Computational analysis of epigenetic information in human DNA sequences

Over the last few years, investigations of human epigenetic profiles have identified key elements of change to be Histone Modifications, stable and heritable DNA methylation and Chromatin remodeling. These factors determine gene expression levels and characterise conditions leading to disease. In order to extract information embedded in long DNA sequences, data mining and pattern recognition tools are widely used, but efforts have been limited to date with respect to analyzing epigenetic changes, and their role as catalysts in disease onset. Useful insight, however, can be gained by investigation of associated dinucleotide distributions. The focus of this paper is to explore specific dinucleotides frequencies across defined regions within the human genome, and to identify new patterns between epigenetic mechanisms and DNA content. Signal processing methods, including Fourier and Wavelet Transformations, are employed and principal results are reported.

Complexity and high-end computing in biology and medicine

Biomedical systems involve a large number of entities and intricate interactions between these. Their direct analysis is, therefore, difficult, and it is often necessary to rely on computational models. These models require significant resources and parallel computing solutions. These approaches are particularly suited, given parallel aspects in the nature of biomedical systems. Model hybridisation also permits the integration and simultaneous study of multiple aspects and scales of these systems, thus providing an efficient platform for multidisciplinary research.

From bio-inspired computing to e-Biology

Several algorithms and techniques widely used in Computer Science have been adapted from, or inspired by, known biological phenomena. This is a consequence of the multidisciplinary background of most early computer scientists. The field has now matured, and permits development of tools and collaborative frameworks which play a vital role in advancing current biomedical research. In this paper, we briefly present examples of the former, and elaborate upon two of the latter, applied to immunological modelling and as a new paradigm in gene expression.

Impact of mobility and topology on information diffusion in MANETs

In some delay-tolerant communication systems such as vehicular ad-hoc networks, information flow can be represented as an infectious process, where each entity having already received the information will try to share it with its neighbours. The random walk and random waypoint models are popular analysis tools for these epidemic broadcasts, and represent two types of random mobility. In this paper, we introduce a simulation framework investigating the impact of a gradual increase of bias in path selection (i.e. reduction of randomness), when moving from the former to the latter. Randomness in path selection can significantly alter the system performances, in both regular and irregular network structures. The implications of these results for real systems are discussed in details.

Building cross-scale models of epigenetic mechanisms

Epigenetic changes correspond to heritable modifications of the chromosome structure, which do not involve alteration of the DNA sequence but do affect gene expression. These mechanisms play an important role in normal cell differentiation, but aberration is associated also with several diseases, including cancer and neural disorders. In consequence, despite intensive studies in recent years, the contribution of modifications remains largely unquantified due to overall system complexity and insufficient data. Computational models can provide powerful auxiliary tools to experimentation, not least as scales from the sub-cellular through cell populations (or to networks of genes) can be spanned. In this paper, the challenges to development, of realistic cross-scale models, are discussed and illustrated with respect to current work.

Characterisation of the cascode gate drive of power MOSFETs in clamped inductive switching applications

This thesis proposes a novel gate drive circuit to improve the switching performance of MOSFET power switches in power electronic converters. The proposed topology exploits the cascode configuration, allowing the minimisation of switching losses in the presence of practical circuit constraints, which enables efficiency and power density improvements. Switching characteristics of the new topology are investigated and key mechanisms that control the switching process are identified. Unique analysis tools and techniques are also developed to demonstrate the application of the cascode gate drive circuit for switching performance optimisation.

Household financial systems

In this paper we discuss some preliminary results of an ethnographic study focused on the ways money and financial issues are collaboratively handled within families. Families develop ‘systems’ or methods through which they organize and manage their everyday financial activities. These systems not only organize everyday family finances, but represent and shape family relationships. Through analysis of our ethnographic field study data, we develop four types of financial systems that we observed in the field: banking arrangements, physical hubs, goal-oriented systems and spatio-temporal organization. In this paper, we discuss examples of these systems and their implications for designing tools to support household financial practices.

Affordances of ICTs: an environmental study of a French language unit offered at university level

This project investigates the integration of Information Communication Technologies (ICTs) into educational settings by closely looking at the uptake of the perceived affordances offered by ICTs by students enrolled in a French language course at Queensland University of Technology. This cross-disciplinary research uses the theoretical concepts of: Ecological Psychology (Gibson, 1979; Good, 2007; Reed, 1996); Ecological Linguistics (Greeno, 1994; Leather & van Dam, 2003; van Lier 2000, 2003, 2004a, 2004b); Design (Norman, 1988, 1999); Software Design/ Human-Computer Interaction (Hartson, 2003; McGrenere & Ho, 2000); Learning Design (Conole & Dyke, 2004a, 2004b; Laurillard et al. 2000;); Education (Kirschner, 2002; Salomon, 1993; Wijekumar et al., 2006) and Educational Psychology (Greeno, 1994). In order to investigate this subject, the following research questions, rooted in the theoretical foundations of the thesis, were formulated: (1) What are the learners’ attitudes towards the ICT tools used in the project?; (2) What are the affordances offered by ICTs used in a specific French language course at university level from the perspective of the teacher and from the perspective of language learners?; (3) What affordances offered by ICT tools used by the teacher within the specific teaching and learning environment have been taken up by learners?; and (4) What factors influence the uptake by learners of the affordances created by ICT tools used by the teacher within the specific teaching and learning environment? The teaching phase of this project, conducted between 2006 and 2008, used Action Research procedures (Hopkins, 2002; McNiff & Whitehead, 2002; van Lier 1994) as a research framework. The data were collected using the following combination of qualitative and quantitative methods: (1) questionnaires administered to students (Hopkins, 2002; McNiff & Whitehead, 2002) using Likert-scale questions, open questions, yes/no questions; (2) partnership classroom observations of research participants conducted by Research Participant Advocates (Hopkins, 2002; McNiff & Whitehead, 2002); and (3) a focus group with volunteering students who participated in the unit (semi-structured interview) (Hopkins, 2002; McNiff & Whitehead, 2002). The data analysis confirms the importance of a careful examination of the teaching and learning environment and reveals differences in the ways in which the opportunities for an action offered by the ICTs were perceived by teacher and students, which impacted on the uptake of affordances. The author applied the model of affordance, as described by Good (2007), to explain these differences and to investigate their consequences. In conclusion, the teacher-researcher considers that the discrepancies in perceiving the affordances result from the disparities between the frames of reference and the functional contexts of the teacher-researcher and students. Based on the results of the data analysis, a series of recommendations is formulated supporting calls for careful analysis of frames of reference and the functional contexts of all participants in the learning and teaching process. The author also suggests a modified model of affordance, outlining the important characteristics of its constituents.

Decision support system for infrastructure sustainability in operations

There is an increasing awareness of sustainability and climate change and its impact on infrastructure and engineering asset management in design, construction, and operations. Sustainability rating tools have been proposed and/or developed that provide ratings of infrastructure projects in differing phases of their life cycle on sustainability. This paper provides an overview of decision support systems using sustainability rating framework that can be used to prioritize or select tasks and activities within projects to enhance levels of sustainability outcomes. These systems can also be used to prioritize projects within an organization to optimize sustainability outcomes within an allocated budget.

Sustainability in infrastructure asset management

The expectation to integrate sustainability aspects (social, environmental, and economic success) into the design, delivery, and operation of infrastructure assets is growing rapidly and globally. There are now several tools and frameworks available to benchmark and measure sustainable performance of infrastructure projects and assets. This paper briefly describes the infrastructure sustainability (IS) rating tool developed by the Australian Green Infrastructure Council (AGIC) that was launched in February 2012. This tool evaluates sustainability initiatives and potential environmental, social, and economic impacts of infrastructure projects and assets. The rating tool provides the following benefits to industry: a common national language for sustainability; a vehicle for consistent application and evaluation of sustainability in tendering processes; assists in scoping whole-of-life sustainability risks, enabling smarter solutions that reduce risks and costs; fosters resource efficiency and waste reduction, reducing costs; fosters innovation and continuous improvement in sustainability outcomes; and builds an organization’s credentials and reputation in its approach to sustainability. The infrastructure types covered by this tool include transport, energy, water, and communication. The key themes of sustainability evaluation will be briefly presented in this paper, and they include management and governance; use of resources; emissions, pollution, and waste; ecology; people and place; and innovation.

Success factors of engaging higher education students and staff with e-learning tools within Learning Management Systems

This thesis explored the state of the use of e-learning tools within Learning Management Systems in higher education and developed a distinct framework to explain the factors influencing users' engagement with these tools. The study revealed that the Learning Management System design, preferences for other tools, availability of time, lack of adequate knowledge about tools, pedagogical practices, and social influences affect the uptake of Learning Management System tools. Semi structured interviews with 74 students and lecturers of a major Australian university were used as a source of data. The applied thematic analysis method was used to analyse the collected data.

Evolutionary optimization and game strategies for advanced multi-disciplinary design : applications to aeronautics and UAV design

Many complex aeronautical design problems can be formulated with efficient multi-objective evolutionary optimization methods and game strategies. This book describes the role of advanced innovative evolution tools in the solution, or the set of solutions of single or multi disciplinary optimization. These tools use the concept of multi-population, asynchronous parallelization and hierarchical topology which allows different models including precise, intermediate and approximate models with each node belonging to the different hierarchical layer handled by a different Evolutionary Algorithm. The efficiency of evolutionary algorithms for both single and multi-objective optimization problems are significantly improved by the coupling of EAs with games and in particular by a new dynamic methodology named “Hybridized Nash-Pareto games”. Multi objective Optimization techniques and robust design problems taking into account uncertainties are introduced and explained in detail. Several applications dealing with civil aircraft and UAV, UCAV systems are implemented numerically and discussed. Applications of increasing optimization complexity are presented as well as two hands-on test cases problems. These examples focus on aeronautical applications and will be useful to the practitioner in the laboratory or in industrial design environments. The evolutionary methods coupled with games presented in this volume can be applied to other areas including surface and marine transport, structures, biomedical engineering, renewable energy and environmental problems.

A technique for analysing GOOSE packets when testing relays in an IEC 61850-8-1 environment

While the implementation of the IEC 61850 standard has significantly enhanced the performance of communications in electrical substations, it has also increased the complexity of the system. Subsequently, these added elaborations have introduced new challenges in relation to the skills and tools required for the design, test and maintenance of 61850-compatible substations. This paper describes a practical experience of testing a protection relay using a non-conventional test equipment; in addition, it proposes a third party software technique to reveal the contents of the packets transferred on the substation network. Using this approach, the standard objects can be linked and interpreted to what the end-users normally see in the IED and test equipment proprietary software programs.

Participatory action research for civic engagement

The future of civic engagement is characterised by both technological innovation as well as new technological user practices that are fuelled by trends towards mobile, personal devices; broadband connectivity; open data; urban interfaces; and, cloud computing. These technology trends are progressing at a rapid pace, and have led global technology vendors to package and sell the ‘Smart City’ as a centralized service delivery platform predicted to optimize and enhance cities’ key performance indicators – and generate a profitable market. The top-down deployment of these large and proprietary technology platforms have helped sectors such as energy, transport, and healthcare to increase efficiencies. However, an increasing number of scholars and commentators warn of another ‘IT bubble’ emerging. Along with some city leaders, they argue that the top-down approach does not fit the governance dynamics and values of a liberal democracy when applied across sectors. A thorough understanding is required, of the socio-cultural nuances of how people work, live, play across different environments, and how they employ social media and mobile devices to interact with, engage in, and constitute public realms. Although the term ‘slacktivism’ is sometimes used to denote a watered down version of civic engagement and activism that is reduced to clicking a ‘Like’ button and signing online petitions, we believe that we are far from witnessing another Biedermeier period that saw people focus on the domestic and the non-political. There is plenty of evidence to the contrary, such as post-election violence in Kenya in 2008, the Occupy movements in New York, Hong Kong and elsewhere, the Arab Spring, Stuttgart 21, Fukushima, the Taksim Gezi Park in Istanbul, and the Vinegar Movement in Brazil in 2013. These examples of civic action shape the dynamics of governments, and in turn, call for new processes to be incorporated into governance structures. Participatory research into these new processes across the triad of people, place and technology is a significant and timely investment to foster productive, sustainable, and livable human habitats. With this chapter, we want to reframe the current debates in academia and priorities in industry and government to allow citizens and civic actors to take their rightful centerpiece place in civic movements. This calls for new participatory approaches for co-inquiry and co-design. It is an evolving process with an explicit agenda to facilitate change, and we propose participatory action research (PAR) as an indispensable component in the journey to develop new governance infrastructures and practices for civic engagement. This chapter proposes participatory action research as a useful and fitting research paradigm to guide methodological considerations surrounding the study, design, development, and evaluation of civic technologies. We do not limit our definition of civic technologies to tools specifically designed to simply enhance government and governance, such as renewing your car registration online or casting your vote electronically on election day. Rather, we are interested in civic media and technologies that foster citizen engagement in the widest sense, and particularly the participatory design of such civic technologies that strive to involve citizens in political debate and action as well as question conventional approaches to political issues (DiSalvo, 2012; Dourish, 2010; Foth et al., 2013). Following an outline of some underlying principles and assumptions behind participatory action research, especially as it applies to cities, we will critically review case studies to illustrate the application of this approach with a view to engender robust, inclusive, and dynamic societies built on the principles of engaged liberal democracy. The rationale for this approach is an alternative to smart cities in a ‘perpetual tomorrow,’ (cf. e.g. Dourish & Bell, 2011), based on many weak and strong signals of civic actions revolving around technology seen today. It seeks to emphasize and direct attention to active citizenry over passive consumerism, human actors over human factors, culture over infrastructure, and prosperity over efficiency. First, we will have a look at some fundamental issues arising from applying simplistic smart city visions to the kind of a problem a city is (cf. Jacobs, 1961). We focus on the touch points between “the city” and its civic body, the citizens. In order to provide for meaningful civic engagement, the city must provide appropriate interfaces.