Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma

Background:
The physical periphery of a biological cell is mainly described by signaling pathways which are triggered by transmembrane proteins and receptors that are sentinels to control the whole gene regulatory network of a cell. However, our current knowledge about the gene regulatory mechanisms that are governed by extracellular signals is severely limited.Results: The purpose of this paper is three fold. First, we infer a gene regulatory network from a large-scale B-cell lymphoma expression data set using the C3NET algorithm. Second, we provide a functional and structural analysis of the largest connected component of this network, revealing that this network component corresponds to the peripheral region of a cell. Third, we analyze the hierarchical organization of network components of the whole inferred B-cell gene regulatory network by introducing a new approach which exploits the variability within the data as well as the inferential characteristics of C3NET. As a result, we find a functional bisection of the network corresponding to different cellular components.

Conclusions:
Overall, our study allows to highlight the peripheral gene regulatory network of B-cells and shows that it is centered around hub transmembrane proteins located at the physical periphery of the cell. In addition, we identify a variety of novel pathological transmembrane proteins such as ion channel complexes and signaling receptors in B-cell lymphoma. © 2012 Simoes et al.; licensee BioMed Central Ltd.

A multiagent network for peer norm enforcement

In a multiagent system where norms are used to regulate the actions agents ought to execute, some agents may decide not to abide by the norms if this can benefit them. Norm enforcement mechanisms are designed to counteract these benefits and thus the motives for not abiding by the norms. In this work we propose a distributed mechanism through which agents in the multiagent system that do not abide by the norms can be ostracised by their peers. An ostracised agent cannot interact anymore and looses all benefits from future interactions. We describe a model for multiagent systems structured as networks of agents, and a behavioural model for the agents in such systems. Furthermore, we provide analytical results which show that there exists an upper bound to the number of potential norm violations when all the agents exhibit certain behaviours. We also provide experimental results showing that both stricter enforcement behaviours and larger percentage of agents exhibiting these behaviours reduce the number of norm violations, and that the network topology influences the number of norm violations. These experiments have been executed under varying scenarios with different values for the number of agents, percentage of enforcers, percentage of violators, network topology, and agent behaviours. Finally, we give examples of applications where the enforcement techniques we provide could be used.

Parallel patterns + Macro Data Flow for multi-core programming

Data flow techniques have been around since the early '70s when they were used in compilers for sequential languages. Shortly after their introduction they were also consideredas a possible model for parallel computing, although the impact here was limited. Recently, however, data flow has been identified as a candidate for efficient implementation of various programming models on multi-core architectures. In most cases, however, the burden of determining data flow "macro" instructions is left to the programmer, while the compiler/run time system manages only the efficient scheduling of these instructions. We discuss a structured parallel programming approach supporting automatic compilation of programs to macro data flow and we show experimental results demonstrating the feasibility of the approach and the efficiency of the resulting "object" code on different classes of state-of-the-art multi-core architectures. The experimental results use different base mechanisms to implement the macro data flow run time support, from plain pthreads with condition variables to more modern and effective lock- and fence-free parallel frameworks. Experimental results comparing efficiency of the proposed approach with those achieved using other, more classical, parallel frameworks are also presented. © 2012 IEEE.

Multi-access communication system in a highly reverberant environment

We investigate by numerical EM simulation the potential communication channel capacity of a reverberant environment using the time reversal approach, excited at 2.4 GHz by ON-OFF keyed RF pulse excitation. It is shown that approximately 725 1.25MHz propagation channels can be allocated with the cavity contains a 4×4 ? or 1×1 ? LOS obstruction positioned between the transceiver antenna and the time reversal unit. Furthermore the results show that two co-located transceiver dipoles separated by a spacing of 3?/4 can successfully resolve a 10ns pulse. Our findings suggest that different independent channels with identical operating frequency can be realized in an enclosed environment such as ventilation duct or underground tunnel. This suggests that there is a possibility of implementing a parallel channel radio link with the minimum inter-antenna spacing of 3?/4 between the transceivers in a rich multipath environment. © 2012 IEEE.

Association Study of 167 Candidate Genes for Schizophrenia Selected by a Multi-Domain Evidence-Based Prioritization Algorithm and Neurodevelopmental Hypothesis

Integrating evidence from multiple domains is useful in prioritizing disease candidate genes for subsequent testing. We ranked all known human genes (n = 3819) under linkage peaks in the Irish Study of High-Density Schizophrenia Families using three different evidence domains: 1) a meta-analysis of microarray gene expression results using the Stanley Brain collection, 2) a schizophrenia protein-protein interaction network, and 3) a systematic literature search. Each gene was assigned a domain-specific p-value and ranked after evaluating the evidence within each domain. For comparison to this
ranking process, a large-scale candidate gene hypothesis was also tested by including genes with Gene Ontology terms related to neurodevelopment. Subsequently, genotypes of 3725 SNPs in 167 genes from a custom Illumina iSelect array were used to evaluate the top ranked vs. hypothesis selected genes. Seventy-three genes were both highly ranked and involved in neurodevelopment (category 1) while 42 and 52 genes were exclusive to neurodevelopment (category 2) or highly ranked (category 3), respectively. The most significant associations were observed in genes PRKG1, PRKCE, and CNTN4 but no individual SNPs were significant after correction for multiple testing. Comparison of the approaches showed an excess of significant tests using the hypothesis-driven neurodevelopment category. Random selection of similar sized genes from two independent genome-wide association studies (GWAS) of schizophrenia showed the excess was unlikely by chance. In a further meta-analysis of three GWAS datasets, four candidate SNPs reached nominal significance. Although gene ranking using integrated sources of prior information did not enrich for significant results in the current experiment, gene selection using an a priori hypothesis (neurodevelopment) was superior to random selection. As such, further development of gene ranking strategies using more carefully selected sources of information is warranted.

Novel Radio Link Buffer Management Schemes for End-User Multi-class Traffic in High Speed Packet Access Networks

The requirement to provide multimedia services with QoS support in mobile networks has led to standardization and deployment of high speed data access technologies such as the High Speed Downlink Packet Access (HSDPA) system. HSDPA improves downlink packet data and multimedia services support in WCDMA-based cellular networks. As is the trend in emerging wireless access technologies, HSDPA supports end-user multi-class sessions comprising parallel flows with diverse Quality of Service (QoS) requirements, such as real-time (RT) voice or video streaming concurrent with non real-time (NRT) data service being transmitted to the same user, with differentiated queuing at the radio link interface. Hence, in this paper we present and evaluate novel radio link buffer management schemes for QoS control of multimedia traffic comprising concurrent RT and NRT flows in the same HSDPA end-user session. The new buffer management schemes—Enhanced Time Space Priority (E-TSP) and Dynamic Time Space Priority (D-TSP)—are designed to improve radio link and network resource utilization as well as optimize end-to-end QoS performance of both RT and NRT flows in the end-user session. Both schemes are based on a Time-Space Priority (TSP) queuing system, which provides joint delay and loss differentiation between the flows by queuing (partially) loss tolerant RT flow packets for higher transmission priority but with restricted access to the buffer space, whilst allowing unlimited access to the buffer space for delay-tolerant NRT flow but with queuing for lower transmission priority. Experiments by means of extensive system-level HSDPA simulations demonstrates that with the proposed TSP-based radio link buffer management schemes, significant end-to-end QoS performance gains accrue to end-user traffic with simultaneous RT and NRT flows, in addition to improved resource utilization in the radio access network.

End-to-End QoS Enhancement ofHSDPA End-User Multi-flow Traffic Using RAN Buffer Management

High speed downlink packet access (HSDPA) was introduced to UMTS radio access segment to provide higher capacity for new packet switched services. As a result, packet switched sessions with multiple diverse traffic flows such as concurrent voice and data, or video and data being transmitted to the same user are a likely commonplace cellular packet data scenario. In HSDPA, radio access network (RAN) buffer management schemes are essential to support the end-to-end QoS of such sessions. Hence in this paper we present the end-to-end performance study of a proposed RAN buffer management scheme for multi-flow sessions via dynamic system-level HSDPA simulations. The scheme is an enhancement of a time-space priority (TSP) queuing strategy applied to the node B MAC-hs buffer allocated to an end user with concurrent real-time (RT) and non-real-time (NRT) flows during a multi-flow session. The experimental multi- flow scenario is a packet voice call with concurrent TCP-based file download to the same user. Results show that with the proposed enhancements to the TSP-based RAN buffer management, end-to-end QoS performance gains accrue to the NRT flow without compromising RT flow QoS of the same end user session

A Dynamic Buffer Management Scheme for End-to-End QoS Enhancement of Multi-flow Services in HSDPA

End-user multi-flow services support is a crucial aspect of current and next generation mobile networks. This paper presents a dynamic buffer management strategy for HSDPA end-user multi-flow traffic with aggregated real-time and non-real-time flows. The scheme incorporates dynamic priority switching between the flows for transmission on the HSDPA radio channel. The end-to-end performance of the proposed strategy is investigated with an end-user multi-flow session of simultaneous VoIP and TCP-based downlink traffic using detailed HSDPA system-level simulations. Compared to an equivalent static buffer management scheme, the results show that end-to-end throughput performance gains in the non-real-time flow and better HSDPA channel utilization is attainable without compromising the real-time VoIP flow QoS constraints

Fault Location on a Distribution Network Using a Decentralised Analysis Process

A reduction in the time required to locate and restore faults on a utility's distribution network improves the customer minutes lost (CML) measurement and hence brings direct cost savings to the operating company. The traditional approach to fault location involves fault impedance determination from high volume waveform files dispatched across a communications channel to a central location for processing and analysis. This paper examines an alternative scheme where data processing is undertaken locally within a recording instrument thus reducing the volume of data to be transmitted. Processed event fault reports may be emailed to relevant operational staff for the timely repair and restoration of the line.

Body shadowing mitigation using differentiated LOS/NLOS channel models for RSSI-based Monte Carlo personnel localization

Research into localization has produced a wealth of algorithms and techniques to estimate the location of wireless network nodes, however the majority of these schemes do not explicitly account for non-line of sight conditions. Disregarding this common situation reduces their accuracy and their potential for exploitation in real world applications. This is a particular problem for personnel tracking where the user's body itself will inherently cause time-varying blocking according to their movements. Using empirical data, this paper demonstrates that, by accounting for non-line of sight conditions and using received signal strength based Monte Carlo localization, meter scale accuracy can be achieved for a wrist-worn personnel tracking tag in a 120 m indoor office environment. © 2012 IEEE.

Channel Time Allocation PSO for Gigabit Multimedia Wireless Networks

This article introduces a resource allocation solution capable of handling mixed media applications within the constraints of a 60 GHz wireless network. The challenges of multimedia wireless transmission include high bandwidth requirements, delay intolerance and wireless channel availability. A new Channel Time Allocation Particle Swarm Optimization (CTA-PSO) is proposed to solve the network utility maximization (NUM) resource allocation problem. CTA-PSO optimizes the time allocated to each device in the network in order to maximize the Quality of Service (QoS) experienced by each user. CTA-PSO introduces network-linked swarm size, an increased diversity function and a learning method based on the personal best, Pbest, results of the swarm. These additional developments to the PSO produce improved convergence speed with respect to Adaptive PSO while maintaining the QoS improvement of the NUM. Specifically, CTA-PSO supports applications described by both convex and non-convex utility functions. The multimedia resource allocation solution presented in this article provides a practical solution for real-time wireless networks.

Human body shadowing in cellular device-to-device communications: channel modeling using the shadowed κ−μ fading model

Using device-to-device communications as an underlay for cellular communications will provide an exciting opportunity to increase network capacity as well as improving spectral efficiency. The unique geometry of device-to-device links, where user equipment is often held or carried at low elevation and in close proximity to the human body, will mean that they are particularly susceptible to shadowing events caused not only by the local environment but also by the user's body. In this paper, the shadowed κ - μ fading model is proposed, which is capable of characterizing shadowed fading in wireless communication channels. In this model, the statistics of the received signal are manifested by the clustering of multipath components. Within each of these clusters, a dominant signal component with arbitrary power may exist. The resultant dominant signal component, which is formed by the phasor addition of these leading contributions, is assumed to follow a Nakagami- m distribution. The probability density function, moments, and the moment-generating function are also derived. The new model is then applied to device-to-device links operating at 868 MHz in an outdoor urban environment. It was found that shadowing of the resultant dominant component can vary significantly depending upon the position of the user equipment relative to the body and the link geometry. Overall, the shadowed κ - μ fading model is shown to provide a good fit to the field data as well as providing a useful insight into the characteristics of the received signal.

Distributed MPC for Frequency Regulation in Multi-Terminal HVDC Grids

High Voltage Direct Current (HVDC) lines allow large quantities of power to be
transferred between two points in an electrical power system. A Multi-Terminal HVDC (MTDC) grid consists of a meshed network of HVDC lines, and this allows energy reserves to be shared between a number of AC areas in an efficient manner. Secondary Frequency Control (SFC) algorithms return the frequencies in areas connected by AC or DC lines to their original setpoints after Primary Frequency Controllers have been called following a contingency. Where multiple
TSOs are responsible for different parts of a MTDC grid it may not be possible to implement SFC from a centralised location. Thus, in this paper a simple gain based distributed Model Predictive Control strategy is proposed for Secondary Frequency Control of MTDC grids which allows TSOs to cooperatively perform SFC without the need for centralised coordination.

On the Security of Cognitive Radio Networks

Cognitive radio has emerged as an essential recipe for future high-capacity high-coverage multi-tier hierarchical networks. Securing data transmission in these networks is of utmost importance. In this paper, we consider the cognitive wiretap channel and propose multiple antennas to secure the transmission at the physical layer, where the eavesdropper overhears the transmission from the secondary transmitter to the secondary receiver. The secondary receiver and the eavesdropper are equipped with multiple antennas, and passive eavesdropping is considered where the channel state information of the eavesdropper’s channel is not available at the secondary transmitter. We present new closedform expressions for the exact and asymptotic secrecy outage probability. Our results reveal the impact of the primary network on the secondary network in the presence of a multi-antenna wiretap channel.

Cognitive amplify-and-forward relay networks with beamforming under primary user power constraint over Nakagami-m fading channels

In this paper, we analyze the performance of cognitive amplify-and-forward (AF) relay networks with beamforming under the peak interference power constraint of the primary user (PU). We focus on the scenario that beamforming is applied at the multi-antenna secondary transmitter and receiver. Also, the secondary relay network operates in channel state information-assisted AF mode, and the signals undergo independent Nakagami-m fading. In particular, closed-form expressions for the outage probability and symbol error rate (SER) of the considered network over Nakagami-m fading are presented. More importantly, asymptotic closed-form expressions for the outage probability and SER are derived. These tractable closed-form expressions for the network performance readily enable us to evaluate and examine the impact of network parameters on the system performance. Specifically, the impact of the number of antennas, the fading severity parameters, the channel mean powers, and the peak interference power is addressed. The asymptotic analysis manifests that the peak interference power constraint imposed on the secondary relay network has no effect on the diversity gain. However, the coding gain is affected by the fading parameters of the links from the primary receiver to the secondary relay network