaka, Yukiko; Aoshima, Hitoshi; Doi, Atsushi; Matsui, Mika; Miyano, Satoru

2011-01-01

The following two matters should be resolved in order for biosimulation tools to be accepted by users in biology/medicine: (1) remove issues which are irrelevant to biological importance, and (2) allow users to represent biopathways intuitively and understand/manage easily the details of representation and simulation mechanism. From these criteria, we firstly define a novel notion of Petri net called Hybrid Functional Petri Net (HFPN). Then, we introduce a software tool, Genomic Object Net, for representing and simulating biopathways, which we have developed by employing the architecture of HFPN. In order to show the usefulness of Genomic Object Net for representing and simulating biopathways, we show two HFPN representations of gene regulation mechanisms of Drosophila melanogaster (fruit fly) circadian rhythm and apoptosis induced by Fas ligand. The simulation results of these biopathways are also correlated with biological observations. The software is available to academic users from http://www.GenomicObject.Net/.

Neural system modeling and simulation using Hybrid Functional Petri Net.

PubMed

Tang, Yin; Wang, Fei

2012-02-01

The Petri net formalism has been proved to be powerful in biological modeling. It not only boasts of a most intuitive graphical presentation but also combines the methods of classical systems biology with the discrete modeling technique. Hybrid Functional Petri Net (HFPN) was proposed specially for biological system modeling. An array of well-constructed biological models using HFPN yielded very interesting results. In this paper, we propose a method to represent neural system behavior, where biochemistry and electrical chemistry are both included using the Petri net formalism. We built a model for the adrenergic system using HFPN and employed quantitative analysis. Our simulation results match the biological data well, showing that the model is very effective. Predictions made on our model further manifest the modeling power of HFPN and improve the understanding of the adrenergic system. The file of our model and more results with their analysis are available in our supplementary material.

Modelling of Biometric Identification System with Given Parameters Using Colored Petri Nets

NASA Astrophysics Data System (ADS)

Petrosyan, G.; Ter-Vardanyan, L.; Gaboutchian, A.

2017-05-01

Biometric identification systems use given parameters and function on the basis of Colored Petri Nets as a modelling language developed for systems in which communication, synchronization and distributed resources play an important role. Colored Petri Nets combine the strengths of Classical Petri Nets with the power of a high-level programming language. Coloured Petri Nets have both, formal intuitive and graphical presentations. Graphical CPN model consists of a set of interacting modules which include a network of places, transitions and arcs. Mathematical representation has a well-defined syntax and semantics, as well as defines system behavioural properties. One of the best known features used in biometric is the human finger print pattern. During the last decade other human features have become of interest, such as iris-based or face recognition. The objective of this paper is to introduce the fundamental concepts of Petri Nets in relation to tooth shape analysis. Biometric identification systems functioning has two phases: data enrollment phase and identification phase. During the data enrollment phase images of teeth are added to database. This record contains enrollment data as a noisy version of the biometrical data corresponding to the individual. During the identification phase an unknown individual is observed again and is compared to the enrollment data in the database and then system estimates the individual. The purpose of modeling biometric identification system by means of Petri Nets is to reveal the following aspects of the functioning model: the efficiency of the model, behavior of the model, mistakes and accidents in the model, feasibility of the model simplification or substitution of its separate components for more effective components without interfering system functioning. The results of biometric identification system modeling and evaluating are presented and discussed.

An assembly process model based on object-oriented hierarchical time Petri Nets

NASA Astrophysics Data System (ADS)

Wang, Jiapeng; Liu, Shaoli; Liu, Jianhua; Du, Zenghui

2017-04-01

In order to improve the versatility, accuracy and integrity of the assembly process model of complex products, an assembly process model based on object-oriented hierarchical time Petri Nets is presented. A complete assembly process information model including assembly resources, assembly inspection, time, structure and flexible parts is established, and this model describes the static and dynamic data involved in the assembly process. Through the analysis of three-dimensional assembly process information, the assembly information is hierarchically divided from the whole, the local to the details and the subnet model of different levels of object-oriented Petri Nets is established. The communication problem between Petri subnets is solved by using message database, and it reduces the complexity of system modeling effectively. Finally, the modeling process is presented, and a five layer Petri Nets model is established based on the hoisting process of the engine compartment of a wheeled armored vehicle.

A versatile petri net based architecture for modeling and simulation of complex biological processes.

PubMed

Nagasaki, Masao; Doi, Atsushi; Matsuno, Hiroshi; Miyano, Satoru

2004-01-01

The research on modeling and simulation of complex biological systems is getting more important in Systems Biology. In this respect, we have developed Hybrid Function Petri net (HFPN) that was newly developed from existing Petri net because of their intuitive graphical representation and their capabilities for mathematical analyses. However, in the process of modeling metabolic, gene regulatory or signal transduction pathways with the architecture, we have realized three extensions of HFPN, (i) an entity should be extended to contain more than one value, (ii) an entity should be extended to handle other primitive types, e.g. boolean, string, (iii) an entity should be extended to handle more advanced type called object that consists of variables and methods, are necessary for modeling biological systems with Petri net based architecture. To deal with it, we define a new enhanced Petri net called hybrid functional Petri net with extension (HFPNe). To demonstrate the effectiveness of the enhancements, we model and simulate with HFPNe four biological processes that are diffcult to represent with the previous architecture HFPN.

Necessary and sufficient liveness condition of GS3PR Petri nets

NASA Astrophysics Data System (ADS)

Liu, GaiYun; Barkaoui, Kamel

2015-05-01

Structural analysis is one of the most important and efficient methods to investigate the behaviour of Petri nets. Liveness is a significant behavioural property of Petri nets. Siphons, as structural objects of a Petri net, are closely related to its liveness. Many deadlock control policies for flexible manufacturing systems (FMS) modelled by Petri nets are implemented via siphon control. Most of the existing methods design liveness-enforcing supervisors by adding control places for siphons based on their controllability conditions. To compute a liveness-enforcing supervisor with as much as permissive behaviour, it is both theoretically and practically significant to find an exact controllability condition for siphons. However, the existing conditions, max, max‧, and max″-controllability of siphons are all overly restrictive and generally sufficient only. This paper develops a new condition called max*-controllability of the siphons in generalised systems of simple sequential processes with resources (GS3PR), which are a net subclass that can model many real-world automated manufacturing systems. We show that a GS3PR is live if all its strict minimal siphons (SMS) are max*-controlled. Compared with the existing conditions, i.e., max-, max‧-, and max″-controllability of siphons, max*-controllability of the SMS is not only sufficient but also necessary. An example is used to illustrate the proposed method.

Modeling biological gradient formation: combining partial differential equations and Petri nets.

PubMed

Bertens, Laura M F; Kleijn, Jetty; Hille, Sander C; Heiner, Monika; Koutny, Maciej; Verbeek, Fons J

2016-01-01

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.

Realization of planning design of mechanical manufacturing system by Petri net simulation model

NASA Astrophysics Data System (ADS)

Wu, Yanfang; Wan, Xin; Shi, Weixiang

1991-09-01

Planning design is to work out a more overall long-term plan. In order to guarantee a mechanical manufacturing system (MMS) designed to obtain maximum economical benefit, it is necessary to carry out a reasonable planning design for the system. First, some principles on planning design for MMS are introduced. Problems of production scheduling and their decision rules for computer simulation are presented. Realizable method of each production scheduling decision rule in Petri net model is discussed. Second, the solution of conflict rules for conflict problems during running Petri net is given. Third, based on the Petri net model of MMS which includes part flow and tool flow, according to the principle of minimum event time advance, a computer dynamic simulation of the Petri net model, that is, a computer dynamic simulation of MMS, is realized. Finally, the simulation program is applied to a simulation exmple, so the scheme of a planning design for MMS can be evaluated effectively.

Optimal management of reconfigurable manufacturing system modeling with Petri nets developed three-dimensional - RPD3D

NASA Astrophysics Data System (ADS)

Teodor, F.; Marinescu, V.; Epureanu, A.

2016-11-01

Modeling of reconfigurable manufacturing systems would have done using existing Petri net types, but the complexity and dynamics of the new manufacturing system, mainly data reconfiguration feature, required looking for a more compact representation with many variables that to model as accurately not only the normal operation of the production system but can capture and model and reconfiguration process. Thus, it was necessary to create a new class of Petri nets, called RPD3D (Developed Petri nets with three dimensional) showing the name of both lineage (new class derived from Petri nets developed, created in 2000 by Prof. Dr. Ing Vasile Marinescu in his doctoral thesis) [1], but the most important of the new features defining (transformation from one 2D model into a 3D model).The idea was to introduce the classical model of a Petri third dimension to be able to overlay multiple levels (layers) formed in 2D or 3D Petri nets that interact with each other (receiving or giving commands to enable or disable the various modules together simulating the operation of reconfigurable manufacturing systems). The aim is to present a new type of Petri nets called RPD3D - Developed Petri three-dimensional model used for optimal control and simulation of reconfigurable manufacturing systems manufacture of products such systems.

Automation of Presentation Record Production Based on Rich-Media Technology Using SNT Petri Nets Theory.

PubMed

Martiník, Ivo

2015-01-01

Rich-media describes a broad range of digital interactive media that is increasingly used in the Internet and also in the support of education. Last year, a special pilot audiovisual lecture room was built as a part of the MERLINGO (MEdia-rich Repository of LearnING Objects) project solution. It contains all the elements of the modern lecture room determined for the implementation of presentation recordings based on the rich-media technologies and their publication online or on-demand featuring the access of all its elements in the automated mode including automatic editing. Property-preserving Petri net process algebras (PPPA) were designed for the specification and verification of the Petri net processes. PPPA does not need to verify the composition of the Petri net processes because all their algebraic operators preserve the specified set of the properties. These original PPPA are significantly generalized for the newly introduced class of the SNT Petri process and agent nets in this paper. The PLACE-SUBST and ASYNC-PROC algebraic operators are defined for this class of Petri nets and their chosen properties are proved. The SNT Petri process and agent nets theory were significantly applied at the design, verification, and implementation of the programming system ensuring the pilot audiovisual lecture room functionality.

Automation of Presentation Record Production Based on Rich-Media Technology Using SNT Petri Nets Theory

PubMed Central

Martiník, Ivo

2015-01-01

Rich-media describes a broad range of digital interactive media that is increasingly used in the Internet and also in the support of education. Last year, a special pilot audiovisual lecture room was built as a part of the MERLINGO (MEdia-rich Repository of LearnING Objects) project solution. It contains all the elements of the modern lecture room determined for the implementation of presentation recordings based on the rich-media technologies and their publication online or on-demand featuring the access of all its elements in the automated mode including automatic editing. Property-preserving Petri net process algebras (PPPA) were designed for the specification and verification of the Petri net processes. PPPA does not need to verify the composition of the Petri net processes because all their algebraic operators preserve the specified set of the properties. These original PPPA are significantly generalized for the newly introduced class of the SNT Petri process and agent nets in this paper. The PLACE-SUBST and ASYNC-PROC algebraic operators are defined for this class of Petri nets and their chosen properties are proved. The SNT Petri process and agent nets theory were significantly applied at the design, verification, and implementation of the programming system ensuring the pilot audiovisual lecture room functionality. PMID:26258164

Robustness analysis of non-ordinary Petri nets for flexible assembly systems

NASA Astrophysics Data System (ADS)

Hsieh, Fu-Shiung

2010-05-01

Non-ordinary controlled Petri nets (NCPNs) have the advantages to model flexible assembly systems in which multiple identical resources may be required to perform an operation. However, existing studies on NCPNs are still limited. For example, the robustness properties of NCPNs have not been studied. This motivates us to develop an analysis method for NCPNs. Robustness analysis concerns the ability for a system to maintain operation in the presence of uncertainties. It provides an alternative way to analyse a perturbed system without reanalysis. In our previous research, we have analysed the robustness properties of several subclasses of ordinary controlled Petri nets. To study the robustness properties of NCPNs, we augment NCPNs with an uncertainty model, which specifies an upper bound on the uncertainties for each reachable marking. The resulting PN models are called non-ordinary controlled Petri nets with uncertainties (NCPNU). Based on NCPNU, the problem is to characterise the maximal tolerable uncertainties for each reachable marking. The computational complexities to characterise maximal tolerable uncertainties for each reachable marking grow exponentially with the size of the nets. Instead of considering general NCPNU, we limit our scope to a subclass of PN models called non-ordinary controlled flexible assembly Petri net with uncertainties (NCFAPNU) for assembly systems and study its robustness. We will extend the robustness analysis to NCFAPNU. We identify two types of uncertainties under which the liveness of NCFAPNU can be maintained.

Hardware implementation of fuzzy Petri net as a controller.

PubMed

Gniewek, Lesław; Kluska, Jacek

2004-06-01

The paper presents a new approach to fuzzy Petri net (FPN) and its hardware implementation. The authors' motivation is as follows. Complex industrial processes can be often decomposed into many parallelly working subprocesses, which can, in turn, be modeled using Petri nets. If all the process variables (or events) are assumed to be two-valued signals, then it is possible to obtain a hardware or software control device, which works according to the algorithm described by conventional Petri net. However, the values of real signals are contained in some bounded interval and can be interpreted as events which are not only true or false, but rather true in some degree from the interval [0, 1]. Such a natural interpretation from multivalued logic (fuzzy logic) point of view, concerns sensor outputs, control signals, time expiration, etc. It leads to the idea of FPN as a controller, which one can rather simply obtain, and which would be able to process both analog, and binary signals. In the paper both graphical, and algebraic representations of the proposed FPN are given. The conditions under which transitions can be fired are described. The algebraic description of the net and a theorem which enables computation of new marking in the net, based on current marking, are formulated. Hardware implementation of the FPN, which uses fuzzy JK flip-flops and fuzzy gates, are proposed. An example illustrating usefulness of the proposed FPN for control algorithm description and its synthesis as a controller device for the concrete production process are presented.

Petri Nets as Modeling Tool for Emergent Agents

NASA Technical Reports Server (NTRS)

Bergman, Marto

2004-01-01

Emergent agents, those agents whose local interactions can cause unexpected global results, require a method of modeling that is both dynamic and structured Petri Nets, a modeling tool developed for dynamic discrete event system of mainly functional agents, provide this, and have the benefit of being an established tool. We present here the details of the modeling method here and discuss how to implement its use for modeling agent-based systems. Petri Nets have been used extensively in the modeling of functional agents, those agents who have defined purposes and whose actions should result in a know outcome. However, emergent agents, those agents who have a defined structure but whose interaction causes outcomes that are unpredictable, have not yet found a modeling style that suits them. A problem with formally modeling emergent agents that any formal modeling style usually expects to show the results of a problem and the results of problems studied using emergent agents are not apparent from the initial construction. However, the study of emergent agents still requires a method to analyze the agents themselves, and have sensible conversation about the differences and similarities between types of emergent agents. We attempt to correct this problem by applying Petri Nets to the characterization of emergent agents. In doing so, the emergent properties of these agents can be highlighted, and conversation about the nature and compatibility of the differing methods of agent creation can begin.

Reachability analysis of real-time systems using time Petri nets.

PubMed

Wang, J; Deng, Y; Xu, G

2000-01-01

Time Petri nets (TPNs) are a popular Petri net model for specification and verification of real-time systems. A fundamental and most widely applied method for analyzing Petri nets is reachability analysis. The existing technique for reachability analysis of TPNs, however, is not suitable for timing property verification because one cannot derive end-to-end delay in task execution, an important issue for time-critical systems, from the reachability tree constructed using the technique. In this paper, we present a new reachability based analysis technique for TPNs for timing property analysis and verification that effectively addresses the problem. Our technique is based on a concept called clock-stamped state class (CS-class). With the reachability tree generated based on CS-classes, we can directly compute the end-to-end time delay in task execution. Moreover, a CS-class can be uniquely mapped to a traditional state class based on which the conventional reachability tree is constructed. Therefore, our CS-class-based analysis technique is more general than the existing technique. We show how to apply this technique to timing property verification of the TPN model of a command and control (C2) system.

Coloured Petri Net Refinement Specification and Correctness Proof with Coq

NASA Technical Reports Server (NTRS)

Choppy, Christine; Mayero, Micaela; Petrucci, Laure

2009-01-01

In this work, we address the formalisation of symmetric nets, a subclass of coloured Petri nets, refinement in COQ. We first provide a formalisation of the net models, and of their type refinement in COQ. Then the COQ proof assistant is used to prove the refinement correctness lemma. An example adapted from a protocol example illustrates our work.

A systematic petri net approach for multiple-scale modeling and simulation of biochemical processes.

PubMed

Chen, Ming; Hu, Minjie; Hofestädt, Ralf

2011-06-01

A method to exploit hybrid Petri nets for modeling and simulating biochemical processes in a systematic way was introduced. Both molecular biology and biochemical engineering aspects are manipulated. With discrete and continuous elements, the hybrid Petri nets can easily handle biochemical factors such as metabolites concentration and kinetic behaviors. It is possible to translate both molecular biological behavior and biochemical processes workflow into hybrid Petri nets in a natural manner. As an example, penicillin production bioprocess is modeled to illustrate the concepts of the methodology. Results of the dynamic of production parameters in the bioprocess were simulated and observed diagrammatically. Current problems and post-genomic perspectives were also discussed.

Petri net-based modelling of human-automation conflicts in aviation.

PubMed

Pizziol, Sergio; Tessier, Catherine; Dehais, Frédéric

2014-01-01

Analyses of aviation safety reports reveal that human-machine conflicts induced by poor automation design are remarkable precursors of accidents. A review of different crew-automation conflicting scenarios shows that they have a common denominator: the autopilot behaviour interferes with the pilot's goal regarding the flight guidance via 'hidden' mode transitions. Considering both the human operator and the machine (i.e. the autopilot or the decision functions) as agents, we propose a Petri net model of those conflicting interactions, which allows them to be detected as deadlocks in the Petri net. In order to test our Petri net model, we designed an autoflight system that was formally analysed to detect conflicting situations. We identified three conflicting situations that were integrated in an experimental scenario in a flight simulator with 10 general aviation pilots. The results showed that the conflicts that we had a-priori identified as critical had impacted the pilots' performance. Indeed, the first conflict remained unnoticed by eight participants and led to a potential collision with another aircraft. The second conflict was detected by all the participants but three of them did not manage the situation correctly. The last conflict was also detected by all the participants but provoked typical automation surprise situation as only one declared that he had understood the autopilot behaviour. These behavioural results are discussed in terms of workload and number of fired 'hidden' transitions. Eventually, this study reveals that both formal and experimental approaches are complementary to identify and assess the criticality of human-automation conflicts. Practitioner Summary: We propose a Petri net model of human-automation conflicts. An experiment was conducted with general aviation pilots performing a scenario involving three conflicting situations to test the soundness of our formal approach. This study reveals that both formal and experimental approaches

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach.

PubMed

Steggles, L Jason; Banks, Richard; Shaw, Oliver; Wipat, Anil

2007-02-01

New developments in post-genomic technology now provide researchers with the data necessary to study regulatory processes in a holistic fashion at multiple levels of biological organization. One of the major challenges for the biologist is to integrate and interpret these vast data resources to gain a greater understanding of the structure and function of the molecular processes that mediate adaptive and cell cycle driven changes in gene expression. In order to achieve this biologists require new tools and techniques to allow pathway related data to be modelled and analysed as network structures, providing valuable insights which can then be validated and investigated in the laboratory. We propose a new technique for constructing and analysing qualitative models of genetic regulatory networks based on the Petri net formalism. We take as our starting point the Boolean network approach of treating genes as binary switches and develop a new Petri net model which uses logic minimization to automate the construction of compact qualitative models. Our approach addresses the shortcomings of Boolean networks by providing access to the wide range of existing Petri net analysis techniques and by using non-determinism to cope with incomplete and inconsistent data. The ideas we present are illustrated by a case study in which the genetic regulatory network controlling sporulation in the bacterium Bacillus subtilis is modelled and analysed. The Petri net model construction tool and the data files for the B. subtilis sporulation case study are available at http://bioinf.ncl.ac.uk/gnapn.

Virtual Control Policy for Binary Ordered Resources Petri Net Class.

PubMed

Rovetto, Carlos A; Concepción, Tomás J; Cano, Elia Esther

2016-08-18

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. The reduced structure of this new class gives advantages that allow analysis of the entire system's behavior, which is a prohibitive task for large systems because of the complexity and routing algorithms.

Virtual Control Policy for Binary Ordered Resources Petri Net Class

PubMed Central

Rovetto, Carlos A.; Concepción, Tomás J.; Cano, Elia Esther

2016-01-01

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. The reduced structure of this new class gives advantages that allow analysis of the entire system’s behavior, which is a prohibitive task for large systems because of the complexity and routing algorithms. PMID:27548170

Petri net modelling of gene regulation of the Duchenne muscular dystrophy.

PubMed

Grunwald, Stefanie; Speer, Astrid; Ackermann, Jörg; Koch, Ina

2008-05-01

Searching for therapeutic strategies for Duchenne muscular dystrophy, it is of great interest to understand the responsible molecular pathways down-stream of dystrophin completely. For this reason we have performed real-time PCR experiments to compare mRNA expression levels of relevant genes in tissues of affected patients and controls. To bring experimental data in context with the underlying pathway theoretical models are needed. Modelling of biological processes in the cell at higher description levels is still an open problem in the field of systems biology. In this paper, a new application of Petri net theory is presented to model gene regulatory processes of Duchenne muscular dystrophy. We have developed a Petri net model, which is based mainly on own experimental and literature data. We distinguish between up- and down-regulated states of gene expression. The analysis of the model comprises the computation of structural and dynamic properties with focus on a thorough T-invariant analysis, including clustering techniques and the decomposition of the network into maximal common transition sets (MCT-sets), which can be interpreted as functionally related building blocks. All possible pathways, which reflect the complex net behaviour in dependence of different gene expression patterns, are discussed. We introduce Mauritius maps of T-invariants, which enable, for example, theoretical knockout analysis. The resulted model serves as basis for a better understanding of pathological processes, and thereby for planning next experimental steps in searching for new therapeutic possibilities. Free availability of the Petri net editor and animator Snoopy and the clustering tool PInA via http://www-dssz.informatik.tu-cottbus.de/~ wwwdssz/. The Petri net models used can be accessed via http://www.tfh-berlin.de/bi/duchenne/.

A distributed Petri Net controller for a dual arm testbed

NASA Technical Reports Server (NTRS)

Bjanes, Atle

1991-01-01

This thesis describes the design and functionality of a Distributed Petri Net Controller (DPNC). The controller runs under X Windows to provide a graphical interface. The DPNC allows users to distribute a Petri Net across several host computers linked together via a TCP/IP interface. A sub-net executes on each host, interacting with the other sub-nets by passing a token vector from host to host. One host has a command window which monitors and controls the distributed controller. The input to the DPNC is a net definition file generated by Great SPN. Thus, a net may be designed, analyzed and verified using this package before implementation. The net is distributed to the hosts by tagging transitions that are host-critical with the appropriate host number. The controller will then distribute the remaining places and transitions to the hosts by generating the local nets, the local marking vectors and the global marking vector. Each transition can have one or more preconditions which must be fulfilled before the transition can fire, as well as one or more post-processes to be executed after the transition fires. These implement the actual input/output to the environment (machines, signals, etc.). The DPNC may also be used to simulate a Great SPN net since stochastic and deterministic firing rates are implemented in the controller for timed transitions.

Runtime Verification of Pacemaker Functionality Using Hierarchical Fuzzy Colored Petri-nets.

PubMed

Majma, Negar; Babamir, Seyed Morteza; Monadjemi, Amirhassan

2017-02-01

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. Accordingly, we supervise the runtime function and status of the software. The software verification means examining limitations and needs of the system users by the system running software. In this paper, a method to verify the pacemaker software, based on the fuzzy function of the device, is presented. So, the function limitations of the device are identified and presented as fuzzy rules and then the device is verified based on the hierarchical Fuzzy Colored Petri-net (FCPN), which is formed considering the software limits. Regarding the experiences of using: 1) Fuzzy Petri-nets (FPN) to verify insulin pumps, 2) Colored Petri-nets (CPN) to verify the pacemaker and 3) To verify the pacemaker by a software agent with Petri-network based knowledge, which we gained during the previous studies, the runtime behavior of the pacemaker software is examined by HFCPN, in this paper. This is considered a developing step compared to the earlier work. HFCPN in this paper, compared to the FPN and CPN used in our previous studies reduces the complexity. By presenting the Petri-net (PN) in a hierarchical form, the verification runtime, decreased as 90.61% compared to the verification runtime in the earlier work. Since we need an inference engine in the runtime verification, we used the HFCPN to enhance the performance of the inference engine.

A Petri-net coordination model for an intelligent mobile robot

NASA Technical Reports Server (NTRS)

Wang, F.-Y.; Kyriakopoulos, K. J.; Tsolkas, A.; Saridis, G. N.

1990-01-01

The authors present a Petri net model of the coordination level of an intelligent mobile robot system (IMRS). The purpose of this model is to specify the integration of the individual efforts on path planning, supervisory motion control, and vision systems that are necessary for the autonomous operation of the mobile robot in a structured dynamic environment. This is achieved by analytically modeling the various units of the system as Petri net transducers and explicitly representing the task precedence and information dependence among them. The model can also be used to simulate the task processing and to evaluate the efficiency of operations and the responsibility of decisions in the coordination level of the IMRS. Some simulation results on the task processing and learning are presented.

A model of airport security work flow based on petri net

NASA Astrophysics Data System (ADS)

Dong, Xinming

2017-09-01

Extremely long lines at airports in the United States have been sharply criticized. In order to find out the bottleneck in the existing security system and put forward reasonable improvement plans and proposal, the Petri net model and the Markov Chain are introduced in this paper. This paper uses data collected by transportation Security Agency (TSA), assuming the data can represent the average level of all airports in the Unites States, to analysis the performance of security check system. By calculating the busy probabilities and the utilization probabilities, the bottleneck is found. Moreover, recommendation is given based on the parameters’ modification in Petri net model.

Petri Net controller synthesis based on decomposed manufacturing models.

PubMed

Dideban, Abbas; Zeraatkar, Hashem

2018-06-01

Utilizing of supervisory control theory on the real systems in many modeling tools such as Petri Net (PN) becomes challenging in recent years due to the significant states in the automata models or uncontrollable events. The uncontrollable events initiate the forbidden states which might be removed by employing some linear constraints. Although there are many methods which have been proposed to reduce these constraints, enforcing them to a large-scale system is very difficult and complicated. This paper proposes a new method for controller synthesis based on PN modeling. In this approach, the original PN model is broken down into some smaller models in which the computational cost reduces significantly. Using this method, it is easy to reduce and enforce the constraints to a Petri net model. The appropriate results of our proposed method on the PN models denote worthy controller synthesis for the large scale systems. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Information flow analysis and Petri-net-based modeling for welding flexible manufacturing cell

NASA Astrophysics Data System (ADS)

Qiu, T.; Chen, Shanben; Wang, Y. T.; Wu, Lin

2000-10-01

Due to the development of advanced manufacturing technology and the introduction of Smart-Manufacturing notion in the field of modern industrial production, welding flexible manufacturing system (WFMS) using robot technology has become the inevitable developing direction on welding automation. In WFMS process, the flexibility for different welding products and the realizing on corresponding welding parameters control are the guarantees for welding quality. Based on a new intelligent arc-welding flexible manufacturing cell (WFMC), the system structure and control policies are studied in this paper. Aiming at the different information flows among every subsystem and central monitoring computer in this WFMC, Petri net theory is introduced into the process of welding manufacturing. With its help, a discrete control model of WFMC has been constructed, in which the system status is regarded as place and the control process is regarded as transition. Moreover, grounded on automation Petri net principle, the judging and utilizing of information obtained from welding sensors are imported into net structure, which extends the traditional Petri net concepts. The control model and policies researched in this paper have established foundation for further intelligent real-time control on WFMC and WFMS.

Aspects regarding at 13C isotope separation column control using Petri nets system

NASA Astrophysics Data System (ADS)

Boca, M. L.; Ciortea, M. E.

2015-11-01

This paper is intended to show that Petri nets can be also applicable in the chemical industry. It used linear programming, modeling underlying Petri nets, especially discrete event systems for isotopic separation, the purpose of considering and control events in real-time through graphical representations. In this paper it is simulate the control of 13C Isotope Separation column using Petri nets. The major problem with 13C comes from the difficulty of obtaining it and raising its natural fraction. Carbon isotopes can be obtained using many methods, one of them being the cryogenic distillation of carbon monoxide. Some few aspects regarding operating conditions and the construction of such cryogenic plants are known today, and even less information are available as far as the separation process modeling and control are concerned. In fact, the efficient control of the carbon monoxide distillation process represents a necessity for large-scale 13C production. Referring to a classic distillation process, some models for carbon isotope separation have been proposed, some based on mass, component and energy balance equations, some on the nonlinear wave theory or the Cohen equations. For modeling the system it was used Petri nets because in this case it is deal with discrete event systems. In use of the non-timed and with auxiliary times Petri model, the transport stream was divided into sections and these sections will be analyzed successively. Because of the complexity of the system and the large amount of calculations required it was not possible to analyze the system as a unitary whole. A first attempt to model the system as a unitary whole led to the blocking of the model during simulation, because of the large processing times.

Threat driven modeling framework using petri nets for e-learning system.

PubMed

Khamparia, Aditya; Pandey, Babita

2016-01-01

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. A case study has been also proposed which shows the need and feasibility of using aspect oriented stochastic petri net models for threat modeling which improves reliability, consistency and robustness of the e-learning system.

A Petri Net-Based Software Process Model for Developing Process-Oriented Information Systems

NASA Astrophysics Data System (ADS)

Li, Yu; Oberweis, Andreas

Aiming at increasing flexibility, efficiency, effectiveness, and transparency of information processing and resource deployment in organizations to ensure customer satisfaction and high quality of products and services, process-oriented information systems (POIS) represent a promising realization form of computerized business information systems. Due to the complexity of POIS, explicit and specialized software process models are required to guide POIS development. In this chapter we characterize POIS with an architecture framework and present a Petri net-based software process model tailored for POIS development with consideration of organizational roles. As integrated parts of the software process model, we also introduce XML nets, a variant of high-level Petri nets as basic methodology for business processes modeling, and an XML net-based software toolset providing comprehensive functionalities for POIS development.

Phenomenological and molecular-level Petri net modeling and simulation of long-term potentiation.

PubMed

Hardy, S; Robillard, P N

2005-10-01

Petri net-based modeling methods have been used in many research projects to represent biological systems. Among these, the hybrid functional Petri net (HFPN) was developed especially for biological modeling in order to provide biologists with a more intuitive Petri net-based method. In the literature, HFPNs are used to represent kinetic models at the molecular level. We present two models of long-term potentiation previously represented by differential equations which we have transformed into HFPN models: a phenomenological synapse model and a molecular-level model of the CaMKII regulation pathway. Through simulation, we obtained results similar to those of previous studies using these models. Our results open the way to a new type of modeling for systems biology where HFPNs are used to combine different levels of abstraction within one model. This approach can be useful in fully modeling a system at the molecular level when kinetic data is missing or when a full study of a system at the molecular level it is not within the scope of the research.

Performance evaluation of automated manufacturing systems using generalized stochastic Petri Nets. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Al-Jaar, Robert Y.; Desrochers, Alan A.

1989-01-01

The main objective of this research is to develop a generic modeling methodology with a flexible and modular framework to aid in the design and performance evaluation of integrated manufacturing systems using a unified model. After a thorough examination of the available modeling methods, the Petri Net approach was adopted. The concurrent and asynchronous nature of manufacturing systems are easily captured by Petri Net models. Three basic modules were developed: machine, buffer, and Decision Making Unit. The machine and buffer modules are used for modeling transfer lines and production networks. The Decision Making Unit models the functions of a computer node in a complex Decision Making Unit Architecture. The underlying model is a Generalized Stochastic Petri Net (GSPN) that can be used for performance evaluation and structural analysis. GSPN's were chosen because they help manage the complexity of modeling large manufacturing systems. There is no need to enumerate all the possible states of the Markov Chain since they are automatically generated from the GSPN model.

A new approach for modular robot system behavioral modeling: Base on Petri net and category theory

NASA Astrophysics Data System (ADS)

Zhang, Yun; Wei, Hongxing; Yang, Bo

2018-04-01

To design modular robot system, Petri nets and category theory are combined and the ability of simulation of Petri net is discussed. According to category theory, the method of describing the category of components in the dynamic characteristics of the system is deduced. Moreover, a modular robot system is analyzed, which provides a verifiable description of the dynamic characteristics of the system.

Applying a semantic information Petri Net modeling method to AUV systems design

NASA Astrophysics Data System (ADS)

Feng, Xiao-Ning; Wang, Shuo; Wang, Zhuo; Liu, Qun

2008-12-01

This paper informally introduces colored object-oriented Petri Nets(COOPN) with the application of the AUV system. According to the characteristic of the AUV system’s running environment, the object-oriented method is used in this paper not only to dispart system modules but also construct the refined running model of AUV system, then the colored Petri Net method is used to establish hierarchically detailed model in order to get the performance analyzing information of the system. After analyzing the model implementation, the errors of architecture designing and function realization can be found. If the errors can be modified on time, the experiment time in the pool can be reduced and the cost can be saved.

Applying Dynamic Fuzzy Petri Net to Web Learning System

ERIC Educational Resources Information Center

Chen, Juei-Nan; Huang, Yueh-Min; Chu, William

2005-01-01

This investigation presents a DFPN (Dynamic Fuzzy Petri Net) model to increase the flexibility of the tutoring agent's behaviour and thus provide a learning content structure for a lecture course. The tutoring agent is a software assistant for a single user, who may be an expert in an e-Learning course. Based on each learner's behaviour, the…

Modelling and simulating reaction-diffusion systems using coloured Petri nets.

PubMed

Liu, Fei; Blätke, Mary-Ann; Heiner, Monika; Yang, Ming

2014-10-01

Reaction-diffusion systems often play an important role in systems biology when developmental processes are involved. Traditional methods of modelling and simulating such systems require substantial prior knowledge of mathematics and/or simulation algorithms. Such skills may impose a challenge for biologists, when they are not equally well-trained in mathematics and computer science. Coloured Petri nets as a high-level and graphical language offer an attractive alternative, which is easily approachable. In this paper, we investigate a coloured Petri net framework integrating deterministic, stochastic and hybrid modelling formalisms and corresponding simulation algorithms for the modelling and simulation of reaction-diffusion processes that may be closely coupled with signalling pathways, metabolic reactions and/or gene expression. Such systems often manifest multiscaleness in time, space and/or concentration. We introduce our approach by means of some basic diffusion scenarios, and test it against an established case study, the Brusselator model. Copyright © 2014 Elsevier Ltd. All rights reserved.

Coloured Logic Petri Nets and analysis of their reachable trees

NASA Astrophysics Data System (ADS)

Wang, Jing; Du, YuYue; Yu, ShuXia

2015-11-01

Logic Petri nets (LPNs) can describe and analyse the batch processing function and passing value indeterminacy in cooperative systems, and alleviate the state space explosion problem. However, the indeterminate data of logical output transitions cannot be described explicitly in LPNs. Therefore, Coloured Logic Petri nets (CLPNs) are defined in this paper. It can determine the indeterminate data of logic output transitions in LPNs, i.e., the indeterminate data can be represented definitely in CLPNs. A vector matching method is proposed to judge the enabling transitions and analyse CLPNs. From the marking equation and the proposed reachable tree generation algorithm of CLPNs, a reachable tree can be built, and reachable markings are calculated. The advantage of CLPNs can be shown based on the number of leaf nodes of the reachability tree, and CLPNs can solve the indeterminate data of logical output transitions. Finally, an example shows that CLPNs can further reduce the dimensionality of reachable markings.

Petri net modelling of biological networks.

PubMed

Chaouiya, Claudine

2007-07-01

Mathematical modelling is increasingly used to get insights into the functioning of complex biological networks. In this context, Petri nets (PNs) have recently emerged as a promising tool among the various methods employed for the modelling and analysis of molecular networks. PNs come with a series of extensions, which allow different abstraction levels, from purely qualitative to more complex quantitative models. Noteworthily, each of these models preserves the underlying graph, which depicts the interactions between the biological components. This article intends to present the basics of the approach and to foster the potential role PNs could play in the development of the computational systems biology.

Modeling and Simulation of Metallurgical Process Based on Hybrid Petri Net

NASA Astrophysics Data System (ADS)

Ren, Yujuan; Bao, Hong

2016-11-01

In order to achieve the goals of energy saving and emission reduction of iron and steel enterprises, an increasing number of modeling and simulation technologies are used to research and analyse metallurgical production process. In this paper, the basic principle of Hybrid Petri net is used to model and analyse the Metallurgical Process. Firstly, the definition of Hybrid Petri Net System of Metallurgical Process (MPHPNS) and its modeling theory are proposed. Secondly, the model of MPHPNS based on material flow is constructed. The dynamic flow of materials and the real-time change of each technological state in metallurgical process are simulated vividly by using this model. The simulation process can implement interaction between the continuous event dynamic system and the discrete event dynamic system at the same level, and play a positive role in the production decision.

Neural networks with fuzzy Petri nets for modeling a machining process

NASA Astrophysics Data System (ADS)

Hanna, Moheb M.

1998-03-01

The paper presents an intelligent architecture based a feedforward neural network with fuzzy Petri nets for modeling product quality in a CNC machining center. It discusses how the proposed architecture can be used for modeling, monitoring and control a product quality specification such as surface roughness. The surface roughness represents the output quality specification manufactured by a CNC machining center as a result of a milling process. The neural network approach employed the selected input parameters which defined by the machine operator via the CNC code. The fuzzy Petri nets approach utilized the exact input milling parameters, such as spindle speed, feed rate, tool diameter and coolant (off/on), which can be obtained via the machine or sensors system. An aim of the proposed architecture is to model the demanded quality of surface roughness as high, medium or low.

Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets.

PubMed

Kielbassa, J; Bortfeldt, R; Schuster, S; Koch, I

2009-02-01

The investigation of spliceosomal processes is currently a topic of intense research in molecular biology. In the molecular mechanism of alternative splicing, a multi-protein-RNA complex - the spliceosome - plays a crucial role. To understand the biological processes of alternative splicing, it is essential to comprehend the biogenesis of the spliceosome. In this paper, we propose the first abstract model of the regulatory assembly pathway of the human spliceosomal subunit U1. Using Petri nets, we describe its highly ordered assembly that takes place in a stepwise manner. Petri net theory represents a mathematical formalism to model and analyze systems with concurrent processes at different abstraction levels with the possibility to combine them into a uniform description language. There exist many approaches to determine static and dynamic properties of Petri nets, which can be applied to analyze biochemical systems. In addition, Petri net tools usually provide intuitively understandable graphical network representations, which facilitate the dialog between experimentalists and theoreticians. Our Petri net model covers binding, transport, signaling, and covalent modification processes. Through the computation of structural and behavioral Petri net properties and their interpretation in biological terms, we validate our model and use it to get a better understanding of the complex processes of the assembly pathway. We can explain the basic network behavior, using minimal T-invariants which represent special pathways through the network. We find linear as well as cyclic pathways. We determine the P-invariants that represent conserved moieties in a network. The simulation of the net demonstrates the importance of the stability of complexes during the maturation pathway. We can show that complexes that dissociate too fast, hinder the formation of the complete U1 snRNP.

An Extended Petri-Net Based Approach for Supply Chain Process Enactment in Resource-Centric Web Service Environment

NASA Astrophysics Data System (ADS)

Wang, Xiaodong; Zhang, Xiaoyu; Cai, Hongming; Xu, Boyi

Enacting a supply-chain process involves variant partners and different IT systems. REST receives increasing attention for distributed systems with loosely coupled resources. Nevertheless, resource model incompatibilities and conflicts prevent effective process modeling and deployment in resource-centric Web service environment. In this paper, a Petri-net based framework for supply-chain process integration is proposed. A resource meta-model is constructed to represent the basic information of resources. Then based on resource meta-model, XML schemas and documents are derived, which represent resources and their states in Petri-net. Thereafter, XML-net, a high level Petri-net, is employed for modeling control and data flow of process. From process model in XML-net, RESTful services and choreography descriptions are deduced. Therefore, unified resource representation and RESTful services description are proposed for cross-system integration in a more effective way. A case study is given to illustrate the approach and the desirable features of the approach are discussed.

Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters

PubMed Central

Liu, Fei; Heiner, Monika; Yang, Ming

2016-01-01

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. FSPNs combine SPNs and fuzzy sets, thereby taking into account both randomness and fuzziness of biological systems. For a biological system, SPNs model the randomness, while fuzzy sets model kinetic parameters with fuzzy uncertainty or variability by associating each parameter with a fuzzy number instead of a crisp real value. We introduce a simulation-based analysis method for FSPNs to explore the uncertainties of outputs resulting from the uncertainties associated with input parameters, which works equally well for bounded and unbounded models. We illustrate our approach using a yeast polarization model having an infinite state space, which shows the appropriateness of FSPNs in combination with simulation-based analysis for modeling and analyzing biological systems with uncertain information. PMID:26910830

An analysis of the Petri net based model of the human body iron homeostasis process.

PubMed

Sackmann, Andrea; Formanowicz, Dorota; Formanowicz, Piotr; Koch, Ina; Blazewicz, Jacek

2007-02-01

In the paper a Petri net based model of the human body iron homeostasis is presented and analyzed. The body iron homeostasis is an important but not fully understood complex process. The modeling of the process presented in the paper is expressed in the language of Petri net theory. An application of this theory to the description of biological processes allows for very precise analysis of the resulting models. Here, such an analysis of the body iron homeostasis model from a mathematical point of view is given.

On determining firing delay time of transitions for Petri net based signaling pathways by introducing stochastic decision rules.

PubMed

Miwa, Yoshimasa; Li, Chen; Ge, Qi-Wei; Matsuno, Hiroshi; Miyano, Satoru

2010-01-01

Parameter determination is important in modeling and simulating biological pathways including signaling pathways. Parameters are determined according to biological facts obtained from biological experiments and scientific publications. However, such reliable data describing detailed reactions are not reported in most cases. This prompted us to develop a general methodology of determining the parameters of a model in the case of that no information of the underlying biological facts is provided. In this study, we use the Petri net approach for modeling signaling pathways, and propose a method to determine firing delay times of transitions for Petri net models of signaling pathways by introducing stochastic decision rules. Petri net technology provides a powerful approach to modeling and simulating various concurrent systems, and recently have been widely accepted as a description method for biological pathways. Our method enables to determine the range of firing delay time which realizes smooth token flows in the Petri net model of a signaling pathway. The availability of this method has been confirmed by the results of an application to the interleukin-1 induced signaling pathway.

On determining firing delay time of transitions for petri net based signaling pathways by introducing stochastic decision rules.

PubMed

Miwa, Yoshimasa; Li, Chen; Ge, Qi-Wei; Matsuno, Hiroshi; Miyano, Satoru

2011-01-01

Parameter determination is important in modeling and simulating biological pathways including signaling pathways. Parameters are determined according to biological facts obtained from biological experiments and scientific publications. However, such reliable data describing detailed reactions are not reported in most cases. This prompted us to develop a general methodology of determining the parameters of a model in the case of that no information of the underlying biological facts is provided. In this study, we use the Petri net approach for modeling signaling pathways, and propose a method to determine firing delay times of transitions for Petri net models of signaling pathways by introducing stochastic decision rules. Petri net technology provides a powerful approach to modeling and simulating various concurrent systems, and recently have been widely accepted as a description method for biological pathways. Our method enables to determine the range of firing delay time which realizes smooth token flows in the Petri net model of a signaling pathway. The availability of this method has been confirmed by the results of an application to the interleukin-1 induced signaling pathway.

Health Monitoring of a Planetary Rover Using Hybrid Particle Petri Nets

NASA Technical Reports Server (NTRS)

Gaudel, Quentin; Ribot, Pauline; Chanthery, Elodie; Daigle, Matthew J.

2016-01-01

This paper focuses on the application of a Petri Net-based diagnosis method on a planetary rover prototype.The diagnosis is performed by using a model-based method in the context of health management of hybrid systems.In system health management, the diagnosis task aims at determining the current health state of a system and the fault occurrences that lead to this state. The Hybrid Particle Petri Nets (HPPN) formalism is used to model hybrid systems behavior and degradation, and to define the generation of diagnosers to monitor the health states of such systems under uncertainty. At any time, the HPPN-based diagnoser provides the current diagnosis represented by a distribution of beliefs over the health states. The health monitoring methodology is demonstrated on the K11 rover. A hybrid model of the K11 is proposed and experimental results show that the approach is robust to real system data and constraints.

Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber.

PubMed

Koch, Ina; Junker, Björn H; Heiner, Monika

2005-04-01

Because of the complexity of metabolic networks and their regulation, formal modelling is a useful method to improve the understanding of these systems. An essential step in network modelling is to validate the network model. Petri net theory provides algorithms and methods, which can be applied directly to metabolic network modelling and analysis in order to validate the model. The metabolism between sucrose and starch in the potato tuber is of great research interest. Even if the metabolism is one of the best studied in sink organs, it is not yet fully understood. We provide an approach for model validation of metabolic networks using Petri net theory, which we demonstrate for the sucrose breakdown pathway in the potato tuber. We start with hierarchical modelling of the metabolic network as a Petri net and continue with the analysis of qualitative properties of the network. The results characterize the net structure and give insights into the complex net behaviour.

Using Colored Stochastic Petri Net (CS-PN) software for protocol specification, validation, and evaluation

NASA Technical Reports Server (NTRS)

Zenie, Alexandre; Luguern, Jean-Pierre

1987-01-01

The specification, verification, validation, and evaluation, which make up the different steps of the CS-PN software are outlined. The colored stochastic Petri net software is applied to a Wound/Wait protocol decomposable into two principal modules: request or couple (transaction, granule) treatment module and wound treatment module. Each module is specified, verified, validated, and then evaluated separately, to deduce a verification, validation and evaluation of the complete protocol. The colored stochastic Petri nets tool is shown to be a natural extension of the stochastic tool, adapted to distributed systems and protocols, because the color conveniently takes into account the numerous sites, transactions, granules and messages.

Approximation methods for stochastic petri nets

NASA Technical Reports Server (NTRS)

Jungnitz, Hauke Joerg

1992-01-01

Stochastic Marked Graphs are a concurrent decision free formalism provided with a powerful synchronization mechanism generalizing conventional Fork Join Queueing Networks. In some particular cases the analysis of the throughput can be done analytically. Otherwise the analysis suffers from the classical state explosion problem. Embedded in the divide and conquer paradigm, approximation techniques are introduced for the analysis of stochastic marked graphs and Macroplace/Macrotransition-nets (MPMT-nets), a new subclass introduced herein. MPMT-nets are a subclass of Petri nets that allow limited choice, concurrency and sharing of resources. The modeling power of MPMT is much larger than that of marked graphs, e.g., MPMT-nets can model manufacturing flow lines with unreliable machines and dataflow graphs where choice and synchronization occur. The basic idea leads to the notion of a cut to split the original net system into two subnets. The cuts lead to two aggregated net systems where one of the subnets is reduced to a single transition. A further reduction leads to a basic skeleton. The generalization of the idea leads to multiple cuts, where single cuts can be applied recursively leading to a hierarchical decomposition. Based on the decomposition, a response time approximation technique for the performance analysis is introduced. Also, delay equivalence, which has previously been introduced in the context of marked graphs by Woodside et al., Marie's method and flow equivalent aggregation are applied to the aggregated net systems. The experimental results show that response time approximation converges quickly and shows reasonable accuracy in most cases. The convergence of Marie's method and flow equivalent aggregation are applied to the aggregated net systems. The experimental results show that response time approximation converges quickly and shows reasonable accuracy in most cases. The convergence of Marie's is slower, but the accuracy is generally better. Delay

Modeling and performance analysis using extended fuzzy-timing Petri nets for networked virtual environments.

PubMed

Zhou, Y; Murata, T; Defanti, T A

2000-01-01

Despite their attractive properties, networked virtual environments (net-VEs) are notoriously difficult to design, implement, and test due to the concurrency, real-time and networking features in these systems. Net-VEs demand high quality-of-service (QoS) requirements on the network to maintain natural and real-time interactions among users. The current practice for net-VE design is basically trial and error, empirical, and totally lacks formal methods. This paper proposes to apply a Petri net formal modeling technique to a net-VE-NICE (narrative immersive constructionist/collaborative environment), predict the net-VE performance based on simulation, and improve the net-VE performance. NICE is essentially a network of collaborative virtual reality systems called the CAVE-(CAVE automatic virtual environment). First, we introduce extended fuzzy-timing Petri net (EFTN) modeling and analysis techniques. Then, we present EFTN models of the CAVE, NICE, and transport layer protocol used in NICE: transmission control protocol (TCP). We show the possibility analysis based on the EFTN model for the CAVE. Then, by using these models and design/CPN as the simulation tool, we conducted various simulations to study real-time behavior, network effects and performance (latencies and jitters) of NICE. Our simulation results are consistent with experimental data.

Task sequence planning in a robot workcell using AND/OR nets

NASA Technical Reports Server (NTRS)

Cao, Tiehua; Sanderson, Arthur C.

1991-01-01

An approach to task sequence planning for a generalized robotic manufacturing or material handling workcell is described. Given the descriptions of the objects in this system and all feasible geometric relationships among these objects, an AND/OR net which describes the relationships of all feasible geometric states and associated feasibility criteria for net transitions is generated. This AND/OR net is mapped into a Petri net which incorporates all feasible sequences of operations. The resulting Petri net is shown to be bounded and have guaranteed properties of liveness, safeness, and reversibility. Sequences are found from the reachability tree of the Petri net. Feasibility criteria for net transitions may be used to generate an extended Petri net representation of lower level command sequences. The resulting Petri net representation may be used for on-line scheduling and control of the system of feasible sequences. A simulation example of the sequences is described.

A Petri net synthesis theory for modeling flexible manufacturing systems.

PubMed

Jeng, M D

1997-01-01

A theory that synthesizes Petri nets for modeling flexible manufacturing systems is presented. The theory adopts a bottom-up or modular-composition approach to construct net models. Each module is modeled as a resource control net (RCN), which represents a subsystem that controls a resource type in a flexible manufacturing system. Interactions among the modules are described as the common transition and transition subnets. The net obtained by merging the modules with two minimal restrictions is shown to be conservative and thus bounded. An algorithm is developed to detect two sufficient conditions for structural liveness of the net. The algorithm examines only the net's structure and the initial marking, and appears to be more efficient than state enumeration techniques such as the reachability tree method. In this paper, the sufficient conditions for liveness are shown to be related to some structural objects called siphons. To demonstrate the applicability of the theory, a flexible manufacturing system of a moderate size is modeled and analyzed using the proposed theory.

Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems.

PubMed

Radom, Marcin; Rybarczyk, Agnieszka; Szawulak, Bartlomiej; Andrzejewski, Hubert; Chabelski, Piotr; Kozak, Adam; Formanowicz, Piotr

2017-12-01

Model development and its analysis is a fundamental step in systems biology. The theory of Petri nets offers a tool for such a task. Since the rapid development of computer science, a variety of tools for Petri nets emerged, offering various analytical algorithms. From this follows a problem of using different programs to analyse a single model. Many file formats and different representations of results make the analysis much harder. Especially for larger nets the ability to visualize the results in a proper form provides a huge help in the understanding of their significance. We present a new tool for Petri nets development and analysis called Holmes. Our program contains algorithms for model analysis based on different types of Petri nets, e.g. invariant generator, Maximum Common Transitions (MCT) sets and cluster modules, simulation algorithms or knockout analysis tools. A very important feature is the ability to visualize the results of almost all analytical modules. The integration of such modules into one graphical environment allows a researcher to fully devote his or her time to the model building and analysis. Available at http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html. piotr@cs.put.poznan.pl. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Analysis of Phase-Type Stochastic Petri Nets With Discrete and Continuous Timing

NASA Technical Reports Server (NTRS)

Jones, Robert L.; Goode, Plesent W. (Technical Monitor)

2000-01-01

The Petri net formalism is useful in studying many discrete-state, discrete-event systems exhibiting concurrency, synchronization, and other complex behavior. As a bipartite graph, the net can conveniently capture salient aspects of the system. As a mathematical tool, the net can specify an analyzable state space. Indeed, one can reason about certain qualitative properties (from state occupancies) and how they arise (the sequence of events leading there). By introducing deterministic or random delays, the model is forced to sojourn in states some amount of time, giving rise to an underlying stochastic process, one that can be specified in a compact way and capable of providing quantitative, probabilistic measures. We formalize a new non-Markovian extension to the Petri net that captures both discrete and continuous timing in the same model. The approach affords efficient, stationary analysis in most cases and efficient transient analysis under certain restrictions. Moreover, this new formalism has the added benefit in modeling fidelity stemming from the simultaneous capture of discrete- and continuous-time events (as opposed to capturing only one and approximating the other). We show how the underlying stochastic process, which is non-Markovian, can be resolved into simpler Markovian problems that enjoy efficient solutions. Solution algorithms are provided that can be easily programmed.

Application of Petri net based analysis techniques to signal transduction pathways.

PubMed

Sackmann, Andrea; Heiner, Monika; Koch, Ina

2006-11-02

Signal transduction pathways are usually modelled using classical quantitative methods, which are based on ordinary differential equations (ODEs). However, some difficulties are inherent in this approach. On the one hand, the kinetic parameters involved are often unknown and have to be estimated. With increasing size and complexity of signal transduction pathways, the estimation of missing kinetic data is not possible. On the other hand, ODEs based models do not support any explicit insights into possible (signal-) flows within the network. Moreover, a huge amount of qualitative data is available due to high-throughput techniques. In order to get information on the systems behaviour, qualitative analysis techniques have been developed. Applications of the known qualitative analysis methods concern mainly metabolic networks. Petri net theory provides a variety of established analysis techniques, which are also applicable to signal transduction models. In this context special properties have to be considered and new dedicated techniques have to be designed. We apply Petri net theory to model and analyse signal transduction pathways first qualitatively before continuing with quantitative analyses. This paper demonstrates how to build systematically a discrete model, which reflects provably the qualitative biological behaviour without any knowledge of kinetic parameters. The mating pheromone response pathway in Saccharomyces cerevisiae serves as case study. We propose an approach for model validation of signal transduction pathways based on the network structure only. For this purpose, we introduce the new notion of feasible t-invariants, which represent minimal self-contained subnets being active under a given input situation. Each of these subnets stands for a signal flow in the system. We define maximal common transition sets (MCT-sets), which can be used for t-invariant examination and net decomposition into smallest biologically meaningful functional units. The

Reconstructing the regulatory network controlling commitment and sporulation in Physarum polycephalum based on hierarchical Petri Net modelling and simulation.

PubMed

Marwan, Wolfgang; Sujatha, Arumugam; Starostzik, Christine

2005-10-21

We reconstruct the regulatory network controlling commitment and sporulation of Physarum polycephalum from experimental results using a hierarchical Petri Net-based modelling and simulation framework. The stochastic Petri Net consistently describes the structure and simulates the dynamics of the molecular network as analysed by genetic, biochemical and physiological experiments within a single coherent model. The Petri Net then is extended to simulate time-resolved somatic complementation experiments performed by mixing the cytoplasms of mutants altered in the sporulation response, to systematically explore the network structure and to probe its dynamics. This reverse engineering approach presumably can be employed to explore other molecular or genetic signalling systems where the activity of genes or their products can be experimentally controlled in a time-resolved manner.

Yeast pheromone pathway modeling using Petri nets

PubMed Central

2014-01-01

Background Our environment is composed of biological components of varying magnitude. The relationships between the different biological elements can be represented as a biological network. The process of mating in S. cerevisiae is initiated by secretion of pheromone by one of the cells. Our interest lies in one particular question: how does a cell dynamically adapt the pathway to continue mating under severe environmental changes or under mutation (which might result in the loss of functionality of some proteins known to participate in the pheromone pathway). Our work attempts to answer this question. To achieve this, we first propose a model to simulate the pheromone pathway using Petri nets. Petri nets are directed graphs that can be used for describing and modeling systems characterized as concurrent, asynchronous, distributed, parallel, non-deterministic, and/or stochastic. We then analyze our Petri net-based model of the pathway to investigate the following: 1) Given the model of the pheromone response pathway, under what conditions does the cell respond positively, i.e., mate? 2) What kinds of perturbations in the cell would result in changing a negative response to a positive one? Method In our model, we classify proteins into two categories: core component proteins (set ψ) and additional proteins (set λ). We randomly generate our model's parameters in repeated simulations. To simulate the pathway, we carry out three different experiments. In the experiments, we simply change the concentration of the additional proteins (λ) available to the cell. The concentration of proteins in ψ is varied consistently from 300 to 400. In Experiment 1, the range of values for λ is set to be 100 to 150. In Experiment 2, it is set to be 151 to 200. In Experiment 3, the set λ is further split into σ and ς, with the idea that proteins in σ are more important than those in ς. The range of values for σ is set to be between 151 to 200 while that of ς is 100 to 150

Yeast pheromone pathway modeling using Petri nets.

PubMed

Majumdar, Abhishek; Scott, Stephen D; Deogun, Jitender S; Harris, Steven

2014-01-01

Our environment is composed of biological components of varying magnitude. The relationships between the different biological elements can be represented as a biological network. The process of mating in S. cerevisiae is initiated by secretion of pheromone by one of the cells. Our interest lies in one particular question: how does a cell dynamically adapt the pathway to continue mating under severe environmental changes or under mutation (which might result in the loss of functionality of some proteins known to participate in the pheromone pathway). Our work attempts to answer this question. To achieve this, we first propose a model to simulate the pheromone pathway using Petri nets. Petri nets are directed graphs that can be used for describing and modeling systems characterized as concurrent, asynchronous, distributed, parallel, non-deterministic, and/or stochastic. We then analyze our Petri net-based model of the pathway to investigate the following: 1) Given the model of the pheromone response pathway, under what conditions does the cell respond positively, i.e., mate? 2) What kinds of perturbations in the cell would result in changing a negative response to a positive one? In our model, we classify proteins into two categories: core component proteins (set ψ) and additional proteins (set λ). We randomly generate our model's parameters in repeated simulations. To simulate the pathway, we carry out three different experiments. In the experiments, we simply change the concentration of the additional proteins (λ) available to the cell. The concentration of proteins in ψ is varied consistently from 300 to 400. In Experiment 1, the range of values for λ is set to be 100 to 150. In Experiment 2, it is set to be 151 to 200. In Experiment 3, the set λ is further split into σ and ς, with the idea that proteins in σ are more important than those in ς. The range of values for σ is set to be between 151 to 200 while that of ς is 100 to 150. Decision trees were

Petri nets as a modeling tool for discrete concurrent tasks of the human operator. [describing sequential and parallel demands on human operators

NASA Technical Reports Server (NTRS)

Schumacher, W.; Geiser, G.

1978-01-01

The basic concepts of Petri nets are reviewed as well as their application as the fundamental model of technical systems with concurrent discrete events such as hardware systems and software models of computers. The use of Petri nets is proposed for modeling the human operator dealing with concurrent discrete tasks. Their properties useful in modeling the human operator are discussed and practical examples are given. By means of and experimental investigation of binary concurrent tasks which are presented in a serial manner, the representation of human behavior by Petri nets is demonstrated.

Modularization of biochemical networks based on classification of Petri net t-invariants.

PubMed

Grafahrend-Belau, Eva; Schreiber, Falk; Heiner, Monika; Sackmann, Andrea; Junker, Björn H; Grunwald, Stefanie; Speer, Astrid; Winder, Katja; Koch, Ina

2008-02-08

Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior.With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system. Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted as modules. To find

Modularization of biochemical networks based on classification of Petri net t-invariants

PubMed Central

Grafahrend-Belau, Eva; Schreiber, Falk; Heiner, Monika; Sackmann, Andrea; Junker, Björn H; Grunwald, Stefanie; Speer, Astrid; Winder, Katja; Koch, Ina

2008-01-01

Background Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior. With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system. Methods Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted

Petri net model for analysis of concurrently processed complex algorithms

NASA Technical Reports Server (NTRS)

Stoughton, John W.; Mielke, Roland R.

1986-01-01

This paper presents a Petri-net model suitable for analyzing the concurrent processing of computationally complex algorithms. The decomposed operations are to be processed in a multiple processor, data driven architecture. Of particular interest is the application of the model to both the description of the data/control flow of a particular algorithm, and to the general specification of the data driven architecture. A candidate architecture is also presented.

Application of Petri net based analysis techniques to signal transduction pathways

PubMed Central

Sackmann, Andrea; Heiner, Monika; Koch, Ina

2006-01-01

Background Signal transduction pathways are usually modelled using classical quantitative methods, which are based on ordinary differential equations (ODEs). However, some difficulties are inherent in this approach. On the one hand, the kinetic parameters involved are often unknown and have to be estimated. With increasing size and complexity of signal transduction pathways, the estimation of missing kinetic data is not possible. On the other hand, ODEs based models do not support any explicit insights into possible (signal-) flows within the network. Moreover, a huge amount of qualitative data is available due to high-throughput techniques. In order to get information on the systems behaviour, qualitative analysis techniques have been developed. Applications of the known qualitative analysis methods concern mainly metabolic networks. Petri net theory provides a variety of established analysis techniques, which are also applicable to signal transduction models. In this context special properties have to be considered and new dedicated techniques have to be designed. Methods We apply Petri net theory to model and analyse signal transduction pathways first qualitatively before continuing with quantitative analyses. This paper demonstrates how to build systematically a discrete model, which reflects provably the qualitative biological behaviour without any knowledge of kinetic parameters. The mating pheromone response pathway in Saccharomyces cerevisiae serves as case study. Results We propose an approach for model validation of signal transduction pathways based on the network structure only. For this purpose, we introduce the new notion of feasible t-invariants, which represent minimal self-contained subnets being active under a given input situation. Each of these subnets stands for a signal flow in the system. We define maximal common transition sets (MCT-sets), which can be used for t-invariant examination and net decomposition into smallest biologically

A colored petri nets based workload evaluation model and its validation through Multi-Attribute Task Battery-II.

PubMed

Wang, Peng; Fang, Weining; Guo, Beiyuan

2017-04-01

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. Verify experiments were carried out based on Multi-Attribute Task Battery-II software. Our results show that there is a strong correlation between the model values and NASA -Task Load Index scores (r=0.9513). In addition, this method can also distinguish behavior characteristics between different people. Copyright © 2016 Elsevier Ltd. All rights reserved.

Modeling and implementation of concurrent logic controllers with use of Petri nets, LSMs, and sequent calculus

NASA Astrophysics Data System (ADS)

Tkacz, J.; Bukowiec, A.; Doligalski, M.

2017-08-01

The paper presentes the method of modeling and implementation of concurrent controllers. Concurrent controllers are specified by Petri nets. Then Petri nets are decomposed using symbolic deduction method of analysis. Formal methods like sequent calculus system with considered elements of Thelen's algorithm have been used here. As a result, linked state machines (LSMs) are received. Each FSM is implemented using methods of structural decomposition during process of logic synthesis. The method of multiple encoding of microinstruction has been applied. It leads to decreased number of Boolean function realized by combinational part of FSM. The additional decoder could be implemented with the use of memory blocks.

Hybrid modeling in biochemical systems theory by means of functional petri nets.

PubMed

Wu, Jialiang; Voit, Eberhard

2009-02-01

Many biological systems are genuinely hybrids consisting of interacting discrete and continuous components and processes that often operate at different time scales. It is therefore desirable to create modeling frameworks capable of combining differently structured processes and permitting their analysis over multiple time horizons. During the past 40 years, Biochemical Systems Theory (BST) has been a very successful approach to elucidating metabolic, gene regulatory, and signaling systems. However, its foundation in ordinary differential equations has precluded BST from directly addressing problems containing switches, delays, and stochastic effects. In this study, we extend BST to hybrid modeling within the framework of Hybrid Functional Petri Nets (HFPN). First, we show how the canonical GMA and S-system models in BST can be directly implemented in a standard Petri Net framework. In a second step we demonstrate how to account for different types of time delays as well as for discrete, stochastic, and switching effects. Using representative test cases, we validate the hybrid modeling approach through comparative analyses and simulations with other approaches and highlight the feasibility, quality, and efficiency of the hybrid method.

High performance hybrid functional Petri net simulations of biological pathway models on CUDA.

PubMed

Chalkidis, Georgios; Nagasaki, Masao; Miyano, Satoru

2011-01-01

Hybrid functional Petri nets are a wide-spread tool for representing and simulating biological models. Due to their potential of providing virtual drug testing environments, biological simulations have a growing impact on pharmaceutical research. Continuous research advancements in biology and medicine lead to exponentially increasing simulation times, thus raising the demand for performance accelerations by efficient and inexpensive parallel computation solutions. Recent developments in the field of general-purpose computation on graphics processing units (GPGPU) enabled the scientific community to port a variety of compute intensive algorithms onto the graphics processing unit (GPU). This work presents the first scheme for mapping biological hybrid functional Petri net models, which can handle both discrete and continuous entities, onto compute unified device architecture (CUDA) enabled GPUs. GPU accelerated simulations are observed to run up to 18 times faster than sequential implementations. Simulating the cell boundary formation by Delta-Notch signaling on a CUDA enabled GPU results in a speedup of approximately 7x for a model containing 1,600 cells.

Research on user behavior authentication model based on stochastic Petri nets

NASA Astrophysics Data System (ADS)

Zhang, Chengyuan; Xu, Haishui

2017-08-01

A behavioural authentication model based on stochastic Petri net is proposed to meet the randomness, uncertainty and concurrency characteristics of user behaviour. The use of random models in the location, changes, arc and logo to describe the characteristics of a variety of authentication and game relationships, so as to effectively implement the graphical user behaviour authentication model analysis method, according to the corresponding proof to verify the model is valuable.

Models of the Behavior of People Searching the Internet: A Petri Net Approach.

ERIC Educational Resources Information Center

Kantor, Paul B.; Nordlie, Ragnar

1999-01-01

Illustrates how various key abstractions of information finding, such as document relevance, a desired number of relevant documents, discouragement, exhaustion, and satisfaction can be modeled using the Petri Net framework. Shows that this model leads naturally to a new approach to collection of user data, and to analysis of transaction logs.…

Applications of the Petri net to simulate, test, and validate the performance and safety of complex, heterogeneous, multi-modality patient monitoring alarm systems.

PubMed

Sloane, E B; Gelhot, V

2004-01-01

This research is motivated by the rapid pace of medical device and information system integration. Although the ability to interconnect many medical devices and information systems may help improve patient care, there is no way to detect if incompatibilities between one or more devices might cause critical events such as patient alarms to go unnoticed or cause one or more of the devices to become stuck in a disabled state. Petri net tools allow automated testing of all possible states and transitions between devices and/or systems to detect potential failure modes in advance. This paper describes an early research project to use Petri nets to simulate and validate a multi-modality central patient monitoring system. A free Petri net tool, HPSim, is used to simulate two wireless patient monitoring networks: one with 44 heart monitors and a central monitoring system and a second version that includes an additional 44 wireless pulse oximeters. In the latter Petri net simulation, a potentially dangerous heart arrhythmia and pulse oximetry alarms were detected.

Specification and Verification of Medical Monitoring System Using Petri-nets.

PubMed

Majma, Negar; Babamir, Seyed Morteza

2014-07-01

To monitor the patient behavior, data are collected from patient's body by a medical monitoring device so as to calculate the output using embedded software. Incorrect calculations may endanger the patient's life if the software fails to meet the patient's requirements. Accordingly, the veracity of the software behavior is a matter of concern in the medicine; moreover, the data collected from the patient's body are fuzzy. Some methods have already dealt with monitoring the medical monitoring devices; however, model based monitoring fuzzy computations of such devices have been addressed less. The present paper aims to present synthesizing a fuzzy Petri-net (FPN) model to verify behavior of a sample medical monitoring device called continuous infusion insulin (INS) because Petri-net (PN) is one of the formal and visual methods to verify the software's behavior. The device is worn by the diabetic patients and then the software calculates the INS dose and makes a decision for injection. The input and output of the infusion INS software are not crisp in the real world; therefore, we present them in fuzzy variables. Afterwards, we use FPN instead of clear PN to model the fuzzy variables. The paper follows three steps to synthesize an FPN to deal with verification of the infusion INS device: (1) Definition of fuzzy variables, (2) definition of fuzzy rules and (3) design of the FPN model to verify the software behavior.

A Petri Net model for distributed energy system

NASA Astrophysics Data System (ADS)

Konopko, Joanna

2015-12-01

Electrical networks need to evolve to become more intelligent, more flexible and less costly. The smart grid is the next generation power energy, uses two-way flows of electricity and information to create a distributed automated energy delivery network. Building a comprehensive smart grid is a challenge for system protection, optimization and energy efficient. Proper modeling and analysis is needed to build an extensive distributed energy system and intelligent electricity infrastructure. In this paper, the whole model of smart grid have been proposed using Generalized Stochastic Petri Nets (GSPN). The simulation of created model is also explored. The simulation of the model has allowed the analysis of how close the behavior of the model is to the usage of the real smart grid.

A vector matching method for analysing logic Petri nets

NASA Astrophysics Data System (ADS)

Du, YuYue; Qi, Liang; Zhou, MengChu

2011-11-01

Batch processing function and passing value indeterminacy in cooperative systems can be described and analysed by logic Petri nets (LPNs). To directly analyse the properties of LPNs, the concept of transition enabling vector sets is presented and a vector matching method used to judge the enabling transitions is proposed in this article. The incidence matrix of LPNs is defined; an equation about marking change due to a transition's firing is given; and a reachable tree is constructed. The state space explosion is mitigated to a certain extent from directly analysing LPNs. Finally, the validity and reliability of the proposed method are illustrated by an example in electronic commerce.

Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy.

PubMed

Jung, Jinmyung; Kwon, Mijin; Bae, Sunghwa; Yim, Soorin; Lee, Doheon

2018-03-05

Muscle atrophy, an involuntary loss of muscle mass, is involved in various diseases and sometimes leads to mortality. However, therapeutics for muscle atrophy thus far have had limited effects. Here, we present a new approach for therapeutic target prediction using Petri net simulation of the status of phosphorylation, with a reasonable assumption that the recovery of abnormally phosphorylated proteins can be a treatment for muscle atrophy. The Petri net model was employed to simulate phosphorylation status in three states, i.e. reference, atrophic and each gene-inhibited state based on the myocyte-specific phosphorylation network. Here, we newly devised a phosphorylation specific Petri net that involves two types of transitions (phosphorylation or de-phosphorylation) and two types of places (activation with or without phosphorylation). Before predicting therapeutic targets, the simulation results in reference and atrophic states were validated by Western blotting experiments detecting five marker proteins, i.e. RELA, SMAD2, SMAD3, FOXO1 and FOXO3. Finally, we determined 37 potential therapeutic targets whose inhibition recovers the phosphorylation status from an atrophic state as indicated by the five validated marker proteins. In the evaluation, we confirmed that the 37 potential targets were enriched for muscle atrophy-related terms such as actin and muscle contraction processes, and they were also significantly overlapping with the genes associated with muscle atrophy reported in the Comparative Toxicogenomics Database (p-value < 0.05). Furthermore, we noticed that they included several proteins that could not be characterized by the shortest path analysis. The three potential targets, i.e. BMPR1B, ROCK, and LEPR, were manually validated with the literature. In this study, we suggest a new approach to predict potential therapeutic targets of muscle atrophy with an analysis of phosphorylation status simulated by Petri net. We generated a list of the potential

Design and verification of distributed logic controllers with application of Petri nets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wiśniewski, Remigiusz; Grobelna, Iwona; Grobelny, Michał

2015-12-31

The paper deals with the designing and verification of distributed logic controllers. The control system is initially modelled with Petri nets and formally verified against structural and behavioral properties with the application of the temporal logic and model checking technique. After that it is decomposed into separate sequential automata that are working concurrently. Each of them is re-verified and if the validation is successful, the system can be finally implemented.

Design and verification of distributed logic controllers with application of Petri nets

NASA Astrophysics Data System (ADS)

Wiśniewski, Remigiusz; Grobelna, Iwona; Grobelny, Michał; Wiśniewska, Monika

2015-12-01

The paper deals with the designing and verification of distributed logic controllers. The control system is initially modelled with Petri nets and formally verified against structural and behavioral properties with the application of the temporal logic and model checking technique. After that it is decomposed into separate sequential automata that are working concurrently. Each of them is re-verified and if the validation is successful, the system can be finally implemented.

Modelling the protocol stack in NCS with deterministic and stochastic petri net

NASA Astrophysics Data System (ADS)

Hui, Chen; Chunjie, Zhou; Weifeng, Zhu

2011-06-01

Protocol stack is the basis of the networked control systems (NCS). Full or partial reconfiguration of protocol stack offers both optimised communication service and system performance. Nowadays, field testing is unrealistic to determine the performance of reconfigurable protocol stack; and the Petri net formal description technique offers the best combination of intuitive representation, tool support and analytical capabilities. Traditionally, separation between the different layers of the OSI model has been a common practice. Nevertheless, such a layered modelling analysis framework of protocol stack leads to the lack of global optimisation for protocol reconfiguration. In this article, we proposed a general modelling analysis framework for NCS based on the cross-layer concept, which is to establish an efficiency system scheduling model through abstracting the time constraint, the task interrelation, the processor and the bus sub-models from upper and lower layers (application, data link and physical layer). Cross-layer design can help to overcome the inadequacy of global optimisation based on information sharing between protocol layers. To illustrate the framework, we take controller area network (CAN) as a case study. The simulation results of deterministic and stochastic Petri-net (DSPN) model can help us adjust the message scheduling scheme and obtain better system performance.

Modeling Cyber Conflicts Using an Extended Petri Net Formalism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zakrzewska, Anita N; Ferragut, Erik M

2011-01-01

When threatened by automated attacks, critical systems that require human-controlled responses have difficulty making optimal responses and adapting protections in real- time and may therefore be overwhelmed. Consequently, experts have called for the development of automatic real-time reaction capabilities. However, a technical gap exists in the modeling and analysis of cyber conflicts to automatically understand the repercussions of responses. There is a need for modeling cyber assets that accounts for concurrent behavior, incomplete information, and payoff functions. Furthermore, we address this need by extending the Petri net formalism to allow real-time cyber conflicts to be modeled in a way thatmore » is expressive and concise. This formalism includes transitions controlled by players as well as firing rates attached to transitions. This allows us to model both player actions and factors that are beyond the control of players in real-time. We show that our formalism is able to represent situational aware- ness, concurrent actions, incomplete information and objective functions. These factors make it well-suited to modeling cyber conflicts in a way that allows for useful analysis. MITRE has compiled the Common Attack Pattern Enumera- tion and Classification (CAPEC), an extensive list of cyber attacks at various levels of abstraction. CAPEC includes factors such as attack prerequisites, possible countermeasures, and attack goals. These elements are vital to understanding cyber attacks and to generating the corresponding real-time responses. We demonstrate that the formalism can be used to extract precise models of cyber attacks from CAPEC. Several case studies show that our Petri net formalism is more expressive than other models, such as attack graphs, for modeling cyber conflicts and that it is amenable to exploring cyber strategies.« less

A Petri Net model for distributed energy system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konopko, Joanna

2015-12-31

Electrical networks need to evolve to become more intelligent, more flexible and less costly. The smart grid is the next generation power energy, uses two-way flows of electricity and information to create a distributed automated energy delivery network. Building a comprehensive smart grid is a challenge for system protection, optimization and energy efficient. Proper modeling and analysis is needed to build an extensive distributed energy system and intelligent electricity infrastructure. In this paper, the whole model of smart grid have been proposed using Generalized Stochastic Petri Nets (GSPN). The simulation of created model is also explored. The simulation of themore » model has allowed the analysis of how close the behavior of the model is to the usage of the real smart grid.« less

Applying generalized stochastic Petri nets to manufacturing systems containing nonexponential transition functions

NASA Technical Reports Server (NTRS)

Watson, James F., III; Desrochers, Alan A.

1991-01-01

Generalized stochastic Petri nets (GSPNs) are applied to flexible manufacturing systems (FMSs). Throughput subnets and s-transitions are presented. Two FMS examples containing nonexponential distributions which were analyzed in previous papers by queuing theory and probability theory, respectively, are treated using GSPNs developed using throughput subnets and s-transitions. The GSPN results agree with the previous results, and developing and analyzing the GSPN models are straightforward and relatively easy compared to other methodologies.

Colored petri net modeling of small interfering RNA-mediated messenger RNA degradation.

PubMed

Nickaeen, Niloofar; Moein, Shiva; Heidary, Zarifeh; Ghaisari, Jafar

2016-01-01

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. In the process of degradation of RNA sequence, small-noncoding RNA molecules known as small interfering RNA (siRNA) match the target RNA sequence. As a result of this matching, the target RNA sequence is destroyed. In this context, the process of matching and destruction is modeled using Colored Petri Nets (CPNs). The model is constructed using CPNs which allow tokens to have a value or type on them. Thus, CPN is a suitable tool to model string structures in which each element of the string has a different type. Using CPNs, long RNA, and siRNA strings are modeled with a finite set of colors. The model is simulated via CPN Tools. A CPN model of the matching between RNA and siRNA strings is constructed in CPN Tools environment. In previous studies, a network of stoichiometric equations was modeled. However, in this particular study, we modeled the mechanism behind the silencing process. Modeling this kind of mechanisms provides us with a tool to examine the effects of different factors such as mutation or drugs on the process.

Some aspects of the anemia of chronic disorders modeled and analyzed by petri net based approach.

PubMed

Formanowicz, Dorota; Sackmann, Andrea; Kozak, Adam; Błażewicz, Jacek; Formanowicz, Piotr

2011-06-01

Anemia of chronic disorders is a very important phenomenon and iron is a crucial factor of this complex process. To better understand this process and its influence on some other factors we have built a mathematical model of the human body iron homeostasis, which possibly most exactly would reflect the metabolism of iron in the case of anemia and inflammation. The model has been formulated in the language of Petri net theory, which allows for its simulation and precise analysis. The obtained results of the analysis of the model's behavior, concerning the influence of anemia and inflammation on the transferrin receptors, and hepcidin concentration changes are the valuable complements to the knowledge following from clinical research. This analysis is one of the first attempts to investigate properties and behavior of a not fully understood biological system on a basis of its Petri net based model.

C code generation from Petri-net-based logic controller specification

NASA Astrophysics Data System (ADS)

Grobelny, Michał; Grobelna, Iwona; Karatkevich, Andrei

2017-08-01

The article focuses on programming of logic controllers. It is important that a programming code of a logic controller is executed flawlessly according to the primary specification. In the presented approach we generate C code for an AVR microcontroller from a rule-based logical model of a control process derived from a control interpreted Petri net. The same logical model is also used for formal verification of the specification by means of the model checking technique. The proposed rule-based logical model and formal rules of transformation ensure that the obtained implementation is consistent with the already verified specification. The approach is validated by practical experiments.

Petri net modeling of encrypted information flow in federated cloud

NASA Astrophysics Data System (ADS)

Khushk, Abdul Rauf; Li, Xiaozhong

2017-08-01

Solutions proposed and developed for the cost-effective cloud systems suffer from a combination of secure private clouds and less secure public clouds. Need to locate applications within different clouds poses a security risk to the information flow of the entire system. This study addresses this by assigning security levels of a given lattice to the entities of a federated cloud system. A dynamic flow sensitive security model featuring Bell-LaPadula procedures is explored that tracks and authenticates the secure information flow in federated clouds. Additionally, a Petri net model is considered as a case study to represent the proposed system and further validate the performance of the said system.

Parallelizing Timed Petri Net simulations

NASA Technical Reports Server (NTRS)

Nicol, David M.

1993-01-01

The possibility of using parallel processing to accelerate the simulation of Timed Petri Nets (TPN's) was studied. It was recognized that complex system development tools often transform system descriptions into TPN's or TPN-like models, which are then simulated to obtain information about system behavior. Viewed this way, it was important that the parallelization of TPN's be as automatic as possible, to admit the possibility of the parallelization being embedded in the system design tool. Later years of the grant were devoted to examining the problem of joint performance and reliability analysis, to explore whether both types of analysis could be accomplished within a single framework. In this final report, the results of our studies are summarized. We believe that the problem of parallelizing TPN's automatically for MIMD architectures has been almost completely solved for a large and important class of problems. Our initial investigations into joint performance/reliability analysis are two-fold; it was shown that Monte Carlo simulation, with importance sampling, offers promise of joint analysis in the context of a single tool, and methods for the parallel simulation of general Continuous Time Markov Chains, a model framework within which joint performance/reliability models can be cast, were developed. However, very much more work is needed to determine the scope and generality of these approaches. The results obtained in our two studies, future directions for this type of work, and a list of publications are included.

Utilizing semantic networks to database and retrieve generalized stochastic colored Petri nets

NASA Technical Reports Server (NTRS)

Farah, Jeffrey J.; Kelley, Robert B.

1992-01-01

Previous work has introduced the Planning Coordinator (PCOORD), a coordinator functioning within the hierarchy of the Intelligent Machine Mode. Within the structure of the Planning Coordinator resides the Primitive Structure Database (PSDB) functioning to provide the primitive structures utilized by the Planning Coordinator in the establishing of error recovery or on-line path plans. This report further explores the Primitive Structure Database and establishes the potential of utilizing semantic networks as a means of efficiently storing and retrieving the Generalized Stochastic Colored Petri Nets from which the error recovery plans are derived.

Bi-directional transition nets

NASA Astrophysics Data System (ADS)

Staines, Anthony Spiteri

2017-06-01

Ordinary Petri nets are forward directed transition systems. Modern transition systems events and event flows are reversible. Hence modeling structures that reflect this are important. The creation of a bi-directional Petri net extends the modeling power of Petri nets. This work presents the successful implementation of a bi-directional transition net. Some toy examples in comparison to Petri nets are given showing the increased modeling power in a compacted form. The results show some interesting findings on how the expressive power of these structures has been increased.

Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks

PubMed Central

2011-01-01

Background Network inference methods reconstruct mathematical models of molecular or genetic networks directly from experimental data sets. We have previously reported a mathematical method which is exclusively data-driven, does not involve any heuristic decisions within the reconstruction process, and deliveres all possible alternative minimal networks in terms of simple place/transition Petri nets that are consistent with a given discrete time series data set. Results We fundamentally extended the previously published algorithm to consider catalysis and inhibition of the reactions that occur in the underlying network. The results of the reconstruction algorithm are encoded in the form of an extended Petri net involving control arcs. This allows the consideration of processes involving mass flow and/or regulatory interactions. As a non-trivial test case, the phosphate regulatory network of enterobacteria was reconstructed using in silico-generated time-series data sets on wild-type and in silico mutants. Conclusions The new exact algorithm reconstructs extended Petri nets from time series data sets by finding all alternative minimal networks that are consistent with the data. It suggested alternative molecular mechanisms for certain reactions in the network. The algorithm is useful to combine data from wild-type and mutant cells and may potentially integrate physiological, biochemical, pharmacological, and genetic data in the form of a single model. PMID:21762503

A Binary Array Asynchronous Sorting Algorithm with Using Petri Nets

NASA Astrophysics Data System (ADS)

Voevoda, A. A.; Romannikov, D. O.

2017-01-01

Nowadays the tasks of computations speed-up and/or their optimization are actual. Among the approaches on how to solve these tasks, a method applying approaches of parallelization and asynchronization to a sorting algorithm is considered in the paper. The sorting methods are ones of elementary methods and they are used in a huge amount of different applications. In the paper, we offer a method of an array sorting that based on a division into a set of independent adjacent pairs of numbers and their parallel and asynchronous comparison. And this one distinguishes the offered method from the traditional sorting algorithms (like quick sorting, merge sorting, insertion sorting and others). The algorithm is implemented with the use of Petri nets, like the most suitable tool for an asynchronous systems description.

Petri net siphon analysis and graph theoretic measures for identifying combination therapies in cancer.

PubMed

Behinaein, Behnam; Rudie, Karen; Sangrar, Waheed

2016-10-03

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. A physiochemical model of EGFR-Ras-MAPK signaling is implemented and calibrated to experimental data. Essential topological features of the model are converted into a Petri net and nodes that behave as siphons-a structural property of Petri nets-are identified. Siphons represent potential drug-targets since they are unrecoverable if their values fall below a threshold. Centrality measures are then used to prioritize siphons identified as candidate drug-targets. Single and multiple drug-target combinations are identified which correspond to clinically relevant drug targets and exhibit inhibition synergy in physiochemical simulations of EGF-induced EGFR-Ras-MAPK signaling. Taken together, these studies suggest that siphons and centrality analyses are a promising computational strategy to identify and rank drug-targetable nodes in larger networks as they do not require knowledge of the dynamics of the system, but rely solely on topology.

Deciding the liveness for a subclass of weighted Petri nets based on structurally circular wait

NASA Astrophysics Data System (ADS)

Liu, GuanJun; Chen, LiJing

2016-05-01

Weighted Petri nets as a kind of formal language are widely used to model and verify discrete event systems related to resource allocation like flexible manufacturing systems. System of Simple Sequential Processes with Multi-Resources (S3PMR, a subclass of weighted Petri nets and an important extension to the well-known System of Simple Sequential Processes with Resources, can model many discrete event systems in which (1) multiple processes may run in parallel and (2) each execution step of each process may use multiple units from multiple resource types. This paper gives a necessary and sufficient condition for the liveness of S3PMR. A new structural concept called Structurally Circular Wait (SCW) is proposed for S3PMR. Blocking Marking (BM) associated with an SCW is defined. It is proven that a marked S3PMR is live if and only if each SCW has no BM. We use an example of multi-processor system-on-chip to show that SCW and BM can precisely characterise the (partial) deadlocks for S3PMR. Simultaneously, two examples are used to show the advantages of SCW in preventing deadlocks of S3PMR. These results are significant for the further research on dealing with the deadlock problem.

STEPP--Search Tool for Exploration of Petri net Paths: a new tool for Petri net-based path analysis in biochemical networks.

PubMed

Koch, Ina; Schueler, Markus; Heiner, Monika

2005-01-01

To understand biochemical processes caused by, e. g., mutations or deletions in the genome, the knowledge of possible alternative paths between two arbitrary chemical compounds is of increasing interest for biotechnology, pharmacology, medicine, and drug design. With the steadily increasing amount of data from high-throughput experiments new biochemical networks can be constructed and existing ones can be extended, which results in many large metabolic, signal transduction, and gene regulatory networks. The search for alternative paths within these complex and large networks can provide a huge amount of solutions, which can not be handled manually. Moreover, not all of the alternative paths are generally of interest. Therefore, we have developed and implemented a method, which allows us to define constraints to reduce the set of all structurally possible paths to the truly interesting path set. The paper describes the search algorithm and the constraints definition language. We give examples for path searches using this dedicated special language for a Petri net model of the sucrose-to-starch breakdown in the potato tuber.

STEPP - Search Tool for Exploration of Petri net Paths: A New Tool for Petri Net-Based Path Analysis in Biochemical Networks.

PubMed

Koch, Ina; Schüler, Markus; Heiner, Monika

2011-01-01

To understand biochemical processes caused by, e.g., mutations or deletions in the genome, the knowledge of possible alternative paths between two arbitrary chemical compounds is of increasing interest for biotechnology, pharmacology, medicine, and drug design. With the steadily increasing amount of data from high-throughput experiments new biochemical networks can be constructed and existing ones can be extended, which results in many large metabolic, signal transduction, and gene regulatory networks. The search for alternative paths within these complex and large networks can provide a huge amount of solutions, which can not be handled manually. Moreover, not all of the alternative paths are generally of interest. Therefore, we have developed and implemented a method, which allows us to define constraints to reduce the set of all structurally possible paths to the truly interesting path set. The paper describes the search algorithm and the constraints definition language. We give examples for path searches using this dedicated special language for a Petri net model of the sucrose-to-starch breakdown in the potato tuber. http://sanaga.tfh-berlin.de/~stepp/

Liveness-enforcing supervisors synthesis for a class of generalised Petri nets based on two-stage deadlock control and mathematical programming

NASA Astrophysics Data System (ADS)

Zhao, Mi; Hou, Yifan; Liu, Ding

2010-10-01

In this article we deal with deadlock prevention problems for S4PR, a class of generalised Petri nets, which can well model a large class of flexible manufacturing systems where deadlocks are caused by insufficiently marked siphons. We present a deadlock prevention methodology that is an iterative approach consisting of two stages. The first one is called siphon control, which is to add for each insufficiently marked minimal siphon a control place to the original net. Its objective is to prevent a minimal siphon from being insufficiently marked. The second one, called control-induced siphon control, is to add a control place to the augmented net with its output arcs connecting to the source transitions, which assures that there are no new insufficiently marked siphons generated. At each iteration, a mixed integer programming approach is adopted for generalised Petri nets to obtain an insufficiently marked minimal siphon from the maximal deadly siphon. This way complete siphon enumeration is avoided that is much more time-consuming for a sizeable plant model than the proposed method. The relation of the proposed method and the liveness and reversibility of the controlled net is obtained. Examples are presented to demonstrate the presented method.

Modelling safety of gantry crane operations using Petri nets.

PubMed

Singh, Karmveer; Raj, Navneet; Sahu, S K; Behera, R K; Sarkar, Sobhan; Maiti, J

2017-03-01

Being a powerful tool in modelling industrial and service operations, Petri net (PN) has been extremely used in different domains, but its application in safety study is limited. In this study, we model the gantry crane operations used for industrial activities using generalized stochastic PNs. The complete cycle of operations of the gantry crane is split into three parts namely inspection and loading, movement of load, and unloading of load. PN models are developed for all three parts and the whole system as well. The developed PN models have captured the safety issues through reachability tree. The hazardous states are identified and how they ultimately lead to some unwanted accidents is demonstrated. The possibility of falling of load and failure of hook, sling, attachment and hoist rope are identified. Possible suggestions based on the study are presented for redesign of the system. For example, mechanical stoppage of operations in case of loosely connected load, and warning system for use of wrong buttons is tested using modified models.

Stochastic Petri net analysis of a replicated file system

NASA Technical Reports Server (NTRS)

Bechta Dugan, Joanne; Ciardo, Gianfranco

1989-01-01

A stochastic Petri-net model of a replicated file system is presented for a distributed environment where replicated files reside on different hosts and a voting algorithm is used to maintain consistency. Witnesses, which simply record the status of the file but contain no data, can be used in addition to or in place of files to reduce overhead. A model sufficiently detailed to include file status (current or out-of-date), as well as failure and repair of hosts where copies or witnesses reside, is presented. The number of copies and witnesses is a parameter of the model. Two different majority protocols are examined, one where a majority of all copies and witnesses is necessary to form a quorum, and the other where only a majority of the copies and witnesses on operational hosts is needed. The latter, known as adaptive voting, is shown to increase file availability in most cases.

Modeling and control of operator functional state in a unified framework of fuzzy inference petri nets.

PubMed

Zhang, Jian-Hua; Xia, Jia-Jun; Garibaldi, Jonathan M; Groumpos, Petros P; Wang, Ru-Bin

2017-06-01

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. Petri net is an effective tool for modeling discrete event systems, but for hybrid system involving discrete dynamics, generally Petri net model has to be extended. Instead of using different tools to represent continuous and discrete components of a hybrid system, this paper proposed a method of fuzzy inference Petri nets (FIPN) to represent the HM hybrid system comprising a Mamdani-type fuzzy model of OFS and a logical switching controller in a unified framework, in which the task-load level is dynamically reallocated between the operator and machine based on the model-predicted OFS. Furthermore, this paper used a multi-model approach to predict the operator performance based on three electroencephalographic (EEG) input variables (features) via the Wang-Mendel (WM) fuzzy modeling method. The membership function parameters of fuzzy OFS model for each experimental participant were optimized using artificial bee colony (ABC) evolutionary algorithm. Three performance indices, RMSE, MRE, and EPR, were computed to evaluate the overall modeling accuracy. Experiment data from six participants are analyzed. The results show that the proposed method (FIPN with adaptive task allocation) yields lower breakdown rate (from 14.8% to 3.27%) and higher human performance (from 90.30% to 91.99%). The simulation results of the FIPN-based adaptive HM (AHM) system on six experimental participants demonstrate that the FIPN

A Petri net approach to the study of persistence in chemical reaction networks.

PubMed

Angeli, David; De Leenheer, Patrick; Sontag, Eduardo D

2007-12-01

Persistence is the property, for differential equations in R(n), that solutions starting in the positive orthant do not approach the boundary of the orthant. For chemical reactions and population models, this translates into the non-extinction property: provided that every species is present at the start of the reaction, no species will tend to be eliminated in the course of the reaction. This paper provides checkable conditions for persistence of chemical species in reaction networks, using concepts and tools from Petri net theory, and verifies these conditions on various systems which arise in the modeling of cell signaling pathways.

Suboptimal liveness-enforcing supervisor design for a class of generalised Petri nets using partial siphon enumeration and mathematical programming

NASA Astrophysics Data System (ADS)

Zhao, Mi; Li, ZhiWu; Hu, HeSuan

2010-09-01

This article develops a deadlock prevention policy for a class of generalised Petri nets, which can well model a large class of flexible manufacturing systems. The analysis of such a system leads us to characterise the deadlock situations in terms of the insufficiently marked siphons in its generalised Petri-net model. The proposed policy is carried out in an iterative way. At each step a minimal siphon is derived from a maximal deadly marked siphon that is found by solving a mixed integer programming (MIP) problem. An algorithm is formalised that can efficiently compute such a minimal siphon from a maximal one. A monitor is added for a derived minimal siphon such that it is max-controlled if it is elementary with respect to the siphons that have been derived. The liveness of the controlled system is decided by the fact that no siphon can be derived due to the MIP solution. After a liveness-enforcing net supervisor computed without complete siphon enumeration, the output-arcs of the additional monitors are rearranged such that the monitors act while restricting the system less. Examples are presented to demonstrate the proposed method.

Stochastic Petri Net extension of a yeast cell cycle model.

PubMed

Mura, Ivan; Csikász-Nagy, Attila

2008-10-21

This paper presents the definition, solution and validation of a stochastic model of the budding yeast cell cycle, based on Stochastic Petri Nets (SPN). A specific family of SPNs is selected for building a stochastic version of a well-established deterministic model. We describe the procedure followed in defining the SPN model from the deterministic ODE model, a procedure that can be largely automated. The validation of the SPN model is conducted with respect to both the results provided by the deterministic one and the experimental results available from literature. The SPN model catches the behavior of the wild type budding yeast cells and a variety of mutants. We show that the stochastic model matches some characteristics of budding yeast cells that cannot be found with the deterministic model. The SPN model fine-tunes the simulation results, enriching the breadth and the quality of its outcome.

The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks.

PubMed

Ruths, Derek; Muller, Melissa; Tseng, Jen-Te; Nakhleh, Luay; Ram, Prahlad T

2008-02-29

Reconstructing cellular signaling networks and understanding how they work are major endeavors in cell biology. The scale and complexity of these networks, however, render their analysis using experimental biology approaches alone very challenging. As a result, computational methods have been developed and combined with experimental biology approaches, producing powerful tools for the analysis of these networks. These computational methods mostly fall on either end of a spectrum of model parameterization. On one end is a class of structural network analysis methods; these typically use the network connectivity alone to generate hypotheses about global properties. On the other end is a class of dynamic network analysis methods; these use, in addition to the connectivity, kinetic parameters of the biochemical reactions to predict the network's dynamic behavior. These predictions provide detailed insights into the properties that determine aspects of the network's structure and behavior. However, the difficulty of obtaining numerical values of kinetic parameters is widely recognized to limit the applicability of this latter class of methods. Several researchers have observed that the connectivity of a network alone can provide significant insights into its dynamics. Motivated by this fundamental observation, we present the signaling Petri net, a non-parametric model of cellular signaling networks, and the signaling Petri net-based simulator, a Petri net execution strategy for characterizing the dynamics of signal flow through a signaling network using token distribution and sampling. The result is a very fast method, which can analyze large-scale networks, and provide insights into the trends of molecules' activity-levels in response to an external stimulus, based solely on the network's connectivity. We have implemented the signaling Petri net-based simulator in the PathwayOracle toolkit, which is publicly available at http://bioinfo.cs.rice.edu/pathwayoracle. Using

The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks

PubMed Central

Ruths, Derek; Muller, Melissa; Tseng, Jen-Te; Nakhleh, Luay; Ram, Prahlad T.

2008-01-01

Reconstructing cellular signaling networks and understanding how they work are major endeavors in cell biology. The scale and complexity of these networks, however, render their analysis using experimental biology approaches alone very challenging. As a result, computational methods have been developed and combined with experimental biology approaches, producing powerful tools for the analysis of these networks. These computational methods mostly fall on either end of a spectrum of model parameterization. On one end is a class of structural network analysis methods; these typically use the network connectivity alone to generate hypotheses about global properties. On the other end is a class of dynamic network analysis methods; these use, in addition to the connectivity, kinetic parameters of the biochemical reactions to predict the network's dynamic behavior. These predictions provide detailed insights into the properties that determine aspects of the network's structure and behavior. However, the difficulty of obtaining numerical values of kinetic parameters is widely recognized to limit the applicability of this latter class of methods. Several researchers have observed that the connectivity of a network alone can provide significant insights into its dynamics. Motivated by this fundamental observation, we present the signaling Petri net, a non-parametric model of cellular signaling networks, and the signaling Petri net-based simulator, a Petri net execution strategy for characterizing the dynamics of signal flow through a signaling network using token distribution and sampling. The result is a very fast method, which can analyze large-scale networks, and provide insights into the trends of molecules' activity-levels in response to an external stimulus, based solely on the network's connectivity. We have implemented the signaling Petri net-based simulator in the PathwayOracle toolkit, which is publicly available at http://bioinfo.cs.rice.edu/pathwayoracle. Using

Application of Petri Nets in Bone Remodeling

PubMed Central

Li, Lingxi; Yokota, Hiroki

2009-01-01

Understanding a mechanism of bone remodeling is a challenging task for both life scientists and model builders, since this highly interactive and nonlinear process can seldom be grasped by simple intuition. A set of ordinary differential equations (ODEs) have been built for simulating bone formation as well as bone resorption. Although solving ODEs numerically can provide useful predictions for dynamical behaviors in a continuous time frame, an actual bone remodeling process in living tissues is driven by discrete events of molecular and cellular interactions. Thus, an event-driven tool such as Petri nets (PNs), which may dynamically and graphically mimic individual molecular collisions or cellular interactions, seems to augment the existing ODE-based systems analysis. Here, we applied PNs to expand the ODE-based approach and examined discrete, dynamical behaviors of key regulatory molecules and bone cells. PNs have been used in many engineering areas, but their application to biological systems needs to be explored. Our PN model was based on 8 ODEs that described an osteoprotegerin linked molecular pathway consisting of 4 types of bone cells. The models allowed us to conduct both qualitative and quantitative evaluations and evaluate homeostatic equilibrium states. The results support that application of PN models assists understanding of an event-driven bone remodeling mechanism using PN-specific procedures such as places, transitions, and firings. PMID:19838338

Developmental switching in Physarum polycephalum: Petri net analysis of single cell trajectories of gene expression indicates responsiveness and genetic plasticity of the Waddington quasipotential landscape

NASA Astrophysics Data System (ADS)

Werthmann, Britta; Marwan, Wolfgang

2017-11-01

The developmental switch to sporulation in Physarum polycephalum is a phytochrome-mediated far-red light-induced cell fate decision that synchronously encompasses the entire multinucleate plasmodial cell and is associated with extensive reprogramming of the transcriptome. By repeatedly taking samples of single cells after delivery of a light stimulus pulse, we analysed differential gene expression in two mutant strains and in a heterokaryon of the two strains all of which display a different propensity for making the cell fate decision. Multidimensional scaling of the gene expression data revealed individually different single cell trajectories eventually leading to sporulation. Characterization of the trajectories as walks through states of gene expression discretized by hierarchical clustering allowed the reconstruction of Petri nets that model and predict the observed behavior. Structural analyses of the Petri nets indicated stimulus- and genotype-dependence of both, single cell trajectories and of the quasipotential landscape through which these trajectories are taken. The Petri net-based approach to the analysis and decomposition of complex cellular responses and of complex mutant phenotypes may provide a scaffold for the data-driven reconstruction of causal molecular mechanisms that shape the topology of the quasipotential landscape.

A fuzzy Petri-net-based mode identification algorithm for fault diagnosis of complex systems

NASA Astrophysics Data System (ADS)

Propes, Nicholas C.; Vachtsevanos, George

2003-08-01

Complex dynamical systems such as aircraft, manufacturing systems, chillers, motor vehicles, submarines, etc. exhibit continuous and event-driven dynamics. These systems undergo several discrete operating modes from startup to shutdown. For example, a certain shipboard system may be operating at half load or full load or may be at start-up or shutdown. Of particular interest are extreme or "shock" operating conditions, which tend to severely impact fault diagnosis or the progression of a fault leading to a failure. Fault conditions are strongly dependent on the operating mode. Therefore, it is essential that in any diagnostic/prognostic architecture, the operating mode be identified as accurately as possible so that such functions as feature extraction, diagnostics, prognostics, etc. can be correlated with the predominant operating conditions. This paper introduces a mode identification methodology that incorporates both time- and event-driven information about the process. A fuzzy Petri net is used to represent the possible successive mode transitions and to detect events from processed sensor signals signifying a mode change. The operating mode is initialized and verified by analysis of the time-driven dynamics through a fuzzy logic classifier. An evidence combiner module is used to combine the results from both the fuzzy Petri net and the fuzzy logic classifier to determine the mode. Unlike most event-driven mode identifiers, this architecture will provide automatic mode initialization through the fuzzy logic classifier and robustness through the combining of evidence of the two algorithms. The mode identification methodology is applied to an AC Plant typically found as a component of a shipboard system.

A Concurrent Multiple Negotiation Protocol Based on Colored Petri Nets.

PubMed

Niu, Lei; Ren, Fenghui; Zhang, Minjie; Bai, Quan

2017-11-01

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. This paper: 1) comprehensively highlights research problems of negotiations at concurrent negotiation level; 2) provides a graph-based CMN model with consideration of the interdependency relationships; and 3) proposes a colored Petri net-based negotiation protocol for conducting CMNs. With the proposed protocol, a CMN can be efficiently and concurrently processed and negotiation agreements can be efficiently achieved. Experimental results indicate the effectiveness and efficiency of the proposed protocol in terms of the negotiation success rate, the negotiation time and the negotiation outcome.

Petri-net-based 2D design of DNA walker circuits.

PubMed

Gilbert, David; Heiner, Monika; Rohr, Christian

2018-01-01

We consider localised DNA computation, where a DNA strand walks along a binary decision graph to compute a binary function. One of the challenges for the design of reliable walker circuits consists in leakage transitions, which occur when a walker jumps into another branch of the decision graph. We automatically identify leakage transitions, which allows for a detailed qualitative and quantitative assessment of circuit designs, design comparison, and design optimisation. The ability to identify leakage transitions is an important step in the process of optimising DNA circuit layouts where the aim is to minimise the computational error inherent in a circuit while minimising the area of the circuit. Our 2D modelling approach of DNA walker circuits relies on coloured stochastic Petri nets which enable functionality, topology and dimensionality all to be integrated in one two-dimensional model. Our modelling and analysis approach can be easily extended to 3-dimensional walker systems.

How to Construct an Automated Warehouse Based on Colored Timed Petri Nets

NASA Astrophysics Data System (ADS)

Cheng, Fei; He, Shanjun

The automated warehouse considered here consists of a number of rack locations with three cranes, a narrow aisle shuttle, and several buffer stations with the roller. Based on analyzing of the behaviors of the active resources in the system, a modular and computerized model is presented via a colored timed Petri net approach, in which places are multicolored to simplify model and characterize control flow of the resources, and token colors are defined as the routes of storage/retrieval operations. In addition, an approach for realization of model via visual c++ is briefly given. These facts allow us to render an emulate system to simulate a discrete control application for online monitoring, dynamic dispatching control and off-line revising scheduler policies.

Safety analysis of discrete event systems using a simplified Petri net controller.

PubMed

Zareiee, Meysam; Dideban, Abbas; Asghar Orouji, Ali

2014-01-01

This paper deals with the problem of forbidden states in discrete event systems based on Petri net models. So, a method is presented to prevent the system from entering these states by constructing a small number of generalized mutual exclusion constraints. This goal is achieved by solving three types of Integer Linear Programming problems. The problems are designed to verify the constraints that some of them are related to verifying authorized states and the others are related to avoiding forbidden states. The obtained constraints can be enforced on the system using a small number of control places. Moreover, the number of arcs related to these places is small, and the controller after connecting them is maximally permissive. © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

Improving the Quality of Alerts and Predicting Intruder's Next Goal with Hidden Colored Petri-Net

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Dong; Frincke, Deb A.

2006-06-22

Intrusion detection systems (IDS) often provide poor quality alerts, which are insufficient to support rapid identification of ongoing attacks or predict an intruder’s next likely goal. In this paper, we propose a novel approach to alert post-processing and correlation, the Hidden Colored Petri-Net (HCPN). Different from most other alert correlation methods, our approach treats the alert correlation problem as an inference problem rather than a filter problem. Our approach assumes that the intruder’s actions are unknown to the IDS and can be inferred only from the alerts generated by the IDS sensors. HCPN can describe the relationship between different stepsmore » carried out by intruders, model observations (alerts) and transitions (actions) separately, and associate each token element (system state) with a probability (or confidence). The model is an extension to Colored Petri-Net (CPN) .It is so called “hidden” because the transitions (actions) are not directly observable but can be inferred by looking through the observations (alerts). These features make HCPN especially suitable for discovering intruders’ actions from their partial observations (alerts,) and predicting intruders’ next goal. Our experiments on DARPA evaluation datasets and the attack scenarios from the Grand Challenge Problem (GCP) show that HCPN has promise as a way to reducing false positives and negatives, predicting intruder’s next possible action, uncovering intruders’ intrusion strategies after the attack scenario has happened, and providing confidence scores.« less

Petri Net and Probabilistic Model Checking Based Approach for the Modelling, Simulation and Verification of Internet Worm Propagation

PubMed Central

Razzaq, Misbah; Ahmad, Jamil

2015-01-01

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. We investigate Susceptible-Exposed-Infectious-Recovered (SEIR) model and propose a new model Susceptible-Exposed-Infectious-Recovered-Delayed-Quarantined (Susceptible/Recovered) (SEIDQR(S/I)) along with hybrid quarantine strategy, which is then constructed and analysed using Stochastic Petri Nets and Continuous Time Markov Chain. The analysis shows that the hybrid quarantine strategy is extremely effective in reducing the risk of propagating the worm. Through Model Checking, we gained insight into the functionality of compartmental models. Model Checking results validate simulation ones well, which fully support the proposed framework. PMID:26713449

Petri Net and Probabilistic Model Checking Based Approach for the Modelling, Simulation and Verification of Internet Worm Propagation.

PubMed

Razzaq, Misbah; Ahmad, Jamil

2015-01-01

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. We investigate Susceptible-Exposed-Infectious-Recovered (SEIR) model and propose a new model Susceptible-Exposed-Infectious-Recovered-Delayed-Quarantined (Susceptible/Recovered) (SEIDQR(S/I)) along with hybrid quarantine strategy, which is then constructed and analysed using Stochastic Petri Nets and Continuous Time Markov Chain. The analysis shows that the hybrid quarantine strategy is extremely effective in reducing the risk of propagating the worm. Through Model Checking, we gained insight into the functionality of compartmental models. Model Checking results validate simulation ones well, which fully support the proposed framework.

A PetriNet-Based Approach for Supporting Traceability in Cyber-Physical Manufacturing Systems.

PubMed

Huang, Jiwei; Zhu, Yeping; Cheng, Bo; Lin, Chuang; Chen, Junliang

2016-03-17

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. A practical prototype system for supporting traceability is designed, and a real-life case study of a quality control system for bee products is presented to validate the effectiveness of the approach.

MONALISA for stochastic simulations of Petri net models of biochemical systems.

PubMed

Balazki, Pavel; Lindauer, Klaus; Einloft, Jens; Ackermann, Jörg; Koch, Ina

2015-07-10

The concept of Petri nets (PN) is widely used in systems biology and allows modeling of complex biochemical systems like metabolic systems, signal transduction pathways, and gene expression networks. In particular, PN allows the topological analysis based on structural properties, which is important and useful when quantitative (kinetic) data are incomplete or unknown. Knowing the kinetic parameters, the simulation of time evolution of such models can help to study the dynamic behavior of the underlying system. If the number of involved entities (molecules) is low, a stochastic simulation should be preferred against the classical deterministic approach of solving ordinary differential equations. The Stochastic Simulation Algorithm (SSA) is a common method for such simulations. The combination of the qualitative and semi-quantitative PN modeling and stochastic analysis techniques provides a valuable approach in the field of systems biology. Here, we describe the implementation of stochastic analysis in a PN environment. We extended MONALISA - an open-source software for creation, visualization and analysis of PN - by several stochastic simulation methods. The simulation module offers four simulation modes, among them the stochastic mode with constant firing rates and Gillespie's algorithm as exact and approximate versions. The simulator is operated by a user-friendly graphical interface and accepts input data such as concentrations and reaction rate constants that are common parameters in the biological context. The key features of the simulation module are visualization of simulation, interactive plotting, export of results into a text file, mathematical expressions for describing simulation parameters, and up to 500 parallel simulations of the same parameter sets. To illustrate the method we discuss a model for insulin receptor recycling as case study. We present a software that combines the modeling power of Petri nets with stochastic simulation of dynamic

Using Petri nets for experimental design in a multi-organ elimination pathway.

PubMed

Reshetova, Polina; Smilde, Age K; Westerhuis, Johan A; van Kampen, Antoine H C

2015-08-01

Genistein is a soy metabolite with estrogenic activity that may result in (un)favorable effects on human health. Elucidation of the mechanisms through which food additives such as genistein exert their beneficiary effects is a major challenge for the food industry. A better understanding of the genistein elimination pathway could shed light on such mechanisms. We developed a Petri net model that represents this multi-organ elimination pathway and which assists in the design of future experiments. Using this model we show that metabolic profiles solely measured in venous blood are not sufficient to uniquely parameterize the model. Based on simulations we suggest two solutions that provide better results: parameterize the model using gut epithelium profiles or add additional biological constrains in the model. Copyright © 2015 Elsevier Ltd. All rights reserved.

On the Use of Kronecker Operators for the Solution of Generalized Stochastic Petri Nets

NASA Technical Reports Server (NTRS)

Ciardo, Gianfranco; Tilgner, Marco

1996-01-01

We discuss how to describe the Markov chain underlying a generalized stochastic Petri net using Kronecker operators on smaller matrices. We extend previous approaches by allowing both an extensive type of marking-dependent behavior for the transitions and the presence of immediate synchronizations. The derivation of the results is thoroughly formalized, including the use of Kronecker operators in the treatment of the vanishing markings and the computation of impulse-based reward measures. We use our techniques to analyze a model whose solution using conventional methods would fail because of the state-space explosion. In the conclusion, we point out ideas to parallelize our approach.

The use of the Petri net method in the simulation modeling of mitochondrial swelling.

PubMed

Danylovych, Yu V; Chunikhin, A Y; Danylovych, G V; Kolomiets, O V

2016-01-01

Using photon correlation spectroscopy, which allows investigating changes in the hydrodynamic dia­meter of the particles in suspension, it was shown that ultrahigh concentrations of Ca2+ (over 10 mM) induce swelling of isolated mitochondria. An increase in hydrodynamic diameter was caused by an increase of non-specific mitochondrial membrane permeability to Ca ions, matrix Ca2+ overload, activation of ATP- and Ca2+-sensitive K+-channels, as well as activation of cyclosporin-sensitive permeability transition pore. To formalize the experimental data and to assess conformity of experimental results with theoretical predictions we developed a simulation model using the hybrid functional Petri net method.

A PetriNet-Based Approach for Supporting Traceability in Cyber-Physical Manufacturing Systems

PubMed Central

Huang, Jiwei; Zhu, Yeping; Cheng, Bo; Lin, Chuang; Chen, Junliang

2016-01-01

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. A practical prototype system for supporting traceability is designed, and a real-life case study of a quality control system for bee products is presented to validate the effectiveness of the approach. PMID:26999141

Quasi-Steady-State Analysis based on Structural Modules and Timed Petri Net Predict System's Dynamics: The Life Cycle of the Insulin Receptor.

PubMed

Scheidel, Jennifer; Lindauer, Klaus; Ackermann, Jörg; Koch, Ina

2015-12-17

The insulin-dependent activation and recycling of the insulin receptor play an essential role in the regulation of the energy metabolism, leading to a special interest for pharmaceutical applications. Thus, the recycling of the insulin receptor has been intensively investigated, experimentally as well as theoretically. We developed a time-resolved, discrete model to describe stochastic dynamics and study the approximation of non-linear dynamics in the context of timed Petri nets. Additionally, using a graph-theoretical approach, we analyzed the structure of the regulatory system and demonstrated the close interrelation of structural network properties with the kinetic behavior. The transition invariants decomposed the model into overlapping subnetworks of various sizes, which represent basic functional modules. Moreover, we computed the quasi-steady states of these subnetworks and demonstrated that they are fundamental to understand the dynamic behavior of the system. The Petri net approach confirms the experimental results of insulin-stimulated degradation of the insulin receptor, which represents a common feature of insulin-resistant, hyperinsulinaemic states.

Supervisory control based on minimal cuts and Petri net sub-controllers coordination

NASA Astrophysics Data System (ADS)

Rezig, Sadok; Achour, Zied; Rezg, Nidhal; Kammoun, Mohamed-Ali

2016-10-01

This paper addresses the synthesis of Petri net (PN) controller for the forbidden state transition problem with a new utilisation of the theory of regions. Moreover, as any method of control synthesis based on a reachability graph, the theory of regions suffers from the combinatorial explosion problem. The proposed work minimises the number of equations in the linear system of theory of regions and therefore one can reduce the computation time. In this paper, two different approaches are proposed to select minimal cuts in the reachability graph in order to synthesise a PN controller. Thanks to a switch from one cut to another, one can activate and deactivate the corresponding PNcontroller. An application is implemented in a flexible manufacturing system to illustrate the present method. Finally, comparison with previous works with experimental results in obtaining a maximally permissive controller is presented.

Fault detection and initial state verification by linear programming for a class of Petri nets

NASA Technical Reports Server (NTRS)

Rachell, Traxon; Meyer, David G.

1992-01-01

The authors present an algorithmic approach to determining when the marking of a LSMG (live safe marked graph) or a LSFC (live safe free choice) net is in the set of live safe markings M. Hence, once the marking of a net is determined to be in M, then if at some time thereafter the marking of this net is determined not to be in M, this indicates a fault. It is shown how linear programming can be used to determine if m is an element of M. The worst-case computational complexity of each algorithm is bounded by the number of linear programs necessary to compute.

Modeling shared resources with generalized synchronization within a Petri net bottom-up approach.

PubMed

Ferrarini, L; Trioni, M

1996-01-01

This paper proposes a simple and effective way to represent shared resources in manufacturing systems within a Petri net model previously developed. Such a model relies on the bottom-up and modular approach to synthesis and analysis. The designer may define elementary tasks and then connect them with one another with three kinds of connections: self-loops, inhibitor arcs and simple synchronizations. A theoretical framework has been established for the analysis of liveness and reversibility of such models. The generalized synchronization, here formalized, represents an extension of the simple synchronization, allowing the merging of suitable subnets among elementary tasks. It is proved that under suitable, but not restrictive, hypotheses the generalized synchronization may be substituted for a simple one, thus being compatible with all the developed theoretical body.

Structural analysis of a Petri net model of oxidative stress in atherosclerosis.

PubMed

Kozak, Adam; Formanowicz, Dorota; Formanowicz, Piotr

2018-06-01

Atherosclerosis is a complex process of gathering sub-endothelial plaques decreasing lumen of the blood vessels. This disorder affects people of all ages, but its progression is asymptomatic for many years. It is regulated by many typical and atypical factors including the immune system response, a chronic kidney disease, a diet rich in lipids, a local inflammatory process and a local oxidative stress that is here one of the key factors. In this study, a Petri net model of atherosclerosis regulation is presented. This model includes also some information about stoichiometric relationships between its components and covers all mentioned factors. For the model, a structural analysis based on invariants was made and biological conclusions are presented. Since the model contains inhibitor arcs, a heuristic method for analysis of such cases is presented. This method can be used to extend the concept of feasible t -invariants.

Using Petri Net Tools to Study Properties and Dynamics of Biological Systems

PubMed Central

Peleg, Mor; Rubin, Daniel; Altman, Russ B.

2005-01-01

Petri Nets (PNs) and their extensions are promising methods for modeling and simulating biological systems. We surveyed PN formalisms and tools and compared them based on their mathematical capabilities as well as by their appropriateness to represent typical biological processes. We measured the ability of these tools to model specific features of biological systems and answer a set of biological questions that we defined. We found that different tools are required to provide all capabilities that we assessed. We created software to translate a generic PN model into most of the formalisms and tools discussed. We have also made available three models and suggest that a library of such models would catalyze progress in qualitative modeling via PNs. Development and wide adoption of common formats would enable researchers to share models and use different tools to analyze them without the need to convert to proprietary formats. PMID:15561791

Designing software for operational decision support through coloured Petri nets

NASA Astrophysics Data System (ADS)

Maggi, F. M.; Westergaard, M.

2017-05-01

Operational support provides, during the execution of a business process, replies to questions such as 'how do I end the execution of the process in the cheapest way?' and 'is my execution compliant with some expected behaviour?' These questions may be asked several times during a single execution and, to answer them, dedicated software components (the so-called operational support providers) need to be invoked. Therefore, an infrastructure is needed to handle multiple providers, maintain data between queries about the same execution and discard information when it is no longer needed. In this paper, we use coloured Petri nets (CPNs) to model and analyse software implementing such an infrastructure. This analysis is needed to clarify the requirements before implementation and to guarantee that the resulting software is correct. To this aim, we present techniques to represent and analyse state spaces with 250 million states on a normal PC. We show how the specified requirements have been implemented as a plug-in of the process mining tool ProM and how the operational support in ProM can be used in combination with an existing operational support provider.

New insights into the human body iron metabolism analyzed by a Petri net based approach.

PubMed

Sackmann, Andrea; Formanowicz, Dorota; Formanowicz, Piotr; Blazewicz, Jacek

2009-04-01

Iron homeostasis is one of the most important biochemical processes in the human body. Despite this fact, the process is not fully understood and until recently only rough descriptions of parts of the process could be found in the literature. Here, an extension of the recently published formal model of the main part of the process is presented. This extension consists in including all known mechanisms of hepcidin regulation. Hepcidin is a hormone synthesized in the liver which is mainly responsible for an inhibition of iron absorption in the small intestine during an inflammatory process. The model is expressed in the language of Petri net theory which allows for its relatively easy analysis and simulation.

Continuous Petri Nets and microRNA analysis in melanoma.

PubMed

Russo, Giulia; Pennisi, Marzio; Boscarino, Roberta; Pappalardo, Francesco

2017-07-31

Personalized target therapies represent one of the possible treatment strategies to fight the ongoing battle against cancer. New treatment interventions are still needed for an effective and successful cancer therapy. In this scenario, we simulated and analyzed the dynamics of BRAF V600E melanoma patients treated with BRAF inhibitors in order to find potentially interesting targets that may make standard treatments more effective in particularly aggressive tumors that may not respond to selective inhibitor drugs. To this aim, we developed a continuous Petri Net model that simulates fundamental signalling cascades involved in melanoma development, such as MAPK and PI3K/AKT, in order to deeply analyze these complex kinase cascades and predict new crucial nodes involved in melanomagenesis. The model pointed out that some microRNAs, like hsa-mir-132, downregulates expression levels of p120RasGAP: under high concentrations of p120RasGAP, MAPK pathway activation is significantly decreased and consequently also PI3K/PDK1/AKT activation. Furthermore, our analysis carried out through the Genomic Data Commons (GDC) Data Portal, shows the evidence that hsa-mir-132 is significantly associated with clinical outcome in melanoma cancer genomic data sets of BRAF-mutated patients. In conclusion, targeting miRNAs through antisense oligonucleotides technology, may suggest the way to enhance the action of of BRAF-inhibitors.

Development of petri net-based dynamic model for improved production of farnesyl pyrophosphate by integrating mevalonate and methylerythritol phosphate pathways in yeast.

PubMed

Baadhe, Rama Raju; Mekala, Naveen Kumar; Palagiri, Satwik Reddy; Parcha, Sreenivasa Rao

2012-07-01

In this case study, we designed a farnesyl pyrophosphate (FPP) biosynthetic network using hybrid functional Petri net with extension (HFPNe) which is derived from traditional Petri net theory and allows easy modeling with graphical approach of various types of entities in the networks together. Our main objective is to improve the production of FPP in yeast, which is further converted to amorphadiene (AD), a precursor of artemisinin (antimalarial drug). Natively, mevalonate (MEV) pathway is present in yeast. Methyl erythritol phosphate pathways (MEP) are present only in higher plant plastids and eubacteria, but not present in yeast. IPP and DAMP are common isomeric intermediate in these two pathways, which immediately yields FPP. By integrating these two pathways in yeast, we augmented the FPP synthesis approximately two folds higher (431.16 U/pt) than in MEV pathway alone (259.91 U/pt) by using HFPNe technique. Further enhanced FPP levels converted to AD by amorphadiene synthase gene yielding 436.5 U/pt of AD which approximately two folds higher compared to the AD (258.5 U/pt) synthesized by MEV pathway exclusively. Simulation and validation processes performed using these models are reliable with identified biological information and data.

Robustness analysis of non-ordinary Petri nets for flexible assembly/disassembly processes based on structural decomposition

NASA Astrophysics Data System (ADS)

Hsieh, Fu-Shiung

2011-03-01

Design of robust supervisory controllers for manufacturing systems with unreliable resources has received significant attention recently. Robustness analysis provides an alternative way to analyse a perturbed system to quickly respond to resource failures. Although we have analysed the robustness properties of several subclasses of ordinary Petri nets (PNs), analysis for non-ordinary PNs has not been done. Non-ordinary PNs have weighted arcs and have the advantage to compactly model operations requiring multiple parts or resources. In this article, we consider a class of flexible assembly/disassembly manufacturing systems and propose a non-ordinary flexible assembly/disassembly Petri net (NFADPN) model for this class of systems. As the class of flexible assembly/disassembly manufacturing systems can be regarded as the integration and interactions of a set of assembly/disassembly subprocesses, a bottom-up approach is adopted in this article to construct the NFADPN models. Due to the routing flexibility in NFADPN, there may exist different ways to accomplish the tasks. To characterise different ways to accomplish the tasks, we propose the concept of completely connected subprocesses. As long as there exists a set of completely connected subprocesses for certain type of products, the production of that type of products can still be maintained without requiring the whole NFADPN to be live. To take advantage of the alternative routes without enforcing liveness for the whole system, we generalise the concept of persistent production proposed to NFADPN. We propose a condition for persistent production based on the concept of completely connected subprocesses. We extend robustness analysis to NFADPN by exploiting its structure. We identify several patterns of resource failures and characterise the conditions to maintain operation in the presence of resource failures.

Applying Petri nets to modeling the chemical stage of radiobiological mechanism

NASA Astrophysics Data System (ADS)

Barilla, J.; Lokajíček, M.; Pisaková, H.; Simr, P.

2015-03-01

The chemical stage represents important part of radiological mechanism as double strand breaks of DNA molecules represent main damages leading to final biological effect. These breaks are formed mainly by water radicals arising in clusters formed by densely ionizing ends of primary or secondary charged particles in neighborhood of a DNA molecule. The given effect may be significantly influenced by other species present in water, which may depend on the size and diffusion of corresponding clusters. We have already proposed a model describing the corresponding process (i.e., the combined effect of cluster diffusion and chemical reactions) running in individual radical clusters and influencing the formation probability of main damages (i.e., DSBs). Now a full number of corresponding species will be considered. With the help of Continuous Petri nets it will then be possible to follow the time evolution of corresponding species in individual clusters, which might be important especially in the case of studying the biological effect of very low-LET radiation. The results in deoxygenated water will be presented; the ratio of final and initial contents of corresponding species being in good agreement with values established experimentally.

A Novel Petri Nets-Based Modeling Method for the Interaction between the Sensor and the Geographic Environment in Emerging Sensor Networks

PubMed Central

Zhang, Feng; Xu, Yuetong; Chou, Jarong

2016-01-01

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. The feature of the sensor device service in ESNs is more easily affected by the geographic environment than the traditional Web service. Therefore, the response time, the fault-tolerant ability and the resource consumption become important factors in the performance of the whole sensor application system. Thus, this paper classified IoT services as Sensing services and Controlling services according to the interaction between IoT service and geographic entity, and classified GIS services as data services and processing services. Then, this paper designed and analyzed service algebra and Colored Petri Nets model to modeling the geo-feature, IoT service, GIS service and the interaction process between the sensor and the geographic enviroment. At last, the modeling process is discussed by examples. PMID:27681730

Applications of colored petri net and genetic algorithms to cluster tool scheduling

NASA Astrophysics Data System (ADS)

Liu, Tung-Kuan; Kuo, Chih-Jen; Hsiao, Yung-Chin; Tsai, Jinn-Tsong; Chou, Jyh-Horng

2005-12-01

In this paper, we propose a method, which uses Coloured Petri Net (CPN) and genetic algorithm (GA) to obtain an optimal deadlock-free schedule and to solve re-entrant problem for the flexible process of the cluster tool. The process of the cluster tool for producing a wafer usually can be classified into three types: 1) sequential process, 2) parallel process, and 3) sequential parallel process. But these processes are not economical enough to produce a variety of wafers in small volume. Therefore, this paper will propose the flexible process where the operations of fabricating wafers are randomly arranged to achieve the best utilization of the cluster tool. However, the flexible process may have deadlock and re-entrant problems which can be detected by CPN. On the other hand, GAs have been applied to find the optimal schedule for many types of manufacturing processes. Therefore, we successfully integrate CPN and GAs to obtain an optimal schedule with the deadlock and re-entrant problems for the flexible process of the cluster tool.

QoS measurement of workflow-based web service compositions using Colored Petri net.

PubMed

Nematzadeh, Hossein; Motameni, Homayun; Mohamad, Radziah; Nematzadeh, Zahra

2014-01-01

Workflow-based web service compositions (WB-WSCs) is one of the main composition categories in service oriented architecture (SOA). Eflow, polymorphic process model (PPM), and business process execution language (BPEL) are the main techniques of the category of WB-WSCs. Due to maturity of web services, measuring the quality of composite web services being developed by different techniques becomes one of the most important challenges in today's web environments. Business should try to provide good quality regarding the customers' requirements to a composed web service. Thus, quality of service (QoS) which refers to nonfunctional parameters is important to be measured since the quality degree of a certain web service composition could be achieved. This paper tried to find a deterministic analytical method for dependability and performance measurement using Colored Petri net (CPN) with explicit routing constructs and application of theory of probability. A computer tool called WSET was also developed for modeling and supporting QoS measurement through simulation.

A methodological approach for using high-level Petri Nets to model the immune system response.

PubMed

Pennisi, Marzio; Cavalieri, Salvatore; Motta, Santo; Pappalardo, Francesco

2016-12-22

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. Petri Nets (PN) are a graphical modeling tool developed to model concurrency and synchronization in distributed systems. Their use has become increasingly marked also thanks to the introduction in the years of many features and extensions which lead to the born of "high level" PN. We propose a novel methodological approach that is based on high level PN, and in particular on Colored Petri Nets (CPN), that can be used to model the immune system response at the cellular scale. To demonstrate the potentiality of the approach we provide a simple model of the humoral immune system response that is able of reproducing some of the most complex well-known features of the adaptive response like memory and specificity features. The methodology we present has advantages of both the two classical approaches based on continuous and discrete models, since it allows to gain good level of granularity in the description of cells behavior without losing the possibility of having a qualitative analysis. Furthermore, the presented methodology based on CPN allows the adoption of the same graphical modeling technique well known to life scientists that use PN for the modeling of signaling pathways. Finally, such an approach may open the floodgates to the realization of multi scale models that integrate both signaling pathways (intra

Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net.

PubMed

Doi, Atsushi; Nagasaki, Masao; Matsuno, Hiroshi; Miyano, Satoru

2011-01-01

MDM2 and p19ARF are essential proteins in cancer pathways forming a complex with protein p53 to control the transcriptional activity of protein p53. It is confirmed that protein p53 loses its transcriptional activity by forming the functional dimer with protein MDM2. However, it is still unclear that protein p53 keeps its transcriptional activity when it forms the trimer with proteins MDM2 and p19ARF. We have observed mutual behaviors among genes p53, MDM2, p19ARF and their products on a computational model with hybrid functional Petri net (HFPN) which is constructed based on information described in the literature. The simulation results suggested that protein p53 should have the transcriptional activity in the forms of the trimer of proteins p53, MDM2, and p19ARF. This paper also discusses the advantages of HFPN based modeling method in terms of pathway description for simulations.

Petri Nets with Fuzzy Logic (PNFL): Reverse Engineering and Parametrization

PubMed Central

Küffner, Robert; Petri, Tobias; Windhager, Lukas; Zimmer, Ralf

2010-01-01

Background The recent DREAM4 blind assessment provided a particularly realistic and challenging setting for network reverse engineering methods. The in silico part of DREAM4 solicited the inference of cycle-rich gene regulatory networks from heterogeneous, noisy expression data including time courses as well as knockout, knockdown and multifactorial perturbations. Methodology and Principal Findings We inferred and parametrized simulation models based on Petri Nets with Fuzzy Logic (PNFL). This completely automated approach correctly reconstructed networks with cycles as well as oscillating network motifs. PNFL was evaluated as the best performer on DREAM4 in silico networks of size 10 with an area under the precision-recall curve (AUPR) of 81%. Besides topology, we inferred a range of additional mechanistic details with good reliability, e.g. distinguishing activation from inhibition as well as dependent from independent regulation. Our models also performed well on new experimental conditions such as double knockout mutations that were not included in the provided datasets. Conclusions The inference of biological networks substantially benefits from methods that are expressive enough to deal with diverse datasets in a unified way. At the same time, overly complex approaches could generate multiple different models that explain the data equally well. PNFL appears to strike the balance between expressive power and complexity. This also applies to the intuitive representation of PNFL models combining a straightforward graphical notation with colloquial fuzzy parameters. PMID:20862218

Comparing digraph and Petri net approaches to deadlock avoidance in FMS.

PubMed

Fanti, M P; Maione, B; Turchiano, B

2000-01-01

Flexible manufacturing systems (FMSs) are modern production facilities with easy adaptability to variable production plans and goals. These systems may exhibit deadlock situations occurring when a circular wait arises because each piece in a set requires a resource currently held by another job in the same set. Several authors have proposed different policies to control resource allocation in order to avoid deadlock problems. These approaches are mainly based on some formal models of manufacturing systems, such as Petri nets (PNs), directed graphs, etc. Since they describe various peculiarities of the FMS operation in a modular and systematic way, PNs are the most extensively used tool to model such systems. On the other hand, digraphs are more synthetic than PNs because their vertices are just the system resources. So, digraphs describe the interactions between jobs and resources only, while neglecting other details on the system operation. The aim of this paper is to show the tight connections between the two approaches to the deadlock problem, by proposing a unitary framework that links graph-theoretic and PN models and results. In this context, we establish a direct correspondence between the structural elements of the PN (empty siphons) and those of the digraphs (maximal-weight zero-outdegree strong components) characterizing a deadlock occurrence. The paper also shows that the avoidance policies derived from digraphs can be implemented by controlled PNs.

Modelling and Analysis of the Feeding Regimen Induced Entrainment of Hepatocyte Circadian Oscillators Using Petri Nets

PubMed Central

Tareen, Samar Hayat Khan; Ahmad, Jamil

2015-01-01

Circadian rhythms are certain periodic behaviours exhibited by living organism at different levels, including cellular and system-wide scales. Recent studies have found that the circadian rhythms of several peripheral organs in mammals, such as the liver, are able to entrain their clocks to received signals independent of other system level clocks, in particular when responding to signals generated during feeding. These studies have found SIRT1, PARP1, and HSF1 proteins to be the major influencers of the core CLOCKBMAL1:PER-CRY circadian clock. These entities, along with abstracted feeding induced signals were modelled collectively in this study using Petri Nets. The properties of the model show that the circadian system itself is strongly robust, and is able to continually evolve. The modelled feeding regimens suggest that the usual 3 meals/day and 2 meals/day feeding regimens are beneficial with any more or less meals/day negatively affecting the system. PMID:25789928

Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways.

PubMed

Hardy, Simon; Robillard, Pierre N

2008-01-15

Cellular signaling networks are dynamic systems that propagate and process information, and, ultimately, cause phenotypical responses. Understanding the circuitry of the information flow in cells is one of the keys to understanding complex cellular processes. The development of computational quantitative models is a promising avenue for attaining this goal. Not only does the analysis of the simulation data based on the concentration variations of biological compounds yields information about systemic state changes, but it is also very helpful for obtaining information about the dynamics of signal propagation. This article introduces a new method for analyzing the dynamics of signal propagation in signaling pathways using Petri net theory. The method is demonstrated with the Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) regulation network. The results constitute temporal information about signal propagation in the network, a simplified graphical representation of the network and of the signal propagation dynamics and a characterization of some signaling routes as regulation motifs.

Reliability apportionment approach for spacecraft solar array using fuzzy reasoning Petri net and fuzzy comprehensive evaluation

NASA Astrophysics Data System (ADS)

Wu, Jianing; Yan, Shaoze; Xie, Liyang; Gao, Peng

2012-07-01

The reliability apportionment of spacecraft solar array is of significant importance for spacecraft designers in the early stage of design. However, it is difficult to use the existing methods to resolve reliability apportionment problem because of the data insufficiency and the uncertainty of the relations among the components in the mechanical system. This paper proposes a new method which combines the fuzzy comprehensive evaluation with fuzzy reasoning Petri net (FRPN) to accomplish the reliability apportionment of the solar array. The proposed method extends the previous fuzzy methods and focuses on the characteristics of the subsystems and the intrinsic associations among the components. The analysis results show that the synchronization mechanism may obtain the highest reliability value and the solar panels and hinges may get the lowest reliability before design and manufacturing. Our developed method is of practical significance for the reliability apportionment of solar array where the design information has not been clearly identified, particularly in early stage of design.

Application of modified Martinez-Silva algorithm in determination of net cover

NASA Astrophysics Data System (ADS)

Stefanowicz, Łukasz; Grobelna, Iwona

2016-12-01

In the article we present the idea of modifications of Martinez-Silva algorithm, which allows for determination of place invariants (p-invariants) of Petri net. Their generation time is important in the parallel decomposition of discrete systems described by Petri nets. Decomposition process is essential from the point of view of discrete system design, as it allows for separation of smaller sequential parts. The proposed modifications of Martinez-Silva method concern the net cover by p-invariants and are focused on two important issues: cyclic reduction of invariant matrix and cyclic checking of net cover.

Knowledge acquisition and representation using fuzzy evidential reasoning and dynamic adaptive fuzzy Petri nets.

PubMed

Liu, Hu-Chen; Liu, Long; Lin, Qing-Lian; Liu, Nan

2013-06-01

The two most important issues of expert systems are the acquisition of domain experts' professional knowledge and the representation and reasoning of the knowledge rules that have been identified. First, during expert knowledge acquisition processes, the domain expert panel often demonstrates different experience and knowledge from one another and produces different types of knowledge information such as complete and incomplete, precise and imprecise, and known and unknown because of its cross-functional and multidisciplinary nature. Second, as a promising tool for knowledge representation and reasoning, fuzzy Petri nets (FPNs) still suffer a couple of deficiencies. The parameters in current FPN models could not accurately represent the increasingly complex knowledge-based systems, and the rules in most existing knowledge inference frameworks could not be dynamically adjustable according to propositions' variation as human cognition and thinking. In this paper, we present a knowledge acquisition and representation approach using the fuzzy evidential reasoning approach and dynamic adaptive FPNs to solve the problems mentioned above. As is illustrated by the numerical example, the proposed approach can well capture experts' diversity experience, enhance the knowledge representation power, and reason the rule-based knowledge more intelligently.

Performance and state-space analyses of systems using Petri nets

NASA Technical Reports Server (NTRS)

Watson, James Francis, III

1992-01-01

The goal of any modeling methodology is to develop a mathematical description of a system that is accurate in its representation and also permits analysis of structural and/or performance properties. Inherently, trade-offs exist between the level detail in the model and the ease with which analysis can be performed. Petri nets (PN's), a highly graphical modeling methodology for Discrete Event Dynamic Systems, permit representation of shared resources, finite capacities, conflict, synchronization, concurrency, and timing between state changes. By restricting the state transition time delays to the family of exponential density functions, Markov chain analysis of performance problems is possible. One major drawback of PN's is the tendency for the state-space to grow rapidly (exponential complexity) compared to increases in the PN constructs. It is the state space, or the Markov chain obtained from it, that is needed in the solution of many problems. The theory of state-space size estimation for PN's is introduced. The problem of state-space size estimation is defined, its complexities are examined, and estimation algorithms are developed. Both top-down and bottom-up approaches are pursued, and the advantages and disadvantages of each are described. Additionally, the author's research in non-exponential transition modeling for PN's is discussed. An algorithm for approximating non-exponential transitions is developed. Since only basic PN constructs are used in the approximation, theory already developed for PN's remains applicable. Comparison to results from entropy theory show the transition performance is close to the theoretic optimum. Inclusion of non-exponential transition approximations improves performance results at the expense of increased state-space size. The state-space size estimation theory provides insight and algorithms for evaluating this trade-off.

Identification of key regulators in glycogen utilization in E. coli based on the simulations from a hybrid functional Petri net model.

PubMed

Tian, Zhongyuan; Fauré, Adrien; Mori, Hirotada; Matsuno, Hiroshi

2013-01-01

Glycogen and glucose are two sugar sources available during the lag phase of E. coli, but the mechanism that regulates their utilization is still unclear. Attempting to unveil the relationship between glucose and glycogen, we propose an integrated hybrid functional Petri net (HFPN) model including glycolysis, PTS, glycogen metabolic pathway, and their internal regulatory systems. By comparing known biological results to this model, basic necessary regulatory mechanism for utilizing glucose and glycogen were identified as a feedback circuit in which HPr and EIIAGlc play key roles. Based on this regulatory HFPN model, we discuss the process of glycogen utilization in E. coli in the context of a systematic understanding of carbohydrate metabolism.

Reliability analysis of repairable systems using Petri nets and vague Lambda-Tau methodology.

PubMed

Garg, Harish

2013-01-01

The main objective of the paper is to developed a methodology, named as vague Lambda-Tau, for reliability analysis of repairable systems. Petri net tool is applied to represent the asynchronous and concurrent processing of the system instead of fault tree analysis. To enhance the relevance of the reliability study, vague set theory is used for representing the failure rate and repair times instead of classical(crisp) or fuzzy set theory because vague sets are characterized by a truth membership function and false membership functions (non-membership functions) so that sum of both values is less than 1. The proposed methodology involves qualitative modeling using PN and quantitative analysis using Lambda-Tau method of solution with the basic events represented by intuitionistic fuzzy numbers of triangular membership functions. Sensitivity analysis has also been performed and the effects on system MTBF are addressed. The methodology improves the shortcomings of the existing probabilistic approaches and gives a better understanding of the system behavior through its graphical representation. The washing unit of a paper mill situated in a northern part of India, producing approximately 200 ton of paper per day, has been considered to demonstrate the proposed approach. The results may be helpful for the plant personnel for analyzing the systems' behavior and to improve their performance by adopting suitable maintenance strategies. Copyright © 2012 ISA. Published by Elsevier Ltd. All rights reserved.

Reliability prediction of ontology-based service compositions using Petri net and time series models.

PubMed

Li, Jia; Xia, Yunni; Luo, Xin

2014-01-01

OWL-S, one of the most important Semantic Web service ontologies proposed to date, provides a core ontological framework and guidelines for describing the properties and capabilities of their web services in an unambiguous, computer interpretable form. Predicting the reliability of composite service processes specified in OWL-S allows service users to decide whether the process meets the quantitative quality requirement. In this study, we consider the runtime quality of services to be fluctuating and introduce a dynamic framework to predict the runtime reliability of services specified in OWL-S, employing the Non-Markovian stochastic Petri net (NMSPN) and the time series model. The framework includes the following steps: obtaining the historical response times series of individual service components; fitting these series with a autoregressive-moving-average-model (ARMA for short) and predicting the future firing rates of service components; mapping the OWL-S process into a NMSPN model; employing the predicted firing rates as the model input of NMSPN and calculating the normal completion probability as the reliability estimate. In the case study, a comparison between the static model and our approach based on experimental data is presented and it is shown that our approach achieves higher prediction accuracy.

Reliability Prediction of Ontology-Based Service Compositions Using Petri Net and Time Series Models

PubMed Central

Li, Jia; Xia, Yunni; Luo, Xin

2014-01-01

OWL-S, one of the most important Semantic Web service ontologies proposed to date, provides a core ontological framework and guidelines for describing the properties and capabilities of their web services in an unambiguous, computer interpretable form. Predicting the reliability of composite service processes specified in OWL-S allows service users to decide whether the process meets the quantitative quality requirement. In this study, we consider the runtime quality of services to be fluctuating and introduce a dynamic framework to predict the runtime reliability of services specified in OWL-S, employing the Non-Markovian stochastic Petri net (NMSPN) and the time series model. The framework includes the following steps: obtaining the historical response times series of individual service components; fitting these series with a autoregressive-moving-average-model (ARMA for short) and predicting the future firing rates of service components; mapping the OWL-S process into a NMSPN model; employing the predicted firing rates as the model input of NMSPN and calculating the normal completion probability as the reliability estimate. In the case study, a comparison between the static model and our approach based on experimental data is presented and it is shown that our approach achieves higher prediction accuracy. PMID:24688429

Classical workflow nets and workflow nets with reset arcs: using Lyapunov stability for soundness verification

NASA Astrophysics Data System (ADS)

Clempner, Julio B.

2017-01-01

This paper presents a novel analytical method for soundness verification of workflow nets and reset workflow nets, using the well-known stability results of Lyapunov for Petri nets. We also prove that the soundness property is decidable for workflow nets and reset workflow nets. In addition, we provide evidence of several outcomes related with properties such as boundedness, liveness, reversibility and blocking using stability. Our approach is validated theoretically and by a numerical example related to traffic signal-control synchronisation.

SafeNet: a methodology for integrating general-purpose unsafe devices in safe-robot rehabilitation systems.

PubMed

Vicentini, Federico; Pedrocchi, Nicola; Malosio, Matteo; Molinari Tosatti, Lorenzo

2014-09-01

Robot-assisted neurorehabilitation often involves networked systems of sensors ("sensory rooms") and powerful devices in physical interaction with weak users. Safety is unquestionably a primary concern. Some lightweight robot platforms and devices designed on purpose include safety properties using redundant sensors or intrinsic safety design (e.g. compliance and backdrivability, limited exchange of energy). Nonetheless, the entire "sensory room" shall be required to be fail-safe and safely monitored as a system at large. Yet, sensor capabilities and control algorithms used in functional therapies require, in general, frequent updates or re-configurations, making a safety-grade release of such devices hardly sustainable in cost-effectiveness and development time. As such, promising integrated platforms for human-in-the-loop therapies could not find clinical application and manufacturing support because of lacking in the maintenance of global fail-safe properties. Under the general context of cross-machinery safety standards, the paper presents a methodology called SafeNet for helping in extending the safety rate of Human Robot Interaction (HRI) systems using unsafe components, including sensors and controllers. SafeNet considers, in fact, the robotic system as a device at large and applies the principles of functional safety (as in ISO 13489-1) through a set of architectural procedures and implementation rules. The enabled capability of monitoring a network of unsafe devices through redundant computational nodes, allows the usage of any custom sensors and algorithms, usually planned and assembled at therapy planning-time rather than at platform design-time. A case study is presented with an actual implementation of the proposed methodology. A specific architectural solution is applied to an example of robot-assisted upper-limb rehabilitation with online motion tracking. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Design and analysis of a Petri net model of the Von Hippel-Lindau (VHL) tumor suppressor interaction network.

PubMed

Minervini, Giovanni; Panizzoni, Elisabetta; Giollo, Manuel; Masiero, Alessandro; Ferrari, Carlo; Tosatto, Silvio C E

2014-01-01

Von Hippel-Lindau (VHL) syndrome is a hereditary condition predisposing to the development of different cancer forms, related to germline inactivation of the homonymous tumor suppressor pVHL. The best characterized function of pVHL is the ubiquitination dependent degradation of Hypoxia Inducible Factor (HIF) via the proteasome. It is also involved in several cellular pathways acting as a molecular hub and interacting with more than 200 different proteins. Molecular details of pVHL plasticity remain in large part unknown. Here, we present a novel manually curated Petri Net (PN) model of the main pVHL functional pathways. The model was built using functional information derived from the literature. It includes all major pVHL functions and is able to credibly reproduce VHL syndrome at the molecular level. The reliability of the PN model also allowed in silico knockout experiments, driven by previous model analysis. Interestingly, PN analysis suggests that the variability of different VHL manifestations is correlated with the concomitant inactivation of different metabolic pathways.

Reliability analysis method of a solar array by using fault tree analysis and fuzzy reasoning Petri net

NASA Astrophysics Data System (ADS)

Wu, Jianing; Yan, Shaoze; Xie, Liyang

2011-12-01

To address the impact of solar array anomalies, it is important to perform analysis of the solar array reliability. This paper establishes the fault tree analysis (FTA) and fuzzy reasoning Petri net (FRPN) models of a solar array mechanical system and analyzes reliability to find mechanisms of the solar array fault. The index final truth degree (FTD) and cosine matching function (CMF) are employed to resolve the issue of how to evaluate the importance and influence of different faults. So an improvement reliability analysis method is developed by means of the sorting of FTD and CMF. An example is analyzed using the proposed method. The analysis results show that harsh thermal environment and impact caused by particles in space are the most vital causes of the solar array fault. Furthermore, other fault modes and the corresponding improvement methods are discussed. The results reported in this paper could be useful for the spacecraft designers, particularly, in the process of redesigning the solar array and scheduling its reliability growth plan.

Stochastic Petri Net Modeling of Hypoxia Pathway Predicts a Novel Incoherent Feed-Forward Loop Controlling SDF-1 Expression in Acute Kidney Injury.

PubMed

Heidary, Zarifeh; Ghaisari, Jafar; Moein, Shiva; Naderi, Mahmood; Gheisari, Yousof

2016-01-01

Homing of stem cells to the sites of injury is crucial for tissue regeneration. Stromal derived factor 1 (SDF-1) is among the most important chemokines recruiting these cells. Unexpectedly, our previous experimental data on mouse models of acute kidney injury showed that SDF-1 has a declining trend following ischemic kidney insult. To describe this unforeseen observation, a stochastic Petri net model of SDF-1 regulation in the hypoxia pathway was constructed based on main related components extracted from literature. Using this strategy, predictions regarding the underlying mechanisms of SDF-1 kinetics are generated and a novel incoherent feed forward loop regulating SDF-1 expression is proposed. The computational approach suggested here can be exploited to propose novel therapies for debilitating disorders such as kidney injury.

Ensuring Patient Safety by using Colored Petri Net Simulation in the Design of Heterogeneous, Multi-Vendor, Integrated, Life-Critical Wireless (802.x) Patient Care Device Networks.

PubMed

Sloane, Elliot; Gehlot, Vijay

2005-01-01

Hospitals and manufacturers are designing and deploying the IEEE 802.x wireless technologies in medical devices to promote patient mobility and flexible facility use. There is little information, however, on the reliability or ultimate safety of connecting multiple wireless life-critical medical devices from multiple vendors using commercial 802.11a, 802.11b, 802.11g or pre-802.11n devices. It is believed that 802.11-type devices can introduce unintended life-threatening risks unless delivery of critical patient alarms to central monitoring systems and/or clinical personnel is assured by proper use of 802.11e Quality of Service (QoS) methods. Petri net tools can be used to simulate all possible states and transitions between devices and/or systems in a wireless device network, and can identify failure modes in advance. Colored Petri Net (CPN) tools are ideal, in fact, as they allow tracking and controlling each message in a network based on pre-selected criteria. This paper describes a research project using CPN to simulate and validate alarm integrity in a small multi-modality wireless patient monitoring system. A 20-monitor wireless patient monitoring network is created in two versions: one with non-prioritized 802.x CSM protocols and the second with simulated Quality of Service (QoS) capabilities similar to 802.11e (i.e., the second network allows message priority management.) In the standard 802.x network, dangerous heart arrhythmia and pulse oximetry alarms could not be reliably and rapidly communicated, but the second network's QoS priority management reduced that risk significantly.

Action-based verification of RTCP-nets with CADP

NASA Astrophysics Data System (ADS)

Biernacki, Jerzy; Biernacka, Agnieszka; Szpyrka, Marcin

2015-12-01

The paper presents an RTCP-nets' (real-time coloured Petri nets) coverability graphs into Aldebaran format translation algorithm. The approach provides the possibility of automatic RTCP-nets verification using model checking techniques provided by the CADP toolbox. An actual fire alarm control panel system has been modelled and several of its crucial properties have been verified to demonstrate the usability of the approach.

SHER: a colored petri net based random mobility model for wireless communications.

PubMed

Khan, Naeem Akhtar; Ahmad, Farooq; Khan, Sher Afzal

2015-01-01

In wireless network research, simulation is the most imperative technique to investigate the network's behavior and validation. Wireless networks typically consist of mobile hosts; therefore, the degree of validation is influenced by the underlying mobility model, and synthetic models are implemented in simulators because real life traces are not widely available. In wireless communications, mobility is an integral part while the key role of a mobility model is to mimic the real life traveling patterns to study. The performance of routing protocols and mobility management strategies e.g. paging, registration and handoff is highly dependent to the selected mobility model. In this paper, we devise and evaluate the Show Home and Exclusive Regions (SHER), a novel two-dimensional (2-D) Colored Petri net (CPN) based formal random mobility model, which exhibits sociological behavior of a user. The model captures hotspots where a user frequently visits and spends time. Our solution eliminates six key issues of the random mobility models, i.e., sudden stops, memoryless movements, border effect, temporal dependency of velocity, pause time dependency, and speed decay in a single model. The proposed model is able to predict the future location of a mobile user and ultimately improves the performance of wireless communication networks. The model follows a uniform nodal distribution and is a mini simulator, which exhibits interesting mobility patterns. The model is also helpful to those who are not familiar with the formal modeling, and users can extract meaningful information with a single mouse-click. It is noteworthy that capturing dynamic mobility patterns through CPN is the most challenging and virulent activity of the presented research. Statistical and reachability analysis techniques are presented to elucidate and validate the performance of our proposed mobility model. The state space methods allow us to algorithmically derive the system behavior and rectify the errors

SHER: A Colored Petri Net Based Random Mobility Model for Wireless Communications

PubMed Central

Khan, Naeem Akhtar; Ahmad, Farooq; Khan, Sher Afzal

2015-01-01

In wireless network research, simulation is the most imperative technique to investigate the network’s behavior and validation. Wireless networks typically consist of mobile hosts; therefore, the degree of validation is influenced by the underlying mobility model, and synthetic models are implemented in simulators because real life traces are not widely available. In wireless communications, mobility is an integral part while the key role of a mobility model is to mimic the real life traveling patterns to study. The performance of routing protocols and mobility management strategies e.g. paging, registration and handoff is highly dependent to the selected mobility model. In this paper, we devise and evaluate the Show Home and Exclusive Regions (SHER), a novel two-dimensional (2-D) Colored Petri net (CPN) based formal random mobility model, which exhibits sociological behavior of a user. The model captures hotspots where a user frequently visits and spends time. Our solution eliminates six key issues of the random mobility models, i.e., sudden stops, memoryless movements, border effect, temporal dependency of velocity, pause time dependency, and speed decay in a single model. The proposed model is able to predict the future location of a mobile user and ultimately improves the performance of wireless communication networks. The model follows a uniform nodal distribution and is a mini simulator, which exhibits interesting mobility patterns. The model is also helpful to those who are not familiar with the formal modeling, and users can extract meaningful information with a single mouse-click. It is noteworthy that capturing dynamic mobility patterns through CPN is the most challenging and virulent activity of the presented research. Statistical and reachability analysis techniques are presented to elucidate and validate the performance of our proposed mobility model. The state space methods allow us to algorithmically derive the system behavior and rectify the

Design and Analysis of a Petri Net Model of the Von Hippel-Lindau (VHL) Tumor Suppressor Interaction Network

PubMed Central

Minervini, Giovanni; Panizzoni, Elisabetta; Giollo, Manuel; Masiero, Alessandro; Ferrari, Carlo; Tosatto, Silvio C. E.

2014-01-01

Von Hippel-Lindau (VHL) syndrome is a hereditary condition predisposing to the development of different cancer forms, related to germline inactivation of the homonymous tumor suppressor pVHL. The best characterized function of pVHL is the ubiquitination dependent degradation of Hypoxia Inducible Factor (HIF) via the proteasome. It is also involved in several cellular pathways acting as a molecular hub and interacting with more than 200 different proteins. Molecular details of pVHL plasticity remain in large part unknown. Here, we present a novel manually curated Petri Net (PN) model of the main pVHL functional pathways. The model was built using functional information derived from the literature. It includes all major pVHL functions and is able to credibly reproduce VHL syndrome at the molecular level. The reliability of the PN model also allowed in silico knockout experiments, driven by previous model analysis. Interestingly, PN analysis suggests that the variability of different VHL manifestations is correlated with the concomitant inactivation of different metabolic pathways. PMID:24886840

State-based verification of RTCP-nets with nuXmv

NASA Astrophysics Data System (ADS)

Biernacka, Agnieszka; Biernacki, Jerzy; Szpyrka, Marcin

2015-12-01

The paper deals with an algorithm of translation of RTCP-nets' (real-time coloured Petri nets) coverability graphs into nuXmv state machines. The approach enables users to verify RTCP-nets with model checking techniques provided by the nuXmv tool. Full details of the algorithm are presented and an illustrative example of the approach usefulness is provided.

A Petri net model of granulomatous inflammation: implications for IL-10 mediated control of Leishmania donovani infection.

PubMed

Albergante, Luca; Timmis, Jon; Beattie, Lynette; Kaye, Paul M

2013-01-01

Experimental visceral leishmaniasis, caused by infection of mice with the protozoan parasite Leishmania donovani, is characterized by focal accumulation of inflammatory cells in the liver, forming discrete "granulomas" within which the parasite is eventually eliminated. To shed new light on fundamental aspects of granuloma formation and function, we have developed an in silico Petri net model that simulates hepatic granuloma development throughout the course of infection. The model was extensively validated by comparison with data derived from experimental studies in mice, and the model robustness was assessed by a sensitivity analysis. The model recapitulated the progression of disease as seen during experimental infection and also faithfully predicted many of the changes in cellular composition seen within granulomas over time. By conducting in silico experiments, we have identified a previously unappreciated level of inter-granuloma diversity in terms of the development of anti-leishmanial activity. Furthermore, by simulating the impact of IL-10 gene deficiency in a variety of lymphocyte and myeloid cell populations, our data suggest a dominant local regulatory role for IL-10 produced by infected Kupffer cells at the core of the granuloma.

A Petri Net Model of Granulomatous Inflammation: Implications for IL-10 Mediated Control of Leishmania donovani Infection

PubMed Central

Albergante, Luca; Timmis, Jon; Beattie, Lynette; Kaye, Paul M.

2013-01-01

Experimental visceral leishmaniasis, caused by infection of mice with the protozoan parasite Leishmania donovani, is characterized by focal accumulation of inflammatory cells in the liver, forming discrete “granulomas” within which the parasite is eventually eliminated. To shed new light on fundamental aspects of granuloma formation and function, we have developed an in silico Petri net model that simulates hepatic granuloma development throughout the course of infection. The model was extensively validated by comparison with data derived from experimental studies in mice, and the model robustness was assessed by a sensitivity analysis. The model recapitulated the progression of disease as seen during experimental infection and also faithfully predicted many of the changes in cellular composition seen within granulomas over time. By conducting in silico experiments, we have identified a previously unappreciated level of inter-granuloma diversity in terms of the development of anti-leishmanial activity. Furthermore, by simulating the impact of IL-10 gene deficiency in a variety of lymphocyte and myeloid cell populations, our data suggest a dominant local regulatory role for IL-10 produced by infected Kupffer cells at the core of the granuloma. PMID:24363630

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2011-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier. Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2010-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier.Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome

Sociophysics of sexism: normal and anomalous petrie multipliers

NASA Astrophysics Data System (ADS)

Eliazar, Iddo

2015-07-01

A recent mathematical model by Karen Petrie explains how sexism towards women can arise in organizations where male and female are equally sexist. Indeed, the Petrie model predicts that such sexism will emerge whenever there is a male majority, and quantifies this majority bias by the ‘Petrie multiplier’: the square of the male/female ratio. In this paper—emulating the shift from ‘normal’ to ‘anomalous’ diffusion—we generalize the Petrie model to a stochastic Poisson model that accommodates heterogeneously sexist men and woman, and that extends the ‘normal’ quadratic Petrie multiplier to ‘anomalous’ non-quadratic multipliers. The Petrie multipliers span a full spectrum of behaviors which we classify into four universal types. A variation of the stochastic Poisson model and its Petrie multipliers is further applied to the context of cyber warfare.

The role of Fenton reaction in ROS-induced toxicity underlying atherosclerosis - modeled and analyzed using a Petri net-based approach.

PubMed

Formanowicz, Dorota; Radom, Marcin; Rybarczyk, Agnieszka; Formanowicz, Piotr

2018-03-01

The superoxide-driven Fenton reaction plays an important role in the transformation of poorly reactive radicals into highly reactive ones. These highly reactive species (ROS), especially hydroxyl radicals can lead to many disturbances contributing to the endothelial dysfunction being a starting point for atherosclerosis. Although, iron has been identified as a possible culprit influencing formation of ROS, its significance in this process is still debatable. To better understand this phenomenon, the influence of blockade of Fenton reaction in a proposed Petri net-based model of the selected aspects of the iron ROS-induced toxicity in atherosclerosis has been evaluated. As a result of the blockade of iron ions formation in the model, even up to 70% of the paths leading to the progression of atherosclerosis in this model has been blocked. In addition, after adding to the model, the blockade of the lipids peroxidation paths, progression of atherosclerotic plaque has been not observed. This allowed to conclude that the superoxide-driven Fenton reaction plays a significant role in the atherosclerosis. Copyright © 2018 Elsevier B.V. All rights reserved.

Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data.

PubMed

Nagasaki, Masao; Yamaguchi, Rui; Yoshida, Ryo; Imoto, Seiya; Doi, Atsushi; Tamada, Yoshinori; Matsuno, Hiroshi; Miyano, Satoru; Higuchi, Tomoyuki

2006-01-01

We propose an automatic construction method of the hybrid functional Petri net as a simulation model of biological pathways. The problems we consider are how we choose the values of parameters and how we set the network structure. Usually, we tune these unknown factors empirically so that the simulation results are consistent with biological knowledge. Obviously, this approach has the limitation in the size of network of interest. To extend the capability of the simulation model, we propose the use of data assimilation approach that was originally established in the field of geophysical simulation science. We provide genomic data assimilation framework that establishes a link between our simulation model and observed data like microarray gene expression data by using a nonlinear state space model. A key idea of our genomic data assimilation is that the unknown parameters in simulation model are converted as the parameter of the state space model and the estimates are obtained as the maximum a posteriori estimators. In the parameter estimation process, the simulation model is used to generate the system model in the state space model. Such a formulation enables us to handle both the model construction and the parameter tuning within a framework of the Bayesian statistical inferences. In particular, the Bayesian approach provides us a way of controlling overfitting during the parameter estimations that is essential for constructing a reliable biological pathway. We demonstrate the effectiveness of our approach using synthetic data. As a result, parameter estimation using genomic data assimilation works very well and the network structure is suitably selected.

Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram.

PubMed

Li, Chen; Nagasaki, Masao; Saito, Ayumu; Miyano, Satoru

2010-04-01

With an accumulation of in silico data obtained by simulating large-scale biological networks, a new interest of research is emerging for elucidating how living organism functions over time in cells. Investigating the dynamic features of current computational models promises a deeper understanding of complex cellular processes. This leads us to develop a method that utilizes structural properties of the model over all simulation time steps. Further, user-friendly overviews of dynamic behaviors can be considered to provide a great help in understanding the variations of system mechanisms. We propose a novel method for constructing and analyzing a so-called active state transition diagram (ASTD) by using time-course simulation data of a high-level Petri net. Our method includes two new algorithms. The first algorithm extracts a series of subnets (called temporal subnets) reflecting biological components contributing to the dynamics, while retaining positive mathematical qualities. The second one creates an ASTD composed of unique temporal subnets. ASTD provides users with concise information allowing them to grasp and trace how a key regulatory subnet and/or a network changes with time. The applicability of our method is demonstrated by the analysis of the underlying model for circadian rhythms in Drosophila. Building ASTD is a useful means to convert a hybrid model dealing with discrete, continuous and more complicated events to finite time-dependent states. Based on ASTD, various analytical approaches can be applied to obtain new insights into not only systematic mechanisms but also dynamics.

Petri Net computational modelling of Langerhans cell Interferon Regulatory Factor Network predicts their role in T cell activation.

PubMed

Polak, Marta E; Ung, Chuin Ying; Masapust, Joanna; Freeman, Tom C; Ardern-Jones, Michael R

2017-04-06

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. Applying Boolean logic we assembled a Petri net-based model of the IRF-GRN which provides molecular pathway predictions for the induction of different transcriptional programmes in LCs. In silico simulations performed after model parameterisation with transcription factor expression values predicted that human LC activation of antigen-specific CD8 T cells would be differentially regulated by epidermal cytokine induction of specific IRF-controlled pathways. This was confirmed by in vitro measurement of IFN-γ production by activated T cells. As a proof of concept, this approach shows that stochastic modelling of a specific immune networks renders transcriptome data valuable for the prediction of functional outcomes of immune responses.

Construction and Experimental Validation of a Petri Net Model of Wnt/β-Catenin Signaling.

PubMed

Jacobsen, Annika; Heijmans, Nika; Verkaar, Folkert; Smit, Martine J; Heringa, Jaap; van Amerongen, Renée; Feenstra, K Anton

2016-01-01

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. The destruction complex is inhibited during active WNT signaling, leading to β-catenin stabilization and induction of β-catenin/TCF target genes. In this study we investigated the mechanism and effect of β-catenin stabilization during active and hyperactive WNT signaling in a combined in silico and in vitro approach. We constructed a Petri net model of Wnt/β-catenin signaling including main players from the plasma membrane (WNT ligands and receptors), cytoplasmic effectors and the downstream negative feedback target gene AXIN2. We validated that our model can be used to simulate both active (WNT stimulation) and hyperactive (GSK3 inhibition) signaling by comparing our simulation and experimental data. We used this experimentally validated model to get further insights into the effect of the negative feedback regulator AXIN2 upon WNT stimulation and observed an attenuated β-catenin stabilization. We furthermore simulated the effect of APC inactivating mutations, yielding a stabilization of β-catenin levels comparable to the Wnt-pathway activities observed in colorectal and breast cancer. Our model can be used for further investigation and viable predictions of the role of Wnt/β-catenin signaling in oncogenesis and development.

Construction and Experimental Validation of a Petri Net Model of Wnt/β-Catenin Signaling

PubMed Central

Heijmans, Nika; Verkaar, Folkert; Smit, Martine J.; Heringa, Jaap

2016-01-01

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. The destruction complex is inhibited during active WNT signaling, leading to β-catenin stabilization and induction of β-catenin/TCF target genes. In this study we investigated the mechanism and effect of β-catenin stabilization during active and hyperactive WNT signaling in a combined in silico and in vitro approach. We constructed a Petri net model of Wnt/β-catenin signaling including main players from the plasma membrane (WNT ligands and receptors), cytoplasmic effectors and the downstream negative feedback target gene AXIN2. We validated that our model can be used to simulate both active (WNT stimulation) and hyperactive (GSK3 inhibition) signaling by comparing our simulation and experimental data. We used this experimentally validated model to get further insights into the effect of the negative feedback regulator AXIN2 upon WNT stimulation and observed an attenuated β-catenin stabilization. We furthermore simulated the effect of APC inactivating mutations, yielding a stabilization of β-catenin levels comparable to the Wnt-pathway activities observed in colorectal and breast cancer. Our model can be used for further investigation and viable predictions of the role of Wnt/β-catenin signaling in oncogenesis and development. PMID:27218469

Target-based drug discovery for [Formula: see text]-globin disorders: drug target prediction using quantitative modeling with hybrid functional Petri nets.

PubMed

Mehraei, Mani; Bashirov, Rza; Tüzmen, Şükrü

2016-10-01

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. In accordance with the reverse pharmacology approach, we pose a hypothesis regarding modulation of specific protein targets that induce [Formula: see text]-globin and consequently fetal hemoglobin. Comparison of simulation results for the proposed strategy with the ones obtained for already existing drugs shows that our strategy is the optimal as it leads to highest level of [Formula: see text]-globin induction and thereby has potential beneficial therapeutic effects on [Formula: see text]-globin disorders. Simulation results enable verification of model coherence demonstrating that it is consistent with qPCR data available for known strategies and/or drugs.

Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram

PubMed Central

2010-01-01

Background With an accumulation of in silico data obtained by simulating large-scale biological networks, a new interest of research is emerging for elucidating how living organism functions over time in cells. Investigating the dynamic features of current computational models promises a deeper understanding of complex cellular processes. This leads us to develop a method that utilizes structural properties of the model over all simulation time steps. Further, user-friendly overviews of dynamic behaviors can be considered to provide a great help in understanding the variations of system mechanisms. Results We propose a novel method for constructing and analyzing a so-called active state transition diagram (ASTD) by using time-course simulation data of a high-level Petri net. Our method includes two new algorithms. The first algorithm extracts a series of subnets (called temporal subnets) reflecting biological components contributing to the dynamics, while retaining positive mathematical qualities. The second one creates an ASTD composed of unique temporal subnets. ASTD provides users with concise information allowing them to grasp and trace how a key regulatory subnet and/or a network changes with time. The applicability of our method is demonstrated by the analysis of the underlying model for circadian rhythms in Drosophila. Conclusions Building ASTD is a useful means to convert a hybrid model dealing with discrete, continuous and more complicated events to finite time-dependent states. Based on ASTD, various analytical approaches can be applied to obtain new insights into not only systematic mechanisms but also dynamics. PMID:20356411

Coverability graphs for a class of synchronously executed unbounded Petri net

NASA Technical Reports Server (NTRS)

Stotts, P. David; Pratt, Terrence W.

1990-01-01

After detailing a variant of the concurrent-execution rule for firing of maximal subsets, in which the simultaneous firing of conflicting transitions is prohibited, an algorithm is constructed for generating the coverability graph of a net executed under this synchronous firing rule. The omega insertion criteria in the algorithm are shown to be valid for any net on which the algorithm terminates. It is accordingly shown that the set of nets on which the algorithm terminates includes the 'conflict-free' class.

An integrated pathway system modeling of Saccharomyces cerevisiae HOG pathway: a Petri net based approach.

PubMed

Tomar, Namrata; Choudhury, Olivia; Chakrabarty, Ankush; De, Rajat K

2013-02-01

Biochemical networks comprise many diverse components and interactions between them. It has intracellular signaling, metabolic and gene regulatory pathways which are highly integrated and whose responses are elicited by extracellular actions. Previous modeling techniques mostly consider each pathway independently without focusing on the interrelation of these which actually functions as a single system. In this paper, we propose an approach of modeling an integrated pathway using an event-driven modeling tool, i.e., Petri nets (PNs). PNs have the ability to simulate the dynamics of the system with high levels of accuracy. The integrated set of signaling, regulatory and metabolic reactions involved in Saccharomyces cerevisiae's HOG pathway has been collected from the literature. The kinetic parameter values have been used for transition firings. The dynamics of the system has been simulated and the concentrations of major biological species over time have been observed. The phenotypic characteristics of the integrated system have been investigated under two conditions, viz., under the absence and presence of osmotic pressure. The results have been validated favorably with the existing experimental results. We have also compared our study with the study of idFBA (Lee et al., PLoS Comput Biol 4:e1000-e1086, 2008) and pointed out the differences between both studies. We have simulated and monitored concentrations of multiple biological entities over time and also incorporated feedback inhibition by Ptp2 which has not been included in the idFBA study. We have concluded that our study is the first to the best of our knowledge to model signaling, metabolic and regulatory events in an integrated form through PN model framework. This study is useful in computational simulation of system dynamics for integrated pathways as there are growing evidences that the malfunctioning of the interplay among these pathways is associated with disease.

Contribution to the modelling and analysis of logistics system performance by Petri nets and simulation models: Application in a supply chain

NASA Astrophysics Data System (ADS)

Azougagh, Yassine; Benhida, Khalid; Elfezazi, Said

2016-02-01

In this paper, the focus is on studying the performance of complex systems in a supply chain context by developing a structured modelling approach based on the methodology ASDI (Analysis, Specification, Design and Implementation) by combining the modelling by Petri nets and simulation using ARENA. The linear approach typically followed in conducting of this kind of problems has to cope with a difficulty of modelling due to the complexity and the number of parameters of concern. Therefore, the approach used in this work is able to structure modelling a way to cover all aspects of the performance study. The modelling structured approach is first introduced before being applied to the case of an industrial system in the field of phosphate. Results of the performance indicators obtained from the models developed, permitted to test the behaviour and fluctuations of this system and to develop improved models of the current situation. In addition, in this paper, it was shown how Arena software can be adopted to simulate complex systems effectively. The method in this research can be applied to investigate various improvements scenarios and their consequences before implementing them in reality.

Petri net-based dependability modeling methodology for reconfigurable field programmable gate arrays

NASA Astrophysics Data System (ADS)

Graczyk, Rafał; Orleański, Piotr; Poźniak, Krzysztof

2015-09-01

Dependability modeling is an important issue for aerospace and space equipment designers. From system level perspective, one has to choose from multitude of possible architectures, redundancy levels, component combinations in a way to meet desired properties and dependability and finally fit within required cost and time budgets. Modeling of such systems is getting harder as its levels of complexity grow together with demand for more functional and flexible, yet more available systems that govern more and more crucial parts of our civilization's infrastructure (aerospace transport systems, telecommunications, exploration probes). In this article promising method of modeling complex systems using Petri networks is introduced in context of qualitative and quantitative dependability analysis. This method, although with some limitation and drawback offer still convenient visual formal method of describing system behavior on different levels (functional, timing, random events) and offers straight correspondence to underlying mathematical engine, perfect for simulations and engineering support.

An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data.

PubMed

Jin, Guangxu; Zhao, Hong; Zhou, Xiaobo; Wong, Stephen T C

2011-07-01

Prediction of synergistic effects of drug combinations has traditionally been relied on phenotypic response data. However, such methods cannot be used to identify molecular signaling mechanisms of synergistic drug combinations. In this article, we propose an enhanced Petri-Net (EPN) model to recognize the synergistic effects of drug combinations from the molecular response profiles, i.e. drug-treated microarray data. We addressed the downstream signaling network of the targets for the two individual drugs used in the pairwise combinations and applied EPN to the identified targeted signaling network. In EPN, drugs and signaling molecules are assigned to different types of places, while drug doses and molecular expressions are denoted by color tokens. The changes of molecular expressions caused by treatments of drugs are simulated by two actions of EPN: firing and blasting. Firing is to transit the drug and molecule tokens from one node or place to another, and blasting is to reduce the number of molecule tokens by drug tokens in a molecule node. The goal of EPN is to mediate the state characterized by control condition without any treatment to that of treatment and to depict the drug effects on molecules by the drug tokens. We applied EPN to our generated pairwise drug combination microarray data. The synergistic predictions using EPN are consistent with those predicted using phenotypic response data. The molecules responsible for the synergistic effects with their associated feedback loops display the mechanisms of synergism. The software implemented in Python 2.7 programming language is available from request. stwong@tmhs.org.

OR.NET: a service-oriented architecture for safe and dynamic medical device interoperability.

PubMed

Kasparick, Martin; Schmitz, Malte; Andersen, Björn; Rockstroh, Max; Franke, Stefan; Schlichting, Stefan; Golatowski, Frank; Timmermann, Dirk

2018-02-23

Modern surgical departments are characterized by a high degree of automation supporting complex procedures. It recently became apparent that integrated operating rooms can improve the quality of care, simplify clinical workflows, and mitigate equipment-related incidents and human errors. Particularly using computer assistance based on data from integrated surgical devices is a promising opportunity. However, the lack of manufacturer-independent interoperability often prevents the deployment of collaborative assistive systems. The German flagship project OR.NET has therefore developed, implemented, validated, and standardized concepts for open medical device interoperability. This paper describes the universal OR.NET interoperability concept enabling a safe and dynamic manufacturer-independent interconnection of point-of-care (PoC) medical devices in the operating room and the whole clinic. It is based on a protocol specifically addressing the requirements of device-to-device communication, yet also provides solutions for connecting the clinical information technology (IT) infrastructure. We present the concept of a service-oriented medical device architecture (SOMDA) as well as an introduction to the technical specification implementing the SOMDA paradigm, currently being standardized within the IEEE 11073 service-oriented device connectivity (SDC) series. In addition, the Session concept is introduced as a key enabler for safe device interconnection in highly dynamic ensembles of networked medical devices; and finally, some security aspects of a SOMDA are discussed.

The fundamental closed-form solution of control-related states of kth order S3PR system with left-side non-sharing resource places of Petri nets

NASA Astrophysics Data System (ADS)

Chao, Daniel Yuh; Yu, Tsung Hsien

2016-01-01

Due to the state explosion problem, it has been unimaginable to enumerate reachable states for Petri nets. Chao broke the barrier earlier by developing the very first closed-form solution of the number of reachable and other states for marked graphs and the kth order system. Instead of using first-met bad marking, we propose 'the moment to launch resource allocation' (MLR) as a partial deadlock avoidance policy for a large, real-time dynamic resource allocation system. Presently, we can use the future deadlock ratio of the current state as the indicator of MLR due to which the ratio can be obtained real-time by a closed-form formula. This paper progresses the application of an MLR concept one step further on Gen-Left kth order systems (one non-sharing resource place in any position of the left-side process), which is also the most fundamental asymmetric net structure, by the construction of the system's closed-form solution of the control-related states (reachable, forbidden, live and deadlock states) with a formula depending on the parameters of k and the location of the non-sharing resource. Here, we kick off a new era of real-time, dynamic resource allocation decisions by constructing a generalisation formula of kth order systems (Gen-Left) with r* on the left side but at arbitrary locations.

Petri net-based approach to modeling and analysis of selected aspects of the molecular regulation of angiogenesis

PubMed Central

Formanowicz, Dorota; Radom, Marcin; Zawierucha, Piotr; Formanowicz, Piotr

2017-01-01

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. A systems approach is necessary for these studies because it is not sufficient to analyze the properties of the building blocks separately and an analysis of the whole network of interactions is essential. This approach is based on building a mathematical model of the system, while the model is expressed in the formal language of a mathematical theory. Recently, the theory of Petri nets was shown to be especially promising for the modeling and analysis of biological phenomena. This analysis, based mainly on t-invariants, has led to a particularly important finding that a direct link (close connection) exist between transforming growth factor β1 (TGF-β1), endothelial nitric oxide synthase (eNOS), nitric oxide (NO), and hypoxia-inducible factor 1, the molecules that play a crucial roles during angiogenesis. We have shown that TGF-β1 may participate in the inhibition of angiogenesis through the upregulation of eNOS expression, which is responsible for catalyzing NO production. The results obtained in the previous studies, concerning the effects of NO on angiogenesis, have not been conclusive, and therefore, our study may contribute to a better understanding of this phenomenon. PMID:28253310

Petri net-based approach to modeling and analysis of selected aspects of the molecular regulation of angiogenesis.

PubMed

Formanowicz, Dorota; Radom, Marcin; Zawierucha, Piotr; Formanowicz, Piotr

2017-01-01

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. A systems approach is necessary for these studies because it is not sufficient to analyze the properties of the building blocks separately and an analysis of the whole network of interactions is essential. This approach is based on building a mathematical model of the system, while the model is expressed in the formal language of a mathematical theory. Recently, the theory of Petri nets was shown to be especially promising for the modeling and analysis of biological phenomena. This analysis, based mainly on t-invariants, has led to a particularly important finding that a direct link (close connection) exist between transforming growth factor β1 (TGF-β1), endothelial nitric oxide synthase (eNOS), nitric oxide (NO), and hypoxia-inducible factor 1, the molecules that play a crucial roles during angiogenesis. We have shown that TGF-β1 may participate in the inhibition of angiogenesis through the upregulation of eNOS expression, which is responsible for catalyzing NO production. The results obtained in the previous studies, concerning the effects of NO on angiogenesis, have not been conclusive, and therefore, our study may contribute to a better understanding of this phenomenon.

Petri Net-Based Model of Helicobacter pylori Mediated Disruption of Tight Junction Proteins in Stomach Lining during Gastric Carcinoma

PubMed Central

Naz, Anam; Obaid, Ayesha; Awan, Faryal M.; Ikram, Aqsa; Ahmad, Jamil; Ali, Amjad

2017-01-01

Tight junctions help prevent the passage of digestive enzymes and microorganisms through the space between adjacent epithelial cells lining. However, Helicobacter pylori encoded virulence factors negatively regulate these tight junctions and contribute to dysfunction of gastric mucosa. Here, we have predicted the regulation of important tight junction proteins, such as Zonula occludens-1, Claudin-2 and Connexin32 in the presence of pathogenic proteins. Molecular events such as post translational modifications and crosstalk between phosphorylation, O-glycosylation, palmitoylation and methylation are explored which may compromise the integrity of these tight junction proteins. Furthermore, the signaling pathways disrupted by dysregulated kinases, proteins and post-translational modifications are reviewed to design an abstracted computational model showing the situation-dependent dynamic behaviors of these biological processes and entities. A qualitative hybrid Petri Net model is therefore constructed showing the altered host pathways in the presence of virulence factor cytotoxin-associated gene A, leading to the disruption of tight junction proteins. The model is qualitative logic-based, which does not depend on any kinetic parameter and quantitative data and depends on knowledge derived from experiments. The designed model provides insights into the tight junction disruption and disease progression. Model is then verified by the available experimental data, nevertheless formal in vitro experimentation is a promising way to ensure its validation. The major findings propose that H. pylori activated kinases are responsible to trigger specific post translational modifications within tight junction proteins, at specific sites. These modifications may favor alterations in gastric barrier and provide a route to bacterial invasion into host cells. PMID:28932213

Petri Net-Based Model of Helicobacter pylori Mediated Disruption of Tight Junction Proteins in Stomach Lining during Gastric Carcinoma.

PubMed

Naz, Anam; Obaid, Ayesha; Awan, Faryal M; Ikram, Aqsa; Ahmad, Jamil; Ali, Amjad

2017-01-01

Tight junctions help prevent the passage of digestive enzymes and microorganisms through the space between adjacent epithelial cells lining. However, Helicobacter pylori encoded virulence factors negatively regulate these tight junctions and contribute to dysfunction of gastric mucosa. Here, we have predicted the regulation of important tight junction proteins, such as Zonula occludens-1, Claudin-2 and Connexin32 in the presence of pathogenic proteins. Molecular events such as post translational modifications and crosstalk between phosphorylation, O-glycosylation, palmitoylation and methylation are explored which may compromise the integrity of these tight junction proteins. Furthermore, the signaling pathways disrupted by dysregulated kinases, proteins and post-translational modifications are reviewed to design an abstracted computational model showing the situation-dependent dynamic behaviors of these biological processes and entities. A qualitative hybrid Petri Net model is therefore constructed showing the altered host pathways in the presence of virulence factor cytotoxin-associated gene A, leading to the disruption of tight junction proteins. The model is qualitative logic-based, which does not depend on any kinetic parameter and quantitative data and depends on knowledge derived from experiments. The designed model provides insights into the tight junction disruption and disease progression. Model is then verified by the available experimental data, nevertheless formal in vitro experimentation is a promising way to ensure its validation. The major findings propose that H. pylori activated kinases are responsible to trigger specific post translational modifications within tight junction proteins, at specific sites. These modifications may favor alterations in gastric barrier and provide a route to bacterial invasion into host cells.

CyberPetri at CDX 2016: Real-time Network Situation Awareness

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arendt, Dustin L.; Best, Daniel M.; Burtner, Edwin R.

CyberPetri is a novel visualization technique that provides a flexible map of the network based on available characteristics, such as IP address, operating system, or service. Previous work introduced CyberPetri as a visualization feature in Ocelot, a network defense tool that helped security analysts understand and respond to an active defense scenario. In this paper we present a case study in which we use the CyberPetri visualization technique to support real-time situation awareness during the 2016 Cyber Defense Exercise.

Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets.

PubMed

Koch, Ina; Nöthen, Joachim; Schleiff, Enrico

2017-01-01

Motivation: Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. Nevertheless, the system is not yet fully understood, although many mechanisms are described, and information for many processes exists. However, the combination and interpretation of the large amount of biological data remain a big challenge, not only because data sets for metabolic paths are still incomplete. Moreover, they are often inconsistent, because they are coming from different experiments of various scales, regarding, for example, accuracy and/or significance. Here, theoretical modeling is powerful to formulate hypotheses for pathways and the dynamics of the metabolism, even if the biological data are incomplete. To develop reliable mathematical models they have to be proven for consistency. This is still a challenging task because many verification techniques fail already for middle-sized models. Consequently, new methods, like decomposition methods or reduction approaches, are developed to circumvent this problem. Methods: We present a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana . We used the Petri net formalism to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency we applied concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs. Results: We formulated the core metabolism of Arabidopsis thaliana based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism. By applying network decomposition and reduction techniques at steady-state conditions, we suggest a straightforward mathematical modeling process. We demonstrate that potential steady-state pathways exist, which provide the fixed carbon to

Task planning with uncertainty for robotic systems. Thesis

NASA Technical Reports Server (NTRS)

Cao, Tiehua

1993-01-01

In a practical robotic system, it is important to represent and plan sequences of operations and to be able to choose an efficient sequence from them for a specific task. During the generation and execution of task plans, different kinds of uncertainty may occur and erroneous states need to be handled to ensure the efficiency and reliability of the system. An approach to task representation, planning, and error recovery for robotic systems is demonstrated. Our approach to task planning is based on an AND/OR net representation, which is then mapped to a Petri net representation of all feasible geometric states and associated feasibility criteria for net transitions. Task decomposition of robotic assembly plans based on this representation is performed on the Petri net for robotic assembly tasks, and the inheritance of properties of liveness, safeness, and reversibility at all levels of decomposition are explored. This approach provides a framework for robust execution of tasks through the properties of traceability and viability. Uncertainty in robotic systems are modeled by local fuzzy variables, fuzzy marking variables, and global fuzzy variables which are incorporated in fuzzy Petri nets. Analysis of properties and reasoning about uncertainty are investigated using fuzzy reasoning structures built into the net. Two applications of fuzzy Petri nets, robot task sequence planning and sensor-based error recovery, are explored. In the first application, the search space for feasible and complete task sequences with correct precedence relationships is reduced via the use of global fuzzy variables in reasoning about subgoals. In the second application, sensory verification operations are modeled by mutually exclusive transitions to reason about local and global fuzzy variables on-line and automatically select a retry or an alternative error recovery sequence when errors occur. Task sequencing and task execution with error recovery capability for one and multiple soft

Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension.

PubMed

Li, Chen; Nagasaki, Masao; Koh, Chuan Hock; Miyano, Satoru

2011-05-01

Mathematical modeling and simulation studies are playing an increasingly important role in helping researchers elucidate how living organisms function in cells. In systems biology, researchers typically tune many parameters manually to achieve simulation results that are consistent with biological knowledge. This severely limits the size and complexity of simulation models built. In order to break this limitation, we propose a computational framework to automatically estimate kinetic parameters for a given network structure. We utilized an online (on-the-fly) model checking technique (which saves resources compared to the offline approach), with a quantitative modeling and simulation architecture named hybrid functional Petri net with extension (HFPNe). We demonstrate the applicability of this framework by the analysis of the underlying model for the neuronal cell fate decision model (ASE fate model) in Caenorhabditis elegans. First, we built a quantitative ASE fate model containing 3327 components emulating nine genetic conditions. Then, using our developed efficient online model checker, MIRACH 1.0, together with parameter estimation, we ran 20-million simulation runs, and were able to locate 57 parameter sets for 23 parameters in the model that are consistent with 45 biological rules extracted from published biological articles without much manual intervention. To evaluate the robustness of these 57 parameter sets, we run another 20 million simulation runs using different magnitudes of noise. Our simulation results concluded that among these models, one model is the most reasonable and robust simulation model owing to the high stability against these stochastic noises. Our simulation results provide interesting biological findings which could be used for future wet-lab experiments.

Community pharmacist participation in a practice-based research network: a report from the Medication Safety Research Network of Indiana (Rx-SafeNet).

PubMed

Patel, Puja; Hemmeger, Heather; Kozak, Mary Ann; Gernant, Stephanie A; Snyder, Margie E

2015-01-01

To describe the experiences and opinions of pharmacists serving as site coordinators for the Medication Safety Research Network of Indiana (Rx-SafeNet). Retail chain, independent, and hospital/health system outpatient community pharmacies throughout Indiana, with a total of 127 pharmacy members represented by 26 site coordinators. Rx-SafeNet, a statewide practice-based research network (PBRN) formed in 2010 and administered by the Purdue University College of Pharmacy. Barriers and facilitators to participation in available research studies, confidence participating in research, and satisfaction with overall network communication. 22 of 26 site coordinators participated, resulting in an 85% response rate. Most (72.2%) of the respondents had received a doctor of pharmacy degree, and 13.6% had postgraduate year (PGY)1 residency training. The highest reported benefits of PBRN membership were an enhanced relationship with the Purdue University College of Pharmacy (81% agreed or strongly agreed) and enhanced professional development (80% agreed or strongly agreed). Time constraints were identified as the greatest potential barrier to network participation, reported by 62% of respondents. In addition, the majority (59%) of survey respondents identified no prior research experience. Last, respondents' confidence in performing research appeared to increase substantially after becoming network members, with 43% reporting a lack of confidence in engaging in research before joining the network compared with 90% reporting confidence after joining the network. In general, Rx-SafeNet site coordinators appeared to experience increased confidence in research engagement after joining the network. While respondents identified a number of benefits associated with network participation, concerns about potential time constraints remained a key barrier to participation. These findings will assist network leadership in identifying opportunities to positively increase member participation

Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets

PubMed Central

Koch, Ina; Nöthen, Joachim; Schleiff, Enrico

2017-01-01

Motivation: Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. Nevertheless, the system is not yet fully understood, although many mechanisms are described, and information for many processes exists. However, the combination and interpretation of the large amount of biological data remain a big challenge, not only because data sets for metabolic paths are still incomplete. Moreover, they are often inconsistent, because they are coming from different experiments of various scales, regarding, for example, accuracy and/or significance. Here, theoretical modeling is powerful to formulate hypotheses for pathways and the dynamics of the metabolism, even if the biological data are incomplete. To develop reliable mathematical models they have to be proven for consistency. This is still a challenging task because many verification techniques fail already for middle-sized models. Consequently, new methods, like decomposition methods or reduction approaches, are developed to circumvent this problem. Methods: We present a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana. We used the Petri net formalism to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency we applied concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs. Results: We formulated the core metabolism of Arabidopsis thaliana based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism. By applying network decomposition and reduction techniques at steady-state conditions, we suggest a straightforward mathematical modeling process. We demonstrate that potential steady-state pathways exist, which provide the fixed carbon to

The education on landslides through the "BE-SAFE-NET" web-portal on Disaster Awareness.

NASA Astrophysics Data System (ADS)

Maquaire, O.; Castaldini, D.; Malet, J.-P.; von Elverfeldt, K.; Pla, F.; Soldati, M.; Greco, R.; Pasuto, A.

2009-04-01

The website on Disaster Awareness with the use of the internet "BE-SAFE-NET" is developed within the framework of the FORM-OSE programme (European Training Programme for South, East and West) of the EUR-OPA Major Hazards Agreement, hosted by the European Centre for Disaster Awareness with the use of the internet (BE-SAFE-NET, Nicosia, Cyprus). The website is dedicated for school actors (school-level children, teachers, administrative and technical staff, families and local authorities) in order to: - Inform on regulations, on tools for raising awareness for natural and man-made risks and on preventative measures; - Train children, teachers, administrative and technical staff and local authorities; - Produce interactive figures, photographs, videos and games; - Interact with newsgroups and electronic conferences. Together with the EUR-OPA Centre of Nicosia, the project associates several centres of the Major Hazards Agreement network: the European University for the Cultural Heritage (CUEBC) of Ravello (Italy) the European Centre for Risk Prevention (ECRP) of Sofia (Bulgaria), and the European Centre on Geomorphological Hazards (CERG) of Strasbourg (France). "BE-SAFE-NET" is defined as a network among European countries in order to provide e-learning material on natural hazards and risks primarily for schools (secondary school teachers), but also for the public in general. On the webpage, teachers, pupils and the interested public should find information on disaster prevention, preparation, immediate reaction and rehabilitation. The aim of the paper is to present the structure and the organisation of the web-portal following the pilot project focused on landslides and managed by CERG. Some examples of landslides pedagogical material are also presented. The website is structured in five main sections: 1. About the initiative; 2. Definition of common concepts (e.g. hazard (natural and man made), vulnerability, risk, disaster); 3. Pedagogical material (e.g. case

Wakata performs microscopic analysis of the NanoRacks Module-38 Petri Dishes

NASA Image and Video Library

2014-01-13

ISS038-E-029082 (12 Jan. 2014) --- Japan Aerospace Exploration Agency astronaut Koichi Wakata, Expedition 38 flight engineer, performs microscopic analysis of the NanoRacks Module-38 Petri Dishes, using Celestron Reflective Microscope, in the Kibo laboratory of the International Space Station. These Module-38 experiments are designed by students as part of a competition sponsored by the International Space School Educational Trust (ISSET). This experiment examines three-dimensional growth of slime mold in petri dishes utilizing the NanoRacks Microscopes Facility.

Resource conflict detection and removal strategy for nondeterministic emergency response processes using Petri nets

NASA Astrophysics Data System (ADS)

Zeng, Qingtian; Liu, Cong; Duan, Hua

2016-09-01

Correctness of an emergency response process specification is critical to emergency mission success. Therefore, errors in the specification should be detected and corrected at build-time. In this paper, we propose a resource conflict detection approach and removal strategy for emergency response processes constrained by resources and time. In this kind of emergency response process, there are two timing functions representing the minimum and maximum execution time for each activity, respectively, and many activities require resources to be executed. Based on the RT_ERP_Net, the earliest time to start each activity and the ideal execution time of the process can be obtained. To detect and remove the resource conflicts in the process, the conflict detection algorithms and a priority-activity-first resolution strategy are given. In this way, real execution time for each activity is obtained and a conflict-free RT_ERP_Net is constructed by adding virtual activities. By experiments, it is proved that the resolution strategy proposed can shorten the execution time of the whole process to a great degree.

A New ’Availability-Payment’ Model for Pricing Performance-Based Logistics Contracts

DTIC Science & Technology

2014-04-30

maintenance network connected to the inventory and Original Equipment Manufacturer (OEM) used in this paper. The input to the Petri net in Figure 2 is the...contract structures. The model developed in this paper uses an affine controller to drive a discrete event simulator ( Petri net ) that produces...discrete event simulator ( Petri net ) that produces availability and cost measures. The model is used to explore the optimum availability assessment

An advanced environment for hybrid modeling of biological systems based on modelica.

PubMed

Pross, Sabrina; Bachmann, Bernhard

2011-01-20

Biological systems are often very complex so that an appropriate formalism is needed for modeling their behavior. Hybrid Petri Nets, consisting of time-discrete Petri Net elements as well as continuous ones, have proven to be ideal for this task. Therefore, a new Petri Net library was implemented based on the object-oriented modeling language Modelica which allows the modeling of discrete, stochastic and continuous Petri Net elements by differential, algebraic and discrete equations. An appropriate Modelica-tool performs the hybrid simulation with discrete events and the solution of continuous differential equations. A special sub-library contains so-called wrappers for specific reactions to simplify the modeling process. The Modelica-models can be connected to Simulink-models for parameter optimization, sensitivity analysis and stochastic simulation in Matlab. The present paper illustrates the implementation of the Petri Net component models, their usage within the modeling process and the coupling between the Modelica-tool Dymola and Matlab/Simulink. The application is demonstrated by modeling the metabolism of Chinese Hamster Ovary Cells.

Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension.

PubMed

Li, Chen; Nagasaki, Masao; Ueno, Kazuko; Miyano, Satoru

2009-04-27

Model checking approaches were applied to biological pathway validations around 2003. Recently, Fisher et al. have proved the importance of model checking approach by inferring new regulation of signaling crosstalk in C. elegans and confirming the regulation with biological experiments. They took a discrete and state-based approach to explore all possible states of the system underlying vulval precursor cell (VPC) fate specification for desired properties. However, since both discrete and continuous features appear to be an indispensable part of biological processes, it is more appropriate to use quantitative models to capture the dynamics of biological systems. Our key motivation of this paper is to establish a quantitative methodology to model and analyze in silico models incorporating the use of model checking approach. A novel method of modeling and simulating biological systems with the use of model checking approach is proposed based on hybrid functional Petri net with extension (HFPNe) as the framework dealing with both discrete and continuous events. Firstly, we construct a quantitative VPC fate model with 1761 components by using HFPNe. Secondly, we employ two major biological fate determination rules - Rule I and Rule II - to VPC fate model. We then conduct 10,000 simulations for each of 48 sets of different genotypes, investigate variations of cell fate patterns under each genotype, and validate the two rules by comparing three simulation targets consisting of fate patterns obtained from in silico and in vivo experiments. In particular, an evaluation was successfully done by using our VPC fate model to investigate one target derived from biological experiments involving hybrid lineage observations. However, the understandings of hybrid lineages are hard to make on a discrete model because the hybrid lineage occurs when the system comes close to certain thresholds as discussed by Sternberg and Horvitz in 1986. Our simulation results suggest that: Rule I

An object-oriented description method of EPMM process

NASA Astrophysics Data System (ADS)

Jiang, Zuo; Yang, Fan

2017-06-01

In order to use the object-oriented mature tools and language in software process model, make the software process model more accord with the industrial standard, it’s necessary to study the object-oriented modelling of software process. Based on the formal process definition in EPMM, considering the characteristics that Petri net is mainly formal modelling tool and combining the Petri net modelling with the object-oriented modelling idea, this paper provides this implementation method to convert EPMM based on Petri net into object models based on object-oriented description.

Analysis hierarchical model for discrete event systems

NASA Astrophysics Data System (ADS)

Ciortea, E. M.

2015-11-01

The This paper presents the hierarchical model based on discrete event network for robotic systems. Based on the hierarchical approach, Petri network is analysed as a network of the highest conceptual level and the lowest level of local control. For modelling and control of complex robotic systems using extended Petri nets. Such a system is structured, controlled and analysed in this paper by using Visual Object Net ++ package that is relatively simple and easy to use, and the results are shown as representations easy to interpret. The hierarchical structure of the robotic system is implemented on computers analysed using specialized programs. Implementation of hierarchical model discrete event systems, as a real-time operating system on a computer network connected via a serial bus is possible, where each computer is dedicated to local and Petri model of a subsystem global robotic system. Since Petri models are simplified to apply general computers, analysis, modelling, complex manufacturing systems control can be achieved using Petri nets. Discrete event systems is a pragmatic tool for modelling industrial systems. For system modelling using Petri nets because we have our system where discrete event. To highlight the auxiliary time Petri model using transport stream divided into hierarchical levels and sections are analysed successively. Proposed robotic system simulation using timed Petri, offers the opportunity to view the robotic time. Application of goods or robotic and transmission times obtained by measuring spot is obtained graphics showing the average time for transport activity, using the parameters sets of finished products. individually.

Industry Strength Tool and Technology for Automated Synthesis of Safety-Critical Applications from Formal Specifications

DTIC Science & Technology

2015-11-01

28 2.3.4 Input/Output Automata ...various other modeling frameworks such as I/O Automata , Kahn Process Networks, Petri-nets, Multi-dimensional SDF, etc. are also used for designing...Formal Ideally suited to model DSP applications 3 Petri Nets Graphical Formal Used for modeling distributed systems 4 I/O Automata Both Formal

Evaluation of sunlight-exposed pyrethroid-treated netting for the control of face fly and housefly (Diptera: Muscidae).

PubMed

Peck, George W; Ferguson, Holly J; LePage, Jane T; Hebert, Vincent R; O'Neal, Sally D; Walsh, Douglas B

2014-01-01

Face flies, Musca autumnalis De Geer (Diptera: Muscidae), and houseflies, Musca domestica L. (Diptera: Muscidae), have a significant impact on livestock and dairy production throughout North America. Pyrethroid insecticide efficacy can be affected by exposure to direct sunlight, and the rate of photodegradation is substrate and formulation dependent. Insecticide-treated netting (ITN) is finding new applications in crop and livestock production systems. A baseline study using long-duration no-choice assays has been carried out to gauge the effectiveness of ITN treated with β-cyfluthrin, λ-cyhalothrin and bifenthrin on face flies and houseflies. After 12 weeks in direct sunlight, ITN treated with β-cyfluthrin was still highly insecticidal to face flies and houseflies, producing 100% mortality in petri dish assays. However, sunlight reduced the insecticidal activity of λ-cyhalothrin, with 3% of face flies and 50% of houseflies surviving after exposure to ITN that had been deployed for 10 weeks. Insecticidal activity was greatly reduced on bifenthrin-treated netting, with 20% of face flies and 50% of houseflies surviving in assays with netting deployed for only 3 weeks. With careful choice of the pyrethroid applied, treated netting could be an important component of livestock integrated pest management programs focused on sustainable practices. © 2013 Society of Chemical Industry.

Microstamped Petri Dishes for Scanning Electrochemical Microscopy Analysis of Arrays of Microtissues

PubMed Central

Sridhar, Adithya; de Boer, Hans L.; van den Berg, Albert; Le Gac, Séverine

2014-01-01

While scanning electrochemical microscopy (SECM) is a powerful technique for non-invasive analysis of cells, SECM-based assays remain scarce and have been mainly limited so far to single cells, which is mostly due to the absence of suitable platform for experimentation on 3D cellular aggregates or microtissues. Here, we report stamping of a Petri dish with a microwell array for large-scale production of microtissues followed by their in situ analysis using SECM. The platform is realized by hot embossing arrays of microwells (200 μm depth; 400 μm diameter) in commercially available Petri dishes, using a PDMS stamp. Microtissues form spontaneously in the microwells, which is demonstrated here using various cell lines (e.g., HeLa, C2C12, HepG2 and MCF-7). Next, the respiratory activity of live HeLa microtissues is assessed by monitoring the oxygen reduction current in constant height mode and at various distances above the platform surface. Typically, at a 40 μm distance from the microtissue, a 30% decrease in the oxygen reduction current is measured, while above 250 μm, no influence of the presence of the microtissues is detected. After exposure to a model drug (50% ethanol), no such changes in oxygen concentration are found at any height in solution, which reflects that microtissues are not viable anymore. This is furthermore confirmed using conventional live/dead fluorescent stains. This live/dead assay demonstrates the capability of the proposed approach combining SECM and microtissue arrays formed in a stamped Petri dish for conducting cellular assays in a non-invasive way on 3D cellular models. PMID:24690887

Modeling of wastewater treatment system of car parks from petroleum products

NASA Astrophysics Data System (ADS)

Savdur, S. N.; Stepanova, Yu V.; Kodolova, I. A.; Fesina, E. L.

2018-05-01

The paper discusses the technological complex of wastewater treatment of car parks from petroleum products. Based on the review of the main modeling methods of discrete-continuous chemical and engineering processes, it substantiates expediency of using the theory of Petri nets (PN) for modeling the process of wastewater treatment of car parks from petroleum products. It is proposed to use a modification of Petri nets which is focused on modeling and analysis of discrete-continuous chemical and engineering processes by prioritizing transitions, timing marks in positions and transitions. A model in the form of modified Petri nets (MPN) is designed. A software package to control the process for wastewater treatment is designed by means of SCADA TRACE MODE.

Modelling and analysis of workflow for lean supply chains

NASA Astrophysics Data System (ADS)

Ma, Jinping; Wang, Kanliang; Xu, Lida

2011-11-01

Cross-organisational workflow systems are a component of enterprise information systems which support collaborative business process among organisations in supply chain. Currently, the majority of workflow systems is developed in perspectives of information modelling without considering actual requirements of supply chain management. In this article, we focus on the modelling and analysis of the cross-organisational workflow systems in the context of lean supply chain (LSC) using Petri nets. First, the article describes the assumed conditions of cross-organisation workflow net according to the idea of LSC and then discusses the standardisation of collaborating business process between organisations in the context of LSC. Second, the concept of labelled time Petri nets (LTPNs) is defined through combining labelled Petri nets with time Petri nets, and the concept of labelled time workflow nets (LTWNs) is also defined based on LTPNs. Cross-organisational labelled time workflow nets (CLTWNs) is then defined based on LTWNs. Third, the article proposes the notion of OR-silent CLTWNS and a verifying approach to the soundness of LTWNs and CLTWNs. Finally, this article illustrates how to use the proposed method by a simple example. The purpose of this research is to establish a formal method of modelling and analysis of workflow systems for LSC. This study initiates a new perspective of research on cross-organisational workflow management and promotes operation management of LSC in real world settings.

Distributed intelligent scheduling of FMS

NASA Astrophysics Data System (ADS)

Wu, Zuobao; Cheng, Yaodong; Pan, Xiaohong

1995-08-01

In this paper, a distributed scheduling approach of a flexible manufacturing system (FMS) is presented. A new class of Petri nets called networked time Petri nets (NTPN) for system modeling of networking environment is proposed. The distributed intelligent scheduling is implemented by three schedulers which combine NTPN models with expert system techniques. The simulation results are shown.

Modeling integrated cellular machinery using hybrid Petri-Boolean networks.

PubMed

Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay

2013-01-01

The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM) that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them using such more

Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks

PubMed Central

Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay

2013-01-01

The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM) that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them using such more

Petri-Net Simulations of Communications Networks.

DTIC Science & Technology

1980-03-01

place, althcugh in reality they may be buried several deep. As the total network is conceptualized by the user. he irust betin by mappinp out all oripins...8217 . (choCk~mahes(z*11)!1𔃺’) 957 ockt2(x,y,’nark-,colour);’I 95 elsef 960 if((check~namesrz.Il 1:’) rt(xl405.(v2i"mr) 134 traflloraph.c PaQ * 17 Fri Feb 8...Iaxnctrk+*) l0g0 intbl1.; 164 lirnkgrach.c paq * 19 Fri Feb 8 07:0q:45 1980 1081 in (k[) miot I Iintbi I; 10(42 1 1083 iawoutctr:iolr,1(outtb1l; 1084

Nano Petri dishes: a new polystyrene platform for studying cell-nanoengineered surface interactions

NASA Astrophysics Data System (ADS)

Cha, Kyoung Je; Na, Moon-Hee; Kim, Hyung Woo; Kim, Dong Sung

2014-05-01

In this study, we fabricated and fully characterized a new type of polystyrene (PS) cell-culture platform containing nanoengineered surfaces (NES), referred to as a nano Petri dish, which can be used at the transition stage of basic cell-NES interaction studies for clinical applications. Nano-injection molding in this study was used for the mass production of the nano Petri dish having nanopore arrays. The effects of processing parameters of the injection molding on the replication quality of the nanopore arrays were quantitatively evaluated by means of design of experiments based on the Taguchi method. This allowed efficient and reliable cell culture studies by providing large numbers of the same dishes, in addition to removing the fixation step of the NES plates inside the cell-culture container. Physical, chemical and mechanical properties of the NES, as well as cell behavior including attachment and proliferation of human osteosarcoma MG-63 cells on the NES, were then characterized, with and without the oxygen plasma surface treatment.

Formalization, implementation, and modeling of institutional controllers for distributed robotic systems.

PubMed

Pereira, José N; Silva, Porfírio; Lima, Pedro U; Martinoli, Alcherio

2014-01-01

The work described is part of a long term program of introducing institutional robotics, a novel framework for the coordination of robot teams that stems from institutional economics concepts. Under the framework, institutions are cumulative sets of persistent artificial modifications made to the environment or to the internal mechanisms of a subset of agents, thought to be functional for the collective order. In this article we introduce a formal model of institutional controllers based on Petri nets. We define executable Petri nets-an extension of Petri nets that takes into account robot actions and sensing-to design, program, and execute institutional controllers. We use a generalized stochastic Petri net view of the robot team controlled by the institutional controllers to model and analyze the stochastic performance of the resulting distributed robotic system. The ability of our formalism to replicate results obtained using other approaches is assessed through realistic simulations of up to 40 e-puck robots. In particular, we model a robot swarm and its institutional controller with the goal of maintaining wireless connectivity, and successfully compare our model predictions and simulation results with previously reported results, obtained by using finite state automaton models and controllers.

A Design Verification of the Parallel Pipelined Image Processings

NASA Astrophysics Data System (ADS)

Wasaki, Katsumi; Harai, Toshiaki

2008-11-01

This paper presents a case study of the design and verification of a parallel and pipe-lined image processing unit based on an extended Petri net, which is called a Logical Colored Petri net (LCPN). This is suitable for Flexible-Manufacturing System (FMS) modeling and discussion of structural properties. LCPN is another family of colored place/transition-net(CPN) with the addition of the following features: integer value assignment of marks, representation of firing conditions as marks' value based formulae, and coupling of output procedures with transition firing. Therefore, to study the behavior of a system modeled with this net, we provide a means of searching the reachability tree for markings.

STS-93 MS Tognini checks the BRIC experiment petri dishes on the middeck

NASA Image and Video Library

2013-11-18

STS093-350-008 (22-27 July 1999) --- Astronaut Michel Tognini, mission specialist representing France’s Centre National d’Etudes Spatiales (CNES), checks the Biological Research in Canisters (BRIC) payload petri dishes on the mid deck of the Space Shuttle Columbia. BRIC was designed to investigate the effects of space flight on small arthropod animals and plant specimens.

A New Availability-Payment Model for Pricing Performance-Based Logistics Contracts

DTIC Science & Technology

2014-05-01

Petri   net ) is used to  capture concurrency and  synchronization...properties of the  system. Petri   Net Available IN 1`A failure indication IN Down Repair Shop IN Down Replace Order IN Replace Order U costs PC (1,2) time...action (expTime(50*w)); INT Repairs AV Replaces AV AV av.req AV DOWNTIME 0 INT 0 INT Manufacturer Quantity Inventory 5 Quantity stock Cost Book

A Method to Preclude Moisture Condensation in Plated Tissue Cultures

Treesearch

Alex M. Diner

1992-01-01

Excessive condensate normally accumulates in in vitro-illuminated petri dishes containing plant tissue cultures, causing avariety of problems. A dark-colored rubber net-mesh placed over the petri dishes prevented such condensation, even when charcoal-supplemented media are used under high light intensity in a growth chamber.

Multi-tasking arbitration and behaviour design for human-interactive robots

NASA Astrophysics Data System (ADS)

Kobayashi, Yuichi; Onishi, Masaki; Hosoe, Shigeyuki; Luo, Zhiwei

2013-05-01

Robots that interact with humans in household environments are required to handle multiple real-time tasks simultaneously, such as carrying objects, collision avoidance and conversation with human. This article presents a design framework for the control and recognition processes to meet these requirements taking into account stochastic human behaviour. The proposed design method first introduces a Petri net for synchronisation of multiple tasks. The Petri net formulation is converted to Markov decision processes and processed in an optimal control framework. Three tasks (safety confirmation, object conveyance and conversation) interact and are expressed by the Petri net. Using the proposed framework, tasks that normally tend to be designed by integrating many if-then rules can be designed in a systematic manner in a state estimation and optimisation framework from the viewpoint of the shortest time optimal control. The proposed arbitration method was verified by simulations and experiments using RI-MAN, which was developed for interactive tasks with humans.

Gods, Germs, and Petri Dishes: Toward a Nonsecular Medical Anthropology.

PubMed

Roberts, Elizabeth F S

2016-01-01

This commentary calls on medical anthropology to become programmatically non-secular. Despite recent anthropological critiques of secularity, within and outside of anthropology, most contemporary medical anthropologists continue to leave deities and religiosity out of their examinations of healing practices, especially in their accounts of biomedicine. Through a critical, relational constructionist lens, which traces how all entities are both constructed and real, a non-secular medical anthropology would insist that when deities are part of medical practice, they are integral to analysis. Importantly then, within the symmetrical nature of this same constructionist lens, biomedical entities like germs and petri dishes need to be accounted for just as much as deities.

Extension of the lower bound of monitor solutions of maximally permissive supervisors to non-α net systems

NASA Astrophysics Data System (ADS)

Wu, W. H.; Chao, D. Y.

2016-07-01

Traditional region-based liveness-enforcing supervisors focus on (1) maximal permissiveness of not losing legal states, (2) structural simplicity of minimal number of monitors, and (3) fast computation. Lately, a number of similar approaches can achieve minimal configuration using efficient linear programming. However, it is unclear as to the relationship between the minimal configuration and the net structure. It is important to explore the structures involved for the fewest monitors required. Once the lower bound is achieved, further iteration to merge (or reduce the number of) monitors is not necessary. The minimal strongly connected resource subnet (i.e., all places are resources) that contains the set of resource places in a basic siphon is an elementary circuit. Earlier, we showed that the number of monitors required for liveness-enforcing and maximal permissiveness equals that of basic siphons for a subclass of Petri nets modelling manufacturing, called α systems. This paper extends this to systems more powerful than the α one so that the number of monitors in a minimal configuration remains to be lower bounded by that of basic siphons. This paper develops the theory behind and shows examples.

Executable Architecture Modeling and Simulation Based on fUML

DTIC Science & Technology

2014-06-01

SoS behaviors. Wang et al.[9] use SysML sequence diagram to model the behaviors and translate the models into Colored Petri Nets (CPN). Staines T.S...Renzhong and Dagli C H. An executable system architecture approach to discrete events system modeling using SysML in conjunction with colored Petri

Shuttle Net, Tuna Net

NASA Technical Reports Server (NTRS)

1983-01-01

Rockwell International, NASA's prime contractor for the Space Shuttle, asked West Coast Netting (WCN) to develop a safety net for personnel working on the Shuttle Orbiter. This could not be an ordinary net, it had to be relatively small, yet have extraordinary tensile strength. It also had to be fire resistant and resistant to ultraviolet (UV) light. After six months, WCN found the requisite fiber, a polyester-like material called NOMEX. The company was forced to invent a more sophisticated twisting process since conventional methods did not approach specified breaking strength. The resulting product, the Hyperester net, sinks faster and fishes deeper, making it attractive to fishing fleets. A patented treatment for UV protection and greater abrasion resistance make Hyperester nets last longer, and the no-shrink feature is an economic bonus.

Helminth.net: expansions to Nematode.net and an introduction to Trematode.net

PubMed Central

Martin, John; Rosa, Bruce A.; Ozersky, Philip; Hallsworth-Pepin, Kymberlie; Zhang, Xu; Bhonagiri-Palsikar, Veena; Tyagi, Rahul; Wang, Qi; Choi, Young-Jun; Gao, Xin; McNulty, Samantha N.; Brindley, Paul J.; Mitreva, Makedonka

2015-01-01

Helminth.net (http://www.helminth.net) is the new moniker for a collection of databases: Nematode.net and Trematode.net. Within this collection we provide services and resources for parasitic roundworms (nematodes) and flatworms (trematodes), collectively known as helminths. For over a decade we have provided resources for studying nematodes via our veteran site Nematode.net (http://nematode.net). In this article, (i) we provide an update on the expansions of Nematode.net that hosts omics data from 84 species and provides advanced search tools to the broad scientific community so that data can be mined in a useful and user-friendly manner and (ii) we introduce Trematode.net, a site dedicated to the dissemination of data from flukes, flatworm parasites of the class Trematoda, phylum Platyhelminthes. Trematode.net is an independent component of Helminth.net and currently hosts data from 16 species, with information ranging from genomic, functional genomic data, enzymatic pathway utilization to microbiome changes associated with helminth infections. The databases’ interface, with a sophisticated query engine as a backbone, is intended to allow users to search for multi-factorial combinations of species’ omics properties. This report describes updates to Nematode.net since its last description in NAR, 2012, and also introduces and presents its new sibling site, Trematode.net. PMID:25392426

Field measurements of dry deposition to spruce foliage and petri dishes in the Black Forest, F.R.G.

USGS Publications Warehouse

Shanley, J.B.

1989-01-01

Dry deposition fluxes Ca2+, Mg2+, K+, Mn2+, Pb2+ and SO42- to spruce foliage and petri dishes were measured in two high-elevation sites (>900 m) in the southern Black Forest, F.R.G., during 12 periods (2-7 days, each) from mid-September to mid-November, 1983, In situ extraction of deposited material from small spruce branches allowed repeated use of the same foliar collecting surfaces for a direct comparison of deposition between periods. Fluxes were corrected for leaching of internally cycled constituents using factors determined from serial extraction experiments. The ratio of flux to petri dishes vs foliage (P/F) was >1.0 for Ca2+, Pb2+ and SO42-, and somewhat 900 m) in the southern Black Forest, F.R.G., during 12 periods (2-7 days, each) from mid-September to mid-November, 1983. The ratio of flux to petri dishes vs foliage (P/F) was >1.0 for Ca2+, Pb2+, and SO42-, and somewhat <1.0 but more constant for Mg2+. Temporal variations in dry deposition fluxes at an exposed site near the industrialized Rhine Valley correlated with variations in total air particulate concentrations at a nearby air quality station. Deposition rates were comparable in magnitude but different in temporal pattern at a remote site in the Black Forest interior. Fluxes at each site reached a minimum during the period of 4-9 November when a regional air inversion confined pollutants to the Rhine Valley below the study sites. High fluxes accompanied the inversion break-up.

A suspended dive-net technique for catching territorial divers

USGS Publications Warehouse

Uher-Koch, Brian D.; Rizzolo, Daniel; Wright, Kenneth G.; Schmutz, Joel A.

2016-01-01

A variety of methods such as night-lighting and lift nets have been used to catch divers (Gavidae), although 24-hour daylight in the Arctic summer and the remote nature of field sites can make the use of these traditional methods impossible. Our research required capture of adult divers at remote locations in northern Alaska. Here we describe a suspended dive-net technique that we used to safely capture territorial White-billed Gavia adamsii and Pacific Divers G. pacifica and that is lightweight and easy to set up. We also were able to capture divers with chicks, and failed breeders, and suggest that this method could be used to catch other territorial aquatic diving birds, especially other diver species.

Microscale Chemistry in a Plastic Petri Dish: Preparation and Chemical Properties of Chlorine Gas

NASA Astrophysics Data System (ADS)

Choi, Martin M. F.

2002-08-01

This experiment demonstrates some of the chemistry of chlorine on a microscale, about the size of a water droplet. Chlorine gas was prepared from an acidified bleach solution in a plastic petri dish. The chlorine gas generated in situ reacted with other chemical reagents in the dish by diffusion. Some of the oxidizing properties and bleaching power of chlorine gas were shown visually and could be observed within 10 minutes. These experiments provide suitable hands-on experience for students at secondary-school level.

Working towards an international consensus on criteria for assessing internet gaming disorder: a critical commentary on Petry et al. (2014)

PubMed Central

GRIFFITHS, MARK D.; VAN ROOIJ, ANTONIUS J.; KARDEFELT-WINTHER, DANIEL; STARCEVIC, VLADAN; KIRÁLY, ORSOLYA; PALLESEN, STÅLE; MÜLLER, KAI; DREIER, MICHAEL; CARRAS, MICHELLE; PRAUSE, NICOLE; KING, DANIEL L.; ABOUJAOUDE, ELLIAS; KUSS, DARIA J.; PONTES, HALLEY M.; FERNANDEZ, OLATZ LOPEZ; NAGYGYORGY, KATALIN; ACHAB, SOPHIA; BILLIEUX, JOËL; QUANDT, THORSTEN; CARBONELL, XAVIER; FERGUSON, CHRISTOPHER J.; HOFF, RANI A.; DEREVENSKY, JEFFREY; HAAGSMA, MARIA C.; DELFABBRO, PAUL; COULSON, MARK; HUSSAIN, ZAHEER; DEMETROVICS, ZSOLT

2017-01-01

This commentary paper critically discusses the recent debate paper by Petry et al. (2014) that argued there was now an international consensus for assessing Internet Gaming Disorder (IGD). Our collective opinions vary considerably regarding many different aspects of online gaming. However, we contend that the paper by Petry and colleagues does not provide a true and representative international community of researchers in this area. This paper critically discusses and provides commentary on (i) the representativeness of the international group that wrote the ‘consensus’ paper, and (ii) each of the IGD criteria. The paper also includes a brief discussion on initiatives that could be taken to move the field towards consensus. It is hoped that this paper will foster debate in the IGD field and lead to improved theory, better methodologically designed studies, and more robust empirical evidence as regards problematic gaming and its psychosocial consequences and impact. PMID:26669530

Methodology for automating software systems

NASA Technical Reports Server (NTRS)

Moseley, Warren

1990-01-01

Applying ITS technology to the shuttle diagnostics would not require the rigor of the Petri Net representation, however it is important in providing the animated simulated portion of the interface and the demands placed on the system to support the training aspects to have a homogeneous and consistent underlying knowledge representation. By keeping the diagnostic rule base, the hardware description, the software description, user profiles, desired behavioral knowledge, and the user interface in the same notation, it is possible to reason about the all of the properties of petri nets, on any selected portion of the simulation. This reasoning provides foundation for utilization of intelligent tutoring systems technology.

Why the Eurocontrol Safety Regulation Commission Policy on Safety Nets and Risk Assessment is Wrong

NASA Astrophysics Data System (ADS)

Brooker, Peter

2004-05-01

Current Eurocontrol Safety Regulation Commission (SRC) policy says that the Air Traffic Management (ATM) system (including safety minima) must be demonstrated through risk assessments to meet the Target Level of Safety (TLS) without needing to take safety nets (such as Short Term Conflict Alert) into account. This policy is wrong. The policy is invalid because it does not build rationally and consistently from ATM's firm foundations of TLS and hazard analysis. The policy is bad because it would tend to retard safety improvements. Safety net policy must rest on a clear and rational treatment of integrated ATM system safety defences. A new safety net policy, appropriate to safe ATM system improvements, is needed, which recognizes that safety nets are an integrated part of ATM system defences. The effects of safety nets in reducing deaths from mid-air collisions should be fully included in hazard analysis and safety audits in the context of the TLS for total system design.

Horizontal ichthyoplankton tow-net system with unobstructed net opening

USGS Publications Warehouse

Nester, Robert T.

1987-01-01

The larval fish sampler described here consists of a modified bridle, frame, and net system with an obstruction-free net opening and is small enough for use on boats 10 m or less in length. The tow net features a square net frame attached to a 0.5-m-diameter cylinder-on-cone plankton net with a bridle designed to eliminate all obstructions forward of the net opening, significantly reducing currents and vibrations in the water directly preceding the net. This system was effective in collecting larvae representing more than 25 species of fish at sampling depths ranging from surface to 10 m and could easily be used at greater depths.

Basic characteristics and realization of production system control

NASA Astrophysics Data System (ADS)

Cheng, Shaopeng; Shell, Richard; Hall, Ernest L.

1992-11-01

This paper analyzes the issues involved in developing an intelligent production control system. It describes the basic characteristics of a production control system and an effective design methodology to realize the production control functions. Petri net, subsystem and hierarchical control concepts are applied to a computer integrated material handling system (MHS). Some communication and interface requirements of the MHS are also considered in this paper. The control system solution is illustrated with an actual MHS operation case which indicates that a truly flexible and integrated production system can be realized with a Petri net operation model and a hierarchical control structure. The significance of this work is related to the different operation testing and evaluation requirements encountered in manufacturing.

VizieR Online Data Catalog: Catalog of Hγ measures (Petrie+ 1973)

NASA Astrophysics Data System (ADS)

Petrie, R. M.; Crampton, D.; Leir, A. Younger F.

2016-02-01

The catalog is a compilation of equivalent widths of H-γ for early-type stars, not only from published material but also from the numerous card files kept by R.M. Petrie. The luminosities of early-type stars through the measurement of the equivalent width of H-γ are relatively precise, although the early work was hampered by systematic errors in the absolute magnitude calibrations. In a number of cases, the values of the equivalent width for a given star differ slightly from publication to publication. There are three possible reasons for this: 1) The later publications may include measurements of additional spectra; 2) in some cases the values were included in the average; 3) some initial measures had not included the extremities of the very extensive wings of H-γ in the spectra of A stars. (2 data files).

Materials Research of Novel Organic Piezoelectric/Ferroelectric Compounds at a H.S.I

DTIC Science & Technology

2015-07-06

analysis 4. http://wavefun.com 5. MOPAC2012, James J. P. Stewart, Stewart Computational Chemistry, Colorado Springs, CO, USA, HTTP://OpenMOPAC. net ... petri dish of mineral oil (to prevent electrical arcing) ripples in the mineral oil are clearly visible when a voltage is applied to the sample. We...acid. It does not appear to be ferroelectric. However, it is piezoelectric. When placed in a petri dish of mineral oil (to prevent electrical arcing

NetCDF-U - Uncertainty conventions for netCDF datasets

NASA Astrophysics Data System (ADS)

Bigagli, Lorenzo; Nativi, Stefano; Domenico, Ben

2013-04-01

To facilitate the automated processing of uncertain data (e.g. uncertainty propagation in modeling applications), we have proposed a set of conventions for expressing uncertainty information within the netCDF data model and format: the NetCDF Uncertainty Conventions (NetCDF-U). From a theoretical perspective, it can be said that no dataset is a perfect representation of the reality it purports to represent. Inevitably, errors arise from the observation process, including the sensor system and subsequent processing, differences in scales of phenomena and the spatial support of the observation mechanism, lack of knowledge about the detailed conversion between the measured quantity and the target variable. This means that, in principle, all data should be treated as uncertain. The most natural representation of an uncertain quantity is in terms of random variables, with a probabilistic approach. However, it must be acknowledged that almost all existing data resources are not treated in this way. Most datasets come simply as a series of values, often without any uncertainty information. If uncertainty information is present, then it is typically within the metadata, as a data quality element. This is typically a global (dataset wide) representation of uncertainty, often derived through some form of validation process. Typically, it is a statistical measure of spread, for example the standard deviation of the residuals. The introduction of a mechanism by which such descriptions of uncertainty can be integrated into existing geospatial applications is considered a practical step towards a more accurate modeling of our uncertain understanding of any natural process. Given the generality and flexibility of the netCDF data model, conventions on naming, syntax, and semantics have been adopted by several communities of practice, as a means of improving data interoperability. Some of the existing conventions include provisions on uncertain elements and concepts, but, to our

Successful Implantation of a Left Ventricular Assist Device After Treatment With the Paracor HeartNet.

PubMed

Schweiger, Martin; Stepanenko, Alexander; Potapov, Evgenji; Drews, Thorsten; Hetzer, Roland; Krabatsch, Thomas

2010-01-01

The Paracor HeartNet, a ventricular constraint device for the treatment of heart failure (HF), is implanted through a left lateral thoracotomy. It envelopes the heart like a mesh "bag." This method of application raises the question of whether adhesions with the pericardium allow the safe implantation of a left ventricular assist device (LVAD) if HF worsens. A male patient who had undergone implantation of the Paracor HeartNet 42 months earlier presented with advanced HF for cardiac transplantation. The patient's condition deteriorated, and because no suitable organ for transplantation was available, implantation of an LVAD became necessary. Surgery was performed via a median sternotomy without complications. No severe adhesions were found. This is the first report on "how to do" LVAD implantation after Paracor HeartNet implantation with images and information about cutting the constraint. Because the Paracor HeartNet is "wrapped" around the heart, concerns persist that severe adhesions with the pericardium might occur. In this case, LVAD implantation after therapy with the Paracor HeartNet was without complications, and the expected massive adhesions were absent.

Monetary benefits of preventing childhood lead poisoning with lead-safe window replacement.

PubMed

Nevin, Rick; Jacobs, David E; Berg, Michael; Cohen, Jonathan

2008-03-01

Previous estimates of childhood lead poisoning prevention benefits have quantified the present value of some health benefits, but not the costs of lead paint hazard control or the benefits associated with housing and energy markets. Because older housing with lead paint constitutes the main exposure source today in the US, we quantify health benefits, costs, market value benefits, energy savings, and net economic benefits of lead-safe window replacement (which includes paint stabilization and other measures). The benefit per resident child from improved lifetime earnings alone is $21,195 in pre-1940 housing and $8685 in 1940-59 housing (in 2005 dollars). Annual energy savings are $130-486 per housing unit, with or without young resident children, with an associated increase in housing market value of $5900-14,300 per housing unit, depending on home size and number of windows replaced. Net benefits are $4490-5,629 for each housing unit built before 1940, and $491-1629 for each unit built from 1940-1959, depending on home size and number of windows replaced. Lead-safe window replacement in all pre-1960 US housing would yield net benefits of at least $67 billion, which does not include many other benefits. These other benefits, which are shown in this paper, include avoided Attention Deficit Hyperactivity Disorder, other medical costs of childhood lead exposure, avoided special education, and reduced crime and juvenile delinquency in later life. In addition, such a window replacement effort would reduce peak demand for electricity, carbon emissions from power plants, and associated long-term costs of climate change.

Initial Results from the Micro-pulse Lidar Network (MPL-Net)

NASA Technical Reports Server (NTRS)

Welton, Ellsworth J.; Campbell, James R.; Berkoff, Timothy A.; Spinhirne, James D.; Ginoux, Paul; Starr, David OC. (Technical Monitor)

2001-01-01

The micro-pulse lidar system (MPL) was developed in the early 1990s and was the first small, eye-safe, and autonomous lidar built for full time monitoring of cloud and aerosol vertical distributions. In 2000, a new project using MPL systems was started at NASA Goddard Space Flight Center. This new project, the Micro-pulse Lidar Network or MPL-Net, was created to provide long-term observations of aerosol and cloud vertical profiles at key sites around the world. This is accomplished using both NASA operated sites and partnerships with other organizations owning MPL systems. The MPL-Net sites are co-located with NASA AERONET sunphotometers to provide aerosol optical depth data needed for calibration of the MPL. In addition to the long-term sites, MPL-Net provides lidar support for a limited number of field experiments and ocean cruises each year. We will present an overview of the MPL-Net project and show initial results from the first two MPL-Net sites at the South Pole and at Goddard Space Flight Center. Observations of dust layers transported from the Gobi desert, across the Pacific Ocean, to the east coast of the United States will also be shown. MPL-Net affiliated instruments were in place at the desert source region in China, on a research vessel in the Sea of Japan, at ARM sites in Alaska and Oklahoma, and finally at our home site in Maryland (GSFC) during the massive dust storms that occurred in April 2001. The MPL observations of dust layers at each location are shown in comparison to dust layers predicted using the Georgia Tech/Goddard Global Ozone Chemistry Aerosol Radiation and Transport model (GOCART). Finally, the MPL-Net project is the primary ground-validation program for the Geo-Science Laser Altimeter System (GLAS) satellite lidar project (launch date 2002). We will present an overview demonstrating how MPL-Net results are used to help prepare the GLAS data processing algorithms and assist in the calibration/validation of the GLAS data products.

Initial Results From The Micro-pulse Lidar Network (MPL-Net)

NASA Astrophysics Data System (ADS)

Welton, E. J.; Campbell, J. R.; Berkoff, T. A.; Spinhirne, J. D.; Ginoux, P.

2001-12-01

The micro-pulse lidar system (MPL) was developed in the early 1990s and was the first small, eye-safe, and autonomous lidar built for fulltime monitoring of cloud and aerosol vertical distributions. In 2000, a new project using MPL systems was started at NASA Goddard Space Flight Center. This new project, the Micro-pulse Lidar Network or MPL-Net, was created to provide long-term observations of aerosol and cloud vertical profiles at key sites around the world. This is accomplished using both NASA operated sites and partnerships with other organizations owning MPL systems. The MPL-Net sites are co-located with NASA AERONET sunphotometers to provide aerosol optical depth data needed for calibration of the MPL. In addition to the long-term sites, MPL-Net provides lidar support for a limited number of field experiments and ocean cruises each year. We will present an overview of the MPL-Net project and show initial results from the first two MPL-Net sites at the South Pole and at Goddard Space Flight Center. Observations of dust layers transported from the desert regions of China, across the Pacific Ocean, to the east coast of the United States will also be shown. MPL-Net affiliated instruments were in place at the desert source region in China, on a research vessel in the Sea of Japan, at ARM sites in Alaska and Oklahoma, and finally at our home site in Maryland (GSFC) during the massive dust storms that occurred in April 2001. The MPL observations of dust layers at each location are shown in comparison to dust layers predicted using the Georgia Tech/Goddard Global Ozone Chemistry Aerosol Radiation and Transport model (GOCART). Finally, the MPL-Net project is the primary ground-validation program for the Geo-Science Laser Altimeter System (GLAS) satellite lidar project (launch date 2002). We will present an overview demonstrating how MPL-Net results are used to help prepare the GLAS data processing algorithms and assist in the calibration/validation of the GLAS data

Research and realization of info-net security controlling system

NASA Astrophysics Data System (ADS)

Xu, Tao; Zhang, Wei; Li, Xuhong; Wang, Xia; Pan, Wenwen

2017-03-01

The thesis introduces some relative concepts about Network Cybernetics, and we design and realize a new info-net security controlling system based on Network Cybernetics. The system can control the endpoints, safely save files, encrypt communication, supervise actions of users and show security conditions, in order to realize full-scale security management. At last, we simulate the functions of the system. The results show, the system can ensure the controllability of users and devices, and supervise them real-time. The system can maximize the security of the network and users.

Safe sex

MedlinePlus

... sex; Sexually transmitted - safe sex; GC - safe sex; Gonorrhea - safe sex; Herpes - safe sex; HIV - safe sex; ... contact. STIs include: Chlamydia Genital herpes Genital warts Gonorrhea Hepatitis HIV HPV Syphilis STIs are also called ...

Net one, net two: the primary care network income statement.

PubMed

Halley, M D; Little, A W

1999-10-01

Although hospital-owned primary care practices have been unprofitable for most hospitals, some hospitals are achieving competitive advantage and sustainable practice operations. A key to the success of some has been a net income reporting tool that separates practice operating expenses from the costs of creating and operating a network of practices to help healthcare organization managers, physicians, and staff to identify opportunities to improve the network's financial performance. This "Net One, Net Two" reporting allows operations leadership to be held accountable for Net One expenses and strategic leadership to be held accountable for Net Two expenses.

A proposal of an architecture for the coordination level of intelligent machines

NASA Technical Reports Server (NTRS)

Beard, Randall; Farah, Jeff; Lima, Pedro

1993-01-01

The issue of obtaining a practical, structured, and detailed description of an architecture for the Coordination Level of Center for Intelligent Robotic Systems for Sapce Exploration (CIRSSE) Testbed Intelligent Controller is addressed. Previous theoretical and implementation works were the departure point for the discussion. The document is organized as follows: after this introductory section, section 2 summarizes the overall view of the Intelligent Machine (IM) as a control system, proposing a performance measure on which to base its design. Section 3 addresses with some detail implementation issues. An hierarchic petri-net with feedback-based learning capabilities is proposed. Finally, section 4 is an attempt to address the feedback problem. Feedback is used for two functions: error recovery and reinforcement learning of the correct translations for the petri-net transitions.

Catamaran Nets

NASA Technical Reports Server (NTRS)

1990-01-01

West Coast Netting, Inc.'s net of Hyperester twine, is made of three strands of fiber twisted together by a company-invented sophisticated twisting machine and process that maintain precisely the same tension on each strand. The resulting twine offers higher strength and improved abrasion resistance. The technology that created the Hyperester supertwine has found spinoff applications, first as an extra-efficient seine for tuna fishing, then as a capture net for law enforcement agencies. The newest one is as a deck for racing catamarans. Hyperester twine net has been used on most of the high performance racing catamarans of recent years, including the America's Cup Challenge boats. They are tough and hold up well in the continual exposure to sunlight and saltwater.

Application of deconvolution interferometry with both Hi-net and KiK-net data

NASA Astrophysics Data System (ADS)

Nakata, N.

2013-12-01

Application of deconvolution interferometry to wavefields observed by KiK-net, a strong-motion recording network in Japan, is useful for estimating wave velocities and S-wave splitting in the near surface. Using this technique, for example, Nakata and Snieder (2011, 2012) found changed in velocities caused by Tohoku-Oki earthquake in Japan. At the location of the borehole accelerometer of each KiK-net station, a velocity sensor is also installed as a part of a high-sensitivity seismograph network (Hi-net). I present a technique that uses both Hi-net and KiK-net records for computing deconvolution interferometry. The deconvolved waveform obtained from the combination of Hi-net and KiK-net data is similar to the waveform computed from KiK-net data only, which indicates that one can use Hi-net wavefields for deconvolution interferometry. Because Hi-net records have a high signal-to-noise ratio (S/N) and high dynamic resolution, the S/N and the quality of amplitude and phase of deconvolved waveforms can be improved with Hi-net data. These advantages are especially important for short-time moving-window seismic interferometry and deconvolution interferometry using later coda waves.

Factors associated with mosquito net use by individuals in households owning nets in Ethiopia

PubMed Central

2011-01-01

Background Ownership of insecticidal mosquito nets has dramatically increased in Ethiopia since 2006, but the proportion of persons with access to such nets who use them has declined. It is important to understand individual level net use factors in the context of the home to modify programmes so as to maximize net use. Methods Generalized linear latent and mixed models (GLLAMM) were used to investigate net use using individual level data from people living in net-owning households from two surveys in Ethiopia: baseline 2006 included 12,678 individuals from 2,468 households and a sub-sample of the Malaria Indicator Survey (MIS) in 2007 included 14,663 individuals from 3,353 households. Individual factors (age, sex, pregnancy); net factors (condition, age, net density); household factors (number of rooms [2006] or sleeping spaces [2007], IRS, women's knowledge and school attendance [2007 only], wealth, altitude); and cluster level factors (rural or urban) were investigated in univariate and multi-variable models for each survey. Results In 2006, increased net use was associated with: age 25-49 years (adjusted (a) OR = 1.4, 95% confidence interval (CI) 1.2-1.7) compared to children U5; female gender (aOR = 1.4; 95% CI 1.2-1.5); fewer nets with holes (Ptrend = 0.002); and increasing net density (Ptrend < 0.001). Reduced net use was associated with: age 5-24 years (aOR = 0.2; 95% CI 0.2-0.3). In 2007, increased net use was associated with: female gender (aOR = 1.3; 95% CI 1.1-1.6); fewer nets with holes (aOR [all nets in HH good] = 1.6; 95% CI 1.2-2.1); increasing net density (Ptrend < 0.001); increased women's malaria knowledge (Ptrend < 0.001); and urban clusters (aOR = 2.5; 95% CI 1.5-4.1). Reduced net use was associated with: age 5-24 years (aOR = 0.3; 95% CI 0.2-0.4); number of sleeping spaces (aOR [per additional space] = 0.6, 95% CI 0.5-0.7); more old nets (aOR [all nets in HH older than 12 months] = 0.5; 95% CI 0.3-0.7); and increasing household altitude

Command and Control for Large-Scale Hybrid Warfare Systems

DTIC Science & Technology

2014-06-05

Prescribed by ANSI Std Z39-18 2 CK Pang et al. in C2 architectures was proposed using Petri nets (PNs).10 Liao in [11] reported an architecture for...arises from the chal- lenging and often-conflicting user requirements, scale, scope, inter-connectivity with different large-scale net - worked teams and...resources can be easily modelled and reconfigured by the notion of block matrix. At any time, the various missions of the net - worked team can be added

Event-driven management algorithm of an Engineering documents circulation system

NASA Astrophysics Data System (ADS)

Kuzenkov, V.; Zebzeev, A.; Gromakov, E.

2015-04-01

Development methodology of an engineering documents circulation system in the design company is reviewed. Discrete event-driven automatic models using description algorithms of project management is offered. Petri net use for dynamic design of projects is offered.

Connecting the dots between genes, biochemistry, and disease susceptibility: systems biology modeling in human genetics.

PubMed

Moore, Jason H; Boczko, Erik M; Summar, Marshall L

2005-02-01

Understanding how DNA sequence variations impact human health through a hierarchy of biochemical and physiological systems is expected to improve the diagnosis, prevention, and treatment of common, complex human diseases. We have previously developed a hierarchical dynamic systems approach based on Petri nets for generating biochemical network models that are consistent with genetic models of disease susceptibility. This modeling approach uses an evolutionary computation approach called grammatical evolution as a search strategy for optimal Petri net models. We have previously demonstrated that this approach routinely identifies biochemical network models that are consistent with a variety of genetic models in which disease susceptibility is determined by nonlinear interactions between two or more DNA sequence variations. We review here this approach and then discuss how it can be used to model biochemical and metabolic data in the context of genetic studies of human disease susceptibility.

Modeling and performance analysis of QoS data

NASA Astrophysics Data System (ADS)

Strzeciwilk, Dariusz; Zuberek, Włodzimierz M.

2016-09-01

The article presents the results of modeling and analysis of data transmission performance on systems that support quality of service. Models are designed and tested, taking into account multiservice network architecture, i.e. supporting the transmission of data related to different classes of traffic. Studied were mechanisms of traffic shaping systems, which are based on the Priority Queuing with an integrated source of data and the various sources of data that is generated. Discussed were the basic problems of the architecture supporting QoS and queuing systems. Designed and built were models based on Petri nets, supported by temporal logics. The use of simulation tools was to verify the mechanisms of shaping traffic with the applied queuing algorithms. It is shown that temporal models of Petri nets can be effectively used in the modeling and analysis of the performance of computer networks.

Simulation in a dynamic prototyping environment: Petri nets or rules?

NASA Technical Reports Server (NTRS)

Moore, Loretta A.; Price, Shannon W.; Hale, Joseph P.

1994-01-01

An evaluation of a prototyped user interface is best supported by a simulation of the system. A simulation allows for dynamic evaluation of the interface rather than just a static evaluation of the screen's appearance. This allows potential users to evaluate both the look (in terms of the screen layout, color, objects, etc.) and feel (in terms of operations and actions which need to be performed) of a system's interface. Because of the need to provide dynamic evaluation of an interface, there must be support for producing active simulations. The high-fidelity training simulators are normally delivered too late to be effectively used in prototyping the displays. Therefore, it is important to build a low fidelity simulator, so that the iterative cycle of refining the human computer interface based upon a user's interactions can proceed early in software development.

Electronic Business Transaction Infrastructure Analysis Using Petri Nets and Simulation

ERIC Educational Resources Information Center

Feller, Andrew Lee

2010-01-01

Rapid growth in eBusiness has made industry and commerce increasingly dependent on the hardware and software infrastructure that enables high-volume transaction processing across the Internet. Large transaction volumes at major industrial-firm data centers rely on robust transaction protocols and adequately provisioned hardware capacity to ensure…

Simulation in a dynamic prototyping environment: Petri nets or rules?

NASA Technical Reports Server (NTRS)

Moore, Loretta A.; Price, Shannon; Hale, Joseph P.

1994-01-01

An evaluation of a prototyped user interface is best supported by a simulation of the system. A simulation allows for dynamic evaluation of the interface rather than just a static evaluation of the screen's appearance. This allows potential users to evaluate both the look (in terms of the screen layout, color, objects, etc.) and feel (in terms of operations and actions which need to be performed) of a system's interface. Because of the need to provide dynamic evaluation of an interface, there must be support for producing active simulations. The high-fidelity training simulators are delivered too late to be effectively used in prototyping the displays. Therefore, it is important to build a low fidelity simulator, so that the iterative cycle of refining the human computer interface based upon a user's interactions can proceed early in software development.

Stochastic Petri Net Modeling of Wave Sequences in Cardiac Arrhythmias.

DTIC Science & Technology

1987-11-01

Wolff - Parkinson - White syndrome . The ventricles are divided into two parts. One of these is excited normally and produces R...example, in a condition called the Wolff - Parkinson - White syn- drome the ECG displays an abnormally early onset of the ventricular activity. It also...8217. , ’ ", -’ , .’ %,,? .’ ,; ’ .- ’ ’ -’ € ’ , . ’ - I. 32 Wolfe- Parkinson - White Syndrome (Fig. 8c) This model uses "basic" elements for the

Therapeutic Phlebotomy is Safe in Children with Sickle Cell Anaemia and can be Effective Treatment for Transfusional Iron Overload

PubMed Central

Aygun, Banu; Mortier, Nicole A.; Kesler, Karen; Lockhart, Alexandre; Schultz, William H.; Cohen, Alan R.; Alvarez, Ofelia; Rogers, Zora R.; Kwiatkowski, Janet L.; Miller, Scott T.; Sylvestre, Pamela; Iyer, Rathi; Lane, Peter A.; Ware, Russell E.

2015-01-01

SUMMARY Serial phlebotomy was performed on sixty children with sickle cell anaemia, stroke and transfusional iron overload randomized to hydroxycarbamide in the Stroke With Transfusions Changing to Hydroxyurea trial. There were 927 phlebotomy procedures with only 33 adverse events, all of which were grade 2. Among 23 children completing 30 months of study treatment, the net iron balance was favourable (−8.7 mg Fe/kg) with significant decrease in ferritin, although liver iron concentration remained unchanged. Therapeutic phlebotomy was safe and well-tolerated, with net iron removal in most children who completed 30 months of protocol-directed treatment. PMID:25612463

Net Gains

ERIC Educational Resources Information Center

Fielker, David

2008-01-01

The Easter conference 2008 had several activities which for the author raised the same questions on cube nets in some work with eight-year-olds some time ago. In this article, the author muses on some problems from the Easter conference regarding nets of shapes. (Contains 1 note.)

The NetQuakes Project - Seeking a Balance Between Science and Citizens.

NASA Astrophysics Data System (ADS)

Luetgert, J. H.; Oppenheimer, D. H.

2012-12-01

The challenge for any system that uses volunteer help to do science is to dependably acquire quality data without unduly burdening the volunteer. The NetQuakes accelerograph and its data acquisition system were created to address the recognized need for more densely sampled strong ground motion recordings in urban areas to provide more accurate ShakeMaps for post-earthquake disaster assessment and to provide data for structural engineers to improve design standards. The recorder has 18 bit resolution with ±3g internal tri-axial MEMS accelerometers. Data are continuously recorded at 200 sps into a 1-2 week ringbuffer. When triggered, a miniSEED file is sent to USGS servers via the Internet. Data can also be recovered from the ringbuffer by a remote request through the NetQuakes servers. Following a power failure, the instrument can run for 36 hours using its internal battery. We rely upon cooperative citizens to host the dataloggers, provide power and Internet connectivity and perform minor servicing. Instrument and battery replacement are simple tasks that can be performed by hosts, thus reducing maintenance costs. Communication with the instrument to acquire data or deliver firmware is accomplished by file transfers using NetQuakes servers. The client instrument initiates all client-server interactions, so it safely resides behind a host's firewall. A connection to the host's LAN, and from there to the public Internet, can be made using WiFi to minimize cabling. Although timing using a cable to an external GPS antenna is possible, it is simpler to use the Network Time Protocol (NTP) to discipline the internal clock. This approach achieves timing accuracy substantially better than a sample interval. Since 2009, we have installed more than 140 NetQuakes instruments in the San Francisco Bay Area and have successfully integrated their data into the near real time data stream of the Northern California Seismic System. An additional 235 NetQuakes instruments have been

Net Zero Water Update

DTIC Science & Technology

2011-05-12

www.epa.gov/nrmrl/pubs/600r09048/600r09048.pdf • http://www.epa.gov/awi/res_rehabilitation.html Net Zero Waste • http://www.army.mil/-news/2011/02...24/52403-net- zero - waste -goal-becoming-a-reality- at-jblm/ • http://www.operationfree.net/2011/04/11/u-s-army-looks-to-net- zero - waste / 27

Experiments and simulation of a net closing mechanism for tether-net capture of space debris

NASA Astrophysics Data System (ADS)

Sharf, Inna; Thomsen, Benjamin; Botta, Eleonora M.; Misra, Arun K.

2017-10-01

This research addresses the design and testing of a debris containment system for use in a tether-net approach to space debris removal. The tether-net active debris removal involves the ejection of a net from a spacecraft by applying impulses to masses on the net, subsequent expansion of the net, the envelopment and capture of the debris target, and the de-orbiting of the debris via a tether to the chaser spacecraft. To ensure a debris removal mission's success, it is important that the debris be successfully captured and then, secured within the net. To this end, we present a concept for a net closing mechanism, which we believe will permit consistently successful debris capture via a simple and unobtrusive design. This net closing system functions by extending the main tether connecting the chaser spacecraft and the net vertex to the perimeter and around the perimeter of the net, allowing the tether to actuate closure of the net in a manner similar to a cinch cord. A particular embodiment of the design in a laboratory test-bed is described: the test-bed itself is comprised of a scaled-down tether-net, a supporting frame and a mock-up debris. Experiments conducted with the facility demonstrate the practicality of the net closing system. A model of the net closure concept has been integrated into the previously developed dynamics simulator of the chaser/tether-net/debris system. Simulations under tether tensioning conditions demonstrate the effectiveness of the closure concept for debris containment, in the gravity-free environment of space, for a realistic debris target. The on-ground experimental test-bed is also used to showcase its utility for validating the dynamics simulation of the net deployment, and a full-scale automated setup would make possible a range of validation studies of other aspects of a tether-net debris capture mission.

Pull-Up Nets

ERIC Educational Resources Information Center

Meenan, Liz

2008-01-01

When the author began teaching, she always hit a problem when it came to 3D shapes. She wanted the pupils to get a feel for them, and she would get them to make the shapes from their nets. The pupils would first try to visualize how the 2D nets could become 3D shapes and then they would physically fold the nets into the shapes for themselves.…

An economic analysis of a safe resident handling program in nursing homes.

PubMed

Lahiri, Supriya; Latif, Saira; Punnett, Laura

2013-04-01

Occupational injuries, especially back problems related to resident handling, are common in nursing home employees and their prevention may require substantial up-front investment. This study evaluated the economics of a safe resident handling program (SRHP), in a large chain of skilled nursing facilities, from the corporation's perspective. The company provided data on program costs, compensation claims, and turnover rates (2003-2009). Workers' compensation and turnover costs before and after the intervention were compared against investment costs using the "net-cost model." Among 110 centers, the overall benefit-to-cost ratio was 1.7-3.09 and the payback period was 1.98-1.06 year (using alternative turnover cost estimates). The average annualized net savings per bed for the 110 centers (using company based turnover cost estimates) was $143, with a 95% confidence interval of $22-$264. This was very similar to the average annualized net savings per full time equivalent (FTE) staff member, which was $165 (95% confidence interval $22-$308). However, at 49 centers costs exceeded benefits. Decreased costs of worker injury compensation claims and turnover appear at least partially attributable to the SRHP. Future research should examine center-specific factors that enhance program success, and improve measures of turnover costs and healthcare productivity. Copyright © 2012 Wiley Periodicals, Inc.

ROOT.NET: Using ROOT from .NET languages like C# and F#

NASA Astrophysics Data System (ADS)

Watts, G.

2012-12-01

ROOT.NET provides an interface between Microsoft's Common Language Runtime (CLR) and .NET technology and the ubiquitous particle physics analysis tool, ROOT. ROOT.NET automatically generates a series of efficient wrappers around the ROOT API. Unlike pyROOT, these wrappers are statically typed and so are highly efficient as compared to the Python wrappers. The connection to .NET means that one gains access to the full series of languages developed for the CLR including functional languages like F# (based on OCaml). Many features that make ROOT objects work well in the .NET world are added (properties, IEnumerable interface, LINQ compatibility, etc.). Dynamic languages based on the CLR can be used as well, of course (Python, for example). Additionally it is now possible to access ROOT objects that are unknown to the translation tool. This poster will describe the techniques used to effect this translation, along with performance comparisons, and examples. All described source code is posted on the open source site CodePlex.

A Fuzzy Reasoning Design for Fault Detection and Diagnosis of a Computer-Controlled System

PubMed Central

Ting, Y.; Lu, W.B.; Chen, C.H.; Wang, G.K.

2008-01-01

A Fuzzy Reasoning and Verification Petri Nets (FRVPNs) model is established for an error detection and diagnosis mechanism (EDDM) applied to a complex fault-tolerant PC-controlled system. The inference accuracy can be improved through the hierarchical design of a two-level fuzzy rule decision tree (FRDT) and a Petri nets (PNs) technique to transform the fuzzy rule into the FRVPNs model. Several simulation examples of the assumed failure events were carried out by using the FRVPNs and the Mamdani fuzzy method with MATLAB tools. The reasoning performance of the developed FRVPNs was verified by comparing the inference outcome to that of the Mamdani method. Both methods result in the same conclusions. Thus, the present study demonstratrates that the proposed FRVPNs model is able to achieve the purpose of reasoning, and furthermore, determining of the failure event of the monitored application program. PMID:19255619

Polynomial algebra of discrete models in systems biology.

PubMed

Veliz-Cuba, Alan; Jarrah, Abdul Salam; Laubenbacher, Reinhard

2010-07-01

An increasing number of discrete mathematical models are being published in Systems Biology, ranging from Boolean network models to logical models and Petri nets. They are used to model a variety of biochemical networks, such as metabolic networks, gene regulatory networks and signal transduction networks. There is increasing evidence that such models can capture key dynamic features of biological networks and can be used successfully for hypothesis generation. This article provides a unified framework that can aid the mathematical analysis of Boolean network models, logical models and Petri nets. They can be represented as polynomial dynamical systems, which allows the use of a variety of mathematical tools from computer algebra for their analysis. Algorithms are presented for the translation into polynomial dynamical systems. Examples are given of how polynomial algebra can be used for the model analysis. alanavc@vt.edu Supplementary data are available at Bioinformatics online.

Nested Interrupt Analysis of Low Cost and High Performance Embedded Systems Using GSPN Framework

NASA Astrophysics Data System (ADS)

Lin, Cheng-Min

Interrupt service routines are a key technology for embedded systems. In this paper, we introduce the standard approach for using Generalized Stochastic Petri Nets (GSPNs) as a high-level model for generating CTMC Continuous-Time Markov Chains (CTMCs) and then use Markov Reward Models (MRMs) to compute the performance for embedded systems. This framework is employed to analyze two embedded controllers with low cost and high performance, ARM7 and Cortex-M3. Cortex-M3 is designed with a tail-chaining mechanism to improve the performance of ARM7 when a nested interrupt occurs on an embedded controller. The Platform Independent Petri net Editor 2 (PIPE2) tool is used to model and evaluate the controllers in terms of power consumption and interrupt overhead performance. Using numerical results, in spite of the power consumption or interrupt overhead, Cortex-M3 performs better than ARM7.

WhaleNet/environet

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williamson, J.M.

1994-12-31

WhaleNet has established a network where students, educators, and scientists can interact and share data for use in interdisciplinary curricular and student research activities in classrooms around the world by utilizing telecommunication. This program enables students to participate in marine/whale research programs in real-time with WhaleNet data and supplementary curriculum materials regardless of their geographic location. Systems have been established with research organizations and whale watch companies whereby research data is posted by scientists and students participating in whale watches on the WhaleNet bulletin board and shared with participating classrooms. WhaleNet presently has contacts with classrooms across the nation, andmore » with research groups, whale watch organizations, science museums, and universities from Alaska to North Carolina, Hawaii to Maine, and Belize to Norway. WhaleNet has plans to make existing whale and fisheries research databases available for classroom use and to have research data from satellite tagging programs on various species of whales available for classroom access in real-time.« less

Therapeutic phlebotomy is safe in children with sickle cell anaemia and can be effective treatment for transfusional iron overload.

PubMed

Aygun, Banu; Mortier, Nicole A; Kesler, Karen; Lockhart, Alexandre; Schultz, William H; Cohen, Alan R; Alvarez, Ofelia; Rogers, Zora R; Kwiatkowski, Janet L; Miller, Scott T; Sylvestre, Pamela; Iyer, Rathi; Lane, Peter A; Ware, Russell E

2015-04-01

Serial phlebotomy was performed on sixty children with sickle cell anaemia, stroke and transfusional iron overload randomized to hydroxycarbamide in the Stroke With Transfusions Changing to Hydroxyurea trial. There were 927 phlebotomy procedures with only 33 adverse events, all of which were grade 2. Among 23 children completing 30 months of study treatment, the net iron balance was favourable (-8·7 mg Fe/kg) with significant decrease in ferritin, although liver iron concentration remained unchanged. Therapeutic phlebotomy was safe and well-tolerated, with net iron removal in most children who completed 30 months of protocol-directed treatment. © 2015 John Wiley & Sons Ltd.

Freeze-out conditions from net-proton and net-charge fluctuations at RHIC

DOE PAGES

Alba, Paolo; Alberico, Wanda; Bellwied, Rene; ...

2014-09-26

We calculate ratios of higher-order susceptibilities quantifying fluctuations in the number of net-protons and in the net-electric charge using the Hadron Resonance Gas (HRG) model. We take into account the effect of resonance decays, the kinematic acceptance cuts in rapidity, pseudo-rapidity and transverse momentum used in the experimental analysis, as well as a randomization of the isospin of nucleons in the hadronic phase. By comparing these results to the latest experimental data from the STAR Collaboration, we determine the freeze-out conditions from net-electric charge and net-proton distributions and discuss their consistency.

Cool and Safe: Multiplicity in Safe Innovation at Unilever

ERIC Educational Resources Information Center

Penders, Bart

2011-01-01

This article presents the making of a safe innovation: the application of ice structuring protein (ISP) in edible ices. It argues that safety is not the absence of risk but is an active accomplishment; innovations are not "made safe afterward" but "safe innovations are made". Furthermore, there are multiple safeties to be accomplished in the…

No Safety Net Required

ERIC Educational Resources Information Center

Benigni, Mark D.; Moylan, Maureen

2009-01-01

This article discusses the Berlin (Connecticut) High School's NET (Non-Traditional Educational Training) program. NET is a self-contained program that is composed of three components: academics, social and emotional support, and vocational training. Rather than treat students alike, the NET program tailors their high school experience to meet…

INMARSAT-C SafetyNET

Science.gov Websites

Tsunamis 406 EPIRB's National Weather Service Marine Forecasts INMARSAT-C SafetyNET Marine Forecast Offices greater danger near shore or any shallow waters? NATIONAL WEATHER SERVICE PRODUCTS VIA INMARSAT-C SafetyNET Inmarsat-C SafetyNET is an internationally adopted, automated satellite system for promulgating

Planning long lasting insecticide treated net campaigns: should households’ existing nets be taken into account?

PubMed Central

2013-01-01

Background Mass distribution of long-lasting insecticide treated bed nets (LLINs) has led to large increases in LLIN coverage in many African countries. As LLIN ownership levels increase, planners of future mass distributions face the challenge of deciding whether to ignore the nets already owned by households or to take these into account and attempt to target individuals or households without nets. Taking existing nets into account would reduce commodity costs but require more sophisticated, and potentially more costly, distribution procedures. The decision may also have implications for the average age of nets in use and therefore on the maintenance of universal LLIN coverage over time. Methods A stochastic simulation model based on the NetCALC algorithm was used to determine the scenarios under which it would be cost saving to take existing nets into account, and the potential effects of doing so on the age profile of LLINs owned. The model accounted for variability in timing of distributions, concomitant use of continuous distribution systems, population growth, sampling error in pre-campaign coverage surveys, variable net ‘decay’ parameters and other factors including the feasibility and accuracy of identifying existing nets in the field. Results Results indicate that (i) where pre-campaign coverage is around 40% (of households owning at least 1 LLIN), accounting for existing nets in the campaign will have little effect on the mean age of the net population and (ii) even at pre-campaign coverage levels above 40%, an approach that reduces LLIN distribution requirements by taking existing nets into account may have only a small chance of being cost-saving overall, depending largely on the feasibility of identifying nets in the field. Based on existing literature the epidemiological implications of such a strategy is likely to vary by transmission setting, and the risks of leaving older nets in the field when accounting for existing nets must be considered

Planning long lasting insecticide treated net campaigns: should households' existing nets be taken into account?

PubMed

Yukich, Joshua; Bennett, Adam; Keating, Joseph; Yukich, Rudy K; Lynch, Matt; Eisele, Thomas P; Kolaczinski, Kate

2013-06-14

Mass distribution of long-lasting insecticide treated bed nets (LLINs) has led to large increases in LLIN coverage in many African countries. As LLIN ownership levels increase, planners of future mass distributions face the challenge of deciding whether to ignore the nets already owned by households or to take these into account and attempt to target individuals or households without nets. Taking existing nets into account would reduce commodity costs but require more sophisticated, and potentially more costly, distribution procedures. The decision may also have implications for the average age of nets in use and therefore on the maintenance of universal LLIN coverage over time. A stochastic simulation model based on the NetCALC algorithm was used to determine the scenarios under which it would be cost saving to take existing nets into account, and the potential effects of doing so on the age profile of LLINs owned. The model accounted for variability in timing of distributions, concomitant use of continuous distribution systems, population growth, sampling error in pre-campaign coverage surveys, variable net 'decay' parameters and other factors including the feasibility and accuracy of identifying existing nets in the field. Results indicate that (i) where pre-campaign coverage is around 40% (of households owning at least 1 LLIN), accounting for existing nets in the campaign will have little effect on the mean age of the net population and (ii) even at pre-campaign coverage levels above 40%, an approach that reduces LLIN distribution requirements by taking existing nets into account may have only a small chance of being cost-saving overall, depending largely on the feasibility of identifying nets in the field. Based on existing literature the epidemiological implications of such a strategy is likely to vary by transmission setting, and the risks of leaving older nets in the field when accounting for existing nets must be considered. Where pre-campaign coverage

Pt-coated cylindrical micropatterned honeycomb Petri dishes as an efficient TCO-free counter electrode in liquid junction photovoltaic devices

NASA Astrophysics Data System (ADS)

Dao, Van-Duong; Bui, Van-Tien; Choi, Ho-Suk

2018-02-01

The Pt layer deposited on a cylindrical micro cavity patterned Petri dish, which is produced using a one-step solvent-immersion phase separation, is fabricated for the first time as an FTO-free counter electrode (CE) for dye-sensitized solar cells (DSCs). Due to the high specific active surface area of the Pt-deposited honeycomb substrate CE, the efficiency of the DSC using the developed CE substrate is enhanced by 14.5% compared with the device using a Pt-sputtered flat substrate. This design strategy has potential in fabricating highly efficient and low-cost CE materials with FTO-free substrates for DSCs.

Function Allocation between Automation and Human Pilot for Airborne Separation Assurance

NASA Technical Reports Server (NTRS)

Idris, Husni; Enea, Gabriele; Lewis, TImothy A.

2016-01-01

Maintaining safe separation between aircraft is a key determinant of the airspace capacity to handle air transportation. With the advent of satellite-based surveillance, aircraft equipped with the needed technologies are now capable of maintaining awareness of their location in the airspace and sharing it with their surrounding traffic. As a result, concepts and cockpit automation are emerging to enable delegating the responsibility of maintaining safe separation from traffic to the pilot; thus increasing the airspace capacity by alleviating the limitation of the current non-scalable centralized ground-based system. In this paper, an analysis of allocating separation assurance functions to the human pilot and cockpit automation is presented to support the design of these concepts and technologies. A task analysis was conducted with the help of Petri nets to identify the main separation assurance functions and their interactions. Each function was characterized by three behavior levels that may be needed to perform the task: skill, rule and knowledge based levels. Then recommendations are made for allocating each function to an automation scale based on their behavior level characterization and with the help of Subject matter experts.

KM3NeT

NASA Astrophysics Data System (ADS)

de Jong, M.

2015-07-01

KM3NeT is a large research infrastructure, that will consist of a network of deep-sea neutrino telescopes in the Mediterranean Sea. The main objective of KM3NeT is the discovery and subsequent observation of high-energy neutrino sources in the Universe. A further physics perspective is the measurement of the mass hierarchy of neutrinos. A corresponding study, ORCA, is ongoing within KM3NeT. A cost effective technology for (very) large water Cherenkov detectors has been developed based on a new generation of low price 3-inch photo-multiplier tubes. Following the successful deployment and operation of two prototypes, the construction of the KM3NeT research infrastructure has started. The prospects of the different phases of the implementation of KM3NeT are summarised.

Chinese farmers' willingness to accept compensation to practice safe disposal of HPAI infected chicken.

PubMed

Huang, Zeying; Wang, Jimin; Zuo, Alec

2017-04-01

Highly Pathogenic Avian Influenza (HPAI) is a high morbidity and mortality zoonotic disease, which threatens poultry and human health. An outbreak of disease in China requires strict slaughter and disposal of all chickens within a three-kilometer radius, incurring large private costs for farmers and encouraging black market transactions. A stated preference survey of 331 farmers across six provinces in China was conducted in 2015, in order to measure the responsiveness of farmers to accept various compensation prices for safely disposing of HPAI infected chicken. Findings suggest that about 25% and 40% of farmers in South and North China respectively would not adopt safe disposal at the current compensation price (10 yuan/bird) offered by the government. However, 80% of farmers would adopt safe disposal if the compensation price increased to 14.1 yuan in South China and 18.9 yuan in North China. The adoption of safe disposal by farmers was positively and significantly influenced by compensation price (p=0.000) and regular contact with epidemic prevention staff (p=0.094). However, adoption was negatively and significantly influenced by net farm income (p=0.100) and chicken production income percentage (p=0.014). Although half of (51%) of farmers were willing to receive zero compensation, a reasonable compensation scheme along with strengthened supervision, may be considered the most effective strategy to encourage safe disposal of HPAI infected chicken and reduce the risks associated with black market transactions. Copyright © 2017 Elsevier B.V. All rights reserved.

[Safe school].

PubMed

Liberal, Edson Ferreira; Aires, Roberto Tschoepke; Aires, Mariana Tschoepke; Osório, Ana Carla de Albuquerque

2005-11-01

To review the strategies to make school a safe environment. The paper first addresses the social context of accidents and violence in the school environment, and makes recommendations, based on the literature data, for the implementation of safe schools. Articles published between 1993 and 2005 in the MEDLINE database. Brazilian epidemiological and literature data have also been searched. There is growing evidence that intervention has multiple components, focusing on health education practices, with the participation of the whole community. The aim of those interventions is to help students and community members to adopt healthy and safe behaviors. Schools are taking on an increasing role in health promotion, disease prevention, and injury prevention. In the context of prevention of external causes of morbidity and mortality, it is important to recognize a risky environment, places, and risk behaviors as favorable to injury and violence, as well as the concept of accident as something one can avoid. Implementation of safe schools represents a promising new direction for school-based preventive work. It is important to note that a safe school should intervene not only in its physical structure, but it should also make it as safe as possible by gathering the school community through health education, and mainly encouraging healthy behavior.

An Economic Analysis of a Safe Resident Handling Program in Nursing Homes

PubMed Central

Lahiri, Supriya; Latif, Saira; Punnett, Laura

2018-01-01

Background Occupational injuries, especially back problems related to resident handling, are common in nursing home employees and their prevention may require substantial up-front investment. This study evaluated the economics of a safe resident handling program (SRHP), in a large chain of skilled nursing facilities, from the corporation's perspective. Methods The company provided data on program costs, compensation claims, and turnover rates (2003-2009). Workers' compensation and turnover costs before and after the intervention were compared against investment costs using the “net-cost model”. Results Among 110 centers, the overall benefit-to-cost ratio was 1.7–3.09 and the payback period was 1.98–1.06 year (using alternative turnover cost estimates). The average annualized net savings per bed for the 110 centers (using company based turnover cost estimates) was $143, with a 95% confidence interval of $22–$264. This was very similar to the average annualized net savings per full time equivalent (FTE) staff member, which was $165 (95% confidence interval $22–$308). However, at 49 centers costs exceeded benefits. Conclusions Decreased costs of worker injury compensation claims and turnover appear at least partially attributable to the SRHP. Future research should examine center-specific factors that enhance program success, and improve measures of turnover costs and healthcare productivity. PMID:23203729

KM3NeT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jong, M. de; Leiden Institute of Physics, Leiden University, Leiden; Collaboration: KM3NeT Collaboration

2015-07-15

KM3NeT is a large research infrastructure, that will consist of a network of deep-sea neutrino telescopes in the Mediterranean Sea. The main objective of KM3NeT is the discovery and subsequent observation of high-energy neutrino sources in the Universe. A further physics perspective is the measurement of the mass hierarchy of neutrinos. A corresponding study, ORCA, is ongoing within KM3NeT. A cost effective technology for (very) large water Cherenkov detectors has been developed based on a new generation of low price 3-inch photo-multiplier tubes. Following the successful deployment and operation of two prototypes, the construction of the KM3NeT research infrastructure hasmore » started. The prospects of the different phases of the implementation of KM3NeT are summarised.« less

AdaNET executive summary

NASA Technical Reports Server (NTRS)

Digman, R. Michael

1988-01-01

The goal of AdaNET is to transfer existing and emerging software engineering technology from the Federal government to the private sector. The views and perspectives of the current project participants on long and short term goals for AdaNET; organizational structure; resources and returns; summary of identified AdaNET services; and the summary of the organizational model currently under discussion are presented.

Software reuse issues affecting AdaNET

NASA Technical Reports Server (NTRS)

Mcbride, John G.

1989-01-01

The AdaNet program is reviewing its long-term goals and strategies. A significant concern is whether current AdaNet plans adequately address the major strategic issues of software reuse technology. The major reuse issues of providing AdaNet services that should be addressed as part of future AdaNet development are identified and reviewed. Before significant development proceeds, a plan should be developed to resolve the aforementioned issues. This plan should also specify a detailed approach to develop AdaNet. A three phased strategy is recommended. The first phase would consist of requirements analysis and produce an AdaNet system requirements specification. It would consider the requirements of AdaNet in terms of mission needs, commercial realities, and administrative policies affecting development, and the experience of AdaNet and other projects promoting the transfer software engineering technology. Specifically, requirements analysis would be performed to better understand the requirements for AdaNet functions. The second phase would provide a detailed design of the system. The AdaNet should be designed with emphasis on the use of existing technology readily available to the AdaNet program. A number of reuse products are available upon which AdaNet could be based. This would significantly reduce the risk and cost of providing an AdaNet system. Once a design was developed, implementation would proceed in the third phase.

Investigation of safe-life fail-safe criteria for the space shuttle

NASA Technical Reports Server (NTRS)

1972-01-01

An investigation was made to determine the effects of a safe-life design approach and a fail-safe design approach on the space shuttle booster vehicle structure, and to recommend any changes to the structural design criteria. Two configurations of the booster vehicle were considered, one incorporating a delta wing (B-9U configuration) and the other a swept wing (B-16B configuration). Several major structural components of the booster were studied to determine the fatigue life, safe-life, and fail-safe capabilities of the baseline design. Each component was investigated to determine the practicability of applying a safe-life or fail-safe design philosophy, the changes such design approaches might require, and the impact of these changes on weight, cost, development plans, and performance.

Cell illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2011-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

Transactions in domain-specific information systems

NASA Astrophysics Data System (ADS)

Zacek, Jaroslav

2017-07-01

Substantial number of the current information system (IS) implementations is based on transaction approach. In addition, most of the implementations are domain-specific (e.g. accounting IS, resource planning IS). Therefore, we have to have a generic transaction model to build and verify domain-specific IS. The paper proposes a new transaction model for domain-specific ontologies. This model is based on value oriented business process modelling technique. The transaction model is formalized by the Petri Net theory. First part of the paper presents common business processes and analyses related to business process modeling. Second part defines the transactional model delimited by REA enterprise ontology paradigm and introduces states of the generic transaction model. The generic model proposal is defined and visualized by the Petri Net modelling tool. Third part shows application of the generic transaction model. Last part of the paper concludes results and discusses a practical usability of the generic transaction model.

Cell Illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2010-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

Multiflavor string-net models

NASA Astrophysics Data System (ADS)

Lin, Chien-Hung

2017-05-01

We generalize the string-net construction to multiple flavors of strings, each of which is labeled by the elements of an Abelian group Gi. The same flavor of strings can branch, while different flavors of strings can cross one another and thus they form intersecting string nets. We systematically construct the exactly soluble lattice Hamiltonians and the ground-state wave functions for the intersecting string-net condensed phases. We analyze the braiding statistics of the low-energy quasiparticle excitations and find that our model can realize all the topological phases as the string-net model with group G =∏iGi . In this respect, our construction provides various ways of building lattice models which realize topological order G , corresponding to different partitions of G and thus different flavors of string nets. In fact, our construction concretely demonstrates the Künneth formula by constructing various lattice models with the same topological order. As an example, we construct the G =Z2×Z2×Z2 string-net model which realizes a non-Abelian topological phase by properly intersecting three copies of toric codes.

Limitations of shallow nets approximation.

PubMed

Lin, Shao-Bo

2017-10-01

In this paper, we aim at analyzing the approximation abilities of shallow networks in reproducing kernel Hilbert spaces (RKHSs). We prove that there is a probability measure such that the achievable lower bound for approximating by shallow nets can be realized for all functions in balls of reproducing kernel Hilbert space with high probability, which is different with the classical minimax approximation error estimates. This result together with the existing approximation results for deep nets shows the limitations for shallow nets and provides a theoretical explanation on why deep nets perform better than shallow nets. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Mixed-Methods Study of Patient-Provider E-mail Content in a Safety-Net Setting

PubMed Central

Mirsky, Jacob B.; Tieu, Lina; Lyles, Courtney; Sarkar, Urmimala

2016-01-01

Objective To explore the content of patient-provider e-mails in a safety-net primary care clinic. Methods We conducted a content analysis using inductive and deductive coding of e-mail exchanges (n=31) collected from January through November of 2013. Participants were English-speaking adult patients with a chronic condition (or their caregivers) cared for at a single publicly-funded general internal medicine clinic and their primary care providers (attending general internist physicians, clinical fellows, internal medicine residents, and nurse practitioners). Results All e-mails were non-urgent. Patients included a medical update in 19% of all e-mails. Patients requested action in 77% of e-mails, and the most common requests overall were for action regarding medications or treatment (29%). Requests for information were less common (45% of e-mails). Patient requests (n=56) were resolved in 84% of e-mail exchanges, resulting in 63 actions. Conclusion Patients in safety-net clinics are capable of safely and effectively using electronic messaging for between-visit communication with providers. Practical Implications Safety-net systems should implement electronic communications tools as soon as possible to increase healthcare access and enhance patient involvement in their care. PMID:26332306

Racial/ethnic differences in obesity and comorbidities between safety-net- and non safety-net integrated health systems

PubMed Central

Balasubramanian, Bijal A.; Garcia, Michael P.; Corley, Douglas A.; Doubeni, Chyke A.; Haas, Jennifer S.; Kamineni, Aruna; Quinn, Virginia P.; Wernli, Karen; Zheng, Yingye; Skinner, Celette Sugg

2017-01-01

Abstract Previous research shows that patients in integrated health systems experience fewer racial disparities compared with more traditional healthcare systems. Little is known about patterns of racial/ethnic disparities between safety-net and non safety-net integrated health systems. We evaluated racial/ethnic differences in body mass index (BMI) and the Charlson comorbidity index from 3 non safety-net- and 1 safety-net integrated health systems in a cross-sectional study. Multinomial logistic regression modeled comorbidity and BMI on race/ethnicity and health care system type adjusting for age, sex, insurance, and zip-code-level income The study included 1.38 million patients. Higher proportions of safety-net versus non safety-net patients had comorbidity score of 3+ (11.1% vs. 5.0%) and BMI ≥35 (27.7% vs. 15.8%). In both types of systems, blacks and Hispanics were more likely than whites to have higher BMIs. Whites were more likely than blacks or Hispanics to have higher comorbidity scores in a safety net system, but less likely to have higher scores in the non safety-nets. The odds of comorbidity score 3+ and BMI 35+ in blacks relative to whites were significantly lower in safety-net than in non safety-net settings. Racial/ethnic differences were present within both safety-net and non safety-net integrated health systems, but patterns differed. Understanding patterns of racial/ethnic differences in health outcomes in safety-net and non safety-net integrated health systems is important to tailor interventions to eliminate racial/ethnic disparities in health and health care. PMID:28296752

Safe Zones: Creating LGBT Safe Space Ally Programs

ERIC Educational Resources Information Center

Poynter, Kerry John; Tubbs, Nancy Jean

2008-01-01

This article discusses model LGBT Safe Space Ally programs. These programs, often called "Safe Zones," include self selected students, faculty, and employees who publicly show support by displaying stickers, signs, and other identifiable items. Issues covered in the article include history, development, training, membership, assessment, and…

The effect of netting solidity ratio and inclined angle on the hydrodynamic characteristics of knotless polyethylene netting

NASA Astrophysics Data System (ADS)

Tang, Hao; Hu, Fuxiang; Xu, Liuxiong; Dong, Shuchuang; Zhou, Cheng; Wang, Xuefang

2017-10-01

Knotless polyethylene (PE) netting has been widely used in aquaculture cages and fishing gears, especially in Japan. In this study, the hydrodynamic coefficient of six knotless PE netting panels with different solidity ratios were assessed in a flume tank under various attack angles of netting from 0° (parallel to flow) to 90° (perpendicular to flow) and current speeds from 40 cm s-1 to 130 cm s-1. It was found that the drag coefficient was related to Reynolds number, solidity ratio and attack angle of netting. The solidity ratio was positively related with drag coefficient for netting panel perpendicular to flow, whereas when setting the netting panel parallel to the flow the opposite result was obtained. For netting panels placed at an angle to the flow, the lift coefficient reached the maximum at an attack angle of 50° and then decreased as the attack angle further increased. The solidity ratio had a dual influence on drag coefficient of inclined netting panels. Compared to result in the literature, the normal drag coefficient of knotless PE netting measured in this study is larger than that of nylon netting or Dyneema netting.

NetView technical research

NASA Technical Reports Server (NTRS)

1993-01-01

This is the Final Technical Report for the NetView Technical Research task. This report is prepared in accordance with Contract Data Requirements List (CDRL) item A002. NetView assistance was provided and details are presented under the following headings: NetView Management Systems (NMS) project tasks; WBAFB IBM 3090; WPAFB AMDAHL; WPAFB IBM 3084; Hill AFB; McClellan AFB AMDAHL; McClellan AFB IBM 3090; and Warner-Robins AFB.

Use of bed nets and factors that influence bed net use among Jinuo Ethnic Minority in southern China.

PubMed

Xu, Jian-wei; Liao, Yuan-mei; Liu, Hui; Nie, Ren-hua; Havumaki, Joshua

2014-01-01

Insecticide-treated nets (ITNs) are an integral part of vector control recommendations for malaria elimination in China. This study investigated the extent to which bed nets were used and which factors influence bed net use among Jinuo Ethnic Minority in China-Myanmar-Laos border areas. This study combined a quantitative household questionnaire survey and qualitative semi-structured in-depth interviews (SDI). Questionnaires were administered to 352 heads of households. SDIs were given to 20 key informants. The bed net to person ratio was 1∶2.1 (i.e., nearly one net for every two people), however only 169 (48.0%) households owned at least one net and 623 (47.2%) residents slept under bed nets the prior night. The percentages of residents who regularly slept under nets (RSUN) and slept under nets the prior night (SUNPN) were similar (48.0% vs. 47.2%, P>0.05), however the percentage correct use of nets (CUN) was significantly lower (34.5%, P<0.0001). The annual cash income per person (ACIP) was an independent factor that influenced bed net use (P<0.0001), where families with an ACIP of CNY10000 or more were much more likely to use nets. House type was strongly associated with bed net use (OR: 4.71, 95% CI: 2.81, 7.91; P<0.0001), where those with traditional wood walls and terracotta roofs were significantly more likely to use nets, and the head of household's knowledge was an independent factor (OR: 5.04, 95% CI: 2.72, 9.35; P<0.0001), where those who knew bed nets prevent malaria were significantly more likely to use nets too. High bed net availability does not necessarily mean higher coverage or bed net use. Household income, house type and knowledge of the ability of bed nets to prevent malaria are all independent factors that influence bed net use among Jinuo Ethnic Minority.

Net alkalinity and net acidity 2: Practical considerations

USGS Publications Warehouse

Kirby, C.S.; Cravotta, C.A.

2005-01-01

The pH, alkalinity, and acidity of mine drainage and associated waters can be misinterpreted because of the chemical instability of samples and possible misunderstandings of standard analytical method results. Synthetic and field samples of mine drainage having various initial pH values and concentrations of dissolved metals and alkalinity were titrated by several methods, and the results were compared to alkalinity and acidity calculated based on dissolved solutes. The pH, alkalinity, and acidity were compared between fresh, unoxidized and aged, oxidized samples. Data for Pennsylvania coal mine drainage indicates that the pH of fresh samples was predominantly acidic (pH 2.5-4) or near neutral (pH 6-7); ??? 25% of the samples had pH values between 5 and 6. Following oxidation, no samples had pH values between 5 and 6. The Standard Method Alkalinity titration is constrained to yield values >0. Most calculated and measured alkalinities for samples with positive alkalinities were in close agreement. However, for low-pH samples, the calculated alkalinity can be negative due to negative contributions by dissolved metals that may oxidize and hydrolyze. The Standard Method hot peroxide treatment titration for acidity determination (Hot Acidity) accurately indicates the potential for pH to decrease to acidic values after complete degassing of CO2 and oxidation of Fe and Mn, and it indicates either the excess alkalinity or that required for neutralization of the sample. The Hot Acidity directly measures net acidity (= -net alkalinity). Samples that had near-neutral pH after oxidation had negative Hot Acidity; samples that had pH < 6.3 after oxidation had positive Hot Acidity. Samples with similar pH values before oxidation had dissimilar Hot Acidities due to variations in their alkalinities and dissolved Fe, Mn, and Al concentrations. Hot Acidity was approximately equal to net acidity calculated based on initial pH and dissolved concentrations of Fe, Mn, and Al minus the

Efficacy of PermaNet® 3.0 and PermaNet® 2.0 nets against laboratory-reared and wild Anopheles gambiae sensu lato populations in northern Tanzania.

PubMed

Kweka, Eliningaya J; Lyaruu, Lucile J; Mahande, Aneth M

2017-01-18

Mosquitoes have developed resistance against pyrethroids, the only class of insecticides approved for use on long-lasting insecticidal nets (LLINs). The present study sought to evaluate the efficacy of the pyrethroid synergist PermaNet® 3.0 LLIN versus the pyrethroid-only PermaNet® 2.0 LLIN, in an East African hut design in Lower Moshi, northern Tanzania. In this setting, resistance to pyrethroid insecticides has been identified in Anopheles gambiae mosquitoes. Standard World Health Organization bioefficacy evaluations were conducted in both laboratory and experimental huts. Experimental hut evaluations were conducted in an area where there was presence of a population of highly pyrethroid-resistant An. arabiensis mosquitoes. All nets used were subjected to cone bioassays and then to experimental hut trials. Mosquito mortality, blood-feeding inhibition and personal protection rate were compared between untreated nets, unwashed LLINs and LLINs that were washed 20 times. Both washed and unwashed PermaNet® 2.0 and PermaNet® 3.0 LLINs had knockdown and mortality rates of 100% against a susceptible strain of An. gambiae sensu stricto. The adjusted mortality rate of the wild mosquito population after use of the unwashed PermaNet® 3.0 and PermaNet® 2.0 nets was found to be higher than after use of the washed PermaNet® 2.0 and PermaNet® 3.0 nets. Given the increasing incidence of pyrethroid resistance in An. gambiae mosquitoes in Tanzania, we recommend that consideration is given to its distribution in areas with pyrethroid-resistant malaria vectors within the framework of a national insecticide-resistance management plan.

Recapture Heterogeneity in Cliff Swallows: Increased Exposure to Mist Nets Leads to Net Avoidance

PubMed Central

Roche, Erin A.; Brown, Charles R.; Brown, Mary Bomberger; Lear, Kristen M.

2013-01-01

Ecologists often use mark-recapture to estimate demographic variables such as abundance, growth rate, or survival for samples of wild animal populations. A common assumption underlying mark-recapture is that all animals have an equal probability of detection, and failure to meet or correct for this assumption–as when certain members of the population are either easier or more difficult to capture than other animals–can lead to biased and inaccurate demographic estimates. We built within-year and among-years Cormack-Jolly-Seber recaptures-only models to identify causes of capture heterogeneity for a population of colonially nesting cliff swallows (Petrochelidon pyrrhonota) caught using mist-netting as a part of a 20-year mark-recapture study in southwestern Nebraska, U.S.A. Daily detection of cliff swallows caught in stationary mist nets at their colony sites declined as the birds got older and as the frequency of netting at a site within a season increased. Experienced birds’ avoidance of the net could be countered by sudden disturbances that startled them into a net, such as when we dropped a net over the side of a bridge or flushed nesting cliff swallows into a stationary net positioned at a colony entrance. Our results support the widely held, but seldom tested, belief that birds learn to avoid stationary mist nets over time, but also show that modifications of traditional field methods can reduce this source of recapture heterogeneity. PMID:23472138

Current Status and Future Prospect of K-NET and KiK-net

NASA Astrophysics Data System (ADS)

Aoi, S.; Kunugi, T.; Suzuki, W.; Nakamura, H.; Fujiwara, H.

2014-12-01

During 18 years since the deployment of K-NET following the Kobe earthquake, our attention has mainly focused on rapidity of the data collection and an unfailing and reliable observation. In this presentation, we review three generations of the instruments employed by K-NET and KiK-net from these two points of view.At beginning of the 2000's, we newly developed the second generation instruments (K-NET02, K-NET02A, KiK-net06) to replace the first generation instruments (K-NET95, SMAC-MDK) employed when the networks were constructed in the 1990's. These instruments have an automatic dial-out function. It takes typically 2-5 s to establish communication and a few seconds to send the pre-trigger data. After that, data is available typically within a 1.5 s delay. Not only waveform data but also strong motion indexes such as real-time intensity, PGA, PGV, PGD, and response spectra are continuously sent once a second.After the 2011 Tohoku earthquake, we have developed the third generation instruments (K-NET11, KiK-net11) and have replaced almost half of the all stations country wide. Main improvement of this instrument is more unfailing and reliable observation. Because we have often experienced very large ground motions (e.g. 45 records exceeding gravity), the maximum measureable range was expanded from 2000 gal to 4000 gal for the second generation instrument, and to 8000 gal for the third. For the third generation instrument, in case of power failure, observation (including transmission of data) works for seven days thanks to the backup battery, while for the second generation instruments it works only for one day. By adding an oblique component to the three-component accelerometers, we could automatically distinguish shaking data from noise such as electric pulses which may cause a false alarm in EEW. Implementation to guarantee the continuity of observation under severe conditions such as during the Tohoku earthquake is very important, as well as a highly efficient

"When I sleep under the net, nothing bothers me; I sleep well and I'm happy": Senegal's culture of net use and how inconveniences to net use do not translate to net abandonment.

PubMed

Berthe, Sara; Loll, Dana; Faye, Sylvain L; Wone, Issa; Koenker, Hannah; Arnold, Bethany; Weber, Rachel

2014-09-12

Despite recent advances in the fight against the disease, malaria remains a serious threat to the health and well-being of populations in endemic countries. The use of long-lasting insecticidal nets (LLIN) reduces contact between the vector and humans, thereby reducing transmission of the disease. LLINs have become an essential component of malaria control programmes worldwide. The Culture of Net Use study used qualitative and quantitative methods in a longitudinal and iterative design over two phases, in order to capture changes in net use over a year and a half period and covering both dry and rainy seasons. Data were collected from a total of 56 households in eight regions to understand variations due to geographical, cultural, and universal coverage differences. At the time of the data collection, the universal coverage campaign had been completed in six of the eight regions (Dakar and Thies excluded). Perceived barriers to use were primarily related to the characteristics of the net itself, include shape, insecticide, and a variety of minority responses, such as perceived lack of mosquito density and being unaccustomed to using nets. Insecticide-related complaints found that insecticide did not present a significant barrier to use, but was cited as a nuisance. Feelings of suffocation continued to be the most commonly cited nuisance. Respondents who favoured the use of insecticide on nets appeared to be more aware of the health and malaria prevention benefits of the insecticide than those who perceived it negatively. Despite prior evidence that barriers such as heat, shape, insecticide and perceived mosquito density contribute to non-use of LLINs in other countries, this study has shown that these factors are considered more as nuisances and that they do not consistently prevent the use of nets among respondents in Senegal. Of those who cited inconveniences with their nets, few were moved to stop using a net. Respondents from this study overcame these barriers

Markets, voucher subsidies and free nets combine to achieve high bed net coverage in rural Tanzania.

PubMed

Khatib, Rashid A; Killeen, Gerry F; Abdulla, Salim M K; Kahigwa, Elizeus; McElroy, Peter D; Gerrets, Rene P M; Mshinda, Hassan; Mwita, Alex; Kachur, S Patrick

2008-06-02

Tanzania has a well-developed network of commercial ITN retailers. In 2004, the government introduced a voucher subsidy for pregnant women and, in mid 2005, helped distribute free nets to under-fives in small number of districts, including Rufiji on the southern coast, during a child health campaign. Contributions of these multiple insecticide-treated net delivery strategies existing at the same time and place to coverage in a poor rural community were assessed. Cross-sectional household survey in 6,331 members of randomly selected 1,752 households of 31 rural villages of Demographic Surveillance System in Rufiji district, Southern Tanzania was conducted in 2006. A questionnaire was administered to every consenting respondent about net use, treatment status and delivery mechanism. Net use was 62.7% overall, 87.2% amongst infants (0 to 1 year), 81.8% amongst young children (>1 to 5 years), 54.5% amongst older children (6 to 15 years) and 59.6% amongst adults (>15 years). 30.2% of all nets had been treated six months prior to interview. The biggest source of nets used by infants was purchase from the private sector with a voucher subsidy (41.8%). Half of nets used by young children (50.0%) and over a third of those used by older children (37.2%) were obtained free of charge through the vaccination campaign. The largest source of nets amongst the population overall was commercial purchase (45.1% use) and was the primary means for protecting adults (60.2% use). All delivery mechanisms, especially sale of nets at full market price, under-served the poorest but no difference in equity was observed between voucher-subsidized and freely distributed nets. All three delivery strategies enabled a poor rural community to achieve net coverage high enough to yield both personal and community level protection for the entire population. Each of them reached their relevant target group and free nets only temporarily suppressed the net market, illustrating that in this setting that

QuarkNet Stories

Science.gov Websites

      Stories of QuarkNet Teachers and Students   and labs 18 HEP experiments 475 high schools in 28 states 60 ,000 students per year The focus of QuarkNet is to involve teachers and students in our experiments: Teachers do research with us and bring

Net alkalinity and net acidity 1: Theoretical considerations

USGS Publications Warehouse

Kirby, C.S.; Cravotta, C.A.

2005-01-01

Net acidity and net alkalinity are widely used, poorly defined, and commonly misunderstood parameters for the characterization of mine drainage. The authors explain theoretical expressions of 3 types of alkalinity (caustic, phenolphthalein, and total) and acidity (mineral, CO2, and total). Except for rarely-invoked negative alkalinity, theoretically defined total alkalinity is closely analogous to measured alkalinity and presents few practical interpretation problems. Theoretically defined "CO 2-acidity" is closely related to most standard titration methods with an endpoint pH of 8.3 used for determining acidity in mine drainage, but it is unfortunately named because CO2 is intentionally driven off during titration of mine-drainage samples. Using the proton condition/mass- action approach and employing graphs to illustrate speciation with changes in pH, the authors explore the concept of principal components and how to assign acidity contributions to aqueous species commonly present in mine drainage. Acidity is defined in mine drainage based on aqueous speciation at the sample pH and on the capacity of these species to undergo hydrolysis to pH 8.3. Application of this definition shows that the computed acidity in mg L -1 as CaCO3 (based on pH and analytical concentrations of dissolved FeII, FeIII, Mn, and Al in mg L -1):aciditycalculated=50{1000(10-pH)+[2(FeII)+3(FeIII)]/56+2(Mn)/ 55+3(Al)/27}underestimates contributions from HSO4- and H+, but overestimates the acidity due to Fe3+ and Al3+. However, these errors tend to approximately cancel each other. It is demonstrated that "net alkalinity" is a valid mathematical construction based on theoretical definitions of alkalinity and acidity. Further, it is shown that, for most mine-drainage solutions, a useful net alkalinity value can be derived from: (1) alkalinity and acidity values based on aqueous speciation, (2) measured alkalinity minus calculated acidity, or (3) taking the negative of the value obtained in a

Curved Solids Nets

ERIC Educational Resources Information Center

Cohen, Nitsa

2003-01-01

The transformation of a solid to its net is based on something quite different from simple perceptual impression. It is a mental operation performed by manipulating mental images. The aim of this study was to observe pre-service and in-service teachers' ability to visualize the transformation of a curved solid to its net and vice versa, and to try…

NETS

NASA Technical Reports Server (NTRS)

Baffes, Paul T.

1993-01-01

NETS development tool provides environment for simulation and development of neural networks - computer programs that "learn" from experience. Written in ANSI standard C, program allows user to generate C code for implementation of neural network.

Safe Schools, Safe Communities.

ERIC Educational Resources Information Center

Lewis, Julie E.; Pickett, Dean; Pulliam, Janet L.; Schwartz, Richard A.; St. Germaine, Anne-Marie; Underwood, Julie; Worona, Jay

Schools must work together with agencies, groups, and individuals to eliminate the forces leading children to violence. Chapter 1, "School Safety: Working Together to Keep Schools Safe," stresses the importance of community collaboration in violence prevention. Effective prevention requires sharing information about students, consistent…

Patient-Reported Burden of a Neuroendocrine Tumor (NET) Diagnosis: Results From the First Global Survey of Patients With NETs

PubMed Central

Granberg, Dan; Wolin, Edward; Warner, Richard; Sissons, Maia; Kolarova, Teodora; Goldstein, Grace; Pavel, Marianne; Öberg, Kjell; Leyden, John

2017-01-01

Purpose Despite the considerable impact of neuroendocrine tumors (NETs) on patients’ daily lives, the journey of the patient with a NET has rarely been documented, with published data to date being limited to small qualitative studies. NETs are heterogeneous malignancies with nonspecific symptomology, leading to extensive health care use and diagnostic delays that affect survival. A large, international patient survey was conducted to increase understanding of the experience of the patient with a NET and identify unmet needs, with the aim of improving disease awareness and care worldwide. Methods An anonymous, self-reported survey was conducted (online or on paper) from February to May 2014, recruiting patients with NETs from > 12 countries as a collaboration between the International Neuroendocrine Cancer Alliance and Novartis Pharmaceuticals. Survey questions captured information on sociodemographics, clinical characteristics, NET diagnostic experience, disease impact/management, interaction with medical teams, NET knowledge/awareness, and sources of information. This article reports the most relevant findings on patient experience with NETs and the impact of NETs on health care system resources. Results A total of 1,928 patients with NETs participated. A NET diagnosis had a substantially negative impact on patients’ personal and work lives. Patients reported delayed diagnosis and extensive NET-related health care resource use. Patients desired improvement in many aspects of NET care, including availability of a wider range of NET-specific treatment options, better access to NET experts or specialist centers, and a more knowledgeable, better-coordinated/-aligned NET medical team. Conclusion This global patient-reported survey demonstrates the considerable burden of NETs with regard to symptoms, work and daily life, and health care resource use, and highlights considerable unmet needs. Further intervention is required to improve the patient experience among

Patient-Reported Burden of a Neuroendocrine Tumor (NET) Diagnosis: Results From the First Global Survey of Patients With NETs.

PubMed

Singh, Simron; Granberg, Dan; Wolin, Edward; Warner, Richard; Sissons, Maia; Kolarova, Teodora; Goldstein, Grace; Pavel, Marianne; Öberg, Kjell; Leyden, John

2017-02-01

Despite the considerable impact of neuroendocrine tumors (NETs) on patients' daily lives, the journey of the patient with a NET has rarely been documented, with published data to date being limited to small qualitative studies. NETs are heterogeneous malignancies with nonspecific symptomology, leading to extensive health care use and diagnostic delays that affect survival. A large, international patient survey was conducted to increase understanding of the experience of the patient with a NET and identify unmet needs, with the aim of improving disease awareness and care worldwide. An anonymous, self-reported survey was conducted (online or on paper) from February to May 2014, recruiting patients with NETs from > 12 countries as a collaboration between the International Neuroendocrine Cancer Alliance and Novartis Pharmaceuticals. Survey questions captured information on sociodemographics, clinical characteristics, NET diagnostic experience, disease impact/management, interaction with medical teams, NET knowledge/awareness, and sources of information. This article reports the most relevant findings on patient experience with NETs and the impact of NETs on health care system resources. A total of 1,928 patients with NETs participated. A NET diagnosis had a substantially negative impact on patients' personal and work lives. Patients reported delayed diagnosis and extensive NET-related health care resource use. Patients desired improvement in many aspects of NET care, including availability of a wider range of NET-specific treatment options, better access to NET experts or specialist centers, and a more knowledgeable, better-coordinated/-aligned NET medical team. This global patient-reported survey demonstrates the considerable burden of NETs with regard to symptoms, work and daily life, and health care resource use, and highlights considerable unmet needs. Further intervention is required to improve the patient experience among those with NETs.

Adaptive Decision Making and Coordination in Variable Structure Organizations

DTIC Science & Technology

1994-09-01

behavior of the net. The design problem is addressed by (a) focusing on algorithms that relate structural properties of’ the Petri Net model to... behavioral characteristics; and (b) by incorporating design requirements in the Lattice algorithm. ’K94-30756 9 4 9 2 P 0 8 II083II Bl l~ll i1111 I! 14...the more resource- consuming the process is. The architecture designer has to deal with these two parameters and perform some tradeoffs. The more

7 CFR 51.489 - Well netted.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 2 2011-01-01 2011-01-01 false Well netted. 51.489 Section 51.489 Agriculture... Standards for Grades of Cantaloups 1 Definitions § 51.489 Well netted. Well netted means that to an extent characteristic of the variety the cantaloup is well covered with fully developed, well raised netting, some...

7 CFR 51.489 - Well netted.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 2 2012-01-01 2012-01-01 false Well netted. 51.489 Section 51.489 Agriculture... Standards for Grades of Cantaloups 1 Definitions § 51.489 Well netted. Well netted means that to an extent characteristic of the variety the cantaloup is well covered with fully developed, well raised netting, some...

The Net Advance of Physics

Science.gov Websites

THE NET ADVANCE OF PHYSICS Review Articles and Tutorials in an Encyclopædic Format Established 1995 [Link to MIT] Computer support for The Net Advance of Physics is furnished by The Massachusetts Newest Additions SPECIAL FEATURES: Net Advance RETRO: Nineteenth Century Physics History of Science

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments

PubMed Central

Thomas, Brandon R.; Chylek, Lily A.; Colvin, Joshua; Sirimulla, Suman; Clayton, Andrew H.A.; Hlavacek, William S.; Posner, Richard G.

2016-01-01

Summary: Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive. Availability and implementation: BioNetFit can be used on stand-alone Mac, Windows/Cygwin, and Linux platforms and on Linux-based clusters running SLURM, Torque/PBS, or SGE. The BioNetFit source code (Perl) is freely available (http://bionetfit.nau.edu). Supplementary information: Supplementary data are available at Bioinformatics online. Contact: bionetgen.help@gmail.com PMID:26556387

Methods of verifying net carbon

DOE Office of Scientific and Technical Information (OSTI.GOV)

McClung, M.

1996-10-01

Problems currently exist with using net carbon as an industrial standard to gauge smelter performance. First, throughout the industry there are a number of different methods used for determining net carbon. Also, until recently there has not been a viable method to cross check or predict change in net carbon. This inherently leads to differences and most likely inaccuracies when comparing performances of different plants using a net carbon number. Ravenswood uses specific methods when calculating the net carbon balance. The R and D Carbon, Ltd. formula developed by Verner Fisher, et al, to predict and cross check net carbonmore » based on baked carbon core analysis has been successfully used. Another method is used, as a cross check, which is based on the raw materials (cokes and pitch) usage as related to the metal produced. The combination of these methods gives a definitive representation of the carbon performance in the reduction cell. This report details the methods Ravenswood Aluminum uses and the information derived from it.« less

27 CFR 4.37 - Net contents.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Net contents. 4.37 Section 4.37 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS LABELING AND ADVERTISING OF WINE Labeling Requirements for Wine § 4.37 Net contents. (a) Statement of net contents. The net...

27 CFR 4.37 - Net contents.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Net contents. 4.37 Section 4.37 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL LABELING AND ADVERTISING OF WINE Labeling Requirements for Wine § 4.37 Net contents. (a) Statement of net contents. The net...

27 CFR 4.37 - Net contents.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false Net contents. 4.37 Section 4.37 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL LABELING AND ADVERTISING OF WINE Labeling Requirements for Wine § 4.37 Net contents. (a) Statement of net contents. The net...

27 CFR 4.37 - Net contents.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Net contents. 4.37 Section 4.37 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS LABELING AND ADVERTISING OF WINE Labeling Requirements for Wine § 4.37 Net contents. (a) Statement of net contents. The net...

27 CFR 4.37 - Net contents.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Net contents. 4.37 Section 4.37 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS LABELING AND ADVERTISING OF WINE Labeling Requirements for Wine § 4.37 Net contents. (a) Statement of net contents. The net...

NASA Net Zero Energy Buildings Roadmap

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pless, S.; Scheib, J.; Torcellini, P.

In preparation for the time-phased net zero energy requirement for new federal buildings starting in 2020, set forth in Executive Order 13514, NASA requested that the National Renewable Energy Laboratory (NREL) to develop a roadmap for NASA's compliance. NASA detailed a Statement of Work that requested information on strategic, organizational, and tactical aspects of net zero energy buildings. In response, this document presents a high-level approach to net zero energy planning, design, construction, and operations, based on NREL's first-hand experience procuring net zero energy construction, and based on NREL and other industry research on net zero energy feasibility. The strategicmore » approach to net zero energy starts with an interpretation of the executive order language relating to net zero energy. Specifically, this roadmap defines a net zero energy acquisition process as one that sets an aggressive energy use intensity goal for the building in project planning, meets the reduced demand goal through energy efficiency strategies and technologies, then adds renewable energy in a prioritized manner, using building-associated, emission- free sources first, to offset the annual energy use required at the building; the net zero energy process extends through the life of the building, requiring a balance of energy use and production in each calendar year.« less

AdaNET research project

NASA Technical Reports Server (NTRS)

Digman, R. Michael

1988-01-01

The components necessary for the success of the commercialization of an Ada Technology Transition Network are reported in detail. The organizational plan presents the planned structure for services development and technical transition of AdaNET services to potential user communities. The Business Plan is the operational plan for the AdaNET service as a commercial venture. The Technical Plan is the plan from which the AdaNET can be designed including detailed requirements analysis. Also contained is an analysis of user fees and charges, and a proposed user fee schedule.

29 CFR 4062.4 - Determinations of net worth and collective net worth.

Code of Federal Regulations, 2011 CFR

2011-07-01

... section, have been improperly transferred. In making such determinations, the PBGC will consider... determining net worth. A person's net worth is equal to its fair market value and fair market value shall be... financial condition, and business history. (6) The economic outlook for the person's industry and the market...

Exploring the long-term balance between net precipitation and net groundwater exchange in Florida seepage lakes

USGS Publications Warehouse

Lee, Terrie M.; Sacks, Laura A.; Swancar, Amy

2014-01-01

The long-term balance between net precipitation and net groundwater exchange that maintains thousands of seepage lakes in Florida’s karst terrain is explored at a representative lake basin and then regionally for the State’s peninsular lake district. The 15-year water budget of Lake Starr includes El Niño Southern Oscillation (ENSO)-related extremes in rainfall, and provides the longest record of Bowen ratio energy-budget (BREB) lake evaporation and lake-groundwater exchanges in the southeastern United States. Negative net precipitation averaging -25 cm/yr at Lake Starr overturns the previously-held conclusion that lakes in this region receive surplus net precipitation. Net groundwater exchange with the lake was positive on average but too small to balance the net precipitation deficit. Groundwater pumping effects and surface-water withdrawals from the lake widened the imbalance. Satellite-based regional estimates of potential evapotranspiration at five large lakes in peninsular Florida compared well with basin-scale evaporation measurements from seven open-water sites that used BREB methods. The regional average lake evaporation estimated for Lake Starr during 1996-2011 was within 5 percent of its measured average, and regional net precipitation agreed within 10 percent. Regional net precipitation to lakes was negative throughout central peninsular Florida and the net precipitation deficit increased by about 20 cm from north to south. Results indicate that seepage lakes farther south on the peninsula receive greater net groundwater inflow than northern lakes and imply that northern lakes are in comparatively leakier hydrogeologic settings. Findings reveal the peninsular lake district to be more vulnerable than was previously realized to drier climate, surface-water withdrawals from lakes, and groundwater pumping effects.

Decision net, directed graph, and neural net processing of imaging spectrometer data

NASA Technical Reports Server (NTRS)

Casasent, David; Liu, Shiaw-Dong; Yoneyama, Hideyuki; Barnard, Etienne

1989-01-01

A decision-net solution involving a novel hierarchical classifier and a set of multiple directed graphs, as well as a neural-net solution, are respectively presented for large-class problem and mixture problem treatments of imaging spectrometer data. The clustering method for hierarchical classifier design, when used with multiple directed graphs, yields an efficient decision net. New directed-graph rules for reducing local maxima as well as the number of perturbations required, and the new starting-node rules for extending the reachability and reducing the search time of the graphs, are noted to yield superior results, as indicated by an illustrative 500-class imaging spectrometer problem.

Principles of E-network modelling of heterogeneous systems

NASA Astrophysics Data System (ADS)

Tarakanov, D.; Tsapko, I.; Tsapko, S.; Buldygin, R.

2016-04-01

The present article is concerned with the analytical and simulation modelling of heterogeneous technical systems using E-network mathematical apparatus (the expansion of Petri nets). The distinguishing feature of the given system is the presence of the module6 which identifies the parameters of the controlled object as well as the external environment.

Entomological evaluation of PermaNet 2.0® and K-O Tab 1-2-3® treated nets in comparison to nets conventionally treated with deltamethrin, after repeated washing.

PubMed

Kayedi, Mohammad Hassan; Khamisabadi, Kiumars; Dehghani, Nader; Haghdoost, Ali Akbar

2015-06-01

The residual insecticidal power of two types of ITNs (PermaNet 2.0® (PN2) and K-O Tab 1-2-3® (KO 123)), compared to K-O Tab® (KO) treated nets, was assessed. The nets were tested unwashed, and after being washed, by hand 5, 15 and 21 times, respectively. After each wash, the nets were dried vertically on a line, in the shade. Two types of bioassays (mean median knock down times (MMKDT) and mortality 24 hours after a 3-minute exposure (%mortality)) were used, along with reared female Anopheles stephensi. The number of washes had a great impact on MMKDT and %mortality of all types of nets. This impact was greater for conventionally treated nets, indicating that PN2 and KO 123 nets are significantly more wash resistant than KO nets after 21 washes. There was no significant difference between PN2 and KO 123 with respect to %mortality 24 hours after a 3-minute exposure at 0, 15 and 21 washes. Similarly, the same results were obtained for MMKDT, and the differences between PN2 and KO 123 were not statistically significant. This study demonstrates that the efficacy of KO 123 nets is as beneficial as the efficacy of PN2 nets up to 21 washes.

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments

DOE PAGES

Thomas, Brandon R.; Chylek, Lily A.; Colvin, Joshua; ...

2015-11-09

Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here in this paper, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive.

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.

PubMed

Thomas, Brandon R; Chylek, Lily A; Colvin, Joshua; Sirimulla, Suman; Clayton, Andrew H A; Hlavacek, William S; Posner, Richard G

2016-03-01

Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive. BioNetFit can be used on stand-alone Mac, Windows/Cygwin, and Linux platforms and on Linux-based clusters running SLURM, Torque/PBS, or SGE. The BioNetFit source code (Perl) is freely available (http://bionetfit.nau.edu). Supplementary data are available at Bioinformatics online. bionetgen.help@gmail.com. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Bed Net Durability Assessments: Exploring a Composite Measure of Net Damage

PubMed Central

Vanden Eng, Jodi L.; Chan, Adeline; Abílio, Ana Paula; Wolkon, Adam; Ponce de Leon, Gabriel; Gimnig, John; Morgan, Juliette

2015-01-01

Background The durability of Long Lasting Insecticidal Nets (LLINs) in field conditions is of great importance for malaria prevention and control efforts; however, the physical integrity of the net fabric is not well understood making it challenging to determine overall effectiveness of nets as they age. The 2011 World Health Organization Pesticide Evaluation Scheme (WHOPES) guidelines provide a simple, standardized method using a proportional hole index (PHI) for assessing net damage with the intent to provide national malaria control programs with guidelines to assess the useful life of LLINS and estimate the rate of replacement. Methods We evaluated the utility of the PHI measure using 409 LLINs collected over three years in Nampula Province, Mozambique following a mass distribution campaign in 2008. For each LLIN the diameter and distance from the bottom of the net were recorded for every hole. Holes were classified into four size categories and a PHI was calculated following WHOPES guidelines. We investigate how the size, shape, and location of holes influence the PHI. The areas of the WHOPES defined categories were compared to circular and elliptical areas based on approximate shape and actual measured axes of each hole and the PHI was compared to cumulative damaged surface area of the LLIN. Results The damaged area of small, medium, large, and extra-large holes was overestimated using the WHOPES categories compared to elliptical areas using the actual measured axes. Similar results were found when comparing to circular areas except for extra-large holes which were underestimated. (Wilcoxon signed rank test of differences p< 0.0001 for all sizes). Approximating holes as circular overestimated hole surface area by 1.5 to 2 times or more. There was a significant difference in the mean number of holes < 0.5 cm by brand and there were more holes of all sizes on the bottom of nets than the top. For a range of hypothetical PHI thresholds used to designate a �

Bed Net Durability Assessments: Exploring a Composite Measure of Net Damage.

PubMed

Vanden Eng, Jodi L; Chan, Adeline; Abílio, Ana Paula; Wolkon, Adam; Ponce de Leon, Gabriel; Gimnig, John; Morgan, Juliette

2015-01-01

The durability of Long Lasting Insecticidal Nets (LLINs) in field conditions is of great importance for malaria prevention and control efforts; however, the physical integrity of the net fabric is not well understood making it challenging to determine overall effectiveness of nets as they age. The 2011 World Health Organization Pesticide Evaluation Scheme (WHOPES) guidelines provide a simple, standardized method using a proportional hole index (PHI) for assessing net damage with the intent to provide national malaria control programs with guidelines to assess the useful life of LLINS and estimate the rate of replacement. We evaluated the utility of the PHI measure using 409 LLINs collected over three years in Nampula Province, Mozambique following a mass distribution campaign in 2008. For each LLIN the diameter and distance from the bottom of the net were recorded for every hole. Holes were classified into four size categories and a PHI was calculated following WHOPES guidelines. We investigate how the size, shape, and location of holes influence the PHI. The areas of the WHOPES defined categories were compared to circular and elliptical areas based on approximate shape and actual measured axes of each hole and the PHI was compared to cumulative damaged surface area of the LLIN. The damaged area of small, medium, large, and extra-large holes was overestimated using the WHOPES categories compared to elliptical areas using the actual measured axes. Similar results were found when comparing to circular areas except for extra-large holes which were underestimated. (Wilcoxon signed rank test of differences p< 0.0001 for all sizes). Approximating holes as circular overestimated hole surface area by 1.5 to 2 times or more. There was a significant difference in the mean number of holes < 0.5 cm by brand and there were more holes of all sizes on the bottom of nets than the top. For a range of hypothetical PHI thresholds used to designate a "failed LLIN", roughly 75 to 80

MetNet - Martian Network Mission

NASA Astrophysics Data System (ADS)

Harri, A.-M.

2009-04-01

We are developing a new kind of planetary exploration mission for Mars - MetNet in situ observation network based on a new semi-hard landing vehicle called the Met-Net Lander (MNL). The actual practical mission development work started in January 2009 with participation from various countries and space agencies. The scientific rationale and goals as well as key mission solutions will be discussed. The eventual scope of the MetNet Mission is to deploy some 20 MNLs on the Martian surface using inflatable descent system structures, which will be supported by observations from the orbit around Mars. Currently we are working on the MetNet Mars Precursor Mission (MMPM) to deploy one MetNet Lander to Mars in the 2009/2011 launch window as a technology and science demonstration mission. The MNL will have a versatile science payload focused on the atmospheric science of Mars. Detailed characterization of the Martian atmospheric circulation patterns, boundary layer phenomena, and climatology cycles, require simultaneous in-situ measurements by a network of observation posts on the Martian surface. The scientific payload of the MetNet Mission encompasses separate instrument packages for the atmospheric entry and descent phase and for the surface operation phase. The MetNet mission concept and key probe technologies have been developed and the critical subsystems have been qualified to meet the Martian environmental and functional conditions. This development effort has been fulfilled in collaboration between the Finnish Meteorological Institute (FMI), the Russian Lavoschkin Association (LA) and the Russian Space Research Institute (IKI) since August 2001. Currently the INTA (Instituto Nacional de Técnica Aeroespacial) from Spain is also participating in the MetNet payload development.

Safe sex self-efficacy and safe sex practice in a Southern United States College

PubMed Central

Addoh, Ovuokerie; Sng, Eveleen; Loprinzi, Paul D.

2017-01-01

Background: The purpose of this study was to assess the association between safe sex self-efficacy and safe-sex practice in a Southern college setting. Methods: Multivariable logistic regression models were used to examine the association between safe sex self-efficacy in four domains (mechanics, partner disapproval, assertiveness, intoxicants) and safe sex practice (outcome variable). Results: For every 1-unit increase in the composite condom use self-efficacy score, there was an 8% increase in the odds of being beyond the median safe-sex practice score (odds ration [OR]: 1.08, 95% CI: 1.02-1.15). Additionally, for every 1-unit increase in intoxicants self-efficacy score, there was a 31% increase in the odds of being beyond the median safe-sex practice score (OR: 1.31, 95% CI: 1.08-1.58). Conclusion: A greater degree of safe-sex self-efficacy is associated with increased odds of safe-sex practice. These findings are informative for the development of targeted approaches to foster safe-sex behavior in Southern US colleges. PMID:28326287

The dental safety net in Connecticut.

PubMed

Beazoglou, Tryfon; Heffley, Dennis; Lepowsky, Steven; Douglass, Joanna; Lopez, Monica; Bailit, Howard

2005-10-01

Many poor, medically disabled and geographically isolated populations have difficulty accessing private-sector dental care and are considered underserved. To address this problem, public- and voluntary-sector organizations have established clinics and provide care to the underserved. Collectively, these clinics are known as "the dental safety net." The authors describe the dental safety net in Connecticut and examine the capacity and efficiency of this system to provide care to the noninstitutionalized underserved population of the state. The authors describe Connecticut's dental safety net in terms of dentists, allied health staff members, operatories, patient visits and patients treated per dentist per year. The authors compare the productivity of safety-net dentists with that of private practitioners. They also estimate the capacity of the safety net to treat people enrolled in Medicaid and the State Children's Health Insurance Program. The safety net is made up of dental clinics in community health centers, hospitals, the dental school and public schools. One hundred eleven dentists, 38 hygienists and 95 dental assistants staff the clinics. Safety-net dentists have fewer patient visits and patients than do private practitioners. The Connecticut safety-net system has the capacity to treat about 28.2 percent of publicly insured patients. The dental safety net is an important community resource, and greater use of allied dental personnel could substantially improve the capacity of the system to care for the poor and other underserved populations.

DroidSafe

DTIC Science & Technology

2016-12-01

branches of our work . 3.1 Understanding Sensitive API Call and API Information Usage Android applications are written in a type- safe language (Java...directly invoke resolved targets. Because DroidSafe works with a comprehensive model of the Android environment , it supports precise resolution of...STATEMENT. FOR THE CHIEF ENGINEER: / S / / S / MARK K. WILLIAMS WARREN H. DEBANY, JR. Work Unit Manager

Modelling a radiology department service using a VDL integrated approach.

PubMed

Guglielmino, Maria Gabriella; Celano, Giovanni; Costa, Antonio; Fichera, Sergio

2009-01-01

The healthcare industry is facing several challenges such as the reduction of costs and quality improvement of the provided services. Engineering studies could be very useful in supporting organizational and management processes. Healthcare service efficiency depends on a strong collaboration between clinical and engineering experts, especially when it comes to analyzing the system and its constraints in detail and subsequently, when it comes to deciding on the reengineering of some key activities. The purpose of this paper is to propose a case study showing how a mix of representation tools allow a manager of a radiology department to solve some human and technological resource re-organizational issues, which have to be faced due to the introduction of a new technology and a new portfolio of services. In order to simulate the activities within the radiology department and examine the relationship between human and technological resources, different visual diagrammatic language (VDL) techniques have been implemented to get knowledge about the heterogeneous factors related to the healthcare service delivery. In particular, flow charts, IDEFO diagrams and Petri nets have been integrated each other with success as a modelisation tools. The simulation study performed through the application of the aforementioned VDL techniques suggests the opportunity of re-organizing the nurse activities within the radiology department. The re-organization of a healthcare service and in particular of a radiology department by means of joint flow charts, IDEF0 diagrams and Petri nets is a poorly investigated topic in literature. This paper demonstrates how flow charts and IDEF0 can help people working within the department to understand the weak points of their organization and constitute an efficient base of knowledge for the implementation of a Petri net aimed at improving the departmental performance.

Constant speed control of four-stroke micro internal combustion swing engine

NASA Astrophysics Data System (ADS)

Gao, Dedong; Lei, Yong; Zhu, Honghai; Ni, Jun

2015-09-01

The increasing demands on safety, emission and fuel consumption require more accurate control models of micro internal combustion swing engine (MICSE). The objective of this paper is to investigate the constant speed control models of four-stroke MICSE. The operation principle of the four-stroke MICSE is presented based on the description of MICSE prototype. A two-level Petri net based hybrid model is proposed to model the four-stroke MICSE engine cycle. The Petri net subsystem at the upper level controls and synchronizes the four Petri net subsystems at the lower level. The continuous sub-models, including breathing dynamics of intake manifold, thermodynamics of the chamber and dynamics of the torque generation, are investigated and integrated with the discrete model in MATLAB Simulink. Through the comparison of experimental data and simulated DC voltage output, it is demonstrated that the hybrid model is valid for the four-stroke MICSE system. A nonlinear model is obtained from the cycle average data via the regression method, and it is linearized around a given nominal equilibrium point for the controller design. The feedback controller of the spark timing and valve duration timing is designed with a sequential loop closing design approach. The simulation of the sequential loop closure control design applied to the hybrid model is implemented in MATLAB. The simulation results show that the system is able to reach its desired operating point within 0.2 s, and the designed controller shows good MICSE engine performance with a constant speed. This paper presents the constant speed control models of four-stroke MICSE and carries out the simulation tests, the models and the simulation results can be used for further study on the precision control of four-stroke MICSE.

A Safe Ride to School; A Safe Ride Home.

ERIC Educational Resources Information Center

Illinois State Board of Education, Springfield.

Text and illustrations are used to teach safe school bus riding practices. The guide begins with instructions to parents or guardians to set a good example of safe behavior, and to help children learn safety rules and be on time. Instructions to children concern obeying the bus driver, boarding the bus, riding the bus, crossing the road, and using…

Capturing birds with mist nets: A review

USGS Publications Warehouse

Keyes, B.E.; Grue, C.E.

1982-01-01

Herein we have tried to provide a comprehensive review of mist-netting techniques suitable for both novice and experienced netters. General mist-netting procedures and modifications developed by netters for particular bird species and habitats are included. Factors which influence capture success, including site selection, net specifications and placement, weather, and time of day, are discussed. Guidelines are presented for the care of netted birds and the use of mist-net data in the study of bird communities. The advantages of the use of mist nets over other methods of capturing birds are also discussed.

Performance modeling of automated manufacturing systems

NASA Astrophysics Data System (ADS)

Viswanadham, N.; Narahari, Y.

A unified and systematic treatment is presented of modeling methodologies and analysis techniques for performance evaluation of automated manufacturing systems. The book is the first treatment of the mathematical modeling of manufacturing systems. Automated manufacturing systems are surveyed and three principal analytical modeling paradigms are discussed: Markov chains, queues and queueing networks, and Petri nets.

Bed net ownership in Kenya: the impact of 3.4 million free bed nets.

PubMed

Hightower, Allen; Kiptui, Rebecca; Manya, Ayub; Wolkon, Adam; Vanden Eng, Jodi Leigh; Hamel, Mary; Noor, Abdisalan; Sharif, Shahnaz K; Buluma, Robert; Vulule, John; Laserson, Kayla; Slutsker, Laurence; Akhwale, Willis

2010-06-24

In July and September 2006, 3.4 million long-lasting insecticide-treated bed nets (LLINs) were distributed free in a campaign targeting children 0-59 months old (CU5s) in the 46 districts with malaria in Kenya. A survey was conducted one month after the distribution to evaluate who received campaign LLINs, who owned insecticide-treated bed nets and other bed nets received through other channels, and how these nets were being used. The feasibility of a distribution strategy aimed at a high-risk target group to meet bed net ownership and usage targets is evaluated. A stratified, two-stage cluster survey sampled districts and enumeration areas with probability proportional to size. Handheld computers (PDAs) with attached global positioning systems (GPS) were used to develop the sampling frame, guide interviewers back to chosen households, and collect survey data. In targeted areas, 67.5% (95% CI: 64.6, 70.3%) of all households with CU5s received campaign LLINs. Including previously owned nets, 74.4% (95% CI: 71.8, 77.0%) of all households with CU5s had an ITN. Over half of CU5s (51.7%, 95% CI: 48.8, 54.7%) slept under an ITN during the previous evening. Nearly forty percent (39.1%) of all households received a campaign net, elevating overall household ownership of ITNs to 50.7% (95% CI: 48.4, 52.9%). The campaign was successful in reaching the target population, families with CU5s, the risk group most vulnerable to malaria. Targeted distribution strategies will help Kenya approach indicator targets, but will need to be combined with other strategies to achieve desired population coverage levels.

Mars MetNet Mission Status

NASA Astrophysics Data System (ADS)

Harri, A.-M.; Aleksashkin, S.; Arruego, I.; Schmidt, W.; Genzer, M.; Vazquez, L.; Haukka, H.; Palin, M.; Nikkanen, T.

2015-10-01

New kind of planetary exploration mission for Mars is under development in collaboration between the Finnish Meteorological Institute (FMI), Lavochkin Association (LA), Space Research Institute (IKI) and Institutio Nacional de Tecnica Aerospacial (INTA). The Mars MetNet mission is based on a new semihard landing vehicle called MetNet Lander (MNL). The scientific payload of the Mars MetNet Precursor [1] mission is divided into three categories: Atmospheric instruments, Optical devices and Composition and structure devices. Each of the payload instruments will provide significant insights in to the Martian atmospheric behavior. The key technologies of the MetNet Lander have been qualified and the electrical qualification model (EQM) of the payload bay has been built and successfully tested.

Distributed state-space generation of discrete-state stochastic models

NASA Technical Reports Server (NTRS)

Ciardo, Gianfranco; Gluckman, Joshua; Nicol, David

1995-01-01

High-level formalisms such as stochastic Petri nets can be used to model complex systems. Analysis of logical and numerical properties of these models of ten requires the generation and storage of the entire underlying state space. This imposes practical limitations on the types of systems which can be modeled. Because of the vast amount of memory consumed, we investigate distributed algorithms for the generation of state space graphs. The distributed construction allows us to take advantage of the combined memory readily available on a network of workstations. The key technical problem is to find effective methods for on-the-fly partitioning, so that the state space is evenly distributed among processors. In this paper we report on the implementation of a distributed state-space generator that may be linked to a number of existing system modeling tools. We discuss partitioning strategies in the context of Petri net models, and report on performance observed on a network of workstations, as well as on a distributed memory multi-computer.

Method for hierarchical modeling of the command of flexible manufacturing systems

NASA Astrophysics Data System (ADS)

Ausfelder, Christian; Castelain, Emmanuel; Gentina, Jean-Claude

1994-04-01

The present paper focuses on the modeling of the command and proposes a hierarchical and modular approach which is oriented on the physical structure of FMS. The requirements issuing from monitoring of FMS are discussed and integrated in the proposed model. Its modularity makes the approach open for extensions concerning as well the production resources as the products. As a modeling tool, we have chosen Object Petri nets. The first part of the paper describes desirable features of an FMS command such as safety, robustness, and adaptability. As it is shown, these features result from the flexibility of the installation. The modeling method presented in the second part of the paper begins with a structural analysis of FMS and defines a natural command hierarchy, where the coordination of the production process, the synchronization of production resources on products, and the internal coordination are treated separately. The method is rigorous and leads to a structured and modular Petri net model which can be used for FMS simulation or translated into the final command code.

Catch of channel catfish with tandem-set hoop nets and gill nets in lentic systems of Nebraska

USGS Publications Warehouse

Richters, Lindsey K.; Pope, Kevin L.

2011-01-01

Twenty-six Nebraska water bodies representing two ecosystem types (small standing waters and large standing waters) were surveyed during 2008 and 2009 with tandem-set hoop nets and experimental gill nets to determine if similar trends existed in catch rates and size structures of channel catfish Ictalurus punctatus captured with these gears. Gear efficiency was assessed as the number of sets (nets) that would be required to capture 100 channel catfish given observed catch per unit effort (CPUE). Efficiency of gill nets was not correlated with efficiency of hoop nets for capturing channel catfish. Small sample sizes prohibited estimation of proportional size distributions in most surveys; in the four surveys for which sample size was sufficient to quantify length-frequency distributions of captured channel catfish, distributions differed between gears. The CPUE of channel catfish did not differ between small and large water bodies for either gear. While catch rates of hoop nets were lower than rates recorded in previous studies, this gear was more efficient than gill nets at capturing channel catfish. However, comparisons of size structure between gears may be problematic.

Bed net ownership in Kenya: the impact of 3.4 million free bed nets

PubMed Central

2010-01-01

Background In July and September 2006, 3.4 million long-lasting insecticide-treated bed nets (LLINs) were distributed free in a campaign targeting children 0-59 months old (CU5s) in the 46 districts with malaria in Kenya. A survey was conducted one month after the distribution to evaluate who received campaign LLINs, who owned insecticide-treated bed nets and other bed nets received through other channels, and how these nets were being used. The feasibility of a distribution strategy aimed at a high-risk target group to meet bed net ownership and usage targets is evaluated. Methods A stratified, two-stage cluster survey sampled districts and enumeration areas with probability proportional to size. Handheld computers (PDAs) with attached global positioning systems (GPS) were used to develop the sampling frame, guide interviewers back to chosen households, and collect survey data. Results In targeted areas, 67.5% (95% CI: 64.6, 70.3%) of all households with CU5s received campaign LLINs. Including previously owned nets, 74.4% (95% CI: 71.8, 77.0%) of all households with CU5s had an ITN. Over half of CU5s (51.7%, 95% CI: 48.8, 54.7%) slept under an ITN during the previous evening. Nearly forty percent (39.1%) of all households received a campaign net, elevating overall household ownership of ITNs to 50.7% (95% CI: 48.4, 52.9%). Conclusions The campaign was successful in reaching the target population, families with CU5s, the risk group most vulnerable to malaria. Targeted distribution strategies will help Kenya approach indicator targets, but will need to be combined with other strategies to achieve desired population coverage levels. PMID:20576145

Use Medicines Safely

MedlinePlus

... Medicines Safely Print This Topic En español Use Medicines Safely Browse Sections The Basics Overview Prescription Medicines ... Medicines 1 of 7 sections The Basics: Prescription Medicines There are different types of medicine. The 2 ...

BreadNet: An On-Line Community.

ERIC Educational Resources Information Center

Walker, Susan

1987-01-01

Describes BreadNet, a computer network linking Middlebury College English teachers, their associates, and students. Network extends to rural English teachers and their K-8 students. BreadNet used for student pen pal program, teacher teleconferencing, information access. Also describes BreadNet's problems and future possibilities. (TES)

The Micro-Pulse Lidar Network (MPL-Net)

NASA Technical Reports Server (NTRS)

Welton, Ellsworth J.; Campbell, James R.; Berkoff, Timothy A.; Spinhirne, James D.; Tsay, Si-Chee; Holben, Brent; Shiobara, Masataka; Starr, David OC. (Technical Monitor)

2002-01-01

In the early 1990s, the first small, eye-safe, and autonomous lidar system was developed, the Micro-pulse Lidar (MPL). The MPL has proven to be useful in the field because it can be automated, runs continuously (day and night), is eye-safe, can easily be transported and set up, and has a small field-of-view which limits multiple scattering concerns. The MPL acquires signal profiles of backscattered laser light from aerosols and clouds. The signals are analyzed to yield multiple layer heights, optical depths of each layer, average extinction-to-backscatter ratio of each layer, and profiles of extinction in each layer. The MPL has been used in a wide variety of field studies over the past 10 years, leading to nearly 20 papers and many conference presentations. In 2000, a new project using MPL systems was started at NASA Goddard Space Flight Center. The MPL-Net project is currently working to establish a worldwide network of MPL systems, all co-located with NASA's AERONET sunphotometers for joint measurements of optical depth and sky radiance. Automated processing algorithms have been developed to produce data products on a next day basis for all sites and some field experiments. Initial results from the first several sites are shown, along with aerosol data collected during several major field campaigns. Measurements of the aerosol extinction-to-backscatter ratio at several different geographic regions, and for various aerosol types are shown. This information is used to improve the construction of look up tables of the ratio, needed to process aerosol profiles acquired with satellite based lidars.

Business Profile of Boat Lift Net and Stationary Lift Net Fishing Gear in Morodemak Waters Central Java

NASA Astrophysics Data System (ADS)

Hapsari, Trisnani D.; Jayanto, Bogi B.; Fitri, Aristi D. P.; Triarso, I.

2018-02-01

Lift net is one of the fishing gears that is used widely in the Morodemak coastal fishing port (PPP) for catching pelagic fish. The yield of fish captured by these fishing gear has high economic value, such as fish belt (Trichiurus sp), squids (Loligo sp) and anchovies (Stelophorus sp). The aims of this research were to determine the technical aspects of boat lift net and stationary lift net fishing gear in Morodemak Waters Demak Regency; to find out the financial aspect of those fishing gears and to analyze the financial feasibility by counting PP, NPV, IRR, and B/C ratio criteria. This research used case study method with descriptive analysis. The sampling method was purposive sampling with 22 fishermen as respondents. The result of the research showed that the average of boat lift net acceptance was Rp 388,580,000. The financial analysis of fisheries boat lift net with the result of NPV Rp 836,149,272, PP 2.44 years, IRR value 54%, and B/C ratio 1.73. The average of stationary lift net acceptance was Rp 27,750,000. The financial analysis lift net with the result of NPV Rp 37,937,601; PP 1.96 years, IRR value 86%, and B/C ratio 1.32. This research had a positive NPV value, B/C ratio >1, and IRR > discount rate (12 %). This study concluded that the fishery business of boat lift net and stationary lift net in Morodemak coastal fishing port (PPP) was worth running.

47 CFR 65.500 - Net income.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Net income. 65.500 Section 65.500... OF RETURN PRESCRIPTION PROCEDURES AND METHODOLOGIES Interexchange Carriers § 65.500 Net income. The net income methodology specified in § 65.450 shall be utilized by all interexchange carriers that are...

Picture Me Safe

ERIC Educational Resources Information Center

Irvin, Daniel W.

1977-01-01

The validity of well-written articles can be destroyed by poor illustration, especially when the pictures show unsafe practices. The responsibility lies with the author to provide clear printable pictures showing safe working environments and safe practices. (Editor)

UChicago-FNAL QuarkNet

Science.gov Websites

QuarkNet group has high school teachers from the Chicago suburbs. We meet twice in the summer, and a few classroom activities. During the summer, we host teams of high school students and teachers. These teams work on research projects with scientists at Fermilab. Read more about the QuarkNet program. High

7 CFR 51.489 - Well netted.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 2 2014-01-01 2014-01-01 false Well netted. 51.489 Section 51.489 Agriculture..., CERTIFICATION, AND STANDARDS) United States Standards for Grades of Cantaloups 1 Definitions § 51.489 Well netted. Well netted means that to an extent characteristic of the variety the cantaloup is well covered...

7 CFR 51.489 - Well netted.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 2 2013-01-01 2013-01-01 false Well netted. 51.489 Section 51.489 Agriculture..., CERTIFICATION, AND STANDARDS) United States Standards for Grades of Cantaloups 1 Definitions § 51.489 Well netted. Well netted means that to an extent characteristic of the variety the cantaloup is well covered...

MPL-Net Measurements of Aerosol and Cloud Vertical Distributions at Co-Located AERONET Sites

NASA Technical Reports Server (NTRS)

Welton, Ellsworth J.; Campbell, James R.; Berkoff, Timothy A.; Spinhirne, James D.; Tsay, Si-Chee; Holben, Brent; Starr, David OC. (Technical Monitor)

2002-01-01

In the early 1990s, the first small, eye-safe, and autonomous lidar system was developed, the Micropulse Lidar (MPL). The MPL acquires signal profiles of backscattered laser light from aerosols and clouds. The signals are analyzed to yield multiple layer heights, optical depths of each layer, average extinction-to-backscatter ratios for each layer, and profiles of extinction in each layer. In 2000, several MPL sites were organized into a coordinated network, called MPL-Net, by the Cloud and Aerosol Lidar Group at NASA Goddard Space Flight Center (GSFC) using funding provided by the NASA Earth Observing System. tn addition to the funding provided by NASA EOS, the NASA CERES Ground Validation Group supplied four MPL systems to the project, and the NASA TOMS group contributed their MPL for work at GSFC. The Atmospheric Radiation Measurement Program (ARM) also agreed to make their data available to the MPL-Net project for processing. In addition to the initial NASA and ARM operated sites, several other independent research groups have also expressed interest in joining the network using their own instruments. Finally, a limited amount of EOS funding was set aside to participate in various field experiments each year. The NASA Sensor Intercomparison and Merger for Biological and Interdisciplinary Oceanic Studies (SIMBIOS) project also provides funds to deploy their MPL during ocean research cruises. All together, the MPL-Net project has participated in four major field experiments since 2000. Most MPL-Net sites and field experiment locations are also co-located with sunphotometers in the NASA Aerosol Robotic Network. (AERONET). Therefore, at these locations data is collected on both aerosol and cloud vertical structure as well as column optical depth and sky radiance. Real-time data products are now available from most MPL-Net sites. Our real-time products are generated at times of AERONET aerosol optical depth (AOD) measurements. The AERONET AOD is used as input to our

Traditional nets interfere with the uptake of long-lasting insecticidal nets in the Peruvian Amazon: the relevance of net preference for achieving high coverage and use.

PubMed

Grietens, Koen Peeters; Muela Ribera, Joan; Soto, Veronica; Tenorio, Alex; Hoibak, Sarah; Aguirre, Angel Rosas; Toomer, Elizabeth; Rodriguez, Hugo; Llanos Cuentas, Alejandro; D'Alessandro, Umberto; Gamboa, Dionicia; Erhart, Annette

2013-01-01

While coverage of long-lasting insecticide-treated nets (LLIN) has steadily increased, a growing number of studies report gaps between net ownership and use. We conducted a mixed-methods social science study assessing the importance of net preference and use after Olyset® LLINs were distributed through a mass campaign in rural communities surrounding Iquitos, the capital city of the Amazonian region of Peru. The study was conducted in the catchment area of the Paujil and Cahuide Health Centres (San Juan district) between July 2007 and November 2008. During a first qualitative phase, participant observation and in-depth interviews collected information on key determinants for net preference and use. In a second quantitative phase, a survey among recently confirmed malaria patients evaluated the acceptability and use of both LLINs and traditional nets, and a case control study assessed the association between net preference/use and housing structure (open vs. closed houses). A total of 10 communities were selected for the anthropological fieldwork and 228 households participated in the quantitative studies. In the study area, bed nets are considered part of the housing structure and are therefore required to fulfil specific architectural and social functions, such as providing privacy and shelter, which the newly distributed Olyset® LLINs ultimately did not. The LLINs' failure to meet these criteria could mainly be attributed to their large mesh size, transparency and perceived ineffectiveness to protect against mosquitoes and other insects, resulting in 63.3% of households not using any of the distributed LLINs. Notably, LLIN usage was significantly lower in houses with no interior or exterior walls (35.2%) than in those with walls (73.8%) (OR = 5.2, 95CI [2.2; 12.3], p<0.001). Net preference can interfere with optimal LLIN use. In order to improve the number of effective days of LLIN protection per dollar spent, appropriate quantitative and qualitative methods

Traditional Nets Interfere with the Uptake of Long-Lasting Insecticidal Nets in the Peruvian Amazon: The Relevance of Net Preference for Achieving High Coverage and Use

PubMed Central

Grietens, Koen Peeters; Muela Ribera, Joan; Soto, Veronica; Tenorio, Alex; Hoibak, Sarah; Aguirre, Angel Rosas; Toomer, Elizabeth; Rodriguez, Hugo; Llanos Cuentas, Alejandro; D'Alessandro, Umberto; Gamboa, Dionicia; Erhart, Annette

2013-01-01

Background While coverage of long-lasting insecticide-treated nets (LLIN) has steadily increased, a growing number of studies report gaps between net ownership and use. We conducted a mixed-methods social science study assessing the importance of net preference and use after Olyset® LLINs were distributed through a mass campaign in rural communities surrounding Iquitos, the capital city of the Amazonian region of Peru. Methods The study was conducted in the catchment area of the Paujil and Cahuide Health Centres (San Juan district) between July 2007 and November 2008. During a first qualitative phase, participant observation and in-depth interviews collected information on key determinants for net preference and use. In a second quantitative phase, a survey among recently confirmed malaria patients evaluated the acceptability and use of both LLINs and traditional nets, and a case control study assessed the association between net preference/use and housing structure (open vs. closed houses). Results A total of 10 communities were selected for the anthropological fieldwork and 228 households participated in the quantitative studies. In the study area, bed nets are considered part of the housing structure and are therefore required to fulfil specific architectural and social functions, such as providing privacy and shelter, which the newly distributed Olyset® LLINs ultimately did not. The LLINs' failure to meet these criteria could mainly be attributed to their large mesh size, transparency and perceived ineffectiveness to protect against mosquitoes and other insects, resulting in 63.3% of households not using any of the distributed LLINs. Notably, LLIN usage was significantly lower in houses with no interior or exterior walls (35.2%) than in those with walls (73.8%) (OR = 5.2, 95CI [2.2; 12.3], p<0.001). Conclusion Net preference can interfere with optimal LLIN use. In order to improve the number of effective days of LLIN protection per dollar spent

MPL-Net data products available at co-located AERONET sites and field experiment locations

NASA Astrophysics Data System (ADS)

Welton, E. J.; Campbell, J. R.; Berkoff, T. A.

2002-05-01

Micro-pulse lidar (MPL) systems are small, eye-safe lidars capable of profiling the vertical distribution of aerosol and cloud layers. There are now over 20 MPL systems around the world, and they have been used in numerous field experiments. A new project was started at NASA Goddard Space Flight Center in 2000. The new project, MPL-Net, is a coordinated network of long-time MPL sites. The network also supports a limited number of field experiments each year. Most MPL-Net sites and field locations are co-located with AERONET sunphotometers. At these locations, the AERONET and MPL-Net data are combined together to provide both column and vertically resolved aerosol and cloud measurements. The MPL-Net project coordinates the maintenance and repair for all instruments in the network. In addition, data is archived and processed by the project using common, standardized algorithms that have been developed and utilized over the past 10 years. These procedures ensure that stable, calibrated MPL systems are operating at sites and that the data quality remains high. Rigorous uncertainty calculations are performed on all MPL-Net data products. Automated, real-time level 1.0 data processing algorithms have been developed and are operational. Level 1.0 algorithms are used to process the raw MPL data into the form of range corrected, uncalibrated lidar signals. Automated, real-time level 1.5 algorithms have also been developed and are now operational. Level 1.5 algorithms are used to calibrate the MPL systems, determine cloud and aerosol layer heights, and calculate the optical depth and extinction profile of the aerosol boundary layer. The co-located AERONET sunphotometer provides the aerosol optical depth, which is used as a constraint to solve for the extinction-to-backscatter ratio and the aerosol extinction profile. Browse images and data files are available on the MPL-Net web-site. An overview of the processing algorithms and initial results from selected sites and field

User-determined end of net life in Senegal: a qualitative assessment of decision-making related to the retirement of expired nets

PubMed Central

2013-01-01

Background Procurement and distribution of long-lasting insecticidal nets (LLINs) in the African region has decreased from 145 million in 2010 to 66 million nets in 2012. As resources for LLIN distribution appear to stagnate, it is important to understand the users’ perception of the life span of a net and at what point and why they stop using it. In order to get the most value out of distributed nets and to ensure that they are used for as long as possible, programmes must communicate to users about how to assess useful net life and how to extend it. Methods Data were collected from 114 respondents who participated in 56 in-depth interviews (IDIs) and eight focus group discussions (FGDs) in August 2012 in eight regions in Senegal. Households were eligible for the study if they owned at least one net and had an available household member over the age of 18. Data were coded by a team of four coders in ATLAS.ti using a primarily deductive approach. Results Respondents reported assessing useful net life using the following criteria: the age of net, the number and size of holes and the presence of mosquitoes in the net at night. If they had the means to do so, many respondents preferred the acquisition of a new net rather than the continued use of a very torn net. However, respondents would preferentially use newer nets, saving older, but useable nets for the future or sharing them with family or friends. Participants reported observing alternative uses of nets, primarily for nets that were considered expired. Conclusions The results indicate that decisions regarding the end of net life vary among community members in Senegal, but are primarily related to net integrity. Additional research is needed into user-determined end of net life as well as care and repair behaviours, which could extend useful net life. The results from this study and from future research on this topic should be used to understand current behaviours and develop communication programmes to

Hydrophilic group formation and cell culturing on polystyrene Petri-dish modified by ion-assisted reaction

NASA Astrophysics Data System (ADS)

Kim, Ki-Hwan; Cho, Jun-Sik; Choi, Doo-Jin; Koh, Seok-Keun

2001-04-01

Polystyrene (PS) Petri-dishes were modified by an ion-assisted reaction (IAR) to improve wettability and to supply a suitable surface for cell culturing. Low energy Ar + ions with 1000 eV were irradiated on the surface of PS in oxygen gas environment. Water contact angles of PS were not reduced much by ion irradiation without oxygen gas and had a value of 40°. In the case of ion irradiation with flowing oxygen gas, however, the water contact angles were dropped significantly from 73° to 19°. X-ray photoelectron spectroscopy analysis showed that the hydrophilic groups were formed on the surface of PS by a chemical reaction between unstable chains induced by ion irradiation and the oxygen gas. Newly formed hydrophilic groups were identified as -(C-O)-, -(CO)- and -(CO)-O- bonds. The influence of the surface modification on growth of the rat pheochromocytoma (PC12) cells was investigated. The IAR-treated PS surfaces showed enhanced attachment and growth in PC12 cell culture test.

Safe Schools/Safe Communities: A Directory of Resources for Pennsylvania.

ERIC Educational Resources Information Center

Pennsylvania State Dept. of Education, Harrisburg.

This document contains a directory of resources available in Pennsylvania to help achieve the goal of safe schools. Following a copy of the Safe Schools Act of 1993, nine sections list agencies that provide services and products under the headings of: conflict resolution/mediation, gangs, suicide, crisis response, family violence, diversity,…

Lessons Learned from Safe Kids/Safe Streets. Juvenile Justice Bulletin

ERIC Educational Resources Information Center

Cronin, Roberta; Gragg, Frances; Schultz, Dana; Eisen, Karla

2006-01-01

This bulletin reports results from an evaluation of six sites of the Safe Kids/Safe Streets (SK/SS) program, which applies a comprehensive, collaborative approach to the child maltreatment field. The bulletin provides insights into collaboration building, systems reform, service options, and other strategies. Among the findings were that the SK/SS…

NetFlow Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Corbet Jr., Thomas F; Beyeler, Walter E; Vanwestrienen, Dirk

NetFlow Dynamics is a web-accessible analysis environment for simulating dynamic flows of materials on model networks. Performing a simulation requires both the NetFlow Dynamics application and a network model which is a description of the structure of the nodes and edges of a network including the flow capacity of each edge and the storage capacity of each node, and the sources and sinks of the material flowing on the network. NetFlow Dynamics consists of databases for storing network models, algorithms to calculate flows on networks, and a GIS-based graphical interface for performing simulations and viewing simulation results. Simulated flows aremore » dynamic in the sense that flows on each edge of the network and inventories at each node change with time and can be out of equilibrium with boundary conditions. Any number of network models could be simulated using Net Flow Dynamics. To date, the models simulated have been models of petroleum infrastructure. The main model has been the National Transportation Fuels Model (NTFM), a network of U.S. oil fields, transmission pipelines, rail lines, refineries, tank farms, and distribution terminals. NetFlow Dynamics supports two different flow algorithms, the Gradient Flow algorithm and the Inventory Control algorithm, that were developed specifically for the NetFlow Dynamics application. The intent is to add additional algorithms in the future as needed. The ability to select from multiple algorithms is desirable because a single algorithm never covers all analysis needs. The current algorithms use a demand-driven capacity-constrained formulation which means that the algorithms strive to use all available capacity and stored inventory to meet desired flows to sinks, subject to the capacity constraints of each network component. The current flow algorithms are best suited for problems in which a material flows on a capacity-constrained network representing a supply chain in which the material supplied can be stored

47 CFR 69.302 - Net investment.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Net investment. 69.302 Section 69.302... Apportionment of Net Investment § 69.302 Net investment. (a) Investment in Accounts 2001, 1220 and Class B Rural...) Investment in Accounts 2002, 2003 and to the extent such inclusions are allowed by this Commission, Account...

47 CFR 69.302 - Net investment.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 3 2011-10-01 2011-10-01 false Net investment. 69.302 Section 69.302... Apportionment of Net Investment § 69.302 Net investment. (a) Investment in Accounts 2001, 1220 and Class B Rural...) Investment in Accounts 2002, 2003 and to the extent such inclusions are allowed by this Commission, Account...

RadNet Databases and Reports

EPA Pesticide Factsheets

EPA’s RadNet data are available for viewing in a searchable database or as PDF reports. Historical and current RadNet monitoring data are used to estimate long-term trends in environmental radiation levels.

BioFrameNet: A FrameNet Extension to the Domain of Molecular Biology

ERIC Educational Resources Information Center

Dolbey, Andrew Eric

2009-01-01

In this study I introduce BioFrameNet, an extension of the Berkeley FrameNet lexical database to the domain of molecular biology. I examine the syntactic and semantic combinatorial possibilities exhibited in the lexical items used in this domain in order to get a better understanding of the grammatical properties of the language used in scientific…

10 CFR 436.20 - Net savings.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Life Cycle Cost Analyses § 436.20 Net savings. For a retrofit project, net savings may be found by subtracting life cycle costs based on the proposed project from life cycle costs based on not having it. For a new building design, net savings is the difference between the life cycle costs of an alternative...

10 CFR 436.20 - Net savings.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Life Cycle Cost Analyses § 436.20 Net savings. For a retrofit project, net savings may be found by subtracting life cycle costs based on the proposed project from life cycle costs based on not having it. For a new building design, net savings is the difference between the life cycle costs of an alternative...

10 CFR 436.20 - Net savings.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Life Cycle Cost Analyses § 436.20 Net savings. For a retrofit project, net savings may be found by subtracting life cycle costs based on the proposed project from life cycle costs based on not having it. For a new building design, net savings is the difference between the life cycle costs of an alternative...

10 CFR 436.20 - Net savings.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Life Cycle Cost Analyses § 436.20 Net savings. For a retrofit project, net savings may be found by subtracting life cycle costs based on the proposed project from life cycle costs based on not having it. For a new building design, net savings is the difference between the life cycle costs of an alternative...

10 CFR 436.20 - Net savings.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Life Cycle Cost Analyses § 436.20 Net savings. For a retrofit project, net savings may be found by subtracting life cycle costs based on the proposed project from life cycle costs based on not having it. For a new building design, net savings is the difference between the life cycle costs of an alternative...

76 FR 12719 - Safe Schools/Healthy Students Program; Office of Safe and Drug-Free Schools; Safe Schools/Healthy...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-08

... official version of this document is the document published in the Federal Register. Free Internet access... DEPARTMENT OF EDUCATION Safe Schools/Healthy Students Program; Office of Safe and Drug- Free... telecommunications device for the deaf (TDD), call the Federal Relay Service (FRS), toll free, at 1-800-877-8339...

Safe syringe disposal is related to safe syringe access among HIV-positive injection drug users.

PubMed

Coffin, Phillip O; Latka, Mary H; Latkin, Carl; Wu, Yingfeng; Purcell, David W; Metsch, Lisa; Gomez, Cynthia; Gourevitch, Marc N

2007-09-01

We evaluated the effect of syringe acquisition on syringe disposal among HIV-positive injection drug users (IDUs) in Baltimore, New York City, and San Francisco (N = 680; mean age 42 years, 62% male, 59% African-American, 21% Hispanic, 12% White). Independent predictors of safe disposal were acquiring syringes through a safe source and ever visiting a syringe exchange program. Weaker predictors included living in San Francisco, living in the area longer, less frequent binge drinking, injecting with an HIV+ partner, peer norms supporting safe injection, and self-empowerment. Independent predictors of safe "handling"-both acquiring and disposing of syringes safely-also included being from New York and being older. HIV-positive IDUs who obtain syringes from a safe source are more likely to safely dispose; peer norms contribute to both acquisition and disposal. Interventions to improve disposal should include expanding sites of safe syringe acquisition while enhancing disposal messages, alternatives, and convenience.

Design for Maintainability with Modified Petri Nets (MPNs): Shipboard Propulsion System Application.

DTIC Science & Technology

1984-11-01

hazard (in acco- Fance with current environmental protection requirements). P20 YES T20 T2 1 EOOW report to 000, "Fire hazards removed from No engine room...8217-..! AARCA: GAS TURBINE MAIN ENGINE - GENERATOR Room NO 2 , .’ .- " SE7 NO. 2 \\ N 2 GEN MRGA GTM ,RZT 4o i .. .E rAF- _....Pr AJ*~ IAMR...GA Z0GYM GEN "-- ~ ~ P LL-L GIM. I I - GT MAIN ENGINE/ \\ t I . ROOM NO. I GAS 7RBINE ALIX MCHRY AUX MCHRY O OROO NO OOM NO. GENEU.ATOF ROOM NO 2 R

27 CFR 7.27 - Net contents.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false Net contents. 7.27 Section 7.27 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL LABELING AND ADVERTISING OF MALT BEVERAGES Labeling Requirements for Malt Beverages § 7.27 Net contents. (a) Net contents shall...

27 CFR 7.27 - Net contents.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Net contents. 7.27 Section 7.27 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL LABELING AND ADVERTISING OF MALT BEVERAGES Labeling Requirements for Malt Beverages § 7.27 Net contents. (a) Net contents shall...

27 CFR 7.27 - Net contents.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Net contents. 7.27 Section 7.27 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS LABELING AND ADVERTISING OF MALT BEVERAGES Labeling Requirements for Malt Beverages § 7.27 Net contents. (a) Net contents shall...

27 CFR 7.27 - Net contents.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Net contents. 7.27 Section 7.27 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS LABELING AND ADVERTISING OF MALT BEVERAGES Labeling Requirements for Malt Beverages § 7.27 Net contents. (a) Net contents shall...

27 CFR 7.27 - Net contents.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Net contents. 7.27 Section 7.27 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS LABELING AND ADVERTISING OF MALT BEVERAGES Labeling Requirements for Malt Beverages § 7.27 Net contents. (a) Net contents shall...

27 CFR 19.644 - Net contents.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Net contents. 19.644 Section 19.644 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS DISTILLED SPIRITS PLANTS Liquor Bottle and Label Requirements Bottle Label Requirements § 19.644 Net contents. The net...

Modelling of current loads on aquaculture net cages

NASA Astrophysics Data System (ADS)

Kristiansen, Trygve; Faltinsen, Odd M.

2012-10-01

In this paper we propose and discuss a screen type of force model for the viscous hydrodynamic load on nets. The screen model assumes that the net is divided into a number of flat net panels, or screens. It may thus be applied to any kind of net geometry. In this paper we focus on circular net cages for fish farms. The net structure itself is modelled by an existing truss model. The net shape is solved for in a time-stepping procedure that involves solving a linear system of equations for the unknown tensions at each time step. We present comparisons to experiments with circular net cages in steady current, and discuss the sensitivity of the numerical results to a set of chosen parameters. Satisfactory agreement between experimental and numerical prediction of drag and lift as function of the solidity ratio of the net and the current velocity is documented.

Measures of net oxidant concentration in seawater

NASA Astrophysics Data System (ADS)

Jackson, George A.; Williams, Peter M.

1988-02-01

Dissolved oxygen deficits in the ocean have been used as a measure of the organic matter oxidized in a volume of water. Such organic matter is usually assumed to be predominantly settled particles. Using dissolved oxygen concentration in this way has two problems: first, it does not differentiate between oxidant consumed by the pool of dissolved organic matter present near the ocean surface and oxidant consumed by organic matter contained by falling particles; second, it does not account for other oxidant sources, such as nitrate, which can be as important to organic matter decay as oxygen in low-oxygen water, such as off Peru or in the Southern California submarine basins. New parameters provide better measures of the net oxidant concentration in a water parcel. One such, NetOx, is changed only by gaseous exchange with the atmosphere, exchange with the benthos, or the production or consumption of sinking particles. A simplified version of NetOx, NetOx = [O2] + 1.25[NO3-] - [TOC], where TOC (total organic carbon), the dissolved organic carbon (DOC) plus the suspended particulate organic carbon (POC), provides an index based on the usually dominant variables. Calculation of NetOx and a second property, NetOC ([O2] - [TOC]), for data from GEOSECS and ourselves in the Atlantic and Pacific oceans using property-property graphs show differences from those from oxygen deficits alone. Comparison of NetOx and NetOC concentrations at high and low latitudes of the Pacific Ocean shows the difference in surface water oxidant concentrations is even larger than the difference in oxygen concentration. Vertical particle fluxes off Peru calculated from NetOx gradients are much greater than those calculated from oxygen gradients. The potential value of NetOx and NetOC as parameters to understand particle fluxes implies that determination of TOC should be a routine part of hydrographic measurements.

Which family members use the best nets? An analysis of the condition of mosquito nets and their distribution within households in Tanzania.

PubMed

Tsuang, Angela; Lines, Jo; Hanson, Kara

2010-07-22

Household ownership of insecticide-treated mosquito nets (ITNs) is increasing, and coverage targets have been revised to address universal coverage with ITNs. However, many households do not have enough nets to cover everyone, and the nets available vary in physical condition and insecticide treatment status. Since 2004, the Government of Tanzania has been implementing the Tanzania National Voucher Scheme (TNVS), which distributes vouchers for ITNs through antenatal clinics to target pregnant women and their infants. This analysis aimed to determine the following: (1) coverage patterns of bed nets within households according to physical condition and treatment status; (2) who might be at risk if mosquitoes were diverted from occupants of untreated nets to those not using nets? (3) the degree to which those at highest risk of malaria use the most protective nets. Data from the 2006 TNVS household survey were analysed to assess within-household distribution of net use. The associations between net characteristics and net user were also evaluated. Multivariate analysis was applied to the relationship between the number of holes per net and user characteristics while adjusting for confounders. In households with a net:person ratio better than 1:4 (one net for every four household members), more than 80% of the people in such households reported using a net the previous night. ITNs were most likely to be used by infants, young children (1-4 y), and women of childbearing age; they were least likely to be used by older women (>or=50 y), older children (5-14 y), and adult men. The nets used by infants and women of childbearing age were in better-than-average physical condition; the nets used by older women and older children were in worse-than-average condition; while young children and adult men used nets in intermediate (average) condition. When adjusted for confounders, the nets used by young and older children had more holes than nets used by infants. Infants and other

Implementation of the NANoREG Safe-by-Design approach for different nanomaterial applications

NASA Astrophysics Data System (ADS)

Micheletti, C.; Roman, M.; Tedesco, E.; Olivato, I.; Benetti, F.

2017-06-01

The Safe-by-Design (SbD) concept is already in use in different industrial sectors as an integral part of the innovation process management. However, the adopted approach is often limited to design solutions aiming at hazard reduction. Safety is not always considered during the innovation process, mainly due to the lack of knowledge (e.g. in small and medium companies, SMEs) and the lack of dialogue between actors along the innovation chain. The net result is that safety is considered only at the end of the innovation process at the market authorization phase, with potential loss of time and money. This is especially valid for manufactured nanomaterials (MNM) for which the regulatory context is not completely developed, and the safety knowledge is not readily available. In order to contribute to a sustainable innovation process in the nanotechnology field by maximising both benefits and safety, the NANoREG project developed a Safe Innovation approach, based on two elements: the Safe-by-Design approach which aims at including risk assessment into all innovation stages; and the Regulatory Preparedness, focused on the dialogue with stakeholders along the innovation chain. In this work we present some examples about the implementation in our Laboratory of this approach for different MNM applications, covering different steps of the innovation chain. The case studies include: the feasibility study of a medical device including substances, for topical application; the testing of two potential nanotech solutions for the consolidation of cultural heritage artifacts; the testing of coatings already on the market for other uses, which was tested as food contact materials (FCM) to evaluate the conformity to food applications. These three examples represent a good opportunity to show the importance of NANoREG SbD and Safe Innovation Approach in general, for developing new nanotechnology-based products, also highlighting the crucial role of EU ProSafe project in promoting this

Which nets are being used: factors associated with mosquito net use in Amhara, Oromia and Southern Nations, Nationalities and Peoples' Regions of Ethiopia.

PubMed

Ngondi, Jeremiah M; Graves, Patricia M; Gebre, Teshome; Mosher, Aryc W; Shargie, Estifanos B; Emerson, Paul M; Richards, Frank O

2011-04-17

There has been recent large scale-up of malaria control interventions in Ethiopia where transmission is unstable. While household ownership of long-lasting insecticidal nets (LLIN) has increased greatly, there are concerns about inadequate net use. This study aimed to investigate factors associated with net use at two time points, before and after mass distribution of nets. Two cross sectional surveys were carried out in 2006 and 2007 in Amhara, Oromia and SNNP regions. The latter was a sub-sample of the national Malaria Indicator Survey (MIS 3R). Each survey wave used multi-stage cluster random sampling with 25 households per cluster (224 clusters with 5,730 households in Baseline 2006 and 245 clusters with 5,910 households in MIS 3R 2007). Net ownership was assessed by visual inspection while net utilization was reported as use of the net the previous night. This net level analysis was restricted to households owning at least one net of any type. Logistic regression models of association between net use and explanatory variables including net type, age, condition, cost and other household characteristics were undertaken using generalized linear latent and mixed models (GLLAMM). A total of 3,784 nets in 2,430 households were included in the baseline 2006 analysis while the MIS 3R 2007 analysis comprised 5,413 nets in 3,328 households. The proportion of nets used the previous night decreased from 85.1% to 56.0% between baseline 2006 and MIS 3R 2007, respectively. Factors independently associated with increased proportion of nets used were: LLIN net type (at baseline 2006); indoor residual spraying (at MIS 3R 2007); and increasing wealth index at both surveys. At both baseline 2006 and MIS 3R 2007, reduced proportion of nets used was independently associated with increasing net age, increasing damage of nets, increasing household net density, and increasing altitude (>2,000 m). This study identified modifiable factors affecting use of nets that were consistent

Netting bias in tropical bird studies

USGS Publications Warehouse

Coates-Estrada, R.; Dowell, B.A.; Fallon, J.E.; Robbins, C.S.; Wilson, Marcia H.; Sader, Steven A.

1995-01-01

Mist netting is the method most commonly used for gathering quantitative information on birds in the American tropics. Point count surveys or other methods often are used in conjunction with netting to reduce some of the many biases associated with netting, specially the failure of stationary nets within 2 m of the ground to sample birds of the tall canopy. We compare totals by both methods. Even close to the ground there are biases related to time of day and mesh size that have not been addressed in tropical studies. Some researchers operate nets all day, others only in the morning or in the morning and evening. Since 1986 we have netted birds and conducted point count surveys at more than 130 sites representing a broad spectrum of habitats in Mexico, Belize, and Guatemala. Using data only from those days when we could operate nets continuously from about dawn to dusk, we compare capture rates throughout the day to show the bias per part-day operations for certain families and species of birds and for the ratio of neotropical migrants to resident birds. More than half of 5000+ birds captured were caught after noon. Trochilidae and parulinae were captured primarily in the morning, Dendrocolaptidae in the middle of the day. Tyrannidae were more active than most birds in early afternoon, and Turdinae had morning and evening peaks. At each site we use a combination of 30-mm and 36-mm nets. The 30-mm mesh consistently captured more seedeaters, gnatcatchers, and small warblers, whereas the 36-mm mesh was more effective for birds of thrush size and larger.

NetProt: Complex-based Feature Selection.

PubMed

Goh, Wilson Wen Bin; Wong, Limsoon

2017-08-04

Protein complex-based feature selection (PCBFS) provides unparalleled reproducibility with high phenotypic relevance on proteomics data. Currently, there are five PCBFS paradigms, but not all representative methods have been implemented or made readily available. To allow general users to take advantage of these methods, we developed the R-package NetProt, which provides implementations of representative feature-selection methods. NetProt also provides methods for generating simulated differential data and generating pseudocomplexes for complex-based performance benchmarking. The NetProt open source R package is available for download from https://github.com/gohwils/NetProt/releases/ , and online documentation is available at http://rpubs.com/gohwils/204259 .

Safe Grid

NASA Technical Reports Server (NTRS)

Chow, Edward T.; Stewart, Helen; Korsmeyer, David (Technical Monitor)

2003-01-01

The biggest users of GRID technologies came from the science and technology communities. These consist of government, industry and academia (national and international). The NASA GRID is moving into a higher technology readiness level (TRL) today; and as a joint effort among these leaders within government, academia, and industry, the NASA GRID plans to extend availability to enable scientists and engineers across these geographical boundaries collaborate to solve important problems facing the world in the 21 st century. In order to enable NASA programs and missions to use IPG resources for program and mission design, the IPG capabilities needs to be accessible from inside the NASA center networks. However, because different NASA centers maintain different security domains, the GRID penetration across different firewalls is a concern for center security people. This is the reason why some IPG resources are been separated from the NASA center network. Also, because of the center network security and ITAR concerns, the NASA IPG resource owner may not have full control over who can access remotely from outside the NASA center. In order to obtain organizational approval for secured remote access, the IPG infrastructure needs to be adapted to work with the NASA business process. Improvements need to be made before the IPG can be used for NASA program and mission development. The Secured Advanced Federated Environment (SAFE) technology is designed to provide federated security across NASA center and NASA partner's security domains. Instead of one giant center firewall which can be difficult to modify for different GRID applications, the SAFE "micro security domain" provide large number of professionally managed "micro firewalls" that can allow NASA centers to accept remote IPG access without the worry of damaging other center resources. The SAFE policy-driven capability-based federated security mechanism can enable joint organizational and resource owner approved remote

The NetLogger Toolkit V2.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunter, Dan; Lee, Jason; Stoufer, Martin

2003-03-28

The NetLogger Toolkit is designed to monitor, under actual operating conditions, the behavior of all the elements of the application-to-application communication path in order to determine exactly where time is spent within a complex system Using NetLogger, distnbuted application components are modified to produce timestamped logs of "interesting" events at all the critical points of the distributed system Events from each component are correlated, which allov^ one to characterize the performance of all aspects of the system and network in detail. The NetLogger Toolkit itself consists of four components an API and library of functions to simplify the generation ofmore » application-level event logs, a set of tools for collecting and sorting log files, an event archive system, and a tool for visualization and analysis of the log files In order to instrument an application to produce event logs, the application developer inserts calls to the NetLogger API at all the critical points in the code, then links the application with the NetLogger library All the tools in the NetLogger Toolkit share a common log format, and assume the existence of accurate and synchronized system clocks NetLogger messages can be logged using an easy-to-read text based format based on the lETF-proposed ULM format, or a binary format that can still be used through the same API but that is several times faster and smaller, with performance comparable or better than binary message formats such as MPI, XDR, SDDF-Binary, and PBIO. The NetLogger binary format is both highly efficient and self-describing, thus optimized for the dynamic message construction and parsing of application instrumentation. NetLogger includes an "activation" API that allows NetLogger logging to be turned on, off, or modified by changing an external file This IS useful for activating logging in daemons/services (e g GndFTP server). The NetLogger reliability API provides the ability to specify backup logging locations and

UltraNet Target Parameters. Chapter 1

NASA Technical Reports Server (NTRS)

Kislitzin, Katherine T.; Blaylock, Bruce T. (Technical Monitor)

1992-01-01

The UltraNet is a high speed network capable of rates up to one gigabit per second. It is a hub based network with four optical fiber links connecting each hub. Each link can carry up to 256 megabits of data, and the hub backplane is capable of one gigabit aggregate throughput. Host connections to the hub may be fiber, coax, or channel based. Bus based machines have adapter boards that connect to transceivers in the hub, while channel based machines use a personality module in the hub. One way that the UltraNet achieves its high transfer rates is by off-loading the protocol processing from the hosts to special purpose protocol engines in the UltraNet hubs. In addition, every hub has a PC connected to it by StarLAN for network management purposes. Although there is hub resident and PC resident UltraNet software, this document treats only the host resident UltraNet software.

Net nitrogen mineralization and net nitrification rates in soils following deforestation for pasture across the southwestern Brazilian Amazon Basin landscape.

PubMed

Neill, Christopher; Piccolo, Marisa C; Cerri, Carlos C; Steudler, Paul A; Melillo, Jerry M; Brito, Marciano

1997-04-01

Previous studies of the effect of tropical forest conversion to cattle pasture on soil N dynamics showed that rates of net N mineralization and net nitrification were lower in pastures compared with the original forest. In this study, we sought to determine the generality of these patterns by examining soil inorganic N concentrations, net mineralization and nitrification rates in 6 forests and 11 pastures 3 years old or older on ultisols and oxisols that encompassed a wide variety of soil textures and spanned a 700-km geographical range in the southwestern Brazilian Amazon Basin state of Rondônia. We sampled each site during October-November and April-May. Forest soils had higher extractable NO 3 - -N and total inorganic N concentrations than pasture soils, but substantial NO 3 - -N occurred in both forest and pasture soils. Rates of net N mineralization and net nitrification were higher in forest soils. Greater concentrations of soil organic matter in finer textured soils were associated with greater rates of net N mineralization and net nitrification, but this relationship was true only under native forest vegetation; rates were uniformly low in pastures, regardless of soil type or texture. Net N mineralization and net nitrification rates per unit of total soil organic matter showed no pattern across the different forest sites, suggesting that controls of net N mineralization may be broadly similar across a wide range of soil types. Similar reductions in rates of net N transformations in pastures 3 years old or older across a range of textures on these soils suggest that changes to soil N cycling caused by deforestation for pasture may be Basin-wide in extent. Lower net N mineralization and net nitrification rates in established pastures suggest that annual N losses from largely deforested landscapes may be lower than losses from the original forest. Total ecosystem N losses since deforestation are likely to depend on the balance between lower N loss rates from

Safe Manual Jettison

NASA Technical Reports Server (NTRS)

Barton, Jay

2008-01-01

In space, the controlled release of certain cargoes is no less useful than the maritime jettisons from which they take their name but is also much more dangerous. Experience has shown that jettisons can be performed safely, but the process is complicated with the path to performing a jettison taking months or even years. In the background, time is also required to write procedures, train the crew, configure the vehicle, and many other activities. This paper outlines the current process used by the National Aeronautics and Space Administration (NASA) for manual jettisons, detailing the methods used to assure that the jettisons and the jettisoned objects are as safe as achievable and that the crew is adequately trained to be able to affect the safe jettison. The goal of this paper is not only to capture what it takes to perform safe jettisons in the near Earth environment but to extrapolate this knowledge to future space exploration scenarios that will likely have Extravehicular Activity (EVA) and International Partner (IP) interfaces.

Infrared video tracking of Anopheles gambiae at insecticide-treated bed nets reveals rapid decisive impact after brief localised net contact

PubMed Central

Parker, Josephine E.A.; Angarita-Jaimes, Natalia; Abe, Mayumi; Towers, Catherine E.; Towers, David; McCall, Philip J.

2015-01-01

Long-lasting insecticidal bed nets (LLINs) protect humans from malaria transmission and are fundamental to malaria control worldwide, but little is known of how mosquitoes interact with nets. Elucidating LLIN mode of action is essential to maintain or improve efficacy, an urgent need as emerging insecticide resistance threatens their future. Tracking multiple free-flying Anopheles gambiae responding to human-occupied bed nets in a novel large-scale system, we characterised key behaviours and events. Four behavioural modes with different levels of net contact were defined: swooping, visiting, bouncing and resting. Approximately 75% of all activity occurred at the bed net roof where multiple brief contacts were focussed above the occupant’s torso. Total flight and net contact times were lower at LLINs than untreated nets but the essential character of the response was unaltered. LLINs did not repel mosquitoes but impacted rapidly: LLIN contact of less than 1 minute per mosquito during the first ten minutes reduced subsequent activity; after thirty minutes, activity at LLINs was negligible. Velocity measurements showed that mosquitoes detected nets, including unbaited untreated nets, prior to contact. This is the most complete characterisation of mosquito-LLIN interactions to date, and reveals many aspects of LLIN mode of action, important for developing the next generation of LLINs. PMID:26323965

SkyNet: Modular nuclear reaction network library

NASA Astrophysics Data System (ADS)

Lippuner, Jonas; Roberts, Luke F.

2017-10-01

The general-purpose nuclear reaction network SkyNet evolves the abundances of nuclear species under the influence of nuclear reactions. SkyNet can be used to compute the nucleosynthesis evolution in all astrophysical scenarios where nucleosynthesis occurs. Any list of isotopes can be evolved and SkyNet supports various different types of nuclear reactions. SkyNet is modular, permitting new or existing physics, such as nuclear reactions or equations of state, to be easily added or modified.

[Chemotherapy for GI and pancreatic NETs].

PubMed

Doi, Toshihiko

2013-07-01

Neuroendocrine tumors(NETs)describe a heterogeneous group of tumors with a wide range of morphologic, functional, and behavioral characteristics. Pancreatic neuroendocrine tumors(pNET)are a subset of NETs which are increasing in incidence and prevalence. These tumors are generally slow growing and behave in an indolent fashion. However, when these tumors spread they can be life threatening and difficult to treat with current modalities. Recently, the basic treatment for pNET was changed with the approval of two targeted agents, sunitinib and everolimus. Clinical trials conducting various combinations of somatostatin analogues, mTOR inhibitors, tyrosine kinase inhibitors, and cytotoxic agents are ongoing under-evaluation, and a multitargeted approach to therapy will translate into improved patient outcomes.

Elliptic net and its cryptographic application

NASA Astrophysics Data System (ADS)

Muslim, Norliana; Said, Mohamad Rushdan Md

2017-11-01

Elliptic net is a generalization of elliptic divisibility sequence and in cryptography field, most cryptographic pairings that are based on elliptic curve such as Tate pairing can be improved by applying elliptic nets algorithm. The elliptic net is constructed by using n dimensional array of values in rational number satisfying nonlinear recurrence relations that arise from elliptic divisibility sequences. The two main properties hold in the recurrence relations are for all positive integers m>n, hm +nhm -n=hm +1hm -1hn2-hn +1hn -1hm2 and hn divides hm whenever n divides m. In this research, we discuss elliptic divisibility sequence associated with elliptic nets based on cryptographic perspective and its possible research direction.

Streptococcus suis DNase SsnA contributes to degradation of neutrophil extracellular traps (NETs) and evasion of NET-mediated antimicrobial activity.

PubMed

de Buhr, Nicole; Neumann, Ariane; Jerjomiceva, Natalja; von Köckritz-Blickwede, Maren; Baums, Christoph G

2014-02-01

Streptococcus suis is an important cause of different pathologies in pigs and humans, most importantly fibrinosuppurative meningitis. Tissue infected with this pathogen is substantially infiltrated with neutrophils, but the function of neutrophil extracellular traps (NETs) - a more recently discovered antimicrobial strategy of neutrophils - in host defence against Strep. suis has not been investigated. The objective of this work was to investigate the interaction of Strep. suis with NETs in vitro. Strep. suis induced NET formation in porcine neutrophils and was entrapped but not killed by those NETs. As the amount of NETs decreased over time, we hypothesized that a known extracellular DNase of Strep. suis degrades NETs. Though this nuclease was originally designated Strep. suis-secreted nuclease A (SsnA), this work demonstrated surface association in accordance with an LPXTG cell wall anchor motif and partial release into the supernatant. Confirming our hypothesis, an isogenic ssnA mutant was significantly attenuated in NET degradation and in protection against the antimicrobial activity of NETs as determined in assays with phorbol myristate acetate (PMA)-stimulated human neutrophils. Though assays with PMA-stimulated porcine neutrophils suggested that SsnA also degrades porcine NETs, phenotypic differences between wt and the isogenic ssnA mutant were less distinct. As SsnA expression was crucial for neither growth in vitro nor for survival in porcine or human blood, the results indicated that SsnA is the first specific NET evasion factor to be identified in Strep. suis.

The EuroNet paediatric hodgkin network - modern imaging data management for real time central review in multicentre trials.

PubMed

Kurch, L; Mauz-Körholz, C; Bertling, S; Wallinder, M; Kaminska, M; Marwede, D; Tchavdarova, L; Georgi, T W; Elsner, A; Barthel, A; Stoevesandt, D; Hasenclever, D; Sattler, B; Sabri, O; Körholz, D; Kluge, R

2013-11-01

Since 2007, children and adolescents with Hodgkin lymphomas are treated in the Europe-wide EuroNet-PHL trials. A real time central review process for stratification of the patients enhances quality control and efficient therapy management. This process includes reading of all cross-sectional-images. Since reference evaluation is time critical, a fast, easy to handle and safe data transfer is important. In addition, immediate and constant access to all the data has to be guaranteed in case of queries and for regulatory reasons. To meet the mentioned requirements the EuroNet Paediatric Hodgkin Data Network (funded by the European Union - Project Number: 2007108) was established between 2008 and 2011. A respective tailored data protection plan was formulated. The aim of this article is to describe the networks' mode of operation and the advantages for multi-centre trials that include centralized image review. © Georg Thieme Verlag KG Stuttgart · New York.

Inferring Phylogenetic Networks Using PhyloNet.

PubMed

Wen, Dingqiao; Yu, Yun; Zhu, Jiafan; Nakhleh, Luay

2018-07-01

PhyloNet was released in 2008 as a software package for representing and analyzing phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of measures for comparing network topologies and a single heuristic for reconciling gene trees with a species tree. Since then, PhyloNet has grown significantly. The software package now includes a wide array of methods for inferring phylogenetic networks from data sets of unlinked loci while accounting for both reticulation (e.g., hybridization) and incomplete lineage sorting. In particular, PhyloNet now allows for maximum parsimony, maximum likelihood, and Bayesian inference of phylogenetic networks from gene tree estimates. Furthermore, Bayesian inference directly from sequence data (sequence alignments or biallelic markers) is implemented. Maximum parsimony is based on an extension of the "minimizing deep coalescences" criterion to phylogenetic networks, whereas maximum likelihood and Bayesian inference are based on the multispecies network coalescent. All methods allow for multiple individuals per species. As computing the likelihood of a phylogenetic network is computationally hard, PhyloNet allows for evaluation and inference of networks using a pseudolikelihood measure. PhyloNet summarizes the results of the various analyzes and generates phylogenetic networks in the extended Newick format that is readily viewable by existing visualization software.

Impact of a behaviour change intervention on long-lasting insecticidal net care and repair behaviour and net condition in Nasarawa State, Nigeria.

PubMed

Koenker, Hannah; Kilian, Albert; Hunter, Gabrielle; Acosta, Angela; Scandurra, Leah; Fagbemi, Babafunke; Onyefunafoa, Emmanuel O; Fotheringham, Megan; Lynch, Matthew

2015-01-21

While some data on net durability have been accumulating in recent years, including formative qualitative research on attitudes towards net care and repair, no data are available on how the durability of a net is influenced by behaviour of net maintenance, care and repair, and whether behavioural change interventions (BCC) could substantially impact on the average useful life of the net. The study used an intervention-control design with before-after assessment through repeated cross-sectional household surveys with two-stage cluster sampling following Nasarawa State's December 2010 mass campaign. All campaign nets were 100-denier polyester, long-lasting insecticidal nets (LLIN). Baseline, midline, and endline surveys occurred at one-year intervals, in March 2012, March 2013, and April 2014, respectively. Outcome measures were the proportion of confirmed campaign nets with observed repairs, and the proportion in serviceable condition, measured with proportionate hole index (pHI) and according to WHO guidelines. For all respondents, exposure to BCC messages was strongly correlated with increased positive attitude towards care and repair, and increases in attitude were positively correlated with observed net repairs, and with the proportion of nets in serviceable condition. In a multivariate regression model, positive care and repair attitude (OR 6.17 p = 0.001) and level of exposure (1 source: OR 4.00 p = 0.000; 3 sources: OR 9.34 p = 0.000) remained the most significant predictors of net condition, controlling for background and environmental factors. Nets that were tied up had 2.70 higher odds of being in serviceable condition (p = 0.001), while repairs made to nets were not sufficient to improve their pHI category. Estimated median net lifespan was approximately one full year longer for nets in households with a positive compared to a negative attitude. Exposure to multiple channels of a comprehensive BCC intervention was associated with improved

Association mapping utilizing diverse barley lines reveals net form net blotch seedling resistance/susceptibility loci

USDA-ARS?s Scientific Manuscript database

Pyrenophora teres f. teres is a necrotrophic fungal pathogen and the causal agent of the economically important foliar disease net form net blotch (NFNB) of barley. The deployment of effective and durable resistance against P. teres f. teres has been hindered by the complexity of quantitative resist...

Conformal Nets II: Conformal Blocks

NASA Astrophysics Data System (ADS)

Bartels, Arthur; Douglas, Christopher L.; Henriques, André

2017-08-01

Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

Safety of MRI with metallic middle ear implants.