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.

Scheduling multirobot operations in manufacturing by truncated Petri nets

NASA Astrophysics Data System (ADS)

Chen, Qin; Luh, J. Y.

1995-08-01

Scheduling of operational sequences in manufacturing processes is one of the important problems in automation. Methods of applying Petri nets to model and analyze the problem with constraints on precedence relations, multiple resources allocation, etc. have been available in literature. Searching for an optimum schedule can be implemented by combining the branch-and-bound technique with the execution of the timed Petri net. The process usually produces a large Petri net which is practically not manageable. This disadvantage, however, can be handled by a truncation technique which divides the original large Petri net into several smaller size subnets. The complexity involved in the analysis of each subnet individually is greatly reduced. However, when the locally optimum schedules of the resulting subnets are combined together, it may not yield an overall optimum schedule for the original Petri net. To circumvent this problem, algorithms are developed based on the concepts of Petri net execution and modified branch-and-bound process. The developed technique is applied to a multi-robot task scheduling problem of the manufacturing work cell.

Software Tool Integrating Data Flow Diagrams and Petri Nets

NASA Technical Reports Server (NTRS)

Thronesbery, Carroll; Tavana, Madjid

2010-01-01

Data Flow Diagram - Petri Net (DFPN) is a software tool for analyzing other software to be developed. The full name of this program reflects its design, which combines the benefit of data-flow diagrams (which are typically favored by software analysts) with the power and precision of Petri-net models, without requiring specialized Petri-net training. (A Petri net is a particular type of directed graph, a description of which would exceed the scope of this article.) DFPN assists a software analyst in drawing and specifying a data-flow diagram, then translates the diagram into a Petri net, then enables graphical tracing of execution paths through the Petri net for verification, by the end user, of the properties of the software to be developed. In comparison with prior means of verifying the properties of software to be developed, DFPN makes verification by the end user more nearly certain, thereby making it easier to identify and correct misconceptions earlier in the development process, when correction is less expensive. After the verification by the end user, DFPN generates a printable system specification in the form of descriptions of processes and data.

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).

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.

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.

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.

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.

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.

Isomorphisms between Petri nets and dataflow graphs

NASA Technical Reports Server (NTRS)

Kavi, Krishna M.; Buckles, Billy P.; Bhat, U. Narayan

1987-01-01

Dataflow graphs are a generalized model of computation. Uninterpreted dataflow graphs with nondeterminism resolved via probabilities are shown to be isomorphic to a class of Petri nets known as free choice nets. Petri net analysis methods are readily available in the literature and this result makes those methods accessible to dataflow research. Nevertheless, combinatorial explosion can render Petri net analysis inoperative. Using a previously known technique for decomposing free choice nets into smaller components, it is demonstrated that, in principle, it is possible to determine aspects of the overall behavior from the particular behavior of components.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

The equivalency between logic Petri workflow nets and workflow nets.

PubMed

Wang, Jing; Yu, ShuXia; Du, YuYue

2015-01-01

Logic Petri nets (LPNs) can describe and analyze batch processing functions and passing value indeterminacy in cooperative systems. Logic Petri workflow nets (LPWNs) are proposed based on LPNs in this paper. Process mining is regarded as an important bridge between modeling and analysis of data mining and business process. Workflow nets (WF-nets) are the extension to Petri nets (PNs), and have successfully been used to process mining. Some shortcomings cannot be avoided in process mining, such as duplicate tasks, invisible tasks, and the noise of logs. The online shop in electronic commerce in this paper is modeled to prove the equivalence between LPWNs and WF-nets, and advantages of LPWNs are presented.

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.

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.

The Equivalency between Logic Petri Workflow Nets and Workflow Nets

PubMed Central

Wang, Jing; Yu, ShuXia; Du, YuYue

2015-01-01

Logic Petri nets (LPNs) can describe and analyze batch processing functions and passing value indeterminacy in cooperative systems. Logic Petri workflow nets (LPWNs) are proposed based on LPNs in this paper. Process mining is regarded as an important bridge between modeling and analysis of data mining and business process. Workflow nets (WF-nets) are the extension to Petri nets (PNs), and have successfully been used to process mining. Some shortcomings cannot be avoided in process mining, such as duplicate tasks, invisible tasks, and the noise of logs. The online shop in electronic commerce in this paper is modeled to prove the equivalence between LPWNs and WF-nets, and advantages of LPWNs are presented. PMID:25821845

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.

Modeling safety requirements of an FMS using Petri-nets

NASA Astrophysics Data System (ADS)

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

1993-08-01

This paper is concerned with the modelling of safety requirements using Petri nets as a tool to model and simulate a Flexible Manufacturing System (FMS). The FMS cell described comprises a pick and place robot, a multi-head drilling machine together with a vision system and illustrates how the hierarchical structure of Petri nets can be used to ensure that all fail- safe requirements are satisfied; block diagrams together with fully detailed example Petri nets are given. The work demonstrates the use of cell and robot control Petro nets together with robot subnets for the x, y and z axes and associated output nets; the control and output nets are linked together with a safety net. Individual machines are linked with the control and safety nets of an FMS at cell level. The paper also illustrates how a Petri net can act as a decision maker during image inspection and identifies the unsafe conditions that can arise within an FMS.

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.

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.

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

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.

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.

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.

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.

Testing of Compounds for Efficacy against Schistosomiasis.

DTIC Science & Technology

1986-07-22

4); 2) a petri dish containing a centrally placed mud mound, blue-green aglae ( Nostoc muscorum) and water Is used for rearing young snails and...maintaining both pre-exposed and exposed snails (5); 3) a petri dish containing small amounts of blue-green algae ( Nostoc muscoru), mud and water is used...25-27 C. 4. Food. Blue-green algae ( Nostoc muscorum) grown in petri dishes with mud (5) is used exclusively as the food source. C. Breedin A

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.

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.

Photocatalytic bacterial inactivation by TiO2-coated surfaces

PubMed Central

2013-01-01

The aim of this study was the evaluation of the photoactivated antibacterial activity of titanium dioxide (TiO2)-coated surfaces. Bacterial inactivation was evaluated using TiO2-coated Petri dishes. The experimental conditions optimized with Petri dishes were used to test the antibacterial effect of TiO2-coated ceramic tiles. The best antibacterial effect with Petri dishes was observed at 180, 60, 30 and 20 min of exposure for Escherichia coli, Staphylococcus aureus, Pseudomonas putida and Listeria innocua, respectively. The ceramic tiles demonstrated a photoactivated bactericidal effect at the same exposure time. In general, no differences were observed between the antibacterial effect obtained with Petri dishes and tiles. However, the photochemical activity of Petri dishes was greater than the activity of the tiles. Results obtained indicates that the TiO2-coated surfaces showed a photoactivated bactericidal effect with all bacteria tested highlighting that the titania could be used in the ceramic and building industry for the production of coated surfaces to be placed in microbiologically sensitive environments, such as the hospital and food industry. PMID:24090112

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

United States Navy Oceanic Armed Reconnaissance System

DTIC Science & Technology

2011-12-12

This report was prepared by: Rahul Petrie Daniel Reese Kurtis Hoots Robert Taylor Drew Nash Bunny Cooper Jonathan Trdan-Schmidt Marshall...NPS – Cohort 311-102S, Team OARS: Mr. Marshall Rice, Mr. Rahul Petrie, Mr. Daniel Reese, Mr. Kurtis Hoots, Mr. Robert Taylor, Mr. Drew Nash

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.

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

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.

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.

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.

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.

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.

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.

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

Rotational Motion of Axisymmetric Marangoni Swimmers

NASA Astrophysics Data System (ADS)

Rothstein, Jonathan; Uvanovic, Nick

2017-11-01

A series of experiments will be presented investigating the motion of millimeter-sized particles on the surface of water. The particles were partially coated with ethanol and carefully placed on a water interface in a series of Petri dishes with different diameters. High speed particle motion was driven by strong surface tension gradients as the ethanol slowly diffuses from the particles into the water resulting in a Marangoni flow. The velocity and acceleration of the particles where measured. In addition to straight line motion, the presence of the bounding walls of the circular Petri dish was found to induce an asymmetric, rotational motion of the axisymmetric Marangoni swimmers. The rotation rate and radius of curvature was found to be a function of the size of the Petri dish and the curvature of the air-water interface near the edge of the dish. For large Petri dishes or small particles, rotation motion was observed far from the bounding walls. In these cases, the symmetry break appears to be the result of the onset of votex shedding. Finally, multiple spherical particles were observed to undergo assembly driven by capillary forces followed by explosive disassembly.

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.

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.

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.

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.

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.

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…

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.…

In Italy, a Partisan Defender of Foreign Professors

ERIC Educational Resources Information Center

Rocca, Francis X.

2007-01-01

Over the past quarter-century David Petrie, a 56-year-old Scotsman has attended, in the capacity of plaintiff or interested observer, at least 80 court hearings at various levels of the Italian and pan-European judicial systems--all in cases of alleged job discrimination by Italian universities. In the process, Mr. Petrie has become the public…

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.

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.

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.

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.

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

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.

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.

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

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.

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.

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.

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.

Safety of MRI with metallic middle ear implants.

PubMed

Tohme, Souheil M; Karkas, Alexandre A; Romanos, Bassam H

2003-01-01

Investigation of the effects of magnetic resonance fields on commonly used metallic middle ear implants. Nine middle ear prostheses (seven containing stainless steel and two made of pure gold used as control) were tested in vitro and one stainless steel stapedectomy prosthesis was tested on a cadaveric temporal bone. Each metallic prosthesis was placed in an empty Petri dish and introduced into a 1.5-tesla (T) magnetic resonance imaging (MRI) unit. Most of the prostheses were then placed in a water-filled Petri dish and reintroduced into the MRI unit. Eventual in vitro displacement was assessed visually by two means. In situ testing was done by implanting a piston in a cadaveric temporal bone and performing MR sequences ; any possible displacement was then assessed by CT scan and under microscopic vision. None of the prostheses was displaced in the empty Petri dish. However, while in the water-filled Petri dish, three of these moved with the flux. The implanted piston in the temporal bone did not move. The displacement of three of the prostheses in water is not relevant in real clinical situations. MRI can thus be considered safe in usual clinical settings, as far as our studied implants are concerned.

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.

Petri net modelling of buffers in automated manufacturing systems.

PubMed

Zhou, M; Dicesare, F

1996-01-01

This paper presents Petri net models of buffers and a methodology by which buffers can be included in a system without introducing deadlocks or overflows. The context is automated manufacturing. The buffers and models are classified as random order or order preserved (first-in-first-out or last-in-first-out), single-input-single-output or multiple-input-multiple-output, part type and/or space distinguishable or indistinguishable, and bounded or safe. Theoretical results for the development of Petri net models which include buffer modules are developed. This theory provides the conditions under which the system properties of boundedness, liveness, and reversibility are preserved. The results are illustrated through two manufacturing system examples: a multiple machine and multiple buffer production line and an automatic storage and retrieval system in the context of flexible manufacturing.

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.

Building a better sticky trap: description of an easy-to-use trap and pole mount for quantifying the abundance of adult aquatic insects

USGS Publications Warehouse

Smith, Joshua T.; Kennedy, Theodore A.; Muehlbauer, Jeffrey D.

2014-01-01

Insect emergence is a fundamental process in freshwaters. It is a critical life-history stage for aquatic insects and provides an important prey resource for terrestrial and aquatic consumers. Sticky traps are increasingly being used to sample these insects. The most common design consists of an acetate sheet coated with a nondrying adhesive that is attached to a wire frame or cylinder. These traps must be prepared at the deployment site, a process that can be time consuming and difficult given the vagaries of field conditions. Our goals were to develop a sturdy, low-cost sticky trap that could be prepared in advance, rapidly deployed and recovered in the field, and used to estimate the flight direction of insects. We used 150-mm Petri dishes with lids. The dishes can be coated cleanly and consistently with Tangle-Trap® adhesive. Deploying traps is simple and requires only a pole set near the body of water being sampled. Four dishes can be attached to the pole using Velcro and aligned in 4 different directions to enable quantification of insect flight direction. After sampling, Petri dishes can be taped closed, packed in boxes, and stored indefinitely. Petri traps are comparable in price to standard acetate sheet traps at ∼US$0.50/directional deployment, but they require more space for storage than acetate sheet traps. However, a major benefit of Petri traps is that field deployment times are ⅓ those of acetate traps. Our study demonstrated that large Petri dishes are an ideal platform for sampling postemergent adult aquatic insects, particularly when the study design involves estimating flight direction and when rapid deployment and recovery of traps is critical.

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/.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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/.

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.

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.

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.

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

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.

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.

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

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

Comparison of functional assays used in the clinical development of a placental malaria vaccine.

PubMed

Pehrson, Caroline; Heno, Kristine K; Adams, Yvonne; Resende, Mafalda; Mathiesen, Line; Soegaard, Max; de Jongh, Willem A; Theander, Thor G; Salanti, Ali; Nielsen, Morten A

2017-01-23

Malaria in pregnancy is associated with significant morbidity in pregnant women and their offspring. Plasmodium falciparum infected erythrocytes (IE) express VAR2CSA that mediates binding to chondroitin sulphate A (CSA) in the placenta. Two VAR2CSA-based vaccines for placental malaria are in clinical development. The purpose of this study was to evaluate the robustness and comparability of binding inhibition assays used in the clinical development of placental malaria vaccines. The ability of sera from animals immunised with different VAR2CSA constructs to inhibit IE binding to CSA was investigated in three in vitro assays using 96-well plates, petri dishes, capillary flow and an ex vivo placental perfusion assay. The inter-assay variation was not uniform between assays and ranged from above ten-fold in the flow assay to two-fold in the perfusion assay. The intra-assay variation was highest in the petri dish assay. A positive correlation between IE binding avidity and the level of binding after antibody inhibition in the petri dish assay indicate that high avidity IE binding is more difficult to inhibit. The highest binding inhibition sensitivity was found in the 96-well and petri dish assays compared to the flow and perfusion assays where binding inhibition required higher antibody titers. The inhibitory capacity of antibodies is not easily translated between assays and the high sensitivity of the 96-well and petri dish assays stresses the need for comparing serial dilutions of serum. Furthermore, IE binding avidity must be in the same range when comparing data from different days. There was an overall concordance in the capacity of antibody-mediated inhibition, when comparing the in vitro assays with the perfusion assay, which more closely represents in vivo conditions. Importantly the ID1-ID2a protein in a liposomal formulation, currently in a phase I trial, effectively induced antibodies that inhibited IE adhesion in placental tissue. Copyright © 2016. Published by Elsevier Ltd.

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 are complementary to identify and assess the criticality conflicts.

Testing of Compounds for Efficacy against Schistosomiasis.

DTIC Science & Technology

1987-08-25

Nostoc muscorU) has been grown (Liang, 1974) is placed in all glass aquaria, and plastic trays to serve as an additional food source. Snails in petri...supplemented with blue-green algae ( Nostoc muscoru) and mud forms the diet of stock snails in glass aquaria as well as those kept in plastic trays. The agar...green algae ( Nostoc muscorum) and water is used for rearing young * snails and maintaining both pre-patent and patent snails V (Liang, 1974); 3) a petri

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

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.

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

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.

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.

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.

Characterizing parameters of Jatropha curcas cell cultures for microgravity studies

NASA Astrophysics Data System (ADS)

Vendrame, Wagner A.; Pinares, Ania

2013-06-01

Jatropha (Jatropha curcas) is a tropical perennial species identified as a potential biofuel crop. The oil is of excellent quality and it has been successfully tested as biodiesel and in jet fuel mixes. However, studies on breeding and genetic improvement of jatropha are limited. Space offers a unique environment for experiments aiming at the assessment of mutations and differential gene expression of crops and in vitro cultures of plants are convenient for studies of genetic variation as affected by microgravity. However, before microgravity studies can be successfully performed, pre-flight experiments are necessary to characterize plant material and validate flight hardware environmental conditions. Such preliminary studies set the ground for subsequent spaceflight experiments. The objectives of this study were to compare the in vitro growth of cultures from three explant sources (cotyledon, leaf, and stem sections) of three jatropha accessions (Brazil, India, and Tanzania) outside and inside the petriGAP, a modified group activation pack (GAP) flight hardware to fit petri dishes. In vitro jatropha cell cultures were established in petri dishes containing a modified MS medium and maintained in a plant growth chamber at 25 ± 2 °C in the dark. Parameters evaluated were surface area of the explant tissue (A), fresh weight (FW), and dry weight (DW) for a period of 12 weeks. Growth was observed for cultures from all accessions at week 12, including subsequent plantlet regeneration. For all accessions differences in A, FW and DW were observed for inside vs. outside the PetriGAPs. Growth parameters were affected by accession (genotype), explant type, and environment. The type of explant influenced the type of cell growth and subsequent plantlet regeneration capacity. However, overall cell growth showed no abnormalities. The present study demonstrated that jatropha in vitro cell cultures are suitable for growth inside PetriGAPs for a period of 12 weeks. The parameters evaluated in this study provide the basic ground work and pre-flight assessment needed to justify a model for microgravity studies with jatropha in vitro cell cultures. Future studies should focus on results of experiments performed with jatropha in vitro cultures in microgravity.

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 therapeutic targets whose inhibition recovers abnormally phosphorylated proteins in an atrophic state. They were evaluated by various approaches, such as Western blotting, GO terms, literature, known muscle atrophy-related genes and shortest path analysis. We expect the new proposed strategy to provide an understanding of phosphorylation status in muscle atrophy and to provide assistance towards identifying new therapies.

Efficacy of entomopathogenic nematode Steinernema feltiae (Rhabditida: Steinernematidae) as influenced by Frankliniella occidentalis (Thysanoptera: Thripidae) developmental stage and host plant stage.

PubMed

Buitenhuis, R; Shipp, J L

2005-10-01

Entomopathogenic nematodes were investigated as an alternative biological control strategy for western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), in ornamental greenhouse crops, by using potted chrysanthemum as a model crop. The susceptibility of various life stages of F. occidentalis to different concentrations of the nematode Steinernema feltiae (Filipjev) (Rhabditida: Steinernematidae) was investigated in petri dish bioassays. This was followed with trials using potted chrysanthemums comparing the efficacy of nematode application to plants in vegetative (exposed habitat) versus flowering (cryptic habitat) stages. In both trials, the effect of the wetting agent Agral 90 (nonylphenoxy polyethoxyethanol), which is used in combination with the nematode spray, on F. occidentalis mortality was assessed. In petri dish trials, the prepupae and pupae were the most susceptible developmental stages of F. occidentalis to infection by S. feltiae. First and second instars were killed by very high rates of nematodes (> or =20,000 infective juveniles per milliliter), but corrected mortality was only approximately 28-37%. No significant mortality was observed for adult thrips. Results from the petri dish trials were confirmed on chrysanthemum plants. Foliar application of S. feltiae did not result in significant mortality in larvae or adults. No significant differences in efficacy were detected by application of nematodes on vegetative versus flowering chrysanthemum. Agral 90 had a significant impact on mortality on the first stage larvae and prepupae in the petri dish trials but not in the plant trials. Thrips control by S. feltiae in greenhouses may be partly or completely due to prepupal and pupal mortality.

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.

Calculations of the Acceleration of Centrifugal Loading on Adherent Cells

NASA Astrophysics Data System (ADS)

Chen, Kang; Song, Yang; Liu, Qing; Zhang, Chunqiu

2017-07-01

Studies have shown that the morphology and function of living cells are greatly affected by the state of different high acceleration. Based on the centrifuge, we designed a centrifugal cell loading machine for the mechanical biology of cells under high acceleration loading. For the machine, the feasibility of the experiment was studied by means of constant acceleration or variable acceleration loading in the Petri dish fixture and/or culture flask. Here we analyzed the distribution of the acceleration of the cells with the change of position and size of the culturing device quantitatively. It is obtained that Petri dish fixture and/or culture flask can be used for constant acceleration loading by experiments; the centripetal acceleration of the adherent cells increases with the increase of the distance between the rotor center of the centrifuge and the fixture of the Petri dish and the size of the fixture. It achieves the idea that the general biology laboratory can conduct the study of mechanical biology at high acceleration. It also provides a basis for more accurate study of the law of high acceleration on mechanobiology of cells.

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.

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.

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.

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/

Contemporary Records of the (1492) Ensisheim Fall

NASA Astrophysics Data System (ADS)

Levi, F. A.; Levi-Donati, G. R.

1992-07-01

On the occasion of the five-hundredth anniversary of the Ensisheim (LL6) stone (November 16, 1492), five rare documents on this fall are presented: 1) Anonymous, Annali del Convento di S. Domenico. (in Italian) Manuscript n. 1151, Biblioteca Com. "Augusta", Perugia. 2) Eusebii Pamphili C. (1570) Chronicon. Petri, Basilea. (in Latin). 3) Lycosthenes (Wolffhart) C. (1557) Prodigiorum ac ostentorum Chronicon. Petri, Basilea. (in Latin). 4) Sansovino F. (1582) Cronologia del Mondo. Salicato, Vinegia. (in Italian). 5) Schedel H. (1492) Liber Chronicarum cum figuris et ymagi(ni)bus ab inicio mu(n)di. Koberger, Nuremberga. (in Latin).

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.

Apex-4 for SpaceX CRS-10

NASA Image and Video Library

2017-02-16

Drs. Rob Ferl and Anna-Lisa Paul in a cold room in the Kennedy Space Center Processing Facility with the petri plates they prepped at the University of Florida for APEX-04. Paul is the principal investigator (PI) and Ferl is co-PI. Apex-04 is an experiment involving Arabidopsis in petri plates inside the Veggie facility aboard the International Space Station. Since Arabidopsis is the genetic model of the plant world, it is a perfect sample organism for performing genetic studies in spaceflight. The experiment is the result of a grant from NASA’s Space Life and Physical Sciences division.

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.

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.

Number of nitrate groups determines reactivity and potency of organic nitrates: a proof of concept study in ALDH-2−/− mice

PubMed Central

Wenzel, P; Hink, U; Oelze, M; Seeling, A; Isse, T; Bruns, K; Steinhoff, L; Brandt, M; Kleschyov, A L; Schulz, E; Lange, K; Weiner, H; Lehmann, J; Lackner, K J; Kawamoto, T; Münzel, T; Daiber, A

2007-01-01

Background and purpose: Mitochondrial aldehyde dehydrogenase (ALDH-2) has been shown to provide a pathway for bioactivation of organic nitrates and to be prone to desensitization in response to highly potent, but not to less potent, nitrates. We therefore sought to support the hypothesis that bioactivation by ALDH-2 critically depends on the number of nitrate groups within the nitrovasodilator. Experimental approach: Nitrates with one (PEMN), two (PEDN; GDN), three (PETriN; glyceryl trinitrate, GTN) and four (pentaerithrityl tetranitrate, PETN) nitrate groups were investigated. Vasodilatory potency was measured in isometric tension studies using isolated aortic segments of wild type (WT) and ALDH-2−/− mice. Activity of the cGMP-dependent kinase-I (reflected by levels of phosphorylated VAsodilator Stimulated Phosphoprotein, P-VASP) was quantified by Western blot analysis, mitochondrial dehydrogenase activity by HPLC. Following incubation of isolated mitochondria with PETN, PETriN-chromophore and PEDN, metabolites were quantified using chemiluminescence nitrogen detection and mass spectrometry. Key results: Compared to WT, vasorelaxation in response to PETN, PETriN and GTN was attenuated about 10fold in ALDH-2−/− mice, identical to WT vessels preincubated with inhibitors of ALDH-2. Reduced vasodilator potency correlated with reduced P-VASP formation and diminished biotransformation of the tetranitrate- and trinitrate-compounds. None of these findings were observed for PEDN, GDN and PEMN. Conclusions and implications: Our results support the crucial role of ALDH-2 in bioactivating highly reactive nitrates like GTN, PETN and PETriN. ALDH-2-mediated relaxation by organic nitrates therefore depends mainly on the number of nitrate groups. Less potent nitrates like PEDN, GDN and PEMN are apparently biotransformed by other pathways. PMID:17220910

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

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.

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.

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.

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.

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.

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.

Antagonism of Trichoderma isolates against Leucoagaricus gongylophorus (Singer) Möller.

PubMed

do Nascimento, Mariela Otoni; de Almeida Sarmento, Renato; Dos Santos, Gil Rodrigues; de Oliveira, Cléia Almeida; de Souza, Danival José

2017-08-01

Filamentous fungi from the genus Trichoderma are commonly found in soil. They are considered facultative mycoparasites, and are antagonists of other fungi such as the cultivar of leaf-cutting ants (Leucoagaricus gongylophorus). The aim of the present study was to bioprospect Trichoderma spp. from different soils collected from Gurupi, Tocantins, Brazil, for antagonistic effects against the mutualistic fungus of leaf-cutting ants. To isolate filamentous fungi, samples were collected from six locations. Preliminarily, isolates were identified by morphological analysis as belonging to Trichoderma. Trichoderma spp. had their internal transcribed spacer region (ITS) of ribosomal RNA genes (rRNA) sequenced to confirm species-level taxonomy. L. gongylophorus was isolated from a laboratory ant colony. Antagonistic properties of seven isolates of Trichoderma against L. gongylophorus were measured using paired disks in Petri dishes with potato dextrose agar medium (PDA). All Trichoderma isolates inhibited the growth of L. gongylophorus in Petri dishes. Isolate 2 of Trichoderma spirale group exhibited slow mycelial growth in the Petri dish, and a high rate of inhibition against L. gongylophorus. This isolate is a promising fungus for field tests of biological control methods for leaf-cutting ants. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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.

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.

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 this method, we studied a MAPK1,2 and AKT signaling network downstream from EGFR in two breast tumor cell lines. We analyzed, both experimentally and computationally, the activity level of several molecules in response to a targeted manipulation of TSC2 and mTOR-Raptor. The results from our method agreed with experimental results in greater than 90% of the cases considered, and in those where they did not agree, our approach provided valuable insights into discrepancies between known network connectivities and experimental observations.

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 this method, we studied a MAPK1,2 and AKT signaling network downstream from EGFR in two breast tumor cell lines. We analyzed, both experimentally and computationally, the activity level of several molecules in response to a targeted manipulation of TSC2 and mTOR-Raptor. The results from our method agreed with experimental results in greater than 90% of the cases considered, and in those where they did not agree, our approach provided valuable insights into discrepancies between known network connectivities and experimental observations. PMID:18463702

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 the optimal number of t-clusters to consider for interpretation, the cluster validity measure, Silhouette Width, is applied. We considered two different case studies as examples: a small signal transduction pathway (pheromone response pathway in Saccharomyces cerevisiae) and a medium-sized gene regulatory network (gene regulation of Duchenne muscular dystrophy). We automatically classified the t-invariants into functionally distinct t-clusters, which could be interpreted biologically as functional modules in the network. We found differences in the suitability of the various distance measures as well as the clustering methods. In terms of a biologically meaningful classification of t-invariants, the best results are obtained using the Tanimoto distance measure. Considering clustering methods, the obtained results suggest that UPGMA and Complete Linkage are suitable for clustering t-invariants with respect to the biological interpretability. We propose a new approach for the biological classification of Petri net t-invariants based on cluster analysis. Due to the biologically meaningful data reduction and structuring of network processes, large sets of t-invariants can be evaluated, allowing for model validation of qualitative biochemical Petri nets. This approach can also be applied to elementary mode analysis.

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 as modules. To find the optimal number of t-clusters to consider for interpretation, the cluster validity measure, Silhouette Width, is applied. Results We considered two different case studies as examples: a small signal transduction pathway (pheromone response pathway in Saccharomyces cerevisiae) and a medium-sized gene regulatory network (gene regulation of Duchenne muscular dystrophy). We automatically classified the t-invariants into functionally distinct t-clusters, which could be interpreted biologically as functional modules in the network. We found differences in the suitability of the various distance measures as well as the clustering methods. In terms of a biologically meaningful classification of t-invariants, the best results are obtained using the Tanimoto distance measure. Considering clustering methods, the obtained results suggest that UPGMA and Complete Linkage are suitable for clustering t-invariants with respect to the biological interpretability. Conclusion We propose a new approach for the biological classification of Petri net t-invariants based on cluster analysis. Due to the biologically meaningful data reduction and structuring of network processes, large sets of t-invariants can be evaluated, allowing for model validation of qualitative biochemical Petri nets. This approach can also be applied to elementary mode analysis. PMID:18257938

Apparatus and process for microbial detection and enumeration

NASA Technical Reports Server (NTRS)

Wilkins, J. R.; Grana, D. (Inventor)

1982-01-01

An apparatus and process for detecting and enumerating specific microorganisms from large volume samples containing small numbers of the microorganisms is presented. The large volume samples are filtered through a membrane filter to concentrate the microorganisms. The filter is positioned between two absorbent pads and previously moistened with a growth medium for the microorganisms. A pair of electrodes are disposed against the filter and the pad electrode filter assembly is retained within a petri dish by retainer ring. The cover is positioned on base of petri dish and sealed at the edges by a parafilm seal prior to being electrically connected via connectors to a strip chart recorder for detecting and enumerating the microorganisms collected on filter.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Selective sweeps in growing microbial colonies

NASA Astrophysics Data System (ADS)

Korolev, Kirill S.; Müller, Melanie J. I.; Karahan, Nilay; Murray, Andrew W.; Hallatschek, Oskar; Nelson, David R.

2012-04-01

Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These experiments, however, are often limited to the well-mixed environments of a test tube or a chemostat. Since spatial organization can significantly affect evolutionary dynamics, the need is growing for evolutionary experiments in spatially structured environments. The surface of a Petri dish provides such an environment, but a more detailed understanding of microbial growth on Petri dishes is necessary to interpret such experiments. We formulate a simple deterministic reaction-diffusion model, which successfully predicts the spatial patterns created by two competing species during colony expansion. We also derive the shape of these patterns analytically without relying on microscopic details of the model. In particular, we find that the relative fitness of two microbial strains can be estimated from the logarithmic spirals created by selective sweeps. The theory is tested with strains of the budding yeast Saccharomyces cerevisiae for spatial competitions with different initial conditions and for a range of relative fitnesses. The reaction-diffusion model also connects the microscopic parameters like growth rates and diffusion constants with macroscopic spatial patterns and predicts the relationship between fitness in liquid cultures and on Petri dishes, which we confirmed experimentally. Spatial sector patterns therefore provide an alternative fitness assay to the commonly used liquid culture fitness assays.

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 components in robotic systems are investigated.

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

Ethylene induced shikonin biosynthesis in shoot culture of Lithospermum erythrorhizon.

PubMed

Touno, Kaori; Tamaoka, Jin; Ohashi, Yuko; Shimomura, Koichiro

2005-02-01

Lithospermum erythrorhizon shoots, cultured on phytohormone-free Murashige and Skoog solid medium, produced shikonin derivatives, whereas shoots cultured in well-ventilated petri dishes, produced small amount. Analysis by gas chromatography revealed the presence of ethylene in non-ventilated petri dishes where the shoots, producing shikonin derivatives, were cultured. Therefore, the possible involvement of ethylene in shikonin biosynthesis of shoot cultures was investigated. Treatment of ethylene or the ethylene precursor, 1-aminocyclopropane-1-carboxylic acid, resulted in increasing shikonin derivatives contents in cultured shoots. Silver ion, an ethylene-response inhibitor, or aminoethoxyvinylglycine, an ethylene biosynthesis inhibitor, decreased production of shikonin derivatives in cultured shoots. Our results indicate that ethylene is one of the regulatory elements of shikonin biosynthesis in L. erythrorhizon shoot culture.

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.

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.

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.

Machine for Automatic Bacteriological Pour Plate Preparation

PubMed Central

Sharpe, A. N.; Biggs, D. R.; Oliver, R. J.

1972-01-01

A fully automatic system for preparing poured plates for bacteriological analyses has been constructed and tested. The machine can make decimal dilutions of bacterial suspensions, dispense measured amounts into petri dishes, add molten agar, mix the dish contents, and label the dishes with sample and dilution numbers at the rate of 2,000 dishes per 8-hr day. In addition, the machine can be programmed to select different media so that plates for different types of bacteriological analysis may be made automatically from the same sample. The machine uses only the components of the media and sterile polystyrene petri dishes; requirements for all other materials, such as sterile pipettes and capped bottles of diluents and agar, are eliminated. Images PMID:4560475

Apex-4 for SpaceX CRS-10

NASA Image and Video Library

2017-02-16

APEX-04, or Advanced Plant EXperiments-04, is being prepared in a cold room in the Kennedy Space Center Processing Facility for SpaceX-10. The petri plates are wrapped in black cloth and kept cold (+4 degrees Celsius) to prevent them from germinating prior to the experiment start on station. Dr. Anna Lisa Paul of the University of Florida is the principal investigator for APEX-04. Apex-04 is an experiment involving Arabidopsis in petri plates inside the Veggie facility aboard the International Space Station. Since Arabidopsis is the genetic model of the plant world, it is a perfect sample organism for performing genetic studies in spaceflight. The experiment is the result of a grant from NASA’s Space Life and Physical Sciences division.

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.

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.

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

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.

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.

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.

Natural Selection in a Petri Dish.

ERIC Educational Resources Information Center

McCarty, Robbie V.; Marek, Edmund A.

1997-01-01

Presents an activity to teach natural selection that involves students in a microbiological investigation. Students discover that a change in environmental conditions tests a species' range of adaptations. (DDR)

Antimicrobial Testing Methods & Procedures: MB-33-00

EPA Pesticide Factsheets

Information about ATMP - SOP Quantitative Petri Plate Method (QPM) for Determining the Effectiveness of Antimicrobial Towelettes Against Vegetative Bacteria on Inanimate, Hard, Non-porous Surfaces - MB-33-00

Hollow-Fiber Membrane Chamber as a Device for In Situ Environmental Cultivation▿

PubMed Central

Aoi, Yoshiteru; Kinoshita, Tomoyuki; Hata, Toru; Ohta, Hiroaki; Obokata, Haruko; Tsuneda, Satoshi

2009-01-01

A hollow-fiber membrane chamber (HFMC) was developed as an in situ cultivation device for environmental microorganisms. The HFMC system consists of 48 to 96 pieces of porous hollow-fiber membrane connected with injectors. The system allows rapid exchange of chemical compounds, thereby simulating a natural environment. Comparative analysis through the cultivation of three types of environmental samples was performed using this newly designed device and a conventional agar-based petri dish. The results show that the ratios of novel phylotypes in isolates, species-level diversities, and cultivabilities in HFMC-based cultivation are higher than those in an agar-based petri dish for all three samples, suggesting that the new in situ cultivation device is effective for cultivation of various environmental microorganisms. PMID:19329655

Apex-4 for SpaceX CRS-10

NASA Image and Video Library

2017-02-16

APEX-04, or Advanced Plant EXperiments-04, is being prepared in a cold room in the Kennedy Space Center Processing Facility for SpaceX-10. Eric Morris from the cold stowage group fits items into the Double Cold Bag (DCB) which is a non-powered container that keeps the APEX petri plates at +4 degrees Celsius during launch and ascent.. Dr. Anna Lisa Paul of the University of Florida is the principal investigator for APEX-04. Apex-04 is an experiment involving Arabidopsis in petri plates inside the Veggie facility aboard the International Space Station. Since Arabidopsis is the genetic model of the plant world, it is a perfect sample organism for performing genetic studies in spaceflight. The experiment is the result of a grant from NASA’s Space Life and Physical Sciences division.

Apex-4 for SpaceX CRS-10

NASA Image and Video Library

2017-02-16

APEX-04, or Advanced Plant EXperiments-04, is being prepared in a cold room in the Kennedy Space Center Processing Facility for SpaceX-10. The 30 petri plates are bundled into groups of 10 and placed into one of three science kits. The science kits allow easy handling when the crew removes the plates from cold stowage on station. Dr. Anna Lisa Paul of the University of Florida is the principal investigator for APEX-04. Apex-04 is an experiment involving Arabidopsis in petri plates inside the Veggie facility aboard the International Space Station. Since Arabidopsis is the genetic model of the plant world, it is a perfect sample organism for performing genetic studies in spaceflight. The experiment is the result of a grant from NASA’s Space Life and Physical Sciences division.

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.

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

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.

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.

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.

Rapid fibroblast activation in mammalian cells induced by silicon nanowire arrays

NASA Astrophysics Data System (ADS)

Ha, Qing; Yang, Gao; Ao, Zhuo; Han, Dong; Niu, Fenglan; Wang, Shutao

2014-06-01

Activated tumor-associated fibroblasts (TAFs) with abundant fibroblast activation protein (FAP) expression attract tremendous attention in tumor progression studies. In this work, we report a rapid 24 h FAP activation method for fibroblasts using silicon nanowires (SiNWs) as culture substrates instead of growth factors or chemokines. In contrast with cells cultured on flat silicon which rarely express FAP, SiNW cultivated cells exhibit FAP levels similar to those found in cancerous tissue. We demonstrated that activated cells grown on SiNWs maintain their viability and proliferation in a time-dependent manner. Moreover, environmental scanning electron microscopy (ESEM) and focused ion beam and scanning electron microscopy (FIB-SEM) analysis clearly revealed that activated cells on SiNWs adapt to the structure of their substrates by filling inter-wire cavities via filopodia in contrast to cells cultured on flat silicon which spread freely. We further illustrated that the expression of FAP was rarely detected in activated cells after being re-cultured in Petri dishes, suggesting that the unique structure of SiNWs may have a certain influence on FAP activation.Activated tumor-associated fibroblasts (TAFs) with abundant fibroblast activation protein (FAP) expression attract tremendous attention in tumor progression studies. In this work, we report a rapid 24 h FAP activation method for fibroblasts using silicon nanowires (SiNWs) as culture substrates instead of growth factors or chemokines. In contrast with cells cultured on flat silicon which rarely express FAP, SiNW cultivated cells exhibit FAP levels similar to those found in cancerous tissue. We demonstrated that activated cells grown on SiNWs maintain their viability and proliferation in a time-dependent manner. Moreover, environmental scanning electron microscopy (ESEM) and focused ion beam and scanning electron microscopy (FIB-SEM) analysis clearly revealed that activated cells on SiNWs adapt to the structure of their substrates by filling inter-wire cavities via filopodia in contrast to cells cultured on flat silicon which spread freely. We further illustrated that the expression of FAP was rarely detected in activated cells after being re-cultured in Petri dishes, suggesting that the unique structure of SiNWs may have a certain influence on FAP activation. Electronic supplementary information (ESI) available: (1) ESEM cross-sectional view images of the flat silicon and SiNW substrates. (2) Bright field morphology images of fibroblasts cultured in Petri dishes. (3) FIB/SEM 52° tilt images of fibroblasts cultured on SiNW 2 and SiNW 3. (4) Immunofluorescence images of FAP expression in fibroblasts re-cultured in Petri dishes after detachment from flat silicon and a series of SiNW substrates. (5) ESEM images of cells re-cultured in Petri dishes after detachment from each group. See DOI: 10.1039/c4nr01415d

New Directions for Corporate Careers.

ERIC Educational Resources Information Center

Lemke, James M.; And Others

1995-01-01

Includes "Introduction" (Lemke); "Career Sidestepping" (Prescott); "Temporary Work Life" (Farrugia); "Electronic Recruiter" (Lemke); "Aerospace Network" (Hoffner); "Multimedia: The Future of Adult Learning" (Golub); and "Teleworking: Commuting on the Information Highway" (Petrie). (JOW)

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 framework provides an effective way to model and regulate/optimize the OFS in HM hybrid systems composed of continuous-time OFS model and discrete-event switching controller. Copyright © 2017 Elsevier B.V. All rights reserved.

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).

Highly effective fungal inactivation in He+O2 atmospheric-pressure nonequilibrium plasmas

NASA Astrophysics Data System (ADS)

Xiong, Z.; Lu, X. P.; Feng, A.; Pan, Y.; Ostrikov, K.

2010-12-01

Highly effective (more than 99.9%) inactivation of a pathogenic fungus Candida albicans commonly found in oral, respiratory, digestive, and reproduction systems of a human body using atmospheric-pressure plasma jets sustained in He+O2 gas mixtures is reported. The inactivation is demonstrated in two fungal culture configurations with open (Petri dish without a cover) and restricted access to the atmosphere (Petri dish with a cover) under specific experimental conditions. It is shown that the fungal inactivation is remarkably more effective in the second configuration. This observation is supported by the scanning and transmission electron microscopy of the fungi before and after the plasma treatment. The inactivation mechanism explains the experimental observations under different experimental conditions and is consistent with the reports by other authors. The results are promising for the development of advanced health care applications.

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.

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.

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.

Ovicidal activity of different concentrations of Pochonia chlamydosporia chlamydospores on Taenia taeniaeformis eggs.

PubMed

Braga, F R; Silva, A R; Carvalho, R O; Araújo, J V; Pinto, P S A

2011-03-01

Three concentrations of chlamydospores of the nematophagous fungus Pochonia chlamydosporia (1000, 10,000 and 20,000 per Petri dish) were evaluated in vitro on Taenia taeniaeformis eggs. Chlamydospores at each concentration were cultured in two different media: 2% water-agar (2%WA) and 2% corn-meal-agar (2%CMA). Taenia taeniaeformis eggs were plated in each chlamydospore concentration in 2%WA and 2%CMA (treated groups) and without fungus (control group). Eggs were removed from each Petri dish at intervals of 7, 14 and 21 days and classified according to ovicidal activity (type 1, type 2 and type 3 effects). Plates containing 2%CMA showed the highest percentages for type 3 effect (81.3%) on the 21st day of observation. A difference (P < 0.01) between the media 2%WA and 2%CMA for type 1 effect was observed only at a concentration of 1000 chlamydospores on the 7th day. There were differences (P < 0.01) between 2%WA and 2%CMA on the 14th and 21st days, at the concentration of 20,000 chlamydospores, for type 1 and type 3 effects. Regression curves for type 3 effect in 2%WA and 2%CMA at the tested concentrations showed higher ovicidal activity with increasing chlamydospore concentrations. Results indicate that, at concentrations of 1000, 10,000 and 20,000 per Petri dish, chlamydospores of P. chlamydosporia effectively destroyed T. taeniaeformis eggs and can be considered a potential biological control agent for this cestode.

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

Reusable anaerobic system for microbiological studies - A concept

NASA Technical Reports Server (NTRS)

Murawczyk, C.

1971-01-01

Simple, low cost system consists of semirigid incubation chamber with clear Teflon window, airtight zipper and internal compartments for petri dishes or microbial plates. Device interests schools, medical laboratories, and manufacturers of biological and pharmaceutical supplies.

The Blue Bottle Experiment--Simple Demonstration of Self-Organization.

ERIC Educational Resources Information Center

Adamcikova, L'ubica; Sevcik, Peter

1998-01-01

Explains a way of observing pattern formation in the Blue Bottle chemistry demonstration by pouring a solution containing sodium hydroxide, glucose, and dye into a Petri dish and placing the dish on an overhead projector. (WRM)

Overhead Projector Demonstrations: A Classroom Demonstration of Aliphatic Substitution.

ERIC Educational Resources Information Center

Perina, Ivo; Mihanovic, Branka

1989-01-01

Presents a halogen substitution of an alkane using a compartmentalized Petri dish or Conway dish on an overhead projector. Provides methodology and several modifications for different reactions. Uses hexane, methyl orange, bromine, and silver nitrate. (MVL)

Swanson configures LMM for CARA-Petri Plant Experiment

NASA Image and Video Library

2014-05-05

ISS039-E-018472 (5 May 2014) --? NASA astronaut Steve Swanson, Expedition 39 flight engineer, works in the U.S. laboratory Destiny of the International Space Station, preparing the Light Microscopy Module (LMM) for a planet experiment.

Dispersal of Beauveria bassiana by the activity of nettle insects.

PubMed

Meyling, Nicolai V; Pell, Judith K; Eilenberg, Jørgen

2006-10-01

Recent studies have shown that the entomopathogenic fungus Beauveria bassiana occurs naturally on the phylloplanes of several plants, including nettles. Insects could, by their activity, be contributing to this inoculum by dispersing it from other sites. The potential of nettle aphids Microlophium carnosum and their predator Anthocoris nemorum to disperse conidia of B. bassiana from soil to nettles and from sporulating cadavers in the nettle canopy was investigated in laboratory experiments. In petri dish assays, aphids showed potential to distribute B. bassiana from soil to nettle leaves. Predators dispersed inoculum from both soil and cadavers to nettle leaves in petri dishes. In microcosms, aphids did not disperse B. bassiana from the soil or from cadavers confined in the canopy, but A. nemorum were able to transfer inoculum from soil into the nettle canopy and to distribute conidia from cryptic cadavers. In some instances, infections were initiated in aphids and predators as a consequence of dispersal.

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.

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.

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

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.

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.

Apex-4 for SpaceX CRS-10

NASA Image and Video Library

2017-02-16

APEX-04, or Advanced Plant EXperiments-04, is being prepared in a cold room in the Kennedy Space Center Processing Facility for SpaceX-10. Eric Morris from the cold stowage group places the APEX-04 science kits into the Double Cold Bag (DCB), which is a non-powered container that keeps the APEX petri plates at +4 degrees Celsius during launch and ascent. The cold bricks in the lower right of the photo are placed in the DCB prior to closure. Dr. Anna Lisa Paul of the University of Florida is the principal investigator for APEX-04. Apex-04 is an experiment involving Arabidopsis in petri plates inside the Veggie facility aboard the International Space Station. Since Arabidopsis is the genetic model of the plant world, it is a perfect sample organism for performing genetic studies in spaceflight. The experiment is the result of a grant from NASA’s Space Life and Physical Sciences division.

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.

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.

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.

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.

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.

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

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.

Adaptation of plastic surfaces for tissue culture by glow discharge.

PubMed Central

Amstein, C F; Hartman, P A

1975-01-01

Plastic petri dishes and microtitration plates were electrically charged by a glow discharge unit installed in a vacuum evaporator. Charged and uncharged plates, as well as plates commercially treated for tissue culture, were inoculated with Vero and BHK-21 cell lines; secondary cultures of monkey kidney, chicken lung, canine kidney, and embryonic bovine kidney; and primary chicken embryo fibroblasts and chicken lung cells. All cell cultures grew normally on petri plates charged with the covers open. Growth rate and cell density compared favorably with growth on the commercial tissue culture plates; cell growth was somewhat less dense, however, on plates charged with the covers closed. Charged plates could be sterilized by ultraviolet light and ethylene oxide with no adverse effects on cell growth. Cells inoculated onto plates charged up to 7 months before inoculation grew as well as on freshly charged plates. Images PMID:818106

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.

Highly effective fungal inactivation in He+O{sub 2} atmospheric-pressure nonequilibrium plasmas

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

Xiong, Z.; Lu, X. P.; Pan, Y.

2010-12-15

Highly effective (more than 99.9%) inactivation of a pathogenic fungus Candida albicans commonly found in oral, respiratory, digestive, and reproduction systems of a human body using atmospheric-pressure plasma jets sustained in He+O{sub 2} gas mixtures is reported. The inactivation is demonstrated in two fungal culture configurations with open (Petri dish without a cover) and restricted access to the atmosphere (Petri dish with a cover) under specific experimental conditions. It is shown that the fungal inactivation is remarkably more effective in the second configuration. This observation is supported by the scanning and transmission electron microscopy of the fungi before and aftermore » the plasma treatment. The inactivation mechanism explains the experimental observations under different experimental conditions and is consistent with the reports by other authors. The results are promising for the development of advanced health care applications.« less

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.

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.

Centripetal Force on an Overhead Projector.

ERIC Educational Resources Information Center

Rheam, Harry

1995-01-01

Describes two simple demonstrations of an object moving in a straight line tangent to the circle if centripetal force is removed. Demonstrations use a pie plate and petri dish with ball bearings to illustrate the phenomena on an overhead projector. (LZ)

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.

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 paper demonstrates how Petri net analysis techniques can promote a deeper understanding of signal transduction pathways. The new concepts of feasible t-invariants and MCT-sets have been proven to be useful for model validation and the interpretation of the biological system behaviour. Whereas MCT-sets provide a decomposition of the net into disjunctive subnets, feasible t-invariants describe subnets, which generally overlap. This work contributes to qualitative modelling and to the analysis of large biological networks by their fully automatic decomposition into biologically meaningful modules.

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 meaningful functional units. Conclusion The paper demonstrates how Petri net analysis techniques can promote a deeper understanding of signal transduction pathways. The new concepts of feasible t-invariants and MCT-sets have been proven to be useful for model validation and the interpretation of the biological system behaviour. Whereas MCT-sets provide a decomposition of the net into disjunctive subnets, feasible t-invariants describe subnets, which generally overlap. This work contributes to qualitative modelling and to the analysis of large biological networks by their fully automatic decomposition into biologically meaningful modules. PMID:17081284

The Forgotten Disaster Victim: Reducing Responder Injury

DTIC Science & Technology

2017-03-01

Approved by: Anke Richter Thesis Advisor Michael Petrie EMS Bureau, County of Monterey Second Reader Erik Dahl Associate Chair for Instruction...RESPONDERS IN DISASTERS .............20 1. Oklahoma City Bombing .............................................................20 2. World Trade Center...Categories, 2008–2014..................................................................................................19 Figure 4. Oklahoma City Bombing

Why cage a tree? Use of whole-tree enclosures to assess introduced predators of hemlock woolly adelgid, Adelges tsugae

Treesearch

Jerome F. Grant; James Rusty Rhea; Paris Lambdin; Greg Wiggins; Abdul Hakeem

2009-01-01

While commonly used approaches (petri dishes, small arenas, growth chambers, greenhouse studies, sleeve cages, etc.) for evaluation of natural enemies provide important information, does the small size of these arenas limit their...

Overhead Projector Demonstrations.

ERIC Educational Resources Information Center

Kolb, Doris, Ed.

1988-01-01

Provides two demonstrations: (1) electrolyte migration of ions using colored ions which cross a strip of gelatin allowing for noticeable migration; and (2) photochemical reduction of Fe+3 by the citrate ion. Points out both reactions can be done in a Petri dish using common lab materials. (MVL)

Vector potential of houseflies (Musca domestica) for Helicobacter pylori.

PubMed

Grübel, P; Hoffman, J S; Chong, F K; Burstein, N A; Mepani, C; Cave, D R

1997-06-01

The mode of transmission of Helicobacter pylori is unknown. Since viable bacteria have been shown to be excreted in feces from infected individuals and houseflies habitually develop and feed on excrement, we hypothesized that flies ingest and harbor H. pylori and, in turn, contaminate the human environment. This study examined the possible vector potential of houseflies (Musca domestica) for H. pylori. Caged houseflies were exposed to freshly grown H. pylori on agar plates. After a 6-h feeding period, the plates were removed and were replaced with sterile petri dishes containing a droplet of sterile brucella broth. At regular intervals, small numbers of houseflies were removed for microbiological and histological analysis, and the petri dishes were replaced with fresh sterile plates with fresh drops of brucella broth. The flies' bodies, the flies' dissected alimentary tracts, and excreta on the petri dishes were cultured for H. pylori, whose identity was confirmed by the urease, catalase, and oxidase reactions and Gram staining. In contrast to control flies, viable H. pylori could be isolated from external surfaces for up to 12 h and from gut and excreta for as long as 30 h after the initial feeding period. After 30 h other gram-negative bacteria overgrew the cultures of samples from all locations tested, rendering the selective culture of H. pylori colonies impossible. Histological analysis revealed Helicobacter-like organisms in the gut lumen and attached to intestinal epithelial cells. We conclude that houseflies can harbor viable H. pylori on their bodies and in their intestinal tracts. They are also able to disseminate viable H. pylori in excreta, and they may therefore present a significant reservoir and be a vector in the transmission of H. pylori.

Vector potential of houseflies (Musca domestica) for Helicobacter pylori.

PubMed Central

Grübel, P; Hoffman, J S; Chong, F K; Burstein, N A; Mepani, C; Cave, D R

1997-01-01

The mode of transmission of Helicobacter pylori is unknown. Since viable bacteria have been shown to be excreted in feces from infected individuals and houseflies habitually develop and feed on excrement, we hypothesized that flies ingest and harbor H. pylori and, in turn, contaminate the human environment. This study examined the possible vector potential of houseflies (Musca domestica) for H. pylori. Caged houseflies were exposed to freshly grown H. pylori on agar plates. After a 6-h feeding period, the plates were removed and were replaced with sterile petri dishes containing a droplet of sterile brucella broth. At regular intervals, small numbers of houseflies were removed for microbiological and histological analysis, and the petri dishes were replaced with fresh sterile plates with fresh drops of brucella broth. The flies' bodies, the flies' dissected alimentary tracts, and excreta on the petri dishes were cultured for H. pylori, whose identity was confirmed by the urease, catalase, and oxidase reactions and Gram staining. In contrast to control flies, viable H. pylori could be isolated from external surfaces for up to 12 h and from gut and excreta for as long as 30 h after the initial feeding period. After 30 h other gram-negative bacteria overgrew the cultures of samples from all locations tested, rendering the selective culture of H. pylori colonies impossible. Histological analysis revealed Helicobacter-like organisms in the gut lumen and attached to intestinal epithelial cells. We conclude that houseflies can harbor viable H. pylori on their bodies and in their intestinal tracts. They are also able to disseminate viable H. pylori in excreta, and they may therefore present a significant reservoir and be a vector in the transmission of H. pylori. PMID:9163433

Interwoven four-compartment capillary membrane technology for three-dimensional perfusion with decentralized mass exchange to scale up embryonic stem cell culture.

PubMed

Gerlach, Jörg C; Lübberstedt, Marc; Edsbagge, Josefina; Ring, Alexander; Hout, Mariah; Baun, Matt; Rossberg, Ingrid; Knöspel, Fanny; Peters, Grant; Eckert, Klaus; Wulf-Goldenberg, Annika; Björquist, Petter; Stachelscheid, Harald; Urbaniak, Thomas; Schatten, Gerald; Miki, Toshio; Schmelzer, Eva; Zeilinger, Katrin

2010-01-01

We describe hollow fiber-based three-dimensional (3D) dynamic perfusion bioreactor technology for embryonic stem cells (ESC) which is scalable for laboratory and potentially clinical translation applications. We added 2 more compartments to the typical 2-compartment devices, namely an additional media capillary compartment for countercurrent 'arteriovenous' flow and an oxygenation capillary compartment. Each capillary membrane compartment can be perfused independently. Interweaving the 3 capillary systems to form repetitive units allows bioreactor scalability by multiplying the capillary units and provides decentralized media perfusion while enhancing mass exchange and reducing gradient distances from decimeters to more physiologic lengths of <1 mm. The exterior of the resulting membrane network, the cell compartment, is used as a physically active scaffold for cell aggregation; adjusting intercapillary distances enables control of the size of cell aggregates. To demonstrate the technology, mouse ESC (mESC) were cultured in 8- or 800-ml cell compartment bioreactors. We were able to confirm the hypothesis that this bioreactor enables mESC expansion qualitatively comparable to that obtained with Petri dishes, but on a larger scale. To test this, we compared the growth of 129/SVEV mESC in static two-dimensional Petri dishes with that in 3D perfusion bioreactors. We then tested the feasibility of scaling up the culture. In an 800-ml prototype, we cultured approximately 5 x 10(9) cells, replacing up to 800 conventional 100-mm Petri dishes. Teratoma formation studies in mice confirmed protein expression and gene expression results with regard to maintaining 'stemness' markers during cell expansion. Copyright 2010 S. Karger AG, Basel.

The Effect of Various Oral Hygiene Products on Bacterial Growth

NASA Astrophysics Data System (ADS)

Viswanath, S.; Aggrawal, A.; Vazirani, S.

2017-12-01

In this experiment, we tested the antimicrobial effectiveness of six different oral hygiene products. We used three natural cleansing products (coconut oil, sea salt, and baking soda), as well as three synthetic products, which were the Colgate toothpaste varieties of sensitivity, cavity protection, and whitening. We mixed water with each of the products to create a paste that could be uniformly applied to the surface of a disc. We then dipped the discs into the solutions and placed them in petri dishes that were pre-treated with bacterial cells. After 72 hours, we measured the area around the disc that was bacteria-free, which is known as the zone of inhibition. This experiment was repeated twice, with one petri dish per product for each trial, and two different types of agar. We were surprised to discover that almost all the products had no zone of inhibition, with bacteria growing throughout the petri dish, and to the disc. The only cleaning product that showed a significant antibacterial result was the Colgate sensitivity toothpaste. During the two trials, the sensitivity toothpaste had a zone of inhibition of 14.8 cm2 and 8.7 cm2, respectively. Coconut oil was the only other product to have a measurable zone of inhibition with an area of 0.3 cm2. We concluded that only the sensitivity toothpaste was effective in killing bacteria, perhaps due to its different hygienic goal of protecting the tooth's nerves. This toothpaste contains ingredients called potassium nitrate and strontium chloride, which blocks tubules in the dentin, the hard, bony tissue beneath the enamel. Sensitivity toothpaste strengthens the tooth, by blocking decaying substances such as oral bacteria (Knights, 2014).

Effective allergen avoidance for reducing exposure to house dust mite allergens and improving disease management in adult atopic asthmatics.

PubMed

Tsurikisawa, Naomi; Saito, Akemi; Oshikata, Chiyako; Yasueda, Hiroshi; Akiyama, Kazuo

2016-10-01

We investigated the best strategy for adult asthmatics to avoid exposure to Dermatophagoides group (Der-1) allergens. Adult atopic asthmatics (n = 111) followed a 32-item checklist for avoiding Der-1 allergen exposure. Twenty-five patients were excluded through incomplete sampling; 50 remaining patients encased their pillows/futons/mattresses in microfine-fiber covers, 13 used vacuum cleaners with dust-mite-collection nozzles, and 23 acted as non-intervention controls. During August-October 2010 and August-October 2011, dust samples were collected in Petri dishes placed in bedrooms for 2 weeks and from mattresses/futons by using adhesive tape on one morning. A Der-1 level decrease was defined as a mean 2011 Der-1 level of <1 as a ratio of the 2010 level on tape or Petri dish samples. We analyzed the associations between Der-1 level change (by ELISA) and % weekly variability in peak expiratory flow (PEF) or fraction of exhaled nitric oxide (FeNO) after intervention. Der-1 levels decreased significantly in the covers group but not the vacuuming group. FeNO levels and PEF variability were unchanged in both groups. In patients whose Petri dish or tape samples showed decreased Der-1 levels, the % PEF variability was lower in 2011 than in 2010, but FeNO levels were unchanged. Three interventions (vacuuming all family members' mattress/futon surfaces at least weekly or after exposure of the futons to sunlight, and floor wiping before vacuuming), plus using covers, were the most effective management strategy in reducing Der-1 levels. This environmental and bedding maintenance program may help manage adult atopic asthma.

Exogenous hydrogen peroxide reversibly inhibits root gravitropism and induces horizontal curvature of primary root during grass pea germination.

PubMed

Jiang, Jinglong; Su, Miao; Wang, Liyan; Jiao, Chengjin; Sun, Zhengxi; Cheng, Wei; Li, Fengmin; Wang, Chongying

2012-04-01

During germination in distilled water (dH(2)O) on a horizontally positioned Petri dish, emerging primary roots of grass pea (Lathyrus sativus L.) grew perpendicular to the bottom of the Petri dish, due to gravitropism. However, when germinated in exogenous hydrogen peroxide (H(2)O(2)), the primary roots grew parallel to the bottom of the Petri dish and asymmetrically, forming a horizontal curvature. Time-course experiments showed that the effect was strongest when H(2)O(2) was applied prior to the emergence of the primary root. H(2)O(2) failed to induce root curvature when applied post-germination. Dosage studies revealed that the frequency of primary root curvature was significantly enhanced with increased H(2)O(2) concentrations. This curvature could be directly counteracted by dimethylthiourea (DMTU), a scavenger of H(2)O(2), but not by diphenylene iodonium (DPI) and pyridine, inhibitors of H(2)O(2) production. Exogenous H(2)O(2) treatment caused both an increase in the activities of H(2)O(2)-scavenging enzymes [including ascorbate peroxidase (APX: EC 1.11.1.11), catalase (CAT: EC 1.11.1.6) and peroxidase (POD: EC 1.11.1.7)] and a reduction in endogenous H(2)O(2) levels and root vitality. Although grass pea seeds absorbed exogenous H(2)O(2) during seed germination, DAB staining of paraffin sections revealed that exogenous H(2)O(2) only entered the root epidermis and not inner tissues. These data indicated that exogenously applied H(2)O(2) could lead to a reversible loss of the root gravitropic response and a horizontal curvature in primary roots during radicle emergence of the seedling. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Post-accident recovery of hardware and moss cultures from STS-107

NASA Astrophysics Data System (ADS)

Kern, V. D.; Reed, D. W.; Sack, F. D.

In a follow-up investigation to our STS-87 moss experiment, 99 cultures of the moss Ceratodon purpureus were launched on January 16, 2003, and incubated under microgravity conditions for up to 15 days onboard the orbiter Columbia during the STS-107 mission. Following a flawless performance during the on-orbit experiment phase, cultures were chemically fixed in space by the crew at pre-determined intervals. After the accidental break up of Columbia during descent on February 1, 2003, it was assumed that no results would be available since all cultures and data were to be retrieved for analysis post-landing. However, during the subsequent months seven out of eight BRIC (Biological Research in Canisters)-LED containers were recovered on the ground by searchers in Eastern Texas. Each canister housed six polycarbonate Petri Dish Fixation Units (PDFUs) containing petri dishes with 1 or 3 moss cultures each. When these canisters were opened in late April at Kennedy Space Center, 86 out of 87 moss cultures were recovered. Many but not all cultures were severely fragmented and it was impossible to discern growth patterns. However, thousands of well-fixed moss apical cells were found and documented by microscopy. Data retrieved from an internal temperature logger indicated that the canisters experienced intense but transient heat shortly after Columbia broke apart. Some PDFU polycarbonate had fused to the aluminum canister wall. Interior temperatures were sufficient to melt the agarose substrate (˜ 88C), but none of the 41 petri dishes was heat damaged. Initial results from the examination of culture and cell morphology will be presented. (Supported by NASA: NAG10-0179.)

Simultaneous recording of electrical activity and the underlying ionic currents in NG108-15 cells cultured on gold substrate.

PubMed

Acosta-García, Ma Cristina; Morales-Reyes, Israel; Jiménez-Anguiano, Anabel; Batina, Nikola; Castellanos, N P; Godínez-Fernández, R

2018-02-01

This paper shows the simultaneous recording of electrical activity and the underlying ionic currents by using a gold substrate to culture NG108-15 cells. Cells grown on two different substrates (plastic Petri dishes and gold substrates) were characterized quantitatively through scanning electron microscopy (SEM) as well as qualitatively by optical and atomic force microscopy (AFM). No significant differences were observed between the surface area of cells cultured on gold substrates and Petri dishes, as indicated by measurements performed on SEM images. We also evaluated the electrophysiological compatibility of the cells through standard patch-clamp experiments by analyzing features such as the resting potential, membrane resistance, ionic currents, etc. Cells grown on both substrates showed no significant differences in their dependency on voltage, as well as in the magnitude of the Na+ and K+ current density; however, cells cultured on the gold substrate showed a lower membrane capacitance when compared to those grown on Petri dishes. By using two separate patch-clamp amplifiers, we were able to record the membrane current with the conventional patch-clamp technique and through the gold substrate simultaneously. Furthermore, the proposed technique allowed us to obtain simultaneous recordings of the electrical activity (such as action potentials firing) and the underlying membrane ionic currents. The excellent conductivity of gold makes it possible to overcome important difficulties found in conventional electrophysiological experiments such as those presented by the resistance of the electrolytic bath solution. We conclude that the technique here presented constitutes a solution to the problem of the simultaneous recording of electrical activity and the underlying ionic currents, which for decades, had been solved only partially.

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.

Rhinitis, Ocular, Throat and Dermal Symptoms, Headache and Tiredness among Students in Schools from Johor Bahru, Malaysia: Associations with Fungal DNA and Mycotoxins in Classroom Dust

PubMed Central

Norbäck, Dan; Hashim, Jamal Hisham; Cai, Gui-Hong; Hashim, Zailina; Ali, Faridah; Bloom, Erica; Larsson, Lennart

2016-01-01

There are few studies on rhinitis and sick building syndrome (SBS) among students in tropical countries. We studied associations between levels of five fungal DNA sequences, two mycotoxins (sterigmatocystin and verrucarol) and cat allergen (Fel d 1) levels in schools and rhinitis and other weekly SBS symptoms in the students. Fungal DNA was measured by quantitative PCR and cat allergen by ELISA. Pupils (N = 462) from eight randomly selected schools in Johor Bahru, Malaysia participated (96%). Dust samples were collected by cotton swabs and Petri dishes exposed for one week. None of the schools had a mechanical ventilation system, but all classrooms had openable windows that were kept open during lectures and indoor CO2 levels were low (mean 492 ppm; range 380–690 ppm). Weekly nasal symptoms (rhinitis) (18.8%), ocular (11.6%), throat (11.1%), dermal symptoms, headache (20.6%) and tiredness (22.1%) were common. Total fungal DNA in swab samples was associated with rhinitis (p = 0.02), ocular symptoms (p = 0.009) and tiredness (p = 0.001). There were positive associations between Aspergillus versicolor DNA in Petri dish samples, ocular symptoms (p = 0.02) and tiredness (p = 0.001). The level of the mycotoxin verrucarol (produced by Stachybotrys chartarum) in swab samples was positively associated with tiredness (p = 0.04). Streptomyces DNA in swab samples (p = 0.03) and Petri dish samples (p = 0.03) were negatively associated with tiredness. In conclusion, total fungal contamination, measured as total fungal DNA) in the classrooms, Aspergillus versicolor and verrucarol can be risk factors for rhinitis and SBS symptoms among students in the tropical country Malaysia. PMID:26829324

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

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.

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.

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.

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

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.

Evaluation of predation of the mite Lasioseius penicilliger (Aracnida: Mesostigmata) on Haemonchus contortus and bacteria-feeding nematodes.

PubMed

Aguilar-Marcelino, L; Quintero-Martínez, M T; Mendoza de Gives, P; López-Arellano, M E; Liébano-Hernández, E; Torres-Hernández, G; González-Camacho, J M; Cid del Prado, I

2014-03-01

Predation by the mite Lasioseius penicilliger was studied on three nematode species, i.e. infective larval stages (L3) of Haemonchus contortus and adults of Panagrellus redivivus and Rhabditis sp. Experiments were carried out in 5.5-cm diameter Petri dishes containing 2% water-agar over a period of 5 days. Batches of up to 1500 third-stage larvae (L3) of H. contortus and 1000 adult nematodes of P. redivivus and Rhabditis sp. were exposed to five mites in separate Petri dishes. Upon contact, each mite used its pedipalp and legs to identify and hold its prey and then used its chelicerae to feed upon the prey. Predation by L. penicilliger was chance dependent but mites became aggregated around any injured/damaged prey, thereby suggesting some form of chemoperception. The rate of predation on the three species of nematodes was high but L3 of H. contortus and adult Rhabditis sp. were preferred.

Effects of diesel and kerosene on germination and growth of coastal wetland plant species.

PubMed

Kim, Kee Dae

2014-11-01

This study aims to investigate effects of diesel and kerosene on seed germination and seedling growth among coastal wetland plants to select species that can be used for the restoration and revegetation of oil-polluted habitats. Tests on 51 species were performed in Petri dishes containing 0 %, 6 %, 12 %, and 18 % diesel, 20 %, 40 %, and 60 % kerosene; each treatment combination was replicated five times with 20 seeds in each Petri dish. All dishes were held in a growth chamber with 20°C day of 12 h/15°C night of 12 h in 80 % humidity for 20 days for calculating the germination percentage, seedling weight, and seedling vitality. The germination percentage of Rumex stenophyllus decreased significantly in diesel and kerosene treatments. The weights of seedlings treated with diesel and kerosene either increased or decreased in comparison with controls depending on the species. Vitality percentage values were high for seedlings of Chenopodium ficifolium. Thus, herbaceous plant responses to oil treatments are species-specific.

Nonlinearity in bacterial population dynamics: Proposal for experiments for the observation of abrupt transitions in patches

PubMed Central

Kenkre, V. M.; Kumar, Niraj

2008-01-01

An explicit proposal for experiments leading to abrupt transitions in spatially extended bacterial populations in a Petri dish is presented on the basis of an exact formula obtained through an analytic theory. The theory provides accurately the transition expressions despite the fact that the actual solutions, which involve strong nonlinearity, are inaccessible to it. The analytic expressions are verified through numerical solutions of the relevant nonlinear equation. The experimental setup suggested uses opaque masks in a Petri dish bathed in ultraviolet radiation [Lin A-L, et al. (2004) Biophys J 87:75–80 and Perry N (2005) J R Soc Interface 2:379–387], but is based on the interplay of two distances the bacteria must traverse, one of them favorable and the other adverse. As a result of this interplay feature, the experiments proposed introduce highly enhanced reliability in interpretation of observations and in the potential for extraction of system parameters. PMID:19033185

Modelling of different enzyme productions by solid-state fermentation on several agro-industrial residues.

PubMed

Diaz, Ana Belen; Blandino, Ana; Webb, Colin; Caro, Ildefonso

2016-11-01

A simple kinetic model, with only three fitting parameters, for several enzyme productions in Petri dishes by solid-state fermentation is proposed in this paper, which may be a valuable tool for simulation of this type of processes. Basically, the model is able to predict temporal fungal enzyme production by solid-state fermentation on complex substrates, maximum enzyme activity expected and time at which these maxima are reached. In this work, several fermentations in solid state were performed in Petri dishes, using four filamentous fungi grown on different agro-industrial residues, measuring xylanase, exo-polygalacturonase, cellulose and laccase activities over time. Regression coefficients after fitting experimental data to the proposed model turned out to be quite high in all cases. In fact, these results are very interesting considering, on the one hand, the simplicity of the model and, on the other hand, that enzyme activities correspond to different enzymes, produced by different fungi on different substrates.

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.

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.

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.

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.

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.

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.

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.

Using Photographs from American Memory.

ERIC Educational Resources Information Center

Singleton, Laurel R., Ed.

2001-01-01

This publication contains teaching ideas generated by classroom teachers. For grades K-4, elementary teacher Doris Waud and media specialist Gail Petri developed "Celebrate America with Symbols from American Memory," in which students explore the American memory and symbols. For grades 5-8, media specialist Mary Alice Anderson developed…

Essential oils as fumigants for bed bugs (Hemiptera: Cimicidae)

USDA-ARS?s Scientific Manuscript database

In Petri dish assays, fumigation of a pyrethroid-susceptible strain of bed bugs Cimex lectularius L. (Hemiptera: Cimicidae) with various essential oils resulted in mortality that approached or equaled 100%, after 5 days. However, when bed bugs were exposed to the same essential oils in sealed, comme...

ACTION OF 50 HZ MAGNETIC FIELDS ON NEURITE OUTGROWTH IN PHEOCHROMOCYTOMA CELLS

EPA Science Inventory

This study tests the capacity of 50-Hz magnetic and electric fields to stimulate neurite outgrowth in PC-12D cells, a cell line which originated from a pheochromocytoma in rat adrenal medulla. he cells were plated on collagen-coated plastic petri dishes and exposed to sinusoidal ...

The Roots of Individuality: Brain Waves and Perception.

ERIC Educational Resources Information Center

Rosenfeld, Anne H.; Rosenfeld, Sam A.

Described is research using computer techniques to study the brain's perceptual systems in both normal and pathological groups, including hyperactive children (6-12 years old). Reviewed are the early studies of A. Petrie, M. Buchsbaum, and J. Silverman using the electroencephalograph to obtain AER (average evoked response) records of…

Recommendations for treated-area choice assays with termites (Isoptera)

Treesearch

Chris J. Peterson; Patrick D. Gerard; Janice Ems-Wilson

2005-01-01

The repellency of catnip (Nepeta cataria) essential oil was evaluated in a treated-area choice assay with subterranean termites (Reticulitermes spp.). It appeared that fewer R. virginicus were found on the treated portion of a petri dish within a period of about 7d; R. flavipes was not...

Energy and Economic Impacts of H.R.5049, the Keep America Competitive Global Warming Policy

EIA Publications

2006-01-01

This report responds to a May 2, 2006 request from Congressmen Tom Udall and Tom Petri asking the Energy Information Administration to analyze the impacts of their legislation implementing a market-based allowance program to cap greenhouse gas emissions at 2009 levels.

Computerunterstütztes Modellieren mit Musiknetzen

NASA Astrophysics Data System (ADS)

Levens, Ulla

In der folgenden Ausführung geht es um eine Anwendung von Petri-Netzen im Bereich Musik. Ausgehend von der Implementierung einer speziellen Anwendung, dem Programmsystem ScoreSynth, wird das zugrundeliegende Konzept erläutert und anschließend an einem kleinen Beispiel veranschaulicht. Dieser Beitrag ist ein Auszug aus [Lev95b].

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…

78 FR 36549 - Sunshine Act; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-18

..., Office of External Affairs, (202) 942-1640. Dated: June 13, 2013. James B. Petri, Secretary, Federal Retirement Thrift Investment Board. [FR Doc. 2013-14524 Filed 6-14-13; 11:15 am] BILLING CODE 6760-01-P ... of Financial Management Report 5. FY 2013-2017 Strategic Plan Update [[Page 36550

A Content Analysis of News Reports of Averted School Rampages

ERIC Educational Resources Information Center

Daniels, Jeffrey A.; Buck, Ilene; Croxall, Susan; Gruber, Julia; Kime, Peter; Govert, Heidi

2007-01-01

Although the majority of research into school violence have focused attention on lethal or injury-producing incidents, this focus provides only partial information about school violence prevention. Moore, Petrie, Braga, and McLaughlin (2003) suggested that researchers turn their attention to those incidents in which a potentially lethal situation…

Spectrum Project

NASA Image and Video Library

2017-10-16

Inside the Spectrum prototype unit, organisms in a Petri plate are exposed to blue excitation lighting. The device works by exposing organisms to different colors of fluorescent light while a camera records what's happening with time-lapse photography. Results from the Spectrum project will shed light on which living things are best suited for long-duration flights into deep space.

Body Dissatisfaction, Ethnic Identity, and Disordered Eating among African American Women

ERIC Educational Resources Information Center

Rogers Wood, Nikel A.; Petrie, Trent A.

2010-01-01

Initial research suggested that only European American women developed eating disorders (Garner, 1993), yet recent studies have shown that African American women do experience them (e.g., Lester & Petrie, 1998b; Mulholland & Mintz, 2001) and also may be negatively affected by similar sociocultural variables. In this study, we examined a…

Bibliometric and Social Network Analysis of Doctoral Research: Research Trends in Distance Learning

ERIC Educational Resources Information Center

Skinner, Jason Kirtland

2015-01-01

The study investigated research topics of doctoral dissertations that examined issues in distance learning from 2000-2014. Twelve reviews of research on distance learning, spanning from 1997-2015, were identified. It was found that only one of these reviews of research (Davies, Howell, & Petri, 2010) looked at doctoral dissertations. The…

A filter paper-based liquid culture system for citrus shoot organogenesis - a mixture-amount experiment

USDA-ARS?s Scientific Manuscript database

The objective of this study was to determine the effects of a static liquid culture system on shoot regeneration from citrus epicotyl explants. Two citrus types were used, Carrizo citrange and Ridge Pineapple sweet orange. A liquid culture system comprised of a Petri dish, cellulose filter paper dis...

40 CFR 92.128 - Particulate handling and weighing.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Particulate handling and weighing. (a) At least 1 hour before the test, place each filter in a closed (to... stabilization period, weigh each filter on the microbalance. This reading is the tare weight and must be recorded. (c) The filter shall then be stored in a covered petri dish or a sealed filter holder until...

40 CFR 92.128 - Particulate handling and weighing.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Particulate handling and weighing. (a) At least 1 hour before the test, place each filter in a closed (to... stabilization period, weigh each filter on the microbalance. This reading is the tare weight and must be recorded. (c) The filter shall then be stored in a covered petri dish or a sealed filter holder until...

40 CFR 92.128 - Particulate handling and weighing.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Particulate handling and weighing. (a) At least 1 hour before the test, place each filter in a closed (to... stabilization period, weigh each filter on the microbalance. This reading is the tare weight and must be recorded. (c) The filter shall then be stored in a covered petri dish or a sealed filter holder until...

40 CFR 92.128 - Particulate handling and weighing.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Particulate handling and weighing. (a) At least 1 hour before the test, place each filter in a closed (to... stabilization period, weigh each filter on the microbalance. This reading is the tare weight and must be recorded. (c) The filter shall then be stored in a covered petri dish or a sealed filter holder until...

40 CFR 92.128 - Particulate handling and weighing.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Particulate handling and weighing. (a) At least 1 hour before the test, place each filter in a closed (to... stabilization period, weigh each filter on the microbalance. This reading is the tare weight and must be recorded. (c) The filter shall then be stored in a covered petri dish or a sealed filter holder until...

The Petri Project Pipeline for Education, Training Resources, and Innovation

ERIC Educational Resources Information Center

Adams, Cindy; Bortz, Carolyn

2010-01-01

Northampton Community College (NCC) responded to an industry identified need within the regional biotechnology community for entry-level production workers in biomanufacturing. In an effort to meet this need and create a transitional program of study for dislocated and incumbent workers, NCC partnered with the local Workforce Investment Boards,…

Research Staff | Bioenergy | NREL

Science.gov Websites

-275-4798 Alahuhta, Markus Researcher IV-Molecular Biology Petri.Alahuhta@nrel.gov 303-384-7850 Amore Katherine.Chou@nrel.gov 303-384-7626 Chou, Yat Researcher IV-Molecular Biology Yat.Chen.Chou@nrel.gov 303-384 Emeritus Researcher Helena.Chum@nrel.gov 303-275-4668 Chung, Daehwan Researcher III-Molecular Biology

Laboratory and Field Evaluations of Two Bacillus thuringiensis Formulations, Novodor and Raven, for Control of Cottonwood Leaf Beetle (Coleoptera: Chrysomelidae)

Treesearch

David R. Coyle; Joel D. McMillin; Steven C. Krause; Elwood R. Hart

2000-01-01

Laboratory and field experiments were conducted to determine the efficacy of two Bacillus thuringiensis Berliner formulations, Novodor and Raven, for controlling cottonwood leaf beetle, Chrysomela scripta F. (Coleoptera: Chrysomelidae). In laboratory bioassays, larvae or adults were added to petri dishes containing ...

Explaining Learning: Biological And Cybernetic Metaphors. Occasional Paper No. 99.

ERIC Educational Resources Information Center

Floden, Robert E.

The cognitive learning processes of assimilation and accommodation are critically examined in this paper. A special focus is given to an analysis of the process of assimilation as it is proposed in Hugh Petrie's book, "The Dilemma of Enquiry and Learning." Initially, Piaget's biological metaphor of assimilation-accommodation is reviewed…

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.

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.

Polarity of Spore Germination in Funaria hygrometrica Hedw.

NASA Astrophysics Data System (ADS)

Pundyak, O. I.; Demkiv, O. T.; Khorkavtsiv, O. Ya; Bagrii, B. B.

It is shown that in darkness the spores of moss Funaria hygrometrica Hedw. germinated polarly under the influence of gravity. At the beginning the rhizoids appeared. They grew downwards. Then future chloronematical stolons started to form a germination spore. Usually, they grew upwards. Clinorotation or horizontal placing of Petry dishes could discoordinate such a gravisensitivity.

Spectrum Project

NASA Image and Video Library

2017-10-16

Inside the Spectrum prototype unit, organisms in a Petri plate are exposed to different colors of lighting. The device works by exposing organisms to different colors of fluorescent light while a camera records what's happening with time-lapse photography. Results from the Spectrum project will shed light on which living things are best suited for long-duration flights into deep space.

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.

Effects of irradiation distance on supply of reactive oxygen species to the bottom of a Petri dish filled with liquid by an atmospheric O{sub 2}/He plasma jet

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

Kawasaki, Toshiyuki, E-mail: kawasaki@nbu.ac.jp; Kusumegi, Shota; Kudo, Akihiro

The impact of irradiation distances on plasma jet-induced specific effects on the supply of reactive oxygen species (ROS) to the bottom of a Petri dish filled with liquid was investigated using a KI-starch gel reagent that can be employed as a ROS indicator even in water. O{sub 3} exposure experiments without plasma irradiation were also performed to elucidate the specific effects of the plasma jet. Relative concentrations of ROS transported to the bottom were evaluated using absorbance measurements. The results indicated that ROS supply to the bottom is markedly enhanced by the plasma jet irradiation at shorter irradiation distances, whereasmore » similar results could not be obtained for the O{sub 3} exposure. In these cases, the liquid mixing in the depth direction was also enhanced by the plasma jet irradiation only, and the supply of reactive atomic oxygen to the liquid surface was markedly increased as well.« less

An evaluation of various methods of treatment for Legg-Calvé-Perthes disease.

PubMed

Wang, L; Bowen, J R; Puniak, M A; Guille, J T; Glutting, J

1995-05-01

An analysis of 5 methods of treatment for Legg-Calvé-Perthes disease was done on 124 patients with 141 affected hips. Before treatment, all groups were statistically similar concerning initial Mose measurement, age at onset of the disease, gender, and Catterall class. Treatments included the Scottish Rite orthosis (41 hips), nonweight bearing and exercises (41 hips), Petrie cast (29 hips), femoral varus osteotomy (15 hips), or Salter osteotomy (15 hips). Hips treated by the Scottish Rite orthosis had a significantly worse Mose measurement across time interaction (repeated measures analysis of variance, post hoc analyses, p < 0.05). For the other 4 treatment methods, there was no statistically different change. At followup, the Mose measurements for hips treated with the Scottish Rite orthosis were significantly worse than those for hips treated by nonweight bearing and exercises, Petrie cast, varus osteotomy, or Salter osteotomy (repeated measures analysis of variance, post hoc analyses, p < 0.05). There was, however, no significant difference in the distribution of hips according to the Stulberg et al classification at the last followup.

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.

Pathogenicity of Steinernema carpocapsae and Steinernema glaseri (Nematoda:Steinernematidae) to Ixodes Scapularis (Acari:Ixodidae)

USGS Publications Warehouse

Zhioua, E.; LeBrun, R.A.; Ginsberg, H.S.; Aeschliman, A.

1995-01-01

The entomopathogenic nematodes Steinernema carpocapsae (Weiser) and S. glaseri (Steiner) are pathogenic to engorged adult, blacklegged ticks, Ixodes scapularis (Say), but not to unfed females, engorged nymphs, or engorged larvae. Nematodes apparently enter the tick through the genital pore, thus precluding infection of immature ticks. The timing of tick mortality, and overall mortality after 17 d, did not differ between infections by S. carpocapsae and S. glaseri. These nematodes typically do not complete their life cycles or produce infective juveniles in I. scapularis. However, both species successfully produced infective juveniles when the tick body was slit before nematode infection. Mortality of engorged I. scapularis females infected by S. carpocapsae was greater than uninfected controls, but did not vary significantly with nematode concentration (50-3,000 infective juveniles per 5-cm-diameter petri dish). The LC50 was 347.8 infective juveniles per petri dish (5 ticks per dish). Hatched egg masses of infected ticks weighed less than those of uninfected controls. Mortality of infected ticks was greatest between 20 and 30?C, and was lower at 15?C.

Architectures for intelligent machines

NASA Technical Reports Server (NTRS)

Saridis, George N.

1991-01-01

The theory of intelligent machines has been recently reformulated to incorporate new architectures that are using neural and Petri nets. The analytic functions of an intelligent machine are implemented by intelligent controls, using entropy as a measure. The resulting hierarchical control structure is based on the principle of increasing precision with decreasing intelligence. Each of the three levels of the intelligent control is using different architectures, in order to satisfy the requirements of the principle: the organization level is moduled after a Boltzmann machine for abstract reasoning, task planning and decision making; the coordination level is composed of a number of Petri net transducers supervised, for command exchange, by a dispatcher, which also serves as an interface to the organization level; the execution level, include the sensory, planning for navigation and control hardware which interacts one-to-one with the appropriate coordinators, while a VME bus provides a channel for database exchange among the several devices. This system is currently implemented on a robotic transporter, designed for space construction at the CIRSSE laboratories at the Rensselaer Polytechnic Institute. The progress of its development is reported.

Attractants from Bartlett pear for codling moth, Cydia pomonella (L.), larvae

NASA Astrophysics Data System (ADS)

Knight, Alan L.; Light, Douglas M.

2001-08-01

The alkyl ethyl and methyl esters of (2 E,4 Z)-2,4-decadienoic acid found in head-space samples of ripe Bartlett pear ( Pyrus communis L.) stimulated a response from neonate larvae of the codling moth (CM), Cydia pomonella (L.), in both static-air Petri-plate and in upwind Y-tube and straight-tube olfactometer bioassays. In comparison with the known CM neonate attractant, ( E,E)-α-farnesene, ethyl (2 E,4 Z)-2,4-decadienoate was attractive at 10-fold and 1,000-fold lower threshold dosages in the Petri-plate and in the Y-tube bioassays, respectively. Methyl (2 E,4 Z)-2,4-decadienoate was attractive to CM neonates in these bioassays at much higher doses than ethyl (2 E,4 Z)-2,4-decadienoate. Other principal head-space volatiles from ripe pear fruit and pear leaves, including butyl acetate, hexyl acetate, ( Z)-3-hexenyl acetate, and ( E)-β-ocimene, were not attractive to CM neonates. The potential uses of these pear kairomones for monitoring and control of CM in walnuts and apple are discussed.

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

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.

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.

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.

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.

In vitro ovine articular chondrocyte proliferation: experiments and modelling.

PubMed

Mancuso, L; Liuzzo, M I; Fadda, S; Pisu, M; Cincotti, A; Arras, M; La Nasa, G; Concas, A; Cao, G

2010-06-01

This study focuses on analysis of in vitro cultures of chondrocytes from ovine articular cartilage. Isolated cells were seeded in Petri dishes, then expanded to confluence and phenotypically characterized by flow cytometry. The sigmoidal temporal profile of total counts was obtained by classic haemocytometry and corresponding cell size distributions were measured electronically using a Coulter Counter. A mathematical model recently proposed (1) was adopted for quantitative interpretation of these experimental data. The model is based on a 1-D (that is, mass-structured), single-staged population balance approach capable of taking into account contact inhibition at confluence. The model's parameters were determined by fitting measured total cell counts and size distributions. Model reliability was verified by predicting cell proliferation counts and corresponding size distributions at culture times longer than those used when tuning the model's parameters. It was found that adoption of cell mass as the intrinsic characteristic of a growing chondrocyte population enables sigmoidal temporal profiles of total counts in the Petri dish, as well as cell size distributions at 'balanced growth', to be adequately predicted.

Biocontrol of ticks by entomopathogenic nematodes. Research update.

PubMed

Samish, M; Alekseev, E; Glazer, I

2000-01-01

Entomopathogenic nematodes (EPNs) are lethal to ticks even though they do not use their normal propagation cycle within tick cadavers. The tick Boophilus annulatus was found to be far more susceptible to EPNs than Hyalomma excavatum, Rhipicephalus bursa, or Rhipicephalus sanguineus. Ticks seem to be less susceptible to nematodes when feeding on a host. Preimaginal tick stages were less susceptible to nematodes than adult ticks. The mortality rate of unfed females was highest, followed by unfed males, and engorged females. The virulence of nematodes to ticks varied greatly among different nematode strains. In most cases, the Heterorhabditis sp. strains were the most virulent strains tested in petri dishes. In buckets containing sandy soil sprayed with 50 nematodes/cm2 and engorged B. annulatus females, the LT50 of the ticks was less than five days. The addition of manure to soil or a manure extract to petri dishes reduced nematode virulence. Since ticks spend most of their life cycle in the upper humid layer of the ground, and many nematode strains share this same ecological niche, the use of EPNs for biocontrol of ticks appears promising.

Phage-mediated counting by the naked eye of miRNA molecules at attomolar concentrations in a Petri dish.

PubMed

Zhou, Xin; Cao, Peng; Zhu, Ye; Lu, Wuguang; Gu, Ning; Mao, Chuanbin

2015-10-01

The ability to count biomolecules such as cancer-biomarker miRNAs with the naked eye is seemingly impossible in molecular diagnostics. Here, we show an ultrasensitive naked-eye-counting strategy for quantifying miRNAs by employing T7 phage-a bacteria-specific virus nanoparticle-as a surrogate. The phage is genetically engineered to become fluorescent and capable of binding a miRNA-capturing gold nanoparticle (GNP) in a one-to-one manner. Target miRNAs crosslink the resultant phage-GNP couple and miRNA-capturing magnetic microparticles, forming a sandwich complex containing equimolar phage and miRNA. The phage is then released from the complex and developed into one macroscopic fluorescent plaque in a Petri dish by plating it in a host bacterial medium. Counting the plaques by the naked eye enables the quantification of miRNAs with detection limits of ∼3 and ∼5 aM for single-target and two-target miRNAs, respectively. This approach offers ultrasensitive and convenient quantification of disease biomarkers by the naked eye.

Phage-mediated counting by the naked eye of miRNA molecules at attomolar concentrations in a Petri dish

NASA Astrophysics Data System (ADS)

Zhou, Xin; Cao, Peng; Zhu, Ye; Lu, Wuguang; Gu, Ning; Mao, Chuanbin

2015-10-01

The ability to count biomolecules such as cancer-biomarker miRNAs with the naked eye is seemingly impossible in molecular diagnostics. Here, we show an ultrasensitive naked-eye-counting strategy for quantifying miRNAs by employing T7 phage--a bacteria-specific virus nanoparticle--as a surrogate. The phage is genetically engineered to become fluorescent and capable of binding a miRNA-capturing gold nanoparticle (GNP) in a one-to-one manner. Target miRNAs crosslink the resultant phage-GNP couple and miRNA-capturing magnetic microparticles, forming a sandwich complex containing equimolar phage and miRNA. The phage is then released from the complex and developed into one macroscopic fluorescent plaque in a Petri dish by plating it in a host bacterial medium. Counting the plaques by the naked eye enables the quantification of miRNAs with detection limits of ~3 and ~5 aM for single-target and two-target miRNAs, respectively. This approach offers ultrasensitive and convenient quantification of disease biomarkers by the naked eye.

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 cellular) models and cellular (population) models built upon the same technique and software.

Wavelength dependent recovery of UV-mediated damage: Tying up the loose ends of optical based powdery mildew management.

PubMed

Suthaparan, Aruppillai; Pathak, Ranjana; Solhaug, Knut Asbjørn; Gislerød, Hans Ragnar

2018-01-01

Controlled environment chamber experiments at Petri dish level were conducted to examine the wavelength and dose dependent efficacy of ultraviolet (UV) radiation, the recovery action potential of optical radiation applied concomitantly/subsequently to effective UV treatment, and the lapse time between UV treatment and subsequent exposure to recovery wavelength on germination efficiency of Oidium neolycopersici conidia. Conidia of eight- to nine-day-old colonies were dusted on water agar surface in Petri dishes and exposed to UV treatments (without lid). Immediately after UV treatments, Petri dishes were sealed and incubated in darkness or differing optical environments generated using seven different radiation sources (range 290nm to 780nm). Twenty-four hours after UV treatment, fifty conidia from each sample were assessed for germination. Compared to non-UV controls, <10% of the conidia germinated after 30s of exposure to 254nm or 283nm UV and subsequent dark incubation. Conidia germination was almost negligible if the exposure duration increased to 4min. Germination was about 60% with broad spectrum UV after 1min of exposure, and about 35% after 2 to 4min of exposure. There was no reduction of conidia germination with the exposure of ≤4min with 310nm. With the tested wavelength and dose ranges, germination recovery was effective in the 350nm to 500nm range. Germination efficiency of conidia treated with effective UV was significantly higher (>73%) if incubated subsequently in the 350nm to 500nm range (germination recovery). Furthermore, germination recovery depends on the characteristics of UV treatment (wavelength, and duration of exposure) and the lapse time between UV treatment and subsequent exposure to optical radiation in the recovery range. The findings of this study provide key criteria for wavelength selection, combination and application time in the optical radiation range, enabling improved design of optical based management strategies against powdery mildews. Copyright © 2017 Elsevier B.V. All rights reserved.

Diagnostic value of morphological, physiological and biochemical tests in distinguishing Trichophyton rubrum from Trichophyton mentagrophytes complex.

PubMed

Ates, Aylin; Ozcan, Kadri; Ilkit, Macit

2008-12-01

The two most frequently encountered dermatophyte etiologic agents of glabrous skin and nail dermatophytoses are Trichophyton rubrum and T. mentagrophytes. This study was aimed to discuss the efficacy of morphological, physiological and biochemical diagnostic tests commonly used in the identification of T. rubrum and members of the T. mentagrophytes complex. In this study, we evaluated; hydrolysis of urea in broth and on urea agar slants and Petri plates incubated at 22 degrees C, 28 degrees C and 37 degrees C, in vitro hair perforation (blond child, sheep and goat hair), pigment production on cornmeal dextrose agar (CMDA) and bromcresol purple-milk solids-glucose agar (BCP-MS-G), Tween opacity, sorbitol assimilation, and salt tolerance. Additionally, the production of micro- and macroconidia was investigated by using brain heart infusion agar (BHIA), Christensen's urea agar in Petri plates (UPA), CMDA, Lowenstein-Jensen agar (LJA), malt extract agar, oatmeal agar, Oxoid chromogenic Candida agar, and potato dextrose agar. All cultures were incubated at 28 degrees C, and conidial production was compared on days 5, 10 and 15. It was found that the urea hydrolysis test yielded more rapid and significant results when urea medium was prepared in Petri plates and incubated at 28 degrees C (P<0.01). LJA supported the highest production of microconidia after 15 days (P<0.001). Additionally, it was found that T. rubrum strains produced red pigment on CMDA (P<0.01) and BCP-MS-G, while strains of the T. mentagrophytes species complex did not. A special algorithm containing the various test procedures employed in these studies is presented which was found to be useful in the differentiation of T. rubrum strains from T. mentagrophytes complex. Our results revealed that UPA, CMDA, BCP-MS-G, LJA, and BHIA may be used as common mycological agars in routine practice.

Rapid Turn Around BRIC-PDFU Payload: A New Paradigm for Spaceflight Experiments

NASA Technical Reports Server (NTRS)

Levine, Howard G.; Slater, K. A.; Cox, D. R.

2010-01-01

In 2009, NASA's Fundamental Space Biology program provided an opportunity for investigators to propose for a quick-turn-around multi-user spaceflight experiment that focused on the model plant species Arabidopsis thaliana. This was a passive payload with no on-orbit power or communications available. An NRA was rapidly written (8/09), released (NNH09ZTT004N; 9/09), proposals were received (11/09) and peer reviewed with 3 PI groups selected for flight (1/10): (1) A-L Paul, University of Florida, (2) E. Blancaflor, Noble Foundation, (3) J. Kiss, Miami University. The investigators flew Arabidopsis seeds or callus cultures of their choosing (plated onto 60 mm diameter Petri dishes containing agarsolidified media) on the STS-131 Space Shuttle mission (launched 4/5/10) and the resulting plant tissues returned to earth on 4/20/10. Each petri dish was placed inside its own Petri Dish Fixation Unit (PDFU), which was assembled and loaded with either formaldehyde, glutaraldehyde or RNAlater for crew-facilitated on-orbit fixation. Five PDFUs plus a temperature data logger were loaded into each of 8 BRIC-PDFUs (Biological Research In Canisters PDFU). All eight BRIC-PDFUs were loaded into a half tray along with actuator equipment that the crew used for the fixations. Pre-flight turn-over was 28 hours prior to launch. The BRIC-PDFU assemblies were removed from the orbiter and handed over to the investigator teams for processing 5-6 hours after landing. This payload demonstrated a rapid response turnaround for flying multiple peer-reviewed science investigations using previously flown hardware and minimal ISS-resources. The approach used reduced both hardware/certification and PI costs. The time waiting for a flight opportunity for the selected Pls was minimal. This new paradigm for spaceflight experiments may provide a model for future flight research opportunities. The ultimate goal is to fly as many investigators as rapidly as possible and reinvigorate the space biology community while obtaining high-quality, peer-reviewed science.

Pure culture response of ectomycorrhizal fungi to imposed water stress

Treesearch

Mark D. Coleman; Caroline S. Bledsoe; William Lopushinsky

1989-01-01

The ability of ectomycorrhizal fungal isolates to tolerate imposed water stress in pure culture was examined in 55 isolates of 18 species. Water potential treatments, adjusted with polyethylene glycol, were applied to Petri dish units. These units allowed colony diameter measurements of fungi grown on liquid media. Delayed growth initiation and inhibition of growth...

Advanced Plant Experiment, APEX-4

NASA Image and Video Library

2017-03-10

Advanced Plant Experiment, APEX-4, support in the Telescience Support Center at NASA Glenn. APEX-4 continues a highly successful investigation into the effects of microgravity on the development of roots and cells on plant seedlings. After four days of growth, the petri plate will be inserted into the Fluids Integrated Rack (FIR) Light Microscopy Module (LMM) facility for detailed imaging.

Cytology and Genetics of Sexual Incompatibility in Didymella rabiei

Treesearch

A. Dan Wilson; W.J. Kaiser

1995-01-01

Mating crosses in all possible combinations between 15 monoascosporic isolates of Didymella rabiei (Ascomycotina, Dothideales), derived from diseased chickpea stems collected at a single location in Genesee, Idaho, were prepared on sterile chickpea stem pieces incubated on moist sterile filter papers in glass petri dishes for 5-6 weeks at 10°C or in...

Improved efficiency of plant regeneration from protoplasts of eggplant Solanum melongena L.

PubMed

Guri, A; Izhar, S

1984-12-01

Eggplant (Solanum melongena L.) mesophyll protoplasts were obtained from in vitro growing plants of line 410 and cv. 'Classic'. Relatively high (15%) plating efficiency was achieved using petri dishes with alternate quadrants containing reservoir medium (R medium + 1% activated charcoal) and culture medium. Shoot regeneration occurred within 6 weeks following initiation of protoplast culture.

Undesirable dispersal of eggs and early-stage nymphs of the bed bug Hemiptera: cimicidae) by static electricity and air currents

USDA-ARS?s Scientific Manuscript database

Movement of whole live insects or other small arthropods attributed to static electricity has been reported only rarely. While viewing bed bugs in plastic or glass Petri dishes using a dissecting microscope, individual eggs and early stage nymphs were occasionally observed to move suddenly and rapid...

Basil oil fumigation increases radiation sensitivity in adult Sitophilus oryzae (Coleoptera: Curculionidae).

USDA-ARS?s Scientific Manuscript database

The biological activity of basil (Ocimum basilicum L.) oil was tested against the stored product pest rice weevil, Sitophilus oryzae(L.). Adult weevils were exposed to seven different concentrations of basil oil ranging from 0.12 µl/ml-0.60 µl/ml in Petri dishes and mortality was assessed at 3,4 and...

30 CFR 7.89 - Test to determine the particulate index.

Code of Federal Regulations, 2012 CFR

2012-07-01

... filters as follows: (i) At least 1 hour before the test, each filter (pair) shall be placed in a closed... the stabilization period, each filter (pair) shall be weighed. The reading is the tare weight. (iii) The filter (pair) shall then be stored in a closed petri dish or a filter holder, both of which shall...

30 CFR 7.89 - Test to determine the particulate index.

Code of Federal Regulations, 2010 CFR

2010-07-01

... filters as follows: (i) At least 1 hour before the test, each filter (pair) shall be placed in a closed... the stabilization period, each filter (pair) shall be weighed. The reading is the tare weight. (iii) The filter (pair) shall then be stored in a closed petri dish or a filter holder, both of which shall...

30 CFR 7.89 - Test to determine the particulate index.

Code of Federal Regulations, 2014 CFR

2014-07-01

... filters as follows: (i) At least 1 hour before the test, each filter (pair) shall be placed in a closed... the stabilization period, each filter (pair) shall be weighed. The reading is the tare weight. (iii) The filter (pair) shall then be stored in a closed petri dish or a filter holder, both of which shall...

30 CFR 7.89 - Test to determine the particulate index.

Code of Federal Regulations, 2011 CFR

2011-07-01

... filters as follows: (i) At least 1 hour before the test, each filter (pair) shall be placed in a closed... the stabilization period, each filter (pair) shall be weighed. The reading is the tare weight. (iii) The filter (pair) shall then be stored in a closed petri dish or a filter holder, both of which shall...

30 CFR 7.89 - Test to determine the particulate index.

Code of Federal Regulations, 2013 CFR

2013-07-01

... filters as follows: (i) At least 1 hour before the test, each filter (pair) shall be placed in a closed... the stabilization period, each filter (pair) shall be weighed. The reading is the tare weight. (iii) The filter (pair) shall then be stored in a closed petri dish or a filter holder, both of which shall...

Behavior Performance of Diuraphis noxia (Homoptera: Aphididae) on Fungal Endophyte-Infected and Uninfected Perennial Ryegrass

Treesearch

S.L. Clement; D.G. Lester; A. Dan Wilson; K.S. Pike

1992-01-01

The behavior and performance of the Russian wheat aphid, Diuraphis noxia (Mordvilko), on fungal endophyte-infected and endophyte-free perennial ryegrass, Lolium perenne L., was investigated in the laboratory and field. Aphids did not select endophyte-free over endophyte-infected leaf sheaths and stem segments in petri dish preference tests....

Demonstrations of the Action and Reaction Law and the Energy Conservation Law Using Fine Spherical Plastic Beads

ERIC Educational Resources Information Center

Khumaeni, A.; Tanaka, S.; Kobayashi, A.; Lee, Y. I.; Kurniawan, K. H.; Ishii, K.; Kagawa, K.

2008-01-01

Equipment for demonstrating Newton's third law and the energy conservation law in mechanics have successfully been constructed utilizing fine spherical plastic beads in place of metal ball bearings. To demonstrate Newton's third law, special magnetized Petri dishes were employed as objects, while to examine the energy conservation law, a…

Induction of soybean resistance to the Mexican bean beetle (Coleoptera: Coccinellidae)

Treesearch

A.L. Iverson; R.B. Hammond; L.R. Iverson

2001-01-01

We tested chemical and insect feeding-induced insect resistance on soybean plants.The chemical induction effects of jasmonic acid (JA) and salicylic acid (SA) were investigated. We also evaluated the effects of plants stressed with previous insect herbivory. A larval antibiosis screening technique (LAST) and a preference test were performed in petri dishes using...

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.

Microecology: Using Fast-Growing Filamentous Fungi to Study the Effects of Environmental Gradients on the Growth Patterns of Hyphae

ERIC Educational Resources Information Center

Delpech, Roger

2004-01-01

This paper describes some simple and rapid techniques for examining the growth responses of fungal hyphae cultivated on environmental gradients. The creation of such gradients using agar-based growth media in petri dishes is explained, along with recommendations for quantitative macroscopic and microscopic measurements. The intention is to provide…

Minibrain Storm : Cerebral Organoids Aren't Real Brains?But They Provide a Powerful Platform for Modeling Brain Diseases Like Zika Infection, Alzheimer's, and Even Autism.

PubMed

Fischer, Shannon

2017-01-01

Floating in a Petri dish, they look like tiny tapioca pearls in peach broth, a couple dozen in number and none much larger than the tip of a ballpoint pen. But under a microscope, dense, lumpy bodies come into focus, outlined by wispy coronas.

The Effect of Culture Methods and Serum Supplementation on Developmental Competence of Bovine Embryos Cultured In Vitro

USDA-ARS?s Scientific Manuscript database

The objective of this study was to compare the developmental competence of bovine in vitro fertilized embryos in three different culture methods; microdrop method (50 µl of medium under mineral oil in petri dishes) compared to tube methods (1 ml of medium in tubes) with or without oil overlay, and t...

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.

Transportation Planning with Immune System Derived Approach

NASA Astrophysics Data System (ADS)

Sugiyama, Kenji; Yaji, Yasuhito; Ootsuki, John Takuya; Fujimoto, Yasutaka; Sekiguchi, Takashi

This paper presents an immune system derived approach for planning transportation of materials between manufacturing processes in the factory. Transportation operations are modeled by Petri Net, and divided into submodels. Transportation orders are derived from the firing sequences of those submodels through convergence calculation by the immune system derived excitation and suppression operations. Basic evaluation of this approach is conducted by simulation-based investigation.

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.

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.

Growth of Pleurotus ostreatus on wheat straw and wheat-grain-based media: Biochemical aspects and preparation of mushroom inoculum.

PubMed

Sainos, E; Díaz-Godínez, G; Loera, O; Montiel-González, A M; Sánchez, C

2006-10-01

Mycelial growth, intracellular activity of proteases, laccases and beta-1,3-glucanases, and cytoplasmic protein were evaluated in the vegetative phase of Pleurotus ostreatus grown on wheat straw and in wheat-grain-based media in Petri dishes and in bottles. The productivity of the wheat straw and wheat-grain-based spawn in cylindrical polyethylene bags containing 5 kg of chopped straw was also determined. We observed high activity of proteases and high content of intracellular protein in cultures grown on wheat straw. This suggests that the proteases are not secreted into the medium and that the protein is an important cellular reserve. On the contrary, cultures grown on wheat straw secreted laccases into the medium, which could be induced by this substrate. P. ostreatus grown on media prepared with a combination of wheat straw and wheat grain showed a high radial growth rate in Petri dishes and a high level of mycelial growth in bottles. The productivities of wheat straw and wheat-grain-based spawn were similar. Our results show that cheaper and more productive mushroom spawn can be prepared by developing the mycelium on wheat straw and wheat-grain-based substrates.

Differentiation and Tropisms in Space-Grown Moss

NASA Technical Reports Server (NTRS)

Sack, Fred D.; Kern, Volker

1999-01-01

This grant supported a Space Shuttle experiment on the effects of microgravity on moss cells. Moss provides a rich system for gravitational and spaceflight research. The early phase of the moss life cycle consists of chains of cells that only grow only at their tips. In the moss Ceratodon purpureus these filaments (protonemata) grow away from gravity in the dark, in a process called gravitropism. The tipmost cells, the apical cells, contain heavy starch-filled bodies called amyloplasts that probably function in g-sensing and that sediment within the apical cell. The SPM-A (Space Moss aka SPAM) experiment flew in November - December, 1997 on STS-87 as part of the Collaborative US Ukrainian Experiment (CLTE). The experiment was accommodated in hardware purpose-built by NASA KSC and Bionetics and included Petri Dish Fixation Units (PDFU) and BRIC-LEDs. Together, this hardware allowed for the culture of the moss on agar in commercial petri dishes, for unilateral illumination with red light of varying intensity, and for chemical fixation in situ. The key findings of the spaceflight were quite unexpected. Neither the orientation of tip-growth nor the distribution of amyloplasts was random in microgravity.

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.

The Effect of Antibacterial Formula Hand Cleaners on the Elimination of Microbes on Hands

NASA Astrophysics Data System (ADS)

Coleman, J. R.

2002-05-01

: The purpose of this project is to find out which one of the antibacterial hand cleanser (antibacterial bar soap, antibacterial liquid hand soap, and liquid hand sanitizer) is more effective in eliminating microbes. If antibacterial- formula liquid hand soap is used on soiled hands, then it will be more effective in eliminating microbes. Germs are microorganisms that cause disease and can spread from person-to-person. Bacteria are a kind of microbe, an example of which is Transient Flora that is often found on hands. Hand washing prevents germs from spreading to others. During the procedure, swabs were used to take samples before and after the soiled hands had been washed with one of the antibacterial hand cleansers. Nutrient Easygel was poured into petri dishes to harden for 1 day, and then samples were swabbed on the gel. The Petri dishes were placed in an incubator for 24 hours, and then data was recorded accordingly. The antibacterial liquid hand soap was sufficient in eliminating the majority of bacteria. The hands had 65% of the bacteria on them, and after the liquid hand soap was used only 37% of the bacteria remained.

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.

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.

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.

Metabolic Profiling Directly from the Petri Dish Using Nanospray Desorption Electrospray Ionization Imaging Mass Spectrometry

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

Watrous, Jeramie D.; Roach, Patrick J.; Heath, Brandi S.

2013-11-05

Understanding molecular interaction pathways in complex biological systems constitutes a treasure trove of knowledge that might facilitate the specific, chemical manipulation of the countless microbiological systems that occur throughout our world. However, there is a lack of methodologies that allow the direct investigation of chemical gradients and interactions in living biological systems, in real time. Here, we report the use of nanospray desorption electrospray ionization (nanoDESI) imaging mass spectrometry for in vivo metabolic profiling of living bacterial colonies directly from the Petri dish with absolutely no sample preparation needed. Using this technique, we investigated single colonies of Shewanella oneidensis MR-1,more » Bacillus subtilis 3610, and Streptomyces coelicolor A3(2) as well as a mixed biofilm of S. oneidensis MR-1 and B. subtilis 3610. Data from B. subtilis 3610 and S. coelicolor A3(2) provided a means of validation for the method while data from S. oneidensis MR-1 and the mixed biofilm showed a wide range of compounds that this bacterium uses for the dissimilatory reduction of extracellular metal oxides, including riboflavin, iron-bound heme and heme biosynthetic intermediates, and the siderophore putrebactin.« less

Coordination control of flexible manufacturing systems

NASA Astrophysics Data System (ADS)

Menon, Satheesh R.

One of the first attempts was made to develop a model driven system for coordination control of Flexible Manufacturing Systems (FMS). The structure and activities of the FMS are modeled using a colored Petri Net based system. This approach has the advantage of being able to model the concurrency inherent in the system. It provides a method for encoding the system state, state transitions and the feasible transitions at any given state. Further structural analysis (for detecting conflicting actions, deadlocks which might occur during operation, etc.) can be performed. The problem is also addressed of implementing and testing the behavior of existing dynamic scheduling approaches in simulations of realistic situations. A simulation architecture was proposed and performance evaluation was carried out for establishing the correctness of the model, stability of the system from a structural (deadlocks) and temporal (boundedness of backlogs) points of view, and for collection of statistics for performance measures such as machine and robot utilizations, average wait times and idle times of resources. A real-time implementation architecture for the coordination controller was also developed and implemented in a software simulated environment. Given the current technology of FMS control, the model-driven colored Petri net-based approach promises to develop a very flexible control environment.

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

A hybrid-system model of the coagulation cascade: simulation, sensitivity, and validation.

PubMed

Makin, Joseph G; Narayanan, Srini

2013-10-01

The process of human blood clotting involves a complex interaction of continuous-time/continuous-state processes and discrete-event/discrete-state phenomena, where the former comprise the various chemical rate equations and the latter comprise both threshold-limited behaviors and binary states (presence/absence of a chemical). Whereas previous blood-clotting models used only continuous dynamics and perforce addressed only portions of the coagulation cascade, we capture both continuous and discrete aspects by modeling it as a hybrid dynamical system. The model was implemented as a hybrid Petri net, a graphical modeling language that extends ordinary Petri nets to cover continuous quantities and continuous-time flows. The primary focus is simulation: (1) fidelity to the clinical data in terms of clotting-factor concentrations and elapsed time; (2) reproduction of known clotting pathologies; and (3) fine-grained predictions which may be used to refine clinical understanding of blood clotting. Next we examine sensitivity to rate-constant perturbation. Finally, we propose a method for titrating between reliance on the model and on prior clinical knowledge. For simplicity, we confine these last two analyses to a critical purely-continuous subsystem of the model.

Process-oriented integration and coordination of healthcare services across organizational boundaries.

PubMed

Tello-Leal, Edgar; Chiotti, Omar; Villarreal, Pablo David

2012-12-01

The paper presents a methodology that follows a top-down approach based on a Model-Driven Architecture for integrating and coordinating healthcare services through cross-organizational processes to enable organizations providing high quality healthcare services and continuous process improvements. The methodology provides a modeling language that enables organizations conceptualizing an integration agreement, and identifying and designing cross-organizational process models. These models are used for the automatic generation of: the private view of processes each organization should perform to fulfill its role in cross-organizational processes, and Colored Petri Net specifications to implement these processes. A multi-agent system platform provides agents able to interpret Colored Petri-Nets to enable the communication between the Healthcare Information Systems for executing the cross-organizational processes. Clinical documents are defined using the HL7 Clinical Document Architecture. This methodology guarantees that important requirements for healthcare services integration and coordination are fulfilled: interoperability between heterogeneous Healthcare Information Systems; ability to cope with changes in cross-organizational processes; guarantee of alignment between the integrated healthcare service solution defined at the organizational level and the solution defined at technological level; and the distributed execution of cross-organizational processes keeping the organizations autonomy.

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. Decision trees were derived from each of the first two experiments to allow us to more easily analyze the conditions under which the pheromone is expressed. Conclusion The simulation results reveal that a cell can overcome the detrimental effects of the conditions by using more concentration of additional proteins in λ. The first two experiments provide evidence that employing more concentration of proteins might be one of the ways that the cell uses to adapt itself in inhibiting conditions to facilitate mating. The results of the third experiment reveal that in some case the protein set σ is sufficient in regulating the response of the cell. Results of Experiments 4 and 5 reveal that there are certain conditions (parameters) in the model that are more important in determining whether a cell will respond positively or not. PMID:25080237

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 derived from each of the first two experiments to allow us to more easily analyze the conditions under which the pheromone is expressed. The simulation results reveal that a cell can overcome the detrimental effects of the conditions by using more concentration of additional proteins in λ. The first two experiments provide evidence that employing more concentration of proteins might be one of the ways that the cell uses to adapt itself in inhibiting conditions to facilitate mating. The results of the third experiment reveal that in some case the protein set σ is sufficient in regulating the response of the cell. Results of Experiments 4 and 5 reveal that there are certain conditions (parameters) in the model that are more important in determining whether a cell will respond positively or not.

BRIC-60: Biological Research in Canisters (BRIC)-60

NASA Technical Reports Server (NTRS)

Richards, Stephanie E. (Compiler); Levine, Howard G.; Romero, Vergel

2016-01-01

The Biological Research in Canisters (BRIC) is an anodized-aluminum cylinder used to provide passive stowage for investigations evaluating the effects of space flight on small organisms. Specimens flown in the BRIC 60 mm petri dish (BRIC-60) hardware include Lycoperscion esculentum (tomato), Arabidopsis thaliana (thale cress), Glycine max (soybean) seedlings, Physarum polycephalum (slime mold) cells, Pothetria dispar (gypsy moth) eggs and Ceratodon purpureus (moss).

Testimony Presented at an Open Hearing of the National Commission on Excellence in Teacher Education (New York, New York, October 18-19, 1984). Volume III.

ERIC Educational Resources Information Center

1984

Included are presentations on (or entitled): (1) role of schools of education (Lia Gelb); (2) teacher education programs (Katherine Sid); (3) "Quality and Quality Control in the Teaching Profession" (Hugh J. Scott); (4) "Educational Reform and Teacher Education" (Hugh G. Petrie); (5) teacher recruitment (Gladys M. Hannon); (6)…

The Effects of Ammonium Perchlorate on Reproduction and Development of Amphibians

DTIC Science & Technology

2008-01-01

Abstract: Ammonium perchlorate is a pervasive pollutant primarily from rocket fuel and fertilizers . It is know , among other things , to affect...females, their ovulated eggs collected, and in vitro fertilization conducted. Healthy ovulated eggs were selected and placed in Petri dishes...used and fertilization accomplished in vitro in the presence of perchlorate concentrations. *These tasks were not completed. Studies with Sodium

Summary Report on Visit to Departamento de Investigation Centro Ramon Y Cajal Madrid, Spain.

DTIC Science & Technology

1984-10-30

Over one hundred colonies of Gram negative bacteria ( Lactobacillus acidophilus ) were cultured at 380 C in Petri dishes for 72 hours. The inoculum...within the various laboratories. He was particularly excited about studies using Lactobacillus bacteria and the work involving Drosophila melanogaster...therapy (0-40 Gauss) caUsed a 40 %reduction in the number of Lactobacillus colonies. ........................ . . .. . .. . .. . .. . . RAT MODEL TO

Polymeric Microelectronics.

DTIC Science & Technology

1981-06-01

Swelling Procedure For Crosslinked Gel 2A.1 Materials: Spectral grade hexane Petri dish with glass plate cover Planchette Balance Vacuum oven 2A.2...Uncrosslinked Material) To determine the amount of uncrosslinked material decant the dupernatant hexane into a weighed planchette . Wash the gel and...swelling flask or dish with hexane again and pour into planchette . Place the planchette and its contents into a vacuum oven at 350C until the contents

System Behavior Models: A Survey of Approaches

DTIC Science & Technology

2016-06-01

MODELS: A SURVEY OF APPROACHES by Scott R. Ruppel June 2016 Thesis Advisor: Kristin Giammarco Second Reader: John M. Green THIS PAGE...Thesis 4. TITLE AND SUBTITLE SYSTEM BEHAVIOR MODELS: A SURVEY OF APPROACHES 5. FUNDING NUMBERS 6. AUTHOR(S) Scott R. Ruppel 7. PERFORMING...Monterey Phoenix, Petri nets, behavior modeling, model-based systems engineering, modeling approaches, modeling survey 15. NUMBER OF PAGES 85 16

Biological control of infective larvae of Ancylostoma spp. in beach sand.

PubMed

De Mello, Ingrid Ney Kramer; Braga, Fabio R; Monteiro, Thalita S Avelar; Freitas, Leandro G; Araujo, Juliana M; Soares, Filippe E Freitas; Araújo, Jackson V

2014-01-01

Geohelminths are parasites that stand out for their prevalence and wide distribution, depending on the soil for their transmission. The aim of this work was to evaluate the predatory capacity of the fungal isolate of the genus Duddingtonia (CG768) on third stage larvae (L3) of Ancylostoma spp. in beach sand under laboratory conditions. In the assay A five treatment groups and 1 control group were formed. The treatment groups contained 5000, 10,000, 15,000, 20,000 or 25,000 chlamydospores of the fungal isolate and 1000 Ancylostoma spp. L3 in pots containing 30g of sand. The control group (without fungus) contained only 1000 Ancylostoma spp. L3 and distilled water in pots with 30g of sand. Evidence of predatory activity was observed at the end of 15 days, where we observed the following percentages of reduction of L3: Group 1 (4.5%); Group 2 (24.5%); Group 3 (59.2%); Group 4 (58.8%); Group 5 (63%). However, difference was noted (p<0.01) only at concentrations 15,000, 20,000 and 25,000 in relation to control group. In the assay B two groups were formed in Petri dishes of 9cm in diameter containing agar water 2% medium. In the treated group, each Petri dish contained 500 Ancylostoma spp. L3 and 5g of sand containing the isolate CG 768 at a concentration of 25,000 chlamydospores/g of sand, and the control group (without fungus) contained only 500 L3. At the end of 7 days the non-predation L3 of Petri dishes using the method of Baermann were recovered. Difference (p<0.01) between groups on reducing the average number of Ancylostoma spp. L3 (percent reduction of 84%) was observed. The results of this study confirm earlier work on the efficiency of the Duddingtonia genus in the control of Ancylostoma spp. infective larvae. Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Developmental capacity of Ascaridia galli eggs is preserved after anaerobic storage in faeces.

PubMed

Tarbiat, B; Rahimian, S; Jansson, D S; Halvarsson, P; Höglund, J

2018-05-15

The reliability of the results of in vitro studies such as detection of anthelmintic resistance often depends on the ability of the parasite eggs to develop under laboratory conditions. The aim of this study was to assess the embryonation capability of the chicken roundworm Ascaridia galli eggs after storage under different conditions. Two storage media for parasite eggs were used; faeces or water. Eggs in petri dishes (90 dishes in total) containing faces or water media were first exposed either to aerobic or anaerobic conditions at different temperatures (4 °C /+O 2 , 4 °C /-O 2 , 25 °C/-O 2 ) for a maximum of 72 days. Every second week, materials from petri dishes in triplicates were recovered and incubated aerobically for two weeks at 25 °C. After the incubation, 200-300 eggs from each petri shish (sampling unit) were counted and the number of embryonated eggs was determined. Data was analyzed in R (version 3.4.3) A logistic regression model with the probability of an egg to embryonate as dependent variable and conditions, storage medium and time points as fixed effects with quasibinomial distribution was run. Least-square means were calculated and pairwise comparisons were made with the fixed effect factors (condition, storage medium and time point). Eggs in faeces had a significantly (p ˂ 0.05) higher embryonation than those in water, irrespective of storage conditions. At 4 °C embryonation tended to decline over time under aerobic conditions irrespective of the storage medium, whereas it remained constant following storage at anaerobic conditions. In contrast, anaerobic storage at the 25 °C negatively affected egg development in both media, except for day 14 in faeces. Our major finding was that eggs in faeces under anaerobic conditions and at 4 °C retained the highest rate of development, with a minimum decline in their developmental capacity over time compared to cleaned eggs stored in water. Copyright © 2018 Elsevier B.V. All rights reserved.

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 processes in a user-friendly environment supported by an intuitive graphical interface. The program offers a valuable alternative to modeling, using ordinary differential equations, especially when simulating single-cell experiments with low molecule counts. The ability to use mathematical expressions provides an additional flexibility in describing the simulation parameters. The open-source distribution allows further extensions by third-party developers. The software is cross-platform and is licensed under the Artistic License 2.0.

Evaluating the effectiveness of a Mexican strain of Duddingtonia flagrans as a biological control agent against gastrointestinal nematodes in goat faeces.

PubMed

Ojeda-Robertos, N F; Mendoza-de Gives, P; Torres-Acosta, J F J; Rodríguez-Vivas, R I; Aguilar-Caballero, A J

2005-06-01

The use of Duddingtonia flagrans in the control of goat nematodes was investigated. Initially, the time of passage of chlamydospores through the digestive tract of goats was evaluated. Two groups of seven parasite-free kids were formed. Group A received a single dose of 3.5x10(6) D. flagrans chlamydospores (FTHO-8 strain) per kg of live weight. Group B did not receive any chlamydospores. Faeces were obtained from each kid daily from day 4 prior to inoculation until day 5 post-inoculation (PI) and were placed in Petri dishes containing water agar. Gastrointestinal nematode infective larvae were added to each Petri dish and incubated at 25 degrees C for 7 days. Petri dishes were examined to detect the fungus and trapped nematodes. A second trial evaluated the effect of D. flagrans on the number of gastrointestinal nematode larvae harvested from goat faecal cultures in naturally infected goats. Two groups of seven goats were formed. The treated group received a single dose of 3.5x10(6) D. flagrans chlamydospores per kg of liveweight. The control group did not receive any chlamydospores. Faeces were obtained twice daily from each kid. Two faecal cultures were made for each kid. One was incubated for 7 days and the other for 14 days. Gastrointestinal nematode larvae were recovered from each culture and counted. Percentage of larval development reduction was determined using a ratio of larvae/eggs deposited in the control and treated groups. Duddingtonia flagrans survived the digestive process of goats, and maintained its predatory activity, being observed from 21 to 81 h PI (3 to 4 days). A reduction in the infective larvae population in the treated group compared to the non-treated group was observed in both incubation periods (7 days: 5.3-36.0%; 14 days: 0-52.8%, P>0.05). Although a single inoculation of D. flagrans can induce a reduction of infective larvae collected from faeces, a different scheme of dosing may be needed to enhance the efficacy of D. flagrans in goats.

Structured, Graphical Analysis of C2 Teams and their Technologies

DTIC Science & Technology

2011-01-01

Two Fratricide Cases Revisited. Paper presented at the 15th International Command and Control Reserach and Technology Symposium (ICCRTS), June 22-24...network-enabled ADF. The paper is thus organized in three sections. The first section introduces the graphics for analyzing the formation and use...summarize, Colored Petri Nets center on networks in which tokens are created, moved, copied, or destroyed (Figure 1). An ellipse denotes a space for

Simulation Modeling of Software Development Processes

NASA Technical Reports Server (NTRS)

Calavaro, G. F.; Basili, V. R.; Iazeolla, G.

1996-01-01

A simulation modeling approach is proposed for the prediction of software process productivity indices, such as cost and time-to-market, and the sensitivity analysis of such indices to changes in the organization parameters and user requirements. The approach uses a timed Petri Net and Object Oriented top-down model specification. Results demonstrate the model representativeness, and its usefulness in verifying process conformance to expectations, and in performing continuous process improvement and optimization.

2006 Program of Study: Ice

DTIC Science & Technology

2007-03-01

Balmforth University of British Columbia Andrew Belmonte Penn State University Robert Bindschadler NASA Goddard Space Flight Center Goran Bjork Goteborg...Friday, July 7 10:30 AM Charles Doering, University of Michigan Twist and shout ! Maximal enstrophy generation in the 3-D Navier-Stokes equation July 10...shear flows Thursday, July 27 10:30 AM Robert Bindschadler, NASA Goddard Space Flight Center The new view of ice sheet dynamics 2:30 PM Petri Fast

Microcalorimetric studies on metabolic and germination response to temperature for three populations of winterfat (Eurotia lanata)

Treesearch

Tonya Thygerson; D. Terrance Booth; Jennifer M. Harris; Lee D. Hansen; Bruce N. Smith

2001-01-01

Eurotia lanata (Pursh) Moq. (winterfat) is a boreal cold-desert subshrub, seldom more than 2 feet tall, that thrives in dry climates at cool temperatures. Diaspore collections from Matador, Saskatchewan, Canada; Pine Bluffs, Wyoming; and Sterling, Colorado, were cleaned and placed on moistened filter paper in petri dishes maintained at 0, 5, 10, 15, and 20 °C to study...

Scalable Adaptive Architectures for Maritime Operations Center Command and Control

DTIC Science & Technology

2011-05-06

the project to investigate the possibility of using earlier work on the validation and verification of rule bases in addressing the dynamically ...support the organization. To address the dynamically changing rules of engagement of a maritime force as it crosses different geographical areas, GMU... dynamic analysis, makes use of an Occurrence Graph that corresponds to the dynamics (or execution) of the Petri Net, to capture properties

Airport security inspection process model and optimization based on GSPN

NASA Astrophysics Data System (ADS)

Mao, Shuainan

2018-04-01

Aiming at the efficiency of airport security inspection process, Generalized Stochastic Petri Net is used to establish the security inspection process model. The model is used to analyze the bottleneck problem of airport security inspection process. The solution to the bottleneck is given, which can significantly improve the efficiency and reduce the waiting time by adding the place for people to remove their clothes and the X-ray detector.

Desorption of SVOCs from Heated Surfaces in the Form of Ultrafine Particles.

PubMed

Wallace, Lance A; Ott, Wayne R; Weschler, Charles J; Lai, Alvin C K

2017-02-07

Ultrafine particles (UFP) produced by electric heating of stoves and metal cooking pans, absent food, have been hypothesized to be created from a surface film of semivolatile organic compounds (SVOCs) sorbed from the surrounding air. This study tests that hypothesis by size-resolved measurements extending the lower range of the UFP studied from 10 to 2.3 nm, and including other surfaces (glass, aluminum, and porcelain). Heating glass Petri dishes or squares of aluminum foil to about 350-400 °C for 4-6 min removed all sorbed organic substances completely. Subsequent exposure of these "clean" Petri dishes and foil squares to indoor air in two different residences for successively longer periods (1 h to 281 days), followed by heating the materials for 4-6 min, indicated a strong relationship of the number, size distribution, and mass of the UFP to the time exposed. Estimates of the accumulation rate of SVOCs on surfaces were similar to those in studies of organic film buildup on indoor windows. Transfer of skin oils by touching the glass or foil surfaces, or after washing the glass surface with detergent and bare hands, was also observed, with measured particle production comparable with that produced by long-term exposure to indoor air.

Comparative rice seed toxicity tests using filter paper, growth pouch-tm, and seed tray methods

USGS Publications Warehouse

Wang, W.

1993-01-01

Paper substrate, especially circular filter paper placed inside a Petri dish, has long been used for the plant seed toxicity test (PSTT). Although this method is simple and inexpensive, recent evidence indicates that it gives results that are significantly different from those obtained using a method that does not involve paper, especially when testing metal cations. The study compared PSTT using three methods: filter paper, Growth Pouch-TM, and seed tray. The Growth Pouch-TM is a commercially available device. The seed tray is a newly designed plastic receptacle placed inside a Petri dish. The results of the Growth Pouch-TM method showed no toxic effects on rice for Ag up to 40 mg L-1 and Cd up to 20 mg L-1. Using the seed tray method, IC50 (50% inhibitory effect concentration) values were 0.55 and 1.4 mg L-1 for Ag and Cd, respectively. Although results of filter paper and seed tray methods were nearly identical for NaF, Cr(VI), and phenol, the toxicities of cations Ag and Cd were reduced by using the filter paper method; IC50 values were 22 and 18 mg L-1, respectively. The results clearly indicate that paper substrate is not advisable for PSTT.

Singlet oxygen luminescence kinetics under PDI relevant conditions of pathogenic dermatophytes and molds.

PubMed

Bornhütter, Tobias; Shamali, Nedaa; Saltsman, Irena; Mahammed, Atif; Gross, Zeev; Däschlein, Georg; Röder, Beate

2018-01-01

A treatment of onychomycosis using the photodynamic effect would be a favorable alternative to currently used antimycotic drugs. This study should be considered as a first step towards development and control of an efficient photodynamic inactivation of onychomycosis causative pathogens. Here, we evaluate the usage of time-resolved 2D singlet oxygen luminescence detection in combination with 2D fluorescence scanning as a tool to understand the behavior of the photosensitizer when applied to fungi on Petri dishes. To investigate the interaction of photosensitizer with fungi in various concentrations and in different stages of live, a photodynamic inactivation was avoided by keeping the samples in darkness. Scans of singlet oxygen luminescence and photosensitizer fluorescence were performed over a period of 24days. Two different photosensitizer, a cationic porphyrin and cationic corrole and two fungi strains, the dermatophyte Trichophyton rubrum and the mold Scopulariopsis brevicaulis, were investigated in this study. The two-dimensional correlation of photosensitizer fluorescence and singlet oxygen luminescence revealed differences in the diffusion of both photosensitizer. Even though the singlet oxygen luminescence was quenched with increasing growth of fungi, it was found that the kinetics of singlet oxygen luminescence could be detected on Petri dishes for both photosensitizers and both fungi strains for up to seven days. Copyright © 2017 Elsevier B.V. All rights reserved.

Radiofrequency radiation effects on the common bean

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

Thomkins, K.; Griggs, L.; Myles, E.L.

Our environment is bombarded daily with thousands of objects we can visually detect. However, invisible to humans are the electromagnetic waves that penetrate our environment. Electromagnetic waves consist of a large spectrum of waves including the harmful gamma rays, x-rays, and ultraviolet rays. The question that has increased tremendously is: can low energy electromagnetic waves become harmful to living organisms? The purpose of this study is to determine the effect of radiofrequency radiation on protein synthesis of the common bean. Phaseolus vulgaris (kidney bean) was surface-sterilized and allowed to germinate on Mushurage and Skoog`s medium for 1 week. Hypocotyls weremore » wounded and placed on media to initiate callus production. Six petri dishes containing 1 g of callus were used in the experiment. Three dishes were exposed to 100kH in a Crawford cell for 24h. The remaining three petri dishes with callus were used as a control. After the exposure period, the protein from callus was extracted and analyzed by one-dimensional gel electrophoresis. The results show that hypocotyl growth was not different between control and experimental groups after 24 h. The result of one-dimensional gel electrophoresis did not show observable differences in protein synthesized by the control and experimental groups. Analysis of protein synthesis is still ongoing.« less

Syntax for calculation of discounting indices from the monetary choice questionnaire and probability discounting questionnaire.

PubMed

Gray, Joshua C; Amlung, Michael T; Palmer, Abraham A; MacKillop, James

2016-09-01

The 27-item Monetary Choice Questionnaire (MCQ; Kirby, Petry, & Bickel, 1999) and 30-item Probability Discounting Questionnaire (PDQ; Madden, Petry, & Johnson, 2009) are widely used, validated measures of preferences for immediate versus delayed rewards and guaranteed versus risky rewards, respectively. The MCQ measures delayed discounting by asking individuals to choose between rewards available immediately and larger rewards available after a delay. The PDQ measures probability discounting by asking individuals to choose between guaranteed rewards and a chance at winning larger rewards. Numerous studies have implicated these measures in addiction and other health behaviors. Unlike typical self-report measures, the MCQ and PDQ generate inferred hyperbolic temporal and probability discounting functions by comparing choice preferences to arrays of functions to which the individual items are preconfigured. This article provides R and SPSS syntax for processing the MCQ and PDQ. Specifically, for the MCQ, the syntax generates k values, consistency of the inferred k, and immediate choice ratios; for the PDQ, the syntax generates h indices, consistency of the inferred h, and risky choice ratios. The syntax is intended to increase the accessibility of these measures, expedite the data processing, and reduce risk for error. © 2016 Society for the Experimental Analysis of Behavior.

Determination of chlorimuron and metsulfuron residues in two soils of Argentina using a rapid seed-bioassay.

PubMed

Castro, M C; Bedmar, F; Monterubbianesi, M G; Peretti, A; Barassi, C A

2002-10-01

The presence of chlorimuron ethyl and metsulfuron methyl in two soils was determined by a modified petri dish bioassay. Pregerminated seeds of maize and sunflower were placed in petri dishes containing 85 to 100 g of treated soil. Radicle root lengths were measured after 24 h. Chlorimuron had no effect on maize on the Balcarce soil, however 0.007 microg g(-1) decreased sunflower root length. Chlorimuron decreased maize and sunflower root length regardless application dose on the San Cayetano soil. Metsulfuron decreased maize root length at 0.04 microg g(-1) and sunflower at 0.021 microg g(-1) on the Balcarce soil. On the San Cayetano soil metsulfuron at 0.001 microg g(-1) decreased maize and sunflower root length. The phytotoxicity of chlorimuron and metsulfuron changed according to soil type and dose. Maize and sunflower were 1.3-1.5 and 1.3-1.8 times respectively more sensitive to chlorimuron on the San Cayetano soil than on the Balcarce soil. In the case of metsulfuron, maize was similarly sensitive on both soils but sunflower was 1.7-2.0 times more sensitive on the San Cayetano soil than on the Balcarce soil. Phytotoxicity increased as organic matter (OM) content decreased and/or when the soil pH and concentration increased.

Optimising the performance of an outpatient setting.

PubMed

Sendi, Pedram; Al, Maiwenn J; Battegay, Manuel; Al Maiwenn, J

2004-01-24

An outpatient setting typically includes experienced and novice resident physicians who are supervised by senior staff physicians. The performance of this kind of outpatient setting, for a given mix of experienced and novice resident physicians, is determined by the number of senior staff physicians available for supervision. The optimum mix of human resources may be determined using discrete-event simulation. An outpatient setting represents a system where concurrency and resource sharing are important. These concepts can be modelled by means of timed Coloured Petri Nets (CPN), which is a discrete-event simulation formalism. We determined the optimum mix of resources (i.e. the number of senior staff physicians needed for a given number of experienced and novice resident physicians) to guarantee efficient overall system performance. In an outpatient setting with 10 resident physicians, two staff physicians are required to guarantee a minimum level of system performance (42-52 patients are seen per 5-hour period). However, with 3 senior staff physicians system performance can be improved substantially (49-56 patients per 5-hour period). An additional fourth staff physician does not substantially enhance system performance (50-57 patients per 5-hour period). Coloured Petri Nets provide a flexible environment in which to simulate an outpatient setting and assess the impact of any staffing changes on overall system performance, to promote informed resource allocation decisions.

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.

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.

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

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

Larvicidal effects of mineral turpentine, low aromatic white spirits, aqueous extracts of Cassia alata, and aqueous extracts, ethanolic extracts and essential oil of betel leaf (Piper betle) on Chrysomya megacephala.

PubMed

Kumarasinghe, Sujith Prasad W; Karunaweera, Nadira D; Ihalamulla, Ranjan L; Arambewela, Lakshmi S R; Dissanayake, Roshinie D S C T

2002-12-01

Many methods have been employed, with variable success, in the treatment of cutaneous myiasis caused by Chrysomya species. Experiment 1: to assess the larvicidal effect of mineral turpentine (MT) and the main ingredient of MT, low aromatic white spirits (LAWS), on Chrysomya megacephala larvae in vitro. Experiment 2: to assess the larvicidal effects of aqueous extracts of winged senna (Cassia alata), and aqueous extracts, ethanolic extracts and essential oil of betel leaf (Piper betle). In experiment 1, two samples of LAWS were obtained from two industrialists (samples 1 and 2). Adult flies of C. megacephala were bred in the insectory of the Department of Parasitology, Faculty of Medicine, University of Colombo. Petri dishes were prepared with pads of cotton wool. These cotton pads were soaked separately in MT, LAWS samples 1 and 2, and normal saline as a control. Ten larvae were placed in each Petri dish. The activity of the larvae was observed and recorded half-hourly. MT and the two samples of LAWS were analyzed by chromatography. In experiment 2, volatile essential oil of betel was prepared using a standard steam distillation process. An ethanolic extract of betel was obtained after boiling the crushed leaf with water, and mixing the stock with ethanol. Betel oil dilutions of 1-4% were prepared using 1% Tween 80 (v/v aq) as a solvent, with 0.05 g/100 mL sodium lauryl sulphate (as stabilizer) and 0.01 g/100 mL methyl paraben (as a preservative). Cotton wool swabs soaked in 1, 2, 3 and 4% essential oil of betel in 1% Tween 80 (v/v aq) prepared as above, 1, 2, 3 and 4% ethanolic extract of betel, 50 and 25% aqueous extract of C. alata, and 50 and 25% aqueous extract of betel were placed in separate Petri dishes. Ten larvae were placed in each Petri dish. 1% Tween 80 solvent with the stabilizer and the preservative, but without betel essential oil, was used as a negative control and MT was used as a positive control. Larval motility was assessed as before. MT and the two LAWS samples killed the larvae in vitro within 4 h. Chromatography showed more unidentified constituents in MT than in pure LAWS, indicating additional substances in MT. The 4 and 3% preparations of the essential oil of betel were effective in killing 100% of the larvae of Chrysomya within 3 h 30 min. The 2% extract of betel essential oil killed 96.7% of larvae in 4 h. Ethanolic and aqueous extracts of betel, the aqueous extract of C. alata, normal saline and the Tween 80 solvent were not larvicidal. MT and LAWS, the main ingredient of MT, were effective in killing Chrysomya larvae. Essential oil obtained from betel leaves also showed a dose-dependent larvicidal effect on Chrysomya larvae. This natural product may be effective in the treatment of wound myiasis.

Investigation of Immunoregulatory Alphaglobulin (IRA) in Shock and Trauma.

DTIC Science & Technology

1980-07-01

rice whose limbs were amputated 2 days earlier Were fraction by adherence to glass Petri dishes or nylon wool columns (2 cycl,7), or by treatin Wi...to alloantigens. suggesting the presence of suppressor cells. The suppressor cells were found to adhere to glass and to nylon wool columns. They were...negative cell population capable of adhering to glass and nylon wool, Presumably macrophages. was responsible for inhibiting the response of lymphocytes

Ki-67 Expression in Human Tumors Measured by Flow Cytometry

DTIC Science & Technology

1990-01-01

Analyzed Fresh tissues obtained from the lymph node biopsies of 30 patients diagnosed as having non-Hodgkin’s lymphoma, nine biopsies identified as...breast tumors, and eight biopsies identified as colon tumors were included in this study. Cell Lines K562 Cell Line The human ervthroleukemia cell line...petri dish. While holding the tissue with toothed forceps , it wa,-is minced with scissors. Ujsing at transfer pip:., tissue fragments we re aspirated

Dissociation of Hexavalent Chromium from Sanded Paint Particles into a Simulated Lung Fluid

DTIC Science & Technology

2006-06-01

was simulated with a porcine based mucin . Sanded particles were collected based on particle size into the impactor’s six petri dishes, which...was used to imitate particle deposition onto a layer of lung fluid. The lung fluid was simulated with a porcine based mucin . Sanded particles were...documented as those directly related to corrosion control such as maintenance, repair, treatment , washing, painting, depainting, and sealing. These

Conception of discrete systems decomposition algorithm using p-invariants and hypergraphs

NASA Astrophysics Data System (ADS)

Stefanowicz, Ł.

2016-09-01

In the article author presents an idea of decomposition algorithm of discrete systems described by Petri Nets using pinvariants. Decomposition process is significant from the point of view of discrete systems design, because it allows separation of the smaller sequential parts. Proposed algorithm uses modified Martinez-Silva method as well as author's selection algorithm. The developed method is a good complement of classical decomposition algorithms using graphs and hypergraphs.

Mississippi State University Center for Air Sea Technology. FY93 and FY 94 Research Program in Navy Ocean Modeling and Prediction

DTIC Science & Technology

1994-09-30

relational versus object oriented DBMS, knowledge discovery, data models, rnetadata, data filtering, clustering techniques, and synthetic data. A secondary...The first was the investigation of Al/ES Lapplications (knowledge discovery, data mining, and clustering ). Here CAST collabo.rated with Dr. Fred Petry...knowledge discovery system based on clustering techniques; implemented an on-line data browser to the DBMS; completed preliminary efforts to apply object

High Temperature Studies of La-Monazite

DTIC Science & Technology

2004-07-01

Hay, E. Boakeye, M. D. Petry, Y. Berta, K. Von Lehmden, and J. Welch, " 5 A. Meldrum , L. A. Boatner, and R. C. Ewing, "Electron-Irradiation-Induced... Meldrum , L. A. Boatner, and R. C. Ewing, "A Comparison of Radiation Alumina-based Fiber for High Temperature Composite Reinforcement," Ceram. Eng... acid . The processing included procedures that allowed the La/P ratio to be controlled to be very close to the stoichiometric value of unity (within less

Some remarks on quantum physics, stochastic processes, and nonlinear filtering theory

NASA Astrophysics Data System (ADS)

Balaji, Bhashyam

2016-05-01

The mathematical similarities between quantum mechanics and stochastic processes has been studied in the literature. Some of the major results are reviewed, such as the relationship between the Fokker-Planck equation and the Schrödinger equation. Also reviewed are more recent results that show the mathematical similarities between quantum many particle systems and concepts in other areas of applied science, such as stochastic Petri nets. Some connections to filtering theory are discussed.

Optical Data Processing in Europe,

DTIC Science & Technology

1981-12-31

PROCESSING IN EUROPE4 _____________ 6PERFORMING ORG. REPORT NUMBER 7. AUTIKOR(eJ G . CONTRACT OR GRANT NUMBER(&) /7David/)Casasent 9. PERFORMING ORGANIZATION...Direction Des Recherches, Etudes et Techniques (DRET]). Present at this meeting were J. Graf, M. Petri and G . Marie of LEP as well as M. Constans and M...be useful in sonai , and processing studies. I visited Henri at Elf Aquitaine in Pau, Frarce. wt- w,-1. overall view of the company and a summary of

A pipette-based calibration system for fast-scan cyclic voltammetry with fast response times.

PubMed

Ramsson, Eric S

2016-01-01

Fast-scan cyclic voltammetry (FSCV) is an electrochemical technique that utilizes the oxidation and/or reduction of an analyte of interest to infer rapid changes in concentrations. In order to calibrate the resulting oxidative or reductive current, known concentrations of an analyte must be introduced under controlled settings. Here, I describe a simple and cost-effective method, using a Petri dish and pipettes, for the calibration of carbon fiber microelectrodes (CFMs) using FSCV.

Ignition of Liquid Fuel Spray and Simulated Solid Rocket Fuel by Photoignition of Carbon Nanotube Utilizing a Camera Flash

DTIC Science & Technology

2011-12-01

10,11 There has been a recent report on the photoignition of graphene oxide for fuel ignition applications.12 In this report, we will describe the...slide Aluminum foil Glass petri dish Xe flash Camera Sample Black spray paint Figure 2- Schematic and photographs of the experimental setup...Gilje, Sergey Dubin, Alireza Badakhshan, Jabari Farrar, Stephen. A. Danczyk, Richard B. Kaner, “Photothermal Deoxygenation of Graphene Oxide for

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

Biological control of Ascaris suum eggs by Pochonia chlamydosporia fungus.

PubMed

Ferreira, Sebastião Rodrigo; de Araújo, Jackson Victor; Braga, Fábio Ribeiro; Araujo, Juliana Milani; Frassy, Luiza Neme; Ferreira, Aloízio Soares

2011-12-01

Ascaris suum is a gastrointestinal nematode parasite of swines. The aim of this study was to observe Pochonia chlamydosporia fungus on biological control of A. suum eggs after fungus passage through swines gastrointestinal tract. Eighteen pigs, previously dewormed, were randomly divided into three groups: group 1, treated with the fungus isolate VC4; group 2, treated with the fungus isolate VC1 and group 3 did not receive fungus (control). In the treated groups, each animal received a 9 g single dose of mycelium mass containing P. chlamydosporia (VC1 or VC4). Thereafter, animal fecal samples were collected at the following intervals: 8, 12, 24, 36, 48, 72 and 96 h after treatment beginning and these were poured in Petri dishes containing 2% water-agar culture medium. Then, 1,000 A. suum eggs were poured into each dish and kept in an incubator at 26 °C and in the dark for 30 days. After this period, approximately 100 eggs were removed from each Petri dish and morphologically analyzed under light microscopy following the ovicidal activity parameters. The higher percentage observed for isolated VC4 eggs destruction was 57.5% (36 h) after fungus administration and for isolate VC1 this percentage was 45.8% (24 h and 72 h) (p > 0.01). P. chlamydosporia remained viable after passing through the gastrointestinal tract of swines, maintaining its ability of destroying A. suum eggs.

Highly concentrated, ring-shaped phase conversion laser-induced breakdown spectroscopy technology for liquid sample analysis.

PubMed

Lin, Qingyu; Wei, Zhimei; Guo, Hongli; Wang, Shuai; Guo, Guangmeng; Zhang, Zhi; Duan, Yixiang

2017-06-10

A highly concentrated, ring-shaped phase conversion (RSPC) method was developed for liquid sample analysis using the laser-induced breakdown spectroscopy (LIBS) technique. In this work, test samples were prepared by mixing the metal particles with polyvinyl alcohol (PVA) supporter in liquid phase. With heat, the PVA solution solidified inside a modified glass petri dish, forming a metal-enriched polymer ring film. Distinguished from other traditional liquid-to-solid conversing methods, the proposed new method takes advantage of enhanced homogeneity for the target elements inside the ring film. The modified glass petri dish was used to control the ring-shaped concentration. Due to the specially designed circular groove at the bottom of this dish, where the PVA solution and liquid sample mixture accumulated, the target elements were concentrated in this small ring, which is beneficial for enhancing and stabilizing the plasma signals compared to the direct liquid sample analysis using LIBS. The limits of detection for Ag, Cu, Cr, and Ba obtained with the RSPC-LIBS technology were 0.098  μg·mL -1 , 0.18  μg·mL -1 , 0.83  μg·mL -1 , and 0.046  μg·mL -1 , respectively, which provided greater improvement than the direct bulk liquid analysis using LIBS.

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

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.

Modelling of Safety Instrumented Systems by using Bernoulli trials: towards the notion of odds on for SIS failures analysis

NASA Astrophysics Data System (ADS)

Cauffriez, Laurent

2017-01-01

This paper deals with the modeling of a random failures process of a Safety Instrumented System (SIS). It aims to identify the expected number of failures for a SIS during its lifecycle. Indeed, the fact that the SIS is a system being tested periodically gives the idea to apply Bernoulli trials to characterize the random failure process of a SIS and thus to verify if the PFD (Probability of Failing Dangerously) experimentally obtained agrees with the theoretical one. Moreover, the notion of "odds on" found in Bernoulli theory allows engineers and scientists determining easily the ratio between “outcomes with success: failure of SIS” and “outcomes with unsuccess: no failure of SIS” and to confirm that SIS failures occur sporadically. A Stochastic P-temporised Petri net is proposed and serves as a reference model for describing the failure process of a 1oo1 SIS architecture. Simulations of this stochastic Petri net demonstrate that, during its lifecycle, the SIS is rarely in a state in which it cannot perform its mission. Experimental results are compared to Bernoulli trials in order to validate the powerfulness of Bernoulli trials for the modeling of the failures process of a SIS. The determination of the expected number of failures for a SIS during its lifecycle opens interesting research perspectives for engineers and scientists by completing the notion of PFD.

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.

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.

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.

Role of Stat3 and ErbB2 in Breast Cancer

DTIC Science & Technology

2013-12-01

required for cell motility, through the formation of lamellipodia at the leading edge of cells in a wound healing assay29. Since cadherin-11 leads...cells in medium lacking the inhibitor. 2.2. Wound healing assay Cells were plated in 3 cm tissue culture petri dishes in DMEM/10% fetal calf serum...solve this apparent paradox,we examined the ability of IL6 it- self , whose synthesis is induced upon cadherin engagement and is the trigger of Stat3

Fate of Bacterial and Viral Bio-Warfare Agents in Disinfected Waters

DTIC Science & Technology

2010-10-01

600 nm; approximately 4 h). An aliquot of 0.4 mL bacterial culture is spread onto the surface of Sporulation Media A Medium (SMA) and incubated at...dishes containing Sporulation Medium Sterile distilled water at 4 °C 70% EtOH Crystal violet Stain 1.2 Sporulation media A: Nutrient broth 8g/L...phase (approximately 4 h). 2.2 Seeding the Sporulation Plates 1. Label 150 mm Petri dishes of SM A Medium. 2. Inoculate, by aseptically spreading

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.

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

AFRRI (Armed Forces Radiobiology Research Institute) Reports, July, August and September 1987.

DTIC Science & Technology

1987-11-01

mononuclear cell layer obtained after Percol isolation contained approximately 90% mono- cytes as assessed by esterase staining. In most experiments...forming cell) were assayed using the double layer agar technique basically as described by Hagan et al. (22). The culture medium was double strength CMRL...trypticase soy broth, 20 g/ml L-asparagine. and penicillin-streptomycin. In the bottom layer of 35 mm plastic Petri dishes was 1 ml of a 1:1 mixture of culture

Estimation and enhancement of real-time software reliability through mutation analysis

NASA Technical Reports Server (NTRS)

Geist, Robert; Offutt, A. J.; Harris, Frederick C., Jr.

1992-01-01

A simulation-based technique for obtaining numerical estimates of the reliability of N-version, real-time software is presented. An extended stochastic Petri net is employed to represent the synchronization structure of N versions of the software, where dependencies among versions are modeled through correlated sampling of module execution times. Test results utilizing specifications for NASA's planetary lander control software indicate that mutation-based testing could hold greater potential for enhancing reliability than the desirable but perhaps unachievable goal of independence among N versions.

UML activity diagram swimlanes in logic controller design

NASA Astrophysics Data System (ADS)

Grobelny, Michał; Grobelna, Iwona

2015-12-01

Logic controller behavior can be specified using various techniques, including UML activity diagrams and control Petri nets. Each technique has its advantages and disadvantages. Application of both specification types in one project allows to take benefits from both of them. Additional elements of UML models make it possible to divide a specification into some parts, considered from other point of view (logic controller, user or system). The paper introduces an idea to use UML activity diagrams with swimlanes to increase the understandability of design models.

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.

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

Microgravity Effects on the Early Events of Biological Nitrogen Fixation in Medicago Truncatula: Results from the SyNRGE Experiment

NASA Technical Reports Server (NTRS)

Stutte, Gary W.; Roberts, Michael

2012-01-01

SyNRGE (Symbiotic Nodulation in a Reduced Gravity Environment) was a sortie mission on STS-135 in the Biological Research in Canisters (BRIC) hardware to study the effect of microgravity on a plant-microbe symbiosis resulting in biological nitrogen fixation. Medicago truncatula, a model species for th legume family, was inoculated with its bacterial symbiont, Sinorhizobium meliloti, to observe early biomolecular events associated with infection and nodulation in Petri Dish Fixation Units (PDFU's).

Biological Research in Canisters (BRIC) - Light Emitting Diode (LED)

NASA Technical Reports Server (NTRS)

Levine, Howard G.; Caron, Allison

2016-01-01

The Biological Research in Canisters - LED (BRIC-LED) is a biological research system that is being designed to complement the capabilities of the existing BRIC-Petri Dish Fixation Unit (PDFU) for the Space Life and Physical Sciences (SLPS) Program. A diverse range of organisms can be supported, including plant seedlings, callus cultures, Caenorhabditis elegans, microbes, and others. In the event of a launch scrub, the entire assembly can be replaced with an identical back-up unit containing freshly loaded specimens.

Decontamination of laboratory microbiological waste by steam sterilization.

PubMed Central

Rutala, W A; Stiegel, M M; Sarubbi, F A

1982-01-01

A steam sterilizer (autoclave) was tested to determine the operating parameters that affected sterilization of microbiological waste. Tests involved standardized loads (5, 10 ad 15 lb [ca. 2.27, 4.54, and 6.80 kg, respectively]) contaminated petri plates in autoclave bags placed in polypropylene or stainless steel containers. Thermal and biological data were obtained by using a digital potentiometer and a biological indicator containing spores of Bacillus stearothermophilus, respectively. The transfer of heat was more efficient when smaller loads of microbiological waste were tested and stainless steel rather than polypropylene containers were used. A single bag with the sides rolled down to expose the top layer of petri plates allowed heat to pass better than did a single bag with the top constricted by a twist-tie. The presence of water in the autoclave bag did not significantly improve heat-up time in stainless steel or polypropylene containers. The results of biological tests substantiated the temperature data. When 10 or 15 lb of microbiological waste was exposed to various test conditions, the only condition that ensured the destruction of B. stearothermophilus involved the use of a stainless steel container (with or without water) for 90 min. Autoclaving for 45 min resulted in the destruction of bacteria included in 10 lb (136 +/- 3 plates) or 15 lb (205 +/- 6 plates) of microbiological waste when stainless steel containers with or without water or polypropylene containers with water used, whereas 60 min was required to kill all bacteria if polypropylene containers without water were used. PMID:7103486

Pollution biomarkers in two estuarine invertebrates, Nereis diversicolor and Scrobicularia plana, from a Marsh ecosystem in SW Spain.

PubMed

Solé, Montserrat; Kopecka-Pilarczyk, Justyna; Blasco, Julián

2009-04-01

The polychaete worm Nereis diversicolor and the clam Scrobicularia plana were collected from several sites, affected by different types of contamination, in a littoral enclosure in the SW Spain (Caño Sancti-Petri and Rio San Pedro). N. diversicolor was present in 6 sampling sites whereas S. plana in 4 of them. The aim of our study was to relate several pollution biomarkers to chemical sources (metals and organic pollutants e.g. PCB, PAH) in these species, thereby confirming their adequacy as sentinels for this habitat. The biomarkers surveyed in the two invertebrates were the activities of the antioxidant enzyme catalase (CAT), the phase II detoxifying enzyme glutathione S-transferase (GST) and the neurotoxicity marker acetylcholinesterase (AChE). Metallothionein (MT) levels were measured as a biomarker of exposure to metals. The results suggested a different response in the two sediment-dwelling organisms, the sediment-eating polychaete and the water-filtering clam, probably as a consequence of different contamination exposures. The results also suggested that samples from the "Caño Sancti-Petri" were exposed to biologically active compounds that altered some of their biochemical responses. Of all the biomarkers tested, AChE was the most sensitive one and N. diversicolor the potentially most robust sentinel in this ecosystem. In this low to moderately polluted environment, the biochemical approach better reflected temporal trends than site-related differences although it was also able to detect punctual chemical insults.

BRIC-100VC Biological Research in Canisters (BRIC)-100VC

NASA Technical Reports Server (NTRS)

Richards, Stephanie E.; Levine, Howard G. (Compiler); Romero, Vergel

2016-01-01

The Biological Research in Canisters (BRIC) is an anodized-aluminum cylinder used to provide passive stowage for investigations of the effects of space flight on small specimens. The BRIC 100 mm petri dish vacuum containment unit (BRIC-100VC) has supported Dugesia japonica (flatworm) within spring under normal atmospheric conditions for 29 days in space and Hemerocallis lilioasphodelus L. (daylily) somatic embryo development within a 5% CO2 gaseous environment for 4.5 months in space. BRIC-100VC is a completely sealed, anodized-aluminum cylinder (Fig. 1) providing containment and structural support of the experimental specimens. The top and bottom lids of the canister include rapid disconnect valves for filling the canister with selected gases. These specialized valves allow for specific atmospheric containment within the canister, providing a gaseous environment defined by the investigator. Additionally, the top lid has been designed with a toggle latch and O-ring assembly allowing for prompt sealing and removal of the lid. The outside dimensions of the BRIC-100VC canisters are 16.0 cm (height) x 11.4 cm (outside diameter). The lower portion of the canister has been equipped with sufficient storage space for passive temperature and relative humidity data loggers. The BRIC- 100VC canister has been optimized to accommodate standard 100 mm laboratory petri dishes or 50 mL conical tubes. Depending on storage orientation, up to 6 or 9 canisters have been flown within an International Space Station (ISS) stowage locker.

Video Tracking Protocol to Screen Deterrent Chemistries for Honey Bees.

PubMed

Larson, Nicholas R; Anderson, Troy D

2017-06-12

The European honey bee, Apis mellifera L., is an economically and agriculturally important pollinator that generates billions of dollars annually. Honey bee colony numbers have been declining in the United States and many European countries since 1947. A number of factors play a role in this decline, including the unintentional exposure of honey bees to pesticides. The development of new methods and regulations are warranted to reduce pesticide exposures to these pollinators. One approach is the use of repellent chemistries that deter honey bees from a recently pesticide-treated crop. Here, we describe a protocol to discern the deterrence of honey bees exposed to select repellent chemistries. Honey bee foragers are collected and starved overnight in an incubator 15 h prior to testing. Individual honey bees are placed into Petri dishes that have either a sugar-agarose cube (control treatment) or sugar-agarose-compound cube (repellent treatment) placed into the middle of the dish. The Petri dish serves as the arena that is placed under a camera in a light box to record the honey bee locomotor activities using video tracking software. A total of 8 control and 8 repellent treatments were analyzed for a 10 min period with each treatment was duplicated with new honey bees. Here, we demonstrate that honey bees are deterred from the sugar-agarose cubes with a compound treatment whereas honey bees are attracted to the sugar-agarose cubes without an added compound.

[How do metallic middle ear implants behave in the MRI?].

PubMed

Kwok, P; Waldeck, A; Strutz, J

2003-01-01

Magnetic resonance imaging (MRI) has gained in frequency and importance as a diagnostic procedure. In respect to the close anatomical relationship in the temporal bone it is necessary to know whether it is hazardous to patients with metallic middle ear implants regarding displacement and rise in temperature. For the MR image quality artefacts caused by metallic prostheses should be low. Four different stapes prostheses made from titanium, gold, teflon/platinum and teflon/steel, a titanium total ossicular reconstruction prosthesis (TORP) and two ventilation tubes (made from titanium and gold) were tested in a 1.5 Tesla MRI machine regarding their displacement. All objects were first placed in a petri dish, then suspended from a thread and finally immersed in a dish filled with Gadolinium. Temperature changes of the implants were recorded by a pyrometer. None of the implants moved when they were placed in the petri dish or suspended from the thread. On the water surface the teflon/platinum and the teflon/steel pistons adjusted their direction with their axis longitudinally to the MRI scanner opening and the teflon/steel piston floated towards the MRI-machine when put close enough to the scanner opening. No rise in temperature was recorded. All implants showed as little artefacts that would still make an evaluation of the surrounding tissue possible. Patients with any of the metallic middle ear implants that were examined in this study may undergo MRI-investigations without significant adverse effects.

Early development of fern gametophytes in microgravity

NASA Technical Reports Server (NTRS)

Roux, Stanley J.; Chatterjee, Ani; Hillier, Sheila; Cannon, Tom

2003-01-01

Dormant spores of the fern Ceratopteris richardii were flown on Shuttle mission STS-93 to evaluate the effects of micro-g on their development and on their pattern of gene expression. Prior to flight the spores were sterilized and sown into one of two environments: (1) Microscope slides in a video-microscopy module; and (2) Petri dishes. All spores were then stored in darkness until use. Spore germination was initiated on orbit after exposure to light. For the spores on microscope slides, cell level changes were recorded through the clear spore coat of the spores by video microscopy. After their exposure to light, spores in petri dishes were frozen in orbit at four different time points during which on earth gravity fixes the polarity of their development. Spores were then stored frozen in Biological Research in Canister units until recovery on earth. The RNAs from these cells and from 1-g control cells were extracted and analyzed on earth after flight to assay changes in gene expression. Video microscopy results revealed that the germinated spores developed normally in microgravity, although the polarity of their development, which is guided by gravity on earth, was random in space. Differential Display-PCR analyses of RNA extracted from space-flown cells showed that there was about a 5% change in the pattern of gene expression between cells developing in micro-g compared to those developing on earth. c2002 Published by Elsevier Science Ltd on behalf of COSPAR.

Growth in spaceflight hardware results in alterations to the transcriptome and proteome

NASA Astrophysics Data System (ADS)

Basu, Proma; Kruse, Colin P. S.; Luesse, Darron R.; Wyatt, Sarah E.

2017-11-01

The Biological Research in Canisters (BRIC) hardware has been used to house many biology experiments on both the Space Transport System (STS, commonly known as the space shuttle) and the International Space Station (ISS). However, microscopic examination of Arabidopsis seedlings by Johnson et al. (2015) indicated the hardware itself may affect cell morphology. The experiment herein was designed to assess the effects of the BRIC-Petri Dish Fixation Units (BRIC-PDFU) hardware on the transcriptome and proteome of Arabidopsis seedlings. To our knowledge, this is the first transcriptomic and proteomic comparison of Arabidopsis seedlings grown with and without hardware. Arabidopsis thaliana wild-type Columbia (Col-0) seeds were sterilized and bulk plated on forty-four 60 mm Petri plates, of which 22 were integrated into the BRIC-PDFU hardware and 22 were maintained in closed containers at Ohio University. Seedlings were grown for approximately 3 days, fixed with RNAlater® and stored at -80 °C prior to RNA and protein extraction, with proteins separated into membrane and soluble fractions prior to analysis. The RNAseq analysis identified 1651 differentially expressed genes; MS/MS analysis identified 598 soluble and 589 membrane proteins differentially abundant both at p < .05. Fold enrichment analysis of gene ontology terms related to differentially expressed transcripts and proteins highlighted a variety of stress responses. Some of these genes and proteins have been previously identified in spaceflight experiments, indicating that these genes and proteins may be perturbed by both conditions.

A new UV-LED device for automatic disinfection of stethoscope membranes.

PubMed

Messina, Gabriele; Burgassi, Sandra; Messina, Daniele; Montagnani, Valerio; Cevenini, Gabriele

2015-10-01

Stethoscopes are widely used by doctors and nurses. Poor stethoscope hygiene is a potential source of nosocomial infection. This study aimed to propose an innovative solution, based on the latest advances in ultraviolet (UV) light-emitting diodes (LEDs), for disinfecting stethoscope membranes automatically and efficiently. Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Enterococcus faecalis were sown on 28 stethoscope membranes and then transferred to Petri dishes. Treatment involved illuminating exposed Petri dishes with a UVC LED for 1 minute. For each microbe, the number of colony-forming units (cfu) at 36°C was compared in control and treated dishes using the Wilcoxon signed-rank test. The Kruskal-Wallis test was used to assess percent reductions in bacteria. Statistical significance was set at 99%. A significant reduction in cfu counts after UV treatment (P < .01) was found for all bacteria: 85.5% for E faecalis, 87.5% for S aureus, 94.3% for E coli, and 94.9% for P aeruginosa . No significant differences in percent reduction in cfu were found between bacteria (P > .01). The stethoscope, symbol of medicine and health care professionals, has been demonstrated to be a carrier of microorganisms. The treatment technique was effective and efficient in disinfecting the membranes. These promising results represent a step forward toward eliminating stethoscope membrane contamination with an innovative approach. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

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.

Event Detection for Hydrothermal Plumes: A case study at Grotto Vent

NASA Astrophysics Data System (ADS)

Bemis, K. G.; Ozer, S.; Xu, G.; Rona, P. A.; Silver, D.

2012-12-01

Evidence is mounting that geologic events such as volcanic eruptions (and intrusions) and earthquakes (near and far) influence the flow rates and temperatures of hydrothermal systems. Connecting such suppositions to observations of hydrothermal output is challenging, but new ongoing time series have the potential to capture such events. This study explores using activity detection, a technique modified from computer vision, to identify pre-defined events within an extended time series recorded by COVIS (Cabled Observatory Vent Imaging Sonar) and applies it to a time series, with gaps, from Sept 2010 to the present; available measurements include plume orientation, plume rise rate, and diffuse flow area at the NEPTUNE Canada Observatory at Grotto Vent, Main Endeavour Field, Juan de Fuca Ridge. Activity detection is the process of finding a pattern (activity) in a data set containing many different types of patterns. Among many approaches proposed to model and detect activities, we have chosen a graph-based technique, Petri Nets, as they do not require training data to model the activity. They use the domain expert's knowledge to build the activity as a combination of feature states and their transitions (actions). Starting from a conceptual model of how hydrothermal plumes respond to daily tides, we have developed a Petri Net based detection algorithm that identifies deviations from the specified response. Initially we assumed that the orientation of the plume would change smoothly and symmetrically in a consistent daily pattern. However, results indicate that the rate of directional changes varies. The present Petri Net detects unusually large and rapid changes in direction or amount of bending; however inspection of Figure 1 suggests that many of the events detected may be artifacts resulting from gaps in the data or from the large temporal spacing. Still, considerable complexity overlies the "normal" tidal response pattern (the data has a dominant frequency of ~12.9 hours). We are in the process of defining several events of particular scientific interest: 1) transient behavioral changes associated with atmospheric storms, earthquakes or volcanic intrusions or eruptions, 2) mutual interaction of neighboring plumes on each other's behavior, and 3) rapid shifts in plume direction that indicate the presence of unusual currents or changes in currents. We will query the existing data to see if these relationships are ever observed as well as testing our understanding of the "normal" pattern of response to tidal currents.Figure 1. Arrows indicate plume orientation at a given time (time axis in days after 9/29/10) and stars indicate times when orientation changes rapidly.

Portable Fiber Laser System and Method to Remove Pits and Cracks on Sensitized Surfaces of Aluminum Alloys

DTIC Science & Technology

2015-08-01

resistant 5083- H116 aluminum, sheet, 1/4" thick, 2" x 24", 2 pieces 71.60 5 Reagent VWR & Fisher Nitric acid and sodium hydroxide for mass loss...Temperature stability ±0.1oC @37oC Temperature uniformity ±0.2oC @37oC 693.55 4 5083-H116 Al-Mg alloy materials McMaster Carr Strengthened corrosion ...test, other acids for etching, electrochemical polishing, and anodizing 700.28 6 Containers VWR Beakers, petri dishes, bottles, graduated cylinders

Modeling and optimum time performance for concurrent processing

NASA Technical Reports Server (NTRS)

Mielke, Roland R.; Stoughton, John W.; Som, Sukhamoy

1988-01-01

The development of a new graph theoretic model for describing the relation between a decomposed algorithm and its execution in a data flow environment is presented. Called ATAMM, the model consists of a set of Petri net marked graphs useful for representing decision-free algorithms having large-grained, computationally complex primitive operations. Performance time measures which determine computing speed and throughput capacity are defined, and the ATAMM model is used to develop lower bounds for these times. A concurrent processing operating strategy for achieving optimum time performance is presented and illustrated by example.

A Dermatologist's Ammunition in the War Against Smoking: A Photoaging App.

PubMed

Brinker, Titus Josef; Enk, Alexander; Gatzka, Martina; Nakamura, Yasuhiro; Sondermann, Wiebke; Omlor, Albert Joachim; Petri, Maximilian Philip; Karoglan, Ante; Seeger, Werner; Klode, Joachim; von Kalle, Christof; Schadendorf, Dirk

2017-09-21

This viewpoint reviews the perspectives for dermatology as a specialty to go beyond the substantial impact of smoking on skin disease and leverage the impact of skin changes on a person's self-concept and behavior in the design of effective interventions for smoking prevention and cessation. ©Titus Josef Brinker, Alexander Enk, Martina Gatzka, Yasuhiro Nakamura, Wiebke Sondermann, Albert Joachim Omlor, Maximilian Philip Petri, Ante Karoglan, Werner Seeger, Joachim Klode, Christof von Kalle, Dirk Schadendorf. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 21.09.2017.

Culture without the petri-dish.

PubMed

Thompson, Jeremy G

2007-01-01

Automation of oocyte maturation and embryo production techniques is a new and exciting development in the field of reproductive technologies. There are two areas where increased automation is having an impact: in the area of embryo diagnostics and in the process of embryo production itself. Benefits include decreased staffing and skill requirements for production and assessment of embryos, as well as increasing quality management systems by removing the "human" factor. However, the uptake of new technologies is likely to be slow, as costs and the conservative nature of the Assisted Reproduction Technology industry to adopt new techniques.

Effect of mycorrhization on the accumulation of rishitin and solavetivone in potato plantlets challenged with Rhizoctonia solani.

PubMed

Yao, M K; Désilets, H; Charles, M T; Boulanger, R; Tweddell, R J

2003-12-01

The effect of colonization with the vesicular-arbuscular mycorrhizal fungus Glomus etunicatum on the content of rishitin and solavetivone was determined in potato plants cv. Goldrush challenged with Rhizoctonia solani. Mycorrhization stimulated significantly the accumulation of both phytoalexins in roots of plantlets challenged with R. solani but did not influence phytoalexin levels in non-challenged plantlet roots. No accumulation of solavetivone or rishitin was detected in shoots. In Petri dish bioassays, rishitin and solavetivone inhibited mycelial growth of R. solani.

Practical direct plaque assay for coliphages in 100-ml samples of drinking water.

PubMed Central

Grabow, W O; Coubrough, P

1986-01-01

A practical single-agar-layer plaque assay for the direct detection of coliphages in 100-ml samples of water was designed and evaluated. With this assay a 100-ml sample of water, an agar medium containing divalent cations, and the host Escherichia coli C (ATCC 13706) were mixed in a single container, and the mixture was plated on 10 14-cm-diameter petri dishes. It was more sensitive, reliable, and accurate than various other methods and proved rapid, simple, and economic. PMID:3532952

The dizzying material evolution of the toothbrush

NASA Astrophysics Data System (ADS)

Salveson, Paul

The toothbrush has evolved a highly specialized material aura over the last 150 years in the petri dish of capitalism. It has been bred to appear cutting edge to the culturally trained eye, much like the bird of paradise has developed beautiful ornate plumage to attract a mate. As the toothbrush's formal evolution becomes more detailed and specific, the transparency of its purpose becomes increasingly convoluted and easily detached from its material reality. An alien object is slowly emerging from a complex set of cultural conditions. It lives in our houses and cleans our teeth.

An Initial Critical Summary of Models for Predicting the Attenuation of Radio Waves by Trees

DTIC Science & Technology

1982-07-01

International Telecommunication Union, Geneva, Switzerland, 1978. 1 1Krevsky, S., "HF and VHF Radio Wave Attenuation Through Jungle and Woods ," IEEE...see Reference 7) summarized groups of measurements taken by Saxton, Trevor,𔃻 3 and IHoPetrie 1 4 in nontropical deciduous woods . In TABLE 1, the subset...a 0. 26 F0.77 (5) I ŕ 3Trevor, B., "Ultra-High-Frequency Propagation Through Woods and Underbrush," RCA Review, July 1940. 14%cPstrie, J.S. and

Mathematical Foundations of Programming Semantics International Conference (9th) Held in New Orleans, Louisiana, April 1993

DTIC Science & Technology

1993-04-01

Informatica 23, pp. 9 - 66 [10] Petri, C.A., Kommunikation mit Automaten, Institut fiir Instrumentelle Mathematik, Schriften des IIM, Nr. 2, Bonn 1962...Flow 122 J. W. de Bakker and Franck van Breugel An Investigation into Functions as Processes 143 Davide Sangiorgi Time Abstracted Bisimulation: Implicit...Jagadeesan: By De Morgan laws, finding a winning strategy in AOB-oA amounts to find a winning strategy in (A-oA)V’B± (where V is the dual of ®). Let A be an

The development of advanced manufacturing systems

NASA Astrophysics Data System (ADS)

Doumeingts, Guy; Vallespir, Bruno; Darricau, Didier; Roboam, Michel

Various methods for the design of advanced manufacturing systems (AMSs) are reviewed. The specifications for AMSs and problems inherent in their development are first discussed. Three models, the Computer Aided Manufacturing-International model, the National Bureau of Standards model, and the GRAI model, are considered in detail. Hierarchical modeling tools such as structured analysis and design techniques, Petri nets, and the Icam definition method are used in the development of integrated manufacturing models. Finally, the GRAI method is demonstrated in the design of specifications for the production management system of the Snecma AMS.

Surface-Acoustic-Wave (SAW)-Driven Device for Dynamic Cell Cultures.

PubMed

Greco, Gina; Agostini, Matteo; Tonazzini, Ilaria; Sallemi, Damiano; Barone, Stefano; Cecchini, Marco

2018-06-19

In the last few decades, new types of cell cultures have been introduced to provide better cell survival and development, with micro- and nanoenvironmental physicochemical conditions aimed at mimicking those present in vivo. However, despite the efforts made, the systems available to date are often difficult to replicate and use. Here, an easy-to-use surface-acoustic-wave (SAW)-based platform is presented for realizing dynamic cell cultures that is compatible with standard optical microscopes, incubators, and cell-culture dishes. The SAW chip is coupled to a standard Petri dish via a polydimethylsiloxane (PDMS) disc and consists of a lithium niobate (LN) substrate on which gold interdigital transducers (IDTs) are patterned to generate the SAWs and induce acoustic streaming in the dish. SAW excitation is verified and characterized by laser Doppler vibrometry, and the fluid dynamics is studied by microparticle image velocimetry (μPIV). Heating is measured by an infrared (IR) thermal camera. We finally tested this device with the U-937 monocyte cell line for viability and proliferation and cell-morphological analysis. The data demonstrate that it is possible to induce significant fluid recirculation within the Petri dish while maintaining negligible heating. Remarkably, cell proliferation in this condition was enhanced by 36 ± 12% with respect to those of standard static cultures. Finally, we show that cell death does not increase and that cell morphology is not altered in the presence of SAWs. This device is the first demonstration that SAW-induced streaming can mechanically improve cell proliferation and further supports the great versatility and biocompatibility of the SAW technology for cell manipulation.

Systematic reconstruction of TRANSPATH data into Cell System Markup Language

PubMed Central

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

2008-01-01

Background Many biological repositories store information based on experimental study of the biological processes within a cell, such as protein-protein interactions, metabolic pathways, signal transduction pathways, or regulations of transcription factors and miRNA. Unfortunately, it is difficult to directly use such information when generating simulation-based models. Thus, modeling rules for encoding biological knowledge into system-dynamics-oriented standardized formats would be very useful for fully understanding cellular dynamics at the system level. Results We selected the TRANSPATH database, a manually curated high-quality pathway database, which provides a plentiful source of cellular events in humans, mice, and rats, collected from over 31,500 publications. In this work, we have developed 16 modeling rules based on hybrid functional Petri net with extension (HFPNe), which is suitable for graphical representing and simulating biological processes. In the modeling rules, each Petri net element is incorporated with Cell System Ontology to enable semantic interoperability of models. As a formal ontology for biological pathway modeling with dynamics, CSO also defines biological terminology and corresponding icons. By combining HFPNe with the CSO features, it is possible to make TRANSPATH data to simulation-based and semantically valid models. The results are encoded into a biological pathway format, Cell System Markup Language (CSML), which eases the exchange and integration of biological data and models. Conclusion By using the 16 modeling rules, 97% of the reactions in TRANSPATH are converted into simulation-based models represented in CSML. This reconstruction demonstrates that it is possible to use our rules to generate quantitative models from static pathway descriptions. PMID:18570683

Isolation of amylolytic, xylanolytic, and cellulolytic microorganisms extracted from the gut of the termite Reticulitermes santonensis by means of a micro-aerobic atmosphere.

PubMed

Tarayre, Cédric; Brognaux, Alison; Bauwens, Julien; Brasseur, Catherine; Mattéotti, Christel; Millet, Catherine; Destain, Jacqueline; Vandenbol, Micheline; Portetelle, Daniel; De Pauw, Edwin; Eric, Haubruge; Francis, Frédéric; Thonart, Philippe

2014-05-01

The aim of this work was to isolate enzyme-producing microorganisms from the tract of the termite Reticulitermes santonensis. The microorganisms were extracted from the guts and anaerobic (CO₂ or CO₂/H₂) and micro-aerobic atmospheres were used to stimulate growth. Three different strategies were tried out. First, the sample was spread on Petri dishes containing solid media with carboxymethylcellulose, microcrystalline cellulose or cellobiose. This technique allowed us to isolate two bacteria: Streptomyces sp. strain ABGxAviA1 and Pseudomonas sp. strain ABGxCellA. The second strategy consisted in inoculating a specific liquid medium containing carboxymethylcellulose, microcrystalline cellulose, or cellobiose. The samples were then spread on Petri dishes with the same specific medium containing carboxymethylcellulose, microcrystalline cellulose, or cellobiose. This led to the isolation of the mold Aspergillus sp. strain ABGxAviA2. Finally, the third strategy consisted in heating the first culture and spreading samples on agar plates containing rich medium. This led to the isolation of the bacterium Bacillus subtilis strain ABGx. All those steps were achieved in controlled atmospheres. The four enzyme-producing strains which were isolated were obtained by using a micro-aerobic atmosphere. Later, enzymatic assays were performed on the four strains. Streptomyces sp. strain ABGxAviA1 was found to produce only amylase, while Pseudomonas sp. strain ABGxCellA was found to produce β-glucosidase as well. Aspergillus sp. strain ABGxAviA2 showed β-glucosidase, amylase, cellulase, and xylanase activities. Finally, B. subtilis strain ABGx produced xylanase and amylase.

Candidate nematicidal proteins in a new Pseudomonas veronii isolate identified by its antagonistic properties against Xiphinema index.

PubMed

Canchignia, Hayron; Altimira, Fabiola; Montes, Christian; Sánchez, Evelyn; Tapia, Eduardo; Miccono, María; Espinoza, Daniel; Aguirre, Carlos; Seeger, Michael; Prieto, Humberto

2017-03-17

The nematode Xiphinema index affects grape vines and transmits important viruses associated with fanleaf degeneration. Pseudomonas spp. are an extensive bacterial group in which important biodegradation and/or biocontrol properties can occur for several strains in the group. The aim of this study was to identify new Pseudomonas isolates with antagonist activity against X. index. Forty bacterial isolates were obtained from soil and root samples from Chilean vineyards. Thirteen new fluorescent pseudomonads were found and assessed for their antagonistic capability. The nematicide Pseudomonas protegens CHA0 was used as a control. Challenges of nematode individuals in King's B semi-solid agar Petri dishes facilitated the identification of the Pseudomonas veronii isolate R4, as determined by a 16S rRNA sequence comparison. This isolate was as effective as CHA0 as an antagonist of X. index, although it had a different lethality kinetic. Milk-induced R4 cultures exhibited protease and lipase activities in cell supernatants using both gelatin/tributyrin Petri dish assays and zymograms. Three proteins with these activities were isolated and subjected to mass spectrometry. Amino acid partial sequences enabled the identification of a 49-kDa protease similar to metalloprotease AprA and two lipases of 50 kDa and 69 kDa similar to LipA and ExoU, respectively. Electron microscopy analyses of challenged nematodes revealed degraded cuticle after R4 supernatant treatment. These results represent a new and unexplored property in this species associated with the presence of secretable lipases and protease, similar to characterized enzymes present in biocontrol pseudomonads.

Response of Ceratitis capitata, Bactrocera dorsalis, and Bactrocera cucurbitae (Diptera: Tephritidae) to metabolic stress disinfection and disinfestation treatment.

PubMed

Arévalo-Galarza, Lourdes; Follett, Peter A

2011-02-01

Metabolic stress disinfection and disinfestation (MSDD) is a postharvest treatment designed to control pathogens and arthropod pests on commodities that combines short cycles of low pressure/vacuum and high CO2 with ethanol vapor. Experiments were conducted to evaluate the effect of MSDD treatment on various life stages of Ceratitis capitata (Wiedemann), Mediterranean fruit fly; Bactrocera dorsalis Hendel, oriental fruit fly; and Bactrocera cucurbitae Coquillett, melon fly, in petri dishes and in papaya, Carica papaya L., fruit. In some experiments, the ethanol vapor phase was withheld to separate the effects of the physical (low pressure/ambient pressure cycles) and chemical (ethanol vapor plus low pressure) phases of treatment. In the experiments with tephritid fruit fly larvae and adults in petri dishes, mortality was generally high when insects were exposed to ethanol and low when ethanol was withheld during MSDD treatment, suggesting that ethanol vapor is highly lethal but that fruit flies are quite tolerant of short periods of low pressure treatment alone. When papaya fruit infested with fruit fly eggs or larvae were treated by MSDD, they produced fewer pupae than untreated control fruit, but a substantial number of individuals developed nonetheless. This suggests that internally feeding insects in fruit may be partially protected from the toxic effects of the ethanol because the vapor does not easily penetrate the fruit pericarp and pulp. MSDD treatment using the atmospheric conditions tested has limited potential as a disinfestation treatment for internal-feeding quarantine pests such as fruit flies infesting perishable commodities.

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

Climatically sensitive tree-ring chronologies from Crimea, Ukraine

NASA Astrophysics Data System (ADS)

Solomina, O.; Davi, N.; D Arrigo, R.

2003-04-01

Several tree species in Crimea can reach ages of 1000 years or more (Crimea..., 1999), including Taxus baccata L., Arbutus andrachne L., Quercus pubescens Willd, Quercus petraea (Mattuschka) Liebl., Quercus robur L., Juniperus excelsa M.B., and Pistacia mutica Fisch.et Mey. In September 2002, we collected samples from several long-lived tree sites described in the literature (Vulf, 1948, Ivanenko, 1951, Ena, 1983, Podgorniy, 1990), located in the mountains of Central Crimea (Sokolinoye, Chufut-Kale, Chelter) and on the coast of the Black Sea (Ai-Todor, Kharaks, Ai-Petri). The trees sampled generally had 300-350 rings. At Ai-Todor, most oaks, junipers, and pistachio showed decay. However, enough samples of oak, juniper and pine were collected to build three chronologies with good replication over the last 350 years. Long meteorological records (for Sevastopol since 1821, Ai-Petri and Yalta since the 1880's) as well as detailed historical data on extreme climatic events since 1687 (summarized by Borisov 1956) are available for this area and can be used to calibrate and verify the tree growth/climate models. Resulting dendroclimatic reconstructions will be the first from this region. The tree-ring time-series may also be used for archaeological dating of historical wood from several medieval fortresses, towns and palaces. In turn, the archaeological wood could be used to extend the tree-ring time series. Stalactites and stalagmites (Dubliansky, 1977) found in numerous caves, as well as 4000-years old laminated lake sediments (Shostakovich, 1934) are also potentially important sources of paleoclimatic information in the area.

Banana peel culture as an indigenous medium for easy identification of late-sporulation human fungal pathogens.

PubMed

Kindo, A J; Tupaki-Sreepurna, A; Yuvaraj, M

2016-01-01

Fungi are increasing in incidence as human pathogens and newer and rarer species are continuously being encountered. Identifying these species from growth on regular culture media may be challenging due to the absence of typical features. An indigenous and cheap medium, similar to the natural substrate of these fungi, was standardised in our laboratory as an aid to species identification in a conventional laboratory setting. Ripe banana peel pieces, sterilised in an autoclave at 121°C temperature and 15 lbs pressure for 15 min promoted good growth of hyphae and pycnidia or acervuli in coelomycetes, flabelliform and medusoid fruiting bodies of basidiomycetes and fruit bodies such as cleistothecium in ascomycetes. The growth from the primary isolation medium was taken and inoculated onto the pieces of double-autoclaved ripe banana peel pieces in a sterile glass Petri dish with some moisture (sprinkles of sterile distilled water). A few sterile coverslips were placed randomly inside the Petri dish for the growing fungus to stick on to it. The plates were kept at room temperature and left undisturbed for 15-20 days. At a time, one coverslip was taken out and placed on a slide with lactophenol cotton blue and focused under the microscope to look for fruit bodies. Lasiodiplodia theobromae, Macrophomina phaseolina, Nigrospora sphaerica, Chaetomium murorum, Nattrassia mangiferae and Schizophyllum commune were identified by characteristic features from growth on banana peel culture. Banana peel culture is a cheap and effective medium resembling the natural substrate of fungi and is useful for promoting characteristic reproductive structures that aid identification.

Comparative study of the antimutagenic properties of vitamins C and E against mutation induced by norfloxacin

PubMed Central

Alba, Myriam Arriaga; Sánchez, Roberto Rivera; Pérez, Nancy Jannet Ruíz; Navarrete, Jaime Sánchez; Paz, Rocío Flores; Montoya-Estrada, Araceli; Gómez, Juan José Hicks

2008-01-01

Background Norfloxacin like other fluoroquinolones, is known to be mutagenic for Salmonella typhimurium TA102 strain. This mutagenic effect is due to free oxygen radicals (ROS), because it is inhibited by antioxidants such as β-carotene and naturally occurring antioxidants of Roheo discolor and other plants. The aim of this work was to evaluate combination therapy with norfloxacin and vitamins C and E, to reduce the possible genotoxic risk associated with fluoroquinolones. Method The antimutagenicity of α-tocoferol (Vitamin E) and ascorbic acid (Vitamin C) against norfloxacin-induced mutation was evaluated on S. typhimurium TA102, using the aroclor-1254-induced S9 rat liver homogenate. The minimum inhibitory concentration (MIC) a measure of the bactericidal effect of norfloxacin, was obtained in vitro by the plate dilution method. Results Vitamin E (0.5 mg per Petri dish) induced a statistically significant reduction (P < 0.001) in the mutagenicity of norfloxacin, whereas Vitamin C (1 mg per Petri dish) had no such effect. Neither of these vitamins altered the MIC for norfloxacin against 25 uropathogenic strains of Escherichia coli. Conclusion These results suggest that Vitamin E is a potent antimutagen that would be worthwhile being used in conjunction with fluoroquinolone treatment. The minimal antimutagenic effect of Vitamin C observed under these experimental conditions may have been because Vitamin C in the Ames test induces a Fenton reaction, and if divalent cations are present, it can act as a pro-oxidant rather than an antioxidant. Ascorbic acid should be further evaluated in the presence of different divalent cations concentrations. PMID:18267022

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.

Long-term three-dimensional perfusion culture of human adult bone marrow mononuclear cells in bioreactors.

PubMed

Schmelzer, Eva; Finoli, Anthony; Nettleship, Ian; Gerlach, Jörg C

2015-04-01

The construction and long-term maintenance of three-dimensional in vitro bone marrow models is of great interest but still quite challenging. Here we describe the use of a multi-compartment hollow-fiber membrane based three-dimensional perfusion bioreactor for long-term culture of whole human bone marrow mononuclear cells. We also investigated bioreactors with incorporated open-porous foamed hydroxyapatite scaffolds, mimicking the in vivo bone matrix. Cells in bioreactors with and without scaffolds were cultured to 6 weeks and compared to Petri dish controls. Cells were analyzed for gene expression, surface markers by flow cytometry, metabolic activity, hematopoietic potential, viability, and attachment by immunocytochemistry. Cells in bioreactors were metabolic active during long-term culture. The percentages of hematopoietic stem cell and mature endothelial cell fractions were maintained in bioreactors. The expression of most of the analyzed genes stabilized and increased after long-term culture of 6 weeks. Compared to Petri dish culture controls, bioreactor perfusion culture improved in both the short and long-term, the colony formation unit capacity of hematopoietic progenitors. Cells attached to the ample surface area provided by hydroxyapatite scaffolds. The implementation of a hydroxyapatite scaffold did not influence colony formation capacity, percentages of cell type specific fractions, gene expression, cell viability or metabolic turnover when compared to control cells cultured in bioreactors without scaffolds. In conclusion, three-dimensional perfusion bioreactor culture enables long-term maintenance of primary human bone marrow cells, with hydroxyapatite scaffolds providing an in vivo-like scaffold for three-dimensional culture. © 2015 Wiley Periodicals, Inc.

Response of coccinellid larvae to conspecific and heterospecific larval tracks: a mechanism that reduces cannibalism and intraguild predation.

PubMed

Meisner, Matthew H; Harmon, Jason P; Ives, Anthony R

2011-02-01

Cannibalism, where one species feeds on individuals of its own species, and intraguild predation (IGP), where a predator feeds on other predatory species, can both pose significant threats to natural enemies and interfere with their biological control of pests. Behavioral mechanisms to avoid these threats, however, could help maintain superior pest control. Here, we ask whether larvae of Coccinella septempunctata (Coleoptera: Coccinellidae) and Harmonia axyridis (Coleoptera: Coccinellidae) respond to larval tracks deposited by the other and whether this behavioral response reduces the threat of cannibalism and IGP. In petri dish experiments, we show that both H. axyridis and C. septempunctata avoid foraging in areas with conspecific larval tracks. Using a method of preventing larvae from depositing tracks, we then demonstrate that the frequency of cannibalism is greater for both species when larvae are prevented from depositing tracks compared with when the tracks are deposited. For multi-species interactions we show in petri dish experiments that C. septempunctata avoids H. axyridis larval tracks but H. axyridis does not avoid C. septempunctata larval tracks, demonstrating an asymmetry in response to larval tracks that parallels the asymmetry in aggressiveness between these species as intraguild predators. On single plants, we show that the presence of H. axyridis larval tracks reduces the risk of IGP by H. axyridis on C. septempunctata. Our study suggests that larval tracks can be used in more ways than previously described, in this case by changing coccinellid larval behavior in a way that reduces cannibalism and IGP. © 2011 Entomological Society of America

Effects of transgenic Bt rice on growth, reproduction, and superoxide dismutase activity of Folsomia candida (Collembola: Isotomidae) in laboratory studies.

PubMed

Bai, Yaoyu; Yan, Ruihong; Ke, Xin; Ye, Gongyin; Huang, Fangneng; Luo, Yongming; Cheng, Jiaan

2011-12-01

Transgenic rice expressing Bacillus thuringiensis (Bt) CrylAb protein is expected to be commercialized in China in the near future. The use of Bt rice for controlling insect pests sparks intensive debates regarding its biosafety. Folsomia candida is an euedaphic species and is often used as a "standard" test organism in assessing effects of environmental pollutants on soil organisms. In this study, growth, development, reproduction, and superoxide dismutase activity (SOD) of F. candida were investigated in the laboratory for populations reared on leaf tissue or leaf-soil mixtures of two CrylAb rice lines and a non-Bt rice isoline. Two independent tests were performed: 1) a 35-d test using petri dishes containing yeast diet (positive control) or fresh rice leaf tissue, and 2) a 28-d test in soil-litter microcosms containing yeast or a mixture of soil and rice leaf tissue. Biological parameters measured in both tests were number of progeny production, population growth rate, and SOD activity. For the petri dish test, data measured also included insect body length and number of exuviation. There were no significant differences between the populations reared on Bt and non-Bt rice leaf tissue in all measured parameters in both tests and for both Bt rice lines, suggesting no significant effects of the CrylAb protein in Bt rice on F. candida in the laboratory studies. Results of this study should add additional biosafety proofs for use of Bt rice to manage rice pests in China.

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

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.

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.

Improvement on `structure of weakly 2-dependent siphons'

NASA Astrophysics Data System (ADS)

Chao, Daniel Y.

2015-01-01

Li and Zhou propose simpler Petri net controllers based on the concept of elementary siphons (generally much smaller than the set of all strict minimum siphons (SMSs) in large Petri nets) to minimise the addition of control places. SMSs can be divided into two groups: elementary and dependant; characteristic T-vectors of the latter are linear combinations of that of the former. A T-vector η is associated with each siphon S such that η(i) is the number of tokens gained in or lost from S by firing transition ti once. A dependent siphon S0 strongly depends on elementary siphons S1, S2, … , Sk if η0 = a1η1 + a2η2 + ṡṡṡ + akηk with all ai (i = 1, 2, 3, … , k) positive. S0 is a weakly dependent siphon if some ai is negative. The T-vectors (resp. number) for elementary siphons are mutually independent (linear to the size of the net). In an earlier paper, we show that there exists a third siphon S3 such that ηβ = η1 + η2 - η3. This equation (called η relationship) plays an important role for optimal control of weakly dependent siphons. However, it assumes that all above S span between exactly two processes. For a well-known benchmark, however, most dependent siphons span more than two processes. This paper improves by removing this restriction and shows that ηβ = η1 + η2 - η3 holds as long as S1∩S2 is another emptiable siphon.

Systematic reconstruction of TRANSPATH data into cell system markup language.

PubMed

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

2008-06-23

Many biological repositories store information based on experimental study of the biological processes within a cell, such as protein-protein interactions, metabolic pathways, signal transduction pathways, or regulations of transcription factors and miRNA. Unfortunately, it is difficult to directly use such information when generating simulation-based models. Thus, modeling rules for encoding biological knowledge into system-dynamics-oriented standardized formats would be very useful for fully understanding cellular dynamics at the system level. We selected the TRANSPATH database, a manually curated high-quality pathway database, which provides a plentiful source of cellular events in humans, mice, and rats, collected from over 31,500 publications. In this work, we have developed 16 modeling rules based on hybrid functional Petri net with extension (HFPNe), which is suitable for graphical representing and simulating biological processes. In the modeling rules, each Petri net element is incorporated with Cell System Ontology to enable semantic interoperability of models. As a formal ontology for biological pathway modeling with dynamics, CSO also defines biological terminology and corresponding icons. By combining HFPNe with the CSO features, it is possible to make TRANSPATH data to simulation-based and semantically valid models. The results are encoded into a biological pathway format, Cell System Markup Language (CSML), which eases the exchange and integration of biological data and models. By using the 16 modeling rules, 97% of the reactions in TRANSPATH are converted into simulation-based models represented in CSML. This reconstruction demonstrates that it is possible to use our rules to generate quantitative models from static pathway descriptions.

On Complex Networks Representation and Computation of Hydrologycal Quantities

NASA Astrophysics Data System (ADS)

Serafin, F.; Bancheri, M.; David, O.; Rigon, R.

2017-12-01

Water is our blue gold. Despite results of discovery-based science keep warning public opinion about the looming worldwide water crisis, water is still treated as a not worth taking resource. Could a different multi-scale perspective affect environmental decision-making more deeply? Can also a further pairing to a new graphical representation of processes interaction sway decision-making more effectively and public opinion consequently?This abstract introduces a complex networks driven way to represent catchments eco-hydrology and related flexible informatics to manage it. The representation is built upon mathematical category. A category is an algebraic structure that comprises "objects" linked by "arrows". It is an evolution of Petri Nets said Time Continuous Petri Nets (TCPN). It aims to display (water) budgets processes and catchment interactions using explicative and self-contained symbolism. The result improves readability of physical processes compared to current descriptions. The IT perspective hinges on the Object Modeling System (OMS) v3. The latter is a non-invasive flexible environmental modeling framework designed to support component-based model development. The implementation of a Directed Acyclic Graph (DAG) data structure, named Net3, has recently enhanced its flexibility. Net3 represents interacting systems as complex networks: vertices match up with any sort of time evolving quantity; edges correspond to their data (fluxes) interchange. It currently hosts JGrass-NewAge components, and those implementing travel time analysis of fluxes. Further bio-physical or management oriented components can be easily added.This talk introduces both graphical representation and related informatics exercising actual applications and examples.

Growth in spaceflight hardware results in alterations to the transcriptome and proteome.

PubMed

Basu, Proma; Kruse, Colin P S; Luesse, Darron R; Wyatt, Sarah E

2017-11-01

The Biological Research in Canisters (BRIC) hardware has been used to house many biology experiments on both the Space Transport System (STS, commonly known as the space shuttle) and the International Space Station (ISS). However, microscopic examination of Arabidopsis seedlings by Johnson et al. (2015) indicated the hardware itself may affect cell morphology. The experiment herein was designed to assess the effects of the BRIC-Petri Dish Fixation Units (BRIC-PDFU) hardware on the transcriptome and proteome of Arabidopsis seedlings. To our knowledge, this is the first transcriptomic and proteomic comparison of Arabidopsis seedlings grown with and without hardware. Arabidopsis thaliana wild-type Columbia (Col-0) seeds were sterilized and bulk plated on forty-four 60 mm Petri plates, of which 22 were integrated into the BRIC-PDFU hardware and 22 were maintained in closed containers at Ohio University. Seedlings were grown for approximately 3 days, fixed with RNAlater ® and stored at -80 °C prior to RNA and protein extraction, with proteins separated into membrane and soluble fractions prior to analysis. The RNAseq analysis identified 1651 differentially expressed genes; MS/MS analysis identified 598 soluble and 589 membrane proteins differentially abundant both at p < .05. Fold enrichment analysis of gene ontology terms related to differentially expressed transcripts and proteins highlighted a variety of stress responses. Some of these genes and proteins have been previously identified in spaceflight experiments, indicating that these genes and proteins may be perturbed by both conditions. Copyright © 2017 The Committee on Space Research (COSPAR). Published by Elsevier Ltd. All rights reserved.

Fabrication of High-Performance Polymer Bulk-Heterojunction Solar Cells by Interfacial Modifications I

DTIC Science & Technology

2009-04-30

P3HT:PCBM based polymer BHJ solar cells with configurations of ITO glass /PEDOT:PSS/P3HT:PCBM/PEGDE(0~6nm)/Al(100nm) and ITO glass /PEDOT:PSS/P3HT:PCBM...4% for inverted PV cells was reported using cesium carbonate (Cs2CO3) as ECL and vanadium oxide ( V2O5 ) as the hole collecting layer (HCL)9. However... glass Petri dish. The active film thickness was about 200 nm ±10 nm. SPDPA was dissolved in ethanol with 1 wt%. 10 nm of SPDPA was spin-coated onto the

Biofidelic Three-Dimensional Brain Surrogate Models of mTBI-Induced Alzheimer’s Disease Pathology

DTIC Science & Technology

2016-10-01

incurred during combat in Vietnam by US forces, Acta Chir. Scand. Suppl. 508 (1981) 351–356. [10] J. Grafman, B.S. Jonas, A. Martin , A.M. Salazar, H...29 (16) (2012) 2564–2575. [92] B.R. Huber, J.S. Meabon, T.J. Martin , P.D. Mourad, R. Bennett, B.C. Kraemer, I. Cernak, E.C. Petrie, M.J. Emery, E.R...cerebral vasculature to blast injury in a rat model of mild traumatic brain injury, Acta Neuropathol. Commun. 2 (1) (2014) 1. [122] J.M. Petras , R.A

Proceedings of the Annual National Conference on Ada (Trademark) Technology (7th) Held in Washington, D.C. on March 13-16, 1989

DTIC Science & Technology

1989-03-16

a decreased throughput that is directly proportion - al to the number of customers that ame requesting service 5.! Softuware Development...the ROC. The cost due providing useful feedback to the PM. The to changes in the SOW are directly suitability of using Ada for lower level proportional ...techniques Also here: of Petri Met Synthesis and Analysis. and and T" .1T1 where K is a proportionality consant to be chosen as 1>K>l-2/(inaxt I),.Il 7th

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

Dynamic 3D culture promotes spontaneous embryonic stem cell differentiation in vitro.

PubMed

Gerlach, Jörg C; Hout, Mariah; Edsbagge, Josefina; Björquist, Petter; Lübberstedt, Marc; Miki, Toshio; Stachelscheid, Harald; Schmelzer, Eva; Schatten, Gerald; Zeilinger, Katrin

2010-02-01

Spontaneous in vitro differentiation of mouse embryonic stem cells (mESC) is promoted by a dynamic, three-dimensional (3D), tissue-density perfusion technique with continuous medium perfusion and exchange in a novel four-compartment, interwoven capillary bioreactor. We compared ectodermal, endodermal, and mesodermal immunoreactive tissue structures formed by mESC at culture day 10 with mouse fetal tissue development at gestational day E9.5. The results show that the bioreactor cultures more closely resemble mouse fetal tissue development at gestational day E9.5 than control mESC cultured in Petri dishes.

Temporal logics and real time expert systems.

PubMed

Blom, J A

1996-10-01

This paper introduces temporal logics. Due to the eternal compromise between expressive adequacy and reasoning efficiency that must decided upon in any application, full (first order logic or modal logic based) temporal logics are frequently not suitable. This is especially true in real time expert systems, where a fixed (and usually small) response time must be guaranteed. One such expert system, Fagan's VM, is reviewed, and a delineation is given of how to formally describe and reason with time in medical protocols. It is shown that Petri net theory is a useful tool to check the correctness of formalised protocols.

Phytotoxic clerodane diterpenes from Salvia miniata Fernald (Lamiaceae).

PubMed

Bisio, Angela; Damonte, Gianluca; Fraternale, Daniele; Giacomelli, Emanuela; Salis, Annalisa; Romussi, Giovanni; Cafaggi, Sergio; Ricci, Donata; De Tommasi, Nunziatina

2011-02-01

Our ongoing research to identify natural growth inhibitors with diterpene and triterpene skeletons exuding from the surface of the aerial parts of Salvia species led us to study Salvia miniata Fernald. Ten clerodane diterpenoids were found, along with three known diterpenes. Most of the isolated compounds from S. miniata inhibited the germination of Papaver rhoeas L. and Avena sativa L. in Petri dish experiments. Parallel results have been obtained in experiments carried out to evaluate the subsequent growth of the seedlings of the target species in the presence of the tested compounds. Copyright © 2010 Elsevier Ltd. All rights reserved.

Apex-4 for SpaceX CRS-10

NASA Image and Video Library

2017-02-16

APEX-04, or Advanced Plant EXperiments-04, is being prepared in a cold room in the Kennedy Space Center Processing Facility for SpaceX-10. Dr. Anna Lisa Paul of the University of Florida is the principal investigator for APEX-04. Apex-04 is an experiment involving Arabidopsis in petri plates inside the Veggie facility aboard the International Space Station. Since Arabidopsis is the genetic model of the plant world, it is a perfect sample organism for performing genetic studies in spaceflight. The experiment is the result of a grant from NASA’s Space Life and Physical Sciences division.

Hierarchical analytical and simulation modelling of human-machine systems with interference

NASA Astrophysics Data System (ADS)

Braginsky, M. Ya; Tarakanov, D. V.; Tsapko, S. G.; Tsapko, I. V.; Baglaeva, E. A.

2017-01-01

The article considers the principles of building the analytical and simulation model of the human operator and the industrial control system hardware and software. E-networks as the extension of Petri nets are used as the mathematical apparatus. This approach allows simulating complex parallel distributed processes in human-machine systems. The structural and hierarchical approach is used as the building method for the mathematical model of the human operator. The upper level of the human operator is represented by the logical dynamic model of decision making based on E-networks. The lower level reflects psychophysiological characteristics of the human-operator.

ATAMM enhancement and multiprocessing performance evaluation

NASA Technical Reports Server (NTRS)

Stoughton, John W.

1994-01-01

The algorithm to architecture mapping model (ATAAM) is a Petri net based model which provides a strategy for periodic execution of a class of real-time algorithms on multicomputer dataflow architecture. The execution of large-grained, decision-free algorithms on homogeneous processing elements is studied. The ATAAM provides an analytical basis for calculating performance bounds on throughput characteristics. Extension of the ATAMM as a strategy for cyclo-static scheduling provides for a truly distributed ATAMM multicomputer operating system. An ATAAM testbed consisting of a centralized graph manager and three processors is described using embedded firmware on 68HC11 microcontrollers.

Microscopic optical path length difference and polarization measurement system for cell analysis

NASA Astrophysics Data System (ADS)

Satake, H.; Ikeda, K.; Kowa, H.; Hoshiba, T.; Watanabe, E.

2018-03-01

In recent years, noninvasive, nonstaining, and nondestructive quantitative cell measurement techniques have become increasingly important in the medical field. These cell measurement techniques enable the quantitative analysis of living cells, and are therefore applied to various cell identification processes, such as those determining the passage number limit during cell culturing in regenerative medicine. To enable cell measurement, we developed a quantitative microscopic phase imaging system based on a Mach-Zehnder interferometer that measures the optical path length difference distribution without phase unwrapping using optical phase locking. The applicability of our phase imaging system was demonstrated by successful identification of breast cancer cells amongst normal cells. However, the cell identification method using this phase imaging system exhibited a false identification rate of approximately 7%. In this study, we implemented a polarimetric imaging system by introducing a polarimetric module to one arm of the Mach-Zehnder interferometer of our conventional phase imaging system. This module was comprised of a quarter wave plate and a rotational polarizer on the illumination side of the sample, and a linear polarizer on the optical detector side. In addition, we developed correction methods for the measurement errors of the optical path length and birefringence phase differences that arose through the influence of elements other than cells, such as the Petri dish. As the Petri dish holding the fluid specimens was transparent, it did not affect the amplitude information; however, the optical path length and birefringence phase differences were affected. Therefore, we proposed correction of the optical path length and birefringence phase for the influence of elements other than cells, as a prerequisite for obtaining highly precise phase and polarimetric images.

Dynamic monitoring of horizontal gene transfer in soil

NASA Astrophysics Data System (ADS)

Cheng, H. Y.; Masiello, C. A.; Silberg, J. J.; Bennett, G. N.

2015-12-01

Soil microbial gene expression underlies microbial behaviors (phenotypes) central to many aspects of C, N, and H2O cycling. However, continuous monitoring of microbial gene expression in soils is challenging because genetically-encoded reporter proteins widely used in the lab are difficult to deploy in soil matrices: for example, green fluorescent protein cannot be easily visualized in soils, even in the lab. To address this problem we have developed a reporter protein that releases small volatile gases. Here, we applied this gas reporter in a proof-of-concept soil experiment, monitoring horizontal gene transfer, a microbial activity that alters microbial genotypes and phenotypes. Horizontal gene transfer is central to bacterial evolution and adaptation and is relevant to problems such as the spread of antibiotic resistance, increasing metal tolerance in superfund sites, and bioremediation capability of bacterial consortia. This process is likely to be impacted by a number of matrix properties not well-represented in the petri dish, such as microscale variations in water, nutrients, and O2, making petri-dish experiments a poor proxy for environmental processes. We built a conjugation system using synthetic biology to demonstrate the use of gas-reporting biosensors in safe, lab-based biogeochemistry experiments, and here we report the use of these sensors to monitor horizontal gene transfer in soils. Our system is based on the F-plasmid conjugation in Escherichia coli. We have found that the gas signal reports on the number of cells that acquire F-plasmids (transconjugants) in a loamy Alfisol collected from Kellogg Biological Station. We will report how a gas signal generated by transconjugants varies with the number of F-plasmid donor and acceptor cells seeded in a soil, soil moisture, and soil O2 levels.

Characterization of ligninolytic enzyme production in white-rot wild fungal strains suitable for kraft pulp bleaching.

PubMed

Damián-Robles, Rosa María; Castro-Montoya, Agustín Jaime; Saucedo-Luna, Jaime; Vázquez-Garcidueñas, Ma Soledad; Arredondo-Santoyo, Marina; Vázquez-Marrufo, Gerardo

2017-10-01

Fungal strains identified by phylogenetic analysis of the ITS rDNA region as Trametes versicolor (CMU-TA01), Irpex lacteus (CMU-84/13), and Phlebiopsis sp. (CMU-47/13) are able to grow on and bleach kraft pulp (KP) in a simple solid-state fermentation (SSF) assay conducted in Petri dishes. Kappa number reductions obtained with Phlebiopsis sp. (48.3%), T. versicolor (43%), and I . lacteus (39.3%), evidence their capability for lignin breakdown. Scanning electron microscopy images of KP fibers from SSF assays demonstrated increased roughness and striation, evidencing significant cell wall modification. T. versicolor produces laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) in potato dextrose broth (PDB), PDB + CuSO 4 , and PDB + KP, whereas Phlebiopsis sp. and I. lacteus showed no Lac and low LiP activities in all media. Compared to PDB, the highest increase in Lac (7.25-fold) and MnP (2.37-fold) activities in PDB + CuSO 4 occur in T. versicolor ; for LiP, the greatest changes (6.95-fold) were observed in I. lacteus . Incubation in PDB + KP shows significant increases in Lac and MnP for T. versicolor , MnP and LiP for Phlebiopsis sp., and none for I. lacteus . SSF assays in Petri plates are a valuable tool to select fungi that are able to delignify KP. Here, delignification by Phlebiopsis sp. of this substrate is reported for the first time, and MnP activity was strongly associated with the delignification ability of the studied strains. The obtained results suggest that the studied fungal strains have biotechnological potential for use in the paper industry.

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 detailed mathematical models.

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.

In vitro penetration of swine oocytes by homologous spermatozoa: Distinct systems for gamete's co-incubation and oocyte's cryopreservation.

PubMed

Macedo, M C; Lucia, T; Rambo, G; Ferreira Filho, E B; Rosa, A P; Fabiane, C; Cabral, M; Deschamps, J C

2010-02-01

In vitro penetration (IVP) of swine oocytes by homologous spermatozoa was evaluated in two experiments using four boars as semen donors. In experiment 1, the IVP rate and the number of penetrating spermatozoa (PSP) were compared using three co-incubation systems for vitrified oocytes and fresh sperm: (1) 35mL petri dishes in a CO(2) incubator, (2) 35mL petri dishes in bags (submarine system) and (3) glass flasks partially submerged in water bath with the same gas mixture used for the bag system. Mean PSP was 8.2+/-10.1 and the IVP rate was 90.5%. The PSP differed across all systems (P=0.0006): 15.5+/-0.5 for flasks, 6.3+/-0.4 for CO(2), and 3.9+/-0.4 for bags. The IVP rate for flasks (95.0%) was greater (P=0.01) than for CO(2) and bags (90.8% and 85.0%, respectively), but it did not differ between flasks and CO(2) for three boars (P>0.05). In experiment 2, co-incubation was done as described for glass flasks in experiment 1. The IVP rate and PSP were compared for cryopreserved oocytes: either vitrified in open pulled straws (OPS), or frozen in cryotubes. Mean PSP was 5.4+/-6.5 and IVP rate was 89.6%. Both PSP and IVP rate were greater (P<0.0001) for oocytes frozen in cryotubes (7.0+/-0.3% and 95.8%, respectively) than those frozen in OPS (3.7+/-0.3% and 83.4%, respectively), with no differences found for three boars (P>0.05). In summary, successful IVP of swine oocytes by homologous spermatozoa can be achieved using gametes incubated in glass flasks and oocytes frozen in cryotubes.

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

Chew, K. W.; Chen, S. S.; Pang, W. L.

The effects of Lithium triflate salt (LiCF{sub 3}SO{sub 3}), on the poly (methyl methacrylate)(PMMA)-based solid polymer electrolytes plasticized with propylene carbonate (PC) solvated in Tetrahydrofuran (THF) have been studied through a.c impedance spectroscopy and infrared spectroscopy. Lithium triflate was incorporated into the predetermined PMMA/PC system that has the highest value of ionic conductivity. In current investigations, four combination systems: Pure PMMA, (PMMA+PC) systems, (PMMA+LiCF{sub 3}SO{sub 3}) and (PMMA+PC+LiCF{sub 3}SO{sub 3}) systems were prepared using the solution cast method. Solutions were stirred for numerous hours to obtain a homogenous solution before it is poured into the petri dishes under ambient temperaturemore » to form the solid electrolyte thin film. The films were then removed from petri discs and transferred into the dessicator for further drying prior to the different tests. From the characterization done through the a.c impedance spectroscopy, the highest room temperature ionic conductivity in the pure PMMA sample, (PMMA+PC) system and (PMMA+LiCF{sub 3}SO{sub 3}) system is 2.83x10{sup -12} Scm{sup -1}, 4.39x10{sup -11} Scm{sup -1} and 3.93x10{sup -6} Scm{sup -1} respectively. The conductivity for (PMMA+PC+LiCF{sub 3}SO{sub 3}) system was obtained with the 30 wt% of lithium triflate, which is 2.48x10{sup -5} Scm{sup -1}. Infrared spectroscopy shows that complexation occurred between the polymer and the plasticizer, and the polymer and plasticizer and salt. The interactions have been studied in the C=O band, C-O-C band and the O-CH{sub 3} band.« less

Catalytic Propulsion and Magnetic Steering of Soft, Patchy Microcapsules: Ability to Pick-Up and Drop-Off Microscale Cargo.

PubMed

Lu, Annie Xi; Liu, Yijing; Oh, Hyuntaek; Gargava, Ankit; Kendall, Eric; Nie, Zhihong; DeVoe, Don L; Raghavan, Srinivasa R

2016-06-22

We describe the creation of polymeric microcapsules that can exhibit autonomous motion along defined trajectories. The capsules are made by cross-linking aqueous microdroplets of the biopolymer chitosan using glutaraldehyde. A coflow microfluidic tubing device is used to generate chitosan droplets containing nanoparticles (NPs) with an iron (Fe) core and a platinum (Pt) shell. The droplets are then incubated in a Petri dish with the cross-linking solution, and an external magnet is placed below the Petri dish to pull the NPs together as a collective "patch" on one end of each droplet. This results in cross-linked capsules (∼150 μm in diameter) with an anisotropic (patchy) structure. When these capsules are placed in a solution of H2O2, the Pt shell of the NPs catalyzes the decomposition of H2O2 into O2 gas, which is ejected from the patchy end in the form of bubbles. As a result, the capsules (which are termed micromotors) move in a direction opposite to the bubbles. Furthermore, the micromotors can be steered along specific paths by an external magnet (the magnetic response arises due to the Fe in the core of the NPs). A given micromotor can thus be directed to meet with and adhere to an inert capsule, i.e., a model cargo. Adhesion occurs due to the soft nature of the two structures. Once the cargo is picked up, the micromotor-cargo pair can be moved along a specific path to a destination, whereupon the cargo can be released from the micromotor. We believe these soft micromotors offer significant benefits over their existing hard counterparts because of their biocompatibility, biodegradability, and ability to encapsulate a variety of payloads.

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.

Influence of temperature on rate of uptake and subsequent horizontal transfer of [14C]fipronil by eastern subterranean termites (Isoptera: Rhinotermitidae).

PubMed

Spomer, Neil A; Kamble, Shripat T; Warriner, Richard A; Davis, Robert W

2008-06-01

The effect of temperature on [14C]fipronil uptake and transfer from donor (D) to recipient (R) Reticulitermes flavipes (Kollar) (Isoptera: Rhinotermitidae) workers was evaluated. Test chambers used in the fipronil uptake study were constructed from petri dishes containing autoclaved soil treated with 1 ppm [14C]fipronil (1.14 microCi of total radioactivity per petri dish), distilled water, and R. flavipes workers. Test chambers were held in environmental growth chambers preset at 12, 17, 22, 27, and 32 degrees C. For the fipronil transfer study, donor termites stained with Nile blue-A were exposed to soil treated with 1 ppm [14C]fipronil for 2 h. Donors were then combined with unexposed recipient termite workers at either 1D:5R, 1D:10R, or 1D:20R ratios. Test chambers consisted of a nest and feeding chamber connected by a piece of polyethylene tube and held in growth chambers at 12, 17, 22, 27, and 32 degrees C. Worker termites were sampled over time and the amount of [14C]fipronil present was measured by scintillation counting. Some degree of uptake and transfer occurred at all temperatures and ratios in this study. The highest level of uptake occurred by termites held at 22-32 degrees C, followed decreasingly by 17 and 12 degrees C. Maximum transfer of [14C]fipronil occurred at the higher ratios (1:5 > 1:10 > 1:20) of donors to recipients. Data presented in this study suggest that temperature is one of the key factors affecting the rate of uptake and subsequent horizontal transfer of [14C]fipronil in subterranean termites.

A thin-layer liquid culture technique for the growth of Helicobacter pylori.

PubMed

Joo, Jung-Soo; Park, Kyung-Chul; Song, Jae-Young; Kim, Dong-Hyun; Lee, Kyung-Ja; Kwon, Young-Cheol; Kim, Jung-Min; Kim, Kyung-Mi; Youn, Hee-Shang; Kang, Hyung-Lyun; Baik, Seung-Chul; Lee, Woo-Kon; Cho, Myung-Je; Rhee, Kwang-Ho

2010-08-01

Several attempts have been successful in liquid cultivation of Helicobaccter pylori. However, there is a need to improve the growth of H. pylori in liquid media in order to get affluent growth and a simple approach for examining bacterial properties. We introduce here a thin-layer liquid culture technique for the growth of H. pylori. A thin-layer liquid culture system was established by adding liquid media to a 90-mm diameter Petri dish. Optimal conditions for bacterial growth were investigated and then viability, growth curve, and released proteins were examined. Maximal growth of H. pylori was obtained by adding 3 mL of brucella broth supplemented with 10% horse to a Petri dish. H. pylori grew in both DMEM and RPMI-1640 supplemented with 10% fetal bovine serum and 0.5% yeast extract. Serum-free RPMI-1640 supported the growth of H. pylori when supplemented with dimethyl-beta-cyclodextrin (200 microg/mL) and 1% yeast extract. Under optimal growth, H. pylori grew exponentially for 28 hours, reaching a density of 3.4 OD(600) with a generation time of 3.3 hours. After 24 hours, cultures at a cell density of 1.0 OD(600) contained 1.3 +/- 0.1 x 10(9 )CFU/mL. gamma-Glutamyl transpeptidase, nuclease, superoxide dismutase, and urease were not detected in culture supernatants at 24 hours in thin-layer liquid culture, but were present at 48 hours, whereas alcohol dehydrogenase, alkylhydroperoxide reductase, catalase, and vacuolating cytotoxin were detected at 24 hours. Thin-layer liquid culture technique is feasible, and can serve as a versatile liquid culture technique for investigating bacterial properties of H. pylori.

Automated single cell sorting and deposition in submicroliter drops

NASA Astrophysics Data System (ADS)

Salánki, Rita; Gerecsei, Tamás; Orgovan, Norbert; Sándor, Noémi; Péter, Beatrix; Bajtay, Zsuzsa; Erdei, Anna; Horvath, Robert; Szabó, Bálint

2014-08-01

Automated manipulation and sorting of single cells are challenging, when intact cells are needed for further investigations, e.g., RNA or DNA sequencing. We applied a computer controlled micropipette on a microscope admitting 80 PCR (Polymerase Chain Reaction) tubes to be filled with single cells in a cycle. Due to the Laplace pressure, fluid starts to flow out from the micropipette only above a critical pressure preventing the precise control of drop volume in the submicroliter range. We found an anomalous pressure additive to the Laplace pressure that we attribute to the evaporation of the drop. We have overcome the problem of the critical dropping pressure with sequentially operated fast fluidic valves timed with a millisecond precision. Minimum drop volume was 0.4-0.7 μl with a sorting speed of 15-20 s per cell. After picking NE-4C neuroectodermal mouse stem cells and human primary monocytes from a standard plastic Petri dish we could gently deposit single cells inside tiny drops. 94 ± 3% and 54 ± 7% of the deposited drops contained single cells for NE-4C and monocytes, respectively. 7.5 ± 4% of the drops contained multiple cells in case of monocytes. Remaining drops were empty. Number of cells deposited in a drop could be documented by imaging the Petri dish before and after sorting. We tuned the adhesion force of cells to make the manipulation successful without the application of microstructures for trapping cells on the surface. We propose that our straightforward and flexible setup opens an avenue for single cell isolation, critically needed for the rapidly growing field of single cell biology.

Influence of Light Intensity on Growth and Pigment Production by Monascus ruber in Submerged Fermentation.

PubMed

Bühler, Rose Marie Meinicke; Müller, Bruna Luíse; Moritz, Denise Esteves; Vendruscolo, Francielo; de Oliveira, Debora; Ninow, Jorge Luiz

2015-07-01

To reduce environmental problems caused by glycerine accumulation and to make the production of biodiesel more profitable, crude glycerin without treatment was used as substrate for obtaining higher value-added bioproducts. Monascus ruber is a filamentous fungus that produces pigments, particularly red ones, which are used for coloring foods (rice wine and meat products). The interest in developing pigments from natural sources is increasing due to the restriction of using synthetic dyes. The effects of temperature, pH, microorganism morphology, aeration, nitrogen source, and substrates have been studied in the cultivation of M. ruber. In this work, it was observed that light intensity is also an important factor that should be considered for understanding the metabolism of the fungus. In M. ruber cultivation, inhibition of growth and pigment production was observed in Petri dishes and blaffed flasks exposed to direct illumination. Growth and pigment production were higher in Petri dishes and flasks exposed to red light and in the absence of light. Radial growth rate of M. ruber in plates in darkness was 1.50 mm day(-1) and in plates exposed to direct illumination was 0.59 mm day(-1). Maximum production of red pigments (8.32 UA) and biomass (8.82 g L(-1)) were obtained in baffled flasks covered with red film and 7.17 UA of red pigments, and 7.40 g L(-1) of biomass was obtained in flasks incubated in darkness. Under conditions of 1248 lux of luminance, the maximum pigment production was 4.48 UA, with production of 6.94 g L(-1) of biomass, indicating that the fungus has photoreceptors which influence the physiological responses.

The Presence of Flour Affects the Efficacy of Aerosolized Insecticides used to Treat the Red Flour Beetle, Tribolium castaneum

PubMed Central

Toews, Michael D.; Campbell, James F.; Arthur, Franklin H.

2010-01-01

Experiments were conducted in tightly sealed pilot scale warehouses to assess the efficacy of common aerosolized insecticides on all life stages of Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae) when exposed in dishes containing 0 to 2 g of wheat flour either under pallets or out in the open. Petri dishes containing 0, 0.1, 1, or 2 g of flour were prepared with 25 eggs, 3rd instars, pupae, or adults and then immediately treated with aerosolized solvent, Pyrethrins, or esfenvalerate. Twenty-four h after insecticide exposure, the dishes were brought to the laboratory and placed in a growth chamber and held for a 3 day moribund (knockdown) assessment and a 21 day mortality assessment. Mortality in untreated controls was generally less than 10%, with the exception of the 21 day counts of adults and eggs. Solvent-treated replications followed similar trends, except that additional mortality was observed in exposed larvae and pupae. In the insecticide-treated dishes, mortality of T. castaneum provisioned with flour generally showed a linear decrease with increasing flour deposits. Regardless of life stage, mortality did not exceed 60% when individuals were exposed in petri dishes containing 2 g of flour. Exposure location also made a significant difference in observed mortality. While mortality never exceeded 75% in dishes positioned under pallets, there was never less than 80% mortality in dishes exposed in the open. Although there was a perceptible increase in mortality with esfenvalerate compared to Pyrethrins, these differences were considerably less than the variation observed among flour deposits. The study suggests that sanitation and preparation prior to aerosol insecticide treatments were more important than choice of a particular insecticide. PMID:21268701

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.

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 detailed mathematical models. PMID:24244124

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.

ARG1 Functions in the Physiological Adaptation of Undifferentiated Plant Cells to Spaceflight

NASA Astrophysics Data System (ADS)

Zupanska, Agata K.; Schultz, Eric R.; Yao, JiQiang; Sng, Natasha J.; Zhou, Mingqi; Callaham, Jordan B.; Ferl, Robert J.; Paul, Anna-Lisa

2017-11-01

Scientific access to spaceflight and especially the International Space Station has revealed that physiological adaptation to spaceflight is accompanied or enabled by changes in gene expression that significantly alter the transcriptome of cells in spaceflight. A wide range of experiments have shown that plant physiological adaptation to spaceflight involves gene expression changes that alter cell wall and other metabolisms. However, while transcriptome profiling aptly illuminates changes in gene expression that accompany spaceflight adaptation, mutation analysis is required to illuminate key elements required for that adaptation. Here we report how transcriptome profiling was used to gain insight into the spaceflight adaptation role of Altered response to gravity 1 (Arg1), a gene known to affect gravity responses in plants on Earth. The study compared expression profiles of cultured lines of Arabidopsis thaliana derived from wild-type (WT) cultivar Col-0 to profiles from a knock-out line deficient in the gene encoding ARG1 (ARG1 KO), both on the ground and in space. The cell lines were launched on SpaceX CRS-2 as part of the Cellular Expression Logic (CEL) experiment of the BRIC-17 spaceflight mission. The cultured cell lines were grown within 60 mm Petri plates in Petri Dish Fixation Units (PDFUs) that were housed within the Biological Research In Canisters (BRIC) hardware. Spaceflight samples were fixed on orbit. Differentially expressed genes were identified between the two environments (spaceflight and comparable ground controls) and the two genotypes (WT and ARG1 KO). Each genotype engaged unique genes during physiological adaptation to the spaceflight environment, with little overlap. Most of the genes altered in expression in spaceflight in WT cells were found to be Arg1-dependent, suggesting a major role for that gene in the physiological adaptation of undifferentiated cells to spaceflight.

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

Airborne fungi in child day care centers in Edirne City, Turkey.

PubMed

Aydogdu, Halide; Asan, Ahmet

2008-12-01

The purpose of this study was to determine the concentration, in terms of monthly and seasonal distribution and in relation to meteorological factors, of indoor and outdoor microfungi at selected sites in several child day care centers in the city of Edirne, Turkey. Samples were collected at one month intervals over a period of 12 months between January-December 2004, by exposing petri plates containing Peptone Dextrose Agar with Rose-Bengal and Streptomycin medium to the air for 10-15 min. A total of 2,071 microfungal colonies were counted on 192 petri plates. Thirty microfungal genera (Acremonium, Alternaria, Arthrinium, Aspergillus, Bahusakala, Beauveria, Ceuthospora, Chaetomium, Cladosporium, Curvularia, Drechslera, Epicoccum, Eurotium, Fusarium, Mycotypha, Myrotechium, Paecilomyces, Penicillium, Pestalotiopsis, Phoma, Ramichloridium, Rhizopus, Scopulariopsis, Stachybotrys, Stemphylium, Torula, Trichoderma, Trichothecium, Ulocladium, Verticillium) and 75 microfungal species were isolated from the air indoor and outdoor of the day care centers. The dominant microfungal genera were Cladosporium, Penicillium and Alternaria (44.11%, 18.94%, 14.67% of the total respectively), while the genus with the most species richness was Penicillium (26 species). Alternaria, Cladosporium, Penicillium and non-sporulating microfungi were found every month. Cladosporium was the dominant genus in both indoor and outdoor air. Although the predominant genus was the same in both indoor and outdoor air, Cladosporium was followed by Penicillium, Alternaria and Aspergillus genera in indoor air and by Alternaria, Penicillium and Aspergillus genera in outdoor air. While a positive correlation was found between the concentration of monthly outdoor microfungi and monthly average temperature, a negative correlation was found between the concentration of monthly outdoor microfungi and monthly average wind velocity. Also, some relationships were found between the monthly concentrations of the most predominant microfungal genera (Cladosporium, Penicillium and Alternaria) and various meteorological factors.

Dependability and performability analysis

NASA Technical Reports Server (NTRS)

Trivedi, Kishor S.; Ciardo, Gianfranco; Malhotra, Manish; Sahner, Robin A.

1993-01-01

Several practical issues regarding specifications and solution of dependability and performability models are discussed. Model types with and without rewards are compared. Continuous-time Markov chains (CTMC's) are compared with (continuous-time) Markov reward models (MRM's) and generalized stochastic Petri nets (GSPN's) are compared with stochastic reward nets (SRN's). It is shown that reward-based models could lead to more concise model specifications and solution of a variety of new measures. With respect to the solution of dependability and performability models, three practical issues were identified: largeness, stiffness, and non-exponentiality, and a variety of approaches are discussed to deal with them, including some of the latest research efforts.

Physicochemical studies of equine infectious anemia virus: V. Effect of ultraviolet irradiation on virus infectivity

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

Nakajima, H.; Mizuno, Y.; Yasuda, K.

1973-03-01

The effect of ultraviolet radiation on the infectivity of equine infectious anemia (EIA) virus is described using influenza virus and Rous sarcoma (RSV) virus as controls. Virus preparations were placed in Petri dishes and uv- irradiated by a 15 watt germicidal lamp. At intervals up to 30 min samples were taken to determine the infectivity in surviving fractions. The infectivity of the influenza virus was reduced by four orders about 2 min after irradiation; the EIA virus infectivity was reduced to the same extent in 20 min, and the RSV infectivity was reduced to the same extent in 30 min.

Morphological Diversity of the Colony Produced by Bacteria Proteus mirabilis

NASA Astrophysics Data System (ADS)

Nakahara, Akio; Shimada, Yuji; Wakita, Jun-ichi; Matsushita, Mitsugu; Matsuyama, Tohey

1996-08-01

Morphological changes of colonies have been investigatedfor a bacterial strain of Proteus mirabilis, which is a famous speciesfor producing concentric-ring-like colonies. It was found that colony patterns can be classified into three types,i.e., cyclic spreading, diffusion-limited growth (DLA-like)and three-dimensional growth (inside the agar medium) patterns. Cyclic spreading patterns can further be classifiedinto three subgroups, i.e., concentric-ring, homogeneous and spatiotemporal patterns. These subgroups were classified by examining the development of colony structure after colonies spread all over petri-dishes. Comparison of the results with thoseof another bacterial species Bacillus subtilis is also discussed.

Uncertainty Modeling for Database Design using Intuitionistic and Rough Set Theory

DTIC Science & Technology

2009-01-01

Definition. An intuitionistic rough relation R is a sub- set of the set cross product P(D1)× P(D2) × · · ·× P( Dm )× Dµ.× Dv. For a specific relation, R...that aj ∈ dij for all j. The interpretation space is the cross product D1× D2 × · · ·× Dm × Dµ× Dv but is limited for a given re- lation R to the set...systems, Journal of Information Science 11 (1985), 77–87. [7] T. Beaubouef and F. Petry, Rough Querying of Crisp Data in Relational Databases, Third

Microbial Cellulose Assembly in Microgravity

NASA Technical Reports Server (NTRS)

Brown, R. Malcolm, Jr.

1998-01-01

Based on evidence indicating a possible correlation between hypo-gravity conditions and alteration of cellulose production by the gram negative bacterium, Acetobacter xylinum, a ground-based study for a possible long term Space Shuttle flight has been conducted. The proposed experiment for A. xylinum aboard the Shuttle is the BRIC (Biological Research in a Canister), a metal container containing spaces for nine Petri plates. Using a common experimental design, the cellulose production capability as well as the survivability of the A. xylinum strains NQ5 and AY201 have been described. It should now be possible to use the BRIC for the first long term microgravity experiments involving the biosynthesis of cellulose.