WorldWideScience

Sample records for metabolic network architecture

  1. Signatures of arithmetic simplicity in metabolic network architecture.

    Directory of Open Access Journals (Sweden)

    William J Riehl

    2010-04-01

    Full Text Available Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their evolutionary history and complex wiring constitutes one of the most fascinating open questions in biology, intimately related to the enigma of life's origin itself. Is the evolution of metabolism subject to general principles, beyond the unpredictable accumulation of multiple historical accidents? Here we search for such principles by applying to an artificial chemical universe some of the methodologies developed for the study of genome scale models of cellular metabolism. In particular, we use metabolic flux constraint-based models to exhaustively search for artificial chemistry pathways that can optimally perform an array of elementary metabolic functions. Despite the simplicity of the model employed, we find that the ensuing pathways display a surprisingly rich set of properties, including the existence of autocatalytic cycles and hierarchical modules, the appearance of universally preferable metabolites and reactions, and a logarithmic trend of pathway length as a function of input/output molecule size. Some of these properties can be derived analytically, borrowing methods previously used in cryptography. In addition, by mapping biochemical networks onto a simplified carbon atom reaction backbone, we find that properties similar to those predicted for the artificial chemistry hold also for real metabolic networks. These findings suggest that optimality principles and arithmetic simplicity might lie beneath some aspects of biochemical complexity.

  2. The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture.

    Science.gov (United States)

    Caetano-Anollés, Gustavo; Kim, Hee Shin; Mittenthal, Jay E

    2007-05-29

    Metabolism represents a complex collection of enzymatic reactions and transport processes that convert metabolites into molecules capable of supporting cellular life. Here we explore the origins and evolution of modern metabolism. Using phylogenomic information linked to the structure of metabolic enzymes, we sort out recruitment processes and discover that most enzymatic activities were associated with the nine most ancient and widely distributed protein fold architectures. An analysis of newly discovered functions showed enzymatic diversification occurred early, during the onset of the modern protein world. Most importantly, phylogenetic reconstruction exercises and other evidence suggest strongly that metabolism originated in enzymes with the P-loop hydrolase fold in nucleotide metabolism, probably in pathways linked to the purine metabolic subnetwork. Consequently, the first enzymatic takeover of an ancient biochemistry or prebiotic chemistry was related to the synthesis of nucleotides for the RNA world.

  3. FTS2000 network architecture

    Science.gov (United States)

    Klenart, John

    1991-01-01

    The network architecture of FTS2000 is graphically depicted. A map of network A topology is provided, with interservice nodes. Next, the four basic element of the architecture is laid out. Then, the FTS2000 time line is reproduced. A list of equipment supporting FTS2000 dedicated transmissions is given. Finally, access alternatives are shown.

  4. VRML metabolic network visualizer.

    Science.gov (United States)

    Rojdestvenski, Igor

    2003-03-01

    A successful date collection visualization should satisfy a set of many requirements: unification of diverse data formats, support for serendipity research, support of hierarchical structures, algorithmizability, vast information density, Internet-readiness, and other. Recently, virtual reality has made significant progress in engineering, architectural design, entertainment and communication. We experiment with the possibility of using the immersive abstract three-dimensional visualizations of the metabolic networks. We present the trial Metabolic Network Visualizer software, which produces graphical representation of a metabolic network as a VRML world from a formal description written in a simple SGML-type scripting language.

  5. Cerebral energy metabolism and the brain's functional network architecture: an integrative review

    Science.gov (United States)

    Lord, Louis-David; Expert, Paul; Huckins, Jeremy F; Turkheimer, Federico E

    2013-01-01

    Recent functional magnetic resonance imaging (fMRI) studies have emphasized the contributions of synchronized activity in distributed brain networks to cognitive processes in both health and disease. The brain's ‘functional connectivity' is typically estimated from correlations in the activity time series of anatomically remote areas, and postulated to reflect information flow between neuronal populations. Although the topological properties of functional brain networks have been studied extensively, considerably less is known regarding the neurophysiological and biochemical factors underlying the temporal coordination of large neuronal ensembles. In this review, we highlight the critical contributions of high-frequency electrical oscillations in the γ-band (30 to 100 Hz) to the emergence of functional brain networks. After describing the neurobiological substrates of γ-band dynamics, we specifically discuss the elevated energy requirements of high-frequency neural oscillations, which represent a mechanistic link between the functional connectivity of brain regions and their respective metabolic demands. Experimental evidence is presented for the high oxygen and glucose consumption, and strong mitochondrial performance required to support rhythmic cortical activity in the γ-band. Finally, the implications of mitochondrial impairments and deficits in glucose metabolism for cognition and behavior are discussed in the context of neuropsychiatric and neurodegenerative syndromes characterized by large-scale changes in the organization of functional brain networks. PMID:23756687

  6. Heterogeneous network architectures

    DEFF Research Database (Denmark)

    Christiansen, Henrik Lehrmann

    2006-01-01

    and it is discussed that it is advantageous to heterogeneous networks and illustrated by a number of examples. Modeling and simulation is a well-known way of doing performance evaluation. An approach to event-driven simulation of communication networks is presented and mixed complexity modeling, which can simplify......Future networks will be heterogeneous! Due to the sheer size of networks (e.g., the Internet) upgrades cannot be instantaneous and thus heterogeneity appears. This means that instead of trying to find the olution, networks hould be designed as being heterogeneous. One of the key equirements here...... is flexibility. This thesis investigates such heterogeneous network architectures and how to make them flexible. A survey of algorithms for network design is presented, and it is described how using heuristics can increase the speed. A hierarchical, MPLS based network architecture is described...

  7. Mobile networks architecture

    CERN Document Server

    Perez, Andre

    2013-01-01

    This book explains the evolutions of architecture for mobiles and summarizes the different technologies:- 2G: the GSM (Global System for Mobile) network, the GPRS (General Packet Radio Service) network and the EDGE (Enhanced Data for Global Evolution) evolution;- 3G: the UMTS (Universal Mobile Telecommunications System) network and the HSPA (High Speed Packet Access) evolutions:- HSDPA (High Speed Downlink Packet Access),- HSUPA (High Speed Uplink Packet Access),- HSPA+;- 4G: the EPS (Evolved Packet System) network.The telephone service and data transmission are the

  8. Future Network Architectures

    DEFF Research Database (Denmark)

    Wessing, Henrik; Bozorgebrahimi, Kurosh; Belter, Bartosz

    2015-01-01

    This study identifies key requirements for NRENs towards future network architectures that become apparent as users become more mobile and have increased expectations in terms of availability of data. In addition, cost saving requirements call for federated use of, in particular, the optical...

  9. Quantifying loopy network architectures.

    Directory of Open Access Journals (Sweden)

    Eleni Katifori

    Full Text Available Biology presents many examples of planar distribution and structural networks having dense sets of closed loops. An archetype of this form of network organization is the vasculature of dicotyledonous leaves, which showcases a hierarchically-nested architecture containing closed loops at many different levels. Although a number of approaches have been proposed to measure aspects of the structure of such networks, a robust metric to quantify their hierarchical organization is still lacking. We present an algorithmic framework, the hierarchical loop decomposition, that allows mapping loopy networks to binary trees, preserving in the connectivity of the trees the architecture of the original graph. We apply this framework to investigate computer generated graphs, such as artificial models and optimal distribution networks, as well as natural graphs extracted from digitized images of dicotyledonous leaves and vasculature of rat cerebral neocortex. We calculate various metrics based on the asymmetry, the cumulative size distribution and the Strahler bifurcation ratios of the corresponding trees and discuss the relationship of these quantities to the architectural organization of the original graphs. This algorithmic framework decouples the geometric information (exact location of edges and nodes from the metric topology (connectivity and edge weight and it ultimately allows us to perform a quantitative statistical comparison between predictions of theoretical models and naturally occurring loopy graphs.

  10. Towards a networkArchitecture

    DEFF Research Database (Denmark)

    Rüdiger, Bjarne; Tournay, Bruno

    2001-01-01

    Planche, bidrag til DAL-konkurrencen. Hvor industrien har været inspirationen for udviklingen af den moderne arkitektur, er IT det tekniske og æstetiske grundlag for den spirende NetworkArchitecture. Computeren og netværker af computerne er således mere end en metafor for NetworkArchitecture....... NetworkArchitecture består af intelligente byggekomponenter forbundet med hinanden i et netværk og i interaktion med omgivelser....

  11. Airport Surface Network Architecture Definition

    Science.gov (United States)

    Nguyen, Thanh C.; Eddy, Wesley M.; Bretmersky, Steven C.; Lawas-Grodek, Fran; Ellis, Brenda L.

    2006-01-01

    Currently, airport surface communications are fragmented across multiple types of systems. These communication systems for airport operations at most airports today are based dedicated and separate architectures that cannot support system-wide interoperability and information sharing. The requirements placed upon the Communications, Navigation, and Surveillance (CNS) systems in airports are rapidly growing and integration is urgently needed if the future vision of the National Airspace System (NAS) and the Next Generation Air Transportation System (NGATS) 2025 concept are to be realized. To address this and other problems such as airport surface congestion, the Space Based Technologies Project s Surface ICNS Network Architecture team at NASA Glenn Research Center has assessed airport surface communications requirements, analyzed existing and future surface applications, and defined a set of architecture functions that will help design a scalable, reliable and flexible surface network architecture to meet the current and future needs of airport operations. This paper describes the systems approach or methodology to networking that was employed to assess airport surface communications requirements, analyze applications, and to define the surface network architecture functions as the building blocks or components of the network. The systems approach used for defining these functions is relatively new to networking. It is viewing the surface network, along with its environment (everything that the surface network interacts with or impacts), as a system. Associated with this system are sets of services that are offered by the network to the rest of the system. Therefore, the surface network is considered as part of the larger system (such as the NAS), with interactions and dependencies between the surface network and its users, applications, and devices. The surface network architecture includes components such as addressing/routing, network management, network

  12. Network architecture as internet governance

    Directory of Open Access Journals (Sweden)

    Francesca Musiani

    2013-10-01

    Full Text Available The architecture of a networked system is its underlying technical and logical structure, including transmission equipment, communication protocols, infrastructure, and connectivity between its components or nodes. This article introduces the idea of network architecture as internet governance, and more specifically, it outlines the dialectic between centralised and distributed architectures, institutions and practices, and how they mutually affect each other. The article argues that network architecture is internet governance in the sense that, by changing the design of the networks subtending internet-based services and the global internet itself, its politics are affected – the balance of rights between users and providers, the capacity of online communities to engage in open and direct interaction, the fair competition between actors of the internet market.

  13. Architecture in the network society

    DEFF Research Database (Denmark)

    2004-01-01

    Under the theme Architecture in the Network Society, participants were invited to focus on the dialog and sharing of knowledge between architects and other disciplines and to reflect on, and propose, new methods in the design process, to enhance and improve the impact of information technology on...... on architecture. This conference and the past history of eCAADe is an example on establishing a social network for the sharing of knowledge regarding the use of computers in architectural education and research.......Under the theme Architecture in the Network Society, participants were invited to focus on the dialog and sharing of knowledge between architects and other disciplines and to reflect on, and propose, new methods in the design process, to enhance and improve the impact of information technology...

  14. Network Analysis, Architecture, and Design

    CERN Document Server

    McCabe, James D

    2007-01-01

    Traditionally, networking has had little or no basis in analysis or architectural development, with designers relying on technologies they are most familiar with or being influenced by vendors or consultants. However, the landscape of networking has changed so that network services have now become one of the most important factors to the success of many third generation networks. It has become an important feature of the designer's job to define the problems that exist in his network, choose and analyze several optimization parameters during the analysis process, and then prioritize and evalua

  15. Network architecture for multimedia services

    Science.gov (United States)

    Hayes, John R.; Kerner, Martin

    1995-02-01

    Video on Demand is expected to be the first of many Video Dial Tone services that will bring broadband connections to residential customers. While significant research has been undertaken to identify cost effective access architectures, much less effort has been expended on video servers and backbone architectures, and it may be here that competitive advantage can be obtained. This paper focuses on the placement of key architectural elements within the network to show that a network topology which balances centralized and distributed storage of content minimizes backbone costs. Intuitively, storing copies of popular movies close to consumers reduces demand on the network, while centralizing titles reduces the amount of server resources required due to sharing and hence the cost of storage.

  16. Architecture and Robust Networks

    Science.gov (United States)

    2011-08-18

    layout, to wildfire ecologies , to biological signal transduction, stress response, metabolic control, and disease dynamics. The work is creating new...deal with homeostasis . Homeostasis is not the simple loss of signal variability but rather is the manifestation of working controls (heart rate... homeostasis , the role of physiology, and mechanistic interpretation of signals. In our framework, we propose to combine a black-box model (system ID) with

  17. Architecture in the network society

    DEFF Research Database (Denmark)

    2004-01-01

    Under the theme Architecture in the Network Society, participants were invited to focus on the dialog and sharing of knowledge between architects and other disciplines and to reflect on, and propose, new methods in the design process, to enhance and improve the impact of information technology...

  18. LINCS: Livermore's network architecture

    International Nuclear Information System (INIS)

    Fletcher, J.G.

    1982-01-01

    Octopus, a local computing network that has been evolving at the Lawrence Livermore National Laboratory for over fifteen years, is currently undergoing a major revision. The primary purpose of the revision is to consolidate and redefine the variety of conventions and formats, which have grown up over the years, into a single standard family of protocols, the Livermore Interactive Network Communication Standard (LINCS). This standard treats the entire network as a single distributed operating system such that access to a computing resource is obtained in a single way, whether that resource is local (on the same computer as the accessing process) or remote (on another computer). LINCS encompasses not only communication but also such issues as the relationship of customer to server processes and the structure, naming, and protection of resources. The discussion includes: an overview of the Livermore user community and computing hardware, the functions and structure of each of the seven layers of LINCS protocol, the reasons why we have designed our own protocols and why we are dissatisfied by the directions that current protocol standards are taking

  19. Uncovering transcriptional regulation of metabolism by using metabolic network topology

    DEFF Research Database (Denmark)

    Patil, Kiran Raosaheb; Nielsen, Jens

    2005-01-01

    therefore developed an algorithm that is based on hypothesis-driven data analysis to uncover the transcriptional regulatory architecture of metabolic networks. By using information on the metabolic network topology from genome-scale metabolic reconstruction, we show that it is possible to reveal patterns...... changes induced by complex regulatory mechanisms coordinating the activity of different metabolic pathways. It is difficult to map such global transcriptional responses by using traditional methods, because many genes in the metabolic network have relatively small changes at their transcription level. We...... in the metabolic network that follow a common transcriptional response. Thus, the algorithm enables identification of so-called reporter metabolites (metabolites around which the most significant transcriptional changes occur) and a set of connected genes with significant and coordinated response to genetic...

  20. Data Architecture for Sensor Network

    Directory of Open Access Journals (Sweden)

    Jan Ježek

    2012-03-01

    Full Text Available Fast development of hardware in recent years leads to the high availability of simple sensing devices at minimal cost. As a consequence, there is many of sensor networks nowadays. These networks can continuously produce a large amount of observed data including the location of measurement. Optimal data architecture for such propose is a challenging issue due to its large scale and spatio-temporal nature.  The aim of this paper is to describe data architecture that was used in a particular solution for storage of sensor data. This solution is based on relation data model – concretely PostgreSQL and PostGIS. We will mention out experience from real world projects focused on car monitoring and project targeted on agriculture sensor networks. We will also shortly demonstrate the possibilities of client side API and the potential of other open source libraries that can be used for cartographic visualization (e.g. GeoServer. The main objective is to describe the strength and weakness of usage of relation database system for such propose and to introduce also alternative approaches based on NoSQL concept.

  1. Sensor network architectures for monitoring underwater pipelines.

    Science.gov (United States)

    Mohamed, Nader; Jawhar, Imad; Al-Jaroodi, Jameela; Zhang, Liren

    2011-01-01

    This paper develops and compares different sensor network architecture designs that can be used for monitoring underwater pipeline infrastructures. These architectures are underwater wired sensor networks, underwater acoustic wireless sensor networks, RF (radio frequency) wireless sensor networks, integrated wired/acoustic wireless sensor networks, and integrated wired/RF wireless sensor networks. The paper also discusses the reliability challenges and enhancement approaches for these network architectures. The reliability evaluation, characteristics, advantages, and disadvantages among these architectures are discussed and compared. Three reliability factors are used for the discussion and comparison: the network connectivity, the continuity of power supply for the network, and the physical network security. In addition, the paper also develops and evaluates a hierarchical sensor network framework for underwater pipeline monitoring.

  2. The architectural design of networks of protein domain architectures.

    Science.gov (United States)

    Hsu, Chia-Hsin; Chen, Chien-Kuo; Hwang, Ming-Jing

    2013-08-23

    Protein domain architectures (PDAs), in which single domains are linked to form multiple-domain proteins, are a major molecular form used by evolution for the diversification of protein functions. However, the design principles of PDAs remain largely uninvestigated. In this study, we constructed networks to connect domain architectures that had grown out from the same single domain for every single domain in the Pfam-A database and found that there are three main distinctive types of these networks, which suggests that evolution can exploit PDAs in three different ways. Further analysis showed that these three different types of PDA networks are each adopted by different types of protein domains, although many networks exhibit the characteristics of more than one of the three types. Our results shed light on nature's blueprint for protein architecture and provide a framework for understanding architectural design from a network perspective.

  3. A COMPARATIVE STUDY OF SYSTEM NETWORK ARCHITECTURE Vs DIGITAL NETWORK ARCHITECTURE

    OpenAIRE

    Seema; Mukesh Arya

    2011-01-01

    The efficient managing system of sources is mandatory for the successful running of any network. Here this paper describes the most popular network architectures one of developed by IBM, System Network Architecture (SNA) and other is Digital Network Architecture (DNA). As we know that the network standards and protocols are needed for the network developers as well as users. Some standards are The IEEE 802.3 standards (The Institute of Electrical and Electronics Engineers 1980) (LAN), IBM Sta...

  4. Robustness of metabolic networks

    Science.gov (United States)

    Jeong, Hawoong

    2009-03-01

    We investigated the robustness of cellular metabolism by simulating the system-level computational models, and also performed the corresponding experiments to validate our predictions. We address the cellular robustness from the ``metabolite''-framework by using the novel concept of ``flux-sum,'' which is the sum of all incoming or outgoing fluxes (they are the same under the pseudo-steady state assumption). By estimating the changes of the flux-sum under various genetic and environmental perturbations, we were able to clearly decipher the metabolic robustness; the flux-sum around an essential metabolite does not change much under various perturbations. We also identified the list of the metabolites essential to cell survival, and then ``acclimator'' metabolites that can control the cell growth were discovered. Furthermore, this concept of ``metabolite essentiality'' should be useful in developing new metabolic engineering strategies for improved production of various bioproducts and designing new drugs that can fight against multi-antibiotic resistant superbacteria by knocking-down the enzyme activities around an essential metabolite. Finally, we combined a regulatory network with the metabolic network to investigate its effect on dynamic properties of cellular metabolism.

  5. Security Shift in Future Network Architectures

    NARCIS (Netherlands)

    Hartog, T.; Schotanus, H.A.; Verkoelen, C.A.A.

    2010-01-01

    In current practice military communication infrastructures are deployed as stand-alone networked information systems. Network-Enabled Capabilities (NEC) and combined military operations lead to new requirements which current communication architectures cannot deliver. This paper informs IT

  6. The NASA Space Communications Data Networking Architecture

    Science.gov (United States)

    Israel, David J.; Hooke, Adrian J.; Freeman, Kenneth; Rush, John J.

    2006-01-01

    The NASA Space Communications Architecture Working Group (SCAWG) has recently been developing an integrated agency-wide space communications architecture in order to provide the necessary communication and navigation capabilities to support NASA's new Exploration and Science Programs. A critical element of the space communications architecture is the end-to-end Data Networking Architecture, which must provide a wide range of services required for missions ranging from planetary rovers to human spaceflight, and from sub-orbital space to deep space. Requirements for a higher degree of user autonomy and interoperability between a variety of elements must be accommodated within an architecture that necessarily features minimum operational complexity. The architecture must also be scalable and evolvable to meet mission needs for the next 25 years. This paper will describe the recommended NASA Data Networking Architecture, present some of the rationale for the recommendations, and will illustrate an application of the architecture to example NASA missions.

  7. Tenet: An Architecture for Tiered Embedded Networks

    OpenAIRE

    Ramesh Govindan; Eddie Kohler; Deborah Estrin; Fang Bian; Krishna Chintalapudi; Om Gnawali; Sumit Rangwala; Ramakrishna Gummadi; Thanos Stathopoulos

    2005-01-01

    Future large-scale sensor network deployments will be tiered, with the motes providing dense sensing and a higher tier of 32-bit master nodes with more powerful radios providing increased overall network capacity. In this paper, we describe a functional architecture for wireless sensor networks that leverages this structure to simplify the overall system. Our Tenet architecture has the nice property that the mote-layer software is generic and reusable, and all application functionality reside...

  8. An architecture for human-network interfaces

    DEFF Research Database (Denmark)

    Sonnenwald, Diane H.

    1990-01-01

    Some of the issues (and their consequences) that arise when human-network interfaces (HNIs) are viewed from the perspective of people who use and develop them are examined. Target attributes of HNI architecture are presented. A high-level architecture model that supports the attributes is discussed...

  9. Feedforward Approximations to Dynamic Recurrent Network Architectures.

    Science.gov (United States)

    Muir, Dylan R

    2018-02-01

    Recurrent neural network architectures can have useful computational properties, with complex temporal dynamics and input-sensitive attractor states. However, evaluation of recurrent dynamic architectures requires solving systems of differential equations, and the number of evaluations required to determine their response to a given input can vary with the input or can be indeterminate altogether in the case of oscillations or instability. In feedforward networks, by contrast, only a single pass through the network is needed to determine the response to a given input. Modern machine learning systems are designed to operate efficiently on feedforward architectures. We hypothesized that two-layer feedforward architectures with simple, deterministic dynamics could approximate the responses of single-layer recurrent network architectures. By identifying the fixed-point responses of a given recurrent network, we trained two-layer networks to directly approximate the fixed-point response to a given input. These feedforward networks then embodied useful computations, including competitive interactions, information transformations, and noise rejection. Our approach was able to find useful approximations to recurrent networks, which can then be evaluated in linear and deterministic time complexity.

  10. An Architecture for SCADA Network Forensics

    Science.gov (United States)

    Kilpatrick, Tim; Gonzalez, Jesus; Chandia, Rodrigo; Papa, Mauricio; Shenoi, Sujeet

    Supervisory control and data acquisition (SCADA) systems are widely used in industrial control and automation. Modern SCADA protocols often employ TCP/IP to transport sensor data and control signals. Meanwhile, corporate IT infrastructures are interconnecting with previously isolated SCADA networks. The use of TCP/IP as a carrier protocol and the interconnection of IT and SCADA networks raise serious security issues. This paper describes an architecture for SCADA network forensics. In addition to supporting forensic investigations of SCADA network incidents, the architecture incorporates mechanisms for monitoring process behavior, analyzing trends and optimizing plant performance.

  11. Advancements in metro optical network architectures

    Science.gov (United States)

    Paraschis, Loukas

    2005-02-01

    This paper discusses the innovation in network architectures, and optical transport, that enables metropolitan networks to cost-effectively scale to hundreds Gb/s of capacity, and to hundreds km of reach, and to also meet the diverse service needs of enterprise and residential applications. A converged metro network, where Ethernet/IP services, and traditional TDM traffic operate over an intelligent WDM transport layer is increasingly becoming the most attractive architecture addressing the primary need of network operators for significantly improved capital and operational network cost. At the same time, this converged network has to leverage advanced technology, and introduce intelligence in order to significantly improve the deployment and manageability of WDM transport. The most important system advancements and the associated technology innovations that enhance the cost-effectiveness of metropolitan optical networks are being reviewed.

  12. The functional consequences of mutualistic network architecture.

    Directory of Open Access Journals (Sweden)

    José M Gómez

    Full Text Available The architecture and properties of many complex networks play a significant role in the functioning of the systems they describe. Recently, complex network theory has been applied to ecological entities, like food webs or mutualistic plant-animal interactions. Unfortunately, we still lack an accurate view of the relationship between the architecture and functioning of ecological networks. In this study we explore this link by building individual-based pollination networks from eight Erysimum mediohispanicum (Brassicaceae populations. In these individual-based networks, each individual plant in a population was considered a node, and was connected by means of undirected links to conspecifics sharing pollinators. The architecture of these unipartite networks was described by means of nestedness, connectivity and transitivity. Network functioning was estimated by quantifying the performance of the population described by each network as the number of per-capita juvenile plants produced per population. We found a consistent relationship between the topology of the networks and their functioning, since variation across populations in the average per-capita production of juvenile plants was positively and significantly related with network nestedness, connectivity and clustering. Subtle changes in the composition of diverse pollinator assemblages can drive major consequences for plant population performance and local persistence through modifications in the structure of the inter-plant pollination networks.

  13. Network interconnections: an architectural reference model

    NARCIS (Netherlands)

    Butscher, B.; Lenzini, L.; Morling, R.; Vissers, C.A.; Popescu-Zeletin, R.; van Sinderen, Marten J.; Heger, D.; Krueger, G.; Spaniol, O.; Zorn, W.

    1985-01-01

    One of the major problems in understanding the different approaches in interconnecting networks of different technologies is the lack of reference to a general model. The paper develops the rationales for a reference model of network interconnection and focuses on the architectural implications for

  14. implementation of internet protocol network architecture

    African Journals Online (AJOL)

    User

    ABSTRACT. Advances in multimedia technologies and development of overlay networks foster the opportu- nity for creating new value-added services over the current Internet. In this paper, a new service network architecture that supports multiparty multimedia conferencing applications, character- istics of which include ...

  15. Network architecture functional description and design

    Energy Technology Data Exchange (ETDEWEB)

    Stans, L.; Bencoe, M.; Brown, D.; Kelly, S.; Pierson, L.; Schaldach, C.

    1989-05-25

    This report provides a top level functional description and design for the development and implementation of the central network to support the next generation of SNL, Albuquerque supercomputer in a UNIX{reg sign} environment. It describes the network functions and provides an architecture and topology.

  16. Virtualized cognitive network architecture for 5G cellular networks

    KAUST Repository

    Elsawy, Hesham

    2015-07-17

    Cellular networks have preserved an application agnostic and base station (BS) centric architecture1 for decades. Network functionalities (e.g. user association) are decided and performed regardless of the underlying application (e.g. automation, tactile Internet, online gaming, multimedia). Such an ossified architecture imposes several hurdles against achieving the ambitious metrics of next generation cellular systems. This article first highlights the features and drawbacks of such architectural ossification. Then the article proposes a virtualized and cognitive network architecture, wherein network functionalities are implemented via software instances in the cloud, and the underlying architecture can adapt to the application of interest as well as to changes in channels and traffic conditions. The adaptation is done in terms of the network topology by manipulating connectivities and steering traffic via different paths, so as to attain the applications\\' requirements and network design objectives. The article presents cognitive strategies to implement some of the classical network functionalities, along with their related implementation challenges. The article further presents a case study illustrating the performance improvement of the proposed architecture as compared to conventional cellular networks, both in terms of outage probability and handover rate.

  17. Security Shift in Future Network Architectures

    OpenAIRE

    Hartog, T.; Schotanus, H.A.; Verkoelen, C.A.A.

    2010-01-01

    In current practice military communication infrastructures are deployed as stand-alone networked information systems. Network-Enabled Capabilities (NEC) and combined military operations lead to new requirements which current communication architectures cannot deliver. This paper informs IT architects, information architects and security specialists about the separation of network and information security, the consequences of this shift and our view on future communication infrastructures in d...

  18. Cognitive optical networks: architectures and techniques

    Science.gov (United States)

    Grebeshkov, Alexander Y.

    2017-04-01

    This article analyzes architectures and techniques of the optical networks with taking into account the cognitive methodology based on continuous cycle "Observe-Orient-Plan-Decide-Act-Learn" and the ability of the cognitive systems adjust itself through an adaptive process by responding to new changes in the environment. Cognitive optical network architecture includes cognitive control layer with knowledge base for control of software-configurable devices as reconfigurable optical add-drop multiplexers, flexible optical transceivers, software-defined receivers. Some techniques for cognitive optical networks as flexible-grid technology, broker-oriented technique, machine learning are examined. Software defined optical network and integration of wireless and optical networks with radio over fiber technique and fiber-wireless technique in the context of cognitive technologies are discussed.

  19. Stable architectures for deep neural networks

    Science.gov (United States)

    Haber, Eldad; Ruthotto, Lars

    2018-01-01

    Deep neural networks have become invaluable tools for supervised machine learning, e.g. classification of text or images. While often offering superior results over traditional techniques and successfully expressing complicated patterns in data, deep architectures are known to be challenging to design and train such that they generalize well to new data. Critical issues with deep architectures are numerical instabilities in derivative-based learning algorithms commonly called exploding or vanishing gradients. In this paper, we propose new forward propagation techniques inspired by systems of ordinary differential equations (ODE) that overcome this challenge and lead to well-posed learning problems for arbitrarily deep networks. The backbone of our approach is our interpretation of deep learning as a parameter estimation problem of nonlinear dynamical systems. Given this formulation, we analyze stability and well-posedness of deep learning and use this new understanding to develop new network architectures. We relate the exploding and vanishing gradient phenomenon to the stability of the discrete ODE and present several strategies for stabilizing deep learning for very deep networks. While our new architectures restrict the solution space, several numerical experiments show their competitiveness with state-of-the-art networks.

  20. Phylogeny of metabolic networks: A spectral graph theoretical ...

    Indian Academy of Sciences (India)

    The eigenvalues of this matrix reflect not only the global architecture of a network but also the local topologies that are produced by different graph evolutionary processes like motif duplication or joining. A divergence measure on spectral densities is used to quantify the distances between various metabolic networks, and a ...

  1. Evolution of metabolic network organization

    Directory of Open Access Journals (Sweden)

    Bonchev Danail

    2010-05-01

    Full Text Available Abstract Background Comparison of metabolic networks across species is a key to understanding how evolutionary pressures shape these networks. By selecting taxa representative of different lineages or lifestyles and using a comprehensive set of descriptors of the structure and complexity of their metabolic networks, one can highlight both qualitative and quantitative differences in the metabolic organization of species subject to distinct evolutionary paths or environmental constraints. Results We used a novel representation of metabolic networks, termed network of interacting pathways or NIP, to focus on the modular, high-level organization of the metabolic capabilities of the cell. Using machine learning techniques we identified the most relevant aspects of cellular organization that change under evolutionary pressures. We considered the transitions from prokarya to eukarya (with a focus on the transitions among the archaea, bacteria and eukarya, from unicellular to multicellular eukarya, from free living to host-associated bacteria, from anaerobic to aerobic, as well as the acquisition of cell motility or growth in an environment of various levels of salinity or temperature. Intuitively, we expect organisms with more complex lifestyles to have more complex and robust metabolic networks. Here we demonstrate for the first time that such organisms are not only characterized by larger, denser networks of metabolic pathways but also have more efficiently organized cross communications, as revealed by subtle changes in network topology. These changes are unevenly distributed among metabolic pathways, with specific categories of pathways being promoted to more central locations as an answer to environmental constraints. Conclusions Combining methods from graph theory and machine learning, we have shown here that evolutionary pressures not only affects gene and protein sequences, but also specific details of the complex wiring of functional modules

  2. A DRM Security Architecture for Home Networks

    NARCIS (Netherlands)

    Popescu, B.C.; Crispo, B.; Kamperman, F.L.A.J.; Tanenbaum, A.S.; Kiayias, A.; Yung, M.

    2004-01-01

    This paper describes a security architecture allowing digital rights management in home networks consisting of consumer electronic devices. The idea is to allow devices to establish dynamic groups, so called "Authorized Domains", where legally acquired copyrighted content can seamlessly move from

  3. Architecture of a Personal Network service layer

    NARCIS (Netherlands)

    Joosten, H.J.M.; Hartog, F.T.H. den; Selgert, F.

    2009-01-01

    We describe a basic service architecture that extends the currently dominant device-oriented approach of Personal Networks (PNs). It specifies functionality for runtime selection and execution of appropriate service components available in the PN, resulting in a highly dynamic, personalized, and

  4. An architectural model for network interconnection

    NARCIS (Netherlands)

    van Sinderen, Marten J.; Vissers, C.A.; Kalin, T.

    1983-01-01

    This paper presents a technique of successive decomposition of a common users' activity to illustrate the problems of network interconnection. The criteria derived from this approach offer a structuring principle which is used to develop an architectural model that embeds heterogeneous subnetworks

  5. A Layered Approach To Pacs Network Architecture

    Science.gov (United States)

    Hegde, Shankar S.; Prewitt, Judith M.

    1984-08-01

    Although the functions performed by the different nodes on the PACS network are many, it is possible to formulate a minimum set of service primitives such that the application software residing at the nodes can utilize those primitives to perform the functions. These primitives define the framework for the communication interface. The question of how these primitives fit into the concept of a layered network architecture is explored in this paper. The OSI model as applicable to the PACS network is described, the areas that need standardization are briefly mentioned, and the ongoing standardization efforts are addressed from the OSI perspective.

  6. An Evolutionary Optimization Framework for Neural Networks and Neuromorphic Architectures

    Energy Technology Data Exchange (ETDEWEB)

    Schuman, Catherine D [ORNL; Plank, James [University of Tennessee (UT); Disney, Adam [University of Tennessee (UT); Reynolds, John [University of Tennessee (UT)

    2016-01-01

    As new neural network and neuromorphic architectures are being developed, new training methods that operate within the constraints of the new architectures are required. Evolutionary optimization (EO) is a convenient training method for new architectures. In this work, we review a spiking neural network architecture and a neuromorphic architecture, and we describe an EO training framework for these architectures. We present the results of this training framework on four classification data sets and compare those results to other neural network and neuromorphic implementations. We also discuss how this EO framework may be extended to other architectures.

  7. The plasma automata network (PAN) architecture

    International Nuclear Information System (INIS)

    Cameron-Carey, C.M.

    1991-01-01

    Conventional neural networks consist of processing elements which are interconnected according to a specified topology. Typically, the number of processing elements and the interconnection topology are fixed. A neural network's information processing capability lies mainly in the variability of interconnection strengths, which directly influence activation patterns; these patterns represent entities and their interrelationships. Contrast this architecture, with its fixed topology and variable interconnection strengths, against one having dynamic topology and fixed connection strength. This paper reports on this proposed architecture in which there are no connections between processing elements. Instead, the processing elements form a plasma, exchanging information upon collision. A plasma can be populated with several different types of processing elements, each with their won activation function and self-modification mechanism. The activation patterns that are the plasma;s response to stimulation drive natural selection among processing elements which evolve to optimize performance

  8. Re-engineering Nascom's network management architecture

    Science.gov (United States)

    Drake, Brian C.; Messent, David

    1994-11-01

    The development of Nascom systems for ground communications began in 1958 with Project Vanguard. The low-speed systems (rates less than 9.6 Kbs) were developed following existing standards; but, there were no comparable standards for high-speed systems. As a result, these systems were developed using custom protocols and custom hardware. Technology has made enormous strides since the ground support systems were implemented. Standards for computer equipment, software, and high-speed communications exist and the performance of current workstations exceeds that of the mainframes used in the development of the ground systems. Nascom is in the process of upgrading its ground support systems and providing additional services. The Message Switching System (MSS), Communications Address Processor (CAP), and Multiplexer/Demultiplexer (MDM) Automated Control System (MACS) are all examples of Nascom systems developed using standards such as, X-windows, Motif, and Simple Network Management Protocol (SNMP). Also, the Earth Observing System (EOS) Communications (Ecom) project is stressing standards as an integral part of its network. The move towards standards has produced a reduction in development, maintenance, and interoperability costs, while providing operational quality improvement. The Facility and Resource Manager (FARM) project has been established to integrate the Nascom networks and systems into a common network management architecture. The maximization of standards and implementation of computer automation in the architecture will lead to continued cost reductions and increased operational efficiency. The first step has been to derive overall Nascom requirements and identify the functionality common to all the current management systems. The identification of these common functions will enable the reuse of processes in the management architecture and promote increased use of automation throughout the Nascom network. The MSS, CAP, MACS, and Ecom projects have indicated

  9. Re-engineering Nascom's network management architecture

    Science.gov (United States)

    Drake, Brian C.; Messent, David

    1994-01-01

    The development of Nascom systems for ground communications began in 1958 with Project Vanguard. The low-speed systems (rates less than 9.6 Kbs) were developed following existing standards; but, there were no comparable standards for high-speed systems. As a result, these systems were developed using custom protocols and custom hardware. Technology has made enormous strides since the ground support systems were implemented. Standards for computer equipment, software, and high-speed communications exist and the performance of current workstations exceeds that of the mainframes used in the development of the ground systems. Nascom is in the process of upgrading its ground support systems and providing additional services. The Message Switching System (MSS), Communications Address Processor (CAP), and Multiplexer/Demultiplexer (MDM) Automated Control System (MACS) are all examples of Nascom systems developed using standards such as, X-windows, Motif, and Simple Network Management Protocol (SNMP). Also, the Earth Observing System (EOS) Communications (Ecom) project is stressing standards as an integral part of its network. The move towards standards has produced a reduction in development, maintenance, and interoperability costs, while providing operational quality improvement. The Facility and Resource Manager (FARM) project has been established to integrate the Nascom networks and systems into a common network management architecture. The maximization of standards and implementation of computer automation in the architecture will lead to continued cost reductions and increased operational efficiency. The first step has been to derive overall Nascom requirements and identify the functionality common to all the current management systems. The identification of these common functions will enable the reuse of processes in the management architecture and promote increased use of automation throughout the Nascom network. The MSS, CAP, MACS, and Ecom projects have indicated

  10. NATO Human View Architecture and Human Networks

    Science.gov (United States)

    Handley, Holly A. H.; Houston, Nancy P.

    2010-01-01

    The NATO Human View is a system architectural viewpoint that focuses on the human as part of a system. Its purpose is to capture the human requirements and to inform on how the human impacts the system design. The viewpoint contains seven static models that include different aspects of the human element, such as roles, tasks, constraints, training and metrics. It also includes a Human Dynamics component to perform simulations of the human system under design. One of the static models, termed Human Networks, focuses on the human-to-human communication patterns that occur as a result of ad hoc or deliberate team formation, especially teams distributed across space and time. Parameters of human teams that effect system performance can be captured in this model. Human centered aspects of networks, such as differences in operational tempo (sense of urgency), priorities (common goal), and team history (knowledge of the other team members), can be incorporated. The information captured in the Human Network static model can then be included in the Human Dynamics component so that the impact of distributed teams is represented in the simulation. As the NATO militaries transform to a more networked force, the Human View architecture is an important tool that can be used to make recommendations on the proper mix of technological innovations and human interactions.

  11. The architecture of complex weighted networks

    Science.gov (United States)

    Barrat, A.; Barthélemy, M.; Pastor-Satorras, R.; Vespignani, A.

    2004-03-01

    Networked structures arise in a wide array of different contexts such as technological and transportation infrastructures, social phenomena, and biological systems. These highly interconnected systems have recently been the focus of a great deal of attention that has uncovered and characterized their topological complexity. Along with a complex topological structure, real networks display a large heterogeneity in the capacity and intensity of the connections. These features, however, have mainly not been considered in past studies where links are usually represented as binary states, i.e., either present or absent. Here, we study the scientific collaboration network and the world-wide air-transportation network, which are representative examples of social and large infrastructure systems, respectively. In both cases it is possible to assign to each edge of the graph a weight proportional to the intensity or capacity of the connections among the various elements of the network. We define appropriate metrics combining weighted and topological observables that enable us to characterize the complex statistical properties and heterogeneity of the actual strength of edges and vertices. This information allows us to investigate the correlations among weighted quantities and the underlying topological structure of the network. These results provide a better description of the hierarchies and organizational principles at the basis of the architecture of weighted networks.

  12. Scalable Architecture for Multihop Wireless ad Hoc Networks

    Science.gov (United States)

    Arabshahi, Payman; Gray, Andrew; Okino, Clayton; Yan, Tsun-Yee

    2004-01-01

    A scalable architecture for wireless digital data and voice communications via ad hoc networks has been proposed. Although the details of the architecture and of its implementation in hardware and software have yet to be developed, the broad outlines of the architecture are fairly clear: This architecture departs from current commercial wireless communication architectures, which are characterized by low effective bandwidth per user and are not well suited to low-cost, rapid scaling in large metropolitan areas. This architecture is inspired by a vision more akin to that of more than two dozen noncommercial community wireless networking organizations established by volunteers in North America and several European countries.

  13. Hybrid RRM Architecture for Future Wireless Networks

    DEFF Research Database (Denmark)

    Tragos, Elias; Mihovska, Albena D.; Mino, Emilio

    2007-01-01

    The concept of ubiquitous and scalable system is applied in the IST WINNER II [1] project to deliver optimum performance for different deployment scenarios from local area to wide area wireless networks. The integration of cellular and local area networks in a unique radio system will provide...... a great advantage to final users and operators, compared with the nowadays situation with many disconnected systems and users equipped with different subscriptions, radio interfaces and terminals. To this issue, the IST project WINNER II has defined three system modes suited to local, metropolitan...... and wide area respectively. The aim of this paper is twofold: first, it presents an architectural solution for scalable and hybrid radio resource management to efficiently integrate the different WINNER modes; second, it proposes a hybrid handover mechanism to exploit the availability of the different...

  14. Structural correlations in bacterial metabolic networks

    Directory of Open Access Journals (Sweden)

    Lizana Ludvig

    2011-01-01

    Full Text Available Abstract Background Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple primordial metabolism the organisms living today have evolved complex and highly variable metabolisms. We have studied this phenomenon by comparing the metabolic networks of 134 bacterial species with known phylogenetic relationships, and by studying a neutral model of metabolic network evolution. Results We consider the 'union-network' of 134 bacterial metabolisms, and also the union of two smaller subsets of closely related species. Each reaction-node is tagged with the number of organisms it belongs to, which we denote organism degree (OD, a key concept in our study. Network analysis shows that common reactions are found at the centre of the network and that the average OD decreases as we move to the periphery. Nodes of the same OD are also more likely to be connected to each other compared to a random OD relabelling based on their occurrence in the real data. This trend persists up to a distance of around five reactions. A simple growth model of metabolic networks is used to investigate the biochemical constraints put on metabolic-network evolution. Despite this seemingly drastic simplification, a 'union-network' of a collection of unrelated model networks, free of any selective pressure, still exhibit similar structural features as their bacterial counterpart. Conclusions The OD distribution quantifies topological properties of the evolutionary history of bacterial metabolic networks, and lends additional support to the importance of horizontal gene transfer during bacterial metabolic evolution where new reactions are attached at the periphery of the network. The neutral model of metabolic network growth can reproduce the main features of real networks, but we observe that the real networks contain a smaller common core, while they are more similar at the periphery

  15. Structural correlations in bacterial metabolic networks.

    Science.gov (United States)

    Bernhardsson, Sebastian; Gerlee, Philip; Lizana, Ludvig

    2011-01-20

    Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple primordial metabolism the organisms living today have evolved complex and highly variable metabolisms. We have studied this phenomenon by comparing the metabolic networks of 134 bacterial species with known phylogenetic relationships, and by studying a neutral model of metabolic network evolution. We consider the 'union-network' of 134 bacterial metabolisms, and also the union of two smaller subsets of closely related species. Each reaction-node is tagged with the number of organisms it belongs to, which we denote organism degree (OD), a key concept in our study. Network analysis shows that common reactions are found at the centre of the network and that the average OD decreases as we move to the periphery. Nodes of the same OD are also more likely to be connected to each other compared to a random OD relabelling based on their occurrence in the real data. This trend persists up to a distance of around five reactions. A simple growth model of metabolic networks is used to investigate the biochemical constraints put on metabolic-network evolution. Despite this seemingly drastic simplification, a 'union-network' of a collection of unrelated model networks, free of any selective pressure, still exhibit similar structural features as their bacterial counterpart. The OD distribution quantifies topological properties of the evolutionary history of bacterial metabolic networks, and lends additional support to the importance of horizontal gene transfer during bacterial metabolic evolution where new reactions are attached at the periphery of the network. The neutral model of metabolic network growth can reproduce the main features of real networks, but we observe that the real networks contain a smaller common core, while they are more similar at the periphery of the network. This suggests that natural selection and

  16. Underwater Sensor Networks: A New Energy Efficient and Robust Architecture

    NARCIS (Netherlands)

    Climent, Salvador; Capella, Juan Vincente; Meratnia, Nirvana; Serrano, Juan José

    2012-01-01

    The specific characteristics of underwater environments introduce new challenges for networking protocols. In this paper, a specialized architecture for underwater sensor networks (UWSNs) is proposed and evaluated. Experiments are conducted in order to analyze the suitability of this protocol for

  17. Establishment of a Spaceport Network Architecture

    Science.gov (United States)

    Larson, Wiley J.; Gill, Tracy R.; Mueller, Robert P.; Brink, Jeffrey S.

    2012-01-01

    Since the beginning of the space age, the main actors in space exploration have been governmental agencies, enabling a privileged access to space, but with very restricted and rare missions. The last decade has seen the rise of space tourism, and the founding of ambitious private space mining companies, showing the beginnings of a new exploration era, that is based on a more generalized and regular access to space and which is not limited to the Earth's vicinity. However, the cost of launching sufficient mass into orbit to sustain these inspiring challenges is prohibitive, and the necessary infrastructures to support these missions is still lacking. To provide easy and affordable access into orbital and deep space destinations, there is the need to create a network of spaceports via specific waypoint locations coupled with the use of natural resources, or In Situ Resource Utilization (ISRU), to provide a more economical solution. As part of the International Space University Space Studies Program 2012, the international and intercultural team of Operations and Service Infrastructure for Space (OASIS) proposes an interdisciplinary answer to the problem of economical space access and transportation. This paper presents a summary of a detailed report [1] of the different phases of a project for developing a network of spaceports throughout the Solar System in a timeframe of 50 years. The requirements, functions, critical technologies and mission architecture of this network of spaceports are outlined in a roadmap of the important steps and phases. The economic and financial aspects are emphasized in order to allow a sustainable development of the network in a public-private partnership via the formation of an International Spaceport Authority (ISPA). The approach includes engineering, scientific, financial, legal, policy, and societal aspects. Team OASIS intends to provide guidelines to make the development of space transportation via a spaceports logistics network

  18. MSAT signalling and network management architectures

    Science.gov (United States)

    Garland, Peter; Keelty, J. Malcolm

    1989-01-01

    Spar Aerospace has been active in the design and definition of Mobile Satellite Systems since the mid 1970's. In work sponsored by the Canadian Department of Communications, various payload configurations have evolved. In addressing the payload configuration, the requirements of the mobile user, the service provider and the satellite operator have always been the most important consideration. The current Spar 11 beam satellite design is reviewed, and its capabilities to provide flexibility and potential for network growth within the WARC87 allocations are explored. To enable the full capabilities of the payload to be realized, a large amount of ground based Switching and Network Management infrastructure will be required, when space segment becomes available. Early indications were that a single custom designed Demand Assignment Multiple Access (DAMA) switch should be implemented to provide efficient use of the space segment. As MSAT has evolved into a multiple service concept, supporting many service providers, this architecture should be reviewed. Some possible signalling and Network Management solutions are explored.

  19. Profiling metabolic networks to study cancer metabolism.

    Science.gov (United States)

    Hiller, Karsten; Metallo, Christian M

    2013-02-01

    Cancer is a disease of unregulated cell growth and survival, and tumors reprogram biochemical pathways to aid these processes. New capabilities in the computational and bioanalytical characterization of metabolism have now emerged, facilitating the identification of unique metabolic dependencies that arise in specific cancers. By understanding the metabolic phenotype of cancers as a function of their oncogenic profiles, metabolic engineering may be applied to design synthetically lethal therapies for some tumors. This process begins with accurate measurement of metabolic fluxes. Here we review advanced methods of quantifying pathway activity and highlight specific examples where these approaches have uncovered potential opportunities for therapeutic intervention. Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. The Architecture of Metabolism. Inventing a Culture of Resilience

    Directory of Open Access Journals (Sweden)

    Meike Schalk

    2014-06-01

    Full Text Available The Metabolist movement, with its radical and visionary urban and architectural schemes, drew the attention of an international architecture community to Japan in the 1960s and 1970s. Seen from a contemporary perspective, the movement’s foremost concern was cultural resilience as a notion of national identity. Metabolism responded to the human and environmental catastrophe that followed the atomic bombing of Japan and vulnerability to natural disasters such as earthquakes, with architecture envisioning the complete transformation of Japan as a system of political, social, and physical structures into resilient spatial and organizational patterns adaptable to change. Projecting a utopia of resilience, Metabolism employed biological metaphors and recalled technoscientific images which, together with the vernacular, evoked the notion of a genetic architecture able to be recreated again and again. A specific concern was to mediate between an urbanism of large, technical and institutional infrastructures and the freedom of the individual. My aim is to critically examine the notion of sustainable architecture by rereading Metabolist theories and products, such as terms, models, projects, and buildings. For a better understanding of the present discourse, this text searches for a possible history of sustainable architecture, a subject mostly presented ahistorically.

  1. A research on the application of software defined networking in satellite network architecture

    Science.gov (United States)

    Song, Huan; Chen, Jinqiang; Cao, Suzhi; Cui, Dandan; Li, Tong; Su, Yuxing

    2017-10-01

    Software defined network is a new type of network architecture, which decouples control plane and data plane of traditional network, has the feature of flexible configurations and is a direction of the next generation terrestrial Internet development. Satellite network is an important part of the space-ground integrated information network, while the traditional satellite network has the disadvantages of difficult network topology maintenance and slow configuration. The application of SDN technology in satellite network can solve these problems that traditional satellite network faces. At present, the research on the application of SDN technology in satellite network is still in the stage of preliminary study. In this paper, we start with introducing the SDN technology and satellite network architecture. Then we mainly introduce software defined satellite network architecture, as well as the comparison of different software defined satellite network architecture and satellite network virtualization. Finally, the present research status and development trend of SDN technology in satellite network are analyzed.

  2. Service-Oriented Radio Architecture: A Novel M2M Network Architecture for Cognitive Radio Systems

    OpenAIRE

    Dong, Xu; Wei, Shengqun; Li, Ying; Wang, Lifeng; Bai, Lin

    2012-01-01

    In future cognitive radio networks, a number of spectrum sensors can be distributedly deployed to monitor the surrounding wireless environment, where the machine-to-machine (M2M) technology is considered to provide the interactions among sensors, cognitive engines, and other system modules. Thus, a flexible M2M network architecture is desired to develop cognitive radio networks. As a distributed system framework, service-oriented architecture (SOA) has been well studied to provide the loose c...

  3. Advances in network systems architectures, security, and applications

    CERN Document Server

    Awad, Ali; Furtak, Janusz; Legierski, Jarosław

    2017-01-01

    This book provides the reader with a comprehensive selection of cutting–edge algorithms, technologies, and applications. The volume offers new insights into a range of fundamentally important topics in network architectures, network security, and network applications. It serves as a reference for researchers and practitioners by featuring research contributions exemplifying research done in the field of network systems. In addition, the book highlights several key topics in both theoretical and practical aspects of networking. These include wireless sensor networks, performance of TCP connections in mobile networks, photonic data transport networks, security policies, credentials management, data encryption for network transmission, risk management, live TV services, and multicore energy harvesting in distributed systems. .

  4. Space Mobile Network: A Near Earth Communication and Navigation Architecture

    Science.gov (United States)

    Israel, Dave J.; Heckler, Greg; Menrad, Robert J.

    2016-01-01

    This paper describes a Space Mobile Network architecture, the result of a recently completed NASA study exploring architectural concepts to produce a vision for the future Near Earth communications and navigation systems. The Space Mobile Network (SMN) incorporates technologies, such as Disruption Tolerant Networking (DTN) and optical communications, and new operations concepts, such as User Initiated Services, to provide user services analogous to a terrestrial smartphone user. The paper will describe the SMN Architecture, envisioned future operations concepts, opportunities for industry and international collaboration and interoperability, and technology development areas and goals.

  5. Stability from Structure : Metabolic Networks Are Unlike Other Biological Networks

    NARCIS (Netherlands)

    Van Nes, P.; Bellomo, D.; Reinders, M.J.T.; De Ridder, D.

    2009-01-01

    In recent work, attempts have been made to link the structure of biochemical networks to their complex dynamics. It was shown that structurally stable network motifs are enriched in such networks. In this work, we investigate to what extent these findings apply to metabolic networks. To this end, we

  6. Security Aspects of an Enterprise-Wide Network Architecture.

    Science.gov (United States)

    Loew, Robert; Stengel, Ingo; Bleimann, Udo; McDonald, Aidan

    1999-01-01

    Presents an overview of two projects that concern local area networks and the common point between networks as they relate to network security. Discusses security architectures based on firewall components, packet filters, application gateways, security-management components, an intranet solution, user registration by Web form, and requests for…

  7. A Reference Architecture for Network-Centric Information Systems

    National Research Council Canada - National Science Library

    Renner, Scott; Schaefer, Ronald

    2003-01-01

    This paper presents the "C2 Enterprise Reference Architecture" (C2ERA), which is a new technical concept of operations for building information systems better suited to the Network-Centric Warfare (NCW) environment...

  8. Architectures of electro-optical packet switched networks

    DEFF Research Database (Denmark)

    Berger, Michael Stubert

    2004-01-01

    This thesis focuses on network- andn ode architectuers for electrical and optical packet switched networks. Future packet switched networks could evolve towards many small, distributed units or towards fewer large, centralised switch units. This work assumes the latter evolution scenario and exam......This thesis focuses on network- andn ode architectuers for electrical and optical packet switched networks. Future packet switched networks could evolve towards many small, distributed units or towards fewer large, centralised switch units. This work assumes the latter evolution scenario...... from optics and electronics. An overview of the DAVID network architecture is given, focusing on the MAN and WAN architecture as well as the MPLS based network hierarchy. A statistical model of the optical slot generation process is presented and utilised to evaluate delay vs. efficiency. Furthermore...

  9. Designing Networked Energy Infrastructures with Architectural Flexibility

    NARCIS (Netherlands)

    Melese, Y.G.; Heijnen, P.W.; Stikkelman, R.M.

    2014-01-01

    Development of networked energy infrastructures (like gas pipe networks), generally requires a significant amount of capital investment under resources, market and institutional uncertainties. Several independent suppliers and consumers are to be connected into these networks. However, the actual

  10. Comparing the Complexity of Two Network Architectures

    Directory of Open Access Journals (Sweden)

    Olivier Z. Zheng

    2017-10-01

    Full Text Available A Service Provider has different methods to provide a VPN service to its customers. But which method is the least complex to implement? In this paper, two architectures are described and analysed. Based on the analyses, two methods of complexity calculation are designed to evaluate the complexity of the architecture: the first method evaluates the resources consumed, the second evaluates the number of cases possible.

  11. Seed architecture shapes embryo metabolism in oilseed rape.

    Science.gov (United States)

    Borisjuk, Ljudmilla; Neuberger, Thomas; Schwender, Jörg; Heinzel, Nicolas; Sunderhaus, Stephanie; Fuchs, Johannes; Hay, Jordan O; Tschiersch, Henning; Braun, Hans-Peter; Denolf, Peter; Lambert, Bart; Jakob, Peter M; Rolletschek, Hardy

    2013-05-01

    Constrained to develop within the seed, the plant embryo must adapt its shape and size to fit the space available. Here, we demonstrate how this adjustment shapes metabolism of photosynthetic embryo. Noninvasive NMR-based imaging of the developing oilseed rape (Brassica napus) seed illustrates that, following embryo bending, gradients in lipid concentration became established. These were correlated with the local photosynthetic electron transport rate and the accumulation of storage products. Experimentally induced changes in embryo morphology and/or light supply altered these gradients and were accompanied by alterations in both proteome and metabolome. Tissue-specific metabolic models predicted that the outer cotyledon and hypocotyl/radicle generate the bulk of plastidic reductant/ATP via photosynthesis, while the inner cotyledon, being enclosed by the outer cotyledon, is forced to grow essentially heterotrophically. Under field-relevant high-light conditions, major contribution of the ribulose-1,5-bisphosphate carboxylase/oxygenase-bypass to seed storage metabolism is predicted for the outer cotyledon and the hypocotyl/radicle only. Differences between in vitro- versus in planta-grown embryos suggest that metabolic heterogeneity of embryo is not observable by in vitro approaches. We conclude that in vivo metabolic fluxes are locally regulated and connected to seed architecture, driving the embryo toward an efficient use of available light and space.

  12. DAPNA: an architectural framework for data processing networks

    NARCIS (Netherlands)

    Sözer, Hasan; Nouta, Sander; Wombacher, Andreas; Perona, Paolo

    2013-01-01

    A data processing network is as a set of (software) components connected through communication channels to apply a series of operations on data. Realization and maintenance of large-scale data processing networks necessitate an architectural approach that supports analysis, verification,

  13. Architecture for Cognitive Networking within NASAs Future Space Communications Infrastructure

    Science.gov (United States)

    Clark, Gilbert J., III; Eddy, Wesley M.; Johnson, Sandra K.; Barnes, James; Brooks, David

    2016-01-01

    Future space mission concepts and designs pose many networking challenges for command, telemetry, and science data applications with diverse end-to-end data delivery needs. For future end-to-end architecture designs, a key challenge is meeting expected application quality of service requirements for multiple simultaneous mission data flows with options to use diverse onboard local data buses, commercial ground networks, and multiple satellite relay constellations in LEO, MEO, GEO, or even deep space relay links. Effectively utilizing a complex network topology requires orchestration and direction that spans the many discrete, individually addressable computer systems, which cause them to act in concert to achieve the overall network goals. The system must be intelligent enough to not only function under nominal conditions, but also adapt to unexpected situations, and reorganize or adapt to perform roles not originally intended for the system or explicitly programmed. This paper describes architecture features of cognitive networking within the future NASA space communications infrastructure, and interacting with the legacy systems and infrastructure in the meantime. The paper begins by discussing the need for increased automation, including inter-system collaboration. This discussion motivates the features of an architecture including cognitive networking for future missions and relays, interoperating with both existing endpoint-based networking models and emerging information-centric models. From this basis, we discuss progress on a proof-of-concept implementation of this architecture as a cognitive networking on-orbit application on the SCaN Testbed attached to the International Space Station.

  14. Architecture for Cognitive Networking within NASA's Future Space Communications Infrastructure

    Science.gov (United States)

    Clark, Gilbert; Eddy, Wesley M.; Johnson, Sandra K.; Barnes, James; Brooks, David

    2016-01-01

    Future space mission concepts and designs pose many networking challenges for command, telemetry, and science data applications with diverse end-to-end data delivery needs. For future end-to-end architecture designs, a key challenge is meeting expected application quality of service requirements for multiple simultaneous mission data flows with options to use diverse onboard local data buses, commercial ground networks, and multiple satellite relay constellations in LEO, GEO, MEO, or even deep space relay links. Effectively utilizing a complex network topology requires orchestration and direction that spans the many discrete, individually addressable computer systems, which cause them to act in concert to achieve the overall network goals. The system must be intelligent enough to not only function under nominal conditions, but also adapt to unexpected situations, and reorganize or adapt to perform roles not originally intended for the system or explicitly programmed. This paper describes an architecture enabling the development and deployment of cognitive networking capabilities into the envisioned future NASA space communications infrastructure. We begin by discussing the need for increased automation, including inter-system discovery and collaboration. This discussion frames the requirements for an architecture supporting cognitive networking for future missions and relays, including both existing endpoint-based networking models and emerging information-centric models. From this basis, we discuss progress on a proof-of-concept implementation of this architecture, and results of implementation and initial testing of a cognitive networking on-orbit application on the SCaN Testbed attached to the International Space Station.

  15. Optimizing Neural Network Architectures Using Generalization Error Estimators

    DEFF Research Database (Denmark)

    Larsen, Jan

    1994-01-01

    This paper addresses the optimization of neural network architectures. It is suggested to optimize the architecture by selecting the model with minimal estimated averaged generalization error. We consider a least-squares (LS) criterion for estimating neural network models, i.e., the associated...... neural network applications, it is impossible to suggest a perfect model, and consequently the ability to handle incomplete models is urgent. A concise derivation of the GEN-estimator is provided, and its qualities are demonstrated by comparative numerical studies...

  16. A network perspective on metabolic inconsistency

    Directory of Open Access Journals (Sweden)

    Sonnenschein Nikolaus

    2012-05-01

    Full Text Available Abstract Background Integrating gene expression profiles and metabolic pathways under different experimental conditions is essential for understanding the coherence of these two layers of cellular organization. The network character of metabolic systems can be instrumental in developing concepts of agreement between expression data and pathways. A network-driven interpretation of gene expression data has the potential of suggesting novel classifiers for pathological cellular states and of contributing to a general theoretical understanding of gene regulation. Results Here, we analyze the coherence of gene expression patterns and a reconstruction of human metabolism, using consistency scores obtained from network and constraint-based analysis methods. We find a surprisingly strong correlation between the two measures, demonstrating that a substantial part of inconsistencies between metabolic processes and gene expression can be understood from a network perspective alone. Prompted by this finding, we investigate the topological context of the individual biochemical reactions responsible for the observed inconsistencies. On this basis, we are able to separate the differential contributions that bear physiological information about the system, from the unspecific contributions that unravel gaps in the metabolic reconstruction. We demonstrate the biological potential of our network-driven approach by analyzing transcriptome profiles of aldosterone producing adenomas that have been obtained from a cohort of Primary Aldosteronism patients. We unravel systematics in the data that could not have been resolved by conventional microarray data analysis. In particular, we discover two distinct metabolic states in the adenoma expression patterns. Conclusions The methodology presented here can help understand metabolic inconsistencies from a network perspective. It thus serves as a mediator between the topology of metabolic systems and their dynamical

  17. Optimum Neural Network Architecture for Precipitation Prediction of Myanmar

    OpenAIRE

    Khaing Win Mar; Thinn Thu Naing

    2008-01-01

    Nowadays, precipitation prediction is required for proper planning and management of water resources. Prediction with neural network models has received increasing interest in various research and application domains. However, it is difficult to determine the best neural network architecture for prediction since it is not immediately obvious how many input or hidden nodes are used in the model. In this paper, neural network model is used as a forecasting tool. The major aim is to evaluate a s...

  18. Efficient VLSI Architecture for Training Radial Basis Function Networks

    Science.gov (United States)

    Fan, Zhe-Cheng; Hwang, Wen-Jyi

    2013-01-01

    This paper presents a novel VLSI architecture for the training of radial basis function (RBF) networks. The architecture contains the circuits for fuzzy C-means (FCM) and the recursive Least Mean Square (LMS) operations. The FCM circuit is designed for the training of centers in the hidden layer of the RBF network. The recursive LMS circuit is adopted for the training of connecting weights in the output layer. The architecture is implemented by the field programmable gate array (FPGA). It is used as a hardware accelerator in a system on programmable chip (SOPC) for real-time training and classification. Experimental results reveal that the proposed RBF architecture is an effective alternative for applications where fast and efficient RBF training is desired. PMID:23519346

  19. Operational Concepts for a Generic Space Exploration Communication Network Architecture

    Science.gov (United States)

    Ivancic, William D.; Vaden, Karl R.; Jones, Robert E.; Roberts, Anthony M.

    2015-01-01

    This document is one of three. It describes the Operational Concept (OpsCon) for a generic space exploration communication architecture. The purpose of this particular document is to identify communication flows and data types. Two other documents accompany this document, a security policy profile and a communication architecture document. The operational concepts should be read first followed by the security policy profile and then the architecture document. The overall goal is to design a generic space exploration communication network architecture that is affordable, deployable, maintainable, securable, evolvable, reliable, and adaptable. The architecture should also require limited reconfiguration throughout system development and deployment. System deployment includes: subsystem development in a factory setting, system integration in a laboratory setting, launch preparation, launch, and deployment and operation in space.

  20. Security Policy for a Generic Space Exploration Communication Network Architecture

    Science.gov (United States)

    Ivancic, William D.; Sheehe, Charles J.; Vaden, Karl R.

    2016-01-01

    This document is one of three. It describes various security mechanisms and a security policy profile for a generic space-based communication architecture. Two other documents accompany this document- an Operations Concept (OpsCon) and a communication architecture document. The OpsCon should be read first followed by the security policy profile described by this document and then the architecture document. The overall goal is to design a generic space exploration communication network architecture that is affordable, deployable, maintainable, securable, evolvable, reliable, and adaptable. The architecture should also require limited reconfiguration throughout system development and deployment. System deployment includes subsystem development in a factory setting, system integration in a laboratory setting, launch preparation, launch, and deployment and operation in space.

  1. The Hi-Ring architecture for datacentre networks

    DEFF Research Database (Denmark)

    Galili, Michael; Kamchevska, Valerija; Ding, Yunhong

    2016-01-01

    This paper summarizes recent work on a hierarchical ring-based network architecture (Hi-Ring) for datacentre and short-range applications. The architecture allows leveraging benefits of optical switching technologies while maintaining a high level of connection granularity. We discuss results...... of optical switching in the various physical dimensions incorporated in the hierarchical nodes and we discuss recent results on global synchronisation of nodes in a ring topology....

  2. Hierarchical analysis of dependency in metabolic networks.

    Science.gov (United States)

    Gagneur, Julien; Jackson, David B; Casari, Georg

    2003-05-22

    Elucidation of metabolic networks for an increasing number of organisms reveals that even small networks can contain thousands of reactions and chemical species. The intimate connectivity between components complicates their decomposition into biologically meaningful sub-networks. Moreover, traditional higher-order representations of metabolic networks as metabolic pathways, suffers from the lack of rigorous definition, yielding pathways of disparate content and size. We introduce a hierarchical representation that emphasizes the gross organization of metabolic networks in largely independent pathways and sub-systems at several levels of independence. The approach highlights the coupling of different pathways and the shared compounds responsible for those couplings. By assessing our results on Escherichia coli (E.coli metabolic reactions, Genetic Circuits Research Group, University of California, San Diego, http://gcrg.ucsd.edu/organisms/ecoli.html, 'model v 1.01. reactions') against accepted biochemical annotations, we provide the first systematic synopsis of an organism's metabolism. Comparison with operons of E.coli shows that low-level clusters are reflected in genome organization and gene regulation. Source code, data sets and supplementary information are available at http://www.mas.ecp.fr/labo/equipe/gagneur/hierarchy/hierarchy.html

  3. IDHOCNET: A Novel ID Centric Architecture for Ad Hoc Networks

    Directory of Open Access Journals (Sweden)

    Shahrukh Khalid

    2016-01-01

    Full Text Available Ad hoc networks lack support of infrastructure and operate in a shared bandwidth wireless environment. Presently, such networks have been realized by various adaptations in Internet Protocol (IP architecture which was developed for infrastructure oriented hierarchical networks. The IP architecture has its known problem and issues even in infrastructure settings, like IP address overloading, mobility, multihoming, and so forth. Therefore, when such architecture is implemented in ad hoc scenario the problems get multiplied. Due to this fact, ad hoc networks suffer from additional problems like IP address autoconfiguration, service provisioning, efficient bandwidth utilization, and node identification. In this paper we present IDHOCNET which is a novel implementation of service provisioning and application development framework in the ad hoc context. We illustrate a number of implemented features of the architecture which include IP address autoconfiguration, identification of nodes by using real world identifiers, IP based services support in ad hoc networks, and a new class of application known as ID based application. Moreover how identifiers can completely replace the IP addresses to run the IP based applications is shown. It is expected that this work will open new research horizons and paradigms for ad hoc networks.

  4. Architectural transformations in network services and distributed systems

    CERN Document Server

    Luntovskyy, Andriy

    2017-01-01

    With the given work we decided to help not only the readers but ourselves, as the professionals who actively involved in the networking branch, with understanding the trends that have developed in recent two decades in distributed systems and networks. Important architecture transformations of distributed systems have been examined. The examples of new architectural solutions are discussed. Content Periodization of service development Energy efficiency Architectural transformations in Distributed Systems Clustering and Parallel Computing, performance models Cloud Computing, RAICs, Virtualization, SDN Smart Grid, Internet of Things, Fog Computing Mobile Communication from LTE to 5G, DIDO, SAT-based systems Data Security Guaranteeing Distributed Systems Target Groups Students in EE and IT of universities and (dual) technical high schools Graduated engineers as well as teaching staff About the Authors Andriy Luntovskyy provides classes on networks, mobile communication, software technology, distributed systems, ...

  5. Power, Avionics and Software Communication Network Architecture

    Science.gov (United States)

    Ivancic, William D.; Sands, Obed S.; Bakula, Casey J.; Oldham, Daniel R.; Wright, Ted; Bradish, Martin A.; Klebau, Joseph M.

    2014-01-01

    This document describes the communication architecture for the Power, Avionics and Software (PAS) 2.0 subsystem for the Advanced Extravehicular Mobile Unit (AEMU). The following systems are described in detail: Caution Warn- ing and Control System, Informatics, Storage, Video, Audio, Communication, and Monitoring Test and Validation. This document also provides some background as well as the purpose and goals of the PAS project at Glenn Research Center (GRC).

  6. Design Guidelines for New Generation Network Architecture

    Science.gov (United States)

    Harai, Hiroaki; Fujikawa, Kenji; Kafle, Ved P.; Miyazawa, Takaya; Murata, Masayuki; Ohnishi, Masaaki; Ohta, Masataka; Umezawa, Takeshi

    Limitations are found in the recent Internet because a lot of functions and protocols are patched to the original suite of layered protocols without considering global optimization. This reveals that end-to-end argument in the original Internet was neither sufficient for the current societal network and nor for a sustainable network of the future. In this position paper, we present design guidelines for a future network, which we call the New Generation Network, which provides the inclusion of diverse human requirements, reliable connection between the real-world and virtual network space, and promotion of social potentiality for human emergence. The guidelines consist of the crystal synthesis, the reality connection, and the sustainable & evolutional guidelines.

  7. Robust quantum network architectures and topologies for entanglement distribution

    Science.gov (United States)

    Das, Siddhartha; Khatri, Sumeet; Dowling, Jonathan P.

    2018-01-01

    Entanglement distribution is a prerequisite for several important quantum information processing and computing tasks, such as quantum teleportation, quantum key distribution, and distributed quantum computing. In this work, we focus on two-dimensional quantum networks based on optical quantum technologies using dual-rail photonic qubits for the building of a fail-safe quantum internet. We lay out a quantum network architecture for entanglement distribution between distant parties using a Bravais lattice topology, with the technological constraint that quantum repeaters equipped with quantum memories are not easily accessible. We provide a robust protocol for simultaneous entanglement distribution between two distant groups of parties on this network. We also discuss a memory-based quantum network architecture that can be implemented on networks with an arbitrary topology. We examine networks with bow-tie lattice and Archimedean lattice topologies and use percolation theory to quantify the robustness of the networks. In particular, we provide figures of merit on the loss parameter of the optical medium that depend only on the topology of the network and quantify the robustness of the network against intermittent photon loss and intermittent failure of nodes. These figures of merit can be used to compare the robustness of different network topologies in order to determine the best topology in a given real-world scenario, which is critical in the realization of the quantum internet.

  8. Optimal flux patterns in cellular metabolic networks

    Energy Technology Data Exchange (ETDEWEB)

    Almaas, E

    2007-01-20

    The availability of whole-cell level metabolic networks of high quality has made it possible to develop a predictive understanding of bacterial metabolism. Using the optimization framework of flux balance analysis, I investigate metabolic response and activity patterns to variations in the availability of nutrient and chemical factors such as oxygen and ammonia by simulating 30,000 random cellular environments. The distribution of reaction fluxes is heavy-tailed for the bacteria H. pylori and E. coli, and the eukaryote S. cerevisiae. While the majority of flux balance investigations have relied on implementations of the simplex method, it is necessary to use interior-point optimization algorithms to adequately characterize the full range of activity patterns on metabolic networks. The interior-point activity pattern is bimodal for E. coli and S. cerevisiae, suggesting that most metabolic reaction are either in frequent use or are rarely active. The trimodal activity pattern of H. pylori indicates that a group of its metabolic reactions (20%) are active in approximately half of the simulated environments. Constructing the high-flux backbone of the network for every environment, there is a clear trend that the more frequently a reaction is active, the more likely it is a part of the backbone. Finally, I briefly discuss the predicted activity patterns of the central-carbon metabolic pathways for the sample of random environments.

  9. Public Safety Broadband Network Architecture Description

    Science.gov (United States)

    2013-08-01

    Principal Author Jack Pagotto Section Head, Multi-Agency Crisis Management S&T DRDC Centre for Security Science Approved by Dr...MHz band. It aligns with the governance model as currently endorsed by the senior officials responsible for emergency management in Canada (SOREM...intervenants, et de s’adapter de manière dynamique aux changements de situation.2 Le présent document décrit l’architecture d’un réseau de communication

  10. Architecture Analysis of an FPGA-Based Hopfield Neural Network

    Directory of Open Access Journals (Sweden)

    Miguel Angelo de Abreu de Sousa

    2014-01-01

    Full Text Available Interconnections between electronic circuits and neural computation have been a strongly researched topic in the machine learning field in order to approach several practical requirements, including decreasing training and operation times in high performance applications and reducing cost, size, and energy consumption for autonomous or embedded developments. Field programmable gate array (FPGA hardware shows some inherent features typically associated with neural networks, such as, parallel processing, modular executions, and dynamic adaptation, and works on different types of FPGA-based neural networks were presented in recent years. This paper aims to address different aspects of architectural characteristics analysis on a Hopfield Neural Network implemented in FPGA, such as maximum operating frequency and chip-area occupancy according to the network capacity. Also, the FPGA implementation methodology, which does not employ multipliers in the architecture developed for the Hopfield neural model, is presented, in detail.

  11. Greening radio access networks using distributed base station architectures

    DEFF Research Database (Denmark)

    Kardaras, Georgios; Soler, José; Dittmann, Lars

    2010-01-01

    energy saving. Different subsystems have to be coordinated real-time and intelligent network nodes supporting complicated functionalities are necessary. Distributed base station architectures are ideal for this purpose mainly because of their high degree of configurability and self......Several actions for developing environmentally friendly technologies have been taken in most industrial fields. Significant resources have also been devoted in mobile communications industry. Moving towards eco-friendly alternatives is primarily a social responsibility for network operators....... However besides this, increasing energy efficiency represents a key factor for reducing operating expenses and deploying cost effective mobile networks. This paper presents how distributed base station architectures can contribute in greening radio access networks. More specifically, the advantages...

  12. SYS6: Tenet: An Architecture for Tiered Embedded Networks

    OpenAIRE

    Krishna Chintalapudi; Deborah Estrin; Om Gnawali; Ramesh Govindan; Eddie Kohler; Jeong Paek; Sumit Rangwala; Thanos Sthathopoulos

    2005-01-01

    Over the last five years, sensor network research has seen significant advances in the development of hardware devices and platforms, and in the design of services and infrastructural elements such as routing, localization, and time synchronization. Deployed systems, however, have lagged behind. In this poster, we will describe an alternative architecture, called Tenet, for sensor networks that constrains placement of application-specific functionality on relatively unconstrained nodes. We w...

  13. Software architecture for hybrid electrical/optical data center network

    DEFF Research Database (Denmark)

    Mehmeri, Victor; Vegas Olmos, Juan José; Tafur Monroy, Idelfonso

    2016-01-01

    This paper presents hardware and software architecture based on Software-Defined Networking (SDN) paradigm and OpenFlow/NETCONF protocols for enabling topology management of hybrid electrical/optical switching data center networks. In particular, a development on top of SDN open-source controller...... OpenDaylight is presented to control an optical switching matrix based on Micro-Electro-Mechanical System (MEMS) technology....

  14. An OSI architecture for the deep space network

    Science.gov (United States)

    Heuser, W. Randy; Cooper, Lynne P.

    1993-01-01

    The flexibility and robustness of a monitor and control system are a direct result of the underlying inter-processor communications architecture. A new architecture for monitor & Control at the Deep Space Network Communications Complexes has been developed based on the Open System Interconnection (OSI) standards. The suitability of OSI standards for DSN M&C has been proven in the laboratory. The laboratory success has resulted in choosing an OSI-based architecture for DSS-13 M&C. DSS-13 is the DSN experimental station and is not part of the 'operational' DSN; it's role is to provide an environment to test new communications concepts can be tested and conduct unique science experiments. Therefore, DSS-13 must be robust enough to support operational activities, while also being flexible enough to enable experimentation. This paper describes the M&C architecture developed for DSS-13 and the results from system and operational testing.

  15. Internet of Things Heterogeneous Interoperable Network Architecture Design

    DEFF Research Database (Denmark)

    Bhalerao, Dipashree M.

    2014-01-01

    Internet of Thing‘s (IoT) state of the art deduce that there is no mature Internet of Things architecture available. Thesis contributes an abstract generic IoT system reference architecture development with specifications. Novelties of thesis are proposed solutions and implementations....... It is proved that reduction of data at a source will result in huge vertical scalability and indirectly horizontal also. Second non functional feature contributes in heterogeneous interoperable network architecture for constrained Things. To eliminate increasing number of gateways, Wi-Fi access point...... with Bluetooth, Zigbee (new access point is called as BZ-Fi) is proposed. Co-existence of Wi-Fi, Bluetooth, and Zigbee network technologies results in interference. To reduce the interference, orthogonal frequency division multiplexing (OFDM) is proposed tobe implemented in Bluetooth and Zigbee. The proposed...

  16. Reconfigurable radio systems network architectures and standards

    CERN Document Server

    Iacobucci, Maria Stella

    2013-01-01

    This timely book provides a standards-based view of the development, evolution, techniques and potential future scenarios for the deployment of reconfigurable radio systems.  After an introduction to radiomobile and radio systems deployed in the access network, the book describes cognitive radio concepts and capabilities, which are the basis for reconfigurable radio systems.  The self-organizing network features introduced in 3GPP standards are discussed and IEEE 802.22, the first standard based on cognitive radio, is described. Then the ETSI reconfigurable radio systems functional ar

  17. Agent-based Personal Network (PN) service architecture

    DEFF Research Database (Denmark)

    Jiang, Bo; Olesen, Henning

    2004-01-01

    In this paper we proposte a new concept for a centralized agent system as the solution for the PN service architecture, which aims to efficiently control and manage the PN resources and enable the PN based services to run seamlessly over different networks and devices. The working principle, cont...

  18. Large-Scale Networked Virtual Environments: Architecture and Applications

    Science.gov (United States)

    Lamotte, Wim; Quax, Peter; Flerackers, Eddy

    2008-01-01

    Purpose: Scalability is an important research topic in the context of networked virtual environments (NVEs). This paper aims to describe the ALVIC (Architecture for Large-scale Virtual Interactive Communities) approach to NVE scalability. Design/methodology/approach: The setup and results from two case studies are shown: a 3-D learning environment…

  19. A Security Architecture for Personal Networks

    NARCIS (Netherlands)

    Jehangir, A.

    2009-01-01

    The proliferation of personal mobile computing devices such as laptops and mo- bile phones, as well as wearable computing devices such as belt computers, digital bracelets and bio-medical sensors has created an opportunity to create a wireless network to share information and resources amongst

  20. Towards Dependable Network-on-Chip Architectures

    NARCIS (Netherlands)

    Chen, C.

    2015-01-01

    The aggressive semiconductor technology scaling provides the means for doubling the amount of transistors on a single chip each and every 18 months. To efficiently utilize these vast chip resources, Multi-Processor Systems on Chip (MPSoCs) integrated with a Network-on-Chip (NoC) communication

  1. Robust Networking Architecture and Secure Communication Scheme for Heterogeneous Wireless Sensor Networks

    Science.gov (United States)

    McNeal, McKenzie, III.

    2012-01-01

    Current networking architectures and communication protocols used for Wireless Sensor Networks (WSNs) have been designed to be energy efficient, low latency, and long network lifetime. One major issue that must be addressed is the security in data communication. Due to the limited capabilities of low cost and small sized sensor nodes, designing…

  2. Communication Network Architectures Based on Ethernet Passive Optical Network for Offshore Wind Power Farms

    Directory of Open Access Journals (Sweden)

    Mohamed A. Ahmed

    2016-03-01

    Full Text Available Nowadays, with large-scale offshore wind power farms (WPFs becoming a reality, more efforts are needed to maintain a reliable communication network for WPF monitoring. Deployment topologies, redundancy, and network availability are the main items to enhance the communication reliability between wind turbines (WTs and control centers. Traditional communication networks for monitoring and control (i.e., supervisory control and data acquisition (SCADA systems using switched gigabit Ethernet will not be sufficient for the huge amount of data passing through the network. In this paper, the optical power budget, optical path loss, reliability, and network cost of the proposed Ethernet Passive Optical Network (EPON-based communication network for small-size offshore WPFs have been evaluated for five different network architectures. The proposed network model consists of an optical network unit device (ONU deployed on the WT side for collecting data from different internal networks. All ONUs from different WTs are connected to a central optical line terminal (OLT, placed in the control center. There are no active electronic elements used between the ONUs and the OLT, which reduces the costs and complexity of maintenance and deployment. As fiber access networks without any protection are characterized by poor reliability, three different protection schemes have been configured, explained, and discussed. Considering the cost of network components, the total implementation expense of different architectures with, or without, protection have been calculated and compared. The proposed network model can significantly contribute to the communication network architecture for next generation WPFs.

  3. Mesoscale Architecture Shapes Initiation and Richness of Spontaneous Network Activity.

    Science.gov (United States)

    Okujeni, Samora; Kandler, Steffen; Egert, Ulrich

    2017-04-05

    Spontaneous activity in the absence of external input, including propagating waves of activity, is a robust feature of neuronal networks in vivo and in vitro The neurophysiological and anatomical requirements for initiation and persistence of such activity, however, are poorly understood, as is their role in the function of neuronal networks. Computational network studies indicate that clustered connectivity may foster the generation, maintenance, and richness of spontaneous activity. Since this mesoscale architecture cannot be systematically modified in intact tissue, testing these predictions is impracticable in vivo Here, we investigate how the mesoscale structure shapes spontaneous activity in generic networks of rat cortical neurons in vitro In these networks, neurons spontaneously arrange into local clusters with high neurite density and form fasciculating long-range axons. We modified this structure by modulation of protein kinase C, an enzyme regulating neurite growth and cell migration. Inhibition of protein kinase C reduced neuronal aggregation and fasciculation of axons, i.e., promoted uniform architecture. Conversely, activation of protein kinase C promoted aggregation of neurons into clusters, local connectivity, and bundling of long-range axons. Supporting predictions from theory, clustered networks were more spontaneously active and generated diverse activity patterns. Neurons within clusters received stronger synaptic inputs and displayed increased membrane potential fluctuations. Intensified clustering promoted the initiation of synchronous bursting events but entailed incomplete network recruitment. Moderately clustered networks appear optimal for initiation and propagation of diverse patterns of activity. Our findings support a crucial role of the mesoscale architectures in the regulation of spontaneous activity dynamics. SIGNIFICANCE STATEMENT Computational studies predict richer and persisting spatiotemporal patterns of spontaneous activity in

  4. Design and optimizing factors of PACS network architecture

    International Nuclear Information System (INIS)

    Tao Yonghao; Miao Jingtao

    2001-01-01

    Objective: Exploring the design and optimizing factors of picture archiving and communication system (PACS) network architecture. Methods: Based on the PACS of shanghai first hospital to performed the measurements and tests on the requirements of network bandwidth and transmitting rate for different PACS functions and procedures respectively in static and dynamic network traffic situation, utilizing the network monitoring tools which built-in workstations and provided by Windows NT. Results: No obvious difference between switch equipment and HUB when measurements and tests implemented in static situation except route which slow down the rate markedly. In dynamic environment Switch is able to provide higher bandwidth utilizing than HUB and local system scope communication achieved faster transmitting rate than global system. Conclusion: The primary optimizing factors of PACS network architecture design include concise network topology and disassemble tremendous global traffic to multiple distributed local scope network communication to reduce the traffic of network backbone. The most important issue is guarantee essential bandwidth for diagnosis procedure of medical imaging

  5. Building and measuring a high performance network architecture

    Energy Technology Data Exchange (ETDEWEB)

    Kramer, William T.C.; Toole, Timothy; Fisher, Chuck; Dugan, Jon; Wheeler, David; Wing, William R; Nickless, William; Goddard, Gregory; Corbato, Steven; Love, E. Paul; Daspit, Paul; Edwards, Hal; Mercer, Linden; Koester, David; Decina, Basil; Dart, Eli; Paul Reisinger, Paul; Kurihara, Riki; Zekauskas, Matthew J; Plesset, Eric; Wulf, Julie; Luce, Douglas; Rogers, James; Duncan, Rex; Mauth, Jeffery

    2001-04-20

    Once a year, the SC conferences present a unique opportunity to create and build one of the most complex and highest performance networks in the world. At SC2000, large-scale and complex local and wide area networking connections were demonstrated, including large-scale distributed applications running on different architectures. This project was designed to use the unique opportunity presented at SC2000 to create a testbed network environment and then use that network to demonstrate and evaluate high performance computational and communication applications. This testbed was designed to incorporate many interoperable systems and services and was designed for measurement from the very beginning. The end results were key insights into how to use novel, high performance networking technologies and to accumulate measurements that will give insights into the networks of the future.

  6. Architecture selection for deployable Local Area Networks

    OpenAIRE

    Hunninghake, David Patrick; Ashley, Bradley Keith

    1990-01-01

    Approved for public release, distribution is unlimited The United States Air Force's Headquarters Tactical Air Command (TAC) Communications-Computers staff provides guidance to TAC functional users on the procurement and use of Local Area Networks (LANs) in a deployed environment. Deployable systems may be defined as those systems designed to be transported away from their normal base for semi-fixed or mobile tactical missions. Major deployed LAN concerns include issues related to transmis...

  7. System architecture for ubiquitous live video streaming in university network environment

    CSIR Research Space (South Africa)

    Dludla, AG

    2013-09-01

    Full Text Available an architecture which supports ubiquitous live streaming for university or campus networks using a modified bluetooth inquiry mechanism with extended ID, integrated end-user device usage and adaptation to heterogeneous networks. Riding on that architecture...

  8. The development of brain network architecture.

    Science.gov (United States)

    Wierenga, Lara M; van den Heuvel, Martijn P; van Dijk, Sarai; Rijks, Yvonne; de Reus, Marcel A; Durston, Sarah

    2016-02-01

    Brain connectivity shows protracted development throughout childhood and adolescence, and, as such, the topology of brain networks changes during this period. The complexity of these changes with development is reflected by regional differences in maturation. This study explored age-related changes in network topology and regional developmental patterns during childhood and adolescence. We acquired two sets of Diffusion Weighted Imaging-scans and anatomical T1-weighted scans. The first dataset included 85 typically developing individuals (53 males; 32 females), aged between 7 and 23 years and was acquired on a Philips Achieva 1.5 Tesla scanner. A second dataset (N = 38) was acquired on a different (but identical) 1.5 T scanner and was used for independent replication of our results. We reconstructed whole brain networks using tractography. We operationalized fiber tract development as changes in mean diffusivity and radial diffusivity with age. Most fibers showed maturational changes in mean and radial diffusivity values throughout childhood and adolescence, likely reflecting increasing white matter integrity. The largest age-related changes were observed in association fibers within and between the frontal and parietal lobes. Furthermore, there was a simultaneous age-related decrease in average path length (P Brain Mapp 37:717-729, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  9. Network Architecture: lessons from the past, vision for the future

    CERN Multimedia

    CERN. Geneva

    2004-01-01

    The Architectural Principles of the Internet have dominated the past decade. Orthogonal to the telecommunications industry principles, they dramatically changed the networking landscape because they relied on iconoclastic ideas. First, the Internet end-to-end principle, which stipulates that the network should intervene minimally on the end-to-end traffic, pushing the complexity to the end-systems. Second, the ban of centralized functions: all the Internet techniques (routing, DNS, management) are based on distributed, decentralized mechanisms. Third, the absolute domination of connectionless (stateless) protocols (as with IP, HTTTP). However, when facing new requirements: multimedia traffic, security, Grid applications, these principles appear sometimes as architectural barriers. Multimedia requires QoS guarantees, but stateless systems are not good at QoS. Security requires active, intelligent networks, but dumb routers or plain end-to-end mail systems are insufficient. Grid applications require...

  10. Network architecture in a converged optical + IP network

    Science.gov (United States)

    Wakim, Walid; Zottmann, Harald

    2012-01-01

    As demands on Provider Networks continue to grow at exponential rates, providers are forced to evaluate how to continue to grow the network while increasing service velocity, enhancing resiliency while decreasing the total cost of ownership (TCO). The bandwidth growth that networks are experiencing is in the form packet based multimedia services such as video, video conferencing, gaming, etc... mixed with Over the Top (OTT) content providers such as Netflix, and the customer's expectations that best effort is not enough you end up with a situation that forces the provider to analyze how to gain more out of the network with less cost. In this paper we will discuss changes in the network that are driving us to a tighter integration between packet and optical layers and how to improve on today's multi - layer inefficiencies to drive down network TCO and provide for a fully integrated and dynamic network that will decrease time to revenue.

  11. Nexus network journal patterns in architecture

    CERN Document Server

    2007-01-01

    This issue is dedicated to various kinds of patterns in architecture. Buthayna Eilouti and Amer Al-Jokhadar address patterns in shape grammars in the ground plans of Mamluk madrasas, religious schools. Giulio Magli goes back further in history, to the age of Greek colonies in Italy before they were conquered by the Romans, to examine patterns in urban design. In Traditional Patterns in Pyrgi of Chios: Mathematics and Community Charoula Stathopoulou examines the geometric patterns that decorate the buildings of the town of Pyrgi, on the Greek island of Chios. Curve Fitting is a study of ways to construct a function so that its graph most closely approximates the pattern given by a set of points. Dirk Huylebrouck’s paper examines how a pattern of points extracted from an arch might be associated to a precise mathematical curve. James Harris looks at the designs of Frank Lloyd Wright and Piet Mondrian to extract the rules of their pattern generation and propose possible applications.

  12. Resting state networks' corticotopy: the dual intertwined rings architecture.

    Directory of Open Access Journals (Sweden)

    Salma Mesmoudi

    Full Text Available How does the brain integrate multiple sources of information to support normal sensorimotor and cognitive functions? To investigate this question we present an overall brain architecture (called "the dual intertwined rings architecture" that relates the functional specialization of cortical networks to their spatial distribution over the cerebral cortex (or "corticotopy". Recent results suggest that the resting state networks (RSNs are organized into two large families: 1 a sensorimotor family that includes visual, somatic, and auditory areas and 2 a large association family that comprises parietal, temporal, and frontal regions and also includes the default mode network. We used two large databases of resting state fMRI data, from which we extracted 32 robust RSNs. We estimated: (1 the RSN functional roles by using a projection of the results on task based networks (TBNs as referenced in large databases of fMRI activation studies; and (2 relationship of the RSNs with the Brodmann Areas. In both classifications, the 32 RSNs are organized into a remarkable architecture of two intertwined rings per hemisphere and so four rings linked by homotopic connections. The first ring forms a continuous ensemble and includes visual, somatic, and auditory cortices, with interspersed bimodal cortices (auditory-visual, visual-somatic and auditory-somatic, abbreviated as VSA ring. The second ring integrates distant parietal, temporal and frontal regions (PTF ring through a network of association fiber tracts which closes the ring anatomically and ensures a functional continuity within the ring. The PTF ring relates association cortices specialized in attention, language and working memory, to the networks involved in motivation and biological regulation and rhythms. This "dual intertwined architecture" suggests a dual integrative process: the VSA ring performs fast real-time multimodal integration of sensorimotor information whereas the PTF ring performs multi

  13. Cyber-physical architecture assisted by programmable networking

    DEFF Research Database (Denmark)

    Rubio-Hernan, Jose; Sahay, Rishikesh; De Cicco, Luca

    2018-01-01

    , this letter proposes a new architecture combining control‐theoretic solutions together with programmable networking techniques to jointly handle crucial threats to cyber‐physical systems. The architecture paves the way for new interesting techniques research directions and challenges which we discuss in our......Cyber‐physical technologies are prone to attacks in addition to faults and failures. The issue of protecting cyber‐physical systems should be tackled by jointly addressing security at both cyber and physical domains in order to promptly detect and mitigate cyber‐physical threats. Toward this end...

  14. Genetic networks of liver metabolism revealed by integration of metabolic and transcriptional profiling.

    Directory of Open Access Journals (Sweden)

    Christine T Ferrara

    2008-03-01

    Full Text Available Although numerous quantitative trait loci (QTL influencing disease-related phenotypes have been detected through gene mapping and positional cloning, identification of the individual gene(s and molecular pathways leading to those phenotypes is often elusive. One way to improve understanding of genetic architecture is to classify phenotypes in greater depth by including transcriptional and metabolic profiling. In the current study, we have generated and analyzed mRNA expression and metabolic profiles in liver samples obtained in an F2 intercross between the diabetes-resistant C57BL/6 leptin(ob/ob and the diabetes-susceptible BTBR leptin(ob/ob mouse strains. This cross, which segregates for genotype and physiological traits, was previously used to identify several diabetes-related QTL. Our current investigation includes microarray analysis of over 40,000 probe sets, plus quantitative mass spectrometry-based measurements of sixty-seven intermediary metabolites in three different classes (amino acids, organic acids, and acyl-carnitines. We show that liver metabolites map to distinct genetic regions, thereby indicating that tissue metabolites are heritable. We also demonstrate that genomic analysis can be integrated with liver mRNA expression and metabolite profiling data to construct causal networks for control of specific metabolic processes in liver. As a proof of principle of the practical significance of this integrative approach, we illustrate the construction of a specific causal network that links gene expression and metabolic changes in the context of glutamate metabolism, and demonstrate its validity by showing that genes in the network respond to changes in glutamine and glutamate availability. Thus, the methods described here have the potential to reveal regulatory networks that contribute to chronic, complex, and highly prevalent diseases and conditions such as obesity and diabetes.

  15. On Functional Module Detection in Metabolic Networks

    Science.gov (United States)

    Koch, Ina; Ackermann, Jörg

    2013-01-01

    Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided identification of functional modules becomes more and more important. Since steady states play a key role in biology, many methods have been developed in that context, for example, elementary flux modes, extreme pathways, transition invariants and place invariants. Metabolic networks can be studied also from the point of view of graph theory, and algorithms for graph decomposition have been applied for the identification of functional modules. A prominent and currently intensively discussed field of methods in graph theory addresses the Q-modularity. In this paper, we recall known concepts of module detection based on the steady-state assumption, focusing on transition-invariants (elementary modes) and their computation as minimal solutions of systems of Diophantine equations. We present the Fourier-Motzkin algorithm in detail. Afterwards, we introduce the Q-modularity as an example for a useful non-steady-state method and its application to metabolic networks. To illustrate and discuss the concepts of invariants and Q-modularity, we apply a part of the central carbon metabolism in potato tubers (Solanum tuberosum) as running example. The intention of the paper is to give a compact presentation of known steady-state concepts from a graph-theoretical viewpoint in the context of network decomposition and reduction and to introduce the application of Q-modularity to metabolic Petri net models. PMID:24958145

  16. Hierarchical Communication Network Architectures for Offshore Wind Power Farms

    Directory of Open Access Journals (Sweden)

    Mohamed A. Ahmed

    2014-05-01

    Full Text Available Nowadays, large-scale wind power farms (WPFs bring new challenges for both electric systems and communication networks. Communication networks are an essential part of WPFs because they provide real-time control and monitoring of wind turbines from a remote location (local control center. However, different wind turbine applications have different requirements in terms of data volume, latency, bandwidth, QoS, etc. This paper proposes a hierarchical communication network architecture that consist of a turbine area network (TAN, farm area network (FAN, and control area network (CAN for offshore WPFs. The two types of offshore WPFs studied are small-scale WPFs close to the grid and medium-scale WPFs far from the grid. The wind turbines are modelled based on the logical nodes (LN concepts of the IEC 61400-25 standard. To keep pace with current developments in wind turbine technology, the network design takes into account the extension of the LNs for both the wind turbine foundation and meteorological measurements. The proposed hierarchical communication network is based on Switched Ethernet. Servers at the control center are used to store and process the data received from the WPF. The network architecture is modelled and evaluated via OPNET. We investigated the end-to-end (ETE delay for different WPF applications. The results are validated by comparing the amount of generated sensing data with that of received traffic at servers. The network performance is evaluated, analyzed and discussed in view of end-to-end (ETE delay for different link bandwidths.

  17. Architecture and dynamics of overlapped RNA regulatory networks.

    Science.gov (United States)

    Lapointe, Christopher P; Preston, Melanie A; Wilinski, Daniel; Saunders, Harriet A J; Campbell, Zachary T; Wickens, Marvin

    2017-11-01

    A single protein can bind and regulate many mRNAs. Multiple proteins with similar specificities often bind and control overlapping sets of mRNAs. Yet little is known about the architecture or dynamics of overlapped networks. We focused on three proteins with similar structures and related RNA-binding specificities-Puf3p, Puf4p, and Puf5p of S. cerevisiae Using RNA Tagging, we identified a "super-network" comprised of four subnetworks: Puf3p, Puf4p, and Puf5p subnetworks, and one controlled by both Puf4p and Puf5p. The architecture of individual subnetworks, and thus the super-network, is determined by competition among particular PUF proteins to bind mRNAs, their affinities for binding elements, and the abundances of the proteins. The super-network responds dramatically: The remaining network can either expand or contract. These strikingly opposite outcomes are determined by an interplay between the relative abundance of the RNAs and proteins, and their affinities for one another. The diverse interplay between overlapping RNA-protein networks provides versatile opportunities for regulation and evolution. © 2017 Lapointe et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  18. Mesh Network Architecture for Enabling Inter-Spacecraft Communication

    Science.gov (United States)

    Becker, Christopher; Merrill, Garrick

    2017-01-01

    To enable communication between spacecraft operating in a formation or small constellation, a mesh network architecture was developed and tested using a time division multiple access (TDMA) communication scheme. The network is designed to allow for the exchange of telemetry and other data between spacecraft to enable collaboration between small spacecraft. The system uses a peer-to-peer topology with no central router, so that it does not have a single point of failure. The mesh network is dynamically configurable to allow for addition and subtraction of new spacecraft into the communication network. Flight testing was performed using an unmanned aerial system (UAS) formation acting as a spacecraft analogue and providing a stressing environment to prove mesh network performance. The mesh network was primarily devised to provide low latency, high frequency communication but is flexible and can also be configured to provide higher bandwidth for applications desiring high data throughput. The network includes a relay functionality that extends the maximum range between spacecraft in the network by relaying data from node to node. The mesh network control is implemented completely in software making it hardware agnostic, thereby allowing it to function with a wide variety of existing radios and computing platforms..

  19. Ecological network analysis of China's societal metabolism.

    Science.gov (United States)

    Zhang, Yan; Liu, Hong; Li, Yating; Yang, Zhifeng; Li, Shengsheng; Yang, Naijin

    2012-01-01

    Uncontrolled socioeconomic development has strong negative effects on the ecological environment, including pollution and the depletion and waste of natural resources. These serious consequences result from the high flows of materials and energy through a socioeconomic system produced by exchanges between the system and its surroundings, causing the disturbance of metabolic processes. In this paper, we developed an ecological network model for a societal system, and used China in 2006 as a case study to illustrate application of the model. We analyzed China's basic metabolic processes and used ecological network analysis to study the network relationships within the system. Basic components comprised the internal environment, five sectors (agriculture, exploitation, manufacturing, domestic, and recycling), and the external environment. We defined 21 pairs of ecological relationships in China's societal metabolic system (excluding self-mutualism within a component). Using utility and throughflow analysis, we found that exploitation, mutualism, and competition relationships accounted for 76.2, 14.3, and 9.5% of the total relationships, respectively. In our trophic level analysis, the components were divided into producers, consumers, and decomposers according to their positions in the system. Our analyses revealed ways to optimize the system's structure and adjust its functions, thereby promoting healthier socioeconomic development, and suggested ways to apply ecological network analysis in future socioeconomic research. Copyright © 2011 Elsevier Ltd. All rights reserved.

  20. Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network.

    Science.gov (United States)

    Kim, Hyun Uk; Kim, Tae Yong; Lee, Sang Yup

    2011-01-01

    Genome-scale metabolic network models have contributed to elucidating biological phenomena, and predicting gene targets to engineer for biotechnological applications. With their increasing importance, their precise network characterization has also been crucial for better understanding of the cellular physiology. We herein introduce a framework for network modularization and Bayesian network analysis (FMB) to investigate organism's metabolism under perturbation. FMB reveals direction of influences among metabolic modules, in which reactions with similar or positively correlated flux variation patterns are clustered, in response to specific perturbation using metabolic flux data. With metabolic flux data calculated by constraints-based flux analysis under both control and perturbation conditions, FMB, in essence, reveals the effects of specific perturbations on the biological system through network modularization and Bayesian network analysis at metabolic modular level. As a demonstration, this framework was applied to the genetically perturbed Escherichia coli metabolism, which is a lpdA gene knockout mutant, using its genome-scale metabolic network model. After all, it provides alternative scenarios of metabolic flux distributions in response to the perturbation, which are complementary to the data obtained from conventionally available genome-wide high-throughput techniques or metabolic flux analysis.

  1. Data center networks topologies, architectures and fault-tolerance characteristics

    CERN Document Server

    Liu, Yang; Veeraraghavan, Malathi; Lin, Dong; Hamdi, Mounir

    2013-01-01

    This SpringerBrief presents a survey of data center network designs and topologies and compares several properties in order to highlight their advantages and disadvantages. The brief also explores several routing protocols designed for these topologies and compares the basic algorithms to establish connections, the techniques used to gain better performance, and the mechanisms for fault-tolerance. Readers will be equipped to understand how current research on data center networks enables the design of future architectures that can improve performance and dependability of data centers. This con

  2. A modular architecture for transparent computation in recurrent neural networks.

    Science.gov (United States)

    Carmantini, Giovanni S; Beim Graben, Peter; Desroches, Mathieu; Rodrigues, Serafim

    2017-01-01

    Computation is classically studied in terms of automata, formal languages and algorithms; yet, the relation between neural dynamics and symbolic representations and operations is still unclear in traditional eliminative connectionism. Therefore, we suggest a unique perspective on this central issue, to which we would like to refer as transparent connectionism, by proposing accounts of how symbolic computation can be implemented in neural substrates. In this study we first introduce a new model of dynamics on a symbolic space, the versatile shift, showing that it supports the real-time simulation of a range of automata. We then show that the Gödelization of versatile shifts defines nonlinear dynamical automata, dynamical systems evolving on a vectorial space. Finally, we present a mapping between nonlinear dynamical automata and recurrent artificial neural networks. The mapping defines an architecture characterized by its granular modularity, where data, symbolic operations and their control are not only distinguishable in activation space, but also spatially localizable in the network itself, while maintaining a distributed encoding of symbolic representations. The resulting networks simulate automata in real-time and are programmed directly, in the absence of network training. To discuss the unique characteristics of the architecture and their consequences, we present two examples: (i) the design of a Central Pattern Generator from a finite-state locomotive controller, and (ii) the creation of a network simulating a system of interactive automata that supports the parsing of garden-path sentences as investigated in psycholinguistics experiments. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. ARCHITECTURES AND ALGORITHMS FOR COGNITIVE NETWORKS ENABLED BY QUALITATIVE MODELS

    DEFF Research Database (Denmark)

    Balamuralidhar, P.

    2013-01-01

    Complexity of communication networks is ever increasing and getting complicated by their heterogeneity and dynamism. Traditional techniques are facing challenges in network performance management. Cognitive networking is an emerging paradigm to make networks more intelligent, thereby overcoming...... of the cognitive engine that incorporates a context space based information structure to its knowledge model. I propose a set of guiding principles behind a cognitive system to be autonomic and use them with additional requirements to build a detailed architecture for the cognitive engine. I define a context space...... structure integrating various information structures that are required for the knowledge model. Use graphical models towards representing and reasoning about context space is a direction followed here. Specifically I analyze the framework of qualitative models for their suitability to represent the dynamic...

  4. Genotype networks, innovation, and robustness in sulfur metabolism

    Science.gov (United States)

    2011-01-01

    Background A metabolism is a complex network of chemical reactions. This network synthesizes multiple small precursor molecules of biomass from chemicals that occur in the environment. The metabolic network of any one organism is encoded by a metabolic genotype, defined as the set of enzyme-coding genes whose products catalyze the network's reactions. Each metabolic genotype has a metabolic phenotype. We define this metabolic phenotype as the spectrum of different sources of a chemical element that a metabolism can use to synthesize biomass. We here focus on the element sulfur. We study properties of the space of all possible metabolic genotypes in sulfur metabolism by analyzing random metabolic genotypes that are viable on different numbers of sulfur sources. Results We show that metabolic genotypes with the same phenotype form large connected genotype networks - networks of metabolic networks - that extend far through metabolic genotype space. How far they reach through this space depends linearly on the number of super-essential reactions. A super-essential reaction is an essential reaction that occurs in all networks viable in a given environment. Metabolic networks can differ in how robust their phenotype is to the removal of individual reactions. We find that this robustness depends on metabolic network size, and on other variables, such as the size of minimal metabolic networks whose reactions are all essential in a specific environment. We show that different neighborhoods of any genotype network harbor very different novel phenotypes, metabolic innovations that can sustain life on novel sulfur sources. We also analyze the ability of evolving populations of metabolic networks to explore novel metabolic phenotypes. This ability is facilitated by the existence of genotype networks, because different neighborhoods of these networks contain very different novel phenotypes. Conclusions We show that the space of metabolic genotypes involved in sulfur metabolism

  5. Phenotypic evolution from genetic polymorphisms in a radial network architecture

    Directory of Open Access Journals (Sweden)

    Siegel Paul B

    2007-11-01

    Full Text Available Abstract Background The genetic architecture of a quantitative trait influences the phenotypic response to natural or artificial selection. One of the main objectives of genetic mapping studies is to identify the genetic factors underlying complex traits and understand how they contribute to phenotypic expression. Presently, we are good at identifying and locating individual loci with large effects, but there is a void in describing more complex genetic architectures. Although large networks of connected genes have been reported, there is an almost complete lack of information on how polymorphisms in these networks contribute to phenotypic variation and change. To date, most of our understanding comes from theoretical, model-based studies, and it remains difficult to assess how realistic their conclusions are as they lack empirical support. Results A previous study provided evidence that nearly half of the difference in eight-week body weight between two divergently selected lines of chickens was a result of four loci organized in a 'radial' network (one central locus interacting with three 'radial' loci that, in turn, only interacted with the central locus. Here, we study the relationship between phenotypic change and genetic polymorphism in this empirically detected network. We use a model-free approach to study, through individual-based simulations, the dynamic properties of this polymorphic and epistatic genetic architecture. The study provides new insights to how epistasis can modify the selection response, buffer and reveal effects of major loci leading to a progressive release of genetic variation. We also illustrate the difficulty of predicting genetic architecture from observed selection response, and discuss mechanisms that might lead to misleading conclusions on underlying genetic architectures from quantitative trait locus (QTL experiments in selected populations. Conclusion Considering both molecular (QTL and phenotypic (selection

  6. Cloud Radio Access Network architecture. Towards 5G mobile networks

    DEFF Research Database (Denmark)

    Checko, Aleksandra

    stations into radio and baseband parts, and pool the Baseband Units (BBUs) from multiple base stations into a centralized and virtualized BBU Pool. This gives a number of benefits in terms of cost and capacity. However, the challenge is then to find an optimal functionality splitting point as well...... savings due to the multiplexing gains in the BBU pool and the fronthaul network. The cost of a fronthaul network deployment and operation can be further reduced by sharing infrastructure between fronthaul and other services. The origins of multiplexing gains in terms of traffic burstiness, the tidal...

  7. Cortical network architecture for context processing in primate brain.

    Science.gov (United States)

    Chao, Zenas C; Nagasaka, Yasuo; Fujii, Naotaka

    2015-09-29

    Context is information linked to a situation that can guide behavior. In the brain, context is encoded by sensory processing and can later be retrieved from memory. How context is communicated within the cortical network in sensory and mnemonic forms is unknown due to the lack of methods for high-resolution, brain-wide neuronal recording and analysis. Here, we report the comprehensive architecture of a cortical network for context processing. Using hemisphere-wide, high-density electrocorticography, we measured large-scale neuronal activity from monkeys observing videos of agents interacting in situations with different contexts. We extracted five context-related network structures including a bottom-up network during encoding and, seconds later, cue-dependent retrieval of the same network with the opposite top-down connectivity. These findings show that context is represented in the cortical network as distributed communication structures with dynamic information flows. This study provides a general methodology for recording and analyzing cortical network neuronal communication during cognition.

  8. 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 .

  9. Communication Network Architectures for Smart-Wind Power Farms

    Directory of Open Access Journals (Sweden)

    Mohamed A. Ahmed

    2014-06-01

    Full Text Available Developments in the wind power industry have enabled a new generation of wind turbines with longer blades, taller towers, higher efficiency, and lower maintenance costs due to the maturity of related technologies. Nevertheless, wind turbines are still blind machines because the control center is responsible for managing and controlling individual wind turbines that are turned on or off according to demand for electricity. In this paper, we propose a communication network architecture for smart-wind power farms (Smart-WPFs. The proposed architecture is designed for wind turbines to communicate directly and share sensing data in order to maximize power generation, WPF availability, and turbine efficiency. We also designed a sensor data frame structure to carry sensing data from different wind turbine parts such as the rotor, transformer, nacelle, etc. The data frame includes a logical node ID (LNID, sensor node ID (SNID, sensor type (ST, and sensor data based on the International Electrotechnical Commission (IEC 61400-25 standard. We present an analytical model that describes upstream traffic between the wind turbines and the control center. Using a queueing theory approach, the upstream traffic is evaluated in view of bandwidth utilization and average queuing delay. The performance of the proposed network architectures are evaluated by using analytical and simulation models.

  10. An efficient optical architecture for sparsely connected neural networks

    Science.gov (United States)

    Hine, Butler P., III; Downie, John D.; Reid, Max B.

    1990-01-01

    An architecture for general-purpose optical neural network processor is presented in which the interconnections and weights are formed by directing coherent beams holographically, thereby making use of the space-bandwidth products of the recording medium for sparsely interconnected networks more efficiently that the commonly used vector-matrix multiplier, since all of the hologram area is in use. An investigation is made of the use of computer-generated holograms recorded on such updatable media as thermoplastic materials, in order to define the interconnections and weights of a neural network processor; attention is given to limits on interconnection densities, diffraction efficiencies, and weighing accuracies possible with such an updatable thin film holographic device.

  11. SDN architecture for optical packet and circuit integrated networks

    Science.gov (United States)

    Furukawa, Hideaki; Miyazawa, Takaya

    2016-02-01

    We have been developing an optical packet and circuit integrated (OPCI) network, which realizes dynamic optical path, high-density packet multiplexing, and flexible wavelength resource allocation. In the OPCI networks, a best-effort service and a QoS-guaranteed service are provided by employing optical packet switching (OPS) and optical circuit switching (OCS) respectively, and users can select these services. Different wavelength resources are assigned for OPS and OCS links, and the amount of their wavelength resources are dynamically changed in accordance with the service usage conditions. To apply OPCI networks into wide-area (core/metro) networks, we have developed an OPCI node with a distributed control mechanism. Moreover, our OPCI node works with a centralized control mechanism as well as a distributed one. It is therefore possible to realize SDN-based OPCI networks, where resource requests and a centralized configuration are carried out. In this paper, we show our SDN architecture for an OPS system that configures mapping tables between IP addresses and optical packet addresses and switching tables according to the requests from multiple users via a web interface. While OpenFlow-based centralized control protocol is coming into widespread use especially for single-administrative, small-area (LAN/data-center) networks. Here, we also show an interworking mechanism between OpenFlow-based networks (OFNs) and the OPCI network for constructing a wide-area network, and a control method of wavelength resource selection to automatically transfer diversified flows from OFNs to the OPCI network.

  12. Resting State Networks' Corticotopy: The Dual Intertwined Rings Architecture

    Science.gov (United States)

    Mesmoudi, Salma; Perlbarg, Vincent; Rudrauf, David; Messe, Arnaud; Pinsard, Basile; Hasboun, Dominique; Cioli, Claudia; Marrelec, Guillaume; Toro, Roberto; Benali, Habib; Burnod, Yves

    2013-01-01

    How does the brain integrate multiple sources of information to support normal sensorimotor and cognitive functions? To investigate this question we present an overall brain architecture (called “the dual intertwined rings architecture”) that relates the functional specialization of cortical networks to their spatial distribution over the cerebral cortex (or “corticotopy”). Recent results suggest that the resting state networks (RSNs) are organized into two large families: 1) a sensorimotor family that includes visual, somatic, and auditory areas and 2) a large association family that comprises parietal, temporal, and frontal regions and also includes the default mode network. We used two large databases of resting state fMRI data, from which we extracted 32 robust RSNs. We estimated: (1) the RSN functional roles by using a projection of the results on task based networks (TBNs) as referenced in large databases of fMRI activation studies; and (2) relationship of the RSNs with the Brodmann Areas. In both classifications, the 32 RSNs are organized into a remarkable architecture of two intertwined rings per hemisphere and so four rings linked by homotopic connections. The first ring forms a continuous ensemble and includes visual, somatic, and auditory cortices, with interspersed bimodal cortices (auditory-visual, visual-somatic and auditory-somatic, abbreviated as VSA ring). The second ring integrates distant parietal, temporal and frontal regions (PTF ring) through a network of association fiber tracts which closes the ring anatomically and ensures a functional continuity within the ring. The PTF ring relates association cortices specialized in attention, language and working memory, to the networks involved in motivation and biological regulation and rhythms. This “dual intertwined architecture” suggests a dual integrative process: the VSA ring performs fast real-time multimodal integration of sensorimotor information whereas the PTF ring performs multi

  13. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

    DEFF Research Database (Denmark)

    Förster, Jochen; Famili, I.; Fu, P.

    2003-01-01

    and the environment were included. A total of 708 structural open reading frames (ORFs) were accounted for in the reconstructed network, corresponding to 1035 metabolic reactions. Further, 140 reactions were included on the basis of biochemical evidence resulting in a genome-scale reconstructed metabolic network...... with Escherichia coli. The reconstructed metabolic network is the first comprehensive network for a eukaryotic organism, and it may be used as the basis for in silico analysis of phenotypic functions....

  14. The brain's functional network architecture reveals human motives.

    Science.gov (United States)

    Hein, Grit; Morishima, Yosuke; Leiberg, Susanne; Sul, Sunhae; Fehr, Ernst

    2016-03-04

    Goal-directed human behaviors are driven by motives. Motives are, however, purely mental constructs that are not directly observable. Here, we show that the brain's functional network architecture captures information that predicts different motives behind the same altruistic act with high accuracy. In contrast, mere activity in these regions contains no information about motives. Empathy-based altruism is primarily characterized by a positive connectivity from the anterior cingulate cortex (ACC) to the anterior insula (AI), whereas reciprocity-based altruism additionally invokes strong positive connectivity from the AI to the ACC and even stronger positive connectivity from the AI to the ventral striatum. Moreover, predominantly selfish individuals show distinct functional architectures compared to altruists, and they only increase altruistic behavior in response to empathy inductions, but not reciprocity inductions. Copyright © 2016, American Association for the Advancement of Science.

  15. Wavelet-cellular neural network architecture and learning algorithm

    Science.gov (United States)

    Bal, Abdullah; Ucan, Osman N.; Pastaci, Halit; Alam, Mohammad S.

    2004-04-01

    Cellular Neural Networks (CNN) provides fast parallel computational capability for image processing applications. The behavior of the CNN is defined by two template matrices. In this paper, adjustment of these template-matrix coefficients have been realized using supervised learning algorithm based on back-propagation technique and wavelet function. Back-propagation algorithm has been modified for dynamic behavior of CNN. Wavelet function is utilized to provide the activation function derivation in this learning algorithm. The supervised learning algorithm is then executed to obtain a compact CNN architecture, called as Wave-CNN. The proposed new learning algorithm and Wave-CNN architecture performance have been tested for 2D image processing applications.

  16. Thinking in networks: artistic–architectural responses to ubiquitous information

    Directory of Open Access Journals (Sweden)

    Yvonne Spielmann

    2011-12-01

    Full Text Available The article discusses creative practices that in aesthetical-technical ways intervene into the computer networked communication systems.I am interested in artist practices that use networks in different ways to make us aware about the possibilities to rethink media-cultural environments. I use the example of the Japanese art-architectural group Double Negative Architecture to give an example of creatively thinking in networks.Yvonne Spielmann (Ph.D., Dr. habil. is presently Research Professor and Chair of New Media at The University of the West of Scotland. Her work focuses on inter-relationships between media and culture, technology, art, science and communication, and in particular on Western/European and non-Western/South-East Asian interaction. Milestones of publish research output are four authored monographs and about 90 single authored articles. Her book, “Video, the Reflexive Medium” (published by MIT Press 2008, Japanese edition by Sangen-sha Press 2011 was rewarded the 2009 Lewis Mumford Award for Outstanding Scholarship in the Ecology of Technics. Her most recent book “Hybrid Cultures” was published in German by Suhrkamp Press in 2010, English edition from MIT Press in 2012. Spielmann's work has been published in German and English and has been translated into French, Polish, Croatian, Swedish, Japanese, and Korean. She holds the 2011 Swedish Prize for Swedish–German scientific co-operation.

  17. Network architecture underlying maximal separation of neuronal representations

    Directory of Open Access Journals (Sweden)

    Ron A Jortner

    2013-01-01

    Full Text Available One of the most basic and general tasks faced by all nervous systems is extracting relevant information from the organism’s surrounding world. While physical signals available to sensory systems are often continuous, variable, overlapping and noisy, high-level neuronal representations used for decision-making tend to be discrete, specific, invariant, and highly separable. This study addresses the question of how neuronal specificity is generated. Inspired by experimental findings on network architecture in the olfactory system of the locust, I construct a highly simplified theoretical framework which allows for analytic solution of its key properties. For generalized feed-forward systems, I show that an intermediate range of connectivity values between source- and target-populations leads to a combinatorial explosion of wiring possibilities, resulting in input spaces which are, by their very nature, exquisitely sparsely populated. In particular, connection probability ½, as found in the locust antennal-lobe–mushroom-body circuit, serves to maximize separation of neuronal representations across the target Kenyon-cells, and explains their specific and reliable responses. This analysis yields a function expressing response specificity in terms of lower network-parameters; together with appropriate gain control this leads to a simple neuronal algorithm for generating arbitrarily sparse and selective codes and linking network architecture and neural coding. I suggest a way to easily construct ecologically meaningful representations from this code.

  18. The topology of metabolic isotope labeling networks

    Directory of Open Access Journals (Sweden)

    Wiechert Wolfgang

    2007-08-01

    Full Text Available Abstract Background Metabolic Flux Analysis (MFA based on isotope labeling experiments (ILEs is a widely established tool for determining fluxes in metabolic pathways. Isotope labeling networks (ILNs contain all essential information required to describe the flow of labeled material in an ILE. Whereas recent experimental progress paves the way for high-throughput MFA, large network investigations and exact statistical methods, these developments are still limited by the poor performance of computational routines used for the evaluation and design of ILEs. In this context, the global analysis of ILN topology turns out to be a clue for realizing large speedup factors in all required computational procedures. Results With a strong focus on the speedup of algorithms the topology of ILNs is investigated using graph theoretic concepts and algorithms. A rigorous determination of all cyclic and isomorphic subnetworks, accompanied by the global analysis of ILN connectivity is performed. Particularly, it is proven that ILNs always brake up into a large number of small strongly connected components (SCCs and, moreover, there are natural isomorphisms between many of these SCCs. All presented techniques are universal, i.e. they do not require special assumptions on the network structure, bidirectionality of fluxes, measurement configuration, or label input. The general results are exemplified with a practically relevant metabolic network which describes the central metabolism of E. coli comprising 10390 isotopomer pools. Conclusion Exploiting the topological features of ILNs leads to a significant speedup of all universal algorithms for ILE evaluation. It is proven in theory and exemplified with the E. coli example that a speedup factor of about 1000 compared to standard algorithms is achieved. This widely opens the door for new high performance algorithms suitable for high throughput applications and large ILNs. Moreover, for the first time the global

  19. Phylogeny of metabolic networks: A spectral graph theoretical ...

    Indian Academy of Sciences (India)

    Many methods have been developed for finding the commonalities between different organisms in order to study their phylogeny. The structure of metabolic networks also reveals valuable insights into metabolic capacity of species as well as into the habitats where they have evolved. We constructed metabolic networks of ...

  20. Genetic architecture of obesity and related metabolic traits-recent insights from isolated populations.

    Science.gov (United States)

    Andersen, Mette Korre; Grarup, Niels; Moltke, Ida; Albrechtsen, Anders; Hansen, Torben

    2018-03-03

    In this mini-review, we give an overview of what is known about the genetic architecture of obesity and related metabolic traits with a primary focus on recent insights from studies of historically small and isolated populations. We start by briefly explaining what genetic architecture is and why studies of isolated populations in general are valuable if we want a complete picture of the genetic architecture of diseases and other traits among humans. Then we contrast what is known about the genetic architecture of obesity and related metabolic traits among large outbred populations, like Europeans, with results from recent studies of isolated populations. Finally, we briefly discuss the perspectives of studying isolated populations to gain insight into genetic architecture in humans. Copyright © 2018. Published by Elsevier Ltd.

  1. Using Distributed Sensor Network Architecture to Link Heterogeneous Astronomical Assets

    Science.gov (United States)

    White, R.; Evans, S.; Pergande, J.; Vestrand, W.; Wozniak, P.; Wren, J.

    The internet has brought about great change in the astronomical community, but this interconnectivity is just starting to be exploited for use in this type of instrumentation. Here we present the Telescope ALert Operations Network System (TALONS), a network software suite that allows intercommunication between external and internal astronomical resources and controls the distribution of information to each of the resources. TALONS is an fundamental element of the Thinking Telescopes System, in operation at Los Alamos National Laboratory, and has been enabling great science for the past four years. The system allows a distributed network of telescopes to perform more efficiently in synchronous operation than as individual instruments. TALONS is designed as a merger between a standard server/client architecture and a Distributed Sensor Network (DSN). It can dynamically regulate its client base, allowing any number of heterogeneous resources to be linked together and communicate. TALONS couples that capability with collaborative analysis and maintenance modules so that it can respond quickly to external requests and changing network environments. TALONS clients connect via an intelligent agent, which acts in proxy for the scientist, allowing the telescope to analyze incoming information and respond autonomously. TALONS has a proven track record of effectively supporting the instruments at Los Alamos and other astronomical resources around the world.

  2. Towards A New Opportunistic IoT Network Architecture for Wildlife Monitoring System

    NARCIS (Netherlands)

    Ayele, Eyuel Debebe; Meratnia, Nirvana; Havinga, Paul J.M.

    In this paper we introduce an opportunistic dual radio IoT network architecture for wildlife monitoring systems (WMS). Since data processing consumes less energy than transmitting the raw data, the proposed architecture leverages opportunistic mobile networks in a fixed LPWAN IoT network

  3. Intelligent Approaches in Improving In-vehicle Network Architecture and Minimizing Power Consumption in Combat Vehicles

    Science.gov (United States)

    2011-01-01

    1345– 1361, November 2002. [30] L.F. P. Pollo , J. -Porto, ―A Network-oriented Power Management Architecture,‖ Proc. Integrated Network Management...208, Feb. 2007, doi: 10.1109/TCE.2007.339526. [47] L.F. Pollo and J-Porto, ―A Network-oriented Power Management Architecture,‖ Proc. Integrated

  4. Architectural approach for quality and safety aware healthcare social networks.

    Science.gov (United States)

    López, Diego M; Blobel, Bernd; González, Carolina

    2012-01-01

    Quality of information and privacy and safety issues are frequently identified as main limitations to make most benefit from social media in healthcare. The objective of the paper is to contribute to the analysis of healthcare social networks (SN), and online healthcare social network services (SNS) by proposing a formal architectural analysis of healthcare SN and SNS, considering the complexity of both systems, but stressing on quality, safety and usability aspects. Quality policies are necessary to control the quality of content published by experts and consumers. Privacy and safety policies protect against inappropriate use of information and users responsibility for sharing information. After the policies are established and documented, a proof of concept online SNS supporting primary healthcare promotion is presented in the paper.

  5. An architecture for designing fuzzy logic controllers using neural networks

    Science.gov (United States)

    Berenji, Hamid R.

    1991-01-01

    Described here is an architecture for designing fuzzy controllers through a hierarchical process of control rule acquisition and by using special classes of neural network learning techniques. A new method for learning to refine a fuzzy logic controller is introduced. A reinforcement learning technique is used in conjunction with a multi-layer neural network model of a fuzzy controller. The model learns by updating its prediction of the plant's behavior and is related to the Sutton's Temporal Difference (TD) method. The method proposed here has the advantage of using the control knowledge of an experienced operator and fine-tuning it through the process of learning. The approach is applied to a cart-pole balancing system.

  6. Space Mobile Network: A Near Earth Communications and Navigation Architecture

    Science.gov (United States)

    Israel, David J.; Heckler, Gregory W.; Menrad, Robert J.

    2016-01-01

    This paper shares key findings of NASA's Earth Regime Network Evolution Study (ERNESt) team resulting from its 18-month effort to define a wholly new architecture-level paradigm for the exploitation of space by civil space and commercial sector organizations. Since the launch of Sputnik in October 1957 spaceflight missions have remained highly scripted activities from launch through disposal. The utilization of computer technology has enabled dramatic increases in mission complexity; but, the underlying premise that the diverse actions necessary to meet mission goals requires minute-by-minute scripting, defined weeks in advance of execution, for the life of the mission has remained. This archetype was appropriate for a "new frontier" but now risks overtly constraining the potential market-based opportunities for the innovation considered necessary to efficiently address the complexities associated with meeting communications and navigation requirements projected to be characteristics of the next era of space exploration: a growing number of missions in simultaneous execution, increased variance of mission types and growth in location/orbital regime diversity. The resulting ERNESt architectural cornerstone - the Space Mobile Network (SMN) - was envisioned as critical to creating an environment essential to meeting these future challenges in political, programmatic, technological and budgetary terms. The SMN incorporates technologies such as: Disruption Tolerant Networking (DTN) and optical communications, as well as new operations concepts such as User Initiated Services (UIS) to provide user services analogous to today's terrestrial mobile network user. Results developed in collaboration with NASA's Space Communications and Navigation (SCaN) Division and field centers are reported on. Findings have been validated via briefings to external focus groups and initial ground-based demonstrations. The SMN opens new niches for exploitation by the marketplace of mission

  7. Robust Network Architecture Against Random Threats in WMD Environments: Theoretical Limits and Recovery Strategies

    Science.gov (United States)

    2017-08-01

    Architecture Against Random Threats in WMD Environments: Theoretical Limits and Recovery Strategies Distribution Statement A. Approved for public...international unit. Divide the international unit by the factor to get the U.S. customary unit. Robust Network Architecture Against Random Threats in WMD...network architecture to approach the theoretical limits of network robustness; and how to inter-operate with other available/limited sources for fast

  8. Sensor network architecture for monitoring turtles on seashore

    Science.gov (United States)

    Carvajal-Gámez, Blanca E.; Cruz, Victor; Díaz-Casco, Manuel A.; Franco, Andrea; Escobar, Carolina; Colin, Abilene; Carreto-Arellano, Chadwick

    2017-04-01

    In the last decade, advances in information and communication technologies have made it possible to diversify the use of sensor networks in different areas of knowledge (medicine, education, militia, urbanization, protection of the environment, etc.). At present, this type of tools is used to develop applications that allow the identification and monitoring of endangered animals in their natural habitat; however, there are still limitations because some of the devices used alter the behavior of the animals, as in the case of sea turtles. Research and monitoring of sea turtles is of vital importance in identifying possible threats and ensuring their preservation, the behavior of this species (migration, reproduction, and nesting) is highly related to environmental conditions. Because of this, behavioral changes information of this species can be used to monitor global climatic conditions. This work presents the design, development and implementation of an architecture for the monitoring and identification of the sea turtle using sensor networks. This will allow to obtain information for the different investigations with a greater accuracy than the conventional techniques, through non-invasive means for the species and its habitat. The proposed architecture contemplates the use of new technology devices, selfconfigurable, with low energy consumption, interconnection with various communication protocols and sustainable energy supply (solar, wind, etc.).

  9. Analysis of Terminal Server Architectures for Thin Clients in a High Assurance Network

    National Research Council Canada - National Science Library

    Balmer, Steven R; Irvine, Cynthia E

    2000-01-01

    This paper examines the architectural and security impact of using commercially available, popular terminal servers to support thin clients within the context of a high assurance multilevel network...

  10. Fiber-wireless convergence in next-generation communication networks systems, architectures, and management

    CERN Document Server

    Chang, Gee-Kung; Ellinas, Georgios

    2017-01-01

    This book investigates new enabling technologies for Fi-Wi convergence. The editors discuss Fi-Wi technologies at the three major network levels involved in the path towards convergence: system level, network architecture level, and network management level. The main topics will be: a. At system level: Radio over Fiber (digitalized vs. analogic, standardization, E-band and beyond) and 5G wireless technologies; b. Network architecture level: NGPON, WDM-PON, BBU Hotelling, Cloud Radio Access Networks (C-RANs), HetNets. c. Network management level: SDN for convergence, Next-generation Point-of-Presence, Wi-Fi LTE Handover, Cooperative MultiPoint. • Addresses the Fi-Wi convergence issues at three different levels, namely at the system level, network architecture level, and network management level • Provides approaches in communication systems, network architecture, and management that are expected to steer the evolution towards fiber-wireless convergence • Contributions from leading experts in the field of...

  11. Firewall Architectures for High-Speed Networks: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Errin W. Fulp

    2007-08-20

    Firewalls are a key component for securing networks that are vital to government agencies and private industry. They enforce a security policy by inspecting and filtering traffic arriving or departing from a secure network. While performing these critical security operations, firewalls must act transparent to legitimate users, with little or no effect on the perceived network performance (QoS). Packets must be inspected and compared against increasingly complex rule sets and tables, which is a time-consuming process. As a result, current firewall systems can introduce significant delays and are unable to maintain QoS guarantees. Furthermore, firewalls are susceptible to Denial of Service (DoS) attacks that merely overload/saturate the firewall with illegitimate traffic. Current firewall technology only offers a short-term solution that is not scalable; therefore, the \\textbf{objective of this DOE project was to develop new firewall optimization techniques and architectures} that meet these important challenges. Firewall optimization concerns decreasing the number of comparisons required per packet, which reduces processing time and delay. This is done by reorganizing policy rules via special sorting techniques that maintain the original policy integrity. This research is important since it applies to current and future firewall systems. Another method for increasing firewall performance is with new firewall designs. The architectures under investigation consist of multiple firewalls that collectively enforce a security policy. Our innovative distributed systems quickly divide traffic across different levels based on perceived threat, allowing traffic to be processed in parallel (beyond current firewall sandwich technology). Traffic deemed safe is transmitted to the secure network, while remaining traffic is forwarded to lower levels for further examination. The result of this divide-and-conquer strategy is lower delays for legitimate traffic, higher throughput

  12. FIGARO ( Future Internet Gateway-based Architecture of Residential Networks ) D5.2: Architecture for service federation in residential networks

    NARCIS (Netherlands)

    Hartog, F.T.H. den; Hillen, B.A.G.; Tijmes, M.R.

    2011-01-01

    This document defines the preliminary version of the FIGARO architectural solution for federation within residential networks. The architecture is derived from use cases from the domains of e-health, energy management, domotics and social community services and thus supports requirements from each

  13. Mobile network architecture of the long-range WindScanner system

    DEFF Research Database (Denmark)

    Vasiljevic, Nikola; Lea, Guillaume; Hansen, Per

    the requirements of running the long-range WindScanner system using a mobile network such as 3G. This architecture allows us to have the WindScanners and the master computer in different geographical locations, and in general facilitates deployments of the long-range WindScanner system.......In this report we have presented the network architecture of the long-range WindScanner system that allows utilization of mobile network connections without the use of static public IP addresses. The architecture mitigates the issues of additional fees and contractual obligations that are linked...... to the acquisition of the mobile network connections with static public IP addresses. The architecture consists of a hardware VPN solution based on the network appliances Z1 and MX60 from Cisco Meraki with additional 3G or 4G dongles. With the presented network architecture and appropriate configuration, we fulfill...

  14. Efficient network-matrix architecture for general flow transport inspired by natural pinnate leaves.

    Science.gov (United States)

    Hu, Liguo; Zhou, Han; Zhu, Hanxing; Fan, Tongxiang; Zhang, Di

    2014-11-14

    Networks embedded in three dimensional matrices are beneficial to deliver physical flows to the matrices. Leaf architectures, pervasive natural network-matrix architectures, endow leaves with high transpiration rates and low water pressure drops, providing inspiration for efficient network-matrix architectures. In this study, the network-matrix model for general flow transport inspired by natural pinnate leaves is investigated analytically. The results indicate that the optimal network structure inspired by natural pinnate leaves can greatly reduce the maximum potential drop and the total potential drop caused by the flow through the network while maximizing the total flow rate through the matrix. These results can be used to design efficient networks in network-matrix architectures for a variety of practical applications, such as tissue engineering, cell culture, photovoltaic devices and heat transfer.

  15. Service Oriented Architecture for Wireless Sensor Networks in Agriculture

    Science.gov (United States)

    Sawant, S. A.; Adinarayana, J.; Durbha, S. S.; Tripathy, A. K.; Sudharsan, D.

    2012-08-01

    Rapid advances in Wireless Sensor Network (WSN) for agricultural applications has provided a platform for better decision making for crop planning and management, particularly in precision agriculture aspects. Due to the ever-increasing spread of WSNs there is a need for standards, i.e. a set of specifications and encodings to bring multiple sensor networks on common platform. Distributed sensor systems when brought together can facilitate better decision making in agricultural domain. The Open Geospatial Consortium (OGC) through Sensor Web Enablement (SWE) provides guidelines for semantic and syntactic standardization of sensor networks. In this work two distributed sensing systems (Agrisens and FieldServer) were selected to implement OGC SWE standards through a Service Oriented Architecture (SOA) approach. Online interoperable data processing was developed through SWE components such as Sensor Model Language (SensorML) and Sensor Observation Service (SOS). An integrated web client was developed to visualize the sensor observations and measurements that enables the retrieval of crop water resources availability and requirements in a systematic manner for both the sensing devices. Further, the client has also the ability to operate in an interoperable manner with any other OGC standardized WSN systems. The study of WSN systems has shown that there is need to augment the operations / processing capabilities of SOS in order to understand about collected sensor data and implement the modelling services. Also, the very low cost availability of WSN systems in future, it is possible to implement the OGC standardized SWE framework for agricultural applications with open source software tools.

  16. A guide to integrating transcriptional regulatory and metabolic networks using PROM (probabilistic regulation of metabolism).

    Science.gov (United States)

    Simeonidis, Evangelos; Chandrasekaran, Sriram; Price, Nathan D

    2013-01-01

    The integration of transcriptional regulatory and metabolic networks is a crucial step in the process of predicting metabolic behaviors that emerge from either genetic or environmental changes. Here, we present a guide to PROM (probabilistic regulation of metabolism), an automated method for the construction and simulation of integrated metabolic and transcriptional regulatory networks that enables large-scale phenotypic predictions for a wide range of model organisms.

  17. RoboSmith: Wireless Networked Architecture for Multiagent Robotic System

    Directory of Open Access Journals (Sweden)

    Florin Moldoveanu

    2010-11-01

    Full Text Available In this paper is presented an architecture for a flexible mini robot for a multiagent robotic system. In a multiagent system the value of an individual agent is negligible since the goal of the system is essential. Thus, the agents (robots need to be small, low cost and cooperative. RoboSmith are designed based on these conditions. The proposed architecture divide a robot into functional modules such as locomotion, control, sensors, communication, and actuation. Any mobile robot can be constructed by combining these functional modules for a specific application. An embedded software with dynamic task uploading and multi-tasking abilities is developed in order to create better interface between robots and the command center and among the robots. The dynamic task uploading allows the robots change their behaviors in runtime. The flexibility of the robots is given by facts that the robots can work in multiagent system, as master-slave, or hybrid mode, can be equipped with different modules and possibly be used in other applications such as mobile sensor networks remote sensing, and plant monitoring.

  18. Architecture and Applications of Functional Three-Dimensional Graphene Networks

    DEFF Research Database (Denmark)

    Dey, Ramendra Sundar; Chi, Qijin

    2015-01-01

    building blocksfor the bottom-up architecture of various graphene based nanomaterials. Th eassembly of functionalized GNS into three-dimensional (3D) porous graphenenetworks represents a novel approach. Resulting 3D porous graphene materialsposses unique physicochemical properties such as large surface......As the fi rst atomic-thick two-dimensional crystalline material, graphene has continuouslycreated a wonder land in materials science within the past decade. Anumber of methods have been developed for preparation and functionalizationof single-layered graphene nanosheets (GNS), which are essential...... areas, goodconductivity and mechanical strength, high thermal stability and desirable fl exibility,which altogether makes this new type of porous materials be highly attractivefor a wide range of applications. In this chapter, we will cover some crucialaspects of porous graphene networked materials...

  19. Metabolic networks of Cucurbita maxima phloem.

    Science.gov (United States)

    Fiehn, Oliver

    2003-03-01

    Metabolomic analysis aims at a comprehensive characterization of biological samples. Yet, biologically meaningful interpretations are often limited by the poor spatial and temporal resolution of the acquired data sets. One way to remedy this is to limit the complexity of the cell types being studied. Cucurbita maxima Duch. vascular exudates provide an excellent material for metabolomics in this regard. Using automated mass spectral deconvolution, over 400 components have been detected in these exudates, but only 90 of them were tentatively identified. Many amino compounds were found in vascular exudates from leaf petioles at concentrations several orders of magnitude higher than in tissue disks from the same leaves, whereas hexoses and sucrose were found in far lower amounts. In order to find the expected impact of assimilation rates on sugar levels, total phloem composition of eight leaves from four plants was followed over 4.5 days. Surprisingly, no diurnal rhythm was found for any of the phloem metabolites that was statistically valid for all eight leaves. Instead, each leaf had its own distinct vascular exudate profile similar to leaves from the same plant, but clearly different from leaves harvested from plants at the same developmental stage. Thirty to forty per cent of all metabolite levels of individual leaves were different from the average of all metabolite profiles. Using metabolic co-regulation analysis, similarities and differences between the exudate profiles were more accurately characterized through network computation, specifically with respect to nitrogen metabolism.

  20. Scale-space measures for graph topology link protein network architecture to function

    NARCIS (Netherlands)

    Hulsman, M.; Dimitrakopoulos, C.; De Ridder, J.

    2014-01-01

    MOTIVATION: The network architecture of physical protein interactions is an important determinant for the molecular functions that are carried out within each cell. To study this relation, the network architecture can be characterized by graph topological characteristics such as shortest paths and

  1. Deciphering transcriptional and metabolic networks associated with lysine metabolism during Arabidopsis seed development.

    Science.gov (United States)

    Angelovici, Ruthie; Fait, Aaron; Zhu, Xiaohong; Szymanski, Jedrzej; Feldmesser, Ester; Fernie, Alisdair R; Galili, Gad

    2009-12-01

    In order to elucidate transcriptional and metabolic networks associated with lysine (Lys) metabolism, we utilized developing Arabidopsis (Arabidopsis thaliana) seeds as a system in which Lys synthesis could be stimulated developmentally without application of chemicals and coupled this to a T-DNA insertion knockout mutation impaired in Lys catabolism. This seed-specific metabolic perturbation stimulated Lys accumulation starting from the initiation of storage reserve accumulation. Our results revealed that the response of seed metabolism to the inducible alteration of Lys metabolism was relatively minor; however, that which was observable operated in a modular manner. They also demonstrated that Lys metabolism is strongly associated with the operation of the tricarboxylic acid cycle while largely disconnected from other metabolic networks. In contrast, the inducible alteration of Lys metabolism was strongly associated with gene networks, stimulating the expression of hundreds of genes controlling anabolic processes that are associated with plant performance and vigor while suppressing a small number of genes associated with plant stress interactions. The most pronounced effect of the developmentally inducible alteration of Lys metabolism was an induction of expression of a large set of genes encoding ribosomal proteins as well as genes encoding translation initiation and elongation factors, all of which are associated with protein synthesis. With respect to metabolic regulation, the inducible alteration of Lys metabolism was primarily associated with altered expression of genes belonging to networks of amino acids and sugar metabolism. The combined data are discussed within the context of network interactions both between and within metabolic and transcriptional control systems.

  2. Distributed Prognostics and Health Management with a Wireless Network Architecture

    Science.gov (United States)

    Goebel, Kai; Saha, Sankalita; Sha, Bhaskar

    2013-01-01

    A heterogeneous set of system components monitored by a varied suite of sensors and a particle-filtering (PF) framework, with the power and the flexibility to adapt to the different diagnostic and prognostic needs, has been developed. Both the diagnostic and prognostic tasks are formulated as a particle-filtering problem in order to explicitly represent and manage uncertainties in state estimation and remaining life estimation. Current state-of-the-art prognostic health management (PHM) systems are mostly centralized in nature, where all the processing is reliant on a single processor. This can lead to a loss in functionality in case of a crash of the central processor or monitor. Furthermore, with increases in the volume of sensor data as well as the complexity of algorithms, traditional centralized systems become for a number of reasons somewhat ungainly for successful deployment, and efficient distributed architectures can be more beneficial. The distributed health management architecture is comprised of a network of smart sensor devices. These devices monitor the health of various subsystems or modules. They perform diagnostics operations and trigger prognostics operations based on user-defined thresholds and rules. The sensor devices, called computing elements (CEs), consist of a sensor, or set of sensors, and a communication device (i.e., a wireless transceiver beside an embedded processing element). The CE runs in either a diagnostic or prognostic operating mode. The diagnostic mode is the default mode where a CE monitors a given subsystem or component through a low-weight diagnostic algorithm. If a CE detects a critical condition during monitoring, it raises a flag. Depending on availability of resources, a networked local cluster of CEs is formed that then carries out prognostics and fault mitigation by efficient distribution of the tasks. It should be noted that the CEs are expected not to suspend their previous tasks in the prognostic mode. When the

  3. Low-Cost Hybrid ROADM Architectures for Scalable C/DWDM Metro Networks

    DEFF Research Database (Denmark)

    Nooruzzaman, Md; Halima, Elbiaze

    2016-01-01

    be introduced to merge CWDM and DWDM traffic at the optical layer. This ensures two advantages: reduced initial investment and scalability for deploying DWDM channels in the future. This article presents various ROADM architectures, and explores the novel optical node architecture of hybrid C/DWDM networks......CWDM networks have proven to be a promising first-step metro and access network architecture, offering a significant cost advantage over DWDM due to the lower cost of lasers and the filters used in CWDM modules. If demand grows beyond the capacity covered by CWDM channels, DWDM network elements can......, consisting of CWDM, hybrid C/DWDM, and junction nodes connecting two rings. Evaluation has shown that the hybrid ROADM architecture is superior to other conventional ROADM architectures in terms of scalability and the initial cost of optical nodes and networks....

  4. An Open Distributed Architecture for Sensor Networks for Risk Management

    Directory of Open Access Journals (Sweden)

    Ralf Denzer

    2008-03-01

    Full Text Available Sensors provide some of the basic input data for risk management of natural andman-made hazards. Here the word ‘sensors’ covers everything from remote sensingsatellites, providing invaluable images of large regions, through instruments installed on theEarth’s surface to instruments situated in deep boreholes and on the sea floor, providinghighly-detailed point-based information from single sites. Data from such sensors is used inall stages of risk management, from hazard, vulnerability and risk assessment in the preeventphase, information to provide on-site help during the crisis phase through to data toaid in recovery following an event. Because data from sensors play such an important part inimproving understanding of the causes of risk and consequently in its mitigation,considerable investment has been made in the construction and maintenance of highlysophisticatedsensor networks. In spite of the ubiquitous need for information from sensornetworks, the use of such data is hampered in many ways. Firstly, information about thepresence and capabilities of sensor networks operating in a region is difficult to obtain dueto a lack of easily available and usable meta-information. Secondly, once sensor networkshave been identified their data it is often difficult to access due to a lack of interoperability between dissemination and acquisition systems. Thirdly, the transfer and processing ofinformation from sensors is limited, again by incompatibilities between systems. Therefore,the current situation leads to a lack of efficiency and limited use of the available data thathas an important role to play in risk mitigation. In view of this situation, the EuropeanCommission (EC is funding a number of Integrated Projects within the Sixth FrameworkProgramme concerned with improving the accessibility of data and services for riskmanagement. Two of these projects: ‘Open Architecture and Spatial Data

  5. From genomes to in silico cells via metabolic networks

    DEFF Research Database (Denmark)

    Borodina, Irina; Nielsen, Jens

    2005-01-01

    Genome-scale metabolic models are the focal point of systems biology as they allow the collection of various data types in a form suitable for mathematical analysis. High-quality metabolic networks and metabolic networks with incorporated regulation have been successfully used for the analysis of...... approaches to obtain an in silico prediction of cellular function based on the interaction of all of the cellular components....

  6. The evolution of modularity in bacterial metabolic networks.

    Science.gov (United States)

    Kreimer, Anat; Borenstein, Elhanan; Gophna, Uri; Ruppin, Eytan

    2008-05-13

    Deciphering the modular organization of metabolic networks and understanding how modularity evolves have attracted tremendous interest in recent years. Here, we present a comprehensive large scale characterization of modularity across the bacterial tree of life, systematically quantifying the modularity of the metabolic networks of >300 bacterial species. Three main determinants of metabolic network modularity are identified. First, network size is an important topological determinant of network modularity. Second, several environmental factors influence network modularity, with endosymbionts and mammal-specific pathogens having lower modularity scores than bacterial species that occupy a wider range of niches. Moreover, even among the pathogens, those that alternate between two distinct niches, such as insect and mammal, tend to have relatively high metabolic network modularity. Third, horizontal gene transfer is an important force that contributes significantly to metabolic modularity. We additionally reconstruct the metabolic network of ancestral bacterial species and examine the evolution of modularity across the tree of life. This reveals a trend of modularity decrease from ancestors to descendants that is likely the outcome of niche specialization and the incorporation of peripheral metabolic reactions.

  7. Criteria for Evaluating Alternative Network and Link Layer Protocols for the NASA Constellation Program Communication Architecture

    Science.gov (United States)

    Benbenek, Daniel; Soloff, Jason; Lieb, Erica

    2010-01-01

    Selecting a communications and network architecture for future manned space flight requires an evaluation of the varying goals and objectives of the program, development of communications and network architecture evaluation criteria, and assessment of critical architecture trades. This paper uses Cx Program proposed exploration activities as a guideline; lunar sortie, outpost, Mars, and flexible path options are described. A set of proposed communications network architecture criteria are proposed and described. They include: interoperability, security, reliability, and ease of automating topology changes. Finally a key set of architecture options are traded including (1) multiplexing data at a common network layer vs. at the data link layer, (2) implementing multiple network layers vs. a single network layer, and (3) the use of a particular network layer protocol, primarily IPv6 vs. Delay Tolerant Networking (DTN). In summary, the protocol options are evaluated against the proposed exploration activities and their relative performance with respect to the criteria are assessed. An architectural approach which includes (a) the capability of multiplexing at both the network layer and the data link layer and (b) a single network layer for operations at each program phase, as these solutions are best suited to respond to the widest array of program needs and meet each of the evaluation criteria.

  8. Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network

    OpenAIRE

    Mart?n-Jim?nez, Cynthia A.; Salazar-Barreto, Diego; Barreto, George E.; Gonz?lez, Janneth

    2017-01-01

    Astrocytes are the most abundant cells of the central nervous system; they have a predominant role in maintaining brain metabolism. In this sense, abnormal metabolic states have been found in different neuropathological diseases. Determination of metabolic states of astrocytes is difficult to model using current experimental approaches given the high number of reactions and metabolites present. Thus, genome-scale metabolic networks derived from transcriptomic data can be used as a framework t...

  9. Quantitative Comparison of the Efficiency and Scalability of the Current and Future LTE Network Architectures

    Directory of Open Access Journals (Sweden)

    Morteza Karimzadeh

    2017-01-01

    Full Text Available The core architecture of current mobile networks does not scale well to cope with future traffic demands owing to its highly centralized composition. Typically, it is believed that decentralization of the network architecture would be a sustainable approach to deal with ever growing amount of mobile data traffic. Nevertheless, the decentralization strategy of network architecture has not been properly examined through quantitative performance studies. Given that LTE will be the leading mobile networking technology in the coming 5–10 years, we conduct a hybrid study model to compare performance of current and future (decentralized LTE network architectures. Particularly, our analysis presents numerical results quantifying impact of the number of attached nodes on the load at network routers and links, on the latency, and on the processing cost of the user’s data and control planes. Analytical results demonstrate that decentralization of the LTE network architecture achieves higher performance compared to the current architecture and improves the latency and cost of data packet delivery more than 10 and 6 times, respectively. Furthermore, it is also observed that GTP outperforms PMIP for all studied performance metrics in the decentralized architecture and provides about twofold better latency and cost for data packet delivery and roughly 6 times lower data traffic load on the network routers.

  10. The network architecture and site test of DCIS in Lungmen nuclear power station

    International Nuclear Information System (INIS)

    Lee, C. K.

    2006-01-01

    The Lungmen Nuclear Power Station (LMNPS) is located in North-Eastern Seashore of Taiwan. LMNPP has two units. Each unit generates 1350 Megawatts. It is the first ABWR Plant in Taiwan and is under-construction now. Due to contractual arrangement, there are seven large I and C suppliers/designers, which are GE NUMAC, DRS, Invensys, GEIS, Hitachi, MHI, and Stone and Webster company. The Distributed Control and Information System (DCIS) in Lungmen are fully integrated with the state-of-the-art computer and network technology. General Electric is the leading designer for integration of DCIS. This paper presents Network Architecture and the Site Test of DCIS. The network architectures are follows. GE NUMAC System adopts the point to point architecture, DRS System adopts Ring type architecture with SCRAMNET protocol, Inevnsys system adopts IGiga Byte Backbone mesh network with Rapid Spanning Tree Protocol, GEIS adopts Ethernet network with EGD protocol, Hitachi adopts ring type network with proprietary protocol. MHI adopt Ethernet network with UDP. The data-links are used for connection between different suppliers. The DCIS architecture supports the plant automation, the alarm prioritization and alarm suppression, and uniform MMI screen for entire plant. The Test Program regarding the integration of different network architectures and Initial DCIS architecture Setup for 161KV Energization will be discussed. Test tool for improving site test schedule, and lessons learned from FAT will be discussed too. And conclusions are at the end of this paper. (authors)

  11. The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism.

    Science.gov (United States)

    Goldman, Aaron David; Beatty, Joshua T; Landweber, Laura F

    2016-01-01

    The triosephosphate isomerase (TIM) barrel protein fold is a structurally repetitive architecture that is present in approximately 10% of all enzymes. It is generally assumed that this ubiquity in modern proteomes reflects an essential historical role in early protein-mediated metabolism. Here, we provide quantitative and comparative analyses to support several hypotheses about the early importance of the TIM barrel architecture. An information theoretical analysis of protein structures supports the hypothesis that the TIM barrel architecture could arise more easily by duplication and recombination compared to other mixed α/β structures. We show that TIM barrel enzymes corresponding to the most taxonomically broad superfamilies also have the broadest range of functions, often aided by metal and nucleotide-derived cofactors that are thought to reflect an earlier stage of metabolic evolution. By comparison to other putatively ancient protein architectures, we find that the functional diversity of TIM barrel proteins cannot be explained simply by their antiquity. Instead, the breadth of TIM barrel functions can be explained, in part, by the incorporation of a broad range of cofactors, a trend that does not appear to be shared by proteins in general. These results support the hypothesis that the simple and functionally general TIM barrel architecture may have arisen early in the evolution of protein biosynthesis and provided an ideal scaffold to facilitate the metabolic transition from ribozymes, peptides, and geochemical catalysts to modern protein enzymes.

  12. Neural network architecture for cognitive navigation in dynamic environments.

    Science.gov (United States)

    Villacorta-Atienza, José Antonio; Makarov, Valeri A

    2013-12-01

    Navigation in time-evolving environments with moving targets and obstacles requires cognitive abilities widely demonstrated by even simplest animals. However, it is a long-standing challenging problem for artificial agents. Cognitive autonomous robots coping with this problem must solve two essential tasks: 1) understand the environment in terms of what may happen and how I can deal with this and 2) learn successful experiences for their further use in an automatic subconscious way. The recently introduced concept of compact internal representation (CIR) provides the ground for both the tasks. CIR is a specific cognitive map that compacts time-evolving situations into static structures containing information necessary for navigation. It belongs to the class of global approaches, i.e., it finds trajectories to a target when they exist but also detects situations when no solution can be found. Here we extend the concept of situations with mobile targets. Then using CIR as a core, we propose a closed-loop neural network architecture consisting of conscious and subconscious pathways for efficient decision-making. The conscious pathway provides solutions to novel situations if the default subconscious pathway fails to guide the agent to a target. Employing experiments with roving robots and numerical simulations, we show that the proposed architecture provides the robot with cognitive abilities and enables reliable and flexible navigation in realistic time-evolving environments. We prove that the subconscious pathway is robust against uncertainty in the sensory information. Thus if a novel situation is similar but not identical to the previous experience (because of, e.g., noisy perception) then the subconscious pathway is able to provide an effective solution.

  13. Quantum perceptron over a field and neural network architecture selection in a quantum computer.

    Science.gov (United States)

    da Silva, Adenilton José; Ludermir, Teresa Bernarda; de Oliveira, Wilson Rosa

    2016-04-01

    In this work, we propose a quantum neural network named quantum perceptron over a field (QPF). Quantum computers are not yet a reality and the models and algorithms proposed in this work cannot be simulated in actual (or classical) computers. QPF is a direct generalization of a classical perceptron and solves some drawbacks found in previous models of quantum perceptrons. We also present a learning algorithm named Superposition based Architecture Learning algorithm (SAL) that optimizes the neural network weights and architectures. SAL searches for the best architecture in a finite set of neural network architectures with linear time over the number of patterns in the training set. SAL is the first learning algorithm to determine neural network architectures in polynomial time. This speedup is obtained by the use of quantum parallelism and a non-linear quantum operator. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Graph methods for the investigation of metabolic networks in parasitology.

    Science.gov (United States)

    Cottret, Ludovic; Jourdan, Fabien

    2010-08-01

    Recently, a way was opened with the development of many mathematical methods to model and analyze genome-scale metabolic networks. Among them, methods based on graph models enable to us quickly perform large-scale analyses on large metabolic networks. However, it could be difficult for parasitologists to select the graph model and methods adapted to their biological questions. In this review, after briefly addressing the problem of the metabolic network reconstruction, we propose an overview of the graph-based approaches used in whole metabolic network analyses. Applications highlight the usefulness of this kind of approach in the field of parasitology, especially by suggesting metabolic targets for new drugs. Their development still represents a major challenge to fight against the numerous diseases caused by parasites.

  15. Metabolic pathways variability and sequence/networks comparisons

    Science.gov (United States)

    Tun, Kyaw; Dhar, Pawan K; Palumbo, Maria Concetta; Giuliani, Alessandro

    2006-01-01

    Background In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees amenable to be compared with correspondent sequence based trees. The procedure can be applied to both single metabolic modules and whole metabolic network data without the need of any specific assumption. Results We demonstrate both the ability of the proposed method to build reliable biological classification of a set of microrganisms and the strong correlation between the metabolic network wiringand involved enzymes sequence space. Conclusion The method represents a valuable tool for the investigation of genotype/phenotype correlationsallowing for a direct comparison of different species as for their metabolic machinery. In addition the detection of enzymes whose sequence space is maximally correlated with the metabolicnetwork space gives an indication of the most crucial (on an evolutionary viewpoint) steps of the metabolic process. PMID:16420696

  16. Metabolic pathways variability and sequence/networks comparisons

    Directory of Open Access Journals (Sweden)

    Palumbo Maria

    2006-01-01

    Full Text Available Abstract Background In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees amenable to be compared with correspondent sequence based trees. The procedure can be applied to both single metabolic modules and whole metabolic network data without the need of any specific assumption. Results We demonstrate both the ability of the proposed method to build reliable biological classification of a set of microrganisms and the strong correlation between the metabolic network wiringand involved enzymes sequence space. Conclusion The method represents a valuable tool for the investigation of genotype/phenotype correlationsallowing for a direct comparison of different species as for their metabolic machinery. In addition the detection of enzymes whose sequence space is maximally correlated with the metabolicnetwork space gives an indication of the most crucial (on an evolutionary viewpoint steps of the metabolic process.

  17. CRISP. Distributed Network Architectures D1.7

    International Nuclear Information System (INIS)

    Andrieu, C.; Fontela, M.; Raison, B.; Enacheanu, B.; Pham, H.; Besanger, Y.; Randrup, M.; Nilsson, U.B.; Kamphuis, I.G.; Schaeffer, G.J.

    2005-08-01

    This document summarises a possible evolution of the merge of ICT network and EPS in the scope of a future electrical architecture. A general overview on several aspects of the transmission and the distribution networks (technical operation, trading, securing, defence plan) and on several aspects of ICT improvement and risks has been given in previous work packages of the part I of the CRISP project. This document brings a common point of view between the partners on this future merge of the various domains involved. The approach is based on the study of given application based on chosen cases, trying then to show a more general view on the whole system. The MV network, including of course the main HV/MV substation, has a specific position in our purpose: historical, technical and trading boundary between the transmission and the distribution system, involving new functions in the context of a future massive and dispersed generation. The whole electrical system is not yet ready to work properly (supply performances maintained at the same level) with a lot of DG and DG-RES and at the same time with a new and complete electrical deregulated market. The multiplication of actors (production, transmission, distribution, customers, local networks) led by the rules of deregulation is an additional issue for planning and operating correctly the network in the long term. The interactions expected between the low level of the network (distribution EPS, VPP, customers, small aggregators) and the high level of the network (transmission EPS, large plants, LSVPP, large aggregators) require to structure the system in different integrated levels, allowing the operators at each stage to manage efficiently the power flux for steady-state, transients and temporary electrical variations. Compared with the present SCADA situation, the ICT will allow the needed information to be shared by various tools and actors at various locations, and will allow the local intelligence to be

  18. T-SDN architecture for space and ground integrated optical transport network

    Science.gov (United States)

    Nie, Kunkun; Hu, Wenjing; Gao, Shenghua; Chang, Chengwu

    2015-11-01

    Integrated optical transport network is the development trend of the future space information backbone network. The space and ground integrated optical transport network(SGIOTN) may contain a variety of equipment and systems. Changing the network or meeting some innovation missions in the network will be an expensive implement. Software Defined Network(SDN) provides a good solution to flexibly adding process logic, timely control states and resources of the whole network, as well as shielding the differences of heterogeneous equipment and so on. According to the characteristics of SGIOTN, we propose an transport SDN architecture for it, with hierarchical control plane and data plane composed of packet networks and optical transport networks.

  19. Architecture aspects of optical networks: a Swisscom approach

    Science.gov (United States)

    Schiess, Marcel; Bosshard, Hans Jakob

    2003-04-01

    Swisscom Fixnet Ltd. has evaluated a new platform for the broadband transport requirements. This new platform will be a combination of advanced SDH (Synchronous Digital Hierarchy) and WDM (Wavelength Division Multiplexing) technology and the principal goal is to cover the bandwidth segment between STM-1 and STM-64. In addition new forthcoming data services e.g. Gigabit Ethernet can be delivered on the same platform infrastructure between remote areas. This paper describes the drivers for the project as well as the requirements at the start of the evaluation process of the transport platform. The requirements include technical, operational and financial aspects. The main focus will then be the discussion of the core, metro or regional area architecture. Various scenarios have been analyzed and compared. The main conclusions have been that the number of "flexibility points" should be kept lower than in traditional SDH-network due to cost reasons in a broadband environment with packet oriented services. Furthermore, the WDM technology is not economically reasonable for a low number of channels in the regional area. The paper then summarizes these lessons learned from the project.

  20. Integration of Genome Scale Metabolic Networks and Gene Regulation of Metabolic Enzymes With Physiologically Based Pharmacokinetics

    Science.gov (United States)

    Maldonado, Elaina M.; Leoncikas, Vytautas; Fisher, Ciarán P.; Moore, J. Bernadette; Plant, Nick J.

    2017-01-01

    The scope of physiologically based pharmacokinetic (PBPK) modeling can be expanded by assimilation of the mechanistic models of intracellular processes from systems biology field. The genome scale metabolic networks (GSMNs) represent a whole set of metabolic enzymes expressed in human tissues. Dynamic models of the gene regulation of key drug metabolism enzymes are available. Here, we introduce GSMNs and review ongoing work on integration of PBPK, GSMNs, and metabolic gene regulation. We demonstrate example models. PMID:28782239

  1. Predicting Electrocardiogram and Arterial Blood Pressure Waveforms with Different Echo State Network Architectures

    Science.gov (United States)

    2014-11-01

    Predicting Electrocardiogram and Arterial Blood Pressure Waveforms with Different Echo State Network Architectures Allan Fong, MS1,3, Ranjeev...the medical staff in Intensive Care Units. The ability to predict electrocardiogram and arterial blood pressure waveforms can potentially help the...type of neural network for mining, understanding, and predicting electrocardiogram and arterial blood pressure waveforms. Several network

  2. Internet of Things Heterogeneous Interoperable Network Architecture Design

    OpenAIRE

    Bhalerao, Dipashree M.

    2014-01-01

    Internet of Thing‘s (IoT) state of the art deduce that there is no mature Internet of Things architecture available. Thesis contributes an abstract generic IoT system reference architecture development with specifications. Novelties of thesis are proposed solutions and implementations for Scalability, heterogeneous interoperability, security and extension of IoT architecture for rural, poor and catastrophic (RPC) areas. VLC is proposed and proved as one of the suitable internetwork means to o...

  3. A Formally Verified Decentralized Key Management Architecture for Wireless Sensor Networks

    NARCIS (Netherlands)

    Law, Y.W.; Corin, R.J.; Etalle, Sandro; Hartel, Pieter H.

    We present a decentralized key management architecture for wireless sensor networks, covering the aspects of key deployment, key refreshment and key establishment. Our architecture is based on a clear set of assumptions and guidelines. Balance between security and energy consumption is achieved by

  4. Horizontal and vertical growth of S. cerevisiae metabolic network.

    KAUST Repository

    Grassi, Luigi

    2011-10-14

    BACKGROUND: The growth and development of a biological organism is reflected by its metabolic network, the evolution of which relies on the essential gene duplication mechanism. There are two current views about the evolution of metabolic networks. The retrograde model hypothesizes that a pathway evolves by recruiting novel enzymes in a direction opposite to the metabolic flow. The patchwork model is instead based on the assumption that the evolution is based on the exploitation of broad-specificity enzymes capable of catalysing a variety of metabolic reactions. RESULTS: We analysed a well-studied unicellular eukaryotic organism, S. cerevisiae, and studied the effect of the removal of paralogous gene products on its metabolic network. Our results, obtained using different paralog and network definitions, show that, after an initial period when gene duplication was indeed instrumental in expanding the metabolic space, the latter reached an equilibrium and subsequent gene duplications were used as a source of more specialized enzymes rather than as a source of novel reactions. We also show that the switch between the two evolutionary strategies in S. cerevisiae can be dated to about 350 million years ago. CONCLUSIONS: Our data, obtained through a novel analysis methodology, strongly supports the hypothesis that the patchwork model better explains the more recent evolution of the S. cerevisiae metabolic network. Interestingly, the effects of a patchwork strategy acting before the Euascomycete-Hemiascomycete divergence are still detectable today.

  5. Architecture

    OpenAIRE

    Clear, Nic

    2014-01-01

    When discussing science fiction’s relationship with architecture, the usual practice is to look at the architecture “in” science fiction—in particular, the architecture in SF films (see Kuhn 75-143) since the spaces of literary SF present obvious difficulties as they have to be imagined. In this essay, that relationship will be reversed: I will instead discuss science fiction “in” architecture, mapping out a number of architectural movements and projects that can be viewed explicitly as scien...

  6. Seafloor classification using echo- waveforms: A method employing hybrid neural network architecture

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, B.; Mahale, V.; DeSouza, C.; Das, P.

    This letter presents seafloor classification study results of a hybrid artificial neural network architecture known as learning vector quantization. Single beam echo-sounding backscatter waveform data from three different seafloors of the western...

  7. Slave nodes and the controllability of metabolic networks

    International Nuclear Information System (INIS)

    Kim, Dong-Hee; Motter, Adilson E

    2009-01-01

    Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell behavior of a large metabolic network be controlled by constraining the flux of one or more reactions in the network? This touches upon the issue of the number of degrees of freedom contained by one such network. Using the metabolic network of Escherichia coli as a model system, here we address this question theoretically by exploring not only reaction deletions, but also a continuum of all possible reaction expression levels. We show that the behavior of the metabolic network can be largely manipulated by the pinned expression of a single reaction. In particular, a relevant fraction of the metabolic reactions exhibits canalizing interactions, in that the specification of one reaction flux determines cellular growth as well as the fluxes of most other reactions in optimal steady states. The activity of individual reactions can thus be used as surrogates to monitor and possibly control cellular growth and other whole-cell behaviors. In addition to its implications for the study of control processes, our methodology provides a new approach to study how the integrated dynamics of the entire metabolic network emerges from the coordinated behavior of its component parts.

  8. Does habitat variability really promote metabolic network modularity?

    Science.gov (United States)

    Takemoto, Kazuhiro

    2013-01-01

    The hypothesis that variability in natural habitats promotes modular organization is widely accepted for cellular networks. However, results of some data analyses and theoretical studies have begun to cast doubt on the impact of habitat variability on modularity in metabolic networks. Therefore, we re-evaluated this hypothesis using statistical data analysis and current metabolic information. We were unable to conclude that an increase in modularity was the result of habitat variability. Although horizontal gene transfer was also considered because it may contribute for survival in a variety of environments, closely related to habitat variability, and is known to be positively correlated with network modularity, such a positive correlation was not concluded in the latest version of metabolic networks. Furthermore, we demonstrated that the previously observed increase in network modularity due to habitat variability and horizontal gene transfer was probably due to a lack of available data on metabolic reactions. Instead, we determined that modularity in metabolic networks is dependent on species growth conditions. These results may not entirely discount the impact of habitat variability and horizontal gene transfer. Rather, they highlight the need for a more suitable definition of habitat variability and a more careful examination of relationships of the network modularity with horizontal gene transfer, habitats, and environments.

  9. Modeling of a 3DTV service in the software-defined networking architecture

    Science.gov (United States)

    Wilczewski, Grzegorz

    2014-11-01

    In this article a newly developed concept towards modeling of a multimedia service offering stereoscopic motion imagery is presented. Proposed model is based on the approach of utilization of Software-defined Networking or Software Defined Networks architecture (SDN). The definition of 3D television service spanning SDN concept is identified, exposing basic characteristic of a 3DTV service in a modern networking organization layout. Furthermore, exemplary functionalities of the proposed 3DTV model are depicted. It is indicated that modeling of a 3DTV service in the Software-defined Networking architecture leads to multiplicity of improvements, especially towards flexibility of a service supporting heterogeneity of end user devices.

  10. A compendium of inborn errors of metabolism mapped onto the human metabolic network.

    Science.gov (United States)

    Sahoo, Swagatika; Franzson, Leifur; Jonsson, Jon J; Thiele, Ines

    2012-10-01

    Inborn errors of metabolism (IEMs) are hereditary metabolic defects, which are encountered in almost all major metabolic pathways occurring in man. Many IEMs are screened for in neonates through metabolomic analysis of dried blood spot samples. To enable the mapping of these metabolomic data onto the published human metabolic reconstruction, we added missing reactions and pathways involved in acylcarnitine (AC) and fatty acid oxidation (FAO) metabolism. Using literary data, we reconstructed an AC/FAO module consisting of 352 reactions and 139 metabolites. When this module was combined with the human metabolic reconstruction, the synthesis of 39 acylcarnitines and 22 amino acids, which are routinely measured, was captured and 235 distinct IEMs could be mapped. We collected phenotypic and clinical features for each IEM enabling comprehensive classification. We found that carbohydrate, amino acid, and lipid metabolism were most affected by the IEMs, while the brain was the most commonly affected organ. Furthermore, we analyzed the IEMs in the context of metabolic network topology to gain insight into common features between metabolically connected IEMs. While many known examples were identified, we discovered some surprising IEM pairs that shared reactions as well as clinical features but not necessarily causal genes. Moreover, we could also re-confirm that acetyl-CoA acts as a central metabolite. This network based analysis leads to further insight of hot spots in human metabolism with respect to IEMs. The presented comprehensive knowledge base of IEMs will provide a valuable tool in studying metabolic changes involved in inherited metabolic diseases.

  11. Structuring evolution: biochemical networks and metabolic diversification in birds.

    Science.gov (United States)

    Morrison, Erin S; Badyaev, Alexander V

    2016-08-25

    Recurrence and predictability of evolution are thought to reflect the correspondence between genomic and phenotypic dimensions of organisms, and the connectivity in deterministic networks within these dimensions. Direct examination of the correspondence between opportunities for diversification imbedded in such networks and realized diversity is illuminating, but is empirically challenging because both the deterministic networks and phenotypic diversity are modified in the course of evolution. Here we overcome this problem by directly comparing the structure of a "global" carotenoid network - comprising of all known enzymatic reactions among naturally occurring carotenoids - with the patterns of evolutionary diversification in carotenoid-producing metabolic networks utilized by birds. We found that phenotypic diversification in carotenoid networks across 250 species was closely associated with enzymatic connectivity of the underlying biochemical network - compounds with greater connectivity occurred the most frequently across species and were the hotspots of metabolic pathway diversification. In contrast, we found no evidence for diversification along the metabolic pathways, corroborating findings that the utilization of the global carotenoid network was not strongly influenced by history in avian evolution. The finding that the diversification in species-specific carotenoid networks is qualitatively predictable from the connectivity of the underlying enzymatic network points to significant structural determinism in phenotypic evolution.

  12. Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity.

    Science.gov (United States)

    Rolfsson, Óttar; Paglia, Giuseppe; Magnusdóttir, Manuela; Palsson, Bernhard Ø; Thiele, Ines

    2013-01-15

    Metabolic network reconstructions define metabolic information within a target organism and can therefore be used to address incomplete metabolic information. In the present study we used a computational approach to identify human metabolites whose metabolism is incomplete on the basis of their detection in humans but exclusion from the human metabolic network reconstruction RECON 1. Candidate solutions, composed of metabolic reactions capable of explaining the metabolism of these compounds, were then identified computationally from a global biochemical reaction database. Solutions were characterized with respect to how metabolites were incorporated into RECON 1 and their biological relevance. Through detailed case studies we show that biologically plausible non-intuitive hypotheses regarding the metabolism of these compounds can be proposed in a semi-automated manner, in an approach that is similar to de novo network reconstruction. We subsequently experimentally validated one of the proposed hypotheses and report that C9orf103, previously identified as a candidate tumour suppressor gene, encodes a functional human gluconokinase. The results of the present study demonstrate how semi-automatic gap filling can be used to refine and extend metabolic reconstructions, thereby increasing their biological scope. Furthermore, we illustrate how incomplete human metabolic knowledge can be coupled with gene annotation in order to prioritize and confirm gene functions.

  13. A Reconfigurable Low Power High Throughput Architecture for Deep Network Training

    OpenAIRE

    Hasan, Raqibul; Taha, Tarek

    2016-01-01

    General purpose computing systems are used for a large variety of applications. Extensive supports for flexibility in these systems limit their energy efficiencies. Neural networks, including deep networks, are widely used for signal processing and pattern recognition applications. In this paper we propose a multicore architecture for deep neural network based processing. Memristor crossbars are utilized to provide low power high throughput execution of neural networks. The system has both tr...

  14. Enabling Wireless Power Transfer in Cellular Networks: Architecture, Modeling and Deployment

    OpenAIRE

    Huang, Kaibin; Lau, Vincent K. N.

    2012-01-01

    Microwave power transfer (MPT) delivers energy wirelessly from stations called power beacons (PBs) to mobile devices by microwave radiation. This provides mobiles practically infinite battery lives and eliminates the need of power cords and chargers. To enable MPT for mobile charging, this paper proposes a new network architecture that overlays an uplink cellular network with randomly deployed PBs for powering mobiles, called a hybrid network. The deployment of the hybrid network under an out...

  15. ReNoC: A Network-on-Chip Architecture with Reconfigurable Topology

    DEFF Research Database (Denmark)

    Stensgaard, Mikkel Bystrup; Sparsø, Jens

    2008-01-01

    This paper presents a Network-on-Chip (NoC) architecture that enables the network topology to be reconfigured. The architecture thus enables a generalized System-on-Chip (SoC) platform in which the topology can be customized for the application that is currently running on the chip, including long...... on physical circuit switching as found in FPGAs. The paper presents the ReNoC (Reconfigurable NoC) architecture and evaluates its potential. The evaluation design shows a 56% decrease in power consumption compared to a static 2D mesh topology....

  16. Architectural and operational considerations emerging from hybrid RF-optical network loading simulations

    Science.gov (United States)

    Chen, Yijiang; Abraham, Douglas S.; Heckman, David P.; Kwok, Andrew; MacNeal, Bruce E.; Tran, Kristy; Wu, Janet P.

    2016-03-01

    A technology demonstration of free space optical communication at interplanetary distances is planned via one or more future NASA deep-space missions. Such demonstrations will "pave the way" for operational use of optical communications on future robotic/potential Human missions. Hence, the Deep Space Network architecture will need to evolve. Preliminary attempts to model the anticipated future mission set and simulate how well it loads onto assumed architectures with combinations of RF and optical apertures have been evaluated. This paper discusses the results of preliminary loading simulations for hybrid RF-optical network architectures and highlights key mission and ground infrastructure considerations that emerge.

  17. Space Network IP Services (SNIS): An Architecture for Supporting Low Earth Orbiting IP Satellite Missions

    Science.gov (United States)

    Israel, David J.

    2005-01-01

    The NASA Space Network (SN) supports a variety of missions using the Tracking and Data Relay Satellite System (TDRSS), which includes ground stations in White Sands, New Mexico and Guam. A Space Network IP Services (SNIS) architecture is being developed to support future users with requirements for end-to-end Internet Protocol (IP) communications. This architecture will support all IP protocols, including Mobile IP, over TDRSS Single Access, Multiple Access, and Demand Access Radio Frequency (RF) links. This paper will describe this architecture and how it can enable Low Earth Orbiting IP satellite missions.

  18. Integration of metabolome data with metabolic networks reveals reporter reactions

    DEFF Research Database (Denmark)

    Çakir, Tunahan; Patil, Kiran Raosaheb; Önsan, Zeynep Ilsen

    2006-01-01

    network topology. The algorithm thus enables identification of reporter reactions, which are reactions where there are significant coordinated changes in the level of surrounding metabolites following environmental/genetic perturbations. Applicability of the algorithm is demonstrated by using data from......Interpreting quantitative metabolome data is a difficult task owing to the high connectivity in metabolic networks and inherent interdependency between enzymatic regulation, metabolite levels and fluxes. Here we present a hypothesis-driven algorithm for the integration of such data with metabolic...... is measured. By combining the results with transcriptome data, we further show that it is possible to infer whether the reactions are hierarchically or metabolically regulated. Hereby, the reported approach represents an attempt to map different layers of regulation within metabolic networks through...

  19. A Novel Architecture for Adaptive Traffic Control in Network on Chip using Code Division Multiple Access Technique

    OpenAIRE

    Fatemeh. Dehghani; Shahram. Darooei

    2016-01-01

    Network on chip has emerged as a long-term and effective method in Multiprocessor System-on-Chip communications in order to overcome the bottleneck in bus based communication architectures. Efficiency and performance of network on chip is so dependent on the architecture and structure of the network. In this paper a new structure and architecture for adaptive traffic control in network on chip using Code Division Multiple Access technique is presented. To solve the problem of synchronous acce...

  20. A neural network architecture for implementation of expert systems for real time monitoring

    Science.gov (United States)

    Ramamoorthy, P. A.

    1991-01-01

    Since neural networks have the advantages of massive parallelism and simple architecture, they are good tools for implementing real time expert systems. In a rule based expert system, the antecedents of rules are in the conjunctive or disjunctive form. We constructed a multilayer feedforward type network in which neurons represent AND or OR operations of rules. Further, we developed a translator which can automatically map a given rule base into the network. Also, we proposed a new and powerful yet flexible architecture that combines the advantages of both fuzzy expert systems and neural networks. This architecture uses the fuzzy logic concepts to separate input data domains into several smaller and overlapped regions. Rule-based expert systems for time critical applications using neural networks, the automated implementation of rule-based expert systems with neural nets, and fuzzy expert systems vs. neural nets are covered.

  1. A comparison of neural network architectures for the prediction of MRR in EDM

    Science.gov (United States)

    Jena, A. R.; Das, Raja

    2017-11-01

    The aim of the research work is to predict the material removal rate of a work-piece in electrical discharge machining (EDM). Here, an effort has been made to predict the material removal rate through back-propagation neural network (BPN) and radial basis function neural network (RBFN) for a work-piece of AISI D2 steel. The input parameters for the architecture are discharge-current (Ip), pulse-duration (Ton), and duty-cycle (τ) taken for consideration to obtained the output for material removal rate of the work-piece. In the architecture, it has been observed that radial basis function neural network is comparatively faster than back-propagation neural network but logically back-propagation neural network results more real value. Therefore BPN may consider as a better process in this architecture for consistent prediction to save time and money for conducting experiments.

  2. Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling

    International Nuclear Information System (INIS)

    Chaiboonchoe, Amphun; Dohai, Bushra Saeed; Cai, Hong; Nelson, David R.; Jijakli, Kenan; Salehi-Ashtiani, Kourosh

    2014-01-01

    Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology (Biolog, Hayward, CA, USA) provides an efficient, high-throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverified reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi, but it has not been reported for the phenotyping of microalgae. Here, we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of d-amino acids, l-dipeptides, and l-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates.

  3. Microalgal Metabolic Network Model Refinement through High Throughput Functional Metabolic Profiling

    Directory of Open Access Journals (Sweden)

    Amphun eChaiboonchoe

    2014-12-01

    Full Text Available Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The Phenotype Microarray (PM technology (Biolog, Hayward, CA, USA provides an efficient, high throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverified reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi but it has not been reported for the phenotyping of microalgae. Here we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of D-amino acids, L-dipeptides, and L-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates.

  4. Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling.

    Science.gov (United States)

    Chaiboonchoe, Amphun; Dohai, Bushra Saeed; Cai, Hong; Nelson, David R; Jijakli, Kenan; Salehi-Ashtiani, Kourosh

    2014-01-01

    Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology (Biolog, Hayward, CA, USA) provides an efficient, high-throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverified reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi, but it has not been reported for the phenotyping of microalgae. Here, we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of d-amino acids, l-dipeptides, and l-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates.

  5. Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks

    Science.gov (United States)

    Haraldsdóttir, Hulda S.; Fleming, Ronan M. T.

    2016-01-01

    Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichiometry but their computational complexity has limited their application to relatively small metabolic networks. Moreover, the vectors returned by existing algorithms do not, in general, represent conservation of a specific moiety with a defined atomic structure. Here, we show that identification of conserved moieties requires data on reaction atom mappings in addition to stoichiometry. We present a novel method to identify conserved moieties in metabolic networks by graph theoretical analysis of their underlying atom transition networks. Our method returns the exact group of atoms belonging to each conserved moiety as well as the corresponding vector in the left null space of the stoichiometric matrix. It can be implemented as a pipeline of polynomial time algorithms. Our implementation completes in under five minutes on a metabolic network with more than 4,000 mass balanced reactions. The scalability of the method enables extension of existing applications for moiety conservation relations to genome-scale metabolic networks. We also give examples of new applications made possible by elucidating the atomic structure of conserved moieties. PMID:27870845

  6. A swarm intelligence framework for reconstructing gene networks: searching for biologically plausible architectures.

    Science.gov (United States)

    Kentzoglanakis, Kyriakos; Poole, Matthew

    2012-01-01

    In this paper, we investigate the problem of reverse engineering the topology of gene regulatory networks from temporal gene expression data. We adopt a computational intelligence approach comprising swarm intelligence techniques, namely particle swarm optimization (PSO) and ant colony optimization (ACO). In addition, the recurrent neural network (RNN) formalism is employed for modeling the dynamical behavior of gene regulatory systems. More specifically, ACO is used for searching the discrete space of network architectures and PSO for searching the corresponding continuous space of RNN model parameters. We propose a novel solution construction process in the context of ACO for generating biologically plausible candidate architectures. The objective is to concentrate the search effort into areas of the structure space that contain architectures which are feasible in terms of their topological resemblance to real-world networks. The proposed framework is initially applied to the reconstruction of a small artificial network that has previously been studied in the context of gene network reverse engineering. Subsequently, we consider an artificial data set with added noise for reconstructing a subnetwork of the genetic interaction network of S. cerevisiae (yeast). Finally, the framework is applied to a real-world data set for reverse engineering the SOS response system of the bacterium Escherichia coli. Results demonstrate the relative advantage of utilizing problem-specific knowledge regarding biologically plausible structural properties of gene networks over conducting a problem-agnostic search in the vast space of network architectures.

  7. Observability of plant metabolic networks is reflected in the correlation of metabolic profiles

    DEFF Research Database (Denmark)

    Schwahn, Kevin; Küken, Anika; Kliebenstein, Daniel James

    2016-01-01

    -of-the-art genome-scale metabolic networks. By using metabolic data profiles from a set of seven environmental perturbations as well as from natural variability, we demonstrate that the data profiles of sensor metabolites are more correlated than those of nonsensor metabolites. This pattern was confirmed...

  8. Architecture and System Engineering Development Study of Space-Based Satellite Networks for NASA Missions

    Science.gov (United States)

    Ivancic, William D.

    2003-01-01

    Traditional NASA missions, both near Earth and deep space, have been stovepipe in nature and point-to-point in architecture. Recently, NASA and others have conceptualized missions that required space-based networking. The notion of networks in space is a drastic shift in thinking and requires entirely new architectures, radio systems (antennas, modems, and media access), and possibly even new protocols. A full system engineering approach for some key mission architectures will occur that considers issues such as the science being performed, stationkeeping, antenna size, contact time, data rates, radio-link power requirements, media access techniques, and appropriate networking and transport protocols. This report highlights preliminary architecture concepts and key technologies that will be investigated.

  9. Preferential attachment in the evolution of metabolic networks

    Directory of Open Access Journals (Sweden)

    Elofsson Arne

    2005-11-01

    Full Text Available Abstract Background Many biological networks show some characteristics of scale-free networks. Scale-free networks can evolve through preferential attachment where new nodes are preferentially attached to well connected nodes. In networks which have evolved through preferential attachment older nodes should have a higher average connectivity than younger nodes. Here we have investigated preferential attachment in the context of metabolic networks. Results The connectivities of the enzymes in the metabolic network of Escherichia coli were determined and representatives for these enzymes were located in 11 eukaryotes, 17 archaea and 46 bacteria. E. coli enzymes which have representatives in eukaryotes have a higher average connectivity while enzymes which are represented only in the prokaryotes, and especially the enzymes only present in βγ-proteobacteria, have lower connectivities than expected by chance. Interestingly, the enzymes which have been proposed as candidates for horizontal gene transfer have a higher average connectivity than the other enzymes. Furthermore, It was found that new edges are added to the highly connected enzymes at a faster rate than to enzymes with low connectivities which is consistent with preferential attachment. Conclusion Here, we have found indications of preferential attachment in the metabolic network of E. coli. A possible biological explanation for preferential attachment growth of metabolic networks is that novel enzymes created through gene duplication maintain some of the compounds involved in the original reaction, throughout its future evolution. In addition, we found that enzymes which are candidates for horizontal gene transfer have a higher average connectivity than other enzymes. This indicates that while new enzymes are attached preferentially to highly connected enzymes, these highly connected enzymes have sometimes been introduced into the E. coli genome by horizontal gene transfer. We speculate

  10. An integrated text mining framework for metabolic interaction network reconstruction

    Directory of Open Access Journals (Sweden)

    Preecha Patumcharoenpol

    2016-03-01

    Full Text Available Text mining (TM in the field of biology is fast becoming a routine analysis for the extraction and curation of biological entities (e.g., genes, proteins, simple chemicals as well as their relationships. Due to the wide applicability of TM in situations involving complex relationships, it is valuable to apply TM to the extraction of metabolic interactions (i.e., enzyme and metabolite interactions through metabolic events. Here we present an integrated TM framework containing two modules for the extraction of metabolic events (Metabolic Event Extraction module—MEE and for the construction of a metabolic interaction network (Metabolic Interaction Network Reconstruction module—MINR. The proposed integrated TM framework performed well based on standard measures of recall, precision and F-score. Evaluation of the MEE module using the constructed Metabolic Entities (ME corpus yielded F-scores of 59.15% and 48.59% for the detection of metabolic events for production and consumption, respectively. As for the testing of the entity tagger for Gene and Protein (GP and metabolite with the test corpus, the obtained F-score was greater than 80% for the Superpathway of leucine, valine, and isoleucine biosynthesis. Mapping of enzyme and metabolite interactions through network reconstruction showed a fair performance for the MINR module on the test corpus with F-score >70%. Finally, an application of our integrated TM framework on a big-scale data (i.e., EcoCyc extraction data for reconstructing a metabolic interaction network showed reasonable precisions at 69.93%, 70.63% and 46.71% for enzyme, metabolite and enzyme–metabolite interaction, respectively. This study presents the first open-source integrated TM framework for reconstructing a metabolic interaction network. This framework can be a powerful tool that helps biologists to extract metabolic events for further reconstruction of a metabolic interaction network. The ME corpus, test corpus, source

  11. Metrics of brain network architecture capture the impact of disease in children with epilepsy

    Directory of Open Access Journals (Sweden)

    Michael J. Paldino

    2017-01-01

    Conclusions: We observed that a machine learning algorithm accurately predicted epilepsy duration based on global metrics of network architecture derived from resting state fMRI. These findings suggest that network metrics have the potential to form the basis for statistical models that translate quantitative imaging data into patient-level markers of cognitive deterioration.

  12. ATLANTIDES: An Architecture for Alert Verification in Network Intrusion Detection Systems

    NARCIS (Netherlands)

    Bolzoni, D.; Crispo, Bruno; Etalle, Sandro

    2007-01-01

    We present an architecture designed for alert verification (i.e., to reduce false positives) in network intrusion-detection systems. Our technique is based on a systematic (and automatic) anomaly-based analysis of the system output, which provides useful context information regarding the network

  13. ATLANTIDES: An Architecture for Alert Verification in Network Intrusion Detection Systems

    NARCIS (Netherlands)

    Bolzoni, D.; Crispo, Bruno; Etalle, Sandro

    We present an architecture designed for alert verification (i.e., to reduce false positives) in network intrusion-detection systems. Our technique is based on a systematic (and automatic) anomaly-based analysis of the system output, which provides useful context information regarding the network

  14. OTN Transport of Baseband Radio Serial Protocols in C-RAN Architecture for Mobile Network Applications

    DEFF Research Database (Denmark)

    Checko, Aleksandra; Kardaras, Georgios; Lanzani, Christian Fabio Alessandro

    This white paper presents a proof of concept implementation of digital baseband radio data transport over Optical Transport Network (OTN) compliant to 3GPP Long Term Evolution – Advanced (LTE-A) standard enabling Cloud Radio Access Network (C-RAN) architecture. The transport between the baseband...

  15. mCRAN: A radio access network architecture for 5G indoor ccommunications

    NARCIS (Netherlands)

    Chandra, Kishor; Cao, Zizheng; Bruintjes, Tom; Prasad, R.V.; Karagiannis, Georgios; Tangdiongga, E.; van den Boom, H.P.A.; Kokkeler, Andre B.J.

    2015-01-01

    Millimeter wave (mmWave) communication is being seen as a disruptive technology for 5G era. In particular, 60GHz frequency band has emerged as a promising candidate for multi-Gbps connectivity in indoor and hotspot areas. In terms of network architecture, cloud radio access network (CRAN) has

  16. Modular Neural Tile Architecture for Compact Embedded Hardware Spiking Neural Network

    NARCIS (Netherlands)

    Pande, Sandeep; Morgan, Fearghal; Cawley, Seamus; Bruintjes, Tom; Smit, Gerardus Johannes Maria; McGinley, Brian; Carrillo, Snaider; Harkin, Jim; McDaid, Liam

    2013-01-01

    Biologically-inspired packet switched network on chip (NoC) based hardware spiking neural network (SNN) architectures have been proposed as an embedded computing platform for classification, estimation and control applications. Storage of large synaptic connectivity (SNN topology) information in

  17. Neural networks as a possible architecture for the distributed control of space systems

    Science.gov (United States)

    Fiesler, E.; Choudry, A.

    1987-01-01

    Researchers attempted to identify the features essential for large, complex, multi-modular multi-functional systems possessing a high level of interconnectivity. These features were studied in the context of neural networks with the aim of arriving at a possible architecture of the distributed control system-specific features of the neural networks and their applicability in space systems.

  18. Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles

    Science.gov (United States)

    Jia, Gengjie; Stephanopoulos, Gregory; Gunawan, Rudiyanto

    2012-01-01

    Kinetic modeling of metabolic pathways has important applications in metabolic engineering, but significant challenges still remain. The difficulties faced vary from finding best-fit parameters in a highly multidimensional search space to incomplete parameter identifiability. To meet some of these challenges, an ensemble modeling method is developed for characterizing a subset of kinetic parameters that give statistically equivalent goodness-of-fit to time series concentration data. The method is based on the incremental identification approach, where the parameter estimation is done in a step-wise manner. Numerical efficacy is achieved by reducing the dimensionality of parameter space and using efficient random parameter exploration algorithms. The shift toward using model ensembles, instead of the traditional “best-fit” models, is necessary to directly account for model uncertainty during the application of such models. The performance of the ensemble modeling approach has been demonstrated in the modeling of a generic branched pathway and the trehalose pathway in Saccharomyces cerevisiae using generalized mass action (GMA) kinetics. PMID:24957767

  19. Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles

    Directory of Open Access Journals (Sweden)

    Gengjie Jia

    2012-11-01

    Full Text Available Kinetic modeling of metabolic pathways has important applications in metabolic engineering, but significant challenges still remain. The difficulties faced vary from finding best-fit parameters in a highly multidimensional search space to incomplete parameter identifiability. To meet some of these challenges, an ensemble modeling method is developed for characterizing a subset of kinetic parameters that give statistically equivalent goodness-of-fit to time series concentration data. The method is based on the incremental identification approach, where the parameter estimation is done in a step-wise manner. Numerical efficacy is achieved by reducing the dimensionality of parameter space and using efficient random parameter exploration algorithms. The shift toward using model ensembles, instead of the traditional “best-fit” models, is necessary to directly account for model uncertainty during the application of such models. The performance of the ensemble modeling approach has been demonstrated in the modeling of a generic branched pathway and the trehalose pathway in Saccharomyces cerevisiae using generalized mass action (GMA kinetics.

  20. Pseudomonas fluorescens induces strain-dependent and strain-independent host plant responses in defense networks, primary metabolism and photosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Pelletier, Dale A [ORNL; Morrell-Falvey, Jennifer L [ORNL; Karve, Abhijit A [ORNL; Lu, Tse-Yuan S [ORNL; Tschaplinski, Timothy J [ORNL; Tuskan, Gerald A [ORNL; Chen, Jay [ORNL; Martin, Madhavi Z [ORNL; Jawdy, Sara [ORNL; Weston, David [ORNL; Doktycz, Mitchel John [ORNL; Schadt, Christopher Warren [ORNL

    2012-01-01

    Colonization of plants by nonpathogenic Pseudomonas fluorescens strains can confer enhanced defense capacity against a broad spectrum of pathogens. Few studies, however, have linked defense pathway regulation to primary metabolism and physiology. In this study, physiological data, metabolites, and transcript profiles are integrated to elucidate how molecular networks initiated at the root-microbe interface influence shoot metabolism and whole-plant performance. Experiments with Arabidopsis thaliana were performed using the newly identified P. fluorescens GM30 or P. fluorescens Pf-5 strains. Co-expression networks indicated that Pf-5 and GM30 induced a subnetwork specific to roots enriched for genes participating in RNA regulation, protein degradation, and hormonal metabolism. In contrast, only GM30 induced a subnetwork enriched for calcium signaling, sugar and nutrient signaling, and auxin metabolism, suggesting strain dependence in network architecture. In addition, one subnetwork present in shoots was enriched for genes in secondary metabolism, photosynthetic light reactions, and hormone metabolism. Metabolite analysis indicated that this network initiated changes in carbohydrate and amino acid metabolism. Consistent with this, we observed strain-specific responses in tryptophan and phenylalanine abundance. Both strains reduced host plant carbon gain and fitness, yet provided a clear fitness benefit when plants were challenged with the pathogen P. syringae DC3000.

  1. Design mobile satellite system architecture as an integral part of the cellular access digital network

    Science.gov (United States)

    Chien, E. S. K.; Marinho, J. A.; Russell, J. E., Sr.

    1988-01-01

    The Cellular Access Digital Network (CADN) is the access vehicle through which cellular technology is brought into the mainstream of the evolving integrated telecommunications network. Beyond the integrated end-to-end digital access and per call network services provisioning of the Integrated Services Digital Network (ISDN), the CADN engenders the added capability of mobility freedom via wireless access. One key element of the CADN network architecture is the standard user to network interface that is independent of RF transmission technology. Since the Mobile Satellite System (MSS) is envisioned to not only complement but also enhance the capabilities of the terrestrial cellular telecommunications network, compatibility and interoperability between terrestrial cellular and mobile satellite systems are vitally important to provide an integrated moving telecommunications network of the future. From a network standpoint, there exist very strong commonalities between the terrestrial cellular system and the mobile satellite system. Therefore, the MSS architecture should be designed as an integral part of the CADN. This paper describes the concept of the CADN, the functional architecture of the MSS, and the user-network interface signaling protocols.

  2. Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance

    Science.gov (United States)

    Thomas, Alex; Rahmanian, Sorena; Bordbar, Aarash; Palsson, Bernhard Ø.; Jamshidi, Neema

    2014-01-01

    Recently there has not been a systematic, objective assessment of the metabolic capabilities of the human platelet. A manually curated, functionally tested, and validated biochemical reaction network of platelet metabolism, iAT-PLT-636, was reconstructed using 33 proteomic datasets and 354 literature references. The network contains enzymes mapping to 403 diseases and 231 FDA approved drugs, alluding to an expansive scope of biochemical transformations that may affect or be affected by disease processes in multiple organ systems. The effect of aspirin (ASA) resistance on platelet metabolism was evaluated using constraint-based modeling, which revealed a redirection of glycolytic, fatty acid, and nucleotide metabolism reaction fluxes in order to accommodate eicosanoid synthesis and reactive oxygen species stress. These results were confirmed with independent proteomic data. The construction and availability of iAT-PLT-636 should stimulate further data-driven, systems analysis of platelet metabolism towards the understanding of pathophysiological conditions including, but not strictly limited to, coagulopathies.

  3. The Hi-Ring Architecture for Data Center Networks

    DEFF Research Database (Denmark)

    Kamchevska, Valerija; Ding, Yunhong; Berger, Michael Stübert

    2018-01-01

    Optical technologies have long been used for standard telecom applications ranging from long haul to metro and access networks. With the rapid expansion of traffic in data center networks, the deployment of optical technologies for computationally intensive short reach networking has attracted a ...

  4. Hybrid SDN Architecture for Resource Consolidation in MPLS Networks

    DEFF Research Database (Denmark)

    Katov, Anton Nikolaev; Mihovska, Albena D.; Prasad, Neeli R.

    2015-01-01

    This paper proposes a methodology for resource consolidation towards minimizing the power consumption in a large network, with a substantial resource overprovisioning. The focus is on the operation of the core MPLS networks. The proposed approach is based on a software defined networking (SDN......) scheme with a reconfigurable centralized controller, which turns off certain network elements. The methodology comprises the process of identifying time periods with lower traffic demand; the ranking of the network elements, based on their utilization and criticality; the rerouting of the traffic off...

  5. An MPLS-based Quality of Service Architecture for Heterogeneous Networks

    OpenAIRE

    Raghavan, Srihari

    2001-01-01

    This thesis proposes a multi-protocol label switching (MPLS)-based architecture to provide quality of service (QoS) for both internet service provider (ISP) networks and backbone Internet Protocol (IP) networks that are heterogeneous in nature. Heterogeneous networks are present due to the use of different link-layer mechanisms in the current Internet. Copper-based links, fiber-based links, and wireless links are some examples of different p...

  6. Comparison of different artificial neural network architectures in modeling of Chlorella sp. flocculation.

    Science.gov (United States)

    Zenooz, Alireza Moosavi; Ashtiani, Farzin Zokaee; Ranjbar, Reza; Nikbakht, Fatemeh; Bolouri, Oberon

    2017-07-03

    Biodiesel production from microalgae feedstock should be performed after growth and harvesting of the cells, and the most feasible method for harvesting and dewatering of microalgae is flocculation. Flocculation modeling can be used for evaluation and prediction of its performance under different affective parameters. However, the modeling of flocculation in microalgae is not simple and has not performed yet, under all experimental conditions, mostly due to different behaviors of microalgae cells during the process under different flocculation conditions. In the current study, the modeling of microalgae flocculation is studied with different neural network architectures. Microalgae species, Chlorella sp., was flocculated with ferric chloride under different conditions and then the experimental data modeled using artificial neural network. Neural network architectures of multilayer perceptron (MLP) and radial basis function architectures, failed to predict the targets successfully, though, modeling was effective with ensemble architecture of MLP networks. Comparison between the performances of the ensemble and each individual network explains the ability of the ensemble architecture in microalgae flocculation modeling.

  7. A cluster-based architecture to structure the topology of parallel wireless sensor networks.

    Science.gov (United States)

    Lloret, Jaime; Garcia, Miguel; Bri, Diana; Diaz, Juan R

    2009-01-01

    A wireless sensor network is a self-configuring network of mobile nodes connected by wireless links where the nodes have limited capacity and energy. In many cases, the application environment requires the design of an exclusive network topology for a particular case. Cluster-based network developments and proposals in existence have been designed to build a network for just one type of node, where all nodes can communicate with any other nodes in their coverage area. Let us suppose a set of clusters of sensor nodes where each cluster is formed by different types of nodes (e.g., they could be classified by the sensed parameter using different transmitting interfaces, by the node profile or by the type of device: laptops, PDAs, sensor etc.) and exclusive networks, as virtual networks, are needed with the same type of sensed data, or the same type of devices, or even the same type of profiles. In this paper, we propose an algorithm that is able to structure the topology of different wireless sensor networks to coexist in the same environment. It allows control and management of the topology of each network. The architecture operation and the protocol messages will be described. Measurements from a real test-bench will show that the designed protocol has low bandwidth consumption and also demonstrates the viability and the scalability of the proposed architecture. Our ccluster-based algorithm is compared with other algorithms reported in the literature in terms of architecture and protocol measurements.

  8. Towards Horizontal Architecture for Autonomic M2M Service Networks

    Directory of Open Access Journals (Sweden)

    Juhani Latvakoski

    2014-05-01

    Full Text Available Today, increasing number of industrial application cases rely on the Machine to Machine (M2M services exposed from physical devices. Such M2M services enable interaction of physical world with the core processes of company information systems. However, there are grand challenges related to complexity and “vertical silos” limiting the M2M market scale and interoperability. It is here expected that horizontal approach for the system architecture is required for solving these challenges. Therefore, a set of architectural principles and key enablers for the horizontal architecture have been specified in this work. A selected set of key enablers called as autonomic M2M manager, M2M service capabilities, M2M messaging system, M2M gateways towards energy constrained M2M asset devices and creation of trust to enable end-to-end security for M2M applications have been developed. The developed key enablers have been evaluated separately in different scenarios dealing with smart metering, car sharing and electric bike experiments. The evaluation results shows that the provided architectural principles, and developed key enablers establish a solid ground for future research and seem to enable communication between objects and applications, which are not initially been designed to communicate together. The aim as the next step in this research is to create a combined experimental system to evaluate the system interoperability and performance in a more detailed manner.

  9. Network Coding Parallelization Based on Matrix Operations for Multicore Architectures

    DEFF Research Database (Denmark)

    Wunderlich, Simon; Cabrera, Juan; Fitzek, Frank

    2015-01-01

    such as the Raspberry Pi2 with four cores in the order of up to one full magnitude. The speed increase gain is even higher than the number of cores of the Raspberry Pi2 since the newly introduced approach exploits the cache architecture way better than by-the-book matrix operations. Copyright © 2015 by the Institute...

  10. Reference Architecture for Multi-Layer Software Defined Optical Data Center Networks

    Directory of Open Access Journals (Sweden)

    Casimer DeCusatis

    2015-09-01

    Full Text Available As cloud computing data centers grow larger and networking devices proliferate; many complex issues arise in the network management architecture. We propose a framework for multi-layer; multi-vendor optical network management using open standards-based software defined networking (SDN. Experimental results are demonstrated in a test bed consisting of three data centers interconnected by a 125 km metropolitan area network; running OpenStack with KVM and VMW are components. Use cases include inter-data center connectivity via a packet-optical metropolitan area network; intra-data center connectivity using an optical mesh network; and SDN coordination of networking equipment within and between multiple data centers. We create and demonstrate original software to implement virtual network slicing and affinity policy-as-a-service offerings. Enhancements to synchronous storage backup; cloud exchanges; and Fibre Channel over Ethernet topologies are also discussed.

  11. Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction.

    Directory of Open Access Journals (Sweden)

    Benjamin D Heavner

    2015-11-01

    Full Text Available We have compared 12 genome-scale models of the Saccharomyces cerevisiae metabolic network published since 2003 to evaluate progress in reconstruction of the yeast metabolic network. We compared the genomic coverage, overlap of annotated metabolites, predictive ability for single gene essentiality with a selection of model parameters, and biomass production predictions in simulated nutrient-limited conditions. We have also compared pairwise gene knockout essentiality predictions for 10 of these models. We found that varying approaches to model scope and annotation reflected the involvement of multiple research groups in model development; that single-gene essentiality predictions were affected by simulated medium, objective function, and the reference list of essential genes; and that predictive ability for single-gene essentiality did not correlate well with predictive ability for our reference list of synthetic lethal gene interactions (R = 0.159. We conclude that the reconstruction of the yeast metabolic network is indeed gradually improving through the iterative process of model development, and there remains great opportunity for advancing our understanding of biology through continued efforts to reconstruct the full biochemical reaction network that constitutes yeast metabolism. Additionally, we suggest that there is opportunity for refining the process of deriving a metabolic model from a metabolic network reconstruction to facilitate mechanistic investigation and discovery. This comparative study lays the groundwork for developing improved tools and formalized methods to quantitatively assess metabolic network reconstructions independently of any particular model application, which will facilitate ongoing efforts to advance our understanding of the relationship between genotype and cellular phenotype.

  12. CardioNet: A human metabolic network suited for the study of cardiomyocyte metabolism

    Directory of Open Access Journals (Sweden)

    Karlstädt Anja

    2012-08-01

    Full Text Available Abstract Background Availability of oxygen and nutrients in the coronary circulation is a crucial determinant of cardiac performance. Nutrient composition of coronary blood may significantly vary in specific physiological and pathological conditions, for example, administration of special diets, long-term starvation, physical exercise or diabetes. Quantitative analysis of cardiac metabolism from a systems biology perspective may help to a better understanding of the relationship between nutrient supply and efficiency of metabolic processes required for an adequate cardiac output. Results Here we present CardioNet, the first large-scale reconstruction of the metabolic network of the human cardiomyocyte comprising 1793 metabolic reactions, including 560 transport processes in six compartments. We use flux-balance analysis to demonstrate the capability of the network to accomplish a set of 368 metabolic functions required for maintaining the structural and functional integrity of the cell. Taking the maintenance of ATP, biosynthesis of ceramide, cardiolipin and further important phospholipids as examples, we analyse how a changed supply of glucose, lactate, fatty acids and ketone bodies may influence the efficiency of these essential processes. Conclusions CardioNet is a functionally validated metabolic network of the human cardiomyocyte that enables theorectical studies of cellular metabolic processes crucial for the accomplishment of an adequate cardiac output.

  13. Seed Architecture Shapes Embryo Metabolism in Oilseed Rape[W][OA

    Science.gov (United States)

    Borisjuk, Ljudmilla; Neuberger, Thomas; Schwender, Jörg; Heinzel, Nicolas; Sunderhaus, Stephanie; Fuchs, Johannes; Hay, Jordan O.; Tschiersch, Henning; Braun, Hans-Peter; Denolf, Peter; Lambert, Bart; Jakob, Peter M.; Rolletschek, Hardy

    2013-01-01

    Constrained to develop within the seed, the plant embryo must adapt its shape and size to fit the space available. Here, we demonstrate how this adjustment shapes metabolism of photosynthetic embryo. Noninvasive NMR-based imaging of the developing oilseed rape (Brassica napus) seed illustrates that, following embryo bending, gradients in lipid concentration became established. These were correlated with the local photosynthetic electron transport rate and the accumulation of storage products. Experimentally induced changes in embryo morphology and/or light supply altered these gradients and were accompanied by alterations in both proteome and metabolome. Tissue-specific metabolic models predicted that the outer cotyledon and hypocotyl/radicle generate the bulk of plastidic reductant/ATP via photosynthesis, while the inner cotyledon, being enclosed by the outer cotyledon, is forced to grow essentially heterotrophically. Under field-relevant high-light conditions, major contribution of the ribulose-1,5-bisphosphate carboxylase/oxygenase–bypass to seed storage metabolism is predicted for the outer cotyledon and the hypocotyl/radicle only. Differences between in vitro– versus in planta–grown embryos suggest that metabolic heterogeneity of embryo is not observable by in vitro approaches. We conclude that in vivo metabolic fluxes are locally regulated and connected to seed architecture, driving the embryo toward an efficient use of available light and space. PMID:23709628

  14. Toward a Mobility-Driven Architecture for Multimodal Underwater Networking

    Science.gov (United States)

    2017-02-01

    the Network and Transport layers of the Open Systems Interconnection ( OSI ) model . Specific technology requirements are mentioned as required. Before...functional layers of MobArch and their correspondence to high-level functionalities defined in the classical OSI model . 4.1 NETWORKING LAYER This...described in Section 2.1. Red and green circles correspond to highlighted red and green nodes in (a). 5 2. Network model considered by MobArch. Each

  15. A SECURE MESSAGE TRANSMISSION SYSTEM ARCHITECTURE FOR COMPUTER NETWORKS EMPLOYING SMART CARDS

    Directory of Open Access Journals (Sweden)

    Geylani KARDAŞ

    2008-01-01

    Full Text Available In this study, we introduce a mobile system architecture which employs smart cards for secure message transmission in computer networks. The use of smart card provides two security services as authentication and confidentiality in our design. The security of the system is provided by asymmetric encryption. Hence, smart cards are used to store personal account information as well as private key of each user for encryption / decryption operations. This offers further security, authentication and mobility to the system architecture. A real implementation of the proposed architecture which utilizes the JavaCard technology is also discussed in this study.

  16. A Holistic Management Architecture for Large-Scale Adaptive Networks

    National Research Council Canada - National Science Library

    Clement, Michael R

    2007-01-01

    This thesis extends the traditional notion of network management as an indicator of resource availability and utilization into a systemic model of resource requirements, capabilities, and adaptable...

  17. Marginally Stable Triangular Recurrent Neural Network Architecture for Time Series Prediction.

    Science.gov (United States)

    Sivakumar, Seshadri; Sivakumar, Shyamala

    2017-09-25

    This paper introduces a discrete-time recurrent neural network architecture using triangular feedback weight matrices that allows a simplified approach to ensuring network and training stability. The triangular structure of the weight matrices is exploited to readily ensure that the eigenvalues of the feedback weight matrix represented by the block diagonal elements lie on the unit circle in the complex z-plane by updating these weights based on the differential of the angular error variable. Such placement of the eigenvalues together with the extended close interaction between state variables facilitated by the nondiagonal triangular elements, enhances the learning ability of the proposed architecture. Simulation results show that the proposed architecture is highly effective in time-series prediction tasks associated with nonlinear and chaotic dynamic systems with underlying oscillatory modes. This modular architecture with dual upper and lower triangular feedback weight matrices mimics fully recurrent network architectures, while maintaining learning stability with a simplified training process. While training, the block-diagonal weights (hence the eigenvalues) of the dual triangular matrices are constrained to the same values during weight updates aimed at minimizing the possibility of overfitting. The dual triangular architecture also exploits the benefit of parsing the input and selectively applying the parsed inputs to the two subnetworks to facilitate enhanced learning performance.

  18. A Study of Artificial Neural Network Architectures for Othello Evaluation Functions

    Science.gov (United States)

    Binkley, Kevin J.; Seehart, Ken; Hagiwara, Masafumi

    In this study, we use temporal difference learning (TDL) to investigate the ability of 20 different artificial neural network (ANN) architectures to learn othello game board evaluation functions. The ANN evaluation functions are applied to create a strong othello player using only 1-ply search. In addition to comparing many of the ANN architectures seen in the literature, we introduce several new architectures that consider the game board symmetry. Both embedding the game board symmetry into the network architecture through weight sharing and the outright removal of symmetry through symmetry removal are explored. Experiments varying the number of inputs per game board square from one to three, the number of hidden nodes, and number of hidden layers are also performed. We found it advantageous to consider game board symmetry in the form of symmetry by weight sharing; and that an input encoding of three inputs per square outperformed the one input per square encoding that is commonly seen in the literature. Furthermore, architectures with only one hidden layer were strongly outperformed by architectures with multiple hidden layers. A standard weighted-square board heuristic evaluation function from the literature was used to evaluate the quality of the trained ANN othello players. One of the ANN architectures introduced in this study, an ANN implementing weight sharing and consisting of three hidden layers, using only a 1-ply search, outperformed a weighted-square test heuristic player using a 6-ply minimax search.

  19. Softwarization of Mobile Network Functions towards Agile and Energy Efficient 5G Architectures: A Survey

    Directory of Open Access Journals (Sweden)

    Dlamini Thembelihle

    2017-01-01

    Full Text Available Future mobile networks (MNs are required to be flexible with minimal infrastructure complexity, unlike current ones that rely on proprietary network elements to offer their services. Moreover, they are expected to make use of renewable energy to decrease their carbon footprint and of virtualization technologies for improved adaptability and flexibility, thus resulting in green and self-organized systems. In this article, we discuss the application of software defined networking (SDN and network function virtualization (NFV technologies towards softwarization of the mobile network functions, taking into account different architectural proposals. In addition, we elaborate on whether mobile edge computing (MEC, a new architectural concept that uses NFV techniques, can enhance communication in 5G cellular networks, reducing latency due to its proximity deployment. Besides discussing existing techniques, expounding their pros and cons and comparing state-of-the-art architectural proposals, we examine the role of machine learning and data mining tools, analyzing their use within fully SDN- and NFV-enabled mobile systems. Finally, we outline the challenges and the open issues related to evolved packet core (EPC and MEC architectures.

  20. Design Methodology of a Sensor Network Architecture Supporting Urgent Information and Its Evaluation

    Science.gov (United States)

    Kawai, Tetsuya; Wakamiya, Naoki; Murata, Masayuki

    Wireless sensor networks are expected to become an important social infrastructure which helps our life to be safe, secure, and comfortable. In this paper, we propose design methodology of an architecture for fast and reliable transmission of urgent information in wireless sensor networks. In this methodology, instead of establishing single complicated monolithic mechanism, several simple and fully-distributed control mechanisms which function in different spatial and temporal levels are incorporated on each node. These mechanisms work autonomously and independently responding to the surrounding situation. We also show an example of a network architecture designed following the methodology. We evaluated the performance of the architecture by extensive simulation and practical experiments and our claim was supported by the results of these experiments.

  1. A Novel Buffer Management Architecture for Epidemic Routing in Delay Tolerant Networks (DTNs)

    KAUST Repository

    Elwhishi, Ahmed

    2010-11-17

    Delay tolerant networks (DTNs) are wireless networks in which an end-to-end path for a given node pair can never exist for an extended period. It has been reported as a viable approach in launching multiple message replicas in order to increase message delivery ratio and reduce message delivery delay. This advantage, nonetheless, is at the expense of taking more buffer space at each node. The combination of custody and replication entails high buffer and bandwidth overhead. This paper investigates a new buffer management architecture for epidemic routing in DTNs, which helps each node to make a decision on which message should be forwarded or dropped. The proposed buffer management architecture is characterized by a suite of novel functional modules, including Summary Vector Exchange Module (SVEM), Networks State Estimation Module (NSEM), and Utility Calculation Module (UCM). Extensive simulation results show that the proposed buffer management architecture can achieve superb performance against its counterparts in terms of delivery ratio and delivery delay.

  2. Wireless Mesh Networks to Support Video Surveillance: Architecture, Protocol, and Implementation Issues

    Directory of Open Access Journals (Sweden)

    Francesco Licandro

    2007-03-01

    Full Text Available Current video-surveillance systems typically consist of many video sources distributed over a wide area, transmitting live video streams to a central location for processing and monitoring. The target of this paper is to present an experience of implementation of a large-scale video-surveillance system based on a wireless mesh network infrastructure, discussing architecture, protocol, and implementation issues. More specifically, the paper proposes an architecture for a video-surveillance system, and mainly centers its focus on the routing protocol to be used in the wireless mesh network, evaluating its impact on performance at the receiver side. A wireless mesh network was chosen to support a video-surveillance application in order to reduce the overall system costs and increase scalability and performance. The paper analyzes the performance of the network in order to choose design parameters that will achieve the best trade-off between video encoding quality and the network traffic generated.

  3. Wireless Mesh Networks to Support Video Surveillance: Architecture, Protocol, and Implementation Issues

    Directory of Open Access Journals (Sweden)

    Licandro Francesco

    2007-01-01

    Full Text Available Current video-surveillance systems typically consist of many video sources distributed over a wide area, transmitting live video streams to a central location for processing and monitoring. The target of this paper is to present an experience of implementation of a large-scale video-surveillance system based on a wireless mesh network infrastructure, discussing architecture, protocol, and implementation issues. More specifically, the paper proposes an architecture for a video-surveillance system, and mainly centers its focus on the routing protocol to be used in the wireless mesh network, evaluating its impact on performance at the receiver side. A wireless mesh network was chosen to support a video-surveillance application in order to reduce the overall system costs and increase scalability and performance. The paper analyzes the performance of the network in order to choose design parameters that will achieve the best trade-off between video encoding quality and the network traffic generated.

  4. Time Shared Optical Network (TSON): a novel metro architecture for flexible multi-granular services.

    Science.gov (United States)

    Zervas, Georgios S; Triay, Joan; Amaya, Norberto; Qin, Yixuan; Cervelló-Pastor, Cristina; Simeonidou, Dimitra

    2011-12-12

    This paper presents the Time Shared Optical Network (TSON) as metro mesh network architecture for guaranteed, statistically-multiplexed services. TSON proposes a flexible and tunable time-wavelength assignment along with one-way tree-based reservation and node architecture. It delivers guaranteed sub-wavelength and multi-granular network services without wavelength conversion, time-slice interchange and optical buffering. Simulation results demonstrate high network utilization, fast service delivery, and low end-to-end delay on a contention-free sub-wavelength optical transport network. In addition, implementation complexity in terms of Layer 2 aggregation, grooming and optical switching has been evaluated. © 2011 Optical Society of America

  5. The architecture of dynamic reservoir in the echo state network

    Science.gov (United States)

    Cui, Hongyan; Liu, Xiang; Li, Lixiang

    2012-09-01

    Echo state network (ESN) has recently attracted increasing interests because of its superior capability in modeling nonlinear dynamic systems. In the conventional echo state network model, its dynamic reservoir (DR) has a random and sparse topology, which is far from the real biological neural networks from both structural and functional perspectives. We hereby propose three novel types of echo state networks with new dynamic reservoir topologies based on complex network theory, i.e., with a small-world topology, a scale-free topology, and a mixture of small-world and scale-free topologies, respectively. We then analyze the relationship between the dynamic reservoir structure and its prediction capability. We utilize two commonly used time series to evaluate the prediction performance of the three proposed echo state networks and compare them to the conventional model. We also use independent and identically distributed time series to analyze the short-term memory and prediction precision of these echo state networks. Furthermore, we study the ratio of scale-free topology and the small-world topology in the mixed-topology network, and examine its influence on the performance of the echo state networks. Our simulation results show that the proposed echo state network models have better prediction capabilities, a wider spectral radius, but retain almost the same short-term memory capacity as compared to the conventional echo state network model. We also find that the smaller the ratio of the scale-free topology over the small-world topology, the better the memory capacities.

  6. Network-Attached Solid-State Recorder Architecture

    Science.gov (United States)

    Cox, Brian

    2008-01-01

    A document discusses placing memory modules on the high-speed serial interconnect, which is used by a spacecraft s computer elements for inter-processor communications, to allow all multiple computer system architectures to access the spacecraft data storage at the same time. Each memory board is identical electrically and receives its bus ID upon connection to the system. The computer elements are configured in a similar fashion. The architecture allows for multiple memory boards to be accessed simultaneously by different computer elements, and results in a scalable, strong, fault-tolerant system. The IEEE-1393 ring bus can be routed so that multiple card failures can occur and the mass memory storage will still function.

  7. Experiments on neural network architectures for fuzzy logic

    Science.gov (United States)

    Keller, James M.

    1991-01-01

    The use of fuzzy logic to model and manage uncertainty in a rule-based system places high computational demands on an inference engine. In an earlier paper, the authors introduced a trainable neural network structure for fuzzy logic. These networks can learn and extrapolate complex relationships between possibility distributions for the antecedents and consequents in the rules. Here, the power of these networks is further explored. The insensitivity of the output to noisy input distributions (which are likely if the clauses are generated from real data) is demonstrated as well as the ability of the networks to internalize multiple conjunctive clause and disjunctive clause rules. Since different rules with the same variables can be encoded in a single network, this approach to fuzzy logic inference provides a natural mechanism for rule conflict resolution.

  8. A Combined Network Architecture Using Art2 and Back Propagation for Adaptive Estimation of Dynamic Processes

    Directory of Open Access Journals (Sweden)

    Einar Sørheim

    1990-10-01

    Full Text Available A neural network architecture called ART2/BP is proposed. Thc goal has been to construct an artificial neural network that learns incrementally an unknown mapping, and is motivated by the instability found in back propagation (BP networks: after first learning pattern A and then pattern B, a BP network often has completely 'forgotten' pattern A. A network using both supervised and unsupervised training is proposed, consisting of a combination of ART2 and BP. ART2 is used to build and focus a supervised backpropagation network consisting of many small subnetworks each specialized on a particular domain of the input space. The ART2/BP network has the advantage of being able to dynamically expand itself in response to input patterns containing new information. Simulation results show that the ART2/BP network outperforms a classical maximum likelihood method for the estimation of a discrete dynamic and nonlinear transfer function.

  9. Enumeration of minimal stoichiometric precursor sets in metabolic networks

    NARCIS (Netherlands)

    Andrade, R.; Wannagat, M.; Coimbra Klein, C.; Acuna, V.; Marchetti Spaccamela, A.; Vieira Milreu, P.; Stougie, L.; Sagot, M.-F.

    2016-01-01

    Background: What an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal precursor sets took into account only the topology of the metabolic network

  10. Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism

    DEFF Research Database (Denmark)

    Buescher, Joerg Martin; Liebermeister, Wolfram; Jules, Matthieu

    2012-01-01

    Adaptation of cells to environmental changes requires dynamic interactions between metabolic and regulatory networks, but studies typically address only one or a few layers of regulation. For nutritional shifts between two preferred carbon sources of Bacillus subtilis, we combined statistical and...

  11. Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism

    NARCIS (Netherlands)

    Buescher, Joerg Martin; Liebermeister, Wolfram; Jules, Matthieu; Uhr, Markus; Muntel, Jan; Botella, Eric; Hessling, Bernd; Kleijn, Roelco Jacobus; Le Chat, Ludovic; Lecointe, Francois; Maeder, Ulrike; Nicolas, Pierre; Piersma, Sjouke; Ruegheimer, Frank; Becher, Doerte; Bessieres, Philippe; Bidnenko, Elena; Denham, Emma L.; Dervyn, Etienne; Devine, Kevin M.; Doherty, Geoff; Drulhe, Samuel; Felicori, Liza; Fogg, Mark J.; Goelzer, Anne; Hansen, Annette; Harwood, Colin R.; Hecker, Michael; Hubner, Sebastian; Hultschig, Claus; Jarmer, Hanne; Klipp, Edda; Leduc, Aurelie; Lewis, Peter; Molina, Frank; Noirot, Philippe; Peres, Sabine; Pigeonneau, Nathalie; Pohl, Susanne; Rasmussen, Simon; Rinn, Bernd; Schaffer, Marc; Schnidder, Julian; Schwikowski, Benno; Van Dijl, Jan Maarten; Veiga, Patrick; Walsh, Sean; Wilkinson, Anthony J.; Stelling, Joerg; Aymerich, Stephane; Sauer, Uwe

    2012-01-01

    Adaptation of cells to environmental changes requires dynamic interactions between metabolic and regulatory networks, but studies typically address only one or a few layers of regulation. For nutritional shifts between two preferred carbon sources of Bacillus subtilis, we combined statistical and

  12. Underground metabolism: network-level perspective and biotechnological potential

    DEFF Research Database (Denmark)

    Notebaart, Richard A; Kintses, Bálint; Feist, Adam

    2018-01-01

    A key challenge in molecular systems biology is understanding how new pathways arise during evolution and how to exploit them for biotechnological applications. New pathways in metabolic networks often evolve by recruiting weak promiscuous activities of pre-existing enzymes. Here we describe recent...

  13. Metabolic networks in epilepsy by MR spectroscopic imaging.

    Science.gov (United States)

    Pan, J W; Spencer, D D; Kuzniecky, R; Duckrow, R B; Hetherington, H; Spencer, S S

    2012-12-01

    The concept of an epileptic network has long been suggested from both animal and human studies of epilepsy. Based on the common observation that the MR spectroscopic imaging measure of NAA/Cr is sensitive to neuronal function and injury, we use this parameter to assess for the presence of a metabolic network in mesial temporal lobe epilepsy (MTLE) patients. A multivariate factor analysis is performed with controls and MTLE patients, using NAA/Cr measures from 12 loci: the bilateral hippocampi, thalami, basal ganglia, and insula. The factor analysis determines which and to what extent these loci are metabolically covarying. We extract two independent factors that explain the data's variability in control and MTLE patients. In controls, these factors characterize a 'thalamic' and 'dominant subcortical' function. The MTLE patients also exhibit a 'thalamic' factor, in addition to a second factor involving the ipsilateral insula and bilateral basal ganglia. These data suggest that MTLE patients demonstrate a metabolic network that involves the thalami, also seen in controls. The MTLE patients also display a second set of metabolically covarying regions that may be a manifestation of the epileptic network that characterizes limbic seizure propagation. © 2012 John Wiley & Sons A/S.

  14. Estimating the size of the solution space of metabolic networks

    Directory of Open Access Journals (Sweden)

    Mulet Roberto

    2008-05-01

    Full Text Available Abstract Background Cellular metabolism is one of the most investigated system of biological interactions. While the topological nature of individual reactions and pathways in the network is quite well understood there is still a lack of comprehension regarding the global functional behavior of the system. In the last few years flux-balance analysis (FBA has been the most successful and widely used technique for studying metabolism at system level. This method strongly relies on the hypothesis that the organism maximizes an objective function. However only under very specific biological conditions (e.g. maximization of biomass for E. coli in reach nutrient medium the cell seems to obey such optimization law. A more refined analysis not assuming extremization remains an elusive task for large metabolic systems due to algorithmic limitations. Results In this work we propose a novel algorithmic strategy that provides an efficient characterization of the whole set of stable fluxes compatible with the metabolic constraints. Using a technique derived from the fields of statistical physics and information theory we designed a message-passing algorithm to estimate the size of the affine space containing all possible steady-state flux distributions of metabolic networks. The algorithm, based on the well known Bethe approximation, can be used to approximately compute the volume of a non full-dimensional convex polytope in high dimensions. We first compare the accuracy of the predictions with an exact algorithm on small random metabolic networks. We also verify that the predictions of the algorithm match closely those of Monte Carlo based methods in the case of the Red Blood Cell metabolic network. Then we test the effect of gene knock-outs on the size of the solution space in the case of E. coli central metabolism. Finally we analyze the statistical properties of the average fluxes of the reactions in the E. coli metabolic network. Conclusion We propose a

  15. Evaluation of Flex-Grid architecture for NREN optical networks

    DEFF Research Database (Denmark)

    Turus, Ioan; Kleist, Josva; Fagertun, Anna Manolova

    2014-01-01

    as reference topologies. Flex-Grid technology is suggested as a solution to cope with the different challenges in NREN transport networks such as traffic increase and introduction of novel physical layer services. Flex-Grid refers to narrow channel spacing values and requires a control plane which would enable......The paper presents an in-depth and structured evaluation of the impact that Flex-Grid technology reveals within current NRENs’ core optical networks. The evaluation is based on simulations performed with OPNET Modeler tool and considers NORDUnet as well as a normalized GEANT core optical network...

  16. Use of communication architecture test bed to evaluate data network performance

    International Nuclear Information System (INIS)

    Clapp, N.E. Jr.; Swail, B.K.; Naser, J.A.

    1994-01-01

    Local area networks (LANs) are becoming more prevalent in nuclear power plants. Traditionally, LANs were only used as information highways, providing office automation services. LANs are now being used as data highways for applications in plant data acquisition and control systems. A communication architecture test bed, which contains network simulators, is needed to allow network performance studies and to resolve design issues prior to equipment purchase. Two levels of granularity of simulation are needed to provide the dynamic information about network performance. A coarse-grain simulator is used to estimate the dynamic performance of the network due to major resources such as workstations, gateways, and data acquisition systems. A fine-grain simulator allows a greater level of detail about the underlying network protocol and resources to be simulated. The combination of coarse-grain and fine-grain simulation packages provides the network designer with the required tools to thoroughly understand the behavior of the modeled network. This paper describes the development of a communication architecture test bed using commercial network simulation packages. Network simulators allow the resolution of major design issues in software without the expense of purchasing costly hardware components

  17. Architectural Design for the Global Legal Information Network

    Science.gov (United States)

    Kalpakis, Konstantinos

    1999-01-01

    In this report, we provide a summary of our activities regarding the goals, requirements analysis, design, and prototype implementation for the Global Legal Information Network, a joint effort between the Law Library of Congress and NASA.

  18. Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks.

    Science.gov (United States)

    Kiparissides, A; Hatzimanikatis, V

    2017-01-01

    The increasing availability of large metabolomics datasets enhances the need for computational methodologies that can organize the data in a way that can lead to the inference of meaningful relationships. Knowledge of the metabolic state of a cell and how it responds to various stimuli and extracellular conditions can offer significant insight in the regulatory functions and how to manipulate them. Constraint based methods, such as Flux Balance Analysis (FBA) and Thermodynamics-based flux analysis (TFA), are commonly used to estimate the flow of metabolites through genome-wide metabolic networks, making it possible to identify the ranges of flux values that are consistent with the studied physiological and thermodynamic conditions. However, unless key intracellular fluxes and metabolite concentrations are known, constraint-based models lead to underdetermined problem formulations. This lack of information propagates as uncertainty in the estimation of fluxes and basic reaction properties such as the determination of reaction directionalities. Therefore, knowledge of which metabolites, if measured, would contribute the most to reducing this uncertainty can significantly improve our ability to define the internal state of the cell. In the present work we combine constraint based modeling, Design of Experiments (DoE) and Global Sensitivity Analysis (GSA) into the Thermodynamics-based Metabolite Sensitivity Analysis (TMSA) method. TMSA ranks metabolites comprising a metabolic network based on their ability to constrain the gamut of possible solutions to a limited, thermodynamically consistent set of internal states. TMSA is modular and can be applied to a single reaction, a metabolic pathway or an entire metabolic network. This is, to our knowledge, the first attempt to use metabolic modeling in order to provide a significance ranking of metabolites to guide experimental measurements. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier

  19. Adaptive Monitoring and Control Architectures for Power Distribution Grids over Heterogeneous ICT Networks

    DEFF Research Database (Denmark)

    Olsen, Rasmus Løvenstein; Hägerling, Christian; Kurtz, Fabian M.

    2014-01-01

    ) and the quality of the power may become costly. In this light, Smart Grids may provide an answer towards a more active and efficient electrical network. The EU project SmartC2Net aims to enable smart grid operations over imperfect, heterogeneous general purpose networks which poses a significant challenge...... to the reliability due to the stochastic behaviour found in such networks. Therefore, key concepts are presented in this paper targeting the support of proper smart grid control in these network environments. An overview on the required Information and Communication Technology (ICT) architecture and its...

  20. The maturing architecture of the brain's default network.

    Science.gov (United States)

    Fair, Damien A; Cohen, Alexander L; Dosenbach, Nico U F; Church, Jessica A; Miezin, Francis M; Barch, Deanna M; Raichle, Marcus E; Petersen, Steven E; Schlaggar, Bradley L

    2008-03-11

    In recent years, the brain's "default network," a set of regions characterized by decreased neural activity during goal-oriented tasks, has generated a significant amount of interest, as well as controversy. Much of the discussion has focused on the relationship of these regions to a "default mode" of brain function. In early studies, investigators suggested that, the brain's default mode supports "self-referential" or "introspective" mental activity. Subsequently, regions of the default network have been more specifically related to the "internal narrative," the "autobiographical self," "stimulus independent thought," "mentalizing," and most recently "self-projection." However, the extant literature on the function of the default network is limited to adults, i.e., after the system has reached maturity. We hypothesized that further insight into the network's functioning could be achieved by characterizing its development. In the current study, we used resting-state functional connectivity MRI (rs-fcMRI) to characterize the development of the brain's default network. We found that the default regions are only sparsely functionally connected at early school age (7-9 years old); over development, these regions integrate into a cohesive, interconnected network.

  1. Quantifying sleep architecture dynamics and individual differences using big data and Bayesian networks.

    Science.gov (United States)

    Yetton, Benjamin D; McDevitt, Elizabeth A; Cellini, Nicola; Shelton, Christian; Mednick, Sara C

    2018-01-01

    The pattern of sleep stages across a night (sleep architecture) is influenced by biological, behavioral, and clinical variables. However, traditional measures of sleep architecture such as stage proportions, fail to capture sleep dynamics. Here we quantify the impact of individual differences on the dynamics of sleep architecture and determine which factors or set of factors best predict the next sleep stage from current stage information. We investigated the influence of age, sex, body mass index, time of day, and sleep time on static (e.g. minutes in stage, sleep efficiency) and dynamic measures of sleep architecture (e.g. transition probabilities and stage duration distributions) using a large dataset of 3202 nights from a non-clinical population. Multi-level regressions show that sex effects duration of all Non-Rapid Eye Movement (NREM) stages, and age has a curvilinear relationship for Wake After Sleep Onset (WASO) and slow wave sleep (SWS) minutes. Bayesian network modeling reveals sleep architecture depends on time of day, total sleep time, age and sex, but not BMI. Older adults, and particularly males, have shorter bouts (more fragmentation) of Stage 2, SWS, and they transition less frequently to these stages. Additionally, we showed that the next sleep stage and its duration can be optimally predicted by the prior 2 stages and age. Our results demonstrate the potential benefit of big data and Bayesian network approaches in quantifying static and dynamic architecture of normal sleep.

  2. Using empirical measurements of tree branching architecture to scale whole-tree metabolism along a 4000 m elevation transect in the Peruvian Andes and Amazon

    Science.gov (United States)

    Bentley, L. P.; Shenkin, A.; Enquist, B.; Malhi, Y.

    2014-12-01

    Plant scaling models use measurements of architecture (i.e., length, width, and order of branch or xylem segments) to ultimately predict whole-plant metabolism via mass and water-use allometries. The application of plant scaling models is broad, and holds potential to simplify forest modelling efforts. However little is known regarding the influence of the environment (e.g., temperature, light, etc) on variation in branching architecture traits and how this variation affects scaling. Furthermore, scaling model assumptions of a self-similar and symmetric branching network have not been extensively tested, especially in tropical forests. As such, it is still unclear to what extent tree communities can be approximated by simple geometrical models, and where important functional divergences from theory exist. Here we analyse novel tree architecture data from diverse species along a 4000m elevational gradient spanning the Andes to the Amazon in Peru. Specifically, we calculate and compare inter- and intra-specific scaling exponents related to branch segment length and width within a hierarchical Bayesian framework. Preliminary results indicate that branching architecture significantly varies among and within species especially with respect to light environments. As such, we explore the role of light in driving tree geometry by also analysing differences in light environment and crown shape. Then, we attempt to link branch architecture and crown shape. Using 6 branch-level and whole-tree traits (path length fraction, crown depth, crown width, crown volume, crown depth/width and crown width/depth) we are able to cluster 68 species of trees into 6 unique groups related to architecture and explain ~60% variability in these data. In the future, it will be important to relate these architectural groups to variation in leaf-level traits and physiology. Lastly, we discuss the implications of using these results to understand tropical forest responses to environmental change.

  3. Requirements and System Architecture for a Healthcare Wireless Body Area Network

    DEFF Research Database (Denmark)

    Hansen, Finn Overgaard; Toftegaard, Thomas Skjødeberg

    Wireless body area networks enable new opportunities for personal healthcare monitoring and personal healthcare applications. This paper presents a comprehensive set of requirements and challenges for building a wireless body area network to support diverse user groups and a corresponding set...... of healthcare applications. Based on the identified requirements, the paper presents an architecture for a wireless body area network and describes how this architecture is connected to an existing it-infrastructure supporting healthcare at home. Finally the paper presents our on-going research with development...... of an ASE-BAN test bed. The major goal for this test bed is to be a platform for research and experiments with development of an ultra-low power body area network including sensor, communication nodes, communication protocols and a body gateway component....

  4. The architecture of antagonistic networks: Node degree distribution, compartmentalization and nestedness

    Directory of Open Access Journals (Sweden)

    Savannah Nuwagaba

    2015-12-01

    Full Text Available Describing complex ecosystems as networks of interacting components has proved fruitful - revealing many distinctive patterns and dynamics of ecological systems. Of these patterns, three have often been brought up in literature, including species degree distribution, compartmentalization and nestedness, due largely to their implications for the functionality and stability of communities. Here, using 61 empirical antagonistic networks, we aim to settle the inconsistency in literature by (i fitting their node degree distributions to five different parametric models and identifying the one fits the best, (ii measuring the levels of nestedness and compartmentalization of these 61 networks and testing their significance using different null models, and (iii exploring how network connectance affects these three network architecture metrics. This research showed that most antagonistic networks do not display power law degree distributions and that resource species are generally uniformly distributed. We also clearly showed that the conclusion of whether a network is significantly compartmentalized or nested depends largely on the null model used.

  5. TopoGen: A Network Topology Generation Architecture with application to automating simulations of Software Defined Networks

    CERN Document Server

    Laurito, Andres; The ATLAS collaboration

    2017-01-01

    Simulation is an important tool to validate the performance impact of control decisions in Software Defined Networks (SDN). Yet, the manual modeling of complex topologies that may change often during a design process can be a tedious error-prone task. We present TopoGen, a general purpose architecture and tool for systematic translation and generation of network topologies. TopoGen can be used to generate network simulation models automatically by querying information available at diverse sources, notably SDN controllers. The DEVS modeling and simulation framework facilitates a systematic translation of structured knowledge about a network topology into a formal modular and hierarchical coupling of preexisting or new models of network entities (physical or logical). TopoGen can be flexibly extended with new parsers and generators to grow its scope of applicability. This permits to design arbitrary workflows of topology transformations. We tested TopoGen in a network engineering project for the ATLAS detector ...

  6. TopoGen: A Network Topology Generation Architecture with application to automating simulations of Software Defined Networks

    CERN Document Server

    Laurito, Andres; The ATLAS collaboration

    2018-01-01

    Simulation is an important tool to validate the performance impact of control decisions in Software Defined Networks (SDN). Yet, the manual modeling of complex topologies that may change often during a design process can be a tedious error-prone task. We present TopoGen, a general purpose architecture and tool for systematic translation and generation of network topologies. TopoGen can be used to generate network simulation models automatically by querying information available at diverse sources, notably SDN controllers. The DEVS modeling and simulation framework facilitates a systematic translation of structured knowledge about a network topology into a formal modular and hierarchical coupling of preexisting or new models of network entities (physical or logical). TopoGen can be flexibly extended with new parsers and generators to grow its scope of applicability. This permits to design arbitrary workflows of topology transformations. We tested TopoGen in a network engineering project for the ATLAS detector ...

  7. The P-Mesh: A Commodity-based Scalable Network Architecture for Clusters

    Science.gov (United States)

    Nitzberg, Bill; Kuszmaul, Chris; Stockdale, Ian; Becker, Jeff; Jiang, John; Wong, Parkson; Tweten, David (Technical Monitor)

    1998-01-01

    We designed a new network architecture, the P-Mesh which combines the scalability and fault resilience of a torus with the performance of a switch. We compare the scalability, performance, and cost of the hub, switch, torus, tree, and P-Mesh architectures. The latter three are capable of scaling to thousands of nodes, however, the torus has severe performance limitations with that many processors. The tree and P-Mesh have similar latency, bandwidth, and bisection bandwidth, but the P-Mesh outperforms the switch architecture (a lower bound for tree performance) on 16-node NAB Parallel Benchmark tests by up to 23%, and costs 40% less. Further, the P-Mesh has better fault resilience characteristics. The P-Mesh architecture trades increased management overhead for lower cost, and is a good bridging technology while the price of tree uplinks is expensive.

  8. Modeling, analysis and optimization of network-on-chip communication architectures

    CERN Document Server

    Ogras, Umit Y

    2013-01-01

    Traditionally, design space exploration for Systems-on-Chip (SoCs) has focused on the computational aspects of the problem at hand. However, as the number of components on a single chip and their performance continue to increase, the communication architecture plays a major role in the area, performance and energy consumption of the overall system. As a result, a shift from computation-based to communication-based design becomes mandatory. Towards this end, network-on-chip (NoC) communication architectures have emerged recently as a promising alternative to classical bus and point-to-point communication architectures. This book explores outstanding research problems related to modeling, analysis and optimization of NoC communication architectures. More precisely, we present novel design methodologies, software tools and FPGA prototypes to aid the design of application-specific NoCs.

  9. A self-organized artificial neural network architecture for sensory integration with applications to letter-phoneme integration

    OpenAIRE

    Jantvik, Tamas; Gustafsson, Lennart; Paplinski, Andrew

    2011-01-01

    The multimodal self-organizing network (MMSON), an artificial neural network architecture carrying out sensory integration, is presented here. The architecture is designed using neurophysiological findings and imaging studies that pertain to sensory integration and consists of interconnected lattices of artificial neurons. In this artificial neural architecture, the degree of recognition of stimuli, that is, the perceived reliability of stimuli in the various subnetworks, is included in the c...

  10. Cluster based architecture and network maintenance protocol for medical priority aware cognitive radio based hospital.

    Science.gov (United States)

    Al Mamoon, Ishtiak; Muzahidul Islam, A K M; Baharun, Sabariah; Ahmed, Ashir; Komaki, Shozo

    2016-08-01

    Due to the rapid growth of wireless medical devices in near future, wireless healthcare services may face some inescapable issue such as medical spectrum scarcity, electromagnetic interference (EMI), bandwidth constraint, security and finally medical data communication model. To mitigate these issues, cognitive radio (CR) or opportunistic radio network enabled wireless technology is suitable for the upcoming wireless healthcare system. The up-to-date research on CR based healthcare has exposed some developments on EMI and spectrum problems. However, the investigation recommendation on system design and network model for CR enabled hospital is rare. Thus, this research designs a hierarchy based hybrid network architecture and network maintenance protocols for previously proposed CR hospital system, known as CogMed. In the previous study, the detail architecture of CogMed and its maintenance protocols were not present. The proposed architecture includes clustering concepts for cognitive base stations and non-medical devices. Two cluster head (CH selector equations are formulated based on priority of location, device, mobility rate of devices and number of accessible channels. In order to maintain the integrity of the proposed network model, node joining and node leaving protocols are also proposed. Finally, the simulation results show that the proposed network maintenance time is very low for emergency medical devices (average maintenance period 9.5 ms) and the re-clustering effects for different mobility enabled non-medical devices are also balanced.

  11. Scale-space measures for graph topology link protein network architecture to function.

    Science.gov (United States)

    Hulsman, Marc; Dimitrakopoulos, Christos; de Ridder, Jeroen

    2014-06-15

    The network architecture of physical protein interactions is an important determinant for the molecular functions that are carried out within each cell. To study this relation, the network architecture can be characterized by graph topological characteristics such as shortest paths and network hubs. These characteristics have an important shortcoming: they do not take into account that interactions occur across different scales. This is important because some cellular functions may involve a single direct protein interaction (small scale), whereas others require more and/or indirect interactions, such as protein complexes (medium scale) and interactions between large modules of proteins (large scale). In this work, we derive generalized scale-aware versions of known graph topological measures based on diffusion kernels. We apply these to characterize the topology of networks across all scales simultaneously, generating a so-called graph topological scale-space. The comprehensive physical interaction network in yeast is used to show that scale-space based measures consistently give superior performance when distinguishing protein functional categories and three major types of functional interactions-genetic interaction, co-expression and perturbation interactions. Moreover, we demonstrate that graph topological scale spaces capture biologically meaningful features that provide new insights into the link between function and protein network architecture. Matlab(TM) code to calculate the scale-aware topological measures (STMs) is available at http://bioinformatics.tudelft.nl/TSSA © The Author 2014. Published by Oxford University Press.

  12. Improvements to Integrated Tradespace Analysis of Communications Architectures (ITACA) Network Loading Analysis Tool

    Science.gov (United States)

    Lee, Nathaniel; Welch, Bryan W.

    2018-01-01

    NASA's SCENIC project aims to simplify and reduce the cost of space mission planning by replicating the analysis capabilities of commercially licensed software which are integrated with relevant analysis parameters specific to SCaN assets and SCaN supported user missions. SCENIC differs from current tools that perform similar analyses in that it 1) does not require any licensing fees, 2) will provide an all-in-one package for various analysis capabilities that normally requires add-ons or multiple tools to complete. As part of SCENIC's capabilities, the ITACA network loading analysis tool will be responsible for assessing the loading on a given network architecture and generating a network service schedule. ITACA will allow users to evaluate the quality of service of a given network architecture and determine whether or not the architecture will satisfy the mission's requirements. ITACA is currently under development, and the following improvements were made during the fall of 2017: optimization of runtime, augmentation of network asset pre-service configuration time, augmentation of Brent's method of root finding, augmentation of network asset FOV restrictions, augmentation of mission lifetimes, and the integration of a SCaN link budget calculation tool. The improvements resulted in (a) 25% reduction in runtime, (b) more accurate contact window predictions when compared to STK(Registered Trademark) contact window predictions, and (c) increased fidelity through the use of specific SCaN asset parameters.

  13. An architecture for performance optimization in a collaborative knowledge-based approach for wireless sensor networks.

    Science.gov (United States)

    Gadeo-Martos, Manuel Angel; Fernandez-Prieto, Jose Angel; Canada-Bago, Joaquin; Velasco, Juan Ramon

    2011-01-01

    Over the past few years, Intelligent Spaces (ISs) have received the attention of many Wireless Sensor Network researchers. Recently, several studies have been devoted to identify their common capacities and to set up ISs over these networks. However, little attention has been paid to integrating Fuzzy Rule-Based Systems into collaborative Wireless Sensor Networks for the purpose of implementing ISs. This work presents a distributed architecture proposal for collaborative Fuzzy Rule-Based Systems embedded in Wireless Sensor Networks, which has been designed to optimize the implementation of ISs. This architecture includes the following: (a) an optimized design for the inference engine; (b) a visual interface; (c) a module to reduce the redundancy and complexity of the knowledge bases; (d) a module to evaluate the accuracy of the new knowledge base; (e) a module to adapt the format of the rules to the structure used by the inference engine; and (f) a communications protocol. As a real-world application of this architecture and the proposed methodologies, we show an application to the problem of modeling two plagues of the olive tree: prays (olive moth, Prays oleae Bern.) and repilo (caused by the fungus Spilocaea oleagina). The results show that the architecture presented in this paper significantly decreases the consumption of resources (memory, CPU and battery) without a substantial decrease in the accuracy of the inferred values.

  14. An architecture to offer cloud-based radio access network as a service

    NARCIS (Netherlands)

    Studer Ferreira, Lucio; Pichon, Dominique; Hatefi, Atoosa; Gomes, Andre; Dimitrova, D.C.; Braun, Torsten; Karagiannis, Georgios; Karimzadeh Motallebi Azar, Morteza; Branco, Monica; Correia, Luis M.

    2014-01-01

    This paper addresses the novel notion of offering a radio access network as a service. Its components may be instantiated on general purpose platforms with pooled resources (both radio and hardware ones) dimensioned on-demand, elastically and following the pay-per-use principle. A novel architecture

  15. Engineering tough, highly compressible, biodegradable hydrogels by tuning the network architecture.

    Science.gov (United States)

    Gu, Dunyin; Tan, Shereen; Xu, Chenglong; O'Connor, Andrea J; Qiao, Greg G

    2017-06-20

    By precisely tuning the network architecture, tough, highly compressible hydrogels were engineered. The hydrogels were made by interconnecting high-functionality hydrophobic domains through linear tri-block chains, consisting of soft hydrophilic middle blocks, flanked with flexible hydrophobic blocks. In showing their applicability, the efficient encapsulation and prolonged release of hydrophobic drugs were achieved.

  16. A multi-tiered architecture for content retrieval in mobile peer-to-peer networks.

    Science.gov (United States)

    2012-01-01

    In this paper, we address content retrieval in Mobile Peer-to-Peer (P2P) Networks. We design a multi-tiered architecture for content : retrieval, where at Tier 1, we design a protocol for content similarity governed by a parameter that trades accu...

  17. Dietary pseudopurpurin improves bone geometry architecture and metabolism in red-bone Guishan goats.

    Directory of Open Access Journals (Sweden)

    ChenChen Wu

    Full Text Available Red-colored bones were found initially in some Guishan goats in the 1980s, and they were designated red-boned goats. However, it is not understood what causes the red color in the bone, or whether the red material changes the bone geometry, architecture, and metabolism of red-boned goats. Pseudopurpurin was identified in the red-colored material of the bone in red-boned goats by high-performance liquid chromatography-electrospray ionization-mass spetrometry and nuclear magnetic resonance analysis. Pseudopurpurin is one of the main constituents of Rubia cordifolia L, which is eaten by the goats. The assessment of the mechanical properties and micro-computed tomography showed that the red-boned goats displayed an increase in the trabecular volume fraction, trabecular thickness, and the number of trabeculae in the distal femur. The mean thickness, inner perimeter, outer perimeter, and area of the femoral diaphysis were also increased. In addition, the trabecular separation and structure model index of the distal femur were decreased, but the bone mineral density of the whole femur and the mechanical properties of the femoral diaphysis were enhanced in the red-boned goats. Meanwhile, expression of alkaline phosphatase and osteocalcin mRNA was higher, and the ratio of the receptor activator of the nuclear factor kappa B ligand to osteoprotegerin was markedly lower in the bone marrow of the red-boned goats compared with common goats. To confirm further the effect of pseudopurpurin on bone geometry, architecture, and metabolism, Wistar rats were fed diets to which pseudopurpurin was added for 5 months. Similar changes were observed in the femurs of the treated rats. The above results demonstrate that pseudopurpurin has a close affinity with the mineral salts of bone, and consequently a high level of mineral salts in the bone cause an improvement in bone strength and an enhancement in the structure and metabolic functions of the bone.

  18. An Architecture for Anonymous Mobile Coupons in a Large Network

    Directory of Open Access Journals (Sweden)

    Alberto Bartoli

    2016-01-01

    Full Text Available A mobile coupon (m-coupon can be presented with a smartphone for obtaining a financial discount when purchasing a product or a service. M-coupons are a powerful marketing tool that has enjoyed a huge growth and diffusion, involving tens of millions of people each year. We propose an architecture which may enable significant improvements over current m-coupon technology, in terms of acceptance of potential customers and of marketing actions that become feasible: the customer does not need to install any dedicated app; an m-coupon is not bound to any specific device or customer; an m-coupon may be redeemed at any store in a set of potentially many thousands of stores, without any prior arrangement between customer and store. We are not aware of any proposal with these properties.

  19. Reconfigurable subsampling receiver architecture for wireless body area networks

    NARCIS (Netherlands)

    Zhao, D.; Serdijn, W.A.; Huang, L.; Dolmans, G.

    2011-01-01

    The wide range of wireless body area network (WBAN) applications gives rise to different system requirements for the carrier frequencies and data rates. In order to accommodate various standards in WBAN applications, a universal receiver system with good performance and low power is highly

  20. Dynamic Adaptive Neural Network Arrays: A Neuromorphic Architecture

    Energy Technology Data Exchange (ETDEWEB)

    Disney, Adam [University of Tennessee (UT); Reynolds, John [University of Tennessee (UT)

    2015-01-01

    Dynamic Adaptive Neural Network Array (DANNA) is a neuromorphic hardware implementation. It differs from most other neuromorphic projects in that it allows for programmability of structure, and it is trained or designed using evolutionary optimization. This paper describes the DANNA structure, how DANNA is trained using evolutionary optimization, and an application of DANNA to a very simple classification task.

  1. Feedback Control Architecture and the Bacterial Chemotaxis Network

    Science.gov (United States)

    Hamadeh, Abdullah; Roberts, Mark A. J.; August, Elias; McSharry, Patrick E.; Maini, Philip K.; Armitage, Judith P.; Papachristodoulou, Antonis

    2011-01-01

    Bacteria move towards favourable and away from toxic environments by changing their swimming pattern. This response is regulated by the chemotaxis signalling pathway, which has an important feature: it uses feedback to ‘reset’ (adapt) the bacterial sensing ability, which allows the bacteria to sense a range of background environmental changes. The role of this feedback has been studied extensively in the simple chemotaxis pathway of Escherichia coli. However it has been recently found that the majority of bacteria have multiple chemotaxis homologues of the E. coli proteins, resulting in more complex pathways. In this paper we investigate the configuration and role of feedback in Rhodobacter sphaeroides, a bacterium containing multiple homologues of the chemotaxis proteins found in E. coli. Multiple proteins could produce different possible feedback configurations, each having different chemotactic performance qualities and levels of robustness to variations and uncertainties in biological parameters and to intracellular noise. We develop four models corresponding to different feedback configurations. Using a series of carefully designed experiments we discriminate between these models and invalidate three of them. When these models are examined in terms of robustness to noise and parametric uncertainties, we find that the non-invalidated model is superior to the others. Moreover, it has a ‘cascade control’ feedback architecture which is used extensively in engineering to improve system performance, including robustness. Given that the majority of bacteria are known to have multiple chemotaxis pathways, in this paper we show that some feedback architectures allow them to have better performance than others. In particular, cascade control may be an important feature in achieving robust functionality in more complex signalling pathways and in improving their performance. PMID:21573199

  2. Feedback control architecture and the bacterial chemotaxis network.

    Directory of Open Access Journals (Sweden)

    Abdullah Hamadeh

    2011-05-01

    Full Text Available Bacteria move towards favourable and away from toxic environments by changing their swimming pattern. This response is regulated by the chemotaxis signalling pathway, which has an important feature: it uses feedback to 'reset' (adapt the bacterial sensing ability, which allows the bacteria to sense a range of background environmental changes. The role of this feedback has been studied extensively in the simple chemotaxis pathway of Escherichia coli. However it has been recently found that the majority of bacteria have multiple chemotaxis homologues of the E. coli proteins, resulting in more complex pathways. In this paper we investigate the configuration and role of feedback in Rhodobacter sphaeroides, a bacterium containing multiple homologues of the chemotaxis proteins found in E. coli. Multiple proteins could produce different possible feedback configurations, each having different chemotactic performance qualities and levels of robustness to variations and uncertainties in biological parameters and to intracellular noise. We develop four models corresponding to different feedback configurations. Using a series of carefully designed experiments we discriminate between these models and invalidate three of them. When these models are examined in terms of robustness to noise and parametric uncertainties, we find that the non-invalidated model is superior to the others. Moreover, it has a 'cascade control' feedback architecture which is used extensively in engineering to improve system performance, including robustness. Given that the majority of bacteria are known to have multiple chemotaxis pathways, in this paper we show that some feedback architectures allow them to have better performance than others. In particular, cascade control may be an important feature in achieving robust functionality in more complex signalling pathways and in improving their performance.

  3. Feedback control architecture and the bacterial chemotaxis network.

    Science.gov (United States)

    Hamadeh, Abdullah; Roberts, Mark A J; August, Elias; McSharry, Patrick E; Maini, Philip K; Armitage, Judith P; Papachristodoulou, Antonis

    2011-05-01

    Bacteria move towards favourable and away from toxic environments by changing their swimming pattern. This response is regulated by the chemotaxis signalling pathway, which has an important feature: it uses feedback to 'reset' (adapt) the bacterial sensing ability, which allows the bacteria to sense a range of background environmental changes. The role of this feedback has been studied extensively in the simple chemotaxis pathway of Escherichia coli. However it has been recently found that the majority of bacteria have multiple chemotaxis homologues of the E. coli proteins, resulting in more complex pathways. In this paper we investigate the configuration and role of feedback in Rhodobacter sphaeroides, a bacterium containing multiple homologues of the chemotaxis proteins found in E. coli. Multiple proteins could produce different possible feedback configurations, each having different chemotactic performance qualities and levels of robustness to variations and uncertainties in biological parameters and to intracellular noise. We develop four models corresponding to different feedback configurations. Using a series of carefully designed experiments we discriminate between these models and invalidate three of them. When these models are examined in terms of robustness to noise and parametric uncertainties, we find that the non-invalidated model is superior to the others. Moreover, it has a 'cascade control' feedback architecture which is used extensively in engineering to improve system performance, including robustness. Given that the majority of bacteria are known to have multiple chemotaxis pathways, in this paper we show that some feedback architectures allow them to have better performance than others. In particular, cascade control may be an important feature in achieving robust functionality in more complex signalling pathways and in improving their performance.

  4. Sensitivity of chemical reaction networks: a structural approach. 1. Examples and the carbon metabolic network.

    Science.gov (United States)

    Mochizuki, Atsushi; Fiedler, Bernold

    2015-02-21

    In biological cells, chemical reaction pathways lead to complex network systems like metabolic networks. One experimental approach to the dynamics of such systems examines their "sensitivity": each enzyme mediating a reaction in the system is increased/decreased or knocked out separately, and the responses in the concentrations of chemicals or their fluxes are observed. In this study, we present a mathematical method, named structural sensitivity analysis, to determine the sensitivity of reaction systems from information on the network alone. We investigate how the sensitivity responses of chemicals in a reaction network depend on the structure of the network, and on the position of the perturbed reaction in the network. We establish and prove some general rules which relate the sensitivity response to the structure of the underlying network. We describe a hierarchical pattern in the flux response which is governed by branchings in the network. We apply our method to several hypothetical and real life chemical reaction networks, including the metabolic network of the Escherichia coli TCA cycle. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Context-specific metabolic networks are consistent with experiments.

    Directory of Open Access Journals (Sweden)

    Scott A Becker

    2008-05-01

    Full Text Available Reconstructions of cellular metabolism are publicly available for a variety of different microorganisms and some mammalian genomes. To date, these reconstructions are "genome-scale" and strive to include all reactions implied by the genome annotation, as well as those with direct experimental evidence. Clearly, many of the reactions in a genome-scale reconstruction will not be active under particular conditions or in a particular cell type. Methods to tailor these comprehensive genome-scale reconstructions into context-specific networks will aid predictive in silico modeling for a particular situation. We present a method called Gene Inactivity Moderated by Metabolism and Expression (GIMME to achieve this goal. The GIMME algorithm uses quantitative gene expression data and one or more presupposed metabolic objectives to produce the context-specific reconstruction that is most consistent with the available data. Furthermore, the algorithm provides a quantitative inconsistency score indicating how consistent a set of gene expression data is with a particular metabolic objective. We show that this algorithm produces results consistent with biological experiments and intuition for adaptive evolution of bacteria, rational design of metabolic engineering strains, and human skeletal muscle cells. This work represents progress towards producing constraint-based models of metabolism that are specific to the conditions where the expression profiling data is available.

  6. Hubs of Anticorrelation in High-Resolution Resting-State Functional Connectivity Network Architecture.

    Science.gov (United States)

    Gopinath, Kaundinya; Krishnamurthy, Venkatagiri; Cabanban, Romeo; Crosson, Bruce A

    2015-06-01

    A major focus of brain research recently has been to map the resting-state functional connectivity (rsFC) network architecture of the normal brain and pathology through functional magnetic resonance imaging. However, the phenomenon of anticorrelations in resting-state signals between different brain regions has not been adequately examined. The preponderance of studies on resting-state fMRI (rsFMRI) have either ignored anticorrelations in rsFC networks or adopted methods in data analysis, which have rendered anticorrelations in rsFC networks uninterpretable. The few studies that have examined anticorrelations in rsFC networks using conventional methods have found anticorrelations to be weak in strength and not very reproducible across subjects. Anticorrelations in rsFC network architecture could reflect mechanisms that subserve a number of important brain processes. In this preliminary study, we examined the properties of anticorrelated rsFC networks by systematically focusing on negative cross-correlation coefficients (CCs) among rsFMRI voxel time series across the brain with graph theory-based network analysis. A number of methods were implemented to enhance the neuronal specificity of resting-state functional connections that yield negative CCs, although at the cost of decreased sensitivity. Hubs of anticorrelation were seen in a number of cortical and subcortical brain regions. Examination of the anticorrelation maps of these hubs indicated that negative CCs in rsFC network architecture highlight a number of regulatory interactions between brain networks and regions, including reciprocal modulations, suppression, inhibition, and neurofeedback.

  7. Architecture of the rat nephron-arterial network

    DEFF Research Database (Denmark)

    Marsh, Donald J; Postnov, Dmitry D; Rowland, Douglas

    2017-01-01

    Among solid organs the kidney's vascular network stands out because each nephron has 2 distinct capillary structures in series, and because tubuloglomerular feedback (TGF), one of the mechanisms responsible for blood flow autoregulation, is specific to renal tubules. TGF and the myogenic mechanism......, acting jointly, autoregulate single nephron blood flow. Each generates a self-sustained periodic oscillation and an oscillating electrical signal that propagates upstream along arterioles. Similar electrical signals from other nephrons interact, allowing nephron synchronization. Experimental measurements...... show synchronization over fields of a few nephrons; simulations based on a simplified network structure that could obscure complex interactions predict more widespread synchronization. To permit more realistic simulations we made a cast of blood vessels in a rat kidney, performed micro...

  8. EnzDP: improved enzyme annotation for metabolic network reconstruction based on domain composition profiles.

    Science.gov (United States)

    Nguyen, Nam-Ninh; Srihari, Sriganesh; Leong, Hon Wai; Chong, Ket-Fah

    2015-10-01

    Determining the entire complement of enzymes and their enzymatic functions is a fundamental step for reconstructing the metabolic network of cells. High quality enzyme annotation helps in enhancing metabolic networks reconstructed from the genome, especially by reducing gaps and increasing the enzyme coverage. Currently, structure-based and network-based approaches can only cover a limited number of enzyme families, and the accuracy of homology-based approaches can be further improved. Bottom-up homology-based approach improves the coverage by rebuilding Hidden Markov Model (HMM) profiles for all known enzymes. However, its clustering procedure relies firmly on BLAST similarity score, ignoring protein domains/patterns, and is sensitive to changes in cut-off thresholds. Here, we use functional domain architecture to score the association between domain families and enzyme families (Domain-Enzyme Association Scoring, DEAS). The DEAS score is used to calculate the similarity between proteins, which is then used in clustering procedure, instead of using sequence similarity score. We improve the enzyme annotation protocol using a stringent classification procedure, and by choosing optimal threshold settings and checking for active sites. Our analysis shows that our stringent protocol EnzDP can cover up to 90% of enzyme families available in Swiss-Prot. It achieves a high accuracy of 94.5% based on five-fold cross-validation. EnzDP outperforms existing methods across several testing scenarios. Thus, EnzDP serves as a reliable automated tool for enzyme annotation and metabolic network reconstruction. Available at: www.comp.nus.edu.sg/~nguyennn/EnzDP .

  9. Bacterial Unculturability and the Formation of Intercellular Metabolic Networks.

    Science.gov (United States)

    Pande, Samay; Kost, Christian

    2017-05-01

    The majority of known bacterial species cannot be cultivated under laboratory conditions. Here we argue that the adaptive emergence of obligate metabolic interactions in natural bacterial communities can explain this pattern. Bacteria commonly release metabolites into the external environment. Accumulating pools of extracellular metabolites create an ecological niche that benefits auxotrophic mutants, which have lost the ability to autonomously produce the corresponding metabolites. In addition to a diffusion-based metabolite transfer, auxotrophic cells can use contact-dependent means to obtain nutrients from other co-occurring cells. Spatial colocalisation and a continuous coevolution further increase the nutritional dependency and optimise fluxes through combined metabolic networks. Thus, bacteria likely function as networks of interacting cells that reciprocally exchange nutrients and biochemical functions rather than as physiologically autonomous units. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. The evolution of metabolic networks of E. coli

    Directory of Open Access Journals (Sweden)

    Baumler David J

    2011-11-01

    Full Text Available Abstract Background Despite the availability of numerous complete genome sequences from E. coli strains, published genome-scale metabolic models exist only for two commensal E. coli strains. These models have proven useful for many applications, such as engineering strains for desired product formation, and we sought to explore how constructing and evaluating additional metabolic models for E. coli strains could enhance these efforts. Results We used the genomic information from 16 E. coli strains to generate an E. coli pangenome metabolic network by evaluating their collective 76,990 ORFs. Each of these ORFs was assigned to one of 17,647 ortholog groups including ORFs associated with reactions in the most recent metabolic model for E. coli K-12. For orthologous groups that contain an ORF already represented in the MG1655 model, the gene to protein to reaction associations represented in this model could then be easily propagated to other E. coli strain models. All remaining orthologous groups were evaluated to see if new metabolic reactions could be added to generate a pangenome-scale metabolic model (iEco1712_pan. The pangenome model included reactions from a metabolic model update for E. coli K-12 MG1655 (iEco1339_MG1655 and enabled development of five additional strain-specific genome-scale metabolic models. These additional models include a second K-12 strain (iEco1335_W3110 and four pathogenic strains (two enterohemorrhagic E. coli O157:H7 and two uropathogens. When compared to the E. coli K-12 models, the metabolic models for the enterohemorrhagic (iEco1344_EDL933 and iEco1345_Sakai and uropathogenic strains (iEco1288_CFT073 and iEco1301_UTI89 contained numerous lineage-specific gene and reaction differences. All six E. coli models were evaluated by comparing model predictions to carbon source utilization measurements under aerobic and anaerobic conditions, and to batch growth profiles in minimal media with 0.2% (w/v glucose. An ancestral

  11. Algorithm-structured computer arrays and networks architectures and processes for images, percepts, models, information

    CERN Document Server

    Uhr, Leonard

    1984-01-01

    Computer Science and Applied Mathematics: Algorithm-Structured Computer Arrays and Networks: Architectures and Processes for Images, Percepts, Models, Information examines the parallel-array, pipeline, and other network multi-computers.This book describes and explores arrays and networks, those built, being designed, or proposed. The problems of developing higher-level languages for systems and designing algorithm, program, data flow, and computer structure are also discussed. This text likewise describes several sequences of successively more general attempts to combine the power of arrays wi

  12. Performance and Challenges of Service-Oriented Architecture for Wireless Sensor Networks.

    Science.gov (United States)

    Alshinina, Remah; Elleithy, Khaled

    2017-03-08

    Wireless Sensor Networks (WSNs) have become essential components for a variety of environmental, surveillance, military, traffic control, and healthcare applications. These applications face critical challenges such as communication, security, power consumption, data aggregation, heterogeneities of sensor hardware, and Quality of Service (QoS) issues. Service-Oriented Architecture (SOA) is a software architecture that can be integrated with WSN applications to address those challenges. The SOA middleware bridges the gap between the high-level requirements of different applications and the hardware constraints of WSNs. This survey explores state-of-the-art approaches based on SOA and Service-Oriented Middleware (SOM) architecture that provide solutions for WSN challenges. The categories of this paper are based on approaches of SOA with and without middleware for WSNs. Additionally, features of SOA and middleware architectures for WSNs are compared to achieve more robust and efficient network performance. Design issues of SOA middleware for WSNs and its characteristics are also highlighted. The paper concludes with future research directions in SOM architecture to meet all requirements of emerging application of WSNs.

  13. Performance and Challenges of Service-Oriented Architecture for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Remah Alshinina

    2017-03-01

    Full Text Available Wireless Sensor Networks (WSNs have become essential components for a variety of environmental, surveillance, military, traffic control, and healthcare applications. These applications face critical challenges such as communication, security, power consumption, data aggregation, heterogeneities of sensor hardware, and Quality of Service (QoS issues. Service-Oriented Architecture (SOA is a software architecture that can be integrated with WSN applications to address those challenges. The SOA middleware bridges the gap between the high-level requirements of different applications and the hardware constraints of WSNs. This survey explores state-of-the-art approaches based on SOA and Service-Oriented Middleware (SOM architecture that provide solutions for WSN challenges. The categories of this paper are based on approaches of SOA with and without middleware for WSNs. Additionally, features of SOA and middleware architectures for WSNs are compared to achieve more robust and efficient network performance. Design issues of SOA middleware for WSNs and its characteristics are also highlighted. The paper concludes with future research directions in SOM architecture to meet all requirements of emerging application of WSNs.

  14. Process reveals structure: How a network is traversed mediates expectations about its architecture.

    Science.gov (United States)

    Karuza, Elisabeth A; Kahn, Ari E; Thompson-Schill, Sharon L; Bassett, Danielle S

    2017-10-06

    Network science has emerged as a powerful tool through which we can study the higher-order architectural properties of the world around us. How human learners exploit this information remains an essential question. Here, we focus on the temporal constraints that govern such a process. Participants viewed a continuous sequence of images generated by three distinct walks on a modular network. Walks varied along two critical dimensions: their predictability and the density with which they sampled from communities of images. Learners exposed to walks that richly sampled from each community exhibited a sharp increase in processing time upon entry into a new community. This effect was eliminated in a highly regular walk that sampled exhaustively from images in short, successive cycles (i.e., that increasingly minimized uncertainty about the nature of upcoming stimuli). These results demonstrate that temporal organization plays an essential role in learners' sensitivity to the network architecture underlying sensory input.

  15. Design and architecture of the Mars relay network planning and analysis framework

    Science.gov (United States)

    Cheung, K. M.; Lee, C. H.

    2002-01-01

    In this paper we describe the design and architecture of the Mars Network planning and analysis framework that supports generation and validation of efficient planning and scheduling strategy. The goals are to minimize the transmitting time, minimize the delaying time, and/or maximize the network throughputs. The proposed framework would require (1) a client-server architecture to support interactive, batch, WEB, and distributed analysis and planning applications for the relay network analysis scheme, (2) a high-fidelity modeling and simulation environment that expresses link capabilities between spacecraft to spacecraft and spacecraft to Earth stations as time-varying resources, and spacecraft activities, link priority, Solar System dynamic events, the laws of orbital mechanics, and other limiting factors as spacecraft power and thermal constraints, (3) an optimization methodology that casts the resource and constraint models into a standard linear and nonlinear constrained optimization problem that lends itself to commercial off-the-shelf (COTS)planning and scheduling algorithms.

  16. Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks*

    Science.gov (United States)

    Krumholz, Elias W.; Libourel, Igor G. L.

    2015-01-01

    Genome-scale metabolic models are central in connecting genotypes to metabolic phenotypes. However, even for well studied organisms, such as Escherichia coli, draft networks do not contain a complete biochemical network. Missing reactions are referred to as gaps. These gaps need to be filled to enable functional analysis, and gap-filling choices influence model predictions. To investigate whether functional networks existed where all gap-filling reactions were supported by sequence similarity to annotated enzymes, four draft networks were supplemented with all reactions from the Model SEED database for which minimal sequence similarity was found in their genomes. Quadratic programming revealed that the number of reactions that could partake in a gap-filling solution was vast: 3,270 in the case of E. coli, where 72% of the metabolites in the draft network could connect a gap-filling solution. Nonetheless, no network could be completed without the inclusion of orphaned enzymes, suggesting that parts of the biochemistry integral to biomass precursor formation are uncharacterized. However, many gap-filling reactions were well determined, and the resulting networks showed improved prediction of gene essentiality compared with networks generated through canonical gap filling. In addition, gene essentiality predictions that were sensitive to poorly determined gap-filling reactions were of poor quality, suggesting that damage to the network structure resulting from the inclusion of erroneous gap-filling reactions may be predictable. PMID:26041773

  17. Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks.

    Science.gov (United States)

    Krumholz, Elias W; Libourel, Igor G L

    2015-07-31

    Genome-scale metabolic models are central in connecting genotypes to metabolic phenotypes. However, even for well studied organisms, such as Escherichia coli, draft networks do not contain a complete biochemical network. Missing reactions are referred to as gaps. These gaps need to be filled to enable functional analysis, and gap-filling choices influence model predictions. To investigate whether functional networks existed where all gap-filling reactions were supported by sequence similarity to annotated enzymes, four draft networks were supplemented with all reactions from the Model SEED database for which minimal sequence similarity was found in their genomes. Quadratic programming revealed that the number of reactions that could partake in a gap-filling solution was vast: 3,270 in the case of E. coli, where 72% of the metabolites in the draft network could connect a gap-filling solution. Nonetheless, no network could be completed without the inclusion of orphaned enzymes, suggesting that parts of the biochemistry integral to biomass precursor formation are uncharacterized. However, many gap-filling reactions were well determined, and the resulting networks showed improved prediction of gene essentiality compared with networks generated through canonical gap filling. In addition, gene essentiality predictions that were sensitive to poorly determined gap-filling reactions were of poor quality, suggesting that damage to the network structure resulting from the inclusion of erroneous gap-filling reactions may be predictable. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. An integer programming formulation to identify the sparse network architecture governing differentiation of embryonic stem cells.

    Science.gov (United States)

    Banerjee, Ipsita; Maiti, Spandan; Parashurama, Natesh; Yarmush, Martin

    2010-05-15

    Primary purpose of modeling gene regulatory networks for developmental process is to reveal pathways governing the cellular differentiation to specific phenotypes. Knowledge of differentiation network will enable generation of desired cell fates by careful alteration of the governing network by adequate manipulation of cellular environment. We have developed a novel integer programming-based approach to reconstruct the underlying regulatory architecture of differentiating embryonic stem cells from discrete temporal gene expression data. The network reconstruction problem is formulated using inherent features of biological networks: (i) that of cascade architecture which enables treatment of the entire complex network as a set of interconnected modules and (ii) that of sparsity of interconnection between the transcription factors. The developed framework is applied to the system of embryonic stem cells differentiating towards pancreatic lineage. Experimentally determined expression profile dynamics of relevant transcription factors serve as the input to the network identification algorithm. The developed formulation accurately captures many of the known regulatory modes involved in pancreatic differentiation. The predictive capacity of the model is tested by simulating an in silico potential pathway of subsequent differentiation. The predicted pathway is experimentally verified by concurrent differentiation experiments. Experimental results agree well with model predictions, thereby illustrating the predictive accuracy of the proposed algorithm. ipb1@pitt.edu Supplementary data are available at Bioinformatics online.

  19. An integer programming formulation to identify the sparse network architecture governing differentiation of embryonic stem cells

    Science.gov (United States)

    Banerjee, Ipsita; Maiti, Spandan; Parashurama, Natesh; Yarmush, Martin

    2010-01-01

    Motivation: Primary purpose of modeling gene regulatory networks for developmental process is to reveal pathways governing the cellular differentiation to specific phenotypes. Knowledge of differentiation network will enable generation of desired cell fates by careful alteration of the governing network by adequate manipulation of cellular environment. Results: We have developed a novel integer programming-based approach to reconstruct the underlying regulatory architecture of differentiating embryonic stem cells from discrete temporal gene expression data. The network reconstruction problem is formulated using inherent features of biological networks: (i) that of cascade architecture which enables treatment of the entire complex network as a set of interconnected modules and (ii) that of sparsity of interconnection between the transcription factors. The developed framework is applied to the system of embryonic stem cells differentiating towards pancreatic lineage. Experimentally determined expression profile dynamics of relevant transcription factors serve as the input to the network identification algorithm. The developed formulation accurately captures many of the known regulatory modes involved in pancreatic differentiation. The predictive capacity of the model is tested by simulating an in silico potential pathway of subsequent differentiation. The predicted pathway is experimentally verified by concurrent differentiation experiments. Experimental results agree well with model predictions, thereby illustrating the predictive accuracy of the proposed algorithm. Contact: ipb1@pitt.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20363729

  20. Current Understanding of the Formation and Adaptation of Metabolic Systems Based on Network Theory

    Directory of Open Access Journals (Sweden)

    Kazuhiro Takemoto

    2012-07-01

    Full Text Available Formation and adaptation of metabolic networks has been a long-standing question in biology. With recent developments in biotechnology and bioinformatics, the understanding of metabolism is progressively becoming clearer from a network perspective. This review introduces the comprehensive metabolic world that has been revealed by a wide range of data analyses and theoretical studies; in particular, it illustrates the role of evolutionary events, such as gene duplication and horizontal gene transfer, and environmental factors, such as nutrient availability and growth conditions, in evolution of the metabolic network. Furthermore, the mathematical models for the formation and adaptation of metabolic networks have also been described, according to the current understanding from a perspective of metabolic networks. These recent findings are helpful in not only understanding the formation of metabolic networks and their adaptation, but also metabolic engineering.

  1. Coupling root architecture and pore network modeling - an attempt towards better understanding root-soil interactions

    Science.gov (United States)

    Leitner, Daniel; Bodner, Gernot; Raoof, Amir

    2013-04-01

    Understanding root-soil interactions is of high importance for environmental and agricultural management. Root uptake is an essential component in water and solute transport modeling. The amount of groundwater recharge and solute leaching significantly depends on the demand based plant extraction via its root system. Plant uptake however not only responds to the potential demand, but in most situations is limited by supply form the soil. The ability of the plant to access water and solutes in the soil is governed mainly by root distribution. Particularly under conditions of heterogeneous distribution of water and solutes in the soil, it is essential to capture the interaction between soil and roots. Root architecture models allow studying plant uptake from soil by describing growth and branching of root axes in the soil. Currently root architecture models are able to respond dynamically to water and nutrient distribution in the soil by directed growth (tropism), modified branching and enhanced exudation. The porous soil medium as rooting environment in these models is generally described by classical macroscopic water retention and sorption models, average over the pore scale. In our opinion this simplified description of the root growth medium implies several shortcomings for better understanding root-soil interactions: (i) It is well known that roots grow preferentially in preexisting pores, particularly in more rigid/dry soil. Thus the pore network contributes to the architectural form of the root system; (ii) roots themselves can influence the pore network by creating preferential flow paths (biopores) which are an essential element of structural porosity with strong impact on transport processes; (iii) plant uptake depend on both the spatial location of water/solutes in the pore network as well as the spatial distribution of roots. We therefore consider that for advancing our understanding in root-soil interactions, we need not only to extend our root models

  2. Developmental changes in the metabolic network of snapdragon flowers.

    Directory of Open Access Journals (Sweden)

    Joëlle K Muhlemann

    Full Text Available Evolutionary and reproductive success of angiosperms, the most diverse group of land plants, relies on visual and olfactory cues for pollinator attraction. Previous work has focused on elucidating the developmental regulation of pathways leading to the formation of pollinator-attracting secondary metabolites such as scent compounds and flower pigments. However, to date little is known about how flowers control their entire metabolic network to achieve the highly regulated production of metabolites attracting pollinators. Integrative analysis of transcripts and metabolites in snapdragon sepals and petals over flower development performed in this study revealed a profound developmental remodeling of gene expression and metabolite profiles in petals, but not in sepals. Genes up-regulated during petal development were enriched in functions related to secondary metabolism, fatty acid catabolism, and amino acid transport, whereas down-regulated genes were enriched in processes involved in cell growth, cell wall formation, and fatty acid biosynthesis. The levels of transcripts and metabolites in pathways leading to scent formation were coordinately up-regulated during petal development, implying transcriptional induction of metabolic pathways preceding scent formation. Developmental gene expression patterns in the pathways involved in scent production were different from those of glycolysis and the pentose phosphate pathway, highlighting distinct developmental regulation of secondary metabolism and primary metabolic pathways feeding into it.

  3. Adaptive Security Architecture based on EC-MQV Algorithm in Personal Network (PN)

    DEFF Research Database (Denmark)

    Mihovska, Albena D.; Prasad, Neeli R.

    2007-01-01

    Abstract — Personal Networks (PNs) have been focused on in order to support the user’s business and private activities without jeopardizing privacy and security of the users and their data. In such a network, it is necessary to produce a proper key agreement method according to the feature...... of the network. One of the features of the network is that the personal devices have deferent capabilities such as computational ability, memory size, transmission power, processing speed and implementation cost. Therefore an adaptive security mechanism should be contrived for such a network of various device...... combinations based on user’s location and device’s capability. The paper proposes new adaptive security architecture with three levels of asymmetric key agreement scheme by using context-aware security manager (CASM) based on elliptic curve cryptosystem (EC-MQV)....

  4. Survivable architectures for time and wavelength division multiplexed passive optical networks

    Science.gov (United States)

    Wong, Elaine

    2014-08-01

    The increased network reach and customer base of next-generation time and wavelength division multiplexed PON (TWDM-PONs) have necessitated rapid fault detection and subsequent restoration of services to its users. However, direct application of existing solutions for conventional PONs to TWDM-PONs is unsuitable as these schemes rely on the loss of signal (LOS) of upstream transmissions to trigger protection switching. As TWDM-PONs are required to potentially use sleep/doze mode optical network units (ONU), the loss of upstream transmission from a sleeping or dozing ONU could erroneously trigger protection switching. Further, TWDM-PONs require its monitoring modules for fiber/device fault detection to be more sensitive than those typically deployed in conventional PONs. To address the above issues, three survivable architectures that are compliant with TWDM-PON specifications are presented in this work. These architectures combine rapid detection and protection switching against multipoint failure, and most importantly do not rely on upstream transmissions for LOS activation. Survivability analyses as well as evaluations of the additional costs incurred to achieve survivability are performed and compared to the unprotected TWDM-PON. Network parameters that impact the maximum achievable network reach, maximum split ratio, connection availability, fault impact, and the incremental reliability costs for each proposed survivable architecture are highlighted.

  5. MPTCP Tunnel: An Architecture for Aggregating Bandwidth of Heterogeneous Access Networks

    Directory of Open Access Journals (Sweden)

    Xiaolan Liu

    2018-01-01

    Full Text Available Fixed and cellular networks are two typical access networks provided by operators. Fixed access network is widely employed; nevertheless, its bandwidth is sometimes not sufficient enough to meet user bandwidth requirements. Meanwhile, cellular access network owns unique advantages of wider coverage, faster increasing link speed, more flexible deployment, and so forth. Therefore, it is attractive for operators to mitigate the bandwidth shortage by bundling these two. Actually, there have been existing schemes proposed to aggregate the bandwidth of two access networks, whereas they all have their own problems, like packet reordering or extra latency overhead. To address this problem, we design new architecture, MPTCP Tunnel, to aggregate the bandwidth of multiple heterogeneous access networks from the perspective of operators. MPTCP Tunnel uses MPTCP, which solves the reordering problem essentially, to bundle multiple access networks. Besides, MPTCP Tunnel sets up only one MPTCP connection at play which adapts itself to multiple traffic types and TCP flows. Furthermore, MPTCP Tunnel forwards intact IP packets through access networks, maintaining the end-to-end TCP semantics. Experimental results manifest that MPTCP Tunnel can efficiently aggregate the bandwidth of multiple access networks and is more adaptable to the increasing heterogeneity of access networks than existing mechanisms.

  6. An eConsent-based System Architecture Supporting Cooperation in Integrated Healthcare Networks.

    Science.gov (United States)

    Bergmann, Joachim; Bott, Oliver J; Hoffmann, Ina; Pretschner, Dietrich P

    2005-01-01

    The economical need for efficient healthcare leads to cooperative shared care networks. A virtual electronic health record is required, which integrates patient related information but reflects the distributed infrastructure and restricts access only to those health professionals involved into the care process. Our work aims on specification and development of a system architecture fulfilling these requirements to be used in concrete regional pilot studies. Methodical analysis and specification have been performed in a healthcare network using the formal method and modelling tool MOSAIK-M. The complexity of the application field was reduced by focusing on the scenario of thyroid disease care, which still includes various interdisciplinary cooperation. Result is an architecture for a secure distributed electronic health record for integrated care networks, specified in terms of a MOSAIK-M-based system model. The architecture proposes business processes, application services, and a sophisticated security concept, providing a platform for distributed document-based, patient-centred, and secure cooperation. A corresponding system prototype has been developed for pilot studies, using advanced application server technologies. The architecture combines a consolidated patient-centred document management with a decentralized system structure without needs for replication management. An eConsent-based approach assures, that access to the distributed health record remains under control of the patient. The proposed architecture replaces message-based communication approaches, because it implements a virtual health record providing complete and current information. Acceptance of the new communication services depends on compatibility with the clinical routine. Unique and cross-institutional identification of a patient is also a challenge, but will loose significance with establishing common patient cards.

  7. The Architecture and Performance Evaluation of iSCSI-Based United Storage Network Merging NAS and SAN

    OpenAIRE

    Xianglin Fu; Changsheng Xie; Ruifang Liu; Shenggang Pan

    2012-01-01

    With the ever increasing volume of data in networks, the traditional storage architecture is greatly challenged; more and more people pay attention to network storage. Currently, the main technology of network storage is represented by NAS (Network Attached Storage) and SAN (Storage Area Network). They are different, but mutually complementary and used under different circumstances; however, both NAS and SAN may be needed in the same company. To reduce the TOC (total of cost), for easier impl...

  8. Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

    Directory of Open Access Journals (Sweden)

    Panda Gurudutta

    2011-05-01

    Full Text Available Abstract Background Burkholderia cenocepacia is a threatening nosocomial epidemic pathogen in patients with cystic fibrosis (CF or a compromised immune system. Its high level of antibiotic resistance is an increasing concern in treatments against its infection. Strain B. cenocepacia J2315 is the most infectious isolate from CF patients. There is a strong demand to reconstruct a genome-scale metabolic network of B. cenocepacia J2315 to systematically analyze its metabolic capabilities and its virulence traits, and to search for potential clinical therapy targets. Results We reconstructed the genome-scale metabolic network of B. cenocepacia J2315. An iterative reconstruction process led to the establishment of a robust model, iKF1028, which accounts for 1,028 genes, 859 internal reactions, and 834 metabolites. The model iKF1028 captures important metabolic capabilities of B. cenocepacia J2315 with a particular focus on the biosyntheses of key metabolic virulence factors to assist in understanding the mechanism of disease infection and identifying potential drug targets. The model was tested through BIOLOG assays. Based on the model, the genome annotation of B. cenocepacia J2315 was refined and 24 genes were properly re-annotated. Gene and enzyme essentiality were analyzed to provide further insights into the genome function and architecture. A total of 45 essential enzymes were identified as potential therapeutic targets. Conclusions As the first genome-scale metabolic network of B. cenocepacia J2315, iKF1028 allows a systematic study of the metabolic properties of B. cenocepacia and its key metabolic virulence factors affecting the CF community. The model can be used as a discovery tool to design novel drugs against diseases caused by this notorious pathogen.

  9. Role of graph architecture in controlling dynamical networks with applications to neural systems

    Science.gov (United States)

    Kim, Jason Z.; Soffer, Jonathan M.; Kahn, Ari E.; Vettel, Jean M.; Pasqualetti, Fabio; Bassett, Danielle S.

    2018-01-01

    Networked systems display complex patterns of interactions between components. In physical networks, these interactions often occur along structural connections that link components in a hard-wired connection topology, supporting a variety of system-wide dynamical behaviours such as synchronization. Although descriptions of these behaviours are important, they are only a first step towards understanding and harnessing the relationship between network topology and system behaviour. Here, we use linear network control theory to derive accurate closed-form expressions that relate the connectivity of a subset of structural connections (those linking driver nodes to non-driver nodes) to the minimum energy required to control networked systems. To illustrate the utility of the mathematics, we apply this approach to high-resolution connectomes recently reconstructed from Drosophila, mouse, and human brains. We use these principles to suggest an advantage of the human brain in supporting diverse network dynamics with small energetic costs while remaining robust to perturbations, and to perform clinically accessible targeted manipulation of the brain's control performance by removing single edges in the network. Generally, our results ground the expectation of a control system's behaviour in its network architecture, and directly inspire new directions in network analysis and design via distributed control.

  10. A Smart Gateway Architecture for Improving Efficiency of Home Network Applications

    Directory of Open Access Journals (Sweden)

    Fei Ding

    2016-01-01

    Full Text Available A smart home gateway plays an important role in the Internet of Things (IoT system that takes responsibility for the connection between the network layer and the ubiquitous sensor network (USN layer. Even though the home network application is developing rapidly, researches on the home gateway based open development architecture are less. This makes it difficult to extend the home network to support new applications, share service, and interoperate with other home network systems. An integrated access gateway (IAGW is proposed in this paper which upward connects with the operator machine-to-machine platform (M2M P/F. In this home network scheme, the gateway provides standard interfaces for supporting various applications in home environments, ranging from on-site configuration to node and service access. In addition, communication management ability is also provided by M2M P/F. A testbed of a simple home network application system that includes the IAGW prototype is created to test its user interaction capabilities. Experimental results show that the proposed gateway provides significant flexibility for users to configure and deploy a home automation network; it can be applied to other monitoring areas and simultaneously supports a multi-ubiquitous sensor network.

  11. GEYSERS: a novel architecture for virtualization and co-provisioning of dynamic optical networks and IT services

    NARCIS (Netherlands)

    Escalona, E.; Peng, S.; Nejabati, R.; Simeonidou, D.; García-Espín, J.A.; Ferrer, J.; Figuerola, S.; Landi, G.; Ciulli, N.; Jiménez, J.; Belter, B.; Demchenko, Y.; de Laat, C.; Chen, X.; Yukan, A.; Soudan, S.; Vicat-Blanc, P.; Buysse, J.; de Leenheer, M.; Develder, C.; Tzanakaki, A.; Robinson, P.; Brogle, M.; Bohnert, T.M.

    2011-01-01

    GEYSERS aims at defining an end-to-end network architecture that offers a novel planning, provisioning and operational framework for optical network and IT infrastructure providers and operators. In this framework, physical infrastructure resources (network and IT) are dynamically partitioned to

  12. REAL-TIME VIDEO SCALING BASED ON CONVOLUTION NEURAL NETWORK ARCHITECTURE

    OpenAIRE

    S Safinaz; A V Ravi Kumar

    2017-01-01

    In recent years, video super resolution techniques becomes mandatory requirements to get high resolution videos. Many super resolution techniques researched but still video super resolution or scaling is a vital challenge. In this paper, we have presented a real-time video scaling based on convolution neural network architecture to eliminate the blurriness in the images and video frames and to provide better reconstruction quality while scaling of large datasets from lower resolution frames t...

  13. Lightweight Filter Architecture for Energy Efficient Mobile Vehicle Localization Based on a Distributed Acoustic Sensor Network

    OpenAIRE

    Kim, Keonwook

    2013-01-01

    The generic properties of an acoustic signal provide numerous benefits for localization by applying energy-based methods over a deployed wireless sensor network (WSN). However, the signal generated by a stationary target utilizes a significant amount of bandwidth and power in the system without providing further position information. For vehicle localization, this paper proposes a novel proximity velocity vector estimator (PVVE) node architecture in order to capture the energy from a moving v...

  14. The KISS principle in Software-Defined Networking: An architecture for Keeping It Simple and Secure

    OpenAIRE

    Kreutz, Diego; Verissimo, Paulo; Magalhaes, Catia; Ramos, Fernando M. V.

    2017-01-01

    Security is an increasingly fundamental requirement in Software-Defined Networking (SDN). However, the pace of adoption of secure mechanisms has been slow, which we estimate to be a consequence of the performance overhead of traditional solutions and of the complexity of the support infrastructure required. As a first step to addressing these problems, we propose a modular secure SDN control plane communications architecture, KISS, with innovative solutions in the context of key distribution ...

  15. Architecture, On-Chip Network and Programming Interface Concept for Multiprocessor System-on-Chip

    OpenAIRE

    Samman, Faizal Arya

    2017-01-01

    in Proc. of the International Conference onSmart Green Technology in Electrical and Information Systems (ICSGTEIS), 2016, publised in IEEE Explorer (indexed by SCOPUS) This paper presents a system architecture, data communnication scheme and application programming interface model or concept for a multiprocessor system based on a network-on-chip (NoC) platform. Each processing node connected to a mesh node has its own local (instruction and data) memory portion, and a global (shared) memor...

  16. Enhanced Stochastic Methodology for Combined Architecture of E-Commerce and Security Networks

    OpenAIRE

    Kim, Song-Kyoo

    2009-01-01

    This paper deals with network architecture which is a combination of electronic commerce and security systems in the typical Internet ecosystems. The e-commerce model that is typically known as online shopping can be considered as a multichannel queueing system. In the other hand, stochastic security system is designed for improving the reliability and availability of the e-commerce system. The security system in this paper deals with a complex system that consists of main unrelia...

  17. Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks

    NARCIS (Netherlands)

    Jol, Stefan J; Kümmel, Anne; Hatzimanikatis, Vassily; Beard, Daniel A; Heinemann, Matthias

    2010-01-01

    Thermodynamic analysis of metabolic networks has recently generated increasing interest for its ability to add constraints on metabolic network operation, and to combine metabolic fluxes and metabolite measurements in a mechanistic manner. Concepts for the calculation of the change in Gibbs energy

  18. Novel photonic bandgap based architectures for quantum computers and networks

    Science.gov (United States)

    Guney, Durdu

    All of the approaches for quantum information processing have their own advantages, but unfortunately also their own drawbacks. Ideally, one would merge the most attractive features of those different approaches in a single technology. We envision that large-scale photonic crystal (PC) integrated circuits and fibers could be the basis for robust and compact quantum circuits and processors of the next generation quantum computers and networking devices. Cavity QED, solid-state, and (non)linear optical models for computing, and optical fiber approach for communications are the most promising candidates to be improved through this novel technology. In our work, we consider both digital and analog quantum computing. In the digital domain, we first perform gate-level analysis. To achieve this task, we solve the Jaynes-Cummings Hamiltonian with time-dependent coupling parameters under the dipole and rotating-wave approximations for a 3D PC single-mode cavity with a sufficiently high Q-factor. We then exploit the results to show how to create a maximally entangled state of two atoms and how to implement several quantum logic gates: a dual-rail Hadamard gate, a dual-rail NOT gate, and a SWAP gate. In all of these operations, we synchronize atoms, as opposed to previous studies with PCs. The method has the potential for extension to N-atom entanglement, universal quantum logic operations, and the implementation of other useful, cavity QED-based quantum information processing tasks. In the next part of the digital domain, we study circuit-level implementations. We design and simulate an integrated teleportation and readout circuit on a single PC chip. The readout part of our device can not only be used on its own but can also be integrated with other compatible optical circuits to achieve atomic state detection. Further improvement of the device in terms of compactness and robustness is possible by integrating with sources and detectors in the optical regime. In the analog

  19. Adaptive Security Architecture based on EC-MQV Algorithm in Personal Network (PN)

    DEFF Research Database (Denmark)

    Mihovska, Albena D.; Prasad, Neeli R.

    2007-01-01

    Abstract — Personal Networks (PNs) have been focused on in order to support the user’s business and private activities without jeopardizing privacy and security of the users and their data. In such a network, it is necessary to produce a proper key agreement method according to the feature of the...... combinations based on user’s location and device’s capability. The paper proposes new adaptive security architecture with three levels of asymmetric key agreement scheme by using context-aware security manager (CASM) based on elliptic curve cryptosystem (EC-MQV)....

  20. Principles of Network Architecture Emerging from Comparisons of the Cerebral Cortex in Large and Small Brains.

    Directory of Open Access Journals (Sweden)

    Barbara L Finlay

    2016-09-01

    Full Text Available The cerebral cortex retains its fundamental organization, layering, and input-output relations as it scales in volume over many orders of magnitude in mammals. How is its network architecture affected by size scaling? By comparing network organization of the mouse and rhesus macaque cortical connectome derived from complete neuroanatomical tracing studies, a recent study in PLOS Biology shows that an exponential distance rule emerges that reveals the falloff in connection probability with distance in the two brains that in turn determines common organizational features.

  1. Modeling workplace contact networks: The effects of organizational structure, architecture, and reporting errors on epidemic predictions.

    Science.gov (United States)

    Potter, Gail E; Smieszek, Timo; Sailer, Kerstin

    2015-09-01

    Face-to-face social contacts are potentially important transmission routes for acute respiratory infections, and understanding the contact network can improve our ability to predict, contain, and control epidemics. Although workplaces are important settings for infectious disease transmission, few studies have collected workplace contact data and estimated workplace contact networks. We use contact diaries, architectural distance measures, and institutional structures to estimate social contact networks within a Swiss research institute. Some contact reports were inconsistent, indicating reporting errors. We adjust for this with a latent variable model, jointly estimating the true (unobserved) network of contacts and duration-specific reporting probabilities. We find that contact probability decreases with distance, and that research group membership, role, and shared projects are strongly predictive of contact patterns. Estimated reporting probabilities were low only for 0-5 min contacts. Adjusting for reporting error changed the estimate of the duration distribution, but did not change the estimates of covariate effects and had little effect on epidemic predictions. Our epidemic simulation study indicates that inclusion of network structure based on architectural and organizational structure data can improve the accuracy of epidemic forecasting models.

  2. Predicting selective drug targets in cancer through metabolic networks

    Science.gov (United States)

    Folger, Ori; Jerby, Livnat; Frezza, Christian; Gottlieb, Eyal; Ruppin, Eytan; Shlomi, Tomer

    2011-01-01

    The interest in studying metabolic alterations in cancer and their potential role as novel targets for therapy has been rejuvenated in recent years. Here, we report the development of the first genome-scale network model of cancer metabolism, validated by correctly identifying genes essential for cellular proliferation in cancer cell lines. The model predicts 52 cytostatic drug targets, of which 40% are targeted by known, approved or experimental anticancer drugs, and the rest are new. It further predicts combinations of synthetic lethal drug targets, whose synergy is validated using available drug efficacy and gene expression measurements across the NCI-60 cancer cell line collection. Finally, potential selective treatments for specific cancers that depend on cancer type-specific downregulation of gene expression and somatic mutations are compiled. PMID:21694718

  3. Enumeration of minimal stoichiometric precursor sets in metabolic networks.

    Science.gov (United States)

    Andrade, Ricardo; Wannagat, Martin; Klein, Cecilia C; Acuña, Vicente; Marchetti-Spaccamela, Alberto; Milreu, Paulo V; Stougie, Leen; Sagot, Marie-France

    2016-01-01

    What an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal precursor sets took into account only the topology of the metabolic network (topological precursor sets). Due to cycles and the stoichiometric values of the reactions, it is often not possible to produce the target(s) from a topological precursor set in the sense that there is no feasible flux. Although considering the stoichiometry makes the problem harder, it enables to obtain biologically reasonable precursor sets that we call stoichiometric. Recently a method to enumerate all minimal stoichiometric precursor sets was proposed in the literature. The relationship between topological and stoichiometric precursor sets had however not yet been studied. Such relationship between topological and stoichiometric precursor sets is highlighted. We also present two algorithms that enumerate all minimal stoichiometric precursor sets. The first one is of theoretical interest only and is based on the above mentioned relationship. The second approach solves a series of mixed integer linear programming problems. We compared the computed minimal precursor sets to experimentally obtained growth media of several Escherichia coli strains using genome-scale metabolic networks. The results show that the second approach efficiently enumerates minimal precursor sets taking stoichiometry into account, and allows for broad in silico studies of strains or species interactions that may help to understand e.g. pathotype and niche-specific metabolic capabilities. sasita is written in Java, uses cplex as LP solver and can be downloaded together with all networks and input files used in this paper at http://www.sasita.gforge.inria.fr.

  4. An In-Home Digital Network Architecture for Real-Time and Non-Real-Time Communication

    NARCIS (Netherlands)

    Scholten, Johan; Jansen, P.G.; Hanssen, F.T.Y.; Hattink, Tjalling

    2002-01-01

    This paper describes an in-home digital network architecture that supports both real-time and non-real-time communication. The architecture deploys a distributed token mechanism to schedule communication streams and to offer guaranteed quality-ofservice. Essentially, the token mechanism prevents

  5. An In-Home Digital Network Architecture for Real-Time and Non-Real-Time Communication

    NARCIS (Netherlands)

    Scholten, Johan; Jansen, P.G.; Hanssen, F.T.Y.; Hattink, Tjalling

    2002-01-01

    This paper describes an in-home digital network architecture that supports both realtime and non-real-time communication. The architecture deploys a distributed token mechanism to schedule communication streams and to offer guaranteed quality-ofservice. Essentially, the token mechanism prevents

  6. (Im) Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-expression regulation: marrying control engineering with metabolic control analysis

    NARCIS (Netherlands)

    He, F.; Fromion, V.; Westerhoff, H.V.

    2013-01-01

    Background: Metabolic control analysis (MCA) and supply-demand theory have led to appreciable understanding of the systems properties of metabolic networks that are subject exclusively to metabolic regulation. Supply-demand theory has not yet considered gene-expression regulation explicitly whilst a

  7. Service oriented network architecture for control and management of home appliances

    Science.gov (United States)

    Hayakawa, Hiroshi; Koita, Takahiro; Sato, Kenya

    2005-12-01

    Recent advances in multimedia network systems and mechatronics have led to the development of a new generation of applications that associate the use of various multimedia objects with the behavior of multiple robotic actors. The connection of audio and video devices through high speed multimedia networks is expected to make the system more convenient to use. For example, many home appliances, such as a video camera, a display monitor, a video recorder, an audio system and so on, are being equipped with a communication interface in the near future. Recently some platforms (i.e. UPnP1, HAVi2 and so on) are proposed for constructing home networks; however, there are some issues to be solved to realize various services by connecting different equipment via the pervasive peer-to-peer network. UPnP offers network connectivity of PCs of intelligent home appliances, practically, which means to require a PC in the network to control other devices. Meanwhile, HAVi has been developed for intelligent AV equipments with sophisticated functions using high CPU power and large memory. Considering the targets of home alliances are embedded systems, this situation raises issues of software and hardware complexity, cost, power consumption and so on. In this study, we have proposed and developed the service oriented network architecture for control and management of home appliances, named SONICA (Service Oriented Network Interoperability for Component Adaptation), to address these issues described before.

  8. An Evaluation of Best Effort Traffic Management of Server and Agent-Based Active Network Management (SAAM) Architecture

    National Research Council Canada - National Science Library

    Ayvat, Birol

    2003-01-01

    The Server and Agent-based Active Network Management (SAAM) architecture was initially designed to work with the next generation Internet where increasingly sophisticated applications will require QoS guarantees...

  9. A Neutral-Network-Fusion Architecture for Automatic Extraction of Oceanographic Features from Satellite Remote Sensing Imagery

    National Research Council Canada - National Science Library

    Askari, Farid

    1999-01-01

    This report describes an approach for automatic feature detection from fusion of remote sensing imagery using a combination of neural network architecture and the Dempster-Shafer (DS) theory of evidence...

  10. Insights into brain architectures from the homological scaffolds of functional connectivity networks

    Directory of Open Access Journals (Sweden)

    Louis-David Lord

    2016-11-01

    Full Text Available In recent years, the application of network analysis to neuroimaging data has provided useful insights about the brain’s functional and structural organization in both health and disease. This has proven a significant paradigm shift from the study of individual brain regions in isolation. Graph-based models of the brain consist of vertices, which represent distinct brain areas, and edges which encode the presence (or absence of a structural or functional relationship between each pair of vertices. By definition, any graph metric will be defined upon this dyadic representation of the brain activity. It is however unclear to what extent these dyadic relationships can capture the brain’s complex functional architecture and the encoding of information in distributed networks. Moreover, because network representations of global brain activity are derived from measures that have a continuous response (i.e. interregional BOLD signals, it is methodologically complex to characterize the architecture of functional networks using traditional graph-based approaches. In the present study, we investigate the relationship between standard network metrics computed from dyadic interactions in a functional network, and a metric defined on the persistence homological scaffold of the network, which is a summary of the persistent homology structure of resting-state fMRI data. The persistence homological scaffold is a summary network that differs in important ways from the standard network representations of functional neuroimaging data: i it is constructed using the information from all edge weights comprised in the original network without applying an ad hoc threshold and ii as a summary of persistent homology, it considers the contributions of simplicial structures to the network organization rather than dyadic edge-vertices interactions. We investigated the information domain captured by the persistence homological scaffold by computing the strength of each

  11. Architecture and performance of neural networks for efficient A/C control in buildings

    International Nuclear Information System (INIS)

    Mahmoud, Mohamed A.; Ben-Nakhi, Abdullatif E.

    2003-01-01

    The feasibility of using neural networks (NNs) for optimizing air conditioning (AC) setback scheduling in public buildings was investigated. The main focus is on optimizing the network architecture in order to achieve best performance. To save energy, the temperature inside public buildings is allowed to rise after business hours by setting back the thermostat. The objective is to predict the time of the end of thermostat setback (EoS) such that the design temperature inside the building is restored in time for the start of business hours. State of the art building simulation software, ESP-r, was used to generate a database that covered the years 1995-1999. The software was used to calculate the EoS for two office buildings using the climate records in Kuwait. The EoS data for 1995 and 1996 were used for training and testing the NNs. The robustness of the trained NN was tested by applying them to a 'production' data set (1997-1999), which the networks have never 'seen' before. For each of the six different NN architectures evaluated, parametric studies were performed to determine the network parameters that best predict the EoS. External hourly temperature readings were used as network inputs, and the thermostat end of setback (EoS) is the output. The NN predictions were improved by developing a neural control scheme (NC). This scheme is based on using the temperature readings as they become available. For each NN architecture considered, six NNs were designed and trained for this purpose. The performance of the NN analysis was evaluated using a statistical indicator (the coefficient of multiple determination) and by statistical analysis of the error patterns, including ANOVA (analysis of variance). The results show that the NC, when used with a properly designed NN, is a powerful instrument for optimizing AC setback scheduling based only on external temperature records

  12. Architecture of the Multi-Modal Organizational Research and Production Heterogeneous Network (MORPHnet)

    Energy Technology Data Exchange (ETDEWEB)

    Aiken, R.J.; Carlson, R.A.; Foster, I.T. [and others

    1997-01-01

    The research and education (R&E) community requires persistent and scaleable network infrastructure to concurrently support production and research applications as well as network research. In the past, the R&E community has relied on supporting parallel network and end-node infrastructures, which can be very expensive and inefficient for network service managers and application programmers. The grand challenge in networking is to provide support for multiple, concurrent, multi-layer views of the network for the applications and the network researchers, and to satisfy the sometimes conflicting requirements of both while ensuring one type of traffic does not adversely affect the other. Internet and telecommunications service providers will also benefit from a multi-modal infrastructure, which can provide smoother transitions to new technologies and allow for testing of these technologies with real user traffic while they are still in the pre-production mode. The authors proposed approach requires the use of as much of the same network and end system infrastructure as possible to reduce the costs needed to support both classes of activities (i.e., production and research). Breaking the infrastructure into segments and objects (e.g., routers, switches, multiplexors, circuits, paths, etc.) gives the capability to dynamically construct and configure the virtual active networks to address these requirements. These capabilities must be supported at the campus, regional, and wide-area network levels to allow for collaboration by geographically dispersed groups. The Multi-Modal Organizational Research and Production Heterogeneous Network (MORPHnet) described in this report is an initial architecture and framework designed to identify and support the capabilities needed for the proposed combined infrastructure and to address related research issues.

  13. Genome-scale reconstruction of the Streptococcus pyogenes M49 metabolic network reveals growth requirements and indicates potential drug targets

    NARCIS (Netherlands)

    Levering, J.; Fiedler, T.; Sieg, A.; van Grinsven, K.W.A.; Hering, S.; Veith, N.; Olivier, B.G.; Klett, L.; Hugenholtz, J.; Teusink, B.; Kreikemeyer, B.; Kummer, U.

    2016-01-01

    Genome-scale metabolic models comprise stoichiometric relations between metabolites, as well as associations between genes and metabolic reactions and facilitate the analysis of metabolism. We computationally reconstructed the metabolic network of the lactic acid bacterium Streptococcus pyogenes

  14. Dialogic e-learning2learn: creating global digital networks and educational knowledge building architectures across diversity

    DEFF Research Database (Denmark)

    Sorensen, Elsebeth Korsgaard

    2007-01-01

    Abstract: Purpose – The purpose of this paper is to address the challenge and potential of online higher and continuing education, of fostering and promoting, in a global perspective across time and space, democratic values working for a better world. Design/methodology/approach – The paper...... presents a generalized dialogic learning architecture of networked collaborative learning and makes a plea for a theory-informed networked collaborative learning architecture and methodology appropriate for adult learners in higher and continuing education. Findings – Values include mutual political...... and evaluation of the implementation of the pedagogical architecture into a Danish Master Programme....

  15. Incremental parameter estimation of kinetic metabolic network models

    Directory of Open Access Journals (Sweden)

    Jia Gengjie

    2012-11-01

    Full Text Available Abstract Background An efficient and reliable parameter estimation method is essential for the creation of biological models using ordinary differential equation (ODE. Most of the existing estimation methods involve finding the global minimum of data fitting residuals over the entire parameter space simultaneously. Unfortunately, the associated computational requirement often becomes prohibitively high due to the large number of parameters and the lack of complete parameter identifiability (i.e. not all parameters can be uniquely identified. Results In this work, an incremental approach was applied to the parameter estimation of ODE models from concentration time profiles. Particularly, the method was developed to address a commonly encountered circumstance in the modeling of metabolic networks, where the number of metabolic fluxes (reaction rates exceeds that of metabolites (chemical species. Here, the minimization of model residuals was performed over a subset of the parameter space that is associated with the degrees of freedom in the dynamic flux estimation from the concentration time-slopes. The efficacy of this method was demonstrated using two generalized mass action (GMA models, where the method significantly outperformed single-step estimations. In addition, an extension of the estimation method to handle missing data is also presented. Conclusions The proposed incremental estimation method is able to tackle the issue on the lack of complete parameter identifiability and to significantly reduce the computational efforts in estimating model parameters, which will facilitate kinetic modeling of genome-scale cellular metabolism in the future.

  16. 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

  17. Source-synchronous networks-on-chip circuit and architectural interconnect modeling

    CERN Document Server

    Mandal, Ayan; Mahapatra, Rabi

    2014-01-01

    This book describes novel methods for network-on-chip (NoC) design, using source-synchronous high-speed resonant clocks.  The authors discuss NoCs from the bottom up, providing circuit level details, before providing architectural simulations. As a result, readers will get a complete picture of how a NoC can be designed and optimized.  Using the methods described in this book, readers are enabled to design NoCs that are 5X better than existing approaches in terms of latency and throughput and can also sustain a significantly greater amount of traffic.   • Describes novel methods for high-speed network-on-chip (NoC) design; • Enables readers to understand NoC design from both circuit and architectural levels; • Provides circuit-level details of the NoC (including clocking, router design), along with a high-speed, resonant clocking style which is used in the NoC; • Includes architectural simulations of the NoC, demonstrating significantly superior performance over the state-of-the-art.

  18. Evaluation of an IP Fabric network architecture for CERN's data center

    CERN Document Server

    Garcia Cabot, Carles; Barceló Ordinas, José M.

    CERN has a large-scale data center with over 11500 servers used to analyze massive amounts of data acquired from the physics experiments and to provide IT services to workers. Its current network architecture is based on the classic three-tier design and it uses both IPv4 and IPv6. Between the access and aggregation layers the traffic is switched in Layer 2, while between aggregation and core it is routed using dual-stack OSPF. A new architecture is needed to increase redundancy and to provide virtual machine mobility and traffic isolation. The state-of-the-art architecture IP Fabric with EVPN is evaluated as a possible solution. The evaluation comprises a study of different features and options, including BGP table scalability and autonomous system number distributions. The proposed solution contains eBGP as the routing protocol, a route control policy, fast convergence mechanisms and an EVPN overlay with iBGP routing and VXLAN encapsulation. The solution is tested in the lab with the network equipment curre...

  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. A Performance Analytical Strategy for Network-on-Chip Router with Input Buffer Architecture

    Directory of Open Access Journals (Sweden)

    WANG, J.

    2012-11-01

    Full Text Available In this paper, a performance analytical strategy is proposed for Network-on-Chip router with input buffer architecture. First, an analytical model is developed based on semi-Markov process. For the non-work-conserving router with small buffer size, the model can be used to analyze the schedule delay and the average service time for each buffer when given the related parameters. Then, the packet average delay in router is calculated by using the model. Finally, we validate the effectiveness of our strategy by simulation. By comparing our analytical results to simulation results, we show that our strategy successfully captures the Network-on-Chip router performance and it performs better than the state-of-art technology. Therefore, our strategy can be used as an efficiency performance analytical tool for Network-on-Chip design.

  1. A Networked Perspective on the Engineering Design Process: At the Intersection of Process and Organisation Architectures

    DEFF Research Database (Denmark)

    Parraguez, Pedro

    projects often fail to be on time, on budget, and meeting specifications. Despite the wealth of process models available, previous approaches have been insufficient to provide a networked perspective that allows the challenging combination of organisational and process complexity to unfold. The lack...... of a networked perspective also has limited the study of the relationships between process complexity and process performance. This thesis argues that to understand and improve design processes, we must look beyond the planned process and unfold the network structure and composition that actually implement...... the process. This combination of process structure—how people and activities are connected—and composition—the functional diversity of the groups participating in the process—is referred to as the actual design process architecture. This thesis reports on research undertaken to develop, apply and test...

  2. Extraction of fibre network architecture by X-ray tomography and prediction of elastic properties using an affine analytical model

    International Nuclear Information System (INIS)

    Tsarouchas, D.; Markaki, A.E.

    2011-01-01

    This paper proposes a method for extracting reliable architectural characteristics from complex porous structures using micro-computed tomography (μCT) images. The work focuses on a highly porous material composed of a network of fibres bonded together. The segmentation process, allowing separation of the fibres from the remainder of the image, is the most critical step in constructing an accurate representation of the network architecture. Segmentation methods, based on local and global thresholding, were investigated and evaluated by a quantitative comparison of the architectural parameters they yielded, such as the fibre orientation and segment length (sections between joints) distributions and the number of inter-fibre crossings. To improve segmentation accuracy, a deconvolution algorithm was proposed to restore the original images. The efficacy of the proposed method was verified by comparing μCT network architectural characteristics with those obtained using high resolution CT scans (nanoCT). The results indicate that this approach resolves the architecture of these complex networks and produces results approaching the quality of nanoCT scans. The extracted architectural parameters were used in conjunction with an affine analytical model to predict the axial and transverse stiffnesses of the fibre network. Transverse stiffness predictions were compared with experimentally measured values obtained by vibration testing.

  3. Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria

    Directory of Open Access Journals (Sweden)

    Hou Jing

    2006-04-01

    Full Text Available Abstract Background Chloroplasts descended from cyanobacteria and have a drastically reduced genome following an endosymbiotic event. Many genes of the ancestral cyanobacterial genome have been transferred to the plant nuclear genome by horizontal gene transfer. However, a selective set of metabolism pathways is maintained in chloroplasts using both chloroplast genome encoded and nuclear genome encoded enzymes. As an organelle specialized for carrying out photosynthesis, does the chloroplast metabolic network have properties adapted for higher efficiency of photosynthesis? We compared metabolic network properties of chloroplasts and prokaryotic photosynthetic organisms, mostly cyanobacteria, based on metabolic maps derived from genome data to identify features of chloroplast network properties that are different from cyanobacteria and to analyze possible functional significance of those features. Results The properties of the entire metabolic network and the sub-network that consists of reactions directly connected to the Calvin Cycle have been analyzed using hypergraph representation. Results showed that the whole metabolic networks in chloroplast and cyanobacteria both possess small-world network properties. Although the number of compounds and reactions in chloroplasts is less than that in cyanobacteria, the chloroplast's metabolic network has longer average path length, a larger diameter, and is Calvin Cycle -centered, indicating an overall less-dense network structure with specific and local high density areas in chloroplasts. Moreover, chloroplast metabolic network exhibits a better modular organization than cyanobacterial ones. Enzymes involved in the same metabolic processes tend to cluster into the same module in chloroplasts. Conclusion In summary, the differences in metabolic network properties may reflect the evolutionary changes during endosymbiosis that led to the improvement of the photosynthesis efficiency in higher plants. Our

  4. Resting State fMRI Functional Connectivity-Based Classification Using a Convolutional Neural Network Architecture

    Directory of Open Access Journals (Sweden)

    Regina J. Meszlényi

    2017-10-01

    Full Text Available Machine learning techniques have become increasingly popular in the field of resting state fMRI (functional magnetic resonance imaging network based classification. However, the application of convolutional networks has been proposed only very recently and has remained largely unexplored. In this paper we describe a convolutional neural network architecture for functional connectome classification called connectome-convolutional neural network (CCNN. Our results on simulated datasets and a publicly available dataset for amnestic mild cognitive impairment classification demonstrate that our CCNN model can efficiently distinguish between subject groups. We also show that the connectome-convolutional network is capable to combine information from diverse functional connectivity metrics and that models using a combination of different connectivity descriptors are able to outperform classifiers using only one metric. From this flexibility follows that our proposed CCNN model can be easily adapted to a wide range of connectome based classification or regression tasks, by varying which connectivity descriptor combinations are used to train the network.

  5. Role of architecture in the elastic response of semiflexible polymer and fiber networks

    Science.gov (United States)

    Heussinger, Claus; Frey, Erwin

    2007-01-01

    We study the elasticity of cross-linked networks of thermally fluctuating stiff polymers. As compared to their purely mechanical counterparts, it is shown that these thermal networks have a qualitatively different elastic response. By accounting for the entropic origin of the single-polymer elasticity, the networks acquire a strong susceptibility to polydispersity and structural randomness that is completely absent in athermal models. In extensive numerical studies we systematically vary the architecture of the networks and identify a wealth of phenomena that clearly show the strong dependence of the emergent macroscopic moduli on the underlying mesoscopic network structure. In particular, we highlight the importance of the polymer length, which to a large extent controls the elastic response of the network, surprisingly, even in parameter regions where it does not enter the macroscopic moduli explicitly. Understanding these subtle effects is only possible by going beyond the conventional approach that considers the response of typical polymer segments only. Instead, we propose to describe the elasticity in terms of a typical polymer filament and the spatial distribution of cross-links along its backbone. We provide theoretical scaling arguments to relate the observed macroscopic elasticity to the physical mechanisms on the microscopic and mesoscopic scales.

  6. 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.

  7. Architecture of an antagonistic tree/fungus network: the asymmetric influence of past evolutionary history.

    Science.gov (United States)

    Vacher, Corinne; Piou, Dominique; Desprez-Loustau, Marie-Laure

    2008-03-05

    Compartmentalization and nestedness are common patterns in ecological networks. The aim of this study was to elucidate some of the processes shaping these patterns in a well resolved network of host/pathogen interactions. Based on a long-term (1972-2005) survey of forest health at the regional scale (all French forests; 15 million ha), we uncovered an almost fully connected network of 51 tree taxa and 157 parasitic fungal species. Our analyses revealed that the compartmentalization of the network maps out the ancient evolutionary history of seed plants, but not the ancient evolutionary history of fungal species. The very early divergence of the major fungal phyla may account for this asymmetric influence of past evolutionary history. Unlike compartmentalization, nestedness did not reflect any consistent phylogenetic signal. Instead, it seemed to reflect the ecological features of the current species, such as the relative abundance of tree species and the life-history strategies of fungal pathogens. We discussed how the evolution of host range in fungal species may account for the observed nested patterns. Overall, our analyses emphasized how the current complexity of ecological networks results from the diversification of the species and their interactions over evolutionary times. They confirmed that the current architecture of ecological networks is not only dependent on recent ecological processes.

  8. Resting State fMRI Functional Connectivity-Based Classification Using a Convolutional Neural Network Architecture

    Science.gov (United States)

    Meszlényi, Regina J.; Buza, Krisztian; Vidnyánszky, Zoltán

    2017-01-01

    Machine learning techniques have become increasingly popular in the field of resting state fMRI (functional magnetic resonance imaging) network based classification. However, the application of convolutional networks has been proposed only very recently and has remained largely unexplored. In this paper we describe a convolutional neural network architecture for functional connectome classification called connectome-convolutional neural network (CCNN). Our results on simulated datasets and a publicly available dataset for amnestic mild cognitive impairment classification demonstrate that our CCNN model can efficiently distinguish between subject groups. We also show that the connectome-convolutional network is capable to combine information from diverse functional connectivity metrics and that models using a combination of different connectivity descriptors are able to outperform classifiers using only one metric. From this flexibility follows that our proposed CCNN model can be easily adapted to a wide range of connectome based classification or regression tasks, by varying which connectivity descriptor combinations are used to train the network. PMID:29089883

  9. Reconfiguration of brain network architecture to support executive control in aging.

    Science.gov (United States)

    Gallen, Courtney L; Turner, Gary R; Adnan, Areeba; D'Esposito, Mark

    2016-08-01

    Aging is accompanied by declines in executive control abilities and changes in underlying brain network architecture. Here, we examined brain networks in young and older adults during a task-free resting state and an N-back task and investigated age-related changes in the modular network organization of the brain. Compared with young adults, older adults showed larger changes in network organization between resting state and task. Although young adults exhibited increased connectivity between lateral frontal regions and other network modules during the most difficult task condition, older adults also exhibited this pattern of increased connectivity during less-demanding task conditions. Moreover, the increase in between-module connectivity in older adults was related to faster task performance and greater fractional anisotropy of the superior longitudinal fasciculus. These results demonstrate that older adults who exhibit more pronounced network changes between a resting state and task have better executive control performance and greater structural connectivity of a core frontal-posterior white matter pathway. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. A state of the art of metabolic networks of unicellular microalgae and cyanobacteria for biofuel production.

    Science.gov (United States)

    Baroukh, Caroline; Muñoz-Tamayo, Rafael; Steyer, Jean-Philippe; Bernard, Olivier

    2015-07-01

    The most promising and yet challenging application of microalgae and cyanobacteria is the production of renewable energy: biodiesel from microalgae triacylglycerols and bioethanol from cyanobacteria carbohydrates. A thorough understanding of microalgal and cyanobacterial metabolism is necessary to master and optimize biofuel production yields. To this end, systems biology and metabolic modeling have proven to be very efficient tools if supported by an accurate knowledge of the metabolic network. However, unlike heterotrophic microorganisms that utilize the same substrate for energy and as carbon source, microalgae and cyanobacteria require light for energy and inorganic carbon (CO2 or bicarbonate) as carbon source. This double specificity, together with the complex mechanisms of light capture, makes the representation of metabolic network nonstandard. Here, we review the existing metabolic networks of photoautotrophic microalgae and cyanobacteria. We highlight how these networks have been useful for gaining insight on photoautotrophic metabolism. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  11. A Unified Robotic Software Architecture for Service Robotics and Networks of Smart Sensors

    Science.gov (United States)

    Westhoff, Daniel; Zhang, Jianwei

    This paper proposes a novel architecture for the programming of multi-modal service robots and networked sensors. The presented software framework eases the development of high-level applications for distributed systems. The software architecture is based upon the Roblet-Technology, which is an exceptionally powerful medium in robotics. The possibility to develop, compile and execute an application on one workstation and distribute parts of a program based on the idea of mobile code is pointed out. Since the Roblet-Technology uses Java the development is independent of the operation system. The framework hides the network communication and therefore greatly improves the programming and testing of applications in service robotics. The concept is evaluated in the context of the service robot TASER of the TAMS Institute at the University of Hamburg. This robot consists of a mobile platform with two manipulators equipped with artificial hands. Several multimodal input and output devices for interaction round off the robot. Networked cameras in the working environment of TASER provide additional information to the robot. The integration of these smart sensors shows the extendability of the proposed concept to general distributed systems.

  12. A FD/DAMA network architecture for the first generation land mobile satellite services

    Science.gov (United States)

    Yan, T.-Y.; Wang, C.; Cheng, U.; Dessouky, K.; Rafferty, W.

    1989-01-01

    A frequency division/demand assigned multiple access (FD/DAMA) network architecture for the first-generation land mobile satellite services is presented. Rationales and technical approaches are described. In this architecture, each mobile subscriber must follow a channel access protocol to make a service request to the network management center before transmission for either open-end or closed-end services. Open-end service requests will be processed on a blocked call cleared basis, while closed-end requests will be processed on a first-come-first-served basis. Two channel access protocols are investigated, namely, a recently proposed multiple channel collision resolution scheme which provides a significantly higher useful throughput, and the traditional slotted Aloha scheme. The number of channels allocated for either open-end or closed-end services can be adaptively changed according to aggregated traffic requests. Both theoretical and simulation results are presented. Theoretical results have been verified by simulation on the JPL network testbed.

  13. Communication Network Architectures for Smart-House with Renewable Energy Resources

    Directory of Open Access Journals (Sweden)

    Mohamed A. Ahmed

    2015-08-01

    Full Text Available With the microgrid revolution, each house will have the ability to meet its own energy needs locally from renewable energy sources such as solar or wind. However, real-time data gathering, energy management and control of renewable energy systems will depend mainly on the performance of the communications infrastructure. This paper describes the design of a communication network architecture using both wired and wireless technologies for monitoring and controlling distributed energy systems involving small-scale wind turbines and photovoltaic systems. The proposed communication architecture consists of three layers: device layer, network layer, and application layer. Two scenarios are considered: a smart-house and a smart-building. Various types of sensor nodes and measurement devices are defined to monitor the condition of the renewable energy systems based on the international electrotechnical commission standard. The OPNET Modeler is used for performance evaluation in terms of end-to-end (ETE delay. The network performance is compared in view of ETE delay, reliability and implementation cost for three different technologies: Ethernet-based, WiFi-based, and ZigBee-based.

  14. An Optimal Path Computation Architecture for the Cloud-Network on Software-Defined Networking

    Directory of Open Access Journals (Sweden)

    Hyunhun Cho

    2015-05-01

    Full Text Available Legacy networks do not open the precise information of the network domain because of scalability, management and commercial reasons, and it is very hard to compute an optimal path to the destination. According to today’s ICT environment change, in order to meet the new network requirements, the concept of software-defined networking (SDN has been developed as a technological alternative to overcome the limitations of the legacy network structure and to introduce innovative concepts. The purpose of this paper is to propose the application that calculates the optimal paths for general data transmission and real-time audio/video transmission, which consist of the major services of the National Research & Education Network (NREN in the SDN environment. The proposed SDN routing computation (SRC application is designed and applied in a multi-domain network for the efficient use of resources, selection of the optimal path between the multi-domains and optimal establishment of end-to-end connections.

  15. An Energy-Efficient and High-Quality Video Transmission Architecture in Wireless Video-Based Sensor Networks

    Directory of Open Access Journals (Sweden)

    Yasaman Samei

    2008-08-01

    Full Text Available Technological progress in the fields of Micro Electro-Mechanical Systems (MEMS and wireless communications and also the availability of CMOS cameras, microphones and small-scale array sensors, which may ubiquitously capture multimedia content from the field, have fostered the development of low-cost limited resources Wireless Video-based Sensor Networks (WVSN. With regards to the constraints of videobased sensor nodes and wireless sensor networks, a supporting video stream is not easy to implement with the present sensor network protocols. In this paper, a thorough architecture is presented for video transmission over WVSN called Energy-efficient and high-Quality Video transmission Architecture (EQV-Architecture. This architecture influences three layers of communication protocol stack and considers wireless video sensor nodes constraints like limited process and energy resources while video quality is preserved in the receiver side. Application, transport, and network layers are the layers in which the compression protocol, transport protocol, and routing protocol are proposed respectively, also a dropping scheme is presented in network layer. Simulation results over various environments with dissimilar conditions revealed the effectiveness of the architecture in improving the lifetime of the network as well as preserving the video quality.

  16. A Router Architecture for Connection-Oriented Service Guarantees in the MANGO Clockless Network-on-Chip

    DEFF Research Database (Denmark)

    Bjerregaard, Tobias; Sparsø, Jens

    2005-01-01

    On-chip networks for future system-on-chip designs need simple, high performance implementations. In order to promote system-level integrity, guaranteed services (GS) need to be provided. We propose a network-on-chip (NoC) router architecture to support this, and demonstrate with a CMOS standard...

  17. Space Communications and Navigation (SCaN) Integrated Network Architecture Definition Document (ADD). Volume 1; Executive Summary; Revision 1

    Science.gov (United States)

    Younes, Badri A.; Schier, James S.

    2010-01-01

    The SCaN Program has defined an integrated network architecture that fully meets the Administrator s mandate to the Program, and will result in a NASA infrastructure capable of providing the needed and enabling communications services to future space missions. The integrated network architecture will increase SCaN operational efficiency and interoperability through standardization, commonality and technology infusion. It will enable NASA missions requiring advanced communication and tracking capabilities such as: a. Optical communication b. Antenna arraying c. Lunar and Mars Relays d. Integrated network management (service management and network control) and integrated service execution e. Enhanced tracking for navigation f. Space internetworking with DTN and IP g. End-to-end security h. Enhanced security services Moreover, the SCaN Program has created an Integrated Network Roadmap that depicts an orchestrated and coherent evolution path toward the target architecture, encompassing all aspects that concern network assets (i.e., operations and maintenance, sustaining engineering, upgrade efforts, and major development). This roadmap identifies major NASA ADPs, and shows dependencies and drivers among the various planned undertakings and timelines. The roadmap is scalable to accommodate timely adjustments in response to Agency needs, goals, objectives and funding. Future challenges to implementing this architecture include balancing user mission needs, technology development, and the availability of funding within NASA s priorities. Strategies for addressing these challenges are to: define a flexible architecture, update the architecture periodically, use ADPs to evaluate options and determine when to make decisions, and to engage the stakeholders in these evaluations. In addition, the SCaN Program will evaluate and respond to mission need dates for technical and operational capabilities to be provided by the SCaN integrated network. In that regard, the architecture

  18. Optimal artificial neural network architecture selection for performance prediction of compact heat exchanger with the EBaLM-OTR technique

    International Nuclear Information System (INIS)

    Wijayasekara, Dumidu; Manic, Milos; Sabharwall, Piyush; Utgikar, Vivek

    2011-01-01

    Highlights: → Performance prediction of PCHE using artificial neural networks. → Evaluating artificial neural network performance for PCHE modeling. → Selection of over-training resilient artificial neural networks. → Artificial neural network architecture selection for modeling problems with small data sets. - Abstract: Artificial Neural Networks (ANN) have been used in the past to predict the performance of printed circuit heat exchangers (PCHE) with satisfactory accuracy. Typically published literature has focused on optimizing ANN using a training dataset to train the network and a testing dataset to evaluate it. Although this may produce outputs that agree with experimental results, there is a risk of over-training or over-learning the network rather than generalizing it, which should be the ultimate goal. An over-trained network is able to produce good results with the training dataset but fails when new datasets with subtle changes are introduced. In this paper we present EBaLM-OTR (error back propagation and Levenberg-Marquardt algorithms for over training resilience) technique, which is based on a previously discussed method of selecting neural network architecture that uses a separate validation set to evaluate different network architectures based on mean square error (MSE), and standard deviation of MSE. The method uses k-fold cross validation. Therefore in order to select the optimal architecture for the problem, the dataset is divided into three parts which are used to train, validate and test each network architecture. Then each architecture is evaluated according to their generalization capability and capability to conform to original data. The method proved to be a comprehensive tool in identifying the weaknesses and advantages of different network architectures. The method also highlighted the fact that the architecture with the lowest training error is not always the most generalized and therefore not the optimal. Using the method the

  19. A Unified Network Security Architecture for Large, Distributed Networks, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — In typical, multi-organizational networking environments, it is difficult to define and maintain a uniform authentication scheme that provides users with easy access...

  20. A Neural Network Architecture for Detecting Grammatical Errors in Statistical Machine Translation

    Directory of Open Access Journals (Sweden)

    Tezcan Arda

    2017-06-01

    Full Text Available In this paper we present a Neural Network (NN architecture for detecting grammatical errors in Statistical Machine Translation (SMT using monolingual morpho-syntactic word representations in combination with surface and syntactic context windows. We test our approach on two language pairs and two tasks, namely detecting grammatical errors and predicting overall post-editing effort. Our results show that this approach is not only able to accurately detect grammatical errors but it also performs well as a quality estimation system for predicting overall post-editing effort, which is characterised by all types of MT errors. Furthermore, we show that this approach is portable to other languages.

  1. Compact OXC architecture, design and prototype development for flexible waveband routing optical networks.

    Science.gov (United States)

    Ishikawa, Tomohiro; Mori, Yojiro; Hasegawa, Hiroshi; Subramaniam, Suresh; Sato, Ken-Ichi; Moriwaki, Osamu

    2017-07-10

    A novel compact OXC node architecture that combines WSSs and arrays of small scale optical delivery-coupling type switches ("DCSWs") is proposed. Unlike conventional OXC nodes, the WSSs are only responsible for dynamic path bundling ("flexible waveband") while the small scale optical switches route bundled path groups. A network design algorithm that is aware of the routing scheme is also proposed, and numerical experiments elucidate that the necessary number of WSSs and amplifiers can be significantly reduced. A prototype of the proposed OXC is also developed using monolithic arrayed DCSWs. Transmission experiments on the prototype verify the proposal's technical feasibility.

  2. A Novel Hierarchical Semi-centralized Telemedicine Network Architecture Proposition for Bangladesh

    DEFF Research Database (Denmark)

    Choudhury, Samiul; Peterson, Carrie Beth; Kyriazakos, Sofoklis

    2011-01-01

    where there are extreme paucities of efficient healthcare professionals and equipments, specifically in the rural areas. In this paper a novel, hierarchical and semi-centralized telemedicine network architecture has been proposed holisti-cally focusing on the rural underdeveloped areas of Bangladesh......One of the major functions of telemedicine is the prompt delivery of modern healthcare to the remotest areas with reduced cost and efficient use of communication resources. The establishment of a well organized telemedicine system is therefore exigent for the developing countries like Bangladesh...

  3. A Scalable, Timing-Safe, Network-on-Chip Architecture with an Integrated Clock Distribution Method

    DEFF Research Database (Denmark)

    Bjerregaard, Tobias; Stensgaard, Mikkel Bystrup; Sparsø, Jens

    2007-01-01

    regions concerns the possibility of data corruption caused by metastability. This paper presents an integrated communication and mesochronous clocking strategy, which avoids timing related errors while maintaining a globally synchronous system perspective. The architecture is scalable as timing integrity......Growing system sizes together with increasing performance variability are making globally synchronous operation hard to realize. Mesochronous clocking constitutes a possible solution to the problems faced. The most fundamental of problems faced when communicating between mesochronously clocked...... is based purely on local observations. It is demonstrated with a 90 nm CMOS standard cell network-on-chip design which implements completely timing-safe, global communication in a modular system...

  4. Architecture and biological applications of artificial neural networks: a tuberculosis perspective.

    Science.gov (United States)

    Darsey, Jerry A; Griffin, William O; Joginipelli, Sravanthi; Melapu, Venkata Kiran

    2015-01-01

    Advancement of science and technology has prompted researchers to develop new intelligent systems that can solve a variety of problems such as pattern recognition, prediction, and optimization. The ability of the human brain to learn in a fashion that tolerates noise and error has attracted many researchers and provided the starting point for the development of artificial neural networks: the intelligent systems. Intelligent systems can acclimatize to the environment or data and can maximize the chances of success or improve the efficiency of a search. Due to massive parallelism with large numbers of interconnected processers and their ability to learn from the data, neural networks can solve a variety of challenging computational problems. Neural networks have the ability to derive meaning from complicated and imprecise data; they are used in detecting patterns, and trends that are too complex for humans, or other computer systems. Solutions to the toughest problems will not be found through one narrow specialization; therefore we need to combine interdisciplinary approaches to discover the solutions to a variety of problems. Many researchers in different disciplines such as medicine, bioinformatics, molecular biology, and pharmacology have successfully applied artificial neural networks. This chapter helps the reader in understanding the basics of artificial neural networks, their applications, and methodology; it also outlines the network learning process and architecture. We present a brief outline of the application of neural networks to medical diagnosis, drug discovery, gene identification, and protein structure prediction. We conclude with a summary of the results from our study on tuberculosis data using neural networks, in diagnosing active tuberculosis, and predicting chronic vs. infiltrative forms of tuberculosis.

  5. Impact of an obesogenic diet program on bone densitometry, micro architecture and metabolism in male rat

    Directory of Open Access Journals (Sweden)

    Gerbaix Maude

    2012-07-01

    Full Text Available Abstract Background The relationships between fat mass and bone tissue are complex and not fully elucidated. A high-fat/high-sucrose diet has been shown to induce harmful effects on bone micro architecture and bone biomechanics of rat. When such diet leads to obesity, it may induce an improvement of biomechanical bone parameters in rodent. Here, we examined the impact of a high-fat/high-sucrose diet on the body composition and its resulting effects on bone density and structure in male rats. Forty three Wistar rats aged 7 months were split into 3 groups: 1 sacrificed before diet (BD, n = 14; 1 subjected to 16 weeks of high-fat/high-sucrose diet (HF/HS, n = 14; 1 subjected to standard diet (Control, n = 15. Abdominal circumference and insulin sensitivity were measured and visceral fat mass was weighed. The bone mineral density (BMD was analyzed at the whole body and tibia by densitometry. Microcomputed tomography and histomorphometric analysis were performed at L2 vertebrae and tibia to study the trabecular and cortical bone structures and the bone cell activities. Osteocalcin and CTX levels were performed to assess the relative balance of the bone formation and resorption. Differences between groups have been tested with an ANOVA with subsequent Scheffe post-hoc test. An ANCOVA with global mass and global fat as covariates was used to determine the potential implication of the resulting mechanical loading on bone. Results The HF/HS group had higher body mass, fat masses and abdominal circumference and developed an impaired glucose tolerance (p  Conclusions The HF/HS diet had induced obesity and impaired glucose tolerance. These changes resulted in an improvement of quantitative, qualitative and metabolic bone parameters. The fat mass increase partly explained these observations.

  6. DReAM: Demand Response Architecture for Multi-level District Heating and Cooling Networks

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharya, Saptarshi; Chandan, Vikas; Arya, Vijay; Kar, Koushik

    2017-05-19

    In this paper, we exploit the inherent hierarchy of heat exchangers in District Heating and Cooling (DHC) networks and propose DReAM, a novel Demand Response (DR) architecture for Multi-level DHC networks. DReAM serves to economize system operation while still respecting comfort requirements of individual consumers. Contrary to many present day DR schemes that work on a consumer level granularity, DReAM works at a level of hierarchy above buildings, i.e. substations that supply heat to a group of buildings. This improves the overall DR scalability and reduce the computational complexity. In the first step of the proposed approach, mathematical models of individual substations and their downstream networks are abstracted into appropriately constructed low-complexity structural forms. In the second step, this abstracted information is employed by the utility to perform DR optimization that determines the optimal heat inflow to individual substations rather than buildings, in order to achieve the targeted objectives across the network. We validate the proposed DReAM framework through experimental results under different scenarios on a test network.

  7. Accessibility in networks: A useful measure for understanding social insect nest architecture

    International Nuclear Information System (INIS)

    Viana, Matheus P.; Fourcassié, Vincent; Perna, Andrea; Costa, Luciano da F.; Jost, Christian

    2013-01-01

    Networks and the associated tools from graph theory have now become well-established approaches to study natural as well as human-made systems. While early studies focused on topology and connectivity, the recent literature has acknowledged the importance of the dynamical properties of these networks. Here we focus on such a dynamic measure: accessibility. It characterizes for any given movement dynamics (such as random walks) the average number of nodes that can be reached in exactly h steps (out-accessibility), or the average number of nodes from which a given node can be reached (in-accessibility). This focus on dynamics makes accessibility particularly appropriate to study movement on networks and to detect complementary properties with respect to topology-based measurements such as betweenness centrality. We apply this measure to six nests of Cubitermes termites. Their mushroom-like 3D architectures consist of chambers and connecting tunnels that can be associated to nodes and edges in a communication network. Accessibilities turn out to be particularly low in the bottom part of the nests that link them to their underground tunneling network. We interpret this result in the context of anti-predator (ants) behavior and/or as a side effect of the global nest shape.

  8. A super base station based centralized network architecture for 5G mobile communication systems

    Directory of Open Access Journals (Sweden)

    Manli Qian

    2015-04-01

    Full Text Available To meet the ever increasing mobile data traffic demand, the mobile operators are deploying a heterogeneous network with multiple access technologies and more and more base stations to increase the network coverage and capacity. However, the base stations are isolated from each other, so different types of radio resources and hardware resources cannot be shared and allocated within the overall network in a cooperative way. The mobile operators are thus facing increasing network operational expenses and a high system power consumption. In this paper, a centralized radio access network architecture, referred to as the super base station (super BS, is proposed, as a possible solution for an energy-efficient fifth-generation (5G mobile system. The super base station decouples the logical functions and physical entities of traditional base stations, so different types of system resources can be horizontally shared and statistically multiplexed among all the virtual base stations throughout the entire system. The system framework and main functionalities of the super BS are described. Some key technologies for system implementation, i.e., the resource pooling, real-time virtualization, adaptive hardware resource allocation are also highlighted.

  9. Clearing the Skies: A deep network architecture for single-image rain streaks removal.

    Science.gov (United States)

    Fu, Xueyang; Huang, Jiabin; Ding, Xinghao; Liao, Yinghao; Paisley, John

    2017-04-06

    We introduce a deep network architecture called DerainNet for removing rain streaks from an image. Based on the deep convolutional neural network (CNN), we directly learn the mapping relationship between rainy and clean image detail layers from data. Because we do not possess the ground truth corresponding to real-world rainy images, we synthesize images with rain for training. In contrast to other common strategies that increase depth or breadth of the network, we use image processing domain knowledge to modify the objective function and improve deraining with a modestly-sized CNN. Specifically, we train our DerainNet on the detail (high-pass) layer rather than in the image domain. Though DerainNet is trained on synthetic data, we find that the learned network translates very effectively to real-world images for testing. Moreover, we augment the CNN framework with image enhancement to improve the visual results. Compared with state-of-the-art single image deraining methods, our method has improved rain removal and much faster computation time after network training.

  10. Microbial diversity and metabolic networks in acid mine drainage habitats.

    Science.gov (United States)

    Méndez-García, Celia; Peláez, Ana I; Mesa, Victoria; Sánchez, Jesús; Golyshina, Olga V; Ferrer, Manuel

    2015-01-01

    Acid mine drainage (AMD) emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon, and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics-based methodologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and archaea recovered through sterile filtering (herein referred to as filterable fraction) in these environments demand their inclusion in the microbial characterization of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including filterable fraction), and eukaryotic diversity in these ecosystems, and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.

  11. A Bayesian approach to the evolution of metabolic networks on a phylogeny.

    Directory of Open Access Journals (Sweden)

    Aziz Mithani

    2010-08-01

    Full Text Available The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions or complex (incorporating dependencies among reactions stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. Here, we describe a model that takes the reaction neighborhood into account when modeling metabolic evolution. The model also allows estimation of the strength of the neighborhood effect during the course of evolution. We present Gibbs samplers for sampling networks at the internal node of a phylogeny and for estimating the parameters of evolution over a phylogeny without exploring the whole search space by iteratively sampling from the conditional distributions of the internal networks and parameters. The samplers are used to estimate the parameters of evolution of metabolic networks of bacteria in the genus Pseudomonas and to infer the metabolic networks of the ancestral pseudomonads. The results suggest that pathway maps that are conserved across the Pseudomonas phylogeny have a stronger neighborhood structure than those which have a variable distribution of reactions across the phylogeny, and that some Pseudomonas lineages are going through genome reduction resulting in the loss of a number of reactions from their metabolic networks.

  12. A consensus yeast metabolic network obtained from a community approach to systems biology.

    NARCIS (Netherlands)

    Herrgard, M.J.; Swainston, N.; Dobson, P.; Dunn, W.B.; Arga, K.Y.; Arvas, M.; Bluthgen, N.; Borger, S.; Costenoble, E.R.; Heinemann, M.; Hucka, M.; Li, P.; Liebermeister, W.; Mo, M.L.; Oliveira, A.P.; Petranovic, D.; Pettifer, S.; Simeonides, E.; Smallbone, K.; Spasi, I.; Weichart, D.; Brent, R.; Broomhead, D.S.; Westerhoff, H.V.; Kirdar, B.; Penttila, M.; Klipp, E.; Paton, N.; Palsson, B.O.; Sauer, U.; Oliver, S.G.; Mendes, P.; Nielsen, J.; Kell, D.B.

    2008-01-01

    Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and

  13. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

    NARCIS (Netherlands)

    Herrgård, Markus J.; Swainston, Neil; Dobson, Paul; Dunn, Warwick B.; Arga, K. Yalçin; Arvas, Mikko; Blüthgen, Nils; Borger, Simon; Costenoble, Roeland; Heinemann, Matthias; Hucka, Michael; Novère, Nicolas Le; Li, Peter; Liebermeister, Wolfram; Mo, Monica L.; Oliveira, Ana Paula; Petranovic, Dina; Pettifer, Stephen; Simeonidis, Evangelos; Smallbone, Kieran; Spasić, Irena; Weichart, Dieter; Brent, Roger; Broomhead, David S.; Westerhoff, Hans V.; Kırdar, Betül; Penttilä, Merja; Klipp, Edda; Palsson, Bernhard Ø.; Sauer, Uwe; Oliver, Stephen G.; Mendes, Pedro; Nielsen, Jens; Kell, Douglas B.

    2008-01-01

    Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and

  14. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

    DEFF Research Database (Denmark)

    Herrgard, Markus; Swainston, Neil; Dobson, Paul

    2008-01-01

    a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously...... of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms....

  15. AUTHENTICATION ARCHITECTURE USING THRESHOLD CRYPTOGRAPHY IN KERBEROS FOR MOBILE AD HOC NETWORKS

    Directory of Open Access Journals (Sweden)

    Hadj Gharib

    2014-06-01

    Full Text Available The use of wireless technologies is gradually increasing and risks related to the use of these technologies are considerable. Due to their dynamically changing topology and open environment without a centralized policy control of a traditional network, a mobile ad hoc network (MANET is vulnerable to the presence of malicious nodes and attacks. The ideal solution to overcome a myriad of security concerns in MANET’s is the use of reliable authentication architecture. In this paper we propose a new key management scheme based on threshold cryptography in kerberos for MANET’s, the proposed scheme uses the elliptic curve cryptography method that consumes fewer resources well adapted to the wireless environment. Our approach shows a strength and effectiveness against attacks.

  16. LIDeA: A Distributed Lightweight Intrusion Detection Architecture for Sensor Networks

    DEFF Research Database (Denmark)

    Giannetsos, Athanasios; Krontiris, Ioannis; Dimitriou, Tassos

    2008-01-01

    Wireless sensor networks are vulnerable to adversaries as they are frequently deployed in open and unattended environments. Preventive mechanisms can be applied to protect them from an assortment of attacks. However, more sophisticated methods, like intrusion detection systems, are needed...... to achieve a more autonomic and complete defense mechanism, even against attacks that have not been anticipated in advance. In this paper, we present a lightweight intrusion detection system, called LIDeA, designed for wireless sensor networks. LIDeA is based on a distributed architecture, in which nodes...... overhear their neighboring nodes and collaborate with each other in order to successfully detect an intrusion. We show how such a system can be implemented in TinyOS, which components and interfaces are needed, and what is the resulting overhead imposed....

  17. Understanding the genetic and epigenetic architecture in complex network of rice flowering pathways.

    Science.gov (United States)

    Sun, Changhui; Chen, Dan; Fang, Jun; Wang, Pingrong; Deng, Xiaojian; Chu, Chengcai

    2014-12-01

    Although the molecular basis of flowering time control is well dissected in the long day (LD) plant Arabidopsis, it is still largely unknown in the short day (SD) plant rice. Rice flowering time (heading date) is an important agronomic trait for season adaption and grain yield, which is affected by both genetic and environmental factors. During the last decade, as the nature of florigen was identified, notable progress has been made on exploration how florigen gene expression is genetically controlled. In Arabidopsis expression of certain key flowering integrators such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT) are also epigenetically regulated by various chromatin modifications, however, very little is known in rice on this aspect until very recently. This review summarized the advances of both genetic networks and chromatin modifications in rice flowering time control, attempting to give a complete view of the genetic and epigenetic architecture in complex network of rice flowering pathways.

  18. Architecture and Design of IP Broadcasting System Using Passive Optical Network

    Science.gov (United States)

    Ikeda, Hiroki; Sugawa, Jun; Ashi, Yoshihiro; Sakamoto, Kenichi

    We propose an IP broadcasting system architecture using passive optical networks (PON) utilizing the optical broadcast links of a PON with a downstream bandwidth allocation algorithm to provide a multi-channel IP broadcasting service to home subscribers on single broadband IP network infrastructures. We introduce the design and adaptation of the optical broadcast links to effectively broadcast video contents to home subscribers. We present a performance analysis that includes the downstream bandwidth utilization efficiency of the broadcast link and the bandwidth control of the IP broadcasting and Internet data. Our analysis and simulation results show that the proposed system can provide 100 HDTV channels to every user over fiber lines. We also propose an IPTV channel selection mechanism in an ONT by selecting a broadcast stream. We developed and evaluated a prototype that can achieve a 15-msec IPTV channel selection speed.

  19. A network architecture for precision formation flying using the IEEE 802.11 MAC Protocol

    Science.gov (United States)

    Clare, Loren P.; Gao, Jay L.; Jennings, Esther H.; Okino, Clayton

    2005-01-01

    Precision Formation Flying missions involve the tracking and maintenance of spacecraft in a desired geometric formation. The strong coupling of spacecraft in formation flying control requires inter-spacecraft communication to exchange information. In this paper, we present a network architecture that supports PFF control, from the initial random deployment phase to the final formation. We show that a suitable MAC layer for the application protocol is IEEE's 802.11 MAC protocol. IEEE 802.11 MAC has two modes of operations: DCF and PCF. We show that DCF is suitable for the initial deployment phase while switching to PCF when the spacecraft are in formation improves jitter and throughput. We also consider the effect of routing on protocol performance and suggest when it is profitable to turn off route discovery to achieve better network performance.

  20. Controllability in cancer metabolic networks according to drug targets as driver nodes.

    Science.gov (United States)

    Asgari, Yazdan; Salehzadeh-Yazdi, Ali; Schreiber, Falk; Masoudi-Nejad, Ali

    2013-01-01

    Networks are employed to represent many nonlinear complex systems in the real world. The topological aspects and relationships between the structure and function of biological networks have been widely studied in the past few decades. However dynamic and control features of complex networks have not been widely researched, in comparison to topological network features. In this study, we explore the relationship between network controllability, topological parameters, and network medicine (metabolic drug targets). Considering the assumption that targets of approved anticancer metabolic drugs are driver nodes (which control cancer metabolic networks), we have applied topological analysis to genome-scale metabolic models of 15 normal and corresponding cancer cell types. The results show that besides primary network parameters, more complex network metrics such as motifs and clusters may also be appropriate for controlling the systems providing the controllability relationship between topological parameters and drug targets. Consequently, this study reveals the possibilities of following a set of driver nodes in network clusters instead of considering them individually according to their centralities. This outcome suggests considering distributed control systems instead of nodal control for cancer metabolic networks, leading to a new strategy in the field of network medicine.

  1. Optimization of neural network architecture for classification of radar jamming FM signals

    Science.gov (United States)

    Soto, Alberto; Mendoza, Ariadna; Flores, Benjamin C.

    2017-05-01

    The purpose of this study is to investigate several artificial Neural Network (NN) architectures in order to design a cognitive radar system capable of optimally distinguishing linear Frequency-Modulated (FM) signals from bandlimited Additive White Gaussian Noise (AWGN). The goal is to create a theoretical framework to determine an optimal NN architecture to achieve a Probability of Detection (PD) of 95% or higher and a Probability of False Alarm (PFA) of 1.5% or lower at 5 dB Signal to Noise Ratio (SNR). Literature research reveals that the frequency-domain power spectral densities characterize a signal more efficiently than its time-domain counterparts. Therefore, the input data is preprocessed by calculating the magnitude square of the Discrete Fourier Transform of the digitally sampled bandlimited AWGN and linear FM signals to populate a matrix containing N number of samples and M number of spectra. This matrix is used as input for the NN, and the spectra are divided as follows: 70% for training, 15% for validation, and 15% for testing. The study begins by experimentally deducing the optimal number of hidden neurons (1-40 neurons), then the optimal number of hidden layers (1-5 layers), and lastly, the most efficient learning algorithm. The training algorithms examined are: Resilient Backpropagation, Scaled Conjugate Gradient, Conjugate Gradient with Powell/Beale Restarts, Polak-Ribiére Conjugate Gradient, and Variable Learning Rate Backpropagation. We determine that an architecture with ten hidden neurons (or higher), one hidden layer, and a Scaled Conjugate Gradient for training algorithm encapsulates an optimal architecture for our application.

  2. Designing 2D and 3D network-on-chip architectures

    CERN Document Server

    Tatas, Konstantinos; Soudris, Dimitrios; Jantsch, Axel

    2014-01-01

    This book covers key concepts in the design of 2D and 3D Network-on-Chip interconnect.  It highlights design challenges and discusses fundamentals of NoC technology, including architectures, algorithms and tools.  Coverage focuses on topology exploration for both 2D and 3D NoCs, routing algorithms, NoC router design, NoC-based system integration, verification and testing, and NoC reliabilty.  Case studies are used to illuminate new design methodologies.  ·         Describes essential theory, practice and state-of-the-art applications of 2D and 3D Network-on-Chip interconnect; ·         Enables readers to exploit parallelism in processor architecture, with interconnect design that is efficient in terms of energy and performance; ·         Covers topics not available in other books, such as NoC and distributed memory organization, dynamic memory management and abstract data type support in many-core platforms, and distributed hierarchical power management.

  3. MASM: a market architecture for sensor management in distributed sensor networks

    Science.gov (United States)

    Viswanath, Avasarala; Mullen, Tracy; Hall, David; Garga, Amulya

    2005-03-01

    Rapid developments in sensor technology and its applications have energized research efforts towards devising a firm theoretical foundation for sensor management. Ubiquitous sensing, wide bandwidth communications and distributed processing provide both opportunities and challenges for sensor and process control and optimization. Traditional optimization techniques do not have the ability to simultaneously consider the wildly non-commensurate measures involved in sensor management in a single optimization routine. Market-oriented programming provides a valuable and principled paradigm to designing systems to solve this dynamic and distributed resource allocation problem. We have modeled the sensor management scenario as a competitive market, wherein the sensor manager holds a combinatorial auction to sell the various items produced by the sensors and the communication channels. However, standard auction mechanisms have been found not to be directly applicable to the sensor management domain. For this purpose, we have developed a specialized market architecture MASM (Market architecture for Sensor Management). In MASM, the mission manager is responsible for deciding task allocations to the consumers and their corresponding budgets and the sensor manager is responsible for resource allocation to the various consumers. In addition to having a modified combinatorial winner determination algorithm, MASM has specialized sensor network modules that address commensurability issues between consumers and producers in the sensor network domain. A preliminary multi-sensor, multi-target simulation environment has been implemented to test the performance of the proposed system. MASM outperformed the information theoretic sensor manager in meeting the mission objectives in the simulation experiments.

  4. An efficient architecture for the integration of sensor and actuator networks into the future internet

    Science.gov (United States)

    Schneider, J.; Klein, A.; Mannweiler, C.; Schotten, H. D.

    2011-08-01

    In the future, sensors will enable a large variety of new services in different domains. Important application areas are service adaptations in fixed and mobile environments, ambient assisted living, home automation, traffic management, as well as management of smart grids. All these applications will share a common property, the usage of networked sensors and actuators. To ensure an efficient deployment of such sensor-actuator networks, concepts and frameworks for managing and distributing sensor data as well as for triggering actuators need to be developed. In this paper, we present an architecture for integrating sensors and actuators into the future Internet. In our concept, all sensors and actuators are connected via gateways to the Internet, that will be used as comprehensive transport medium. Additionally, an entity is needed for registering all sensors and actuators, and managing sensor data requests. We decided to use a hierarchical structure, comparable to the Domain Name Service. This approach realizes a cost-efficient architecture disposing of "plug and play" capabilities and accounting for privacy issues.

  5. Routing Protocols for Delay Tolerant Networks: A Reference Architecture and a Thorough Quantitative Evaluation

    Directory of Open Access Journals (Sweden)

    Khalil Massri

    2016-03-01

    Full Text Available In this paper, we propose a reference architecture for Delay-Tolerant Networking (DTN routing protocols and a thorough quantitative evaluation of many protocols proposed in the literature. We categorize DTN protocols according to their use of the three techniques that are the key elements of our reference architecture: queue management, forwarding and replication. Queue management orders and manages the messages in the node’s buffer; forwarding selects the messages to be delivered when there is a contact; and finally, replication bounds the number of replicas in the network. Contrary to most previous papers, where either only qualitative comparisons have been presented or only a single category of protocols has been analyzed, in our work, we discuss the results of our experimental activity on many of the DTN protocols in the literature. Our results, which have been obtained both using synthetic and real mobility traces, show that an effective combination of the proposed techniques can significantly improve the performance of the protocols in terms of delivery ratio, overhead and delay.

  6. Using the reconstructed genome-scale human metabolic network to study physiology and pathology

    OpenAIRE

    Bordbar, Aarash; Palsson, Bernhard O.

    2012-01-01

    Metabolism plays a key role in many major human diseases. Generation of high-throughput omics data has ushered in a new era of systems biology. Genome-scale metabolic network reconstructions provide a platform to interpret omics data in a biochemically meaningful manner. The release of the global human metabolic network, Recon 1, in 2007 has enabled new systems biology approaches to study human physiology, pathology, and pharmacology. There are currently over 20 publications that utilize Reco...

  7. Coordinations between gene modules control the operation of plant amino acid metabolic networks

    Directory of Open Access Journals (Sweden)

    Galili Gad

    2009-01-01

    Full Text Available Abstract Background Being sessile organisms, plants should adjust their metabolism to dynamic changes in their environment. Such adjustments need particular coordination in branched metabolic networks in which a given metabolite can be converted into multiple other metabolites via different enzymatic chains. In the present report, we developed a novel "Gene Coordination" bioinformatics approach and use it to elucidate adjustable transcriptional interactions of two branched amino acid metabolic networks in plants in response to environmental stresses, using publicly available microarray results. Results Using our "Gene Coordination" approach, we have identified in Arabidopsis plants two oppositely regulated groups of "highly coordinated" genes within the branched Asp-family network of Arabidopsis plants, which metabolizes the amino acids Lys, Met, Thr, Ile and Gly, as well as a single group of "highly coordinated" genes within the branched aromatic amino acid metabolic network, which metabolizes the amino acids Trp, Phe and Tyr. These genes possess highly coordinated adjustable negative and positive expression responses to various stress cues, which apparently regulate adjustable metabolic shifts between competing branches of these networks. We also provide evidence implying that these highly coordinated genes are central to impose intra- and inter-network interactions between the Asp-family and aromatic amino acid metabolic networks as well as differential system interactions with other growth promoting and stress-associated genome-wide genes. Conclusion Our novel Gene Coordination elucidates that branched amino acid metabolic networks in plants are regulated by specific groups of highly coordinated genes that possess adjustable intra-network, inter-network and genome-wide transcriptional interactions. We also hypothesize that such transcriptional interactions enable regulatory metabolic adjustments needed for adaptation to the stresses.

  8. Reveal, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures

    Science.gov (United States)

    Liang, Shoudan; Fuhrman, Stefanie; Somogyi, Roland

    1998-01-01

    Given the immanent gene expression mapping covering whole genomes during development, health and disease, we seek computational methods to maximize functional inference from such large data sets. Is it possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables? We investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between input states and output states, one is able to infer the sets of input elements controlling each element or gene in the network. This process is unequivocal and exact for complete state transition tables. We implemented this REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable within the conditions tested so far. For n = 50 (elements) and k = 3 (inputs per element), the analysis of incomplete state transition tables (100 state transition pairs out of a possible 10(exp 15)) reliably produced the original rule and wiring sets. While this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi-state models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields.

  9. A distributed multiagent system architecture for body area networks applied to healthcare monitoring.

    Science.gov (United States)

    Felisberto, Filipe; Laza, Rosalía; Fdez-Riverola, Florentino; Pereira, António

    2015-01-01

    In the last years the area of health monitoring has grown significantly, attracting the attention of both academia and commercial sectors. At the same time, the availability of new biomedical sensors and suitable network protocols has led to the appearance of a new generation of wireless sensor networks, the so-called wireless body area networks. Nowadays, these networks are routinely used for continuous monitoring of vital parameters, movement, and the surrounding environment of people, but the large volume of data generated in different locations represents a major obstacle for the appropriate design, development, and deployment of more elaborated intelligent systems. In this context, we present an open and distributed architecture based on a multiagent system for recognizing human movements, identifying human postures, and detecting harmful activities. The proposed system evolved from a single node for fall detection to a multisensor hardware solution capable of identifying unhampered falls and analyzing the users' movement. The experiments carried out contemplate two different scenarios and demonstrate the accuracy of our proposal as a real distributed movement monitoring and accident detection system. Moreover, we also characterize its performance, enabling future analyses and comparisons with similar approaches.

  10. A Programmer-Interpreter Neural Network Architecture for Prefrontal Cognitive Control.

    Science.gov (United States)

    Donnarumma, Francesco; Prevete, Roberto; Chersi, Fabian; Pezzulo, Giovanni

    2015-09-01

    There is wide consensus that the prefrontal cortex (PFC) is able to exert cognitive control on behavior by biasing processing toward task-relevant information and by modulating response selection. This idea is typically framed in terms of top-down influences within a cortical control hierarchy, where prefrontal-basal ganglia loops gate multiple input-output channels, which in turn can activate or sequence motor primitives expressed in (pre-)motor cortices. Here we advance a new hypothesis, based on the notion of programmability and an interpreter-programmer computational scheme, on how the PFC can flexibly bias the selection of sensorimotor patterns depending on internal goal and task contexts. In this approach, multiple elementary behaviors representing motor primitives are expressed by a single multi-purpose neural network, which is seen as a reusable area of "recycled" neurons (interpreter). The PFC thus acts as a "programmer" that, without modifying the network connectivity, feeds the interpreter networks with specific input parameters encoding the programs (corresponding to network structures) to be interpreted by the (pre-)motor areas. Our architecture is validated in a standard test for executive function: the 1-2-AX task. Our results show that this computational framework provides a robust, scalable and flexible scheme that can be iterated at different hierarchical layers, supporting the realization of multiple goals. We discuss the plausibility of the "programmer-interpreter" scheme to explain the functioning of prefrontal-(pre)motor cortical hierarchies.

  11. The central monitoring station of Indian Environmental Radiation Monitoring Network (IERMON): the architecture and functions

    International Nuclear Information System (INIS)

    Garg, Saurabh; Ratheesh, M.P.; Mukundan, T.; Patel, M.D.; Nair, C.K.G.; Puranik, V.D.

    2010-01-01

    The Indian Environmental Radiation Monitoring Network (IERMON) is being established across the country by the Bhabha Atomic Research Centre, Mumbai. The network consists of stations with automated systems for environmental radiation monitoring with online data communication facility. Currently about 100 stations are operational and additional 500 stations are expected to be installed by March, 2012. The network is established with different objectives, the main objective being the detection and reporting of any nuclear emergency anywhere in the country. The central monitoring station of the network is established in Mumbai. This paper describes the architecture and functions of IERMON Central Station. The Central Station consists of server room for online data collection from remote stations and maintenance of databases for various applications; central monitoring room for user interaction with database and IERMON website maintenance and development room for the development of new applications. The functions of IERMON Central Station include detection and reporting of nuclear emergency, maintenance of remote stations, enhancement of public awareness on environmental radiation through public display systems and website, etc. The details on system layout and data protocols can be found in the paper. (author)

  12. RoCoMAR: Robots’ Controllable Mobility Aided Routing and Relay Architecture for Mobile Sensor Networks

    Directory of Open Access Journals (Sweden)

    Seokhoon Yoon

    2013-07-01

    Full Text Available In a practical deployment, mobile sensor network (MSN suffers from a low performance due to high node mobility, time-varying wireless channel properties, and obstacles between communicating nodes. In order to tackle the problem of low network performance and provide a desired end-to-end data transfer quality, in this paper we propose a novel ad hoc routing and relaying architecture, namely RoCoMAR (Robots’ Controllable Mobility Aided Routing that uses robotic nodes’ controllable mobility. RoCoMAR repeatedly performs link reinforcement process with the objective of maximizing the network throughput, in which the link with the lowest quality on the path is identified and replaced with high quality links by placing a robotic node as a relay at an optimal position. The robotic node resigns as a relay if the objective is achieved or no more gain can be obtained with a new relay. Once placed as a relay, the robotic node performs adaptive link maintenance by adjusting its position according to the movements of regular nodes. The simulation results show that RoCoMAR outperforms existing ad hoc routing protocols for MSN in terms of network throughput and end-to-end delay.

  13. RoCoMAR: robots' controllable mobility aided routing and relay architecture for mobile sensor networks.

    Science.gov (United States)

    Le, Duc Van; Oh, Hoon; Yoon, Seokhoon

    2013-07-05

    In a practical deployment, mobile sensor network (MSN) suffers from a low performance due to high node mobility, time-varying wireless channel properties, and obstacles between communicating nodes. In order to tackle the problem of low network performance and provide a desired end-to-end data transfer quality, in this paper we propose a novel ad hoc routing and relaying architecture, namely RoCoMAR (Robots' Controllable Mobility Aided Routing) that uses robotic nodes' controllable mobility. RoCoMAR repeatedly performs link reinforcement process with the objective of maximizing the network throughput, in which the link with the lowest quality on the path is identified and replaced with high quality links by placing a robotic node as a relay at an optimal position. The robotic node resigns as a relay if the objective is achieved or no more gain can be obtained with a new relay. Once placed as a relay, the robotic node performs adaptive link maintenance by adjusting its position according to the movements of regular nodes. The simulation results show that RoCoMAR outperforms existing ad hoc routing protocols for MSN in terms of network throughput and end-to-end delay.

  14. Effect of chain rigidity on network architecture and deformation behavior of glassy polymer networks

    Science.gov (United States)

    Knowles, Kyler Reser

    Processing carbon fiber composite laminates creates molecular-level strains in the thermoset matrix upon curing and cooling which can lead to failures such as geometry deformations, micro-cracking, and other issues. It is known strain creation is attributed to the significant volume and physical state changes undergone by the polymer matrix throughout the curing process, though storage and relaxation of cure-induced strains remain poorly understood. This dissertation establishes two approaches to address the issue. The first establishes testing methods to simultaneously measure key volumetric properties of a carbon fiber composite laminate and its polymer matrix. The second approach considers the rigidity of the polymer matrix in regards to strain storage and relaxation mechanisms which ultimately control composite performance throughout manufacturing and use. Through the use of a non-contact, full-field strain measurement technique known as digital image correlation (DIC), we describe and implement useful experiments which quantify matrix and composite parameters necessary for simulation efforts and failure models. The methods are compared to more traditional techniques and show excellent correlation. Further, we established relationships which represent matrix-fiber compatibility in regards to critical processing constraints. The second approach involves a systematic study of epoxy-amine networks which are chemically-similar but differ in chain segment rigidity. Prior research has investigated the isomer effect of glassy polymers, showing sizeable differences in thermal, volumetric, physical, and mechanical properties. This work builds on these themes and shows the apparent isomer effect is rather an effect of chain rigidity. Indeed, it was found that structurally-dissimilar polymer networks exhibit very similar properties as a consequence of their shared average network rigidity. Differences in chain packing, as a consequence of chain rigidity, were shown to

  15. A Neural Network Architecture For Rapid Model Indexing In Computer Vision Systems

    Science.gov (United States)

    Pawlicki, Ted

    1988-03-01

    Models of objects stored in memory have been shown to be useful for guiding the processing of computer vision systems. A major consideration in such systems, however, is how stored models are initially accessed and indexed by the system. As the number of stored models increases, the time required to search memory for the correct model becomes high. Parallel distributed, connectionist, neural networks' have been shown to have appealing content addressable memory properties. This paper discusses an architecture for efficient storage and reference of model memories stored as stable patterns of activity in a parallel, distributed, connectionist, neural network. The emergent properties of content addressability and resistance to noise are exploited to perform indexing of the appropriate object centered model from image centered primitives. The system consists of three network modules each of which represent information relative to a different frame of reference. The model memory network is a large state space vector where fields in the vector correspond to ordered component objects and relative, object based spatial relationships between the component objects. The component assertion network represents evidence about the existence of object primitives in the input image. It establishes local frames of reference for object primitives relative to the image based frame of reference. The spatial relationship constraint network is an intermediate representation which enables the association between the object based and the image based frames of reference. This intermediate level represents information about possible object orderings and establishes relative spatial relationships from the image based information in the component assertion network below. It is also constrained by the lawful object orderings in the model memory network above. The system design is consistent with current psychological theories of recognition by component. It also seems to support Marr's notions

  16. Light-emitting conjugated polymers with microporous network architecture: interweaving scaffold promotes electronic conjugation, facilitates exciton migration, and improves luminescence.

    Science.gov (United States)

    Xu, Yanhong; Chen, Long; Guo, Zhaoqi; Nagai, Atsushi; Jiang, Donglin

    2011-11-09

    Herein we report a strategy for the design of highly luminescent conjugated polymers by restricting rotation of the polymer building blocks through a microporous network architecture. We demonstrate this concept using tetraphenylethene (TPE) as a building block to construct a light-emitting conjugated microporous polymer. The interlocked network successfully restricted the rotation of the phenyl units, which are the major cause of fluorescence deactivation in TPE, thus providing intrinsic luminescence activity for the polymers. We show positive "CMP effects" that the network promotes π-conjugation, facilitates exciton migration, and improves luminescence activity. Although the monomer and linear polymer analogue in solvents are nonemissive, the network polymers are highly luminescent in various solvents and the solid state. Because emission losses due to rotation are ubiquitous among small chromophores, this strategy can be generalized for the de novo design of light-emitting materials by integrating the chromophores into an interlocked network architecture.

  17. Improved Vehicular Information Network Architecture Using Fuzzy Based Named Data NetworkingNDN

    Directory of Open Access Journals (Sweden)

    Kanwalpreet Kaur

    2015-08-01

    Full Text Available Vehicular Ad-hoc System VANETs is really a component with smart transport systems. It has ability to prevent accidents and the road congestion issues on highways but it suffers from the accomplishment and scalability issues. To handle these difficulties from the Inter Vehicular Communication IVC we apply Name Data Networking NDN. All though in NDN the users are only concerned about necessary data and give no attention on the number of locations from where the data is coming. The NDN layout is usually much more worthy for IVC circumstance getting the ordered material labeling design as well as amp64258exible material retrieval. In this report we propose vehicular network dependent on fuzzy membership function which offers the fundamental NDN style to improve support location dependent forwarding content aggregation and distributed mobility management. This paper finally winds up the several boundaries regarding earlier approaches.

  18. Comprehensive Mapping of Pluripotent Stem Cell Metabolism Using Dynamic Genome-Scale Network Modeling

    Directory of Open Access Journals (Sweden)

    Sriram Chandrasekaran

    2017-12-01

    Full Text Available Summary: Metabolism is an emerging stem cell hallmark tied to cell fate, pluripotency, and self-renewal, yet systems-level understanding of stem cell metabolism has been limited by the lack of genome-scale network models. Here, we develop a systems approach to integrate time-course metabolomics data with a computational model of metabolism to analyze the metabolic state of naive and primed murine pluripotent stem cells. Using this approach, we find that one-carbon metabolism involving phosphoglycerate dehydrogenase, folate synthesis, and nucleotide synthesis is a key pathway that differs between the two states, resulting in differential sensitivity to anti-folates. The model also predicts that the pluripotency factor Lin28 regulates this one-carbon metabolic pathway, which we validate using metabolomics data from Lin28-deficient cells. Moreover, we identify and validate metabolic reactions related to S-adenosyl-methionine production that can differentially impact histone methylation in naive and primed cells. Our network-based approach provides a framework for characterizing metabolic changes influencing pluripotency and cell fate. : Chandrasekaran et al. use computational modeling, metabolomics, and metabolic inhibitors to discover metabolic differences between various pluripotent stem cell states and infer their impact on stem cell fate decisions. Keywords: systems biology, stem cell biology, metabolism, genome-scale modeling, pluripotency, histone methylation, naive (ground state, primed state, cell fate, metabolic network

  19. Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes

    DEFF Research Database (Denmark)

    Zelezniak, Aleksej; Pers, Tune Hannes; Pinho Soares, Simao Pedro

    2010-01-01

    mechanisms underlying these transcriptional changes and their impact on the cellular metabolic phenotype is a challenging task due to the complexity of transcriptional regulation and the highly interconnected nature of the metabolic network. In this study we integrate skeletal muscle gene expression datasets...... with human metabolic network reconstructions to identify key metabolic regulatory features of T2DM. These features include reporter metabolites—metabolites with significant collective transcriptional response in the associated enzyme-coding genes, and transcription factors with significant enrichment...... factor regulatory network connecting several parts of metabolism. The identified transcription factors include members of the CREB, NRF1 and PPAR family, among others, and represent regulatory targets for further experimental analysis. Overall, our results provide a holistic picture of key metabolic...

  20. Polyethylenimine architecture-dependent metabolic imprints and perturbation of cellular redox homeostasis

    DEFF Research Database (Denmark)

    Hall, Arnaldur; Parhamifar, Ladan; Lange, Marina Krarup

    2015-01-01

    demonstrate that the central mechanisms of PEI architecture- and size-dependent perturbations of integrated cellular metabolomics involve destabilization of plasma membrane and mitochondrial membranes with consequences on mitochondrial oxidative phosphorylation (OXPHOS), glycolytic flux and redox homeostasis...... architectures caused a greater lactate dehydrogenase (LDH) and ATP depletion, activated AMP kinase (AMPK) and disturbed redox homeostasis through diminished availability of nicotinamide adenine dinucleotide phosphate (NADPH), reduced antioxidant capacity of glutathione (GSH) and increased burden of reactive...

  1. eQTL Networks Reveal Complex Genetic Architecture in the Immature Soybean Seed

    Directory of Open Access Journals (Sweden)

    Yung-Tsi Bolon

    2014-03-01

    Full Text Available The complex network of regulatory factors and interactions involved in transcriptional regulation within the seed is not well understood. To evaluate gene expression regulation in the immature seed, we utilized a genetical genomics approach on a soybean [ (L. Merr.] recombinant inbred line (RIL population and produced a genome-wide expression quantitative trait loci (eQTL dataset. The validity of the dataset was confirmed by mapping the eQTL hotspot for flavonoid biosynthesis-related genes to a region containing repeats of chalcone synthase (CHS genes known to correspond to the soybean inhibitor locus that regulates seed color. We then identified eQTL for genes with seed-specific expression and discovered striking eQTL hotspots at distinct genomic intervals on chromosomes (Chr 20, 7, and 13. The main eQTL hotspot for transcriptional regulation of fatty acid biosynthesis genes also coincided with regulation of oleosin genes. Transcriptional upregulation of genesets from eQTL with opposite allelic effects were also found. Gene–eQTL networks were constructed and candidate regulatory genes were identified from these three key loci specific to seed expression and enriched in genes involved in seed oil accumulation. Our data provides new insight into the complex nature of gene networks in the immature soybean seed and the genetic architecture that contributes to seed development.

  2. REAL-TIME VIDEO SCALING BASED ON CONVOLUTION NEURAL NETWORK ARCHITECTURE

    Directory of Open Access Journals (Sweden)

    S Safinaz

    2017-08-01

    Full Text Available In recent years, video super resolution techniques becomes mandatory requirements to get high resolution videos. Many super resolution techniques researched but still video super resolution or scaling is a vital challenge. In this paper, we have presented a real-time video scaling based on convolution neural network architecture to eliminate the blurriness in the images and video frames and to provide better reconstruction quality while scaling of large datasets from lower resolution frames to high resolution frames. We compare our outcomes with multiple exiting algorithms. Our extensive results of proposed technique RemCNN (Reconstruction error minimization Convolution Neural Network shows that our model outperforms the existing technologies such as bicubic, bilinear, MCResNet and provide better reconstructed motioning images and video frames. The experimental results shows that our average PSNR result is 47.80474 considering upscale-2, 41.70209 for upscale-3 and 36.24503 for upscale-4 for Myanmar dataset which is very high in contrast to other existing techniques. This results proves our proposed model real-time video scaling based on convolution neural network architecture’s high efficiency and better performance.

  3. Structural architecture supports functional organization in the human aging brain at a regionwise and network level.

    Science.gov (United States)

    Zimmermann, Joelle; Ritter, Petra; Shen, Kelly; Rothmeier, Simon; Schirner, Michael; McIntosh, Anthony R

    2016-07-01

    Functional interactions in the brain are constrained by the underlying anatomical architecture, and structural and functional networks share network features such as modularity. Accordingly, age-related changes of structural connectivity (SC) may be paralleled by changes in functional connectivity (FC). We provide a detailed qualitative and quantitative characterization of the SC-FC coupling in human aging as inferred from resting-state blood oxygen-level dependent functional magnetic resonance imaging and diffusion-weighted imaging in a sample of 47 adults with an age range of 18-82. We revealed that SC and FC decrease with age across most parts of the brain and there is a distinct age-dependency of regionwise SC-FC coupling and network-level SC-FC relations. A specific pattern of SC-FC coupling predicts age more reliably than does regionwise SC or FC alone (r = 0.73, 95% CI = [0.7093, 0.8522]). Hence, our data propose that regionwise SC-FC coupling can be used to characterize brain changes in aging. Hum Brain Mapp 37:2645-2661, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  4. The probabilistic neural network architecture for high speed classification of remotely sensed imagery

    Science.gov (United States)

    Chettri, Samir R.; Cromp, Robert F.

    1993-01-01

    In this paper we discuss a neural network architecture (the Probabilistic Neural Net or the PNN) that, to the best of our knowledge, has not previously been applied to remotely sensed data. The PNN is a supervised non-parametric classification algorithm as opposed to the Gaussian maximum likelihood classifier (GMLC). The PNN works by fitting a Gaussian kernel to each training point. The width of the Gaussian is controlled by a tuning parameter called the window width. If very small widths are used, the method is equivalent to the nearest neighbor method. For large windows, the PNN behaves like the GMLC. The basic implementation of the PNN requires no training time at all. In this respect it is far better than the commonly used backpropagation neural network which can be shown to take O(N6) time for training where N is the dimensionality of the input vector. In addition the PNN can be implemented in a feed forward mode in hardware. The disadvantage of the PNN is that it requires all the training data to be stored. Some solutions to this problem are discussed in the paper. Finally, we discuss the accuracy of the PNN with respect to the GMLC and the backpropagation neural network (BPNN). The PNN is shown to be better than GMLC and not as good as the BPNN with regards to classification accuracy.

  5. Network Analysis and Application Control Software based on Client-Server Architecture

    Science.gov (United States)

    Mohan, Ramya

    2013-04-01

    This paper outlines a comprehensive model to increase system efficiency, preserve network bandwidth, monitor incoming and outgoing packets, ensure the security of confidential files and reduce power wastage in an organization. This model illustrates the use and potential application of a Network Analysis Tool (NAT) in a multi-computer set-up of any scale. The model is designed to run in the background and not hamper any currently executing applications, while using minimum system resources. It was developed as open source software, using VB. Net, with a view to overcoming limitations of legacy systems and financial restrictions in small-to mid-level organizations like businesses and educational institutes. It is fully-customizable and serves as a simple and open-source alternative to existing software. The NAT relies on simple client-server architecture and uses remote access to monitor and maintain the computers on a network, for example logging off a user or shutting down a computer after a certain "idle" time, enabling and disabling applications, troubleshooting and so on. The NAT was tested in a laboratory and resultant data is presented, along with the results of a survey that was conducted among users.

  6. Next Generation RFID-Based Medical Service Management System Architecture in Wireless Sensor Network

    Science.gov (United States)

    Tolentino, Randy S.; Lee, Kijeong; Kim, Yong-Tae; Park, Gil-Cheol

    Radio Frequency Identification (RFID) and Wireless Sensor Network (WSN) are two important wireless technologies that have wide variety of applications and provide unlimited future potentials most especially in healthcare systems. RFID is used to detect presence and location of objects while WSN is used to sense and monitor the environment. Integrating RFID with WSN not only provides identity and location of an object but also provides information regarding the condition of the object carrying the sensors enabled RFID tag. However, there isn't any flexible and robust communication infrastructure to integrate these devices into an emergency care setting. An efficient wireless communication substrate for medical devices that addresses ad hoc or fixed network formation, naming and discovery, transmission efficiency of data, data security and authentication, as well as filtration and aggregation of vital sign data need to be study and analyze. This paper proposed an efficient next generation architecture for RFID-based medical service management system in WSN that possesses the essential elements of each future medical application that are integrated with existing medical practices and technologies in real-time, remote monitoring, in giving medication, and patient status tracking assisted by embedded wearable wireless sensors which are integrated in wireless sensor network.

  7. Exploiting complexity and the robustness of network architecture for drug discovery.

    Science.gov (United States)

    Hellerstein, Marc K

    2008-04-01

    The issue of complexity stands at the center of contemporary drug discovery and development. The central problem in drug development today is attrition of drug candidates identified by the modern molecular target-based discovery approach, due to two related features of complex metabolic networks: their fundamentally unpredictable response to targeted interventions and their "robustness" (tendency to maintain stable function in the face of internal or external perturbations). Complexity and adaptations are, therefore, generally seen as obstacles to drug discovery. Here, the converse proposition is presented-that the complexity and adaptive responses of highly interconnected metabolic networks can be exploited for therapeutic discovery. Unanticipated connectivity relationships may result in "off-target" changes in metabolic fluxes, leading to unexpected therapeutic actions of agents. Exploiting this approach requires that fully assembled living systems (in vivo models) be studied and that informative in vivo biomarkers of the activity of biochemical pathways responsible for disease be available. These biomarkers should be sensitive, predictive of functional endpoints, and have high enough throughput for efficient screening of large numbers of agents. To the extent that such biomarkers unambiguously reflect the activity of pathways that mediate disease or therapeutic response (i.e., are "authentic"), their utility will be increased. Examples are presented of pathway-based screening of approved drugs for unexpected actions. Results support the principle that agents that have one action typically have many actions, including unanticipated actions, reflecting connectivity relationships of complex networks. Pathway-based screening in vivo represents an alternative to the high attrition of the molecular target-based discovery paradigm.

  8. A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks.

    Science.gov (United States)

    Merlet, Benjamin; Paulhe, Nils; Vinson, Florence; Frainay, Clément; Chazalviel, Maxime; Poupin, Nathalie; Gloaguen, Yoann; Giacomoni, Franck; Jourdan, Fabien

    2016-01-01

    This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc) and flat file formats (SBML and Matlab files). We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics) and Glasgow Polyomics (GP) on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks. In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks. In order to achieve this goal, we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.

  9. Co-regulation of metabolic genes is better explained by flux coupling than by network distance.

    Directory of Open Access Journals (Sweden)

    Richard A Notebaart

    2008-01-01

    Full Text Available To what extent can modes of gene regulation be explained by systems-level properties of metabolic networks? Prior studies on co-regulation of metabolic genes have mainly focused on graph-theoretical features of metabolic networks and demonstrated a decreasing level of co-expression with increasing network distance, a naïve, but widely used, topological index. Others have suggested that static graph representations can poorly capture dynamic functional associations, e.g., in the form of dependence of metabolic fluxes across genes in the network. Here, we systematically tested the relative importance of metabolic flux coupling and network position on gene co-regulation, using a genome-scale metabolic model of Escherichia coli. After validating the computational method with empirical data on flux correlations, we confirm that genes coupled by their enzymatic fluxes not only show similar expression patterns, but also share transcriptional regulators and frequently reside in the same operon. In contrast, we demonstrate that network distance per se has relatively minor influence on gene co-regulation. Moreover, the type of flux coupling can explain refined properties of the regulatory network that are ignored by simple graph-theoretical indices. Our results underline the importance of studying functional states of cellular networks to define physiologically relevant associations between genes and should stimulate future developments of novel functional genomic tools.

  10. Computational solution to automatically map metabolite libraries in the context of genome scale metabolic networks

    Directory of Open Access Journals (Sweden)

    Benjamin eMerlet

    2016-02-01

    Full Text Available This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc and flat file formats (SBML and Matlab files. We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics and Glasgow Polyomics on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks.In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks.In order to achieve this goal we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.

  11. QoS Management and Control for an All-IP WiMAX Network Architecture: Design, Implementation and Evaluation

    Directory of Open Access Journals (Sweden)

    Thomas Michael Bohnert

    2008-01-01

    Full Text Available The IEEE 802.16 standard provides a specification for a fixed and mobile broadband wireless access system, offering high data rate transmission of multimedia services with different Quality-of-Service (QoS requirements through the air interface. The WiMAX Forum, going beyond the air interface, defined an end-to-end WiMAX network architecture, based on an all-IP platform in order to complete the standards required for a commercial rollout of WiMAX as broadband wireless access solution. As the WiMAX network architecture is only a functional specification, this paper focuses on an innovative solution for an end-to-end WiMAX network architecture offering in compliance with the WiMAX Forum specification. To our best knowledge, this is the first WiMAX architecture built by a research consortium globally and was performed within the framework of the European IST project WEIRD (WiMAX Extension to Isolated Research Data networks. One of the principal features of our architecture is support for end-to-end QoS achieved by the integration of resource control in the WiMAX wireless link and the resource management in the wired domains in the network core. In this paper we present the architectural design of these QoS features in the overall WiMAX all-IP framework and their functional as well as performance evaluation. The presented results can safely be considered as unique and timely for any WiMAX system integrator.

  12. Development of an ease-of-use remote healthcare system architecture using RFID and networking technologies.

    Science.gov (United States)

    Lin, Shih-Sung; Hung, Min-Hsiung; Tsai, Chang-Lung; Chou, Li-Ping

    2012-12-01

    The study aims to provide an ease-of-use approach for senior patients to utilize remote healthcare systems. An ease-of-use remote healthcare system (RHS) architecture using RFID (Radio Frequency Identification) and networking technologies is developed. Specifically, the codes in RFID tags are used for authenticating the patients' ID to secure and ease the login process. The patient needs only to take one action, i.e. placing a RFID tag onto the reader, to automatically login and start the RHS and then acquire automatic medical services. An ease-of-use emergency monitoring and reporting mechanism is developed as well to monitor and protect the safety of the senior patients who have to be left alone at home. By just pressing a single button, the RHS can automatically report the patient's emergency information to the clinic side so that the responsible medical personnel can take proper urgent actions for the patient. Besides, Web services technology is used to build the Internet communication scheme of the RHS so that the interoperability and data transmission security between the home server and the clinical server can be enhanced. A prototype RHS is constructed to validate the effectiveness of our designs. Testing results show that the proposed RHS architecture possesses the characteristics of ease to use, simplicity to operate, promptness in login, and no need to preserve identity information. The proposed RHS architecture can effectively increase the willingness of senior patients who act slowly or are unfamiliar with computer operations to use the RHS. The research results can be used as an add-on for developing future remote healthcare systems.

  13. Review of metabolic pathways activated in cancer cells as determined through isotopic labeling and network analysis.

    Science.gov (United States)

    Dong, Wentao; Keibler, Mark A; Stephanopoulos, Gregory

    2017-09-01

    Cancer metabolism has emerged as an indispensable part of contemporary cancer research. During the past 10 years, the use of stable isotopic tracers and network analysis have unveiled a number of metabolic pathways activated in cancer cells. Here, we review such pathways along with the particular tracers and labeling observations that led to the discovery of their rewiring in cancer cells. The list of such pathways comprises the reductive metabolism of glutamine, altered glycolysis, serine and glycine metabolism, mutant isocitrate dehydrogenase (IDH) induced reprogramming and the onset of acetate metabolism. Additionally, we demonstrate the critical role of isotopic labeling and network analysis in identifying these pathways. The alterations described in this review do not constitute a complete list, and future research using these powerful tools is likely to discover other cancer-related pathways and new metabolic targets for cancer therapy. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  14. Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks

    DEFF Research Database (Denmark)

    Brochado, Ana Rita; Andrejev, Sergej; Maranas, Costas D.

    2012-01-01

    Genome-scale metabolic networks provide a comprehensive structural framework for modeling genotype-phenotype relationships through flux simulations. The solution space for the metabolic flux state of the cell is typically very large and optimization-based approaches are often necessary for predic......Genome-scale metabolic networks provide a comprehensive structural framework for modeling genotype-phenotype relationships through flux simulations. The solution space for the metabolic flux state of the cell is typically very large and optimization-based approaches are often necessary...

  15. Trade-offs between efficiency and robustness in bacterial metabolic networks are associated with niche breadth.

    Science.gov (United States)

    Morine, Melissa J; Gu, Hong; Myers, Ransom A; Bielawski, Joseph P

    2009-05-01

    The relation between structure and function in biologic networks is a central point of systems biology research. Key functional features--notably, efficiency and robustness--are linked to the topologic structure of a network, and there appears to be a degree of trade-off between these features, i.e., simulation studies indicate that more efficient networks tend to be less robust. Here, we investigate this issue in metabolic networks from 105 lineages of bacteria having a wide range of ecologies. We take quantitative measurements on each network and integrate this network data with ecologic data using a phylogenetic comparative model. In this setting, we find that biologic conclusions obtained with classical phylogenetic comparative methods are sensitive to correlations between model covariates and phylogenetic branch length. To avoid this problem, we propose a revised statistical framework--hierarchical mixed-effect regression--to accommodate phylogenetic nonindependence. Using this approach, we show that the cartography of metabolic networks does indeed reflect a trade-off between efficiency and robustness. Furthermore, ecologic characteristics related to niche breadth are strong predictors of network shape. Given the broad variation in niche breadth seen among species, we predict that there is no universally optimal balance between efficiency and robustness in bacterial metabolic networks and, thus, no universally optimal network structure. These results highlight the biologic relevance of variation in network structure and the potential role of niche breadth in shaping metabolic strategies of efficiency and robustness.

  16. Historical Building Monitoring Using an Energy-Efficient Scalable Wireless Sensor Network Architecture

    Directory of Open Access Journals (Sweden)

    Alberto Bonastre

    2011-10-01

    Full Text Available We present a set of novel low power wireless sensor nodes designed for monitoring wooden masterpieces and historical buildings, in order to perform an early detection of pests. Although our previous star-based system configuration has been in operation for more than 13 years, it does not scale well for sensorization of large buildings or when deploying hundreds of nodes. In this paper we demonstrate the feasibility of a cluster-based dynamic-tree hierarchical Wireless Sensor Network (WSN architecture where realistic assumptions of radio frequency data transmission are applied to cluster construction, and a mix of heterogeneous nodes are used to minimize economic cost of the whole system and maximize power saving of the leaf nodes. Simulation results show that the specialization of a fraction of the nodes by providing better antennas and some energy harvesting techniques can dramatically extend the life of the entire WSN and reduce the cost of the whole system. A demonstration of the proposed architecture with a new routing protocol and applied to termite pest detection has been implemented on a set of new nodes and should last for about 10 years, but it provides better scalability, reliability and deployment properties.

  17. Developmental gene regulatory network architecture across 500 million years of echinoderm evolution

    Science.gov (United States)

    Hinman, Veronica F.; Nguyen, Albert T.; Cameron, R. Andrew; Davidson, Eric H.

    2003-01-01

    Evolutionary change in morphological features must depend on architectural reorganization of developmental gene regulatory networks (GRNs), just as true conservation of morphological features must imply retention of ancestral developmental GRN features. Key elements of the provisional GRN for embryonic endomesoderm development in the sea urchin are here compared with those operating in embryos of a distantly related echinoderm, a starfish. These animals diverged from their common ancestor 520-480 million years ago. Their endomesodermal fate maps are similar, except that sea urchins generate a skeletogenic cell lineage that produces a prominent skeleton lacking entirely in starfish larvae. A relevant set of regulatory genes was isolated from the starfish Asterina miniata, their expression patterns determined, and effects on the other genes of perturbing the expression of each were demonstrated. A three-gene feedback loop that is a fundamental feature of the sea urchin GRN for endoderm specification is found in almost identical form in the starfish: a detailed element of GRN architecture has been retained since the Cambrian Period in both echinoderm lineages. The significance of this retention is highlighted by the observation of numerous specific differences in the GRN connections as well. A regulatory gene used to drive skeletogenesis in the sea urchin is used entirely differently in the starfish, where it responds to endomesodermal inputs that do not affect it in the sea urchin embryo. Evolutionary changes in the GRNs since divergence are limited sharply to certain cis-regulatory elements, whereas others have persisted unaltered.

  18. Seafloor classification using artificial neural network architecture from central western continental shelf of India

    Science.gov (United States)

    Mahale, Vasudev; Chakraborty, Bishwajit; Navelkar, Gajanan S.; Prabhu Desai, R. G.

    2005-04-01

    Seafloor classification studies are carried out at the central western continental shelf of India employing two frequency normal incidence single beam echo-sounder backscatter data. Echo waveform data from different seafloor sediment areas are utilized for present study. Three artificial neural network (ANN) architectures, e.g., Self-Organization Feature Maps (SOFM), Multi-Layer Perceptron (MLP), and Learning Vector Quantization (LVQ) are applied for seafloor classifications. In case of MLP, features are extracted from the received echo signal, on the basis of which, classification is carried out. In the case of the SOFM, a simple moving average echo waveform pre-processing technique is found to yield excellent classification results. Finally, LVQ, which is known as ANN of hybrid architecture is found to be the efficient seafloor classifier especially from the point of view of the real-time application. The simultaneously acquired sediment sample, multi-beam bathymetry and side scan sonar and echo waveform based seafloor classifications results are indicative of the depositional (inner shelf), non-depositional or erosion (outer shelf) environment and combination of both in the transition zone. [Work supported by DIT.

  19. Deep learning architecture for iris recognition based on optimal Gabor filters and deep belief network

    Science.gov (United States)

    He, Fei; Han, Ye; Wang, Han; Ji, Jinchao; Liu, Yuanning; Ma, Zhiqiang

    2017-03-01

    Gabor filters are widely utilized to detect iris texture information in several state-of-the-art iris recognition systems. However, the proper Gabor kernels and the generative pattern of iris Gabor features need to be predetermined in application. The traditional empirical Gabor filters and shallow iris encoding ways are incapable of dealing with such complex variations in iris imaging including illumination, aging, deformation, and device variations. Thereby, an adaptive Gabor filter selection strategy and deep learning architecture are presented. We first employ particle swarm optimization approach and its binary version to define a set of data-driven Gabor kernels for fitting the most informative filtering bands, and then capture complex pattern from the optimal Gabor filtered coefficients by a trained deep belief network. A succession of comparative experiments validate that our optimal Gabor filters may produce more distinctive Gabor coefficients and our iris deep representations be more robust and stable than traditional iris Gabor codes. Furthermore, the depth and scales of the deep learning architecture are also discussed.

  20. Historical building monitoring using an energy-efficient scalable wireless sensor network architecture.

    Science.gov (United States)

    Capella, Juan V; Perles, Angel; Bonastre, Alberto; Serrano, Juan J

    2011-01-01

    We present a set of novel low power wireless sensor nodes designed for monitoring wooden masterpieces and historical buildings, in order to perform an early detection of pests. Although our previous star-based system configuration has been in operation for more than 13 years, it does not scale well for sensorization of large buildings or when deploying hundreds of nodes. In this paper we demonstrate the feasibility of a cluster-based dynamic-tree hierarchical Wireless Sensor Network (WSN) architecture where realistic assumptions of radio frequency data transmission are applied to cluster construction, and a mix of heterogeneous nodes are used to minimize economic cost of the whole system and maximize power saving of the leaf nodes. Simulation results show that the specialization of a fraction of the nodes by providing better antennas and some energy harvesting techniques can dramatically extend the life of the entire WSN and reduce the cost of the whole system. A demonstration of the proposed architecture with a new routing protocol and applied to termite pest detection has been implemented on a set of new nodes and should last for about 10 years, but it provides better scalability, reliability and deployment properties.

  1. Monitoring Architectural Heritage by Wireless Sensors Networks: San Gimignano — A Case Study

    Science.gov (United States)

    Mecocci, Alessandro; Abrardo, Andrea

    2014-01-01

    This paper describes a wireless sensor network (WSN) used to monitor the health state of architectural heritage in real-time. The WSN has been deployed and tested on the “Rognosa” tower in the medieval village of San Gimignano, Tuscany, Italy. This technology, being non-invasive, mimetic, and long lasting, is particularly well suited for long term monitoring and on-line diagnosis of the conservation state of heritage buildings. The proposed monitoring system comprises radio-equipped nodes linked to suitable sensors capable of monitoring crucial parameters like: temperature, humidity, masonry cracks, pouring rain, and visual light. The access to data is granted by a user interface for remote control. The WSN can autonomously send remote alarms when predefined thresholds are reached. PMID:24394600

  2. Control Architecture for Intentional Island Operation in Distribution Network with High Penetration of Distributed Generation

    DEFF Research Database (Denmark)

    Chen, Yu

    Currently, a high penetration level of Distributed Generations (DGs), such as Wind Turbines (WTs) and Combined Heat and Power plants (CHPs), has been observed in the Danish distribution systems, and even more DGs are foreseen to be present in the coming years. With adequate DGs available, how...... amount of DGs. As part of the NextGen project, this project focuses on the system modeling and simulation regarding the control architecture and recommends the development of a communication and information exchange system based on IEC 61850. This thesis starts with the background of this PhD project......, the feasibility of the application of Artificial Neural Network (ANN) to ICA is studied, in order to improve the computation efficiency for ISR calculation. Finally, the integration of ICA into Dynamic Security Assessment (DSA), the ICA implementation, and the development of ICA are discussed....

  3. Addressing unknown constants and metabolic network behaviors through petascale computing: understanding H2 production in green algae

    International Nuclear Information System (INIS)

    Chang, Christopher; Alber, David; Graf, Peter; Kim, Kwiseon; Seibert, Michael

    2007-01-01

    The Genomics Revolution has resulted in a massive and growing quantity of whole-genome DNA sequences, which encode the metabolic catalysts necessary for life. However, gene annotations can rarely be complete, and measurement of the kinetic constants associated with the encoded enzymes can not possibly keep pace, necessitating the use of careful modeling to explore plausible network behaviors. Key challenges are (1) quantitatively formulating kinetic laws governing each transformation in a fixed model network; (2) characterizing the stable solution (if any) of the associated ordinary differential equations (ODEs); (3) fitting the latter to metabolomics data as it becomes available; and (4) optimizing a model output against the possible space of kinetic parameters, with respect to properties such as robustness of network response, or maximum consumption/production. This SciDAC-2 project addresses this large-scale uncertainty in the genome-scale metabolic network of the water-splitting, H 2 -producing green alga Chlamydomonas reinhardtii. Each metabolic transformation is formulated as an irreversible steady-state process, such that the vast literature on known enzyme mechanisms may be incorporated directly. To start, glycolysis, the tricarboxylic acid cycle, and basic fermentation pathways have been encoded in Systems Biology Markup Language (SBML) with careful annotation and consistency with the KEGG database, yielding a model with 3 compartments, 95 species, 38 reactions, and 109 kinetic constants. To study and optimize such models with a view toward larger models, we have developed a system which takes as input an SBML model, and automatically produces C code that when compiled and executed optimizes the model's kinetic parameters according to test criteria. We describe the system and present numerical results. Further development, including overlaying of a parallel multistart algorithm, will allow optimization of thousands of parameters on high-performance systems

  4. Metabolic networks of Sodalis glossinidius: a systems biology approach to reductive evolution.

    Science.gov (United States)

    Belda, Eugeni; Silva, Francisco J; Peretó, Juli; Moya, Andrés

    2012-01-01

    Genome reduction is a common evolutionary process affecting bacterial lineages that establish symbiotic or pathogenic associations with eukaryotic hosts. Such associations yield highly reduced genomes with greatly streamlined metabolic abilities shaped by the type of ecological association with the host. Sodalis glossinidius, the secondary endosymbiont of tsetse flies, represents one of the few complete genomes available of a bacterium at the initial stages of this process. In the present study, genome reduction is studied from a systems biology perspective through the reconstruction and functional analysis of genome-scale metabolic networks of S. glossinidius. The functional profile of ancestral and extant metabolic networks sheds light on the evolutionary events underlying transition to a host-dependent lifestyle. Meanwhile, reductive evolution simulations on the extant metabolic network can predict possible future evolution of S. glossinidius in the context of genome reduction. Finally, knockout simulations in different metabolic systems reveal a gradual decrease in network robustness to different mutational events for bacterial endosymbionts at different stages of the symbiotic association. Stoichiometric analysis reveals few gene inactivation events whose effects on the functionality of S. glossinidius metabolic systems are drastic enough to account for the ecological transition from a free-living to host-dependent lifestyle. The decrease in network robustness across different metabolic systems may be associated with the progressive integration in the more stable environment provided by the insect host. Finally, reductive evolution simulations reveal the strong influence that external conditions exert on the evolvability of metabolic systems.

  5. Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites.

    Science.gov (United States)

    Hadadi, Noushin; Hafner, Jasmin; Soh, Keng Cher; Hatzimanikatis, Vassily

    2017-01-01

    Reaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely available in the literature. The understanding of metabolic pathways at the atomic level is of great importance as it can deconvolute the overlapping catabolic/anabolic pathways resulting in the observed metabolic phenotype. The automated identification of atom transitions within a metabolic network is a very challenging task since the degree of complexity of metabolic networks dramatically increases when we transit from metabolite-level studies to atom-level studies. Despite being studied extensively in various approaches, the field of atom mapping of metabolic networks is lacking an automated approach, which (i) accounts for the information of reaction mechanism for atom mapping and (ii) is extendable from individual atom-mapped reactions to atom-mapped reaction networks. Hereby, we introduce a computational framework, iAM.NICE (in silico Atom Mapped Network Integrated Computational Explorer), for the systematic atom-level reconstruction of metabolic networks from in silico labelled substrates. iAM.NICE is to our knowledge the first automated atom-mapping algorithm that is based on the underlying enzymatic biotransformation mechanisms, and its application goes beyond individual reactions and it can be used for the reconstruction of atom-mapped metabolic networks. We illustrate the applicability of our method through the reconstruction of atom-mapped reactions of the KEGG database and we provide an example of an atom-level representation of the core metabolic network of E. coli. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. A comprehensive zero-copy architecture for high performance distributed Data Acquisition over advanced network technologies for the CMS experiment

    CERN Document Server

    Bauer, Gerry; Branson, James; Bukowiec, Sebastian Czeslaw; Chaze, Olivier; Cittolin, Sergio; Coarasa, J. A; Deldicque, Christian; Dobson, Marc; Dupont, Aymeric; Erhan, Samim; Gigi, Dominique; Glege, Frank; Gomez-Reino, R; Hartl, Christian; Holzner, Andre Georg; Masetti, Lorenzo; Meijers, Franciscus; Meschi, Emilio; Mommsen, Remigius; Nunez-Barranco, C; O'Dell, Vivian; Orsini, Luciano; Paus, Christoph Maria Ernst; Petrucci, Andrea; Pieri, Marco; Polese, Giovanni; Racz, Attila; Raginel, Olivier; Sakulin, Hannes; Sani, Matteo; Schwick, Christoph; Spataru, Andrei Cristian; Stoeckli, Fabian; Sumorok, Konstanty

    2013-01-01

    This paper outlines a software architecture where zero-copy operations are used comprehensively at every processing point from the Application layer to the Physical layer. The proposed architecture is being used during feasibility studies on advanced networking technologies for the CMS experiment at CERN. The design relies on a homogeneous peer-to-peer message passing system, which is built around memory pool caches allowing efficient and deterministic latency handling of messages of any size through the different software layers. In this scheme portable distributed applications can be programmed to process input to output operations by mere pointer arithmetic and DMA operations only. The approach combined with the open fabric protocol stack (OFED) allows one to attain near wire-speed message transfer at application level. The architecture supports full portability of user applications by encapsulating the protocol details and network into modular peer transport services whereas a transparent replacement of t...

  7. Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain.

    Science.gov (United States)

    Krienen, Fenna M; Yeo, B T Thomas; Ge, Tian; Buckner, Randy L; Sherwood, Chet C

    2016-01-26

    The human brain is patterned with disproportionately large, distributed cerebral networks that connect multiple association zones in the frontal, temporal, and parietal lobes. The expansion of the cortical surface, along with the emergence of long-range connectivity networks, may be reflected in changes to the underlying molecular architecture. Using the Allen Institute's human brain transcriptional atlas, we demonstrate that genes particularly enriched in supragranular layers of the human cerebral cortex relative to mouse distinguish major cortical classes. The topography of transcriptional expression reflects large-scale brain network organization consistent with estimates from functional connectivity MRI and anatomical tracing in nonhuman primates. Microarray expression data for genes preferentially expressed in human upper layers (II/III), but enriched only in lower layers (V/VI) of mouse, were cross-correlated to identify molecular profiles across the cerebral cortex of postmortem human brains (n = 6). Unimodal sensory and motor zones have similar molecular profiles, despite being distributed across the cortical mantle. Sensory/motor profiles were anticorrelated with paralimbic and certain distributed association network profiles. Tests of alternative gene sets did not consistently distinguish sensory and motor regions from paralimbic and association regions: (i) genes enriched in supragranular layers in both humans and mice, (ii) genes cortically enriched in humans relative to nonhuman primates, (iii) genes related to connectivity in rodents, (iv) genes associated with human and mouse connectivity, and (v) 1,454 gene sets curated from known gene ontologies. Molecular innovations of upper cortical layers may be an important component in the evolution of long-range corticocortical projections.

  8. Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation

    International Nuclear Information System (INIS)

    Çakır, Tunahan; Khatibipour, Mohammad Jafar

    2014-01-01

    The primary focus in the network-centric analysis of cellular metabolism by systems biology approaches is to identify the active metabolic network for the condition of interest. Two major approaches are available for the discovery of the condition-specific metabolic networks. One approach starts from genome-scale metabolic networks, which cover all possible reactions known to occur in the related organism in a condition-independent manner, and applies methods such as the optimization-based Flux-Balance Analysis to elucidate the active network. The other approach starts from the condition-specific metabolome data, and processes the data with statistical or optimization-based methods to extract information content of the data such that the active network is inferred. These approaches, termed bottom-up and top-down, respectively, are currently employed independently. However, considering that both approaches have the same goal, they can both benefit from each other paving the way for the novel integrative analysis methods of metabolome data- and flux-analysis approaches in the post-genomic era. This study reviews the strengths of constraint-based analysis and network inference methods reported in the metabolic systems biology field; then elaborates on the potential paths to reconcile the two approaches to shed better light on how the metabolism functions.

  9. Proceedings of the Second Software Architecture Technology User Network (SATURN) Workshop

    Science.gov (United States)

    2006-08-01

    architect for The Open Group Architecture Framework ( TOGAF ), Version 8.1, ATAM Evaluator (SEI), and Software Architecture Profes- 8 | CMU/SEI-2006-TR...quality attribute UML extensions − The DoDAF − The Object Management Group (OMG) − The Open Group Architecture Framework ( TOGAF ) • Describe tactics...Measurement and Analysis SOA service-oriented architecture SoS system of systems TIG Technical Interest Group TOGAF The Open Group Architecture

  10. An Architecture for Performance Optimization in a Collaborative Knowledge-Based Approach for  Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Juan Ramon Velasco

    2011-09-01

    Full Text Available Over the past few years, Intelligent Spaces (ISs have received the attention of many Wireless Sensor Network researchers. Recently, several studies have been devoted to identify their common capacities and to set up ISs over these networks. However, little attention has been paid to integrating Fuzzy Rule-Based Systems into collaborative Wireless Sensor Networks for the purpose of implementing ISs. This work presents a distributed architecture proposal for collaborative Fuzzy Rule-Based Systems embedded in Wireless Sensor Networks, which has been designed to optimize the implementation of ISs. This architecture includes the following: (a an optimized design for the inference engine; (b a visual interface; (c a module to reduce the redundancy and complexity of the knowledge bases; (d a module to evaluate the accuracy of the new knowledge base; (e a module to adapt the format of the rules to the structure used by the inference engine; and (f a communications protocol. As a real-world application of this architecture and the proposed methodologies, we show an application to the problem of modeling two plagues of the olive tree: prays (olive moth, Prays oleae Bern. and repilo (caused by the fungus Spilocaea oleagina. The results show that the architecture presented in this paper significantly decreases the consumption of resources (memory, CPU and battery without a substantial decrease in the accuracy of the inferred values.

  11. Metabolic network reconstruction, growth characterization and 13C-metabolic flux analysis of the extremophile Thermus thermophilus HB8.

    Science.gov (United States)

    Swarup, Aditi; Lu, Jing; DeWoody, Kathleen C; Antoniewicz, Maciek R

    2014-07-01

    Thermus thermophilus is an extremely thermophilic bacterium with significant biotechnological potential. In this work, we have characterized aerobic growth characteristics of T. thermophilus HB8 at temperatures between 50 and 85°C, constructed a metabolic network model of its central carbon metabolism and validated the model using (13)C-metabolic flux analysis ((13)C-MFA). First, cells were grown in batch cultures in custom constructed mini-bioreactors at different temperatures to determine optimal growth conditions. The optimal temperature for T. thermophilus grown on defined medium with glucose was 81°C. The maximum growth rate was 0.25h(-1). Between 50 and 81°C the growth rate increased by 7-fold and the temperature dependence was described well by an Arrhenius model with an activation energy of 47kJ/mol. Next, we performed a (13)C-labeling experiment with [1,2-(13)C] glucose as the tracer and calculated intracellular metabolic fluxes using (13)C-MFA. The results provided support for the constructed network model and highlighted several interesting characteristics of T. thermophilus metabolism. We found that T. thermophilus largely uses glycolysis and TCA cycle to produce biosynthetic precursors, ATP and reducing equivalents needed for cells growth. Consistent with its proposed metabolic network model, we did not detect any oxidative pentose phosphate pathway flux or Entner-Doudoroff pathway activity. The biomass precursors erythrose-4-phosphate and ribose-5-phosphate were produced via the non-oxidative pentose phosphate pathway, and largely via transketolase, with little contribution from transaldolase. The high biomass yield on glucose that was measured experimentally was also confirmed independently by (13)C-MFA. The results presented here provide a solid foundation for future studies of T. thermophilus and its metabolic engineering applications. Copyright © 2014 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  12. Abnormal functional architecture of amygdala-centered networks in adolescent posttraumatic stress disorder.

    Science.gov (United States)

    Aghajani, Moji; Veer, Ilya M; van Hoof, Marie-José; Rombouts, Serge A R B; van der Wee, Nic J; Vermeiren, Robert R J M

    2016-03-01

    Posttraumatic stress disorder (PTSD) is a prevalent, debilitating, and difficult to treat psychiatric disorder. Very little is known of how PTSD affects neuroplasticity in the developing adolescent brain. Whereas multiple lines of research implicate amygdala-centered network dysfunction in the pathophysiology of adult PTSD, no study has yet examined the functional architecture of amygdala subregional networks in adolescent PTSD. Using intrinsic functional connectivity analysis, we investigated functional connectivity of the basolateral (BLA) and centromedial (CMA) amygdala in 19 sexually abused adolescents with PTSD relative to 23 matched controls. Additionally, we examined whether altered amygdala subregional connectivity coincides with abnormal grey matter volume of the amygdaloid complex. Our analysis revealed abnormal amygdalar connectivity and morphology in adolescent PTSD patients. More specifically, PTSD patients showed diminished right BLA connectivity with a cluster including dorsal and ventral portions of the anterior cingulate and medial prefrontal cortices (p PTSD patients showed increased left CMA connectivity with a cluster including the orbitofrontal and subcallosal cortices (p PTSD. These findings provide unique insights into how perturbations in major amygdalar circuits could hamper fear regulation and drive excessive acquisition and expression of fear in PTSD. As such, they represent an important step toward characterizing the neurocircuitry of adolescent PTSD, thereby informing the development of reliable biomarkers and potential therapeutic targets. © 2016 Wiley Periodicals, Inc.

  13. Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions

    Directory of Open Access Journals (Sweden)

    Orth Jeffrey D

    2012-05-01

    Full Text Available Abstract Background The iJO1366 reconstruction of the metabolic network of Escherichia coli is one of the most complete and accurate metabolic reconstructions available for any organism. Still, because our knowledge of even well-studied model organisms such as this one is incomplete, this network reconstruction contains gaps and possible errors. There are a total of 208 blocked metabolites in iJO1366, representing gaps in the network. Results A new model improvement workflow was developed to compare model based phenotypic predictions to experimental data to fill gaps and correct errors. A Keio Collection based dataset of E. coli gene essentiality was obtained from literature data and compared to model predictions. The SMILEY algorithm was then used to predict the most likely missing reactions in the reconstructed network, adding reactions from a KEGG based universal set of metabolic reactions. The feasibility of these putative reactions was determined by comparing updated versions of the model to the experimental dataset, and genes were predicted for the most feasible reactions. Conclusions Numerous improvements to the iJO1366 metabolic reconstruction were suggested by these analyses. Experiments were performed to verify several computational predictions, including a new mechanism for growth on myo-inositol. The other predictions made in this study should be experimentally verifiable by similar means. Validating all of the predictions made here represents a substantial but important undertaking.

  14. A genome-scale metabolic network reconstruction of tomato (Solanum lycopersicum L.) and its application to photorespiratory metabolism.

    Science.gov (United States)

    Yuan, Huili; Cheung, C Y Maurice; Poolman, Mark G; Hilbers, Peter A J; van Riel, Natal A W

    2016-01-01

    Tomato (Solanum lycopersicum L.) has been studied extensively due to its high economic value in the market, and high content in health-promoting antioxidant compounds. Tomato is also considered as an excellent model organism for studying the development and metabolism of fleshy fruits. However, the growth, yield and fruit quality of tomatoes can be affected by drought stress, a common abiotic stress for tomato. To investigate the potential metabolic response of tomato plants to drought, we reconstructed iHY3410, a genome-scale metabolic model of tomato leaf, and used this metabolic network to simulate tomato leaf metabolism. The resulting model includes 3410 genes and 2143 biochemical and transport reactions distributed across five intracellular organelles including cytosol, plastid, mitochondrion, peroxisome and vacuole. The model successfully described the known metabolic behaviour of tomato leaf under heterotrophic and phototrophic conditions. The in silico investigation of the metabolic characteristics for photorespiration and other relevant metabolic processes under drought stress suggested that: (i) the flux distributions through the mevalonate (MVA) pathway under drought were distinct from that under normal conditions; and (ii) the changes in fluxes through core metabolic pathways with varying flux ratio of RubisCO carboxylase to oxygenase may contribute to the adaptive stress response of plants. In addition, we improved on previous studies of reaction essentiality analysis for leaf metabolism by including potential alternative routes for compensating reaction knockouts. Altogether, the genome-scale model provides a sound framework for investigating tomato metabolism and gives valuable insights into the functional consequences of abiotic stresses. © 2015 The Authors.The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

  15. Improving the description of metabolic networks: the TCA cycle as example

    NARCIS (Netherlands)

    Stobbe, Miranda D.; Houten, Sander M.; van Kampen, Antoine H. C.; Wanders, Ronald J. A.; Moerland, Perry D.

    2012-01-01

    To collect the ever-increasing yet scattered knowledge on metabolism, multiple pathway databases like the Kyoto Encyclopedia of Genes and Genomes have been created. A complete and accurate description of the metabolic network for human and other organisms is essential to foster new biological

  16. Success of Anomia Treatment in Aphasia Is Associated With Preserved Architecture of Global and Left Temporal Lobe Structural Networks.

    Science.gov (United States)

    Bonilha, Leonardo; Gleichgerrcht, Ezequiel; Nesland, Travis; Rorden, Chris; Fridriksson, Julius

    2016-03-01

    Targeted speech therapy can lead to substantial naming improvement in some subjects with anomia following dominant-hemisphere stroke. We investigated whether treatment-induced improvement in naming is associated with poststroke preservation of structural neural network architecture. Twenty-four patients with poststroke chronic aphasia underwent 30 hours of speech therapy over a 2-week period and were assessed at baseline and after therapy. Whole brain maps of neural architecture were constructed from pretreatment diffusion tensor magnetic resonance imaging to derive measures of global brain network architecture (network small-worldness) and regional network influence (nodal betweenness centrality). Their relationship with naming recovery was evaluated with multiple linear regressions. Treatment-induced improvement in correct naming was associated with poststroke preservation of global network small worldness and of betweenness centrality in temporal lobe cortical regions. Together with baseline aphasia severity, these measures explained 78% of the variability in treatment response. Preservation of global and left temporal structural connectivity broadly explains the variability in treatment-related naming improvement in aphasia. These findings corroborate and expand on previous classical lesion-symptom mapping studies by elucidating some of the mechanisms by which brain damage may relate to treated aphasia recovery. Favorable naming outcomes may result from the intact connections between spared cortical areas that are functionally responsive to treatment. © The Author(s) 2015.

  17. Metabolic network modeling approaches for investigating the "hungry cancer".

    Science.gov (United States)

    Sharma, Ashwini Kumar; König, Rainer

    2013-08-01

    Metabolism is the functional phenotype of a cell, at a given condition, resulting from an intricate interplay of various regulatory processes. The study of these dynamic metabolic processes and their capabilities help to identify the fundamental properties of living systems. Metabolic deregulation is an emerging hallmark of cancer cells. This deregulation results in rewiring of the metabolic circuitry conferring an exploitative metabolic advantage for the tumor cells which leads to a distinct benefit in survival and lays the basis for unbound progression. Metabolism can be considered as a thermodynamic open-system in which source substrates of high value are being processed through a well established interconnected biochemical conversion system, strictly obeying physiochemical principles, generating useful intermediates and finally resulting in the release of byproducts. Based on this basic principle of an input-output balance, various models have been developed to interrogate metabolism elucidating its underlying functional properties. However, only a few modeling approaches have proved computationally feasible in elucidating the metabolic nature of cancer at a systems level. Besides this, statistical approaches have been set up to identify biochemical pathways being more relevant for specific types of tumor cells. In this review, we are briefly introducing the basic statistical approaches followed by the major modeling concepts. We have put an emphasis on the methods and their applications that have been used to a greater extent in understanding the metabolic remodeling of cancer. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Coastal Ocean Observing Network - Open Source Architecture for Data Management and Web-Based Data Services

    Science.gov (United States)

    Pattabhi Rama Rao, E.; Venkat Shesu, R.; Udaya Bhaskar, T. V. S.

    2012-07-01

    The observations from the oceans are the backbone for any kind of operational services, viz. potential fishing zone advisory services, ocean state forecast, storm surges, cyclones, monsoon variability, tsunami, etc. Though it is important to monitor open Ocean, it is equally important to acquire sufficient data in the coastal ocean through coastal ocean observing systems for re-analysis, analysis and forecast of coastal ocean by assimilating different ocean variables, especially sub-surface information; validation of remote sensing data, ocean and atmosphere model/analysis and to understand the processes related to air-sea interaction and ocean physics. Accurate information and forecast of the state of the coastal ocean at different time scales is vital for the wellbeing of the coastal population as well as for the socio-economic development of the country through shipping, offshore oil and energy etc. Considering the importance of ocean observations in terms of understanding our ocean environment and utilize them for operational oceanography, a large number of platforms were deployed in the Indian Ocean including coastal observatories, to acquire data on ocean variables in and around Indian Seas. The coastal observation network includes HF Radars, wave rider buoys, sea level gauges, etc. The surface meteorological and oceanographic data generated by these observing networks are being translated into ocean information services through analysis and modelling. Centralized data management system is a critical component in providing timely delivery of Ocean information and advisory services. In this paper, we describe about the development of open-source architecture for real-time data reception from the coastal observation network, processing, quality control, database generation and web-based data services that includes on-line data visualization and data downloads by various means.

  19. Implementation of time synchronized cryogenics control system network architecture for SST-1

    Energy Technology Data Exchange (ETDEWEB)

    Patel, Rakesh J., E-mail: rpatel@ipr.res.in; Mahesuria, Gaurang; Panchal, Pradip; Panchal, Rohit; Sonara, Dasarath; Tanna, Vipul; Pradhan, Subrata

    2016-11-15

    Highlights: • SST-1 cryogenics sub-systems are 1.3 kW HRL, LN2 distribution system, current feeders system and 80 K booster system. • GUI developed in SCADA and control program developed in PLC for automation of the above sub-systems. • Implemented the cryogenics control system network to communicate all systems to InSQL server. • InSQL server configured for real time centralized process data acquisition from all connected sub-systems control nodes. • Acquired the process parameters coming from different systems at same time stamp. - Abstract: Under the SST-1 mission mandate, the several cryogenic sub-systems have been developed, upgraded and procured in prior to the SST-1 operation. New developments include 80 K Bubble type thermal shields, LN2 distribution system, LN2 booster system and current feeders system (CFS).Graphical User Interface (GUI) program developed in Wonderware SCADA and control logic program developed in Schneider make PLC for the above sub-systems. Industrial SQL server (InSQL) configured for centralized storage of real time process data coming from various control nodes of cryogenics sub-systems. The cryogenics control system network for communicating all cryogenics sub-system control nodes to InSQL server for centralized data storage and time synchronization among cryogenic sub-systems with centralized InSQL server is successfully implemented. Due to implemented time synchronization among sub-systems control nodes, it is possible to analyze the process parameters coming from different sub-systems at same time stamp. This paper describes the overview of implemented cryogenics control system network architecture for real time cryogenic process data monitor, storage and retrieval.

  20. Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network.

    Science.gov (United States)

    Galhardo, Mafalda; Sinkkonen, Lasse; Berninger, Philipp; Lin, Jake; Sauter, Thomas; Heinäniemi, Merja

    2014-02-01

    Metabolic diseases and comorbidities represent an ever-growing epidemic where multiple cell types impact tissue homeostasis. Here, the link between the metabolic and gene regulatory networks was studied through experimental and computational analysis. Integrating gene regulation data with a human metabolic network prompted the establishment of an open-sourced web portal, IDARE (Integrated Data Nodes of Regulation), for visualizing various gene-related data in context of metabolic pathways. Motivated by increasing availability of deep sequencing studies, we obtained ChIP-seq data from widely studied human umbilical vein endothelial cells. Interestingly, we found that association of metabolic genes with multiple transcription factors (TFs) enriched disease-associated genes. To demonstrate further extensions enabled by examining these networks together, constraint-based modeling was applied to data from human preadipocyte differentiation. In parallel, data on gene expression, genome-wide ChIP-seq profiles for peroxisome proliferator-activated receptor (PPAR) γ, CCAAT/enhancer binding protein (CEBP) α, liver X receptor (LXR) and H3K4me3 and microRNA target identification for miR-27a, miR-29a and miR-222 were collected. Disease-relevant key nodes, including mitochondrial glycerol-3-phosphate acyltransferase (GPAM), were exposed from metabolic pathways predicted to change activity by focusing on association with multiple regulators. In both cell types, our analysis reveals the convergence of microRNAs and TFs within the branched chain amino acid (BCAA) metabolic pathway, possibly providing an explanation for its downregulation in obese and diabetic conditions.

  1. Metabolic pathway of non-alcoholic fatty liver disease: Network properties and robustness

    Directory of Open Access Journals (Sweden)

    WenJun Zhang

    2017-03-01

    Full Text Available Nonalcoholic fatty liver disease (NAFLD is a systematic and complex disease involving various cytokines/metabolites. In present article, we use methodology of network biology to analyze network properties of NAFLD metabolic pathway. It is found that the metabolic pathway of NAFLD is not a typical complex network with power-law degree distribution, p(x=x^(-4.4275, x>=5. There is only one connected component in the metabolic pathway. The calculated cut cytokines/metabolites of the metabolic pathway are SREBP-1c, ChREBP, ObR, AMPK, IRE1alpha, ROS, PERK, elF2alpha, ATF4, CHOP, Bim, CASP8, Bid, CxII, Lipogenic enzymes, XBP1, and FFAs. The most important cytokine/metabolite for possible network robustness is FFAs, seconded by TNF-alpha. It is concluded that FFAs is the most important cytokine/metabolite in the metabolic pathway, seconded by ROS. FFAs, LEP, ACDC, CYP2E1, and Glucose are the only cytokines/metabolites that affect others without influences from other cytokines/metabolites. Finally, the IDs matrix for identifying possible sub-networks/modules is given. However, jointly combining the results of connectedness analysis and sub-networks/modules identification, we hold that there are not significant sub-networks/modules in the pathway.

  2. A self-organized artificial neural network architecture for sensory integration with applications to letter-phoneme integration.

    Science.gov (United States)

    Jantvik, Tamas; Gustafsson, Lennart; Papliński, Andrew P

    2011-08-01

    The multimodal self-organizing network (MMSON), an artificial neural network architecture carrying out sensory integration, is presented here. The architecture is designed using neurophysiological findings and imaging studies that pertain to sensory integration and consists of interconnected lattices of artificial neurons. In this artificial neural architecture, the degree of recognition of stimuli, that is, the perceived reliability of stimuli in the various subnetworks, is included in the computation. The MMSON's behavior is compared to aspects of brain function that deal with sensory integration. According to human behavioral studies, integration of signals from sensory receptors of different modalities enhances perception of objects and events and also reduces time to detection. In neocortex, integration takes place in bimodal and multimodal association areas and result, not only in feedback-mediated enhanced unimodal perception and shortened reaction time, but also in robust bimodal or multimodal percepts. Simulation data from the presented artificial neural network architecture show that it replicates these important psychological and neuroscientific characteristics of sensory integration.

  3. A CDMA Spotbeam Architecture for the Next Generation Satellite System (NGSS) for the Aeronautical Telecommunications Network (ATN)

    Science.gov (United States)

    Raghavan, Rajesh S.; Shamma, Mohammed A.

    2003-01-01

    This paper will present work being done to model and simulate a CDMA based Mobile Satellite System architecture for providing all or part of the future Air Traffic Management (ATM) services. Such a system, will help in relieving the dependence on ground based networks, if not eliminate it. Additionally such an architecture can be used in parallel or as a supplementary service along with ground based links to help alleviate any capacity bottlenecks, or in areas where such services are difficult to make available such as in oceanic, remote areas outside the jet highways, or in developing countries where ground services are less available.

  4. The Importance of Transition Metals in the Expanding Network of Microbial Metabolism in the Archean Eon

    Science.gov (United States)

    Moore, E. K.; Jelen, B. I.; Giovannelli, D.; Prabhu, A.; Raanan, H.; Falkowski, P. G.

    2017-12-01

    Deep time changes in Earth surface redox conditions, particularly due to global oxygenation, has impacted the availability of different metals and substrates that are central in biology. Oxidoreductase proteins are molecular nanomachines responsible for all biological electron transfer processes across the tree of life. These enzymes largely contain transition metals in their active sites. Microbial metabolic pathways form a global network of electron transfer, which expanded throughout the Archean eon. Older metabolisms (sulfur reduction, methanogenesis, anoxygenic photosynthesis) accessed negative redox potentials, while later evolving metabolisms (oxygenic photosynthesis, nitrification/denitrification, aerobic respiration) accessed positive redox potentials. The incorporation of different transition metals facilitated biological innovation and the expansion of the network of microbial metabolism. Network analysis was used to examine the connections between microbial taxa, metabolic pathways, crucial metallocofactors, and substrates in deep time by incorporating biosignatures preserved in the geologic record. Nitrogen fixation and aerobic respiration have the highest level of betweenness among metabolisms in the network, indicating that the oldest metabolisms are not the most central. Fe has by far the highest betweenness among metals. Clustering analysis largely separates High Metal Bacteria (HMB), Low Metal Bacteria (LMB), and Archaea showing that simple un-weighted links between taxa, metabolism, and metals have phylogenetic relevance. On average HMB have the highest betweenness among taxa, followed by Archaea and LMB. There is a correlation between the number of metallocofactors and metabolic pathways in representative bacterial taxa, but Archaea do not follow this trend. In many cases older and more recently evolved metabolisms were clustered together supporting previous findings that proliferation of metabolic pathways is not necessarily chronological.

  5. Analysis of normal human retinal vascular network architecture using multifractal geometry

    Directory of Open Access Journals (Sweden)

    Ştefan Ţălu

    2017-03-01

    Full Text Available AIM: To apply the multifractal analysis method as a quantitative approach to a comprehensive description of the microvascular network architecture of the normal human retina. METHODS: Fifty volunteers were enrolled in this study in the Ophthalmological Clinic of Cluj-Napoca, Romania, between January 2012 and January 2014. A set of 100 segmented and skeletonised human retinal images, corresponding to normal states of the retina were studied. An automatic unsupervised method for retinal vessel segmentation was applied before multifractal analysis. The multifractal analysis of digital retinal images was made with computer algorithms, applying the standard box-counting method. Statistical analyses were performed using the GraphPad InStat software. RESULTS: The architecture of normal human retinal microvascular network was able to be described using the multifractal geometry. The average of generalized dimensions (Dq for q=0, 1, 2, the width of the multifractal spectrum (Δα=αmax - αmin and the spectrum arms’ heights difference (│Δf│ of the normal images were expressed as mean±standard deviation (SD: for segmented versions, D0=1.7014±0.0057; D1=1.6507±0.0058; D2=1.5772±0.0059; Δα=0.92441±0.0085; │Δf│= 0.1453±0.0051; for skeletonised versions, D0=1.6303±0.0051; D1=1.6012±0.0059; D2=1.5531±0.0058; Δα=0.65032±0.0162; │Δf│= 0.0238±0.0161. The average of generalized dimensions (Dq for q=0, 1, 2, the width of the multifractal spectrum (Δα and the spectrum arms’ heights difference (│Δf│ of the segmented versions was slightly greater than the skeletonised versions. CONCLUSION: The multifractal analysis of fundus photographs may be used as a quantitative parameter for the evaluation of the complex three-dimensional structure of the retinal microvasculature as a potential marker for early detection of topological changes associated with retinal diseases.

  6. Adaptive Code Division Multiple Access Protocol for Wireless Network-on-Chip Architectures

    Science.gov (United States)

    Vijayakumaran, Vineeth

    Massive levels of integration following Moore's Law ushered in a paradigm shift in the way on-chip interconnections were designed. With higher and higher number of cores on the same die traditional bus based interconnections are no longer a scalable communication infrastructure. On-chip networks were proposed enabled a scalable plug-and-play mechanism for interconnecting hundreds of cores on the same chip. Wired interconnects between the cores in a traditional Network-on-Chip (NoC) system, becomes a bottleneck with increase in the number of cores thereby increasing the latency and energy to transmit signals over them. Hence, there has been many alternative emerging interconnect technologies proposed, namely, 3D, photonic and multi-band RF interconnects. Although they provide better connectivity, higher speed and higher bandwidth compared to wired interconnects; they also face challenges with heat dissipation and manufacturing difficulties. On-chip wireless interconnects is one other alternative proposed which doesn't need physical interconnection layout as data travels over the wireless medium. They are integrated into a hybrid NOC architecture consisting of both wired and wireless links, which provides higher bandwidth, lower latency, lesser area overhead and reduced energy dissipation in communication. However, as the bandwidth of the wireless channels is limited, an efficient media access control (MAC) scheme is required to enhance the utilization of the available bandwidth. This thesis proposes using a multiple access mechanism such as Code Division Multiple Access (CDMA) to enable multiple transmitter-receiver pairs to send data over the wireless channel simultaneously. It will be shown that such a hybrid wireless NoC with an efficient CDMA based MAC protocol can significantly increase the performance of the system while lowering the energy dissipation in data transfer. In this work it is shown that the wireless NoC with the proposed CDMA based MAC protocol

  7. Integrating data from biological experiments into metabolic networks with the DBE information system.

    Science.gov (United States)

    Borisjuk, Ljudmilla; Hajirezaei, Mohammad-Reza; Klukas, Christian; Rolletschek, Hardy; Schreiber, Falk

    2005-01-01

    Modern 'omics'-technologies result in huge amounts of data about life processes. For analysis and data mining purposes this data has to be considered in the context of the underlying biological networks. This work presents an approach for integrating data from biological experiments into metabolic networks by mapping the data onto network elements and visualising the data enriched networks automatically. This methodology is implemented in DBE, an information system that supports the analysis and visualisation of experimental data in the context of metabolic networks. It consists of five parts: (1) the DBE-Database for consistent data storage, (2) the Excel-Importer application for the data import, (3) the DBE-Website as the interface for the system, (4) the DBE-Pictures application for the up- and download of binary (e. g. image) files, and (5) DBE-Gravisto, a network analysis and graph visualisation system. The usability of this approach is demonstrated in two examples.

  8. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.

    Science.gov (United States)

    Herrgård, Markus J; Swainston, Neil; Dobson, Paul; Dunn, Warwick B; Arga, K Yalçin; Arvas, Mikko; Blüthgen, Nils; Borger, Simon; Costenoble, Roeland; Heinemann, Matthias; Hucka, Michael; Le Novère, Nicolas; Li, Peter; Liebermeister, Wolfram; Mo, Monica L; Oliveira, Ana Paula; Petranovic, Dina; Pettifer, Stephen; Simeonidis, Evangelos; Smallbone, Kieran; Spasić, Irena; Weichart, Dieter; Brent, Roger; Broomhead, David S; Westerhoff, Hans V; Kirdar, Betül; Penttilä, Merja; Klipp, Edda; Palsson, Bernhard Ø; Sauer, Uwe; Oliver, Stephen G; Mendes, Pedro; Nielsen, Jens; Kell, Douglas B

    2008-10-01

    Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.

  9. Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast.

    Science.gov (United States)

    Wang, Zhuo; Danziger, Samuel A; Heavner, Benjamin D; Ma, Shuyi; Smith, Jennifer J; Li, Song; Herricks, Thurston; Simeonidis, Evangelos; Baliga, Nitin S; Aitchison, John D; Price, Nathan D

    2017-05-01

    Gene regulatory and metabolic network models have been used successfully in many organisms, but inherent differences between them make networks difficult to integrate. Probabilistic Regulation Of Metabolism (PROM) provides a partial solution, but it does not incorporate network inference and underperforms in eukaryotes. We present an Integrated Deduced And Metabolism (IDREAM) method that combines statistically inferred Environment and Gene Regulatory Influence Network (EGRIN) models with the PROM framework to create enhanced metabolic-regulatory network models. We used IDREAM to predict phenotypes and genetic interactions between transcription factors and genes encoding metabolic activities in the eukaryote, Saccharomyces cerevisiae. IDREAM models contain many fewer interactions than PROM and yet produce significantly more accurate growth predictions. IDREAM consistently outperformed PROM using any of three popular yeast metabolic models and across three experimental growth conditions. Importantly, IDREAM's enhanced accuracy makes it possible to identify subtle synthetic growth defects. With experimental validation, these novel genetic interactions involving the pyruvate dehydrogenase complex suggested a new role for fatty acid-responsive factor Oaf1 in regulating acetyl-CoA production in glucose grown cells.

  10. Dead end metabolites--defining the known unknowns of the E. coli metabolic network.

    Directory of Open Access Journals (Sweden)

    Amanda Mackie

    Full Text Available The EcoCyc database is an online scientific database which provides an integrated view of the metabolic and regulatory network of the bacterium Escherichia coli K-12 and facilitates computational exploration of this important model organism. We have analysed the occurrence of dead end metabolites within the database--these are metabolites which lack the requisite reactions (either metabolic or transport that would account for their production or consumption within the metabolic network. 127 dead end metabolites were identified from the 995 compounds that are contained within the EcoCyc metabolic network. Their presence reflects either a deficit in our representation of the network or in our knowledge of E. coli metabolism. Extensive literature searches resulted in the addition of 38 transport reactions and 3 metabolic reactions to the database and led to an improved representation of the pathway for Vitamin B12 salvage. 39 dead end metabolites were identified as components of reactions that are not physiologically relevant to E. coli K-12--these reactions are properties of purified enzymes in vitro that would not be expected to occur in vivo. Our analysis led to improvements in the software that underpins the database and to the program that finds dead end metabolites within EcoCyc. The remaining dead end metabolites in the EcoCyc database likely represent deficiencies in our knowledge of E. coli metabolism.

  11. Bacterial metabolism in immediate response to nutritional perturbation with temporal and network view of metabolites.

    Science.gov (United States)

    Yukihira, Daichi; Fujimura, Yoshinori; Wariishi, Hiroyuki; Miura, Daisuke

    2015-09-01

    In this study, the initial propagation of metabolic perturbation in Escherichia coli was visualized to understand the dynamic characteristics of the metabolic pathways without the association of transcription alterations. E. coli cells were exposed to the sudden relief of glucose starvation, and time-dependent variances in metabolite balances were traced in the second scale. The acquired time-course data were represented by structural variations of the metabolite-metabolite correlation network. The initial correlation structure was altered immediately by the glucose pulse, followed by further structural variations within a few minutes. It was demonstrated that one metabolite temporally correlated with distinct metabolites with different timings, and such a behavior could imply a regulatory role for the metabolite in the metabolic network. Centrality analysis of the networks and partial correlation analysis indicated that preparation for growth and oxidative stress could be coupled as a structural property of the metabolic pathways.

  12. Characterization of the Usage of the Serine Metabolic Network in Human Cancer

    Directory of Open Access Journals (Sweden)

    Mahya Mehrmohamadi

    2014-11-01

    Full Text Available The serine, glycine, one-carbon (SGOC metabolic network is implicated in cancer pathogenesis, but its general functions are unknown. We carried out a computational reconstruction of the SGOC network and then characterized its expression across thousands of cancer tissues. Pathways including methylation and redox metabolism exhibited heterogeneous expression indicating a strong context dependency of their usage in tumors. From an analysis of coexpression, simultaneous up- or downregulation of nucleotide synthesis, NADPH, and glutathione synthesis was found to be a common occurrence in all cancers. Finally, we developed a method to trace the metabolic fate of serine using stable isotopes, high-resolution mass spectrometry, and a mathematical model. Although the expression of single genes didn’t appear indicative of flux, the collective expression of several genes in a given pathway allowed for successful flux prediction. Altogether, these findings identify expansive and heterogeneous functions for the SGOC metabolic network in human cancer.

  13. Parallel implementation of high-speed, phase diverse atmospheric turbulence compensation method on a neural network-based architecture

    Science.gov (United States)

    Arrasmith, William W.; Sullivan, Sean F.

    2008-04-01

    Phase diversity imaging methods work well in removing atmospheric turbulence and some system effects from predominantly near-field imaging systems. However, phase diversity approaches can be computationally intensive and slow. We present a recently adapted, high-speed phase diversity method using a conventional, software-based neural network paradigm. This phase-diversity method has the advantage of eliminating many time consuming, computationally heavy calculations and directly estimates the optical transfer function from the entrance pupil phases or phase differences. Additionally, this method is more accurate than conventional Zernike-based, phase diversity approaches and lends itself to implementation on parallel software or hardware architectures. We use computer simulation to demonstrate how this high-speed, phase diverse imaging method can be implemented on a parallel, highspeed, neural network-based architecture-specifically the Cellular Neural Network (CNN). The CNN architecture was chosen as a representative, neural network-based processing environment because 1) the CNN can be implemented in 2-D or 3-D processing schemes, 2) it can be implemented in hardware or software, 3) recent 2-D implementations of CNN technology have shown a 3 orders of magnitude superiority in speed, area, or power over equivalent digital representations, and 4) a complete development environment exists. We also provide a short discussion on processing speed.

  14. Construction and analysis of a genome-scale metabolic network for Bacillus licheniformis WX-02.

    Science.gov (United States)

    Guo, Jing; Zhang, Hong; Wang, Cheng; Chang, Ji-Wei; Chen, Ling-Ling

    2016-05-01

    We constructed the genome-scale metabolic network of Bacillus licheniformis (B. licheniformis) WX-02 by combining genomic annotation, high-throughput phenotype microarray (PM) experiments and literature-based metabolic information. The accuracy of the metabolic network was assessed by an OmniLog PM experiment. The final metabolic model iWX1009 contains 1009 genes, 1141 metabolites and 1762 reactions, and the predicted metabolic phenotypes showed an agreement rate of 76.8% with experimental PM data. In addition, key metabolic features such as growth yield, utilization of different substrates and essential genes were identified by flux balance analysis. A total of 195 essential genes were predicted from LB medium, among which 149 were verified with the experimental essential gene set of B. subtilis 168. With the removal of 5 reactions from the network, pathways for poly-γ-glutamic acid (γ-PGA) synthesis were optimized and the γ-PGA yield reached 83.8 mmol/h. Furthermore, the important metabolites and pathways related to γ-PGA synthesis and bacterium growth were comprehensively analyzed. The present study provides valuable clues for exploring the metabolisms and metabolic regulation of γ-PGA synthesis in B. licheniformis WX-02. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  15. Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning

    Science.gov (United States)

    Hoo-Chang, Shin; Roth, Holger R.; Gao, Mingchen; Lu, Le; Xu, Ziyue; Nogues, Isabella; Yao, Jianhua; Mollura, Daniel

    2016-01-01

    Remarkable progress has been made in image recognition, primarily due to the availability of large-scale annotated datasets (i.e. ImageNet) and the revival of deep convolutional neural networks (CNN). CNNs enable learning data-driven, highly representative, layered hierarchical image features from sufficient training data. However, obtaining datasets as comprehensively annotated as ImageNet in the medical imaging domain remains a challenge. There are currently three major techniques that successfully employ CNNs to medical image classification: training the CNN from scratch, using off-the-shelf pre-trained CNN features, and conducting unsupervised CNN pre-training with supervised fine-tuning. Another effective method is transfer learning, i.e., fine-tuning CNN models (supervised) pre-trained from natural image dataset to medical image tasks (although domain transfer between two medical image datasets is also possible). In this paper, we exploit three important, but previously understudied factors of employing deep convolutional neural networks to computer-aided detection problems. We first explore and evaluate different CNN architectures. The studied models contain 5 thousand to 160 million parameters, and vary in numbers of layers. We then evaluate the influence of dataset scale and spatial image context on performance. Finally, we examine when and why transfer learning from pre-trained ImageNet (via fine-tuning) can be useful. We study two specific computeraided detection (CADe) problems, namely thoraco-abdominal lymph node (LN) detection and interstitial lung disease (ILD) classification. We achieve the state-of-the-art performance on the mediastinal LN detection, with 85% sensitivity at 3 false positive per patient, and report the first five-fold cross-validation classification results on predicting axial CT slices with ILD categories. Our extensive empirical evaluation, CNN model analysis and valuable insights can be extended to the design of high performance

  16. Childhood maltreatment is associated with alteration in global network fiber-tract architecture independent of history of depression and anxiety.

    Science.gov (United States)

    Ohashi, Kyoko; Anderson, Carl M; Bolger, Elizabeth A; Khan, Alaptagin; McGreenery, Cynthia E; Teicher, Martin H

    2017-04-15

    Childhood maltreatment is a major risk factor for psychopathology. It is also associated with alterations in the network architecture of the brain, which we hypothesized may play a significant role in the development of psychopathology. In this study, we analyzed the global network architecture of physically healthy unmedicated 18-25 year old subjects (n=262) using diffusion tensor imaging (DTI) MRI and tractography. Anatomical networks were constructed from fiber streams interconnecting 90 cortical or subcortical regions for subjects with no-to-low (n=122) versus moderate-to-high (n=140) exposure to maltreatment. Graph theory analysis revealed lower degree, strength, global efficiency, and maximum Laplacian spectra, higher pathlength, small-worldness and Laplacian skewness, and less deviation from artificial networks in subjects with moderate-to-high exposure to maltreatment. On balance, local clustering was similar in both groups, but the different clusters were more strongly interconnected in the no-to-low exposure group. History of major depression, anxiety and attention deficit hyperactivity disorder did not have a significant impact on global network measures over and above the effect of maltreatment. Maltreatment is an important factor that needs to be taken into account in studies examining the relationship between network differences and psychopathology. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. SNAIL: A multiprocessor based on the simple serial synchronized multistage interconnection network architecture

    Energy Technology Data Exchange (ETDEWEB)

    Sasahara, M.; Terada, J.; Zhou, L.; Gaye, K.; Yamato, J.; Ogura, S.; Amano, H. [Keio Univ., Yokohama (Japan)

    1994-12-31

    Simple Serial Synchronized (SSS) Multistage Interconnection Network (MIN) is a novel MIN architecture for connecting processors and memory modules in multiprocessors. Synchronized bit-serial communication simplifies the structure/control, and also solves the pin-limitation problem. Here, design, implementation, and evaluation of a multiprocessor prototype called SNAIL with the SSS-MIN are presented. The heart of SNAIL is the prototype 1 {mu} CMOS SSS-MIN gate array chip which exchanges packets from 16 inputs with 50MHz clock. The message combining is implemented only with 20% increases of the hardware. From the empirical evaluation with some application programs, it appears that the latency and synchronization overhead of the SSS-MIN are tolerable, and the bandwidth of the SSS-MIN is sufficient. Although the performance improvement with the bit serial message combine is not so large (1%) when instructions are stored in the local memory, it becomes up to 400% when instructions are stored in the shared memory.

  18. Lightweight filter architecture for energy efficient mobile vehicle localization based on a distributed acoustic sensor network.

    Science.gov (United States)

    Kim, Keonwook

    2013-08-23

    The generic properties of an acoustic signal provide numerous benefits for localization by applying energy-based methods over a deployed wireless sensor network (WSN). However, the signal generated by a stationary target utilizes a significant amount of bandwidth and power in the system without providing further position information. For vehicle localization, this paper proposes a novel proximity velocity vector estimator (PVVE) node architecture in order to capture the energy from a moving vehicle and reject the signal from motionless automobiles around the WSN node. A cascade structure between analog envelope detector and digital exponential smoothing filter presents the velocity vector-sensitive output with low analog circuit and digital computation complexity. The optimal parameters in the exponential smoothing filter are obtained by analytical and mathematical methods for maximum variation over the vehicle speed. For stationary targets, the derived simulation based on the acoustic field parameters demonstrates that the system significantly reduces the communication requirements with low complexity and can be expected to extend the operation time considerably.

  19. An artificial neural network architecture for non-parametric visual odometry in wireless capsule endoscopy

    Science.gov (United States)

    Dimas, George; Iakovidis, Dimitris K.; Karargyris, Alexandros; Ciuti, Gastone; Koulaouzidis, Anastasios

    2017-09-01

    Wireless capsule endoscopy is a non-invasive screening procedure of the gastrointestinal (GI) tract performed with an ingestible capsule endoscope (CE) of the size of a large vitamin pill. Such endoscopes are equipped with a usually low-frame-rate color camera which enables the visualization of the GI lumen and the detection of pathologies. The localization of the commercially available CEs is performed in the 3D abdominal space using radio-frequency (RF) triangulation from external sensor arrays, in combination with transit time estimation. State-of-the-art approaches, such as magnetic localization, which have been experimentally proved more accurate than the RF approach, are still at an early stage. Recently, we have demonstrated that CE localization is feasible using solely visual cues and geometric models. However, such approaches depend on camera parameters, many of which are unknown. In this paper the authors propose a novel non-parametric visual odometry (VO) approach to CE localization based on a feed-forward neural network architecture. The effectiveness of this approach in comparison to state-of-the-art geometric VO approaches is validated using a robotic-assisted in vitro experimental setup.

  20. An artificial neural network architecture for non-parametric visual odometry in wireless capsule endoscopy

    International Nuclear Information System (INIS)

    Dimas, George; Iakovidis, Dimitris K; Karargyris, Alexandros; Ciuti, Gastone; Koulaouzidis, Anastasios

    2017-01-01

    Wireless capsule endoscopy is a non-invasive screening procedure of the gastrointestinal (GI) tract performed with an ingestible capsule endoscope (CE) of the size of a large vitamin pill. Such endoscopes are equipped with a usually low-frame-rate color camera which enables the visualization of the GI lumen and the detection of pathologies. The localization of the commercially available CEs is performed in the 3D abdominal space using radio-frequency (RF) triangulation from external sensor arrays, in combination with transit time estimation. State-of-the-art approaches, such as magnetic localization, which have been experimentally proved more accurate than the RF approach, are still at an early stage. Recently, we have demonstrated that CE localization is feasible using solely visual cues and geometric models. However, such approaches depend on camera parameters, many of which are unknown. In this paper the authors propose a novel non-parametric visual odometry (VO) approach to CE localization based on a feed-forward neural network architecture. The effectiveness of this approach in comparison to state-of-the-art geometric VO approaches is validated using a robotic-assisted in vitro experimental setup. (paper)

  1. A compendium of inborn errors of metabolism mapped onto the human metabolic network.

    OpenAIRE

    Sahoo, Swagatika; Franzson, Leifur; Jonsson, Jon J; Thiele, Ines

    2012-01-01

    Efst á síðunni er hægt að nálgast greinina í heild sinni með því að smella á hlekkinn Inborn errors of metabolism (IEMs) are hereditary metabolic defects, which are encountered in almost all major metabolic pathways occurring in man. Many IEMs are screened for in neonates through metabolomic analysis of dried blood spot samples. To enable the mapping of these metabolomic data onto the published human metabolic reconstruction, we added missing reactions and pathways involved in acylcarnitin...

  2. Genetic architecture of plasma adiponectin overlaps with the genetics of metabolic syndrome-related traits

    NARCIS (Netherlands)

    P. Henneman (Peter); Y.S. Aulchenko (Yurii); R.R. Frants (Rune); I.V. Zorkoltseva (Irina); M.C. Zillikens (Carola); M. Frölich (Marijke); B.A. Oostra (Ben); J.A.P. Willems van Dijk (Ko); P. Tikka-Kleemola (Päivi)

    2010-01-01

    textabstractOBJECTIVE - Adiponectin, a hormone secreted by adipose tissue, is of particular interest in metabolic syndrome, because it is inversely correlated with obesity and insulin sensitivity. However, it is not known to what extent the genetics of plasma adiponectin and the genetics of obesity

  3. Robustness in Regulatory Interaction Networks. A Generic Approach with Applications at Different Levels: Physiologic, Metabolic and Genetic

    Science.gov (United States)

    Demongeot, Jacques; Ben Amor, Hedi; Elena, Adrien; Gillois, Pierre; Noual, Mathilde; Sené, Sylvain

    2009-01-01

    Regulatory interaction networks are often studied on their dynamical side (existence of attractors, study of their stability). We focus here also on their robustness, that is their ability to offer the same spatiotemporal patterns and to resist to external perturbations such as losses of nodes or edges in the networks interactions architecture, changes in their environmental boundary conditions as well as changes in the update schedule (or updating mode) of the states of their elements (e.g., if these elements are genes, their synchronous coexpression mode versus their sequential expression). We define the generic notions of boundary, core, and critical vertex or edge of the underlying interaction graph of the regulatory network, whose disappearance causes dramatic changes in the number and nature of attractors (e.g., passage from a bistable behaviour to a unique periodic regime) or in the range of their basins of stability. The dynamic transition of states will be presented in the framework of threshold Boolean automata rules. A panorama of applications at different levels will be given: brain and plant morphogenesis, bulbar cardio-respiratory regulation, glycolytic/oxidative metabolic coupling, and eventually cell cycle and feather morphogenesis genetic control. PMID:20057955

  4. A general model for metabolic scaling in self-similar asymmetric networks.

    Directory of Open Access Journals (Sweden)

    Alexander Byers Brummer

    2017-03-01

    Full Text Available How a particular attribute of an organism changes or scales with its body size is known as an allometry. Biological allometries, such as metabolic scaling, have been hypothesized to result from selection to maximize how vascular networks fill space yet minimize internal transport distances and resistances. The West, Brown, Enquist (WBE model argues that these two principles (space-filling and energy minimization are (i general principles underlying the evolution of the diversity of biological networks across plants and animals and (ii can be used to predict how the resulting geometry of biological networks then governs their allometric scaling. Perhaps the most central biological allometry is how metabolic rate scales with body size. A core assumption of the WBE model is that networks are symmetric with respect to their geometric properties. That is, any two given branches within the same generation in the network are assumed to have identical lengths and radii. However, biological networks are rarely if ever symmetric. An open question is: Does incorporating asymmetric branching change or influence the predictions of the WBE model? We derive a general network model that relaxes the symmetric assumption and define two classes of asymmetrically bifurcating networks. We show that asymmetric branching can be incorporated into the WBE model. This asymmetric version of the WBE model results in several theoretical predictions for the structure, physiology, and metabolism of organisms, specifically in the case for the cardiovascular system. We show how network asymmetry can now be incorporated in the many allometric scaling relationships via total network volume. Most importantly, we show that the 3/4 metabolic scaling exponent from Kleiber's Law can still be attained within many asymmetric networks.

  5. SCinet Architecture: Featured at the International Conference for High Performance Computing,Networking, Storage and Analysis 2016

    Energy Technology Data Exchange (ETDEWEB)

    Lyonnais, Marc; Smith, Matt; Mace, Kate P.

    2017-02-06

    SCinet is the purpose-built network that operates during the International Conference for High Performance Computing,Networking, Storage and Analysis (Super Computing or SC). Created each year for the conference, SCinet brings to life a high-capacity network that supports applications and experiments that are a hallmark of the SC conference. The network links the convention center to research and commercial networks around the world. This resource serves as a platform for exhibitors to demonstrate the advanced computing resources of their home institutions and elsewhere by supporting a wide variety of applications. Volunteers from academia, government and industry work together to design and deliver the SCinet infrastructure. Industry vendors and carriers donate millions of dollars in equipment and services needed to build and support the local and wide area networks. Planning begins more than a year in advance of each SC conference and culminates in a high intensity installation in the days leading up to the conference. The SCinet architecture for SC16 illustrates a dramatic increase in participation from the vendor community, particularly those that focus on network equipment. Software-Defined Networking (SDN) and Data Center Networking (DCN) are present in nearly all aspects of the design.

  6. Mobility-Aware Modeling and Analysis of Dense Cellular Networks With $C$ -Plane/ $U$ -Plane Split Architecture

    KAUST Repository

    Ibrahim, Hazem

    2016-09-19

    The unrelenting increase in the population of mobile users and their traffic demands drive cellular network operators to densify their network infrastructure. Network densification shrinks the footprint of base stations (BSs) and reduces the number of users associated with each BS, leading to an improved spatial frequency reuse and spectral efficiency, and thus, higher network capacity. However, the densification gain comes at the expense of higher handover rates and network control overhead. Hence, user’s mobility can diminish or even nullifies the foreseen densification gain. In this context, splitting the control plane ( C -plane) and user plane ( U -plane) is proposed as a potential solution to harvest densification gain with reduced cost in terms of handover rate and network control overhead. In this paper, we use stochastic geometry to develop a tractable mobility-aware model for a two-tier downlink cellular network with ultra-dense small cells and C -plane/ U -plane split architecture. The developed model is then used to quantify the effect of mobility on the foreseen densification gain with and without C -plane/ U -plane split. To this end, we shed light on the handover problem in dense cellular environments, show scenarios where the network fails to support certain mobility profiles, and obtain network design insights.

  7. A Simple Network Architecture Accounts for Diverse Reward Time Responses in Primary Visual Cortex.

    Science.gov (United States)

    Huertas, Marco A; Hussain Shuler, Marshall G; Shouval, Harel Z

    2015-09-16

    Many actions performed by animals and humans depend on an ability to learn, estimate, and produce temporal intervals of behavioral relevance. Exemplifying such learning of cued expectancies is the observation of reward-timing activity in the primary visual cortex (V1) of rodents, wherein neural responses to visual cues come to predict the time of future reward as behaviorally experienced in the past. These reward-timing responses exhibit significant heterogeneity in at least three qualitatively distinct classes: sustained increase or sustained decrease in firing rate until the time of expected reward, and a class of cells that reach a peak in firing at the expected delay. We elaborate upon our existing model by including inhibitory and excitatory units while imposing simple connectivity rules to demonstrate what role these inhibitory elements and the simple architectures play in sculpting the response dynamics of the network. We find that simply adding inhibition is not sufficient for obtaining the different distinct response classes, and that a broad distribution of inhibitory projections is necessary for obtaining peak-type responses. Furthermore, although changes in connection strength that modulate the effects of inhibition onto excitatory units have a strong impact on the firing rate profile of these peaked responses, the network exhibits robustness in its overall ability to predict the expected time of reward. Finally, we demonstrate how the magnitude of expected reward can be encoded at the expected delay in the network and how peaked responses express this reward expectancy. Heterogeneity in single-neuron responses is a common feature of neuronal systems, although sometimes, in theoretical approaches, it is treated as a nuisance and seldom considered as conveying a different aspect of a signal. In this study, we focus on the heterogeneous responses in the primary visual cortex of rodents trained with a predictable delayed reward time. We describe under what

  8. The Role of Architectural and Learning Constraints in Neural Network Models: A Case Study on Visual Space Coding.

    Science.gov (United States)

    Testolin, Alberto; De Filippo De Grazia, Michele; Zorzi, Marco

    2017-01-01

    The recent "deep learning revolution" in artificial neural networks had strong impact and widespread deployment for engineering applications, but the use of deep learning for neurocomputational modeling has been so far limited. In this article we argue that unsupervised deep learning represents an important step forward for improving neurocomputational models of perception and cognition, because it emphasizes the role of generative learning as opposed to discriminative (supervised) learning. As a case study, we present a series of simulations investigating the emergence of neural coding of visual space for sensorimotor transformations. We compare different network architectures commonly used as building blocks for unsupervised deep learning by systematically testing the type of receptive fields and gain modulation developed by the hidden neurons. In particular, we compare Restricted Boltzmann Machines (RBMs), which are stochastic, generative networks with bidirectional connections trained using contrastive divergence, with autoencoders, which are deterministic networks trained using error backpropagation. For both learning architectures we also explore the role of sparse coding, which has been identified as a fundamental principle of neural computation. The unsupervised models are then compared with supervised, feed-forward networks that learn an explicit mapping between different spatial reference frames. Our simulations show that both architectural and learning constraints strongly influenced the emergent coding of visual space in terms of distribution of tuning functions at the level of single neurons. Unsupervised models, and particularly RBMs, were found to more closely adhere to neurophysiological data from single-cell recordings in the primate parietal cortex. These results provide new insights into how basic properties of artificial neural networks might be relevant for modeling neural information processing in biological systems.

  9. Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks

    Directory of Open Access Journals (Sweden)

    Chang Jeong-Ho

    2006-06-01

    Full Text Available Abstract Background To infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms. In contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional relationships under different physiological conditions. However, evaluating the similarities or differences between metabolic networks is a computationally challenging problem, and systematic methods of doing this are desirable. Here we introduce a graph-kernel method for computing the similarity between metabolic networks in polynomial time, and use it to profile metabolic pathways and to construct phylogenetic trees. Results To compare the structures of metabolic networks in organisms, we adopted the exponential graph kernel, which is a kernel-based approach with a labeled graph that includes a label matrix and an adjacency matrix. To construct the phylogenetic trees, we used an unweighted pair-group method with arithmetic mean, i.e., a hierarchical clustering algorithm. We applied the kernel-based network profiling method in a comparative analysis of nine carbohydrate metabolic networks from 81 biological species encompassing Archaea, Eukaryota, and Eubacteria. The resulting phylogenetic hierarchies generally support the tripartite scheme of three domains rather than the two domains of prokaryotes and eukaryotes. Conclusion By combining the kernel machines with metabolic information, the method infers the context of biosphere development that covers physiological events required for adaptation by genetic reconstruction. The results show that one may obtain a global view of the tree of life by comparing the metabolic pathway

  10. Dynamic brain glucose metabolism identifies anti-correlated cortical-cerebellar networks at rest.

    Science.gov (United States)

    Tomasi, Dardo G; Shokri-Kojori, Ehsan; Wiers, Corinde E; Kim, Sunny W; Demiral, Şukru B; Cabrera, Elizabeth A; Lindgren, Elsa; Miller, Gregg; Wang, Gene-Jack; Volkow, Nora D

    2017-12-01

    It remains unclear whether resting state functional magnetic resonance imaging (rfMRI) networks are associated with underlying synchrony in energy demand, as measured by dynamic 2-deoxy-2-[ 18 F]fluoroglucose (FDG) positron emission tomography (PET). We measured absolute glucose metabolism, temporal metabolic connectivity (t-MC) and rfMRI patterns in 53 healthy participants at rest. Twenty-two rfMRI networks emerged from group independent component analysis (gICA). In contrast, only two anti-correlated t-MC emerged from FDG-PET time series using gICA or seed-voxel correlations; one included frontal, parietal and temporal cortices, the other included the cerebellum and medial temporal regions. Whereas cerebellum, thalamus, globus pallidus and calcarine cortex arose as the strongest t-MC hubs, the precuneus and visual cortex arose as the strongest rfMRI hubs. The strength of the t-MC linearly increased with the metabolic rate of glucose suggesting that t-MC measures are strongly associated with the energy demand of the brain tissue, and could reflect regional differences in glucose metabolism, counterbalanced metabolic network demand, and/or differential time-varying delivery of FDG. The mismatch between metabolic and functional connectivity patterns computed as a function of time could reflect differences in the temporal characteristics of glucose metabolism as measured with PET-FDG and brain activation as measured with rfMRI.

  11. A Strategy for Functional Interpretation of Metabolomic Time Series Data in Context of Metabolic Network Information

    Directory of Open Access Journals (Sweden)

    Thomas eNägele

    2016-03-01

    Full Text Available The functional connection of experimental metabolic time series data with biochemical network information is an important, yet complex, issue in systems biology. Frequently, experimental analysis of diurnal, circadian or developmental dynamics of metabolism results in a comprehensive and multidimensional data matrix comprising information about metabolite concentrations, protein levels and/or enzyme activities. While, irrespective of the type of organism, the experimental high-throughput analysis of the transcriptome, proteome and metabolome has become a common part of many systems biology studies, functional data integration in a biochemical and physiological context is still challenging. Here, an approach is presented which addresses the functional connection of experimental time series data with biochemical network information which can be inferred, for example, from a metabolic network reconstruction. Based on a time-continuous and variance-weighted regression analysis of experimental data, metabolic functions, i.e. first-order derivatives of metabolite concentrations, were related to time-dependent changes in other biochemically relevant metabolic functions, i.e. second-order derivatives of metabolite concentrations. This finally revealed time points of perturbed dependencies in metabolic functions indicating a modified biochemical interaction. The approach was validated using previously published experimental data on a diurnal time course of metabolite levels, enzyme activities and metabolic flux simulations. To support and ease the presented approach of functional time series analysis, a graphical user interface including a test data set and a manual is provided which can be run within the numerical software environment Matlab®.

  12. A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks.

    Science.gov (United States)

    Röhl, Annika; Bockmayr, Alexander

    2017-01-03

    Constraint-based analysis has become a widely used method to study metabolic networks. While some of the associated algorithms can be applied to genome-scale network reconstructions with several thousands of reactions, others are limited to small or medium-sized models. In 2015, Erdrich et al. introduced a method called NetworkReducer, which reduces large metabolic networks to smaller subnetworks, while preserving a set of biological requirements that can be specified by the user. Already in 2001, Burgard et al. developed a mixed-integer linear programming (MILP) approach for computing minimal reaction sets under a given growth requirement. Here we present an MILP approach for computing minimum subnetworks with the given properties. The minimality (with respect to the number of active reactions) is not guaranteed by NetworkReducer, while the method by Burgard et al. does not allow specifying the different biological requirements. Our procedure is about 5-10 times faster than NetworkReducer and can enumerate all minimum subnetworks in case there exist several ones. This allows identifying common reactions that are present in all subnetworks, and reactions appearing in alternative pathways. Applying complex analysis methods to genome-scale metabolic networks is often not possible in practice. Thus it may become necessary to reduce the size of the network while keeping important functionalities. We propose a MILP solution to this problem. Compared to previous work, our approach is more efficient and allows computing not only one, but even all minimum subnetworks satisfying the required properties.

  13. Metabolomics Approach Reveals Integrated Metabolic Network Associated with Serotonin Deficiency

    Science.gov (United States)

    Weng, Rui; Shen, Sensen; Tian, Yonglu; Burton, Casey; Xu, Xinyuan; Liu, Yi; Chang, Cuilan; Bai, Yu; Liu, Huwei

    2015-07-01

    Serotonin is an important neurotransmitter that broadly participates in various biological processes. While serotonin deficiency has been associated with multiple pathological conditions such as depression, schizophrenia, Alzheimer’s disease and Parkinson’s disease, the serotonin-dependent mechanisms remain poorly understood. This study therefore aimed to identify novel biomarkers and metabolic pathways perturbed by serotonin deficiency using metabolomics approach in order to gain new metabolic insights into the serotonin deficiency-related molecular mechanisms. Serotonin deficiency was achieved through pharmacological inhibition of tryptophan hydroxylase (Tph) using p-chlorophenylalanine (pCPA) or genetic knockout of the neuronal specific Tph2 isoform. This dual approach improved specificity for the serotonin deficiency-associated biomarkers while minimizing nonspecific effects of pCPA treatment or Tph2 knockout (Tph2-/-). Non-targeted metabolic profiling and a targeted pCPA dose-response study identified 21 biomarkers in the pCPA-treated mice while 17 metabolites in the Tph2-/- mice were found to be significantly altered compared with the control mice. These newly identified biomarkers were associated with amino acid, energy, purine, lipid and gut microflora metabolisms. Oxidative stress was also found to be significantly increased in the serotonin deficient mice. These new biomarkers and the overall metabolic pathways may provide new understanding for the serotonin deficiency-associated mechanisms under multiple pathological states.

  14. Large-scale brain networks in affective and social neuroscience: Towards an integrative functional architecture of the brain

    Science.gov (United States)

    Barrett, Lisa Feldman; Satpute, Ajay

    2013-01-01

    Understanding how a human brain creates a human mind ultimately depends on mapping psychological categories and concepts to physical measurements of neural response. Although it has long been assumed that emotional, social, and cognitive phenomena are realized in the operations of separate brain regions or brain networks, we demonstrate that it is possible to understand the body of neuroimaging evidence using a framework that relies on domain general, distributed structure-function mappings. We review current research in affective and social neuroscience and argue that the emerging science of large-scale intrinsic brain networks provides a coherent framework for a domain-general functional architecture of the human brain. PMID:23352202

  15. Suitability of Using Self-Organizing Neural Networks in Configuring P-System Communications Architectures

    OpenAIRE

    Gutierrez Rodriguez, Abraham; Delgado Sanz, Maria Soledad; Fernández Muñoz, Luis

    2009-01-01

    Nowadays, it is possible to find out different viable architectures that implements P Systems in a distributed cluster of processors. These proposed architectures have reached a certain compromise between the massively parallelism character of the system and the evolution step times. They are based in the distribution of several membranes in each processor, the use of proxies to control the communication between membranes and mainly, the suitable distribution of the architecture in a balanced...

  16. A Comprehensive Zero-Copy Architecture for High Performance Distributed Data Acquisition Over Advanced Network Technologies for the CMS Experiment

    Science.gov (United States)

    Bauer, Gerry; Behrens, Ulf; Branson, James; Bukowiec, Sebastian; Chaze, Olivier; Cittolin, Sergio; Perez, Jose Antonio Coarasa; Deldicque, Christian; Dobson, Marc; Dupont, Aymeric; Erhan, Samim; Gigi, Dominique; Glege, Frank; Gomez-Reino, Robert; Hartl, Christian; Holzner, Andre; Masetti, Lorenzo; Meijers, Frans; Meschi, Emilio; Mommsen, Remigius K.; Nunez-Barranco-Fernandez, Carlos; O'Dell, Vivian; Orsini, Luciano; Paus, Christoph; Petrucci, Andrea; Pieri, Marco; Polese, Giovanni; Racz, Attila; Raginel, Olivier; Sakulin, Hannes; Sani, Matteo; Schwick, Christoph; Spataru, Andrei Cristian; Stoeckli, Fabian; Sumorok, Konstanty

    2013-12-01

    This paper outlines a software architecture where zero-copy operations are used comprehensively at every processing point from the Application layer to the Physical layer. The proposed architecture is being used during feasibility studies on advanced networking technologies for the CMS experiment at CERN. The design relies on a homogeneous peer-to-peer message passing system, which is built around memory pool caches allowing efficient and deterministic latency handling of messages of any size through the different software layers. In this scheme portable distributed applications can be programmed to process input to output operations by mere pointer arithmetic and DMA operations only. The approach combined with the open fabric protocol stack (OFED) allows one to attain near wire-speed message transfer at application level. The architecture supports full portability of user applications by encapsulating the protocol details and network into modular peer transport services whereas a transparent replacement of the underlying protocol facilitates deployment of several network technologies like Gigabit Ethernet, Myrinet, Infiniband, etc. Therefore, this solution provides a protocol-independent communication framework and prevents having to deal with potentially difficult couplings when the underlying communication infrastructure is changed. We demonstrate the feasibility of this approach by giving efficiency and performance measurements of the software in the context of the CMS distributed event building studies.

  17. Resource-aware system architecture model for implementation of quantum aided Byzantine agreement on quantum repeater networks

    Science.gov (United States)

    Taherkhani, Mohammand Amin; Navi, Keivan; Van Meter, Rodney

    2018-01-01

    Quantum aided Byzantine agreement is an important distributed quantum algorithm with unique features in comparison to classical deterministic and randomized algorithms, requiring only a constant expected number of rounds in addition to giving a higher level of security. In this paper, we analyze details of the high level multi-party algorithm, and propose elements of the design for the quantum architecture and circuits required at each node to run the algorithm on a quantum repeater network (QRN). Our optimization techniques have reduced the quantum circuit depth by 44% and the number of qubits in each node by 20% for a minimum five-node setup compared to the design based on the standard arithmetic circuits. These improvements lead to a quantum system architecture with 160 qubits per node, space-time product (an estimate of the required fidelity) {KQ}≈ 1.3× {10}5 per node and error threshold 1.1× {10}-6 for the total nodes in the network. The evaluation of the designed architecture shows that to execute the algorithm once on the minimum setup, we need to successfully distribute a total of 648 Bell pairs across the network, spread evenly between all pairs of nodes. This framework can be considered a starting point for establishing a road-map for light-weight demonstration of a distributed quantum application on QRNs.

  18. Comb-Type Grafted Hydrogels of PNIPAM and PDMAEMA with Reversed Network-Graft Architectures from Controlled Radical Polymerizations

    Directory of Open Access Journals (Sweden)

    Sheng-Qi Chen

    2016-02-01

    Full Text Available Dual thermo- and pH-responsive comb-type grafted hydrogels of poly(N,N-dimethylaminoethyl methacrylate (PDMAEMA and poly(N-isopropylacrylamide (PNIPAM with reversed network-graft architectures were synthesized by the combination of atom transfer radical polymerization (ATRP, reversible addition-fragmentation chain transfer (RAFT polymerization and click chemistry. Two kinds of macro-cross-linkers with two azido groups at one chain-end and different chain length [PNIPAM–(N32 and PDMAEMA–(N32] were prepared with N,N-di(β-azidoethyl 2-halocarboxylamide as the ATRP initiator. Through RAFT copolymerization of DMAEMA or NIPAM with propargyl acrylate (ProA using dibenzyltrithiocarbonate as a chain transfer agent, two network precursors with different content of alkynyl side-groups [P(DMAEMA-co-ProA and P(NIPAM-co-ProA] were obtained. The subsequent azido-alkynyl click reaction of macro-cross-linkers and network precursors led to the formation of the network-graft hydrogels. These dual stimulus-sensitive hydrogels exhibited rapid response, high swelling ratio and reproducible swelling/de-swelling cycles under different temperatures and pH values. The influences of cross-linkage density and network-graft architecture on the properties of the hydrogels were investigated. The release of ceftriaxone sodium from these hydrogels showed both thermal- and pH-dependence, suggesting the feasibility of these hydrogels as thermo- and pH-dependent drug release devices.

  19. Comparative analysis of Salmonella genomes identifies a metabolic network for escalating growth in the inflamed gut.

    Science.gov (United States)

    Nuccio, Sean-Paul; Bäumler, Andreas J

    2014-03-18

    The Salmonella genus comprises a group of pathogens associated with illnesses ranging from gastroenteritis to typhoid fever. We performed an in silico analysis of comparatively reannotated Salmonella genomes to identify genomic signatures indicative of disease potential. By removing numerous annotation inconsistencies and inaccuracies, the process of reannotation identified a network of 469 genes involved in central anaerobic metabolism, which was intact in genomes of gastrointestinal pathogens but degrading in genomes of extraintestinal pathogens. This large network contained pathways that enable gastrointestinal pathogens to utilize inflammation-derived nutrients as well as many of the biochemical reactions used for the enrichment and biochemical discrimination of Salmonella serovars. Thus, comparative genome analysis identifies a metabolic network that provides clues about the strategies for nutrient acquisition and utilization that are characteristic of gastrointestinal pathogens. IMPORTANCE While some Salmonella serovars cause infections that remain localized to the gut, others disseminate throughout the body. Here, we compared Salmonella genomes to identify characteristics that distinguish gastrointestinal from extraintestinal pathogens. We identified a large metabolic network that is functional in gastrointestinal pathogens but decaying in extraintestinal pathogens. While taxonomists have used traits from this network empirically for many decades for the enrichment and biochemical discrimination of Salmonella serovars, our findings suggest that it is part of a "business plan" for growth in the inflamed gastrointestinal tract. By identifying a large metabolic network characteristic of Salmonella serovars associated with gastroenteritis, our in silico analysis provides a blueprint for potential strategies to utilize inflammation-derived nutrients and edge out competing gut microbes.

  20. Proceedings of the First Software Architecture Technology User Network (SATURN) Workshop

    National Research Council Canada - National Science Library

    Nord, Robert L; Bass, Len; Clements, Paul; Northrop, Linda; Tomayko, James E

    2005-01-01

    ...: peer collaboration, shared understanding, SEI technical staff presence, developing metrics that measure benefits, exploring case studies that highlight how to apply architecture-centric methods...

  1. 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.

  2. TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

    Directory of Open Access Journals (Sweden)

    Jensen Paul A

    2011-09-01

    Full Text Available Abstract Background Several methods have been developed for analyzing genome-scale models of metabolism and transcriptional regulation. Many of these methods, such as Flux Balance Analysis, use constrained optimization to predict relationships between metabolic flux and the genes that encode and regulate enzyme activity. Recently, mixed integer programming has been used to encode these gene-protein-reaction (GPR relationships into a single optimization problem, but these techniques are often of limited generality and lack a tool for automating the conversion of rules to a coupled regulatory/metabolic model. Results We present TIGER, a Toolbox for Integrating Genome-scale Metabolism, Expression, and Regulation. TIGER converts a series of generalized, Boolean or multilevel rules into a set of mixed integer inequalities. The package also includes implementations of existing algorithms to integrate high-throughput expression data with genome-scale models of metabolism and transcriptional regulation. We demonstrate how TIGER automates the coupling of a genome-scale metabolic model with GPR logic and models of transcriptional regulation, thereby serving as a platform for algorithm development and large-scale metabolic analysis. Additionally, we demonstrate how TIGER's algorithms can be used to identify inconsistencies and improve existing models of transcriptional regulation with examples from the reconstructed transcriptional regulatory network of Saccharomyces cerevisiae. Conclusion The TIGER package provides a consistent platform for algorithm development and extending existing genome-scale metabolic models with regulatory networks and high-throughput data.

  3. Chronic obstructive pulmonary disease candidate gene prioritization based on metabolic networks and functional information.

    Directory of Open Access Journals (Sweden)

    Xinyan Wang

    Full Text Available Chronic obstructive pulmonary disease (COPD is a multi-factor disease, in which metabolic disturbances played important roles. In this paper, functional information was integrated into a COPD-related metabolic network to assess similarity between genes. Then a gene prioritization method was applied to the COPD-related metabolic network to prioritize COPD candidate genes. The gene prioritization method was superior to ToppGene and ToppNet in both literature validation and functional enrichment analysis. Top-ranked genes prioritized from the metabolic perspective with functional information could promote the better understanding about the molecular mechanism of this disease. Top 100 genes might be potential markers for diagnostic and effective therapies.

  4. Understanding the control of acyl flux through the lipid metabolic network of plant oil biosynthesis.

    Science.gov (United States)

    Bates, Philip D

    2016-09-01

    Plant oil biosynthesis involves a complex metabolic network with multiple subcellular compartments, parallel pathways, cycles, and pathways that have a dual function to produce essential membrane lipids and triacylglycerol. Modern molecular biology techniques provide tools to alter plant oil compositions through bioengineering, however with few exceptions the final composition of triacylglycerol cannot be predicted. One reason for limited success in oilseed bioengineering is the inadequate understanding of how to control the flux of fatty acids through various fatty acid modification, and triacylglycerol assembly pathways of the lipid metabolic network. This review focuses on the mechanisms of acyl flux through the lipid metabolic network, and highlights where uncertainty resides in our understanding of seed oil biosynthesis. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. The hypothalamic neural-glial network and the metabolic syndrome

    NARCIS (Netherlands)

    Jastroch, Martin; Morin, Silke; Tschöp, Matthias H.; Yi, Chun-Xia

    2014-01-01

    Despite numerous educational interventions and biomedical research efforts, modern society continues to suffer from obesity and its associated metabolic diseases, such as type 2 diabetes mellitus, and these diseases show little sign of abating. One reason for this is an incomplete understanding of

  6. Genome scale metabolic network reconstruction of Spirochaeta cellobiosiphila

    Directory of Open Access Journals (Sweden)

    Bharat Manna

    2017-10-01

    Full Text Available Substantial rise in the global energy demand is one of the biggest challenges in this century. Environmental pollution due to rapid depletion of the fossil fuel resources and its alarming impact on the climate change and Global Warming have motivated researchers to look for non-petroleum-based sustainable, eco-friendly, renewable, low-cost energy alternatives, such as biofuel. Lignocellulosic biomass is one of the most promising bio-resources with huge potential to contribute to this worldwide energy demand. However, the complex organization of the Cellulose, Hemicellulose and Lignin in the Lignocellulosic biomass requires extensive pre-treatment and enzymatic hydrolysis followed by fermentation, raising overall production cost of biofuel. This encourages researchers to design cost-effective approaches for the production of second generation biofuels. The products from enzymatic hydrolysis of cellulose are mostly glucose monomer or cellobiose unit that are subjected to fermentation. Spirochaeta genus is a well-known group of obligate or facultative anaerobes, living primarily on carbohydrate metabolism. Spirochaeta cellobiosiphila sp. is a facultative anaerobe under this genus, which uses a variety of monosaccharides and disaccharides as energy sources. However, most rapid growth occurs on cellobiose and fermentation yields significant amount of ethanol, acetate, CO2, H2 and small amounts of formate. It is predicted to be promising microbial machinery for industrial fermentation processes for biofuel production. The metabolic pathways that govern cellobiose metabolism in Spirochaeta cellobiosiphila are yet to be explored. The function annotation of the genome sequence of Spirochaeta cellobiosiphila is in progress. In this work we aim to map all the metabolic activities for reconstruction of genome-scale metabolic model of Spirochaeta cellobiosiphila.

  7. Differentially expressed genes in mycorrhized and nodulated roots of common bean are associated with defense, cell wall architecture, N metabolism, and P metabolism

    Science.gov (United States)

    Gómez, Brenda-Mariana; Blanco, Lourdes; Lara, Miguel

    2017-01-01

    Legumes participate in two important endosymbiotic associations, with phosphorus-acquiring arbuscular mycorrhiza (AM, soil fungi) and with nitrogen-fixing bacterial rhizobia. These divergent symbionts share a common symbiotic signal transduction pathway that facilitates the establishment of mycorrhization and nodulation in legumes. However, the unique and shared downstream genes essential for AM and nodule development have not been identified in crop legumes. Here, we used ion torrent next-generation sequencing to perform comparative transcriptomics of common bean (Phaseolus vulgaris) roots colonized by AM or rhizobia. We analyzed global gene expression profiles to identify unique and shared differentially expressed genes (DEGs) that regulate these two symbiotic interactions, and quantitatively compared DEG profiles. We identified 3,219 (1,959 upregulated and 1,260 downregulated) and 2,645 (1,247 upregulated and 1,398 downregulated) unigenes that were differentially expressed in response to mycorrhizal or rhizobial colonization, respectively, compared with uninoculated roots. We obtained quantitative expression profiles of unique and shared genes involved in processes related to defense, cell wall structure, N metabolism, and P metabolism in mycorrhized and nodulated roots. KEGG pathway analysis indicated that most genes involved in jasmonic acid and salicylic acid signaling, N metabolism, and inositol phosphate metabolism are variably expressed during symbiotic interactions. These combined data provide valuable information on symbiotic gene signaling networks that respond to mycorrhizal and rhizobial colonization, and serve as a guide for future genetic strategies to enhance P uptake and N-fixing capacity to increase the net yield of this valuable grain legume. PMID:28771548

  8. Detection of driver metabolites in the human liver metabolic network using structural controllability analysis

    Science.gov (United States)

    2014-01-01

    Background Abnormal states in human liver metabolism are major causes of human liver diseases ranging from hepatitis to hepatic tumor. The accumulation in relevant data makes it feasible to derive a large-scale human liver metabolic network (HLMN) and to discover important biological principles or drug-targets based on network analysis. Some studies have shown that interesting biological phenomenon and drug-targets could be discovered by applying structural controllability analysis (which is a newly prevailed concept in networks) to biological networks. The exploration on the connections between structural controllability theory and the HLMN could be used to uncover valuable information on the human liver metabolism from a fresh perspective. Results We applied structural controllability analysis to the HLMN and detected driver metabolites. The driver metabolites tend to have strong ability to influence the states of other metabolites and weak susceptibility to be influenced by the states of others. In addition, the metabolites were classified into three classes: critical, high-frequency and low-frequency driver metabolites. Among the identified 36 critical driver metabolites, 27 metabolites were found to be essential; the high-frequency driver metabolites tend to participate in different metabolic pathways, which are important in regulating the whole metabolic systems. Moreover, we explored some other possible connections between the structural controllability theory and the HLMN, and find that transport reactions and the environment play important roles in the human liver metabolism. Conclusion There are interesting connections between the structural controllability theory and the human liver metabolism: driver metabolites have essential biological functions; the crucial role of extracellular metabolites and transport reactions in controlling the HLMN highlights the importance of the environment in the health of human liver metabolism. PMID:24885538

  9. Irreversibility of T-Cell Specification: Insights from Computational Modelling of a Minimal Network Architecture.

    Directory of Open Access Journals (Sweden)

    Erica Manesso

    Full Text Available A cascade of gene activations under the control of Notch signalling is required during T-cell specification, when T-cell precursors gradually lose the potential to undertake other fates and become fully committed to the T-cell lineage. We elucidate how the gene/protein dynamics for a core transcriptional module governs this important process by computational means.We first assembled existing knowledge about transcription factors known to be important for T-cell specification to form a minimal core module consisting of TCF-1, GATA-3, BCL11B, and PU.1 aiming at dynamical modeling. Model architecture was based on published experimental measurements of the effects on each factor when each of the others is perturbed. While several studies provided gene expression measurements at different stages of T-cell development, pure time series are not available, thus precluding a straightforward study of the dynamical interactions among these genes. We therefore translate stage dependent data into time series. A feed-forward motif with multiple positive feed-backs can account for the observed delay between BCL11B versus TCF-1 and GATA-3 activation by Notch signalling. With a novel computational approach, all 32 possible interactions among Notch signalling, TCF-1, and GATA-3 are explored by translating combinatorial logic expressions into differential equations for BCL11B production rate.Our analysis reveals that only 3 of 32 possible configurations, where GATA-3 works as a dimer, are able to explain not only the time delay, but very importantly, also give rise to irreversibility. The winning models explain the data within the 95% confidence region and are consistent with regard to decay rates.This first generation model for early T-cell specification has relatively few players. Yet it explains the gradual transition into a committed state with no return. Encoding logics in a rate equation setting allows determination of binding properties beyond what is

  10. Open Architecture in Naval Combat System Computing of the 21st Century: Network-Centric Applications

    Science.gov (United States)

    2003-06-01

    also take advantage of other Navy, as well as other-service, open architecture initiatives. In addition to HiPer -D, several Navy Department programs...February 2003, pp. 42-46, at 43. 5Michael W. Masters, Chief Scientist, Advanced Computing Programs, NSWCDD, “ HiPer -D Open Architecture: Advanced

  11. Do design rules facilitate or complicate architectural innovation in innovation alliance networks?

    NARCIS (Netherlands)

    Hofman, Erwin; Halman, Johannes I.M.; van Looy, Bart

    2016-01-01

    Architectural innovation is fundamental to the renewal of technological systems. However, it can be a real challenge to organize architectural innovation, all the more so when success hinges upon close collaboration with other firms that are responsible for different subsystems of the end product.

  12. Network contingencies in the relationship between design rules and architectural innovation performance

    NARCIS (Netherlands)

    Hofman, Erwin; Halman, Johannes; van Looy, Bart

    2016-01-01

    Architectural innovation is fundamental to the renewal of technological systems. However, it can be a real challenge to organize architectural innovation, all the more so when success hinges upon close collaboration with other firms that are responsible for different subsystems of the end product.

  13. A Client-Server Architecture for an Instructional Environment Based on Computer Networks and the Internet.

    Science.gov (United States)

    Guidon, Jacques; Pierre, Samuel

    1996-01-01

    Discusses the use of computers in education and training and proposes a client-server architecture for an experimental computer environment as an approach to a virtual classroom. Highlights include the World Wide Web and client software, document delivery, hardware architecture, and Internet resources and services. (Author/LRW)

  14. The Salience Network and Its Functional Architecture in a Perceptual Decision: An Effective Connectivity Study.

    Science.gov (United States)

    Lamichhane, Bidhan; Dhamala, Mukesh

    2015-08-01

    The anterior insulae (INSs) are involved in accumulating sensory evidence in perceptual decision-making independent of the motor response, whereas the dorsal anterior cingulate cortex (dACC) is known to play a role in choosing appropriate behavioral responses. Recent evidence suggests that INSs and dACC are part of the salience network (SN), a key network known to be involved in decision-making and thought to be important for the coordination of behavioral responses. However, how these nodes in the SN contribute to the decision-making process from segregation of stimuli to the generation of an appropriate behavioral response remains unknown. In this study, the authors scanned 33 participants in functional magnetic resonance imaging and asked them to decide whether the presented pairs of audio (a beep of sound) and visual (a flash of light) stimuli were synchronous or asynchronous. Participants reported their perception with a button press. Stimuli were presented in block of eight pairs with a temporal lag (ΔT) between the first (audio) and the second (visual) stimulus in each pair. They used dynamic causal modeling (DCM) and the Bayesian model evidence technique to elucidate the functional architecture between the nodes of SN. Both the synchrony and the asynchrony perception resulted in strong activation in the SN. Most importantly, the DCM analyses demonstrated that the INSs were integrating as well as driving hubs in the SN. The INSs were found to a play an important role in the integration of sensory information; input to the SN is most likely through INSs. Furthermore, significant INSs to dACC intrinsic connectivity established by these task conditions help us conclude that INSs drive the dACC to guide the behavior of choosing the appropriate response. The authors therefore argue that the dACC and INS are part of a system involved in the decision-making process from perception to planning of a motor response, and that this observed functional mechanism might

  15. Structural architecture of the social network of a non-human primate (Macaca sylvanus): a study of its topology in La Forêt des Singes, Rocamadour.

    Science.gov (United States)

    Sosa, Sebastian

    2014-01-01

    For a decade, technological or natural networks have appeared to have a common mathematical architecture. This type of architecture has a node connectivity which follows a power law distribution. This architecture confers to these networks a resistance property to the loss of nodes. Such properties are advantageous for evolutional networks through time. Thus, this architecture can be expected in animal social networks. Another characteristic commonly met concerns the structuration of the network into communities by the mechanism of assortative mixing by vertex degree (i.e. by the number of ties individuals have). Such a structure is a reflection of evolutional mechanisms: the preferential attachment and the triadic closure processes. Using recent analytical techniques on an affiliative social network in a non-human primate species (Macaca sylvanus), we analysed the mathematical architecture and its properties. We demonstrate that in spite of the use of a recent protocol supposed to permit this type of analysis, the type of distribution cannot be clearly determined, encouraging us to carefully interpret the results obtained until then. Nevertheless, we observed interesting properties of the network at an ecological and evolutional level with network resilience that allows a cohesive society to be maintained even when faced with a catastrophe (high predation, epidemic).

  16. Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

    Directory of Open Access Journals (Sweden)

    Brian R Granger

    2016-04-01

    Full Text Available The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space, a dynamic stoichiometric modeling framework. Using VisANT's unique metagraph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction network between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues. VisANT is freely available at: http://visant.bu.edu and COMETS at http://comets.bu.edu.

  17. [Gene networks that regulate secondary metabolism in actinomycetes: pleiotropic regulators].

    Science.gov (United States)

    Rabyk, M V; Ostash, B O; Fedorenko, V O

    2014-01-01

    Current advances in the research and practical applications of pleiotropic regulatory genes for antibiotic production in actinomycetes are reviewed. The basic regulatory mechanisms found in these bacteria are outlined. Examples described in the review show the importance of the manipulation of regulatory systems that affect the synthesis of antibiotics for the metabolic engineering of the actinomycetes. Also, the study of these genes is the basis for the development of genetic engineering approaches towards the induction of "cryptic" part of the actinomycetes secondary metabolome, which capacity for production of biologically active compounds is much bigger than the diversity of antibiotics underpinned by traditional microbiological screening. Besides the practical problems, the study of regulatory genes for antibiotic biosynthesis will provide insights into the process of evolution of complex regulatory systems that coordinate the expression of gene operons, clusters and regulons, involved in the control of secondary metabolism and morphogenesis of actinomycetes.

  18. The Large-Scale Organization of Object-Responsive Cortex Is Reflected in Resting-State Network Architecture.

    Science.gov (United States)

    Konkle, Talia; Caramazza, Alfonso

    2017-10-01

    Neural responses to visually presented objects have a large-scale spatial organization across the cortex, related to the dimensions of animacy and object size. Most proposals about the origins of this organization point to the influence of differential connectivity with other cortical regions as the key organizing force that drives distinctions in object-responsive cortex. To explore this possibility, we used resting-state functional connectivity to examine the relationship between stimulus-evoked organization of objects, and distinctions in functional network architecture. Using a data-driven analysis, we found evidence for three distinct whole-brain resting-state networks that route through object-responsive cortex, and these naturally manifest the tripartite structure of the stimulus-evoked organization. However, object-responsive regions were also highly correlated with each other at rest. Together, these results point to a nested network architecture, with a local interconnected network across object-responsive cortex and distinctive subnetworks that specifically route these key object distinctions to distinct long-range regions. Broadly, these results point to the viability that long-range connections are a driving force of the large-scale organization of object-responsive cortex. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. [Controlling arachidonic acid metabolic network: from single- to multi-target inhibitors of key enzymes].

    Science.gov (United States)

    Liu, Ying; Chen, Zheng; Shang, Er-chang; Yang, Kun; Wei, Deng-guo; Zhou, Lu; Jiang, Xiao-lu; He, Chong; Lai, Lu-hua

    2009-03-01

    Inflammatory diseases are common medical conditions seen in disorders of human immune system. There is a great demand for anti-inflammatory drugs. There are major inflammatory mediators in arachidonic acid metabolic network. Several enzymes in this network have been used as key targets for the development of anti-inflammatory drugs. However, specific single-target inhibitors can not sufficiently control the network balance and may cause side effects at the same time. Most inflammation induced diseases come from the complicated coupling of inflammatory cascades involving multiple targets. In order to treat these complicated diseases, drugs that can intervene multi-targets at the same time attracted much attention. The goal of this review is mainly focused on the key enzymes in arachidonic acid metabolic network, such as phospholipase A2, cyclooxygenase, 5-lipoxygenase and eukotriene A4 hydrolase. Advance in single target and multi-targe inhibitors is summarized.

  20. Human-Centered Development of an Online Social Network for Metabolic Syndrome Management.

    Science.gov (United States)

    Núñez-Nava, Jefersson; Orozco-Sánchez, Paola A; López, Diego M; Ceron, Jesus D; Alvarez-Rosero, Rosa E

    2016-01-01

    According to the International Diabetes Federation (IDF), a quarter of the world's population has Metabolic Syndrome (MS). To develop (and assess the users' degree of satisfaction of) an online social network for patients who suffer from Metabolic Syndrome, based on the recommendations and requirements of the Human-Centered Design. Following the recommendations of the ISO 9241-210 for Human-Centered Design (HCD), an online social network was designed to promote physical activity and healthy nutrition. In order to guarantee the active participation of the users during the development of the social network, a survey, an in-depth interview, a focal group, and usability tests were carried out with people suffering from MS. The study demonstrated how the different activities, recommendations, and requirements of the ISO 9241-210 are integrated into a traditional software development process. Early usability tests demonstrated that the user's acceptance and the effectiveness and efficiency of the social network are satisfactory.