Candidate gene association studies : a comprehensive guide to useful in silico tools

The candidate gene approach has been a pioneer in the field of genetic epidemiology, identifying risk alleles and their association with clinical traits. With the advent of rapidly changing technology, there has been an explosion of in silico tools available to researchers, giving them fast, efficient resources and reliable strategies important to find casual gene variants for candidate or genome wide association studies (GWAS). In this review, following a description of candidate gene prioritisation, we summarise the approaches to single nucleotide polymorphism (SNP) prioritisation and discuss the tools available to assess functional relevance of the risk variant with consideration to its genomic location. The strategy and the tools discussed are applicable to any study investigating genetic risk factors associated with a particular disease. Some of the tools are also applicable for the functional validation of variants relevant to the era of GWAS and next generation sequencing (NGS).

Caffeine ingestion and cycling power output in a low or normal muscle glycogen state

Purpose Commencing selected workouts with low muscle glycogen availability augments several markers of training adaptation compared with undertaking the same sessions with normal glycogen content. However, low glycogen availability reduces the capacity to perform high-intensity (>85% of peak aerobic power (V·O2peak)) endurance exercise. We determined whether a low dose of caffeine could partially rescue the reduction in maximal self-selected power output observed when individuals commenced high-intensity interval training with low (LOW) compared with normal (NORM) glycogen availability. Methods Twelve endurance-trained cyclists/triathletes performed four experimental trials using a double-blind Latin square design. Muscle glycogen content was manipulated via exercise–diet interventions so that two experimental trials were commenced with LOW and two with NORM muscle glycogen availability. Sixty minutes before an experimental trial, subjects ingested a capsule containing anhydrous caffeine (CAFF, 3 mg-1·kg-1 body mass) or placebo (PLBO). Instantaneous power output was measured throughout high-intensity interval training (8 × 5-min bouts at maximum self-selected intensity with 1-min recovery). Results There were significant main effects for both preexercise glycogen content and caffeine ingestion on power output. LOW reduced power output by approximately 8% compared with NORM (P < 0.01), whereas caffeine increased power output by 2.8% and 3.5% for NORM and LOW, respectively, (P < 0.01). Conclusion We conclude that caffeine enhanced power output independently of muscle glycogen concentration but could not fully restore power output to levels commensurate with that when subjects commenced exercise with normal glycogen availability. However, the reported increase in power output does provide a likely performance benefit and may provide a means to further enhance the already augmented training response observed when selected sessions are commenced with reduced muscle glycogen availability. It has long been known that endurance training induces a multitude of metabolic and morphological adaptations that improve the resistance of the trained musculature to fatigue and enhance endurance capacity and/or exercise performance (13). Accumulating evidence now suggests that many of these adaptations can be modified by nutrient availability (9–11,21). Growing evidence suggests that training with reduced muscle glycogen using a “train twice every second day” compared with a more traditional “train once daily” approach can enhance the acute training response (29) and markers representative of endurance training adaptation after short-term (3–10 wk) training interventions (8,16,30). Of note is that the superior training adaptation in these previous studies was attained despite a reduction in maximal self-selected power output (16,30). The most obvious factor underlying the reduced intensity during a second training bout is the reduction in muscle glycogen availability. However, there is also the possibility that other metabolic and/or neural factors may be responsible for the power drop-off observed when two exercise bouts are performed in close proximity. Regardless of the precise mechanism(s), there remains the intriguing possibility that the magnitude of training adaptation previously reported in the face of a reduced training intensity (Hulston et al. (16) and Yeo et al.) might be further augmented, and/or other aspects of the training stimulus better preserved, if power output was not compromised. Caffeine ingestion is a possible strategy that might “rescue” the aforementioned reduction in power output that occurs when individuals commence high-intensity interval training (HIT) with low compared with normal glycogen availability. Recent evidence suggests that, at least in endurance-based events, the maximal benefits of caffeine are seen at small to moderate (2–3 mg·kg-1 body mass (BM)) doses (for reviews, see Refs. (3,24)). Accordingly, in this study, we aimed to determine the effect of a low dose of caffeine (3 mg·kg-1 BM) on maximal self-selected power output during HIT commenced with either normal (NORM) or low (LOW) muscle glycogen availability. We hypothesized that even under conditions of low glycogen availability, caffeine would increase maximal self-selected power output and thereby partially rescue the reduction in training intensity observed when individuals commence HIT with low glycogen availability.

Studies on the clarification of juice from whole sugar cane crop

In the sugar industry, processing juice derived from the whole sugar cane plant adversely affects the yield and quality of the product sugar. Dr Thai investigated the aggregation behaviour of sugar cane juice particles and developed strategies to improve the removal of non-sucrose impurities.

Studies of the phase evolution of YBCO materials with different additives

Y123 samples with varying amounts of added Y211, PtO 2 and CeO 2 have been melt processed and quenched from temperatures between 960°C and 1100°C. The microstructures of the quenched samples have been characterized using a combination of x-ray diffractometry, optical microscopy, scanning electron microscopy, microprobe analysis, energy-dispersive x-ray spectroscopy and wavelength-dispersive x-ray spectroscopy. The Ba-Cu-O-rich melt undergoes complex changes as a function of temperature and time. A region of stability of BaCuO 2 (BC1) and BaCu 2O 2 (BC2) exists below 1040°C in samples of Y123 + 20 mol% Y211. Ba 2Cu 3O 5 is stabilized by rapid quenching but appears to separate into BC1 and BC2 at lower quenching rates. PtO 2 and CeO 2 additions affect the distribution and volume fractions of the two Ba-Cu-oxide phases.

The molecular bases of training adaptation

Skeletal muscle is a malleable tissue capable of altering the type and amount of protein in response to disruptions to cellular homeostasis. The process of exercise-induced adaptation in skeletal muscle involves a multitude of signalling mechanisms initiating replication of specific DNA genetic sequences, enabling subsequent translation of the genetic message and ultimately generating a series of amino acids that form new proteins. The functional consequences of these adaptations are determined by training volume, intensity and frequency, and the half-life of the protein. Moreover, many features of the training adaptation are specific to the type of stimulus, such as the mode of exercise. Prolonged endurance training elicits a variety of metabolic and morphological changes, including mitochondrial biogenesis, fast-to-slow fibre-type transformation and substrate metabolism. In contrast, heavy resistance exercise stimulates synthesis of contractile proteins responsible for muscle hypertrophy and increases in maximal contractile force output. Concomitant with the vastly different functional outcomes induced by these diverse exercise modes, the genetic and molecular mechanisms of adaptation are distinct. With recent advances in technology, it is now possible to study the effects of various training interventions on a variety of signalling proteins and early-response genes in skeletal muscle. Although it cannot presently be claimed that such scientific endeavours have influenced the training practices of elite athletes, these new and exciting technologies have provided insight into how current training techniques result in specific muscular adaptations, and may ultimately provide clues for future and novel training methodologies. Greater knowledge of the mechanisms and interaction of exercise-induced adaptive pathways in skeletal muscle is important for our understanding of the aetiology of disease, maintenance of metabolic and functional capacity with aging, and training for athletic performance. This article highlights the effects of exercise on molecular and genetic mechanisms of training adaptation in skeletal muscle.

Fully Bayesian experimental design for pharmacokinetic studies

Utility functions in Bayesian experimental design are usually based on the posterior distribution. When the posterior is found by simulation, it must be sampled from for each future data set drawn from the prior predictive distribution. Many thousands of posterior distributions are often required. A popular technique in the Bayesian experimental design literature to rapidly obtain samples from the posterior is importance sampling, using the prior as the importance distribution. However, importance sampling will tend to break down if there is a reasonable number of experimental observations and/or the model parameter is high dimensional. In this paper we explore the use of Laplace approximations in the design setting to overcome this drawback. Furthermore, we consider using the Laplace approximation to form the importance distribution to obtain a more efficient importance distribution than the prior. The methodology is motivated by a pharmacokinetic study which investigates the effect of extracorporeal membrane oxygenation on the pharmacokinetics of antibiotics in sheep. The design problem is to find 10 near optimal plasma sampling times which produce precise estimates of pharmacokinetic model parameters/measures of interest. We consider several different utility functions of interest in these studies, which involve the posterior distribution of parameter functions.

Curriculum renewal in legal education

This project investigated ways in which the learning experience for students in Australian law schools could be enhanced by renewing final year legal curriculum through the design of effective capstone experiences to close the loop on tertiary legal studies and better prepare students for a smooth transition into the world of work and professional practice. Key project outcomes are a set of final year curriculum design principles and a transferable model for an effective final year program – a final year Toolkit comprising a range of templates, models and specific capstone examples for adoption or adaptation by legal educators. The project found that the efficacy of capstone experiences is affected by the curriculum context within which they are offered. For this reason, a number of ‘favourable conditions’, which promote the effectiveness of capstone experiences, have also been identified. The project’s final year principles and Toolkit promote program coherence and integration, should increase student satisfaction and levels of engagement with their experience of legal education and make a valuable contribution to assurance of learning in the new Tertiary Education Quality and Standards Agency (TEQSA) environment. From the point of view of the student experience, the final year principles and models address the current fragmented approach to final year legal curricula design and delivery. The knowledge and research base acquired under the auspices of this project is of both discipline and national importance as the project’s outcomes are transferable and have the potential to significantly influence the quality and coherence of the program experience of final year students in other tertiary disciplines, both within Australia and beyond. Project outcomes and deliverables are available on both the project’s website http://wiki.qut.edu.au/display/capstone/Home and on the Law Capstone Experience Forum website http://www.lawcapstoneexperience.com/. In the course of developing its deliverables, the project found that the design of capstone experiences varies significantly within and across disciplines; different frameworks may be used (for example, a disciplinary or inter-disciplinary focus, or to satisfy professional accreditation requirements), rationales and objectives may differ, and a variety of models utilised (for example, an integrated final year program, a single subject, a suite of subjects, or modules within several subjects). Broadly however, capstone experiences should provide final year students with an opportunity both to look back over their academic learning, in an effort to make sense of what they have accomplished, and to look forward to their professional and personal futures that build on that foundational learning.

Higher harmonic large-amplitude fourier transformed alternating current voltammetry : analytical attributes derived from studies of the oxidation of ferrocenemethanol and uric acid at a glassy carbon electrode

An analytical evaluation of the higher ac harmonic components derived from large amplitude Fourier transformed voltammetry is provided for the reversible oxidation of ferrocenemethanol (FcMeOH) and oxidation of uric acid by an EEC mechanism in a pH 7.4 phosphate buffer at a glassy carbon (GC) electrode. The small background current in the analytically optimal fifth harmonic is predominantly attributed to faradaic current associated with the presence of electroactive functional groups on the GC electrode surface, rather than to capacitive current which dominates the background in the dc, and the initial three ac harmonics. The detection limits for the dc and the first to fifth harmonic ac components are 1.9, 5.89, 2.1, 2.5, 0.8, and 0.5 µM for FcMeOH, respectively, using a sine wave modulation of 100 mV at 21.46 Hz and a dc sweep rate of 111.76 mV s−1. Analytical performance then progressively deteriorates in the sixth and higher harmonics. For the determination of uric acid, the capacitive background current was enhanced and the reproducibility lowered by the presence of surface active uric acid, but the rapid overall 2e− rather than 1e– electron transfer process gives rise to a significantly enhanced fifth harmonic faradaic current which enabled a detection limit of 0.3 µM to be achieved which is similar to that reported using chemically modified electrodes. Resolution of overlapping voltammetric signals for a mixture of uric acid and dopamine is also achieved using higher fourth or fifth harmonic components, under very low background current conditions. The use of higher fourth and fifth harmonics exhibiting highly favorable faradaic to background (noise) current ratios should therefore be considered in analytical applications under circumstances where the electron transfer rate is fast.

Experimental studies of hollow flange channel beams subject to combined bending and shear actions

This paper presents the details of an experimental study of a cold-formed steel hollow flange channel beam known as LiteSteel Beam (LSB) subject to combined bending and shear actions. The LSB sections are produced by a patented manufacturing process involving simultaneous cold-forming and electric resistance welding. Due to the geometry of the LSB, as well as its unique residual stress characteristics and initial geometric imperfections resultant of manufacturing processes, much of the existing research for common cold-formed steel sections is not directly applicable to LSB. Experimental and numerical studies have been carried out to evaluate the behaviour and design of LSBs subject to pure bending actions and predominant shear actions. To date, however, no investigation has been conducted into the strength of LSB sections under combined bending and shear actions. Combined bending and shear is especially prevalent at the supports of continuous span and cantilever beams, where the interaction of high shear force and bending moment can reduce the capacity of a section to well below that for the same section subject only to pure shear or moment. Hence experimental studies were conducted to assess the combined bending and shear behaviour and strengths of LSBs. Eighteen tests were conducted and the results were compared with current AS/NZS 4600 and AS 4100 design rules. AS/NZS 4600 design rules were shown to grossly underestimate the combined bending and shear capacities of LSBs and hence two lower bound design equations were proposed based on experimental results. Use of these equations will significantly improve the confidence and cost-effectiveness of designing LSBs for combined bending and shear actions.

Rural self-reliance: the impact on health experiences of people living with type II diabetes in rural Queensland, Australia

Objective: The objective of the study was to explore whether and how rural culture influences type II diabetes management and to better understand the social processes that rural people construct in coping with diabetes and its complications. In particular, the study aimed to analyse the interface and interactions between rural people with type II diabetes and the Australian health care system, and to develop a theoretical understanding that reflects constructs that may be more broadly applicable. Methods: The study applied constructivist grounded theory methods within an interpretive interactionist framework. Data from 39 semi-structured interviews with rural and urban type II diabetes patients and a mix of rural health care providers were analysed to develop a theoretical understanding of the social processes that define diabetes management in that context. Results: The analysis suggests that although type II diabetes imposes limitations that require adjustment and adaptation, these processes are actively negotiated by rural people within the environmental context to fit the salient social understandings of autonomy and self-reliance. Thus, people normalized self-reliant diabetes management behaviours because this was congruent with the rural culture. Factors that informed the actions of normalization were relationships between participants and health care professionals, support, and access to individual resources. Conclusions: The findings point to ways in which rural self-reliance is conceived as the primary strategy of diabetes management. People face the paradox of engaging with a health care system that at the same time maximizes individual responsibility for health and minimizes the social support by which individuals manage the condition. The emphasis on self-reliance gives some legitimacy to a lack of prevention and chronic care services. Success of diabetes management behaviours is, however, contingent on relative resources. Where there is good primary care, there develops a number of downstream effects including a sense of empowerment to manage difficult rural environmental circumstances. This has particular bearing on health outcomes for people with fewer resources.

A Sustainable Community for Older People : Case Studies of Green Retirement Villages in Australia

In Australia, the proportion of the population aged 65 years and over reached 13.5% in 2010 and is expected to increase steadily to around 20% by the year 2056 [Australia Bureau of Statistics (ABS), 2010], creating what has been regarded as a looming crisis in how to house and care for older people. As a viable accommodation option, the retirement village is widely accepted as a means of promoting and enhancing independence, choice and quality of life for older people. Recent research by Barker (2010) indicates that the current and potential residents of retirement villages are generally very conscious of resource consumption and would like their residences and community to be more sustainable. The aim of this study was to understand the perception of older people toward sustainability ideas and identify the sustainable practices involved in retirement villages to improve the wellbeing of residents. Multiple research methods, including content analysis, questionnaire survey, interviews and case studies were conducted for the research purpose. The results indicate that most retirement village residents understand and recognize the importance of sustainability in their lifestyle. However, their sustainability requirements need to be supported and enhanced by the provision of affordable sustainability features. Additionally, many retirement village developers and operators realize the importance of providing a sustainable retirement community for their residents, and that a sustainable retirement village (that is environmental-friendly, affordable, and improves social engagement) can be achieved through the consideration of project planning, design, construction, and operations throughout the project life cycle. The clear shift from healthcare to lifestyle-focused services in the recent development of retirement villages together with the increasing number of aged people moving into retirement villages (Simpson and Cheney, 2007) has raised awareness of the need for the retirement village industry to provide a sustainable community for older people to improve their life quality after retirement. This is the first critical study of sustainable development in the retirement village industry and its potential in addressing the housing needs of older people, providing a contribution towards improving the life quality of older people and with direct and immediate significance to the community as a whole.

Incorporating translation in qualitative studies : two case studies in education

Cross-language qualitative research in education continues to increase. However, there has been inadequate discussion in the literature concerning the translation process that ensures research trustworthiness applicable for bilingual researchers. Informed by the literature on evaluation criteria for qualitative data translation, this paper compares two different procedures for incorporating translation in education qualitative research to provide a clear depiction of the complexities involved in translating qualitative data and the strengths and weaknesses of each procedure. To maintain the trustworthiness of the qualitative research, it is necessary to minimise translation errors, provide detailed accounts of the translation process, involve more than one translator and remain open to scrutiny from those seeking to access the translation process. Taking into account the resource constraints often faced by novice qualitative researchers, this paper provides some strategies that can be employed in similar contexts.