In silico biology : making the most of parallel computing

Biological systems are typically complex and adaptive, involving large numbers of entities, or organisms, and many-layered interactions between these. System behaviour evolves over time, and typically benefits from previous experience by retaining memory of previous events. Given the dynamic nature of these phenomena, it is non-trivial to provide a comprehensive description of complex adaptive systems and, in particular, to define the importance and contribution of low-level unsupervised interactions to the overall evolution process. In this chapter, the authors focus on the application of the agent-based paradigm in the context of the immune response to HIV. Explicit implementation of lymph nodes and the associated lymph network, including lymphatic chain structure, is a key objective, and requires parallelisation of the model. Steps taken towards an optimal communication strategy are detailed.

Model refinement through high-performance computing: an agent-based HIV example

Background Recent advances in Immunology highlighted the importance of local properties on the overall progression of HIV infection. In particular, the gastrointestinal tract is seen as a key area during early infection, and the massive cell depletion associated with it may influence subsequent disease progression. This motivated the development of a large-scale agent-based model. Results Lymph nodes are explicitly implemented, and considerations on parallel computing permit large simulations and the inclusion of local features. The results obtained show that GI tract inclusion in the model leads to an accelerated disease progression, during both the early stages and the long-term evolution, compared to a theoretical, uniform model. Conclusions These results confirm the potential of treatment policies currently under investigation, which focus on this region. They also highlight the potential of this modelling framework, incorporating both agent-based and network-based components, in the context of complex systems where scaling-up alone does not result in models providing additional insights.

Efficiency of parallelisation of genetic algorithms in the data analysis context

Most real-life data analysis problems are difficult to solve using exact methods, due to the size of the datasets and the nature of the underlying mechanisms of the system under investigation. As datasets grow even larger, finding the balance between the quality of the approximation and the computing time of the heuristic becomes non-trivial. One solution is to consider parallel methods, and to use the increased computational power to perform a deeper exploration of the solution space in a similar time. It is, however, difficult to estimate a priori whether parallelisation will provide the expected improvement. In this paper we consider a well-known method, genetic algorithms, and evaluate on two distinct problem types the behaviour of the classic and parallel implementations.

Optimisation algorithms for microarray biclustering

In providing simultaneous information on expression profiles for thousands of genes, microarray technologies have, in recent years, been largely used to investigate mechanisms of gene expression. Clustering and classification of such data can, indeed, highlight patterns and provide insight on biological processes. A common approach is to consider genes and samples of microarray datasets as nodes in a bipartite graphs, where edges are weighted e.g. based on the expression levels. In this paper, using a previously-evaluated weighting scheme, we focus on search algorithms and evaluate, in the context of biclustering, several variations of Genetic Algorithms. We also introduce a new heuristic “Propagate”, which consists in recursively evaluating neighbour solutions with one more or one less active conditions. The results obtained on three well-known datasets show that, for a given weighting scheme,optimal or near-optimal solutions can be identified.

The birthday cake: Social relations and professional practices around mealtimes with toddlers and child care

Events that involve food and eating are important parts of the daily routine in which adults and children participate in child care settings. These events can be viewed as cultural practices because they involve certain everyday ways of acting, thinking or feeling (Grusec JE et al, Child Dev 71(1): 205–211, 2000). The cultural practices around food and eating symbolise and guide the social relations, emotions, social structures and behaviours of the participants. Identities and roles for the participants are created in these practices, marked by ambiguity, movement and fluidity through ongoing processes of negotiation (Punch S et al, Child Geogr 8(3): 227–232, 2010). The formal professional systems that guide these practices in early education and care programs often focus on the nutritional value of the food, while the children and teachers involved in these mealtime events account for the intersubjective experiences. Mealtimes provide opportunities for children and teachers to interact and co-construct meaning around the situations that arise. Of special interest in this research are teachers’ and children’s intentions for communication in the context of events involving food and eating and the kind of learning embedded in the communications that occur. Throughout this chapter, these events are referred to as mealtimes. This study is informed by phenomenological theory which aims to reach understandings about interactions and their meaning from the perspective of the participating individuals.

The centrality of ethical leadership

Purpose The central argument in this paper is that ethical school leadership is imperative in a context of increasing performance-driven accountability. The purpose of this paper is to focus on school principals’ perceptions of how they understand ethical leadership and how they lead the ethical use of data. Design/methodology/approach This study utilises semi-structured interviews with six state school principals (one primary and six secondary) to explore their perceptions of ethical leadership practices; and how they balance current competing accountabilities in a context of performance-driven accountability. Findings There were four key findings. First, principals used data to inform and direct their practices and their conversations with teachers. Second, while ethics was a central consideration in how principals’ led, practising in an ethical manner was identified as complex and challenging in the current context. Third, Starratt’s (1996) ethical framework proved to be relevant for interpreting principals’ practices. Finally, all of the principals referred to dilemmas they faced as a result of competing priorities and all used a variety of strategies to deal with these dilemmas. Originality/value While there is a small body of research that explores school leaders’ understandings of ethical tensions and dilemmas, there is little research that has focused on school leaders’ understandings of the ethical use of data. This study, then, contributes to this area as it provides a discussion on school principals’ leadership practices in the current climate driven by data use.

Life storytelling at the ABC: Challenges of 'giving the audience a voice' in the context of public service media

Life storytelling projects have become an important means through which public service media institutions such as the Australian Broadcasting Corporation are seeking to foster audience participation and involve particular cohorts in the creation and distribution of broadcast content. This paper contributes to the wider conversation on audience participation within public service media intuitions (PSMs), and focuses on the opportunities and challenges that arise within life storytelling projects that are facilitated by these institutions, and that aim to ‘give voice’ to members of ‘the audience’. In particular, it focuses on two of the Australian Broadcasting Corporation’s current life storytelling projects: ABC Open and Heywire.

Renewable energy distribution in public spaces: Analyzing the case of Ballast Point Park in Sydney, using a triple bottom line approach

As cities are rapidly developing new interventions against climate change, embedding renewable energy in public spaces is an important strategy. However, most interventions primarily include environmental sustainability while neglecting the social and economic interrelationships of electricity production. Although there is a growing interest in sustainability within environmental design and landscape architecture, public spaces are still awaiting viable energy-conscious design and assessment interventions. The purpose of this paper is to investigate this issue in a renowned public space—Ballast Point Park in Sydney—using a triple bottom line (TBL) case study approach. The emerging factors and relationships of each component of TBL, within the context of public open space, are identified and discussed. With specific focus on renewable energy distribution in and around Ballast Point Park, the paper concludes with a general design framework, which conceptualizes an optimal distribution of onsite electricity produced from renewable sources embedded in public open spaces.

Heavy vehicle safety in Oman: Police interviews and heavy vehicle driver survey and focus groups. Third Report of the Heavy Vehicle Safety Research in Oman Project for The Research Council of Oman.

Over the past six months the project has undertaken three key, separate, data collection rounds. Each of these rounds focused on essentially different issues within the broader common construct of heavy vehicle road safety. This document will initially report on a series of two key qualitative data collections rounds. Firstly it will detail findings and report on discussions held in focus groups with 43 heavy vehicle drivers. The second qualitative study involved a series of interviews undertaken with 19 police officers from various levels of command and operations within the Royal Oman Police. The final data collection round reported on in this document is a roadside survey questionnaire undertaken with 400 heavy vehicle drivers.

Focus group discussions exploring major social influences on young driver safety in Oman. Report to the Research Council of Oman, Muscat.

This report documents the findings of in-depth focus groups conducted with 17 young drivers. The main aim of these focus groups was to explore key themes related to the risky behaviour of young drivers (17-25 years) in Oman. Specifically the interviews explored the influence of parents and peers, who may serve as a source of imitation, reward and punishment. Additionally, the interviews explored the influence of policing and licensing on young driver behaviour.

Emergency department models of care in the context of care quality and cost: A systematic review

To identify current ED models of care and their impact on care quality, care effectiveness, and cost. A systematic search of key health databases (Medline, CINAHL, Cochrane, EMbase) was conducted to identify literature on ED models of care. Additionally, a focused review of the contents of 11 international and national emergency medicine, nursing and health economic journals (published between 2010 and 2013) was undertaken with snowball identification of references of the most recent and relevant papers. Articles published between 1998 and 2013 in the English language were included for initial review by three of the authors. Studies in underdeveloped countries and not addressing the objectives of the present study were excluded. Relevant details were extracted from the retrieved literature, and analysed for relevance and impact. The literature was synthesised around the study's main themes. Models described within the literature mainly focused on addressing issues at the input, throughput or output stages of ED care delivery. Models often varied to account for site specific characteristics (e.g. onsite inpatient units) or to suit staffing profiles (e.g. extended scope physiotherapist), ED geographical location (e.g. metropolitan or rural site), and patient demographic profile (e.g. paediatrics, older persons, ethnicity). Only a few studies conducted cost-effectiveness analysis of service models. Although various models of delivering emergency healthcare exist, further research is required in order to make accurate and reliable assessments of their safety, clinical effectiveness and cost-effectiveness.

Specificity and context in post-exercise recovery: It is not a one-size-fits-all approach

The concept of specificity of exercise prescription and training is a longstanding and widely accepted foundation of the exercise sciences. Simply, the principle holds that training adaptations are achieved relative to the stimulus applied. That is, the manipulation of training variables (e.g. intensity or loading, mode, volume and frequency) directly influences the acute training stimulus, and so the long-term adaptive response (Young et al., 2001; Bird et al., 2005). Translating this concept to practice then recommends that exercise be prescribed specific to the desired outcomes, and the more closely this is achieved, the greater the performance gain is likely to be. However, the cardiovascular and metabolic adaptations traditionally associated with long, slow distance training types, similarly achieved using high-intensity training methods (for a review see Gibala et al., 2012), highlights understanding of underlying physiology as paramount for effective training program design. Various other factors including illness, sleep and psychology also impact on the training stimulus (Halson, 2014) and must be managed collectively with appropriate post-exercise recovery to continue performance improvements and reduce overtraining and injury risks (Kenttä and Hassmén, 1998).

Social media, audiences, and audience co-creativity in contemporary performance: Restoring balance?

Producers, technicians, performers, audiences and critics are all critical components of the performing arts ecology – critical components of an ecosystem that have to come together into some sort of productive relationship if the performing arts are to be vital, viable and successful. Different performance practices developed in different times, spaces and places do, of course, connect these players in different ways as part of their attempt to achieve their own definition of success, be it based on entertainment, educational, expression, empowerment, or something else. In some contemporary performance practices, social media platforms, applications and processes are seen to have significant potential to restore balance to the relationship between performer and audience, providing audiences with more power to participate in a performance event. In this paper, I investigate prevailing assumptions about social media’s power to democratise performance practice, or, at least, develop more co-creative performance practices in which producers, performers and audiences participate actively before, during and after the event. I focus, in particular, on the use of social media as a means of developing a participatory aesthetic in which an audience member is asked to contribute to the cast of characters, plot or progression of a performance. Although diverse – from performances streamed online, to performances that offer transmedia components the audience can use to learn more about character, context and plot online, to performances that incorporate online voting, liking or linking, to performances that unfold fully online on websites, blogs, microblogs or other social media platforms – what a lot of uses of social media in contemporary performance today share is a desire to encourage audiences to reflect on their role in making, and making meaning, of the event. In this paper I interrogate if, and if so how, this democratises or develops deeper levels of co-creativity in the relationship between producers, performers and audiences.

The provision of visitable housing in Australia: Down to the detail

In response to the ratification of the United Nations Convention of the Rights of People with Disabilities (CRPD), Australian housing industry leaders, supported by the Australian Government, committed to transform their practices voluntarily through the adoption of a national guideline, called Livable Housing Design. They set a target in 2010 that all new housing would be visitable by 2020. Research in this area suggests that the anticipated voluntary transformation is unrealistic and that mandatory regulation will be necessary for any lasting transformation to occur. It also suggests that the assumptions underpinning the Livable Housing Design agreement are unfounded. This paper reports on a study that problematised these assumptions. The study used eleven newly-constructed dwellings in three housing contexts in Brisbane, Australia. It sought to understand the logics-of-practice in providing, and not providing, visitable housing. By examining the specific details that make a dwelling visitable, and interpreting the accounts of builders, designers and developers, the study identified three logics-of-practice which challenged the assumptions underpinning the Livable Housing Design agreement: focus on the point of sale; an aversion to change and deference to external regulators on matters of social inclusion. These were evident in all housing contexts indicating a dominant industry culture regardless of housing context or policy intention. The paper suggests that financial incentives for both the builder and the buyer, demonstration by industry leaders and, ultimately, national regulation is a possible pathway for the Livable Housing Design agreement to reach the 2020 goal. The paper concludes that the Australian Government has three options: to ignore its obligations under the CRPD; to revisit the Livable Housing Design agreement in the hope that it works; or to regulate the housing industry through the National Construction Code to ensure the 2020 target is reached.

Collecting in an urban context: Relationships between collections and space in the home

Collecting has become a popular hobby within Western society, with collectables including anything from ‘bottle tops’ to ‘skyscrapers’. As the nature and size of these collections can impact upon the use of space in the home, the purpose of this study is to explore the relationship between the collections, space in the home and the impacts on others. This qualitative study explores the experiences of 11 Australian collectors, investigating the motivations, practices and adaption techniques used within their urban home environment. The themes of sentimentality, sociability and spatial tensions, including physical, personal and use of space are discussed within the context of their home and family environments. Overall the practice of collecting objects is a complex, varied, sentimental and sociable activity, providing enjoyment, knowledge and friendships. Space can be a central consideration to the practice of collecting as collections shape and are shaped by the available space in a household.