Inferring phylogenies of evolving sequences without multiple sequence alignment

Alignment-free methods, in which shared properties of sub-sequences (e.g. identity or match length) are extracted and used to compute a distance matrix, have recently been explored for phylogenetic inference. However, the scalability and robustness of these methods to key evolutionary processes remain to be investigated. Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. We find that compared to a multiple sequence alignment approach, D2 methods are more robust against among-site rate heterogeneity, compositional biases, genetic rearrangements and insertions/deletions, but are more sensitive to recent sequence divergence and sequence truncation. Across diverse empirical datasets, the alignment-free methods perform well for sequences sharing low divergence, at greater computation speed. Our findings provide strong evidence for the scalability and the potential use of alignment-free methods in large-scale phylogenomics.

In pursuit of some appreciation: Assessment and group membership in children’s second stories

Group membership is central to social interaction. Within peer groups, social hierarchies and affiliations are matters to which members seriously attend (Corsaro, 2014). Studies of peer groups highlight how status is achieved through oppositional actions. This paper examines the way in which competition and collaboration in a children’s peer group accomplishes status during the production and management of “second stories” (Sacks 1992). We present analysis of the interaction of young boys in a preparatory year playground who are engaged in a single instance of storytelling “rounds”. Analysis highlights the pivotal role of members’ contributions, assessments and receipts in a series of second stories that enact a simultaneously competitive and collaborative local order.

Analysis of passenger group behaviour and its impact on passenger flow using an agent-based model

Group interaction within crowds is a common phenomenon and has great influence on pedestrian behaviour. This paper investigates the impact of passenger group dynamics using an agent-based simulation method for the outbound passenger process at airports. Unlike most passenger-flow models that treat passengers as individual agents, the proposed model additionally incorporates their group dynamics as well. The simulation compares passenger behaviour at airport processes and discretionary services under different group formations. Results from experiments (both qualitative and quantitative) show that incorporating group attributes, in particular, the interactions with fellow travellers and wavers can have significant influence on passengers activity preference as well as the performance and utilisation of services in airport terminals. The model also provides a convenient way to investigate the effectiveness of airport space design and service allocations, which can contribute to positive passenger experiences. The model was created using AnyLogic software and its parameters were initialised using recent research data published in the literature.

Bricolage and storied selves: Young people's assemblages of narrative and identity in an Australian life storytelling project

Narrating is simultaneously self-interpretation and self-construction. People make sense of their lives and create their identities through an active process of assembling and applying meaning to memories, experiences, thoughts, actions and passions. Such a process can usefully be described as a bricolage: life narratives are created as an assemblage of scattered experiences and events. Through the particular way in which they are arranged, the storyteller constructs what Paul Ricoeur (1992) calls a “narrative identity”; that is, an identity which is organised through and specific to the story told. Applying this notion of narrative as bricolage to ‘Heywire’ – an Australian youth life storytelling project – this paper discusses the unique affordances that the process of storytelling offers in terms of identity and the way new, digital technologies and the internet augment the features of life narratives. It argues that narrative, in addition to new media, offers important tools through which young people who participate in the Heywire project make sense of personal experiences and craft their own identities in powerful and purposeful ways.

Is group more cost effective than individual cognitive behaviour therapy? The evidence is not solid yet

This paper critically evaluates the empirical evidence of 36 studies regarding the comparative cost-effectiveness of group and individual cognitive behaviour therapy (CBT) as a whole, and also for specific mental disorders (e.g. depression, anxiety, substance abuse) or populations (e.g. children). Methods of calculating costs, as well as methods of comparing treatment outcomes were appraised and criticized. Overall, the evidence that group CBT is more cost-effective than individual CBT is mixed, with group CBT appearing to be more cost effective in treating depression and children, but less cost effective in treating drugs and alcohol dependence, anxiety and social phobias. In addition, methodological weaknesses in the studies assessed are noted. There is a need to improve cost calculation methodology, as well as more solid and a greater number of empirical cost-effectiveness studies before a firm conclusion can be reached that group CBT is more cost effective then individual CBT.

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.

Children with gender dysphoria deserve better from the law

An increasing number of Australian children are accessing specialist health services for gender dysphoria treatment, largely because of a growing awareness among doctors about available specialist health services. But the law is not in step with the needs of these children...

Making the transition from pharmacy student to pharmacist: Australian interns' perceptions of professional identity formation

Objectives The experience of transitioning from university to practice influences professional identity formation. It is unclear how this transitioning experience influences pharmacy interns' professional identities. This study aims to examine pharmacy interns' perceptions of their transition from university to the workplace and the influence this had on their pharmacist identities. Methods A qualitative approach using in-depth interviews was adopted for this study. Fifteen interns (community and hospital) from one school of pharmacy in Australia were interviewed. Questions were asked about the nature of their current intern role, their university experiences, how they saw themselves as pharmacists and their perceptions of the transition to practice. Key findings The interns interviewed entered the workplace valuing patient-focused aspects of practice and contributing to patient care. The nature of work meant there were limited opportunities to enact these aspects of their professional identities. The interns were challenged by interactions with patients and doctors, and experienced difficulties reconciling this with their university-derived professional identities. Also, the interns lacked the confidence and strategies to overcome these challenges. Some were exploring alternative ways of being pharmacists. Conclusions This paper argues that graduates' experience of the transition to practice was challenging. This was due to nascent professional identities formed in university and a lack of workplace experiences enabling patient-centred practices. The interns' formation of professional identities was highly responsive to the context of work. To facilitate the development of Australian patient-centred pharmacy practice, supporting professional identity formation should be a focus within pharmacy education.

Friendship group motives for alcohol consumption: A midstream social marketing approach

Alcohol has been estimated to cost Australia $36 Billion per year, almost double that of all illegal drugs combined. This thesis uncovered seven friendship group-level motives for alcohol consumption, these motives were: Competition, Copying, Commitments, Conformity, Winding down, Play, and Confidence. These motives were then measured and their correlation with self-reported alcohol consumption was assessed. Using these results will allow social marketers to design targeted programmes that achieve meaningful behaviour change that goes beyond merely informing or raising awareness about the dangers of alcohol.

The favelas through the lenses of photographers: Photojournalism from community and mainstream media organisations

Photographers from community and mainstream media organisations bring the everyday of favela communities to the attention of Rio de Janeiro’s society from different perspectives. While mainstream photojournalists mainly report on favelas from outside to inside, denouncing wrongdoings and human rights abuses, community photographers do it from the opposite direction, from inside to outside, presenting images of the everyday life of favela communities. This paper takes an ethnographic and discursive approach to comparing these two categories of photographers to ask how their different practices can yield benefits for the people living in marginalised communities. Furthermore, by adapting Foucault and Bourdieu’s theories, this study examines photographers’ habitus so as to determine how cultural capital and economic capital that they possess shape their subjectivity and, as such, the fields of community and mainstream photojournalism. This study has no intention of creating polarised distinctions between community and mainstream photojournalism. Instead, the research aims, through the investigation of the working practices, identities, and discourses of photographers from community and mainstream media organisations, to identify the activities and limitations of both community and mainstream in order to build an understanding about how the media ecology works best within both.

Proceedings of the 3rd International Subtropical Cities Conference 2011 Subtropical Cities: Subtropical Urbanism -Beyond Climate Change

Climate has been, throughout modern history, a primary attribute for attracting residents to the “Sunshine States” of Florida (USA) and Queensland (Australia). The first major group of settlers capitalized on the winter growing season to support a year-­‐round agricultural economy. As these economies developed, the climate attracted tourism and retirement industries. Yet as Florida and Queensland have blossomed under beneficial climates, the stresses acting on the natural environment are exacting a toll. Southeast Florida and eastern Queensland are among the most vulnerable coastal metropolitan areas in the world. In these places the certainty of sea level rise is measurable with impacts, empirically observable, that will continue to increase regardless of any climate change mitigation.1 The cities of the subtropics share a series of paradoxes relating to climate, resources, environment, and culture. As the subtropical climate entices new residents and visitors there are increasing costs associated with urban infrastructure and the ravages of violent weather. The carefree lifestyle of subtropical cities is increasingly dependent on scarce water and energy resources and the flow of tangible goods that support a trade economy. The natural environment is no longer exploitable as the survival of the human environment is contingent upon the ability of natural ecosystems to absorb the impact of human actions. The quality of subtropical living is challenged by the mounting pressures of population growth and rapid urbanization yet urban form and contemporary building design fail to take advantage of the subtropical zone’s natural attributes of abundant sunshine, cooling breezes and warm temperatures. Yet, by building a global network of local knowledge, subtropical cities like Brisbane, the City of Gold Coast and Fort Lauderdale, are confidently leading the way with innovative and inventive solutions for building resiliency and adaptation to climate change. The Centre for Subtropical Design at Queensland University of Technology organized the first international Subtropical Cities conference in Brisbane, Australia, where the “fault-­‐lines” of subtropical cities at breaking points were revealed. The second conference, held in 2008, shed a more optimistic light with the theme "From fault-­‐lines to sight-­‐lines -­‐ subtropical urbanism in 20-­‐20" highlighting the leadership exemplified in the vitality of small and large works from around the subtropical world. Yet beyond these isolated local actions the need for more cooperation and collaboration was identified as the key to moving beyond the problems of the present and foreseeable future. The spirit of leadership and collaboration has taken on new force, as two institutions from opposite sides of the globe joined together to host the 3rd international conference Subtropical Cities 2011 -­‐ Subtropical Urbanism: Beyond Climate Change. The collaboration between Florida Atlantic University and the Queensland University of Technology to host this conference, for the first time in the United States, forges a new direction in international cooperative research to address urban design solutions that support sustainable behaviours, resiliency and adaptation to sea level rise, green house gas (GHG) reduction, and climate change research in the areas of architecture and urban design, planning, and public policy. With southeast Queensland and southern Florida as contributors to this global effort among subtropical urban regions that share similar challenges, opportunities, and vulnerabilities our mutual aim is to advance the development and application of local knowledge to the global problems we share. The conference attracted over 150 participants from four continents. Presentations by authors were organized into three sub-­‐themes: Cultural/Place Identity, Environment and Ecology, and Social Economics. Each of the 22 papers presented underwent a double-­‐blind peer review by a panel of international experts among the disciplines and research areas represented. The Centre for Subtropical Design at the Queensland University of Technology is leading Australia in innovative environmental design with a multi-­‐disciplinary focus on creating places that are ‘at home’ in the warm humid subtropics. The Broward Community Design Collaborative at Florida Atlantic University's College for Design and Social Inquiry has built an interdisciplinary collaboration that is unique in the United States among the units of Architecture, Urban and Regional Planning, Social Work, Public Administration, together with the College of Engineering and Computer Science, the College of Science, and the Center for Environmental Studies, to engage in funded action research through design inquiry to solve the problems of development for urban resiliency and environmental sustainment. As we move beyond debates about climate change -­‐ now acting upon us -­‐ the subtropical urban regions of the world will continue to convene to demonstrate the power of local knowledge against global forces, thereby inspiring us as we work toward everyday engagement and action that can make our cities more livable, equitable, and green.

An individual-based versus group-based exercise and counselling intervention for improving quality of life in breast cancer survivors. A feasibility and efficacy study

Background Cancer and its treatments produce lingering side-effects that undermine the quality of life (QOL) of survivors. Exercise and psycho-therapies increase QOL among survivors, however, research is needed to identify intervention characteristics most associated with such improvements. Objective This research aimed to assess the feasibility of a 9 week individual or group based exercise and counselling program, and to examine if a group based intervention is as effective at improving the QOL of breast cancer survivors as an individual-based intervention. Methods A three group design was implemented to compare the efficacy of a 9 week individual (IEC n = 12) and group based exercise and counselling (GEC n = 14) intervention to a usual care (UsC n = 10) group on QOL of thirty-six breast cancer survivors. Results Across all groups, 90% of participants completed the interventions, with no adverse effects documented. At the completion of the intervention, there was a significant difference between groups for change in global QOL across time (p < 0.023), with IEC improving significantly more (15.0 points) than the UsC group (1.8 points). The effect size was moderate (0.70). Although the GEC improved QOL by almost 10.0 points, this increase did not reach significance. Both increases were above the minimally important difference of 7–8 points. Conclusion These preliminary results suggest a combined exercise and psychological counseling program is both a feasible and acceptable intervention for breast cancer survivors. Whilst both the individual and group interventions improved QOL above the clinically important difference, only the individual based intervention was significant when compared to UsC.