Large scale read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molecular biology, resulting in an explosion of data sets and an increasing role in clinical practice. Such applications necessarily require rapid identification of the organism as a prelude to annotation and further analysis. NGS data consist of a substantial number of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. Highly accurate results have been obtained for restricted sets using SVM classifiers, but such methods are difficult to parallelise and success depends on careful attention to feature selection. This work examines the problem at very large scale, using a mix of synthetic and real data with a view to determining the overall structure of the problem and the effectiveness of parallel ensembles of simpler classifiers (principally random forests) in addressing the challenges of large scale genomics.

A coupled SPH-DEM model for micro-scale structural deformations of plant cells during drying

A single plant cell was modeled with smoothed particle hydrodynamics (SPH) and a discrete element method (DEM) to study the basic micromechanics that govern the cellular structural deformations during drying. This two-dimensional particle-based model consists of two components: a cell fluid model and a cell wall model. The cell fluid was approximated to a highly viscous Newtonian fluid and modeled with SPH. The cell wall was treated as a stiff semi-permeable solid membrane with visco-elastic properties and modeled as a neo-Hookean solid material using a DEM. Compared to existing meshfree particle-based plant cell models, we have specifically introduced cell wall–fluid attraction forces and cell wall bending stiffness effects to address the critical shrinkage characteristics of the plant cells during drying. Also, a moisture domain-based novel approach was used to simulate drying mechanisms within the particle scheme. The model performance was found to be mainly influenced by the particle resolution, initial gap between the outermost fluid particles and wall particles and number of particles in the SPH influence domain. A higher order smoothing kernel was used with adaptive smoothing length to improve the stability and accuracy of the model. Cell deformations at different states of cell dryness were qualitatively and quantitatively compared with microscopic experimental findings on apple cells and a fairly good agreement was observed with some exceptions. The wall–fluid attraction forces and cell wall bending stiffness were found to be significantly improving the model predictions. A detailed sensitivity analysis was also done to further investigate the influence of wall–fluid attraction forces, cell wall bending stiffness, cell wall stiffness and the particle resolution. This novel meshfree based modeling approach is highly applicable for cellular level deformation studies of plant food materials during drying, which characterize large deformations.

The validity and reliability of the Parent Fever Management Scale: A study from Palestine

Background Parental fever phobia and overuse of antipyretics to control fever is increasing. Little is known about childhood fever management among Arab parents. No scales to measure parents’ fever management practices in Palestine are available. Aims The aims of this study were to translate and examine the psychometric properties of the Arabic version of the Parent Fever Management Scale (PFMS). Methods A standard “forward–backward” procedure was used to translate PFMS into Arabic language. It was then validated on a convenience sample of 402 parents between July and October 2012. Descriptive statistics were used, and instrument reliability was assessed for internal consistency using Cronbach's alpha coefficient. Validity was confirmed using convergent and known group validation. Results Applying the recommended scoring method, the median (interquartile range) score of the PFMS was 26 (23-30). Acceptable internal consistency was found (Cronbach’s alpha = 0.733) and the test–retest reliability value was 0.92 (P < 0.001). The chi-squared (χ2) test showed a significant relationship between PFMS groups and frequent daily administration of antipyretic groups (χ2 = 52.86; P < 0.001). The PFMS sensitivity and specificity were 77.67% and 57.75%, respectively. The positive and negative predictive values were 67.89% and 32.11%, respectively. Conclusions The findings of this validation study indicate that the Arabic version of the PFMS is a reliable and valid measure which can be used as a useful tool for health professionals to identify parents’ fever management practices and thus provide targeted education to reduce the unnecessary burden of care they place on themselves when concerned for a febrile child.

Epigenetic mechanisms mediating vulnerability and resilience to psychiatric disorders

The impact that stressful encounters have upon long-lasting behavioural phenotypes is varied. Whereas a significant proportion of the population will develop "stress-related" conditions such as post-traumatic stress disorder or depression in later life, the majority are considered "resilient" and are able to cope with stress and avoid such psychopathologies. The reason for this heterogeneity is undoubtedly multi-factorial, involving a complex interplay between genetic and environmental factors. Both genes and environment are of critical importance when it comes to developmental processes, and it appears that subtle differences in either of these may be responsible for altering developmental trajectories that confer vulnerability or resilience. At the molecular level, developmental processes are regulated by epigenetic mechanisms, with recent clinical and pre-clinical data obtained by ourselves and others suggesting that epigenetic differences in various regions of the brain are associated with a range of psychiatric disorders, including many that are stress-related. Here we provide an overview of how these epigenetic differences, and hence susceptibility to psychiatric disorders, might arise through exposure to stress-related factors during critical periods of development.

On-road driver sleepiness : what are Australian drivers experiences and awareness of sleepiness while driving?

Objectives: Driver sleepiness contributes substantially to road crash incidents. Simulator and on-road studies clearly reveal an impairing effect from sleepiness for driving ability. However, drivers might not appreciate the dangerousness of driving while sleepy and this could translate to their on-road driving behaviours. This study sought to determine drivers’ on-road experiences of sleepiness, their sleep habits, and personal awareness of the signs of sleepiness. Methods: Participants were a random selection of 92 drivers travelling on a major highway in the state of Queensland, Australia, who were stopped by Police as part of routine drink driving operations. Participants completed a brief questionnaire that included: demographic details, awareness and on-road experiences of sleepy driving, and sleep habits. A modified version of the Karolinska Sleepiness Scale (KSS) was used to assess subjective sleepiness during the last 15 minutes of driving. Results: Participants rating of subjective sleepiness was quite low with 90% reporting at or below 3 on the KSS. Participants were reasonably aware of the signs of sleepiness; with a number of these correlated with on-road experiences. The participants sleep debt correlated with their alertness (r = -.30) and the hours spent driving (r = .38). Conclusions: These results suggest that drivers had moderate or substantial experience of driving when sleepy and many were aware of the signs of sleepiness. As many of the participants reported driving long distances after suboptimal sleep durations, it is possible that their risk perception of the dangerousness of sleepy driving maybe erroneous.

Decomposition of the environmental Kuznets curve : scale, technique, and composition effects

This study decomposed the determinants of environmental quality into scale, technique, and composition effects. We applied a semiparametric method of generalized additive models, which enabled us to use flexible functional forms and include several independent variables in the model. The differences in the technique effect were found to play a crucial role in reducing pollution. We found that the technique effect was sufficient to reduce sulfur dioxide emissions. On the other hand, its effect was not enough to reduce carbon dioxide (CO2) emissions and energy use, except for the case of CO2 emissions in high-income countries.

Examining the potential for design and renewable energy to contribute to zero energy housing in Queensland

This was a comparative study of the possibility of a net zero energy house in Queensland, Australia. It examines the actual energy use and thermal comfort conditions of an occupied Brisbane home and compares performance with the 10 star scale rating scheme for Australian residential buildings. An adaptive comfort psychometric chart was developed for this analysis. The house's capacity for the use of the natural ventilation was studied by CFD modelling. This study showed that the house succeeded in achieving the definition of net zero energy on an annual and monthly basis for lighting, cooking and space heating / cooling and for 70% of days for lighting, hot water and cooking services.

Cross cultural adaptation and validation of a Spanish version of the lower limb functional index

Background: The Lower Limb Functional Index (LLFI) is a relatively recently published regional outcome measure. The development article showed the LLFI had robust and valid clinimetric properties with sound psychometric and practical characteristics when compared to the Lower Limb Extremity Scale (LEFS) criterion standard. Objective: The purpose of this study was cross cultural adaptation and validation of the LLFI Spanish-version (LLFI-Sp) in a Spanish population. Methods: A two stage observational study was conducted. The LLFI was initially cross-culturally adapted to Spanish through double forward and single backward translation; then subsequently validated for the psychometric characteristics of validity, internal consistency, reliability, error score and factor structure. Participants (n = 136) with various lower limb conditions of >12 weeks duration completed the LLFI-Sp, Western Ontario and McMaster University Osteoarthritis Index (WOMAC) and the Euroqol Health Questionnaire 5 Dimensions (EQ-5D-3 L). The full sample was employed to determine internal consistency, concurrent criterion validity, construct validity and factor structure; a subgroup (n = 45) determined reliability at seven days concurrently completing a global rating of change scale. Results: The LLFI-Sp demonstrated high but not excessive internal consistency (α = 0.91) and high reliability (ICC = 0.96). The factor structure was one-dimensional which supported the construct validity. Criterion validity with the WOMAC was strong (r = 0.77) and with the EQ-5D-3 L fair and inversely correlated (r = -0.62). The study limitations included the lack of longitudinal data and the determination of responsiveness. Conclusions: The LLFI-Sp supports the findings of the original English version as being a valid lower limb regional outcome measure. It demonstrated similar psychometric properties for internal consistency, validity, reliability, error score and factor structure.

Fire performance and design of cold-formed steel wall systems

Traditionally, the fire resistance rating of Light gauge steel frame (LSF) wall systems is based on approximate prescriptive methods developed using limited fire tests. These fire tests are conducted using standard fire time-temperature curve given in ISO 834. However, in recent times fire has become a major disaster in buildings due to the increase in fire loads as a result of modern furniture and lightweight construction, which make use of thermoplastics materials, synthetic foams and fabrics. Therefore a detailed research study into the performance of load bearing LSF wall systems under both standard and realistic design fires on one side was undertaken to develop improved fire design rules. This study included both full scale fire tests and numerical studies of eight different LSF wall systems conducted for both the standard fire curve and the recently developed realistic design fire curves. The use of previous fire design rules developed for LSF walls subjected to non-uniform elevated temperature distributions based on AISI design manual and Eurocode 3 Parts 1.2 and 1.3 was investigated first. New simplified fire design rules based on AS/NZS 4600, North American Specification and Eurocode 3 Part 1.3 were then proposed with suitable allowances for the interaction effects of compression and bending actions. The importance of considering thermal bowing, magnified thermal bowing and neutral axis shift in the fire design was also investigated and their effects were included. A spread sheet based design tool was developed based on the new design rules to predict the failure load ratio versus time and temperature curves for varying LSF wall configurations. The accuracy of the proposed design rules was verified using the fire test and finite element analysis results for various wall configurations, steel grades, thicknesses and load ratios under both standard and realistic design fire conditions. A simplified method was also proposed to predict the fire resistance rating of LSF walls based on two sets of equations developed for the load ratio-hot flange temperature and the time-temperature relationships. This paper presents the details of this study on LSF wall systems under fire conditions and the results.

A rating aggregation method for generating product reputations

Many websites offer the opportunity for customers to rate items and then use customers' ratings to generate items reputation, which can be used later by other users for decision making purposes. The aggregated value of the ratings per item represents the reputation of this item. The accuracy of the reputation scores is important as it is used to rank items. Most of the aggregation methods didn't consider the frequency of distinct ratings and they didn't test how accurate their reputation scores over different datasets with different sparsity. In this work we propose a new aggregation method which can be described as a weighted average, where weights are generated using the normal distribution. The evaluation result shows that the proposed method outperforms state-of-the-art methods over different sparsity datasets.

Numerical simulation of micro-scale morphological changes of plant food materials during drying - a meshfree approach

This thesis developed a high preforming alternative numerical technique to investigate microscale morphological changes of plant food materials during drying. The technique is based on a novel meshfree method, and is more capable of modeling large deformations of multiphase problem domains, when compared with conventional grid-based numerical modeling techniques. The developed cellular model can effectively replicate dried tissue morphological changes such as shrinkage and cell wall wrinkling, as influenced by moisture reduction and turgor loss.

Storytelling; safeguarding; treatment; and responsibility; attributes of recovery in psychiatric intensive care units

Background and aim In recent years policy in Australia has endorsed recovery-oriented mental health services underpinned by the needs, rights and values of people with lived experience of mental illness. This paper critically reviews the idea of recovery understood by nurses at the frontline of services for people experiencing acute psychiatric distress. Method Data gathered from focus groups held with nurses from two hospitals were used to ascertain their use of terminology, understanding of attributes and current practices that support recovery for people experiencing acute psychiatric distress. A review of literature further examined current nurse based evidence and nurse knowledge of recovery approaches specific to psychiatric intensive care settings. Results Four defining attributes of recovery based on nurses’ perspectives are shared to identify and describe strategies that may help underpin recovery specific to psychiatric intensive care settings. Conclusion The four attributes described in this paper provide a pragmatic framework with which nurses can reinforce their clinical decision-making and negotiate the dynamic and often incongruous challenges they experience to embed recovery-oriented culture in acute psychiatric settings.

Supporting collaboration on very large-scale interactive wall surfaces

In this paper we describe CubIT, a multi-user presentation and collaboration system installed at the Queensland University of Technology’s (QUT) Cube facility. The ‘Cube’ is an interactive visualisation facility made up of five very large-scale interactive multi-panel wall displays, each consisting of up to twelve 55-inch multi-touch screens (48 screens in total) and massive projected display screens situated above the display panels. The paper outlines the unique design challenges, features, implementation and evaluation of CubIT. The system was built to make the Cube facility accessible to QUT’s academic and student population. CubIT enables users to easily upload and share their own media content, and allows multiple users to simultaneously interact with the Cube’s wall displays. The features of CubIT were implemented via three user interfaces, a multi-touch interface working on the wall displays, a mobile phone and tablet application and a web-based content management system. Each of these interfaces plays a different role and offers different interaction mechanisms. Together they support a wide range of collaborative features including multi-user shared workspaces, drag and drop upload and sharing between users, session management and dynamic state control between different parts of the system. The results of our evaluation study showed that CubIT was successfully used for a variety of tasks, and highlighted challenges with regards to user expectations regarding functionality as well as issues arising from public use.