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.

Museums as urban catalysts : the role of urban design in flagship cultural development

A long-held urban redevelopment strategy has been the investment in flagship cultural projects—large-scale, iconic museums and arts centres that are intended to enhance the city image while catalyzing private sector investment and attracting tourists to the surrounding area. This paper concentrates on an aspect of the flagship cultural strategy that has received surprisingly little focused attention—the role that urban design and context play in realizing project outcomes. The analysis concentrates on two established flagship museums in Los Angeles and San Jose, California. The research demonstrates that certain urban design characteristics can negatively affect the ability of a project to attract visitors and generate commercial activity. However, at the same time, factors beyond the local context may be an overriding factor in project outcomes thus calling into question the concept of cultural catalyst.

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 Construction and Performance of Commercial Contracts

This book analyses the principles underlying the construction and application of a number of boilerplate and other clauses commonly included in commercial contracts. The first Part of the work deals with general principles of interpretation. It then considers clauses which allocate commercial risk; clauses relating to performance; clauses introducing new parties by way of assignment, novation or nomination; clauses such as guarantees and indemnities which create liabilities in third parties; and dispute resolution clauses including governing law. The authors highlight common issues surrounding the application of these clauses in practice and, where appropriate, make drafting recommendations based on their analysis of case law and the operation of relevant statutes. This is a very accessible resource for all commercial practitioners.

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.

Changes to commercial service provision among sex workers from Queensland, Australia

Introduction: The role of commercial sex in facilitating infection transmission is a subject of ongoing empirical enquiry, with little attention to the variety and extent of ‘non-traditional’ commercial services that pose a lesser risk of infection. This study sought to examine the supply and demand of a wide range of traditional and non-traditional commercial sexual services among sex workers and their clients from Queensland, Australia. Methods: Cross-sectional convenience sampling was used to compare female sex workers in 1991 (n=200, aged 16-46 years) and 2003 (n=247, aged 18-57 years) and from male clients in 2003. The client sample comprised 160 male clients aged between 19 and 72 years. Results: Over the comparison period there was a significant increase in the provision of ‘exotic’ or non-traditional sexual services. In 2003, the availability of bondage and discipline, submission, fantasy, use of sex toys, golden showers, fisting and lesbian double acts had increased dramatically, while ‘traditional’ services had mostly remained at similar levels. Moreover, the proportion of sex workers in some industry sectors providing ‘exotic’ commercial services seem to have risen over time. Conclusion: Undoubtedly, the sex industry has professionalised and now includes more sophisticated and specialized suppliers. As with any commercial business, the diversification of services is largely driven with client demand, with the ‘menu’ being generally broader than the majority of client preferences. However, although clients demands for particular commercial sexual services seems to have been met, with regard to anal sex and anal play, supply has failed to meet client demand. Disclosure of Interest Statement: Funding for the 2003 study was provided by the Prostitution Licensing Authority. Acknowledgement and sincere thanks to the men and women who participated in this study.

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.

Dosimetry of cone-defined stereotactic radiosurgery fields with a commercial synthetic diamond detector

Purpose Small field x-ray beam dosimetry is difficult due to a lack of lateral electronic equilibrium, source occlusion, high dose gradients and detector volume averaging. Currently there is no single definitive detector recommended for small field dosimetry. The objective of this work was to evaluate the performance of a new commercial synthetic diamond detector, namely the PTW 60019 microDiamond, for the dosimetry of small x-ray fields as used in stereotactic radiosurgery (SRS). Methods Small field sizes were defined by BrainLAB circular cones (4 – 30 mm diameter) on a Novalis Trilogy linear accelerator and using the 6 MV SRS x-ray beam mode for all measurements. Percentage depth doses were measured and compared to an IBA SFD and a PTW 60012 E diode. Cross profiles were measured and compared to an IBA SFD diode. Field factors, Ω_(Q_clin,Q_msr)^(f_clin,f_msr ), were calculated by Monte Carlo methods using BEAMnrc and correction factors, k_(Q_clin,Q_msr)^(f_clin,f_msr ), were derived for the PTW 60019 microDiamond detector. Results For the small fields of 4 to 30 mm diameter, there were dose differences in the PDDs of up to 1.5% when compared to an IBA SFD and PTW 60012 E diode detector. For the cross profile measurements the penumbra values varied, depending upon the orientation of the detector. The field factors, Ω_(Q_clin,Q_msr)^(f_clin,f_msr ), were calculated for these field diameters at a depth of 1.4 cm in water and they were within 2.7% of published values for a similar linear accelerator. The corrections factors, k_(Q_clin,Q_msr)^(f_clin,f_msr ), were derived for the PTW 60019 microDiamond detector. Conclusions We conclude that the new PTW 60019 microDiamond detector is generally suitable for relative dosimetry in small 6 MV SRS beams for a Novalis Trilogy linear equipped with circular cones.

Effect of temperature and moisture on high pressure lipid/oil extraction from microalgae

Commercially viable carbon–neutral biodiesel production from microalgae has potential for replacing depleting petroleum diesel. The process of biodiesel production from microalgae involves harvesting, drying and extraction of lipids which are energy- and cost-intensive processes. The development of effective large-scale lipid extraction processes which overcome the complexity of microalgae cell structure is considered one of the most vital requirements for commercial production. Thus the aim of this work was to investigate suitable extraction methods with optimised conditions to progress opportunities for sustainable microalgal biodiesel production. In this study, the green microalgal species consortium, Tarong polyculture was used to investigate lipid extraction with hexane (solvent) under high pressure and variable temperature and biomass moisture conditions using an Accelerated Solvent Extraction (ASE) method. The performance of high pressure solvent extraction was examined over a range of different process and sample conditions (dry biomass to water ratios (DBWRs): 100%, 75%, 50% and 25% and temperatures from 70 to 120 ºC, process time 5–15 min). Maximum total lipid yields were achieved at 50% and 75% sample dryness at temperatures of 90–120 ºC. We show that individual fatty acids (Palmitic acid C16:0; Stearic acid C18:0; Oleic acid C18:1; Linolenic acid C18:3) extraction optima are influenced by temperature and sample dryness, consequently affecting microalgal biodiesel quality parameters. Higher heating values and kinematic viscosity were compliant with biodiesel quality standards under all extraction conditions used. Our results indicate that biodiesel quality can be positively manipulated by selecting process extraction conditions that favour extraction of saturated and mono-unsaturated fatty acids over optimal extraction conditions for polyunsaturated fatty acids, yielding positive effects on cetane number and iodine values. Exceeding biodiesel standards for these two parameters opens blending opportunities with biodiesels that fall outside the minimal cetane and maximal iodine values.

Commercial Leases in Australia [7th ed.]

Commercial Leases in Australia is a comprehensive guide to understanding and drafting commercial leases agreements in Australia and to managing disputes when they arise.

Development of a dragline in-bucket bulk density monitor

This paper details the implementation and trialling of a prototype in-bucket bulk density monitor on a production dragline. Bulk density information can provide feedback to mine planning and scheduling to improve blasting and consequently facilitating optimal bucket sizing. The bulk density measurement builds upon outcomes presented in the AMTC2009 paper titled ‘Automatic In-Bucket Volume Estimation for Dragline Operations’ and utilises payload information from a commercial dragline monitor. While the previous paper explains the algorithms and theoretical basis for the system design and scaled model testing this paper will focus on the full scale implementation and the challenges involved.

Fire performance of LSF wall panels using numerical parametric studies

Light Gauge Steel Framing (LSF) walls made of cold-formed and thin-walled steel lipped channel studs with plasterboard linings on both sides are commonly used in commercial, industrial and residential buildings. However, there is limited data about their structural and thermal performances under fire conditions. Recent research at the Queensland University of Technology has investigated the structural and thermal behaviour of load bearing LSF wall systems. In this research a series of full scale fire tests was conducted first to evaluate the performance of LSF wall systems with eight different wall configurations under standard fire conditions. Finite element models of LSF walls were then developed, analysed under transient and steady state conditions, and validated using full scale fire tests. This paper presents the details of an investigation into the fire performance of LSF wall panels based on an extensive finite element analysis based parametric study. The LSF wall panels with eight different plasterboard-insulation configurations were considered under standard fire conditions. Effects of varying steel grades, steel thicknesses, screw spacing, plasterboard restraint, insulation materials and load ratio on the fire performance of LSF walls were investigated and the results of extensive fire performance data are presented in the form of load ratio versus time and critical hot flange (failure) temperature curves.

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.