Gene network and proteomic analyses of cardiac responses to pathological and physiological stress

Background—The molecular mechanisms underlying similarities and differences between physiological and pathological left ventricular hypertrophy (LVH) are of intense interest. Most previous work involved targeted analysis of individual signaling pathways or screening of transcriptomic profiles. We developed a network biology approach using genomic and proteomic data to study the molecular patterns that distinguish pathological and physiological LVH. Methods and Results—A network-based analysis using graph theory methods was undertaken on 127 genome-wide expression arrays of in vivo murine LVH. This revealed phenotype-specific pathological and physiological gene coexpression networks. Despite >1650 common genes in the 2 networks, network structure is significantly different. This is largely because of rewiring of genes that are differentially coexpressed in the 2 networks; this novel concept of differential wiring was further validated experimentally. Functional analysis of the rewired network revealed several distinct cellular pathways and gene sets. Deeper exploration was undertaken by targeted proteomic analysis of mitochondrial, myofilament, and extracellular subproteomes in pathological LVH. A notable finding was that mRNA–protein correlation was greater at the cellular pathway level than for individual loci. Conclusions—This first combined gene network and proteomic analysis of LVH reveals novel insights into the integrated pathomechanisms that distinguish pathological versus physiological phenotypes. In particular, we identify differential gene wiring as a major distinguishing feature of these phenotypes. This approach provides a platform for the investigation of potentially novel pathways in LVH and offers a freely accessible protocol (http://sites.google.com/site/cardionetworks) for similar analyses in other cardiovascular diseases.

Learning and change in interorganizational networks:the case for network learning and network change

The ALBA 2002 Call for Papers asks the question ‘How do organizational learning and knowledge management contribute to organizational innovation and change?’. Intuitively, we would argue, the answer should be relatively straightforward as links between learning and change, and knowledge management and innovation, have long been commonly assumed to exist. On the basis of this assumption, theories of learning tend to focus ‘within organizations’, and assume a transfer of learning from individual to organization which in turn leads to change. However, empirically, we find these links are more difficult to articulate. Organizations exist in complex embedded economic, political, social and institutional systems, hence organizational change (or innovation) may be influenced by learning in this wider context. Based on our research in this wider interorganizational setting, we first make the case for the notion of network learning that we then explore to develop our appreciation of change in interorganizational networks, and how it may be facilitated. The paper begins with a brief review of lite rature on learning in the organizational and interorganizational context which locates our stance on organizational learning versus the learning organization, and social, distributed versus technical, centred views of organizational learning and knowledge. Developing from the view that organizational learning is “a normal, if problematic, process in every organization” (Easterby-Smith, 1997: 1109), we introduce the notion of network learning: learning by a group of organizations as a group. We argue this is also a normal, if problematic, process in organizational relationships (as distinct from interorganizational learning), which has particular implications for network change. Part two of the paper develops our analysis, drawing on empirical data from two studies of learning. The first study addresses the issue of learning to collaborate between industrial customers and suppliers, leading to the case for network learning. The second, larger scale study goes on to develop this theme, examining learning around several major change issues in a healthcare service provider network. The learning processes and outcomes around the introduction of a particularly controversial and expensive technology are described, providing a rich and contrasting case with the first study. In part three, we then discuss the implications of this work for change, and for facilitating change. Conclusions from the first study identify potential interventions designed to facilitate individual and organizational learning within the customer organization to develop individual and organizational ‘capacity to collaborate’. Translated to the network example, we observe that network change entails learning at all levels – network, organization, group and individual. However, presenting findings in terms of interventions is less meaningful in an interorganizational network setting given: the differences in authority structures; the less formalised nature of the network setting; and the importance of evaluating performance at the network rather than organizational level. Academics challenge both the idea of managing change and of managing networks. Nevertheless practitioners are faced with the issue of understanding and in fluencing change in the network setting. Thus we conclude that a network learning perspective is an important development in our understanding of organizational learning, capability and change, locating this in the wider context in which organizations are embedded. This in turn helps to develop our appreciation of facilitating change in interorganizational networks, both in terms of change issues (such as introducing a new technology), and change orientation and capability.

Design and evaluation of a framework for cooperative and adaptive QoS control of DSRC network for road safety applications

Dedicated short-range communications (DSRC) are a promising vehicle communication technique for collaborative road safety applications (CSA). However, road safety applications require highly reliable and timely wireless communications, which present big challenges to DSRC based vehicle networks on effective and robust quality of services (QoS) provisioning due to the random channel access method applied in the DSRC technique. In this paper we examine the QoS control problem for CSA in the DSRC based vehicle networks and presented an overview of the research work towards the QoS control problem. After an analysis of the system application requirements and the DSRC vehicle network features, we propose a framework for cooperative and adaptive QoS control, which is believed to be a key for the success of DSRC on supporting effective collaborative road safety applications. A core design in the proposed QoS control framework is that network feedback and cross-layer design are employed to collaboratively achieve targeted QoS. A design example of cooperative and adaptive rate control scheme is implemented and evaluated, with objective of illustrating the key ideas in the framework. Simulation results demonstrate the effectiveness of proposed rate control schemes in providing highly available and reliable channel for emergency safety messages. © 2013 Wenyang Guan et al.

Performance investigation of IEEE 802.11 MAC in multihop wireless networks

Medium access control (MAC) protocols have a large impact on the achievable system performance for wireless ad hoc networks. Because of the limitations of existing analytical models for ad hoc networks, many researchers have opted to study the impact of MAC protocols via discreteevent simulations. However, as the network scenarios, traffic patterns and physical layer techniques may change significantly, simulation alone is not efficient to get insights into the impacts of MAC protocols on system performance. In this paper, we analyze the performance of IEEE 802.11 distributed coordination function (DCF) in multihop network scenario. We are particularly interested in understanding how physical layer techniques may affect the MAC protocol performance. For this purpose, the features of interference range is studied and taken into account of the analytical model. Simulations with OPNET show the effectiveness of the proposed analytical approach. Copyright 2005 ACM.

Socio-economic vision graph generation and handover in distributed smart camera networks

In this article we present an approach to object tracking handover in a network of smart cameras, based on self-interested autonomous agents, which exchange responsibility for tracking objects in a market mechanism, in order to maximise their own utility. A novel ant-colony inspired mechanism is used to learn the vision graph, that is, the camera neighbourhood relations, during runtime, which may then be used to optimise communication between cameras. The key benefits of our completely decentralised approach are on the one hand generating the vision graph online, enabling efficient deployment in unknown scenarios and camera network topologies, and on the other hand relying only on local information, increasing the robustness of the system. Since our market-based approach does not rely on a priori topology information, the need for any multicamera calibration can be avoided. We have evaluated our approach both in a simulation study and in network of real distributed smart cameras.

Learning to be different:heterogeneity and efficiency in distributed smart camera networks

In this paper we study the self-organising behaviour of smart camera networks which use market-based handover of object tracking responsibilities to achieve an efficient allocation of objects to cameras. Specifically, we compare previously known homogeneous configurations, when all cameras use the same marketing strategy, with heterogeneous configurations, when each camera makes use of its own, possibly different marketing strategy. Our first contribution is to establish that such heterogeneity of marketing strategies can lead to system wide outcomes which are Pareto superior when compared to those possible in homogeneous configurations. However, since the particular configuration required to lead to Pareto efficiency in a given scenario will not be known in advance, our second contribution is to show how online learning of marketing strategies at the individual camera level can lead to high performing heterogeneous configurations from the system point of view, extending the Pareto front when compared to the homogeneous case. Our third contribution is to show that in many cases, the dynamic behaviour resulting from online learning leads to global outcomes which extend the Pareto front even when compared to static heterogeneous configurations. Our evaluation considers results obtained from an open source simulation package as well as data from a network of real cameras. © 2013 IEEE.

Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses

We show theoretically and experimentally a mechanismbehind the emergence of wide or bimodal protein distributions in biochemical networks with nonlinear input-output characteristics (the dose-response curve) and variability in protein abundance. Large cell-to-cell variation in the nonlinear dose-response characteristics can be beneficial to facilitate two distinct groups of response levels as opposed to a graded response. Under the circumstances that we quantify mathematically, the two distinct responses can coexist within a cellular population, leading to the emergence of a bimodal protein distribution. Using flow cytometry, we demonstrate the appearance of wide distributions in the hypoxia-inducible factor-mediated response network in HCT116 cells. With help of our theoretical framework, we perform a novel calculation of the magnitude of cell-to-cell heterogeneity in the dose-response obtained experimentally. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Towards the distributed core for ubiquitous superfast broadband optical access

In this paper, we describe recent architectural and technological advances of the end to end optical network architecture proposed by the DISCUS project (the DIStributed Core for unlimited bandwidth supply for all Users and Services). The two main targets of DISCUS are the principle of equivalence in the access and the reduction of optical-to-electronic conversions in the metro-core network. Technological advances and techno-economic evaluation of Long-Reach Passive Optical Networks (LR-PON), as well as the optimal metro-core node architecture and the required network control plane framework are reported. Network infrastructure sharing challenges are also discussed. © 2014 IEEE.

A comparison of two distributed large-volume measurement systems:the mobile spatial co-ordinate measuring system and the indoor global positioning system

Advances in the area of industrial metrology have generated new technologies that are capable of measuring components with complex geometry and large dimensions. However, no standard or best-practice guides are available for the majority of such systems. Therefore, these new systems require appropriate testing and verification in order for the users to understand their full potential prior to their deployment in a real manufacturing environment. This is a crucial stage, especially when more than one system can be used for a specific measurement task. In this paper, two relatively new large-volume measurement systems, the mobile spatial co-ordinate measuring system (MScMS) and the indoor global positioning system (iGPS), are reviewed. These two systems utilize different technologies: the MScMS is based on ultrasound and radiofrequency signal transmission and the iGPS uses laser technology. Both systems have components with small dimensions that are distributed around the measuring area to form a network of sensors allowing rapid dimensional measurements to be performed in relation to large-size objects, with typical dimensions of several decametres. The portability, reconfigurability, and ease of installation make these systems attractive for many industries that manufacture large-scale products. In this paper, the major technical aspects of the two systems are briefly described and compared. Initial results of the tests performed to establish the repeatability and reproducibility of these systems are also presented. © IMechE 2009.

Impact of denial of service solutions on network quality of service

The Internet has become a universal communication network tool. It has evolved from a platform that supports best-effort traffic to one that now carries different traffic types including those involving continuous media with quality of service (QoS) requirements. As more services are delivered over the Internet, we face increasing risk to their availability given that malicious attacks on those Internet services continue to increase. Several networks have witnessed denial of service (DoS) and distributed denial of service (DDoS) attacks over the past few years which have disrupted QoS of network services, thereby violating the Service Level Agreement (SLA) between the client and the Internet Service Provider (ISP). Hence DoS or DDoS attacks are major threats to network QoS. In this paper we survey techniques and solutions that have been deployed to thwart DoS and DDoS attacks and we evaluate them in terms of their impact on network QoS for Internet services. We also present vulnerabilities that can be exploited for QoS protocols and also affect QoS if exploited. In addition, we also highlight challenges that still need to be addressed to achieve end-to-end QoS with recently proposed DoS/DDoS solutions. © 2010 John Wiley & Sons, Ltd.

Benchmarking of distributed computing engines spark and GraphLab for big data analytics

In this paper we evaluate and compare two representativeand popular distributed processing engines for large scalebig data analytics, Spark and graph based engine GraphLab. Wedesign a benchmark suite including representative algorithmsand datasets to compare the performances of the computingengines, from performance aspects of running time, memory andCPU usage, network and I/O overhead. The benchmark suite istested on both local computer cluster and virtual machines oncloud. By varying the number of computers and memory weexamine the scalability of the computing engines with increasingcomputing resources (such as CPU and memory). We also runcross-evaluation of generic and graph based analytic algorithmsover graph processing and generic platforms to identify thepotential performance degradation if only one processing engineis available. It is observed that both computing engines showgood scalability with increase of computing resources. WhileGraphLab largely outperforms Spark for graph algorithms, ithas close running time performance as Spark for non-graphalgorithms. Additionally the running time with Spark for graphalgorithms over cloud virtual machines is observed to increaseby almost 100% compared to over local computer clusters.

Improving energy efficiency in a wireless sensor network by combining cooperative MIMO with data aggregation

In wireless sensor networks where nodes are powered by batteries, it is critical to prolong the network lifetime by minimizing the energy consumption of each node. In this paper, the cooperative multiple-input-multiple-output (MIMO) and data-aggregation techniques are jointly adopted to reduce the energy consumption per bit in wireless sensor networks by reducing the amount of data for transmission and better using network resources through cooperative communication. For this purpose, we derive a new energy model that considers the correlation between data generated by nodes and the distance between them for a cluster-based sensor network by employing the combined techniques. Using this model, the effect of the cluster size on the average energy consumption per node can be analyzed. It is shown that the energy efficiency of the network can significantly be enhanced in cooperative MIMO systems with data aggregation, compared with either cooperative MIMO systems without data aggregation or data-aggregation systems without cooperative MIMO, if sensor nodes are properly clusterized. Both centralized and distributed data-aggregation schemes for the cooperating nodes to exchange and compress their data are also proposed and appraised, which lead to diverse impacts of data correlation on the energy performance of the integrated cooperative MIMO and data-aggregation systems.

Performance optimisation of the MAC protocol with multiple contention slots in MIMO ad hoc networks

The multiple-input multiple-output (MIMO) technique can be used to improve the performance of ad hoc networks. Various medium access control (MAC) protocols with multiple contention slots have been proposed to exploit spatial multiplexing for increasing the transport throughput of MIMO ad hoc networks. However, the existence of multiple request-to-send/clear-to-send (RTS/CTS) contention slots represents a severe overhead that limits the improvement on transport throughput achieved by spatial multiplexing. In addition, when the number of contention slots is fixed, the efficiency of RTS/CTS contention is affected by the transmitting power of network nodes. In this study, a joint optimisation scheme on both transmitting power and contention slots number for maximising the transport throughput is presented. This includes the establishment of an analytical model of a simplified MAC protocol with multiple contention slots, the derivation of transport throughput as a function of both transmitting power and the number of contention slots, and the optimisation process based on the transport throughput formula derived. The analytical results obtained, verified by simulation, show that much higher transport throughput can be achieved using the joint optimisation scheme proposed, compared with the non-optimised cases and the results previously reported.

Learning user and product distributed representations using a sequence model for sentiment analysis

In product reviews, it is observed that the distribution of polarity ratings over reviews written by different users or evaluated based on different products are often skewed in the real world. As such, incorporating user and product information would be helpful for the task of sentiment classification of reviews. However, existing approaches ignored the temporal nature of reviews posted by the same user or evaluated on the same product. We argue that the temporal relations of reviews might be potentially useful for learning user and product embedding and thus propose employing a sequence model to embed these temporal relations into user and product representations so as to improve the performance of document-level sentiment analysis. Specifically, we first learn a distributed representation of each review by a one-dimensional convolutional neural network. Then, taking these representations as pretrained vectors, we use a recurrent neural network with gated recurrent units to learn distributed representations of users and products. Finally, we feed the user, product and review representations into a machine learning classifier for sentiment classification. Our approach has been evaluated on three large-scale review datasets from the IMDB and Yelp. Experimental results show that: (1) sequence modeling for the purposes of distributed user and product representation learning can improve the performance of document-level sentiment classification; (2) the proposed approach achieves state-of-The-Art results on these benchmark datasets.

Verification of the indoor gps system by comparison with points calibrated using a network of laser tracker measurements

This paper details a method of determining the uncertainty of dimensional measurement for a three dimensional coordinate measurement machine. An experimental procedure was developed to compare three dimensional coordinate measurements with calibrated reference points. The reference standard used to calibrate these reference points was a fringe counting interferometer with the multilateration technique employed to establish three dimensional coordinates. This is an extension of the established technique of comparing measured lengths with calibrated lengths. Specifically a distributed coordinate measurement device was tested which consisted of a network of Rotary-Laser Automatic Theodolites (R-LATs), this system is known commercially as indoor GPS (iGPS). The method was found to be practical and able to establish that the expanded uncertainty of the basic iGPS system was approximately 1 mm at a 95% confidence level. © Springer-Verlag Berlin Heidelberg 2010.