Stochastic models for regulatory networks of the genetic toggle switch

Bistability arises within a wide range of biological systems from the λ phage switch in bacteria to cellular signal transduction pathways in mammalian cells. Changes in regulatory mechanisms may result in genetic switching in a bistable system. Recently, more and more experimental evidence in the form of bimodal population distributions indicates that noise plays a very important role in the switching of bistable systems. Although deterministic models have been used for studying the existence of bistability properties under various system conditions, these models cannot realize cell-to-cell fluctuations in genetic switching. However, there is a lag in the development of stochastic models for studying the impact of noise in bistable systems because of the lack of detailed knowledge of biochemical reactions, kinetic rates, and molecular numbers. In this work, we develop a previously undescribed general technique for developing quantitative stochastic models for large-scale genetic regulatory networks by introducing Poisson random variables into deterministic models described by ordinary differential equations. Two stochastic models have been proposed for the genetic toggle switch interfaced with either the SOS signaling pathway or a quorum-sensing signaling pathway, and we have successfully realized experimental results showing bimodal population distributions. Because the introduced stochastic models are based on widely used ordinary differential equation models, the success of this work suggests that this approach is a very promising one for studying noise in large-scale genetic regulatory networks.

Computational approaches for modelling intrinsic noise and delays in genetic regulatory networks

This chapter focuses on the interactions and roles between delays and intrinsic noise effects within cellular pathways and regulatory networks. We address these aspects by focusing on genetic regulatory networks that share a common network motif, namely the negative feedback loop, leading to oscillatory gene expression and protein levels. In this context, we discuss computational simulation algorithms for addressing the interplay of delays and noise within the signaling pathways based on biological data. We address implementational issues associated with efficiency and robustness. In a molecular biology setting we present two case studies of temporal models for the Hes1 gene (Monk, 2003; Hirata et al., 2002), known to act as a molecular clock, and the Her1/Her7 regulatory system controlling the periodic somite segmentation in vertebrate embryos (Giudicelli and Lewis, 2004; Horikawa et al., 2006).

Evolving noisy oscillatory dynamics in genetic regulatory networks

We introduce a genetic programming (GP) approach for evolving genetic networks that demonstrate desired dynamics when simulated as a discrete stochastic process. Our representation of genetic networks is based on a biochemical reaction model including key elements such as transcription, translation and post-translational modifications. The stochastic, reaction-based GP system is similar but not identical with algorithmic chemistries. We evolved genetic networks with noisy oscillatory dynamics. The results show the practicality of evolving particular dynamics in gene regulatory networks when modelled with intrinsic noise.

Planning of distribution networks for medium voltage and low voltage

Determination of the placement and rating of transformers and feeders are the main objective of the basic distribution network planning. The bus voltage and the feeder current are two constraints which should be maintained within their standard range. The distribution network planning is hardened when the planning area is located far from the sources of power generation and the infrastructure. This is mainly as a consequence of the voltage drop, line loss and system reliability. Long distance to supply loads causes a significant amount of voltage drop across the distribution lines. Capacitors and Voltage Regulators (VRs) can be installed to decrease the voltage drop. This long distance also increases the probability of occurrence of a failure. This high probability leads the network reliability to be low. Cross-Connections (CC) and Distributed Generators (DGs) are devices which can be employed for improving system reliability. Another main factor which should be considered in planning of distribution networks (in both rural and urban areas) is load growth. For supporting this factor, transformers and feeders are conventionally upgraded which applies a large cost. Installation of DGs and capacitors in a distribution network can alleviate this issue while the other benefits are gained. In this research, a comprehensive planning is presented for the distribution networks. Since the distribution network is composed of low and medium voltage networks, both are included in this procedure. However, the main focus of this research is on the medium voltage network planning. The main objective is to minimize the investment cost, the line loss, and the reliability indices for a study timeframe and to support load growth. The investment cost is related to the distribution network elements such as the transformers, feeders, capacitors, VRs, CCs, and DGs. The voltage drop and the feeder current as the constraints are maintained within their standard range. In addition to minimizing the reliability and line loss costs, the planned network should support a continual growth of loads, which is an essential concern in planning distribution networks. In this thesis, a novel segmentation-based strategy is proposed for including this factor. Using this strategy, the computation time is significantly reduced compared with the exhaustive search method as the accuracy is still acceptable. In addition to being applicable for considering the load growth, this strategy is appropriate for inclusion of practical load characteristic (dynamic), as demonstrated in this thesis. The allocation and sizing problem has a discrete nature with several local minima. This highlights the importance of selecting a proper optimization method. Modified discrete particle swarm optimization as a heuristic method is introduced in this research to solve this complex planning problem. Discrete nonlinear programming and genetic algorithm as an analytical and a heuristic method respectively are also applied to this problem to evaluate the proposed optimization method.

How long is a tweet? Mapping dynamic conversation networks on Twitter using Gawk and Gephi

Twitter is now well established as the world’s second most important social media platform, after Facebook. Its 140-character updates are designed for brief messaging, and its network structures are kept relatively flat and simple: messages from users are either public and visible to all (even to unregistered visitors using the Twitter website), or private and visible only to approved ‘followers’ of the sender; there are no more complex definitions of degrees of connection (family, friends, friends of friends) as they are available in other social networks. Over time, Twitter users have developed simple, but effective mechanisms for working around these limitations: ‘#hashtags’, which enable the manual or automatic collation of all tweets containing the same #hashtag, as well allowing users to subscribe to content feeds that contain only those tweets which feature specific #hashtags; and ‘@replies’, which allow senders to direct public messages even to users whom they do not already follow. This paper documents a methodology for extracting public Twitter activity data around specific #hashtags, and for processing these data in order to analyse and visualize the @reply networks existing between participating users – both overall, as a static network, and over time, to highlight the dynamic structure of @reply conversations. Such visualizations enable us to highlight the shifting roles played by individual participants, as well as the response of the overall #hashtag community to new stimuli – such as the entry of new participants or the availability of new information. Over longer timeframes, it is also possible to identify different phases in the overall discussion, or the formation of distinct clusters of preferentially interacting participants.

A recommendation method for online dating networks based on social relations and demographic information

A new relationship type of social networks - online dating - are gaining popularity. With a large member base, users of a dating network are overloaded with choices about their ideal partners. Recommendation methods can be utilized to overcome this problem. However, traditional recommendation methods do not work effectively for online dating networks where the dataset is sparse and large, and a two-way matching is required. This paper applies social networking concepts to solve the problem of developing a recommendation method for online dating networks. We propose a method by using clustering, SimRank and adapted SimRank algorithms to recommend matching candidates. Empirical results show that the proposed method can achieve nearly double the performance of the traditional collaborative filtering and common neighbor methods of recommendation.

Microstrip decoupling networks for low-order multi-port arrays with reduced element spacing

An array of monopole elements with reduced element spacing of λ/6 to λ/20 is considered for application in digital beam-forming and direction-finding. The small element spacing introduces strong mutual coupling between the array elements. This paper discusses that decoupling can be achieved analytically for arrays with three elements and describes Kuroda’s identities to realize the lumped elements of the derived decoupling network. Design procedures and equations are proposed. Experimental results are presented. The decoupled array has a bandwidth of 1% and a superdirective radiation pattern.

Diversified service provisioning in global business networks

Companies and their services are being increasingly exposed to global business networks and Internet-based ondemand services. Much of the focus is on flexible orchestration and consumption of services, beyond ownership and operational boundaries of services. However, ways in which third-parties in the “global village” can seamlessly self-create new offers out of existing services remains open. This paper proposes a framework for service provisioning in global business networks that allows an open-ended set of techniques for extending services through a rich, multi-tooling environment. The Service Provisioning Management Framework, as such, supports different modeling techniques, through supportive tools, allowing different parts of services to be integrated into new contexts. Integration of service user interfaces, business processes, operational interfaces and business object are supported. The integration specifications that arise from service extensions are uniformly reflected through a kernel technique, the Service Integration Technique. Thus, the framework preserves coherence of service provisioning tasks without constraining the modeling techniques needed for extending different aspects of services.

Finding and matching communities in social networks using data mining

The rapid growth in the number of users using social networks and the information that a social network requires about their users make the traditional matching systems insufficiently adept at matching users within social networks. This paper introduces the use of clustering to form communities of users and, then, uses these communities to generate matches. Forming communities within a social network helps to reduce the number of users that the matching system needs to consider, and helps to overcome other problems from which social networks suffer, such as the absence of user activities' information about a new user. The proposed system has been evaluated on a dataset obtained from an online dating website. Empirical analysis shows that accuracy of the matching process is increased using the community information.

Ad hoc innovation by users of social networks : the case of Twitter

Generic, flexible social media spaces such as Facebook and Twitter constitute an increasingly important element in our overall media repertoires. They provide a technological basis for instant and world-wide, ad hoc, many-to-many communication, and their effect on global communication patterns has already been highlighted. The short-messaging platform Twitter, for example, caters for uses ranging from interpersonal and quasi-private phatic exchanges to ‘ambient journalism’: ad hoc new reporting and dissemination as major events break. Many such uses have themselves emerged through user-driven processes: even standard Twitter conventions such as the @reply (to publicly address a fellow user) or the #hashtag(to collect related messages in an easily accessible space) are user inventions, in fact, and were incorporated into Twitter’s own infrastructure only subsequently. This demonstrates the substantial potential of social, user-led innovation in social media spaces.

Resourcing Early Learners : New Networks, New Actors

The landscape of early childhood education and care is changing. Governments world-wide are assuming increasing authority in relation to child-rearing in the years before school entry, beyond the traditional role in assisting parents to do the best they can by their children. As part of a social agenda aimed at forming citizens well prepared to play an active part in a globalised knowledge economy, the idea of ‘early learning’ expresses the necessity of engaging caregivers right from the start of children’s lives. Nichols, Rowsell, Rainbird, and Nixon investigate this trend over three years, in two countries, and three contrasting regions, by setting themselves the task of tracing every service and agent offering resources under the banner of early learning. Far from a dry catalogue, the study involves in-depth ethnographic research in fascinating spaces such as a church-run centre for African refugee women and children, a state-of-the-art community library and an Australian country town. Included is an unprecedented inventory of an entire suburban mall. Richly visually documented, the study employs emerging methods such as Google-mapping to trace the travels of actual parents as they search for particular resources. Each chapter features a context investigated in this large, international study: the library, the mall, the clinic, and the church. The author team unravels new spaces and new networks at work in early childhood literacy and development.

Excess power circulation in distribution networks containing distributed energy resources

The presence of large number of single-phase distributed energy resources (DERs) can cause severe power quality problems in distribution networks. The DERs can be installed in random locations. This may cause the generation in a particular phase exceeds the load demand in that phase. Therefore the excess power in that phase will be fed back to the transmission network. To avoid this problem, the paper proposes the use of distribution static compensator (DSTATCOM) that needs to be connected at the first bus following a substation. When operated properly, the DSTATCOM can facilitate a set of balanced current flow from the substation, even when excess power is generated by DERs. The proposals are validated through extensive digital computer simulation studies using PSCAD and MATLAB.

An approach for current balancing in distribution networks with rooftop PVs

Current unbalance is a significant power quality problem in distribution networks. This problem increases further with the increased penetration of single-phase photovoltaic cells. In this paper, a new approach is developed for current unbalance reduction in medium voltage distribution networks. The method is based on utilization of three single-phase voltage source converters connected in delta configuration between the phases. Each converter is controlled to function as a varying capacitor. The combination of the load and the compensator will result in a balanced load with unity power factor. The efficacy of the proposed current unbalance reduction concept is verified through dynamic simulations in PSCAD/EMTDC.

A database for person re-identification in multi-camera surveillance networks

Person re-identification involves recognising individuals in different locations across a network of cameras and is a challenging task due to a large number of varying factors such as pose (both subject and camera) and ambient lighting conditions. Existing databases do not adequately capture these variations, making evaluations of proposed techniques difficult. In this paper, we present a new challenging multi-camera surveillance database designed for the task of person re-identification. This database consists of 150 unscripted sequences of subjects travelling in a building environment though up to eight camera views, appearing from various angles and in varying illumination conditions. A flexible XML-based evaluation protocol is provided to allow a highly configurable evaluation setup, enabling a variety of scenarios relating to pose and lighting conditions to be evaluated. A baseline person re-identification system consisting of colour, height and texture models is demonstrated on this database.

Analyzing the factors influencing the successful design and uptake of interactive systems to support social networks in urban neighborhoods

In urban residential environments in Australia and other developed countries, Internet access is on the verge of becoming a ubiquitous utility like gas or electricity. From an urban sociology and community informatics perspective, this article discusses new emerging social formations of urban residents that are based on networked individualism and the potential of Internet-based systems to support them. It proposes that one of the main reasons for the disappearance or nonexistence of urban residential communities is a lack of appropriate opportunities and instruments to encourage and support local interaction in urban neighborhoods. The article challenges the view that a mere reappropriation of applications used to support dispersed virtual communities is adequate to meet the place and proximity-based design requirements that community networks in urban neighborhoods pose. It argues that the key factors influencing the successful design and uptake of interactive systems to support social networks in urban neighborhoods include the swarming social behavior of urban dwellers; the dynamics of their existing communicative ecology; and the serendipitous, voluntary, and place-based quality of interaction between residents on the basis of choice, like-mindedness, mutual interest and support needs. Drawing on an analysis of these factors, the conceptual design framework of a prototype system — the urban tribe incubator — is presented.