Phylogenetic analysis of polyomaviruses based on their complete genomes

Perez-Losada et al. [1] analyzed 72 complete genomes corresponding to nine mammalian (67 strains) and 2 avian (5 strains) polyomavirus species using maximum likelihood and Bayesian methods of phylogenetic inference. Because some data of 2 genomes in their work are now not available in GenBank, in this work, we analyze the phylogenetic relationship of the remaining 70 complete genomes corresponding to nine mammalian (65 strains) and two avian (5 strains) polyomavirus species using a dynamical language model approach developed by our group (Yu et al., [26]). This distance method does not require sequence alignment for deriving species phylogeny based on overall similarities of the complete genomes. Our best tree separates the bird polyomaviruses (avian polyomaviruses and goose hemorrhagic polymaviruses) from the mammalian polyomaviruses, which supports the idea of splitting the genus into two subgenera. Such a split is consistent with the different viral life strategies of each group. In the mammalian polyomavirus subgenera, mouse polyomaviruses (MPV), simian viruses 40 (SV40), BK viruses (BKV) and JC viruses (JCV) are grouped as different branches as expected. The topology of our best tree is quite similar to that of the tree constructed by Perez-Losada et al.

Variation of the Stiles-Crawford effect with accommodation and myopia

Background: Mechanical forces either due to accommodation or myopia may stretch the retina and/or cause shear between the retina and choroid. This can be investigated by making use of the Stiles-Crawford effect (SCE), which is the phenomenon of light changing in apparent brightness as it enters through different positions in the pupil. The SCE can be measured by psychophysical and objective techniques, with the SCE parameters being directionality (rate of change across the pupil), and orientation (the location of peak sensitivity in the pupil). Aims: 1. To study the changes in foveal SCE with accommodation in emmetropes and myopes using a subjective (psychophysical) technique. 2. To develop and evaluate a quick objective technique of measuring the SCE using the multifocal electroretinogram. Methods: The SCE was measured in 6 young emmetropes and 6 young myopes for up to 8 D accommodation stimulus with a psychophysical technique and its variants. An objective technique using the multifocal electroretinogram was developed and evaluated with 5 emmetropes. Results: Using the psychophysical technique, the SCE directionality increased by similar amounts in both emmetropes and myopes as accommodation increased, with an increase of 15-20% with 6 D of accommodation. However, there were no significant orientation changes. Additional measurements showed that most of the change in the directionality was probably an artefact of optical factors such as higher-order aberrations and accommodative lag rather a true effect of accommodation. The multifocal technique demonstrated the presence of the SCE, but results were noisy and too variable to detect any changes in SCE directionality or orientation with accommodation. Conclusion: There is little true change in the SCE with accommodation responses up to 6 D in either emmetropes or myopes, although it is possible that substantial changes might occur at very high accommodation levels. The objective technique using the multifocal electroretinogram was quicker and less demanding for the subjects than the psychophysical technique, but as implemented in this thesis, it is not a reliable method of measuring the SCE.

Aging and the force-velocity relationship of muscles

Aging in humans is associated with a loss in neuromuscular function and performance. This is related, in part, to the reduction in muscular strength and power caused by a loss of skeletal muscle mass (sarcopenia) and changes in muscle architecture. Due to these changes, the force-velocity (f-v) relationship of human muscles alters with age. This change has functional implications such as slower walking speeds. Different methods to reverse these changes have been investigated, including traditional resistance training, power training and eccentric (or eccentrically-biased) resistance training. This review will summarise the changes of the f-v relationship with age, the functional implications of these changes and the various methods to reverse or at least partly ameliorate these changes.

Involvement of target contrast in visual masking location tasks deficients in myopia

Purpose: There have been few studies of visual temporal processing of myopic eyes. This study investigated the visual performance of emmetropic and myopic eyes using a backward visual masking location task. Methods: Data were collected for 39 subjects (15 emmetropes, 12 stable myopes, 12 progressing myopes). In backward visual masking, a target’s visibility is reduced by a mask presented in quick succession ‘after’ the target. The target and mask stimuli were presented at different interstimulus intervals (from 12 to 300 ms). The task involved locating the position of a target letter with both a higher (seven per cent) and a lower (five per cent) contrast. Results: Emmetropic subjects had significantly better performance for the lower contrast location task than the myopes (F2,36 = 22.88; p < 0.001) but there was no difference between the progressing and stable myopic groups (p = 0.911). There were no differences between the groups for the higher contrast location task (F2,36 = 0.72, p = 0.495). No relationship between task performance and either the magnitude of myopia or axial length was found for either task. Conclusions: A location task deficit was observed in myopes only for lower contrast stimuli. Both emmetropic and myopic groups had better performance for the higher contrast task compared to the lower contrast task, with myopes showing considerable improvement. This suggests that five per cent contrast may be the contrast threshold required to bias the task towards the magnocellular system (where myopes have a temporal processing deficit). Alternatively, the task may be sensitive to the contrast sensitivity of the observer.

View from a bridge : what makes a musical city

The attention paid by the British music press in 1976 to the release of The Saints first single “I’m Stranded” was the trigger for a commercial and academic interest in the Brisbane music scene which still has significant energy. In 2007, Brisbane was identifed by Billboard Magazine as a “hot spot” of independent music. A place to watch. Someone turned a torch on this town, had a quick look, moved on. But this town has always had music in it. Some of it made by me. So, I’m taking this connection of mine, and working it into a contextual historical analysis of the creative lives of Brisbane musicians. I will be interviewing a number of Brisbane musicians. These interviews have begun, and will continue to be be conducted in 2011/2012. I will ask questions and pursue memories that will encompass family, teenage years, siblings, the suburbs, the city, venues, television and radio; but then widen to welcome the river, the hills and mountains, foes and friends, beliefs and death. The wider research will be a contextual historical analysis of the creative lives of Brisbane musicians. It will explore the changing nature of their work practices over time and will consider the notion, among other factors, of ‘place’ in both their creative practice and their creative output. It will also examine how the presence of the practitioners and their work is seen to contribute to the cultural life of the city and the creative lives of its citizens into the future. This paper offers an analysis of this last notion: how does this city see its music-makers? In addition to the interviews, over 300 Brisbane musicians were surveyed in September 2009 as part of a QUT-initiated recorded music event (BIGJAM). Their responses will inform the production of this paper.

Theoretical investigation of mechanisms of formation and interaction of nanoparticles

In this thesis an investigation into theoretical models for formation and interaction of nanoparticles is presented. The work presented includes a literature review of current models followed by a series of five chapters of original research. This thesis has been submitted in partial fulfilment of the requirements for the degree of doctor of philosophy by publication and therefore each of the five chapters consist of a peer-reviewed journal article. The thesis is then concluded with a discussion of what has been achieved during the PhD candidature, the potential applications for this research and ways in which the research could be extended in the future. In this thesis we explore stochastic models pertaining to the interaction and evolution mechanisms of nanoparticles. In particular, we explore in depth the stochastic evaporation of molecules due to thermal activation and its ultimate effect on nanoparticles sizes and concentrations. Secondly, we analyse the thermal vibrations of nanoparticles suspended in a fluid and subject to standing oscillating drag forces (as would occur in a standing sound wave) and finally on lattice surfaces in the presence of high heat gradients. We have described in this thesis a number of new models for the description of multicompartment networks joined by a multiple, stochastically evaporating, links. The primary motivation for this work is in the description of thermal fragmentation in which multiple molecules holding parts of a carbonaceous nanoparticle may evaporate. Ultimately, these models predict the rate at which the network or aggregate fragments into smaller networks/aggregates and with what aggregate size distribution. The models are highly analytic and describe the fragmentation of a link holding multiple bonds using Markov processes that best describe different physical situations and these processes have been analysed using a number of mathematical methods. The fragmentation of the network/aggregate is then predicted using combinatorial arguments. Whilst there is some scepticism in the scientific community pertaining to the proposed mechanism of thermal fragmentation,we have presented compelling evidence in this thesis supporting the currently proposed mechanism and shown that our models can accurately match experimental results. This was achieved using a realistic simulation of the fragmentation of the fractal carbonaceous aggregate structure using our models. Furthermore, in this thesis a method of manipulation using acoustic standing waves is investigated. In our investigation we analysed the effect of frequency and particle size on the ability for the particle to be manipulated by means of a standing acoustic wave. In our results, we report the existence of a critical frequency for a particular particle size. This frequency is inversely proportional to the Stokes time of the particle in the fluid. We also find that for large frequencies the subtle Brownian motion of even larger particles plays a significant role in the efficacy of the manipulation. This is due to the decreasing size of the boundary layer between acoustic nodes. Our model utilises a multiple time scale approach to calculating the long term effects of the standing acoustic field on the particles that are interacting with the sound. These effects are then combined with the effects of Brownian motion in order to obtain a complete mathematical description of the particle dynamics in such acoustic fields. Finally, in this thesis, we develop a numerical routine for the description of "thermal tweezers". Currently, the technique of thermal tweezers is predominantly theoretical however there has been a handful of successful experiments which demonstrate the effect it practise. Thermal tweezers is the name given to the way in which particles can be easily manipulated on a lattice surface by careful selection of a heat distribution over the surface. Typically, the theoretical simulations of the effect can be rather time consuming with supercomputer facilities processing data over days or even weeks. Our alternative numerical method for the simulation of particle distributions pertaining to the thermal tweezers effect use the Fokker-Planck equation to derive a quick numerical method for the calculation of the effective diffusion constant as a result of the lattice and the temperature. We then use this diffusion constant and solve the diffusion equation numerically using the finite volume method. This saves the algorithm from calculating many individual particle trajectories since it is describes the flow of the probability distribution of particles in a continuous manner. The alternative method that is outlined in this thesis can produce a larger quantity of accurate results on a household PC in a matter of hours which is much better than was previously achieveable.

Porous polyurethane coatings bonded onto surface-modified titanium substrates for the growth of an endothelial cell layer

Cardiovascular diseases refer to the class of diseases that involve the heart or blood vessels (arteries and veins). Examples of medical devices for treating the cardiovascular diseases include ventricular assist devices (VADs), artificial heart valves and stents. Metallic biomaterials such as titanium and its alloy are commonly used for ventricular assist devices. However, titanium and its alloy show unacceptable thrombosis, which represents a major obstacle to be overcome. Polyurethane (PU) polymer has better blood compatibility and has been used widely in cardiovascular devices. Thus one aim of the project was to coat a PU polymer onto a titanium substrate by increasing the surface roughness, and surface functionality. Since the endothelium of a blood vessel has the most ideal non-thrombogenic properties, it was the target of this research project to grow an endothelial cell layer as a biological coating based on the tissue engineering strategy. However, seeding endothelial cells on the smooth PU coating surfaces is problematic due to the quick loss of seeded cells which do not adhere to the PU surface. Thus it was another aim of the project to create a porous PU top layer on the dense PU pre-layer-coated titanium substrate. The method of preparing the porous PU layer was based on the solvent casting/particulate leaching (SCPL) modified with centrifugation. Without the step of centrifugation, the distribution of the salt particles was not uniform within the polymer solution, and the degree of interconnection between the salt particles was not well controlled. Using the centrifugal treatment, the pore distribution became uniform and the pore interconnectivity was improved even at a high polymer solution concentration (20%) as the maximal salt weight was added in the polymer solution. The titanium surfaces were modified by alkli and heat treatment, followed by functionlisation using hydrogen peroxide. A silane coupling agent was coated before the application of the dense PU pre-layer and the porous PU top layer. The ability of the porous top layer to grow and retain the endothelial cells was also assessed through cell culture techniques. The bonding strengths of the PU coatings to the modified titanium substrates were measured and related to the surface morphologies. The outcome of the project is that it has laid a foundation to achieve the strategy of endothelialisation for the blood compatibility of medical devices. This thesis is divided into seven chapters. Chapter 2 describes the current state of the art in the field of surface modification in cardiovascular devices such as ventricular assist devices (VADs). It also analyses the pros and cons of the existing coatings, particularly in the context of this research. The surface coatings for VADs have evolved from early organic/ inorganic (passive) coatings, to bioactive coatings (e.g. biomolecules), and to cell-based coatings. Based on the commercial applications and the potential of the coatings, the relevant review is focused on the following six types of coatings: (1) titanium nitride (TiN) coatings, (2) diamond-like carbon (DLC) coatings, (3) 2-methacryloyloxyethyl phosphorylcholine (MPC) polymer coatings, (4) heparin coatings, (5) textured surfaces, and (6) endothelial cell lining. Chapter 3 reviews the polymer scaffolds and one relevant fabrication method. In tissue engineering, the function of a polymeric material is to provide a 3-dimensional architecture (scaffold) which is typically used to accommodate transplanted cells and to guide their growth and the regeneration of tissue. The success of these systems is dependent on the design of the tissue engineering scaffolds. Chapter 4 describes chemical surface treatments for titanium and titanium alloys to increase the bond strength to polymer by altering the substrate surface, for example, by increasing surface roughness or changing surface chemistry. The nature of the surface treatment prior to bonding is found to be a major factor controlling the bonding strength. By increasing surface roughness, an increase in surface area occurs, which allows the adhesive to flow in and around the irregularities on the surface to form a mechanical bond. Changing surface chemistry also results in the formation of a chemical bond. Chapter 5 shows that bond strengths between titanium and polyurethane could be significantly improved by surface treating the titanium prior to bonding. Alkaline heat treatment and H2O2 treatment were applied to change the surface roughness and the surface chemistry of titanium. Surface treatment increases the bond strength by altering the substrate surface in a number of ways, including increasing the surface roughness and changing the surface chemistry. Chapter 6 deals with the characterization of the polyurethane scaffolds, which were fabricated using an enhanced solvent casting/particulate (salt) leaching (SCPL) method developed for preparing three-dimensional porous scaffolds for cardiac tissue engineering. The enhanced method involves the combination of a conventional SCPL method and a step of centrifugation, with the centrifugation being employed to improve the pore uniformity and interconnectivity of the scaffolds. It is shown that the enhanced SCPL method and a collagen coating resulted in a spatially uniform distribution of cells throughout the collagen-coated PU scaffolds.In Chapter 7, the enhanced SCPL method is used to form porous features on the polyurethane-coated titanium substrate. The cavities anchored the endothelial cells to remain on the blood contacting surfaces. It is shown that the surface porosities created by the enhanced SCPL may be useful in forming a stable endothelial layer upon the blood contacting surface. Chapter 8 finally summarises the entire work performed on the fabrication and analysis of the polymer-Ti bonding, the enhanced SCPL method and the PU microporous surface on the metallic substrate. It then outlines the possibilities for future work and research in this area.

Preventing sexual violence?

This article critically assesses the main social policy responses to preventing rape following much feminist struggle to make sexual violence a public matter of legitimate concern. It considers the preventative potential of legal measures, anti-violence campaigns waged by feminist and men's groups in the US and Australia, public education campaigns in Schools and Universities, and public awareness campaigns sponsored by the state.We argue that sexual violence is not amenable to quick fix strategies that place responsibility for prevention entirely on individual men or women. While we recognise that responsibilising victims and individualising offenders is consistent with wider global shifts in social policy calling upon individuals to manage their own risk, we argue that the increasing reliance on such neo-liberal social policy is especially problematic in preventing rape. The paper suggests ways to resist this which place greater emphasis on the promotion of sexual ethics; the eroticisation of consent; the reinvention of the norms of romance to include both these, and the complete separation of the psycho-social-symbolic connections between sex and violence, and ultimately the re-evaluation of the cultural expectations of masculinity and femininity.

Selective growth of carbon nanotubes on bare silicon : MWNT sinthesys on patterned substrates without predeposition of metal catalyst

Carbon nanotubes (CNTs) are expected to become the ideal constituent of many technologes, in particular for future generation electronics. This considerable interest is due to their unique electrical and mechanical properties. They show indeed super-high current-carrying capacity, ballistic electron transport and good field-emission properties. Then, these superior features make CNTs the most promising building blocks for electronic devices, as organic solar cells and organic light emitting devices (OLED). By using Focused Ion Beam (FIB) patterning it is possible to a obtain a high control on position, relative distances and diameter of CNTs. The present work shows how to grow three-dimensional architecture made of vertical-aligned CNTs directly on silicon. Thanks to the higher activity of a pre-patterned surface the synthesis process results very quick, cheap and simple. Such large area growths of CNTs could be used in preliminary test for application as electrodes for organic solar cells.

Technical report : acoustic analysis of the natural environment

This technical report is concerned with one aspect of environmental monitoring—the detection and analysis of acoustic events in sound recordings of the environment. Sound recordings offer ecologists the potential advantages of cheaper and increased sampling. An acoustic event detection algorithm is introduced that outputs a compact rectangular marquee description of each event. It can disentangle superimposed events, which are a common occurrence during morning and evening choruses. Next, three uses to which acoustic event detection can be put are illustrated. These tasks have been selected because they illustrate quite different modes of analysis: (1) the detection of diffuse events caused by wind and rain, which are a frequent contaminant of recordings of the terrestrial environment; (2) the detection of bird calls using the spatial distribution of their component events; and (3) the preparation of acoustic maps for whole ecosystem analysis. This last task utilises the temporal distribution of events over a daily, monthly or yearly cycle.

An optimising compiler for generated tiny virtual machines

VMSCRIPT is a scripting language designed to allow small programs to be compiled for a range of generated tiny virtual machines, suitable for sensor network devices. The VMSCRIPT compiler is an optimising compiler designed to allow quick re-targeting, based on a template, code rewriting model. A compiler backend can be specified at the same time as a virtual machine, with the compiler reading the specification and using it as a code generator.

Personal epistemology in pre-service teachers : belief changes throughout a teacher education course

Classrooms of the 21st century are complex systems. They support diverse learners from varied contexts and function in a “messy” bricolage of policy contexts. This complexity is also evident in the nature of teaching and learning deployed in these classrooms. There is also, in current contexts, a general expectation that teachers will support students to construct, rather than simply receive knowledge. This process of constructing knowledge requires a focus on critical thinking in complex social and real world contexts (see also Elen & Clarebout, 2001; Yang, Chang & Hsu 2008). Critical thinking, which involves the identification and evaluation of multiple perspectives when making decisions, is a process of knowing – a tool of wisdom (Kuhn & Udell, 2001). Schommer-Aikens, Bird and Bakken (2010) refer to classrooms that encourage critical thinking as “epistemologically based” in which “the teacher encourages his/her students to look for connections among concepts within the text, with their prior knowledge, and with concepts found in the world beyond themselves” (p. 48).

Technical report : acoustic analysis of the natural environment

This technical report is concerned with one aspect of environmental monitoring—the detection and analysis of acoustic events in sound recordings of the environment. Sound recordings offer ecologists the potential advantages of cheaper and increased sampling. An acoustic event detection algorithm is introduced that outputs a compact rectangular marquee description of each event. It can disentangle superimposed events, which are a common occurrence during morning and evening choruses. Next, three uses to which acoustic event detection can be put are illustrated. These tasks have been selected because they illustrate quite different modes of analysis: (1) the detection of diffuse events caused by wind and rain, which are a frequent contaminant of recordings of the terrestrial environment; (2) the detection of bird calls using the spatial distribution of their component events; and (3) the preparation of acoustic maps for whole ecosystem analysis. This last task utilises the temporal distribution of events over a daily, monthly or yearly cycle.

Introduction and Epilogue to Special Issue: Re-conceiving the artful in management development and education

The editorial focus of this issue is on artful, aesthetic and artistic endeavours in management. Being artful is not about arts-based quick fixes. In the context of this Special Issue, to be artful is to transform self through profound learning experiences that expand human consciousness, often facilitated by artistic processes. In management education and development this suggests a shift from instrumental management towards a paradigm of artful creation. Why the arts and artfulness? And why now? In what ways can the arts inform, inspire and leverage management development and education?