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.

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

2013-09-01

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.

Architectures of electro-optical packet switched networks

DEFF Research Database (Denmark)

Berger, Michael Stubert

2004-01-01

and examines possible architectures for future high capacity networks with high capacity nodes. It is assumed that optics will play a key role in this scenario, and in this respect, the European IST research project DAVID aimed at proposing viable architectures for optical packet switching, exploiting the best...... 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...... architecture for a buffered crossbar switch is presented. The architecture uses two levels of backpressure (flow control) with different constraints on round trip time. No additional scheduling complexity is introduced, and for the actual example shown, a reduction in memory of 75% was obtained at the cost...

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.

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.

Hybrid architecture for building secure sensor networks

Science.gov (United States)

Owens, Ken R., Jr.; Watkins, Steve E.

2012-04-01

Sensor networks have various communication and security architectural concerns. Three approaches are defined to address these concerns for sensor networks. The first area is the utilization of new computing architectures that leverage embedded virtualization software on the sensor. Deploying a small, embedded virtualization operating system on the sensor nodes that is designed to communicate to low-cost cloud computing infrastructure in the network is the foundation to delivering low-cost, secure sensor networks. The second area focuses on securing the sensor. Sensor security components include developing an identification scheme, and leveraging authentication algorithms and protocols that address security assurance within the physical, communication network, and application layers. This function will primarily be accomplished through encrypting the communication channel and integrating sensor network firewall and intrusion detection/prevention components to the sensor network architecture. Hence, sensor networks will be able to maintain high levels of security. The third area addresses the real-time and high priority nature of the data that sensor networks collect. This function requires that a quality-of-service (QoS) definition and algorithm be developed for delivering the right data at the right time. A hybrid architecture is proposed that combines software and hardware features to handle network traffic with diverse QoS requirements.

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.

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...

Satellite ATM Networks: Architectures and Guidelines Developed

Science.gov (United States)

vonDeak, Thomas C.; Yegendu, Ferit

1999-01-01

An important element of satellite-supported asynchronous transfer mode (ATM) networking will involve support for the routing and rerouting of active connections. Work published under the auspices of the Telecommunications Industry Association (http://www.tiaonline.org), describes basic architectures and routing protocol issues for satellite ATM (SATATM) networks. The architectures and issues identified will serve as a basis for further development of technical specifications for these SATATM networks. Three ATM network architectures for bent pipe satellites and three ATM network architectures for satellites with onboard ATM switches were developed. The architectures differ from one another in terms of required level of mobility, supported data rates, supported terrestrial interfaces, and onboard processing and switching requirements. The documentation addresses low-, middle-, and geosynchronous-Earth-orbit satellite configurations. The satellite environment may require real-time routing to support the mobility of end devices and nodes of the ATM network itself. This requires the network to be able to reroute active circuits in real time. In addition to supporting mobility, rerouting can also be used to (1) optimize network routing, (2) respond to changing quality-of-service requirements, and (3) provide a fault tolerance mechanism. Traffic management and control functions are necessary in ATM to ensure that the quality-of-service requirements associated with each connection are not violated and also to provide flow and congestion control functions. Functions related to traffic management were identified and described. Most of these traffic management functions will be supported by on-ground ATM switches, but in a hybrid terrestrial-satellite ATM network, some of the traffic management functions may have to be supported by the onboard satellite ATM switch. Future work is planned to examine the tradeoffs of placing traffic management functions onboard a satellite as

Intrinsic and task-evoked network architectures of the human brain

Science.gov (United States)

Cole, Michael W.; Bassett, Danielle S.; Power, Jonathan D.; Braver, Todd S.; Petersen, Steven E.

2014-01-01

Summary Many functional network properties of the human brain have been identified during rest and task states, yet it remains unclear how the two relate. We identified a whole-brain network architecture present across dozens of task states that was highly similar to the resting-state network architecture. The most frequent functional connectivity strengths across tasks closely matched the strengths observed at rest, suggesting this is an “intrinsic”, standard architecture of functional brain organization. Further, a set of small but consistent changes common across tasks suggests the existence of a task-general network architecture distinguishing task states from rest. These results indicate the brain’s functional network architecture during task performance is shaped primarily by an intrinsic network architecture that is also present during rest, and secondarily by evoked task-general and task-specific network changes. This establishes a strong relationship between resting-state functional connectivity and task-evoked functional connectivity – areas of neuroscientific inquiry typically considered separately. PMID:24991964

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.

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...

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.

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...

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

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

Mobile network architecture of the long-range WindScanner system

OpenAIRE

Vasiljevic, Nikola; Lea, Guillaume; Hansen, Per; Jensen, Henrik M.

2016-01-01

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...

Optical Neural Network Classifier Architectures

National Research Council Canada - National Science Library

Getbehead, Mark

1998-01-01

We present an adaptive opto-electronic neural network hardware architecture capable of exploiting parallel optics to realize real-time processing and classification of high-dimensional data for Air...

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

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

Software Defined Networking (SDN) controlled all optical switching networks with multi-dimensional switching architecture

Science.gov (United States)

Zhao, Yongli; Ji, Yuefeng; Zhang, Jie; Li, Hui; Xiong, Qianjin; Qiu, Shaofeng

2014-08-01

Ultrahigh throughout capacity requirement is challenging the current optical switching nodes with the fast development of data center networks. Pbit/s level all optical switching networks need to be deployed soon, which will cause the high complexity of node architecture. How to control the future network and node equipment together will become a new problem. An enhanced Software Defined Networking (eSDN) control architecture is proposed in the paper, which consists of Provider NOX (P-NOX) and Node NOX (N-NOX). With the cooperation of P-NOX and N-NOX, the flexible control of the entire network can be achieved. All optical switching network testbed has been experimentally demonstrated with efficient control of enhanced Software Defined Networking (eSDN). Pbit/s level all optical switching nodes in the testbed are implemented based on multi-dimensional switching architecture, i.e. multi-level and multi-planar. Due to the space and cost limitation, each optical switching node is only equipped with four input line boxes and four output line boxes respectively. Experimental results are given to verify the performance of our proposed control and switching architecture.

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...

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

Directory of Open Access Journals (Sweden)

Kim Hyun

2011-12-01

Full Text Available Abstract Background 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. Results 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. Conclusions 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.

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.

dSDiVN: a distributed Software-Defined Networking architecture for Infrastructure-less Vehicular Networks

OpenAIRE

Alioua, Ahmed; Senouci, Sidi-Mohammed; Moussaoui, Samira

2017-01-01

In the last few years, the emerging network architecture paradigm of Software-Defined Networking (SDN), has become one of the most important technology to manage large scale networks such as Vehicular Ad-hoc Networks (VANETs). Recently, several works have shown interest in the use of SDN paradigm in VANETs. SDN brings flexibility, scalability and management facility to current VANETs. However, almost all of proposed Software-Defined VANET (SDVN) architectures are infrastructure-based. This pa...

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...

Scaling architecture-on-demand based optical networks

NARCIS (Netherlands)

Meyer, Hugo; Sancho, Jose Carlos; Mrdakovic, Milica; Peng, Shuping; Simeonidou, Dimitra; Miao, Wang; Calabretta, Nicola

2016-01-01

This paper analyzes methodologies that allow scaling properly Architecture-On-Demand (AoD) based optical networks. As Data Centers and HPC systems are growing in size and complexity, optical networks seem to be the way to scale the bandwidth of current network infrastructures. To scale the number of

Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks.

Science.gov (United States)

Gorochowski, Thomas E; Grierson, Claire S; di Bernardo, Mario

2018-03-01

Network motifs are significantly overrepresented subgraphs that have been proposed as building blocks for natural and engineered networks. Detailed functional analysis has been performed for many types of motif in isolation, but less is known about how motifs work together to perform complex tasks. To address this issue, we measure the aggregation of network motifs via methods that extract precisely how these structures are connected. Applying this approach to a broad spectrum of networked systems and focusing on the widespread feed-forward loop motif, we uncover striking differences in motif organization. The types of connection are often highly constrained, differ between domains, and clearly capture architectural principles. We show how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli . Our findings have implications for understanding how networked systems are constructed from motif parts and elucidate constraints that guide their evolution.

Mobile network architecture of the long-range WindScanner system

DEFF Research Database (Denmark)

Vasiljevic, Nikola; Lea, Guillaume; Hansen, Per

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...

Software Defined Networks in Wireless Sensor Architectures

Directory of Open Access Journals (Sweden)

Jesús Antonio Puente Fernández

2018-03-01

Full Text Available Nowadays, different protocols coexist in Internet that provides services to users. Unfortunately, control decisions and distributed management make it hard to control networks. These problems result in an inefficient and unpredictable network behaviour. Software Defined Networks (SDN is a new concept of network architecture. It intends to be more flexible and to simplify the management in networks with respect to traditional architectures. Each of these aspects are possible because of the separation of control plane (controller and data plane (switches in network devices. OpenFlow is the most common protocol for SDN networks that provides the communication between control and data planes. Moreover, the advantage of decoupling control and data planes enables a quick evolution of protocols and also its deployment without replacing data plane switches. In this survey, we review the SDN technology and the OpenFlow protocol and their related works. Specifically, we describe some technologies as Wireless Sensor Networks and Wireless Cellular Networks and how SDN can be included within them in order to solve their challenges. We classify different solutions for each technology attending to the problem that is being fixed.

Emulation of Neural Networks on a Nanoscale Architecture

International Nuclear Information System (INIS)

Eshaghian-Wilner, Mary M; Friesz, Aaron; Khitun, Alex; Navab, Shiva; Parker, Alice C; Wang, Kang L; Zhou, Chongwu

2007-01-01

In this paper, we propose using a nanoscale spin-wave-based architecture for implementing neural networks. We show that this architecture can efficiently realize highly interconnected neural network models such as the Hopfield model. In our proposed architecture, no point-to-point interconnection is required, so unlike standard VLSI design, no fan-in/fan-out constraint limits the interconnectivity. Using spin-waves, each neuron could broadcast to all other neurons simultaneously and similarly a neuron could concurrently receive and process multiple data. Therefore in this architecture, the total weighted sum to each neuron can be computed by the sum of the values from all the incoming waves to that neuron. In addition, using the superposition property of waves, this computation can be done in O(1) time, and neurons can update their states quite rapidly

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.

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, ...

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

Smart business networks: architectural aspects and risks

NARCIS (Netherlands)

L-F. Pau (Louis-François)

2004-01-01

textabstractThis paper summarizes key attributes and the uniqueness of smart business networks [1], to propose thereafter an operational implementation architecture. It involves, amongst others, the embedding of business logic specific to a network of business partners, inside the communications

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...

Network topology exploration of mesh-based coarse-grain reconfigurable architectures

NARCIS (Netherlands)

Bansal, N.; Gupta, S.; Dutt, N.D.; Nicolau, A.; Gupta, R.

2004-01-01

Several coarse-grain reconfigurable architectures proposed recently consist of a large number of processing elements (PEs) connected in a mesh-like network topology. We study the effects of three aspects of network topology exploration on the performance of applications on these architectures: (a)

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.

Microsoft Windows 2000 Network Architecture Guide

National Research Council Canada - National Science Library

Bartock, Paul

2000-01-01

The purpose of this guide is to inform the reader about the services that are available in the Microsoft Windows 2000 environment and how to integrate these services into their network architecture...

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...

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.

Designing network on-chip architectures in the nanoscale era

CERN Document Server

Flich, Jose

2010-01-01

Going beyond isolated research ideas and design experiences, Designing Network On-Chip Architectures in the Nanoscale Era covers the foundations and design methods of network on-chip (NoC) technology. The contributors draw on their own lessons learned to provide strong practical guidance on various design issues.Exploring the design process of the network, the first part of the book focuses on basic aspects of switch architecture and design, topology selection, and routing implementation. In the second part, contributors discuss their experiences in the industry, offering a roadmap to recent p

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.

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…

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...

Tree-based server-middleman-client architecture: improving scalability and reliability for voting-based network games in ad hoc wireless networks

Science.gov (United States)

Guo, Y.; Fujinoki, H.

2006-10-01

The concept of a new tree-based architecture for networked multi-player games was proposed by Matuszek to improve scalability in network traffic at the same time to improve reliability. The architecture (we refer it as "Tree-Based Server- Middlemen-Client architecture") will solve the two major problems in ad-hoc wireless networks: frequent link failures and significance in battery power consumption at wireless transceivers by using two new techniques, recursive aggregation of client messages and subscription-based propagation of game state. However, the performance of the TBSMC architecture has never been quantitatively studied. In this paper, the TB-SMC architecture is compared with the client-server architecture using simulation experiments. We developed an event driven simulator to evaluate the performance of the TB-SMC architecture. In the network traffic scalability experiments, the TB-SMC architecture resulted in less than 1/14 of the network traffic load for 200 end users. In the reliability experiments, the TB-SMC architecture improved the number of successfully delivered players' votes by 31.6, 19.0, and 12.4% from the clientserver architecture at high (failure probability of 90%), moderate (50%) and low (10%) failure probability.

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…

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.

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

Convolutional neural network architectures for predicting DNA–protein binding

Science.gov (United States)

Zeng, Haoyang; Edwards, Matthew D.; Liu, Ge; Gifford, David K.

2016-01-01

Motivation: Convolutional neural networks (CNN) have outperformed conventional methods in modeling the sequence specificity of DNA–protein binding. Yet inappropriate CNN architectures can yield poorer performance than simpler models. Thus an in-depth understanding of how to match CNN architecture to a given task is needed to fully harness the power of CNNs for computational biology applications. Results: We present a systematic exploration of CNN architectures for predicting DNA sequence binding using a large compendium of transcription factor datasets. We identify the best-performing architectures by varying CNN width, depth and pooling designs. We find that adding convolutional kernels to a network is important for motif-based tasks. We show the benefits of CNNs in learning rich higher-order sequence features, such as secondary motifs and local sequence context, by comparing network performance on multiple modeling tasks ranging in difficulty. We also demonstrate how careful construction of sequence benchmark datasets, using approaches that control potentially confounding effects like positional or motif strength bias, is critical in making fair comparisons between competing methods. We explore how to establish the sufficiency of training data for these learning tasks, and we have created a flexible cloud-based framework that permits the rapid exploration of alternative neural network architectures for problems in computational biology. Availability and Implementation: All the models analyzed are available at http://cnn.csail.mit.edu. Contact: gifford@mit.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307608

Stability of Ecological Communities and the Architecture of Mutualistic and Trophic Networks

NARCIS (Netherlands)

Thebault, E.M.C.; Fontaine, C.

2010-01-01

Research on the relationship between the architecture of ecological networks and community stability has mainly focused on one type of interaction at a time, making difficult any comparison between different network types. We used a theoretical approach to show that the network architecture favoring

Learning, memory, and the role of neural network architecture.

Directory of Open Access Journals (Sweden)

Ann M Hermundstad

2011-06-01

Full Text Available The performance of information processing systems, from artificial neural networks to natural neuronal ensembles, depends heavily on the underlying system architecture. In this study, we compare the performance of parallel and layered network architectures during sequential tasks that require both acquisition and retention of information, thereby identifying tradeoffs between learning and memory processes. During the task of supervised, sequential function approximation, networks produce and adapt representations of external information. Performance is evaluated by statistically analyzing the error in these representations while varying the initial network state, the structure of the external information, and the time given to learn the information. We link performance to complexity in network architecture by characterizing local error landscape curvature. We find that variations in error landscape structure give rise to tradeoffs in performance; these include the ability of the network to maximize accuracy versus minimize inaccuracy and produce specific versus generalizable representations of information. Parallel networks generate smooth error landscapes with deep, narrow minima, enabling them to find highly specific representations given sufficient time. While accurate, however, these representations are difficult to generalize. In contrast, layered networks generate rough error landscapes with a variety of local minima, allowing them to quickly find coarse representations. Although less accurate, these representations are easily adaptable. The presence of measurable performance tradeoffs in both layered and parallel networks has implications for understanding the behavior of a wide variety of natural and artificial learning systems.

Greening radio access networks using distributed base station architectures

DEFF Research Database (Denmark)

Kardaras, Georgios; Soler, José; Dittmann, Lars

2010-01-01

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...... 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...

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...

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.

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

Energy Technology Data Exchange (ETDEWEB)

Chaiboonchoe, Amphun; Dohai, Bushra Saeed; Cai, Hong; Nelson, David R. [Division of Science and Math, New York University Abu Dhabi, Abu Dhabi (United Arab Emirates); Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi Institute, Abu Dhabi (United Arab Emirates); Jijakli, Kenan [Division of Science and Math, New York University Abu Dhabi, Abu Dhabi (United Arab Emirates); Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi Institute, Abu Dhabi (United Arab Emirates); Engineering Division, Biofinery, Manhattan, KS (United States); Salehi-Ashtiani, Kourosh, E-mail: ksa3@nyu.edu [Division of Science and Math, New York University Abu Dhabi, Abu Dhabi (United Arab Emirates); Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi Institute, Abu Dhabi (United Arab Emirates)

2014-12-10

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.

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)

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

Energy Technology Data Exchange (ETDEWEB)

Lee, C. K. [Instrument and Control Section, Lungmen Nuclear Power Station, Taiwan Power Company, Taipei County Taiwan (China)

2006-07-01

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)

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.

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,

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.

Network architectures and protocols for the integration of ACTS and ISDN

Science.gov (United States)

Chitre, D. M.; Lowry, P. A.

1992-01-01

A close integration of satellite networks and the integrated services digital network (ISDN) is essential for satellite networks to carry ISDN traffic effectively. This also shows how a given (pre-ISDN) satellite network architecture can be enhanced to handle ISDN signaling and provide ISDN services. It also describes the functional architecture and high-level protocols that could be implemented in the NASA Advanced Communications Technology Satellite (ACTS) low burst rate communications system to provide ISDN services.

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

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

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

High-performance, scalable optical network-on-chip architectures

Science.gov (United States)

Tan, Xianfang

The rapid advance of technology enables a large number of processing cores to be integrated into a single chip which is called a Chip Multiprocessor (CMP) or a Multiprocessor System-on-Chip (MPSoC) design. The on-chip interconnection network, which is the communication infrastructure for these processing cores, plays a central role in a many-core system. With the continuously increasing complexity of many-core systems, traditional metallic wired electronic networks-on-chip (NoC) became a bottleneck because of the unbearable latency in data transmission and extremely high energy consumption on chip. Optical networks-on-chip (ONoC) has been proposed as a promising alternative paradigm for electronic NoC with the benefits of optical signaling communication such as extremely high bandwidth, negligible latency, and low power consumption. This dissertation focus on the design of high-performance and scalable ONoC architectures and the contributions are highlighted as follow: 1. A micro-ring resonator (MRR)-based Generic Wavelength-routed Optical Router (GWOR) is proposed. A method for developing any sized GWOR is introduced. GWOR is a scalable non-blocking ONoC architecture with simple structure, low cost and high power efficiency compared to existing ONoC designs. 2. To expand the bandwidth and improve the fault tolerance of the GWOR, a redundant GWOR architecture is designed by cascading different type of GWORs into one network. 3. The redundant GWOR built with MRR-based comb switches is proposed. Comb switches can expand the bandwidth while keep the topology of GWOR unchanged by replacing the general MRRs with comb switches. 4. A butterfly fat tree (BFT)-based hybrid optoelectronic NoC (HONoC) architecture is developed in which GWORs are used for global communication and electronic routers are used for local communication. The proposed HONoC uses less numbers of electronic routers and links than its counterpart of electronic BFT-based NoC. It takes the advantages of

Environmental versatility promotes modularity in genome-scale metabolic networks.

Science.gov (United States)

Samal, Areejit; Wagner, Andreas; Martin, Olivier C

2011-08-24

The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new arrangements that may benefit their carrier. Conversely, modularity may emerge as a by-product of some trait. We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chemical environments. For such networks, we define a network module as a maximal set of reactions that are fully coupled, i.e., whose fluxes can only vary in fixed proportions. This definition overcomes limitations of purely graph based analyses of metabolism by exploiting the functional links between reactions. We call a metabolic network viable in a given chemical environment if it can synthesize all of an organism's biomass compounds from nutrients in this environment. An organism's metabolism is highly versatile if it can sustain life in many different chemical environments. We here ask whether versatility affects the modularity of metabolic networks. Using recently developed techniques to randomly sample large numbers of viable metabolic networks from a vast space of metabolic networks, we use flux balance analysis to study in silico metabolic networks that differ in their versatility. We find that highly versatile networks are also highly modular. They contain more modules and more reactions that are organized into modules. Most or all reactions in a module are associated with the same biochemical pathways. Modules that arise in highly versatile networks generally involve reactions that process nutrients or closely related chemicals. We also observe that the metabolism of E. coli is significantly more modular than even our most versatile networks. Our work shows that modularity in metabolic networks can be a by-product of functional constraints, e.g., the need to sustain life in multiple

Environmental versatility promotes modularity in genome-scale metabolic networks

Directory of Open Access Journals (Sweden)

Wagner Andreas

2011-08-01

Full Text Available Abstract Background The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new arrangements that may benefit their carrier. Conversely, modularity may emerge as a by-product of some trait. We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chemical environments. For such networks, we define a network module as a maximal set of reactions that are fully coupled, i.e., whose fluxes can only vary in fixed proportions. This definition overcomes limitations of purely graph based analyses of metabolism by exploiting the functional links between reactions. We call a metabolic network viable in a given chemical environment if it can synthesize all of an organism's biomass compounds from nutrients in this environment. An organism's metabolism is highly versatile if it can sustain life in many different chemical environments. We here ask whether versatility affects the modularity of metabolic networks. Results Using recently developed techniques to randomly sample large numbers of viable metabolic networks from a vast space of metabolic networks, we use flux balance analysis to study in silico metabolic networks that differ in their versatility. We find that highly versatile networks are also highly modular. They contain more modules and more reactions that are organized into modules. Most or all reactions in a module are associated with the same biochemical pathways. Modules that arise in highly versatile networks generally involve reactions that process nutrients or closely related chemicals. We also observe that the metabolism of E. coli is significantly more modular than even our most versatile networks. Conclusions Our work shows that modularity in metabolic networks can be a by-product of functional

Mobile opportunistic networks architectures, protocols and applications

CERN Document Server

Denko, Mieso K

2011-01-01

Widespread availability of pervasive and mobile devices coupled with recent advances in networking technologies make opportunistic networks one of the most promising communication technologies for a growing number of future mobile applications. Covering the basics as well as advanced concepts, this book introduces state-of-the-art research findings, technologies, tools, and innovations. Prominent researchers from academia and industry report on communication architectures, network algorithms and protocols, emerging applications, experimental studies, simulation tools, implementation test beds,

Enabling Tussle-Agile Inter-networking Architectures by Underlay Virtualisation

Science.gov (United States)

Dianati, Mehrdad; Tafazolli, Rahim; Moessner, Klaus

In this paper, we propose an underlay inter-network virtualisation framework in order to enable tussle-agile flexible networking over the existing inter-network infrastructures. The functionalities that inter-networking elements (transit nodes, access networks, etc.) need to support in order to enable virtualisation are discussed. We propose the base architectures of each the abstract elements to support the required inter-network virtualisation functionalities.

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.

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

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.

Flux networks in metabolic graphs

International Nuclear Information System (INIS)

Warren, P B; Queiros, S M Duarte; Jones, J L

2009-01-01

A metabolic model can be represented as a bipartite graph comprising linked reaction and metabolite nodes. Here it is shown how a network of conserved fluxes can be assigned to the edges of such a graph by combining the reaction fluxes with a conserved metabolite property such as molecular weight. A similar flux network can be constructed by combining the primal and dual solutions to the linear programming problem that typically arises in constraint-based modelling. Such constructions may help with the visualization of flux distributions in complex metabolic networks. The analysis also explains the strong correlation observed between metabolite shadow prices (the dual linear programming variables) and conserved metabolite properties. The methods were applied to recent metabolic models for Escherichia coli, Saccharomyces cerevisiae and Methanosarcina barkeri. Detailed results are reported for E. coli; similar results were found for other organisms

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

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. .

Noise effect in metabolic networks

International Nuclear Information System (INIS)

Zheng-Yan, Li; Zheng-Wei, Xie; Tong, Chen; Qi, Ouyang

2009-01-01

Constraint-based models such as flux balance analysis (FBA) are a powerful tool to study biological metabolic networks. Under the hypothesis that cells operate at an optimal growth rate as the result of evolution and natural selection, this model successfully predicts most cellular behaviours in growth rate. However, the model ignores the fact that cells can change their cellular metabolic states during evolution, leaving optimal metabolic states unstable. Here, we consider all the cellular processes that change metabolic states into a single term 'noise', and assume that cells change metabolic states by randomly walking in feasible solution space. By simulating a state of a cell randomly walking in the constrained solution space of metabolic networks, we found that in a noisy environment cells in optimal states tend to travel away from these points. On considering the competition between the noise effect and the growth effect in cell evolution, we found that there exists a trade-off between these two effects. As a result, the population of the cells contains different cellular metabolic states, and the population growth rate is at suboptimal states. (cross-disciplinary physics and related areas of science and technology)

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.

Separating VNF and Network Control for Hardware‐Acceleration of SDN/NFV Architecture

Directory of Open Access Journals (Sweden)

Tong Duan

2017-08-01

Full Text Available A hardware‐acceleration architecture that separates virtual network functions (VNFs and network control (called HSN is proposed to solve the mismatch between the simple flow steering requirements and strong packet processing abilities of software‐defined networking (SDN forwarding elements (FEs in SDN/network function virtualization (NFV architecture, while improving the efficiency of NFV infrastructure and the performance of network‐intensive functions. HSN makes full use of FEs and accelerates VNFs through two mechanisms: (1 separation of traffic steering and packet processing in the FEs; (2 separation of SDN and NFV control in the FEs. Our HSN prototype, built on NetFPGA‐10G, demonstrates that the processing performance can be greatly improved with only a small modification of the traditional SDN/NFV architecture.

Network architecture test-beds as platforms for ubiquitous computing.

Science.gov (United States)

Roscoe, Timothy

2008-10-28

Distributed systems research, and in particular ubiquitous computing, has traditionally assumed the Internet as a basic underlying communications substrate. Recently, however, the networking research community has come to question the fundamental design or 'architecture' of the Internet. This has been led by two observations: first, that the Internet as it stands is now almost impossible to evolve to support new functionality; and second, that modern applications of all kinds now use the Internet rather differently, and frequently implement their own 'overlay' networks above it to work around its perceived deficiencies. In this paper, I discuss recent academic projects to allow disruptive change to the Internet architecture, and also outline a radically different view of networking for ubiquitous computing that such proposals might facilitate.

Design of Network Architectures: Role of Game Theory and Economics

OpenAIRE

Shetty, Nikhil

2010-01-01

The economics of the market that a network architecture enables has a important bearing on its success and eventual adoption. Some of these economic issues are tightly coupled with the design of the network architecture. A poor design could end up making certain markets very difficult to enable, even if they are in the better interest of society. Theanalysis of these cross-disciplinary problems requires understanding both the technology and the economic aspects. This thesis introduces three m...

A multi-agent system architecture for sensor networks.

Science.gov (United States)

Fuentes-Fernández, Rubén; Guijarro, María; Pajares, Gonzalo

2009-01-01

The design of the control systems for sensor networks presents important challenges. Besides the traditional problems about how to process the sensor data to obtain the target information, engineers need to consider additional aspects such as the heterogeneity and high number of sensors, and the flexibility of these networks regarding topologies and the sensors in them. Although there are partial approaches for resolving these issues, their integration relies on ad hoc solutions requiring important development efforts. In order to provide an effective approach for this integration, this paper proposes an architecture based on the multi-agent system paradigm with a clear separation of concerns. The architecture considers sensors as devices used by an upper layer of manager agents. These agents are able to communicate and negotiate services to achieve the required functionality. Activities are organized according to roles related with the different aspects to integrate, mainly sensor management, data processing, communication and adaptation to changes in the available devices and their capabilities. This organization largely isolates and decouples the data management from the changing network, while encouraging reuse of solutions. The use of the architecture is facilitated by a specific modelling language developed through metamodelling. A case study concerning a generic distributed system for fire fighting illustrates the approach and the comparison with related work.

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

Network based control point for UPnP QoS architecture

DEFF Research Database (Denmark)

Brewka, Lukasz Jerzy; Wessing, Henrik; Rossello Busquet, Ana

2011-01-01

Enabling coexistence of non-UPnP Devices in an UPnP QoS Architecture is an important issue that might have a major impact on the deployment and usability of UPnP in future home networks. The work presented here shows potential issues of placing non-UPnP Device in the network managed by UPnP QoS. We...... address this issue by extensions to the UPnP QoS Architecture that can prevent non-UPnP Devices from degrading the overall QoS level. The obtained results show that deploying Network Based Control Point service with efficient traffic classifier, improves significantly the end-to-end packet delay...

Routing architecture and security for airborne networks

Science.gov (United States)

Deng, Hongmei; Xie, Peng; Li, Jason; Xu, Roger; Levy, Renato

2009-05-01

Airborne networks are envisioned to provide interconnectivity for terrestial and space networks by interconnecting highly mobile airborne platforms. A number of military applications are expected to be used by the operator, and all these applications require proper routing security support to establish correct route between communicating platforms in a timely manner. As airborne networks somewhat different from traditional wired and wireless networks (e.g., Internet, LAN, WLAN, MANET, etc), security aspects valid in these networks are not fully applicable to airborne networks. Designing an efficient security scheme to protect airborne networks is confronted with new requirements. In this paper, we first identify a candidate routing architecture, which works as an underlying structure for our proposed security scheme. And then we investigate the vulnerabilities and attack models against routing protocols in airborne networks. Based on these studies, we propose an integrated security solution to address routing security issues in airborne networks.

Control of fluxes in metabolic networks

Science.gov (United States)

Basler, Georg; Nikoloski, Zoran; Larhlimi, Abdelhalim; Barabási, Albert-László; Liu, Yang-Yu

2016-01-01

Understanding the control of large-scale metabolic networks is central to biology and medicine. However, existing approaches either require specifying a cellular objective or can only be used for small networks. We introduce new coupling types describing the relations between reaction activities, and develop an efficient computational framework, which does not require any cellular objective for systematic studies of large-scale metabolism. We identify the driver reactions facilitating control of 23 metabolic networks from all kingdoms of life. We find that unicellular organisms require a smaller degree of control than multicellular organisms. Driver reactions are under complex cellular regulation in Escherichia coli, indicating their preeminent role in facilitating cellular control. In human cancer cells, driver reactions play pivotal roles in malignancy and represent potential therapeutic targets. The developed framework helps us gain insights into regulatory principles of diseases and facilitates design of engineering strategies at the interface of gene regulation, signaling, and metabolism. PMID:27197218

Small-worldness and gender differences of large scale brain metabolic covariance networks in young adults: a FDG PET study of 400 subjects.

Science.gov (United States)

Hu, Yuxiao; Xu, Qiang; Shen, Junkang; Li, Kai; Zhu, Hong; Zhang, Zhiqiang; Lu, Guangming

2015-02-01

Many studies have demonstrated the small-worldness of the human brain, and have revealed a sexual dimorphism in brain network properties. However, little is known about the gender effects on the topological organization of the brain metabolic covariance networks. To investigate the small-worldness and the gender differences in the topological architectures of human brain metabolic networks. FDG-PET data of 400 healthy right-handed subjects (200 women and 200 age-matched men) were involved in the present study. Metabolic networks of each gender were constructed by calculating the covariance of regional cerebral glucose metabolism (rCMglc) across subjects on the basis of AAL parcellation. Gender differences of network and nodal properties were investigated by using the graph theoretical approaches. Moreover, the gender-related difference of rCMglc in each brain region was tested for investigating the relationships between the hub regions and the brain regions showing significant gender-related differences in rCMglc. We found prominent small-world properties in the domain of metabolic networks in each gender. No significant gender difference in the global characteristics was found. Gender differences of nodal characteristic were observed in a few brain regions. We also found bilateral and lateralized distributions of network hubs in the females and males. Furthermore, we first reported that some hubs of a gender located in the brain regions showing weaker rCMglc in this gender than the other gender. The present study demonstrated that small-worldness was existed in metabolic networks, and revealed gender differences of organizational patterns in metabolic network. These results maybe provided insights into the understanding of the metabolic substrates underlying individual differences in cognition and behaviors. © The Foundation Acta Radiologica 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

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.

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.

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.

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.

Pathway discovery in metabolic networks by subgraph extraction.

Science.gov (United States)

Faust, Karoline; Dupont, Pierre; Callut, Jérôme; van Helden, Jacques

2010-05-01

Subgraph extraction is a powerful technique to predict pathways from biological networks and a set of query items (e.g. genes, proteins, compounds, etc.). It can be applied to a variety of different data types, such as gene expression, protein levels, operons or phylogenetic profiles. In this article, we investigate different approaches to extract relevant pathways from metabolic networks. Although these approaches have been adapted to metabolic networks, they are generic enough to be adjusted to other biological networks as well. We comparatively evaluated seven sub-network extraction approaches on 71 known metabolic pathways from Saccharomyces cerevisiae and a metabolic network obtained from MetaCyc. The best performing approach is a novel hybrid strategy, which combines a random walk-based reduction of the graph with a shortest paths-based algorithm, and which recovers the reference pathways with an accuracy of approximately 77%. Most of the presented algorithms are available as part of the network analysis tool set (NeAT). The kWalks method is released under the GPL3 license.

SELECTING NEURAL NETWORK ARCHITECTURE FOR INVESTMENT PROFITABILITY PREDICTIONS

Directory of Open Access Journals (Sweden)

Marijana Zekić-Sušac

2012-07-01

Full Text Available After production and operations, finance and investments are one of the mostfrequent areas of neural network applications in business. The lack of standardizedparadigms that can determine the efficiency of certain NN architectures in a particularproblem domain is still present. The selection of NN architecture needs to take intoconsideration the type of the problem, the nature of the data in the model, as well as somestrategies based on result comparison. The paper describes previous research in that areaand suggests a forward strategy for selecting best NN algorithm and structure. Since thestrategy includes both parameter-based and variable-based testings, it can be used forselecting NN architectures as well as for extracting models. The backpropagation, radialbasis,modular, LVQ and probabilistic neural network algorithms were used on twoindependent sets: stock market and credit scoring data. The results show that neuralnetworks give better accuracy comparing to multiple regression and logistic regressionmodels. Since it is model-independant, the strategy can be used by researchers andprofessionals in other areas of application.

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 phenotypes from phenotypic arrays and in gene-deletion studies. They have also been used for gene expression analysis guided by metabolic network structure, leading to the identification of commonly regulated genes. Thus, genome-scale metabolic modeling currently stands out as one of the most promising...

A Multi-Agent System Architecture for Sensor Networks

Directory of Open Access Journals (Sweden)

María Guijarro

2009-12-01

Full Text Available The design of the control systems for sensor networks presents important challenges. Besides the traditional problems about how to process the sensor data to obtain the target information, engineers need to consider additional aspects such as the heterogeneity and high number of sensors, and the flexibility of these networks regarding topologies and the sensors in them. Although there are partial approaches for resolving these issues, their integration relies on ad hoc solutions requiring important development efforts. In order to provide an effective approach for this integration, this paper proposes an architecture based on the multi-agent system paradigm with a clear separation of concerns. The architecture considers sensors as devices used by an upper layer of manager agents. These agents are able to communicate and negotiate services to achieve the required functionality. Activities are organized according to roles related with the different aspects to integrate, mainly sensor management, data processing, communication and adaptation to changes in the available devices and their capabilities. This organization largely isolates and decouples the data management from the changing network, while encouraging reuse of solutions. The use of the architecture is facilitated by a specific modelling language developed through metamodelling. A case study concerning a generic distributed system for fire fighting illustrates the approach and the comparison with related work.

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.

Regulation of metabolic networks by small molecule metabolites

Directory of Open Access Journals (Sweden)

Kanehisa Minoru

2007-03-01

Full Text Available Abstract Background The ability to regulate metabolism is a fundamental process in living systems. We present an analysis of one of the mechanisms by which metabolic regulation occurs: enzyme inhibition and activation by small molecules. We look at the network properties of this regulatory system and the relationship between the chemical properties of regulatory molecules. Results We find that many features of the regulatory network, such as the degree and clustering coefficient, closely match those of the underlying metabolic network. While these global features are conserved across several organisms, we do find local differences between regulation in E. coli and H. sapiens which reflect their different lifestyles. Chemical structure appears to play an important role in determining a compounds suitability for use in regulation. Chemical structure also often determines how groups of similar compounds can regulate sets of enzymes. These groups of compounds and the enzymes they regulate form modules that mirror the modules and pathways of the underlying metabolic network. We also show how knowledge of chemical structure and regulation could be used to predict regulatory interactions for drugs. Conclusion The metabolic regulatory network shares many of the global properties of the metabolic network, but often varies at the level of individual compounds. Chemical structure is a key determinant in deciding how a compound is used in regulation and for defining modules within the regulatory system.

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...

Cloud Radio Access Network architecture. Towards 5G mobile networks

DEFF Research Database (Denmark)

Checko, Aleksandra

Cloud Radio Access Network (C-RAN) is a novel mobile network architecture which can address a number of challenges that mobile operators face while trying to support ever-growing end-users’ needs towards 5th generation of mobile networks (5G). The main idea behind C-RAN is to split the base...... 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...... as to design the socalled fronthaul network, interconnecting those parts. This thesis focuses on quantifying those benefits and proposing a flexible and capacity-optimized fronthaul network. It is shown that a C-RAN with a functional split resulting in a variable bit rate on the fronthaul links brings cost...

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.

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.

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 .

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.

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...

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

Development of the network architecture of the Canadian MSAT system

Science.gov (United States)

Davies, N. George; Shoamanesh, Alireza; Leung, Victor C. M.

1988-05-01

A description is given of the present concept for the Canadian Mobile Satellite (MSAT) System and the development of the network architecture which will accommodate the planned family of three categories of service: a mobile radio service (MRS), a mobile telephone service (MTS), and a mobile data service (MDS). The MSAT satellite will have cross-strapped L-band and Ku-band transponders to provide communications services between L-band mobile terminals and fixed base stations supporting dispatcher-type MRS, gateway stations supporting MTS interconnections to the public telephone network, data hub stations supporting the MDS, and the network control center. The currently perceived centralized architecture with demand assignment multiple access for the circuit switched MRS, MTS and permanently assigned channels for the packet switched MDS is discussed.

Sirtuins as regulators of the yeast metabolic network

Directory of Open Access Journals (Sweden)

Markus eRalser

2012-03-01

Full Text Available There is growing evidence that the metabolic network is an integral regulator of cellularphysiology. Dynamic changes in metabolite concentrations, metabolic flux, or networktopology act as reporters of biological or environmental signals, and are required for the cellto trigger an appropriate biological reaction. Changes in the metabolic network are recognizedby specific sensory macromolecules and translated into a transcriptional or translationalresponse. The protein family of sirtuins, discovered more than 30 years ago as regulators ofsilent chromatin, seems to fulfill the role of a metabolic sensor during aging and conditions ofcaloric restriction. NAD+/NADH interconverting metabolic enzymes glyceraldehyde-3-phosphate dehydrogenase and alcohol dehydrogenase, as well as enzymes involved inNAD(H, synthesis provide or deprive NAD+ in close proximity to Sir2. This influence sirtuinactivity, and facilitates a dynamic response of the metabolic network to changes inmetabolism with effects on physiology and aging. The molecular network downstream Sir2,however, is complex. In just two orders, Sir2’s metabolism-related interactions span half ofthe yeast proteome, and are connected with virtually every physiological process. Thus,although it is fundamental to analyze single molecular mechanisms, it is at the same timecrucial to consider this genome-scale complexity when correlating single molecular eventswith phenotypes such as aging, cell growth, or stress resistance.

Area analysis of interconnection networks implemented on the honeycomb architecture

Energy Technology Data Exchange (ETDEWEB)

Milutinovic, D

1996-12-31

The are utilization of interconnection networks for parallel processing on one form of uniform parallel architecture of cellular type is analyzed. Formulae for the number of cells necessity to realize a networks and the efficiency factor of the system are derived. 15 refs.

Framewise phoneme classification with bidirectional LSTM and other neural network architectures.

Science.gov (United States)

Graves, Alex; Schmidhuber, Jürgen

2005-01-01

In this paper, we present bidirectional Long Short Term Memory (LSTM) networks, and a modified, full gradient version of the LSTM learning algorithm. We evaluate Bidirectional LSTM (BLSTM) and several other network architectures on the benchmark task of framewise phoneme classification, using the TIMIT database. Our main findings are that bidirectional networks outperform unidirectional ones, and Long Short Term Memory (LSTM) is much faster and also more accurate than both standard Recurrent Neural Nets (RNNs) and time-windowed Multilayer Perceptrons (MLPs). Our results support the view that contextual information is crucial to speech processing, and suggest that BLSTM is an effective architecture with which to exploit it.

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.

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

Science.gov (United States)

Aghdasi, Hadi S; Abbaspour, Maghsoud; Moghadam, Mohsen Ebrahimi; Samei, Yasaman

2008-08-04

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.

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

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.

Energy-aware architecture for multi-rate ad hoc networks

Directory of Open Access Journals (Sweden)

Ahmed Yahya

2010-06-01

Full Text Available The backbone of ad hoc network design is energy performance and bandwidth resources limitations. Multi-rate adaptation architectures have been proposed to reduce the control overhead and to increase bandwidth utilization efficiency. In this paper, we propose a multi-rate protocol to provide the highest network performance under very low control overhead. The efficiency of the proposed auto multi-rate protocol is validated extensive simulations using QualNet network simulator. The simulation results demonstrate that our solution significantly improves the overall network performance.

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

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.

Reconfiguration of Brain Network Architectures between Resting-State and Complexity-Dependent Cognitive Reasoning.

Science.gov (United States)

Hearne, Luke J; Cocchi, Luca; Zalesky, Andrew; Mattingley, Jason B

2017-08-30

Our capacity for higher cognitive reasoning has a measurable limit. This limit is thought to arise from the brain's capacity to flexibly reconfigure interactions between spatially distributed networks. Recent work, however, has suggested that reconfigurations of task-related networks are modest when compared with intrinsic "resting-state" network architecture. Here we combined resting-state and task-driven functional magnetic resonance imaging to examine how flexible, task-specific reconfigurations associated with increasing reasoning demands are integrated within a stable intrinsic brain topology. Human participants (21 males and 28 females) underwent an initial resting-state scan, followed by a cognitive reasoning task involving different levels of complexity, followed by a second resting-state scan. The reasoning task required participants to deduce the identity of a missing element in a 4 × 4 matrix, and item difficulty was scaled parametrically as determined by relational complexity theory. Analyses revealed that external task engagement was characterized by a significant change in functional brain modules. Specifically, resting-state and null-task demand conditions were associated with more segregated brain-network topology, whereas increases in reasoning complexity resulted in merging of resting-state modules. Further increments in task complexity did not change the established modular architecture, but affected selective patterns of connectivity between frontoparietal, subcortical, cingulo-opercular, and default-mode networks. Larger increases in network efficiency within the newly established task modules were associated with higher reasoning accuracy. Our results shed light on the network architectures that underlie external task engagement, and highlight selective changes in brain connectivity supporting increases in task complexity. SIGNIFICANCE STATEMENT Humans have clear limits in their ability to solve complex reasoning problems. It is thought that

Multi-equilibrium property of metabolic networks: SSI module

Directory of Open Access Journals (Sweden)

Chen Luonan

2011-06-01

Full Text Available Abstract Background Revealing the multi-equilibrium property of a metabolic network is a fundamental and important topic in systems biology. Due to the complexity of the metabolic network, it is generally a difficult task to study the problem as a whole from both analytical and numerical viewpoint. On the other hand, the structure-oriented modularization idea is a good choice to overcome such a difficulty, i.e. decomposing the network into several basic building blocks and then studying the whole network through investigating the dynamical characteristics of the basic building blocks and their interactions. Single substrate and single product with inhibition (SSI metabolic module is one type of the basic building blocks of metabolic networks, and its multi-equilibrium property has important influence on that of the whole metabolic networks. Results In this paper, we describe what the SSI metabolic module is, characterize the rates of the metabolic reactions by Hill kinetics and give a unified model for SSI modules by using a set of nonlinear ordinary differential equations with multi-variables. Specifically, a sufficient and necessary condition is first given to describe the injectivity of a class of nonlinear systems, and then, the sufficient condition is used to study the multi-equilibrium property of SSI modules. As a main theoretical result, for the SSI modules in which each reaction has no more than one inhibitor, a sufficient condition is derived to rule out multiple equilibria, i.e. the Jacobian matrix of its rate function is nonsingular everywhere. Conclusions In summary, we describe SSI modules and give a general modeling framework based on Hill kinetics, and provide a sufficient condition for ruling out multiple equilibria of a key type of SSI module.

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

A network architecture supporting consistent rich behavior in collaborative interactive applications.

Science.gov (United States)

Marsh, James; Glencross, Mashhuda; Pettifer, Steve; Hubbold, Roger

2006-01-01

Network architectures for collaborative virtual reality have traditionally been dominated by client-server and peer-to-peer approaches, with peer-to-peer strategies typically being favored where minimizing latency is a priority, and client-server where consistency is key. With increasingly sophisticated behavior models and the demand for better support for haptics, we argue that neither approach provides sufficient support for these scenarios and, thus, a hybrid architecture is required. We discuss the relative performance of different distribution strategies in the face of real network conditions and illustrate the problems they face. Finally, we present an architecture that successfully meets many of these challenges and demonstrate its use in a distributed virtual prototyping application which supports simultaneous collaboration for assembly, maintenance, and training applications utilizing haptics.

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...

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.

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.

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....

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.

Predicting metabolic pathways by sub-network extraction.

Science.gov (United States)

Faust, Karoline; van Helden, Jacques

2012-01-01

Various methods result in groups of functionally related genes obtained from genomes (operons, regulons, syntheny groups, and phylogenetic profiles), transcriptomes (co-expression groups) and proteomes (modules of interacting proteins). When such groups contain two or more enzyme-coding genes, graph analysis methods can be applied to extract a metabolic pathway that interconnects them. We describe here the way to use the Pathway extraction tool available on the NeAT Web server ( http://rsat.ulb.ac.be/neat/ ) to piece together the metabolic pathway from a group of associated, enzyme-coding genes. The tool identifies the reactions that can be catalyzed by the products of the query genes (seed reactions), and applies sub-graph extraction algorithms to extract from a metabolic network a sub-network that connects the seed reactions. This sub-network represents the predicted metabolic pathway. We describe here the pathway prediction process in a step-by-step way, give hints about the main parametric choices, and illustrate how this tool can be used to extract metabolic pathways from bacterial genomes, on the basis of two study cases: the isoleucine-valine operon in Escherichia coli and a predicted operon in Cupriavidus (Ralstonia) metallidurans.

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.

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.

Navigation Architecture for a Space Mobile Network

Science.gov (United States)

Valdez, Jennifer E.; Ashman, Benjamin; Gramling, Cheryl; Heckler, Gregory W.; Carpenter, Russell

2016-01-01

The Tracking and Data Relay Satellite System (TDRSS) Augmentation Service for Satellites (TASS) is a proposed beacon service to provide a global, space based GPS augmentation service based on the NASA Global Differential GPS (GDGPS) System. The TASS signal will be tied to the GPS time system and usable as an additional ranging and Doppler radiometric source. Additionally, it will provide data vital to autonomous navigation in the near Earth regime, including space weather information, TDRS ephemerides, Earth Orientation Parameters (EOP), and forward commanding capability. TASS benefits include enhancing situational awareness, enabling increased autonomy, and providing near real-time command access for user platforms. As NASA Headquarters' Space Communication and Navigation Office (SCaN) begins to move away from a centralized network architecture and towards a Space Mobile Network (SMN) that allows for user initiated services, autonomous navigation will be a key part of such a system. This paper explores how a TASS beacon service enables the Space Mobile Networking paradigm, what a typical user platform would require, and provides an in-depth analysis of several navigation scenarios and operations concepts. This paper provides an overview of the TASS beacon and its role within the SMN and user community. Supporting navigation analysis is presented for two user mission scenarios: an Earth observing spacecraft in low earth orbit (LEO), and a highly elliptical spacecraft in a lunar resonance orbit. These diverse flight scenarios indicate the breadth of applicability of the TASS beacon for upcoming users within the current network architecture and in the SMN.

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...

Ensemble Network Architecture for Deep Reinforcement Learning

Directory of Open Access Journals (Sweden)

Xi-liang Chen

2018-01-01

Full Text Available The popular deep Q learning algorithm is known to be instability because of the Q-value’s shake and overestimation action values under certain conditions. These issues tend to adversely affect their performance. In this paper, we develop the ensemble network architecture for deep reinforcement learning which is based on value function approximation. The temporal ensemble stabilizes the training process by reducing the variance of target approximation error and the ensemble of target values reduces the overestimate and makes better performance by estimating more accurate Q-value. Our results show that this architecture leads to statistically significant better value evaluation and more stable and better performance on several classical control tasks at OpenAI Gym environment.

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

SANDS: an architecture for clinical decision support in a National Health Information Network.

Science.gov (United States)

Wright, Adam; Sittig, Dean F

2007-10-11

A new architecture for clinical decision support called SANDS (Service-oriented Architecture for NHIN Decision Support) is introduced and its performance evaluated. The architecture provides a method for performing clinical decision support across a network, as in a health information exchange. Using the prototype we demonstrated that, first, a number of useful types of decision support can be carried out using our architecture; and, second, that the architecture exhibits desirable reliability and performance characteristics.

Saccharomyces cerevisiae metabolism in ecological context

OpenAIRE

Jouhten, Paula; Ponomarova, Olga; González García, Ramón; Patil, Kiran R.

2016-01-01

The architecture and regulation of Saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry. Yet, several recent studies have revealed notable limitations in explaining genotype?metabolic phenotype relations in this yeast, especially when concerning multiple genetic/environmental perturbations. Apparently unexpected genotype?phenotype relations may originate in the evolutionarily shaped cellular operating principles ...

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.

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.

Metabolite coupling in genome-scale metabolic networks

Directory of Open Access Journals (Sweden)

Palsson Bernhard Ø

2006-03-01

Full Text Available Abstract Background Biochemically detailed stoichiometric matrices have now been reconstructed for various bacteria, yeast, and for the human cardiac mitochondrion based on genomic and proteomic data. These networks have been manually curated based on legacy data and elementally and charge balanced. Comparative analysis of these well curated networks is now possible. Pairs of metabolites often appear together in several network reactions, linking them topologically. This co-occurrence of pairs of metabolites in metabolic reactions is termed herein "metabolite coupling." These metabolite pairs can be directly computed from the stoichiometric matrix, S. Metabolite coupling is derived from the matrix ŜŜT, whose off-diagonal elements indicate the number of reactions in which any two metabolites participate together, where Ŝ is the binary form of S. Results Metabolite coupling in the studied networks was found to be dominated by a relatively small group of highly interacting pairs of metabolites. As would be expected, metabolites with high individual metabolite connectivity also tended to be those with the highest metabolite coupling, as the most connected metabolites couple more often. For metabolite pairs that are not highly coupled, we show that the number of reactions a pair of metabolites shares across a metabolic network closely approximates a line on a log-log scale. We also show that the preferential coupling of two metabolites with each other is spread across the spectrum of metabolites and is not unique to the most connected metabolites. We provide a measure for determining which metabolite pairs couple more often than would be expected based on their individual connectivity in the network and show that these metabolites often derive their principal biological functions from existing in pairs. Thus, analysis of metabolite coupling provides information beyond that which is found from studying the individual connectivity of individual

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.

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

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

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...

Architecture, design and protection of electrical distribution networks

Energy Technology Data Exchange (ETDEWEB)

Sorrel, J.P. [Schneider electric Industries SA (France)

2000-07-01

Architectures related to AII Electric Ship (AES) require high level of propulsion power. Merchant ships and obviously warships require a low vulnerability, a high reliability and availability, a simple maintainability as well as an ordinary ode of operation. These constraints converge to an optimum single line diagram. We will focus on the mode of operation of the network, its constraints, the facilities to use a ring distribution for the ship service distribution system, the earthing of HV network as well as future developments. (author)

A Smart Gateway Architecture for Improving Efficiency of Home Network Applications

OpenAIRE

Ding, Fei; Song, Aiguo; Tong, En; Li, Jianqing

2016-01-01

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 integr...

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

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

Business architecture for inter-organisational innovation networks: A case study comparison from South Africa and Germany

CSIR Research Space (South Africa)

Gous, H

2011-06-01

Full Text Available systems architectures. An important step towards a deeper understanding of inter-organisational innovation networks is to compare the business architectures of network case studies to identify similarities and differences in terms of scope and context...

Deep Space Network information system architecture study

Science.gov (United States)

Beswick, C. A.; Markley, R. W. (Editor); Atkinson, D. J.; Cooper, L. P.; Tausworthe, R. C.; Masline, R. C.; Jenkins, J. S.; Crowe, R. A.; Thomas, J. L.; Stoloff, M. J.

1992-01-01

The purpose of this article is to describe an architecture for the DSN information system in the years 2000-2010 and to provide guidelines for its evolution during the 1990's. The study scope is defined to be from the front-end areas at the antennas to the end users (spacecraft teams, principal investigators, archival storage systems, and non-NASA partners). The architectural vision provides guidance for major DSN implementation efforts during the next decade. A strong motivation for the study is an expected dramatic improvement in information-systems technologies--i.e., computer processing, automation technology (including knowledge-based systems), networking and data transport, software and hardware engineering, and human-interface technology. The proposed Ground Information System has the following major features: unified architecture from the front-end area to the end user; open-systems standards to achieve interoperability; DSN production of level 0 data; delivery of level 0 data from the Deep Space Communications Complex, if desired; dedicated telemetry processors for each receiver; security against unauthorized access and errors; and highly automated monitor and control.

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.

Interconnection network architectures based on integrated orbital angular momentum emitters

Science.gov (United States)

Scaffardi, Mirco; Zhang, Ning; Malik, Muhammad Nouman; Lazzeri, Emma; Klitis, Charalambos; Lavery, Martin; Sorel, Marc; Bogoni, Antonella

2018-02-01

Novel architectures for two-layer interconnection networks based on concentric OAM emitters are presented. A scalability analysis is done in terms of devices characteristics, power budget and optical signal to noise ratio by exploiting experimentally measured parameters. The analysis shows that by exploiting optical amplifications, the proposed interconnection networks can support a number of ports higher than 100. The OAM crosstalk induced-penalty, evaluated through an experimental characterization, do not significantly affect the interconnection network performance.

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.

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.

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.

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.

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.

Fluid and flexible minds: Intelligence reflects synchrony in the brain’s intrinsic network architecture

Directory of Open Access Journals (Sweden)

Michael A. Ferguson

2017-06-01

Full Text Available Human intelligence has been conceptualized as a complex system of dissociable cognitive processes, yet studies investigating the neural basis of intelligence have typically emphasized the contributions of discrete brain regions or, more recently, of specific networks of functionally connected regions. Here we take a broader, systems perspective in order to investigate whether intelligence is an emergent property of synchrony within the brain’s intrinsic network architecture. Using a large sample of resting-state fMRI and cognitive data (n = 830, we report that the synchrony of functional interactions within and across distributed brain networks reliably predicts fluid and flexible intellectual functioning. By adopting a whole-brain, systems-level approach, we were able to reliably predict individual differences in human intelligence by characterizing features of the brain’s intrinsic network architecture. These findings hold promise for the eventual development of neural markers to predict changes in intellectual function that are associated with neurodevelopment, normal aging, and brain disease. In our study, we aimed to understand how individual differences in intellectual functioning are reflected in the intrinsic network architecture of the human brain. We applied statistical methods, known as spectral decompositions, in order to identify individual differences in the synchronous patterns of spontaneous brain activity that reliably predict core aspects of human intelligence. The synchrony of brain activity at rest across multiple discrete neural networks demonstrated positive relationships with fluid intelligence. In contrast, global synchrony within the brain’s network architecture reliably, and inversely, predicted mental flexibility, a core facet of intellectual functioning. The multinetwork systems approach described here represents a methodological and conceptual extension of earlier efforts that related differences in

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

Energy Technology Data Exchange (ETDEWEB)

Wijayasekara, Dumidu, E-mail: wija2589@vandals.uidaho.edu [Department of Computer Science, University of Idaho, 1776 Science Center Drive, Idaho Falls, ID 83402 (United States); Manic, Milos [Department of Computer Science, University of Idaho, 1776 Science Center Drive, Idaho Falls, ID 83402 (United States); Sabharwall, Piyush [Idaho National Laboratory, Idaho Falls, ID (United States); Utgikar, Vivek [Department of Chemical Engineering, University of Idaho, Idaho Falls, ID 83402 (United States)

2011-07-15

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 testing

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

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.

Cyber-Physical Architecture Assisted by Programmable Networking

OpenAIRE

Rubio-Hernan, Jose; Sahay, Rishikesh; De Cicco, Luca; Garcia-Alfaro, Joaquin

2018-01-01

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. Towards this end, 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 arch...

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.

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...

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

KAUST Repository

Elwhishi, Ahmed; Ho, Pin-Han; Naik, K.; Shihada, Basem

2010-01-01

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.

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.

Development of the brain's functional network architecture.

Science.gov (United States)

Vogel, Alecia C; Power, Jonathan D; Petersen, Steven E; Schlaggar, Bradley L

2010-12-01

A full understanding of the development of the brain's functional network architecture requires not only an understanding of developmental changes in neural processing in individual brain regions but also an understanding of changes in inter-regional interactions. Resting state functional connectivity MRI (rs-fcMRI) is increasingly being used to study functional interactions between brain regions in both adults and children. We briefly review methods used to study functional interactions and networks with rs-fcMRI and how these methods have been used to define developmental changes in network functional connectivity. The developmental rs-fcMRI studies to date have found two general properties. First, regional interactions change from being predominately anatomically local in children to interactions spanning longer cortical distances in young adults. Second, this developmental change in functional connectivity occurs, in general, via mechanisms of segregation of local regions and integration of distant regions into disparate subnetworks.

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.

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.

Signalling design and architecture for a proposed mobile satellite network

Science.gov (United States)

Yan, T.-Y.; Cheng, U.; Wang, C.

1990-01-01

In a frequency-division/demand-assigned multiple-access (FD/DAMA) architecture, each mobile subscriber must make a connection request to the Network Management Center before transmission for either open-end or closed-end services. Open-end services are for voice calls and long file transfer and are processed on a blocked-call-cleared basis. Closed-end services are for transmitting burst data and are processed on a first-come first-served basis. This paper presents the signalling design and architecture for non-voice services of an FD/DAMA mobile satellite network. The connection requests are made through the recently proposed multiple channel collision resolution scheme which provides a significantly higher throughput than the traditional slotted ALOHA scheme. For non-voice services, it is well known that retransmissions are necessary to ensure the delivery of a message in its entirety from the source to destination. Retransmission protocols for open-end and closed-end data transfer are investigated. The signal structure for the proposed network is derived from X-25 standards with appropriate modifications. The packet types and their usages are described in this paper.

Toward the automated generation of genome-scale metabolic networks in the SEED.

Science.gov (United States)

DeJongh, Matthew; Formsma, Kevin; Boillot, Paul; Gould, John; Rycenga, Matthew; Best, Aaron

2007-04-26

Current methods for the automated generation of genome-scale metabolic networks focus on genome annotation and preliminary biochemical reaction network assembly, but do not adequately address the process of identifying and filling gaps in the reaction network, and verifying that the network is suitable for systems level analysis. Thus, current methods are only sufficient for generating draft-quality networks, and refinement of the reaction network is still largely a manual, labor-intensive process. We have developed a method for generating genome-scale metabolic networks that produces substantially complete reaction networks, suitable for systems level analysis. Our method partitions the reaction space of central and intermediary metabolism into discrete, interconnected components that can be assembled and verified in isolation from each other, and then integrated and verified at the level of their interconnectivity. We have developed a database of components that are common across organisms, and have created tools for automatically assembling appropriate components for a particular organism based on the metabolic pathways encoded in the organism's genome. This focuses manual efforts on that portion of an organism's metabolism that is not yet represented in the database. We have demonstrated the efficacy of our method by reverse-engineering and automatically regenerating the reaction network from a published genome-scale metabolic model for Staphylococcus aureus. Additionally, we have verified that our method capitalizes on the database of common reaction network components created for S. aureus, by using these components to generate substantially complete reconstructions of the reaction networks from three other published metabolic models (Escherichia coli, Helicobacter pylori, and Lactococcus lactis). We have implemented our tools and database within the SEED, an open-source software environment for comparative genome annotation and analysis. Our method sets the

Toward the automated generation of genome-scale metabolic networks in the SEED

Directory of Open Access Journals (Sweden)

Gould John

2007-04-01

Full Text Available Abstract Background Current methods for the automated generation of genome-scale metabolic networks focus on genome annotation and preliminary biochemical reaction network assembly, but do not adequately address the process of identifying and filling gaps in the reaction network, and verifying that the network is suitable for systems level analysis. Thus, current methods are only sufficient for generating draft-quality networks, and refinement of the reaction network is still largely a manual, labor-intensive process. Results We have developed a method for generating genome-scale metabolic networks that produces substantially complete reaction networks, suitable for systems level analysis. Our method partitions the reaction space of central and intermediary metabolism into discrete, interconnected components that can be assembled and verified in isolation from each other, and then integrated and verified at the level of their interconnectivity. We have developed a database of components that are common across organisms, and have created tools for automatically assembling appropriate components for a particular organism based on the metabolic pathways encoded in the organism's genome. This focuses manual efforts on that portion of an organism's metabolism that is not yet represented in the database. We have demonstrated the efficacy of our method by reverse-engineering and automatically regenerating the reaction network from a published genome-scale metabolic model for Staphylococcus aureus. Additionally, we have verified that our method capitalizes on the database of common reaction network components created for S. aureus, by using these components to generate substantially complete reconstructions of the reaction networks from three other published metabolic models (Escherichia coli, Helicobacter pylori, and Lactococcus lactis. We have implemented our tools and database within the SEED, an open-source software environment for comparative

SNMS: an intelligent transportation system network architecture based on WSN and P2P network

Institute of Scientific and Technical Information of China (English)

LI Li; LIU Yuan-an; TANG Bi-hua

2007-01-01

With the development of city road networks, the question of how to obtain information about the roads is becoming more and more important. In this article, sensor network with mobile station (SNMS), a novel two-tiered intelligent transportation system (ITS) network architecture based on wireless sensor network (WSN) and peer-to-peer (P2P) network, is proposed to provide significant traffic information about the road and thereby, assist travelers to take optimum decisions when they are driving. A detailed explanation with regard to the strategy of each level as well as the design of two main components in the network, sensor unit (SU) and mobile station (MS), is presented. Finally, a representative scenario is described to display the operation of the system.

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

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...... 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...... 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...

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

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..

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

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

mCRAN : a radio access network architecture for 5G indoor communications

NARCIS (Netherlands)

Chandra, Kishor; Cao, Zizheng; Bruintjes, T. M.; Prasad, R. Venkatesha; Karagiannis, G.; Tangdiongga, Eduward; van den Boom, H.P.A.; Kokkeler, A. 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

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

CERN Document Server

AUTHOR|(CDS)2156318; 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...

Second Law of Thermodynamics Applied to Metabolic Networks

Science.gov (United States)

Nigam, R.; Liang, S.

2003-01-01

We present a simple algorithm based on linear programming, that combines Kirchoff's flux and potential laws and applies them to metabolic networks to predict thermodynamically feasible reaction fluxes. These law's represent mass conservation and energy feasibility that are widely used in electrical circuit analysis. Formulating the Kirchoff's potential law around a reaction loop in terms of the null space of the stoichiometric matrix leads to a simple representation of the law of entropy that can be readily incorporated into the traditional flux balance analysis without resorting to non-linear optimization. Our technique is new as it can easily check the fluxes got by applying flux balance analysis for thermodynamic feasibility and modify them if they are infeasible so that they satisfy the law of entropy. We illustrate our method by applying it to the network dealing with the central metabolism of Escherichia coli. Due to its simplicity this algorithm will be useful in studying large scale complex metabolic networks in the cell of different organisms.

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

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

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.

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.

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

Blueprint for antimicrobial hit discovery targeting metabolic networks.

Science.gov (United States)

Shen, Y; Liu, J; Estiu, G; Isin, B; Ahn, Y-Y; Lee, D-S; Barabási, A-L; Kapatral, V; Wiest, O; Oltvai, Z N

2010-01-19

Advances in genome analysis, network biology, and computational chemistry have the potential to revolutionize drug discovery by combining system-level identification of drug targets with the atomistic modeling of small molecules capable of modulating their activity. To demonstrate the effectiveness of such a discovery pipeline, we deduced common antibiotic targets in Escherichia coli and Staphylococcus aureus by identifying shared tissue-specific or uniformly essential metabolic reactions in their metabolic networks. We then predicted through virtual screening dozens of potential inhibitors for several enzymes of these reactions and showed experimentally that a subset of these inhibited both enzyme activities in vitro and bacterial cell viability. This blueprint is applicable for any sequenced organism with high-quality metabolic reconstruction and suggests a general strategy for strain-specific antiinfective therapy.

Research on the Architecture of a Basic Reconfigurable Information Communication Network

Directory of Open Access Journals (Sweden)

Ruimin Wang

2013-01-01

Full Text Available The current information network cannot fundamentally meet some urgent requirements, such as providing ubiquitous information services and various types of heterogeneous network, supporting diverse and comprehensive network services, possessing high quality communication effects, ensuring the security and credibility of information interaction, and implementing effective supervisory control. This paper provides the theory system for the basic reconfigurable information communication network based on the analysis of present problems on the Internet and summarizes the root of these problems. It also provides an in-depth discussion about the related technologies and the prime components of the architecture.

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.

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

Shifts in the architecture of the Nationwide Health Information Network.

Science.gov (United States)

Lenert, Leslie; Sundwall, David; Lenert, Michael Edward

2012-01-01

In the midst of a US $30 billion USD investment in the Nationwide Health Information Network (NwHIN) and electronic health records systems, a significant change in the architecture of the NwHIN is taking place. Prior to 2010, the focus of information exchange in the NwHIN was the Regional Health Information Organization (RHIO). Since 2010, the Office of the National Coordinator (ONC) has been sponsoring policies that promote an internet-like architecture that encourages point to-point information exchange and private health information exchange networks. The net effect of these activities is to undercut the limited business model for RHIOs, decreasing the likelihood of their success, while making the NwHIN dependent on nascent technologies for community level functions such as record locator services. These changes may impact the health of patients and communities. Independent, scientifically focused debate is needed on the wisdom of ONC's proposed changes in its strategy for the NwHIN.

Integration of metabolic and gene regulatory networks modulates the C. elegans dietary response.

Science.gov (United States)

Watson, Emma; MacNeil, Lesley T; Arda, H Efsun; Zhu, Lihua Julie; Walhout, Albertha J M

2013-03-28

Expression profiles are tailored according to dietary input. However, the networks that control dietary responses remain largely uncharacterized. Here, we combine forward and reverse genetic screens to delineate a network of 184 genes that affect the C. elegans dietary response to Comamonas DA1877 bacteria. We find that perturbation of a mitochondrial network composed of enzymes involved in amino acid metabolism and the TCA cycle affects the dietary response. In humans, mutations in the corresponding genes cause inborn diseases of amino acid metabolism, most of which are treated by dietary intervention. We identify several transcription factors (TFs) that mediate the changes in gene expression upon metabolic network perturbations. Altogether, our findings unveil a transcriptional response system that is poised to sense dietary cues and metabolic imbalances, illustrating extensive communication between metabolic networks in the mitochondria and gene regulatory networks in the nucleus. Copyright © 2013 Elsevier Inc. All rights reserved.

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.

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.

Optical home network based on an N×N multimode fiber architecture and CWDM technology

NARCIS (Netherlands)

Richard, F.; Guignard, P.; Pizzinat, A.; Guillo, L.; Guillory, J.; Charbonnier, B; Koonen, A.M.J.; Martinez, E.O.; Tanguy, E.; Li, H.W.

2011-01-01

With this optical home network solution associating an N×N multimode architecture and CWDM technology, various applications and network topologies are supported by a unique multiformat infrastructure. Issues related to the use of MMF are discussed.

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.

Evolution of bow-tie architectures in biology.

Directory of Open Access Journals (Sweden)

Tamar Friedlander

2015-03-01

Full Text Available Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal determines the size of the narrowest part of the network-that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.

Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

DEFF Research Database (Denmark)

Förster, Jochen; Famili, I.; Fu, P.

2003-01-01

The metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information. The metabolic reactions were compartmentalized between the cytosol and the mitochondria, and transport steps between the compartments...

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.

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

Limited Influence of Oxygen on the Evolution of Chemical Diversity in Metabolic Networks

Directory of Open Access Journals (Sweden)

Kazuhiro Takemoto

2013-10-01

Full Text Available Oxygen is thought to promote species and biomolecule diversity. Previous studies have suggested that oxygen expands metabolic networks by acquiring metabolites with different chemical properties (higher hydrophobicity, for example. However, such conclusions are typically based on biased evaluation, and are therefore non-conclusive. Thus, we re-investigated the effect of oxygen on metabolic evolution using a phylogenetic comparative method and metadata analysis to reduce the bias as much as possible. Notably, we found no difference in metabolic network expansion between aerobes and anaerobes when evaluating phylogenetic relationships. Furthermore, we showed that previous studies have overestimated or underestimated the degrees of differences in the chemical properties (e.g., hydrophobicity between oxic and anoxic metabolites in metabolic networks of unicellular organisms; however, such overestimation was not observed when considering the metabolic networks of multicellular organisms. These findings indicate that the contribution of oxygen to increased chemical diversity in metabolic networks is lower than previously thought; rather, phylogenetic signals and cell-cell communication result in increased chemical diversity. However, this conclusion does not contradict the effect of oxygen on metabolic evolution; instead, it provides a deeper understanding of how oxygen contributes to metabolic evolution despite several limitations in data analysis methods.

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.

Time analysis of interconnection network implemented on the honeycomb architecture

Energy Technology Data Exchange (ETDEWEB)

Milutinovic, D [Inst. Michael Pupin, Belgrade (Yugoslavia)

1996-12-31

Problems of time domains analysis of the mapping of interconnection networks for parallel processing on one form of uniform massively parallel architecture of the cellular type are considered. The results of time analysis are discussed. It is found that changing the technology results in changing the mapping rules. 17 refs.

Structure versus time in the evolutionary diversification of avian carotenoid metabolic networks.

Science.gov (United States)

Morrison, Erin S; Badyaev, Alexander V

2018-05-01

Historical associations of genes and proteins are thought to delineate pathways available to subsequent evolution; however, the effects of past functional involvements on contemporary evolution are rarely quantified. Here, we examined the extent to which the structure of a carotenoid enzymatic network persists in avian evolution. Specifically, we tested whether the evolution of carotenoid networks was most concordant with phylogenetically structured expansion from core reactions of common ancestors or with subsampling of biochemical pathway modules from an ancestral network. We compared structural and historical associations in 467 carotenoid networks of extant and ancestral species and uncovered the overwhelming effect of pre-existing metabolic network structure on carotenoid diversification over the last 50 million years of avian evolution. Over evolutionary time, birds repeatedly subsampled and recombined conserved biochemical modules, which likely maintained the overall structure of the carotenoid metabolic network during avian evolution. These findings explain the recurrent convergence of evolutionary distant species in carotenoid metabolism and weak phylogenetic signal in avian carotenoid evolution. Remarkable retention of an ancient metabolic structure throughout extensive and prolonged ecological diversification in avian carotenoid metabolism illustrates a fundamental requirement of organismal evolution - historical continuity of a deterministic network that links past and present functional associations of its components. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

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.

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...

FluxVisualizer, a Software to Visualize Fluxes through Metabolic Networks

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Tim Daniel Rose

2018-04-01

Full Text Available FluxVisualizer (Version 1.0, 2017, freely available at https://fluxvisualizer.ibgc.cnrs.fr is a software to visualize fluxes values on a scalable vector graphic (SVG representation of a metabolic network by colouring or increasing the width of reaction arrows of the SVG file. FluxVisualizer does not aim to draw metabolic networks but to use a customer’s SVG file allowing him to exploit his representation standards with a minimum of constraints. FluxVisualizer is especially suitable for small to medium size metabolic networks, where a visual representation of the fluxes makes sense. The flux distribution can either be an elementary flux mode (EFM, a flux balance analysis (FBA result or any other flux distribution. It allows the automatic visualization of a series of pathways of the same network as is needed for a set of EFMs. The software is coded in python3 and provides a graphical user interface (GUI and an application programming interface (API. All functionalities of the program can be used from the API and the GUI and allows advanced users to add their own functionalities. The software is able to work with various formats of flux distributions (Metatool, CellNetAnalyzer, COPASI and FAME export files as well as with Excel files. This simple software can save a lot of time when evaluating fluxes simulations on a metabolic network.

EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT.

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Kumari Sonal Choudhary

2016-06-01

Full Text Available Epithelial to mesenchymal transition (EMT is an important event during development and cancer metastasis. There is limited understanding of the metabolic alterations that give rise to and take place during EMT. Dysregulation of signalling pathways that impact metabolism, including epidermal growth factor receptor (EGFR, are however a hallmark of EMT and metastasis. In this study, we report the investigation into EGFR signalling and metabolic crosstalk of EMT through constraint-based modelling and analysis of the breast epithelial EMT cell model D492 and its mesenchymal counterpart D492M. We built an EGFR signalling network for EMT based on stoichiometric coefficients and constrained the network with gene expression data to build epithelial (EGFR_E and mesenchymal (EGFR_M networks. Metabolic alterations arising from differential expression of EGFR genes was derived from a literature review of AKT regulated metabolic genes. Signaling flux differences between EGFR_E and EGFR_M models subsequently allowed metabolism in D492 and D492M cells to be assessed. Higher flux within AKT pathway in the D492 cells compared to D492M suggested higher glycolytic activity in D492 that we confirmed experimentally through measurements of glucose uptake and lactate secretion rates. The signaling genes from the AKT, RAS/MAPK and CaM pathways were predicted to revert D492M to D492 phenotype. Follow-up analysis of EGFR signaling metabolic crosstalk in three additional breast epithelial cell lines highlighted variability in in vitro cell models of EMT. This study shows that the metabolic phenotype may be predicted by in silico analyses of gene expression data of EGFR signaling genes, but this phenomenon is cell-specific and does not follow a simple trend.

EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT.

Science.gov (United States)

Choudhary, Kumari Sonal; Rohatgi, Neha; Halldorsson, Skarphedinn; Briem, Eirikur; Gudjonsson, Thorarinn; Gudmundsson, Steinn; Rolfsson, Ottar

2016-06-01

Epithelial to mesenchymal transition (EMT) is an important event during development and cancer metastasis. There is limited understanding of the metabolic alterations that give rise to and take place during EMT. Dysregulation of signalling pathways that impact metabolism, including epidermal growth factor receptor (EGFR), are however a hallmark of EMT and metastasis. In this study, we report the investigation into EGFR signalling and metabolic crosstalk of EMT through constraint-based modelling and analysis of the breast epithelial EMT cell model D492 and its mesenchymal counterpart D492M. We built an EGFR signalling network for EMT based on stoichiometric coefficients and constrained the network with gene expression data to build epithelial (EGFR_E) and mesenchymal (EGFR_M) networks. Metabolic alterations arising from differential expression of EGFR genes was derived from a literature review of AKT regulated metabolic genes. Signaling flux differences between EGFR_E and EGFR_M models subsequently allowed metabolism in D492 and D492M cells to be assessed. Higher flux within AKT pathway in the D492 cells compared to D492M suggested higher glycolytic activity in D492 that we confirmed experimentally through measurements of glucose uptake and lactate secretion rates. The signaling genes from the AKT, RAS/MAPK and CaM pathways were predicted to revert D492M to D492 phenotype. Follow-up analysis of EGFR signaling metabolic crosstalk in three additional breast epithelial cell lines highlighted variability in in vitro cell models of EMT. This study shows that the metabolic phenotype may be predicted by in silico analyses of gene expression data of EGFR signaling genes, but this phenomenon is cell-specific and does not follow a simple trend.

Software defined network architecture based research on load balancing strategy

Science.gov (United States)

You, Xiaoqian; Wu, Yang

2018-05-01

As a new type network architecture, software defined network has the key idea of separating the control place of the network from the transmission plane, to manage and control the network in a concentrated way; in addition, the network interface is opened on the control layer and the data layer, so as to achieve programmable control of the network. Considering that only the single shortest route is taken into the calculation of traditional network data flow transmission, and congestion and resource consumption caused by excessive load of link circuits are ignored, a link circuit load based flow media business QoS gurantee system is proposed in this article to divide the flow in the network into ordinary data flow and QoS flow. In this way, it supervises the link circuit load with the controller so as to calculate reasonable route rapidly and issue the flow table to the exchanger, to finish rapid data transmission. In addition, it establishes a simulation platform to acquire optimized result through simulation experiment.

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

SANDS: a service-oriented architecture for clinical decision support in a National Health Information Network.

Science.gov (United States)

Wright, Adam; Sittig, Dean F

2008-12-01

In this paper, we describe and evaluate a new distributed architecture for clinical decision support called SANDS (Service-oriented Architecture for NHIN Decision Support), which leverages current health information exchange efforts and is based on the principles of a service-oriented architecture. The architecture allows disparate clinical information systems and clinical decision support systems to be seamlessly integrated over a network according to a set of interfaces and protocols described in this paper. The architecture described is fully defined and developed, and six use cases have been developed and tested using a prototype electronic health record which links to one of the existing prototype National Health Information Networks (NHIN): drug interaction checking, syndromic surveillance, diagnostic decision support, inappropriate prescribing in older adults, information at the point of care and a simple personal health record. Some of these use cases utilize existing decision support systems, which are either commercially or freely available at present, and developed outside of the SANDS project, while other use cases are based on decision support systems developed specifically for the project. Open source code for many of these components is available, and an open source reference parser is also available for comparison and testing of other clinical information systems and clinical decision support systems that wish to implement the SANDS architecture. The SANDS architecture for decision support has several significant advantages over other architectures for clinical decision support. The most salient of these are:

Addressing unknown constants and metabolic network behaviors through petascale computing: understanding H{sub 2} production in green algae

Energy Technology Data Exchange (ETDEWEB)

Chang, Christopher; Alber, David; Graf, Peter; Kim, Kwiseon; Seibert, Michael [National Renewable Energy Laboratory (NREL), Golden, CO 80401 (United States)

2007-07-15

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{sub 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

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

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...... cell design. Our implementation is based on clockless circuit techniques, and thus inherently supports a modular, GALS-oriented design flow. Our router exploits virtual channels to provide connection-oriented GS, as well as connection-less best-effort (BE) routing. The architecture is highly flexible...

Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation

Energy Technology Data Exchange (ETDEWEB)

Çakır, Tunahan, E-mail: tcakir@gyte.edu.tr [Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University (formerly known as Gebze Institute of Technology), Gebze (Turkey); Khatibipour, Mohammad Jafar [Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University (formerly known as Gebze Institute of Technology), Gebze (Turkey); Department of Chemical Engineering, Gebze Technical University (formerly known as Gebze Institute of Technology), Gebze (Turkey)

2014-12-03

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.

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.

Ensuring Data Storage Security in Tree cast Routing Architecture for Sensor Networks

Science.gov (United States)

Kumar, K. E. Naresh; Sagar, U. Vidya; Waheed, Mohd. Abdul

2010-10-01

In this paper presents recent advances in technology have made low-cost, low-power wireless sensors with efficient energy consumption. A network of such nodes can coordinate among themselves for distributed sensing and processing of certain data. For which, we propose an architecture to provide a stateless solution in sensor networks for efficient routing in wireless sensor networks. This type of architecture is known as Tree Cast. We propose a unique method of address allocation, building up multiple disjoint trees which are geographically inter-twined and rooted at the data sink. Using these trees, routing messages to and from the sink node without maintaining any routing state in the sensor nodes is possible. In contrast to traditional solutions, where the IT services are under proper physical, logical and personnel controls, this routing architecture moves the application software and databases to the large data centers, where the management of the data and services may not be fully trustworthy. This unique attribute, however, poses many new security challenges which have not been well understood. In this paper, we focus on data storage security, which has always been an important aspect of quality of service. To ensure the correctness of users' data in this architecture, we propose an effective and flexible distributed scheme with two salient features, opposing to its predecessors. By utilizing the homomorphic token with distributed verification of erasure-coded data, our scheme achieves the integration of storage correctness insurance and data error localization, i.e., the identification of misbehaving server(s). Unlike most prior works, the new scheme further supports secure and efficient dynamic operations on data blocks, including: data update, delete and append. Extensive security and performance analysis shows that the proposed scheme is highly efficient and resilient against Byzantine failure, malicious data modification attack, and even server

A Novel Architectural Concept for Enhanced 5G Network Facilities

Directory of Open Access Journals (Sweden)

Chochliouros Ioannis P.

2017-01-01

Full Text Available The 5G ESSENCE project’s context is based on the concept of Edge Cloud Computing and Small Cell-as-a-Service (SCaaS -as both have been previously identified in the SESAME 5G-PPP project of phase 1- and further “promotes” their role and/or influences within the related 5G vertical markets. 5G ESSENCE’s core innovation is focused upon the development/provision of a highly flexible and scalable platform, offering benefits to the involved market actors. The present work identifies a variety of challenges to be fulfilled by the 5G ESSENCE, in the scope of an enhanced architectural framework. The proposed technical approach exploits the profits of the centralization of Small Cell functions as scale grows through an edge cloud environment, based on a two-tier architecture with the first distributed tier being for offering low latency services and the second centralized tier being for the provision of high processing power for computing-intensive network applications. This permits decoupling the control and user planes of the Radio Access Network (RAN and achieving the advantages of Cloud-RAN without the enormous fronthaul latency restrictions. The use of end-to-end network slicing mechanisms allows for sharing the related infrastructure among multiple operators/vertical industries and customizing its capabilities on a per-tenant basis, creating a neutral host market and reducing operational costs.

An Architecture to Manage Incoming Traffic of Inter-Domain Routing Using OpenFlow Networks

Directory of Open Access Journals (Sweden)

Walber José Adriano Silva

2018-04-01

Full Text Available The Border Gateway Protocol (BGP is the current state-of-the-art inter-domain routing between Autonomous Systems (ASes. Although BGP has different mechanisms to manage outbound traffic in an AS domain, it lacks an efficient tool for inbound traffic control from transit ASes such as Internet Service Providers (ISPs. For inter-domain routing, the BGP’s destination-based forwarding paradigm limits the granularity of distributing the network traffic among the multiple paths of the current Internet topology. Thus, this work offered a new architecture to manage incoming traffic in the inter-domain using OpenFlow networks. The architecture explored direct inter-domain communication to exchange control information and the functionalities of the OpenFlow protocol. Based on the achieved results of the size of exchanging messages, the proposed architecture is not only scalable, but also capable of performing load balancing for inbound traffic using different strategies.

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.

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.

Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data

Directory of Open Access Journals (Sweden)

Klipp Edda

2006-12-01

Full Text Available Abstract Background Translating a known metabolic network into a dynamic model requires reasonable guesses of all enzyme parameters. In Bayesian parameter estimation, model parameters are described by a posterior probability distribution, which scores the potential parameter sets, showing how well each of them agrees with the data and with the prior assumptions made. Results We compute posterior distributions of kinetic parameters within a Bayesian framework, based on integration of kinetic, thermodynamic, metabolic, and proteomic data. The structure of the metabolic system (i.e., stoichiometries and enzyme regulation needs to be known, and the reactions are modelled by convenience kinetics with thermodynamically independent parameters. The parameter posterior is computed in two separate steps: a first posterior summarises the available data on enzyme kinetic parameters; an improved second posterior is obtained by integrating metabolic fluxes, concentrations, and enzyme concentrations for one or more steady states. The data can be heterogenous, incomplete, and uncertain, and the posterior is approximated by a multivariate log-normal distribution. We apply the method to a model of the threonine synthesis pathway: the integration of metabolic data has little effect on the marginal posterior distributions of individual model parameters. Nevertheless, it leads to strong correlations between the parameters in the joint posterior distribution, which greatly improve the model predictions by the following Monte-Carlo simulations. Conclusion We present a standardised method to translate metabolic networks into dynamic models. To determine the model parameters, evidence from various experimental data is combined and weighted using Bayesian parameter estimation. The resulting posterior parameter distribution describes a statistical ensemble of parameter sets; the parameter variances and correlations can account for missing knowledge, measurement

Convolutional neural networks for event-related potential detection: impact of the architecture.

Science.gov (United States)

Cecotti, H

2017-07-01

The detection of brain responses at the single-trial level in the electroencephalogram (EEG) such as event-related potentials (ERPs) is a difficult problem that requires different processing steps to extract relevant discriminant features. While most of the signal and classification techniques for the detection of brain responses are based on linear algebra, different pattern recognition techniques such as convolutional neural network (CNN), as a type of deep learning technique, have shown some interests as they are able to process the signal after limited pre-processing. In this study, we propose to investigate the performance of CNNs in relation of their architecture and in relation to how they are evaluated: a single system for each subject, or a system for all the subjects. More particularly, we want to address the change of performance that can be observed between specifying a neural network to a subject, or by considering a neural network for a group of subjects, taking advantage of a larger number of trials from different subjects. The results support the conclusion that a convolutional neural network trained on different subjects can lead to an AUC above 0.9 by using an appropriate architecture using spatial filtering and shift invariant layers.

Data-driven integration of genome-scale regulatory and metabolic network models

Science.gov (United States)

Imam, Saheed; Schäuble, Sascha; Brooks, Aaron N.; Baliga, Nitin S.; Price, Nathan D.

2015-01-01

Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription, and signaling) have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert—a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. In this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system. PMID:25999934

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 ...

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 ...

Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization.

Science.gov (United States)

Nair, Govind; Jungreuthmayer, Christian; Zanghellini, Jürgen

2017-02-01

Knockout strategies, particularly the concept of constrained minimal cut sets (cMCSs), are an important part of the arsenal of tools used in manipulating metabolic networks. Given a specific design, cMCSs can be calculated even in genome-scale networks. We would however like to find not only the optimal intervention strategy for a given design but the best possible design too. Our solution (PSOMCS) is to use particle swarm optimization (PSO) along with the direct calculation of cMCSs from the stoichiometric matrix to obtain optimal designs satisfying multiple objectives. To illustrate the working of PSOMCS, we apply it to a toy network. Next we show its superiority by comparing its performance against other comparable methods on a medium sized E. coli core metabolic network. PSOMCS not only finds solutions comparable to previously published results but also it is orders of magnitude faster. Finally, we use PSOMCS to predict knockouts satisfying multiple objectives in a genome-scale metabolic model of E. coli and compare it with OptKnock and RobustKnock. PSOMCS finds competitive knockout strategies and designs compared to other current methods and is in some cases significantly faster. It can be used in identifying knockouts which will force optimal desired behaviors in large and genome scale metabolic networks. It will be even more useful as larger metabolic models of industrially relevant organisms become available.

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

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

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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.

Network analysis of metabolic enzyme evolution in Escherichia coli

Directory of Open Access Journals (Sweden)

Kraulis Per

2004-02-01

Full Text Available Abstract Background The two most common models for the evolution of metabolism are the patchwork evolution model, where enzymes are thought to diverge from broad to narrow substrate specificity, and the retrograde evolution model, according to which enzymes evolve in response to substrate depletion. Analysis of the distribution of homologous enzyme pairs in the metabolic network can shed light on the respective importance of the two models. We here investigate the evolution of the metabolism in E. coli viewed as a single network using EcoCyc. Results Sequence comparison between all enzyme pairs was performed and the minimal path length (MPL between all enzyme pairs was determined. We find a strong over-representation of homologous enzymes at MPL 1. We show that the functionally similar and functionally undetermined enzyme pairs are responsible for most of the over-representation of homologous enzyme pairs at MPL 1. Conclusions The retrograde evolution model predicts that homologous enzymes pairs are at short metabolic distances from each other. In general agreement with previous studies we find that homologous enzymes occur close to each other in the network more often than expected by chance, which lends some support to the retrograde evolution model. However, we show that the homologous enzyme pairs which may have evolved through retrograde evolution, namely the pairs that are functionally dissimilar, show a weaker over-representation at MPL 1 than the functionally similar enzyme pairs. Our study indicates that, while the retrograde evolution model may have played a small part, the patchwork evolution model is the predominant process of metabolic enzyme evolution.

Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling

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Mahadevan Radhakrishnan

2010-05-01

Full Text Available Abstract Background Geobacter sulfurreducens is a member of the Geobacter species, which are capable of oxidation of organic waste coupled to the reduction of heavy metals and electrode with applications in bioremediation and bioenergy generation. While the metabolism of this organism has been studied through the development of a stoichiometry based genome-scale metabolic model, the associated regulatory network has not yet been well studied. In this manuscript, we report on the implementation of a thermodynamics based metabolic flux model for Geobacter sulfurreducens. We use this updated model to identify reactions that are subject to regulatory control in the metabolic network of G. sulfurreducens using thermodynamic variability analysis. Findings As a first step, we have validated the regulatory sites and bottleneck reactions predicted by the thermodynamic flux analysis in E. coli by evaluating the expression ranges of the corresponding genes. We then identified ten reactions in the metabolic network of G. sulfurreducens that are predicted to be candidates for regulation. We then compared the free energy ranges for these reactions with the corresponding gene expression fold changes under conditions of different environmental and genetic perturbations and show that the model predictions of regulation are consistent with data. In addition, we also identify reactions that operate close to equilibrium and show that the experimentally determined exchange coefficient (a measure of reversibility is significant for these reactions. Conclusions Application of the thermodynamic constraints resulted in identification of potential bottleneck reactions not only from the central metabolism but also from the nucleotide and amino acid subsystems, thereby showing the highly coupled nature of the thermodynamic constraints. In addition, thermodynamic variability analysis serves as a valuable tool in estimating the ranges of ΔrG' of every reaction in the model

Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders.

Science.gov (United States)

Meng, Qingying; Ying, Zhe; Noble, Emily; Zhao, Yuqi; Agrawal, Rahul; Mikhail, Andrew; Zhuang, Yumei; Tyagi, Ethika; Zhang, Qing; Lee, Jae-Hyung; Morselli, Marco; Orozco, Luz; Guo, Weilong; Kilts, Tina M; Zhu, Jun; Zhang, Bin; Pellegrini, Matteo; Xiao, Xinshu; Young, Marian F; Gomez-Pinilla, Fernando; Yang, Xia

2016-05-01

Nutrition plays a significant role in the increasing prevalence of metabolic and brain disorders. Here we employ systems nutrigenomics to scrutinize the genomic bases of nutrient-host interaction underlying disease predisposition or therapeutic potential. We conducted transcriptome and epigenome sequencing of hypothalamus (metabolic control) and hippocampus (cognitive processing) from a rodent model of fructose consumption, and identified significant reprogramming of DNA methylation, transcript abundance, alternative splicing, and gene networks governing cell metabolism, cell communication, inflammation, and neuronal signaling. These signals converged with genetic causal risks of metabolic, neurological, and psychiatric disorders revealed in humans. Gene network modeling uncovered the extracellular matrix genes Bgn and Fmod as main orchestrators of the effects of fructose, as validated using two knockout mouse models. We further demonstrate that an omega-3 fatty acid, DHA, reverses the genomic and network perturbations elicited by fructose, providing molecular support for nutritional interventions to counteract diet-induced metabolic and brain disorders. Our integrative approach complementing rodent and human studies supports the applicability of nutrigenomics principles to predict disease susceptibility and to guide personalized medicine. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Effective Utilization of Resources and Infrastructure for a Spaceport Network Architecture

Science.gov (United States)

Gill, Tracy; Larson, Wiley; Mueller, Robert; Roberson, Luke

2012-01-01

Providing routine, affordable access to a variety of orbital and deep space destinations requires an intricate network of ground, planetary surface, and space-based spaceports like those on Earth (land and sea), in various Earth orbits, and on other extraterrestrial surfaces. Advancements in technology and international collaboration are critical to establish a spaceport network that satisfies the requirements for private and government research, exploration, and commercial objectives. Technologies, interfaces, assembly techniques, and protocols must be adapted to enable mission critical capabilities and interoperability throughout the spaceport network. The conceptual space mission architecture must address the full range of required spaceport services, from managing propellants for a variety of spacecraft to governance structure. In order to accomplish affordability and sustainability goals, the network architecture must consider deriving propellants from in situ planetary resources to the maximum extent possible. Water on the Moon and Mars, Mars' atmospheric CO2, and O2 extracted from lunar regolith are examples of in situ resources that could be used to generate propellants for various spacecraft, orbital stages and trajectories, and the commodities to support habitation and human operations at these destinations. The ability to use in-space fuel depots containing in situ derived propellants would drastically reduce the mass required to launch long-duration or deep space missions from Earth's gravity well. Advances in transformative technologies and common capabilities, interfaces, umbilicals, commodities, protocols, and agreements will facilitate a cost-effective, safe, reliable infrastructure for a versatile network of Earth- and extraterrestrial spaceports. Defining a common infrastructure on Earth, planetary surfaces, and in space, as well as deriving propellants from in situ planetary resources to construct in-space propellant depots to serve the spaceport

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 ...

LIDeA: A Distributed Lightweight Intrusion Detection Architecture for Sensor Networks

DEFF Research Database (Denmark)

Giannetsos, Athanasios; Krontiris, Ioannis; Dimitriou, Tassos

2008-01-01

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......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...

An Internet of Things Generic Reference Architecture

DEFF Research Database (Denmark)

Bhalerao, Dipashree M.; Riaz, Tahir; Madsen, Ole Brun

2013-01-01

Internet of things Network is a future application of Internet. This network has three major basic blocks as business process or Application, core network or internetwork and peripheral network as Things or objects. The assembly has the basic intention of connecting all physical and virtual things......, and keeping track of all these things for monitoring and controlling some information. IoT architecture is studied from software architecture, overall system architecture and network architecture point of view. Paper puts forward the requirements of software architecture along with, its component...... and deployment diagram, process and interface diagram at abstract level. Paper proposes the abstract generic IoT reference and concrete abstract generic IoT reference architectures. Network architecture is also put up as a state of the art. Paper shortly gives overviews of protocols used for IoT. Some...

Comprehensive Mapping of Pluripotent Stem Cell Metabolism Using Dynamic Genome-Scale Network Modeling

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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

Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis

Directory of Open Access Journals (Sweden)

Reifman Jaques

2010-11-01

Full Text Available Abstract Background During infection, Mycobacterium tuberculosis confronts a generally hostile and nutrient-poor in vivo host environment. Existing models and analyses of M. tuberculosis metabolic networks are able to reproduce experimentally measured cellular growth rates and identify genes required for growth in a range of different in vitro media. However, these models, under in vitro conditions, do not provide an adequate description of the metabolic processes required by the pathogen to infect and persist in a host. Results To better account for the metabolic activity of M. tuberculosis in the host environment, we developed a set of procedures to systematically modify an existing in vitro metabolic network by enhancing the agreement between calculated and in vivo-measured gene essentiality data. After our modifications, the new in vivo network contained 663 genes, 838 metabolites, and 1,049 reactions and had a significantly increased sensitivity (0.81 in predicted gene essentiality than the in vitro network (0.31. We verified the modifications generated from the purely computational analysis through a review of the literature and found, for example, that, as the analysis suggested, lipids are used as the main source for carbon metabolism and oxygen must be available for the pathogen under in vivo conditions. Moreover, we used the developed in vivo network to predict the effects of double-gene deletions on M. tuberculosis growth in the host environment, explore metabolic adaptations to life in an acidic environment, highlight the importance of different enzymes in the tricarboxylic acid-cycle under different limiting nutrient conditions, investigate the effects of inhibiting multiple reactions, and look at the importance of both aerobic and anaerobic cellular respiration during infection. Conclusions The network modifications we implemented suggest a distinctive set of metabolic conditions and requirements faced by M. tuberculosis during

Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface

Directory of Open Access Journals (Sweden)

Bushell Michael E

2011-05-01

Full Text Available Abstract Background Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering. These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment. Results Here, we present Acorn, an open source (GNU GPL grid computing system for constraint-based simulations of genome scale metabolic reaction networks within an interactive web environment. The grid-based architecture allows efficient execution of computationally intensive, iterative protocols such as Flux Variability Analysis, which can be readily scaled up as the numbers of models (and users increase. The web interface uses AJAX, which facilitates efficient model browsing and other search functions, and intuitive implementation of appropriate simulation conditions. Research groups can install Acorn locally and create user accounts. Users can also import models in the familiar SBML format and link reaction formulas to major functional genomics portals of choice. Selected models and simulation results can be shared between different users and made publically available. Users can construct pathway map layouts and import them into the server using a desktop editor integrated within the system. Pathway maps are then used to visualise numerical results within the web environment. To illustrate these features we have deployed Acorn and created a

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.

Co-regulation of metabolic genes is better explained by flux coupling than by network distance.

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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.

Data-driven integration of genome-scale regulatory and metabolic network models

Directory of Open Access Journals (Sweden)

Saheed eImam

2015-05-01

Full Text Available Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription and signaling have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert – a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. In this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system.

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

Expanded flux variability analysis on metabolic network of Escherichia coli

Institute of Scientific and Technical Information of China (English)

CHEN Tong; XIE ZhengWei; OUYANG Qi

2009-01-01

Flux balance analysis,based on the mass conservation law in a cellular organism,has been extensively employed to study the interplay between structures and functions of cellular metabolic networks.Consequently,the phenotypes of the metabolism can be well elucidated.In this paper,we introduce the Expanded Flux Variability Analysis (EFVA) to characterize the intrinsic nature of metabolic reactions,such as flexibility,modularity and essentiality,by exploring the trend of the range,the maximum and the minimum flux of reactions.We took the metabolic network of Escherichia coli as an example and analyzed the variability of reaction fluxes under different growth rate constraints.The average variability of all reactions decreases dramatically when the growth rate increases.Consider the noise effect on the metabolic system,we thus argue that the microorganism may practically grow under a suboptimal state.Besides,under the EFVA framework,the reactions are easily to be grouped into catabolic and anabolic groups.And the anabolic groups can be further assigned to specific biomass constitute.We also discovered the growth rate dependent essentiality of reactions.

Validation of a metabolic network for Saccharomyces cerevisiae using mixed substrate studies.

Science.gov (United States)

Vanrolleghem, P A; de Jong-Gubbels, P; van Gulik, W M; Pronk, J T; van Dijken, J P; Heijnen, S

1996-01-01

Setting up a metabolic network model for respiratory growth of Saccharomyces cerevisiae requires the estimation of only two (energetic) stoichiometric parameters: (1) the operational PO ratio and (2) a growth-related maintenance factor k. It is shown, both theoretically and practically, how chemostat cultivations with different mixtures of two substrates allow unique values to be given to these unknowns of the proposed metabolic model. For the yeast and model considered, an effective PO ratio of 1.09 mol of ATP/mol of O (95% confidence interval 1.07-1.11) and a k factor of 0.415 mol of ATP/C-mol of biomass (0.385-0.445) were obtained from biomass substrate yield data on glucose/ethanol mixtures. Symbolic manipulation software proved very valuable in this study as it supported the proof of theoretical identifiability and significantly reduced the necessary computations for parameter estimation. In the transition from 100% glucose to 100% ethanol in the feed, four metabolic regimes occur. Switching between these regimes is determined by cessation of an irreversible reaction and initiation of an alternative reaction. Metabolic network predictions of these metabolic switches compared well with activity measurements of key enzymes. As a second validation of the network, the biomass yield of S. cerevisiae on acetate was also compared to the network prediction. An excellent agreement was found for a network in which acetate transport was modeled with a proton symport, while passive diffusion of acetate gave significantly higher yield predictions.

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.

Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks.

Science.gov (United States)

Oh, S June; Joung, Je-Gun; Chang, Jeong-Ho; Zhang, Byoung-Tak

2006-06-06

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. 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. 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 structures using meta-level information rather than sequence

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

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)....

A single network adaptive critic (SNAC) architecture for optimal control synthesis for a class of nonlinear systems.

Science.gov (United States)

Padhi, Radhakant; Unnikrishnan, Nishant; Wang, Xiaohua; Balakrishnan, S N

2006-12-01

Even though dynamic programming offers an optimal control solution in a state feedback form, the method is overwhelmed by computational and storage requirements. Approximate dynamic programming implemented with an Adaptive Critic (AC) neural network structure has evolved as a powerful alternative technique that obviates the need for excessive computations and storage requirements in solving optimal control problems. In this paper, an improvement to the AC architecture, called the "Single Network Adaptive Critic (SNAC)" is presented. This approach is applicable to a wide class of nonlinear systems where the optimal control (stationary) equation can be explicitly expressed in terms of the state and costate variables. The selection of this terminology is guided by the fact that it eliminates the use of one neural network (namely the action network) that is part of a typical dual network AC setup. As a consequence, the SNAC architecture offers three potential advantages: a simpler architecture, lesser computational load and elimination of the approximation error associated with the eliminated network. In order to demonstrate these benefits and the control synthesis technique using SNAC, two problems have been solved with the AC and SNAC approaches and their computational performances are compared. One of these problems is a real-life Micro-Electro-Mechanical-system (MEMS) problem, which demonstrates that the SNAC technique is applicable to complex engineering systems.

Enumeration of smallest intervention strategies in genome-scale metabolic networks.

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Axel von Kamp

2014-01-01

Full Text Available One ultimate goal of metabolic network modeling is the rational redesign of biochemical networks to optimize the production of certain compounds by cellular systems. Although several constraint-based optimization techniques have been developed for this purpose, methods for systematic enumeration of intervention strategies in genome-scale metabolic networks are still lacking. In principle, Minimal Cut Sets (MCSs; inclusion-minimal combinations of reaction or gene deletions that lead to the fulfilment of a given intervention goal provide an exhaustive enumeration approach. However, their disadvantage is the combinatorial explosion in larger networks and the requirement to compute first the elementary modes (EMs which itself is impractical in genome-scale networks. We present MCSEnumerator, a new method for effective enumeration of the smallest MCSs (with fewest interventions in genome-scale metabolic network models. For this we combine two approaches, namely (i the mapping of MCSs to EMs in a dual network, and (ii a modified algorithm by which shortest EMs can be effectively determined in large networks. In this way, we can identify the smallest MCSs by calculating the shortest EMs in the dual network. Realistic application examples demonstrate that our algorithm is able to list thousands of the most efficient intervention strategies in genome-scale networks for various intervention problems. For instance, for the first time we could enumerate all synthetic lethals in E.coli with combinations of up to 5 reactions. We also applied the new algorithm exemplarily to compute strain designs for growth-coupled synthesis of different products (ethanol, fumarate, serine by E.coli. We found numerous new engineering strategies partially requiring less knockouts and guaranteeing higher product yields (even without the assumption of optimal growth than reported previously. The strength of the presented approach is that smallest intervention strategies can be

Integration of Plant Metabolomics Data with Metabolic Networks: Progresses and Challenges.

Science.gov (United States)

Töpfer, Nadine; Seaver, Samuel M D; Aharoni, Asaph

2018-01-01

In the last decade, plant genome-scale modeling has developed rapidly and modeling efforts have advanced from representing metabolic behavior of plant heterotrophic cell suspensions to studying the complex interplay of cell types, tissues, and organs. A crucial driving force for such developments is the availability and integration of "omics" data (e.g., transcriptomics, proteomics, and metabolomics) which enable the reconstruction, extraction, and application of context-specific metabolic networks. In this chapter, we demonstrate a workflow to integrate gas chromatography coupled to mass spectrometry (GC-MS)-based metabolomics data of tomato fruit pericarp (flesh) tissue, at five developmental stages, with a genome-scale reconstruction of tomato metabolism. This method allows for the extraction of context-specific networks reflecting changing activities of metabolic pathways throughout fruit development and maturation.

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

Metabolic network modeling of microbial interactions in natural and engineered environmental systems

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Octavio ePerez-Garcia

2016-05-01

Full Text Available We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA, experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e. i lumped networks, ii compartment per guild networks, iii bi-level optimization simulations and iv dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial

A performance analysis of advanced I/O architectures for PC-based network file servers

Science.gov (United States)

Huynh, K. D.; Khoshgoftaar, T. M.

1994-12-01

In the personal computing and workstation environments, more and more I/O adapters are becoming complete functional subsystems that are intelligent enough to handle I/O operations on their own without much intervention from the host processor. The IBM Subsystem Control Block (SCB) architecture has been defined to enhance the potential of these intelligent adapters by defining services and conventions that deliver command information and data to and from the adapters. In recent years, a new storage architecture, the Redundant Array of Independent Disks (RAID), has been quickly gaining acceptance in the world of computing. In this paper, we would like to discuss critical system design issues that are important to the performance of a network file server. We then present a performance analysis of the SCB architecture and disk array technology in typical network file server environments based on personal computers (PCs). One of the key issues investigated in this paper is whether a disk array can outperform a group of disks (of same type, same data capacity, and same cost) operating independently, not in parallel as in a disk array.

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

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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.

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

Science.gov (United States)

Granger, Brian R; Chang, Yi-Chien; Wang, Yan; DeLisi, Charles; Segrè, Daniel; Hu, Zhenjun

2016-04-01

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.

Characterization of the Usage of the Serine Metabolic Network in Human Cancer

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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.

Robustness in Regulatory Interaction Networks. A Generic Approach with Applications at Different Levels: Physiologic, Metabolic and Genetic

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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

Robustness in Regulatory Interaction Networks. A Generic Approach with Applications at Different Levels: Physiologic, Metabolic and Genetic

Directory of Open Access Journals (Sweden)

Sylvain Sené

2009-10-01

Full Text Available 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.

Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions

DEFF Research Database (Denmark)

Schmidt, R.; Waschina, S.; Boettger-Schmidt, D.

2015-01-01

, the method we report represents a powerful tool to identify inconsistencies in large-scale metabolic networks. AVAILABILITY AND IMPLEMENTATION: The method is available as source code on http://users.minet.uni-jena.de/ approximately m3kach/ASBIG/ASBIG.zip. CONTACT: christoph.kaleta@uni-jena.de SUPPLEMENTARY...... by inherent inconsistencies and gaps. RESULTS: Here we present a novel method to validate metabolic network reconstructions based on the concept of autocatalytic sets. Autocatalytic sets correspond to collections of metabolites that, besides enzymes and a growth medium, are required to produce all biomass...... components in a metabolic model. These autocatalytic sets are well-conserved across all domains of life, and their identification in specific genome-scale reconstructions allows us to draw conclusions about potential inconsistencies in these models. The method is capable of detecting inconsistencies, which...

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

An open, interoperable, and scalable prehospital information technology network architecture.

Science.gov (United States)

Landman, Adam B; Rokos, Ivan C; Burns, Kevin; Van Gelder, Carin M; Fisher, Roger M; Dunford, James V; Cone, David C; Bogucki, Sandy

2011-01-01

Some of the most intractable challenges in prehospital medicine include response time optimization, inefficiencies at the emergency medical services (EMS)-emergency department (ED) interface, and the ability to correlate field interventions with patient outcomes. Information technology (IT) can address these and other concerns by ensuring that system and patient information is received when and where it is needed, is fully integrated with prior and subsequent patient information, and is securely archived. Some EMS agencies have begun adopting information technologies, such as wireless transmission of 12-lead electrocardiograms, but few agencies have developed a comprehensive plan for management of their prehospital information and integration with other electronic medical records. This perspective article highlights the challenges and limitations of integrating IT elements without a strategic plan, and proposes an open, interoperable, and scalable prehospital information technology (PHIT) architecture. The two core components of this PHIT architecture are 1) routers with broadband network connectivity to share data between ambulance devices and EMS system information services and 2) an electronic patient care report to organize and archive all electronic prehospital data. To successfully implement this comprehensive PHIT architecture, data and technology requirements must be based on best available evidence, and the system must adhere to health data standards as well as privacy and security regulations. Recent federal legislation prioritizing health information technology may position federal agencies to help design and fund PHIT architectures.

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.

Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions

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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.

Figure-ground segregation in a recurrent network architecture.

Science.gov (United States)

Roelfsema, Pieter R; Lamme, Victor A F; Spekreijse, Henk; Bosch, Holger

2002-05-15

Here we propose a model of how the visual brain segregates textured scenes into figures and background. During texture segregation, locations where the properties of texture elements change abruptly are assigned to boundaries, whereas image regions that are relatively homogeneous are grouped together. Boundary detection and grouping of image regions require different connection schemes, which are accommodated in a single network architecture by implementing them in different layers. As a result, all units carry signals related to boundary detection as well as grouping of image regions, in accordance with cortical physiology. Boundaries yield an early enhancement of network responses, but at a later point, an entire figural region is grouped together, because units that respond to it are labeled with enhanced activity. The model predicts which image regions are preferentially perceived as figure or as background and reproduces the spatio-temporal profile of neuronal activity in the visual cortex during texture segregation in intact animals, as well as in animals with cortical lesions.

Random sampling of elementary flux modes in large-scale metabolic networks.

Science.gov (United States)

Machado, Daniel; Soons, Zita; Patil, Kiran Raosaheb; Ferreira, Eugénio C; Rocha, Isabel

2012-09-15

The description of a metabolic network in terms of elementary (flux) modes (EMs) provides an important framework for metabolic pathway analysis. However, their application to large networks has been hampered by the combinatorial explosion in the number of modes. In this work, we develop a method for generating random samples of EMs without computing the whole set. Our algorithm is an adaptation of the canonical basis approach, where we add an additional filtering step which, at each iteration, selects a random subset of the new combinations of modes. In order to obtain an unbiased sample, all candidates are assigned the same probability of getting selected. This approach avoids the exponential growth of the number of modes during computation, thus generating a random sample of the complete set of EMs within reasonable time. We generated samples of different sizes for a metabolic network of Escherichia coli, and observed that they preserve several properties of the full EM set. It is also shown that EM sampling can be used for rational strain design. A well distributed sample, that is representative of the complete set of EMs, should be suitable to most EM-based methods for analysis and optimization of metabolic networks. Source code for a cross-platform implementation in Python is freely available at http://code.google.com/p/emsampler. dmachado@deb.uminho.pt Supplementary data are available at Bioinformatics online.

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

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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.

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

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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.

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

Testing a Cloud Provider Network for Hybrid P2P and Cloud Streaming Architectures

OpenAIRE

Cerviño Arriba, Javier; Rodríguez, Pedro; Trajkovska, Irena; Mozo Velasco, Alberto; Salvachúa Rodríguez, Joaquín

2011-01-01

The number of online real-time streaming services deployed over network topologies like P2P or centralized ones has remarkably increased in the recent years. This has revealed the lack of networks that are well prepared to respond to this kind of traffic. A hybrid distribution network can be an efficient solution for real-time streaming services. This paper contains the experimental results of streaming distribution in a hybrid architecture that consist of mixed connections among P2P and Clou...

On the complexity of neural network classifiers: a comparison between shallow and deep architectures.

Science.gov (United States)

Bianchini, Monica; Scarselli, Franco

2014-08-01

Recently, researchers in the artificial neural network field have focused their attention on connectionist models composed by several hidden layers. In fact, experimental results and heuristic considerations suggest that deep architectures are more suitable than shallow ones for modern applications, facing very complex problems, e.g., vision and human language understanding. However, the actual theoretical results supporting such a claim are still few and incomplete. In this paper, we propose a new approach to study how the depth of feedforward neural networks impacts on their ability in implementing high complexity functions. First, a new measure based on topological concepts is introduced, aimed at evaluating the complexity of the function implemented by a neural network, used for classification purposes. Then, deep and shallow neural architectures with common sigmoidal activation functions are compared, by deriving upper and lower bounds on their complexity, and studying how the complexity depends on the number of hidden units and the used activation function. The obtained results seem to support the idea that deep networks actually implements functions of higher complexity, so that they are able, with the same number of resources, to address more difficult problems.

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...

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.

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; Kierzek, Andrzej M

2017-11-01

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. © 2017 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

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...

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.

Study on Optimization of I and C Architecture for Research Reactors Using Bayesian Networks

Energy Technology Data Exchange (ETDEWEB)

Rahman, Khaili Ur; Shin, Jinsoo; Heo, Gyunyoung [Kyung Hee Univ., Yongin (Korea, Republic of)

2013-07-01

The optimization in terms of redundancy of modules and components in Instrumentation and Control (I and C) architecture is based on cost and availability assuming regulatory requirements are satisfied. The motive of this study is to find an optimized I and C architecture, either in hybrid formation, fully digital or analog, with respect to system availability and relative cost of architecture. The cost of research reactors I and C systems is prone to have effect on marketing competitiveness. As a demonstrative example, the reactor protection system of research reactors is selected. The four cases with different architecture formation were developed with single and double redundancy of bi-stable modules, coincidence processor module, and safety or protection circuit actuation logic. The architecture configurations are transformed to reliability block diagram (RBD) based on logical operation and function of modules. A Bayesian Network (BN) model is constructed from RBD to assess availability. The cost estimation was proposed and reliability cost index RI was suggested.

Study on Optimization of I and C Architecture for Research Reactors Using Bayesian Networks

International Nuclear Information System (INIS)

Rahman, Khaili Ur; Shin, Jinsoo; Heo, Gyunyoung

2013-01-01

The optimization in terms of redundancy of modules and components in Instrumentation and Control (I and C) architecture is based on cost and availability assuming regulatory requirements are satisfied. The motive of this study is to find an optimized I and C architecture, either in hybrid formation, fully digital or analog, with respect to system availability and relative cost of architecture. The cost of research reactors I and C systems is prone to have effect on marketing competitiveness. As a demonstrative example, the reactor protection system of research reactors is selected. The four cases with different architecture formation were developed with single and double redundancy of bi-stable modules, coincidence processor module, and safety or protection circuit actuation logic. The architecture configurations are transformed to reliability block diagram (RBD) based on logical operation and function of modules. A Bayesian Network (BN) model is constructed from RBD to assess availability. The cost estimation was proposed and reliability cost index RI was suggested

The Hi-Ring DCN Architecture

DEFF Research Database (Denmark)

Galili, Michael; Kamchevska, Valerija; Ding, Yunhong

2016-01-01

We will review recent work on the proposed hierarchical ring-based architecture (HiRing) proposed for data center networks. We will discuss the architecture and initial demonstrations of optical switching performance and time-domain synchronization......We will review recent work on the proposed hierarchical ring-based architecture (HiRing) proposed for data center networks. We will discuss the architecture and initial demonstrations of optical switching performance and time-domain synchronization...

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.

A 10 Gb/s passive-components-based WDM-TDM reconfigurable optical access network architecture

NARCIS (Netherlands)

Tran, N.C.; Jung, H.D.; Okonkwo, C.M.; Tangdiongga, E.; Koonen, A.M.J.

2011-01-01

We propose a cost-effective, reconfigurable optical access network by employing passive components in the remote node and dual conventional optical transceivers in ONUs. The architecture is demonstrated with bidirectional transmission at 10 Gb/s.

Abnormal metabolic brain networks in Parkinson's disease from blackboard to bedside.

Science.gov (United States)

Tang, Chris C; Eidelberg, David

2010-01-01

Metabolic imaging in the rest state has provided valuable information concerning the abnormalities of regional brain function that underlie idiopathic Parkinson's disease (PD). Moreover, network modeling procedures, such as spatial covariance analysis, have further allowed for the quantification of these changes at the systems level. In recent years, we have utilized this strategy to identify and validate three discrete metabolic networks in PD associated with the motor and cognitive manifestations of the disease. In this chapter, we will review and compare the specific functional topographies underlying parkinsonian akinesia/rigidity, tremor, and cognitive disturbance. While network activity progressed over time, the rate of change for each pattern was distinctive and paralleled the development of the corresponding clinical symptoms in early-stage patients. This approach is already showing great promise in identifying individuals with prodromal manifestations of PD and in assessing the rate of progression before clinical onset. Network modulation was found to correlate with the clinical effects of dopaminergic treatment and surgical interventions, such as subthalamic nucleus (STN) deep brain stimulation (DBS) and gene therapy. Abnormal metabolic networks have also been identified for atypical parkinsonian syndromes, such as multiple system atrophy (MSA) and progressive supranuclear palsy (PSP). Using multiple disease-related networks for PD, MSA, and PSP, we have developed a novel, fully automated algorithm for accurate classification at the single-patient level, even at early disease stages. Copyright © 2010 Elsevier B.V. All rights reserved.

Discovery of Boolean metabolic networks: integer linear programming based approach.

Science.gov (United States)

Qiu, Yushan; Jiang, Hao; Ching, Wai-Ki; Cheng, Xiaoqing

2018-04-11

Traditional drug discovery methods focused on the efficacy of drugs rather than their toxicity. However, toxicity and/or lack of efficacy are produced when unintended targets are affected in metabolic networks. Thus, identification of biological targets which can be manipulated to produce the desired effect with minimum side-effects has become an important and challenging topic. Efficient computational methods are required to identify the drug targets while incurring minimal side-effects. In this paper, we propose a graph-based computational damage model that summarizes the impact of enzymes on compounds in metabolic networks. An efficient method based on Integer Linear Programming formalism is then developed to identify the optimal enzyme-combination so as to minimize the side-effects. The identified target enzymes for known successful drugs are then verified by comparing the results with those in the existing literature. Side-effects reduction plays a crucial role in the study of drug development. A graph-based computational damage model is proposed and the theoretical analysis states the captured problem is NP-completeness. The proposed approaches can therefore contribute to the discovery of drug targets. Our developed software is available at " http://hkumath.hku.hk/~wkc/APBC2018-metabolic-network.zip ".

Identifying all moiety conservation laws in genome-scale metabolic networks.

Science.gov (United States)

De Martino, Andrea; De Martino, Daniele; Mulet, Roberto; Pagnani, Andrea

2014-01-01

The stoichiometry of a metabolic network gives rise to a set of conservation laws for the aggregate level of specific pools of metabolites, which, on one hand, pose dynamical constraints that cross-link the variations of metabolite concentrations and, on the other, provide key insight into a cell's metabolic production capabilities. When the conserved quantity identifies with a chemical moiety, extracting all such conservation laws from the stoichiometry amounts to finding all non-negative integer solutions of a linear system, a programming problem known to be NP-hard. We present an efficient strategy to compute the complete set of integer conservation laws of a genome-scale stoichiometric matrix, also providing a certificate for correctness and maximality of the solution. Our method is deployed for the analysis of moiety conservation relationships in two large-scale reconstructions of the metabolism of the bacterium E. coli, in six tissue-specific human metabolic networks, and, finally, in the human reactome as a whole, revealing that bacterial metabolism could be evolutionarily designed to cover broader production spectra than human metabolism. Convergence to the full set of moiety conservation laws in each case is achieved in extremely reduced computing times. In addition, we uncover a scaling relation that links the size of the independent pool basis to the number of metabolites, for which we present an analytical explanation.

Identifying all moiety conservation laws in genome-scale metabolic networks.

Directory of Open Access Journals (Sweden)

Andrea De Martino

Full Text Available The stoichiometry of a metabolic network gives rise to a set of conservation laws for the aggregate level of specific pools of metabolites, which, on one hand, pose dynamical constraints that cross-link the variations of metabolite concentrations and, on the other, provide key insight into a cell's metabolic production capabilities. When the conserved quantity identifies with a chemical moiety, extracting all such conservation laws from the stoichiometry amounts to finding all non-negative integer solutions of a linear system, a programming problem known to be NP-hard. We present an efficient strategy to compute the complete set of integer conservation laws of a genome-scale stoichiometric matrix, also providing a certificate for correctness and maximality of the solution. Our method is deployed for the analysis of moiety conservation relationships in two large-scale reconstructions of the metabolism of the bacterium E. coli, in six tissue-specific human metabolic networks, and, finally, in the human reactome as a whole, revealing that bacterial metabolism could be evolutionarily designed to cover broader production spectra than human metabolism. Convergence to the full set of moiety conservation laws in each case is achieved in extremely reduced computing times. In addition, we uncover a scaling relation that links the size of the independent pool basis to the number of metabolites, for which we present an analytical explanation.

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

A proposed architecture for a satellite-based mobile communications network - The lowest three layers

Science.gov (United States)

Yan, T. Y.; Naderi, F. M.

1986-01-01

Architecture for a commercial mobile satellite network is proposed. The mobile satellite system (MSS) is composed of a network management center, mobile terminals, base stations, and gateways; the functions of each component are described. The satellite is a 'bent pipe' that performs frequency translations, and it has multiple UHF beams. The development of the MSS design based on the seven-layer open system interconnection model is examined. Consideration is given to the functions of the physical, data link, and network layers and the integrated adaptive mobile access protocol.

A Model of Trusted Connection Architecture

Directory of Open Access Journals (Sweden)

Zhang Xun

2017-01-01

Full Text Available According to that traditional trusted network connection architecture (TNC has limitations on dynamic network environment and the user behavior support, we develop TCA to propose a trusted connection architecture supporting behavior measurement (TCA-SBM, besides, the structure diagram of network architecture is given. Through introducing user behavior measure elements, TCA-SBM can conduct measurement on the whole network in time dimension periodically, and refine the measurement on network behavior in measure dimension to conduct fine-grained dynamic trusted measurement. As a result, TCA-SBM enhances the TCA’s ability to adapt to the dynamic change of network and makes up the deficiency of trusted computing framework in the network connection.

Optimality principles in the regulation of metabolic networks.

Science.gov (United States)

Berkhout, Jan; Bruggeman, Frank J; Teusink, Bas

2012-08-29

One of the challenging tasks in systems biology is to understand how molecular networks give rise to emergent functionality and whether universal design principles apply to molecular networks. To achieve this, the biophysical, evolutionary and physiological constraints that act on those networks need to be identified in addition to the characterisation of the molecular components and interactions. Then, the cellular "task" of the network-its function-should be identified. A network contributes to organismal fitness through its function. The premise is that the same functions are often implemented in different organisms by the same type of network; hence, the concept of design principles. In biology, due to the strong forces of selective pressure and natural selection, network functions can often be understood as the outcome of fitness optimisation. The hypothesis of fitness optimisation to understand the design of a network has proven to be a powerful strategy. Here, we outline the use of several optimisation principles applied to biological networks, with an emphasis on metabolic regulatory networks. We discuss the different objective functions and constraints that are considered and the kind of understanding that they provide.

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.

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.

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.

Optimality Principles in the Regulation of Metabolic Networks

Directory of Open Access Journals (Sweden)

Jan Berkhout

2012-08-01

Full Text Available One of the challenging tasks in systems biology is to understand how molecular networks give rise to emergent functionality and whether universal design principles apply to molecular networks. To achieve this, the biophysical, evolutionary and physiological constraints that act on those networks need to be identified in addition to the characterisation of the molecular components and interactions. Then, the cellular “task” of the network—its function—should be identified. A network contributes to organismal fitness through its function. The premise is that the same functions are often implemented in different organisms by the same type of network; hence, the concept of design principles. In biology, due to the strong forces of selective pressure and natural selection, network functions can often be understood as the outcome of fitness optimisation. The hypothesis of fitness optimisation to understand the design of a network has proven to be a powerful strategy. Here, we outline the use of several optimisation principles applied to biological networks, with an emphasis on metabolic regulatory networks. We discuss the different objective functions and constraints that are considered and the kind of understanding that they provide.

A novel survivable architecture for hybrid WDM/TDM passive optical networks

Science.gov (United States)

Qiu, Yang; Chan, Chun-Kit

2014-02-01

A novel tree-ring survivable architecture, which consists of an organization of a wavelength-division-multiplexing (WDM) tree from optical line terminal (OLT) to remote nodes (RNs) and a time division multiplexing (TDM) ring in each RN, is proposed for hybrid WDM/TDM passive optical networks. By utilizing the cyclic property of arrayed waveguide gratings (AWGs) and the single-ring topology among a group of optical network units (ONUs) in the remote node, not only the feeder and distribution fibers, but also any fiber failures in the RN rings are protected simultaneously. Five-Gbit/s transmissions under both normal working and protection modes were experimentally demonstrated and a traffic restoration time was successfully measured.

SNAVA-A real-time multi-FPGA multi-model spiking neural network simulation architecture.

Science.gov (United States)

Sripad, Athul; Sanchez, Giovanny; Zapata, Mireya; Pirrone, Vito; Dorta, Taho; Cambria, Salvatore; Marti, Albert; Krishnamourthy, Karthikeyan; Madrenas, Jordi

2018-01-01

Spiking Neural Networks (SNN) for Versatile Applications (SNAVA) simulation platform is a scalable and programmable parallel architecture that supports real-time, large-scale, multi-model SNN computation. This parallel architecture is implemented in modern Field-Programmable Gate Arrays (FPGAs) devices to provide high performance execution and flexibility to support large-scale SNN models. Flexibility is defined in terms of programmability, which allows easy synapse and neuron implementation. This has been achieved by using a special-purpose Processing Elements (PEs) for computing SNNs, and analyzing and customizing the instruction set according to the processing needs to achieve maximum performance with minimum resources. The parallel architecture is interfaced with customized Graphical User Interfaces (GUIs) to configure the SNN's connectivity, to compile the neuron-synapse model and to monitor SNN's activity. Our contribution intends to provide a tool that allows to prototype SNNs faster than on CPU/GPU architectures but significantly cheaper than fabricating a customized neuromorphic chip. This could be potentially valuable to the computational neuroscience and neuromorphic engineering communities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Virtualized cognitive network architecture for 5G cellular networks

KAUST Repository

Elsawy, Hesham; Dahrouj, Hayssam; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim

2015-01-01

, 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

Limitations of a metabolic network-based reverse ecology method for inferring host-pathogen interactions.

Science.gov (United States)

Takemoto, Kazuhiro; Aie, Kazuki

2017-05-25

Host-pathogen interactions are important in a wide range of research fields. Given the importance of metabolic crosstalk between hosts and pathogens, a metabolic network-based reverse ecology method was proposed to infer these interactions. However, the validity of this method remains unclear because of the various explanations presented and the influence of potentially confounding factors that have thus far been neglected. We re-evaluated the importance of the reverse ecology method for evaluating host-pathogen interactions while statistically controlling for confounding effects using oxygen requirement, genome, metabolic network, and phylogeny data. Our data analyses showed that host-pathogen interactions were more strongly influenced by genome size, primary network parameters (e.g., number of edges), oxygen requirement, and phylogeny than the reserve ecology-based measures. These results indicate the limitations of the reverse ecology method; however, they do not discount the importance of adopting reverse ecology approaches altogether. Rather, we highlight the need for developing more suitable methods for inferring host-pathogen interactions and conducting more careful examinations of the relationships between metabolic networks and host-pathogen interactions.

Quantitative Tools for Dissection of Hydrogen-Producing Metabolic Networks-Final Report

Energy Technology Data Exchange (ETDEWEB)

Rabinowitz, Joshua D.; Dismukes, G.Charles.; Rabitz, Herschel A.; Amador-Noguez, Daniel

2012-10-19

During this project we have pioneered the development of integrated experimental-computational technologies for the quantitative dissection of metabolism in hydrogen and biofuel producing microorganisms (i.e. C. acetobutylicum and various cyanobacteria species). The application of these new methodologies resulted in many significant advances in the understanding of the metabolic networks and metabolism of these organisms, and has provided new strategies to enhance their hydrogen or biofuel producing capabilities. As an example, using mass spectrometry, isotope tracers, and quantitative flux-modeling we mapped the metabolic network structure in C. acetobutylicum. This resulted in a comprehensive and quantitative understanding of central carbon metabolism that could not have been obtained using genomic data alone. We discovered that biofuel production in this bacterium, which only occurs during stationary phase, requires a global remodeling of central metabolism (involving large changes in metabolite concentrations and fluxes) that has the effect of redirecting resources (carbon and reducing power) from biomass production into solvent production. This new holistic, quantitative understanding of metabolism is now being used as the basis for metabolic engineering strategies to improve solvent production in this bacterium. In another example, making use of newly developed technologies for monitoring hydrogen and NAD(P)H levels in vivo, we dissected the metabolic pathways for photobiological hydrogen production by cyanobacteria Cyanothece sp. This investigation led to the identification of multiple targets for improving hydrogen production. Importantly, the quantitative tools and approaches that we have developed are broadly applicable and we are now using them to investigate other important biofuel producers, such as cellulolytic bacteria.

Reconfigurable FPGA architecture for computer vision applications in Smart Camera Networks

OpenAIRE

Maggiani , Luca; Salvadori , Claudio; Petracca , Matteo; Pagano , Paolo; Saletti , Roberto

2013-01-01

International audience; Smart Camera Networks (SCNs) is nowadays an emerging research field which represents the natural evolution of centralized computer vision applications towards full distributed and pervasive systems. In such a scenario, one of the biggest effort is in the definition of a flexible and reconfigurable SCN node architecture able to remotely support the possibility of updating the application parameters and changing the running computer vision applications at run-time. In th...

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

Directory of Open Access Journals (Sweden)

Ina Koch

2017-06-01

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

AziSA: An architecture for underground measurement and control networks - 2nd CSIR Biennial Conference

CSIR Research Space (South Africa)

Stewart, R

2008-11-01

Full Text Available products from various manufacturers. SOLUTION The architecture that has been developed at the CSIR is called AziSA, an isiZulu word meaning ‘to inform’. The AziSA architecture AziSA is a specification for an open measurement and control network... for in-mine communications even if the link with the outside world is disrupted. This requirement for robustness implies that processing in the system must be distributed and not totally dependent on central coordination. Decisions should be made...

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.

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

Directory of Open Access Journals (Sweden)

Page Michel

2009-12-01

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

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...

Dietary Pseudopurpurin Improves Bone Geometry Architecture and Metabolism in Red-Bone Guishan Goats

Science.gov (United States)

Han, TieSuo; Li, Peng; Wang, JianGuo; Liu, GuoWen; Wang, Zhe; Ge, ChangRong; Gao, ShiZheng

2012-01-01

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. PMID:22624037

Combined metabolomic and correlation networks analyses reveal fumarase insufficiency altered amino acid metabolism.

Science.gov (United States)

Hou, Entai; Li, Xian; Liu, Zerong; Zhang, Fuchang; Tian, Zhongmin

2018-04-01

Fumarase catalyzes the interconversion of fumarate and l-malate in the tricarboxylic acid cycle. Fumarase insufficiencies were associated with increased levels of fumarate, decreased levels of malate and exacerbated salt-induced hypertension. To gain insights into the metabolism profiles induced by fumarase insufficiency and identify key regulatory metabolites, we applied a GC-MS based metabolomics platform coupled with a network approach to analyze fumarase insufficient human umbilical vein endothelial cells (HUVEC) and negative controls. A total of 24 altered metabolites involved in seven metabolic pathways were identified as significantly altered, and enriched for the biological module of amino acids metabolism. In addition, Pearson correlation network analysis revealed that fumaric acid, l-malic acid, l-aspartic acid, glycine and l-glutamic acid were hub metabolites according to Pagerank based on their three centrality indices. Alanine aminotransferase and glutamate dehydrogenase activities increased significantly in fumarase deficiency HUVEC. These results confirmed that fumarase insufficiency altered amino acid metabolism. The combination of metabolomics and network methods would provide another perspective on expounding the molecular mechanism at metabolomics level. Copyright © 2017 John Wiley & Sons, Ltd.

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.

Efficient network reconstruction from dynamical cascades identifies small-world topology of neuronal avalanches.

Directory of Open Access Journals (Sweden)

Sinisa Pajevic

2009-01-01

Full Text Available Cascading activity is commonly found in complex systems with directed interactions such as metabolic networks, neuronal networks, or disease spreading in social networks. Substantial insight into a system's organization can be obtained by reconstructing the underlying functional network architecture from the observed activity cascades. Here we focus on Bayesian approaches and reduce their computational demands by introducing the Iterative Bayesian (IB and Posterior Weighted Averaging (PWA methods. We introduce a special case of PWA, cast in nonparametric form, which we call the normalized count (NC algorithm. NC efficiently reconstructs random and small-world functional network topologies and architectures from subcritical, critical, and supercritical cascading dynamics and yields significant improvements over commonly used correlation methods. With experimental data, NC identified a functional and structural small-world topology and its corresponding traffic in cortical networks with neuronal avalanche dynamics.

Metabolic network prediction through pairwise rational kernels.

Science.gov (United States)

Roche-Lima, Abiel; Domaratzki, Michael; Fristensky, Brian

2014-09-26

Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to another reaction. Many pathways remain incompletely characterized. One of the major challenges of computational biology is to obtain better models of metabolic pathways. Existing models are dependent on the annotation of the genes. This propagates error accumulation when the pathways are predicted by incorrectly annotated genes. Pairwise classification methods are supervised learning methods used to classify new pair of entities. Some of these classification methods, e.g., Pairwise Support Vector Machines (SVMs), use pairwise kernels. Pairwise kernels describe similarity measures between two pairs of entities. Using pairwise kernels to handle sequence data requires long processing times and large storage. Rational kernels are kernels based on weighted finite-state transducers that represent similarity measures between sequences or automata. They have been effectively used in problems that handle large amount of sequence information such as protein essentiality, natural language processing and machine translations. We create a new family of pairwise kernels using weighted finite-state transducers (called Pairwise Rational Kernel (PRK)) to predict metabolic pathways from a variety of biological data. PRKs take advantage of the simpler representations and faster algorithms of transducers. Because raw sequence data can be used, the predictor model avoids the errors introduced by incorrect gene annotations. We then developed several experiments with PRKs and Pairwise SVM to validate our methods using the metabolic network of Saccharomyces cerevisiae. As a result, when PRKs are used, our method executes faster in comparison with other pairwise kernels. Also, when we use PRKs combined with other simple kernels that include evolutionary information, the accuracy

Integration of expression data in genome-scale metabolic network reconstructions

Directory of Open Access Journals (Sweden)

Anna S. Blazier

2012-08-01

Full Text Available With the advent of high-throughput technologies, the field of systems biology has amassed an abundance of omics data, quantifying thousands of cellular components across a variety of scales, ranging from mRNA transcript levels to metabolite quantities. Methods are needed to not only integrate this omics data but to also use this data to heighten the predictive capabilities of computational models. Several recent studies have successfully demonstrated how flux balance analysis (FBA, a constraint-based modeling approach, can be used to integrate transcriptomic data into genome-scale metabolic network reconstructions to generate predictive computational models. In this review, we summarize such FBA-based methods for integrating expression data into genome-scale metabolic network reconstructions, highlighting their advantages as well as their limitations.

A flexible data fusion architecture for persistent surveillance using ultra-low-power wireless sensor networks

Science.gov (United States)

Hanson, Jeffrey A.; McLaughlin, Keith L.; Sereno, Thomas J.

2011-06-01

We have developed a flexible, target-driven, multi-modal, physics-based fusion architecture that efficiently searches sensor detections for targets and rejects clutter while controlling the combinatoric problems that commonly arise in datadriven fusion systems. The informational constraints imposed by long lifetime requirements make systems vulnerable to false alarms. We demonstrate that our data fusion system significantly reduces false alarms while maintaining high sensitivity to threats. In addition, mission goals can vary substantially in terms of targets-of-interest, required characterization, acceptable latency, and false alarm rates. Our fusion architecture provides the flexibility to match these trade-offs with mission requirements unlike many conventional systems that require significant modifications for each new mission. We illustrate our data fusion performance with case studies that span many of the potential mission scenarios including border surveillance, base security, and infrastructure protection. In these studies, we deployed multi-modal sensor nodes - including geophones, magnetometers, accelerometers and PIR sensors - with low-power processing algorithms and low-bandwidth wireless mesh networking to create networks capable of multi-year operation. The results show our data fusion architecture maintains high sensitivities while suppressing most false alarms for a variety of environments and targets.

ARCHITECTURES AND ALGORITHMS FOR COGNITIVE NETWORKS ENABLED BY QUALITATIVE MODELS

DEFF Research Database (Denmark)

Balamuralidhar, P.

2013-01-01

traditional limitations and potentially achieving better performance. The vision is that, networks should be able to monitor themselves, reason upon changes in self and environment, act towards the achievement of specific goals and learn from experience. The concept of a Cognitive Engine (CE) supporting...... cognitive functions, as part of network elements, enabling above said autonomic capabilities is gathering attention. Awareness of the self and the world is an important aspect of the cognitive engine to be autonomic. This is achieved through embedding their models in the engine, but the complexity...... 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...

Gender differences of brain glucose metabolic networks revealed by FDG-PET: evidence from a large cohort of 400 young adults.

Science.gov (United States)

Hu, Yuxiao; Xu, Qiang; Li, Kai; Zhu, Hong; Qi, Rongfeng; Zhang, Zhiqiang; Lu, Guangming

2013-01-01

Gender differences of the human brain are an important issue in neuroscience research. In recent years, an increasing amount of evidence has been gathered from noninvasive neuroimaging studies supporting a sexual dimorphism of the human brain. However, there is a lack of imaging studies on gender differences of brain metabolic networks based on a large population sample. FDG PET data of 400 right-handed, healthy subjects, including 200 females (age: 25:45 years, mean age ± SD: 40.9 ± 3.9 years) and 200 age-matched males were obtained and analyzed in the present study. We first investigated the regional differences of brain glucose metabolism between genders using a voxel-based two-sample t-test analysis. Subsequently, we investigated the gender differences of the metabolic networks. Sixteen metabolic covariance networks using seed-based correlation were analyzed. Seven regions showing significant regional metabolic differences between genders, and nine regions conventionally used in the resting-state network studies were selected as regions-of-interest. Permutation tests were used for comparing within- and between-network connectivity between genders. Compared with the males, females showed higher metabolism in the posterior part and lower metabolism in the anterior part of the brain. Moreover, there were widely distributed patterns of the metabolic networks in the human brain. In addition, significant gender differences within and between brain glucose metabolic networks were revealed in the present study. This study provides solid data that reveal gender differences in regional brain glucose metabolism and brain glucose metabolic networks. These observations might contribute to the better understanding of the gender differences in human brain functions, and suggest that gender should be included as a covariate when designing experiments and explaining results of brain glucose metabolic networks in the control and experimental individuals or patients.

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

Examining the volume efficiency of the cortical architecture in a multi-processor network model.

Science.gov (United States)

Ruppin, E; Schwartz, E L; Yeshurun, Y

1993-01-01

The convoluted form of the sheet-like mammalian cortex naturally raises the question whether there is a simple geometrical reason for the prevalence of cortical architecture in the brains of higher vertebrates. Addressing this question, we present a formal analysis of the volume occupied by a massively connected network or processors (neurons) and then consider the pertaining cortical data. Three gross macroscopic features of cortical organization are examined: the segregation of white and gray matter, the circumferential organization of the gray matter around the white matter, and the folded cortical structure. Our results testify to the efficiency of cortical architecture.

A Novel, Privacy Preserving, Architecture for Online Social Networks

Directory of Open Access Journals (Sweden)

Zhe Wang

2015-12-01

Full Text Available The centralized nature of conventional OSNs poses serious risks to the privacy and security of information exchanged between their members. These risks prompted several attempts to create decentralized OSNs, or DOSNs. The basic idea underlying these attempts, is that each member of a social network keeps its data under its own control, instead of surrendering it to a central host, providing access to it to other members according to its own access-control policy. Unfortunately all existing versions of DOSNs have a very serious limitation. Namely, they are unable to subject the membership of a DOSN, and the interaction between its members, to any global policy—which is essential for many social communities. Moreover, the DOSN architecture is unable to support useful capabilities such as narrowcasting and profile based search. This paper describes a novel architecture of decentralized OSNs—called DOSC, for “online social community”. DOSC adopts the decentralization idea underlying DOSNs, but it is able to subject the membership of a DOSC-community, and the interaction between its members, to a wide range of policies, including privacy-preserving narrowcasting and profile-sensitive search.

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.

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.

Interrogating the architecture of protein assemblies and protein interaction networks by cross-linking mass spectrometry

NARCIS (Netherlands)

Liu, Fan; Heck, Albert J R

2015-01-01

Proteins are involved in almost all processes of the living cell. They are organized through extensive networks of interaction, by tightly bound macromolecular assemblies or more transiently via signaling nodes. Therefore, revealing the architecture of protein complexes and protein interaction

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.

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.

Environmental versatility promotes modularity in large scale metabolic networks

OpenAIRE

Samal A.; Wagner Andreas; Martin O.C.

2011-01-01

Abstract Background The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new arrangements that may benefit their carrier. Conversely, modularity may emerge as a by-product of some trait. We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chem...

Network Thermodynamic Curation of Human and Yeast Genome-Scale Metabolic Models

Science.gov (United States)

Martínez, Verónica S.; Quek, Lake-Ee; Nielsen, Lars K.

2014-01-01

Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as irreversible. However, these specifications are mainly based on biochemical textbooks or on their similarity to other organisms and are rarely underpinned by detailed thermodynamic analysis. In this study, a to our knowledge new workflow combining network-embedded thermodynamic and flux variability analysis was used to evaluate existing irreversibility constraints in Recon 1 and Yeast 5 and to identify new ones. A total of 27 and 16 new irreversible reactions were identified in Recon 1 and Yeast 5, respectively, whereas only four reactions were found with directions incorrectly specified against thermodynamics (three in Yeast 5 and one in Recon 1). The workflow further identified for both models several isolated internal loops that require further curation. The framework also highlighted the need for substrate channeling (in human) and ATP hydrolysis (in yeast) for the essential reaction catalyzed by phosphoribosylaminoimidazole carboxylase in purine metabolism. Finally, the framework highlighted differences in proline metabolism between yeast (cytosolic anabolism and mitochondrial catabolism) and humans (exclusively mitochondrial metabolism). We conclude that network-embedded thermodynamics facilitates the specification and validation of irreversibility constraints in compartmentalized metabolic models, at the same time providing further insight into network properties. PMID:25028891

Introduction to parallel algorithms and architectures arrays, trees, hypercubes

CERN Document Server

Leighton, F Thomson

1991-01-01

Introduction to Parallel Algorithms and Architectures: Arrays Trees Hypercubes provides an introduction to the expanding field of parallel algorithms and architectures. This book focuses on parallel computation involving the most popular network architectures, namely, arrays, trees, hypercubes, and some closely related networks.Organized into three chapters, this book begins with an overview of the simplest architectures of arrays and trees. This text then presents the structures and relationships between the dominant network architectures, as well as the most efficient parallel algorithms for

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.

, neural network architecture, seafloor classification, self-organizing feature map (SOFM). I. INTRODUCTION S EAFLOOR classification and characterization using re- mote high-frequency acoustic system has been recognized as a useful tool (see [1...] and references therein). The seafloor’s characteristics are extremely complicated due to variations of the many parameters at different scales. The parameters include sediment grain size, relief height at the water–sediment inter- face, and variations within...

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.

Mimoza: web-based semantic zooming and navigation in metabolic networks.

Science.gov (United States)

Zhukova, Anna; Sherman, David J

2015-02-26

The complexity of genome-scale metabolic models makes them quite difficult for human users to read, since they contain thousands of reactions that must be included for accurate computer simulation. Interestingly, hidden similarities between groups of reactions can be discovered, and generalized to reveal higher-level patterns. The web-based navigation system Mimoza allows a human expert to explore metabolic network models in a semantically zoomable manner: The most general view represents the compartments of the model; the next view shows the generalized versions of reactions and metabolites in each compartment; and the most detailed view represents the initial network with the generalization-based layout (where similar metabolites and reactions are placed next to each other). It allows a human expert to grasp the general structure of the network and analyze it in a top-down manner Mimoza can be installed standalone, or used on-line at http://mimoza.bordeaux.inria.fr/ , or installed in a Galaxy server for use in workflows. Mimoza views can be embedded in web pages, or downloaded as COMBINE archives.

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.

Seamless interworking architecture for WBAN in heterogeneous wireless networks with QoS guarantees.

Science.gov (United States)

Khan, Pervez; Ullah, Niamat; Ullah, Sana; Kwak, Kyung Sup

2011-10-01

The IEEE 802.15.6 standard is a communication standard optimized for low-power and short-range in-body/on-body nodes to serve a variety of medical, consumer electronics and entertainment applications. Providing high mobility with guaranteed Quality of Service (QoS) to a WBAN user in heterogeneous wireless networks is a challenging task. A WBAN uses a Personal Digital Assistant (PDA) to gather data from body sensors and forwards it to a remote server through wide range wireless networks. In this paper, we present a coexistence study of WBAN with Wireless Local Area Networks (WLAN) and Wireless Wide Area Networks (WWANs). The main issue is interworking of WBAN in heterogenous wireless networks including seamless handover, QoS, emergency services, cooperation and security. We propose a Seamless Interworking Architecture (SIA) for WBAN in heterogenous wireless networks based on a cost function. The cost function is based on power consumption and data throughput costs. Our simulation results show that the proposed scheme outperforms typical approaches in terms of throughput, delay and packet loss rate.

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

OpenAIRE

Checko, Aleksandra; Kardaras, Georgios; Lanzani, Christian Fabio Alessandro; Temple, Dan; Mathiasen, Carsten; Pedersen, Lars A.; Klaps, Bert

2014-01-01

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 module and a remote radio module is compliant to Common Public Radio Interface (CPRI) and to the OBSAI reference point 3 - 01 (RP3-01) interface protocols, respectively. The purpose is to demonstrate ...

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.

Integration of genome-scale metabolic networks into whole-body PBPK models shows phenotype-specific cases of drug-induced metabolic perturbation.

Science.gov (United States)

Cordes, Henrik; Thiel, Christoph; Baier, Vanessa; Blank, Lars M; Kuepfer, Lars

2018-01-01

Drug-induced perturbations of the endogenous metabolic network are a potential root cause of cellular toxicity. A mechanistic understanding of such unwanted side effects during drug therapy is therefore vital for patient safety. The comprehensive assessment of such drug-induced injuries requires the simultaneous consideration of both drug exposure at the whole-body and resulting biochemical responses at the cellular level. We here present a computational multi-scale workflow that combines whole-body physiologically based pharmacokinetic (PBPK) models and organ-specific genome-scale metabolic network (GSMN) models through shared reactions of the xenobiotic metabolism. The applicability of the proposed workflow is illustrated for isoniazid, a first-line antibacterial agent against Mycobacterium tuberculosis , which is known to cause idiosyncratic drug-induced liver injuries (DILI). We combined GSMN models of a human liver with N-acetyl transferase 2 (NAT2)-phenotype-specific PBPK models of isoniazid. The combined PBPK-GSMN models quantitatively describe isoniazid pharmacokinetics, as well as intracellular responses, and changes in the exometabolome in a human liver following isoniazid administration. Notably, intracellular and extracellular responses identified with the PBPK-GSMN models are in line with experimental and clinical findings. Moreover, the drug-induced metabolic perturbations are distributed and attenuated in the metabolic network in a phenotype-dependent manner. Our simulation results show that a simultaneous consideration of both drug pharmacokinetics at the whole-body and metabolism at the cellular level is mandatory to explain drug-induced injuries at the patient level. The proposed workflow extends our mechanistic understanding of the biochemistry underlying adverse events and may be used to prevent drug-induced injuries in the future.

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.

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.

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.

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.

Network thermodynamic curation of human and yeast genome-scale metabolic models.

Science.gov (United States)

Martínez, Verónica S; Quek, Lake-Ee; Nielsen, Lars K

2014-07-15

Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as irreversible. However, these specifications are mainly based on biochemical textbooks or on their similarity to other organisms and are rarely underpinned by detailed thermodynamic analysis. In this study, a to our knowledge new workflow combining network-embedded thermodynamic and flux variability analysis was used to evaluate existing irreversibility constraints in Recon 1 and Yeast 5 and to identify new ones. A total of 27 and 16 new irreversible reactions were identified in Recon 1 and Yeast 5, respectively, whereas only four reactions were found with directions incorrectly specified against thermodynamics (three in Yeast 5 and one in Recon 1). The workflow further identified for both models several isolated internal loops that require further curation. The framework also highlighted the need for substrate channeling (in human) and ATP hydrolysis (in yeast) for the essential reaction catalyzed by phosphoribosylaminoimidazole carboxylase in purine metabolism. Finally, the framework highlighted differences in proline metabolism between yeast (cytosolic anabolism and mitochondrial catabolism) and humans (exclusively mitochondrial metabolism). We conclude that network-embedded thermodynamics facilitates the specification and validation of irreversibility constraints in compartmentalized metabolic models, at the same time providing further insight into network properties. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

MWAHCA: a multimedia wireless ad hoc cluster architecture.

Science.gov (United States)

Diaz, Juan R; Lloret, Jaime; Jimenez, Jose M; Sendra, Sandra

2014-01-01

Wireless Ad hoc networks provide a flexible and adaptable infrastructure to transport data over a great variety of environments. Recently, real-time audio and video data transmission has been increased due to the appearance of many multimedia applications. One of the major challenges is to ensure the quality of multimedia streams when they have passed through a wireless ad hoc network. It requires adapting the network architecture to the multimedia QoS requirements. In this paper we propose a new architecture to organize and manage cluster-based ad hoc networks in order to provide multimedia streams. Proposed architecture adapts the network wireless topology in order to improve the quality of audio and video transmissions. In order to achieve this goal, the architecture uses some information such as each node's capacity and the QoS parameters (bandwidth, delay, jitter, and packet loss). The architecture splits the network into clusters which are specialized in specific multimedia traffic. The real system performance study provided at the end of the paper will demonstrate the feasibility of the proposal.

MWAHCA: A Multimedia Wireless Ad Hoc Cluster Architecture

Directory of Open Access Journals (Sweden)

Juan R. Diaz

2014-01-01

Full Text Available Wireless Ad hoc networks provide a flexible and adaptable infrastructure to transport data over a great variety of environments. Recently, real-time audio and video data transmission has been increased due to the appearance of many multimedia applications. One of the major challenges is to ensure the quality of multimedia streams when they have passed through a wireless ad hoc network. It requires adapting the network architecture to the multimedia QoS requirements. In this paper we propose a new architecture to organize and manage cluster-based ad hoc networks in order to provide multimedia streams. Proposed architecture adapts the network wireless topology in order to improve the quality of audio and video transmissions. In order to achieve this goal, the architecture uses some information such as each node’s capacity and the QoS parameters (bandwidth, delay, jitter, and packet loss. The architecture splits the network into clusters which are specialized in specific multimedia traffic. The real system performance study provided at the end of the paper will demonstrate the feasibility of the proposal.

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

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Feng Xueyang

2012-08-01

Full Text Available Abstract Background Concurrent with the efforts currently underway in mapping microbial genomes using high-throughput sequencing methods, systems biologists are building metabolic models to characterize and predict cell metabolisms. One of the key steps in building a metabolic model is using multiple databases to collect and assemble essential information about genome-annotations and the architecture of the metabolic network for a specific organism. To speed up metabolic model development for a large number of microorganisms, we need a user-friendly platform to construct metabolic networks and to perform constraint-based flux balance analysis based on genome databases and experimental results. Results We have developed a semi-automatic, web-based platform (MicrobesFlux for generating and reconstructing metabolic models for annotated microorganisms. MicrobesFlux is able to automatically download the metabolic network (including enzymatic reactions and metabolites of ~1,200 species from the KEGG database (Kyoto Encyclopedia of Genes and Genomes and then convert it to a metabolic model draft. The platform also provides diverse customized tools, such as gene knockouts and the introduction of heterologous pathways, for users to reconstruct the model network. The reconstructed metabolic network can be formulated to a constraint-based flux model to predict and analyze the carbon fluxes in microbial metabolisms. The simulation results can be exported in the SBML format (The Systems Biology Markup Language. Furthermore, we also demonstrated the platform functionalities by developing an FBA model (including 229 reactions for a recent annotated bioethanol producer, Thermoanaerobacter sp. strain X514, to predict its biomass growth and ethanol production. Conclusion MicrobesFlux is an installation-free and open-source platform that enables biologists without prior programming knowledge to develop metabolic models for annotated microorganisms in the KEGG

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

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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.

Sensing and Measurement Architecture for Grid Modernization

Energy Technology Data Exchange (ETDEWEB)

Taft, Jeffrey D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); De Martini, Paul [California Inst. of Technology (CalTech), Pasadena, CA (United States)

2016-02-01

This paper addresses architecture for grid sensor networks, with primary emphasis on distribution grids. It describes a forward-looking view of sensor network architecture for advanced distribution grids, and discusses key regulatory, financial, and planning issues.

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...

The compositional and evolutionary logic of metabolism

International Nuclear Information System (INIS)

Braakman, Rogier; Smith, Eric

2013-01-01

Metabolism is built on a foundation of organic chemistry, and employs structures and interactions at many scales. Despite these sources of complexity, metabolism also displays striking and robust regularities in the forms of modularity and hierarchy, which may be described compactly in terms of relatively few principles of composition. These regularities render metabolic architecture comprehensible as a system, and also suggests the order in which layers of that system came into existence. In addition metabolism also serves as a foundational layer in other hierarchies, up to at least the levels of cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, motivates us to interpret metabolism as a source of causation or constraint on many forms of organization in the biosphere. Many of the forms of modularity and hierarchy exhibited by metabolism are readily interpreted as stages in the emergence of catalytic control by living systems over organic chemistry, sometimes recapitulating or incorporating geochemical mechanisms. We identify as modules, either subsets of chemicals and reactions, or subsets of functions, that are re-used in many contexts with a conserved internal structure. At the small molecule substrate level, module boundaries are often associated with the most complex reaction mechanisms, catalyzed by highly conserved enzymes. Cofactors form a biosynthetically and functionally distinctive control layer over the small-molecule substrate. The most complex members among the cofactors are often associated with the reactions at module boundaries in the substrate networks, while simpler cofactors participate in widely generalized reactions. The highly tuned chemical structures of cofactors (sometimes exploiting distinctive properties of the elements of the periodic table) thereby act as ‘keys’ that incorporate classes of organic reactions

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

Cable-telco architectures

Science.gov (United States)

McGrath, Carl J.

1994-11-01

Continued evolution of consumer broadband services such as digital video and digital multimedia has placed renewed emphasis on the need for network solutions to the broadband connectivity challenge. Although still important to architectural planners, connection oriented broadband services based on ISDN concepts must now compete with a wider array of broadcast and highly asymmetrical services for bandwidth on the network. For network operators, the business imperative is to identify and execute a network rebuild plan that will meet the capacity and flexibility needs of these services and compete with the inevitable alternate paths into the home. This paper focuses on some of the key issues facing broadband network planners as they search for the best architecture to meet the business and operations goals in their segment of the market. It will be apparent that no single optimum solution exists for all deployment scenarios, emphasizing the need for flexible and modular sources (such as servers) and network interfaces (such as set tops) which preserve the value of content, the ultimate driver in this round of network revolution.

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.

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.

ESnet4: next generation network strategy, architecture, and implementation for DOE Science

International Nuclear Information System (INIS)

Collins, Michael; Burrescia, Joseph; Dart, Eli; Gagliardi, Jim; Guok, Chin; Johnston, William; Metzger, Joe; Oberman, Kevin; O'Connor, Mike

2006-01-01

The Department of Energy's (DOE) Office of Science is the largest supporter of basic research in the physical sciences in the US. It directly supports the research of 15,000 PhDs, PostDocs and Graduate Students, and operates major scientific facilities at DOE laboratories that serve the entire US research community: other Federal agencies, universities, and industry, as well as the international research and education (R and E) community. ESnet's mission is to provide the network infrastructure that supports the mission of the Office of Science (SC). ESnet must evolve substantially in order to continue meeting the Office of Science mission needs and this paper discusses the development of ESnet's strategy to meet these requirements through a new network architecture and implementation approach

Connexin 43-Mediated Astroglial Metabolic Networks Contribute to the Regulation of the Sleep-Wake Cycle.

Science.gov (United States)

Clasadonte, Jerome; Scemes, Eliana; Wang, Zhongya; Boison, Detlev; Haydon, Philip G

2017-09-13

Astrocytes produce and supply metabolic substrates to neurons through gap junction-mediated astroglial networks. However, the role of astroglial metabolic networks in behavior is unclear. Here, we demonstrate that perturbation of astroglial networks impairs the sleep-wake cycle. Using a conditional Cre-Lox system in mice, we show that knockout of the gap junction subunit connexin 43 in astrocytes throughout the brain causes excessive sleepiness and fragmented wakefulness during the nocturnal active phase. This astrocyte-specific genetic manipulation silenced the wake-promoting orexin neurons located in the lateral hypothalamic area (LHA) by impairing glucose and lactate trafficking through astrocytic networks. This global wakefulness instability was mimicked with viral delivery of Cre recombinase to astrocytes in the LHA and rescued by in vivo injections of lactate. Our findings propose a novel regulatory mechanism critical for maintaining normal daily cycle of wakefulness and involving astrocyte-neuron metabolic interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Integration of metabolomics data into metabolic networks.

Science.gov (United States)

Töpfer, Nadine; Kleessen, Sabrina; Nikoloski, Zoran

2015-01-01

Metabolite levels together with their corresponding metabolic fluxes are integrative outcomes of biochemical transformations and regulatory processes and they can be used to characterize the response of biological systems to genetic and/or environmental changes. However, while changes in transcript or to some extent protein levels can usually be traced back to one or several responsible genes, changes in fluxes and particularly changes in metabolite levels do not follow such rationale and are often the outcome of complex interactions of several components. The increasing quality and coverage of metabolomics technologies have fostered the development of computational approaches for integrating metabolic read-outs with large-scale models to predict the physiological state of a system. Constraint-based approaches, relying on the stoichiometry of the considered reactions, provide a modeling framework amenable to analyses of large-scale systems and to the integration of high-throughput data. Here we review the existing approaches that integrate metabolomics data in variants of constrained-based approaches to refine model reconstructions, to constrain flux predictions in metabolic models, and to relate network structural properties to metabolite levels. Finally, we discuss the challenges and perspectives in the developments of constraint-based modeling approaches driven by metabolomics data.

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.

An Overview on SDN Architectures with Multiple Controllers

Directory of Open Access Journals (Sweden)

Othmane Blial

2016-01-01

Full Text Available Software-defined networking offers several benefits for networking by separating the control plane from the data plane. However, networks’ scalability, reliability, and availability remain as a big issue. Accordingly, multicontroller architectures are important for SDN-enabled networks. This paper gives a comprehensive overview of SDN multicontroller architectures. It presents SDN and its main instantiation OpenFlow. Then, it explains in detail the differences between multiple types of multicontroller architectures, like the distribution method and the communication system. Furthermore, it provides already implemented and under research examples of multicontroller architectures by describing their design, their communication process, and their performance results.

Multiobjective flux balancing using the NISE method for metabolic network analysis.

Science.gov (United States)

Oh, Young-Gyun; Lee, Dong-Yup; Lee, Sang Yup; Park, Sunwon

2009-01-01

Flux balance analysis (FBA) is well acknowledged as an analysis tool of metabolic networks in the framework of metabolic engineering. However, FBA has a limitation for solving a multiobjective optimization problem which considers multiple conflicting objectives. In this study, we propose a novel multiobjective flux balance analysis method, which adapts the noninferior set estimation (NISE) method (Solanki et al., 1993) for multiobjective linear programming (MOLP) problems. NISE method can generate an approximation of the Pareto curve for conflicting objectives without redundant iterations of single objective optimization. Furthermore, the flux distributions at each Pareto optimal solution can be obtained for understanding the internal flux changes in the metabolic network. The functionality of this approach is shown by applying it to a genome-scale in silico model of E. coli. Multiple objectives for the poly(3-hydroxybutyrate) [P(3HB)] production are considered simultaneously, and relationships among them are identified. The Pareto curve for maximizing succinic acid production vs. maximizing biomass production is used for the in silico analysis of various combinatorial knockout strains. This proposed method accelerates the strain improvement in the metabolic engineering by reducing computation time of obtaining the Pareto curve and analysis time of flux distribution at each Pareto optimal solution. (c) 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009.

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.

Artificial Neural Networks for differential diagnosis of breast lesions in MR-Mammography: A systematic approach addressing the influence of network architecture on diagnostic performance using a large clinical database

International Nuclear Information System (INIS)

Dietzel, Matthias; Baltzer, Pascal A.T.; Dietzel, Andreas; Zoubi, Ramy; Gröschel, Tobias; Burmeister, Hartmut P.; Bogdan, Martin; Kaiser, Werner A.

2012-01-01

Rationale and objectives: Differential diagnosis of lesions in MR-Mammography (MRM) remains a complex task. The aim of this MRM study was to design and to test robustness of Artificial Neural Network architectures to predict malignancy using a large clinical database. Materials and methods: For this IRB-approved investigation standardized protocols and study design were applied (T1w-FLASH; 0.1 mmol/kgBW Gd-DTPA; T2w-TSE; histological verification after MRM). All lesions were evaluated by two experienced (>500 MRM) radiologists in consensus. In every lesion, 18 previously published descriptors were assessed and documented in the database. An Artificial Neural Network (ANN) was developed to process this database (The-MathWorks/Inc., feed-forward-architecture/resilient back-propagation-algorithm). All 18 descriptors were set as input variables, whereas histological results (malignant vs. benign) was defined as classification variable. Initially, the ANN was optimized in terms of “Training Epochs” (TE), “Hidden Layers” (HL), “Learning Rate” (LR) and “Neurons” (N). Robustness of the ANN was addressed by repeated evaluation cycles (n: 9) with receiver operating characteristics (ROC) analysis of the results applying 4-fold Cross Validation. The best network architecture was identified comparing the corresponding Area under the ROC curve (AUC). Results: Histopathology revealed 436 benign and 648 malignant lesions. Enhancing the level of complexity could not increase diagnostic accuracy of the network (P: n.s.). The optimized ANN architecture (TE: 20, HL: 1, N: 5, LR: 1.2) was accurate (mean-AUC 0.888; P: <0.001) and robust (CI: 0.885–0.892; range: 0.880–0.898). Conclusion: The optimized neural network showed robust performance and high diagnostic accuracy for prediction of malignancy on unknown data.

Artificial Neural Networks for differential diagnosis of breast lesions in MR-Mammography: a systematic approach addressing the influence of network architecture on diagnostic performance using a large clinical database.

Science.gov (United States)

Dietzel, Matthias; Baltzer, Pascal A T; Dietzel, Andreas; Zoubi, Ramy; Gröschel, Tobias; Burmeister, Hartmut P; Bogdan, Martin; Kaiser, Werner A

2012-07-01

Differential diagnosis of lesions in MR-Mammography (MRM) remains a complex task. The aim of this MRM study was to design and to test robustness of Artificial Neural Network architectures to predict malignancy using a large clinical database. For this IRB-approved investigation standardized protocols and study design were applied (T1w-FLASH; 0.1 mmol/kgBW Gd-DTPA; T2w-TSE; histological verification after MRM). All lesions were evaluated by two experienced (>500 MRM) radiologists in consensus. In every lesion, 18 previously published descriptors were assessed and documented in the database. An Artificial Neural Network (ANN) was developed to process this database (The-MathWorks/Inc., feed-forward-architecture/resilient back-propagation-algorithm). All 18 descriptors were set as input variables, whereas histological results (malignant vs. benign) was defined as classification variable. Initially, the ANN was optimized in terms of "Training Epochs" (TE), "Hidden Layers" (HL), "Learning Rate" (LR) and "Neurons" (N). Robustness of the ANN was addressed by repeated evaluation cycles (n: 9) with receiver operating characteristics (ROC) analysis of the results applying 4-fold Cross Validation. The best network architecture was identified comparing the corresponding Area under the ROC curve (AUC). Histopathology revealed 436 benign and 648 malignant lesions. Enhancing the level of complexity could not increase diagnostic accuracy of the network (P: n.s.). The optimized ANN architecture (TE: 20, HL: 1, N: 5, LR: 1.2) was accurate (mean-AUC 0.888; P: <0.001) and robust (CI: 0.885-0.892; range: 0.880-0.898). The optimized neural network showed robust performance and high diagnostic accuracy for prediction of malignancy on unknown data. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

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.

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.

Homogeneous and Heterogeneous MPSoC Architectures with Network-On-Chip Connectivity for Low-Power and Real-Time Multimedia Signal Processing

Directory of Open Access Journals (Sweden)

Sergio Saponara

2012-01-01

Full Text Available Two multiprocessor system-on-chip (MPSoC architectures are proposed and compared in the paper with reference to audio and video processing applications. One architecture exploits a homogeneous topology; it consists of 8 identical tiles, each made of a 32-bit RISC core enhanced by a 64-bit DSP coprocessor with local memory. The other MPSoC architecture exploits a heterogeneous-tile topology with on-chip distributed memory resources; the tiles act as application specific processors supporting a different class of algorithms. In both architectures, the multiple tiles are interconnected by a network-on-chip (NoC infrastructure, through network interfaces and routers, which allows parallel operations of the multiple tiles. The functional performances and the implementation complexity of the NoC-based MPSoC architectures are assessed by synthesis results in submicron CMOS technology. Among the large set of supported algorithms, two case studies are considered: the real-time implementation of an H.264/MPEG AVC video codec and of a low-distortion digital audio amplifier. The heterogeneous architecture ensures a higher power efficiency and a smaller area occupation and is more suited for low-power multimedia processing, such as in mobile devices. The homogeneous scheme allows for a higher flexibility and easier system scalability and is more suited for general-purpose DSP tasks in power-supplied devices.

Microgrid cyber security reference architecture.

Energy Technology Data Exchange (ETDEWEB)

Veitch, Cynthia K.; Henry, Jordan M.; Richardson, Bryan T.; Hart, Derek H.

2013-07-01

This document describes a microgrid cyber security reference architecture. First, we present a high-level concept of operations for a microgrid, including operational modes, necessary power actors, and the communication protocols typically employed. We then describe our motivation for designing a secure microgrid; in particular, we provide general network and industrial control system (ICS)-speci c vulnerabilities, a threat model, information assurance compliance concerns, and design criteria for a microgrid control system network. Our design approach addresses these concerns by segmenting the microgrid control system network into enclaves, grouping enclaves into functional domains, and describing actor communication using data exchange attributes. We describe cyber actors that can help mitigate potential vulnerabilities, in addition to performance bene ts and vulnerability mitigation that may be realized using this reference architecture. To illustrate our design approach, we present a notional a microgrid control system network implementation, including types of communica- tion occurring on that network, example data exchange attributes for actors in the network, an example of how the network can be segmented to create enclaves and functional domains, and how cyber actors can be used to enforce network segmentation and provide the neces- sary level of security. Finally, we describe areas of focus for the further development of the reference architecture.

Architecture for an integrated real-time air combat and sensor network simulation

Science.gov (United States)

Criswell, Evans A.; Rushing, John; Lin, Hong; Graves, Sara

2007-04-01

An architecture for an integrated air combat and sensor network simulation is presented. The architecture integrates two components: a parallel real-time sensor fusion and target tracking simulation, and an air combat simulation. By integrating these two simulations, it becomes possible to experiment with scenarios in which one or both sides in a battle have very large numbers of primitive passive sensors, and to assess the likely effects of those sensors on the outcome of the battle. Modern Air Power is a real-time theater-level air combat simulation that is currently being used as a part of the USAF Air and Space Basic Course (ASBC). The simulation includes a variety of scenarios from the Vietnam war to the present day, and also includes several hypothetical future scenarios. Modern Air Power includes a scenario editor, an order of battle editor, and full AI customization features that make it possible to quickly construct scenarios for any conflict of interest. The scenario editor makes it possible to place a wide variety of sensors including both high fidelity sensors such as radars, and primitive passive sensors that provide only very limited information. The parallel real-time sensor network simulation is capable of handling very large numbers of sensors on a computing cluster of modest size. It can fuse information provided by disparate sensors to detect and track targets, and produce target tracks.

Design requirements of communication architecture of SMART safety system

International Nuclear Information System (INIS)

Park, H. Y.; Kim, D. H.; Sin, Y. C.; Lee, J. Y.

2001-01-01

To develop the communication network architecture of safety system of SMART, the evaluation elements for reliability and performance factors are extracted from commercial networks and classified the required-level by importance. A predictable determinacy, status and fixed based architecture, separation and isolation from other systems, high reliability, verification and validation are introduced as the essential requirements of safety system communication network. Based on the suggested requirements, optical cable, star topology, synchronous transmission, point-to-point physical link, connection-oriented logical link, MAC (medium access control) with fixed allocation are selected as the design elements. The proposed architecture will be applied as basic communication network architecture of SMART safety system

Experimental demonstration of OpenFlow-enabled media ecosystem architecture for high-end applications over metro and core networks.

Science.gov (United States)

Ntofon, Okung-Dike; Channegowda, Mayur P; Efstathiou, Nikolaos; Rashidi Fard, Mehdi; Nejabati, Reza; Hunter, David K; Simeonidou, Dimitra

2013-02-25

In this paper, a novel Software-Defined Networking (SDN) architecture is proposed for high-end Ultra High Definition (UHD) media applications. UHD media applications require huge amounts of bandwidth that can only be met with high-capacity optical networks. In addition, there are requirements for control frameworks capable of delivering effective application performance with efficient network utilization. A novel SDN-based Controller that tightly integrates application-awareness with network control and management is proposed for such applications. An OpenFlow-enabled test-bed demonstrator is reported with performance evaluations of advanced online and offline media- and network-aware schedulers.

Unravelling Darwin's entangled bank: architecture and robustness of mutualistic networks with multiple interaction types.

Science.gov (United States)

Dáttilo, Wesley; Lara-Rodríguez, Nubia; Jordano, Pedro; Guimarães, Paulo R; Thompson, John N; Marquis, Robert J; Medeiros, Lucas P; Ortiz-Pulido, Raul; Marcos-García, Maria A; Rico-Gray, Victor

2016-11-30

Trying to unravel Darwin's entangled bank further, we describe the architecture of a network involving multiple forms of mutualism (pollination by animals, seed dispersal by birds and plant protection by ants) and evaluate whether this multi-network shows evidence of a structure that promotes robustness. We found that species differed strongly in their contributions to the organization of the multi-interaction network, and that only a few species contributed to the structuring of these patterns. Moreover, we observed that the multi-interaction networks did not enhance community robustness compared with each of the three independent mutualistic networks when analysed across a range of simulated scenarios of species extinction. By simulating the removal of highly interacting species, we observed that, overall, these species enhance network nestedness and robustness, but decrease modularity. We discuss how the organization of interlinked mutualistic networks may be essential for the maintenance of ecological communities, and therefore the long-term ecological and evolutionary dynamics of interactive, species-rich communities. We suggest that conserving these keystone mutualists and their interactions is crucial to the persistence of species-rich mutualistic assemblages, mainly because they support other species and shape the network organization. © 2016 The Author(s).