WorldWideScience

Sample records for network formal specifications

  1. Formal Specification and Validation of a Hybrid Connectivity Restoration Algorithm for Wireless Sensor and Actor Networks

    Directory of Open Access Journals (Sweden)

    Nazir Ahmad Zafar

    2012-08-01

    Full Text Available Maintaining inter-actor connectivity is extremely crucial in mission-critical applications of Wireless Sensor and Actor Networks (WSANs, as actors have to quickly plan optimal coordinated responses to detected events. Failure of a critical actor partitions the inter-actor network into disjoint segments besides leaving a coverage hole, and thus hinders the network operation. This paper presents a Partitioning detection and Connectivity Restoration (PCR algorithm to tolerate critical actor failure. As part of pre-failure planning, PCR determines critical/non-critical actors based on localized information and designates each critical node with an appropriate backup (preferably non-critical. The pre-designated backup detects the failure of its primary actor and initiates a post-failure recovery process that may involve coordinated multi-actor relocation. To prove the correctness, we construct a formal specification of PCR using Z notation. We model WSAN topology as a dynamic graph and transform PCR to corresponding formal specification using Z notation. Formal specification is analyzed and validated using the Z Eves tool. Moreover, we simulate the specification to quantitatively analyze the efficiency of PCR. Simulation results confirm the effectiveness of PCR and the results shown that it outperforms contemporary schemes found in the literature.

  2. Comparing Formal Specification Languages

    NARCIS (Netherlands)

    Harmelen, van F.A.H.; Lopez de Mantaras, R.; Malec, J.; Treur, J.

    This paper presents a comparison between eight specification languages discussed during the Workshop on Formal Specification Techniques for Complex Reasoning Systems held in Vienna during the ECAI'92 conference. The languages as discussed here possess many important common characteristics, but also

  3. Formal Specification and Validation of Secure Connection Establishment in a Generic Access Network Scenario

    DEFF Research Database (Denmark)

    Fleischer, Paul; Kristensen, Lars Michael

    2008-01-01

    The Generic Access Network (GAN) architecture is defined by the 3rd Generation Partnership Project (3GPP), and allows telephone services, such as SMS and voice-calls, to be accessed via generic IP networks. The main usage of this is to allow mobile phones to use WiFi in addition to the usual GSM...... network. The GAN specification relies on the Internet Protocol Security layer (IPSec) and the Internet Key Exchange protocol (IKEv2) to provide encryption across IP networks, and thus avoid compromising the security of the telephone networks. The detailed usage of these two Internet protocols (IPSec...

  4. Formal Specification and Validation of a Hybrid Connectivity Restoration Algorithm for Wireless Sensor and Actor Networks

    Science.gov (United States)

    Imran, Muhammad; Zafar, Nazir Ahmad

    2012-01-01

    Maintaining inter-actor connectivity is extremely crucial in mission-critical applications of Wireless Sensor and Actor Networks (WSANs), as actors have to quickly plan optimal coordinated responses to detected events. Failure of a critical actor partitions the inter-actor network into disjoint segments besides leaving a coverage hole, and thus hinders the network operation. This paper presents a Partitioning detection and Connectivity Restoration (PCR) algorithm to tolerate critical actor failure. As part of pre-failure planning, PCR determines critical/non-critical actors based on localized information and designates each critical node with an appropriate backup (preferably non-critical). The pre-designated backup detects the failure of its primary actor and initiates a post-failure recovery process that may involve coordinated multi-actor relocation. To prove the correctness, we construct a formal specification of PCR using Z notation. We model WSAN topology as a dynamic graph and transform PCR to corresponding formal specification using Z notation. Formal specification is analyzed and validated using the Z Eves tool. Moreover, we simulate the specification to quantitatively analyze the efficiency of PCR. Simulation results confirm the effectiveness of PCR and the results shown that it outperforms contemporary schemes found in the literature.

  5. Formal Women-only Networks

    DEFF Research Database (Denmark)

    Villesèche, Florence; Josserand, Emmanuel

    2017-01-01

    implications: The paper contributes to research showing that the social structure of interactions and context can impact women’s standing in the workplace. Originality/value: The paper sheds light on the under-studied and under-theorised phenomenon of formal women-only business networks. Beyond the individual...... member level, the authors suggest that such networks can be of value for organisations and the wider social group of women in management and leadership positions....

  6. Integrating Semi-formal and Formal Software Specification Techniques

    NARCIS (Netherlands)

    Wieringa, Roelf J.; Dubois, Eric

    1998-01-01

    In this paper, we report on the integration of informal, semiformal and formal system specification techniques. We present a framework for system specification called TRADE, within which several well-known semiformal specification techniques are placed. TRADE is based on an analysis of structured

  7. Formal specification of human-computer interfaces

    Science.gov (United States)

    Auernheimer, Brent

    1990-01-01

    A high-level formal specification of a human computer interface is described. Previous work is reviewed and the ASLAN specification language is described. Top-level specifications written in ASLAN for a library and a multiwindow interface are discussed.

  8. Graphical And Textual Notations In Formal Specification

    Energy Technology Data Exchange (ETDEWEB)

    Bove, Rocco; Dipoppa, Giovanni; Groven, Arne-Kristian; Sivertsen, Terje

    1996-07-01

    The present report describes the current status of the co-operative project between ENEA and the OECD Halden Reactor Project on graphical and formal methods for software specification. The aim of this project is to contribute to a clarification of the relationship between graphical descriptions and formal specifications, and to provide guidelines for how they can be combined in order to utilize the strengths of' each approach. The overall aim of such a combination is to improve the formal basis of graphical descriptions and make formal specifications more generally comprehensible. The research reported includes the application of the IPTES technology on the APRM case example, an approach to the translation of Petri nets into algebraic specification, and the specification of real-time distributed systems using time-extended LOTOS. (author)

  9. Formal balancing of chemical reaction networks

    NARCIS (Netherlands)

    van der Schaft, Abraham; Rao, S.; Jayawardhana, B.

    2016-01-01

    In this paper we recall and extend the main results of Van der Schaft, Rao, Jayawardhana (2015) concerning the use of Kirchhoff’s Matrix Tree theorem in the explicit characterization of complex-balanced reaction networks and the notion of formal balancing. The notion of formal balancing corresponds

  10. User Interface Technology for Formal Specification Development

    Science.gov (United States)

    Lowry, Michael; Philpot, Andrew; Pressburger, Thomas; Underwood, Ian; Lum, Henry, Jr. (Technical Monitor)

    1994-01-01

    Formal specification development and modification are an essential component of the knowledge-based software life cycle. User interface technology is needed to empower end-users to create their own formal specifications. This paper describes the advanced user interface for AMPHION1 a knowledge-based software engineering system that targets scientific subroutine libraries. AMPHION is a generic, domain-independent architecture that is specialized to an application domain through a declarative domain theory. Formal specification development and reuse is made accessible to end-users through an intuitive graphical interface that provides semantic guidance in creating diagrams denoting formal specifications in an application domain. The diagrams also serve to document the specifications. Automatic deductive program synthesis ensures that end-user specifications are correctly implemented. The tables that drive AMPHION's user interface are automatically compiled from a domain theory; portions of the interface can be customized by the end-user. The user interface facilitates formal specification development by hiding syntactic details, such as logical notation. It also turns some of the barriers for end-user specification development associated with strongly typed formal languages into active sources of guidance, without restricting advanced users. The interface is especially suited for specification modification. AMPHION has been applied to the domain of solar system kinematics through the development of a declarative domain theory. Testing over six months with planetary scientists indicates that AMPHION's interactive specification acquisition paradigm enables users to develop, modify, and reuse specifications at least an order of magnitude more rapidly than manual program development.

  11. Ontology Assisted Formal Specification Extraction from Text

    Directory of Open Access Journals (Sweden)

    Andreea Mihis

    2010-12-01

    Full Text Available In the field of knowledge processing, the ontologies are the most important mean. They make possible for the computer to understand better the natural language and to make judgments. In this paper, a method which use ontologies in the semi-automatic extraction of formal specifications from a natural language text is proposed.

  12. Formal Specification of Real-Time Systems

    Energy Technology Data Exchange (ETDEWEB)

    Groven, Arne-Kristian

    1996-07-01

    This report presents the results of a study on formal specification of real-time distributed control systems. Emphasis has been but on the ability to describe both system architecture, system functionality and timed system behaviour inside the same formal framework. A timed extension of the ISO standardized formal description language LOTOS (ISO 8807), called TE-LOTOS, has been used for describing the timed behaviour. The functionality can be described in LOTOS, which is a subset of the timed extension. A graphical notation has been used for describing system architecture, transformable to a subset of LOTOS. This methodology has been used to specify a test example, a steam-boiler control system. Modularization of the specification is an important issue. This is achieved by isolating the time-dependent aspect in one part of the specification, and the system functionality in another. This modularization facilitates the separation of general aspect from the more specific aspects. This is demonstrated by comparison with another type of control systems, the APRM system (HWR-397). (author)

  13. Formal specification level concepts, methods, and algorithms

    CERN Document Server

    Soeken, Mathias

    2015-01-01

    This book introduces a new level of abstraction that closes the gap between the textual specification of embedded systems and the executable model at the Electronic System Level (ESL). Readers will be enabled to operate at this new, Formal Specification Level (FSL), using models which not only allow significant verification tasks in this early stage of the design flow, but also can be extracted semi-automatically from the textual specification in an interactive manner.  The authors explain how to use these verification tasks to check conceptual properties, e.g. whether requirements are in conflict, as well as dynamic behavior, in terms of execution traces. • Serves as a single-source reference to a new level of abstraction for embedded systems, known as the Formal Specification Level (FSL); • Provides a variety of use cases which can be adapted to readers’ specific design flows; • Includes a comprehensive illustration of Natural Language Processing (NLP) techniques, along with examples of how to i...

  14. A Formal Model and Verification Problems for Software Defined Networks

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    V. A. Zakharov

    2013-01-01

    Full Text Available Software-defined networking (SDN is an approach to building computer networks that separate and abstract data planes and control planes of these systems. In a SDN a centralized controller manages a distributed set of switches. A set of open commands for packet forwarding and flow-table updating was defined in the form of a protocol known as OpenFlow. In this paper we describe an abstract formal model of SDN, introduce a tentative language for specification of SDN forwarding policies, and set up formally model-checking problems for SDN.

  15. Formal specification is an experimental science

    Energy Technology Data Exchange (ETDEWEB)

    Bjorner, D. [Technical Univ., Lyngby (Denmark)

    1992-09-01

    Traditionally, abstract models of large, complex systems have been given in free-form mathematics, combining - often in ad-hoc, not formally supported ways - notions from the disciplines of partial differential equations, functional analysis, mathematical statistics, etc. Such models have been very useful for assimilation of information, analysis (investigation), and prediction (simulation). These models have, however, usually not been helpful in deriving computer representations of the modelled systems - for the purposes of computerized monitoring and control, Computing science, concerned with how to construct objects that can exist within the computer, offers ways of complementing, and in some cases, replacing or combining traditional mathematical models. Formal, model-, as well as property-oriented, specifications in the styles of denotational (respectively, algebraic semantics) represent major approaches to such modelling. In this expository, discursive paper we illustrate what we mean by model-oriented specifications of large, complex technological computing systems. The three modelling examples covers the introvert programming methodological subject of SDEs: software development environments, the distributed computing system subject of wfs`s: (transaction) work flow systems, and the extrovert subject of robots: robotics! the thesis is, just as for mathematical modelling, that we can derive much understanding, etc., from experimentally creating such formally specified models - on paper - and that we gain little in additionally building ad-hoc prototypes. Our models are expressed in a model-oriented style using the VDM specification language Meta-IV In this paper the models only reflect the {open_quotes}data modelling{close_quotes} aspects. We observe that such data models are more easily captured in the model-oriented siyle than in the algebraic semantics property-oriented style which originally was built of the abstraction of operations. 101 refs., 4 figs.

  16. Formal Verification of Security Policy Implementations in Enterprise Networks

    Science.gov (United States)

    Bera, P.; Ghosh, S. K.; Dasgupta, Pallab

    In enterprise networks, the management of security policies and their configurations becoming increasingly difficult due to complex security constraints of the organizations. In such networks, the overall organizational security policy (global policy) is defined as a collection of rules for providing service accesses between various network zones. Often, the specification of the global policy is incomplete; where all possible service access paths may not be covered explicitly by the "permit" and "deny" rules. This policy is implemented in a distributed manner through appropriate sets of access control rules (ACL rules) in the network interfaces. However, the implementation must be complete i.e., all service access paths across the network must be implemented as "permit" and "deny" ACL rules. In that case, the unspecified access paths in a given policy must be implemented as either "permit" or "deny" rules; hence there may exist multiple ACL implementations corresponding to that policy. Formally verifying that the ACL rules distributed across the network interfaces guarantees proper enforcement of the global security policy is an important requirement and a major technical challenge. The complexity of the problem is compounded by the fact that some combination of network services may lead to inconsistent hidden access paths in the network. The ACL implementations ignoring these hidden access paths may result in violation of one or more policy rules implicitly. This paper presents a formal verification framework for analyzing security policy implementations in enterprise networks. It stems from boolean modeling of the network topology, network services and security policy where the unspecified access paths are modeled as "don't-care" rules. The framework formally models the hidden access rules and incorporates them in the distributed ACL implementations for extracting a security implementation model, and finally formulates a QSAT (satisfiability of quantified boolean

  17. Blending Formal and Informal Learning Networks for Online Learning

    Science.gov (United States)

    Czerkawski, Betül C.

    2016-01-01

    With the emergence of social software and the advance of web-based technologies, online learning networks provide invaluable opportunities for learning, whether formal or informal. Unlike top-down, instructor-centered, and carefully planned formal learning settings, informal learning networks offer more bottom-up, student-centered participatory…

  18. Enhancing Formal E-Learning with Edutainment on Social Networks

    Science.gov (United States)

    Labus, A.; Despotovic-Zrakic, M.; Radenkovic, B.; Bogdanovic, Z.; Radenkovic, M.

    2015-01-01

    This paper reports on the investigation of the possibilities of enhancing the formal e-learning process by harnessing the potential of informal game-based learning on social networks. The goal of the research is to improve the outcomes of the formal learning process through the design and implementation of an educational game on a social network…

  19. Formal Specification of the OpenMP Memory Model

    Energy Technology Data Exchange (ETDEWEB)

    Bronevetsky, G; de Supinski, B

    2006-12-19

    OpenMP [2] is an important API for shared memory programming, combining shared memory's potential for performance with a simple programming interface. Unfortunately, OpenMP lacks a critical tool for demonstrating whether programs are correct: a formal memory model. Instead, the current official definition of the OpenMP memory model (the OpenMP 2.5 specification [2]) is in terms of informal prose. As a result, it is impossible to verify OpenMP applications formally since the prose does not provide a formal consistency model that precisely describes how reads and writes on different threads interact. We expand on our previous work that focused on the formal verification of OpenMP programs through a formal memory model [?]. As in that work, our formalization, which is derived from the existing prose model [2], provides a two-step process to verify whether an observed OpenMP execution is conformant. This paper extends the model to cover the entire specification. In addition to this formalization, our contributions include a discussion of ambiguities in the current prose-based memory model description. Although our formal model may not capture the current informal memory model perfectly, in part due to these ambiguities, our model reflects our understanding of the informal model's intent. We conclude with several examples that may indicate areas of the OpenMP memory model that need further refinement, however it is specified. Our goal is to motivate the OpenMP community to adopt those refinements eventually, ideally through a formal model, in later OpenMP specifications.

  20. On Formal Specification of Emergent Behaviours in Swarm Robotic Systems

    Directory of Open Access Journals (Sweden)

    Alan FT Winfield

    2005-12-01

    Full Text Available It is a characteristic of swarm robotics that specifying overall emergent swarm behaviours in terms of the low-level behaviours of individual robots is very difficult. Yet if swarm robotics is to make the transition from the laboratory to real-world engineering realisation we need such specifications. This paper explores the use of temporal logic to formally specify, and possibly also prove, the emergent behaviours of a robotic swarm. The paper makes use of a simplified wireless connected swarm as a case study with which to illustrate the approach. Such a formal approach could be an important step toward a disciplined design methodology for swarm robotics.

  1. Formal Methods for Abstract Specifications – A Comparison of Concepts

    DEFF Research Database (Denmark)

    Instenberg, Martin; Schneider, Axel; Schnetter, Sabine

    2006-01-01

    inspections and tests are usual means. To facilitate the introduction of formal methods in the development process of complex systems and protocols, two different tools evolved from research activities – UPPAAL and SpecEdit – have been investigated and compared regarding their concepts and functionality......In industry formal methods are becoming increasingly important for the verification of hardware and software designs. However current practice for specification of system and protocol functionality on high level of abstraction is textual description. For verification of the system behavior manual...

  2. Incremental and unifying modelling formalism for biological interaction networks

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    Képès François

    2007-11-01

    Full Text Available Abstract Background An appropriate choice of the modeling formalism from the broad range of existing ones may be crucial for efficiently describing and analyzing biological systems. Results We propose a new unifying and incremental formalism for the representation and modeling of biological interaction networks. This formalism allows automated translations into other formalisms, thus enabling a thorough study of the dynamic properties of a biological system. As a first illustration, we propose a translation into the R. Thomas' multivalued logical formalism which provides a possible semantics; a methodology for constructing such models is presented on a classical benchmark: the λ phage genetic switch. We also show how to extract from our model a classical ODE description of the dynamics of a system. Conclusion This approach provides an additional level of description between the biological and mathematical ones. It yields, on the one hand, a knowledge expression in a form which is intuitive for biologists and, on the other hand, its representation in a formal and structured way.

  3. The Impact of Formal Hierarchies on Enterprise Social Networking Behavior

    DEFF Research Database (Denmark)

    Behrendt, Sebastian; Klier, Julia; Klier, Mathias

    2015-01-01

    With more and more companies using enterprise social networks (ESN) for employee communication and collaboration, the influence of ESN on organizational hierarchies has been subject of countless discussions in practice-oriented media and first academic studies. Conversely, the question whether...... impact on social networking behavior. By applying means of social network analysis and supported by statements from interviews, we illustrate how deeply formal hierarchy impacts the three examined types of relationships. Our results motivate academics to further study the interrelation between hierarchy...... und ESN and hierarchy’s effects regarding the sociotechnical design and implementation of related systems....

  4. A two-level formal specification of a defense communications system

    Energy Technology Data Exchange (ETDEWEB)

    Chisholm, G.H. [Argonne National Lab., IL (United States). Decision and Information Sciences Div.; Kemmerer, R.A. [Univ. of California, Santa Barbara, CA (United States). Reliable Software Group

    1994-04-01

    Computer systems are being used in critical situations with sensitive data, which makes it very important to ensure that these systems perform as desired. The defense communications system contains particularly sensitive data. A two-level ASLAN formal specification of a defense communications system is presented. The ASLAN model is designed to enhance the understanding of critical requirements and demands of the defense communications system. For the top-level (high-level) specifications, the structural details of the actual network are actual network are abstracted to allow more time for examining the interactions between the sites and the network. At this level, DataGrams move through the network, although the actual routing decisions are not specified. More details are added in the second-level specification. At this level, structure is added to the network.

  5. Factors Influencing the Performance of German Food SME Formal Networks

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    Jivka Deiters

    2014-08-01

    Full Text Available The food sector in Europe can be characterized as a complex, global and dynamically changing network of trade streams, food supply network relations and related product flows which offers a big spectrum for economic output and employment. Innovation is important for the competitiveness of the food industry that is to a large extent comprised of small and medium sized enterprises (SMEs. For them, innovation has grown extremely subordinate to interaction in networks. Network initiatives that could provide appropriate support involve social interaction and knowledge exchange, learning and competence development, and coordination (organization and management ofimplementation. This paper is designed to assess the factors that affect the performance of German food SME formal networks. It also addresses the consequences at the network and macro level. The analysis was explored by using the laddering technique based on the means‐end chain theory. The findings will help to build up a “network learning toolbox” that is adapted to the particular requirements of the different target groups such as of SMEs, network managers and policy makers. The “network learning toolbox” should improve network learning, which is adriver for improvements in innovation, economic growth and sustainable competitive advantage for food SMEs.

  6. A Formal Approach to the Verification of Networks on Chip

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    Schmaltz Julien

    2009-01-01

    Full Text Available Abstract The current technology allows the integration on a single die of complex systems-on-chip (SoCs that are composed of manufactured blocks (IPs, interconnected through specialized networks on chip (NoCs. IPs have usually been validated by diverse techniques (simulation, test, formal verification and the key problem remains the validation of the communication infrastructure. This paper addresses the formal verification of NoCs by means of a mechanized proof tool, the ACL2 theorem prover. A metamodel for NoCs has been developed and implemented in ACL2. This metamodel satisfies a generic correctness statement. Its verification for a particular NoC instance is reduced to discharging a set of proof obligations for each one of the NoC constituents. The methodology is demonstrated on a realistic and state-of-the-art design, the Spidergon network from STMicroelectronics.

  7. Network Learning and Innovation in SME Formal Networks

    Directory of Open Access Journals (Sweden)

    Jivka Deiters

    2013-02-01

    Full Text Available The driver for this paper is the need to better understand the potential for learning and innovation that networks canprovide especially for small and medium sized enterprises (SMEs which comprise by far the majority of enterprises in the food sector. With the challenges the food sector is facing in the near future, learning and innovation or more focused, as it is being discussed in the paper, ‘learning for innovation’ are not just opportunities but pre‐conditions for the sustainability of the sector. Network initiatives that could provide appropriate support involve social interaction and knowledge exchange, learning, competence development, and coordination (organization and management of implementation. The analysis identifies case studies in any of these orientations which serve different stages of the innovation process: invention and implementation. The variety of network case studies cover networks linked to a focus group for training, research, orconsulting, networks dealing with focused market oriented product or process development, promotional networks, and networks for open exchange and social networking.

  8. ASLan++ — A Formal Security Specification Language for Distributed Systems

    DEFF Research Database (Denmark)

    Von Oheimb, David; Mödersheim, Sebastian Alexander

    2010-01-01

    This paper introduces ASLan++, the AVANTSSAR Specification Language. ASLan++ has been designed for formally specifying dynamically composed security-sensitive web services and service-oriented architectures, their associated security policies, as well as their security properties, at both...... credentialsbased authentication mechanism, dynamic access control policies, and the related security goals. This demonstrates the flexibility and expressiveness of the language, and that the resulting models are logically adequate, while on the other hand they are clear to read and feasible to construct for system...

  9. From Wireless Sensor Networks to Wireless Body Area Networks: Formal Modeling and Verification on Security Using PAT

    Directory of Open Access Journals (Sweden)

    Tieming Chen

    2016-01-01

    Full Text Available Model checking has successfully been applied on verification of security protocols, but the modeling process is always tedious and proficient knowledge of formal method is also needed although the final verification could be automatic depending on specific tools. At the same time, due to the appearance of novel kind of networks, such as wireless sensor networks (WSN and wireless body area networks (WBAN, formal modeling and verification for these domain-specific systems are quite challenging. In this paper, a specific and novel formal modeling and verification method is proposed and implemented using an expandable tool called PAT to do WSN-specific security verification. At first, an abstract modeling data structure for CSP#, which is built in PAT, is developed to support the node mobility related specification for modeling location-based node activity. Then, the traditional Dolev-Yao model is redefined to facilitate modeling of location-specific attack behaviors on security mechanism. A throughout formal verification application on a location-based security protocol in WSN is described in detail to show the usability and effectiveness of the proposed methodology. Furthermore, also a novel location-based authentication security protocol in WBAN can be successfully modeled and verified directly using our method, which is, to the best of our knowledge, the first effort on employing model checking for automatic analysis of authentication protocol for WBAN.

  10. Systems, methods and apparatus for implementation of formal specifications derived from informal requirements

    Science.gov (United States)

    Hinchey, Michael G. (Inventor); Rash, James L. (Inventor); Erickson, John D. (Inventor); Gracinin, Denis (Inventor); Rouff, Christopher A. (Inventor)

    2010-01-01

    Systems, methods and apparatus are provided through which in some embodiments an informal specification is translated without human intervention into a formal specification. In some embodiments the formal specification is a process-based specification. In some embodiments, the formal specification is translated into a high-level computer programming language which is further compiled into a set of executable computer instructions.

  11. Fuzzy operators and cyclic behavior in formal neuronal networks

    Science.gov (United States)

    Labos, E.; Holden, A. V.; Laczko, J.; Orzo, L.; Labos, A. S.

    1992-01-01

    Formal neuronal networks (FNN), which are comprised of threshold gates, make use of the unit step function. It is regarded as a degenerated distribution function (DDF) and will be referred to here as a non-fuzzy threshold operator (nFTO). Special networks of this kind generating long cycles of states are modified by introduction of fuzzy threshold operators (FTO), i.e., non-degenerated distribution functions (nDDF). The cyclic behavior of the new nets is compared with the original ones. The interconnection matrix and threshold values are not modified. It is concluded that the original long cycles change the fixed points and short cycles, and as the computer simulations demonstrate, the aperiodic motion that is associated with chaotic behavior appears. The emergence of the above changes depend on the steepness of the threshold operators.

  12. Formal Variability of Terms in the Sphere of Network Technologies

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    Roman Viktorovich Deniko

    2015-09-01

    Full Text Available The article addresses the problem of formal variability of terms in the sphere of network terminology in the Russian language. The research is based on data from the Internet communication in the sphere of network technologies. Such formal variability types as graphical, phonemic, word building and complex (graphic and phonetic, morphologic and accentual are discussed in this article. The authors reveal the reasons for graphic variability of foreign origin terms making up the international terminological fund. These reasons cover such aspects as the use of graphics of source language and recipient language; the presence or absence of hyphenation, etc. It is determined that the phonemic variants of terms appear as a result of oral or written borrowings. The existence of such variants is also connected with the stage of their adaptation in the Russian language after borrowing. In this case the variants are related with soft or hard pronunciation of consonants. There are also some cases of phonemic variability on the graphic level. The complex variability is regarded as a part of active processes taking place in the modern Russian language, and these processes involve both native and foreign origin terms. The particular attention is paid to the word-building variants – word-building affixes the variability of which is peculiar of network technologies. The results of the research show that the variability of professional units belonging to the network technologies sublanguage is caused by the active process of borrowing of specialpurpose vocabulary into the Russian language. The process is due to the intensification of intercultural communication in the professional spheres.

  13. On the Formal Specification of Computer Communication Protocols.

    Science.gov (United States)

    1980-12-01

    lUodule: Inet-rt ..................................... 67 e. ’odule: Peasserble ................................... 71 f. ?.odule: Send- frap ...specification on a network access protocol. - 56 - , 7 A trial deconposition is given In figure 7. The II Is decomposed into four layers: Hlost-Host...updated. After a few trials the decomposition in figure 8 was arrived at and used. H H H-H Virt I ------------------ Virtual to physical Virtual to

  14. Registration of an enterprise information system development by formal specifications

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    Milan Mišovič

    2006-01-01

    Full Text Available The economical view from the Enterprise process sets ERP, SCM, CRM, BI, … to a functionality and Enterprise Information System structure by informaticians is demonstrable reality. A comprehensive Enterprise Information System software solution, that respects the mentioned economical platform by large software firms, has got required attributes of a data, process and communication integrity but there is not financially sustainable for small enterprises. These enterprises are predominantly oriented to progressive computerization of enterprise processes and rather gradually buy application packages for individual process sets. Large and small software firms provide needed partial solutions, nevertheless small firms solutions are connected with the data, process and communication disintegration. Since the compatibility requirement is not generally accepted, finding of an EAI solution have become one of the main System Integration tasks. This article provides one specific style for a complex or partial Enterprise Information System solution. This solution is founded on formal and descriptive specifications that can sustain required data, process and communication integration among packages of applications. As a result, this style provides the new view for the effectiveness of the associated process of information modeling.

  15. Formal derivation of qualitative dynamical models from biochemical networks.

    Science.gov (United States)

    Abou-Jaoudé, Wassim; Thieffry, Denis; Feret, Jérôme

    2016-11-01

    As technological advances allow a better identification of cellular networks, large-scale molecular data are swiftly produced, allowing the construction of large and detailed molecular interaction maps. One approach to unravel the dynamical properties of such complex systems consists in deriving coarse-grained dynamical models from these maps, which would make the salient properties emerge. We present here a method to automatically derive such models, relying on the abstract interpretation framework to formally relate model behaviour at different levels of description. We illustrate our approach on two relevant case studies: the formation of a complex involving a protein adaptor, and a race between two competing biochemical reactions. States and traces of reaction networks are first abstracted by sampling the number of instances of chemical species within a finite set of intervals. We show that the qualitative models induced by this abstraction are too coarse to reproduce properties of interest. We then refine our approach by taking into account additional constraints, the mass invariants and the limiting resources for interval crossing, and by introducing information on the reaction kinetics. The resulting qualitative models are able to capture sophisticated properties of interest, such as a sequestration effect, which arise in the case studies and, more generally, participate in shaping the dynamics of cell signaling and regulatory networks. Our methodology offers new trade-offs between complexity and accuracy, and clarifies the implicit assumptions made in the process of qualitative modelling of biological networks. Copyright © 2016 The Author(s). Published by Elsevier Ireland Ltd.. All rights reserved.

  16. Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes.

    Directory of Open Access Journals (Sweden)

    Abibatou Mbodj

    2016-09-01

    Full Text Available Given the complexity of developmental networks, it is often difficult to predict the effect of genetic perturbations, even within coding genes. Regulatory factors generally have pleiotropic effects, exhibit partially redundant roles, and regulate highly interconnected pathways with ample cross-talk. Here, we delineate a logical model encompassing 48 components and 82 regulatory interactions involved in mesoderm specification during Drosophila development, thereby providing a formal integration of all available genetic information from the literature. The four main tissues derived from mesoderm correspond to alternative stable states. We demonstrate that the model can predict known mutant phenotypes and use it to systematically predict the effects of over 300 new, often non-intuitive, loss- and gain-of-function mutations, and combinations thereof. We further validated several novel predictions experimentally, thereby demonstrating the robustness of model. Logical modelling can thus contribute to formally explain and predict regulatory outcomes underlying cell fate decisions.

  17. A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks.

    Science.gov (United States)

    Monteiro, Pedro T; Dumas, Estelle; Besson, Bruno; Mateescu, Radu; Page, Michel; Freitas, Ana T; de Jong, Hidde

    2009-12-30

    The study of biological networks has led to the development of increasingly large and detailed models. Computer tools are essential for the simulation of the dynamical behavior of the networks from the model. However, as the size of the models grows, it becomes infeasible to manually verify the predictions against experimental data or identify interesting features in a large number of simulation traces. Formal verification based on temporal logic and model checking provides promising methods to automate and scale the analysis of the models. However, a framework that tightly integrates modeling and simulation tools with model checkers is currently missing, on both the conceptual and the implementational level. We have developed a generic and modular web service, based on a service-oriented architecture, for integrating the modeling and formal verification of genetic regulatory networks. The architecture has been implemented in the context of the qualitative modeling and simulation tool GNA and the model checkers NUSMV and CADP. GNA has been extended with a verification module for the specification and checking of biological properties. The verification module also allows the display and visual inspection of the verification results. The practical use of the proposed web service is illustrated by means of a scenario involving the analysis of a qualitative model of the carbon starvation response in E. coli. The service-oriented architecture allows modelers to define the model and proceed with the specification and formal verification of the biological properties by means of a unified graphical user interface. This guarantees a transparent access to formal verification technology for modelers of genetic regulatory networks.

  18. A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks

    Directory of Open Access Journals (Sweden)

    Page Michel

    2009-12-01

    Full Text Available Abstract Background The study of biological networks has led to the development of increasingly large and detailed models. Computer tools are essential for the simulation of the dynamical behavior of the networks from the model. However, as the size of the models grows, it becomes infeasible to manually verify the predictions against experimental data or identify interesting features in a large number of simulation traces. Formal verification based on temporal logic and model checking provides promising methods to automate and scale the analysis of the models. However, a framework that tightly integrates modeling and simulation tools with model checkers is currently missing, on both the conceptual and the implementational level. Results We have developed a generic and modular web service, based on a service-oriented architecture, for integrating the modeling and formal verification of genetic regulatory networks. The architecture has been implemented in the context of the qualitative modeling and simulation tool GNA and the model checkers NUSMV and CADP. GNA has been extended with a verification module for the specification and checking of biological properties. The verification module also allows the display and visual inspection of the verification results. Conclusions The practical use of the proposed web service is illustrated by means of a scenario involving the analysis of a qualitative model of the carbon starvation response in E. coli. The service-oriented architecture allows modelers to define the model and proceed with the specification and formal verification of the biological properties by means of a unified graphical user interface. This guarantees a transparent access to formal verification technology for modelers of genetic regulatory networks.

  19. A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks

    Science.gov (United States)

    2009-01-01

    Background The study of biological networks has led to the development of increasingly large and detailed models. Computer tools are essential for the simulation of the dynamical behavior of the networks from the model. However, as the size of the models grows, it becomes infeasible to manually verify the predictions against experimental data or identify interesting features in a large number of simulation traces. Formal verification based on temporal logic and model checking provides promising methods to automate and scale the analysis of the models. However, a framework that tightly integrates modeling and simulation tools with model checkers is currently missing, on both the conceptual and the implementational level. Results We have developed a generic and modular web service, based on a service-oriented architecture, for integrating the modeling and formal verification of genetic regulatory networks. The architecture has been implemented in the context of the qualitative modeling and simulation tool GNA and the model checkers NUSMV and CADP. GNA has been extended with a verification module for the specification and checking of biological properties. The verification module also allows the display and visual inspection of the verification results. Conclusions The practical use of the proposed web service is illustrated by means of a scenario involving the analysis of a qualitative model of the carbon starvation response in E. coli. The service-oriented architecture allows modelers to define the model and proceed with the specification and formal verification of the biological properties by means of a unified graphical user interface. This guarantees a transparent access to formal verification technology for modelers of genetic regulatory networks. PMID:20042075

  20. Centrality measures and thermodynamic formalism for complex networks.

    Science.gov (United States)

    Delvenne, Jean-Charles; Libert, Anne-Sophie

    2011-04-01

    In the study of small and large networks it is customary to perform a simple random walk where the random walker jumps from one node to one of its neighbors with uniform probability. The properties of this random walk are intimately related to the combinatorial properties of the network. In this paper we propose to use the Ruelle-Bowens random walk instead, whose probability transitions are chosen in order to maximize the entropy rate of the walk on an unweighted graph. If the graph is weighted, then a free energy is optimized instead of the entropy rate. Specifically, we introduce a centrality measure for large networks, which is the stationary distribution attained by the Ruelle-Bowens random walk; we name it entropy rank. We introduce a more general version, which is able to deal with disconnected networks, under the name of free-energy rank. We compare the properties of those centrality measures with the classic PageRank and hyperlink-induced topic search (HITS) on both toy and real-life examples, in particular their robustness to small modifications of the network. We show that our centrality measures are more discriminating than PageRank, since they are able to distinguish clearly pages that PageRank regards as almost equally interesting, and are more sensitive to the medium-scale details of the graph.

  1. On the design and formal specification of a transaction processing protocol

    NARCIS (Netherlands)

    van Sinderen, Marten J.; Widya, I.A.; Quemada, J.; Manas, J.; Vazquez, E.

    1991-01-01

    This paper presents the design and formal specification of a protocol that provides support for online transaction processing. The design approach taken is one that supports stepwise refinement and incorporates formal methods based on the formal description technique LOTIOS. The concepts of the

  2. Enhancing Formal Specification and Verification of Temporal Constraints in Business Processes

    OpenAIRE

    Cheikhrouhou, Saoussen; Kallel, Slim; Guermouche, Nawal; Jmaiel, Mohamed

    2014-01-01

    International audience; Formal specification and verification support of time-related constraints constitute fundamental challenges for any Business Process Management (BPM) system. Reluctantly, the literature on the subject of formal specification and verification of advanced temporal constraints such as absolute temporal constraints associated with relative temporal constraints is scarce. In this paper, we propose a novel approach enabling the formal specification and verification of advanc...

  3. Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes

    National Research Council Canada - National Science Library

    Mbodj, Abibatou; Gustafson, E Hilary; Ciglar, Lucia; Junion, Guillaume; Gonzalez, Aitor; Girardot, Charles; Perrin, Laurent; Furlong, Eileen E M; Thieffry, Denis

    2016-01-01

    .... Here, we delineate a logical model encompassing 48 components and 82 regulatory interactions involved in mesoderm specification during Drosophila development, thereby providing a formal integration...

  4. Slice-Based Formal Specification Measures -- Mapping Coupling and Cohesion Measures to Formal Z

    Science.gov (United States)

    Bollin, Andreas

    2010-01-01

    This paper demonstrates that existing slice-based measures can reasonably be mapped to the field of state-based specification languages. By making use of Z specifications this contribution renews the idea of slice-profiles and derives coupling and cohesion measures for them. The measures are then assessed by taking a critical look at their sensitiveness in respect to modifications on the specification source. The presented study shows that slice-based coupling and cohesion measures have the potential to be used as quality indicators for specifications as they reflect the changes in the structure of a specification as accustomed from their program-related pendants.

  5. Formal analysis of executions of organizational scenarios based on process-oriented specifications

    NARCIS (Netherlands)

    Popova, V.; Sharpanskykh, O.

    2011-01-01

    Abstract This paper presents various formal techniques for analysis of executions of organizational scenarios based on specifications of organizations. Organizational specifications describe (prescribe) ordering and timing relations on organizational processes, modes of use of resources, allocations

  6. Modeling signaling networks with different formalisms: a preview.

    Science.gov (United States)

    MacNamara, Aidan; Henriques, David; Saez-Rodriguez, Julio

    2013-01-01

    In the last 30 years, many of the mechanisms behind signal transduction, the process by which the cell takes extracellular signals as an input and converts them to a specific cellular phenotype, have been experimentally determined. With these discoveries, however, has come the realization that the architecture of signal transduction, the signaling network, is incredibly complex. Although the main pathways between receptor and output are well-known, there is a complex net of regulatory features that include crosstalk between different pathways, spatial and temporal effects, and positive and negative feedbacks. Hence, modeling approaches have been used to try and unravel some of these complexities. We use the mitogen-activated protein kinase cascade to illustrate chemical kinetic and logic approaches to modeling signaling networks. By using a common well-known model, we illustrate here the assumptions and level of detail behind each modeling approach, which serves as an introduction to the more detailed discussions of each in the accompanying chapters in this book.

  7. Formal Models of the Network Co-occurrence Underlying Mental Operations.

    Directory of Open Access Journals (Sweden)

    Danilo Bzdok

    2016-06-01

    Full Text Available Systems neuroscience has identified a set of canonical large-scale networks in humans. These have predominantly been characterized by resting-state analyses of the task-unconstrained, mind-wandering brain. Their explicit relationship to defined task performance is largely unknown and remains challenging. The present work contributes a multivariate statistical learning approach that can extract the major brain networks and quantify their configuration during various psychological tasks. The method is validated in two extensive datasets (n = 500 and n = 81 by model-based generation of synthetic activity maps from recombination of shared network topographies. To study a use case, we formally revisited the poorly understood difference between neural activity underlying idling versus goal-directed behavior. We demonstrate that task-specific neural activity patterns can be explained by plausible combinations of resting-state networks. The possibility of decomposing a mental task into the relative contributions of major brain networks, the "network co-occurrence architecture" of a given task, opens an alternative access to the neural substrates of human cognition.

  8. Formal Models of the Network Co-occurrence Underlying Mental Operations

    Science.gov (United States)

    Bzdok, Danilo; Varoquaux, Gaël; Grisel, Olivier; Eickenberg, Michael; Poupon, Cyril; Thirion, Bertrand

    2016-01-01

    Systems neuroscience has identified a set of canonical large-scale networks in humans. These have predominantly been characterized by resting-state analyses of the task-unconstrained, mind-wandering brain. Their explicit relationship to defined task performance is largely unknown and remains challenging. The present work contributes a multivariate statistical learning approach that can extract the major brain networks and quantify their configuration during various psychological tasks. The method is validated in two extensive datasets (n = 500 and n = 81) by model-based generation of synthetic activity maps from recombination of shared network topographies. To study a use case, we formally revisited the poorly understood difference between neural activity underlying idling versus goal-directed behavior. We demonstrate that task-specific neural activity patterns can be explained by plausible combinations of resting-state networks. The possibility of decomposing a mental task into the relative contributions of major brain networks, the "network co-occurrence architecture" of a given task, opens an alternative access to the neural substrates of human cognition. PMID:27310288

  9. Architecture and specification style in formal descriptions of distributed systems

    NARCIS (Netherlands)

    Vissers, C.A.; Scollo, Giuseppe; van Sinderen, Marten J.; Aggarwal, S.; Sabnani, K.

    1988-01-01

    Objective of this paper is to illustrate relationships that exist between architecture, the abstract subject of distributed system design, and specification style, the way of using a given language to design and implement the architecture. We advocate for a few specification styles thate allow to

  10. A Formal Model for Trust in Dynamic Networks

    DEFF Research Database (Denmark)

    Carbone, Marco; Nielsen, Mogens; Sassone, Vladimiro

    2003-01-01

    We propose a formal model of trust informed by the Global Computing scenario and focusing on the aspects of trust formation, evolution, and propagation. The model is based on a novel notion of trust structures which, building on concepts from trust management and domain theory, feature at the same...

  11. Impact of informal networks on opinion dynamics in hierarchically formal organization

    Science.gov (United States)

    Song, Xiao; Shi, Wen; Ma, Yaofei; Yang, Chen

    2015-10-01

    Traditional opinion dynamics model focused mainly on the conditions under which a group of agents would reach a consensus. Conclusion has been gained that continuous opinion dynamics are subject to the constraint that convergent opinion adjustment only proceeds when opinion difference is below a given tolerance. This conclusion is useful but neglected the fact that an organization often consists of overlapped networks including formally hierarchical network and small-world/scale-free informal networks. To study the impact of different types of informal networks on converging speed or the number of opinion clusters, four typical types of informal networks (small-world, scale-free, tree and fully connected) are modeled and proposed as complements to formal communications. Experiments to compare formal network and hybrid networks are then carried out. It is observed that opinion dynamics with supplemented communications of informal networks can benefit convergence speed and reduce opinion clusters. More importantly, it is revealed that three key factors of informal networks affect their impact on formal network. These factors of informal network in descending orders are: agents' tolerances, scale and number of links.

  12. Formal specification of a query expression generator using RSL ...

    African Journals Online (AJOL)

    From the specification, an implementation of our generator is generated in C++ using a command within the RSL project support environment that translates RSL to C++. The preliminary results with our generator show that it holds promise as a stand-alone tool as well. (Botswana Journal of Technology: 2002 11(2): 9-17) ...

  13. The Formal Specification of an Abstract Database: Design and Implementation.

    Science.gov (United States)

    1985-12-01

    manageable. For example, although we can not put the object STUDENT into a database, it is no problem to store the characterstring ’ STUDENT ’ as a conceptual...his attention into one specific direction, since our methodology €I focuses on representation independence. The only reason for choosing this approach...dblist.iritlst: -~dap; dblist.madlst: -*tap; dblist.memblst: -4rap; /* database part * isbaal: -~ bap ; isnat: -~ bap ; 225 isint: -~bop; ischar: -*bop; isstr.char

  14. Formal Specification and Verification of a Coordination Protocol for an Automated Air Traffic Control System

    Data.gov (United States)

    National Aeronautics and Space Administration — We detail all of the facets of adapting classical model checking to a real aerospace system, in- cluding deriving the formal model and a set of specifications from...

  15. Women in formal corporate networks: an organisational citizenship perspective.

    OpenAIRE

    Singh, Val; Vinnicombe, Susan; Kumra, Savita

    2006-01-01

    To investigate women's corporate networks, and the reported benefits for the women and their employers. To gain insight into the motivation for these voluntary activities, by drawing on organisational citizenship theory.

  16. Formally Verifying Human-Automaton Interaction with Specification Properties Generated from Task Analytic Models

    Science.gov (United States)

    Bolton, M. L.; Jimenez, N.; van Paassen, M. M.; Trujillo, M.

    2013-09-01

    Human-automation interaction (HAI) is a major contributor to failures in aerospace systems, often due to unexpected interactions between system components. Formal verification is a method of analysis that exhaustively examines all of the interaction in a formal system model to determine if it adheres to desirable specification properties. Task analytic models can be included in formal system models to allow HAI to be evaluated with formal verification. However, previous work required analysts to manually formulate specification properties they wished to check. A practice which can result in unexpected, dangerous HAI conditions not being checked. This paper presents a method for generating specification properties from task models to allow analysts to automatically check for HAI problems they may not have anticipated. The paper describes the design and implementation of the method. An example (a pilot performing a before landing checklist) is presented to illustrate its utility.

  17. Formal Methods for Verification and Validation of Partial Specifications: A Case Study

    Science.gov (United States)

    Easterbrook, Steve; Callahan, John

    1997-01-01

    This paper describes our work exploring the suitability of formal specification methods for independent verification and validation (IV&V) of software specifications for large, safety critical systems. An IV&V contractor often has to perform rapid analysis on incomplete specifications, with no control over how those specifications are represented. Lightweight formal methods show significant promise in this context, as they offer a way of uncovering major errors, without the burden of full proofs of correctness. We describe a case study of the use of partial formal models for V&V of the requirements for Fault Detection Isolation and Recovery on the space station. We conclude that the insights gained from formalizing a specification are valuable, and it is the process of formalization, rather than the end product that is important. It was only necessary to build enough of the formal model to test the properties in which we were interested. Maintenance of fidelity between multiple representations of the same requirements (as they evolve) is still a problem, and deserves further study.

  18. An Approach to Formal Description of One Class of Automata Networks

    CERN Document Server

    Severyanov, V M

    2003-01-01

    Hyperbolic Cellular Automata, a special class of Automata Networks, are based on Iterated Function Systems and originally were designed for constructing fractal objects. However, they are in their own right and can be studied, for example, in the context of the computer simulation theory. Hyperbolic Cellular Automata can be considered as a generalization of Cellular Automata. The main difference lies in the fact that a hyperbolic cellular automaton has a nonregular structure of the cell neighborhood system. Evolving Algebras (known also as Abstract State Machines) have been proposed by Yuri Gurevich as the models for arbitrary computational processes. They are finite many-sorted dynamic algebras representing state transitions and describing operational semantics of discrete dynamical systems. System states are represented here as static algebras, the dynamics is described by a set of transition rules. Evolving Algebras provide a formal method for executable specifications. An evolving algebra approach to form...

  19. An Entry Point for Formal Methods: Specification and Analysis of Event Logs

    Directory of Open Access Journals (Sweden)

    Howard Barringer

    2010-03-01

    Full Text Available Formal specification languages have long languished, due to the grave scalability problems faced by complete verification methods. Runtime verification promises to use formal specifications to automate part of the more scalable art of testing, but has not been widely applied to real systems, and often falters due to the cost and complexity of instrumentation for online monitoring. In this paper we discuss work in progress to apply an event-based specification system to the logging mechanism of the Mars Science Laboratory mission at JPL. By focusing on log analysis, we exploit the "instrumentation" already implemented and required for communicating with the spacecraft. We argue that this work both shows a practical method for using formal specifications in testing and opens interesting research avenues, including a challenging specification learning problem.

  20. Formal Food-related Networks in Ireland: A Case Study Analysis

    Directory of Open Access Journals (Sweden)

    Maeve Henchion

    2012-03-01

    Full Text Available  Strategic networking is of crucial importance for innovation in small and medium sized enterprises (SMEs as it enables these companies access external resources and overcome internal constraints. However, SMEs often lack the skills and competencies to engage in and benefit from networks. Consequently SMEs often fail in establishing strategic and efficient networks. To date, there is limited guidance available on the optimal design of such networks. Furthermore, limited guidance is available on the number of networks, and level of engagement therein, that companies should be involved with. Using case studies across a range of formal networks within the food sector in Ireland, insights into the success factors and barriers to network learning are presented, which provide a foundation for such guidelines. Three case studies were selected for analysis in Ireland. Up to ten in-depth interviews were scheduled with the network managers and key informants from the triple helix (i.e. policy, research and industry sectors within each formal network. Initially, interviewees were identified as a result of a review of secondary sources and personal knowledge of the authors. The snowball sampling technique was then employed to identify additional interviewees within each network. The findings from this study revealed that some formal networks had a strong institutional influence, including significant financial inputs, whilst others had bottom-up origins. Many networks had strong levels of interaction prior to formalisation, which provided solid trust-based foundations. Innovation and/or learning were not the expressed objectives of all networks at the outset. However, interviewees across all three networks felt that positive impacts had been achieved in these areas. Whilst being involved in a broad network can provide access to a wider range of ideas, these case studies suggest that being involved in a smaller, dense network, with high levels of IP

  1. Revealing dynamics and consequences of fit and misfit between formal and informal networks in multi-institutional product development collaborations

    NARCIS (Netherlands)

    Kratzer, J.; Gemuenden, Hans G.; Lettl, Christopher

    The study presents a longitudinal examination about dynamics and consequences of fit and misfit between formally ascribed design interfaces and informal communication networks in two large multi-institutional product development collaborations in space industry. Findings: (1) formally ascribed

  2. Revealing dynamics and consequences of fit and misfit between formal and informal networks in multi-institutional product development collaborations

    DEFF Research Database (Denmark)

    Kratzer, Jan; Gemünden, Hans Georg; Lettl, Christopher

    2008-01-01

    The study presents a longitudinal examination about dynamics and consequences of fit and misfit between formally ascribed design interfaces and informal communication networks in two large multi-institutional product development collaborations in space industry. Findings: (1) formally ascribed...

  3. Formal reconstruction of attack scenarios in mobile ad hoc and sensor networks

    Directory of Open Access Journals (Sweden)

    Rekhis Slim

    2011-01-01

    Full Text Available Abstract Several techniques of theoretical digital investigation are presented in the literature but most of them are unsuitable to cope with attacks in wireless networks, especially in Mobile Ad hoc and Sensor Networks (MASNets. In this article, we propose a formal approach for digital investigation of security attacks in wireless networks. We provide a model for describing attack scenarios in a wireless environment, and system and network evidence generated consequently. The use of formal approaches is motivated by the need to avoid ad hoc generation of results that impedes the accuracy of analysis and integrity of investigation. We develop an inference system that integrates the two types of evidence, handles incompleteness and duplication of information in them, and allows possible and provable actions and attack scenarios to be generated. To illustrate the proposal, we consider a case study dealing with the investigation of a remote buffer overflow attack.

  4. Online Social Networks as Formal Learning Environments: Learner Experiences and Activities

    Science.gov (United States)

    Veletsianos, George; Navarrete, Cesar C.

    2012-01-01

    While the potential of social networking sites to contribute to educational endeavors is highlighted by researchers and practitioners alike, empirical evidence on the use of such sites for formal online learning is scant. To fill this gap in the literature, we present a case study of learners' perspectives and experiences in an online course…

  5. Developing Formal Object-oriented Requirements Specifications: A Model, Tool and Technique.

    Science.gov (United States)

    Jackson, Robert B.; And Others

    1995-01-01

    Presents a formal object-oriented specification model (OSS) for computer software system development that is supported by a tool that automatically generates a prototype from an object-oriented analysis model (OSA) instance, lets the user examine the prototype, and permits the user to refine the OSA model instance to generate a requirements…

  6. COORDINATION IN MULTILEVEL NETWORK-CENTRIC CONTROL SYSTEMS OF REGIONAL SECURITY: APPROACH AND FORMAL MODEL

    Directory of Open Access Journals (Sweden)

    A. V. Masloboev

    2015-01-01

    Full Text Available The paper deals with development of methods and tools for mathematical and computer modeling of the multilevel network-centric control systems of regional security. This research is carried out under development strategy implementation of the Arctic zone of the Russian Federation and national safeguarding for the period before 2020 in the Murmansk region territory. Creation of unified interdepartmental multilevel computer-aided system is proposed intended for decision-making information support and socio-economic security monitoring of the Arctic regions of Russia. The distinctive features of the investigated system class are openness, self-organization, decentralization of management functions and decision-making, weak hierarchy in the decision-making circuit and goal generation capability inside itself. Research techniques include functional-target approach, mathematical apparatus of multilevel hierarchical system theory and principles of network-centric control of distributed systems with pro-active components and variable structure. The work considers network-centric management local decisions coordination problem-solving within the multilevel distributed systems intended for information support of regional security. The coordination problem-solving approach and problem formalization in the multilevel network-centric control systems of regional security have been proposed based on developed multilevel recurrent hierarchical model of regional socio-economic system complex security. The model provides coordination of regional security indexes, optimized by the different elements of multilevel control systems, subject to decentralized decision-making. The model specificity consists in application of functional-target technology and mathematical apparatus of multilevel hierarchical system theory for coordination procedures implementation of the network-centric management local decisions. The work-out and research results can find further

  7. A Polyadic pi-Calculus Approach for the Formal Specification of UML-RT

    Directory of Open Access Journals (Sweden)

    J. M. Bezerra

    2009-01-01

    Full Text Available UML-RT is a UML real-time profile that allows modeling event-driven and distributed systems; however it is not a formal specification language. This paper proposes a formal approach for UML-RT through a mapping of the UML-RT communicating elements into the -calculus (or pi-calculus process algebra. The formal approach both captures the intended behavior of the system being modeled and provides a rigorous and nonambiguous system description. Our proposal differentiates from other research work because we map UML-RT to -calculus, and we allow the mapping of dynamic reconfiguration of UML-RT unwired ports. We illustrate the usage and applicability of the mapping through three examples. The first example focuses on explaining the mapping; the second one aims to demonstrate the use of the -calculus definitions to verify system requirements; the third case is an example of mobile processes called Handover protocol.

  8. Analysis of Formal Methods for Specification of E-Commerce Applications

    Directory of Open Access Journals (Sweden)

    Sadiq Ali Khan

    2016-01-01

    Full Text Available E-commerce based application characteristics portray elevated dynamics while incorporating decentralized nature. Extreme emphasis influencing structural design plus implementation, positions such applications highly appreciated. Significant research articles reveal that, applying formal methods addressing challenges incumbent with E-commerce based applications, contribute towards reliability and robustness obliging the system. Anticipating and designing sturdy e-process and concurrent implementation, allows application behavior extra strength against errors, frauds and hacking, minimizing program faults during application operations. Programmers find extreme difficulty guaranteeing correct processing under all circumstances, however, not impossible. Concealed flaws and errors, triggered only under unexpected and unanticipated scenarios, pilot subtle mistakes and appalling failures. Code authors utilize various formal methods for reducing these flaws. Mentioning prominent methods would include, ASM (Abstract State Machines, B-Method, z-Language, UML (Unified Modelling Language etc. This paper primarily focuses different formal methods applied while deliberating specification and verification techniques for cost effective.

  9. A Formal Methodology to Design and Deploy Dependable Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Alessandro Testa

    2016-12-01

    Full Text Available Wireless Sensor Networks (WSNs are being increasingly adopted in critical applications, where verifying the correct operation of sensor nodes is a major concern. Undesired events may undermine the mission of the WSNs. Hence, their effects need to be properly assessed before deployment, to obtain a good level of expected performance; and during the operation, in order to avoid dangerous unexpected results. In this paper, we propose a methodology that aims at assessing and improving the dependability level of WSNs by means of an event-based formal verification technique. The methodology includes a process to guide designers towards the realization of a dependable WSN and a tool (“ADVISES” to simplify its adoption. The tool is applicable to homogeneous WSNs with static routing topologies. It allows the automatic generation of formal specifications used to check correctness properties and evaluate dependability metrics at design time and at runtime for WSNs where an acceptable percentage of faults can be defined. During the runtime, we can check the behavior of the WSN accordingly to the results obtained at design time and we can detect sudden and unexpected failures, in order to trigger recovery procedures. The effectiveness of the methodology is shown in the context of two case studies, as proof-of-concept, aiming to illustrate how the tool is helpful to drive design choices and to check the correctness properties of the WSN at runtime. Although the method scales up to very large WSNs, the applicability of the methodology may be compromised by the state space explosion of the reasoning model, which must be faced by partitioning large topologies into sub-topologies.

  10. A Formal Methodology to Design and Deploy Dependable Wireless Sensor Networks.

    Science.gov (United States)

    Testa, Alessandro; Cinque, Marcello; Coronato, Antonio; Augusto, Juan Carlos

    2016-12-23

    Wireless Sensor Networks (WSNs) are being increasingly adopted in critical applications, where verifying the correct operation of sensor nodes is a major concern. Undesired events may undermine the mission of the WSNs. Hence, their effects need to be properly assessed before deployment, to obtain a good level of expected performance; and during the operation, in order to avoid dangerous unexpected results. In this paper, we propose a methodology that aims at assessing and improving the dependability level of WSNs by means of an event-based formal verification technique. The methodology includes a process to guide designers towards the realization of a dependable WSN and a tool ("ADVISES") to simplify its adoption. The tool is applicable to homogeneous WSNs with static routing topologies. It allows the automatic generation of formal specifications used to check correctness properties and evaluate dependability metrics at design time and at runtime for WSNs where an acceptable percentage of faults can be defined. During the runtime, we can check the behavior of the WSN accordingly to the results obtained at design time and we can detect sudden and unexpected failures, in order to trigger recovery procedures. The effectiveness of the methodology is shown in the context of two case studies, as proof-of-concept, aiming to illustrate how the tool is helpful to drive design choices and to check the correctness properties of the WSN at runtime. Although the method scales up to very large WSNs, the applicability of the methodology may be compromised by the state space explosion of the reasoning model, which must be faced by partitioning large topologies into sub-topologies.

  11. Exploring the dynamics of formal and informal networks in complex multi-team development projects

    DEFF Research Database (Denmark)

    Kratzer, Jan; Gemünden, Hans Georg; Lettl, Christopher

    The increasing number of complex multi-team projects and the scarcity of knowledge about how to run them successfully, create a need for systematic empirical studies. We attempt to lessen this empirical gap by examining the overlap and structure of formally ascribed design interfaces and informal...... communication networks overlap only marginally. Second, the structure of informal communication remains largely stable in the transition from the design to the integration phase. The third and most intriguing finding is that the weak overlap between formally ascribed design interfaces and the informal...

  12. Exploring the dynamics of formal and informal networks in complex multi-team development projects

    DEFF Research Database (Denmark)

    Kratzer, J.; Gemuenden, H. G.; Lettl, Christopher

    2007-01-01

    The increasing number of complex multi-team projects and the scarcity of knowledge about how to run them successfully, create a need for systematic empirical studies. We attempt to lessen this empirical gap by examining the overlap and structure of formally ascribed design interfaces and informal...... communication networks overlap only marginally. Second, the structure of informal communication remains largely stable in the transition from the design to the integration phase. The third and most intriguing finding is that the weak overlap between formally ascribed design interfaces and the informal...

  13. Specification and Validation of an Edge Router Discovery Protocol for Mobile Ad Hoc Networks

    DEFF Research Database (Denmark)

    Kristensen, Lars Michael; Jensen, Kurt

    2004-01-01

    core network in assigning network address prefixes to gateways in mobile ad-hoc networks. This paper focuses on how CP-nets and the CPN computer tools have been applied in the development of ERDP. A CPN model has been constructed that constitutes a formal executable specification of ERDP. Simulation...

  14. Computational network design from functional specifications

    KAUST Repository

    Peng, Chi Han

    2016-07-11

    Connectivity and layout of underlying networks largely determine agent behavior and usage in many environments. For example, transportation networks determine the flow of traffic in a neighborhood, whereas building floorplans determine the flow of people in a workspace. Designing such networks from scratch is challenging as even local network changes can have large global effects. We investigate how to computationally create networks starting from only high-level functional specifications. Such specifications can be in the form of network density, travel time versus network length, traffic type, destination location, etc. We propose an integer programming-based approach that guarantees that the resultant networks are valid by fulfilling all the specified hard constraints and that they score favorably in terms of the objective function. We evaluate our algorithm in two different design settings, street layout and floorplans to demonstrate that diverse networks can emerge purely from high-level functional specifications.

  15. Formal Specification and Verification of Total Order Broadcast through Destination Agreement Using Event-B

    OpenAIRE

    Arun Kumar Singh; Divakar Yadav

    2015-01-01

    A reliable broadcast is communication primitive used to develop fault tolerant distributed applications. It in due course delivers messages to all participating sites irrespective of their ordering. Total order broadcast impose restriction on message ordering and satisfies total order requirement. A clear specifications, rigorous validation and verification is key to obtain better design of dependable services in such applications. With the help of formal methods one can specify a...

  16. A method for building and evaluating formal specifications of object-oriented conceptual models of database systems

    NARCIS (Netherlands)

    Wieringa, Roelf J.

    1993-01-01

    This report describes a method called MCM (Method for Conceptual Modeling) for building and evaluating formal specifications of object-oriented models of database system behavior. An important aim of MCM is to bridge the gap between formal specification and informal understanding. Building a MCM

  17. Specifics of Formal and Legal Issues in Processes of Revitalizing Post-Industrial Buildings

    Science.gov (United States)

    Kochański, Paweł

    2016-12-01

    The article deals with issues from the initial phase of the investment process connected with revitalizing postindustrial buildings: planning and programming investments in the functional and financial scope, as well as designing. The described formal and legal aspects are the result of a study of a few projects concerning the adaptation of buildings to serving a new function in Zielona Góra and Żaganie. The conclusions drawn from an individual view into each of the described problems are no different than when designing new buildings. It is not until we look into the whole preparation and design process, and gathering all experiences from the formal-legal sphere, that allows us to notice that, in the case of revitalizing postindustrial buildings and their adaptation to serve modern-day functions, a multifaceted but also specific approach is required.

  18. Specifics of Formal and Legal Issues in Processes of Revitalizing Post-Industrial Buildings

    Directory of Open Access Journals (Sweden)

    Kochański Paweł

    2016-12-01

    Full Text Available The article deals with issues from the initial phase of the investment process connected with revitalizing postindustrial buildings: planning and programming investments in the functional and financial scope, as well as designing. The described formal and legal aspects are the result of a study of a few projects concerning the adaptation of buildings to serving a new function in Zielona Góra and Żaganie. The conclusions drawn from an individual view into each of the described problems are no different than when designing new buildings. It is not until we look into the whole preparation and design process, and gathering all experiences from the formal-legal sphere, that allows us to notice that, in the case of revitalizing postindustrial buildings and their adaptation to serve modern-day functions, a multifaceted but also specific approach is required.

  19. Automated Mapping of UML Activity Diagrams to Formal Specifications for Supporting Containment Checking

    Directory of Open Access Journals (Sweden)

    Faiz UL Muram

    2014-04-01

    Full Text Available Business analysts and domain experts are often sketching the behaviors of a software system using high-level models that are technology- and platform-independent. The developers will refine and enrich these high-level models with technical details. As a consequence, the refined models can deviate from the original models over time, especially when the two kinds of models evolve independently. In this context, we focus on behavior models; that is, we aim to ensure that the refined, low-level behavior models conform to the corresponding high-level behavior models. Based on existing formal verification techniques, we propose containment checking as a means to assess whether the system's behaviors described by the low-level models satisfy what has been specified in the high-level counterparts. One of the major obstacles is how to lessen the burden of creating formal specifications of the behavior models as well as consistency constraints, which is a tedious and error-prone task when done manually. Our approach presented in this paper aims at alleviating the aforementioned challenges by considering the behavior models as verification inputs and devising automated mappings of behavior models onto formal properties and descriptions that can be directly used by model checkers. We discuss various challenges in our approach and show the applicability of our approach in illustrative scenarios.

  20. SOCIAL NETWORK ANALYSIS FOR THE MEASUREMENT OF FORMAL AND INFORMAL STRUCTURES

    Directory of Open Access Journals (Sweden)

    Siomara Maria Pierangeli Pascotto,

    2013-03-01

    Full Text Available A discussion around the application of the social network analysis methodology has being helped to understand the social dynamic operation of organizations, including governments, which are subject to different management structures that have a high degree of functional hierarchy. This study was developed in a Federal School Institution in Sao Paulo State – Brazil searching to identify the link developed between Institution administrative support staff members and their social networks. The research objective is to establish a comparison between the link data facts with Social Networks Theories which says that the more ties (contacts exist in an informal group, the more the network promotes an open environment for exchanging knowledge and information. The research looked forward to identify how do the social networks are developed, how common objectives and subjects turns people closely connected, how do the focal points and main contacts emerge from this community and what are their influences in the rest of the group. It was applied social network measurement methodologies, combined with qualitative instrument analysis. As a conclusion, was found that the informal structure has influence over the formal structure providing an environment for exchanging knowledge and information, pointing out that some characters are actually responsible for the dynamic of networks, occupying driver and strategic position that gives them recognition as such by the other agents in the net.

  1. Theory of electromagnetic transmission structures. I - Relativistic foundation and network formalisms

    Science.gov (United States)

    Gabriel, G. J.

    1980-01-01

    A new theorem on a class of four-dimensional skew-symmetric tensors is demonstrated. Coupled with the relativistic covariant form of Maxwell's equations, this theorem consolidates the classifications of guided waves by combining the three types - TE, TM, TEM - under a uniform condition applied to the generating four-potential which is Lorentz invariant. Each type corresponds to a potential of which a pair of the four components vanishes in a particular frame. Through appropriate normalization conditions, the resulting time-domain equations for the field amplitudes are readily reduced to modified telegraphist equations, which in turn lead to distributed network representations for each of the three types. The ambiguity of distributed network formalisms in general is elucidated and the concept of network parameter densities such as traditionally employed in TEM transmission line theory is questioned.

  2. Formal Specification and Analysis of Danish and Irish Ballot Counting Algorithms

    DEFF Research Database (Denmark)

    Cochran, Dermot

    There are many valid arguments both for and against the use of electronic voting in real world elections. My thesis is that a verification-centric software implementation of a particular algorithm for counting of ballots can be proven correct or shown to be incorrect by an appropriate combination...... of formal specification, static analysis and testing. Hand counting of paper ballots might no longer be necessary, if we can assume that the digital ballots are valid, not tampered with and a true representation of the paper ballots etc. As a case study, the Danish and Irish voting schemes are analyzed...

  3. Linking Simulation with Formal Verification and Modeling of Wireless Sensor Network in TLA+

    Science.gov (United States)

    Martyna, Jerzy

    In this paper, we present the results of the simulation of a wireless sensor network based on the flooding technique and SPIN protocols. The wireless sensor network was specified and verified by means of the TLA+ specification language [1]. For a model of wireless sensor network built this way simulation was carried with the help of specially constructed software tools. The obtained results allow us to predict the behaviour of the wireless sensor network in various topologies and spatial densities. Visualization of the output data enable precise examination of some phenomenas in wireless sensor networks, such as a hidden terminal, etc.

  4. Balancing creativity and time efficiency in multi-team R&D projects: The alignment of formal and informal networks

    DEFF Research Database (Denmark)

    Kratzer, Jan; Gemuenden, Hans Georg; Lettl, Christopher

    2008-01-01

    The business world is denoted by an increasing number of multi-team R&D projects, however, managerial knowledge about how to run them successfully is scarce. The present study attempts to shed light at this kind of projects by investigating the alignment of formal and informal network structures...... interfaces and informal communication networks overlap only marginally because the informal communication networks are characterized by many more linkages. Second, the weak overlap between formally ascribed design interfaces and the informal communication networks is inversely U-shaped associated...

  5. Coexistence or Operational Necessity: The Role of Formally Structured Organisation and Informal Networks during Deployments

    Science.gov (United States)

    2011-06-01

    organisations decide to outsource services and labour . Possibly the most well known reason for outsourcing anything regarded as not a core organisational...competency, is to access cheaper labour and cut costs (Eliot 1998). Although the interviews did not probe this issue and the data does not provide specific...is followed up by formal means • Degree of risks • Relies on personal judgment • Lack of auditability of informal Coexistence or

  6. Application of different entropy formalisms in a neural network for novel word learning

    Science.gov (United States)

    Khordad, R.; Rastegar Sedehi, H. R.

    2015-12-01

    In this paper novel word learning in adults is studied. For this goal, four entropy formalisms are employed to include some degree of non-locality in a neural network. The entropy formalisms are Tsallis, Landsberg-Vedral, Kaniadakis, and Abe entropies. First, we have analytically obtained non-extensive cost functions for the all entropies. Then, we have used a generalization of the gradient descent dynamics as a learning rule in a simple perceptron. The Langevin equations are numerically solved and the error function (learning curve) is obtained versus time for different values of the parameters. The influence of index q and number of neuron N on learning is investigated for the all entropies. It is found that learning is a decreasing function of time for the all entropies. The rate of learning for the Landsberg-Vedral entropy is slower than other entropies. The variation of learning with time for the Landsberg-Vedral entropy is not appreciable when the number of neurons increases. It is said that entropy formalism can be used as a means for studying the learning.

  7. Neural Schematics as a unified formal graphical representation of large-scale Neural Network Structures

    Directory of Open Access Journals (Sweden)

    Matthias eEhrlich

    2013-10-01

    Full Text Available One of the major outcomes of neuroscientific research are models of Neural Network Structures. Descriptions of these models usually consist of a non-standardized mixture of text, figures, and other means of visual information communication in print media. However, as neuroscience is an interdisciplinary domain by nature, a standardized way of consistently representing models of Neural Network Structures is required. While generic descriptions of such models in textual form have recently been developed, a formalized way of schematically expressing them does not exist to date. Hence, in this paper we present Neural Schematics as a concept inspired by similar approaches from other disciplines for a generic two dimensional representation of said structures. After introducing Neural Network Structures in general, a set of current visualizations of models of Neural Network Structures is reviewed and analyzed for what information they convey and how their elements are rendered. This analysis then allows for the definition of general items and symbols to consistently represent these models as Neural Schematics on a two dimensional plane. We will illustrate the possibilities an agreed upon standard can yield on sampled diagrams transformed into Neural Schematics and an example application for the design and modeling of large-scale Neural Network Structures.

  8. Reaction-diffusion-like formalism for plastic neural networks reveals dissipative solitons at criticality

    Science.gov (United States)

    Grytskyy, Dmytro; Diesmann, Markus; Helias, Moritz

    2016-06-01

    Self-organized structures in networks with spike-timing dependent synaptic plasticity (STDP) are likely to play a central role for information processing in the brain. In the present study we derive a reaction-diffusion-like formalism for plastic feed-forward networks of nonlinear rate-based model neurons with a correlation sensitive learning rule inspired by and being qualitatively similar to STDP. After obtaining equations that describe the change of the spatial shape of the signal from layer to layer, we derive a criterion for the nonlinearity necessary to obtain stable dynamics for arbitrary input. We classify the possible scenarios of signal evolution and find that close to the transition to the unstable regime metastable solutions appear. The form of these dissipative solitons is determined analytically and the evolution and interaction of several such coexistent objects is investigated.

  9. VSAT networks in India - Specifications and applications

    Science.gov (United States)

    Ghose, A. K.

    1993-08-01

    This paper describes briefly the evolution of VSATs in India, including the existing and proposed networks and their applications. The salient specifications of the various types of VSATs are described. Some of the VSATs under advanced stages of development as well as those to be used in proposed networks due for implementation soon are also covered.

  10. Toward a formalized account of attitudes: The Causal Attitude Network (CAN) model.

    Science.gov (United States)

    Dalege, Jonas; Borsboom, Denny; van Harreveld, Frenk; van den Berg, Helma; Conner, Mark; van der Maas, Han L J

    2016-01-01

    This article introduces the Causal Attitude Network (CAN) model, which conceptualizes attitudes as networks consisting of evaluative reactions and interactions between these reactions. Relevant evaluative reactions include beliefs, feelings, and behaviors toward the attitude object. Interactions between these reactions arise through direct causal influences (e.g., the belief that snakes are dangerous causes fear of snakes) and mechanisms that support evaluative consistency between related contents of evaluative reactions (e.g., people tend to align their belief that snakes are useful with their belief that snakes help maintain ecological balance). In the CAN model, the structure of attitude networks conforms to a small-world structure: evaluative reactions that are similar to each other form tight clusters, which are connected by a sparser set of "shortcuts" between them. We argue that the CAN model provides a realistic formalized measurement model of attitudes and therefore fills a crucial gap in the attitude literature. Furthermore, the CAN model provides testable predictions for the structure of attitudes and how they develop, remain stable, and change over time. Attitude strength is conceptualized in terms of the connectivity of attitude networks and we show that this provides a parsimonious account of the differences between strong and weak attitudes. We discuss the CAN model in relation to possible extensions, implication for the assessment of attitudes, and possibilities for further study. (c) 2015 APA, all rights reserved).

  11. Protege Career Aspirations: The Influence of Formal E-Mentor Networks and Family-Based Role Models

    Science.gov (United States)

    DiRenzo, Marco S.; Weer, Christy H.; Linnehan, Frank

    2013-01-01

    Using longitudinal data from a nine-month e-mentoring program, we analyzed the influence of formal e-mentor networks and family-based role models on increases in both psychosocial and career-related outcomes. Findings indicate that e-mentor network relationship quality positively influenced general- and career-based self-efficacy which, in turn,…

  12. Formal modeling and analysis of ER-α associated Biological Regulatory Network in breast cancer

    Directory of Open Access Journals (Sweden)

    Samra Khalid

    2016-10-01

    Full Text Available Background Breast cancer (BC is one of the leading cause of death among females worldwide. The increasing incidence of BC is due to various genetic and environmental changes which lead to the disruption of cellular signaling network(s. It is a complex disease in which several interlinking signaling cascades play a crucial role in establishing a complex regulatory network. The logical modeling approach of René Thomas has been applied to analyze the behavior of estrogen receptor-alpha (ER-α associated Biological Regulatory Network (BRN for a small part of complex events that leads to BC metastasis. Methods A discrete model was constructed using the kinetic logic formalism and its set of logical parameters were obtained using the model checking technique implemented in the SMBioNet software which is consistent with biological observations. The discrete model was further enriched with continuous dynamics by converting it into an equivalent Petri Net (PN to analyze the logical parameters of the involved entities. Results In-silico based discrete and continuous modeling of ER-α associated signaling network involved in BC provides information about behaviors and gene-gene interaction in detail. The dynamics of discrete model revealed, imperative behaviors represented as cyclic paths and trajectories leading to pathogenic states such as metastasis. Results suggest that the increased expressions of receptors ER-α, IGF-1R and EGFR slow down the activity of tumor suppressor genes (TSGs such as BRCA1, p53 and Mdm2 which can lead to metastasis. Therefore, IGF-1R and EGFR are considered as important inhibitory targets to control the metastasis in BC. Conclusion The in-silico approaches allow us to increase our understanding of the functional properties of living organisms. It opens new avenues of investigations of multiple inhibitory targets (ER-α, IGF-1R and EGFR for wet lab experiments as well as provided valuable insights in the treatment of cancers

  13. Analysis of formal methods for specification of e-Commerce applications

    National Research Council Canada - National Science Library

    Khan, Sadiq Ali; Jamshed, Huma

    2016-01-01

    .... Significant research articles reveal that, applying formal methods addressing challenges incumbent with E-commerce based applications, contribute towards reliability and robustness obliging the system...

  14. Clustering context-specific gene regulatory networks.

    Science.gov (United States)

    Ramesh, Archana; Trevino, Robert; VON Hoff, Daniel D; Kim, Seungchan

    2010-01-01

    Gene regulatory networks (GRNs) learned from high throughput genomic data are often hard to visualize due to the large number of nodes and edges involved, rendering them difficult to appreciate. This becomes an important issue when modular structures are inherent in the inferred networks, such as in the recently proposed context-specific GRNs.(12) In this study, we investigate the application of graph clustering techniques to discern modularity in such highly complex graphs, focusing on context-specific GRNs. Identified modules are then associated with a subset of samples and the key pathways enriched in the module. Specifically, we study the use of Markov clustering and spectral clustering on cancer datasets to yield evidence on the possible association amongst different tumor types. Two sets of gene expression profiling data were analyzed to reveal context-specificity as well as modularity in genomic regulations.

  15. Understanding the Construction of Personal Learning Networks to Support Non-Formal Workplace Learning of Training Professionals

    Science.gov (United States)

    Manning, Christin

    2013-01-01

    Workers in the 21st century workplace are faced with rapid and constant developments that place a heavy demand on them to continually learn beyond what the Human Resources and Training groups can meet. As a consequence, professionals must rely on non-formal learning approaches through the development of a personal learning network to keep…

  16. Modality-specificity of selective attention networks

    Directory of Open Access Journals (Sweden)

    Hannah Jamieson Stewart

    2015-11-01

    Full Text Available Objective: To establish the modality specificity and generality of selective attention networks. Method: Forty-eight young adults completed a battery of four auditory and visual selective attention tests based upon the Attention Network framework: the visual and auditory Attention Network Tests (vANT, aANT, the Test of Everyday Attention (TEA, and the Test of Attention in Listening (TAiL. These provided independent measures for auditory and visual alerting, orienting, and conflict resolution networks. The measures were subjected to an exploratory factor analysis to assess underlying attention constructs. Results: The analysis yielded a four-component solution. The first component comprised of a range of measures from the TEA and was labeled ‘general attention’. The third component was labeled ‘auditory attention’, as it only contained measures from the TAiL using pitch as the attended stimulus feature. The second and fourth components were labeled as ‘spatial orienting’ and ‘spatial conflict’, respectively – they were comprised of orienting and conflict resolution measures from the vANT, aANT and TAiL attend-location task – all tasks based upon spatial judgments (e.g., the direction of a target arrow or sound location. Conclusions: These results do not support our a-priori hypothesis that attention networks are either modality specific or supramodal. Auditory attention separated into selectively attending to spatial and non-spatial features, with the auditory spatial attention loading onto the same factor as visual spatial attention, suggesting spatial attention is supramodal. However, since our study did not include a non-spatial measure of visual attention, further research will be required to ascertain whether non-spatial attention is modality-specific.

  17. Formal Proof of the Dependable Bypassing Routing Algorithm Suitable for Adaptive Networks on Chip QnoC Architecture

    Directory of Open Access Journals (Sweden)

    Hayat Daoud

    2017-02-01

    Full Text Available Approaches for the design of fault tolerant Network-on-Chip (NoC for use in System-on-Chip (SoC reconfigurable technology using Field-Programmable Gate Array (FPGA technology are challenging, especially in Multiprocessor System-on-Chip (MPSoC design. To achieve this, the use of rigorous formal approaches, based on incremental design and proof theory, has become an essential step in the validation process. The Event-B method is a promising formal approach that can be used to develop, model and prove accurately SoC and MPSoC architectures. This paper proposes a formal verification approach for NoC architecture including the dependability constraints relating to the choice of the path routing of data packets and the strategy imposed for diversion when faulty routers are detected. The formalization process is incremental and validated by correct-by-construction development of the NoC architecture. Using the concepts of graph colouring and B-event formalism, the results obtained have demonstrated its efficiency for determining the bugs, and a solution to ensure a fast and reliable operation of the network when compared to existing similar methods.

  18. Split, Send, Reassemble: A Formal Specification of a CAN Bus Protocol Stack

    OpenAIRE

    van Glabbeek, Rob; Höfner, Peter

    2017-01-01

    We present a formal model for a fragmentation and a reassembly protocol running on top of the standardised CAN bus, which is widely used in automotive and aerospace applications. Although the CAN bus comes with an in-built mechanism for prioritisation, we argue that this is not sufficient and provide another protocol to overcome this shortcoming.

  19. Linkages between informal and formal caregivers in home-care networks of frail older adults

    NARCIS (Netherlands)

    Jacobs, M.T.; van Tilburg, T.G.; Groenewegen, P.; Broese Van Groenou, M.I.

    2016-01-01

    In ageing societies, policy makers aim for more contact between informal and formal care-givers as it may enhance the quality of care. So far, the linkage between formal and informal care-givers is generally studied from a one-sided or a single dyadic perspective, without taking into account that

  20. Formal Specification and Verification of Fully Asynchronous Implementations of the Data Encryption Standard

    Directory of Open Access Journals (Sweden)

    Wendelin Serwe

    2015-11-01

    Full Text Available This paper presents two formal models of the Data Encryption Standard (DES, a first using the international standard LOTOS, and a second using the more recent process calculus LNT. Both models encode the DES in the style of asynchronous circuits, i.e., the data-flow blocks of the DES algorithm are represented by processes communicating via rendezvous. To ensure correctness of the models, several techniques have been applied, including model checking, equivalence checking, and comparing the results produced by a prototype automatically generated from the formal model with those of existing implementations of the DES. The complete code of the models is provided as appendices and also available on the website of the CADP verification toolbox.

  1. Formal semantic specifications as implementation blueprints for real-time programming languages

    Science.gov (United States)

    Feyock, S.

    1981-01-01

    Formal definitions of language and system semantics provide highly desirable checks on the correctness of implementations of programming languages and their runtime support systems. If these definitions can give concrete guidance to the implementor, major increases in implementation accuracy and decreases in implementation effort can be achieved. It is shown that of the wide variety of available methods the Hgraph (hypergraph) definitional technique (Pratt, 1975), is best suited to serve as such an implementation blueprint. A discussion and example of the Hgraph technique is presented, as well as an overview of the growing body of implementation experience of real-time languages based on Hgraph semantic definitions.

  2. Developing a Formal Specification for the Mission Systems of a Maritime Surveillance Aircraft

    DEFF Research Database (Denmark)

    Petrucci, Laure; Billington, Jonathan; Kristensen, Lars Michael

    2003-01-01

    The mission system of an aircraft is a complex real-time distributed system consisting of a mission control computer, different kinds of devices interconnected by a number of serial data buses. The complexity and real-time requirements of mission systems have motivated research into the application...... system with Coloured Petri Nets and analysed the model using state spaces. Here, we describe how this model was refined and modified to obtain a Coloured Petri Net model for the AP-3C Orion maritime surveillance aircraft....... of formal techniques to investigate and predict the effects of upgrades on mission system behaviour. This paper reports on a joint research project between the University of South Australia and Australia's Defence Science and Technology Organisation. In previous work we modelled a generic avionics mission...

  3. Combining the GW formalism with the polarizable continuum model: A state-specific non-equilibrium approach

    Energy Technology Data Exchange (ETDEWEB)

    Duchemin, Ivan, E-mail: ivan.duchemin@cea.fr [INAC, SP2M/L-Sim, CEA/UJF Cedex 09, 38054 Grenoble (France); Jacquemin, Denis [Laboratoire CEISAM - UMR CNR 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3 (France); Institut Universitaire de France, 1 rue Descartes, 75005 Paris Cedex 5 (France); Blase, Xavier [CNRS, Inst. NÉEL, F-38000 Grenoble (France); Univ. Grenoble Alpes, Inst. NÉEL, F-38000 Grenoble (France)

    2016-04-28

    We have implemented the polarizable continuum model within the framework of the many-body Green’s function GW formalism for the calculation of electron addition and removal energies in solution. The present formalism includes both ground-state and non-equilibrium polarization effects. In addition, the polarization energies are state-specific, allowing to obtain the bath-induced renormalisation energy of all occupied and virtual energy levels. Our implementation is validated by comparisons with ΔSCF calculations performed at both the density functional theory and coupled-cluster single and double levels for solvated nucleobases. The present study opens the way to GW and Bethe-Salpeter calculations in disordered condensed phases of interest in organic optoelectronics, wet chemistry, and biology.

  4. Toward a formalized account of attitudes: The Causal Attitude Network (CAN) Model

    NARCIS (Netherlands)

    Dalege, J.; Borsboom, D.; Harreveld, F. van; Berg, H. van den; Conner, M.; Maas, H.L.J. van der

    2016-01-01

    This article introduces the Causal Attitude Network (CAN) model, which conceptualizes attitudes as networks consisting of evaluative reactions and interactions between these reactions. Relevant evaluative reactions include beliefs, feelings, and behaviors toward the attitude object. Interactions

  5. Toward a formalized account of attitudes: the Causal Attitude Network (CAN) model

    NARCIS (Netherlands)

    Dalege, J.; Borsboom, D.; van Harreveld, F.; van den Berg, H.; Conner, M.; van der Maas, H.L.J.

    2016-01-01

    This article introduces the Causal Attitude Network (CAN) model, which conceptualizes attitudes as networks consisting of evaluative reactions and interactions between these reactions. Relevant evaluative reactions include beliefs, feelings, and behaviors toward the attitude object. Interactions

  6. A Formal Verification Model for Performance Analysis of Reinforcement Learning Algorithms Applied t o Dynamic Networks

    OpenAIRE

    Shrirang Ambaji KULKARNI; Raghavendra G . RAO

    2017-01-01

    Routing data packets in a dynamic network is a difficult and important problem in computer networks. As the network is dynamic, it is subject to frequent topology changes and is subject to variable link costs due to congestion and bandwidth. Existing shortest path algorithms fail to converge to better solutions under dynamic network conditions. Reinforcement learning algorithms posses better adaptation techniques in dynamic environments. In this paper we apply model based Q-Routing technique ...

  7. Formal Methods Specification and Verification Guidebook for Software and Computer Systems. Volume 1; Planning and Technology Insertion

    Science.gov (United States)

    1995-01-01

    The Formal Methods Specification and Verification Guidebook for Software and Computer Systems describes a set of techniques called Formal Methods (FM), and outlines their use in the specification and verification of computer systems and software. Development of increasingly complex systems has created a need for improved specification and verification techniques. NASA's Safety and Mission Quality Office has supported the investigation of techniques such as FM, which are now an accepted method for enhancing the quality of aerospace applications. The guidebook provides information for managers and practitioners who are interested in integrating FM into an existing systems development process. Information includes technical and administrative considerations that must be addressed when establishing the use of FM on a specific project. The guidebook is intended to aid decision makers in the successful application of FM to the development of high-quality systems at reasonable cost. This is the first volume of a planned two-volume set. The current volume focuses on administrative and planning considerations for the successful application of FM.

  8. The Importance of Being an Insider: How Networks Influence the Small Firm's Engagement with Formal Training

    Science.gov (United States)

    Bishop, Dan

    2011-01-01

    Purpose: The purpose of this paper is to examine the ways in which the small firm's external relationships influence its approach to formal training and training providers. Design/methodology/approach: A qualitative approach was adopted, involving semi-structured interviews with senior managers, in 25 small firms in South Wales. These interviews…

  9. Job advertisements and personal networks: two specific channels in the Spanish labour market

    OpenAIRE

    Rieucau, Géraldine

    2008-01-01

    Drawing on an employee labour survey, this article explores job-finding channels in the Spanish labour market and points out that social networks are the most important way of finding a job. It focuses on a comparison between an informal channel (relatives and close personal relationships) and a formal one (job advertisements), and demonstrates that these channels serve two specific segments in the labour market. The most important results concern workers' profiles: advertisements are highly ...

  10. Identifying condition-specific modules by clustering multiple networks.

    Science.gov (United States)

    Ma, Xiaoke; Sun, Penggang; Qin, Guimin

    2017-10-10

    Condition-specific modules in multiple networks must be determined to reveal the underlying molecular mechanisms of diseases. Current algorithms exhibit limitations such as low accuracy and high sensitivity to the number of networks because these algorithms discover condition-specific modules in multiple networks by separating specificity and modularity of modules. To overcome these limitations, we characterize condition-specific module as a group of genes whose connectivity is strong in the corresponding network and weak in other networks; this strategy can accurately depict the topological structure of condition-specific modules. We then transform the condition-specific module discovery problem into a clustering problem in multiple networks. We develop an efficient heuristic algorithm for the Specific Modules in Multiple Networks (SMMN), which discovers the condition-specific modules by considering multiple networks. By using the artificial networks, we demonstrate that SMMN outperforms state-of-the-art methods. In breast cancer networks, stage-specific modules discovered by SMMN are more discriminative in predicting cancer stages than those obtained by other techniques. In pan-cancer networks, cancer-specific modules are more likely to associate with survival time of patients, which is critical for cancer therapy.

  11. A social network model of supply chain management in formal and informal inter-firm engagement

    Directory of Open Access Journals (Sweden)

    Lokhman Hakim Osman

    2015-12-01

    Full Text Available Background: This research looks into the different effects of firms' network structural positions in an upstream supply network upon the firms' level of relational capital outcomes.  Previous research has largely focus on the context of decentralized network structure.  However, the supply network is a centralized network because of the existence of the focal firm.  The existence of the focal firm may influence the impact of relational capital outcomes.  Methods: The objective of this research is to determine the type of network structural positions required to obtain reasonable relational capital outcome in upstream supply network.  Results and conclusions: This study found that, network structural positions i.e. betweeness centrality contributed to firms' level of relational capital influence. In conclusion, firms, embedded in upstream supply network benefits differently in terms of relational capital through different degree of embeddedness.  Firms' resources should be re-aligned to match the benefits with the different network structural positions.

  12. Autonomic networking-on-chip bio-inspired specification, development, and verification

    CERN Document Server

    Cong-Vinh, Phan

    2011-01-01

    Despite the growing mainstream importance and unique advantages of autonomic networking-on-chip (ANoC) technology, Autonomic Networking-On-Chip: Bio-Inspired Specification, Development, and Verification is among the first books to evaluate research results on formalizing this emerging NoC paradigm, which was inspired by the human nervous system. The FIRST Book to Assess Research Results, Opportunities, & Trends in ""BioChipNets"" The third book in the Embedded Multi-Core Systems series from CRC Press, this is an advanced technical guide and reference composed of contributions from prominent re

  13. Uncovering the Hidden Structure of Platoons: Formal and Emergent Leaders’ Perceptions of Organizational Networks

    Science.gov (United States)

    2008-12-01

    tested by calculating the Quadratic Assignment Procedure ( QAP ) correlation between leadership ratings and advice network ties as well as the QAP ...correlation between leadership ratings and friendship network ties, in each of the three infantry platoons. QAP correlations (Hubert & Schultz, 1976...inflated estimates of statistical significance if ordinary least squares (OLS) regression is used. The QAP technique is designed to provide unbiased

  14. A Formal Verification Model for Performance Analysis of Reinforcement Learning Algorithms Applied t o Dynamic Networks

    Directory of Open Access Journals (Sweden)

    Shrirang Ambaji KULKARNI

    2017-04-01

    Full Text Available Routing data packets in a dynamic network is a difficult and important problem in computer networks. As the network is dynamic, it is subject to frequent topology changes and is subject to variable link costs due to congestion and bandwidth. Existing shortest path algorithms fail to converge to better solutions under dynamic network conditions. Reinforcement learning algorithms posses better adaptation techniques in dynamic environments. In this paper we apply model based Q-Routing technique for routing in dynamic network. To analyze the correctness of Q-Routing algorithms mathematically, we provide a proof and also implement a SPIN based verification model. We also perform simulation based analysis of Q-Routing for given metrics.

  15. The connection-set algebra--a novel formalism for the representation of connectivity structure in neuronal network models.

    Science.gov (United States)

    Djurfeldt, Mikael

    2012-07-01

    The connection-set algebra (CSA) is a novel and general formalism for the description of connectivity in neuronal network models, from small-scale to large-scale structure. The algebra provides operators to form more complex sets of connections from simpler ones and also provides parameterization of such sets. CSA is expressive enough to describe a wide range of connection patterns, including multiple types of random and/or geometrically dependent connectivity, and can serve as a concise notation for network structure in scientific writing. CSA implementations allow for scalable and efficient representation of connectivity in parallel neuronal network simulators and could even allow for avoiding explicit representation of connections in computer memory. The expressiveness of CSA makes prototyping of network structure easy. A C+ + version of the algebra has been implemented and used in a large-scale neuronal network simulation (Djurfeldt et al., IBM J Res Dev 52(1/2):31-42, 2008b) and an implementation in Python has been publicly released.

  16. Formal Methods for Information Protection Technology. Task 1: Formal Grammar-Based Approach and Tool for Simulation Attacks against Computer Network. Part 1

    National Research Council Canada - National Science Library

    Karsayev, O

    2004-01-01

    .... Integrity, confidentiality and availability of the network resources must be assured. To detect and suppress different types of computer unauthorized intrusions, modern network security systems (NSS...

  17. The reconstruction and analysis of tissue specific human metabolic networks.

    Science.gov (United States)

    Hao, Tong; Ma, Hong-Wu; Zhao, Xue-Ming; Goryanin, Igor

    2012-02-01

    Human tissues have distinct biological functions. Many proteins/enzymes are known to be expressed only in specific tissues and therefore the metabolic networks in various tissues are different. Though high quality global human metabolic networks and metabolic networks for certain tissues such as liver have already been studied, a systematic study of tissue specific metabolic networks for all main tissues is still missing. In this work, we reconstruct the tissue specific metabolic networks for 15 main tissues in human based on the previously reconstructed Edinburgh Human Metabolic Network (EHMN). The tissue information is firstly obtained for enzymes from Human Protein Reference Database (HPRD) and UniprotKB databases and transfers to reactions through the enzyme-reaction relationships in EHMN. As our knowledge of tissue distribution of proteins is still very limited, we replenish the tissue information of the metabolic network based on network connectivity analysis and thorough examination of the literature. Finally, about 80% of proteins and reactions in EHMN are determined to be in at least one of the 15 tissues. To validate the quality of the tissue specific network, the brain specific metabolic network is taken as an example for functional module analysis and the results reveal that the function of the brain metabolic network is closely related with its function as the centre of the human nervous system. The tissue specific human metabolic networks are available at .

  18. Formal Analysis of Privacy Requirements Specifications for Multi-Tier Applications

    Science.gov (United States)

    2013-07-30

    Platform for Privacy Preferences ( P3P ), a website XML- based policy language aimed to align web browser user privacy preferences with website...practices [10]. While P3P has experienced wide spread adoption, the P3P is a declarative language, and website operators often make mistakes in how they...Computers & Security, 30(4): 178–193. 2011. [10] L. Cranor et al., “Platform for Privacy Preferences ( P3P ) Specification,” W3C Working Group Note

  19. A Formal Method for Verification and Validation of Neural Network High Assurance Systems Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Our proposed innovation is to develop neural network (NN) rule extraction technology to a level where it can be incorporated into a software tool, we are calling...

  20. Deploying Crowd-Sourced Formal Verification Systems in a DoD Network

    Science.gov (United States)

    2013-09-01

    Kerckhoffs, 1883). The network security concept also includes practical applications such as IPsec technology, firewalls and authentication...Tanenbaum, 2003). Some of these applications will be used as system security measures in the experimentation sections of this thesis. IPsec (IP Security...Being originally a communications security measure, IPsec was created to fill the security gap throughout Internet. The argument at the first point

  1. How the Formal and Informal Social Networks of Special Education Teachers Shape Their Practice

    Science.gov (United States)

    Wong, Amie

    2016-01-01

    Teacher collaboration has long been considered to be a vehicle for educational improvement. Meanwhile, some teachers find themselves disconnected and isolated from their colleagues, in part due to the roles they serve in schools. There is little research information on the social networks of special education teachers. This study is intended to…

  2. Formal assessment instrument for ensuring the security of NASA's networks, systems and software

    Science.gov (United States)

    Gilliam, D. P.; Powell, J. D.; Sherif, J.

    2002-01-01

    To address the problem of security for NASA's networks, systems and software, NASA has funded the Jet Propulsion Lab in conjunction with UC Davis to begin work on developing a software security assessment instrument for use in the software development and maintenance life cycle.

  3. Information and knowledge flows in product development of automotive industry – a comparison between formal and informal networks

    Directory of Open Access Journals (Sweden)

    Renelson Ribeiro Sampaio

    2013-03-01

    Full Text Available To maintain competitive advantage, companies must innovate. Thus, high quality, low cost and diversity of products became the starting condition for competitiveness. As a result, speed and flexibility in the design of new products are crucial, as these factors are related to the ability of companies to respond adequately to the pressures from the market. Innovation is usually related to the introduction of something new in a particular work process, which lead to new products or services. The ability for people to share information is then to be seen as a factor of strengthening of the work processes in order to contribute substantially to the company's competitive advantage in this new context. Considering these aspects, this paper seeks to map the processes of product development for an automobile company, analyzing and mapping the flow of information. The main contribution of this study is the critical analysis of social network established in a time of development of a project. This analysis provides an estimate of the level of diffusion of information and knowledge among team members, as well as the comparison between social networking and formal network mapped empirically defined a priori in the company's written procedures.

  4. COORDINATION IN MULTILEVEL NETWORK-CENTRIC CONTROL SYSTEMS OF REGIONAL SECURITY: APPROACH AND FORMAL MODEL

    OpenAIRE

    A. V. Masloboev; V. A. Putilov; A. V. Sioutine

    2015-01-01

    The paper deals with development of methods and tools for mathematical and computer modeling of the multilevel network-centric control systems of regional security. This research is carried out under development strategy implementation of the Arctic zone of the Russian Federation and national safeguarding for the period before 2020 in the Murmansk region territory. Creation of unified interdepartmental multilevel computer-aided system is proposed intended for decision-making information suppo...

  5. Identifying Anomalous Port-Specific Network Behavior

    Science.gov (United States)

    2010-05-01

    ANY KIND WITH RESPECT TO FREEDOM FROM PATENT, TRADEMARK , OR COPYRIGHT INFRINGEMENT. Use of any trademarks in this report is not intended in any way...to infringe on the rights of the trademark holder. Internal use. Permission to reproduce this document and to prepare derivative works from this...applications (registered or unregistered ). 5 | CMU/SEI-2010-TR-010 Port values play an important role in network flow monitoring. A flow record is an

  6. A Collaborative Diagonal Learning Network: The role of formal and informal professional development in elementary science reform

    Science.gov (United States)

    Cooke-Nieves, Natasha Anika

    Science education research has consistently shown that elementary teachers have a low self-efficacy and background knowledge to teach science. When they teach science, there is a lack of field experiences and inquiry-based instruction at the elementary level due to limited resources, both material and pedagogical. This study focused on an analysis of a professional development (PD) model designed by the author known as the Collaborative Diagonal Learning Network (CDLN). The purpose of this study was to examine elementary school teacher participants pedagogical content knowledge related to their experiences in a CDLN model. The CDLN model taught formal and informal instruction using a science coach and an informal educational institution. Another purpose for this research included a theoretical analysis of the CDLN model to see if its design enabled teachers to expand their resource knowledge of available science education materials. The four-month-long study used qualitative data obtained during an in-service professional development program facilitated by a science coach and educators from a large natural history museum. Using case study as the research design, four elementary school teachers were asked to evaluate the effectiveness of their science coach and museum educator workshop sessions. During the duration of this study, semi-structured individual/group interviews and open-ended pre/post PD questionnaires were used. Other data sources included researcher field notes from lesson observations, museum field trips, audio-recorded workshop sessions, email correspondence, and teacher-created artifacts. The data were analyzed using a constructivist grounded theory approach. Themes that emerged included increased self-efficacy; increased pedagogical content knowledge; increased knowledge of museum education resources and access; creation of a professional learning community; and increased knowledge of science notebooking. Implications for formal and informal

  7. A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method.

    Science.gov (United States)

    Luna, Augustin; Karac, Evrim I; Sunshine, Margot; Chang, Lucas; Nussinov, Ruth; Aladjem, Mirit I; Kohn, Kurt W

    2011-05-17

    The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation. A formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification. The work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://discover.nci.nih.gov/mim.

  8. A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method

    Science.gov (United States)

    2011-01-01

    Background The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation. Results A formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification. Conclusions The work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://discover.nci.nih.gov/mim. PMID:21586134

  9. Experiences with Formal Engineering: Model-Based Specification, Implementation and Testing of a Software Bus at Neopost

    NARCIS (Netherlands)

    Sijtema, Marten; Stoelinga, Mariëlle Ida Antoinette; Belinfante, Axel; Marinelli, Lawrence; Salaün, Gwen; Schätz, Bernhard

    We report on the actual industrial use of formal methods during the development of a software bus. At Neopost Inc., we developed the server component of a software bus, called the XBus, using formal methods during the design, validation and testing phase: We modeled our design of the XBus in the

  10. Experiences with formal engineering: model-based specification, implementation and testing of a software bus at Neopost

    NARCIS (Netherlands)

    Sijtema, M.; Salaün, G.; Schätz, B.; Belinfante, Axel; Stoelinga, Mariëlle Ida Antoinette; Marinelli, L.

    2014-01-01

    We report on the actual industrial use of formal methods during the development of a software bus. During an internship at Neopost Inc., of 14 weeks, we developed the server component of a software bus, called the XBus, using formal methods during the design, validation and testing phase: we modeled

  11. Formal Methods Specification and Analysis Guidebook for the Verification of Software and Computer Systems. Volume 2; A Practitioner's Companion

    Science.gov (United States)

    1995-01-01

    This guidebook, the second of a two-volume series, is intended to facilitate the transfer of formal methods to the avionics and aerospace community. The 1st volume concentrates on administrative and planning issues [NASA-95a], and the second volume focuses on the technical issues involved in applying formal methods to avionics and aerospace software systems. Hereafter, the term "guidebook" refers exclusively to the second volume of the series. The title of this second volume, A Practitioner's Companion, conveys its intent. The guidebook is written primarily for the nonexpert and requires little or no prior experience with formal methods techniques and tools. However, it does attempt to distill some of the more subtle ingredients in the productive application of formal methods. To the extent that it succeeds, those conversant with formal methods will also nd the guidebook useful. The discussion is illustrated through the development of a realistic example, relevant fragments of which appear in each chapter. The guidebook focuses primarily on the use of formal methods for analysis of requirements and high-level design, the stages at which formal methods have been most productively applied. Although much of the discussion applies to low-level design and implementation, the guidebook does not discuss issues involved in the later life cycle application of formal methods.

  12. Do Specific Types of Networking Predict Specific Mobility Outcomes? A Two-Year Prospective Study

    Science.gov (United States)

    Wolff, Hans-Georg; Moser, Klaus

    2010-01-01

    Previous research has established a general relation between networking and career outcomes, as postulated by theories on protean careers and career self management. We suggest that specific facets of networking behavior differentially affect specific career mobility outcomes over time. In a 2-year prospective study, we examined the impact of six…

  13. Student Agency: an Analysis of Students' Networked Relations Across the Informal and Formal Learning Domains

    Science.gov (United States)

    Rappa, Natasha Anne; Tang, Kok-Sing

    2017-06-01

    Agency is a construct facilitating our examination of when and how young people extend their own learning across contexts. However, little is known about the role played by adolescent learners' sense of agency. This paper reports two cases of students' agentively employing and developing science literacy practices—one in Singapore and the other in the USA. The paper illustrates how these two adolescent learners in different ways creatively accessed, navigated and integrated in-school and out-of-school discourses to support and nurture their learning of physics. Data were gleaned from students' work and interviews with students participating in a physics curricular programme in which they made linkages between their chosen out-of-school texts and several physics concepts learnt in school. The students' agentive moves were identified by means of situational mapping, which involved a relational analysis of the students' chosen artefacts and discourses across time and space. This relational analysis enabled us to address questions of student agency—how it can be effected, realised, construed and examined. It highlights possible ways to intervene in these networked relations to facilitate adolescents' agentive moves in their learning endeavours.

  14. Specification Mining for Intrusion Detection in Networked Control Systems

    NARCIS (Netherlands)

    Caselli, M.; Zambon, Emmanuele; Amann, Johanna; Sommer, Robin; Kargl, Frank

    2016-01-01

    This paper discusses a novel approach to specification-based intrusion detection in the field of networked control systems. Our approach reduces the substantial human effort required to deploy a specification-based intrusion detection system by automating the development of its specification rules.

  15. Utility communication networks and services specification, deployment and operation

    CERN Document Server

    2017-01-01

    This CIGRE green book begins by addressing the specification and provision of communication services in the context of operational applications for electrical power utilities, before subsequently providing guidelines on the deployment or transformation of networks to deliver these specific communication services. Lastly, it demonstrates how these networks and their services can be monitored, operated, and maintained to ensure that the requisite high level of service quality is consistently achieved.

  16. Formalized Informal Learning

    DEFF Research Database (Denmark)

    Levinsen, Karin Tweddell; Sørensen, Birgitte Holm

    2013-01-01

    are examined and the relation between network society competences, learners’ informal learning strategies and ICT in formalized school settings over time is studied. The authors find that aspects of ICT like multimodality, intuitive interaction design and instant feedback invites an informal bricoleur approach....... When integrated into certain designs for teaching and learning, this allows for Formalized Informal Learning and support is found for network society competences building....

  17. Navigating cancer network attractors for tumor-specific therapy

    DEFF Research Database (Denmark)

    Creixell, Pau; Schoof, Erwin; Erler, Janine Terra

    2012-01-01

    Cells employ highly dynamic signaling networks to drive biological decision processes. Perturbations to these signaling networks may attract cells to new malignant signaling and phenotypic states, termed cancer network attractors, that result in cancer development. As different cancer cells reach...... these malignant states by accumulating different molecular alterations, uncovering these mechanisms represents a grand challenge in cancer biology. Addressing this challenge will require new systems-based strategies that capture the intrinsic properties of cancer signaling networks and provide deeper...... understanding of the processes by which genetic lesions perturb these networks and lead to disease phenotypes. Network biology will help circumvent fundamental obstacles in cancer treatment, such as drug resistance and metastasis, empowering personalized and tumor-specific cancer therapies....

  18. Broker Positions in Task-Specific Knowledge Networks

    NARCIS (Netherlands)

    D.J. Dekker (David); F. Stokman; Ph.H.B.F. Franses (Philip Hans)

    2000-01-01

    textabstractIn this paper we empirically investigate various benefits and costs associated with broker characteristics of individuals who operate in the account management system of financial service providers. We narrow our focus to broker positions in two specific task-specific knowledge networks

  19. Specificity, promiscuity, and the structure of complex information processing networks

    Science.gov (United States)

    Myers, Christopher

    2006-03-01

    Both the top-down designs of engineered systems and the bottom-up serendipities of biological evolution must negotiate tradeoffs between specificity and control: overly specific interactions between components can make systems brittle and unevolvable, while more generic interactions can require elaborate control in order to aggregate specificity from distributed pieces. Complex information processing systems reveal network organizations that navigate this landscape of constraints: regulatory and signaling networks in cells involve the coordination of molecular interactions that are surprisingly promiscuous, and object-oriented design in software systems emphasizes the polymorphic composition of objects of minimal necessary specificity [C.R. Myers, Phys Rev E 68, 046116 (2003)]. Models of information processing arising both in systems biology and engineered computation are explored to better understand how particular network organizations can coordinate the activity of promiscuous components to achieve robust and evolvable function.

  20. Emergence of Functional Specificity in Balanced Networks with Synaptic Plasticity.

    Directory of Open Access Journals (Sweden)

    Sadra Sadeh

    2015-06-01

    Full Text Available In rodent visual cortex, synaptic connections between orientation-selective neurons are unspecific at the time of eye opening, and become to some degree functionally specific only later during development. An explanation for this two-stage process was proposed in terms of Hebbian plasticity based on visual experience that would eventually enhance connections between neurons with similar response features. For this to work, however, two conditions must be satisfied: First, orientation selective neuronal responses must exist before specific recurrent synaptic connections can be established. Second, Hebbian learning must be compatible with the recurrent network dynamics contributing to orientation selectivity, and the resulting specific connectivity must remain stable for unspecific background activity. Previous studies have mainly focused on very simple models, where the receptive fields of neurons were essentially determined by feedforward mechanisms, and where the recurrent network was small, lacking the complex recurrent dynamics of large-scale networks of excitatory and inhibitory neurons. Here we studied the emergence of functionally specific connectivity in large-scale recurrent networks with synaptic plasticity. Our results show that balanced random networks, which already exhibit highly selective responses at eye opening, can develop feature-specific connectivity if appropriate rules of synaptic plasticity are invoked within and between excitatory and inhibitory populations. If these conditions are met, the initial orientation selectivity guides the process of Hebbian learning and, as a result, functionally specific and a surplus of bidirectional connections emerge. Our results thus demonstrate the cooperation of synaptic plasticity and recurrent dynamics in large-scale functional networks with realistic receptive fields, highlight the role of inhibition as a critical element in this process, and paves the road for further computational

  1. Book Titled Autonomic Networking-on-Chip: Bio-Inspired Specification, Development, and Verification: An Introduction

    Directory of Open Access Journals (Sweden)

    Phan Cong Vinh

    2015-03-01

    Full Text Available Despite the growing mainstream importance and unique advantages of autonomic networking-onchip (ANoC technology, Autonomic Networking-On-Chip: Bio-Inspired Specification, Development, and Verification is among the first books to evaluate research results on formalizing this emerging NoC paradigm, which was inspired by the human nervous system. The third book in the Embedded Multi-Core Systems series from CRC Press, this is an advanced technical guide and reference composed of contributions from prominent researchers in industry and academia around the world. A response to the critical need for a global information exchange and dialogue, it is written for engineers, scientists, practitioners, and other researchers who have a basic understanding of NoC and are now ready to learn how to specify, develop, and verify ANoC using rigorous approaches.

  2. Processing of Feature Selectivity in Cortical Networks with Specific Connectivity.

    Directory of Open Access Journals (Sweden)

    Sadra Sadeh

    Full Text Available Although non-specific at the onset of eye opening, networks in rodent visual cortex attain a non-random structure after eye opening, with a specific bias for connections between neurons of similar preferred orientations. As orientation selectivity is already present at eye opening, it remains unclear how this specificity in network wiring contributes to feature selectivity. Using large-scale inhibition-dominated spiking networks as a model, we show that feature-specific connectivity leads to a linear amplification of feedforward tuning, consistent with recent electrophysiological single-neuron recordings in rodent neocortex. Our results show that optimal amplification is achieved at an intermediate regime of specific connectivity. In this configuration a moderate increase of pairwise correlations is observed, consistent with recent experimental findings. Furthermore, we observed that feature-specific connectivity leads to the emergence of orientation-selective reverberating activity, and entails pattern completion in network responses. Our theoretical analysis provides a mechanistic understanding of subnetworks' responses to visual stimuli, and casts light on the regime of operation of sensory cortices in the presence of specific connectivity.

  3. A comparison between state-specific and linear-response formalisms for the calculation of vertical electronic transition energy in solution with the CCSD-PCM method.

    Science.gov (United States)

    Caricato, Marco

    2013-07-28

    The calculation of vertical electronic transition energies of molecular systems in solution with accurate quantum mechanical methods requires the use of approximate and yet reliable models to describe the effect of the solvent on the electronic structure of the solute. The polarizable continuum model (PCM) of solvation represents a computationally efficient way to describe this effect, especially when combined with coupled cluster (CC) methods. Two formalisms are available to compute transition energies within the PCM framework: State-Specific (SS) and Linear-Response (LR). The former provides a more complete account of the solute-solvent polarization in the excited states, while the latter is computationally very efficient (i.e., comparable to gas phase) and transition properties are well defined. In this work, I review the theory for the two formalisms within CC theory with a focus on their computational requirements, and present the first implementation of the LR-PCM formalism with the coupled cluster singles and doubles method (CCSD). Transition energies computed with LR- and SS-CCSD-PCM are presented, as well as a comparison between solvation models in the LR approach. The numerical results show that the two formalisms provide different absolute values of transition energy, but similar relative solvatochromic shifts (from nonpolar to polar solvents). The LR formalism may then be used to explore the solvent effect on multiple states and evaluate transition probabilities, while the SS formalism may be used to refine the description of specific states and for the exploration of excited state potential energy surfaces of solvated systems.

  4. Formal matrices

    CERN Document Server

    Krylov, Piotr

    2017-01-01

    This monograph is a comprehensive account of formal matrices, examining homological properties of modules over formal matrix rings and summarising the interplay between Morita contexts and K theory. While various special types of formal matrix rings have been studied for a long time from several points of view and appear in various textbooks, for instance to examine equivalences of module categories and to illustrate rings with one-sided non-symmetric properties, this particular class of rings has, so far, not been treated systematically. Exploring formal matrix rings of order 2 and introducing the notion of the determinant of a formal matrix over a commutative ring, this monograph further covers the Grothendieck and Whitehead groups of rings. Graduate students and researchers interested in ring theory, module theory and operator algebras will find this book particularly valuable. Containing numerous examples, Formal Matrices is a largely self-contained and accessible introduction to the topic, assuming a sol...

  5. Fast reconstruction of compact context-specific metabolic network models.

    Directory of Open Access Journals (Sweden)

    Nikos Vlassis

    2014-01-01

    Full Text Available Systemic approaches to the study of a biological cell or tissue rely increasingly on the use of context-specific metabolic network models. The reconstruction of such a model from high-throughput data can routinely involve large numbers of tests under different conditions and extensive parameter tuning, which calls for fast algorithms. We present fastcore, a generic algorithm for reconstructing context-specific metabolic network models from global genome-wide metabolic network models such as Recon X. fastcore takes as input a core set of reactions that are known to be active in the context of interest (e.g., cell or tissue, and it searches for a flux consistent subnetwork of the global network that contains all reactions from the core set and a minimal set of additional reactions. Our key observation is that a minimal consistent reconstruction can be defined via a set of sparse modes of the global network, and fastcore iteratively computes such a set via a series of linear programs. Experiments on liver data demonstrate speedups of several orders of magnitude, and significantly more compact reconstructions, over a rival method. Given its simplicity and its excellent performance, fastcore can form the backbone of many future metabolic network reconstruction algorithms.

  6. Specific non-monotonous interactions increase persistence of ecological networks.

    Science.gov (United States)

    Yan, Chuan; Zhang, Zhibin

    2014-03-22

    The relationship between stability and biodiversity has long been debated in ecology due to opposing empirical observations and theoretical predictions. Species interaction strength is often assumed to be monotonically related to population density, but the effects on stability of ecological networks of non-monotonous interactions that change signs have not been investigated previously. We demonstrate that for four kinds of non-monotonous interactions, shifting signs to negative or neutral interactions at high population density increases persistence (a measure of stability) of ecological networks, while for the other two kinds of non-monotonous interactions shifting signs to positive interactions at high population density decreases persistence of networks. Our results reveal a novel mechanism of network stabilization caused by specific non-monotonous interaction types through either increasing stable equilibrium points or reducing unstable equilibrium points (or both). These specific non-monotonous interactions may be important in maintaining stable and complex ecological networks, as well as other networks such as genes, neurons, the internet and human societies.

  7. Specific and Complete Local Integration of Patterns in Bayesian Networks

    Directory of Open Access Journals (Sweden)

    Martin Biehl

    2017-05-01

    Full Text Available We present a first formal analysis of specific and complete local integration. Complete local integration was previously proposed as a criterion for detecting entities or wholes in distributed dynamical systems. Such entities in turn were conceived to form the basis of a theory of emergence of agents within dynamical systems. Here, we give a more thorough account of the underlying formal measures. The main contribution is the disintegration theorem which reveals a special role of completely locally integrated patterns (what we call ι-entities within the trajectories they occur in. Apart from proving this theorem we introduce the disintegration hierarchy and its refinement-free version as a way to structure the patterns in a trajectory. Furthermore, we construct the least upper bound and provide a candidate for the greatest lower bound of specific local integration. Finally, we calculate the ι -entities in small example systems as a first sanity check and find that ι -entities largely fulfil simple expectations.

  8. Human brain networks function in connectome-specific harmonic waves.

    Science.gov (United States)

    Atasoy, Selen; Donnelly, Isaac; Pearson, Joel

    2016-01-21

    A key characteristic of human brain activity is coherent, spatially distributed oscillations forming behaviour-dependent brain networks. However, a fundamental principle underlying these networks remains unknown. Here we report that functional networks of the human brain are predicted by harmonic patterns, ubiquitous throughout nature, steered by the anatomy of the human cerebral cortex, the human connectome. We introduce a new technique extending the Fourier basis to the human connectome. In this new frequency-specific representation of cortical activity, that we call 'connectome harmonics', oscillatory networks of the human brain at rest match harmonic wave patterns of certain frequencies. We demonstrate a neural mechanism behind the self-organization of connectome harmonics with a continuous neural field model of excitatory-inhibitory interactions on the connectome. Remarkably, the critical relation between the neural field patterns and the delicate excitation-inhibition balance fits the neurophysiological changes observed during the loss and recovery of consciousness.

  9. Undocumented Latina networks and responses to domestic violence in a new immigrant gateway: toward a place-specific analysis.

    Science.gov (United States)

    Reina, Angelica S; Maldonado, Marta María; Lohman, Brenda J

    2013-12-01

    New immigrant gateways differ significantly from areas of established settlement, with repercussions for domestic violence situations. Through interviews and a focus group with undocumented Latinas, we examine one specific area of such difference, that of formal and informal networks. These networks affect women's ability to seek and obtain help and procure their overall well-being. Findings suggest that the incorporation of Latinas into new gateways entails a reconfiguration of social ties and an increased level of isolation that renders immigrant women particularly vulnerable and ill-equipped to respond to domestic violence situations. We examine the theoretical and practical implications of our findings.

  10. Adaptive NetworkProfiler for Identifying Cancer Characteristic-Specific Gene Regulatory Networks.

    Science.gov (United States)

    Park, Heewon; Shimamura, Teppei; Imoto, Seiya; Miyano, Satoru

    2017-10-20

    There is currently much discussion about sample (patient)-specific gene regulatory network identification, since the efficiently constructed sample-specific gene networks lead to effective personalized cancer therapy. Although statistical approaches have been proposed for inferring gene regulatory networks, the methods cannot reveal sample-specific characteristics because the existing methods, such as an L1-type regularization, provide averaged results for all samples. Thus, we cannot reveal sample-specific characteristics in transcriptional regulatory networks. To settle on this issue, the NetworkProfiler was proposed based on the kernel-based L1-type regularization. The NetworkProfiler imposes a weight on each sample based on the Gaussian kernal function for controlling effect of samples on modeling a target sample, where the amount of weight depends on similarity of cancer characteristics between samples. The method, however, cannot perform gene regulatory network identification well for a target sample in a sparse region (i.e., for a target sample, there are only a few samples having a similar characteristic of the target sample, where the characteristic is considered as a modulator in sample-specific gene network construction), since a constant bandwidth in the Gaussian kernel function cannot effectively group samples for modeling a target sample in sparse region. The cancer characteristics, such as an anti-cancer drug sensitivity, are usually nonuniformly distributed, and thus modeling for samples in a sparse region is also a crucial issue. We propose a novel kernel-based L1-type regularization method based on a modified k-nearest neighbor (KNN)-Gaussian kernel function, called an adaptive NetworkProfiler. By using the modified KNN-Gaussian kernel function, our method provides robust results against the distribution of modulators, and properly groups samples according to a cancer characteristic for sample-specific analysis. Furthermore, we propose a sample-specific

  11. An Implementation of the Task Algebra, a Formal Specification for the Task Model in the Discovery Method

    Directory of Open Access Journals (Sweden)

    C.A. Fernández-Fernández

    2014-10-01

    Full Text Available This paper describes an implementation of the Task Algebra, a formal model of hierarchical tasks and workflows, in the Haskell programming language. Previously we presented the Task Algebra as a formal, unambiguous notation capturing the kinds of activity and workflow typically seen in business analysis diagrams, similar to UML use case and activity diagrams. Here, we show how the abstract syntax for the Task Algebra may be parsed and then semantically analysed, by a suite of Haskell functions, to compute the execution traces of a system. The approach is illustrated with a case study of a journal management system. The results show how it is possible to automate the semantic analysis of requirements diagrams, as a precursor to developing a logical design.

  12. Internet factories: Creating application-specific networks on-demand

    NARCIS (Netherlands)

    Strijkers, R.J.; Makkes, M.X.; Laat, C. de; Meijer, R.J.

    2014-01-01

    We introduce the concept of Internet factories. Internet factories structure the task of creating and managing application-specific overlay networks using infrastructure-as-a-service clouds. We describe the Internet factory architecture and report on a proof of concept with three examples that

  13. Artificial neural network approach for estimation of surface specific ...

    Indian Academy of Sciences (India)

    Microwave sensor MSMR (Multifrequency Scanning Microwave Radiometer) data onboard Oceansat-1 was used for retrieval of monthly averages of near surface specific humidity (a) and air temperature (a) by means of Artificial Neural Network (ANN). The MSMR measures the microwave radiances in 8 channels at ...

  14. Differential dependency network analysis to identify condition-specific topological changes in biological networks.

    Science.gov (United States)

    Zhang, Bai; Li, Huai; Riggins, Rebecca B; Zhan, Ming; Xuan, Jianhua; Zhang, Zhen; Hoffman, Eric P; Clarke, Robert; Wang, Yue

    2009-02-15

    Significant efforts have been made to acquire data under different conditions and to construct static networks that can explain various gene regulation mechanisms. However, gene regulatory networks are dynamic and condition-specific; under different conditions, networks exhibit different regulation patterns accompanied by different transcriptional network topologies. Thus, an investigation on the topological changes in transcriptional networks can facilitate the understanding of cell development or provide novel insights into the pathophysiology of certain diseases, and help identify the key genetic players that could serve as biomarkers or drug targets. Here, we report a differential dependency network (DDN) analysis to detect statistically significant topological changes in the transcriptional networks between two biological conditions. We propose a local dependency model to represent the local structures of a network by a set of conditional probabilities. We develop an efficient learning algorithm to learn the local dependency model using the Lasso technique. A permutation test is subsequently performed to estimate the statistical significance of each learned local structure. In testing on a simulation dataset, the proposed algorithm accurately detected all the genes with network topological changes. The method was then applied to the estrogen-dependent T-47D estrogen receptor-positive (ER+) breast cancer cell line datasets and human and mouse embryonic stem cell datasets. In both experiments using real microarray datasets, the proposed method produced biologically meaningful results. We expect DDN to emerge as an important bioinformatics tool in transcriptional network analyses. While we focus specifically on transcriptional networks, the DDN method we introduce here is generally applicable to other biological networks with similar characteristics. The DDN MATLAB toolbox and experiment data are available at http://www.cbil.ece.vt.edu/software.htm.

  15. Formal Modeling of mTOR Associated Biological Regulatory Network Reveals Novel Therapeutic Strategy for the Treatment of Cancer

    Directory of Open Access Journals (Sweden)

    Zurah Bibi

    2017-06-01

    Full Text Available Cellular homeostasis is a continuous phenomenon that if compromised can lead to several disorders including cancer. There is a need to understand the dynamics of cellular proliferation to get deeper insights into the prevalence of cancer. Mechanistic Target of Rapamycin (mTOR is implicated as the central regulator of the metabolic pathway involved in growth whereas its two distinct complexes mTORC1 and mTORC2 perform particular functions in cellular propagation. To date, mTORC1 is a well defined therapeutic target to inhibit uncontrolled cell division, while the role of mTORC2 is not well characterized. Therefore, the current study is designed to understand the signaling dynamics of mTOR and its partner proteins such as PI3K, PTEN, mTORC2, PKB (Akt, mTORC1, and FOXO. For this purpose, a qualitative model of mTOR-associated Biological Regulatory Network (BRN is constructed to predict its regulatory behaviors which may not be predictable otherwise. The depleted expression of PTEN and FOXO along with the overexpression of PI3K, mTORC2, mTORC1 and Akt is predicted as a stable steady state which is in accordance with their observed expression levels in the progression of various cancers. The qualitative model also predicts the homeostasis of all the entities in the form of qualitative cycles. The significant qualitative (discrete cycle is identified by analyzing betweenness centralities of the qualitative (discrete states. This cycle is further refined as a linear hybrid automaton model with the production (activation and degradation (inhibition time delays in order to analyze the real-time constraints for its existence. The analysis of the hybrid model provides a formal proof that during homeostasis the inhibition time delay of Akt is less than the inhibition time delay of mTORC2. In conclusion, our observations characterize that in homeostasis Akt is degraded with a faster rate than mTORC2 which suggests that the inhibition of Akt along with the

  16. Context-specific protein network miner - an online system for exploring context-specific protein interaction networks from the literature

    KAUST Repository

    Chowdhary, Rajesh

    2012-04-06

    Background: Protein interaction networks (PINs) specific within a particular context contain crucial information regarding many cellular biological processes. For example, PINs may include information on the type and directionality of interaction (e.g. phosphorylation), location of interaction (i.e. tissues, cells), and related diseases. Currently, very few tools are capable of deriving context-specific PINs for conducting exploratory analysis. Results: We developed a literature-based online system, Context-specific Protein Network Miner (CPNM), which derives context-specific PINs in real-time from the PubMed database based on a set of user-input keywords and enhanced PubMed query system. CPNM reports enriched information on protein interactions (with type and directionality), their network topology with summary statistics (e.g. most densely connected proteins in the network; most densely connected protein-pairs; and proteins connected by most inbound/outbound links) that can be explored via a user-friendly interface. Some of the novel features of the CPNM system include PIN generation, ontology-based PubMed query enhancement, real-time, user-queried, up-to-date PubMed document processing, and prediction of PIN directionality. Conclusions: CPNM provides a tool for biologists to explore PINs. It is freely accessible at http://www.biotextminer.com/CPNM/. © 2012 Chowdhary et al.

  17. Specificity and evolvability in eukaryotic protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Pedro Beltrao

    2007-02-01

    Full Text Available Progress in uncovering the protein interaction networks of several species has led to questions of what underlying principles might govern their organization. Few studies have tried to determine the impact of protein interaction network evolution on the observed physiological differences between species. Using comparative genomics and structural information, we show here that eukaryotic species have rewired their interactomes at a fast rate of approximately 10(-5 interactions changed per protein pair, per million years of divergence. For Homo sapiens this corresponds to 10(3 interactions changed per million years. Additionally we find that the specificity of binding strongly determines the interaction turnover and that different biological processes show significantly different link dynamics. In particular, human proteins involved in immune response, transport, and establishment of localization show signs of positive selection for change of interactions. Our analysis suggests that a small degree of molecular divergence can give rise to important changes at the network level. We propose that the power law distribution observed in protein interaction networks could be partly explained by the cell's requirement for different degrees of protein binding specificity.

  18. Cell-specific synaptic plasticity induced by network oscillations.

    Science.gov (United States)

    Zarnadze, Shota; Bäuerle, Peter; Santos-Torres, Julio; Böhm, Claudia; Schmitz, Dietmar; Geiger, Jörg Rp; Dugladze, Tamar; Gloveli, Tengis

    2016-05-24

    Gamma rhythms are known to contribute to the process of memory encoding. However, little is known about the underlying mechanisms at the molecular, cellular and network levels. Using local field potential recording in awake behaving mice and concomitant field potential and whole-cell recordings in slice preparations we found that gamma rhythms lead to activity-dependent modification of hippocampal networks, including alterations in sharp wave-ripple complexes. Network plasticity, expressed as long-lasting increases in sharp wave-associated synaptic currents, exhibits enhanced excitatory synaptic strength in pyramidal cells that is induced postsynaptically and depends on metabotropic glutamate receptor-5 activation. In sharp contrast, alteration of inhibitory synaptic strength is independent of postsynaptic activation and less pronounced. Further, we found a cell type-specific, directionally biased synaptic plasticity of two major types of GABAergic cells, parvalbumin- and cholecystokinin-expressing interneurons. Thus, we propose that gamma frequency oscillations represent a network state that introduces long-lasting synaptic plasticity in a cell-specific manner.

  19. A gene regulatory network armature for T-lymphocyte specification

    Energy Technology Data Exchange (ETDEWEB)

    Fung, Elizabeth-sharon [Los Alamos National Laboratory

    2008-01-01

    Choice of a T-lymphoid fate by hematopoietic progenitor cells depends on sustained Notch-Delta signaling combined with tightly-regulated activities of multiple transcription factors. To dissect the regulatory network connections that mediate this process, we have used high-resolution analysis of regulatory gene expression trajectories from the beginning to the end of specification; tests of the short-term Notchdependence of these gene expression changes; and perturbation analyses of the effects of overexpression of two essential transcription factors, namely PU.l and GATA-3. Quantitative expression measurements of >50 transcription factor and marker genes have been used to derive the principal components of regulatory change through which T-cell precursors progress from primitive multipotency to T-lineage commitment. Distinct parts of the path reveal separate contributions of Notch signaling, GATA-3 activity, and downregulation of PU.l. Using BioTapestry, the results have been assembled into a draft gene regulatory network for the specification of T-cell precursors and the choice of T as opposed to myeloid dendritic or mast-cell fates. This network also accommodates effects of E proteins and mutual repression circuits of Gfil against Egr-2 and of TCF-l against PU.l as proposed elsewhere, but requires additional functions that remain unidentified. Distinctive features of this network structure include the intense dose-dependence of GATA-3 effects; the gene-specific modulation of PU.l activity based on Notch activity; the lack of direct opposition between PU.l and GATA-3; and the need for a distinct, late-acting repressive function or functions to extinguish stem and progenitor-derived regulatory gene expression.

  20. An automatic method to generate domain-specific investigator networks using PubMed abstracts

    Directory of Open Access Journals (Sweden)

    Gwinn Marta

    2007-06-01

    Full Text Available Abstract Background Collaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts. Results We developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8% and from 94.2% of HuGE PubMed records (accuracy 87.0. We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit, indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70–90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network. Conclusion We successfully created a

  1. Frequency-specific network topologies in the resting human brain

    Directory of Open Access Journals (Sweden)

    Shuntaro eSasai

    2014-12-01

    Full Text Available A community is a set of nodes with dense inter-connections, while there are sparse connections between different communities. A hub is a highly connected node with high centrality. It has been shown that both communities and hubs exist simultaneously in the brain’s functional connectivity network, as estimated by correlations among low-frequency spontaneous fluctuations in functional magnetic resonance imaging (fMRI signal changes (0.01–0.10 Hz. This indicates that the brain has a spatial organization that promotes both segregation and integration of information. Here, we demonstrate that frequency-specific network topologies that characterize segregation and integration also exist within this frequency range. In investigating the coherence spectrum among 87 brain regions, we found that two frequency bands, 0.01–0.03 Hz (very low frequency [VLF] band and 0.07–0.09 Hz (low frequency [LF] band, mainly contributed to functional connectivity. Comparing graph theoretical indices for the VLF and LF bands revealed that the network in the former had a higher capacity for information segregation between identified communities than the latter. Hubs in the VLF band were mainly located within the anterior cingulate cortices, whereas those in the LF band were located in the posterior cingulate cortices and thalamus. Thus, depending on the timescale of brain activity, at least two distinct network topologies contributed to information segregation and integration. This suggests that the brain intrinsically has timescale-dependent functional organizations.

  2. Formalizing physical security procedures

    NARCIS (Netherlands)

    Meadows, C.; Pavlovic, Dusko

    Although the problems of physical security emerged more than 10,000 years before the problems of computer security, no formal methods have been developed for them, and the solutions have been evolving slowly, mostly through social procedures. But as the traffic on physical and social networks is now

  3. SPECIFICITY OF COMMUNICATION DOCTOR – PATIENT, ONLINE, THROUGH SOCIAL NETWORKS

    Directory of Open Access Journals (Sweden)

    Florin-Alexandru LUCA

    2014-12-01

    Full Text Available A survey in 2013 of Division Market Research Group Rentrop Straton Romanian-German - "state services and private clinics. Comparative Analysis ", highlights the fact that into urban population in Romania, the internet is the most popular source of information on health services. According to the survey, 81.9% of respondents use the Internet to find out about the best doctors available to them. Preferences of respondents to the online environment as the main source of information translates into ease of access and the possibility of interaction, but also trust recommendations based on personal experiences, recommendations can be found through discussion forums, mostly or comments left on pages on social networking sites. In the present study we try to emphasize the specificity of communication physician - patient online through social networks.

  4. A Formal Approach to the Selection by Minimum Error and Pattern Method for Sensor Data Loss Reduction in Unstable Wireless Sensor Network Communications.

    Science.gov (United States)

    Kim, Changhwa; Shin, DongHyun

    2017-05-12

    There are wireless networks in which typically communications are unsafe. Most terrestrial wireless sensor networks belong to this category of networks. Another example of an unsafe communication network is an underwater acoustic sensor network (UWASN). In UWASNs in particular, communication failures occur frequently and the failure durations can range from seconds up to a few hours, days, or even weeks. These communication failures can cause data losses significant enough to seriously damage human life or property, depending on their application areas. In this paper, we propose a framework to reduce sensor data loss during communication failures and we present a formal approach to the Selection by Minimum Error and Pattern (SMEP) method that plays the most important role for the reduction in sensor data loss under the proposed framework. The SMEP method is compared with other methods to validate its effectiveness through experiments using real-field sensor data sets. Moreover, based on our experimental results and performance comparisons, the SMEP method has been validated to be better than others in terms of the average sensor data value error rate caused by sensor data loss.

  5. Formal modeling of robot behavior with learning.

    Science.gov (United States)

    Kirwan, Ryan; Miller, Alice; Porr, Bernd; Di Prodi, P

    2013-11-01

    We present formal specification and verification of a robot moving in a complex network, using temporal sequence learning to avoid obstacles. Our aim is to demonstrate the benefit of using a formal approach to analyze such a system as a complementary approach to simulation. We first describe a classical closed-loop simulation of the system and compare this approach to one in which the system is analyzed using formal verification. We show that the formal verification has some advantages over classical simulation and finds deficiencies our classical simulation did not identify. Specifically we present a formal specification of the system, defined in the Promela modeling language and show how the associated model is verified using the Spin model checker. We then introduce an abstract model that is suitable for verifying the same properties for any environment with obstacles under a given set of assumptions. We outline how we can prove that our abstraction is sound: any property that holds for the abstracted model will hold in the original (unabstracted) model.

  6. Reconstructing context-specific gene regulatory network and identifying modules and network rewiring through data integration.

    Science.gov (United States)

    Ma, Tianle; Zhang, Aidong

    2017-07-15

    Reconstructing context-specific transcriptional regulatory network is crucial for deciphering principles of regulatory mechanisms underlying various conditions. Recently studies that reconstructed transcriptional networks have focused on individual organisms or cell types and relied on data repositories of context-free regulatory relationships. Here we present a comprehensive framework to systematically derive putative regulator-target pairs in any given context by integrating context-specific transcriptional profiling and public data repositories of gene regulatory networks. Moreover, our framework can identify core regulatory modules and signature genes underlying global regulatory circuitry, and detect network rewiring and core rewired modules in different contexts by considering gene modules and edge (gene interaction) modules collaboratively. We applied our methods to analyzing Autism RNA-seq experiment data and produced biologically meaningful results. In particular, all 11 hub genes in a predicted rewired autistic regulatory subnetwork have been linked to autism based on literature review. The predicted rewired autistic regulatory network may shed some new insight into disease mechanism. Published by Elsevier Inc.

  7. Livelihood Networks and Decision-making Among Congolese Young People in Formal and Informal Refugee Contexts in Uganda

    OpenAIRE

    Christina Clark

    2006-01-01

    Refugee young people who are without their biological parents are often assumed to be among the most disempowered members of displaced populations. This paper interrogates this assumption by exploring Congolese young people’s access to decision-making in a variety of household contexts in Kampala and Kyaka II refugee settlement, western Uganda. Using a network approach to household and family, research findings reveal shrinking networks, increasing delinkage between household and family, and ...

  8. Formalization of Database Systems -- and a Formal Definition of {IMS}

    DEFF Research Database (Denmark)

    Bjørner, Dines; Løvengreen, Hans Henrik

    1982-01-01

    come ueee of formal definitions of data models and databaee management systems. A formal model of INS will carry this discussion. Finally we survey some of the exkting literature on formal definitions of database systems. The emphasis will be on constructive definitions in the denotationul semantics......Drawing upon an analogy between Programming Language Systems and Database Systems we outline the requirements that architectural specifications of database systems must futfitl, and argue that only formal, mathematical definitions may 6atisfy these. Then we illustrate home aspects and touch upon...... style of the VCM: Vienna Development Nethd. The role of formal definitions in international standardiaation efforts is briefly mentioned....

  9. Stimulus-Specific Transcriptional Regulation Within the p53 Network

    Science.gov (United States)

    Donner, Aaron Joseph; Hoover, Jennifer Michelle; Szostek, Stephanie Aspen; Espinosa, Joaquín Maximiliano

    2010-01-01

    The p53 transcriptional network is composed of hundreds of effector genes involved in varied stress-response pathways, including cell cycle arrest and apoptosis. It is not clear how distinct p53 target genes are differentially activated to trigger stress-specific biological responses. We analyzed the p53 transcriptional program upon activation by two DNA-damaging agents, UVC and doxorubicin, versus the non-genotoxic molecule Nutlin-3. In colorectal cancer cells, UVC triggers apoptosis, doxorubicin induces transient cell cycle arrest followed by apoptosis, and Nutlin-3 leads to cell cycle arrest with no significant apoptosis. Quantitative gene expression analysis allowed us to group p53 target genes into three main classes according to their activation profiles in each scenario. The CDK-inhibitor p21 was classified as a Class I gene, being significantly activated under cell cycle arrest conditions (i.e., doxorubicin and Nutlin-3) but not during UVC-induced apoptosis. Chromatin immunoprecipitation analysis of the p21 locus indicates that the level of p53-dependent transcription is determined by the effects of stimulus-specific transcriptional coregulators acting downstream of p53 binding and histone acetylation. In particular, our analysis indicates that the subunits of the CDK-module of the human Mediator complex function as stimulus-specific positive coregulators of p21 transcription. PMID:17957141

  10. Human-specific transcriptional networks in the brain

    Science.gov (United States)

    Konopka, Genevieve; Friedrich, Tara; Davis-Turak, Jeremy; Winden, Kellen; Oldham, Michael C.; Gao, Fuying; Chen, Leslie; Wang, Guang-Zhong; Luo, Rui; Preuss, Todd M.; Geschwind, Daniel H.

    2013-01-01

    Summary Understanding human-specific patterns of brain gene expression and regulation can provide key insights into human brain evolution and speciation. Here, we use next generation sequencing, and Illumina and Affymetrix microarray platforms, to compare the transcriptome of human, chimpanzee, and macaque telencephalon. Our analysis reveals a predominance of genes differentially expressed within human frontal lobe and a striking increase in transcriptional complexity specific to the human lineage in the frontal lobe. In contrast, caudate nucleus gene expression is highly conserved. We also identify gene co-expression signatures related to either neuronal processes or neuropsychiatric diseases, including a human-specific module with CLOCK as its hub gene and another module enriched for neuronal morphological processes and genes co-expressed with FOXP2, a gene important for language evolution. These data demonstrate that transcriptional networks have undergone evolutionary remodeling even within a given brain region, providing a new window through which to view the foundation of uniquely human cognitive capacities. PMID:22920253

  11. Integrated formal operations plan

    Energy Technology Data Exchange (ETDEWEB)

    Cort, G.; Dearholt, W.; Donahue, S.; Frank, J.; Perkins, B.; Tyler, R.; Wrye, J.

    1994-01-05

    The concept of formal operations (that is, a collection of business practices to assure effective, accountable operations) has vexed the Laboratory for many years. To date most attempts at developing such programs have been based upon rigid, compliance-based interpretations of a veritable mountain of Department of Energy (DOE) orders, directives, notices, and standards. These DOE dictates seldom take the broad view but focus on highly specialized programs isolated from the overall context of formal operations. The result is a confusing array of specific, and often contradictory, requirements that produce a patchwork of overlapping niche programs. This unnecessary duplication wastes precious resources, dramatically increases the complexity of our work processes, and communicates a sense of confusion to our customers and regulators. Coupled with the artificial divisions that have historically existed among the Laboratory`s formal operations organizations (quality assurance, configuration management, records management, training, etc.), this approach has produced layers of increasingly vague and complex formal operations plans, each of which interprets its parent and adds additional requirements of its own. Organizational gridlock ensues whenever an activity attempts to implement these bureaucratic monstrosities. The integrated formal operations plan presented is to establish a set of requirements that must be met by an integrated formal operations program, assign responsibilities for implementation and operation of the program, and specify criteria against which the performance of the program will be measured. The accountable line manager specifies the items, processes, and information (the controlled elements) to which the formal operations program specified applies. The formal operations program is implemented using a graded approach based on the level of importance of the various controlled elements and the scope of the activities in which they are involved.

  12. Formal verification of a deadlock detection algorithm

    Directory of Open Access Journals (Sweden)

    Freek Verbeek

    2011-10-01

    Full Text Available Deadlock detection is a challenging issue in the analysis and design of on-chip networks. We have designed an algorithm to detect deadlocks automatically in on-chip networks with wormhole switching. The algorithm has been specified and proven correct in ACL2. To enable a top-down proof methodology, some parts of the algorithm have been left unimplemented. For these parts, the ACL2 specification contains constrained functions introduced with defun-sk. We used single-threaded objects to represent the data structures used by the algorithm. In this paper, we present details on the proof of correctness of the algorithm. The process of formal verification was crucial to get the algorithm flawless. Our ultimate objective is to have an efficient executable, and formally proven correct implementation of the algorithm running in ACL2.

  13. Origins of Specificity and Promiscuity in Metabolic Networks

    Science.gov (United States)

    Carbonell, Pablo; Lecointre, Guillaume; Faulon, Jean-Loup

    2011-01-01

    How enzymes have evolved to their present form is linked to the question of how pathways emerged and evolved into extant metabolic networks. To investigate this mechanism, we have explored the chemical diversity present in a largely unbiased data set of catalytic reactions processed by modern enzymes across the tree of life. In order to get a quantitative estimate of enzyme chemical diversity, we measure enzyme multispecificity or promiscuity using the reaction molecular signatures. Our main finding is that reactions that are catalyzed by a highly specific enzyme are shared by poorly divergent species, suggesting a later emergence of this function during evolution. In contrast, reactions that are catalyzed by highly promiscuous enzymes are more likely to appear uniformly distributed across species in the tree of life. From a functional point of view, promiscuous enzymes are mainly involved in amino acid and lipid metabolisms, which might be associated with the earliest form of biochemical reactions. In this way, results presented in this paper might assist us with the identification of primeval promiscuous catalytic functions contributing to life's minimal metabolism. PMID:22052908

  14. The challenge of religious and language diversity in Burkina Faso formal education: students’ mobility and social networks

    Directory of Open Access Journals (Sweden)

    Pingrewaoga Bema Abdoul Hadi Savadogo

    2014-09-01

    Full Text Available This paper addresses the education of young Muslims in Burkina Faso through relevant literature analysis and the authors’ observations, highlighting the pathways of study in Arabic-speaking countries and the social dynamics around them. The central theme is associated with the more general debate about education and diversity, because it discusses, on the one hand, the educational hegemony of secular orientation carried out in French adopted by part of the society and made official by the nation-state; on the other hand, it stresses the movement of another part of society that continues to enroll their children in Muslim schools where teaching is conducted in Arabic or bilingual (French and Arabic. The study describes the sociopolitical contexts that constitute the institutions of Islamic education, emphasizing the importance of Franco-Arabic schools and new Muslim private universities from the non-public higher education network. Following this discussion, there is a debate about the contribution of these young graduated men and women (inside and outside the country to hold and maintain the educational system. This paper also highlights the political action of these groups that claims for citizenship through religious practices. We conclude by stressing the existence of the fundamental contribution of Islam, which remains a powerful space for the construction of social and interpersonal meanings even in post-colonial dynamics. This is the scenario in which the reconstruction of networks may be converted into an overall challenge for social occupational therapy to mediate conflicts emerging from the confrontation of values and social practices.

  15. Disease gene prioritization by integrating tissue-specific molecular networks using a robust multi-network model.

    Science.gov (United States)

    Ni, Jingchao; Koyuturk, Mehmet; Tong, Hanghang; Haines, Jonathan; Xu, Rong; Zhang, Xiang

    2016-11-10

    Accurately prioritizing candidate disease genes is an important and challenging problem. Various network-based methods have been developed to predict potential disease genes by utilizing the disease similarity network and molecular networks such as protein interaction or gene co-expression networks. Although successful, a common limitation of the existing methods is that they assume all diseases share the same molecular network and a single generic molecular network is used to predict candidate genes for all diseases. However, different diseases tend to manifest in different tissues, and the molecular networks in different tissues are usually different. An ideal method should be able to incorporate tissue-specific molecular networks for different diseases. In this paper, we develop a robust and flexible method to integrate tissue-specific molecular networks for disease gene prioritization. Our method allows each disease to have its own tissue-specific network(s). We formulate the problem of candidate gene prioritization as an optimization problem based on network propagation. When there are multiple tissue-specific networks available for a disease, our method can automatically infer the relative importance of each tissue-specific network. Thus it is robust to the noisy and incomplete network data. To solve the optimization problem, we develop fast algorithms which have linear time complexities in the number of nodes in the molecular networks. We also provide rigorous theoretical foundations for our algorithms in terms of their optimality and convergence properties. Extensive experimental results show that our method can significantly improve the accuracy of candidate gene prioritization compared with the state-of-the-art methods. In our experiments, we compare our methods with 7 popular network-based disease gene prioritization algorithms on diseases from Online Mendelian Inheritance in Man (OMIM) database. The experimental results demonstrate that our methods

  16. Formal verification of AI software

    Science.gov (United States)

    Rushby, John; Whitehurst, R. Alan

    1989-01-01

    The application of formal verification techniques to Artificial Intelligence (AI) software, particularly expert systems, is investigated. Constraint satisfaction and model inversion are identified as two formal specification paradigms for different classes of expert systems. A formal definition of consistency is developed, and the notion of approximate semantics is introduced. Examples are given of how these ideas can be applied in both declarative and imperative forms.

  17. Formal Testing of Correspondence Carrying Software

    NARCIS (Netherlands)

    Bujorianu, M.C.; Bujorianu, L.M.; Maharaj, S.

    2008-01-01

    Nowadays formal software development is characterised by use of multitude formal specification languages. Test case generation from formal specifications depends in general on a specific language, and, moreover, there are competing methods for each language. There is a need for a generic approach to

  18. A Domain-Specific Language for Incremental and Modular Design of Large-Scale Verifiably-Safe Flow Networks (Preliminary Report

    Directory of Open Access Journals (Sweden)

    Azer Bestavros

    2011-09-01

    Full Text Available We define a domain-specific language (DSL to inductively assemble flow networks from small networks or modules to produce arbitrarily large ones, with interchangeable functionally-equivalent parts. Our small networks or modules are "small" only as the building blocks in this inductive definition (there is no limit on their size. Associated with our DSL is a type theory, a system of formal annotations to express desirable properties of flow networks together with rules that enforce them as invariants across their interfaces, i.e, the rules guarantee the properties are preserved as we build larger networks from smaller ones. A prerequisite for a type theory is a formal semantics, i.e, a rigorous definition of the entities that qualify as feasible flows through the networks, possibly restricted to satisfy additional efficiency or safety requirements. This can be carried out in one of two ways, as a denotational semantics or as an operational (or reduction semantics; we choose the first in preference to the second, partly to avoid exponential-growth rewriting in the operational approach. We set up a typing system and prove its soundness for our DSL.

  19. EEG classification of emotions using emotion-specific brain functional network.

    Science.gov (United States)

    Gonuguntla, V; Shafiq, G; Wang, Y; Veluvolu, K C

    2015-08-01

    The brain functional network perspective forms the basis to relate mechanisms of brain functions. This work analyzes the network mechanisms related to human emotion based on synchronization measure - phase-locking value in EEG to formulate the emotion specific brain functional network. Based on network dissimilarities between emotion and rest tasks, most reactive channel pairs and the reactive band corresponding to emotions are identified. With the identified most reactive pairs, the subject-specific functional network is formed. The identified subject-specific and emotion-specific dynamic network pattern show significant synchrony variation in line with the experiment protocol. The same network pattern are then employed for classification of emotions. With the study conducted on the 4 subjects, an average classification accuracy of 62 % was obtained with the proposed technique.

  20. Landslide susceptibility and risk assessment: specificities for road networks

    Science.gov (United States)

    Pellicani, Roberta; Argentiero, Ilenia; Parisi, Alessandro; Spilotro, Giuseppe

    2017-04-01

    A regional-scale assessment of landslide susceptibility and risk along the main road corridors crossing the provincial territory of Matera (Basilicata Region, Southern Italy) was carried out. The entire provincial road network extends for about 1,320 km through a territory, of which represents the main connection infrastructure among thirty-one municipalities due to the lack of an efficient integrated transportation system through the whole regional territory. For this reason, the strategic importance of these roads consists in their uniqueness in connecting every urban center with the socio-economic surrounding context. These roads and their vehicular traffic are continuously exposed to instability processes (about the 40% of the total length is disrupted by landslides), characterized both by high intensity and low frequency and by low intensity and high frequency. This last typology, consisting in small shallow landslides, is particularly hazardous for the roads since it is widespread along the road network, its occurrence is connected to rainfalls and determines high vulnerability conditions for the road in terms of interruption of vehicular traffic. A GIS-based heuristic-bivariate statistical predictive model was performed to assess and map the landslide susceptibility in the study area, by using a polynomial function of eight predisposing factors, weighted according to their influence on the landslide phenomena, recognized and collected in an inventory. Susceptibility associated to small shallow phenomena was assessed by using a polynomial function of specific factors, such as slope angle and aspect, lithological outcrops, rainfalls, etc. In absence of detailed input data, the spatial distribution of landslide risk along the road corridors was assessed and mapped using a qualitative hazard-consequence matrix approach, by which risk is obtained by combining hazard categories with consequence classes pairwise in a two-dimensional table or matrix. Landslide

  1. Proceedings of the Second NASA Formal Methods Symposium

    Science.gov (United States)

    Munoz, Cesar (Editor)

    2010-01-01

    This publication contains the proceedings of the Second NASA Formal Methods Symposium sponsored by the National Aeronautics and Space Administration and held in Washington D.C. April 13-15, 2010. Topics covered include: Decision Engines for Software Analysis using Satisfiability Modulo Theories Solvers; Verification and Validation of Flight-Critical Systems; Formal Methods at Intel -- An Overview; Automatic Review of Abstract State Machines by Meta Property Verification; Hardware-independent Proofs of Numerical Programs; Slice-based Formal Specification Measures -- Mapping Coupling and Cohesion Measures to Formal Z; How Formal Methods Impels Discovery: A Short History of an Air Traffic Management Project; A Machine-Checked Proof of A State-Space Construction Algorithm; Automated Assume-Guarantee Reasoning for Omega-Regular Systems and Specifications; Modeling Regular Replacement for String Constraint Solving; Using Integer Clocks to Verify the Timing-Sync Sensor Network Protocol; Can Regulatory Bodies Expect Efficient Help from Formal Methods?; Synthesis of Greedy Algorithms Using Dominance Relations; A New Method for Incremental Testing of Finite State Machines; Verification of Faulty Message Passing Systems with Continuous State Space in PVS; Phase Two Feasibility Study for Software Safety Requirements Analysis Using Model Checking; A Prototype Embedding of Bluespec System Verilog in the PVS Theorem Prover; SimCheck: An Expressive Type System for Simulink; Coverage Metrics for Requirements-Based Testing: Evaluation of Effectiveness; Software Model Checking of ARINC-653 Flight Code with MCP; Evaluation of a Guideline by Formal Modelling of Cruise Control System in Event-B; Formal Verification of Large Software Systems; Symbolic Computation of Strongly Connected Components Using Saturation; Towards the Formal Verification of a Distributed Real-Time Automotive System; Slicing AADL Specifications for Model Checking; Model Checking with Edge-valued Decision Diagrams

  2. Attention reorganizes connectivity across networks in a frequency specific manner

    DEFF Research Database (Denmark)

    Kwon, Soyoung; Watanabe, Masataka; Fischer, Elvira

    2017-01-01

    modulations that can be cleanly attributed to attention compared to matched visual processing. In contrast to prior approaches, we used an ultra-long trial design that avoided transients from trial onsets, included slow fluctuations (...Attention allows our brain to focus its limited resources on a given task. It does so by selective modulation of neural activity and of functional connectivity (FC) across brain-wide networks. While there is extensive literature on activity changes, surprisingly few studies examined brain-wide FC......-segregated analyses. We found that FC derived from long blocks had a nearly two-fold higher gain compared to FC derived from traditional (short) block designs. Second, attention enhanced intrinsic (negative or positive) correlations across networks, such as between the default-mode network (DMN), the dorsal attention...

  3. Microsolvation of Mg²⁺, Ca²⁺: strong influence of formal charges in hydrogen bond networks.

    Science.gov (United States)

    Gonzalez, Juan David; Florez, Elizabeth; Romero, Jonathan; Reyes, Andrés; Restrepo, Albeiro

    2013-04-01

    A stochastic exploration of the quantum conformational spaces in the microsolvation of divalent cations with explicit consideration of up to six solvent molecules [Mg (H₂O)n)](2+), (n=3, 4, 5, 6) at the B3LYP, MP2, CCSD(T) levels is presented. We find several cases in which the formal charge in Mg²⁺ causes dissociation of water molecules in the first solvation shell, leaving a hydroxide ion available to interact with the central cation, the released proton being transferred to outer solvation shells in a Grotthus type mechanism; this particular finding sheds light on the capacity of Mg²⁺ to promote formation of hydroxide anions, a process necessary to regulate proton transfer in enzymes with exonuclease activity. Two distinct types of hydrogen bonds, scattered over a wide range of distances (1.35-2.15 Å) were identified. We find that in inner solvation shells, where hydrogen bond networks are severely disturbed, most of the interaction energies come from electrostatic and polarization+charge transfer, while in outer solvation shells the situation approximates that of pure water clusters.

  4. Multi-Objective Optimization Algorithm to Discover Condition-Specific Modules in Multiple Networks

    Directory of Open Access Journals (Sweden)

    Xiaoke Ma

    2017-12-01

    Full Text Available The advances in biological technologies make it possible to generate data for multiple conditions simultaneously. Discovering the condition-specific modules in multiple networks has great merit in understanding the underlying molecular mechanisms of cells. The available algorithms transform the multiple networks into a single objective optimization problem, which is criticized for its low accuracy. To address this issue, a multi-objective genetic algorithm for condition-specific modules in multiple networks (MOGA-CSM is developed to discover the condition-specific modules. By using the artificial networks, we demonstrate that the MOGA-CSM outperforms state-of-the-art methods in terms of accuracy. Furthermore, MOGA-CSM discovers stage-specific modules in breast cancer networks based on The Cancer Genome Atlas (TCGA data, and these modules serve as biomarkers to predict stages of breast cancer. The proposed model and algorithm provide an effective way to analyze multiple networks.

  5. Network Traffic Features for Anomaly Detection in Specific Industrial Control System Network

    Directory of Open Access Journals (Sweden)

    Matti Mantere

    2013-09-01

    Full Text Available The deterministic and restricted nature of industrial control system networks sets them apart from more open networks, such as local area networks in office environments. This improves the usability of network security, monitoring approaches that would be less feasible in more open environments. One of such approaches is machine learning based anomaly detection. Without proper customization for the special requirements of the industrial control system network environment, many existing anomaly or misuse detection systems will perform sub-optimally. A machine learning based approach could reduce the amount of manual customization required for different industrial control system networks. In this paper we analyze a possible set of features to be used in a machine learning based anomaly detection system in the real world industrial control system network environment under investigation. The network under investigation is represented by architectural drawing and results derived from network trace analysis. The network trace is captured from a live running industrial process control network and includes both control data and the data flowing between the control network and the office network. We limit the investigation to the IP traffic in the traces.

  6. Specification and Estimation of Network Formation and Network Interaction Models with the Exponential Probability Distribution

    OpenAIRE

    Hsieh, Chih-Sheng; Lee, Lung fei

    2017-01-01

    In this paper, we model network formation and network interactions under a unified framework. The key feature of our model is to allow individuals to respond to incentives stemming from interaction benefits on certain activities when they choose friends (network links), while capturing homophily in terms of unobserved characteristic variables in network formation and activities. There are two advantages of this modeling approach: first, one can evaluate whether incentives from certain interac...

  7. MOOCs, Open educational resources and social networking: bridging the gap between informal and formal learning//MOOC, recursos de educación abierto y redes sociales: acortando la distancia entre aprendizaje informal y formal

    Directory of Open Access Journals (Sweden)

    Niall Sclater

    2016-07-01

    Full Text Available MOOCs and open educational resources (OER provide a wealth of learning opportunities for people around the globe, many of whom have no access to formal higher education. OER are often difficult to locate and are accessed on their own without support from or dialogue with subject experts and peers. This paper looks at whether it is possible to develop effective learning communities around OER and whether these communities can emerge spontaneously and in a self-organised way without moderation. It examines the complex interplay between formal and informal learning, and examines whether MOOCs are the answer to providing effective interaction and dialogue for those wishing to study at university level for free on the Internet.

  8. Formalizing Arrow's theorem

    Indian Academy of Sciences (India)

    Section 4 describes my first, aborted, attempt at a formalization, while Sections 5 to 7 present the formalization that was finished. Section 5 explains how I formalized orders and preorders. Section 6 presents a fragment of the formalization in detail, and Section 7 gives an example of how the formalization can be used to get ...

  9. De novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity

    Science.gov (United States)

    Boyken, Scott E.; Chen, Zibo; Groves, Benjamin; Langan, Robert A.; Oberdorfer, Gustav; Ford, Alex; Gilmore, Jason; Xu, Chunfu; DiMaio, Frank; Pereira, Jose Henrique; Sankaran, Banumathi; Seelig, Georg; Zwart, Peter H.; Baker, David

    2017-01-01

    In nature, structural specificity in DNA and proteins is encoded quite differently: in DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen bond networks with atomic accuracy is a milestone for protein design and enables the programming of protein interaction specificity for a broad range of synthetic biology applications. PMID:27151862

  10. HF beacon network for ionospheric specification in Peru

    Science.gov (United States)

    Hysell, D. L.; Milla, M. A.; Vierinen, J.

    2016-12-01

    A growing network of HF beacon transmitters and receivers is being deployed in Peru for specifying the F region ionosphere regionally. The effort is motivated by ionospheric disturbances associated with equatorial spread F (ESF), especially disturbances arising under inauspicious ESF conditions. The beacons use dual frequencies (2.72 and 3.64 MHz). They incorporate PRN coding to afford group-delay measurements. Scatered power, Doppler shift, bearing, and polarization are also measured. An algorithm for inverting the beacon data combined with electron density profiles from Jicamarca is described. Data and representative solutions from recent campaigns will be reviewed.

  11. Differential synchronization in default and task-specific networks of the human brain

    Directory of Open Access Journals (Sweden)

    Aaron eKirschner

    2012-05-01

    Full Text Available On a regional scale the brain is organized into dynamic functional networks. The activity within one of these, the default network, can be dissociated from that in other task-specific networks. All brain networks are connected structurally, but evidently are only transiently connected functionally. One hypothesis as to how such transient functional coupling occurs is that network formation and dissolution is mediated, or at least accompanied, by increases and decreases in oscillatory synchronization between constituent brain regions. If so, then we should be able to find transient differences in intra-network synchronization between the default network and a task-specific network. In order to investigate this hypothesis we conducted two experiments in which subjects engaged in a Sustained Attention to Response Task (SART while having brain activity recorded via high-density electroencephalography (EEG. We found that during periods when attention was focused internally (mind-wandering there was significantly more neural phase synchronization between brain regions associated with the default network, whereas during periods when subjects were focused on performing the visual task there was significantly more neural phase synchrony within a task-specific brain network that shared some of the same brain regions. These differences in network synchrony occurred in each of theta, alpha, and gamma frequency bands. A similar pattern of differential oscillatory power changes, indicating modulation of local synchronization by attention state, was also found. These results provide further evidence that the human brain is intrinsically organized into default and task-specific brain networks, and confirm that oscillatory synchronization is a potential mechanism for functional coupling within these networks.

  12. Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers

    Science.gov (United States)

    Chen, Hao; Zhu, Zhitu; Zhu, Yichun; Wang, Jian; Mei, Yunqing; Cheng, Yunfeng

    2015-01-01

    It is known that a disease is rarely a consequence of an abnormality of a single gene, but reflects the interactions of various processes in a complex network. Annotated molecular networks offer new opportunities to understand diseases within a systems biology framework and provide an excellent substrate for network-based identification of biomarkers. The network biomarkers and dynamic network biomarkers (DNBs) represent new types of biomarkers with protein–protein or gene–gene interactions that can be monitored and evaluated at different stages and time-points during development of disease. Clinical bioinformatics as a new way to combine clinical measurements and signs with human tissue-generated bioinformatics is crucial to translate biomarkers into clinical application, validate the disease specificity, and understand the role of biomarkers in clinical settings. In this article, the recent advances and developments on network biomarkers and DNBs are comprehensively reviewed. How network biomarkers help a better understanding of molecular mechanism of diseases, the advantages and constraints of network biomarkers for clinical application, clinical bioinformatics as a bridge to the development of diseases-specific, stage-specific, severity-specific and therapy predictive biomarkers, and the potentials of network biomarkers are also discussed. PMID:25560835

  13. Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers.

    Science.gov (United States)

    Chen, Hao; Zhu, Zhitu; Zhu, Yichun; Wang, Jian; Mei, Yunqing; Cheng, Yunfeng

    2015-02-01

    It is known that a disease is rarely a consequence of an abnormality of a single gene, but reflects the interactions of various processes in a complex network. Annotated molecular networks offer new opportunities to understand diseases within a systems biology framework and provide an excellent substrate for network-based identification of biomarkers. The network biomarkers and dynamic network biomarkers (DNBs) represent new types of biomarkers with protein-protein or gene-gene interactions that can be monitored and evaluated at different stages and time-points during development of disease. Clinical bioinformatics as a new way to combine clinical measurements and signs with human tissue-generated bioinformatics is crucial to translate biomarkers into clinical application, validate the disease specificity, and understand the role of biomarkers in clinical settings. In this article, the recent advances and developments on network biomarkers and DNBs are comprehensively reviewed. How network biomarkers help a better understanding of molecular mechanism of diseases, the advantages and constraints of network biomarkers for clinical application, clinical bioinformatics as a bridge to the development of diseases-specific, stage-specific, severity-specific and therapy predictive biomarkers, and the potentials of network biomarkers are also discussed. © 2015 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

  14. A validated regulatory network for Th17 cell specification

    Science.gov (United States)

    Ciofani, Maria; Madar, Aviv; Galan, Carolina; Sellars, Maclean; Mace, Kieran; Pauli, Florencia; Agarwal, Ashish; Huang, Wendy; Parkhurst, Christopher N.; Muratet, Michael; Newberry, Kim M.; Meadows, Sarah; Greenfield, Alex; Yang, Yi; Jain, Preti; Kirigin, Francis F.; Birchmeier, Carmen; Wagner, Erwin F.; Murphy, Kenneth M.; Myers, Richard M.; Bonneau, Richard; Littman, Dan R.

    2012-01-01

    Th17 cells have critical roles in mucosal defense and are major contributors to inflammatory disease. Their differentiation requires the nuclear hormone receptor RORγt working with multiple other essential transcription factors (TFs). We have used an iterative systems approach, combining genome-wide TF occupancy, expression profiling of TF mutants, and expression time series to delineate the Th17 global transcriptional regulatory network. We find that cooperatively-bound BATF and IRF4 contribute to initial chromatin accessibility, and with STAT3 initiate a transcriptional program that is then globally tuned by the lineage-specifying TF RORγt, which plays a focal deterministic role at key loci. Integration of multiple datasets allowed inference of an accurate predictive model that we computationally and experimentally validated, identifying multiple new Th17 regulators, including Fosl2, a key determinant of cellular plasticity. This interconnected network can be used to investigate new therapeutic approaches to manipulate Th17 functions in the setting of inflammatory disease. PMID:23021777

  15. Adolescent social networks: general and smoking-specific characteristics associated with smoking.

    Science.gov (United States)

    Roberts, Megan E; Nargiso, Jessica E; Gaitonde, Linda Brazil; Stanton, Cassandra A; Colby, Suzanne M

    2015-03-01

    Converging lines of research suggest that adolescents' smoking behaviors are strongly influenced by the characteristics of their social network and the social processes their network facilitates. The primary goal of this study was to conduct a detailed comparison of the social networks of adolescent smokers and nonsmokers to determine what aspects relate the most to smoking status. A secondary goal was to conduct within-group analyses to examine relationships between key measures of behavior-specific social support and (a) smoking susceptibility among nonsmokers, and (b) readiness to quit smoking among smokers. A matched sample of 190 adolescent smokers and nonsmokers (Mage = 16.8 years; 51% female) completed a questionnaire in which they nominated and reported on up to 10 important people in their lives. This measure allowed us to examine adolescents' overall networks (both peers and family) and to investigate numerous aspects, including general network characteristics (e.g., size of network, average contact with network members), social support (e.g., importance of people in the network), and the pervasiveness of smoking in the network (e.g., percentage of smoking peers). The pervasiveness of smoking in adolescents' social network was the strongest distinguisher of smokers versus nonsmokers. In addition, behavior-specific social support was strongly associated with susceptibility to initiate smoking among nonsmokers and readiness to quit among smokers. This research offers insight into potential targets for prevention and early intervention by demonstrating how social networks can both promote and attenuate risk for smoking.

  16. Adolescent Social Networks: General and Smoking-Specific Characteristics Associated With Smoking

    Science.gov (United States)

    Roberts, Megan E.; Nargiso, Jessica E.; Gaitonde, Linda Brazil; Stanton, Cassandra A.; Colby, Suzanne M.

    2015-01-01

    Objective: Converging lines of research suggest that adolescents’ smoking behaviors are strongly influenced by the characteristics of their social network and the social processes their network facilitates. The primary goal of this study was to conduct a detailed comparison of the social networks of adolescent smokers and nonsmokers to determine what aspects relate the most to smoking status. A secondary goal was to conduct within-group analyses to examine relationships between key measures of behavior-specific social support and (a) smoking susceptibility among nonsmokers, and (b) readiness to quit smoking among smokers. Method: A matched sample of 190 adolescent smokers and nonsmokers (Mage = 16.8 years; 51% female) completed a questionnaire in which they nominated and reported on up to 10 important people in their lives. This measure allowed us to examine adolescents’ overall networks (both peers and family) and to investigate numerous aspects, including general network characteristics (e.g., size of network, average contact with network members), social support (e.g., importance of people in the network), and the pervasiveness of smoking in the network (e.g., percentage of smoking peers). Results: The pervasiveness of smoking in adolescents’ social network was the strongest distinguisher of smokers versus nonsmokers. In addition, behavior-specific social support was strongly associated with susceptibility to initiate smoking among nonsmokers and readiness to quit among smokers. Conclusions: This research offers insight into potential targets for prevention and early intervention by demonstrating how social networks can both promote and attenuate risk for smoking. PMID:25785800

  17. Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees

    Directory of Open Access Journals (Sweden)

    Chen Xiaoyu

    2007-12-01

    Full Text Available Abstract Background In vertebrates, a large part of gene transcriptional regulation is operated by cis-regulatory modules. These modules are believed to be regulating much of the tissue-specificity of gene expression. Results We develop a Bayesian network approach for identifying cis-regulatory modules likely to regulate tissue-specific expression. The network integrates predicted transcription factor binding site information, transcription factor expression data, and target gene expression data. At its core is a regression tree modeling the effect of combinations of transcription factors bound to a module. A new unsupervised EM-like algorithm is developed to learn the parameters of the network, including the regression tree structure. Conclusion Our approach is shown to accurately identify known human liver and erythroid-specific modules. When applied to the prediction of tissue-specific modules in 10 different tissues, the network predicts a number of important transcription factor combinations whose concerted binding is associated to specific expression.

  18. Formal Methods: Practice and Experience

    DEFF Research Database (Denmark)

    Woodcock, Jim; Larsen, Peter Gorm; Bicarregui, Juan

    2009-01-01

    Formal methods use mathematical models for analysis and verification at any part of the program life-cycle. We describe the state of the art in the industrial use of formal methods, concentrating on their increasing use at the earlier stages of specification and design. We do this by reporting....... Based on this, we discuss the issues surrounding the industrial adoption of formal methods. Finally, we look to the future and describe the development of a Verified Software Repository, part of the worldwide Verified Software Initiative. We introduce the initial projects being used to populate...

  19. Formal Verification of UML Profil

    DEFF Research Database (Denmark)

    Bhutto, Arifa; Hussain, Dil Muhammad Akbar

    2011-01-01

    The Unified Modeling Language (UML) is based on the Model Driven Development (MDD) approach which capturing the system functionality using the platform-independent model (PMI) and appropriate domain-specific languages. In UML base system notations, structural view is model by the class, components...... and object diagrams and behavioral view model by the activity, use case, state, and sequence diagram. However, UML does not provide the formal syntax, therefore its semantics is not formally definable, so for assure of correctness, we need to incorporate semantic reasoning through verification, specification......, refinement, and incorporate into the development process. Our motivation of research is to make an easy structural view and suggest formal technique/ method which can be best applied or used for the UML based development system. We investigate the tools and methods, which broadly used for the formal...

  20. Network Analysis Identifies Disease-Specific Pathways for Parkinson's Disease.

    Science.gov (United States)

    Monti, Chiara; Colugnat, Ilaria; Lopiano, Leonardo; Chiò, Adriano; Alberio, Tiziana

    2018-01-01

    Neurodegenerative diseases are characterized by the progressive loss of specific neurons in selected regions of the central nervous system. The main clinical manifestation (movement disorders, cognitive impairment, and/or psychiatric disturbances) depends on the neuron population being primarily affected. Parkinson's disease is a common movement disorder, whose etiology remains mostly unknown. Progressive loss of dopaminergic neurons in the substantia nigra causes an impairment of the motor control. Some of the pathogenetic mechanisms causing the progressive deterioration of these neurons are not specific for Parkinson's disease but are shared by other neurodegenerative diseases, like Alzheimer's disease and amyotrophic lateral sclerosis. Here, we performed a meta-analysis of the literature of all the quantitative proteomic investigations of neuronal alterations in different models of Parkinson's disease, Alzheimer's disease, and amyotrophic lateral sclerosis to distinguish between general and Parkinson's disease-specific pattern of neurodegeneration. Then, we merged proteomics data with genetics information from the DisGeNET database. The comparison of gene and protein information allowed us to identify 25 proteins involved uniquely in Parkinson's disease and we verified the alteration of one of them, i.e., transaldolase 1 (TALDO1), in the substantia nigra of 5 patients. By using open-source bioinformatics tools, we identified the biological processes specifically affected in Parkinson's disease, i.e., proteolysis, mitochondrion organization, and mitophagy. Eventually, we highlighted four cellular component complexes mostly involved in the pathogenesis: the proteasome complex, the protein phosphatase 2A, the chaperonins CCT complex, and the complex III of the respiratory chain.

  1. The Global Genome Biodiversity Network (GGBN) Data Standard specification

    Science.gov (United States)

    Droege, G.; Barker, K.; Seberg, O.; Coddington, J.; Benson, E.; Berendsohn, W. G.; Bunk, B.; Butler, C.; Cawsey, E. M.; Deck, J.; Döring, M.; Flemons, P.; Gemeinholzer, B.; Güntsch, A.; Hollowell, T.; Kelbert, P.; Kostadinov, I.; Kottmann, R.; Lawlor, R. T.; Lyal, C.; Mackenzie-Dodds, J.; Meyer, C.; Mulcahy, D.; Nussbeck, S. Y.; O'Tuama, É.; Orrell, T.; Petersen, G.; Robertson, T.; Söhngen, C.; Whitacre, J.; Wieczorek, J.; Yilmaz, P.; Zetzsche, H.; Zhang, Y.; Zhou, X.

    2016-01-01

    Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today’s ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard. Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard PMID:27694206

  2. The Global Genome Biodiversity Network (GGBN) Data Standard specification.

    Science.gov (United States)

    Droege, G; Barker, K; Seberg, O; Coddington, J; Benson, E; Berendsohn, W G; Bunk, B; Butler, C; Cawsey, E M; Deck, J; Döring, M; Flemons, P; Gemeinholzer, B; Güntsch, A; Hollowell, T; Kelbert, P; Kostadinov, I; Kottmann, R; Lawlor, R T; Lyal, C; Mackenzie-Dodds, J; Meyer, C; Mulcahy, D; Nussbeck, S Y; O'Tuama, É; Orrell, T; Petersen, G; Robertson, T; Söhngen, C; Whitacre, J; Wieczorek, J; Yilmaz, P; Zetzsche, H; Zhang, Y; Zhou, X

    2016-01-01

    Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today's ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard.Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard. © The Author(s) 2016. Published by Oxford University Press.

  3. A disease-specific metabolic brain network associated with corticobasal degeneration

    NARCIS (Netherlands)

    Niethammer, Martin; Tang, Chris C.; Feigin, Andrew; Allen, Patricia J.; Heinen, Lisette; Hellwig, Sabine; Amtage, Florian; Hanspal, Era; Vonsattel, Jean Paul; Poston, Kathleen L.; Meyer, Philipp T.; Leenders, Klaus L.; Eidelberg, David

    2014-01-01

    Corticobasal degeneration is an uncommon parkinsonian variant condition that is diagnosed mainly on clinical examination. To facilitate the differential diagnosis of this disorder, we used metabolic brain imaging to characterize a specific network that can be used to discriminate corticobasal

  4. Analysis of network architecture reveals phylogenetic constraints on mycorrhizal specificity in the genus Orchis (Orchidaceae)

    National Research Council Canada - National Science Library

    Hans Jacquemyn; Vincent Merckx; Rein Brys; Daniel Tyteca; Bruno P. A. Cammue; Olivier Honnay; Bart Lievens

    2011-01-01

    ... of the mycorrhizal specificity of orchids. Here, we used a network analysis approach to investigate orchid mycorrhizal associations in 16 species of the genus Orchis sampled across 11 different regions in Europe...

  5. Identification of context-specific gene regulatory networks with GEMULA--Gene Expression Modeling Using LAsso

    NARCIS (Netherlands)

    Geeven, G.; van Kesteren, R.E.; Smit, A.B.; de Gunst, M.C.M.

    2012-01-01

    Motivation: Gene regulatory networks, in which edges between nodes describe interactions between transcriptional regulators and their target genes, determine the coordinated spatiotemporal expression of genes. Especially in higher organisms, context-specific combinatorial regulation by transcription

  6. Masses of Formal Philosophy

    DEFF Research Database (Denmark)

    Masses of Formal Philosophy is an outgrowth of Formal Philosophy. That book gathered the responses of some of the most prominent formal philosophers to five relatively open and broad questions initiating a discussion of metaphilosophical themes and problems surrounding the use of formal methods...... in philosophy. Including contributions from a wide range of philosophers, Masses of Formal Philosophy contains important new responses to the original five questions....

  7. Assessing the Increase in Specific Surface Area for Electrospun Fibrous Network due to Pore Induction.

    Science.gov (United States)

    Katsogiannis, Konstantinos Alexandros G; Vladisavljević, Goran T; Georgiadou, Stella; Rahmani, Ramin

    2016-10-26

    The effect of pore induction on increasing electrospun fibrous network specific surface area was investigated in this study. Theoretical models based on the available surface area of the fibrous network and exclusion of the surface area lost due to fiber-to-fiber contacts were developed. The models for calculation of the excluded area are based on Hertzian, Derjaguin-Muller-Toporov (DMT), and Johnson-Kendall-Roberts (JKR) contact models. Overall, the theoretical models correlated the network specific surface area to the material properties including density, surface tension, Young's modulus, Poisson's ratio, as well as network physical properties, such as density and geometrical characteristics including fiber radius, fiber aspect ratio and network thickness. Pore induction proved to increase the network specific surface area up to 52%, compared to the maximum surface area that could be achieved by nonporous fiber network with the same physical properties and geometrical characteristics. The model based on Johnson-Kendall-Roberts contact model describes accurately the fiber-to-fiber contact area under the experimental conditions used for pore generation. The experimental results and the theoretical model based on Johnson-Kendall-Roberts contact model show that the increase in network surface area due to pore induction can reach to up to 58%.

  8. Current and emerging approaches to define intestinal epithelium-specific transcriptional networks

    DEFF Research Database (Denmark)

    Olsen, Anders Krûger; Boyd, Mette; Danielsen, Erik Thomas

    2012-01-01

    Upon developmental or environmental cues, the composition of transcription factors in a transcriptional regulatory network is deeply implicated in controlling the signature of the gene expression and thereby specifies the cell- or tissue-type. Novel methods including ChIP-chip and ChIP-Seq have......, specific regulatory networks of transcription factors are activated to target specific genes, which determine the intestinal cell fate. The expanding genome-wide mapping of transcription factor binding sites and construction of transcriptional regulatory networks provide new insight into how intestinal...... differentiation is occurring. This review summarizes the current overview of the transcriptional regulatory networks driving the intestinal epithelial differentiation in adult. The novel technologies that have been implied to study these networks are presented and their prospects for implications in future...

  9. Automatic Testing with Formal Methods

    NARCIS (Netherlands)

    Tretmans, G.J.; Belinfante, Axel

    1999-01-01

    The use of formal system specifications makes it possible to automate the derivation of test cases from specifications. This allows to automate the whole testing process, not only the test execution part of it. This paper presents the state of the art and future perspectives in testing based on

  10. Polarity-specific high-level information propagation in neural networks.

    Science.gov (United States)

    Lin, Yen-Nan; Chang, Po-Yen; Hsiao, Pao-Yueh; Lo, Chung-Chuan

    2014-01-01

    Analyzing the connectome of a nervous system provides valuable information about the functions of its subsystems. Although much has been learned about the architectures of neural networks in various organisms by applying analytical tools developed for general networks, two distinct and functionally important properties of neural networks are often overlooked. First, neural networks are endowed with polarity at the circuit level: Information enters a neural network at input neurons, propagates through interneurons, and leaves via output neurons. Second, many functions of nervous systems are implemented by signal propagation through high-level pathways involving multiple and often recurrent connections rather than by the shortest paths between nodes. In the present study, we analyzed two neural networks: the somatic nervous system of Caenorhabditis elegans (C. elegans) and the partial central complex network of Drosophila, in light of these properties. Specifically, we quantified high-level propagation in the vertical and horizontal directions: the former characterizes how signals propagate from specific input nodes to specific output nodes and the latter characterizes how a signal from a specific input node is shared by all output nodes. We found that the two neural networks are characterized by very efficient vertical and horizontal propagation. In comparison, classic small-world networks show a trade-off between vertical and horizontal propagation; increasing the rewiring probability improves the efficiency of horizontal propagation but worsens the efficiency of vertical propagation. Our result provides insights into how the complex functions of natural neural networks may arise from a design that allows them to efficiently transform and combine input signals.

  11. On the existence of a generalized non-specific task-dependent network

    Directory of Open Access Journals (Sweden)

    Kenneth eHugdahl

    2015-08-01

    Full Text Available In this paper we suggest the existence of a generalized task-related cortical network that is up-regulated whenever the task to be performed requires the allocation of generalized non-specific cognitive resources, independent of the specifics of the task to be performed. We have labelled this general purpose network, the extrinsic mode network (EMN as complementary to the default mode network (DMN, such that the EMN is down-regulated during periods of task-absence, when the DMN is up-regulated, and vice versa. We conceptualize the EMN as a cortical network for extrinsic neuronal activity, similar to the DMN as being a cortical network for intrinsic neuronal activity. The EMN has essentially a fronto-temporo-parietal spatial distribution, including the inferior and middle frontal gyri, inferior parietal lobule, supplementary motor area, inferior temporal gyrus, We further hypothesize that this network is always active regardless of the cognitive task being performed. We suggest that failure of network up- and down-regulation dynamics may provide neuronal underpinnings for cognitive impairments seen in many mental disorders, such as e.g. schizophrenia. We start by describing a common observation in functional imaging, the close overlap in fronto-parietal activations in healthy individuals to tasks that denote very different cognitive processes. We now suggest that this is because the brain utilizes the EMN network as a generalized response to tasks that exceeds a cognitive demand threshold and/or requires the processing of novel information. We further discuss how the EMN is related to the DMN, and how a network for extrinsic activity is related to a network for intrinsic activity. Finally we discuss whether the EMN and DMN networks interact in a common single brain system, rather than being two separate and independent brain systems.

  12. A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo

    Science.gov (United States)

    Davidson, Eric H.; Rast, Jonathan P.; Oliveri, Paola; Ransick, Andrew; Calestani, Cristina; Yuh, Chiou-Hwa; Minokawa, Takuya; Amore, Gabriele; Hinman, Veronica; Arenas-Mena, Cesar; hide

    2002-01-01

    We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see http://www.its.caltech.edu/mirsky/endomeso.htm (End-mes Gene Network Update) for the latest version. The network contains over 40 genes at present, many newly uncovered in the course of this work, and most encoding DNA-binding transcriptional regulatory factors. The architecture of the network was approached initially by construction of a logic model that integrated the extensive experimental evidence now available on endomesoderm specification. The internal linkages between genes in the network have been determined functionally, by measurement of the effects of regulatory perturbations on the expression of all relevant genes in the network. Five kinds of perturbation have been applied: (1) use of morpholino antisense oligonucleotides targeted to many of the key regulatory genes in the network; (2) transformation of other regulatory factors into dominant repressors by construction of Engrailed repressor domain fusions; (3) ectopic expression of given regulatory factors, from genetic expression constructs and from injected mRNAs; (4) blockade of the beta-catenin/Tcf pathway by introduction of mRNA encoding the intracellular domain of cadherin; and (5) blockade of the Notch signaling pathway by introduction of mRNA encoding the extracellular domain of the Notch receptor. The network model predicts the cis-regulatory inputs that link each gene into the network. Therefore, its architecture is testable by cis-regulatory analysis. Strongylocentrotus purpuratus and Lytechinus variegatus genomic BAC recombinants that include a large number of the genes in the network have been sequenced and annotated. Tests of the cis-regulatory predictions of

  13. Allele-specific behavior of molecular networks: understanding small-molecule drug response in yeast.

    Directory of Open Access Journals (Sweden)

    Fan Zhang

    Full Text Available The study of systems genetics is changing the way the genetic and molecular basis of phenotypic variation, such as disease susceptibility and drug response, is being analyzed. Moreover, systems genetics aids in the translation of insights from systems biology into genetics. The use of systems genetics enables greater attention to be focused on the potential impact of genetic perturbations on the molecular states of networks that in turn affects complex traits. In this study, we developed models to detect allele-specific perturbations on interactions, in which a genetic locus with alternative alleles exerted a differing influence on an interaction. We utilized the models to investigate the dynamic behavior of an integrated molecular network undergoing genetic perturbations in yeast. Our results revealed the complexity of regulatory relationships between genetic loci and networks, in which different genetic loci perturb specific network modules. In addition, significant within-module functional coherence was found. We then used the network perturbation model to elucidate the underlying molecular mechanisms of individual differences in response to 100 diverse small molecule drugs. As a result, we identified sub-networks in the integrated network that responded to variations in DNA associated with response to diverse compounds and were significantly enriched for known drug targets. Literature mining results provided strong independent evidence for the effectiveness of these genetic perturbing networks in the elucidation of small-molecule responses in yeast.

  14. Building Real World Domain-Specific Social Network Websites as a Capstone Project

    Science.gov (United States)

    Yue, Kwok-Bun; De Silva, Dilhar; Kim, Dan; Aktepe, Mirac; Nagle, Stewart; Boerger, Chris; Jain, Anubha; Verma, Sunny

    2009-01-01

    This paper describes our experience of using Content Management Software (CMS), specifically Joomla, to build a real world domain-specific social network site (SNS) as a capstone project for graduate information systems and computer science students. As Web 2.0 technologies become increasingly important in driving business application development,…

  15. Motif formation and industry specific topologies in the Japanese business firm network

    Science.gov (United States)

    Maluck, Julian; Donner, Reik V.; Takayasu, Hideki; Takayasu, Misako

    2017-05-01

    Motifs and roles are basic quantities for the characterization of interactions among 3-node subsets in complex networks. In this work, we investigate how the distribution of 3-node motifs can be influenced by modifying the rules of an evolving network model while keeping the statistics of simpler network characteristics, such as the link density and the degree distribution, invariant. We exemplify this problem for the special case of the Japanese Business Firm Network, where a well-studied and relatively simple yet realistic evolving network model is available, and compare the resulting motif distribution in the real-world and simulated networks. To better approximate the motif distribution of the real-world network in the model, we introduce both subgraph dependent and global additional rules. We find that a specific rule that allows only for the merging process between nodes with similar link directionality patterns reduces the observed excess of densely connected motifs with bidirectional links. Our study improves the mechanistic understanding of motif formation in evolving network models to better describe the characteristic features of real-world networks with a scale-free topology.

  16. Optimizing the District Heating Primary Network from the Perspective of Economic-Specific Pressure Loss

    Directory of Open Access Journals (Sweden)

    Haichao Wang

    2017-07-01

    Full Text Available A district heating (DH system is one of the most important components of infrastructures in cold areas. Proper DH network design should balance the initial investment and the heat distribution cost of the DH network. Currently, this design is often based on a recommended value for specific pressure loss (R = ∆P/L in the main lines. This will result in a feasible network design, but probably not be optimal in most cases. The paper develops a novel optimization model to facilitate the design by considering the initial investment in the pipes and the heat distribution costs. The model will generate all possible network scenarios consisting of different series of diameters for each pipe in the flow direction of the network. Then, the annuity on the initial investment, the heat distribution cost, and the total annual cost will be calculated for each network scenario, taking into account the uncertainties of the material prices and the yearly operating time levels. The model is applied to a sample DH network and the results indicate that the model works quite well, clearly identifying the optimal network design and demonstrating that the heat distribution cost is more important than the initial investment in DH network design.

  17. A Network Analysis Approach to fMRI Condition-Specific Functional Connectivity

    CERN Document Server

    Shinkareva, Svetlana V; Wang, Jing

    2010-01-01

    In this work we focus on examination and comparison of whole-brain functional connectivity patterns measured with fMRI across experimental conditions. Direct examination and comparison of condition-specific matrices is challenging due to the large number of elements in a connectivity matrix. We present a framework that uses network analysis to describe condition-specific functional connectivity. Treating the brain as a complex system in terms of a network, we extract the most relevant connectivity information by partitioning each network into clusters representing functionally connected brain regions. Extracted clusters are used as features for predicting experimental condition in a new data set. The approach is illustrated on fMRI data examining functional connectivity patterns during processing of abstract and concrete concepts. Topological (brain regions) and functional (level of connectivity and information flow) systematic differences in the ROI-based functional networks were identified across participan...

  18. Pragmatics for formal semantics

    DEFF Research Database (Denmark)

    Danvy, Olivier

    2011-01-01

    This tech talk describes how to write and how to inter-derive formal semantics for sequential programming languages. The progress reported here is (1) concrete guidelines to write each formal semantics to alleviate their proof obligations, and (2) simple calculational tools to obtain a formal...

  19. Security Analysis of DTN Architecture and Bundle Protocol Specification for Space-Based Networks

    Science.gov (United States)

    Ivancic, William D.

    2009-01-01

    A Delay-Tolerant Network (DTN) Architecture (Request for Comment, RFC-4838) and Bundle Protocol Specification, RFC-5050, have been proposed for space and terrestrial networks. Additional security specifications have been provided via the Bundle Security Specification (currently a work in progress as an Internet Research Task Force internet-draft) and, for link-layer protocols applicable to Space networks, the Licklider Transport Protocol Security Extensions. This document provides a security analysis of the current DTN RFCs and proposed security related internet drafts with a focus on space-based communication networks, which is a rather restricted subset of DTN networks. Note, the original focus and motivation of DTN work was for the Interplanetary Internet . This document does not address general store-and-forward network overlays, just the current work being done by the Internet Research Task Force (IRTF) and the Consultative Committee for Space Data Systems (CCSDS) Space Internetworking Services Area (SIS) - DTN working group under the DTN and Bundle umbrellas. However, much of the analysis is relevant to general store-and-forward overlays.

  20. Formal aspects of resilience

    Directory of Open Access Journals (Sweden)

    Diana-Maria Drigă

    2015-12-01

    Full Text Available The concept of resilience has represented during the recent years a leading concern both in Romania, within the European Union and worldwide. Specialists in economics, management, finance, legal sciences, political sciences, sociology, psychology, grant a particular interest to this concept. Multidisciplinary research of resilience has materialized throughout the time in multiple conceptualizations and theorizing, but without being a consensus between specialists in terms of content, specificity and scope. Through this paper it is intended to clarify the concept of resilience, achieving an exploration of the evolution of this concept in ecological, social and economic environment. At the same time, the paper presents aspects of feedback mechanisms and proposes a formalization of resilience using the logic and mathematical analysis.

  1. Preliminary Proceedings First International Workshop on Formal Methods for WirelessSystems

    DEFF Research Database (Denmark)

    The FMWS workshops aim at bringing together researchers interested in formal methods for wireless systems, more specifically in theories for semantics, logics, and verification techniques for wireless systems. Wireless systems are rapidly increasing their success in real-world applications while...... formal methods for modelling, analysing, and verifying the systems are lacking behind. Recently however much attention has been carried out to model, analyse and verify Sensor Networks and, more generally, Ad Hoc Networks. This very first FMWS workshop is co-located with CONCUR '08, held in Toronto...

  2. Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.

    Directory of Open Access Journals (Sweden)

    Marco Galardini

    2015-09-01

    Full Text Available Reconstruction of the regulatory network is an important step in understanding how organisms control the expression of gene products and therefore phenotypes. Recent studies have pointed out the importance of regulatory network plasticity in bacterial adaptation and evolution. The evolution of such networks within and outside the species boundary is however still obscure. Sinorhizobium meliloti is an ideal species for such study, having three large replicons, many genomes available and a significant knowledge of its transcription factors (TF. Each replicon has a specific functional and evolutionary mark; which might also emerge from the analysis of their regulatory signatures. Here we have studied the plasticity of the regulatory network within and outside the S. meliloti species, looking for the presence of 41 TFs binding motifs in 51 strains and 5 related rhizobial species. We have detected a preference of several TFs for one of the three replicons, and the function of regulated genes was found to be in accordance with the overall replicon functional signature: house-keeping functions for the chromosome, metabolism for the chromid, symbiosis for the megaplasmid. This therefore suggests a replicon-specific wiring of the regulatory network in the S. meliloti species. At the same time a significant part of the predicted regulatory network is shared between the chromosome and the chromid, thus adding an additional layer by which the chromid integrates itself in the core genome. Furthermore, the regulatory network distance was found to be correlated with both promoter regions and accessory genome evolution inside the species, indicating that both pangenome compartments are involved in the regulatory network evolution. We also observed that genes which are not included in the species regulatory network are more likely to belong to the accessory genome, indicating that regulatory interactions should also be considered to predict gene conservation in

  3. Rotor and wind turbine formalism

    DEFF Research Database (Denmark)

    Branlard, Emmanuel Simon Pierre

    2017-01-01

    The main conventions used in this book for the study of rotors are introduced in this chapter. The main assumptions and notations are provided. The formalism specific to wind turbines is presented. The forces, moments, velocities and dimensionless coefficients used in the study of rotors...

  4. Repetitive Transcranial Magnetic Stimulation Educes Frequency-Specific Causal Relationships in the Motor Network.

    Science.gov (United States)

    Salinas, Felipe S; Franklin, Crystal; Narayana, Shalini; Szabó, C Ákos; Fox, Peter T

    2016-01-01

    Repetitive transcranial magnetic stimulation (rTMS) has the potential to treat brain disorders by modulating the activity of disease-specific brain networks, yet the rTMS frequencies used are delivered in a binary fashion - excitatory (>1 Hz) and inhibitory (≤1 Hz). To assess the effective connectivity of the motor network at different rTMS stimulation rates during positron-emission tomography (PET) and confirm that not all excitatory rTMS frequencies act on the motor network in the same manner. We delivered image-guided, supra-threshold rTMS at 3 Hz, 5 Hz, 10 Hz, 15 Hz and rest (in separate randomized sessions) to the primary motor cortex (M1) of the lightly anesthetized baboon during PET imaging. Each rTMS/PET session was analyzed using normalized cerebral blood flow (CBF) measurements. Path analysis - using structural equation modeling (SEM) - was employed to determine the effective connectivity of the motor network at all rTMS frequencies. Once determined, the final model of the motor network was used to assess any differences in effective connectivity at each rTMS frequency. The exploratory SEM produced a very well fitting final network model (χ(2) = 18.04, df = 21, RMSEA = 0.000, p = 0.647, TLI = 1.12) using seven nodes of the motor network. 5 Hz rTMS produced the strongest path coefficients in four of the seven connections, suggesting that this frequency is the optimal rTMS frequency for stimulation the motor network (as a whole); however, the premotor cerebellum connection was optimally stimulated at 10 Hz rTMS and the supplementary motor area caudate connection was optimally driven at 15 Hz rTMS. We have demonstrated that 1) 5 Hz rTMS revealed the strongest path coefficients (i.e. causal influence) on the nodes of the motor network, 2) stimulation at "excitatory" rTMS frequencies did not produce increased CBF in all nodes of the motor network, 3) specific rTMS frequencies may be used to target specific none

  5. Identification and characterization of the leaf specific networks of inner and rosette leaves in Brassica rapa.

    Science.gov (United States)

    Kim, Man-Sun; Hong, Seongmin; Devaraj, Sangeeth Prasath; Im, Subin; Kim, Jeong-Rae; Lim, Yong Pyo

    2017-08-26

    Inner and rosette leaves of Chinese cabbage (Brassica rapa) have different characteristics in terms of nutritional value, appearance, taste, color and texture. Many researchers have utilized differentially expressed genes for exploring the difference between inner and rosette leaves of Brassica rapa. The functional characteristics of a gene, however, is determined by complex interactions between genes. Hence, a noble network approach is required for elucidating such functional difference that is not captured by gene expression profiles alone. In this study, we measured gene expression in the standard cabbage genome by RNA-Sequencing and constructed rosette and inner leaf networks based on the gene expression profiles. Furthermore, we compared the topological and functional characteristics of these networks. We found significant functional difference between the rosette and inner leaf networks. Specifically, we found that the genes in the rosette leaf network were associated with homeostasis and response to external stimuli whereas the genes in the inner leaf network were mainly related to the glutamine biosynthesis processes and developmental processes with hormones. Overall, the network approach provides an insight into the functional difference of the two leaves. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Molecular evolution constraints in the floral organ specification gene regulatory network module across 18 angiosperm genomes.

    Science.gov (United States)

    Davila-Velderrain, Jose; Servin-Marquez, Andres; Alvarez-Buylla, Elena R

    2014-03-01

    The gene regulatory network of floral organ cell fate specification of Arabidopsis thaliana is a robust developmental regulatory module. Although such finding was proposed to explain the overall conservation of floral organ types and organization among angiosperms, it has not been confirmed that the network components are conserved at the molecular level among flowering plants. Using the genomic data that have accumulated, we address the conservation of the genes involved in this network and the forces that have shaped its evolution during the divergence of angiosperms. We recovered the network gene homologs for 18 species of flowering plants spanning nine families. We found that all the genes are highly conserved with no evidence of positive selection. We studied the sequence conservation features of the genes in the context of their known biological function and the strength of the purifying selection acting upon them in relation to their placement within the network. Our results suggest an association between protein length and sequence conservation, evolutionary rates, and functional category. On the other hand, we found no significant correlation between the strength of purifying selection and gene placement. Our results confirm that the studied robust developmental regulatory module has been subjected to strong functional constraints. However, unlike previous studies, our results do not support the notion that network topology plays a major role in constraining evolutionary rates. We speculate that the dynamical functional role of genes within the network and not just its connectivity could play an important role in constraining evolution.

  7. Industrial use of formal methods formal verification

    CERN Document Server

    Boulanger, Jean-Louis

    2012-01-01

    At present the literature gives students and researchers of the very general books on the formal technics. The purpose of this book is to present in a single book, a return of experience on the used of the "formal technics" (such proof and model-checking) on industrial examples for the transportation domain. This book is based on the experience of people which are completely involved in the realization and the evaluation of safety critical system software based.  The implication of the industrialists allows to raise the problems of confidentiality which could appear and so allow

  8. Current and emerging approaches to define intestinal epithelium-specific transcriptional networks

    DEFF Research Database (Denmark)

    Olsen, Anders Krüger; Boyd, Mette; Danielsen, Erik Thomas

    2012-01-01

    Upon developmental or environmental cues, the composition of transcription factors in a transcriptional regulatory network is deeply implicated in controlling the signature of the gene expression and thereby specifies the cell or tissue type. Novel methods including ChIP-chip and ChIP-Seq have been...... applied to analyze known transcription factors and their interacting regulatory DNA elements in the intestine. The intestine is an example of a dynamic tissue where stem cells in the crypt proliferate and undergo a differentiation process toward the villus. During this differentiation process, specific...... regulatory networks of transcription factors are activated to target specific genes, which determine the intestinal cell fate. The expanding genomewide mapping of transcription factor binding sites and construction of transcriptional regulatory networks provide new insight into how intestinal differentiation...

  9. PROCEED and Crowd-sourced Formal Verification

    Science.gov (United States)

    2011-11-07

    VA November 7, 2011 PROCEED and Crowd-sourced Formal Verification Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting...TITLE AND SUBTITLE PROCEED and Crowd-sourced Formal Verification 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d... Formal Verification (CSFV) Approved for Public Release, Distribution Unlimited. The Problem Application specific functions Are there fundamental

  10. Formal Verification of Mathematical Software. Volume 2

    Science.gov (United States)

    1990-05-01

    copy RAfJC-TR-90-53, Vol I (of twol Final Techrical Report ?"ay 1990 AD-A223 633 FORMAL VERIFICATION OF MATHEMATICAL SOFTWARE DTIC ELECTE Odyssey...copies of this report unless contractual obligations or notices on a specific document require that it be returned. FORMAL VERIFICATION OF...1 May 1986 Contract Expiration Date: 31 July 1989 Short Title of Work: Formal Verification of SDI Mathematical Software Period of Work Covered: May 86

  11. The binding problem in population neurodynamics: a network model for stimulus-specific coherent oscillations.

    Science.gov (United States)

    Pavlásek, J

    1998-12-01

    A hypothesis is presented that coherent oscillatory discharges of spatially distributed neuronal groups (the supposed binding mechanism) are the result of the convergence of stimulus-dependent activity in modality-specific afferent pathways with oscillatory activity generated in unspecific sensory systems. This view is supported by simulation experiments on model networks.

  12. Chromatin states modify network motifs contributing to cell-specific functions

    Science.gov (United States)

    Zhao, Hongying; Liu, Tingting; Liu, Ling; Zhang, Guanxiong; Pang, Lin; Yu, Fulong; Fan, Huihui; Ping, Yanyan; Wang, Li; Xu, Chaohan; Xiao, Yun; Li, Xia

    2015-01-01

    Epigenetic modification can affect many important biological processes, such as cell proliferation and apoptosis. It can alter chromatin conformation and contribute to gene regulation. To investigate how chromatin states associated with network motifs, we assembled chromatin state-modified regulatory networks by combining 269 ChIP-seq data and chromatin states in four cell types. We found that many chromatin states were significantly associated with network motifs, especially for feedforward loops (FFLs). These distinct chromatin state compositions contribute to different expression levels and translational control of targets in FFLs. Strikingly, the chromatin state-modified FFLs were highly cell-specific and, to a large extent, determined cell-selective functions, such as the embryonic stem cell-specific bivalent modification-related FFL with an important role in poising developmentally important genes for expression. Besides, comparisons of chromatin state-modified FFLs between cancerous/stem and primary cell lines revealed specific type of chromatin state alterations that may act together with motif structural changes cooperatively contribute to cell-to-cell functional differences. Combination of these alterations could be helpful in prioritizing candidate genes. Together, this work highlights that a dynamic epigenetic dimension can help network motifs to control cell-specific functions. PMID:26169043

  13. A Specification-Based IDS for Detecting Attacks on RPL-Based Network Topology

    Directory of Open Access Journals (Sweden)

    Anhtuan Le

    2016-05-01

    Full Text Available Routing Protocol for Low power and Lossy network (RPL topology attacks can downgrade the network performance significantly by disrupting the optimal protocol structure. To detect such threats, we propose a RPL-specification, obtained by a semi-auto profiling technique that constructs a high-level abstract of operations through network simulation traces, to use as reference for verifying the node behaviors. This specification, including all the legitimate protocol states and transitions with corresponding statistics, will be implemented as a set of rules in the intrusion detection agents, in the form of the cluster heads propagated to monitor the whole network. In order to save resources, we set the cluster members to report related information about itself and other neighbors to the cluster head instead of making the head overhearing all the communication. As a result, information about a cluster member will be reported by different neighbors, which allow the cluster head to do cross-check. We propose to record the sequence in RPL Information Object (DIO and Information Solicitation (DIS messages to eliminate the synchronized issue created by the delay in transmitting the report, in which the cluster head only does cross-check on information that come from sources with the same sequence. Simulation results show that the proposed Intrusion Detection System (IDS has a high accuracy rate in detecting RPL topology attacks, while only creating insignificant overhead (about 6.3% that enable its scalability in large-scale network.

  14. A Hh-driven gene network controls specification, pattern and size of the Drosophila simple eyes.

    Science.gov (United States)

    Aguilar-Hidalgo, Daniel; Domínguez-Cejudo, María A; Amore, Gabriele; Brockmann, Anette; Lemos, María C; Córdoba, Antonio; Casares, Fernando

    2013-01-01

    During development, extracellular signaling molecules interact with intracellular gene networks to control the specification, pattern and size of organs. One such signaling molecule is Hedgehog (Hh). Hh is known to act as a morphogen, instructing different fates depending on the distance to its source. However, how Hh, when signaling across a cell field, impacts organ-specific transcriptional networks is still poorly understood. Here, we investigate this issue during the development of the Drosophila ocellar complex. The development of this sensory structure, which is composed of three simple eyes (or ocelli) located at the vertices of a triangular patch of cuticle on the dorsal head, depends on Hh signaling and on the definition of three domains: two areas of eya and so expression--the prospective anterior and posterior ocelli--and the intervening interocellar domain. Our results highlight the role of the homeodomain transcription factor engrailed (en) both as a target and as a transcriptional repressor of hh signaling in the prospective interocellar region. Furthermore, we identify a requirement for the Notch pathway in the establishment of en maintenance in a Hh-independent manner. Therefore, hh signals transiently during the specification of the interocellar domain, with en being required here for hh signaling attenuation. Computational analysis further suggests that this network design confers robustness to signaling noise and constrains phenotypic variation. In summary, using genetics and modeling we have expanded the ocellar gene network to explain how the interaction between the Hh gradient and this gene network results in the generation of stable mutually exclusive gene expression domains. In addition, we discuss some general implications our model may have in some Hh-driven gene networks.

  15. Enhancing System Realisation in Formal Model Development

    DEFF Research Database (Denmark)

    Tran-Jørgensen, Peter Würtz Vinther

    – a formal methods tool that supports the Vienna Development Method. The development of the code generation infrastructure has involved the re-design of the software architecture of Overture. The new architecture brings forth the reuse and extensibility features of Overture to take into account the needs......Software for mission-critical systems is sometimes analysed using formal specification to increase the chances of the system behaving as intended. When sufficient insights into the system have been obtained from the formal analysis, the formal specification is realised in the form of a software...... implementation. One way to realise the system’s software is by automatically generating it from the formal specification – a technique referred to as code generation. However, in general it is difficult to make guarantees about the correctness of the generated code – especially while requiring automation...

  16. Geometry and Formal Linguistics.

    Science.gov (United States)

    Huff, George A.

    This paper presents a method of encoding geometric line-drawings in a way which allows sets of such drawings to be interpreted as formal languages. A characterization of certain geometric predicates in terms of their properties as languages is obtained, and techniques usually associated with generative grammars and formal automata are then applied…

  17. Fear of the Formal

    DEFF Research Database (Denmark)

    du Gay, Paul; Lopdrup-Hjorth, Thomas

    Over recent decades, institutions exhibiting high degrees of formality have come in for severe criticism. From the private to the public sector, and across a whole spectrum of actors spanning from practitioners to academics, formal organization is viewed with increasing doubt and skepticism. In a...

  18. Formality in Brackets

    DEFF Research Database (Denmark)

    Garsten, Christina; Nyqvist, Anette

    Ethnographic work in formal organizations involves learning to recognize the many layers of front stage and back stage of organized life, and to bracket formality. It means to be alert to the fact that what is formal and front stage for one some actors, and in some situations, may in fact be back...... stage and informal for others. Walking the talk, donning the appropriate attire, wearing the proper suit, may be part of what is takes to figure out the code of formal organizational settings – an entrance ticket to the backstage, as it were. Oftentimes, it involves a degree of mimicry, of ‘following...... suits’ (Nyqvist 2013), and of doing ‘ethnography by failure’ (Garsten 2013). In this paper, we explore the layers of informality and formality in our fieldwork experiences among financial investors and policy experts, and discuss how to ethnographically represent embodied fieldwork practices. How do we...

  19. Network Delays and Link Capacities in Application-Specific Wormhole NoCs

    Directory of Open Access Journals (Sweden)

    Zvika Guz

    2007-01-01

    Full Text Available Network-on-chip- (NoC- based application-specific systems on chip, where information traffic is heterogeneous and delay requirements may largely vary, require individual capacity assignment for each link in the NoC. This is in contrast to the standard approach of on- and off-chip interconnection networks which employ uniform-capacity links. Therefore, the allocation of link capacities is an essential step in the automated design process of NoC-based systems. The algorithm should minimize the communication resource costs under Quality-of-Service timing constraints. This paper presents a novel analytical delay model for virtual channeled wormhole networks with nonuniform links and applies the analysis in devising an efficient capacity allocation algorithm which assigns link capacities such that packet delay requirements for each flow are satisfied.

  20. Disease-specific clinical trials networks: the example of cystic fibrosis.

    Science.gov (United States)

    De Boeck, Kris; Bulteel, Veerle; Fajac, Isabelle

    2016-06-01

    This article describes the steps of the development and the structure of a disease-specific clinical trials network for cystic fibrosis in Europe. Activities such as reviewing study protocols, feasibility assessments, training and standardizing of procedures, and outcome measurements help to bring high-quality clinical trials to the patients. Cooperation with the pharmaceutical industry, other research networks, patient organizations, and regulatory agencies is very important throughout all activities. The European Cystic Fibrosis Society-Clinical Trials Network facilitates the development of new treatments for a rare disease and could be a prototype for other diseases. • Clinical research has led to the first approved treatments targeting the basic Cystic Fibrosis defect. • For a rare disease like Cystic Fibrosis, multicenter international collaboration is needed to obtain solid evidence when testing possible new treatments. What is New: • The Clinical Trials Network established by the European Cystic Fibrosis Society has grown to a fully operational network with well-defined structures, procedures and partnerships. • Standardization of outcome parameters, protocol review, feasibility assessment and other activities help to develop high quality, efficient, relevant and feasible clinical trials, with the aim to bring new treatments to the patients.

  1. Symptom-specific amygdala hyperactivity modulates motor control network in conversion disorder

    Directory of Open Access Journals (Sweden)

    Thomas Hassa

    2017-01-01

    Full Text Available Initial historical accounts as well as recent data suggest that emotion processing is dysfunctional in conversion disorder patients and that this alteration may be the pathomechanistic neurocognitive basis for symptoms in conversion disorder. However, to date evidence of direct interaction of altered negative emotion processing with motor control networks in conversion disorder is still lacking. To specifically study the neural correlates of emotion processing interacting with motor networks we used a task combining emotional and sensorimotor stimuli both separately as well as simultaneously during functional magnetic resonance imaging in a well characterized group of 13 conversion disorder patients with functional hemiparesis and 19 demographically matched healthy controls. We performed voxelwise statistical parametrical mapping for a priori regions of interest within emotion processing and motor control networks. Psychophysiological interaction (PPI was used to test altered functional connectivity of emotion and motor control networks. Only during simultaneous emotional stimulation and passive movement of the affected hand patients displayed left amygdala hyperactivity. PPI revealed increased functional connectivity in patients between the left amygdala and the (pre-supplemental motor area and the subthalamic nucleus, key regions within the motor control network. These findings suggest a novel mechanistic direct link between dysregulated emotion processing and motor control circuitry in conversion disorder.

  2. Transnational issue-specific expert networking: A pathway to local policy change.

    Science.gov (United States)

    O'Brien, Cheryl

    2015-12-01

    This article reports on key findings from a study of subnational governments in Mexico and Nigeria (O'Brien, 2013). With empirical richness of the case study method and small-n statistical analysis across the subnational units for each country, this study asks: How can we push the needle toward more progressive policy change on violence against women in developing and democratizing contexts? This study finds that issue-specific expert networking is a civic pathway to subnational policy responsiveness in Mexico and Nigeria. The dynamics of this pathway illuminate local-global political connections, and this study shows how issue-specific expert networking is important for the diffusion of an international norm and policies on violence against women. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. The Benefits of Formalization

    DEFF Research Database (Denmark)

    Rand, John; Torm, Nina Elisabeth

    2012-01-01

    Based on unique panel data consisting of both formal and informal firms, this paper uses a matched double difference approach to examine the relationship between legal status and firm level outcomes in micro, small and medium manufacturing enterprises (SMEs) in Vietnam. Controlling for determining...... factors and observable time-variant factors that may simultaneously influence the decision to formalize and subsequent firm performance, we find evidence that becoming officially registered leads to an increase in profits and investments, and a decrease in the use of casual labor (improved contract...... conditions for workers). Thus, we conclude that formalizing is beneficial both to firms and the workers in these firms....

  4. Formal description of board games

    OpenAIRE

    Nowak, Stanislav

    2011-01-01

    The aim of thesis was to design a mathematical formalism that allows describing and exploring the properties of board games. The work benefits from the findings of automata theory and logic programming. First part of thesis deals with finite automata and their possible applications for the needs of board games. The result is an extension of finite-state automaton covering the specifics of board games called game automaton. Board games are a complex domain hight level tools should be used. Suc...

  5. Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.

    Directory of Open Access Journals (Sweden)

    Todd P Michael

    2008-02-01

    Full Text Available Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation.

  6. Overview of Distributed Control Systems Formalisms

    Directory of Open Access Journals (Sweden)

    Peter Holecko

    2008-01-01

    Full Text Available This paper discusses a chosen set of mainly object-oriented formal and semiformal methods, methodics, environments and tools for specification, analysis, modeling, simulation, verification, development and synthesis of distributed control systems (DCS.

  7. Optimization of a hydrometric network extension using specific flow, kriging and simulated annealing

    Science.gov (United States)

    Chebbi, Afef; Kebaili Bargaoui, Zoubeida; Abid, Nesrine; da Conceição Cunha, Maria

    2017-12-01

    In hydrometric stations, water levels are continuously observed and discharge rating curves are constantly updated to achieve accurate river levels and discharge observations. An adequate spatial distribution of hydrological gauging stations presents a lot of interest in linkage with the river regime characterization, water infrastructures design, water resources management and ecological survey. Due to the increase of riverside population and the associated flood risk, hydrological networks constantly need to be developed. This paper suggests taking advantage of kriging approaches to improve the design of a hydrometric network. The context deals with the application of an optimization approach using ordinary kriging and simulated annealing (SA) in order to identify the best locations to install new hydrometric gauges. The task at hand is to extend an existing hydrometric network in order to estimate, at ungauged sites, the average specific annual discharge which is a key basin descriptor. This methodology is developed for the hydrometric network of the transboundary Medjerda River in the North of Tunisia. A Geographic Information System (GIS) is adopted to delineate basin limits and centroids. The latter are adopted to assign the location of basins in kriging development. Scenarios where the size of an existing 12 stations network is alternatively increased by 1, 2, 3, 4 and 5 new station(s) are investigated using geo-regression and minimization of the variance of kriging errors. The analysis of the optimized locations from a scenario to another shows a perfect conformity with respect to the location of the new sites. The new locations insure a better spatial coverage of the study area as seen with the increase of both the average and the maximum of inter-station distances after optimization. The optimization procedure selects the basins that insure the shifting of the mean drainage area towards higher specific discharges.

  8. Formalizing Arrow's theorem

    Indian Academy of Sciences (India)

    Keywords. formalization of mathematics; Mizar; social choice theory; Arrow's theorem; Gibbard–Satterthwaite theorem; proof errors. ... Author Affiliations. Freek Wiedijk1. Institute for Computing and Information Sciences, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands ...

  9. Frequency-specific electrophysiologic correlates of resting state fMRI networks.

    Science.gov (United States)

    Hacker, Carl D; Snyder, Abraham Z; Pahwa, Mrinal; Corbetta, Maurizio; Leuthardt, Eric C

    2017-04-01

    Resting state functional MRI (R-fMRI) studies have shown that slow (<0.1Hz), intrinsic fluctuations of the blood oxygen level dependent (BOLD) signal are temporally correlated within hierarchically organized functional systems known as resting state networks (RSNs) (Doucet et al., 2011). Most broadly, this hierarchy exhibits a dichotomy between two opposed systems (Fox et al., 2005). One system engages with the environment and includes the visual, auditory, and sensorimotor (SMN) networks as well as the dorsal attention network (DAN), which controls spatial attention. The other system includes the default mode network (DMN) and the fronto-parietal control system (FPC), RSNs that instantiate episodic memory and executive control, respectively. Here, we test the hypothesis, based on the spectral specificity of electrophysiologic responses to perceptual vs. memory tasks (Klimesch, 1999; Pfurtscheller and Lopes da Silva, 1999), that these two large-scale neural systems also manifest frequency specificity in the resting state. We measured the spatial correspondence between electrocorticographic (ECoG) band-limited power (BLP) and R-fMRI correlation patterns in awake, resting, human subjects. Our results show that, while gamma BLP correspondence was common throughout the brain, theta (4-8Hz) BLP correspondence was stronger in the DMN and FPC, whereas alpha (8-12Hz) correspondence was stronger in the SMN and DAN. Thus, the human brain, at rest, exhibits frequency specific electrophysiology, respecting both the spectral structure of task responses and the hierarchical organization of RSNs. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  10. A biochemical network can control formation of a synthetic material by sensing numerous specific stimuli.

    Science.gov (United States)

    Hun Yeon, Ju; Chan, Karen Y T; Wong, Ting-Chia; Chan, Kelvin; Sutherland, Michael R; Ismagilov, Rustem F; Pryzdial, Edward L G; Kastrup, Christian J

    2015-05-15

    Developing bio-compatible smart materials that assemble in response to environmental cues requires strategies that can discriminate multiple specific stimuli in a complex milieu. Synthetic materials have yet to achieve this level of sensitivity, which would emulate the highly evolved and tailored reaction networks of complex biological systems. Here we show that the output of a naturally occurring network can be replaced with a synthetic material. Exploiting the blood coagulation system as an exquisite biological sensor, the fibrin clot end-product was replaced with a synthetic material under the biological control of a precisely regulated cross-linking enzyme. The functions of the coagulation network remained intact when the material was incorporated. Clot-like polymerization was induced in indirect response to distinct small molecules, phospholipids, enzymes, cells, viruses, an inorganic solid, a polyphenol, a polysaccharide, and a membrane protein. This strategy demonstrates for the first time that an existing stimulus-responsive biological network can be used to control the formation of a synthetic material by diverse classes of physiological triggers.

  11. Electro-acupuncture at different acupoints modulating the relative specific brain functional network

    Science.gov (United States)

    Fang, Jiliang; Wang, Xiaoling; Wang, Yin; Liu, Hesheng; Hong, Yang; Liu, Jun; Zhou, Kehua; Wang, Lei; Xue, Chao; Song, Ming; Liu, Baoyan; Zhu, Bing

    2010-11-01

    Objective: The specific brain effects of acupoint are important scientific concern in acupuncture. However, previous acupuncture fMRI studies focused on acupoints in muscle layer on the limb. Therefore, researches on acupoints within connective tissue at trunk are warranted. Material and Methods: Brain effects of acupuncture on abdomen at acupoints Guanyuan (CV4) and Zhongwan (CV12) were tested using fMRI on 21 healthy volunteers. The data acquisition was performed at resting state, during needle retention, electroacupuncture (EA) and post-EA resting state. Needling sensations were rated after every electroacupuncture (EA) procedure. The needling sensations and the brain functional activity and connectivity were compared between CV4 and CV12 using SPSS, SPM2 and the local and remote connectivity maps. Results and conclusion: EA at CV4 and CV12 induced apparent deactivation effects in the limbic-paralimbic-neocortical network. The default mode of the brain was modified by needle retention and EA, respectively. The functional brain network was significantly changed post EA. However, the minor differences existed between these two acupoints. The results demonstrated similarity between functional brain network mode of acupuncture modulation and functional circuits of emotional and cognitive regulation. Acupuncture may produce analgesia, anti-anxiety and anti-depression via the limbic-paralimbic-neocortical network (LPNN).

  12. A new training algorithm using artificial neural networks to classify gender-specific dynamic gait patterns.

    Science.gov (United States)

    Andrade, Andre; Costa, Marcelo; Paolucci, Leopoldo; Braga, Antônio; Pires, Flavio; Ugrinowitsch, Herbert; Menzel, Hans-Joachim

    2015-01-01

    The aim of this study was to present a new training algorithm using artificial neural networks called multi-objective least absolute shrinkage and selection operator (MOBJ-LASSO) applied to the classification of dynamic gait patterns. The movement pattern is identified by 20 characteristics from the three components of the ground reaction force which are used as input information for the neural networks in gender-specific gait classification. The classification performance between MOBJ-LASSO (97.4%) and multi-objective algorithm (MOBJ) (97.1%) is similar, but the MOBJ-LASSO algorithm achieved more improved results than the MOBJ because it is able to eliminate the inputs and automatically select the parameters of the neural network. Thus, it is an effective tool for data mining using neural networks. From 20 inputs used for training, MOBJ-LASSO selected the first and second peaks of the vertical force and the force peak in the antero-posterior direction as the variables that classify the gait patterns of the different genders.

  13. Reconstruction and Analysis of Human Kidney-Specific Metabolic Network Based on Omics Data

    Directory of Open Access Journals (Sweden)

    Ai-Di Zhang

    2013-01-01

    Full Text Available With the advent of the high-throughput data production, recent studies of tissue-specific metabolic networks have largely advanced our understanding of the metabolic basis of various physiological and pathological processes. However, for kidney, which plays an essential role in the body, the available kidney-specific model remains incomplete. This paper reports the reconstruction and characterization of the human kidney metabolic network based on transcriptome and proteome data. In silico simulations revealed that house-keeping genes were more essential than kidney-specific genes in maintaining kidney metabolism. Importantly, a total of 267 potential metabolic biomarkers for kidney-related diseases were successfully explored using this model. Furthermore, we found that the discrepancies in metabolic processes of different tissues are directly corresponding to tissue's functions. Finally, the phenotypes of the differentially expressed genes in diabetic kidney disease were characterized, suggesting that these genes may affect disease development through altering kidney metabolism. Thus, the human kidney-specific model constructed in this study may provide valuable information for the metabolism of kidney and offer excellent insights into complex kidney diseases.

  14. A new method for discovering disease-specific MiRNA-target regulatory networks.

    Directory of Open Access Journals (Sweden)

    Miriam Baglioni

    Full Text Available Genes and their expression regulation are among the key factors in the comprehension of the genesis and development of complex diseases. In this context, microRNAs (miRNAs are post-transcriptional regulators that play an important role in gene expression since they are frequently deregulated in pathologies like cardiovascular disease and cancer. In vitro validation of miRNA--targets regulation is often too expensive and time consuming to be carried out for every possible alternative. As a result, a tool able to provide some criteria to prioritize trials is becoming a pressing need. Moreover, before planning in vitro experiments, the scientist needs to evaluate the miRNA-target genes interaction network. In this paper we describe the miRable method whose purpose is to identify new potentially relevant genes and their interaction networks associate to a specific pathology. To achieve this goal miRable follows a system biology approach integrating together general-purpose medical knowledge (literature, Protein-Protein Interaction networks, prediction tools and pathology specific data (gene expression data. A case study on Prostate Cancer has shown that miRable is able to: 1 find new potential miRNA-targets pairs, 2 highlight novel genes potentially involved in a disease but never or little studied before, 3 reconstruct all possible regulatory subnetworks starting from the literature to expand the knowledge on the regulation of miRNA regulatory mechanisms.

  15. Topological specificity and hierarchical network of the circadian calcium rhythm in the suprachiasmatic nucleus.

    Science.gov (United States)

    Enoki, Ryosuke; Kuroda, Shigeru; Ono, Daisuke; Hasan, Mazahir T; Ueda, Tetsuo; Honma, Sato; Honma, Ken-ichi

    2012-12-26

    The circadian pacemaker in the hypothalamic suprachiasmatic nucleus (SCN) is a hierarchical multioscillator system in which neuronal networks play crucial roles in expressing coherent rhythms in physiology and behavior. However, our understanding of the neuronal network is still incomplete. Intracellular calcium mediates the input signals, such as phase-resetting stimuli, to the core molecular loop involving clock genes for circadian rhythm generation and the output signals from the loop to various cellular functions, including changes in neurotransmitter release. Using a unique large-scale calcium imaging method with genetically encoded calcium sensors, we visualized intracellular calcium from the entire surface of SCN slice in culture including the regions where autonomous clock gene expression was undetectable. We found circadian calcium rhythms at a single-cell level in the SCN, which were topologically specific with a larger amplitude and more delayed phase in the ventral region than the dorsal. The robustness of the rhythm was reduced but persisted even after blocking the neuronal firing with tetrodotoxin (TTX). Notably, TTX dissociated the circadian calcium rhythms between the dorsal and ventral SCN. In contrast, a blocker of gap junctions, carbenoxolone, had only a minor effect on the calcium rhythms at both the single-cell and network levels. These results reveal the topological specificity of the circadian calcium rhythm in the SCN and the presence of coupled regional pacemakers in the dorsal and ventral regions. Neuronal firings are not necessary for the persistence of the calcium rhythms but indispensable for the hierarchical organization of rhythmicity in the SCN.

  16. Structural and metabolic changes in language areas linked to formal thought disorder.

    Science.gov (United States)

    Horn, Helge; Federspiel, Andrea; Wirth, Miranka; Müller, Thomas J; Wiest, Roland; Wang, Jiong-Jiong; Strik, Werner

    2009-02-01

    The role of the language network in the pathophysiology of formal thought disorder has yet to be elucidated. To investigate whether specific grey-matter deficits in schizophrenic formal thought disorder correlate with resting perfusion in the left-sided language network. We investigated 13 right-handed patients with schizophrenia and formal thought disorder of varying severity and 13 matched healthy controls, using voxel-based morphometry and magnetic resonance imaging perfusion measurement (arterial spin labelling). We found positive correlations between perfusion and the severity of formal thought disorder in the left frontal and left temporoparietal language areas. We also observed bilateral deficits in grey-matter volume, positively correlated with the severity of thought disorder in temporoparietal areas and other brain regions. The results of the voxel-based morphometry and the arterial spin labelling measurements overlapped in the left posterior superior temporal gyrus and left angular gyrus. Specific grey-matter deficits may be a risk factor for state-related dysfunctions of the left-sided language system, leading to local hyperperfusion and formal thought disorder.

  17. Formal methods in software development: A road less travelled

    Directory of Open Access Journals (Sweden)

    John A van der Poll

    2010-08-01

    Full Text Available An integration of traditional verification techniques and formal specifications in software engineering is presented. Advocates of such techniques claim that mathematical formalisms allow them to produce quality, verifiably correct, or at least highly dependable software and that the testing and maintenance phases are shortened. Critics on the other hand maintain that software formalisms are hard to master, tedious to use and not well suited for the fast turnaround times demanded by industry. In this paper some popular formalisms and the advantages of using these during the early phases of the software development life cycle are presented. Employing the Floyd-Hoare verification principles during the formal specification phase facilitates reasoning about the properties of a specification. Some observations that may help to alleviate the formal-methods controversy are established and a number of formal methods successes is presented. Possible conditions for an increased acceptance of formalisms in oftware development are discussed.

  18. Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network.

    Science.gov (United States)

    Pacheco, Maria Pires; John, Elisabeth; Kaoma, Tony; Heinäniemi, Merja; Nicot, Nathalie; Vallar, Laurent; Bueb, Jean-Luc; Sinkkonen, Lasse; Sauter, Thomas

    2015-10-19

    The reconstruction of context-specific metabolic models from easily and reliably measurable features such as transcriptomics data will be increasingly important in research and medicine. Current reconstruction methods suffer from high computational effort and arbitrary threshold setting. Moreover, understanding the underlying epigenetic regulation might allow the identification of putative intervention points within metabolic networks. Genes under high regulatory load from multiple enhancers or super-enhancers are known key genes for disease and cell identity. However, their role in regulation of metabolism and their placement within the metabolic networks has not been studied. Here we present FASTCORMICS, a fast and robust workflow for the creation of high-quality metabolic models from transcriptomics data. FASTCORMICS is devoid of arbitrary parameter settings and due to its low computational demand allows cross-validation assays. Applying FASTCORMICS, we have generated models for 63 primary human cell types from microarray data, revealing significant differences in their metabolic networks. To understand the cell type-specific regulation of the alternative metabolic pathways we built multiple models during differentiation of primary human monocytes to macrophages and performed ChIP-Seq experiments for histone H3 K27 acetylation (H3K27ac) to map the active enhancers in macrophages. Focusing on the metabolic genes under high regulatory load from multiple enhancers or super-enhancers, we found these genes to show the most cell type-restricted and abundant expression profiles within their respective pathways. Importantly, the high regulatory load genes are associated to reactions enriched for transport reactions and other pathway entry points, suggesting that they are critical regulatory control points for cell type-specific metabolism. By integrating metabolic modelling and epigenomic analysis we have identified high regulatory load as a common feature of metabolic

  19. Especificación formal en OCL de reglas de consistencia entre los diagramas de clases y casos de uso de UML y el modelo de interfaces Formal OCL specification of consistency rules between the UML class and the use case models and the interfaces model

    Directory of Open Access Journals (Sweden)

    Carlos Mario Zapata

    2008-01-01

    Full Text Available En el ciclo de vida del software, durante las fases de definición y análisis, se realiza una especificación de los requisitos. Para ello, es necesario realizar un proceso de captura de las necesidades y expectativas de los interesados, que se traduce posteriormente en un conjunto de modelos que representan tanto el problema como su solución. Por lo general, la mayoría de esos modelos se expresan en el lenguaje de modelado unificado -UML-, que define un conjunto de artefactos que permiten especificar los requisitos del software, los cuales deberían guardar consistencia, cuando se trate del mismo modelo. Sin embargo, la consistencia entre diferentes artefactos no se encuentra definida en la especificación de UML y poco se ha trabajado con este tipo de consistencia. En este artículo se propone un método para verificar la consistencia entre el diagrama de clases y el diagrama de casos de uso de UML de una manera formal. Dicho proceso se lleva a cabo evaluando una serie de reglas definidas en el lenguaje de restricciones de objetos -OCL- que se deben cumplir para garantizar que la información brindada por dichos modelos sea consistente. Como se reconoce la participación de los dos diagramas en la elaboración de las interfaces gráficas de usuario -GUI-, se define adicionalmente la consistencia con este artefacto.In a software lifetime, during definition and analysis stages, a specification of requirements is carried out. For such a purpose, it is necessary to get through a process to capture interested persons’ needs and expectations, which will later be translated into a set of models representing both the problem and the solution. Most models are frequently expressed by the UML (Unified Modeling Language which defines a set of devices for specifying software requirements which should be consistent with the same model. However, consistency among several devices is not defined in the UML specification and not too much work has been made

  20. Formal Specification and Verification of Distributed System.

    Science.gov (United States)

    1983-06-01

    a->b); A distributed design [HOA78] to generate prime numbers using the " sieve of Eratosthenes " method, is depicted in Figure 11. PNG consists of two... Sieve . 22 5.4.1.2 The Printer. 23 5.4.2 The Verification of PNG. 23 6. Conclusions and Comparisons to Other Approaches ..............25 6.1 The Temporal...types of processes: sieves and a printer. To simplify the description, assume there are infinite number of sieve processes, denoted by Sieve [l], Sieve

  1. From Safety Analysis to Formal Specification

    DEFF Research Database (Denmark)

    Hansen, Kirsten Mark; Ravn, Anders P.; Stavridou, Victoria

    1998-01-01

    Software for safety critical systems must deal with the hazards identified bysafety analysis. This paper investigates, how the results of onesafety analysis technique, fault trees, are interpreted as software safetyrequirements to be used in the program design process. We propose thatfault tree a...... requirements for software components....

  2. Activity and High-Order Effective Connectivity Alterations in Sanfilippo C Patient-Specific Neuronal Networks

    Directory of Open Access Journals (Sweden)

    Isaac Canals

    2015-10-01

    Full Text Available Induced pluripotent stem cell (iPSC technology has been successfully used to recapitulate phenotypic traits of several human diseases in vitro. Patient-specific iPSC-based disease models are also expected to reveal early functional phenotypes, although this remains to be proved. Here, we generated iPSC lines from two patients with Sanfilippo type C syndrome, a lysosomal storage disorder with inheritable progressive neurodegeneration. Mature neurons obtained from patient-specific iPSC lines recapitulated the main known phenotypes of the disease, not present in genetically corrected patient-specific iPSC-derived cultures. Moreover, neuronal networks organized in vitro from mature patient-derived neurons showed early defects in neuronal activity, network-wide degradation, and altered effective connectivity. Our findings establish the importance of iPSC-based technology to identify early functional phenotypes, which can in turn shed light on the pathological mechanisms occurring in Sanfilippo syndrome. This technology also has the potential to provide valuable readouts to screen compounds, which can prevent the onset of neurodegeneration.

  3. Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex

    Science.gov (United States)

    Gray, Lucas T; Yao, Zizhen; Nguyen, Thuc Nghi; Kim, Tae Kyung; Zeng, Hongkui; Tasic, Bosiljka

    2017-01-01

    Mammalian cortex is a laminar structure, with each layer composed of a characteristic set of cell types with different morphological, electrophysiological, and connectional properties. Here, we define chromatin accessibility landscapes of major, layer-specific excitatory classes of neurons, and compare them to each other and to inhibitory cortical neurons using the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq). We identify a large number of layer-specific accessible sites, and significant association with genes that are expressed in specific cortical layers. Integration of these data with layer-specific transcriptomic profiles and transcription factor binding motifs enabled us to construct a regulatory network revealing potential key layer-specific regulators, including Cux1/2, Foxp2, Nfia, Pou3f2, and Rorb. This dataset is a valuable resource for identifying candidate layer-specific cis-regulatory elements in adult mouse cortex. DOI: http://dx.doi.org/10.7554/eLife.21883.001 PMID:28112643

  4. A gene network that coordinates preplacodal competence and neural crest specification in zebrafish.

    Science.gov (United States)

    Bhat, Neha; Kwon, Hye-Joo; Riley, Bruce B

    2013-01-01

    Preplacodal ectoderm (PPE) and neural crest (NC) are specified at the interface of neural and nonneural ectoderm and together contribute to the peripheral nervous system in all vertebrates. Bmp activates early steps for both fates during late blastula stage. Low Bmp activates expression of transcription factors Tfap2a and Tfap2c in the lateral neural plate, thereby specifying neural crest fate. Elevated Bmp establishes preplacodal competence throughout the ventral ectoderm by coinducing Tfap2a, Tfap2c, Foxi1 and Gata3. PPE specification occurs later at the end of gastrulation and requires complete attenuation of Bmp, yet expression of PPE competence factors continues well past gastrulation. Here we show that competence factors positively regulate each other's expression during gastrulation, forming a self-sustaining network that operates independently of Bmp. Misexpression of Tfap2a in embryos blocked for Bmp from late blastula stage can restore development of both PPE and NC. However, Tfap2a alone is not sufficient to activate any other competence factors nor does it rescue individual placodes. On the other hand, misexpression of any two competence factors in Bmp-blocked embryos can activate the entire transcription factor network and support the development of NC, PPE and some individual placodes. We also show that while these factors are partially redundant with respect to PPE specification, they later provide non-redundant functions needed for development of specific placodes. Thus, we have identified a gene regulatory network that coordinates development of NC, PPE and individual placodes in zebrafish. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. Formalizing Restriction Categories

    Directory of Open Access Journals (Sweden)

    James Chapman

    2017-03-01

    Full Text Available Restriction categories are an abstract axiomatic framework by Cockett and Lack for reasoning about (generalizations of the idea of partiality of functions. In a restriction category, every map defines an endomap on its domain, the corresponding partial identity map. Restriction categories cover a number of examples of different flavors and are sound and complete with respect to the more synthetic and concrete partial map categories. A partial map category is based on a given category (of total maps and a map in it is a map from a subobject of the domain. In this paper, we report on an Agda formalization of the first chapters of the theory of restriction categories, including the challenging completeness result. We explain the mathematics formalized, comment on the design decisions we made for the formalization, and illustrate them at work.

  6. Formalizing Probabilistic Safety Claims

    Science.gov (United States)

    Herencia-Zapana, Heber; Hagen, George E.; Narkawicz, Anthony J.

    2011-01-01

    A safety claim for a system is a statement that the system, which is subject to hazardous conditions, satisfies a given set of properties. Following work by John Rushby and Bev Littlewood, this paper presents a mathematical framework that can be used to state and formally prove probabilistic safety claims. It also enables hazardous conditions, their uncertainties, and their interactions to be integrated into the safety claim. This framework provides a formal description of the probabilistic composition of an arbitrary number of hazardous conditions and their effects on system behavior. An example is given of a probabilistic safety claim for a conflict detection algorithm for aircraft in a 2D airspace. The motivation for developing this mathematical framework is that it can be used in an automated theorem prover to formally verify safety claims.

  7. Ontology or formal ontology

    Science.gov (United States)

    Žáček, Martin

    2017-07-01

    Ontology or formal ontology? Which word is correct? The aim of this article is to introduce correct terms and explain their basis. Ontology describes a particular area of interest (domain) in a formal way - defines the classes of objects that are in that area, and relationships that may exist between them. Meaning of ontology consists mainly in facilitating communication between people, improve collaboration of software systems and in the improvement of systems engineering. Ontology in all these areas offer the possibility of unification of view, maintaining consistency and unambiguity.

  8. Formality theorem for gerbes

    DEFF Research Database (Denmark)

    Bressler, Paul; Gorokhovsky, Alexander; Nest, Ryszard

    2015-01-01

    The main result of the present paper is an analogue of Kontsevich formality theorem in the context of the deformation theory of gerbes. We construct an L∞L∞ deformation of the Schouten algebra of multi-vectors which controls the deformation theory of a gerbe.......The main result of the present paper is an analogue of Kontsevich formality theorem in the context of the deformation theory of gerbes. We construct an L∞L∞ deformation of the Schouten algebra of multi-vectors which controls the deformation theory of a gerbe....

  9. Content-specific network analysis of peer-to-peer communication in an online community for smoking cessation.

    Science.gov (United States)

    Myneni, Sahiti; Cobb, Nathan K; Cohen, Trevor

    2016-01-01

    Analysis of user interactions in online communities could improve our understanding of health-related behaviors and inform the design of technological solutions that support behavior change. However, to achieve this we would need methods that provide granular perspective, yet are scalable. In this paper, we present a methodology for high-throughput semantic and network analysis of large social media datasets, combining semi-automated text categorization with social network analytics. We apply this method to derive content-specific network visualizations of 16,492 user interactions in an online community for smoking cessation. Performance of the categorization system was reasonable (average F-measure of 0.74, with system-rater reliability approaching rater-rater reliability). The resulting semantically specific network analysis of user interactions reveals content- and behavior-specific network topologies. Implications for socio-behavioral health and wellness platforms are also discussed.

  10. Formal verification of an avionics microprocessor

    Science.gov (United States)

    Srivas, Mandayam, K.; Miller, Steven P.

    1995-01-01

    Formal specification combined with mechanical verification is a promising approach for achieving the extremely high levels of assurance required of safety-critical digital systems. However, many questions remain regarding their use in practice: Can these techniques scale up to industrial systems, where are they likely to be useful, and how should industry go about incorporating them into practice? This report discusses a project undertaken to answer some of these questions, the formal verification of the AAMPS microprocessor. This project consisted of formally specifying in the PVS language a rockwell proprietary microprocessor at both the instruction-set and register-transfer levels and using the PVS theorem prover to show that the microcode correctly implemented the instruction-level specification for a representative subset of instructions. Notable aspects of this project include the use of a formal specification language by practicing hardware and software engineers, the integration of traditional inspections with formal specifications, and the use of a mechanical theorem prover to verify a portion of a commercial, pipelined microprocessor that was not explicitly designed for formal verification.

  11. Time Is Not Space: Core Computations and Domain-Specific Networks for Mental Travels.

    Science.gov (United States)

    Gauthier, Baptiste; van Wassenhove, Virginie

    2016-11-23

    Humans can consciously project themselves in the future and imagine themselves at different places. Do mental time travel and mental space navigation abilities share common cognitive and neural mechanisms? To test this, we recorded fMRI while participants mentally projected themselves in time or in space (e.g., 9 years ago, in Paris) and ordered historical events from their mental perspective. Behavioral patterns were comparable for mental time and space and shaped by self-projection and by the distance of historical events to the mental position of the self, suggesting the existence of egocentric mapping in both dimensions. Nonetheless, self-projection in space engaged the medial and lateral parietal cortices, whereas self-projection in time engaged a widespread parietofrontal network. Moreover, while a large distributed network was found for spatial distances, temporal distances specifically engaged the right inferior parietal cortex and the anterior insula. Across these networks, a robust overlap was only found in a small region of the inferior parietal lobe, adding evidence for its role in domain-general egocentric mapping. Our findings suggest that mental travel in time or space capitalizes on egocentric remapping and on distance computation, which are implemented in distinct dimension-specific cortical networks converging in inferior parietal lobe. As humans, we can consciously imagine ourselves at a different time (mental time travel) or at a different place (mental space navigation). Are such abilities domain-general, or are the temporal and spatial dimensions of our conscious experience separable? Here, we tested the hypothesis that mental time travel and mental space navigation required the egocentric remapping of events, including the estimation of their distances to the self. We report that, although both remapping and distance computation are foundational for the processing of the temporal and spatial dimensions of our conscious experience, their

  12. Methodological remarks about comparing formal frameworks for narratives

    NARCIS (Netherlands)

    Löwe, B.

    2011-01-01

    The paper by Benedikt Löwe is devoted to formal modelling, and in particular to the question of how we should model narratives, and assess their equivalence on the basis of these formal models. Specifically, in this paper, Löwe gives an overview of several formal frameworks, draws some

  13. Formalizing narratives using nested circumscription

    Energy Technology Data Exchange (ETDEWEB)

    Baral, C.; Gabaldon, A. [Univ. of Texas, El Paso, TX (United States); Provetti, A. [Universita di Bologna (Italy)

    1996-12-31

    The representation of narratives of actions and observations is a current issue in Knowledge Representation, where traditional plan-oriented treatments of action seem to fall short. To address narratives, Pinto and Reiter have extended Situation Calculus axioms, Kowalski and Sergot have introduced the Event Calculus in Logic Programming, and Baral et al. have defined the specification language L which allows to express actual and hypothetical situations in a uniform setting. The L entailment relation can formalize several forms of reasoning about actions and change. In this paper we illustrate a translation of L theories into Nested Abnormality Theories, a novel form of circumscription. The proof of soundness and completeness of the translation is the main technical result of the paper, but attention is also devoted to the features of Nested Abnormality Theories to capture commonsense reasoning in general and to clarify which assumptions a logical formalization forces upon a domain. These results also help clarifying the relationship between L and other recent circumscriptive formalization for narratives, such as Miller and Shanahan`s.

  14. A Subject-Specificity Analysis of Radio Channels in Wireless Body Area Networks

    Directory of Open Access Journals (Sweden)

    Yang Hao

    2011-07-01

    Full Text Available This paper presents an analysis of subject-specific radio channels in wireless body area networks (WBANs using a simulation tool based on the parallel finite-difference time-domain (FDTD technique. This technique is well suited to model radio propagations around complex, inhomogeneous objects such as the human body. The impacts of different subjects varying in size on on-body, inter-body, and off-body radio channels are studied. The analysis demonstrates that the characteristics of on-body radio channels are subject-specific and are associated with human gender, height, and body mass index. On the other hand, when waves propagate away from the body, such as in the inter-body and off-body cases, the impacts of different subjects on the channel characteristics are found to be negligible.

  15. Cell type specific alterations in interchromosomal networks across the cell cycle.

    Directory of Open Access Journals (Sweden)

    Andrew J Fritz

    2014-10-01

    Full Text Available The interchromosomal organization of a subset of human chromosomes (#1, 4, 11, 12, 16, 17, and 18 was examined in G1 and S phase of human WI38 lung fibroblast and MCF10A breast epithelial cells. Radial positioning of the chromosome territories (CTs was independent of gene density, but size dependent. While no changes in radial positioning during the cell cycle were detected, there were stage-specific differences between cell types. Each CT was in close proximity (interaction with a similar number of other CT except the gene rich CT17 which had significantly more interactions. Furthermore, CT17 was a member of the highest pairwise CT combinations with multiple interactions. Major differences were detected in the pairwise interaction profiles of MCF10A versus WI38 including cell cycle alterations from G1 to S. These alterations in interaction profiles were subdivided into five types: overall increase, overall decrease, switching from 1 to ≥2 interactions, vice versa, or no change. A global data mining program termed the chromatic median determined the most probable overall association network for the entire subset of CT. This probabilistic interchromosomal network was nearly completely different between the two cell lines. It was also strikingly altered across the cell cycle in MCF10A, but only slightly in WI38. We conclude that CT undergo multiple and preferred interactions with other CT in the nucleus and form preferred -albeit probabilistic- interchromosomal networks. This network of interactions is altered across the cell cycle and between cell types. It is intriguing to consider the relationship of these alterations to the corresponding changes in the gene expression program across the cell cycle and in different cell types.

  16. Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle

    Directory of Open Access Journals (Sweden)

    Liu Liwen

    2009-09-01

    Full Text Available Abstract Background Fission yeast Schizosaccharomyces pombe and budding yeast Saccharomyces cerevisiae are among the original model organisms in the study of the cell-division cycle. Unlike budding yeast, no large-scale regulatory network has been constructed for fission yeast. It has only been partially characterized. As a result, important regulatory cascades in budding yeast have no known or complete counterpart in fission yeast. Results By integrating genome-wide data from multiple time course cell cycle microarray experiments we reconstructed a gene regulatory network. Based on the network, we discovered in addition to previously known regulatory hubs in M phase, a new putative regulatory hub in the form of the HMG box transcription factor SPBC19G7.04. Further, we inferred periodic activities of several less known transcription factors over the course of the cell cycle, identified over 500 putative regulatory targets and detected many new phase-specific and conserved cis-regulatory motifs. In particular, we show that SPBC19G7.04 has highly significant periodic activity that peaks in early M phase, which is coordinated with the late G2 activity of the forkhead transcription factor fkh2. Finally, using an enhanced Bayesian algorithm to co-cluster the expression data, we obtained 31 clusters of co-regulated genes 1 which constitute regulatory modules from different phases of the cell cycle, 2 whose phase order is coherent across the 10 time course experiments, and 3 which lead to identification of phase-specific control elements at both the transcriptional and post-transcriptional levels in S. pombe. In particular, the ribosome biogenesis clusters expressed in G2 phase reveal new, highly conserved RNA motifs. Conclusion Using a systems-level analysis of the phase-specific nature of the S. pombe cell cycle gene regulation, we have provided new testable evidence for post-transcriptional regulation in the G2 phase of the fission yeast cell cycle

  17. Formal fault tree semantics

    OpenAIRE

    Schellhorn, Gerhard

    2002-01-01

    Formal fault tree semantics / G. Schellhorn, A. Thums, and W. Reif. - In: IDPT : Proceedings of the Sixth World Conference on Integrated Design and Process Technology : June 23 - 27, 2003, Pasadena, California / SDPS, Society for Design & Process Science. - 2002. - 1CD-ROM

  18. Fear of the Formal

    DEFF Research Database (Denmark)

    du Gay, Paul; Lopdrup-Hjorth, Thomas

    2016-01-01

    term this ‘fear of the formal’, outlining key elements of its genealogy and exploring its contemporary manifestation in relation to recent and ongoing reforms of organisational life in a range of contexts. At the same time, we seek to indicate the continuing constitutive significance of formality...

  19. Formal Methods for Privacy

    Science.gov (United States)

    2009-09-01

    automated enforcement [52]. Other policy languages such as P3P [15], which has a formal notation, inform website visitors of the site’s privacy practices...Lorrie Faith Cranor. Web Privacy with P3P . O’Reilly, September 2002. [16] Lorrie Faith Cranor, Praveen Guduru, and Manjula Arjula. User interfaces for

  20. Resting-state networks predict individual differences in common and specific aspects of executive function.

    Science.gov (United States)

    Reineberg, Andrew E; Andrews-Hanna, Jessica R; Depue, Brendan E; Friedman, Naomi P; Banich, Marie T

    2015-01-01

    The goal of the present study was to examine relationships between individual differences in resting state functional connectivity as ascertained by fMRI (rs-fcMRI) and performance on tasks of executive function (EF), broadly defined as the ability to regulate thoughts and actions. Unlike most previous research that focused on the relationship between rs-fcMRI and a single behavioral measure of EF, in the current study we examined the relationship of rs-fcMRI with individual differences in subcomponents of EF. Ninety-one adults completed a resting state fMRI scan and three separate EF tasks outside the magnet: inhibition of prepotent responses, task set shifting, and working memory updating. From these three measures, we derived estimates of common aspects of EF, as well as abilities specific to working memory updating and task shifting. Using Independent Components Analysis (ICA), we identified across the group of participants several networks of regions (Resting State Networks, RSNs) with temporally correlated time courses. We then used dual regression to explore how these RSNs covaried with individual differences in EF. Dual regression revealed that increased higher common EF was associated with connectivity of a) frontal pole with an attentional RSN, and b) Crus I and II of the cerebellum with the right frontoparietal RSN. Moreover, higher shifting-specific abilities were associated with increased connectivity of angular gyrus with a ventral attention RSN. The results of the current study suggest that the organization of the brain at rest may have important implications for individual differences in EF, and that individuals higher in EF may have expanded resting state networks as compared to individuals with lower EF. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Bottle-neck type of neural network as a mapping device towards food specifications.

    Science.gov (United States)

    Novic, Marjana; Groselj, Neva

    2009-09-01

    A novel methodology is proposed for food specifications associated with the origin of food. The methodology was tested on honey samples collected within the TRACE EU project. The data were sampled in various regions in Europe and analysed for the trace elements content. The sampling sites were characterized by different geological origins, such as limestone, shale, or magmatic. We have chosen 14 elements, B, Na, Mg, A, K, Ca, Mn, Co, Ni, Cu, Zn, Rb, Sr, and Ba, due to their influence on the separation of samples regarding the geology of the sampling sites. A special architecture of an error back-propagation neural network, so called bottle-neck type of neural network was used to project the data into a 2D plane. The data were fed into the 14-nodes input layer and then transferred through the 2-nodes hidden layer (compared to a bottle-neck) to the 14-nodes output layer. The two hidden nodes representing the two coordinates of the projection plane enable us to map the samples used for training of the bottle-neck network. With the knowledge about the classes of individual samples we determine the clusters in the projection plane and consequently obtain the coordinates of the centroid (gravity point) of a particular cluster. The clusters are characterized with an ellipse shape borders spanning the length of up to 3sigma in each dimension. Since the data were classified as regard to the geology, three main clusters were sought: (i) limestone, (ii) shale/mudstone/clay/loess, and (iii) acid-magmatic origin of honey samples. The novel methodology proposed for food specifications was demonstrated on a reduced set of samples, which shows good clustering of all three classes in the projection plane, and on the third class of the original data set.

  2. Network-specific resting-state connectivity changes in the premotor-parietal axis in writer's cramp.

    Science.gov (United States)

    Mantel, Tobias; Meindl, Tobias; Li, Yong; Jochim, Angela; Gora-Stahlberg, Gina; Kräenbring, Jona; Berndt, Maria; Dresel, Christian; Haslinger, Bernhard

    2018-01-01

    Writer's cramp is a task-specific dystonia impairing writing and sometimes other fine motor tasks. Neuroimaging studies using manifold designs have shown varying results regarding the nature of changes in the disease. To clarify and extend the knowledge of underlying changes by investigating functional connectivity (FC) in intrinsic connectivity networks with putative sensorimotor function at rest in an increased number of study subjects. Resting-state functional magnetic resonance imaging with independent component analysis was performed in 26/27 writer's cramp patients/healthy controls, and FC within and between resting state networks with putative sensorimotor function was compared. Additionally, voxel-based morphometry was carried out on the subjects' structural images. Patients displayed increased left- and reduced right-hemispheric primary sensorimotor FC in the premotor-parietal network. Mostly bilaterally altered dorsal/ventral premotor FC, as well as altered parietal FC were observed within multiple sensorimotor networks and showed differing network-dependent directionality. Beyond within-network FC changes and reduced right cerebellar grey matter volume in the structural analysis, the positive between-network FC of the cerebellar network and the basal ganglia network was reduced. Abnormal resting-state FC in multiple networks with putative sensorimotor function may act as basis of preexisting observations made during task-related neuroimaging. Further, altered connectivity between the cerebellar and basal ganglia network underlines the important role of these structures in the disease.

  3. Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis

    Directory of Open Access Journals (Sweden)

    Chen Jiun-Ching

    2007-05-01

    Full Text Available Abstract Background Genome-wide identification of specific oligonucleotides (oligos is a computationally-intensive task and is a requirement for designing microarray probes, primers, and siRNAs. An artificial neural network (ANN is a machine learning technique that can effectively process complex and high noise data. Here, ANNs are applied to process the unique subsequence distribution for prediction of specific oligos. Results We present a novel and efficient algorithm, named the integration of ANN and BLAST (IAB algorithm, to identify specific oligos. We establish the unique marker database for human and rat gene index databases using the hash table algorithm. We then create the input vectors, via the unique marker database, to train and test the ANN. The trained ANN predicted the specific oligos with high efficiency, and these oligos were subsequently verified by BLAST. To improve the prediction performance, the ANN over-fitting issue was avoided by early stopping with the best observed error and a k-fold validation was also applied. The performance of the IAB algorithm was about 5.2, 7.1, and 6.7 times faster than the BLAST search without ANN for experimental results of 70-mer, 50-mer, and 25-mer specific oligos, respectively. In addition, the results of polymerase chain reactions showed that the primers predicted by the IAB algorithm could specifically amplify the corresponding genes. The IAB algorithm has been integrated into a previously published comprehensive web server to support microarray analysis and genome-wide iterative enrichment analysis, through which users can identify a group of desired genes and then discover the specific oligos of these genes. Conclusion The IAB algorithm has been developed to construct SpecificDB, a web server that provides a specific and valid oligo database of the probe, siRNA, and primer design for the human genome. We also demonstrate the ability of the IAB algorithm to predict specific oligos through

  4. Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.

    Science.gov (United States)

    Liu, Chun-Chi; Lin, Chin-Chung; Li, Ker-Chau; Chen, Wen-Shyen E; Chen, Jiun-Ching; Yang, Ming-Te; Yang, Pan-Chyr; Chang, Pei-Chun; Chen, Jeremy J W

    2007-05-22

    Genome-wide identification of specific oligonucleotides (oligos) is a computationally-intensive task and is a requirement for designing microarray probes, primers, and siRNAs. An artificial neural network (ANN) is a machine learning technique that can effectively process complex and high noise data. Here, ANNs are applied to process the unique subsequence distribution for prediction of specific oligos. We present a novel and efficient algorithm, named the integration of ANN and BLAST (IAB) algorithm, to identify specific oligos. We establish the unique marker database for human and rat gene index databases using the hash table algorithm. We then create the input vectors, via the unique marker database, to train and test the ANN. The trained ANN predicted the specific oligos with high efficiency, and these oligos were subsequently verified by BLAST. To improve the prediction performance, the ANN over-fitting issue was avoided by early stopping with the best observed error and a k-fold validation was also applied. The performance of the IAB algorithm was about 5.2, 7.1, and 6.7 times faster than the BLAST search without ANN for experimental results of 70-mer, 50-mer, and 25-mer specific oligos, respectively. In addition, the results of polymerase chain reactions showed that the primers predicted by the IAB algorithm could specifically amplify the corresponding genes. The IAB algorithm has been integrated into a previously published comprehensive web server to support microarray analysis and genome-wide iterative enrichment analysis, through which users can identify a group of desired genes and then discover the specific oligos of these genes. The IAB algorithm has been developed to construct SpecificDB, a web server that provides a specific and valid oligo database of the probe, siRNA, and primer design for the human genome. We also demonstrate the ability of the IAB algorithm to predict specific oligos through polymerase chain reaction experiments. Specific

  5. Sequence-specific bias correction for RNA-seq data using recurrent neural networks.

    Science.gov (United States)

    Zhang, Yao-Zhong; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru

    2017-01-25

    The recent success of deep learning techniques in machine learning and artificial intelligence has stimulated a great deal of interest among bioinformaticians, who now wish to bring the power of deep learning to bare on a host of bioinformatical problems. Deep learning is ideally suited for biological problems that require automatic or hierarchical feature representation for biological data when prior knowledge is limited. In this work, we address the sequence-specific bias correction problem for RNA-seq data redusing Recurrent Neural Networks (RNNs) to model nucleotide sequences without pre-determining sequence structures. The sequence-specific bias of a read is then calculated based on the sequence probabilities estimated by RNNs, and used in the estimation of gene abundance. We explore the application of two popular RNN recurrent units for this task and demonstrate that RNN-based approaches provide a flexible way to model nucleotide sequences without knowledge of predetermined sequence structures. Our experiments show that training a RNN-based nucleotide sequence model is efficient and RNN-based bias correction methods compare well with the-state-of-the-art sequence-specific bias correction method on the commonly used MAQC-III data set. RNNs provides an alternative and flexible way to calculate sequence-specific bias without explicitly pre-determining sequence structures.

  6. {\\delta}M Formalism

    CERN Document Server

    Talebian-Ashkezari, Alireza; Abolhasani, Ali Akbar

    2016-01-01

    We study the evolution of the "non-perturbative" metric perturbations in a Bianchi background in the long-wavelength limit. By applying the gradient expansion to the equations of motion we exhibit a generalized "Separate Universe" approach to the cosmological perturbation theory. Having found this consistent separate universe picture, we introduce the "{\\delta}M formalism" for calculating the evolution of the tensor perturbations in anisotropic inflation models in almost similar way as the so-called {\\delta}N formula for the super-horizon dynamics of the curvature perturbations. Likewise its ancestor, {\\delta}N formalism, this new method can substantially reduce the amount of calculations related to the evolution of the tensor modes.

  7. Readings in Formal Epistemology

    DEFF Research Database (Denmark)

    Formal epistemology’ is a term coined in the late 1990s for a new constellation of interests in philosophy,the roots of which are found in earlier works of epistemologists, philosophers of science, and logicians. It addresses a growing agenda of problems concerning knowledge, belief, certainty......, rationality, deliberation, decision, strategy, action and agent interaction – and it does so using methods from logic, probability, computability, decision, and game theory. This volume presents 42 classic texts in formal epistemology, and strengthens the ties between research into this area of philosophy...... and its neighbouring intellectual disciplines. The editors provide introductions to five basic subsections: Bayesian Epistemology, Belief Change, Decision Theory, Interactive Epistemology and Logics of Knowledge and Belief. The volume also includes a thorough index and suggestions for further reading...

  8. {\\delta}M Formalism

    OpenAIRE

    Talebian-Ashkezari, Alireza; Ahmadi, Nahid; Abolhasani, Ali Akbar

    2016-01-01

    We study the evolution of the "non-perturbative" metric perturbations in a Bianchi background in the long-wavelength limit. By applying the gradient expansion to the equations of motion we exhibit a generalized "Separate Universe" approach to the cosmological perturbation theory. Having found this consistent separate universe picture, we introduce the "{\\delta}M formalism" for calculating the evolution of the tensor perturbations in anisotropic inflation models in almost similar way as the so...

  9. Formal groups and applications

    CERN Document Server

    Hazewinkel, Michiel

    2012-01-01

    This book is a comprehensive treatment of the theory of formal groups and its numerous applications in several areas of mathematics. The seven chapters of the book present basics and main results of the theory, as well as very important applications in algebraic topology, number theory, and algebraic geometry. Each chapter ends with several pages of historical and bibliographic summary. One prerequisite for reading the book is an introductory graduate algebra course, including certain familiarity with category theory.

  10. Dense fibrillar collagen is a potent inducer of invadopodia via a specific signaling network.

    Science.gov (United States)

    Artym, Vira V; Swatkoski, Stephen; Matsumoto, Kazue; Campbell, Catherine B; Petrie, Ryan J; Dimitriadis, Emilios K; Li, Xin; Mueller, Susette C; Bugge, Thomas H; Gucek, Marjan; Yamada, Kenneth M

    2015-02-02

    Cell interactions with the extracellular matrix (ECM) can regulate multiple cellular activities and the matrix itself in dynamic, bidirectional processes. One such process is local proteolytic modification of the ECM. Invadopodia of tumor cells are actin-rich proteolytic protrusions that locally degrade matrix molecules and mediate invasion. We report that a novel high-density fibrillar collagen (HDFC) matrix is a potent inducer of invadopodia, both in carcinoma cell lines and in primary human fibroblasts. In carcinoma cells, HDFC matrix induced formation of invadopodia via a specific integrin signaling pathway that did not require growth factors or even altered gene and protein expression. In contrast, phosphoproteomics identified major changes in a complex phosphosignaling network with kindlin2 serine phosphorylation as a key regulatory element. This kindlin2-dependent signal transduction network was required for efficient induction of invadopodia on dense fibrillar collagen and for local degradation of collagen. This novel phosphosignaling mechanism regulates cell surface invadopodia via kindlin2 for local proteolytic remodeling of the ECM.

  11. Dense fibrillar collagen is a potent inducer of invadopodia via a specific signaling network

    Science.gov (United States)

    Swatkoski, Stephen; Matsumoto, Kazue; Campbell, Catherine B.; Petrie, Ryan J.; Dimitriadis, Emilios K.; Li, Xin; Mueller, Susette C.; Bugge, Thomas H.; Gucek, Marjan

    2015-01-01

    Cell interactions with the extracellular matrix (ECM) can regulate multiple cellular activities and the matrix itself in dynamic, bidirectional processes. One such process is local proteolytic modification of the ECM. Invadopodia of tumor cells are actin-rich proteolytic protrusions that locally degrade matrix molecules and mediate invasion. We report that a novel high-density fibrillar collagen (HDFC) matrix is a potent inducer of invadopodia, both in carcinoma cell lines and in primary human fibroblasts. In carcinoma cells, HDFC matrix induced formation of invadopodia via a specific integrin signaling pathway that did not require growth factors or even altered gene and protein expression. In contrast, phosphoproteomics identified major changes in a complex phosphosignaling network with kindlin2 serine phosphorylation as a key regulatory element. This kindlin2-dependent signal transduction network was required for efficient induction of invadopodia on dense fibrillar collagen and for local degradation of collagen. This novel phosphosignaling mechanism regulates cell surface invadopodia via kindlin2 for local proteolytic remodeling of the ECM. PMID:25646088

  12. Formal verification: will the seedling ever flower?

    Science.gov (United States)

    White, Neil; Matthews, Stuart; Chapman, Roderick

    2017-10-13

    In one sense, formal specification and verification have been highly successful: techniques have been developed in pioneering academic research, transferred to software companies through training and partnerships, and successfully deployed in systems with national significance. Altran UK has been in the vanguard of this movement. This paper summarizes some of our key deployments of formal techniques over the past 20 years, including both security- and safety-critical systems. The impact of formal techniques, however, remains within an industrial niche, and while government and suppliers across industry search for solutions to the problems of poor-quality software, the wider software industry remains resistant to adoption of this proven solution. We conclude by reflecting on some of the challenges we face as a community in ensuring that formal techniques achieve their true potential impact on society.This article is part of the themed issue 'Verified trustworthy software systems'. © 2017 The Author(s).

  13. Formalisms for reuse and systems integration

    CERN Document Server

    Rubin, Stuart

    2015-01-01

    Reuse and integration are defined as synergistic concepts, where reuse addresses how to minimize redundancy in the creation of components; while, integration focuses on component composition. Integration supports reuse and vice versa. These related concepts support the design of software and systems for maximizing performance while minimizing cost. Knowledge, like data, is subject to reuse; and, each can be interpreted as the other. This means that inherent complexity, a measure of the potential utility of a system, is directly proportional to the extent to which it maximizes reuse and integration. Formal methods can provide an appropriate context for the rigorous handling of these synergistic concepts. Furthermore, formal languages allow for non ambiguous model specification; and, formal verification techniques provide support for insuring the validity of reuse and integration mechanisms.   This edited book includes 12 high quality research papers written by experts in formal aspects of reuse and integratio...

  14. Towards a Formal Model of Social Data

    DEFF Research Database (Denmark)

    Mukkamala, Raghava Rao; Vatrapu, Ravi; Hussain, Abid

    network analysis. As far as we know, there are no integrated modeling approaches to social data across the conceptual, formal and software realms. Social media analytics can be undertaken in two main ways - ”Social Graph Analytics” and ”Social Text Analytics” (Vatrapu, in press/2013). Social graph......, we exemplify the semantics of the formal model with real-world social data examples. Third, we briefly present and discuss the Social Data Analytics Tool (SODATO) that realizes the conceptual model in software and provisions social data for computational social science analysis based on the formal...... model. Finally, we exemplify our approach with help of a case study on big social data of the fast fashion company, H&M. from its Facebook page....

  15. Formal verification of an oral messages algorithm for interactive consistency

    Science.gov (United States)

    Rushby, John

    1992-01-01

    The formal specification and verification of an algorithm for Interactive Consistency based on the Oral Messages algorithm for Byzantine Agreement is described. We compare our treatment with that of Bevier and Young, who presented a formal specification and verification for a very similar algorithm. Unlike Bevier and Young, who observed that 'the invariant maintained in the recursive subcases of the algorithm is significantly more complicated than is suggested by the published proof' and who found its formal verification 'a fairly difficult exercise in mechanical theorem proving,' our treatment is very close to the previously published analysis of the algorithm, and our formal specification and verification are straightforward. This example illustrates how delicate choices in the formulation of the problem can have significant impact on the readability of its formal specification and on the tractability of its formal verification.

  16. The African American Student Network: An Informal Networking Group as a Therapeutic Intervention for Black College Students on a Predominantly White Campus

    Science.gov (United States)

    Grier-Reed, Tabitha

    2013-01-01

    Informal support networks as opposed to formal mental health counseling may represent a culture-specific, indigenous style of coping for Black college students. Using the African American Student Network (or as students refer to it AFAM), this article comments on the potential of an informal networking group as a culturally sensitive therapeutic…

  17. Networks of phobic fear: Functional connectivity shifts in two subtypes of specific phobia.

    Science.gov (United States)

    Stefanescu, Maria R; Endres, Ralph J; Hilbert, Kevin; Wittchen, Hans-Ulrich; Lueken, Ulrike

    2018-01-01

    Anxiety disorders can be conceptualized by an abnormal interplay of emotion-processing brain circuits; however, knowledge of brain connectivity measures in specific phobia is still limited. To explore functional interactions within selected fear-circuitry structures (anterior cingulate cortex (ACC), amygdala, insula), we re-examined three task-based fMRI studies using a symptom provocation approach (n=94 subjects in total) on two different phobia subtypes (animal subtype as represented by snake phobia (SP) and blood-injection-injury subtype as represented by dental phobia (DP)), and a non-phobic healthy control group (HC). Functional connectivity (FC) analyses detected a negative coupling between the amygdala and the ACC in HC for both classes of phobic stimuli, while SP and DP lacked this inhibitory relationship during visual stimulus presentation. However, a negative FC between the insula and the amygdala was observed in DP during visual symptom provocation, which reversed to a positive FC under auditory symptom provocation pointing to effects depending on stimulus modality in DP. SP showed significantly higher FC towards snake-anxiety eliciting stimuli than HC on an average measure of FC, while DP showed a similar pattern under auditory stimulation only. These findings altogether indicate FC shifts during symptom provocation in specific phobia possibly reflecting impaired emotion regulation processes within fear-circuitry networks. FC hence could represent a prime target for neuroscience-informed augmentation strategies when treating pathological forms of fear. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Formal Methods in Industry

    Directory of Open Access Journals (Sweden)

    Alexei Serna A.

    2012-12-01

    Full Text Available The application of formal methods in industry has progressed extensively over the past decade and the results are promising. But despite these achievements and it have been documented in numerous studies, it is still very common the skepticism about its usefulness and applicability. The goal of this paper is to show that its evolution over the past decade exceeds all previous processes and each time they do a better job to satisfy industrial needs. This is achieved by the description of some experiments and the result of various applications in industry and through an analyzing of the needs of companies that must be satisfy the research community in this field.

  19. Langevin formalism for solidification

    Energy Technology Data Exchange (ETDEWEB)

    Karma, A. (Department of Physics, Northeastern University, Boston, Massachusetts 02115 (United States))

    1993-05-31

    The question of how thermal noise should be incorporated in the continuum equations of solidification in a way which is consistent with both bulk and interfacial equilibrium fluctuations is investigated. The proper Langevin formalism which accomplishes this task is found to consist of the usual bulk forces, which remain unaffected by the presence of a two-phase boundary, and an extra stochastic force on the interface associated with its kinetics. The relevance of this force in the context of pattern formation is examined.

  20. Diffusion formalism and applications

    CERN Document Server

    Dattagupta, Sushanta

    2013-01-01

    Within a unifying framework, Diffusion: Formalism and Applications covers both classical and quantum domains, along with numerous applications. The author explores the more than two centuries-old history of diffusion, expertly weaving together a variety of topics from physics, mathematics, chemistry, and biology. The book examines the two distinct paradigms of diffusion-physical and stochastic-introduced by Fourier and Laplace and later unified by Einstein in his groundbreaking work on Brownian motion. The author describes the role of diffusion in probability theory and stochastic calculus and

  1. Temporal stability of network centrality in control and default mode networks: Specific associations with externalizing psychopathology in children and adolescents.

    Science.gov (United States)

    Sato, João Ricardo; Biazoli, Claudinei Eduardo; Salum, Giovanni Abrahão; Gadelha, Ary; Crossley, Nicolas; Satterthwaite, Theodore D; Vieira, Gilson; Zugman, André; Picon, Felipe Almeida; Pan, Pedro Mario; Hoexter, Marcelo Queiroz; Anés, Mauricio; Moura, Luciana Monteiro; Del'aquilla, Marco Antonio Gomes; Amaro, Edson; McGuire, Philip; Lacerda, Acioly L T; Rohde, Luis Augusto; Miguel, Euripedes Constantino; Jackowski, Andrea Parolin; Bressan, Rodrigo Affonseca

    2015-12-01

    Abnormal connectivity patterns have frequently been reported as involved in pathological mental states. However, most studies focus on "static," stationary patterns of connectivity, which may miss crucial biological information. Recent methodological advances have allowed the investigation of dynamic functional connectivity patterns that describe non-stationary properties of brain networks. Here, we introduce a novel graphical measure of dynamic connectivity, called time-varying eigenvector centrality (tv-EVC). In a sample 655 children and adolescents (7-15 years old) from the Brazilian "High Risk Cohort Study for Psychiatric Disorders" who were imaged using resting-state fMRI, we used this measure to investigate age effects in the temporal in control and default-mode networks (CN/DMN). Using support vector regression, we propose a network maturation index based on the temporal stability of tv-EVC. Moreover, we investigated whether the network maturation is associated with the overall presence of behavioral and emotional problems with the Child Behavior Checklist. As hypothesized, we found that the tv-EVC at each node of CN/DMN become more stable with increasing age (P < 0.001 for all nodes). In addition, the maturity index for this particular network is indeed associated with general psychopathology in children assessed by the total score of Child Behavior Checklist (P = 0.027). Moreover, immaturity of the network was mainly correlated with externalizing behavior dimensions. Taken together, these results suggest that changes in functional network dynamics during neurodevelopment may provide unique insights regarding pathophysiology. © 2015 Wiley Periodicals, Inc.

  2. Formalizing the concept of sound.

    Energy Technology Data Exchange (ETDEWEB)

    Kaper, H. G.; Tipei, S.

    1999-08-03

    The notion of formalized music implies that a musical composition can be described in mathematical terms. In this article we explore some formal aspects of music and propose a framework for an abstract approach.

  3. The specification of weight structures in network autocorrelation models of social influence

    NARCIS (Netherlands)

    Leenders, Roger Th.A.J.

    2002-01-01

    Many physical and social phenomena are embedded within networks of interdependencies, the so-called 'context' of these phenomena. In network analysis, this type of process is typically modeled as a network autocorrelation model. Parameter estimates and inferences based on autocorrelation models,

  4. Exploiting Linkage Information and Problem-Specific Knowledge in Evolutionary Distribution Network Expansion Planning

    NARCIS (Netherlands)

    N.H. Luong (Ngoc Hoang); J.A. La Poutré (Han); P.A.N. Bosman (Peter)

    2015-01-01

    htmlabstractThis paper tackles the Distribution Network Expansion Planning (DNEP) problem that has to be solved by distribution network operators to decide which, where, and/or when enhancements to electricity networks should be introduced to satisfy the future power demands. We compare two

  5. Exploiting linkage information and problem-specific knowledge in evolutionary distribution network expansion planning

    NARCIS (Netherlands)

    N.H. Luong (Ngoc Hoang); J.A. La Poutré (Han); P.A.N. Bosman (Peter)

    2017-01-01

    textabstractThis article tackles the Distribution Network Expansion Planning (DNEP) problem that has to be solved by distribution network operators to decide which, where, and/or when enhancements to electricity networks should be introd uced to satisfy the future power demands. Because of many

  6. Facial Sketch Synthesis Using 2D Direct Combined Model-Based Face-Specific Markov Network.

    Science.gov (United States)

    Tu, Ching-Ting; Chan, Yu-Hsien; Chen, Yi-Chung

    2016-08-01

    A facial sketch synthesis system is proposed, featuring a 2D direct combined model (2DDCM)-based face-specific Markov network. In contrast to the existing facial sketch synthesis systems, the proposed scheme aims to synthesize sketches, which reproduce the unique drawing style of a particular artist, where this drawing style is learned from a data set consisting of a large number of image/sketch pairwise training samples. The synthesis system comprises three modules, namely, a global module, a local module, and an enhancement module. The global module applies a 2DDCM approach to synthesize the global facial geometry and texture of the input image. The detailed texture is then added to the synthesized sketch in a local patch-based manner using a parametric 2DDCM model and a non-parametric Markov random field (MRF) network. Notably, the MRF approach gives the synthesized results an appearance more consistent with the drawing style of the training samples, while the 2DDCM approach enables the synthesis of outcomes with a more derivative style. As a result, the similarity between the synthesized sketches and the input images is greatly improved. Finally, a post-processing operation is performed to enhance the shadowed regions of the synthesized image by adding strong lines or curves to emphasize the lighting conditions. The experimental results confirm that the synthesized facial images are in good qualitative and quantitative agreement with the input images as well as the ground-truth sketches provided by the same artist. The representing power of the proposed framework is demonstrated by synthesizing facial sketches from input images with a wide variety of facial poses, lighting conditions, and races even when such images are not included in the training data set. Moreover, the practical applicability of the proposed framework is demonstrated by means of automatic facial recognition tests.

  7. Bayesian Graphical Network Analyses Reveal Complex Biological Interactions Specific to Alzheimer’s Disease

    Science.gov (United States)

    Rembach, Alan; Stingo, Francesco C.; Peterson, Christine; Vannucci, Marina; Do, Kim-Anh; Wilson, William J.; Macaulay, S. Lance; Ryan, Timothy M.; Martins, Ralph N.; Ames, David; Masters, Colin L.; Doecke, James D.

    2015-01-01

    With different approaches to finding prognostic or diagnostic biomarkers for Alzheimer’s disease (AD), many studies pursue only brief lists of biomarkers or disease specific pathways, potentially dismissing information from groups of correlated biomarkers. Using a novel Bayesian graphical network method, with data from the Australian Imaging, Biomarkers and Lifestyle (AIBL) study of aging, the aim of this study was to assess the biological connectivity between AD associated blood-based proteins. Briefly, three groups of protein markers (18, 37, and 48 proteins, respectively) were assessed for the posterior probability of biological connection both within and between clinical classifications. Clinical classification was defined in four groups: high performance healthy controls (hpHC), healthy controls (HC), participants with mild cognitive impairment (MCI), and participants with AD. Using the smaller group of proteins, posterior probabilities of network similarity between clinical classifications were very high, indicating no difference in biological connections between groups. Increasing the number of proteins increased the capacity to separate both hpHC and HC apart from the AD group (0 for complete separation, 1 for complete similarity), with posterior probabilities shifting from 0.89 for the 18 protein group, through to 0.54 for the 37 protein group, and finally 0.28 for the 48 protein group. Using this approach, we identified beta-2 microglobulin (β2M) as a potential master regulator of multiple proteins across all classifications, demonstrating that this approach can be used across many data sets to identify novel insights into diseases like AD. PMID:25613103

  8. Guidelines for Formal Verification Systems

    Science.gov (United States)

    1989-04-01

    This document explains the requirements for formal verification systems that are candidates for the NCSC’s Endorsed Tools List (ETL). This document...is primarily intended for developers of verification systems to use in the development of production-quality formal verification systems. It explains...the requirements and the process used to evaluate formal verification systems submitted to the NCSC for endorsement.

  9. Topical Roots of Formal Dialectic

    NARCIS (Netherlands)

    Krabbe, Erik C. W.

    Formal dialectic has its roots in ancient dialectic. We can trace this influence in Charles Hamblin's book on fallacies, in which he introduced his first formal dialectical systems. Earlier, Paul Lorenzen proposed systems of dialogical logic, which were in fact formal dialectical systems avant la

  10. Sex-specific effects of social networks on the prevalence, awareness, and control of hypertension among older Korean adults.

    Science.gov (United States)

    Baek, Jiwon; Hur, Nam Wook; Kim, Hyeon Chang; Youm, Yoosik

    2016-07-01

    Hypertension is a common chronic disease among older adults, and is associated with medical complications and mortality. This study aimed to examine the effects of social network characteristics on the prevalence, awareness, and control of hypertension among older adults. The Korean Social Life, Health, and Aging Project (KSHAP) interviewed 814 ≥ 60-year-old residents and their spouses from a rural township between December 2011 and March 2012 (response rate: 95%). We evaluated the data from 595 participants. Multivariate logistic regression models were used to assess the effects of network characteristics on hypertension. We observed strong sex-specific network effects on the prevalence, awareness, and control of hypertension. Among older women, network density was associated with hypertension awareness [odds ratio (OR): 2.63, 95% confidence interval (CI): 1.03-5.37] and control (OR: 1.72; 95% CI: 0.94-3.13). Among older men, large networks were associated with a lower prevalence of hypertension (OR: 0.75; 95% CI: 0.58-0.96). Compared to older women, older men with coarse networks exhibited better hypertension awareness (OR: 0.37; 95% CI: 0.14-0.95) and control (OR: 0.42; 95% CI: 0.19-0.91). Network size interacted with density for hypertension control (P = 0.051), with controlled hypertension being associated with large and course networks. A large network was associated with a lower risk for hypertension, and a coarse network was associated with hypertension awareness and control among older men. Older women with dense networks were most likely to exhibit hypertension awareness and control.

  11. Towards Formal Verification of a Separation Microkernel

    Science.gov (United States)

    Butterfield, Andrew; Sanan, David; Hinchey, Mike

    2013-08-01

    The best approach to verifying an IMA separation kernel is to use a (fixed) time-space partitioning kernel with a multiple independent levels of separation (MILS) architecture. We describe an activity that explores the cost and feasibility of doing a formal verification of such a kernel to the Common Criteria (CC) levels mandated by the Separation Kernel Protection Profile (SKPP). We are developing a Reference Specification of such a kernel, and are using higher-order logic (HOL) to construct formal models of this specification and key separation properties. We then plan to do a dry run of part of a formal proof of those properties using the Isabelle/HOL theorem prover.

  12. Automated Formal Verification for PLC Control Systems

    CERN Multimedia

    Fernández Adiego, Borja

    2014-01-01

    Programmable Logic Controllers (PLCs) are widely used devices used in industrial control systems. Ensuring that the PLC software is compliant with its specification is a challenging task. Formal verification has become a recommended practice to ensure the correctness of the safety-critical software. However, these techniques are still not widely applied in industry due to the complexity of building formal models, which represent the system and the formalization of requirement specifications. We propose a general methodology to perform automated model checking of complex properties expressed in temporal logics (e.g. CTL, LTL) on PLC programs. This methodology is based on an Intermediate Model (IM), meant to transform PLC programs written in any of the languages described in the IEC 61131-3 standard (ST, IL, etc.) to different modeling languages of verification tools. This approach has been applied to CERN PLC programs validating the methodology.

  13. Soil specific re-calibration of water content sensors for a field-scale sensor network

    Science.gov (United States)

    Gasch, Caley K.; Brown, David J.; Anderson, Todd; Brooks, Erin S.; Yourek, Matt A.

    2015-04-01

    Obtaining accurate soil moisture data from a sensor network requires sensor calibration. Soil moisture sensors are factory calibrated, but multiple site specific factors may contribute to sensor inaccuracies. Thus, sensors should be calibrated for the specific soil type and conditions in which they will be installed. Lab calibration of a large number of sensors prior to installation in a heterogeneous setting may not be feasible, and it may not reflect the actual performance of the installed sensor. We investigated a multi-step approach to retroactively re-calibrate sensor water content data from the dielectric permittivity readings obtained by sensors in the field. We used water content data collected since 2009 from a sensor network installed at 42 locations and 5 depths (210 sensors total) within the 37-ha Cook Agronomy Farm with highly variable soils located in the Palouse region of the Northwest United States. First, volumetric water content was calculated from sensor dielectric readings using three equations: (1) a factory calibration using the Topp equation; (2) a custom calibration obtained empirically from an instrumented soil in the field; and (3) a hybrid equation that combines the Topp and custom equations. Second, we used soil physical properties (particle size and bulk density) and pedotransfer functions to estimate water content at saturation, field capacity, and wilting point for each installation location and depth. We also extracted the same reference points from the sensor readings, when available. Using these reference points, we re-scaled the sensor readings, such that water content was restricted to the range of values that we would expect given the physical properties of the soil. The re-calibration accuracy was assessed with volumetric water content measurements obtained from field-sampled cores taken on multiple dates. In general, the re-calibration was most accurate when all three reference points (saturation, field capacity, and wilting

  14. Formalization in Component Based Development

    DEFF Research Database (Denmark)

    Holmegaard, Jens Peter; Knudsen, John; Makowski, Piotr

    2006-01-01

    We present a unifying conceptual framework for components, component interfaces, contracts and composition of components by focusing on the collection of properties or qualities that they must share. A specific property, such as signature, functionality behaviour or timing is an aspect. Each aspect...... may be specified in a formal language convenient for its purpose and, in principle, unrelated to languages for other aspects. Each aspect forms its own semantic domain, although a semantic domain may be parameterized by values derived from other aspects. The proposed conceptual framework is introduced...... by small examples, using UML as concrete syntax for various aspects, and is illustrated by one larger case study based on an industrial prototype of a complex component based system....

  15. A Survey of Formal Methods in Software Development

    DEFF Research Database (Denmark)

    Bjørner, Dines

    2012-01-01

    The use of formal methods and formal techniques in industry is steadily growing. In this survey we shall characterise what we mean by software development and by a formal method; briefly overview a history of formal specification languages - some of which are: VDM (Vienna Development Method, 1974......-..., [1]), Z (Z for Zermelo Fraenkel, 1980-..., [2]), RAISE (Rigorous Approach to Industrial Software Engineering, 1987-..., [3]) Event B (B for Bourbaki, 1990/2000-..., [4]) and Alloy [5]; and outline the basics of a formal development using, for example, RAISE: first developing a domain description D......, then a requirements prescription R, and finally a software design S - showing (arguing or formally proving) that S, in the context of D satisfies (is correct with respect to) R. We shall then mention industries in Japan, Europe and USA which, in a number of projects, use formal methods; discuss what it takes...

  16. Formalized informal learning

    DEFF Research Database (Denmark)

    Levinsen, Karin; Sørensen, Birgitte Holm

    2011-01-01

    This paper presents findings from a large-scale longitudinal, qualitative study - Project ICT and Learning (PIL) - that engaged the participation of eight primary schools in Denmark, and was conducted between 2006 and 2008. The research design was based on action research, involving teachers...... and other relevant stakeholders, as well as participant observations in the classroom documented by thick descriptions, formal and informal interviews and focus group interviews. The aim of the study was to explore and identify relations between designs for teaching and learning and the students' learning...... of school subjects within defined learning goals and curricula, along with various implementations of ICT in the pedagogical everyday practice (Levinsen & Sørensen 2008). However, another research strand - the topic of this paper - emerged during the project's life cycle as a consequence of ongoing changes...

  17. In/formalization

    Directory of Open Access Journals (Sweden)

    Alan Smart

    2017-12-01

    Full Text Available Addressing a variety of locations and subjects across several social contexts and countries, this forum intends to stimulate novel ways of conceptualizing the inevitable interpenetration and entanglement of formalization and informalization as two interlinked social processes. Rather than proposing a new coherent definition of “informality”, we propose to consider “in/formalization” as a space of practice and reflection which is crucial for engaging with contemporary economy, law and politics and their current local and global articulations and scenarios. The forum features contributions by Stamatis Amarianakis, Lenka Brunclíková, Dolores Koenig, B. Lynne Milgram, Sarah Muir, Antonio Maria Pusceddu, Alan Smart, Mechthild von Vacano, Filippo M. Zerilli & Julie Trappe.

  18. Digital recovery management: Characterizing recovery-specific social network site participation and perceived benefit.

    Science.gov (United States)

    Bergman, Brandon G; Kelly, Nathaniel W; Hoeppner, Bettina B; Vilsaint, Corrie L; Kelly, John F

    2017-06-01

    Research shows that digital social network sites (SNSs) may be valuable platforms to effect health behavior change. Little is known specifically about their ability to help address alcohol and other drug problems. This gap is noteworthy, given that individuals are already participating in existing, recovery-specific SNSs (hereafter referred to as recovery SNSs): online communities with the functionality of conventional SNSs (e.g., Facebook) that focus on substance use disorder (SUD) recovery. For example, InTheRooms.com (ITR) is a large, well-known recovery SNS that is available for free 24 hr/day via website and mobile smartphone applications. It offers recovery tools within a digital social milieu for over 430,000 registered users. To augment the knowledge base on recovery SNS platforms, we conducted an online survey of 123 ITR participants (M = 50.8 years old; 56.9% female; 93.5% White; M = 7.3 years of abstinence, range of 0-30 years; 65% cited alcohol as their primary substance). Respondents engaged with ITR, on average, for about 30 min/day several times each week. Daily meditation prompts and live online video meetings were the most commonly utilized resources. Participants generally endorsed ITR as a helpful platform, particularly with respect to increased abstinence/recovery motivation and self-efficacy. Compared to individuals abstinent for 1 or more years, those abstinent less than 1 year (including nonabstinent individuals) showed similar rates of engagement with ITR activities and similar levels of perceived benefit. Our findings suggest that longitudinal studies are warranted to examine the clinical utility of ITR and other recovery SNSs as SUD treatment adjuncts and/or recovery self-management tools. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  19. Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors.

    Science.gov (United States)

    Kemmeren, Patrick; Sameith, Katrin; van de Pasch, Loes A L; Benschop, Joris J; Lenstra, Tineke L; Margaritis, Thanasis; O'Duibhir, Eoghan; Apweiler, Eva; van Wageningen, Sake; Ko, Cheuk W; van Heesch, Sebastiaan; Kashani, Mehdi M; Ampatziadis-Michailidis, Giannis; Brok, Mariel O; Brabers, Nathalie A C H; Miles, Anthony J; Bouwmeester, Diane; van Hooff, Sander R; van Bakel, Harm; Sluiters, Erik; Bakker, Linda V; Snel, Berend; Lijnzaad, Philip; van Leenen, Dik; Groot Koerkamp, Marian J A; Holstege, Frank C P

    2014-04-24

    To understand regulatory systems, it would be useful to uniformly determine how different components contribute to the expression of all other genes. We therefore monitored mRNA expression genome-wide, for individual deletions of one-quarter of yeast genes, focusing on (putative) regulators. The resulting genetic perturbation signatures reflect many different properties. These include the architecture of protein complexes and pathways, identification of expression changes compatible with viability, and the varying responsiveness to genetic perturbation. The data are assembled into a genetic perturbation network that shows different connectivities for different classes of regulators. Four feed-forward loop (FFL) types are overrepresented, including incoherent type 2 FFLs that likely represent feedback. Systematic transcription factor classification shows a surprisingly high abundance of gene-specific repressors, suggesting that yeast chromatin is not as generally restrictive to transcription as is often assumed. The data set is useful for studying individual genes and for discovering properties of an entire regulatory system. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. The coordinating role of IQGAP1 in the regulation of local, endosome-specific actin networks

    Directory of Open Access Journals (Sweden)

    Edward B. Samson

    2017-06-01

    Full Text Available IQGAP1 is a large, multi-domain scaffold that helps orchestrate cell signaling and cytoskeletal mechanics by controlling interactions among a spectrum of receptors, signaling intermediates, and cytoskeletal proteins. While this coordination is known to impact cell morphology, motility, cell adhesion, and vesicular traffic, among other functions, the spatiotemporal properties and regulatory mechanisms of IQGAP1 have not been fully resolved. Herein, we describe a series of super-resolution and live-cell imaging analyses that identified a role for IQGAP1 in the regulation of an actin cytoskeletal shell surrounding a novel membranous compartment that localizes selectively to the basal cortex of polarized epithelial cells (MCF-10A. We also show that IQGAP1 appears to both stabilize the actin coating and constrain its growth. Loss of compartmental IQGAP1 initiates a disassembly mechanism involving rapid and unconstrained actin polymerization around the compartment and dispersal of its vesicle contents. Together, these findings suggest IQGAP1 achieves this control by harnessing both stabilizing and antagonistic interactions with actin. They also demonstrate the utility of these compartments for image-based investigations of the spatial and temporal dynamics of IQGAP1 within endosome-specific actin networks.

  1. The coordinating role of IQGAP1 in the regulation of local, endosome-specific actin networks.

    Science.gov (United States)

    Samson, Edward B; Tsao, David S; Zimak, Jan; McLaughlin, R Tyler; Trenton, Nicholaus J; Mace, Emily M; Orange, Jordan S; Schweikhard, Volker; Diehl, Michael R

    2017-06-15

    IQGAP1 is a large, multi-domain scaffold that helps orchestrate cell signaling and cytoskeletal mechanics by controlling interactions among a spectrum of receptors, signaling intermediates, and cytoskeletal proteins. While this coordination is known to impact cell morphology, motility, cell adhesion, and vesicular traffic, among other functions, the spatiotemporal properties and regulatory mechanisms of IQGAP1 have not been fully resolved. Herein, we describe a series of super-resolution and live-cell imaging analyses that identified a role for IQGAP1 in the regulation of an actin cytoskeletal shell surrounding a novel membranous compartment that localizes selectively to the basal cortex of polarized epithelial cells (MCF-10A). We also show that IQGAP1 appears to both stabilize the actin coating and constrain its growth. Loss of compartmental IQGAP1 initiates a disassembly mechanism involving rapid and unconstrained actin polymerization around the compartment and dispersal of its vesicle contents. Together, these findings suggest IQGAP1 achieves this control by harnessing both stabilizing and antagonistic interactions with actin. They also demonstrate the utility of these compartments for image-based investigations of the spatial and temporal dynamics of IQGAP1 within endosome-specific actin networks. © 2017. Published by The Company of Biologists Ltd.

  2. Patient Specific Seizure Prediction System Using Hilbert Spectrum and Bayesian Networks Classifiers

    Directory of Open Access Journals (Sweden)

    Nilufer Ozdemir

    2014-01-01

    Full Text Available The aim of this paper is to develop an automated system for epileptic seizure prediction from intracranial EEG signals based on Hilbert-Huang transform (HHT and Bayesian classifiers. Proposed system includes decomposition of the signals into intrinsic mode functions for obtaining features and use of Bayesian networks with correlation based feature selection for binary classification of preictal and interictal recordings. The system was trained and tested on Freiburg EEG database. 58 hours of preictal data, 40-minute data blocks prior to each of 87 seizures collected from 21 patients, and 503.1 hours of interictal data were examined resulting in 96.55% sensitivity with 0.21 false alarms per hour, 13.896% average proportion of time spent in warning, and 33.21 minutes of average detection latency using 30-second EEG segments with 50% overlap and a simple postprocessing technique resulting in a decision (a seizure is expected/not expected every 5 minutes. High sensitivity and low false positive rate with reasonable detection latency show that HHT based features are acceptable for patient specific seizure prediction from intracranial EEG data. Time spent for testing an EEG segment was 4.1451 seconds on average, which makes the system viable for use in real-time seizure control systems.

  3. An integrated geometric modelling framework for patient-specific computational haemodynamic study on wide-ranged vascular network.

    Science.gov (United States)

    Torii, Ryo; Oshima, Marie

    2012-01-01

    Patient-specific haemodynamic computations have been used as an effective tool in researches on cardiovascular disease associated with haemodynamics such as atherosclerosis and aneurysm. Recent development of computer resource has enabled 3D haemodynamic computations in wide-spread arterial network but there are still difficulties in modelling vascular geometry because of noise and limited resolution in medical images. In this paper, an integrated framework to model an arterial network tree for patient-specific computational haemodynamic study is developed. With this framework, 3D vascular geometry reconstruction of an arterial network and quantification of its geometric feature are aimed. The combination of 3D haemodynamic computation and vascular morphology quantification helps better understand the relationship between vascular morphology and haemodynamic force behind 'geometric risk factor' for cardiovascular diseases. The proposed method is applied to an intracranial arterial network to demonstrate its accuracy and effectiveness. The results are compared with the marching-cubes (MC) method. The comparison shows that the present modelling method can reconstruct a wide-ranged vascular network anatomically more accurate than the MC method, particularly in peripheral circulation where the image resolution is low in comparison to the vessel diameter, because of the recognition of an arterial network connectivity based on its centreline.

  4. Prediction of disease-related genes based on weighted tissue-specific networks by using DNA methylation.

    Science.gov (United States)

    Li, Min; Zhang, Jiayi; Liu, Qing; Wang, Jianxin; Wu, Fang-Xiang

    2014-01-01

    Predicting disease-related genes is one of the most important tasks in bioinformatics and systems biology. With the advances in high-throughput techniques, a large number of protein-protein interactions are available, which make it possible to identify disease-related genes at the network level. However, network-based identification of disease-related genes is still a challenge as the considerable false-positives are still existed in the current available protein interaction networks (PIN). Considering the fact that the majority of genetic disorders tend to manifest only in a single or a few tissues, we constructed tissue-specific networks (TSN) by integrating PIN and tissue-specific data. We further weighed the constructed tissue-specific network (WTSN) by using DNA methylation as it plays an irreplaceable role in the development of complex diseases. A PageRank-based method was developed to identify disease-related genes from the constructed networks. To validate the effectiveness of the proposed method, we constructed PIN, weighted PIN (WPIN), TSN, WTSN for colon cancer and leukemia, respectively. The experimental results on colon cancer and leukemia show that the combination of tissue-specific data and DNA methylation can help to identify disease-related genes more accurately. Moreover, the PageRank-based method was effective to predict disease-related genes on the case studies of colon cancer and leukemia. Tissue-specific data and DNA methylation are two important factors to the study of human diseases. The same method implemented on the WTSN can achieve better results compared to those being implemented on original PIN, WPIN, or TSN. The PageRank-based method outperforms degree centrality-based method for identifying disease-related genes from WTSN.

  5. Formal refinement of extended state machines

    Directory of Open Access Journals (Sweden)

    Thomas Fayolle

    2016-06-01

    Full Text Available In a traditional formal development process, e.g. using the B method, the informal user requirements are (manually translated into a global abstract formal specification. This translation is especially difficult to achieve. The Event-B method was developed to incrementally and formally construct such a specification using stepwise refinement. Each increment takes into account new properties and system aspects. In this paper, we propose to couple a graphical notation called Algebraic State-Transition Diagrams (ASTD with an Event-B specification in order to provide a better understanding of the software behaviour. The dynamic behaviour is captured by the ASTD, which is based on automata and process algebra operators, while the data model is described by means of an Event-B specification. We propose a methodology to incrementally refine such specification couplings, taking into account new refinement relations and consistency conditions between the control specification and the data specification. We compare the specifications obtained using each approach for readability and proof complexity. The advantages and drawbacks of the traditional approach and of our methodology are discussed. The whole process is illustrated by a railway CBTC-like case study. Our approach is supported by tools for translating ASTD's into B and Event-B into B.

  6. Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks.

    Science.gov (United States)

    Repunte-Canonigo, Vez; Shin, William; Vendruscolo, Leandro F; Lefebvre, Celine; van der Stap, Lena; Kawamura, Tomoya; Schlosburg, Joel E; Alvarez, Mariano; Koob, George F; Califano, Andrea; Sanna, Pietro Paolo

    2015-02-02

    A systems biology approach based on the assembly and interrogation of gene regulatory networks, or interactomes, was used to study neuroadaptation processes associated with the transition to alcohol dependence at the molecular level. Using a rat model of dependent and non-dependent alcohol self-administration, we reverse engineered a global transcriptional regulatory network during protracted abstinence, a period when relapse rates are highest. We then interrogated the network to identify master regulator genes that mechanistically regulate brain region-specific signatures associated with dependent and non-dependent alcohol self-administration. Among these, the gene coding for the glucocorticoid receptor was independently identified as a master regulator in multiple brain regions, including the medial prefrontal cortex, nucleus accumbens, central nucleus of the amygdala, and ventral tegmental area, consistent with the view that brain reward and stress systems are dysregulated during protracted abstinence. Administration of the glucocorticoid antagonist mifepristone in either the nucleus accumbens or ventral tegmental area selectively decreased dependent, excessive, alcohol self-administration in rats but had no effect on non-dependent, moderate, alcohol self-administration. Our study suggests that assembly and analysis of regulatory networks is an effective strategy for the identification of key regulators of long-term neuroplastic changes within specific brain regions that play a functional role in alcohol dependence. More specifically, our results support a key role for regulatory networks downstream of the glucocorticoid receptor in excessive alcohol drinking during protracted alcohol abstinence.

  7. Mixing Formal and Informal Model Elements for Tracing Requirements

    DEFF Research Database (Denmark)

    Jastram, Michael; Hallerstede, Stefan; Ladenberger, Lukas

    2011-01-01

    Tracing between informal requirements and formal models is challenging. A method for such tracing should permit to deal efficiently with changes to both the requirements and the model. A particular challenge is posed by the persisting interplay of formal and informal elements. In this paper, we...... a system for traceability with a state-based formal method that supports refinement. We do not require all specification elements to be modelled formally and support incremental incorporation of new specification elements into the formal model. Refinement is used to deal with larger amounts of requirements...... describe an incremental approach to requirements validation and systems modelling. Formal modelling facilitates a high degree of automation: it serves for validation and traceability. The foundation for our approach are requirements that are structured according to the WRSPM reference model. We provide...

  8. Network strength, transaction-specific investments, inter-personal trust, and relationship satisfaction in Chinese agrifood SMEs

    NARCIS (Netherlands)

    Lu Hualiang,; Feng, S.; Trienekens, J.H.; Omta, S.W.F.

    2012-01-01

    Purpose - The purpose of this paper is to investigate the effects of network strength, transaction-specific investments and inter-personal trust on business relationship satisfaction for small-and-medium-sized enterprises (SMEs) involved in agri-food processing and exporting in China.

  9. Using domain-specific basic functions for the analysis of supervised artificial neural networks

    NARCIS (Netherlands)

    van der Zwaag, B.J.

    2003-01-01

    Since the early development of artificial neural networks, researchers have tried to analyze trained neural networks in order to gain insight into their behavior. For certain applications and in certain problem domains this has been successful, for example by the development of so-called rule

  10. A Formal Model For Declarative Workflows

    DEFF Research Database (Denmark)

    Mukkamala, Raghava Rao

    in highly complex and dynamic environments like healthcare and case management sectors, where the processes ex- hibit a lot of uncertainty and unexpected behavior and thereby require high degree of flexibility. Several research groups have suggested declarative models as a good approach to handle such ad...... using DCR Graphs and to make the formal model available to a wider audience, we have developed prototype tools for specification and a workflow engine for the execution of DCR Graphs. We have also developed tools interfacing SPIN model checker to formally verify safety and liveness properties on the DCR...... Graphs. Case studies from healthcare and case management domains have been modeled in DCR Graphs to show that our formal model is suitable for modeling the workflows from those dynamic sectors. This PhD project is funded by the Danish Strategic Research Council through the Trustworthy Pervasive...

  11. Fourier Series Formalization in ACL2(r

    Directory of Open Access Journals (Sweden)

    Cuong K. Chau

    2015-09-01

    Full Text Available We formalize some basic properties of Fourier series in the logic of ACL2(r, which is a variant of ACL2 that supports reasoning about the real and complex numbers by way of non-standard analysis. More specifically, we extend a framework for formally evaluating definite integrals of real-valued, continuous functions using the Second Fundamental Theorem of Calculus. Our extended framework is also applied to functions containing free arguments. Using this framework, we are able to prove the orthogonality relationships between trigonometric functions, which are the essential properties in Fourier series analysis. The sum rule for definite integrals of indexed sums is also formalized by applying the extended framework along with the First Fundamental Theorem of Calculus and the sum rule for differentiation. The Fourier coefficient formulas of periodic functions are then formalized from the orthogonality relations and the sum rule for integration. Consequently, the uniqueness of Fourier sums is a straightforward corollary. We also present our formalization of the sum rule for definite integrals of infinite series in ACL2(r. Part of this task is to prove the Dini Uniform Convergence Theorem and the continuity of a limit function under certain conditions. A key technique in our proofs of these theorems is to apply the overspill principle from non-standard analysis.

  12. A disease-specific metabolic brain network associated with corticobasal degeneration

    Science.gov (United States)

    Niethammer, Martin; Tang, Chris C.; Feigin, Andrew; Allen, Patricia J.; Heinen, Lisette; Hellwig, Sabine; Amtage, Florian; Hanspal, Era; Vonsattel, Jean Paul; Poston, Kathleen L.; Meyer, Philipp T.; Leenders, Klaus L.

    2014-01-01

    Corticobasal degeneration is an uncommon parkinsonian variant condition that is diagnosed mainly on clinical examination. To facilitate the differential diagnosis of this disorder, we used metabolic brain imaging to characterize a specific network that can be used to discriminate corticobasal degeneration from other atypical parkinsonian syndromes. Ten non-demented patients (eight females/two males; age 73.9 ± 5.7 years) underwent metabolic brain imaging with 18F-fluorodeoxyglucose positron emission tomography for atypical parkinsonism. These individuals were diagnosed clinically with probable corticobasal degeneration. This diagnosis was confirmed in the three subjects who additionally underwent post-mortem examination. Ten age-matched healthy subjects (five females/five males; age 71.7 ± 6.7 years) served as controls for the imaging studies. Spatial covariance analysis was applied to scan data from the combined group to identify a significant corticobasal degeneration-related metabolic pattern that discriminated (P cerebral hemisphere opposite the more clinically affected body side. The presence of this corticobasal degeneration-related metabolic topography was confirmed in two independent testing sets of patient and control scans, with elevated pattern expression (P computed expression values for this pattern accurately discriminated corticobasal degeneration from multiple system atrophy and progressive supranuclear palsy (the two most common atypical parkinsonian syndromes) on a single case basis. Based upon this measure, corticobasal degeneration was successfully distinguished from multiple system atrophy (P palsy, presumably because of the overlap (∼24%) that existed between the corticobasal degeneration- and the progressive supranuclear palsy-related metabolic topographies. Nonetheless, excellent discrimination between these disease entities was achieved by computing hemispheric asymmetry scores for the corticobasal degeneration-related pattern on a

  13. A disease-specific metabolic brain network associated with corticobasal degeneration.

    Science.gov (United States)

    Niethammer, Martin; Tang, Chris C; Feigin, Andrew; Allen, Patricia J; Heinen, Lisette; Hellwig, Sabine; Amtage, Florian; Hanspal, Era; Vonsattel, Jean Paul; Poston, Kathleen L; Meyer, Philipp T; Leenders, Klaus L; Eidelberg, David

    2014-11-01

    Corticobasal degeneration is an uncommon parkinsonian variant condition that is diagnosed mainly on clinical examination. To facilitate the differential diagnosis of this disorder, we used metabolic brain imaging to characterize a specific network that can be used to discriminate corticobasal degeneration from other atypical parkinsonian syndromes. Ten non-demented patients (eight females/two males; age 73.9 ± 5.7 years) underwent metabolic brain imaging with (18)F-fluorodeoxyglucose positron emission tomography for atypical parkinsonism. These individuals were diagnosed clinically with probable corticobasal degeneration. This diagnosis was confirmed in the three subjects who additionally underwent post-mortem examination. Ten age-matched healthy subjects (five females/five males; age 71.7 ± 6.7 years) served as controls for the imaging studies. Spatial covariance analysis was applied to scan data from the combined group to identify a significant corticobasal degeneration-related metabolic pattern that discriminated (P metabolic reductions involving frontal and parietal cortex, thalamus, and caudate nucleus. These pattern-related changes were greater in magnitude in the cerebral hemisphere opposite the more clinically affected body side. The presence of this corticobasal degeneration-related metabolic topography was confirmed in two independent testing sets of patient and control scans, with elevated pattern expression (P disease groups relative to corresponding normal values. We next determined whether prospectively computed expression values for this pattern accurately discriminated corticobasal degeneration from multiple system atrophy and progressive supranuclear palsy (the two most common atypical parkinsonian syndromes) on a single case basis. Based upon this measure, corticobasal degeneration was successfully distinguished from multiple system atrophy (P metabolic topographies. Nonetheless, excellent discrimination between these disease entities was

  14. Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction.

    Science.gov (United States)

    Han, Youngmahn; Kim, Dongsup

    2017-12-28

    Computational scanning of peptide candidates that bind to a specific major histocompatibility complex (MHC) can speed up the peptide-based vaccine development process and therefore various methods are being actively developed. Recently, machine-learning-based methods have generated successful results by training large amounts of experimental data. However, many machine learning-based methods are generally less sensitive in recognizing locally-clustered interactions, which can synergistically stabilize peptide binding. Deep convolutional neural network (DCNN) is a deep learning method inspired by visual recognition process of animal brain and it is known to be able to capture meaningful local patterns from 2D images. Once the peptide-MHC interactions can be encoded into image-like array(ILA) data, DCNN can be employed to build a predictive model for peptide-MHC binding prediction. In this study, we demonstrated that DCNN is able to not only reliably predict peptide-MHC binding, but also sensitively detect locally-clustered interactions. Nonapeptide-HLA-A and -B binding data were encoded into ILA data. A DCNN, as a pan-specific prediction model, was trained on the ILA data. The DCNN showed higher performance than other prediction tools for the latest benchmark datasets, which consist of 43 datasets for 15 HLA-A alleles and 25 datasets for 10 HLA-B alleles. In particular, the DCNN outperformed other tools for alleles belonging to the HLA-A3 supertype. The F1 scores of the DCNN were 0.86, 0.94, and 0.67 for HLA-A*31:01, HLA-A*03:01, and HLA-A*68:01 alleles, respectively, which were significantly higher than those of other tools. We found that the DCNN was able to recognize locally-clustered interactions that could synergistically stabilize peptide binding. We developed ConvMHC, a web server to provide user-friendly web interfaces for peptide-MHC class I binding predictions using the DCNN. ConvMHC web server can be accessible via http://jumong.kaist.ac.kr:8080/convmhc

  15. Specific and evolving resting-state network alterations in post-concussion syndrome following mild traumatic brain injury.

    Directory of Open Access Journals (Sweden)

    Arnaud Messé

    Full Text Available Post-concussion syndrome has been related to axonal damage in patients with mild traumatic brain injury, but little is known about the consequences of injury on brain networks. In the present study, our aim was to characterize changes in functional brain networks following mild traumatic brain injury in patients with post-concussion syndrome using resting-state functional magnetic resonance imaging data. We investigated 17 injured patients with persistent post-concussion syndrome (under the DSM-IV criteria at 6 months post-injury compared with 38 mild traumatic brain injury patients with no post-concussion syndrome and 34 healthy controls. All patients underwent magnetic resonance imaging examinations at the subacute (1-3 weeks and late (6 months phases after injury. Group-wise differences in functional brain networks were analyzed using graph theory measures. Patterns of long-range functional networks alterations were found in all mild traumatic brain injury patients. Mild traumatic brain injury patients with post-concussion syndrome had greater alterations than patients without post-concussion syndrome. In patients with post-concussion syndrome, changes specifically affected temporal and thalamic regions predominantly at the subacute stage and frontal regions at the late phase. Our results suggest that the post-concussion syndrome is associated with specific abnormalities in functional brain network that may contribute to explain deficits typically observed in PCS patients.

  16. Contact networks structured by sex underpin sex-specific epidemiology of infection.

    Science.gov (United States)

    Silk, Matthew J; Weber, Nicola L; Steward, Lucy C; Hodgson, David J; Boots, Mike; Croft, Darren P; Delahay, Richard J; McDonald, Robbie A

    2018-02-01

    Contact networks are fundamental to the transmission of infection and host sex often affects the acquisition and progression of infection. However, the epidemiological impacts of sex-related variation in animal contact networks have rarely been investigated. We test the hypothesis that sex-biases in infection are related to variation in multilayer contact networks structured by sex in a population of European badgers Meles meles naturally infected with Mycobacterium bovis. Our key results are that male-male and between-sex networks are structured at broader spatial scales than female-female networks and that in male-male and between-sex contact networks, but not female-female networks, there is a significant relationship between infection and contacts with individuals in other groups. These sex differences in social behaviour may underpin male-biased acquisition of infection and may result in males being responsible for more between-group transmission. This highlights the importance of sex-related variation in host behaviour when managing animal diseases. © 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

  17. Link-prediction to tackle the boundary specification problem in social network surveys

    Science.gov (United States)

    De Wilde, Philippe; Buarque de Lima-Neto, Fernando

    2017-01-01

    Diffusion processes in social networks often cause the emergence of global phenomena from individual behavior within a society. The study of those global phenomena and the simulation of those diffusion processes frequently require a good model of the global network. However, survey data and data from online sources are often restricted to single social groups or features, such as age groups, single schools, companies, or interest groups. Hence, a modeling approach is required that extrapolates the locally restricted data to a global network model. We tackle this Missing Data Problem using Link-Prediction techniques from social network research, network generation techniques from the area of Social Simulation, as well as a combination of both. We found that techniques employing less information may be more adequate to solve this problem, especially when data granularity is an issue. We validated the network models created with our techniques on a number of real-world networks, investigating degree distributions as well as the likelihood of links given the geographical distance between two nodes. PMID:28426826

  18. Rhythm-specific modulation of the sensorimotor network in drug-naive patients with Parkinson's disease by levodopa.

    Science.gov (United States)

    Esposito, Fabrizio; Tessitore, Alessandro; Giordano, Alfonso; De Micco, Rosita; Paccone, Antonella; Conforti, Renta; Pignataro, Giuseppe; Annunziato, Lucio; Tedeschi, Gioacchino

    2013-03-01

    Brain activity during rest is characterized by slow (0.01-0.1 Hz) fluctuations of blood oxygenation level-dependent functional magnetic resonance imaging signals. These fluctuations are organized as functional connectivity networks called resting-state networks, anatomically corresponding to specific neuronal circuits. As Parkinson's disease is mainly characterized by a dysfunction of the sensorimotor pathways, which can be influenced by levodopa administration, the present study investigated the functional connectivity changes within the sensorimotor resting-state network in drug-naïve patients with Parkinson's disease after acute levodopa administration. Using a double-blind placebo-controlled design, resting-state functional magnetic resonance imaging was carried out in 20 drug-naïve patients with Parkinson's disease, immediately before and 60 min after, oral administration of either levodopa or placebo. Control resting-state functional magnetic resonance imaging data were recorded in 18 age- and sex-matched healthy volunteers. Independent component analysis was performed to extract resting-state network maps and associated time-course spectral features. At the anatomical level, levodopa enhanced the sensorimotor network functional connectivity in the supplementary motor area, a region where drug-naïve patients with Parkinson's disease exhibited reduced signal fluctuations compared with untreated patients. At the spectral frequency level, levodopa stimulated these fluctuations in a selective frequency band of the sensorimotor network. The reported effects induced by levodopa on sensorimotor network topological and spectral features confirm that the sensorimotor system is a target of acute levodopa administration in drug-naïve patients with Parkinson's disease. Moreover, while the regional changes in supplementary motor area reflect the functional improvement in motor function, the rhythm-specific modulation induced by the dopamine precursor discloses a novel

  19. Resonant-state perturbation formalisms

    Energy Technology Data Exchange (ETDEWEB)

    Romo, W.J. (Carleton Univ., Ottawa, Ontario (Canada). Dept. of Physics)

    1983-05-02

    Three different formalisms for determining bound-state, virtual-state, and resonant-state energies of a perturbed system are developed. Two of the formalisms are based on expansions of the unperturbed Green function in terms of bound-state, resonant-state and deformed-continuum-state contributions of the form developed by T. Berggren. The third formalism is based on a Mittag-Leffler expansion of the unperturbed Green function. The three formalisms are compared and the relative merits of calculation schemes based on them are examined.

  20. EHRA: Specification and Analysis of Energy-Harvesting Wireless Sensor Networks

    DEFF Research Database (Denmark)

    Dung, Phan Anh; Hansen, Michael Reichhardt; Madsen, Jan

    2014-01-01

    to study wireless sensor networks (WSN) with energy-harvesting capabilities. The purpose of the framework is to analyze WSNs at a high level of abstraction, that is, before the protocols are implemented and before the WSN is deployed. The conceptual basis of EHRA comprises the environment, the medium...... is developed as a simulator implemented using the functional programming language F#. This simulator is used to analyze global properties of WSNs such as network fragmentation,routing trends, and energy profiles for the nodes. Three routing protocols, with a progression in the energy-harvesting awareness......, are analyzed on a network that is placed in a heterogeneous environment....

  1. Linking social and spatial networks to viral community phylogenetics reveals subtype-specific transmission dynamics in African lions.

    Science.gov (United States)

    Fountain-Jones, Nicholas M; Packer, Craig; Troyer, Jennifer L; VanderWaal, Kimberly; Robinson, Stacie; Jacquot, Maude; Craft, Meggan E

    2017-10-01

    Heterogeneity within pathogen species can have important consequences for how pathogens transmit across landscapes; however, discerning different transmission routes is challenging. Here, we apply both phylodynamic and phylogenetic community ecology techniques to examine the consequences of pathogen heterogeneity on transmission by assessing subtype-specific transmission pathways in a social carnivore. We use comprehensive social and spatial network data to examine transmission pathways for three subtypes of feline immunodeficiency virus (FIVPle ) in African lions (Panthera leo) at multiple scales in the Serengeti National Park, Tanzania. We used FIVPle molecular data to examine the role of social organization and lion density in shaping transmission pathways and tested to what extent vertical (i.e., father- and/or mother-offspring relationships) or horizontal (between unrelated individuals) transmission underpinned these patterns for each subtype. Using the same data, we constructed subtype-specific FIVPle co-occurrence networks and assessed what combination of social networks, spatial networks or co-infection best structured the FIVPle network. While social organization (i.e., pride) was an important component of FIVPle transmission pathways at all scales, we find that FIVPle subtypes exhibited different transmission pathways at within- and between-pride scales. A combination of social and spatial networks, coupled with consideration of subtype co-infection, was likely to be important for FIVPle transmission for the two major subtypes, but the relative contribution of each factor was strongly subtype-specific. Our study provides evidence that pathogen heterogeneity is important in understanding pathogen transmission, which could have consequences for how endemic pathogens are managed. Furthermore, we demonstrate that community phylogenetic ecology coupled with phylodynamic techniques can reveal insights into the differential evolutionary pressures acting on virus

  2. Frequency-specific directed interactions in the human brain network for language

    NARCIS (Netherlands)

    Schoffelen, J.M.; Hultén, A.H.; Lam, N.H.L.; Marquand, A.F.; Uddén, J.U.; Hagoort, P.

    2017-01-01

    The brain's remarkable capacity for language requires bidirectional interactions between functionally specialized brain regions. We used magnetoencephalography to investigate interregional interactions in the brain network for language while 102 participants were reading sentences. Using Granger

  3. The Formalization of Cultural Psychology. Reasons and Functions.

    Science.gov (United States)

    Salvatore, Sergio

    2017-03-01

    In this paper I discuss two basic theses about the formalization of cultural psychology. First, I claim that formalization is a relevant, even necessary stage of development of this domain of science. This is so because formalization allows the scientific language to achieve a much needed autonomy from the commonsensical language of the phenomena that this science deals with. Second, I envisage the two main functions that formalization has to perform in the field of cultural psychology: on the one hand, it has to provide formal rules grounding and constraining the deductive construction of the general theory; on the other hand, it has to provide the devices for supporting the interpretation of local phenomena, in terms of the abductive reconstruction of the network of linkages among empirical occurrences comprising the local phenomena.

  4. Fast-scale network dynamics in human cortex have specific spectral covariance patterns

    OpenAIRE

    Freudenburg, Zachary V.; Gaona, Charles M.; Sharma, Mohit; Bundy, David T.; Breshears, Jonathan D.; Robert B Pless; Leuthardt, Eric C.

    2014-01-01

    How different cortical regions are coordinated during a cognitive task is fundamentally important to understanding brain function. At rest, the brain is subdivided into different functional networks that are bound together at very slow oscillating time scales. Less is understood about how this networked behavior operates during the brief moments of a cognitive operation. By recording brain signals directly from the surface of the human brain, we find that, when performing a simple speech task...

  5. Specifying Geographic Information - Ontology, Knowledge Representation, and Formal Constraints

    DEFF Research Database (Denmark)

    Christensen, Jesper Vinther

    2007-01-01

    of quality requirements and formalization of rules, so that they can be used for verification of produced information. An essential contribution is a formal specification language dedicated to the formulation of formal rules to be observed by the information. The language is based on a formal semantic model...... of geographic information is an essential part of a specification. The thesis contributes a structure of quality descriptions by introducing two notions: "Acceptable Quality Levels" (AQL) and "Quality Element Requirements" (QER), which designate respectively the minimum quality requirements for information...... by writing specifications in the context of one or more other specifications. As an illustration of the applications of specifications written in the developed specification language, a concept is developed in the thesis to make possible a decentralized collection and distribution of information about...

  6. Formal verification of algorithms for critical systems

    Science.gov (United States)

    Rushby, John M.; Von Henke, Friedrich

    1993-01-01

    We describe our experience with formal, machine-checked verification of algorithms for critical applications, concentrating on a Byzantine fault-tolerant algorithm for synchronizing the clocks in the replicated computers of a digital flight control system. First, we explain the problems encountered in unsynchronized systems and the necessity, and criticality, of fault-tolerant synchronization. We give an overview of one such algorithm, and of the arguments for its correctness. Next, we describe a verification of the algorithm that we performed using our EHDM system for formal specification and verification. We indicate the errors we found in the published analysis of the algorithm, and other benefits that we derived from the verification. Based on our experience, we derive some key requirements for a formal specification and verification system adequate to the task of verifying algorithms of the type considered. Finally, we summarize our conclusions regarding the benefits of formal verification in this domain, and the capabilities required of verification systems in order to realize those benefits.

  7. Evolution of the environmental justice movement: activism, formalization and differentiation

    Science.gov (United States)

    Colsa Perez, Alejandro; Grafton, Bernadette; Mohai, Paul; Hardin, Rebecca; Hintzen, Katy; Orvis, Sara

    2015-10-01

    To complement a recent flush of research on transnational environmental justice movements, we sought a deeper organizational history of what we understand as the contemporary environmental justice movement in the United States. We thus conducted in-depth interviews with 31 prominent environmental justice activists, scholars, and community leaders across the US. Today’s environmental justice groups have transitioned from specific local efforts to broader national and global mandates, and more sophisticated political, technological, and activist strategies. One of the most significant transformations has been the number of groups adopting formal legal status, and emerging as registered environmental justice organizations (REJOs) within complex partnerships. This article focuses on the emergence of REJOs, and describes the respondents’ views about the implications of this for more local grassroots groups. It reveals a central irony animating work across groups in today’s movement: legal formalization of many environmental justice organizations has made the movement increasingly internally differentiated, dynamic, and networked, even as the passage of actual national laws on environmental justice has proven elusive.

  8. Formal Test Automation: The Conference Protocol with PHACT

    NARCIS (Netherlands)

    Heerink, A.W.; Ural, Hasan; Probert, Robert L.; Feenstra, J.; Tretmans, G.J.; von Bochmann, Gregor

    2000-01-01

    We discuss a case study of automatic test generation and test execution based on formal methods. The case is the Conference Protocol, a simple, chatbox-like protocol, for which (formal) specifications and multiple implementations are publicly available and which is also used in other case study

  9. Formal structures for extracting analytically justifiable decisions from ...

    African Journals Online (AJOL)

    ... that a business process model “should have a formal foundation” as a major requirement for transforming it into a DSS. The paper further ascertains that formal structures refer to logical representations of the relationships existing between the dependent and the independent variables in a specific architecture description.

  10. RAISE: a Product Supporting Industrial Use of Formal Methods

    DEFF Research Database (Denmark)

    Haxthausen, Anne Elisabeth; Pedersen, J. Storbank; Prehn, Søren

    1993-01-01

    This paper gives an overview of RAISE, a product consisting of a method for developing software, an associated formal specification language and tools supporting the method and the language. The method is based on the notion of stepwise refinement and offers the possibility of formal verification...

  11. Improving 1D Site Specific Velocity Profiles for the Kik-Net Network

    Science.gov (United States)

    Holt, James; Edwards, Benjamin; Pilz, Marco; Fäh, Donat; Rietbrock, Andreas

    2017-04-01

    Ground motion predication equations (GMPEs) form the cornerstone of modern seismic hazard assessments. When produced to a high standard they provide reliable estimates of ground motion/spectral acceleration for a given site and earthquake scenario. This information is crucial for engineers to optimise design and for regulators who enforce legal minimum safe design capacities. Classically, GMPEs were built upon the assumption that variability around the median model could be treated as aleatory. As understanding improved, it was noted that the propagation could be segregated into the response of the average path from the source and the response of the site. This is because the heterogeneity of the near-surface lithology is significantly different from that of the bulk path. It was then suggested that the semi-ergodic approach could be taken if the site response could be determined, moving uncertainty away from aleatory to epistemic. The determination of reliable site-specific response models is therefore becoming increasingly critical for ground motion models used in engineering practice. Today it is common practice to include proxies for site response within the scope of a GMPE, such as Vs30 or site classification, in an effort to reduce the overall uncertainty of the predication at a given site. However, these proxies are not always reliable enough to give confident ground motion estimates, due to the complexity of the near-surface. Other approaches of quantifying the response of the site include detailed numerical simulations (1/2/3D - linear, EQL, non-linear etc.). However, in order to be reliable, they require highly detailed and accurate velocity and, for non-linear analyses, material property models. It is possible to obtain this information through invasive methods, but is expensive, and not feasible for most projects. Here we propose an alternative method to derive reliable velocity profiles (and their uncertainty), calibrated using almost 20 years of

  12. A Formalization of Linkage Analysis

    DEFF Research Database (Denmark)

    Ingolfsdottir, Anna; Christensen, A.I.; Hansen, Jens A.

    In this report a formalization of genetic linkage analysis is introduced. Linkage analysis is a computationally hard biomathematical method, which purpose is to locate genes on the human genome. It is rooted in the new area of bioinformatics and no formalization of the method has previously been ...

  13. Obligationes as Formal Dialogue Systems

    NARCIS (Netherlands)

    Uckelman, S.L.; Ågotnes, T.

    2011-01-01

    Formal Dialogue Systems (FDSs) model rule-based interaction between agents. Their conceptual roots go back to Hamblin's [11,12], which cites the medieval theory of obligationes as inspiration for his development of a formal system of argumentation. In an obligatio, two agents, Opponent and

  14. Formal verification of Simulink/Stateflow diagrams a deductive approach

    CERN Document Server

    Zhan, Naijun; Zhao, Hengjun

    2017-01-01

    This book presents a state-of-the-art technique for formal verification of continuous-time Simulink/Stateflow diagrams, featuring an expressive hybrid system modelling language, a powerful specification logic and deduction-based verification approach, and some impressive, realistic case studies. Readers will learn the HCSP/HHL-based deductive method and the use of corresponding tools for formal verification of Simulink/Stateflow diagrams. They will also gain some basic ideas about fundamental elements of formal methods such as formal syntax and semantics, and especially the common techniques applied in formal modelling and verification of hybrid systems. By investigating the successful case studies, readers will realize how to apply the pure theory and techniques to real applications, and hopefully will be inspired to start to use the proposed approach, or even develop their own formal methods in their future work.

  15. Towards the Formalization of a Factory Demonstrator in BeSpaceD

    OpenAIRE

    Foster, Keith; Blech, Jan Olaf; Prevost, Guillaume

    2016-01-01

    This report gives an overview of our efforts towards a formalization for a food processing demonstrator plant. Our BeSpaceD framework is used for the formalization. The formalization comprises properties of components and relations between components. We present domain-specific constructs for the formalization of industrial automation facilities and provide some insights into the concrete food processing formalization. We are particularly interested in spatio-temporal and other physical chara...

  16. New procedure for departure formalities

    CERN Multimedia

    HR & GS Departments

    2011-01-01

    As part of the process of simplifying procedures and rationalising administrative processes, the HR and GS Departments have introduced new personalised departure formalities on EDH. These new formalities have applied to students leaving CERN since last year and from 17 October 2011 this procedure will be extended to the following categories of CERN personnel: Staff members, Fellows and Associates. It is planned to extend this electronic procedure to the users in due course. What purpose do departure formalities serve? The departure formalities are designed to ensure that members of the personnel contact all the relevant services in order to return any necessary items (equipment, cards, keys, dosimeter, electronic equipment, books, etc.) and are aware of all the benefits to which they are entitled on termination of their contract. The new departure formalities on EDH have the advantage of tailoring the list of services that each member of the personnel must visit to suit his individual contractual and p...

  17. Formal connections in deformation quantization

    DEFF Research Database (Denmark)

    Masulli, Paolo

    manifold. Gammelgaard gave an explicit formula for a class of star products in this setting. We review his construction, which is combinatorial and based on a certain family of graphs and extend it, to provide the graph formalism with the notions of composition and differentiation. We shall focus our...... attention on symplectic manifolds equipped with a family of star products, indexed by a parameter space. In this situation we can define a connection in the trivial bundle over the parameter space with fibres the formal smooth functions on the manifold, which relates the star products in the family...... and is called a formal connection. We study the question of classifying such formal connections. To each star product we can associate a certain cohomology class called the characteristic class. It turns out that a formal connection exists if and only if all the star products in the family have the same...

  18. Formal language constrained path problems

    Energy Technology Data Exchange (ETDEWEB)

    Barrett, C.; Jacob, R.; Marathe, M.

    1997-07-08

    In many path finding problems arising in practice, certain patterns of edge/vertex labels in the labeled graph being traversed are allowed/preferred, while others are disallowed. Motivated by such applications as intermodal transportation planning, the authors investigate the complexity of finding feasible paths in a labeled network, where the mode choice for each traveler is specified by a formal language. The main contributions of this paper include the following: (1) the authors show that the problem of finding a shortest path between a source and destination for a traveler whose mode choice is specified as a context free language is solvable efficiently in polynomial time, when the mode choice is specified as a regular language they provide algorithms with improved space and time bounds; (2) in contrast, they show that the problem of finding simple paths between a source and a given destination is NP-hard, even when restricted to very simple regular expressions and/or very simple graphs; (3) for the class of treewidth bounded graphs, they show that (i) the problem of finding a regular language constrained simple path between source and a destination is solvable in polynomial time and (ii) the extension to finding context free language constrained simple paths is NP-complete. Several extensions of these results are presented in the context of finding shortest paths with additional constraints. These results significantly extend the results in [MW95]. As a corollary of the results, they obtain a polynomial time algorithm for the BEST k-SIMILAR PATH problem studied in [SJB97]. The previous best algorithm was given by [SJB97] and takes exponential time in the worst case.

  19. A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation.

    Directory of Open Access Journals (Sweden)

    Warren D Anderson

    2017-07-01

    Full Text Available Multiple physiological systems interact throughout the development of a complex disease. Knowledge of the dynamics and connectivity of interactions across physiological systems could facilitate the prevention or mitigation of organ damage underlying complex diseases, many of which are currently refractory to available therapeutics (e.g., hypertension. We studied the regulatory interactions operating within and across organs throughout disease development by integrating in vivo analysis of gene expression dynamics with a reverse engineering approach to infer data-driven dynamic network models of multi-organ gene regulatory influences. We obtained experimental data on the expression of 22 genes across five organs, over a time span that encompassed the development of autonomic nervous system dysfunction and hypertension. We pursued a unique approach for identification of continuous-time models that jointly described the dynamics and structure of multi-organ networks by estimating a sparse subset of ∼12,000 possible gene regulatory interactions. Our analyses revealed that an autonomic dysfunction-specific multi-organ sequence of gene expression activation patterns was associated with a distinct gene regulatory network. We analyzed the model structures for adaptation motifs, and identified disease-specific network motifs involving genes that exhibited aberrant temporal dynamics. Bioinformatic analyses identified disease-specific single nucleotide variants within or near transcription factor binding sites upstream of key genes implicated in maintaining physiological homeostasis. Our approach illustrates a novel framework for investigating the pathogenesis through model-based analysis of multi-organ system dynamics and network properties. Our results yielded novel candidate molecular targets driving the development of cardiovascular disease, metabolic syndrome, and immune dysfunction.

  20. On Asymptotic Analysis of Packet and Wormhole Switched Routing Algorithm for Application-Specific Networks-on-Chip

    Directory of Open Access Journals (Sweden)

    Nitin

    2012-01-01

    Full Text Available The application of the multistage interconnection networks (MINs in systems-on-chip (SoC and networks-on-chip (NoC is hottest since year 2002. Nevertheless, nobody used them practically for parallel communication. However, to overcome all the previous problems, a new method is proposed that uses MIN to provide intra-(global communication among application-specific NoCs in networks-in-package (NiP. For this, four fault-tolerant parallel algorithms are proposed. It allows different NoCs to communicate in parallel using either fault-tolerant irregular Penta multistage interconnection network (PNN or fault-tolerant regular Hexa multistage interconnection network (HXN. These two are acting as an interconnects-on-chip (IoC in NiP. Both IoC use packet switching and wormhole switching to route packets from source NoC to destination NoC. The results are compared in terms of packet losses and wormhole switching which comes out to be better than packet switching. The comparison of IoC on cost and MTTR concluded that the HXN has the higher cost than the PNN, but MTTR values of the HXN are low in comparison to the PNN. This signifies that the ability to tolerate faults and online repairing of the HXN is higher and faster than the PNN.

  1. The formal operations: Piaget’s concept, researches and main critics

    Directory of Open Access Journals (Sweden)

    Stepanović Ivana Ž.

    2004-01-01

    Full Text Available This paper deals with Piaget's concept of formal operations, formal operations researches and critics related to the concept. The first part of the work is dedicated to the formal operations concept. The main characteristics of formal operational thought and formal operations structure, as well as structure logical model are presented in that part of the work. The second part is a review of formal operational researches and it is divided in three parts: (1 problems of researches (2 characteristics of applied methodology and (3 author approaches as a specific research context. In the last part of the work the main critics of formal operations concept are presented and discussed.

  2. Formal genetic maps

    African Journals Online (AJOL)

    Mohammad Saad Zaghloul Salem

    2014-12-24

    Dec 24, 2014 ... characteristics of different regions/sequences of both the nuclear and the mitochondrial genomes, ..... DNA markers have major diagnostic implications since they represent characteris- tic structural features of specific regions of the genome. They have, also, critical implications in comparative analysis of.

  3. Provision of specific dental procedures by general dentists in the National Dental Practice-Based Research Network: questionnaire findings

    OpenAIRE

    Gilbert, Gregg H.; Gordan, Valeria V.; Korelitz, James J.; Fellows, Jeffrey L.; Meyerowitz, Cyril; Oates, Thomas W; Rindal, D. Brad; Gregory, Randall J; ,

    2015-01-01

    Background Objectives were to: (1) determine whether and how often general dentists (GDs) provide specific dental procedures; and (2) test the hypothesis that provision is associated with key dentist, practice, and patient characteristics. Methods GDs (n?=?2,367) in the United States National Dental Practice-Based Research Network completed an Enrollment Questionnaire that included: (1) dentist; (2) practice; and (3) patient characteristics, and how commonly they provide each of 10 dental pro...

  4. Formal verification - Robust and efficient code: Introduction to Formal Verification

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    In general, FV means "proving that certain properties hold for a given system using formal mathematics". This definition can certainly feel daunting, however, as we will learn, we can reap benefits from the paradigm without digging too deep into ...

  5. Specification of requirements for health social-network as Personal Health Record (PHR system

    Directory of Open Access Journals (Sweden)

    Mozhgan Tanhapour

    2015-09-01

    Conclusion: The proposed set of requirements are qualitatively compared with the other similar systems. Using the proposed health social network that provides PHR capabilities for its users will have an irrefutable impact on quality and efficiency of patient-centered care, and play an important role in improving the health of society.

  6. Formal Verification of Large Software Systems

    Science.gov (United States)

    Yin, Xiang; Knight, John

    2010-01-01

    We introduce a scalable proof structure to facilitate formal verification of large software systems. In our approach, we mechanically synthesize an abstract specification from the software implementation, match its static operational structure to that of the original specification, and organize the proof as the conjunction of a series of lemmas about the specification structure. By setting up a different lemma for each distinct element and proving each lemma independently, we obtain the important benefit that the proof scales easily for large systems. We present details of the approach and an illustration of its application on a challenge problem from the security domain

  7. The ubiquitous transcription factor CTCF promotes lineage-specific epigenomic remodeling and establishment of transcriptional networks driving cell differentiation.

    Science.gov (United States)

    Dubois-Chevalier, Julie; Staels, Bart; Lefebvre, Philippe; Eeckhoute, Jérôme

    2015-01-01

    Cell differentiation relies on tissue-specific transcription factors (TFs) that cooperate to establish unique transcriptomes and phenotypes. However, the role of ubiquitous TFs in these processes remains poorly defined. Recently, we have shown that the CCCTC-binding factor (CTCF) is required for adipocyte differentiation through epigenomic remodelling of adipose tissue-specific enhancers and transcriptional activation of Peroxisome proliferator-activated receptor gamma (PPARG), the main driver of the adipogenic program (PPARG), and its target genes. Here, we discuss how these findings, together with the recent literature, illuminate a functional role for ubiquitous TFs in lineage-determining transcriptional networks.

  8. Ascl1 as a novel player in the Ptf1a transcriptional network for GABAergic cell specification in the retina.

    Directory of Open Access Journals (Sweden)

    Nicolas Mazurier

    Full Text Available In contrast with the wealth of data involving bHLH and homeodomain transcription factors in retinal cell type determination, the molecular bases underlying neurotransmitter subtype specification is far less understood. Using both gain and loss of function analyses in Xenopus, we investigated the putative implication of the bHLH factor Ascl1 in this process. We found that in addition to its previously characterized proneural function, Ascl1 also contributes to the specification of the GABAergic phenotype. We showed that it is necessary for retinal GABAergic cell genesis and sufficient in overexpression experiments to bias a subset of retinal precursor cells towards a GABAergic fate. We also analysed the relationships between Ascl1 and a set of other bHLH factors using an in vivo ectopic neurogenic assay. We demonstrated that Ascl1 has unique features as a GABAergic inducer and is epistatic over factors endowed with glutamatergic potentialities such as Neurog2, NeuroD1 or Atoh7. This functional specificity is conferred by the basic DNA binding domain of Ascl1 and involves a specific genetic network, distinct from that underlying its previously demonstrated effects on catecholaminergic differentiation. Our data show that GABAergic inducing activity of Ascl1 requires the direct transcriptional regulation of Ptf1a, providing therefore a new piece of the network governing neurotransmitter subtype specification during retinogenesis.

  9. Scalable Techniques for Formal Verification

    CERN Document Server

    Ray, Sandip

    2010-01-01

    This book presents state-of-the-art approaches to formal verification techniques to seamlessly integrate different formal verification methods within a single logical foundation. It should benefit researchers and practitioners looking to get a broad overview of the spectrum of formal verification techniques, as well as approaches to combining such techniques within a single framework. Coverage includes a range of case studies showing how such combination is fruitful in developing a scalable verification methodology for industrial designs. This book outlines both theoretical and practical issue

  10. Formal Component-Based Semantics

    Directory of Open Access Journals (Sweden)

    Ken Madlener

    2011-08-01

    Full Text Available One of the proposed solutions for improving the scalability of semantics of programming languages is Component-Based Semantics, introduced by Peter D. Mosses. It is expected that this framework can also be used effectively for modular meta theoretic reasoning. This paper presents a formalization of Component-Based Semantics in the theorem prover Coq. It is based on Modular SOS, a variant of SOS, and makes essential use of dependent types, while profiting from type classes. This formalization constitutes a contribution towards modular meta theoretic formalizations in theorem provers. As a small example, a modular proof of determinism of a mini-language is developed.

  11. Leibniz' First Formalization of Syllogistics

    DEFF Research Database (Denmark)

    Robering, Klaus

    2014-01-01

    In his Dissertatio de Arte Combinatoria from 1666 Leibniz provides a formal presentation of syllogistics within the framework of his general-combinatoric program. He does not set up an axiomatic system for the derivation of all valid syllogistic mode, rather he formulates a set of rules which...... of letters just those which belong to the useful, i.e., valid, modes. The set of codes of valid modes turns out to be a so-called "regular" language (in the sense of formal-language-theory). Leibniz' formalization of syllogistics in his Dissertatio thus contains an estimation of the computational complexity...

  12. Informal work and formal plans

    DEFF Research Database (Denmark)

    Dalsted, Rikke Juul; Hølge-Hazelton, Bibi; Kousgaard, Marius Brostrøm

    2012-01-01

    INTRODUCTION: Formal pathways models outline that patients should receive information in order to experience a coherent journey but do not describe an active role for patients or their relatives. The aim of this is paper is to articulate and discuss the active role of patients during their cancer....... The patients' requests were not sufficiently supported in the professional organisation of work or formal planning. Patients' insertion and use of information in their trajectories challenged professional views and working processes. And the design of the formal pathway models limits the patients' active...

  13. Formal Foundations for Hierarchical Safety Cases

    Science.gov (United States)

    Denney, Ewen; Pai, Ganesh; Whiteside, Iain

    2015-01-01

    Safety cases are increasingly being required in many safety-critical domains to assure, using structured argumentation and evidence, that a system is acceptably safe. However, comprehensive system-wide safety arguments present appreciable challenges to develop, understand, evaluate, and manage, partly due to the volume of information that they aggregate, such as the results of hazard analysis, requirements analysis, testing, formal verification, and other engineering activities. Previously, we have proposed hierarchical safety cases, hicases, to aid the comprehension of safety case argument structures. In this paper, we build on a formal notion of safety case to formalise the use of hierarchy as a structuring technique, and show that hicases satisfy several desirable properties. Our aim is to provide a formal, theoretical foundation for safety cases. In particular, we believe that tools for high assurance systems should be granted similar assurance to the systems to which they are applied. To this end, we formally specify and prove the correctness of key operations for constructing and managing hicases, which gives the specification for implementing hicases in AdvoCATE, our toolset for safety case automation. We motivate and explain the theory with the help of a simple running example, extracted from a real safety case and developed using AdvoCATE.

  14. Formal Framework for Proof Generating Optimizers

    OpenAIRE

    Gawkowski, Marek Jerzy

    2009-01-01

    Most software systems are described in high-level model or programming languages. Their runtime behavior, however, is determined by the compiled code. For uncritical software, it may be sufficient to test the runtime behavior of the code. For safety-critical software, there is an additional aggravating factor resulting from the fact that the code must satisfy the formal specification which reflects the safety policy of the software consumer and that the software producer is obliged to demonst...

  15. HOMESCHOOLING: PILIHAN DI TENGAH KEGAGALAN SEKOLAH FORMAL

    OpenAIRE

    Sadid, Agus

    2012-01-01

    Homeschooling is a family-based school to provide specific education but referring to nationaleducation curriculum. Homeschooling becomes an effective choice in the failure of formal school to producequalified graduates. Having critically discussing homeschooling in a number of aspects, this article concludes(1) home schooling can be organized as a pure homeschooling, a homeschooling model which independentlydevelop and implement curriculum without others’ assistance; instructional achievemen...

  16. Cell-type-specific predictive network yields novel insights into mouse embryonic stem cell self-renewal and cell fate.

    Directory of Open Access Journals (Sweden)

    Karen G Dowell

    Full Text Available Self-renewal, the ability of a stem cell to divide repeatedly while maintaining an undifferentiated state, is a defining characteristic of all stem cells. Here, we clarify the molecular foundations of mouse embryonic stem cell (mESC self-renewal by applying a proven Bayesian network machine learning approach to integrate high-throughput data for protein function discovery. By focusing on a single stem-cell system, at a specific developmental stage, within the context of well-defined biological processes known to be active in that cell type, we produce a consensus predictive network that reflects biological reality more closely than those made by prior efforts using more generalized, context-independent methods. In addition, we show how machine learning efforts may be misled if the tissue specific role of mammalian proteins is not defined in the training set and circumscribed in the evidential data. For this study, we assembled an extensive compendium of mESC data: ∼2.2 million data points, collected from 60 different studies, under 992 conditions. We then integrated these data into a consensus mESC functional relationship network focused on biological processes associated with embryonic stem cell self-renewal and cell fate determination. Computational evaluations, literature validation, and analyses of predicted functional linkages show that our results are highly accurate and biologically relevant. Our mESC network predicts many novel players involved in self-renewal and serves as the foundation for future pluripotent stem cell studies. This network can be used by stem cell researchers (at http://StemSight.org to explore hypotheses about gene function in the context of self-renewal and to prioritize genes of interest for experimental validation.

  17. Cell-type-specific predictive network yields novel insights into mouse embryonic stem cell self-renewal and cell fate.

    Science.gov (United States)

    Dowell, Karen G; Simons, Allen K; Wang, Zack Z; Yun, Kyuson; Hibbs, Matthew A

    2013-01-01

    Self-renewal, the ability of a stem cell to divide repeatedly while maintaining an undifferentiated state, is a defining characteristic of all stem cells. Here, we clarify the molecular foundations of mouse embryonic stem cell (mESC) self-renewal by applying a proven Bayesian network machine learning approach to integrate high-throughput data for protein function discovery. By focusing on a single stem-cell system, at a specific developmental stage, within the context of well-defined biological processes known to be active in that cell type, we produce a consensus predictive network that reflects biological reality more closely than those made by prior efforts using more generalized, context-independent methods. In addition, we show how machine learning efforts may be misled if the tissue specific role of mammalian proteins is not defined in the training set and circumscribed in the evidential data. For this study, we assembled an extensive compendium of mESC data: ∼2.2 million data points, collected from 60 different studies, under 992 conditions. We then integrated these data into a consensus mESC functional relationship network focused on biological processes associated with embryonic stem cell self-renewal and cell fate determination. Computational evaluations, literature validation, and analyses of predicted functional linkages show that our results are highly accurate and biologically relevant. Our mESC network predicts many novel players involved in self-renewal and serves as the foundation for future pluripotent stem cell studies. This network can be used by stem cell researchers (at http://StemSight.org) to explore hypotheses about gene function in the context of self-renewal and to prioritize genes of interest for experimental validation.

  18. Multilayer Brain Networks

    Science.gov (United States)

    Vaiana, Michael; Muldoon, Sarah Feldt

    2018-01-01

    The field of neuroscience is facing an unprecedented expanse in the volume and diversity of available data. Traditionally, network models have provided key insights into the structure and function of the brain. With the advent of big data in neuroscience, both more sophisticated models capable of characterizing the increasing complexity of the data and novel methods of quantitative analysis are needed. Recently, multilayer networks, a mathematical extension of traditional networks, have gained increasing popularity in neuroscience due to their ability to capture the full information of multi-model, multi-scale, spatiotemporal data sets. Here, we review multilayer networks and their applications in neuroscience, showing how incorporating the multilayer framework into network neuroscience analysis has uncovered previously hidden features of brain networks. We specifically highlight the use of multilayer networks to model disease, structure-function relationships, network evolution, and link multi-scale data. Finally, we close with a discussion of promising new directions of multilayer network neuroscience research and propose a modified definition of multilayer networks designed to unite and clarify the use of the multilayer formalism in describing real-world systems.

  19. Knowledge Production, Urban Locations and the Importance of Local Networks

    DEFF Research Database (Denmark)

    Skytt-Larsen, Christine Benna; Winther, Lars

    2015-01-01

    research on knowledge production, however, reveals that knowledge productive networks are significant for both the competitiveness and location of KIBS. Thus, to understand the urban location of industrial design, it is important to analyse how knowledge production is organized within the industry....... Industrial design is concentrated in urban locations, but most of its clients are located elsewhere. Hence, it seems that industrial design firms concentrate in urban locations mainly because their knowledge networks include specific types of formal and informal local social networks....

  20. Security and Privacy Preservation in Human-Involved Networks

    Science.gov (United States)

    Asher, Craig; Aumasson, Jean-Philippe; Phan, Raphael C.-W.

    This paper discusses security within human-involved networks, with a focus on social networking services (SNS). We argue that more secure networks could be designed using semi-formal security models inspired from cryptography, as well as notions like that of ceremony, which exploits human-specific abilities and psychology to assist creating more secure protocols. We illustrate some of our ideas with the example of the SNS Facebook.

  1. Frequency-specific directed interactions in the human brain network for language.

    Science.gov (United States)

    Schoffelen, Jan-Mathijs; Hultén, Annika; Lam, Nietzsche; Marquand, André F; Uddén, Julia; Hagoort, Peter

    2017-07-25

    The brain's remarkable capacity for language requires bidirectional interactions between functionally specialized brain regions. We used magnetoencephalography to investigate interregional interactions in the brain network for language while 102 participants were reading sentences. Using Granger causality analysis, we identified inferior frontal cortex and anterior temporal regions to receive widespread input and middle temporal regions to send widespread output. This fits well with the notion that these regions play a central role in language processing. Characterization of the functional topology of this network, using data-driven matrix factorization, which allowed for partitioning into a set of subnetworks, revealed directed connections at distinct frequencies of interaction. Connections originating from temporal regions peaked at alpha frequency, whereas connections originating from frontal and parietal regions peaked at beta frequency. These findings indicate that the information flow between language-relevant brain areas, which is required for linguistic processing, may depend on the contributions of distinct brain rhythms.

  2. Readings in Formal Epistemology : Sourcebook

    NARCIS (Netherlands)

    Arló-Costa, H.; Hendricks, V.F.; van Benthem, J.

    2016-01-01

    This volume presents 38 classic texts in formal epistemology, and strengthens the ties between research into this area of philosophy and its neighbouring intellectual disciplines. The editors provide introductions to five subsections: Bayesian Epistemology, Belief Change, Decision Theory,

  3. Concepts of formal concept analysis

    Science.gov (United States)

    Žáček, Martin; Homola, Dan; Miarka, Rostislav

    2017-07-01

    The aim of this article is apply of Formal Concept Analysis on concept of world. Formal concept analysis (FCA) as a methodology of data analysis, information management and knowledge representation has potential to be applied to a verity of linguistic problems. FCA is mathematical theory for concepts and concept hierarchies that reflects an understanding of concept. Formal concept analysis explicitly formalizes extension and intension of a concept, their mutual relationships. A distinguishing feature of FCA is an inherent integration of three components of conceptual processing of data and knowledge, namely, the discovery and reasoning with concepts in data, discovery and reasoning with dependencies in data, and visualization of data, concepts, and dependencies with folding/unfolding capabilities.

  4. El Salvador - Formal Technical Education

    Data.gov (United States)

    Millennium Challenge Corporation — With a budget of nearly $20 million, the Formal Technical Education Sub-Activity was designed to strengthen technical and vocational educational institutions in the...

  5. Applying ADLs to Assess Emerging Industry Specifications for Dynamic Discovery of Ad Hoc Network Services

    Science.gov (United States)

    2001-01-31

    0..1 Contains 1 Contains SERVICE MANAGER discov er Network Context() <<not shr>> Cache Manager Discov ery () <<OPT>> Announce Serv ice Processing...Architectural Layers Approach JINI Entities Service Manager Entity Major Functions Lazy Discovery Directed Discovery Client (s,ra) Aggressive...registered-services SCM SM discovered-SCMs (SU NR SCM): (SU,NR) SCM registered-notifications SCM SU discovered-SCMs • SM is Service Manager • SD is

  6. Tract-specific white matter hyperintensities disrupt neural network function in Alzheimer's disease.

    Science.gov (United States)

    Taylor, Alexander N W; Kambeitz-Ilankovic, Lana; Gesierich, Benno; Simon-Vermot, Lee; Franzmeier, Nicolai; Araque Caballero, Miguel Á; Müller, Sophia; Hesheng, Liu; Ertl-Wagner, Birgit; Bürger, Katharina; Weiner, Michael W; Dichgans, Martin; Duering, Marco; Ewers, Michael

    2017-03-01

    White matter hyperintensities (WMHs) increase the risk of Alzheimer's disease (AD). Whether WMHs are associated with the decline of functional neural networks in AD is debated. Resting-state functional magnetic resonance imaging and WMH were assessed in 78 subjects with increased amyloid levels on AV-45 positron emission tomography (PET) in different clinical stages of AD. We tested the association between WMH volume in major atlas-based fiber tract regions of interest (ROIs) and changes in functional connectivity (FC) between the tracts' projection areas within the default mode network (DMN). WMH volume within the inferior fronto-occipital fasciculus (IFOF) was the highest among all tract ROIs and associated with reduced FC in IFOF-connected DMN areas, independently of global AV-45 PET. Higher AV-45 PET contributed to reduced FC in IFOF-connected, temporal, and parietal DMN areas. High fiber tract WMH burden is associated with reduced FC in connected areas, thus adding to the effects of amyloid pathology on neuronal network function. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  7. Formalism and functionalism in linguistics.

    Science.gov (United States)

    Newmeyer, Frederick J

    2010-05-01

    Formalism and functionalism in linguistics are often taken to be diametrically opposed approaches. However, close examination of the relevant phenomena reveals that the two are complementary, rather than being irrevocably in opposition to each other. One can be a formal linguist and a functional linguist at the same time, without there being any contradiction. Copyright © 2010 John Wiley & Sons, Ltd. For further resources related to this article, please visit the WIREs website. Copyright © 2010 John Wiley & Sons, Ltd.

  8. Terra in K-16 formal education settings

    Science.gov (United States)

    Chambers, L. H.; Fischer, J. D.; Lewis, P. M.; Moore, S. W.; Oots, P. C.; Rogerson, T. M.; Hitke, K. M.; Riebeek, H.

    2009-12-01

    Since it began, the Terra mission has had an active presence in formal education at the K-16 level. This educational presence was provided through the S’COOL project for the first five years of the mission, joined by the MY NASA DATA project for the second five years. The Students’ Cloud Observations On-Line (S’COOL) Project, begun in 1997 under the auspices of the Clouds and the Earth’s Radiant Energy System (CERES) project, seeks to motivate students across the entire K-12 spectrum to learn science basics and how they tie in to a larger picture. Beginning early on, college level participants have also participated in the project, both in science classes and in science education coursework. The project uses the connection to an on-going NASA science investigation as a powerful motivator for student observations, analysis and learning, and has reached around the globe as shown in the world map. This poster will review the impact that Terra, through S’COOL, has made in formal education over the last decade. The MY NASA DATA Project began in 2004 under the NASA Research, Education and Applications Solutions Network (REASoN). A 5-year REASoN grant enabled the creation of an extensive website which wraps easily accessible Earth science data - including Terra parameters from CERES (involving MODIS data fusion), MISR, and MOPITT (an example for carbon monoxide is given in the graph, with dark areas indicating high CO levels) - with explanatory material written at the middle school level, and an extensive collection of peer-reviewed lesson plans. The MY NASA DATA site has a rapidly growing user-base and was recently adopted by a number of NASA Earth Science missions, in addition to Terra, as a formal education arm of their Education and Public Outreach efforts. This poster will summarize the contributions that Terra, through MY NASA DATA, has made to formal education since 2004.

  9. Formal Modeling of Greedy Nodes in 802.15.4 WSN

    Directory of Open Access Journals (Sweden)

    Youcef Hammal

    2015-06-01

    Full Text Available This paper deals with formal specification of the non-slotted CSMA/CA protocol in wireless sensor networks(WSN whose some nodes own a greedy behavior. This protocol requires sensor nodes to wait some time before initiating a transmission, whereas greedy nodes may try to reduce their waiting duration, which may penalize other nodes. To analyze their impact on WSN mode in operation, we use timed automata of the model-checker UPPAAL to capture the abstract behavior of communication medium, sane, and greedy nodes in WSN. This enables the use of analysis tools to check whether these models satisfy intended properties.

  10. Male-to-female gender dysphoria: Gender-specific differences in resting-state networks.

    Science.gov (United States)

    Clemens, Benjamin; Junger, Jessica; Pauly, Katharina; Neulen, Josef; Neuschaefer-Rube, Christiane; Frölich, Dirk; Mingoia, Gianluca; Derntl, Birgit; Habel, Ute

    2017-05-01

    Recent research found gender-related differences in resting-state functional connectivity (rs-FC) measured by functional magnetic resonance imaging (fMRI). To the best of our knowledge, there are no studies examining the differences in rs-FC between men, women, and individuals who report a discrepancy between their anatomical sex and their gender identity, i.e. gender dysphoria (GD). To address this important issue, we present the first fMRI study systematically investigating the differences in typical resting-state networks (RSNs) and hormonal treatment effects in 26 male-to-female GD individuals (MtFs) compared with 19 men and 20 women. Differences between male and female control groups were found only in the auditory RSN, whereas differences between both control groups and MtFs were found in the auditory and fronto-parietal RSNs, including both primary sensory areas (e.g. calcarine gyrus) and higher order cognitive areas such as the middle and posterior cingulate and dorsomedial prefrontal cortex. Overall, differences in MtFs compared with men and women were more pronounced before cross-sex hormonal treatment. Interestingly, rs-FC between MtFs and women did not differ significantly after treatment. When comparing hormonally untreated and treated MtFs, we found differences in connectivity of the calcarine gyrus and thalamus in the context of the auditory network, as well as the inferior frontal gyrus in context of the fronto-parietal network. Our results provide first evidence that MtFs exhibit patterns of rs-FC which are different from both their assigned and their aspired gender, indicating an intermediate position between the two sexes. We suggest that the present study constitutes a starting point for future research designed to clarify whether the brains of individuals with GD are more similar to their assigned or their aspired gender.

  11. Formalization of an environmental model using formal concept analysis - FCA

    Science.gov (United States)

    Bourdon-García, Rubén D.; Burgos-Salcedo, Javier D.

    2016-08-01

    Nowadays, there is a huge necessity to generate novel strategies for social-ecological systems analyses for resolving global sustainability problems. This paper has as main purpose the application of the formal concept analysis to formalize the theory of Augusto Ángel Maya, who without a doubt, was one of the most important environmental philosophers in South America; Ángel Maya proposed and established that Ecosystem-Culture relations, instead Human-Nature ones, are determinants in our understanding and management of natural resources. Based on this, a concept lattice, formal concepts, subconcept-superconcept relations, partially ordered sets, supremum and infimum of the lattice and implications between attributes (Duquenne-Guigues base), were determined for the ecosystem-culture relations.

  12. Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity.

    Science.gov (United States)

    Venkatasubramanian, Prashanna Balaji; Toydemir, Gamze; de Wit, Nicole; Saccenti, Edoardo; Martins Dos Santos, Vitor A P; van Baarlen, Peter; Wells, Jerry M; Suarez-Diez, Maria; Mes, Jurriaan J

    2017-07-28

    Intestinal epithelial cells, like Caco-2, are commonly used to study the interaction between food, other luminal factors and the host, often supported by microarray analysis to study the changes in gene expression as a result of the exposure. However, no compiled dataset for Caco-2 has ever been initiated and Caco-2-dedicated gene expression networks are barely available. Here, 341 Caco-2-specific microarray samples were collected from public databases and from in-house experiments pertaining to Caco-2 cells exposed to pathogens, probiotics and several food compounds. Using these datasets, a gene functional association network specific for Caco-2 was generated containing 8937 nodes 129711 edges. Two in silico methods, a modified version of biclustering and the new Differential Expression Correlation Analysis, were developed to identify Caco-2-specific gene targets within a pathway of interest. These methods were subsequently applied to the AhR and Nrf2 signalling pathways and altered expression of the predicted target genes was validated by qPCR in Caco-2 cells exposed to coffee extracts, known to activate both AhR and Nrf2 pathways. The datasets and in silico method(s) to identify and predict responsive target genes can be used to more efficiently design experiments to study Caco-2/intestinal epithelial-relevant biological processes.

  13. Informal work and formal plans

    DEFF Research Database (Denmark)

    Dalsted, Rikke Juul; Hølge-Hazelton, Bibi; Kousgaard, Marius Brostrøm

    2012-01-01

    INTRODUCTION: Formal pathways models outline that patients should receive information in order to experience a coherent journey but do not describe an active role for patients or their relatives. The aim of this is paper is to articulate and discuss the active role of patients during their cancer...... and care. They initiated processes in the trajectories, and acquired information, which they used to form their trajectories. Patients presented problems to the healthcare professionals in order to get proper help when needed. DISCUSSION: Work done by patients was invisible and not perceived as work....... The patients' requests were not sufficiently supported in the professional organisation of work or formal planning. Patients' insertion and use of information in their trajectories challenged professional views and working processes. And the design of the formal pathway models limits the patients' active...

  14. Formal verification of mathematical software

    Science.gov (United States)

    Sutherland, D.

    1984-01-01

    Methods are investigated for formally specifying and verifying the correctness of mathematical software (software which uses floating point numbers and arithmetic). Previous work in the field was reviewed. A new model of floating point arithmetic called the asymptotic paradigm was developed and formalized. Two different conceptual approaches to program verification, the classical Verification Condition approach and the more recently developed Programming Logic approach, were adapted to use the asymptotic paradigm. These approaches were then used to verify several programs; the programs chosen were simplified versions of actual mathematical software.

  15. Formally Generating Adaptive Security Protocols

    Science.gov (United States)

    2013-03-01

    RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE (DD-MM-YYYY) MAR 2013 2. REPORT TYPE FINAL TECHNICAL REPORT 3. DATES COVERED (From - To) May...receipt of messages. Formally, an event class of type T is a function that takes an event ordering and an event in that event ordering, and returns a bag...and Robert Constable. An exper- iment in formal design using meta-properties. In J. Lala , D. Mughan, C. McCollum, and B. Witten, editors, DARPA

  16. What do tests of formal reasoning actually measure?

    Science.gov (United States)

    Lawson, Anton E.

    Tests of formal operational reasoning derived from Piagetian theory have been found to be effective predictors of academic achievement. Yet Piaget's theory regarding the underlying nature of formal operations and their employment in specific contexts has run into considerable empirical difficulty. The primary purpose of this study was to present the core of an alternative theory of the nature of advanced scientific reasoning. That theory, referred to as the multiple-hypothesis theory, argues that tests of formal operational reasoning actually measure the extent to which persons have acquired the ability to initiate reasoning with more than one specific antecedent condition, or if they are unable to imagine more than one antecedent condition, they are aware that more than one is possible; therefore conclusions that are drawn are tempered by this possibility. As a test of this multiple-hypothesis theory of advanced reasoning and the contrasting Piagetian theory of formal operations, a sample of 922 college students were first classified as concrete operational, transitional, or formal operational, based upon responses to standard Piagetian measures of formal operational reasoning. They were then administered seven logic tasks. Actual response patterns to the tasks were analyzed and found to be similar to predicted response patterns derived from the multiple-hypothesis theory and were different from those predicted by Piagetian theory. Therefore, support was obtained for the multiple-hypothesis theory. The terms intuitive and reflective were suggested to replace the terms concrete operational and formal operational to refer to persons at varying levels of intellectual development.

  17. Preferences for and barriers to formal and informal athletic training continuing education activities.

    Science.gov (United States)

    Armstrong, Kirk J; Weidner, Thomas G

    2011-01-01

    Our previous research determined the frequency of participation and perceived effect of formal and informal continuing education (CE) activities. However, actual preferences for and barriers to CE must be characterized. To determine the types of formal and informal CE activities preferred by athletic trainers (ATs) and barriers to their participation in these activities. Cross-sectional study. Athletic training practice settings. Of a geographically stratified random sample of 1000 ATs, 427 ATs (42.7%) completed the survey. As part of a larger study, the Survey of Formal and Informal Athletic Training Continuing Education Activities (FIATCEA) was developed and administered electronically. The FIATCEA consists of demographic characteristics and Likert scale items (1 = strongly disagree, 5 = strongly agree) about preferred CE activities and barriers to these activities. Internal consistency of survey items, as determined by Cronbach α, was 0.638 for preferred CE activities and 0.860 for barriers to these activities. Descriptive statistics were computed for all items. Differences between respondent demographic characteristics and preferred CE activities and barriers to these activities were determined via analysis of variance and dependent t tests. The α level was set at .05. Hands-on clinical workshops and professional networking were the preferred formal and informal CE activities, respectively. The most frequently reported barriers to formal CE were the cost of attending and travel distance, whereas the most frequently reported barriers to informal CE were personal and job-specific factors. Differences were noted between both the cost of CE and travel distance to CE and all other barriers to CE participation (F(1,411) = 233.54, P Informal CE was highly valued by ATs because it could be individualized.

  18. A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo

    Science.gov (United States)

    Su, Yi-Hsien; Li, Enhu; Geiss, Gary K.; Longabaugh, William J. R.; Krämer, Alexander; Davidson, Eric H.

    2009-01-01

    The current gene regulatory network (GRN) for the sea urchin embryo pertains to pregastrular specification functions in the endomesodermal territories. Here we extend gene regulatory network analysis to the adjacent oral and aboral ectoderm territories over the same period. A large fraction of the regulatory genes predicted by the sea urchin genome project and shown in ancillary studies to be expressed in either oral or aboral ectoderm by 24h are included, though universally expressed and pan-ectodermal regulatory genes are in general not. The loci of expression of these genes have been determined by whole mount in situ hybridization. We have carried out a global perturbation analysis in which expression of each gene was interrupted by introduction of morpholino antisense oligonucleotide, and the effects on all other genes were measured quantitatively, both by QPCR and by a new instrumental technology (NanoString Technologies nCounter Analysis System). At its current stage the network model, built in BioTapestry, includes 22 genes encoding transcription factors, 4 genes encoding known signaling ligands, and 3 genes that are yet unknown but are predicted to perform specific roles. Evidence emerged from the analysis pointing to distinctive subcircuit features observed earlier in other parts of the GRN, including a double negative transcriptional regulatory gate, and dynamic state lockdowns by feedback interactions. While much of the regulatory apparatus is downstream of Nodal signaling, as expected from previous observations, there are also cohorts of independently activated oral and aboral ectoderm regulatory genes, and we predict yet unidentified signaling interactions between oral and aboral territories. PMID:19268450

  19. Self-regulation of circumscribed brain activity modulates spatially selective and frequency specific connectivity of distributed resting state networks

    Directory of Open Access Journals (Sweden)

    Mathias eVukelić

    2015-07-01

    Full Text Available The mechanisms of learning involved in brain self-regulation have still to be unveiled to exploit the full potential of this methodology for therapeutic interventions. This skill of volitionally changing brain activity presumably resembles motor skill learning which in turn is accompanied by plastic changes modulating resting state networks. Along these lines, we hypothesized that brain regulation and neurofeedback would similarly modify intrinsic networks at rest while presenting a distinct spatio-temporal pattern. High-resolution EEG preceded and followed a single neurofeedback training intervention of modulating circumscribed sensorimotor low β -activity by motor imagery in eleven healthy participants. They were kept in the deliberative phase of skill acquisition with high demands for learning self-regulation through stepwise increases of task difficulty. By applying the corrected imaginary part of the coherency function, we observed increased functional connectivity of both the primary motor and the primary somatosensory cortex with their respective contralateral homologous cortices in the low β-frequency band which was self-regulated during feedback. At the same time, the primary motor cortex - but none of the surrounding cortical areas - showed connectivity to contralateral supplementary motor and dorsal premotor areas in the high β-band. Simultaneously, the neurofeedback target displayed a specific increase of functional connectivity with an ipsilateral fronto-parietal network in the α-band while presenting a de-coupling with contralateral primary and secondary sensorimotor areas in the very same frequency band.Brain self-regulating modifies resting state connections spatially selective to the neurofeedback target of the dominant hemisphere. These are anatomically distinct with regard to the cortico-cortical connectivity pattern and are functionally specific with regard to the time domain of coherent activity consistent with a Hebbian

  20. Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts.

    Directory of Open Access Journals (Sweden)

    Jiao Li

    2009-07-01

    Full Text Available The recently proposed concept of molecular connectivity maps enables researchers to integrate experimental measurements of genes, proteins, metabolites, and drug compounds under similar biological conditions. The study of these maps provides opportunities for future toxicogenomics and drug discovery applications. We developed a computational framework to build disease-specific drug-protein connectivity maps. We integrated gene/protein and drug connectivity information based on protein interaction networks and literature mining, without requiring gene expression profile information derived from drug perturbation experiments on disease samples. We described the development and application of this computational framework using Alzheimer's Disease (AD as a primary example in three steps. First, molecular interaction networks were incorporated to reduce bias and improve relevance of AD seed proteins. Second, PubMed abstracts were used to retrieve enriched drug terms that are indirectly associated with AD through molecular mechanistic studies. Third and lastly, a comprehensive AD connectivity map was created by relating enriched drugs and related proteins in literature. We showed that this molecular connectivity map development approach outperformed both curated drug target databases and conventional information retrieval systems. Our initial explorations of the AD connectivity map yielded a new hypothesis that diltiazem and quinidine may be investigated as candidate drugs for AD treatment. Molecular connectivity maps derived computationally can help study molecular signature differences between different classes of drugs in specific disease contexts. To achieve overall good data coverage and quality, a series of statistical methods have been developed to overcome high levels of data noise in biological networks and literature mining results. Further development of computational molecular connectivity maps to cover major disease areas will likely set

  1. A Synthesized Framework for Formal Verification of Computing Systems

    Directory of Open Access Journals (Sweden)

    Nikola Bogunovic

    2003-12-01

    Full Text Available Design process of computing systems gradually evolved to a level that encompasses formal verification techniques. However, the integration of formal verification techniques into a methodical design procedure has many inherent miscomprehensions and problems. The paper explicates the discrepancy between the real system implementation and the abstracted model that is actually used in the formal verification procedure. Particular attention is paid to the seamless integration of all phases of the verification procedure that encompasses definition of the specification language and denotation and execution of conformance relation between the abstracted model and its intended behavior. The concealed obstacles are exposed, computationally expensive steps identified and possible improvements proposed.

  2. Evolution of posterior parietal cortex and parietal-frontal networks for specific actions in primates.

    Science.gov (United States)

    Kaas, Jon H; Stepniewska, Iwona

    2016-02-15

    Posterior parietal cortex (PPC) is an extensive region of the human brain that develops relatively late and is proportionally large compared with that of monkeys and prosimian primates. Our ongoing comparative studies have led to several conclusions about the evolution of this posterior parietal region. In early placental mammals, PPC likely was a small multisensory region much like PPC of extant rodents and tree shrews. In early primates, PPC likely resembled that of prosimian galagos, in which caudal PPC (PPCc) is visual and rostral PPC (PPCr) has eight or more multisensory domains where electrical stimulation evokes different complex motor behaviors, including reaching, hand-to-mouth, looking, protecting the face or body, and grasping. These evoked behaviors depend on connections with functionally matched domains in premotor cortex (PMC) and motor cortex (M1). Domains in each region compete with each other, and a serial arrangement of domains allows different factors to influence motor outcomes successively. Similar arrangements of domains have been retained in New and Old World monkeys, and humans appear to have at least some of these domains. The great expansion and prolonged development of PPC in humans suggest the addition of functionally distinct territories. We propose that, across primates, PMC and M1 domains are second and third levels in a number of parallel, interacting networks for mediating and selecting one type of action over others. © 2015 Wiley Periodicals, Inc.

  3. Vocal Imitation in Parrots Allows Addressing of Specific Individuals in a Dynamic Communication Network

    DEFF Research Database (Denmark)

    Balsby, T.J.S.; Momberg, J.V.; Dabelsteen, T.

    2012-01-01

    Parrots in captivity are known for their ability to vocally imitate humans and recently it has been shown that wild-living orange-fronted conures are able to immediately imitate other individuals´ contact calls. The function of this exceptional ability to imitate remains unclear. However, orangeâ......€“fronted conures live in fission-fusion flocks where they encounter many different individuals every day, and it is possible that their vocal imitation ability is a flexible means to address a specific individual within a flock. We tested this via playback to short-term captive wild conures. Test birds were placed...... together in pairs in outdoor aviaries to form simple flocks. To simulate imitation of a specific individual these pairs received playback of contact calls that primarily imitate one of the two birds. Overall, individuals that received simulated vocal imitations of its calls responded more frequently...

  4. A Cell-Signaling Network Temporally Resolves Specific versus Promiscuous Phosphorylation

    Directory of Open Access Journals (Sweden)

    Evgeny Kanshin

    2015-02-01

    Full Text Available If specific and functional kinase- or phosphatase-substrate interactions are optimized for binding compared to promiscuous interactions, then changes in phosphorylation should occur faster on functional versus promiscuous substrates. To test this hypothesis, we designed a high temporal resolution global phosphoproteomics protocol to study the high-osmolarity glycerol (HOG response in the budding yeast Saccharomyces cerevisiae. The method provides accurate, stimulus-specific measurement of phosphoproteome changes, quantitative analysis of phosphodynamics at sub-minute temporal resolution, and detection of more phosphosites. Rates of evolution of dynamic phosphosites were comparable to those of known functional phosphosites and significantly lower than static or longer-time-frame dynamic phosphosites. Kinetic profile analyses indicated that putatively functional kinase- or phosphatase-substrate interactions occur more rapidly, within 60 s, than promiscuous interactions. Finally, we report many changes in phosphorylation of proteins implicated in cytoskeletal and mitotic spindle dynamics that may underlie regulation of cell cycle and morphogenesis.

  5. Combining Ontologies with Domain Specific Languages: A Case Study from Network Configuration Software

    Science.gov (United States)

    Miksa, Krzysztof; Sabina, Pawel; Kasztelnik, Marek

    One of the important aspects of Model-Driven Engineering (MDE) is to consider application-domain variability, which leads to creation of Domain Specific Languages (DSL). As with DSLs models are concise, easy to understand and maintain, this approach greatly increases the productivity and software quality. Usually, the DSLs in MDE are described with a metamodel and a concrete syntax definition. The models expressed in the DSL are linguistic instantiations of the language concepts found in the metamodel.

  6. Vocal imitation in parrots allows addressing of specific individuals in a dynamic communication network.

    Directory of Open Access Journals (Sweden)

    Thorsten J S Balsby

    Full Text Available Parrots in captivity are known for their ability to vocally imitate humans and recently it has been shown that wild-living orange-fronted conures are able to immediately imitate other individuals' contact calls. The function of this exceptional ability to imitate remains unclear. However, orange-fronted conures live in fission-fusion flocks where they encounter many different individuals every day, and it is possible that their vocal imitation ability is a flexible means to address a specific individual within a flock. We tested this via playback to short-term captive wild conures. Test birds were placed together in pairs in outdoor aviaries to form simple flocks. To simulate imitation of a specific individual these pairs received playback of contact calls that primarily imitate one of the two birds. Overall, individuals that received simulated vocal imitations of its calls responded more frequently and faster than the other individual. This suggests that orange-fronted conures can use imitations of contact calls to address specific individuals of a flock. In the discussion we argue that the fission-fusion flock dynamics of many parrot species has been an important factor in evolving conures' and other parrots' exceptional ability to imitate.

  7. Vocal imitation in parrots allows addressing of specific individuals in a dynamic communication network.

    Science.gov (United States)

    Balsby, Thorsten J S; Momberg, Jane Vestergaard; Dabelsteen, Torben

    2012-01-01

    Parrots in captivity are known for their ability to vocally imitate humans and recently it has been shown that wild-living orange-fronted conures are able to immediately imitate other individuals' contact calls. The function of this exceptional ability to imitate remains unclear. However, orange-fronted conures live in fission-fusion flocks where they encounter many different individuals every day, and it is possible that their vocal imitation ability is a flexible means to address a specific individual within a flock. We tested this via playback to short-term captive wild conures. Test birds were placed together in pairs in outdoor aviaries to form simple flocks. To simulate imitation of a specific individual these pairs received playback of contact calls that primarily imitate one of the two birds. Overall, individuals that received simulated vocal imitations of its calls responded more frequently and faster than the other individual. This suggests that orange-fronted conures can use imitations of contact calls to address specific individuals of a flock. In the discussion we argue that the fission-fusion flock dynamics of many parrot species has been an important factor in evolving conures' and other parrots' exceptional ability to imitate.

  8. Using network screening methods to determine locations with specific safety issues: A design consistency case study.

    Science.gov (United States)

    Butsick, Andrew J; Wood, Jonathan S; Jovanis, Paul P

    2017-09-01

    The Highway Safety Manual provides multiple methods that can be used to identify sites with promise (SWiPs) for safety improvement. However, most of these methods cannot be used to identify sites with specific problems. Furthermore, given that infrastructure funding is often specified for use related to specific problems/programs, a method for identifying SWiPs related to those programs would be very useful. This research establishes a method for Identifying SWiPs with specific issues. This is accomplished using two safety performance functions (SPFs). This method is applied to identifying SWiPs with geometric design consistency issues. Mixed effects negative binomial regression was used to develop two SPFs using 5 years of crash data and over 8754km of two-lane rural roadway. The first SPF contained typical roadway elements while the second contained additional geometric design consistency parameters. After empirical Bayes adjustments, sites with promise (SWiPs) were identified. The disparity between SWiPs identified by the two SPFs was evident; 40 unique sites were identified by each model out of the top 220 segments. By comparing sites across the two models, candidate road segments can be identified where a lack design consistency may be contributing to an increase in expected crashes. Practitioners can use this method to more effectively identify roadway segments suffering from reduced safety performance due to geometric design inconsistency, with detailed engineering studies of identified sites required to confirm the initial assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Formal systems for persuasion dialogue

    NARCIS (Netherlands)

    Prakken, Henry

    This article reviews formal systems that regulate persuasion dialogues. In such dialogues two or more participants aim to resolve a difference of opinion, each trying to persuade the other participants to adopt their point of view. Systems for persuasion dialogue have found application in various

  10. Formal monkey linguistics : The debate

    NARCIS (Netherlands)

    Schlenker, Philippe; Chemla, Emmanuel; Schel, Anne M.; Fuller, James; Gautier, Jean Pierre; Kuhn, Jeremy; Veselinović, Dunja; Arnold, Kate; Cäsar, Cristiane; Keenan, Sumir; Lemasson, Alban; Ouattara, Karim; Ryder, Robin; Zuberbühler, Klaus

    2016-01-01

    We explain why general techniques from formal linguistics can and should be applied to the analysis of monkey communication - in the areas of syntax and especially semantics. An informed look at our recent proposals shows that such techniques needn't rely excessively on categories of human language:

  11. HAMILTONIAN FORMALISM ON CHARACTERISTIC SURFACES.

    Science.gov (United States)

    The problem of the construction of a Hamiltonian formalism suitable for propagation of a field off characteristic or null surfaces is considered. In...is developed on characteristic surfaces. A Hamiltonian for gravitation (general relativity) is constructed, first on null surfaces described only by

  12. Gene networks specific for innate immunity define post-traumatic stress disorder.

    Science.gov (United States)

    Breen, M S; Maihofer, A X; Glatt, S J; Tylee, D S; Chandler, S D; Tsuang, M T; Risbrough, V B; Baker, D G; O'Connor, D T; Nievergelt, C M; Woelk, C H

    2015-12-01

    The molecular factors involved in the development of Post-Traumatic Stress Disorder (PTSD) remain poorly understood. Previous transcriptomic studies investigating the mechanisms of PTSD apply targeted approaches to identify individual genes under a cross-sectional framework lack a holistic view of the behaviours and properties of these genes at the system-level. Here we sought to apply an unsupervised gene-network based approach to a prospective experimental design using whole-transcriptome RNA-Seq gene expression from peripheral blood leukocytes of U.S. Marines (N=188), obtained both pre- and post-deployment to conflict zones. We identified discrete groups of co-regulated genes (i.e., co-expression modules) and tested them for association to PTSD. We identified one module at both pre- and post-deployment containing putative causal signatures for PTSD development displaying an over-expression of genes enriched for functions of innate-immune response and interferon signalling (Type-I and Type-II). Importantly, these results were replicated in a second non-overlapping independent dataset of U.S. Marines (N=96), further outlining the role of innate immune and interferon signalling genes within co-expression modules to explain at least part of the causal pathophysiology for PTSD development. A second module, consequential of trauma exposure, contained PTSD resiliency signatures and an over-expression of genes involved in hemostasis and wound responsiveness suggesting that chronic levels of stress impair proper wound healing during/after exposure to the battlefield while highlighting the role of the hemostatic system as a clinical indicator of chronic-based stress. These findings provide novel insights for early preventative measures and advanced PTSD detection, which may lead to interventions that delay or perhaps abrogate the development of PTSD.

  13. Dynamics of the pionium with the density matrix formalism

    CERN Document Server

    Afanasyev, L; Tarasov, A; Voskresenskaya, O O; 10.1088/0953-4075/37/24/003

    2004-01-01

    The evolution of pionium, the pi /sup +/ pi /sup -/ hydrogen-like atom, passing through matter is described by the density matrix formalism in the first Born approximation. We compare the probability-based calculations with the more precise density matrix formalism which takes into account the interference effects, and consider their influence on the pionium break-up probability. We apply our general result to the specific conditions of the DIRAC experiment at CERN.

  14. Formal Assurance for Cognitive Architecture Based Autonomous Agent

    Science.gov (United States)

    Bhattacharyya, Siddhartha; Eskridge, Thomas; Neogi, Natasha; Carvalho, Marco

    2017-01-01

    Autonomous systems are designed and deployed in different modeling paradigms. These environments focus on specific concepts in designing the system. We focus our effort in the use of cognitive architectures to design autonomous agents to collaborate with humans to accomplish tasks in a mission. Our research focuses on introducing formal assurance methods to verify the behavior of agents designed in Soar, by translating the agent to the formal verification environment Uppaal.

  15. On the Role of Formal Methods in Software Certification: An Experience Report

    Science.gov (United States)

    2009-01-01

    software, formal verification , formal specification, certification 1 Introduction Prior to its deployment, a security-critical software system may undergo a...the assumptions for ED make explicit those routines that the certification authority agreed were outside the scope of the formal verification . C.L...IEEE Computer 25 (1992), pp. 40–51. [14] Owre, S., J. Rushby, N. Shankar and F. von Henke, Formal verification for fault-tolerant architectures

  16. TGF-β Controls miR-181/ERK Regulatory Network during Retinal Axon Specification and Growth.

    Directory of Open Access Journals (Sweden)

    Sabrina Carrella

    Full Text Available Retinal axon specification and growth are critically sensitive to the dosage of numerous signaling molecules and transcription factors. Subtle variations in the expression levels of key molecules may result in a variety of axonal growth anomalies. miR-181a and miR-181b are two eye-enriched microRNAs whose inactivation in medaka fish leads to alterations of the proper establishment of connectivity and function in the visual system. miR-181a/b are fundamental regulators of MAPK signaling and their role in retinal axon growth and specification is just beginning to be elucidated. Here we demonstrate that miR-181a/b are key nodes in the interplay between TGF-β and MAPK/ERK within the functional pathways that control retinal axon specification and growth. Using a variety of in vivo and in vitro approaches in medaka fish, we demonstrate that TGF-β signaling controls the miR-181/ERK regulatory network, which in turn strengthens the TGF-β-mediated regulation of RhoA degradation. Significantly, these data uncover the role of TGF-β signaling in vivo, for the first time, in defining the correct wiring and assembly of functional retina neural circuits and further highlight miR-181a/b as key factors in axon specification and growth.

  17. TGF-β Controls miR-181/ERK Regulatory Network during Retinal Axon Specification and Growth.

    Science.gov (United States)

    Carrella, Sabrina; Barbato, Sara; D'Agostino, Ylenia; Salierno, Francesco Giuseppe; Manfredi, Anna; Banfi, Sandro; Conte, Ivan

    2015-01-01

    Retinal axon specification and growth are critically sensitive to the dosage of numerous signaling molecules and transcription factors. Subtle variations in the expression levels of key molecules may result in a variety of axonal growth anomalies. miR-181a and miR-181b are two eye-enriched microRNAs whose inactivation in medaka fish leads to alterations of the proper establishment of connectivity and function in the visual system. miR-181a/b are fundamental regulators of MAPK signaling and their role in retinal axon growth and specification is just beginning to be elucidated. Here we demonstrate that miR-181a/b are key nodes in the interplay between TGF-β and MAPK/ERK within the functional pathways that control retinal axon specification and growth. Using a variety of in vivo and in vitro approaches in medaka fish, we demonstrate that TGF-β signaling controls the miR-181/ERK regulatory network, which in turn strengthens the TGF-β-mediated regulation of RhoA degradation. Significantly, these data uncover the role of TGF-β signaling in vivo, for the first time, in defining the correct wiring and assembly of functional retina neural circuits and further highlight miR-181a/b as key factors in axon specification and growth.

  18. Closing the gap between formalism and application

    DEFF Research Database (Denmark)

    Christensen, Ole Ravn

    2008-01-01

    A common problem in learning mathematics concerns the gap between, on the one hand, doing the formalisms and calculations of abstract mathematics and, on the other hand, applying these in a specific contextualized setting for example the engineering world. The skills acquired through problem......-based learning (PBL), in the special model used at Aalborg University, Denmark, may give us some idea of how to bridge this gap. Through an investigation of a series of examples of student projects concerning the application of mathematical subjects-such as matrices, differential equations, cluster analysis...

  19. A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks.

    Directory of Open Access Journals (Sweden)

    Hojung Nam

    2014-09-01

    Full Text Available Altered metabolism in cancer cells has been viewed as a passive response required for a malignant transformation. However, this view has changed through the recently described metabolic oncogenic factors: mutated isocitrate dehydrogenases (IDH, succinate dehydrogenase (SDH, and fumarate hydratase (FH that produce oncometabolites that competitively inhibit epigenetic regulation. In this study, we demonstrate in silico predictions of oncometabolites that have the potential to dysregulate epigenetic controls in nine types of cancer by incorporating massive scale genetic mutation information (collected from more than 1,700 cancer genomes, expression profiling data, and deploying Recon 2 to reconstruct context-specific genome-scale metabolic models. Our analysis predicted 15 compounds and 24 substructures of potential oncometabolites that could result from the loss-of-function and gain-of-function mutations of metabolic enzymes, respectively. These results suggest a substantial potential for discovering unidentified oncometabolites in various forms of cancers.

  20. Correlates of formal reasoning: Content and problem effects

    Science.gov (United States)

    Linn, Marcia C.; Pulos, Steven; Gans, Adrienne

    Piaget's structural theory of formal thought suggests that a general construct of formal reasoning exists. The content of the task and type of problem employed are often ignored in Piagetian based studies but are important for generalizing findings to other studies and to educational problems. The study reported here examines content and problem effects of formal thought in 13-year-old adolescents. Specifically, three controlling variables tasks with different content and two question type tests (analysis and controlling questions) were administered to 120 seventh graders. Ability measures and personality dimensions associated with formal reasoning in the literature are used to clarify what formal reasoning is and how content and problem type are involved in formal reasoning. Significant main effects were found for problem and content effects (p = 0.001), and a significant interaction was found between the two (p = 0.001). Across the three tasks general ability, field dependency, and locus of control were consistently and significantly related to the controlling questions. However, only measures of field dependency were related to the analysis questions. Combinations of ability and personality factors were found to be uniquely related to each task, within each question type. Results have implications for a theory of formal thought and the teaching of the controlling variables strategy.

  1. The Generational Impact of Technology on Formal Writing of Rural Middle School Students

    Science.gov (United States)

    Land, Martha Ann

    2012-01-01

    The purpose of this study was to determine the impact text messages, social networks, Instant Messaging, email, and blogging had on rural middle school students' ability to decipher between formal and informal writing. Students completed self-evaluation logs, completed Formal and Informal Writing Assessments, and were scored on their use of…

  2. SCL/TAL1-mediated transcriptional network enhances megakaryocytic specification of human embryonic stem cells.

    Science.gov (United States)

    Toscano, Miguel G; Navarro-Montero, Oscar; Ayllon, Veronica; Ramos-Mejia, Veronica; Guerrero-Carreno, Xiomara; Bueno, Clara; Romero, Tamara; Lamolda, Mar; Cobo, Marien; Martin, Francisco; Menendez, Pablo; Real, Pedro J

    2015-01-01

    Human embryonic stem cells (hESCs) are a unique in vitro model for studying human developmental biology and represent a potential source for cell replacement strategies. Platelets can be generated from cord blood progenitors and hESCs; however, the molecular mechanisms and determinants controlling the in vitro megakaryocytic specification of hESCs remain elusive. We have recently shown that stem cell leukemia (SCL) overexpression accelerates the emergence of hemato-endothelial progenitors from hESCs and promotes their subsequent differentiation into blood cells with higher clonogenic potential. Given that SCL participates in megakaryocytic commitment, we hypothesized that it may potentiate megakaryopoiesis from hESCs. We show that ectopic SCL expression enhances the emergence of megakaryocytic precursors, mature megakaryocytes (MKs), and platelets in vitro. SCL-overexpressing MKs and platelets respond to different activating stimuli similar to their control counterparts. Gene expression profiling of megakaryocytic precursors shows that SCL overexpression renders a megakaryopoietic molecular signature. Connectivity Map analysis reveals that trichostatin A (TSA) and suberoylanilide hydroxamic acid (SAHA), both histone deacetylase (HDAC) inhibitors, functionally mimic SCL-induced effects. Finally, we confirm that both TSA and SAHA treatment promote the emergence of CD34(+) progenitors, whereas valproic acid, another HDAC inhibitor, potentiates MK and platelet production. We demonstrate that SCL and HDAC inhibitors are megakaryopoiesis regulators in hESCs.

  3. Designing area optimized application-specific network-on-chip architectures while providing hard QoS guarantees.

    Science.gov (United States)

    Khawaja, Sajid Gul; Mushtaq, Mian Hamza; Khan, Shoab A; Akram, M Usman; Jamal, Habib Ullah

    2015-01-01

    With the increase of transistors' density, popularity of System on Chip (SoC) has increased exponentially. As a communication module for SoC, Network on Chip (NoC) framework has been adapted as its backbone. In this paper, we propose a methodology for designing area-optimized application specific NoC while providing hard Quality of Service (QoS) guarantees for real time flows. The novelty of the proposed system lies in derivation of a Mixed Integer Linear Programming model which is then used to generate a resource optimal Network on Chip (NoC) topology and architecture while considering traffic and QoS requirements. We also present the micro-architectural design features used for enabling traffic and latency guarantees and discuss how the solution adapts for dynamic variations in the application traffic. The paper highlights the effectiveness of proposed method by generating resource efficient NoC solutions for both industrial and benchmark applications. The area-optimized results are generated in few seconds by proposed technique, without resorting to heuristics, even for an application with 48 traffic flows.

  4. Prioritizing disease candidate proteins in cardiomyopathy-specific protein-protein interaction networks based on "guilt by association" analysis.

    Directory of Open Access Journals (Sweden)

    Wan Li

    Full Text Available The cardiomyopathies are a group of heart muscle diseases which can be inherited (familial. Identifying potential disease-related proteins is important to understand mechanisms of cardiomyopathies. Experimental identification of cardiomyophthies is costly and labour-intensive. In contrast, bioinformatics approach has a competitive advantage over experimental method. Based on "guilt by association" analysis, we prioritized candidate proteins involving in human cardiomyopathies. We first built weighted human cardiomyopathy-specific protein-protein interaction networks for three subtypes of cardiomyopathies using the known disease proteins from Online Mendelian Inheritance in Man as seeds. We then developed a method in prioritizing disease candidate proteins to rank candidate proteins in the network based on "guilt by association" analysis. It was found that most candidate proteins with high scores shared disease-related pathways with disease seed proteins. These top ranked candidate proteins were related with the corresponding disease subtypes, and were potential disease-related proteins. Cross-validation and comparison with other methods indicated that our approach could be used for the identification of potentially novel disease proteins, which may provide insights into cardiomyopathy-related mechanisms in a more comprehensive and integrated way.

  5. Designing area optimized application-specific network-on-chip architectures while providing hard QoS guarantees.

    Directory of Open Access Journals (Sweden)

    Sajid Gul Khawaja

    Full Text Available With the increase of transistors' density, popularity of System on Chip (SoC has increased exponentially. As a communication module for SoC, Network on Chip (NoC framework has been adapted as its backbone. In this paper, we propose a methodology for designing area-optimized application specific NoC while providing hard Quality of Service (QoS guarantees for real time flows. The novelty of the proposed system lies in derivation of a Mixed Integer Linear Programming model which is then used to generate a resource optimal Network on Chip (NoC topology and architecture while considering traffic and QoS requirements. We also present the micro-architectural design features used for enabling traffic and latency guarantees and discuss how the solution adapts for dynamic variations in the application traffic. The paper highlights the effectiveness of proposed method by generating resource efficient NoC solutions for both industrial and benchmark applications. The area-optimized results are generated in few seconds by proposed technique, without resorting to heuristics, even for an application with 48 traffic flows.

  6. Specific gene-regulation networks during the pre-implantation development of the pig embryo as revealed by deep sequencing.

    Science.gov (United States)

    Cao, Suying; Han, Jianyong; Wu, Jun; Li, Qiuyan; Liu, Shichao; Zhang, Wei; Pei, Yangli; Ruan, Xiaoan; Liu, Zhonghua; Wang, Xumin; Lim, Bing; Li, Ning

    2014-01-03

    Because few studies exist to describe the unique molecular network regulation behind pig pre-implantation embryonic development (PED), genetic engineering in the pig embryo is limited. Also, this lack of research has hindered derivation and application of porcine embryonic stem cells and porcine induced pluripotent stem cells (iPSCs). We identified and analyzed the genome wide transcriptomes of pig in vivo-derived and somatic cell nuclear transferred (SCNT) as well as mouse in vivo-derived pre-implantation embryos at different stages using mRNA deep sequencing. Comparison of the pig embryonic transcriptomes with those of mouse and human pre-implantation embryos revealed unique gene expression patterns during pig PED. Pig zygotic genome activation was confirmed to occur at the 4-cell stage via genome-wide gene expression analysis. This activation was delayed to the 8-cell stage in SCNT embryos. Specific gene expression analysis of the putative inner cell mass (ICM) and the trophectoderm (TE) revealed that pig and mouse pre-implantation embryos share regulatory networks during the first lineage segregation and primitive endoderm differentiation, but not during ectoderm commitment. Also, fatty acid metabolism appears to be a unique characteristic of pig pre-implantation embryonic development. In addition, the global gene expression patterns in the pig SCNT embryos were different from those in in vivo-derived pig embryos. Our results provide a resource for pluripotent stem cell engineering and for understanding pig development.

  7. Contextual approach to quantum formalism

    CERN Document Server

    Khrennikov, Andrei

    2009-01-01

    The aim of this book is to show that the probabilistic formalisms of classical statistical mechanics and quantum mechanics can be unified on the basis of a general contextual probabilistic model. By taking into account the dependence of (classical) probabilities on contexts (i.e. complexes of physical conditions), one can reproduce all distinct features of quantum probabilities such as the interference of probabilities and the violation of Bell’s inequality. Moreover, by starting with a formula for the interference of probabilities (which generalizes the well known classical formula of total probability), one can construct the representation of contextual probabilities by complex probability amplitudes or, in the abstract formalism, by normalized vectors of the complex Hilbert space or its hyperbolic generalization. Thus the Hilbert space representation of probabilities can be naturally derived from classical probabilistic assumptions. An important chapter of the book critically reviews known no-go theorems...

  8. Musical Formalism and Political Performances

    Directory of Open Access Journals (Sweden)

    Jonathan A. Neufeld

    2009-01-01

    Full Text Available Musical formalism, which strictly limits the type of thing any description of the music can tell us, is ill-equipped to account for contemporary performance practice. If performative interpretations are in a position to tell us something about musical works—that is if performance is a kind of description, as Peter Kivy argues—then we have to loosen the restrictions on notions of musical relevance to make sense of performance. I argue that musical formalism, which strictly limits the type of thing any description of the music can tell us, is inconsistent with Kivy's quite compelling account of performance. This shows the difficulty that actual performances pose to overly rigid conceptions of music. Daniel Barenboim's unannounced performance of Wagner in Israel in 2001 shows that the problem of the boundaries of musical relevance is no mere philosophical puzzle. It is a pressing problem in the musical public sphere.

  9. Informal work and formal plans

    DEFF Research Database (Denmark)

    Dalsted, Rikke Juul; Hølge-Hazelton, Bibi; Kousgaard, Marius Brostrøm

    2012-01-01

    trajectories. METHODS AND THEORY: An in-depth case study of patient trajectories at a Danish hospital and surrounding municipality using individual interviews with patients. Theory about trajectory and work by Strauss was included. RESULTS: Patients continuously took initiatives to organize their treatment...... and care. They initiated processes in the trajectories, and acquired information, which they used to form their trajectories. Patients presented problems to the healthcare professionals in order to get proper help when needed. DISCUSSION: Work done by patients was invisible and not perceived as work....... The patients' requests were not sufficiently supported in the professional organisation of work or formal planning. Patients' insertion and use of information in their trajectories challenged professional views and working processes. And the design of the formal pathway models limits the patients' active...

  10. Formal Validation of Aerospace Software

    Science.gov (United States)

    Lesens, David; Moy, Yannick; Kanig, Johannes

    2013-08-01

    Any single error in critical software can have catastrophic consequences. Even though failures are usually not advertised, some software bugs have become famous, such as the error in the MIM-104 Patriot. For space systems, experience shows that software errors are a serious concern: more than half of all satellite failures from 2000 to 2003 involved software. To address this concern, this paper addresses the use of formal verification of software developed in Ada.

  11. Stroh formalism and Rayleigh waves

    CERN Document Server

    Tanuma, Kazumi

    2008-01-01

    Introduces a powerful and elegant mathematical method for the analysis of anisotropic elasticity equationsThe reader can grasp the essentials as quickly as possibleCan be used as a textbook, which presents compactly introduction and applications of the Stroh formalismAppeals to the people not only in mathematics but also in mechanics and engineering sciencePrerequisites are only basic linear algebra, calculus and fundamentals of differential equations

  12. UML-ising formal techniques

    DEFF Research Database (Denmark)

    Bjørner, Dines; George, Chris W.; Haxthausen, Anne Elisabeth

    2004-01-01

    these different UML views are unified, integrated, correlated or merely co-located is for others to dispute. We also seek to support multiple views, but are also in no doubt that there must be sound, well defined relations between such views. We thus report on ways and means of integrating formal techniques...... techniques, one that can be believably deployed for as wide a spectrum, or even a wider spectrum of software (and hardware) development, as, respectively than UML....

  13. Teleparallel formalism of galilean gravity

    OpenAIRE

    Ulhoa, S. C.; Khanna, F. C.; Santana, A.E.

    2011-01-01

    A pseudo-Riemannian manifold is introduced, with light-cone coordinates in (4+1) dimensional space-time, to describe a Galilei covariant gravity. The notion of 5-bein and torsion are developed and a galilean version of teleparallelism is constructed in this manifold. The formalism is applied to two spherically symmetric configurations. The first one is an ansatz which is inferred by following the Schwarzschild solution in general relativity. The second one is a solution of galilean covariant ...

  14. Sensitive and specific peak detection for SELDI-TOF mass spectrometry using a wavelet/neural-network based approach.

    Directory of Open Access Journals (Sweden)

    Vincent A Emanuele

    Full Text Available SELDI-TOF mass spectrometer's compact size and automated, high throughput design have been attractive to clinical researchers, and the platform has seen steady-use in biomarker studies. Despite new algorithms and preprocessing pipelines that have been developed to address reproducibility issues, visual inspection of the results of SELDI spectra preprocessing by the best algorithms still shows miscalled peaks and systematic sources of error. This suggests that there continues to be problems with SELDI preprocessing. In this work, we study the preprocessing of SELDI in detail and introduce improvements. While many algorithms, including the vendor supplied software, can identify peak clusters of specific mass (or m/z in groups of spectra with high specificity and low false discover rate (FDR, the algorithms tend to underperform estimating the exact prevalence and intensity of peaks in those clusters. Thus group differences that at first appear very strong are shown, after careful and laborious hand inspection of the spectra, to be less than significant. Here we introduce a wavelet/neural network based algorithm which mimics what a team of expert, human users would call for peaks in each of several hundred spectra in a typical SELDI clinical study. The wavelet denoising part of the algorithm optimally smoothes the signal in each spectrum according to an improved suite of signal processing algorithms previously reported (the LibSELDI toolbox under development. The neural network part of the algorithm combines those results with the raw signal and a training dataset of expertly called peaks, to call peaks in a test set of spectra with approximately 95% accuracy. The new method was applied to data collected from a study of cervical mucus for the early detection of cervical cancer in HPV infected women. The method shows promise in addressing the ongoing SELDI reproducibility issues.

  15. Lifelong Competence Development: On the Advantages of Formal Competence-Performance Modeling

    NARCIS (Netherlands)

    Kickmeier-Rust, Michael D.; Albert, Dietrich; Steiner, Christina

    2006-01-01

    Please, cite this publication as: Kickmeier-Rust, M.D., Albert, D., & Steiner, C. (2006). Lifelong Competence Development: On the Advantages of Formal Competence-Performance Modeling. Proceedings of International Workshop in Learning Networks for Lifelong Competence Development, TENCompetence

  16. Formal and Informal Work Group Relationships With Performance: A Moderation Model Using Social

    National Research Council Canada - National Science Library

    Knost, Benjamin R

    2006-01-01

    .... This field study, conducted at a military training course, attempted to further refine this social network-performance relationship by modeling characteristics of both the formal and informal work...

  17. Developing Modern Niger Delta Formalism

    Directory of Open Access Journals (Sweden)

    Edewor Uyoyou Nelson O

    2014-11-01

    Full Text Available Edewor Nelson (b. 1970 is a sculptor whose works depict configurations that espouse contexts associated with inimical and exploitative tendencies of petroleum oil exploration and exploitation in the Niger Delta region. His expressions represent a new formalism that is iconic of the region’s reality in terms of environmental degradation and fundamental human rights abuses. This motivation became imperative in the seemingly failure of other artistic explorations on the subject to adequately reflect modern formal archetypes for which the region’s dilemma can be expressed. The challenge of analytic study of this effort for attaining interpretative insights into this studio practice is pertinent. To realize this, corresponding Ivri traditional art form associated with the past in the region has been studied alongside petroleum drilling–related forms. This provides the fulcrum on which this article approaches an analysis of contextual and conceptual applications attributable to the stylistic oeuvre of Edewor’s practice since 1997. It uses formalism and iconography interpretative tools for its critical discourse.

  18. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution.

    Directory of Open Access Journals (Sweden)

    Amanda Tse

    Full Text Available Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib and promiscuous (Bosutinib, Dasatinib kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations

  19. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

    Science.gov (United States)

    Tse, Amanda; Verkhivker, Gennady M.

    2015-01-01

    Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating

  20. Proceedings of the First NASA Formal Methods Symposium

    Science.gov (United States)

    Denney, Ewen (Editor); Giannakopoulou, Dimitra (Editor); Pasareanu, Corina S. (Editor)

    2009-01-01

    Topics covered include: Model Checking - My 27-Year Quest to Overcome the State Explosion Problem; Applying Formal Methods to NASA Projects: Transition from Research to Practice; TLA+: Whence, Wherefore, and Whither; Formal Methods Applications in Air Transportation; Theorem Proving in Intel Hardware Design; Building a Formal Model of a Human-Interactive System: Insights into the Integration of Formal Methods and Human Factors Engineering; Model Checking for Autonomic Systems Specified with ASSL; A Game-Theoretic Approach to Branching Time Abstract-Check-Refine Process; Software Model Checking Without Source Code; Generalized Abstract Symbolic Summaries; A Comparative Study of Randomized Constraint Solvers for Random-Symbolic Testing; Component-Oriented Behavior Extraction for Autonomic System Design; Automated Verification of Design Patterns with LePUS3; A Module Language for Typing by Contracts; From Goal-Oriented Requirements to Event-B Specifications; Introduction of Virtualization Technology to Multi-Process Model Checking; Comparing Techniques for Certified Static Analysis; Towards a Framework for Generating Tests to Satisfy Complex Code Coverage in Java Pathfinder; jFuzz: A Concolic Whitebox Fuzzer for Java; Machine-Checkable Timed CSP; Stochastic Formal Correctness of Numerical Algorithms; Deductive Verification of Cryptographic Software; Coloured Petri Net Refinement Specification and Correctness Proof with Coq; Modeling Guidelines for Code Generation in the Railway Signaling Context; Tactical Synthesis Of Efficient Global Search Algorithms; Towards Co-Engineering Communicating Autonomous Cyber-Physical Systems; and Formal Methods for Automated Diagnosis of Autosub 6000.

  1. Context-aware approach for formal verification

    Directory of Open Access Journals (Sweden)

    Amel Benabbou

    2016-02-01

    Full Text Available The Context-aware approach has proven to be an effective technique for software model-checking verification. It focuses on the explicit modelling of environment as one or more contexts. In this area, specifying precise requirement is a challenged task for engineer since often environmental conditions lack of precision. A DSL, called CDL, has been proposed to facilitate the specification of requirement and context. However, such language is still low-level and error prone, difficult to grasp on complex models and assessment about its usability is still mitigated. In this paper, we propose a high level formalism of CDL to facilitate specifying contexts based on interaction overview diagrams that orchestrate activity diagrams automatically transformed from textual use cases. Our approach highlights the boundaries between the system and its environment. It is qualified as model checking context-aware that aims to reduce the semantic gap between informal and formal requirements, hence the objective is to assist and encourage engineers to put sufficient details to accomplish effectively the specification process.

  2. Towards formal evaluation of collaborative work

    Directory of Open Access Journals (Sweden)

    R. Baeza-Yates

    2006-01-01

    Full Text Available Introduction. Computer Supported Cooperative Work (CSCW projects are difficult to evaluate when implemented at most organizations. There are many variables and some of these are qualitative and hard to assess. However, there are other variables that could be measured and, thus, for a specific CSCW system, management could have a performance estimate. Method. A groupware application is modelled, focusing on the work done and time spent on the collaboration. Analysis. The following variables and their relations are studied: quality of the outcomes, number of people involved and time spent on the overall task, and total work done. Results. An application - collaborative retrieval - is formalized to illustrate the model. For this application, a specific heuristic is proposed to the case when many people search for the same information, thereby increasing the recall and precision of the answer. The evaluation methodology is applied to this case, showing some experimental results. Conclusion. We present an initial attempt to formally evaluate performance measures related to CSCW applications.

  3. Noncognitive formal approach to knowledge representation in artificial intelligence

    Energy Technology Data Exchange (ETDEWEB)

    McMannama, J.A.

    1986-01-01

    With the entry of artificial intelligence (Al) into real-time applications, a rigorous analysis of Al expert systems is required in order to validate them for operational use. To satisfy this requirement for analysis of the associated knowledge representations, the techniques of formal language theory are used. A combination of theorems, proofs and problem-solving techniques from formal language theory are employed to analyze language equivalents of the more commonly used Al knowledge representations of production rules (excluding working memory or situation data) and semantic networks. Using formal language characteristics, it is shown that no single support-tool or automatic-programming tool can ever be constructed that can handle all possible production-rule or semantic-network variations. Additionally, it is shown that the entire set of finite production-rule languages is able to be stored in and retrieved from finite semantic-network languages. In effect, the semantic-network structure is shown to be a viable candidate for a centralized database of knowledge.

  4. Formal verification of a fault tolerant clock synchronization algorithm

    Science.gov (United States)

    Rushby, John; Vonhenke, Frieder

    1989-01-01

    A formal specification and mechanically assisted verification of the interactive convergence clock synchronization algorithm of Lamport and Melliar-Smith is described. Several technical flaws in the analysis given by Lamport and Melliar-Smith were discovered, even though their presentation is unusally precise and detailed. It seems that these flaws were not detected by informal peer scrutiny. The flaws are discussed and a revised presentation of the analysis is given that not only corrects the flaws but is also more precise and easier to follow. Some of the corrections to the flaws require slight modifications to the original assumptions underlying the algorithm and to the constraints on its parameters, and thus change the external specifications of the algorithm. The formal analysis of the interactive convergence clock synchronization algorithm was performed using the Enhanced Hierarchical Development Methodology (EHDM) formal specification and verification environment. This application of EHDM provides a demonstration of some of the capabilities of the system.

  5. A Formal Verification Methodology for DDD Mode Pacemaker Control Programs

    Directory of Open Access Journals (Sweden)

    Sana Shuja

    2015-01-01

    Full Text Available Pacemakers are safety-critical devices whose faulty behaviors can cause harm or even death. Often these faulty behaviors are caused due to bugs in programs used for digital control of pacemakers. We present a formal verification methodology that can be used to check the correctness of object code programs that implement the safety-critical control functions of DDD mode pacemakers. Our methodology is based on the theory of Well-Founded Equivalence Bisimulation (WEB refinement, where both formal specifications and implementation are treated as transition systems. We develop a simple and general formal specification for DDD mode pacemakers. We also develop correctness proof obligations that can be applied to validate object code programs used for pacemaker control. Using our methodology, we were able to verify a control program with millions of transitions against the simple specification with only 10 transitions. Our method also found several bugs during the verification process.

  6. Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins.

    Science.gov (United States)

    Le, Nguyen-Quoc-Khanh; Ho, Quang-Thai; Ou, Yu-Yen

    2017-09-05

    In several years, deep learning is a modern machine learning technique using in a variety of fields with state-of-the-art performance. Therefore, utilization of deep learning to enhance performance is also an important solution for current bioinformatics field. In this study, we try to use deep learning via convolutional neural networks and position specific scoring matrices to identify electron transport proteins, which is an important molecular function in transmembrane proteins. Our deep learning method can approach a precise model for identifying of electron transport proteins with achieved sensitivity of 80.3%, specificity of 94.4%, and accuracy of 92.3%, with MCC of 0.71 for independent dataset. The proposed technique can serve as a powerful tool for identifying electron transport proteins and can help biologists understand the function of the electron transport proteins. Moreover, this study provides a basis for further research that can enrich a field of applying deep learning in bioinformatics. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  7. Developing intelligent sensor networks —a technological convergence approach

    OpenAIRE

    Vassev, Emil; Hinchey, Mike; Nixon, Paddy

    2010-01-01

    peer-reviewed We present a technological convergence approach to developing sensor networks capable of self-management. We use ASSL (Autonomic System Specification Language) to formally develop autonomous intelligent sensor nodes and DMF (Demand Migration Framework) to connect these nodes in a sensor network. ASSL provides constructs for modeling special self-management policies that drive the sensor nodes’ behavior and control the communication mechanism provided by DMF.

  8. Temporal network based analysis of cell specific vein graft transcriptome defines key pathways and hub genes in implantation injury.

    Directory of Open Access Journals (Sweden)

    Manoj Bhasin

    Full Text Available Vein graft failure occurs between 1 and 6 months after implantation due to obstructive intimal hyperplasia, related in part to implantation injury. The cell-specific and temporal response of the transcriptome to vein graft implantation injury was determined by transcriptional profiling of laser capture microdissected endothelial cells (EC and medial smooth muscle cells (SMC from canine vein grafts, 2 hours (H to 30 days (D following surgery. Our results demonstrate a robust genomic response beginning at 2 H, peaking at 12-24 H, declining by 7 D, and resolving by 30 D. Gene ontology and pathway analyses of differentially expressed genes indicated that implantation injury affects inflammatory and immune responses, apoptosis, mitosis, and extracellular matrix reorganization in both cell types. Through backpropagation an integrated network was built, starting with genes differentially expressed at 30 D, followed by adding upstream interactive genes from each prior time-point. This identified significant enrichment of IL-6, IL-8, NF-κB, dendritic cell maturation, glucocorticoid receptor, and Triggering Receptor Expressed on Myeloid Cells (TREM-1 signaling, as well as PPARα activation pathways in graft EC and SMC. Interactive network-based analyses identified IL-6, IL-8, IL-1α, and Insulin Receptor (INSR as focus hub genes within these pathways. Real-time PCR was used for the validation of two of these genes: IL-6 and IL-8, in addition to Collagen 11A1 (COL11A1, a cornerstone of the backpropagation. In conclusion, these results establish causality relationships clarifying the pathogenesis of vein graft implantation injury, and identifying novel targets for its prevention.

  9. Informal work and formal plans

    DEFF Research Database (Denmark)

    Dalsted, Rikke Juul; Hølge-Hazelton, Bibi; Kousgaard, Marius Brostrøm

    2012-01-01

    INTRODUCTION: Formal pathways models outline that patients should receive information in order to experience a coherent journey but do not describe an active role for patients or their relatives. The aim of this is paper is to articulate and discuss the active role of patients during their cancer...... trajectories. METHODS AND THEORY: An in-depth case study of patient trajectories at a Danish hospital and surrounding municipality using individual interviews with patients. Theory about trajectory and work by Strauss was included. RESULTS: Patients continuously took initiatives to organize their treatment...

  10. Formal Verification at System Level

    Science.gov (United States)

    Mazzini, S.; Puri, S.; Mari, F.; Melatti, I.; Tronci, E.

    2009-05-01

    System Level Analysis calls for a language comprehensible to experts with different background and yet precise enough to support meaningful analyses. SysML is emerging as an effective balance between such conflicting goals. In this paper we outline some the results obtained as for SysML based system level functional formal verification by an ESA/ESTEC study, with a collaboration among INTECS and La Sapienza University of Roma. The study focuses on SysML based system level functional requirements techniques.

  11. The Bondi-Sachs Formalism

    CERN Document Server

    Mädler, Thomas

    2016-01-01

    The Bondi-Sachs formalism of General Relativity is a metric-based treatment of the Einstein equations in which the coordinates are adapted to the null geodesics of the spacetime. It provided the first convincing evidence that gravitational radiation is a nonlinear effect of general relativity and that the emission of gravitational waves from an isolated system is accompanied by a mass loss from the system. The asymptotic behaviour of the Bondi-Sachs metric revealed the existence of the symmetry group at null infinity, the Bondi-Metzner-Sachs group, which turned out to be larger than the Poincare group.

  12. Understanding Informality and Formality in Learning.

    Science.gov (United States)

    Colley, Helen; Hodkinson, Phil; Malcolm, Janice

    2003-01-01

    Reviews definitions of and debates over distinctions among formal, informal, and nonformal learning. Outlines questions about four aspects of formality/informality with which to analyze learning situations: process, location/setting, purposes, and content. (SK)

  13. Formal Inspection: A Tool for TQM

    Science.gov (United States)

    Welz, L.; Kelly, J.

    1995-01-01

    The goal of the Formal Inspection Program at the Jet Propulsion Laboratory (JPL) is to support projects wishing to use Formal Inspections to improve the quality of software and system level engineering products.

  14. Declarative Networking

    CERN Document Server

    Loo, Boon Thau

    2012-01-01

    Declarative Networking is a programming methodology that enables developers to concisely specify network protocols and services, which are directly compiled to a dataflow framework that executes the specifications. Declarative networking proposes the use of a declarative query language for specifying and implementing network protocols, and employs a dataflow framework at runtime for communication and maintenance of network state. The primary goal of declarative networking is to greatly simplify the process of specifying, implementing, deploying and evolving a network design. In addition, decla

  15. Formal and nonformal SETI education programs

    Science.gov (United States)

    Bhathal, Ragbir

    2001-08-01

    Frank Drake's experiment on the search for extraterrestrial intelligence in 1960 not only generated a new field of observational astronomy but also produced spin-offs in the fields of education and the social science. SETI education programs in formal and non-formal educational institutions provide a powerful tool for educating the public and students about humanity's most profound question: are we alone in the universe? This paper discusses SETI educational programs in both formal and non-formal settings.

  16. Spin response formalism in circular accelerators

    Energy Technology Data Exchange (ETDEWEB)

    Ptitsyn, V.I. [Brookhaven National Laboratory, Upton, NY 11973 (United States)], E-mail: vadimp@bnl.gov; Shatunov, Yu.M. [Budker Institute of Nuclear Physics, Novosibirsk, 630090 (Russian Federation); Mane, S.R. [Convergent Computing Inc., P. O. Box 561, Shoreham, NY 11786 (United States)], E-mail: srmane@optonline.net

    2009-09-11

    We present the principal features of the so-called 'spin response formalism', which is linear response theory applied to the spin dynamics in circular accelerators. The formalism is useful for calculating the resonance strengths of several classes of first-order spin resonances in rings, including those for spin flippers. We describe some of the successful applications of the formalism to various storage rings. We include a brief comparison with other formalisms and indicate topics for future work.

  17. Expression profile and specific network features of the apoptotic machinery explain relapse of acute myeloid leukemia after chemotherapy

    Directory of Open Access Journals (Sweden)

    Di Pietro Cinzia

    2010-07-01

    Full Text Available Abstract Background According to the different sensitivity of their bone marrow CD34+ cells to in vitro treatment with Etoposide or Mafosfamide, Acute Myeloid Leukaemia (AML patients in apparent complete remission (CR after chemotherapy induction may be classified into three groups: (i normally responsive; (ii chemoresistant; (iii highly chemosensitive. This inversely correlates with in vivo CD34+ mobilization and, interestingly, also with the prognosis of the disease: patients showing a good mobilizing activity are resistant to chemotherapy and subject to significantly higher rates of Minimal Residual Disease (MRD and relapse than the others. Based on its known role in patients' response to chemotherapy, we hypothesized an involvement of the Apoptotic Machinery (AM in these phenotypic features. Methods To investigate the molecular bases of the differential chemosensitivity of bone marrow hematopoietic stem cells (HSC in CR AML patients, and the relationship between chemosensitivity, mobilizing activity and relapse rates, we analyzed their AM expression profile by performing Real Time RT-PCR of 84 AM genes in CD34+ pools from the two extreme classes of patients (i.e., chemoresistant and highly chemosensitive, and compared them with normal controls. Results The AM expression profiles of patients highlighted features that could satisfactorily explain their in vitro chemoresponsive phenotype: specifically, in chemoresistant patients we detected up regulation of antiapoptotic BIRC genes and down regulation of proapoptotic APAF1, FAS, FASL, TNFRSF25. Interestingly, our analysis of the AM network showed that the dysregulated genes in these patients are characterized by high network centrality (i.e., high values of betweenness, closeness, radiality, stress and high involvement in drug response. Conclusions AM genes represent critical nodes for the proper execution of cell death following pharmacological induction in patients. We propose that their

  18. Formal Proofs for Nonlinear Optimization

    Directory of Open Access Journals (Sweden)

    Victor Magron

    2015-01-01

    Full Text Available We present a formally verified global optimization framework. Given a semialgebraic or transcendental function f and a compact semialgebraic domain K, we use the nonlinear maxplus template approximation algorithm to provide a certified lower bound of f over K.This method allows to bound in a modular way some of the constituents of f by suprema of quadratic forms with a well chosen curvature. Thus, we reduce the initial goal to a hierarchy of semialgebraic optimization problems, solved by sums of squares relaxations. Our implementation tool interleaves  semialgebraic approximations with sums of squares witnesses to form certificates. It is interfaced with Coq and thus benefits from the trusted arithmetic available inside the proof assistant. This feature is used to produce, from the certificates, both valid underestimators and lower bounds for each approximated constituent.The application range for such a tool is widespread; for instance Hales' proof of Kepler's conjecture yields thousands of multivariate transcendental inequalities. We illustrate the performance of our formal framework on some of these inequalities as well as on examples from the global optimization literature.

  19. Formal Verification of Circuits and Systems

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    methods in the verification task. Today formal verification is finding increasing acceptance ... approaches that are major research issues in formal verification research today. There are four articles in this issue, which show up the different flavours in the approach to formal methods in verification. The first paper by Supratik ...

  20. Comment: universality of formal operational thought.

    Science.gov (United States)

    Mwamwenda, T S

    1992-08-01

    Piaget suggested four stages of development (sensorimotor, preoperational, concrete and formal operations) may be universally observed, but only the first three have been confirmed because few people attain formal operations. Both Westerners and Africans may attain formal operations, however, given the way they reason and interact in their milieu.

  1. Formal analysis of design process dynamics

    NARCIS (Netherlands)

    Bosse, T.; Jonker, C.M.; Treur, J.

    2010-01-01

    This paper presents a formal analysis of design process dynamics. Such a formal analysis is a prerequisite to come to a formal theory of design and for the development of automated support for the dynamics of design processes. The analysis was geared toward the identification of dynamic design

  2. Ego Identity, Egocentrism, and Formal Operations.

    Science.gov (United States)

    Protinsky, Howard; Wilkerson, Jackie

    1986-01-01

    Examined the relationship between ego identity, formal operations, and egocentrism in adolescents. Results indicated significant positive correlations between ego identity and formal operations and between ego identity and grade in school. Grade in school explained 21 percent of the variance while formal operational thinking, egocentrism, and sex…

  3. Hallucination- and speech-specific hypercoupling in frontotemporal auditory and language networks in schizophrenia using combined task-based fMRI data: An fBIRN study.

    Science.gov (United States)

    Lavigne, Katie M; Woodward, Todd S

    2017-12-21

    Hypercoupling of activity in speech-perception-specific brain networks has been proposed to play a role in the generation of auditory-verbal hallucinations (AVHs) in schizophrenia; however, it is unclear whether this hypercoupling extends to nonverbal auditory perception. We investigated this by comparing schizophrenia patients with and without AVHs, and healthy controls, on task-based functional magnetic resonance imaging (fMRI) data combining verbal speech perception (SP), inner verbal thought generation (VTG), and nonverbal auditory oddball detection (AO). Data from two previously published fMRI studies were simultaneously analyzed using group constrained principal component analysis for fMRI (group fMRI-CPCA), which allowed for comparison of task-related functional brain networks across groups and tasks while holding the brain networks under study constant, leading to determination of the degree to which networks are common to verbal and nonverbal perception conditions, and which show coordinated hyperactivity in hallucinations. Three functional brain networks emerged: (a) auditory-motor, (b) language processing, and (c) default-mode (DMN) networks. Combining the AO and sentence tasks allowed the auditory-motor and language networks to separately emerge, whereas they were aggregated when individual tasks were analyzed. AVH patients showed greater coordinated activity (deactivity for DMN regions) than non-AVH patients during SP in all networks, but this did not extend to VTG or AO. This suggests that the hypercoupling in AVH patients in speech-perception-related brain networks is specific to perceived speech, and does not extend to perceived nonspeech or inner verbal thought generation. © 2017 Wiley Periodicals, Inc.

  4. Career Progression and Formal versus on the Job Training

    OpenAIRE

    Adda; Dustmann

    2004-01-01

    This paper evaluates the return to formal education over the life-cycle and compare it to informal, on the job training. More specifically, we assess the apprenticeship system in Germany by comparing the long run value of education choices and subsequent labor market outcomes for apprentices and non-apprentices. We develop a structural model of career progression and educational choice, allowing for unobserved ability, endogenous job to job transition, specific firm-worker matches, specific r...

  5. Entrepreneurial networks as culturally embedded phenomena

    Directory of Open Access Journals (Sweden)

    Vlatka Skokic

    2015-06-01

    Full Text Available Entrepreneurship research concerning networks has largely focused on network structure, content and governance. We believe that further research is required in order to gain a richer understanding of why specific network forms and types originated. The purpose of this paper is to explore the existence, importance, values and meanings of both the informal and formal networks and networking behaviours of small-scale hotel owner-managers embedded in the socio-economic context of Croatia. In order to gain richer and more detailed understanding of entrepreneurial networks and to understand the influence of socio-economic setting on entrepreneurial networking, we have employed qualitative, in-depth study with small hotel owners. Results suggest that entrepreneurs do not establish strong personal and firm-to-firm ties, but rather focus on formal associations. Reported findings identify socio-cultural factors apparently unique to the context of former socialist economy which have the potential to explain the reported networking behaviour. The adopted research approach brings another dimension to existing theoretical underpinnings, which can encourage researchers to extend or revise theories with new contextual variables.

  6. Formalizing the XML Schema Matching Problem as a Constraint Optimization Problem

    NARCIS (Netherlands)

    Smiljanic, M.; van Keulen, Maurice; Jonker, Willem; Andersen, K.V.; Debenham, J.K.; Wagner, R.

    The first step in finding an efficient way to solve any difficult problem is making a complete, possibly formal, problem specification. This paper introduces a formal specification for the problem of semantic XML schema matching. Semantic schema matching has been extensively researched, and many

  7. Provision of specific dental procedures by general dentists in the National Dental Practice-Based Research Network: questionnaire findings.

    Science.gov (United States)

    Gilbert, Gregg H; Gordan, Valeria V; Korelitz, James J; Fellows, Jeffrey L; Meyerowitz, Cyril; Oates, Thomas W; Rindal, D Brad; Gregory, Randall J

    2015-01-22

    Objectives were to: (1) determine whether and how often general dentists (GDs) provide specific dental procedures; and (2) test the hypothesis that provision is associated with key dentist, practice, and patient characteristics. GDs (n = 2,367) in the United States National Dental Practice-Based Research Network completed an Enrollment Questionnaire that included: (1) dentist; (2) practice; and (3) patient characteristics, and how commonly they provide each of 10 dental procedures. We determined how commonly procedures were provided and tested the hypothesis that provision was substantively related to the three sets of characteristics. Two procedure categories were classified as "uncommon" (orthodontics, periodontal surgery), three were "common" (molar endodontics; implants; non-surgical periodontics), and five were "very common" (restorative; esthetic procedures; extractions; removable prosthetics; non-molar endodontics). Dentist, practice, and patient characteristics were substantively related to procedure provision; several characteristics seemed to have pervasive effects, such as dentist gender, training after dental school, full-time/part-time status, private practice vs. institutional practice, presence of a specialist in the same practice, and insurance status of patients. As a group, GDs provide a comprehensive range of procedures. However, provision by individual dentists is substantively related to certain dentist, practice, and patient characteristics. A large number and broad range of factors seem to influence which procedures GDs provide. This may have implications for how GDs respond to the ever-changing landscape of dental care utilization, patient population demography, scope of practice, delivery models and GDs' evolving role in primary care.

  8. Formal Methods at Intel - An Overview

    Science.gov (United States)

    Harrison, John

    2010-01-01

    Since the 1990s, Intel has invested heavily in formal methods, which are now deployed in several domains: hardware, software, firmware, protocols etc. Many different formal methods tools and techniques are in active use, including symbolic trajectory evaluation, temporal logic model checking, SMT-style combined decision procedures, and interactive higher-order logic theorem proving. I will try to give a broad overview of some of the formal methods activities taking place at Intel, and describe the challenges of extending formal verification to new areas and of effectively using multiple formal techniques in combination

  9. Toward a Grid Work flow Formal Composition

    Energy Technology Data Exchange (ETDEWEB)

    Hlaoui, Y. B.; BenAyed, L. J.

    2007-07-01

    This paper exposes a new approach for the composition of grid work flow models. This approach proposes an abstract syntax for the UML Activity Diagrams (UML-AD) and a formal foundation for grid work flow composition in form of a work flow algebra based on UML-AD. This composition fulfils the need for collaborative model development particularly the specification and the reduction of the complexity of grid work flow model verification. This complexity has arisen with the increase in scale of grid work flow applications such as science and e-business applications since large amounts of computational resources are required and multiple parties could be involved in the development process and in the use of grid work flows. Furthermore, the proposed algebra allows the definition of work flow views which are useful to limit the access to predefined users in order to ensure the security of grid work flow applications. (Author)

  10. Towards Safe Navigation by Formalizing Navigation Rules

    Directory of Open Access Journals (Sweden)

    Arne Kreutzmann

    2013-06-01

    Full Text Available One crucial aspect of safe navigation is to obey all navigation regulations applicable, in particular the collision regulations issued by the International Maritime Organization (IMO Colregs. Therefore, decision support systems for navigation need to respect Colregs and this feature should be verifiably correct. We tackle compliancy of navigation regulations from a perspective of software verification. One common approach is to use formal logic, but it requires to bridge a wide gap between navigation concepts and simple logic. We introduce a novel domain specification language based on a spatio-temporal logic that allows us to overcome this gap. We are able to capture complex navigation concepts in an easily comprehensible representation that can direcly be utilized by various bridge systems and that allows for software verification.

  11. Formal modeling of virtual machines

    Science.gov (United States)

    Cremers, A. B.; Hibbard, T. N.

    1978-01-01

    Systematic software design can be based on the development of a 'hierarchy of virtual machines', each representing a 'level of abstraction' of the design process. The reported investigation presents the concept of 'data space' as a formal model for virtual machines. The presented model of a data space combines the notions of data type and mathematical machine to express the close interaction between data and control structures which takes place in a virtual machine. One of the main objectives of the investigation is to show that control-independent data type implementation is only of limited usefulness as an isolated tool of program development, and that the representation of data is generally dictated by the control context of a virtual machine. As a second objective, a better understanding is to be developed of virtual machine state structures than was heretofore provided by the view of the state space as a Cartesian product.

  12. The {\\delta}N Formalism

    CERN Document Server

    Sugiyama, Naonori S; Futamase, Toshifumi

    2013-01-01

    Precise understanding of non-linear evolution of cosmological perturbations during inflation is necessary for the correct interpretation of measurements of non-Gaussian correlations in the cosmic microwave background and the large-scale structure of the universe. The "{\\delta}N formalism" is a popular and powerful technique for computing non-linear evolution of cosmological perturbations on large scales. In particular, it enables us to compute the curvature perturbation, {\\zeta}, on large scales without actually solving perturbed field equations. However, people often wonder why this is the case. In order for this approach to be valid, the perturbed Hamiltonian constraint and matter-field equations on large scales must, with a suitable choice of coordinates, take on the same forms as the corresponding unperturbed equations. We find that this is possible when (1) the unperturbed metric is given by a homogeneous and isotropic Friedmann-Lema\\^itre-Robertson-Walker metric; and (2) on large scales and with a suita...

  13. Formal analysis of electromagnetic optics

    Science.gov (United States)

    Khan-Afshar, Sanaz; Hasan, Osman; Tahar, Sofiène

    2014-09-01

    Optical systems are increasingly being used in safety-critical applications. Due to the complexity and sensitivity of optical systems, their verification raises many challenges for engineers. Traditionally, the analysis of such systems has been carried out by paper-and-pencil based proofs and numerical computations. However, these techniques cannot provide accurate results due to the risk of human error and inherent approximations of numerical algorithms. In order to overcome these limitations, we propose to use theorem proving (i.e., a computer-based technique that allows to express mathematical expressions and reason about their correctness by taking into account all the details of mathematical reasoning) as a complementary approach to improve optical system analysis. This paper provides a higher-order logic (a language used to express mathematical theories) formalization of electromagnetic optics in the HOL Light theorem prover. In order to demonstrate the practical effectiveness of our approach, we present the analysis of resonant cavity enhanced photonic devices.

  14. A Formal Calculus for Categories

    DEFF Research Database (Denmark)

    Cáccamo, Mario José

    This dissertation studies the logic underlying category theory. In particular we present a formal calculus for reasoning about universal properties. The aim is to systematise judgements about functoriality and naturality central to categorical reasoning. The calculus is based on a language which...... extends the typed lambda calculus with new binders to represent universal constructions. The types of the languages are interpreted as locally small categories and the expressions represent functors. The logic supports a syntactic treatment of universality and duality. Contravariance requires a definition...... of universality generous enough to deal with functors of mixed variance. Ends generalise limits to cover these kinds of functors and moreover provide the basis for a very convenient algebraic manipulation of expressions. The equational theory of the lambda calculus is extended with new rules for the definitions...

  15. Matrix formalism of synchrobetatron coupling

    Directory of Open Access Journals (Sweden)

    Xiaobiao Huang

    2007-01-01

    Full Text Available In this paper we present a complete linear synchrobetatron coupling formalism by studying the transfer matrix which describes linear horizontal and longitudinal motions. With the technique established in the linear horizontal-vertical coupling study [D. Sagan and D. Rubin, Phys. Rev. ST Accel. Beams 2, 074001 (1999PRABFM1098-440210.1103/PhysRevSTAB.2.074001], we found a transformation to block diagonalize the transfer matrix and decouple the betatron motion and the synchrotron motion. By separating the usual dispersion term from the horizontal coordinate first, we were able to obtain analytic expressions of the transformation under reasonable approximations. We also obtained the perturbations to the betatron tune and the Courant-Snyder functions. The closed-orbit changes due to finite energy gains at rf cavities and radiation energy losses were studied by the 5×5 extended transfer matrix with the fifth column describing kicks in the 4-dimension phase space.

  16. Formal Aspects of Grid Brokering

    Directory of Open Access Journals (Sweden)

    Attila Kertész

    2009-12-01

    Full Text Available Coordination in distributed environments, like Grids, involves selecting the most appropriate services, resources or compositions to carry out the planned activities. Such functionalities appear at various levels of the infrastructure and in various means forming a blurry domain, where it is hard to see how the participating components are related and what their relevant properties are. In this paper we focus on a subset of these problems: resource brokering in Grid middleware. This paper aims at establishing a semantical model for brokering and related activities by defining brokering agents at three levels of the Grid middleware for resource, host and broker selection. The main contribution of this paper is the definition and decomposition of different brokering components in Grids by providing a formal model using Abstract State Machines.

  17. Region-specific network plasticity in simulated and living cortical networks: comparison of the center of activity trajectory (CAT) with other statistics

    Science.gov (United States)

    Chao, Zenas C.; Bakkum, Douglas J.; Potter, Steve M.

    2007-09-01

    Electrically interfaced cortical networks cultured in vitro can be used as a model for studying the network mechanisms of learning and memory. Lasting changes in functional connectivity have been difficult to detect with extracellular multi-electrode arrays using standard firing rate statistics. We used both simulated and living networks to compare the ability of various statistics to quantify functional plasticity at the network level. Using a simulated integrate-and-fire neural network, we compared five established statistical methods to one of our own design, called center of activity trajectory (CAT). CAT, which depicts dynamics of the location-weighted average of spatiotemporal patterns of action potentials across the physical space of the neuronal circuitry, was the most sensitive statistic for detecting tetanus-induced plasticity in both simulated and living networks. By reducing the dimensionality of multi-unit data while still including spatial information, CAT allows efficient real-time computation of spatiotemporal activity patterns. Thus, CAT will be useful for studies in vivo or in vitro in which the locations of recording sites on multi-electrode probes are important.

  18. Formal Verification of Annotated Textual Use-Cases

    Czech Academy of Sciences Publication Activity Database

    Šimko, V.; Hauzar, D.; Hnětynka, P.; Bureš, Tomáš; Plášil, F.

    2015-01-01

    Roč. 58, č. 7 (2015), s. 1495-1529 ISSN 0010-4620 Grant - others:GA AV ČR(CZ) GAP103/11/1489 Institutional support: RVO:67985807 Keywords : specification * use-cases * behavior modeling * verification * temporal logic * formalization Subject RIV: JC - Computer Hardware ; Software Impact factor: 1.000, year: 2015

  19. FORMED: Bringing Formal Methods to the Engineering Desktop

    Science.gov (United States)

    2016-02-01

    Language and transforming application models into both an ACL2s formal specification for analysis and Java code for deployment. Correspondence testing...Functions ................................................................................................ 19 4.8.4 History variables...with templates that generate Java , C, and C++ code, as well as reports. We wrote new templates that generate the ACL2s functions and theorems, but

  20. Formal and Integrated Strategies for Competence Development in SMEs

    Science.gov (United States)

    Kock, Henrik; Ellstrom, Per-Erik

    2011-01-01

    Purpose: The purpose of this paper is to increase understanding of the relationships among the workplace as a learning environment, strategies for competence development used by SMEs and learning outcomes. Specifically, there is a focus on a distinction between formal and integrated strategies for competence development, the conditions under which…

  1. Formal system specifications: A case study of three diverse representations

    Energy Technology Data Exchange (ETDEWEB)

    Chisholm, G.H. (Argonne National Lab., IL (USA)); Smith, B.T. (Argonne National Lab., IL (USA) New Mexico Univ., Albuquerque, NM (USA). Dept. of Computer Science); Wojcik, A.S. (Argonne National Lab., IL (USA) Michigan State Univ., East Lansing, MI (USA). Dept. of Computer Science)

    1990-12-01

    The only effective way to raise the confidence level of a program significantly is to give a convincing proof of its correctness. But one should not first make the program and then prove its correctness, because then the requirement of providing the proof would only increase the poor programmer's burden. On the contrary: the programmer should let correctness proof and program grow hand in hand. 21 refs., 15 figs.

  2. Formal Specification and Analysis of Cloud Computing Management

    Science.gov (United States)

    2012-01-24

    VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law , no person shall be subject to a penalty for failing to...Mazza, for giving me the possibility to stay in beautiful Cardiff-by-the- Sea where parts of this thesis originated. vii Acknowledgements Anita...Computing in a Nutshell 5 2.1. What is Cloud Computing? . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2.2. Technical definition

  3. Formal Foundations for the Specification of Software Architecture.

    Science.gov (United States)

    1995-03-01

    booloso (orsbrieg oc-)) op sort: ho(S) -> seq(S) osioos (iomplies (and (orderiog a bXordoriog hoa)) definition of ortoord is ( equol a b)) axmose...booloon ( equol ohb)) op ordered oql(IS,eot(1) ->- holeer op ordered soq(et) ->- booleso ester (implies (sod (geq . b)(geq be) op sort: bog(( Seet

  4. AUTOMATIC SECURITY ANALYSIS OF INFORMATION SYSTEMS INDEPENDENTLY OF FORMAL SPECIFICATIONS

    National Research Council Canada - National Science Library

    D A Kavchuk; Y N Matveev

    2017-01-01

    .... The validation is carried out upon the live system in automatic mode, and system reaction to the attacking influences, performed with the Metasploit penetration testing platform, is observed. Method...

  5. Formal specification of a query expression generator using RSL ...

    African Journals Online (AJOL)

    We design a query generator to convert queries expressed in more user-friendly terms to terms (attributes) that change in line with the underlying database structures of an organisation. These latter terms are generated with the aid of a type structure defined over the database structures and perhaps may be optimised for ...

  6. On the formal specification of regulatory compliance : A comprehensive analysis

    NARCIS (Netherlands)

    El Gammal, A.; Turetken, O.; van den Heuvel, W.J.A.M.; Papazoglou, M.; Maglio, P.; Maximilien, E.M.; Rossi, G.; Yuan, S.-T.; Ludwig, H.; Fantinato, M.

    2011-01-01

    Today’s business environment demands a high rate of compliance of service-enabled business processes with which enterprises are required to cope. Thus, a comprehensive compliance management framework is required such that compliance management must crosscut all the stages of the complete business

  7. Prerequisites to Deriving Formal Specifications from Natural Language Requirements.

    Science.gov (United States)

    1981-10-01

    AFOSR-80-0190 9. PERFORMING ORGANIZATION NAME AND ADDRESS 10. PROGRAM ELEMENT. PROJEC7, TASK AREA A WORK UNIT NUMBERS Department of Computer...Watson Research Center, Yorktown Heights, MY, 1976. Wason , P. C. and P. N. Johnson-Laird. Psychology of Reasoning: Structure and Content, Cambridge

  8. Fusing Bayes Nets using Formal Argumentation in Multi-agent Systems

    DEFF Research Database (Denmark)

    Nielsen, Søren Holbech; Parsons, Simon

    2006-01-01

    We consider a multi-agent system where each agent is equipped with a Bayesian network, and present an open framework for the agents to compromise on a possible consensus network. The framework builds on formal argumentation, and unlike previous solutions on graphical consensus belief, it is suffi...

  9. Formal training in forensic mental health: psychiatry and psychology.

    Science.gov (United States)

    Sadoff, Robert L; Dattilio, Frank M

    2012-01-01

    The field of forensic mental health has grown exponentially in the past decades to include forensic psychiatrists and psychologists serving as the primary experts to the court systems. However, many colleagues have chosen to pursue the avenue of serving as forensic experts without obtaining formal training and experience. This article discusses the importance of formal education, training and experience for psychiatrists and psychologists working in forensic settings and the ethical implications that befall those who fail to obtain such credentials. Specific aspects of training and supervised experience are discussed in detail. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. Digital system verification a combined formal methods and simulation framework

    CERN Document Server

    Li, Lun

    2010-01-01

    Integrated circuit capacity follows Moore's law, and chips are commonly produced at the time of this writing with over 70 million gates per device. Ensuring correct functional behavior of such large designs before fabrication poses an extremely challenging problem. Formal verification validates the correctness of the implementation of a design with respect to its specification through mathematical proof techniques. Formal techniques have been emerging as commercialized EDA tools in the past decade. Simulation remains a predominantly used tool to validate a design in industry. After more than 5

  11. PRODUCTION SYSTEM MODELING AND SIMULATION USING DEVS FORMALISM

    Directory of Open Access Journals (Sweden)

    Darío Amaya Hurtado

    Full Text Available This article presents the Discrete Event System Specification (DEVS formalism, in their atomic and coupled configurations; it is used for discrete event systems modeling and simulation. Initially this work describes the analysis of discrete event systems concepts and its applicability. Then a comprehensive description of the DEVS formalism structure is presented, in order to model and simulate an industrial process, taking into account changes in parameters such as process service time, each station storage systems structure and process tasks coupling. For the MatLab® simulation, the Simevents Toolbox was used for theoretical developments validation.

  12. Season-specific climate signal and reconstruction from a new tree-ring network in the southwestern U.S

    Science.gov (United States)

    Griffin, D.; Woodhouse, C. A.; Meko, D. M.; Stahle, D. W.; Faulstich, H.; Leavitt, S. W.; Touchan, R.; Castro, C. L.; Carrillo, C.

    2011-12-01

    Our research group has updated existing tree-ring collections from over 50 sampling sites in the southwestern U.S. The new and archived specimens, carefully dated with dendrochronology, have been analyzed for width variations of "earlywood" and "latewood." These are the two components of annual rings in conifers that form in spring and summer, respectively. The network of primary tree-ring data has been used to develop a suite of well-replicated chronologies that extend through the 2008 growing season and are sensitive to the season-specific climate variability of the Southwest. Correlation function analysis indicates that the earlywood chronologies are closely related to cool season (October-April) precipitation variability and the chronologies derived from latewood are generally sensitive to precipitation and temperature conditions during the warm season (June-August). These proxy data originate from biological organisms and are not without bias; however, they do constitute a new means for evaluating the recent paleoclimatic history of the North American summer monsoon. The monsoon is a major component of the region's climate, impacting social and environmental systems and delivering up to 60% of the annual precipitation in the southwestern U.S. We have developed latewood-based retrodictions of monsoon precipitation that explain over half of the variance in the instrumental record, pass standard verification tests, and point to periods of persistent drought and wetness during the last 300-500 years. These reconstructions are being used to evaluate the monsoon's long-term spatiotemporal variability and its relationship to cool season climate and the major modes of ocean-atmosphere variability.

  13. Formal Analysis of Cognitive Agent Behavior: formal theoretical basis

    NARCIS (Netherlands)

    Sharpanskykh, A.; Treur, J.

    2006-01-01

    In cognitive systems the behavior of an actor (an agent) can be considered from both an external and an internal perspective. This paper contributes an automated procedure for translating a given external behavioral specification into an executable specification of internal dynamics, by which the

  14. Adapting Formal Education Materials for Out-of-School Settings

    Science.gov (United States)

    Smith, Denise A.; Gibbons, H.

    2006-12-01

    Out-of-school programs present significant opportunities to reinforce and extend classroom learning. How can we work effectively with these programs to engage youth in science and technology? What types of materials can be easily integrated into out-of-school learning experiences? How can existing formal education materials be adapted for use in out-of-school settings? To address these questions, the Space Telescope Science Institute and the Pacific Science Center have engaged in a project that builds on a network of informal science education centers and community-based organizations developed for a national outreach program associated with the NOVA/PBS Origins series. As part of this effort, the Pacific Science Center has held a focus group with local community-based organizations serving underserved and underrepresented youth, and engaged 20 sites in Washington, California, and Tennessee in testing formal education materials adapted for use in out-of-school settings. We report preliminary focus group and field-test results, including emerging best practices for adapting formal education materials for use in out-of-time settings. Results from this project will enable a variety of education and public outreach programs to extend the reach of their materials to new audiences in a way that bridges the formal and informal science education realms.

  15. JML- Based formal development of a Java card application for managing medical appointments

    OpenAIRE

    Rodrigues, Ricardo Miguel Soares

    2009-01-01

    Although formal methods can dramatically increase the quality of software systems, they have not widely been adopted in software industry. Many software companies have the perception that formal methods are not cost-effective cause they are plenty of mathematical symbols that are difficult for non-experts to assimilate. The Java Modelling Language (short for JML) Section 3.3 is an academic initiative towards the development of a common formal specification language for Java programs, and the ...

  16. Formal Description of Hybrid Systems

    DEFF Research Database (Denmark)

    Zhou, Chaochen; Ji, Wang; Ravn, Anders P.

    1996-01-01

    A language to describe hybrid systems, i.e. networks of communicating discrete and continuous processes, is proposed. A semantics of the language is given in Extended Duration Calculus, a real-time interval logic with a proof system that allows reasoning in mathematical analysis about continuous ...... processes to be embedded into the logic. The semantics thus provides a secure link to hybrid system models based on a general theory of dynamical systems.......A language to describe hybrid systems, i.e. networks of communicating discrete and continuous processes, is proposed. A semantics of the language is given in Extended Duration Calculus, a real-time interval logic with a proof system that allows reasoning in mathematical analysis about continuous...

  17. CNMO: Towards the Construction of a Communication Network Modelling Ontology

    Science.gov (United States)

    Rahman, Muhammad Azizur; Pakstas, Algirdas; Wang, Frank Zhigang

    Ontologies that explicitly identify objects, properties, and relationships in specific domains are essential for collaboration that involves sharing of data, knowledge or resources. A communications network modelling ontology (CNMO) has been designed to represent a network model as well as aspects related to its development and actual network operation. Network nodes/sites, link, traffic sources, protocols as well as aspects of the modeling/simulation scenario and operational aspects are defined with their formal representation. A CNMO may be beneficial for various network design/simulation/research communities due to the uniform representation of network models. This ontology is designed using terminology and concepts from various network modeling, simulation and topology generation tools.

  18. A survey of formal languages for contracts

    DEFF Research Database (Denmark)

    Hvitved, Tom

    2010-01-01

    In this short paper we present the current status on formal languages and models for contracts. By a formal model is meant an unambiguous and rigorous representation of contracts, in order to enable their automatic validation, execution, and analysis — activates that are collectively referred to ...... to as contract lifecycle management (CLM). We present a set of formalism requirements, which represent features that any ideal contract model should support, based on which we present a comparative survey of existing contract formalisms.......In this short paper we present the current status on formal languages and models for contracts. By a formal model is meant an unambiguous and rigorous representation of contracts, in order to enable their automatic validation, execution, and analysis — activates that are collectively referred...

  19. Universal formalism of Fano resonance

    Directory of Open Access Journals (Sweden)

    Liang Huang

    2015-01-01

    Full Text Available The phenomenon of Fano resonance is ubiquitous in a large variety of wave scattering systems, where the resonance profile is typically asymmetric. Whether the parameter characterizing the asymmetry should be complex or real is an issue of great experimental interest. Using coherent quantum transport as a paradigm and taking into account of the collective contribution from all available scattering channels, we derive a universal formula for the Fano-resonance profile. We show that our formula bridges naturally the traditional Fano formulas with complex and real asymmetry parameters, indicating that the two types of formulas are fundamentally equivalent (except for an offset. The connection also reveals a clear footprint for the conductance resonance during a dephasing process. Therefore, the emergence of complex asymmetric parameter when fitting with experimental data needs to be properly interpreted. Furthermore, we have provided a theory for the width of the resonance, which relates explicitly the width to the degree of localization of the close-by eigenstates and the corresponding coupling matrices or the self-energies caused by the leads. Our work not only resolves the issue about the nature of the asymmetry parameter, but also provides deeper physical insights into the origin of Fano resonance. Since the only assumption in our treatment is that the transport can be described by the Green’s function formalism, our results are also valid for broad disciplines including scattering problems of electromagnetic waves, acoustics, and seismology.

  20. Generalized Boltzmann formalism for oscillating neutrinos

    Science.gov (United States)

    Strack, P.; Burrows, A.

    2005-05-01

    In the standard approaches to neutrino transport in the simulation of core-collapse supernovas, one will often start from the classical Boltzmann equation for the neutrino’s spatial, temporal, and spectral evolution. For each neutrino species, and its antiparticle, the classical density in phase space, or the associated specific intensity, will be calculated as a function of time. The neutrino radiation is coupled to matter by source and sink terms on the “right-hand side” of the transport equation and together with the equations of hydrodynamics this set of coupled partial differential equations for classical densities describes, in principle, the evolution of core collapse and explosion. However, with the possibility of neutrino oscillations between species, a purely quantum-physical effect, how to generalize this set of Boltzmann equations for classical quantities to reflect oscillation physics has not been clear. To date, the formalisms developed have retained the character of quantum operator physics involving complex quantities and have not been suitable for easy incorporation into standard supernova codes. In this paper, we derive generalized Boltzmann equations for quasiclassical, real-valued phase-space densities that retain all the standard oscillation phenomenology, including the matter-enhanced resonant flavor conversion (Mikheev-Smirnov-Wolfenstein effect), neutrino self-interactions, and the interplay between decohering matter coupling and flavor oscillations. With this formalism, any code(s) that can now handle the solution of the classical Boltzmann or transport equation can easily be generalized to include neutrino oscillations in a quantum-physically consistent fashion.