Identification of long intergenic region sequences involved in maize streak virus replication

The main cis-acting control regions for replication of the single-stranded DNA genome of maize streak virus (MSV) are believed to reside within an approximately 310 nt long intergenic region (LIR). However, neither the minimum LIR sequence required nor the sequence determinants of replication specificity have been determined experimentally. There are iterated sequences, or iterons, both within the conserved inverted-repeat sequences with the potential to form a stem-loop structure at the origin of virion-strand replication, and upstream of the rep gene TATA box (the rep-proximal iteron or RPI). Based on experimental analyses of similar iterons in viruses from other geminivirus genera and their proximity to known Rep-binding sites in the distantly related mastrevirus wheat dwarf virus, it has been hypothesized that the iterons may be Rep-binding and/or -recognition sequences. Here, a series of LIR deletion mutants was used to define the upper bounds of the LIR sequence required for replication. After identifying MSV strains and distinct mastreviruses with incompatible replication-specificity determinants (RSDs), LIR chimaeras were used to map the primary MSV RSD to a 67 nt sequence containing the RPI. Although the results generally support the prevailing hypothesis that MSV iterons are functional analogues of those found in other geminivirus genera, it is demonstrated that neither the inverted-repeat nor RPI sequences are absolute determinants of replication specificity. Moreover, widely divergent mastreviruses can trans-replicate one another. These results also suggest that sequences in the 67 nt region surrounding the RPI interact in a sequence-specific manner with those of the inverted repeat.

Meaning or measurement? Researching the social contexts of health and settlement among newly-arrived refugee youth in Melbourne, Australia

What are the most appropriate methodological approaches for researching the psychosocial determinants of health and wellbeing among young people from refugee backgrounds over the resettlement period? What kinds of research models can involve young people in meaningful reflections on their lives and futures while simultaneously yielding valid data to inform services and policy? This paper reports on the methods developed for a longitudinal study of health and wellbeing among young people from refugee backgrounds in Melbourne, Australia. The study involves 100 newly-arrived young people 12 to 18 years of age, and employs a combination of qualitative and quantitative methods implemented as a series of activities carried out by participants in personalized settlement journals. This paper highlights the need to think outside the box of traditional qualitative and/or quantitative approaches for social research into refugee youth health and illustrates how integrated approaches can produce information that is meaningful to policy makers, service providers and to the young people themselves.

The analogue shear zone : from rheology to associated geometry

The geometry of ductile strain localization phenomena is related to the rheology of the deformed rocks. Both qualitative and quantitative rheological properties of natural rocks have been estimated from finite field structures such as folds and shear zones. We apply physical modelling to investigate the relationship between rheology and the temporal evolution of the width and transversal strain distribution in shear zones, both of which have been used previously as rheological proxies. Geologically relevant materials with well-characterized rheological properties (Newtonian, strain hardening, strain softening, Mohr-Coulomb) are deformed in a shear box and observed with Particle Imaging Velocimetry (PIV). It is shown that the width and strain distribution histories in model shear zones display characteristic finite responses related to material properties as predicted by previous studies. Application of the results to natural shear zones in the field is discussed. An investigation of the impact of 3D boundary conditions in the experiments demonstrates that quantitative methods for estimating rheology from finite natural structures must take these into account carefully.

Bear With Me

This project investigates musicalisation and intermediality in the writing and devising of composed theatre. Its research question asks “How does the narrative of a musical play differ when it emerges from a setlist of original songs?”, the aim being to create performance event that is neither music nor theatre. This involves composition of lyrics, music, action and spoken text, projected image: gathered in a script and presented in performance. Scholars such as Kulezic-Wilson(in Kendrick, L and Roesner, D 2011:34) outline the acoustic dimension to the ‘performative turn’ (Mungen, Ernst and Bentzweizer, 2012) as heralding “…a shift of emphasis on how meaning is created (and veiled) and how the spectrum of theatrical creation and reception is widened.” Rebstock and Roesner (2012) capture approaches similar to this, building on Lehmann’s work in the post-dramatic under the new term ‘composed theatre’. This practice led research draws influence from these new theoretical frames, pushing beyond ‘the musical’. Springing from a set of original songs in dialogue with performed narrative, Bear with Me is a 45 minute music driven work for children, involving projected image and participatory action. Bear with Me’s intermedial hybrid of theatrical, screen and concert presentations shows that a simple setlist of original songs can be the starting point for the structure of a complex intermedial performance. Bear with Me was programmed into the Queensland Performing Arts Centre’s Out of the Box Festival. It was first performed in the Tony Gould Gallery at the Queensland in June 2012. The season sold out. A masterclass on my playwriting methodology was presented at the Connecting The Dots Symposium which ran alongside the festival.

Implementation Guide for Surveillance of Staphylococcus aureus Bacteraemia -- [Consultation Edition]

The Implementation Guide for the Hospital Surveillance of SAB has been produced by the Healthcare Associated Infection (HAI) Technical Working Group of the Australian Commission on Safety and Quality in Health Care (ACSQHC), and endorsed by the HAI Advisory Group. The Technical Working Group is made up of representatives invited from surveillance units and the ACSQHC, who have had input into the preparation of this Guide. The Guide has been developed to ensure consistency in reporting of SAB across public and private hospitals to enable accurate national reporting and benchmarking. It is intended to be used by Australian hospitals and organisations to support the implementation of healthcare associated Staphylococcus aureus bacteraemia(SAB) surveillance using the endorsed case definition1 in the box below and further detail in the Data Set Specification.

Static vertical displacement measurement of bridges using Fiber Bragg Grating (FBG) sensors

Vertical displacements are one of the most relevant parameters for structural health monitoring of bridges in both the short and long terms. Bridge managers around the globe are always looking for a simple way to measure vertical displacements of bridges. However, it is difficult to carry out such measurements. On the other hand, in recent years, with the advancement of fiber-optic technologies, fiber Bragg grating (FBG) sensors are more commonly used in structural health monitoring due to their outstanding advantages including multiplexing capability, immunity of electromagnetic interference as well as high resolution and accuracy. For these reasons, using FBG sensors is proposed to develop a simple, inexpensive and practical method to measure vertical displacements of bridges. A curvature approach for vertical displacement measurements using curvature measurements is proposed. In addition, with the successful development of FBG tilt sensors, an inclination approach is also proposed using inclination measurements. A series of simulation tests of a full- scale bridge was conducted. It shows that both of the approaches can be implemented to determine vertical displacements for bridges with various support conditions, varying stiffness (EI) along the spans and without any prior known loading. These approaches can thus measure vertical displacements for most of slab-on-girder and box-girder bridges. Besides, the approaches are feasible to implement for bridges under various loading. Moreover, with the advantages of FBG sensors, they can be implemented to monitor bridge behavior remotely and in real time. A beam loading test was conducted to determine vertical displacements using FBG strain sensors and tilt sensors. The discrepancies as compared with dial gauges reading using the curvature and inclination approaches are 0.14mm (1.1%) and 0.41mm (3.2%), respectively. Further recommendations of these approaches for developments will also be discussed at the end of the paper.

Natural convection flow in a strong cross magnetic field with radiation

The problem of MHD natural convection boundary layer flow of an electrically conducting and optically dense gray viscous fluid along a heated vertical plate is analyzed in the presence of strong cross magnetic field with radiative heat transfer. In the analysis radiative heat flux is considered by adopting optically thick radiation limit. Attempt is made to obtain the solutions valid for liquid metals by taking Pr≪1. Boundary layer equations are transformed in to a convenient dimensionless form by using stream function formulation (SFF) and primitive variable formulation (PVF). Non-similar equations obtained from SFF are then simulated by implicit finite difference (Keller-box) method whereas parabolic partial differential equations obtained from PVF are integrated numerically by hiring direct finite difference method over the entire range of local Hartmann parameter, $xi$ . Further, asymptotic solutions are also obtained for large and small values of local Hartmann parameter $xi$ . A favorable agreement is found between the results for small, large and all values of $xi$ . Numerical results are also demonstrated graphically by showing the effect of various physical parameters on shear stress, rate of heat transfer, velocity and temperature.

Bayesian algorithms with applications

Advances in algorithms for approximate sampling from a multivariable target function have led to solutions to challenging statistical inference problems that would otherwise not be considered by the applied scientist. Such sampling algorithms are particularly relevant to Bayesian statistics, since the target function is the posterior distribution of the unobservables given the observables. In this thesis we develop, adapt and apply Bayesian algorithms, whilst addressing substantive applied problems in biology and medicine as well as other applications. For an increasing number of high-impact research problems, the primary models of interest are often sufficiently complex that the likelihood function is computationally intractable. Rather than discard these models in favour of inferior alternatives, a class of Bayesian "likelihoodfree" techniques (often termed approximate Bayesian computation (ABC)) has emerged in the last few years, which avoids direct likelihood computation through repeated sampling of data from the model and comparing observed and simulated summary statistics. In Part I of this thesis we utilise sequential Monte Carlo (SMC) methodology to develop new algorithms for ABC that are more efficient in terms of the number of model simulations required and are almost black-box since very little algorithmic tuning is required. In addition, we address the issue of deriving appropriate summary statistics to use within ABC via a goodness-of-fit statistic and indirect inference. Another important problem in statistics is the design of experiments. That is, how one should select the values of the controllable variables in order to achieve some design goal. The presences of parameter and/or model uncertainty are computational obstacles when designing experiments but can lead to inefficient designs if not accounted for correctly. The Bayesian framework accommodates such uncertainties in a coherent way. If the amount of uncertainty is substantial, it can be of interest to perform adaptive designs in order to accrue information to make better decisions about future design points. This is of particular interest if the data can be collected sequentially. In a sense, the current posterior distribution becomes the new prior distribution for the next design decision. Part II of this thesis creates new algorithms for Bayesian sequential design to accommodate parameter and model uncertainty using SMC. The algorithms are substantially faster than previous approaches allowing the simulation properties of various design utilities to be investigated in a more timely manner. Furthermore the approach offers convenient estimation of Bayesian utilities and other quantities that are particularly relevant in the presence of model uncertainty. Finally, Part III of this thesis tackles a substantive medical problem. A neurological disorder known as motor neuron disease (MND) progressively causes motor neurons to no longer have the ability to innervate the muscle fibres, causing the muscles to eventually waste away. When this occurs the motor unit effectively ‘dies’. There is no cure for MND, and fatality often results from a lack of muscle strength to breathe. The prognosis for many forms of MND (particularly amyotrophic lateral sclerosis (ALS)) is particularly poor, with patients usually only surviving a small number of years after the initial onset of disease. Measuring the progress of diseases of the motor units, such as ALS, is a challenge for clinical neurologists. Motor unit number estimation (MUNE) is an attempt to directly assess underlying motor unit loss rather than indirect techniques such as muscle strength assessment, which generally is unable to detect progressions due to the body’s natural attempts at compensation. Part III of this thesis builds upon a previous Bayesian technique, which develops a sophisticated statistical model that takes into account physiological information about motor unit activation and various sources of uncertainties. More specifically, we develop a more reliable MUNE method by applying marginalisation over latent variables in order to improve the performance of a previously developed reversible jump Markov chain Monte Carlo sampler. We make other subtle changes to the model and algorithm to improve the robustness of the approach.

Are we keeping the bastards honest? Perceptions of corruption, integrity and influence on politics

The words of the late Don Chipp, the founder of the Australian Democrats, have a perennial relevance to politics. When Chipp talked about ‘keeping the bastards honest’, it related to a minor political party playing a role of keeping the major political parties true to their word (Warhurst 1997). Yet it is also a democratic role that citizens play on an ongoing basis, particularly through the mechanism of elections. At the ballot box, governments that are widely perceived to have acted with a lack of integrity are roundly punished. This chapter explores public opinion on issues of integrity, corruption, influence and trust in politics and politicians in Australia. The evidence paints a differentiated picture of a public which sees little sign of overtly corrupt political practices but on the other hand does not feel terribly influential and is not always confident of fair treatment from public officials...

Nitrous oxide emissions from irrigated wheat in Australia : impact of irrigation management

Background and Aims: Irrigation management affects soil water dynamics as well as the soil microbial carbon and nitrogen turnover and potentially the biosphere-atmosphere exchange of greenhouse gasses (GHG). We present a study on the effect of three irrigation treatments on the emissions of nitrous oxide (N2O) from irrigated wheat on black vertisols in South-Eastern Queensland, Australia. Methods: Soil N2O fluxes from wheat were monitored over one season with a fully automated system that measured emissions on a sub-daily basis. Measurements were taken from 3 subplots for each treatment within a randomized split-plot design. Results: Highest N2O emissions occurred after rainfall or irrigation and the amount of irrigation water applied was found to influence the magnitude of these “emission pulses”. Daily N2O emissions varied from -0.74 to 20.46 g N2O-N ha-1 day-1 resulting in seasonal losses ranging from 0.43 to 0.75 kg N2O N ha-1 season -1 for the different irrigation treatments. Emission factors (EF = proportion of N fertilizer emitted as N2O) over the wheat cropping season, uncorrected for background emissions, ranged from 0.2 to 0.4% of total N applied for the different treatments. Highest seasonal N2O emissions were observed in the treatment with the highest irrigation intensity; however, the N2O intensity (N2O emission per crop yield) was highest in the treatment with the lowest irrigation intensity. Conclusions: Our data suggest that timing and amount of irrigation can effectively be used to reduce N2O losses from irrigated agricultural systems; however, in order to develop sustainable mitigation strategies the N2O intensity of a cropping system is an important concept that needs to be taken into account.

Studios for the masses : can student colaboration replace the master-apprentice relationship in design instruction?

This action research project investigated the use of a collaborative learning approach for addressing issues associated with teaching urban design to large, diverse cohorts. As a case study, I observed two semesters of an urban design unit that I revised between 2011 and 2012 to incorporate collaborative learning activities. Data include instructional materials, participant observations, peer-reviews of collaborative learning activities, feedback from students and instructors and student projects. Themes that emerged through qualitative analysis include the challenge of removing inequalities inherent in the diverse cohort, the challenge of unifying project guidance and marking criteria, and the challenge of providing project guidance for a very large cohort. Most notably, the study revealed a need to clarify learning objectives relating to design principles in order to fully transition to and benefit from a collaborative learning model.