Some comparison on whole-proteome phylogeny of large dsDNA viruses based on dynamical language approach and feature frequency profiles method

There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among them, CVTree method, feature frequency profiles method and dynamical language approach were used to investigate the whole-proteome phylogeny of large dsDNA viruses. Using the data set of large dsDNA viruses from Gao and Qi (BMC Evol. Biol. 2007), the phylogenetic results based on the CVTree method and the dynamical language approach were compared in Yu et al. (BMC Evol. Biol. 2010). In this paper, we first apply dynamical language approach to the data set of large dsDNA viruses from Wu et al. (Proc. Natl. Acad. Sci. USA 2009) and compare our phylogenetic results with those based on the feature frequency profiles method. Then we construct the whole-proteome phylogeny of the larger dataset combining the above two data sets. According to the report of The International Committee on the Taxonomy of Viruses (ICTV), the trees from our analyses are in good agreement to the latest classification of large dsDNA viruses.

Teaching Reflective Learning in Higher Education : A Systematic Approach Using Pedagogic Patterns

This book is about understanding the nature and application of reflection in higher education. It provides a theoretical model to guide the implementation of reflective learning and reflective practice across multiple disciplines and international contexts in higher education. The book presents research into the ways in which reflection is both considered and implemented in different ways across different professional disciplines, while maintaining a common purpose to transform and improve learning and/or practice. Readers will find this book innovative and new in three key ways. First, in its holistic theorisation of reflection within the pedagogic field of higher education; Secondly, in conceptualising reflection in different modes to achieve specific purposes in different disciplines; and finally, in providing conceptual guidance for embedding reflective learning and reflective practice in a systematic way across whole programmes, faculties or institutions in higher education. The book considers important contextual factors that influence the teaching of forms and methods of reflection. It provides a functional analysis of multiple modes of reflection, including written, oral, visual, auditory, and embodied forms. Empirical chapters analyse the application of these modes across disciplines and at different stages of a programme. The theoretical model accounts for students’ stage of development in the disciplinary field, along with progressive and cyclical levels of higher order thinking, and learning and professional practice that are expected within different disciplines and professional fields. The book provides: • A conceptual model for the application of reflection across disciplines in a variety of contexts. • Empirical examples of different modes and pedagogic patterns for reflection. • Guidance and support for embedding systemic pedagogical and curriculum change.

Developing and evaluating interventions that are applicable and relevant to inpatients and those who care for them; a multiphase, pragmatic action research approach

Background Randomised controlled trials may be of limited use to evaluate the multidisciplinary and multimodal interventions required to effectively treat complex patients in routine clinical practice; pragmatic action research approaches may provide a suitable alternative. Methods A multiphase, pragmatic, action research based approach was developed to identify and overcome barriers to nutritional care in patients admitted to a metropolitan hospital hip-fracture unit. Results Four sequential action research cycles built upon baseline data including 614 acute hip-fracture inpatients and 30 purposefully sampled clinicians. Reports from Phase I identified barriers to nutrition screening and assessment. Phase II reported post-fracture protein-energy intakes and intake barriers. Phase III built on earlier results; an explanatory mixed-methods study expanded and explored additional barriers and facilitators to nutritional care. Subsequent changes to routine clinical practice were developed and implemented by the treating team between Phase III and IV. These were implemented as a new multidisciplinary, multimodal nutritional model of care. A quasi-experimental controlled, ‘before-and-after’ study was then used to compare the new model of care with an individualised nutritional care model. Engagement of the multidisciplinary team in a multiphase, pragmatic action research intervention doubled energy and protein intakes, tripled return home discharge rates, and effected a 75% reduction in nutritional deterioration during admission in a reflective cohort of hip-fracture inpatients. Conclusions This approach allowed research to be conducted as part of routine clinical practice, captured a more representative patient cohort than previously reported studies, and facilitated exploration of barriers and engagement of the multidisciplinary healthcare workers to identify and implement practical solutions. This study demonstrates substantially different findings to those previously reported, and is the first to demonstrate that multidisciplinary, multimodal nutrition care reduces intake barriers, delivers a higher proportional increase in protein and energy intake compared with baseline than other published intervention studies, and improves patient outcomes when compared with individualised nutrition care. The findings are considered highly relevant to clinical practice and have high translation validity. The authors strongly encourage the development of similar study designs to investigate complex health problems in elderly, multi-morbid patient populations as a way to evaluate and change clinical practice.

Using personal construct theory and narrative methods to facilitate reflexive constructions of teaching physical education

This paper reports on two lengthy studies in Physical education teacher education (PETE) conducted independently but which are epistemologically and methodologically linked. The paper describes how personal construct theory (PCT) and its associated methods provided a means for PETE students to reflexively construct their ideas about teaching physical education over an extended period. Data are drawn from each study in the form of a story of a single participant to indicate how this came about. Furthermore we suggest that PCT might be both a useful research strategy and an effective approach to facilitate professional development in a teacher education setting.

Finite volume methods for simulating anomalous transport

In this thesis a new approach for solving a certain class of anomalous diffusion equations was developed. The theory and algorithms arising from this work will pave the way for more efficient and more accurate solutions of these equations, with applications to science, health and industry. The method of finite volumes was applied to discretise the spatial derivatives, and this was shown to outperform existing methods in several key respects. The stability and convergence of the new method were rigorously established.

Identifying risk factors and protective factors for venous leg ulcer recurrence using a theoretical approach : a longitudinal study

Background The high recurrence rate of chronic venous leg ulcers has a significant impact on an individual’s quality of life and healthcare costs. Objectives This study aimed to identify risk and protective factors for recurrence of venous leg ulcers using a theoretical approach by applying a framework of self and family management of chronic conditions to underpin the study. Design Secondary analysis of combined data collected from three previous prospective longitudinal studies. Setting The contributing studies’ participants were recruited from two metropolitan hospital outpatient wound clinics and three community-based wound clinics. Participants Data were available on a sample of 250 adults, with a leg ulcer of primarily venous aetiology, who were followed after ulcer healing for a median follow-up time of 17 months after healing (range: 3 to 36 months). Methods Data from the three studies were combined. The original participant data were collected through medical records and self-reported questionnaires upon healing and every 3 months thereafter. A Cox proportion-hazards regression analysis was undertaken to determine the influential factors on leg ulcer recurrence based on the proposed conceptual framework. Results The median time to recurrence was 42 weeks (95% CI 31.9–52.0), with an incidence of 22% (54 of 250 participants) recurrence within three months of healing, 39% (91 of 235 participants) for those who were followed for six months, 57% (111 of 193) by 12 months, 73% (53 of 72) by two years and 78% (41 of 52) of those who were followed up for three years. A Cox proportional-hazards regression model revealed that the risk factors for recurrence included a history of deep vein thrombosis (HR 1.7, 95% CI 1.07–2.67, p=0.024), history of multiple previous leg ulcers (HR 4.4, 95% CI 1.84–10.5, p=0.001), and longer duration (in weeks) of previous ulcer (HR 1.01, 95% CI 1.003–1.01, p<0.001); while the protective factors were elevating legs for at least 30 minutes per day (HR 0.33, 95% CI 0.19–0.56, p<0.001), higher levels of self-efficacy (HR 0.95, 95% CI 0.92–0.99, p=0.016), and walking around for at least three hours/day (HR 0.66, 95% CI 0.44–0.98, p=0.040). Conclusions Results from this study provide a comprehensive examination of risk and protective factors associated with leg ulcer recurrence based on the chronic disease self and family management framework. These results in turn provide essential steps towards developing and testing interventions to promote optimal prevention strategies for venous leg ulcer recurrence.

Evolution of the docklands food hub : a design-led innovation approach to food sovereignty through local food systems

Access to nutritious, safe and culturally appropriate food is a basic human right (Mechlem, 2004). Food sovereignty defines this right through the empowerment of the people to redefine food and agricultural systems, and through ecologically sustainable production methods. At the heart of the food sovereignty movement are the interests of producers, distributors and consumers, rather than the interests of markets and corporations, which dominate the current globalized food system (Hinrichs, 2003). Food sovereignty challenges designers to enable people to innovate the food system. We are yet to develop economically viable solutions for scaling projects and providing citizens, governments and business with tools to develop and promote projects to innovate food systems and promote food sovereignty (Meroni, 2011; Murray, Caulier-Grice and Mulgan, 2010). This article examines how a design-led approach to innovation can assist in the development of new business models and ventures for local food systems: this is presented through an emerging field of research ‘Design-Led Food Communities’. Design-Led Food Communities enables citizens, governments and business to innovate local food projects through the application of design. This article reports on the case study of the Docklands Food Hub Project in Melbourne, Australia. Preliminary findings demonstrate valued outcomes, but also a deficiency in the design process to generate food solutions collaboratively between government, business and citizens.

Locally weighted learning methods for non-rigid robot control

This thesis develops a novel approach to robot control that learns to account for a robot's dynamic complexities while executing various control tasks using inspiration from biological sensorimotor control and machine learning. A robot that can learn its own control system can account for complex situations and adapt to changes in control conditions to maximise its performance and reliability in the real world. This research has developed two novel learning methods, with the aim of solving issues with learning control of non-rigid robots that incorporate additional dynamic complexities. The new learning control system was evaluated on a real three degree-of-freedom elastic joint robot arm with a number of experiments: initially validating the learning method and testing its ability to generalise to new tasks, then evaluating the system during a learning control task requiring continuous online model adaptation.

An agent-based approach to immune modelling

This study focuses on trying to understand why the range of experience with respect to HIV infection is so diverse, especially as regards to the latency period. The challenge is to determine what assumptions can be made about the nature of the experience of antigenic invasion and diversity that can be modelled, tested and argued plausibly. To investigate this, an agent-based approach is used to extract high-level behaviour which cannot be described analytically from the set of interaction rules at the cellular level. A prototype model encompasses local variation in baseline properties contributing to the individual disease experience and is included in a network which mimics the chain of lymphatic nodes. Dealing with massively multi-agent systems requires major computational efforts. However, parallelisation methods are a natural consequence and advantage of the multi-agent approach. These are implemented using the MPI library.

Informing methods for preparing public health overviews of reviews: a comparison of public health overviews with Cochrane Overviews published between 1999 and 2014

Background: Overviews of systematic reviews (SRs) are useful for public health policy; however there is an absence of Cochrane Overviews covering public health (PH) topics. Objectives: We sought to analyze the methodological approaches used in existing Cochrane Overviews and Protocols for overviews (primarily clinical in nature), and compare these to the methods and approaches used in PH overviews (non-Cochrane). The intent was to identify issues that would be relevant for undertaking Cochrane overviews. Methods: We conducted a descriptive analysis of overviews published between 1999 and 2014. We searched the Cochrane Database of Systematic Reviews for Cochrane Protocols for overviews and Cochrane Overviews, and the HealthEvidence.org for PH overviews. The primary characteristics of the overviews and elements of the methodology were extracted and compared. Results: A total of 61 overviews of SRs were included in our analysis; specifically, this included 21 Cochrane Protocols for overviews, 15 Cochrane Overviews, and 27 non-Cochrane PH overviews. Amongst the overviews, the most significant differences are that PH overviews (non-Cochrane) tend to: include earlier and more reviews, greater number of participants, allow lower levels of evidence, use assessment tools other than AMSTAR (A Measurement Tool to Assess Systematic Reviews, i.e. a tool for assessing quality of SRs), not assess quality of evidence in reviews, search more databases overall, specify search limits including English-only reviews, and not consider recent primary studies for inclusion. Some of these differences clearly related to quality, however many relate to the nuances of PH interventions. Conclusions: The methodology in Cochrane overviews and PH overviews varies widely. Future PH overviews may benefit from the Cochrane methodology but the Cochrane approach requires modification to accommodate PH research methodology. Additionally, the use of databases that pre-screen and quality assess relevant PH systematic reviews may help expedite the search process.

A ‘Big Data’ Approach to Mapping the Australian Twittersphere

This chapter discusses the methodological aspects and empirical findings of a large-scale, funded project investigating public communication through social media in Australia. The project concentrates on Twitter, but we approach it as representative of broader current trends toward the integration of large datasets and computational methods into media and communication studies in general, and social media scholarship in particular. The research discussed in this chapter aims to empirically describe networks of affiliation and interest in the Australian Twittersphere, while reflecting on the methodological implications and imperatives of ‘big data’ in the humanities. Using custom network crawling technology, we have conducted a snowball crawl of Twitter accounts operated by Australian users to identify more than one million users and their follower/followee relationships, and have mapped their interconnections. In itself, the map provides an overview of the major clusters of densely interlinked users, largely centred on shared topics of interest (from politics through arts to sport) and/or sociodemographic factors (geographic origins, age groups). Our map of the Twittersphere is the first of its kind for the Australian part of the global Twitter network, and also provides a first independent and scholarly estimation of the size of the total Australian Twitter population. In combination with our investigation of participation patterns in specific thematic hashtags, the map also enables us to examine which areas of the underlying follower/followee network are activated in the discussion of specific current topics – allowing new insights into the extent to which particular topics and issues are of interest to specialised niches or to the Australian public more broadly. Specifically, we examine the Twittersphere footprint of dedicated political discussion, under the #auspol hashtag, and compare it with the heightened, broader interest in Australian politics during election campaigns, using #ausvotes; we explore the different patterns of Twitter activity across the map for major television events (the popular competitive cooking show #masterchef, the British #royalwedding, and the annual #stateoforigin Rugby League sporting contest); and we investigate the circulation of links to the articles published by a number of major Australian news organisations across the network. Such analysis, which combines the ‘big data’-informed map and a close reading of individual communicative phenomena, makes it possible to trace the dynamic formation and dissolution of issue publics against the backdrop of longer-term network connections, and the circulation of information across these follower/followee links. Such research sheds light on the communicative dynamics of Twitter as a space for mediated social interaction. Our work demonstrates the possibilities inherent in the current ‘computational turn’ (Berry, 2010) in the digital humanities, as well as adding to the development and critical examination of methodologies for dealing with ‘big data’ (boyd and Crawford, 2011). Out tools and methods for doing Twitter research, released under Creative Commons licences through our project Website, provide the basis for replicable and verifiable digital humanities research on the processes of public communication which take place through this important new social network.

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).

Influencers on quality of life as reported by people living with dementia in long-term care: A descriptive exploratory approach

Background Over half of the residents in long-term care have a diagnosis of dementia. Maintaining quality of life is important, as there is no cure for dementia. Quality of life may be used as a benchmark for caregiving, and can help to enhance respect for the person with dementia and to improve care provision. The purpose of this study was to describe quality of life as reported by people living with dementia in long-term care in terms of the influencers of, as well as the strategies needed, to improve quality of life. Methods A descriptive exploratory approach. A subsample of twelve residents across two Australian states from a national quantitative study on quality of life was interviewed. Data were analysed thematically from a realist perspective. The approach to the thematic analysis was inductive and data-driven. Results Three themes emerged in relation to influencers and strategies related to quality of life: (a) maintaining independence; (b) having something to do, and; (c) the importance of social interaction. Conclusions The findings highlight the importance of understanding individual resident needs and consideration of the complexity of living in large group living situations, in particular in regard to resident decision-making.

A novel approach to increasing inventory with the current panel: Increasing donation frequency by asking for a different blood product

BACKGROUND Ongoing shortages of blood products may be addressed through additional donations. However, donation frequency rates are typically lower than medically possible. This preliminary study aims to determine voluntary nonremunerated whole blood (WB) and plasmapheresis donors' willingness, and subsequent facilitators and barriers, to make additional donations of a different type. STUDY DESIGN AND METHODS Forty individual telephone interviews were conducted posing two additional donation pattern scenarios: first, making a single and, second, making multiple plasmapheresis donations between WB donations. Stratified purposive sampling was conducted for four samples varying in donation experience: no-plasma, new-to-both-WB-and-plasma, new-to-plasma, and plasma donors. Interviews were analyzed yielding excellent (κ values > 0.81) inter-rater reliability. RESULTS Facilitators were more endorsed than barriers for a single but not multiple plasmapheresis donation. More new-to-both donors (n = 5) were willing to make multiple plasma donations between WB donations than others (n = 1 each) and identified fewer barriers (n = 3) than those more experienced in donation (n = 8 no plasma, n = 10 new to both, n = 11 plasma). Donors in the plasma sample were concerned about the subsequent reduced time between plasma donations by adding WB donations (n = 3). The no-plasma and new-to-plasma donors were concerned about the time commitment required (n = 3). CONCLUSION Current donors are willing to add different product donations but donation history influences their willingness to change. Early introduction of multiple donation types, variation in inventory levels, and addressing barriers will provide blood collection agencies with a novel and cost-effective inventory management strategy.

Structural optimization approach for specially shaped composite tank in spacecrafts

This study proposes an optimized approach of designing in which a model specially shaped composite tank for spacecrafts is built by applying finite element analysis. The composite layers are preliminarily designed by combining quasi-network design method with numerical simulation, which determines the ratio between the angle and the thickness of layers as the initial value of the optimized design. By adopting an adaptive simulated annealing algorithm, the angles and the numbers of layers at each angle are optimized to minimize the weight of structure. Based on this, the stacking sequence of composite layers is formulated according to the number of layers in the optimized structure by applying the enumeration method and combining the general design parameters. Numerical simulation is finally adopted to calculate the buckling limit of tanks in different designing methods. This study takes a composite tank with a cone-shaped cylinder body as example, in which ellipsoid head section and outer wall plate are selected as the object to validate this method. The result shows that the quasi-network design method can improve the design quality of composite material layer in tanks with complex preliminarily loading conditions. The adaptive simulated annealing algorithm can reduce the initial design weight by 30%, which effectively probes the global optimal solution and optimizes the weight of structure. It can be therefore proved that, this optimization method is capable of designing and optimizing specially shaped composite tanks with complex loading conditions.