Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies

As of June 2009, 361 genome-wide association studies (GWAS) had been referenced by the HuGE database. GWAS require DNA from many thousands of individuals, relying on suitable DNA collections. We recently performed a multiple sclerosis (MS) GWAS where a substantial component of the cases (24%) had DNA derived from saliva. Genotyping was done on the Illumina genotyping platform using the Infinium Hap370CNV DUO microarray. Additionally, we genotyped 10 individuals in duplicate using both saliva- and blood-derived DNA. The performance of blood- versus saliva-derived DNA was compared using genotyping call rate, which reflects both the quantity and quality of genotyping per sample and the “GCScore,” an Illumina genotyping quality score, which is a measure of DNA quality. We also compared genotype calls and GCScores for the 10 sample pairs. Call rates were assessed for each sample individually. For the GWAS samples, we compared data according to source of DNA and center of origin. We observed high concordance in genotyping quality and quantity between the paired samples and minimal loss of quality and quantity of DNA in the saliva samples in the large GWAS sample, with the blood samples showing greater variation between centers of origin. This large data set highlights the usefulness of saliva DNA for genotyping, especially in high-density single-nucleotide polymorphism microarray studies such as GWAS.

Sleepiness : how a biological drive can influence other risky road user behaviours

The Safe System approach to road safety utilises a holistic view of the interactions among vehicles, roads and road users. Yet, the contribution of each of these factors to crashes is vastly different. The role of road users is widely acknowledged as an overwhelming contributor to road crashes. Substantial gains have been made with improvements to vehicle and roads over a number of years. However, improvements of the road user’s behaviour has been (in some cases) less substantial. A road user behaviour that is relatively unregulated is driver sleepiness, which is part of the ‘fatal five’ of risky road user behaviours. The effect of sleepiness is ubiquitous – sleepiness is a state that most, if not all drivers on our roads has experienced, and is habitually exposed to. The quality and quantity of daily sleep is integral to our level of neurobehavioural performance during wakefulness and as such can have a compounding effect on a number of other risky driving behaviours. This paper will discuss the potential influence of sleepiness as an interceding factor for a number of risky driving behaviours. Little effort has been given to increasing awareness of the deleterious and wide ranging effects that sleepiness has on road safety. Given the wide ranging influence of sleepiness, improvements of ‘sleep health’ as a protective factor at the community or individual level could lead to significant reductions in road trauma and increases of general well being. A discussion of potential actions to reduce sleepiness is required if reductions of road trauma are to continue.

Mathematical modelling of soft callus formation in early murine bone repair

Fracture healing is a complicated coupling of many processes. Yet despite the apparent complexity, fracture repair is usually effective. There is, however, no comprehensive mathematical model addressing the multiple interactions of cells, cytokines and oxygen that includes extra-cellular matrix production and that results in the formation of the early stage soft callus. This thesis develops a one dimensional continuum transport model in the context of early fracture healing. Although fracture healing is a complex interplay of many local factors, critical components are identified and used to construct an hypothesis about regulation of the evolution of early callus formation. Multiple cell lines, cellular differentiation, oxygen levels and cytokine concentrations are examined as factors affecting this model of early bone repair. The model presumes diffusive and chemotactic cell migration mechanisms. It is proposed that the initial signalling regime and oxygen availability arising as consequences of bone fracture, are sufficient to determine the quantity and quality of early soft callus formation. Readily available software and purpose written algorithms have been used to obtain numerical solutions representative of various initial conditions. These numerical distributions of cellular populations reflect available histology obtained from murine osteotomies. The behaviour of the numerical system in response to differing initial conditions can be described by alternative in vivo healing pathways. An experimental basis, as illustrated in murine fracture histology, has been utilised to validate the mathematical model outcomes. The model developed in this thesis has potential for future extension, to incorporate processes leading to woven bone deposition, while maintaining the characteristics that regulate early callus formation.

A new era : personal technology challenges educational technology

As we race towards a new era, rapid change of conventional models has become the norm. Just as technology has etched itself to the core of society, the sheer quantity of student devices connecting to university networks presents a sector wide challenge coinciding almost perfectly with many universities creating technology rich learning spaces. New fears include future proofing. It is not just a matter of technology becoming outdated. In seeking to accommodate the teaching styles and experience of staff across diverse faculties, is this technology simply too vanilla to meet their needs as they become increasingly skilled and inspired by technology’s potential? Through the early findings of a study into staff use of technology within Queensland University of Technology's next generation collaborative learning spaces, this paper explores whether the answers lie in a model presented by students equipping themselves with the tools they need to learn in the 21st century.

Timing and distribution of protein ingestion during prolonged recovery from resistance exercise alters myofibrillar protein synthesis

Quantity and timing of protein ingestion are major factors regulating myofibrillar protein synthesis (MPS). However, the effect of specific ingestion patterns on MPS throughout a 12 h period is unknown. We determined how different distributions of protein feeding during 12 h recovery after resistance exercise affects anabolic responses in skeletal muscle. Twenty-four healthy trained males were assigned to three groups (n = 8/group) and undertook a bout of resistance exercise followed by ingestion of 80 g of whey protein throughout 12 h recovery in one of the following protocols: 8 × 10 g every 1.5 h (PULSE); 4 × 20 g every 3 h (intermediate: INT); or 2 × 40 g every 6 h (BOLUS). Muscle biopsies were obtained at rest and after 1, 4, 6, 7 and 12 h post exercise. Resting and post-exercise MPS (l-[ring-(13)C6] phenylalanine), and muscle mRNA abundance and cell signalling were assessed. All ingestion protocols increased MPS above rest throughout 1-12 h recovery (88-148%, P < 0.02), but INT elicited greater MPS than PULSE and BOLUS (31-48%, P < 0.02). In general signalling showed a BOLUS>INT>PULSE hierarchy in magnitude of phosphorylation. MuRF-1 and SLC38A2 mRNA were differentially expressed with BOLUS. In conclusion, 20 g of whey protein consumed every 3 h was superior to either PULSE or BOLUS feeding patterns for stimulating MPS throughout the day. This study provides novel information on the effect of modulating the distribution of protein intake on anabolic responses in skeletal muscle and has the potential to maximize outcomes of resistance training for attaining peak muscle mass.

Neurons Activated During Fear Memory Consolidation and Reconsolidation are Mapped to a Common and New Topography in the Lateral Amygdala

A key question in neuroscience is how memory is selectively allocated to neural networks in the brain. This question remains a significant research challenge, in both rodent models and humans alike, because of the inherent difficulty in tracking and deciphering large, highly dimensional neuronal ensembles that support memory (i.e., the engram). In a previous study we showed that consolidation of a new fear memory is allocated to a common topography of amygdala neurons. When a consolidated memory is retrieved, it may enter a labile state, requiring reconsolidation for it to persist. What is not known is whether the original spatial allocation of a consolidated memory changes during reconsolidation. Knowledge about the spatial allocation of a memory, during consolidation and reconsolidation, provides fundamental insight into its core physical structure (i.e., the engram). Using design-based stereology, we operationally define reconsolidation by showing a nearly identical quantity of neurons in the dorsolateral amygdala (LAd) that expressed a plasticity-related protein, phosphorylated mitogen-activated protein kinase, following both memory acquisition and retrieval. Next, we confirm that Pavlovian fear conditioning recruits a stable, topographically organized population of activated neurons in the LAd. When the stored fear memory was briefly reactivated in the presence of the relevant conditioned stimulus, a similar topography of activated neurons was uncovered. In addition, we found evidence for activated neurons allocated to new regions of the LAd. These findings provide the first insight into the spatial allocation of a fear engram in the LAd, during its consolidation and reconsolidation phase.

Hush-a-by mummy : interactions between co-sleeping and maternal sleep disturbance

Childbirth is an extraordinary, everyday experience; in 2011, 301 617 infants were born in Australia [1], resulting in countless potential occurrences of sleep disturbance and subsequent daytime sleepiness. While the relationship between sleep and sleepiness has been heavily investigated in the vulnerable sub-populations of shift workers and patients with sleep disorders, comparatively postpartum women have been overlooked. Previous research has reported slower reaction times to the Psychomotor Vigilance Task [2] and shorter sleep onset in the multiple sleep latency test [3] in new mothers compared with control women. However little is known about change in sleep and sleepiness over time or potential interactions with infant care behaviour choices, such as co-sleeping (mother and infant sharing a bed). This study aims to investigate change in new mothers sleep quantity, sleep quality and resulting daytime sleepiness over postpartum weeks 6, 12 and 18, while evaluating the impact of co-sleeping.

Actigraphy assessment of mother's sleep at 6, 12 & 18 weeks postpartum

Introduction: Mothers’ sleep during the postpartum period is commonly characterised by bouts of sleep across the night, resulting in low sleep efficiency and daytime sleepiness. Understanding of the nature of mothers’ sleep disruption needs to incorporate indices of both sleep quantity and sleep quality, but objective assessment of sleep disturbance experienced during the first postpartum months has not been investigated in great detail. This longitudinal study aimed to objectively measure mothers’ sleep during the first 18 weeks postpartum, to ascertain the level of sleep disturbance experienced. Method: Eleven mothers (Mean age = 29.82, SD = 4.45) from Australia wore Actiwatch-2 devices for up to 7 days and nights at 6, 12 and 18 weeks postpartum. For each night of recording, a number of sleep bouts were identified. Total sleep time (TST) was calculated as the total number of minutes across the night within these bouts. Sleep efficiency was calculated as the percentage of minutes across the night classified as being part of a sleep bout, with higher scores indicating higher efficiency. Sleep quality captured the efficiency of sleep within sleep bouts, and was calculated as the percentage of epochs classified as sleep within sleep bouts, with higher scores indicating higher sleep quality. Results: At 6 weeks postpartum, mean total sleep time was 420.22 minutes (SD = 50.61). Total sleep time did not significantly differ across the assessment; however there was a trend towards an increase over time. Sleep efficiency increased across the time periods (F(2,10) = 10.30, p = .001), with a significant increase between week 12 and week 18. At 6 weeks postpartum, mean sleep quality was 93.15% (SD = 2.68) and scores did not significantly change across the assessment periods. While there was no relationship between sleep efficiency and sleep quality during weeks 6 and 12, a significant positive relationship was observed at week 18, r2 = .52, p = .013. Conclusions: Within this sample, a low level of disruption was consistently shown within the mothers’ night time sleep bouts. However, overall sleep efficiency suggested a significant proportion of time spent awake between sleep bouts. While TST remained stable over time, overall sleep efficiency improved, suggesting the mothers’ sleep was becoming more consolidated. A single sleep bout a night was not often experienced.

The ECOS Project. An interactive simulation to promote an ECO-friendly universe.

Custom designed for display on the Cube Installation situated in the new Science and Engineering Centre (SEC) at QUT, the ECOS project is a playful interface that uses real-time weather data to simulate how a five-star energy building operates in climates all over the world. In collaboration with the SEC building managers, the ECOS Project incorporates energy consumption and generation data of the building into an interactive simulation, which is both engaging to users and highly informative, and which invites play and reflection on the roles of green buildings. ECOS focuses on the principle that humans can have both a positive and negative impact on ecosystems with both local and global consequence. The ECOS project draws on the practice of Eco-Visualisation, a term used to encapsulate the important merging of environmental data visualization with the philosophy of sustainability. Holmes (2007) uses the term Eco-Visualisation (EV) to refer to data visualisations that ‘display the real time consumption statistics of key environmental resources for the goal of promoting ecological literacy’. EVs are commonly artifacts of interaction design, information design, interface design and industrial design, but are informed by various intellectual disciplines that have shared interests in sustainability. As a result of surveying a number of projects, Pierce, Odom and Blevis (2008) outline strategies for designing and evaluating effective EVs, including ‘connecting behavior to material impacts of consumption, encouraging playful engagement and exploration with energy, raising public awareness and facilitating discussion, and stimulating critical reflection.’ Consequently, Froehlich (2010) and his colleagues also use the term ‘Eco-feedback technology’ to describe the same field. ‘Green IT’ is another variation which Tomlinson (2010) describes as a ‘field at the juncture of two trends… the growing concern over environmental issues’ and ‘the use of digital tools and techniques for manipulating information.’ The ECOS Project team is guided by these principles, but more importantly, propose an example for how these principles may be achieved. The ECOS Project presents a simplified interface to the very complex domain of thermodynamic and climate modeling. From a mathematical perspective, the simulation can be divided into two models, which interact and compete for balance – the comfort of ECOS’ virtual denizens and the ecological and environmental health of the virtual world. The comfort model is based on the study of psychometrics, and specifically those relating to human comfort. This provides baseline micro-climatic values for what constitutes a comfortable working environment within the QUT SEC buildings. The difference between the ambient outside temperature (as determined by polling the Google Weather API for live weather data) and the internal thermostat of the building (as set by the user) allows us to estimate the energy required to either heat or cool the building. Once the energy requirements can be ascertained, this is then balanced with the ability of the building to produce enough power from green energy sources (solar, wind and gas) to cover its energy requirements. Calculating the relative amount of energy produced by wind and solar can be done by, in the case of solar for example, considering the size of panel and the amount of solar radiation it is receiving at any given time, which in turn can be estimated based on the temperature and conditions returned by the live weather API. Some of these variables can be altered by the user, allowing them to attempt to optimize the health of the building. The variables that can be changed are the budget allocated to green energy sources such as the Solar Panels, Wind Generator and the Air conditioning to control the internal building temperature. These variables influence the energy input and output variables, modeled on the real energy usage statistics drawn from the SEC data provided by the building managers.

A biomimetic extracellular matrix for cartilage tissue engineering centered on photocurable gelatin, hyaluronic acid and chondroitin sulfate

The development of hydrogels tailored for cartilage tissue engineering has been a research and clinical goal for over a decade. Directing cells towards a chondrogenic phenotype and promoting new matrix formation are significant challenges that must be overcome for the successful application of hydrogels in cartilage tissue therapies. Gelatin-methacrylamide (Gel-MA) hydrogels have shown promise for the repair of some tissues, but they have not been extensively investigated for cartilage tissue engineering. We encapsulated human chondrocytes in gel-MA based hydrogels, and show that with the incorporation of small quantities of photo-crosslinkable hyaluronic acid methacrylate (HA-MA), and to a lesser extent chondroitin sulfate methacrylate (CS-MA), chondrogenesis and mechanical properties can be enhanced. The addition of HA-MA to Gel-MA constructs resulted in more rounded cell morphologies, enhanced chondrogenesis as assessed by gene expression and immunofluorescence, and increased quantity and distribution of the newly synthesised ECM throughout the construct. Consequently, while the compressive moduli of control Gel-MA constructs increased by 26 kPa after 8 weeks culture, constructs with HA-MA and CS-MA increased by 96 kPa. The enhanced chondrogenic differentiation, distribution of ECM, and improved mechanical properties make these materials potential candidates for cartilage tissue engineering applications.

Nondiscretionary residential water use : the impact of habits and water-efficient technologies

Several studies published in the last few decades have demonstrated a low price-elasticity for residential water use. In particular, it has been shown that there is a quantity of water demanded that remains constant regardless of prices and other economic factors. In this research, we characterise residential water demand based on a Stone-Geary utility function. This specification is not only theory-compatible but can also explicitly model a minimum level of consumption not dependent on prices or income. This is described as minimum threshold or nondiscretionary water use. Additionally, the Stone-Geary framework is used to model the subsistence level of water consumption that is dependent on the temporal evolution of consumer habits and stock of physical capital. The main aim of this study is to analyse the impact of water-saving habits and water-efficient technologies on residential water demand, while additionally focusing attention on nondiscretionary uses. This is informed by an empirical application using data from a survey conducted among residents of Brisbane City Council, Australia. The results will be especially useful in the design of water tariffs and other water-saving policies.

Incidence of unilateral arm lymphoedema after breast cancer : a systematic review and meta-analysis

Background The body of evidence related to breast-cancer-related lymphoedema incidence and risk factors has substantially grown and improved in quality over the past decade. We assessed the incidence of unilateral arm lymphoedema after breast cancer and explored the evidence available for lymphoedema risk factors. Methods We searched Academic Search Elite, Cumulative Index to Nursing and Allied Health, Cochrane Central Register of Controlled Trials (clinical trials), and Medline for research articles that assessed the incidence or prevalence of, or risk factors for, arm lymphoedema after breast cancer, published between January 1, 2000, and June 30, 2012. We extracted incidence data and calculated corresponding exact binomial 95% CIs. We used random effects models to calculate a pooled overall estimate of lymphoedema incidence, with subgroup analyses to assess the effect of different study designs, countries of study origin, diagnostic methods, time since diagnosis, and extent of axillary surgery. We assessed risk factors and collated them into four levels of evidence, depending on consistency of findings and quality and quantity of studies contributing to findings. Findings 72 studies met the inclusion criteria for the assessment of lymphoedema incidence, giving a pooled estimate of 16·6% (95% CI 13·6–20·2). Our estimate was 21·4% (14·9–29·8) when restricted to data from prospective cohort studies (30 studies). The incidence of arm lymphoedema seemed to increase up to 2 years after diagnosis or surgery of breast cancer (24 studies with time since diagnosis or surgery of 12 to <24 months; 18·9%, 14·2–24·7), was highest when assessed by more than one diagnostic method (nine studies; 28·2%, 11·8–53·5), and was about four times higher in women who had an axillary-lymph-node dissection (18 studies; 19·9%, 13·5–28·2) than it was in those who had sentinel-node biopsy (18 studies; 5·6%, 6·1–7·9). 29 studies met the inclusion criteria for the assessment of risk factors. Risk factors that had a strong level of evidence were extensive surgery (ie, axillary-lymph-node dissection, greater number of lymph nodes dissected, mastectomy) and being overweight or obese. Interpretation Our findings suggest that more than one in five women who survive breast cancer will develop arm lymphoedema. A clear need exists for improved understanding of contributing risk factors, as well as of prevention and management strategies to reduce the individual and public health burden of this disabling and distressing disorder.

Alcohol ingestion impairs maximal post-exercise rates of myofibrillar protein synthesis following a single bout of concurrent training

Introduction The culture in many team sports involves consumption of large amounts of alcohol after training/competition. The effect of such a practice on recovery processes underlying protein turnover in human skeletal muscle are unknown. We determined the effect of alcohol intake on rates of myofibrillar protein synthesis (MPS) following strenuous exercise with carbohydrate (CHO) or protein ingestion. Methods In a randomized cross-over design, 8 physically active males completed three experimental trials comprising resistance exercise (8×5 reps leg extension, 80% 1 repetition maximum) followed by continuous (30 min, 63% peak power output (PPO)) and high intensity interval (10×30 s, 110% PPO) cycling. Immediately, and 4 h post-exercise, subjects consumed either 500 mL of whey protein (25 g; PRO), alcohol (1.5 g·kg body mass−1, 12±2 standard drinks) co-ingested with protein (ALC-PRO), or an energy-matched quantity of carbohydrate also with alcohol (25 g maltodextrin; ALC-CHO). Subjects also consumed a CHO meal (1.5 g CHO·kg body mass−1) 2 h post-exercise. Muscle biopsies were taken at rest, 2 and 8 h post-exercise. Results Blood alcohol concentration was elevated above baseline with ALC-CHO and ALC-PRO throughout recovery (P<0.05). Phosphorylation of mTORSer2448 2 h after exercise was higher with PRO compared to ALC-PRO and ALC-CHO (P<0.05), while p70S6K phosphorylation was higher 2 h post-exercise with ALC-PRO and PRO compared to ALC-CHO (P<0.05). Rates of MPS increased above rest for all conditions (~29–109%, P<0.05). However, compared to PRO, there was a hierarchical reduction in MPS with ALC-PRO (24%, P<0.05) and with ALC-CHO (37%, P<0.05). Conclusion We provide novel data demonstrating that alcohol consumption reduces rates of MPS following a bout of concurrent exercise, even when co-ingested with protein. We conclude that alcohol ingestion suppresses the anabolic response in skeletal muscle and may therefore impair recovery and adaptation to training and/or subsequent performance.

The Chidiac case : another miscarriage of justice?

On 25 March 1997 the Witness program on Channel 7 screened a story about the conviction of Neil Chidiac in February 1989 for conspiracy to import a trafficable quantity of heroin in NSW. The program questioned the justice of Chidiac's conviction and filmed his recent release from prison on parole after serving over eight years in prison, still protesting his innocence. Witness featured an interview with the chief Crown witness against Chidiac, Alfred Oti, in which Oti completely repudiated the testimony he gave at the trial and admitted to lying at the behest of the police in order to secure advantages for himself...

Australasian nutrition research for prevention and management of child obesity : innovation and progress in the last decade

The Food and Nutrition stream of Australasian Child and Adolescent Obesity Research Network (ACAORN) aims to improve the quality of dietary methodologies and the reporting of dietary intake within Australasian child obesity research (http://www.acaorn.org.au/streams/nutrition/). With 2012 marking ACAORN’s 10th anniversary, this commentary profiles a selection of child obesity nutrition research published over the last decade by Food and Nutrition Stream members. In addition, stream activities have included the development of an online selection guide to assist researchers in their selection of appropriate dietary intake methodologies (http://www.acaorn.org.au/streams/nutrition/dietary-intake/index.php). The quantity and quality of research to guide effective child obesity prevention and treatment has increased substantially over the last decade. ACAORN provides a successful case study of how research networks can provide a collegial atmosphere to foster and co-ordinate research efforts in an otherwise competitive environment.