Information processing in the transcriptional regulatory network of yeast: Functional robustness

Background: Gene networks are considered to represent various aspects of molecular biological systems meaningfully because they naturally provide a systems perspective of molecular interactions. In this respect, the functional understanding of the transcriptional regulatory network is considered as key to elucidate the functional organization of an organism.

Local network-based measures to assess the inferability of different regulatory networks

The purpose of this study is to compare the inferability of various synthetic as well as real biological regulatory networks. In order to assess differences we apply local network-based measures. That means, instead of applying global measures, we investigate and assess an inference algorithm locally, on the level of individual edges and subnetworks. We demonstrate the behaviour of our local network-based measures with respect to different regulatory networks by conducting large-scale simulations. As inference algorithm we use exemplarily ARACNE. The results from our exploratory analysis allow us not only to gain new insights into the strength and weakness of an inference algorithm with respect to characteristics of different regulatory networks, but also to obtain information that could be used to design novel problem-specific statistical estimators.

Coordinated control of DFIG’s rotor and grid side converters during network unbalance

This paper proposes a coordinated control of the rotor and grid side converters (RSC & GSC) of doubly-fed induction generator (DFIG) based wind generation systems under unbalanced voltage conditions. System behaviors and operations of the RSC and GSC under unbalanced voltage are illustrated. To provide enhanced operation, the RSC is controlled to eliminate the torque oscillations at double supply frequency under unbalanced stator supply. The oscillation of the stator output active power is then cancelled by the active power output from the GSC, to ensure constant active power output from the overall DFIG generation system. To provide the required positive and negative sequence currents control for the RSC and GSC, a current control strategy containing a main controller and an auxiliary controller is analyzed. The main controller is implemented in the positive (dq)+ frame without involving positive/negative sequence decomposition whereas the auxiliary controller is implemented in the negative sequence (dq)? frame with negative sequence current extracted. Simulation results using EMTDC/PSCAD are presented for a 2MW DFIG wind generation system to validate the proposed control scheme and to show the enhanced system operation during unbalanced voltage supply.

A fast multi-output RBF neural network construction method

This paper investigates the center selection of multi-output radial basis function (RBF) networks, and a multi-output fast recursive algorithm (MFRA) is proposed. This method can not only reveal the significance of each candidate center based on the reduction in the trace of the error covariance matrix, but also can estimate the network weights simultaneously using a back substitution approach. The main contribution is that the center selection procedure and the weight estimation are performed within a well-defined regression context, leading to a significantly reduced computational complexity. The efficiency of the algorithm is confirmed by a computational complexity analysis, and simulation results demonstrate its effectiveness. (C) 2010 Elsevier B.V. All rights reserved.

Two-stage RBF network construction based on particle swarm optimization

The conventional radial basis function (RBF) network optimization methods, such as orthogonal least squares or the two-stage selection, can produce a sparse network with satisfactory generalization capability. However, the RBF width, as a nonlinear parameter in the network, is not easy to determine. In the aforementioned methods, the width is always pre-determined, either by trial-and-error, or generated randomly. Furthermore, all hidden nodes share the same RBF width. This will inevitably reduce the network performance, and more RBF centres may then be needed to meet a desired modelling specification. In this paper we investigate a new two-stage construction algorithm for RBF networks. It utilizes the particle swarm optimization method to search for the optimal RBF centres and their associated widths. Although the new method needs more computation than conventional approaches, it can greatly reduce the model size and improve model generalization performance. The effectiveness of the proposed technique is confirmed by two numerical simulation examples.

An Autopilot Based on a Local Control Network Design for an Unmanned Surface Vehicle

Over recent years, a number of marine autopilots designed using linear techniques have underperformed owing to their inability to cope with nonlinear vessel dynamics. To this end, a new design framework for the development of nonlinear autopilots is proposed herein. Local control networks (LCNs) can be used in the design of nonlinear control systems. In this paper, a LCN approach is taken in the design of a nonlinear autopilot for controlling the nonlinear yaw dynamics of an unmanned surface vehicle known as Springer. It is considered the approach is the first of its kind to be used in marine control systems design. Simulation results are presented and the performance of the nonlinear autopilot is compared with that of an existing Springer linear quadratic Gaussian (LQG) autopilot using standard system performance criteria. From the results it can be concluded the LCN autopilot out performed that based on LQG techniques in terms of the selected criteria. Also it provided more energy saving control strategies and would thereby increase operational duration times for the vehicle during real-time missions.

Cache-Integrated Network Interfaces: Flexible On-Chip Communication and Synchronization for Large-Scale CMPs

Per-core scratchpad memories (or local stores) allow direct inter-core communication, with latency and energy advantages over coherent cache-based communication, especially as CMP architectures become more distributed. We have designed cache-integrated network interfaces, appropriate for scalable multicores, that combine the best of two worlds – the flexibility of caches and the efficiency of scratchpad memories: on-chip SRAM is configurably shared among caching, scratchpad, and virtualized network interface (NI) functions. This paper presents our architecture, which provides local and remote scratchpad access, to either individual words or multiword blocks through RDMA copy. Furthermore, we introduce event responses, as a technique that enables software configurable communication and synchronization primitives. We present three event response mechanisms that expose NI functionality to software, for multiword transfer initiation, completion notifications for software selected sets of arbitrary size transfers, and multi-party synchronization queues. We implemented these mechanisms in a four-core FPGA prototype, and measure the logic overhead over a cache-only design for basic NI functionality to be less than 20%. We also evaluate the on-chip communication performance on the prototype, as well as the performance of synchronization functions with simulation of CMPs with up to 128 cores. We demonstrate efficient synchronization, low-overhead communication, and amortized-overhead bulk transfers, which allow parallelization gains for fine-grain tasks, and efficient exploitation of the hardware bandwidth.

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.

The p-hub Model with Hub-catchment Areas, Existing Hubs, and Simulation: A Case Study of Serbian Intermodal Terminals

This paper addresses the problem of optimally locating intermodal freight terminals in Serbia. To solve this problem and determine the effects of the resulting scenarios, two modeling approaches were combined. The first approach is based on multiple-assignment hub-network design, and the second is based on simulation. The multiple-assignment p-hub network location model was used to determine the optimal location of intermodal terminals. Simulation was used as a tool to estimate intermodal transport flow volumes, due to the unreliability and unavailability of specific statistical data, and as a method for quantitatively analyzing the economic, time, and environmental effects of different scenarios of intermodal terminal development. The results presented here represent a summary, with some extension, of the research realized in the IMOD-X project (Intermodal Solutions for Competitive Transport in Serbia).

Multi-Objective Reactive Power Support from Wind farms for Network Performance Enhancement

This paper examines the ability of the doubly fed induction generator (DFIG) to deliver multiple reactive power objectives during variable wind conditions. The reactive power requirement is decomposed based on various control objectives (e.g. power factor control, voltage control, loss minimisation, and flicker mitigation) defined around different time frames (i.e. seconds, minutes, and hourly), and the control reference is generated by aggregating the individual reactive power requirement for each control strategy. A novel coordinated controller is implemented for the rotor-side converter and the grid-side converter considering their capability curves and illustrating that it can effectively utilise the aggregated DFIG reactive power capability for system performance enhancement. The performance of the multi-objective strategy is examined for a range of wind and network conditions, and it is shown that for the majority of the scenarios, more than 92% of the main control objective can be achieved while introducing the integrated flicker control scheme with the main reactive power control scheme. Therefore, optimal control coordination across the different control strategies can maximise the availability of ancillary services from DFIG-based wind farms without additional dynamic reactive power devices being installed in power networks.

Fair charging strategies for EVs connected to a low-voltage distribution network

The development of smart grid technologies and appropriate charging strategies are key to accommodating large numbers of Electric Vehicles (EV) charging on the grid. In this paper a general framework is presented for formulating the EV charging optimization problem and three different charging strategies are investigated and compared from the perspective of charging fairness while taking into account power system constraints. Two strategies are based on distributed algorithms, namely, Additive Increase and Multiplicative Decrease (AIMD), and Distributed Price-Feedback (DPF), while the third is an ideal centralized solution used to benchmark performance. The algorithms are evaluated using a simulation of a typical residential low voltage distribution network with 50% EV penetration. © 2013 IEEE.

On-off based charging strategies for EVs connected to a Low Voltage distributon network

The development of appropriate Electric Vehicle (EV) charging strategies has been identified as an effective way to accommodate an increasing number of EVs on Low Voltage (LV) distribution networks. Most research studies to date assume that future charging facilities will be capable of regulating charge rates continuously, while very few papers consider the more realistic situation of EV chargers that support only on-off charging functionality. In this work, a distributed charging algorithm applicable to on-off based charging systems is presented. Then, a modified version of the algorithm is proposed to incorporate real power system constraints. Both algorithms are compared with uncontrolled and centralized charging strategies from the perspective of both utilities and customers. © 2013 IEEE.

Python PSS/E Simulation to Test Efficacy of Proposed PMU Based WAMS and Potential WAMPAC Applications

A PSS/E 32 model of a real section of the Northern Ireland electrical grid was dynamically controlled with Python 2.5. In this manner data from a proposed wide area monitoring system was simulated. The area is of interest as it is a weakly coupled distribution grid with significant distributed generation. The data was used to create an optimization and protection metric that reflected reactive power flow, voltage profile, thermal overload and voltage excursions. Step changes in the metric were introduced upon the operation of special protection systems and voltage excursions. A wide variety of grid conditions were simulated while tap changer positions and switched capacitor banks were iterated through; with the most desirable state returning the lowest optimization and protection metric. The optimized metric was compared against the metric generated from the standard system state returned by PSS/E. Various grid scenarios were explored involving an intact network and compromised networks (line loss) under summer maximum, summer minimum and winter maximum conditions. In each instance the output from the installed distributed generation is varied between 0 MW and 80 MW (120% of installed capacity). It is shown that in grid models the triggering of special protection systems is delayed by between 1 MW and 6 MW (1.5% to 9% of capacity), with 3.5 MW being the average. The optimization and protection metric gives a quantitative value for system health and demonstrates the potential efficacy of wide area monitoring for protection and control.

MIMO cooperative communication network design with relay selection and CSI feedback

In this paper, we investigate an amplify-and-forward (AF) multiple-input multiple-output - spatial division multiplexing (MIMO-SDM) cooperative wireless networks, where each network node is equipped with multiple antennas. In order to deal with the problems of signal combining at the destination and cooperative relay selection, we propose an improved minimum mean square error (MMSE) signal combining scheme for signal recovery at the destination. Additionally, we propose two distributed relay selection algorithms based on the minimum mean squared error (MSE) of the signal estimation for the cases where channel state information (CSI) from the source to the destination is available and unavailable at the candidate nodes. Simulation results demonstrate that the proposed combiner together with the proposed relay selection algorithms achieve higher diversity gain than previous approaches in both flat and frequency-selective fading channels.