Choose wisely: Network, ontology and annotation resources for the analysis of Staphylococcus aureus omics data

Staphylococcus aureus (S. aureus) is a prominent human and livestock pathogen investigated widely using omic technologies. Critically, due to availability, low visibility or scattered resources, robust network and statistical contextualisation of the resulting data is generally under-represented. Here, we present novel meta-analyses of freely-accessible molecular network and gene ontology annotation information resources for S. aureus omics data interpretation. Furthermore, through the application of the gene ontology annotation resources we demonstrate their value and ability (or lack-there-of) to summarise and statistically interpret the emergent properties of gene expression and protein abundance changes using publically available data. This analysis provides simple metrics for network selection and demonstrates the availability and impact that gene ontology annotation selection can have on the contextualisation of bacterial omics data.

Implementation of National Rental Affordability Scheme in Queensland

In 2008 the Australian government introduced the National Rental Affordability Scheme (NRAS) to increase the supply of affordable rental in Australia. This Federal Government initiative was progressively rolled out through four different rounds over the years with fifth round to be announced some time in 2014. Although the scheme has been successful evident there have been numerous setbacks experienced. This paper focuses on understanding lessons learnt from the performance of the scheme to make recommendations for future government initiatives. This evaluation is based on the combination of document analysis, government officers as well as approved NRAS participants operating throughout Queensland. The most significant challenges for the NRAS participants is the involvement of three levels government which cause delays in the scheme approval process.

Submission to Communications Alliance Industry Code: Copyright Notice Scheme

In making this submission, we suggest that Australia learn from the experiences of other jurisdictions, and avoid some of the mistakes that have been made. In particular, this involves: * Ensuring that adequate information is available to evaluate the success of the scheme * Ensuring that notices sent to consumers provide full and accurate information that helps them understand their rights and options * Limiting the potential abuse of the system, and particularly attempts to intimidate consumers into paying unfair penalties through ‘speculative invoicing’ * Avoiding the potential for actual or perceived bias in the scheme’s oversight body

Content-independent embedding scheme for multi-modal medical image watermarking

Background As the increasing adoption of information technology continues to offer better distant medical services, the distribution of, and remote access to digital medical images over public networks continues to grow significantly. Such use of medical images raises serious concerns for their continuous security protection, which digital watermarking has shown great potential to address. Methods We present a content-independent embedding scheme for medical image watermarking. We observe that the perceptual content of medical images varies widely with their modalities. Recent medical image watermarking schemes are image-content dependent and thus they may suffer from inconsistent embedding capacity and visual artefacts. To attain the image content-independent embedding property, we generalise RONI (region of non-interest, to the medical professionals) selection process and use it for embedding by utilising RONI’s least significant bit-planes. The proposed scheme thus avoids the need for RONI segmentation that incurs capacity and computational overheads. Results Our experimental results demonstrate that the proposed embedding scheme performs consistently over a dataset of 370 medical images including their 7 different modalities. Experimental results also verify how the state-of-the-art reversible schemes can have an inconsistent performance for different modalities of medical images. Our scheme has MSSIM (Mean Structural SIMilarity) larger than 0.999 with a deterministically adaptable embedding capacity. Conclusions Our proposed image-content independent embedding scheme is modality-wise consistent, and maintains a good image quality of RONI while keeping all other pixels in the image untouched. Thus, with an appropriate watermarking framework (i.e., with the considerations of watermark generation, embedding and detection functions), our proposed scheme can be viable for the multi-modality medical image applications and distant medical services such as teleradiology and eHealth.

Semi-automated annotation of environmental acoustic recordings

Environmental sensors collect massive amounts of audio data. This thesis investigates computational methods to support human analysts in identifying faunal vocalisations from that audio. A series of experiments was conducted to trial the effectiveness of novel user interfaces. This research examines the rapid scanning of spectrograms, decision support tools for users, and cleaning methods for folksonomies. Together, these investigations demonstrate that providing computational support to human analysts increases their efficiency and accuracy; this allows bioacoustics projects to efficiently utilise their valuable human analysts.

A stochastic exponential Euler scheme for simulation of stiff biochemical reaction systems

In order to simulate stiff biochemical reaction systems, an explicit exponential Euler scheme is derived for multidimensional, non-commutative stochastic differential equations with a semilinear drift term. The scheme is of strong order one half and A-stable in mean square. The combination with this and the projection method shows good performance in numerical experiments dealing with an alternative formulation of the chemical Langevin equation for a human ether a-go-go related gene ion channel mode

A benchmark for numerical scheme validation of airborne particle exposure in street canyons

Measurements of particle concentrations and distributions in terms of number, surface area, and mass were performed simultaneously at eight sampling points within a symmetric street canyon of an Italian city. The aim was to obtain a useful benchmark for validation of wind tunnel experiments and numerical schemes: to this purpose, the influence of wind directions and speeds was considered. Particle number concentrations (PNCs) were higher on the leeward side than the windward side of the street canyon due to the wind vortex effect. Different vertical PNC profiles were observed between the two canyon sides depending on the wind direction and speed at roof level. A decrease in particle concentrations was observed with increasing rooftop wind speed, except for the coarse fraction indicating a possible particle resuspension due to the traffic and wind motion. This study confirms that particle concentration fields in urban street canyons are strongly influenced by traffic emissions and meteorological parameters, especially wind direction and speed.

Evaluation of the relationship between Chlamydia pecorum sequence types and disease using a species-specific multi-locus sequence typing scheme (MLST)

Chlamydia pecorum is globally associated with several ovine diseases including keratoconjunctivitis and polyarthritis. The exact relationship between the variety of C. pecorum strains reported and the diseases described in sheep remains unclear, challenging efforts to accurately diagnose and manage infected flocks. In the present study, we applied C. pecorum multi-locus sequence typing (MLST) to C. pecorum positive samples collected from sympatric flocks of Australian sheep presenting with conjunctivitis, conjunctivitis with polyarthritis, or polyarthritis only and with no clinical disease (NCD) in order to elucidate the exact relationships between the infecting strains and the range of diseases. Using Bayesian phylogenetic and cluster analyses on 62 C. pecorum positive ocular, vaginal and rectal swab samples from sheep presenting with a range of diseases and in a comparison to C. pecorum sequence types (STs) from other hosts, one ST (ST 23) was recognised as a globally distributed strain associated with ovine and bovine diseases such as polyarthritis and encephalomyelitis. A second ST (ST 69) presently only described in Australian animals, was detected in association with ovine as well as koala chlamydial infections. The majority of vaginal and rectal C. pecorum STs from animals with NCD and/or anatomical sites with no clinical signs of disease in diseased animals, clustered together in a separate group, by both analyses. Furthermore, 8/13 detected STs were novel. This study provides a platform for strain selection for further research into the pathogenic potential of C. pecorum in animals and highlights targets for potential strain-specific diagnostic test development.

Grant application: QUT Learning and Teaching scheme 2012 Cracking the Code - A checklist to complement CRAs for first year Justice students.

Widening participation brings with it increasing diversity, increased variation in the level of academic preparedness (Clarke, 2011; Nelson, Clarke, & Kift 2010). Cultural capital coupled with negotiating the academic culture creates an environment based on many assumptions about academic writing and university culture. Variations in staff and student expectations relating to the teaching and learning experience is captured in a range of national and institutional data (AUSSE, CEQ, LEX). Nationally, AUSSE data (2009) indicates that communication, writing, speaking and analytic skills, staff expectations are quite a bit higher than students. The research team noted a recognisable shift in the changing cohort of students and their understanding and engagement with feedback and CRAs, as well as variations in teaching staff and student expectations. The current reality of tutor and student roles is that: - Students self select when/how they access lectures and tutorials. - Shorter tutorial times result in reduced opportunity to develop rapport with students. - CRAs are not always used consistently by staff (different marking styles and levels of feedback). - Marking is not always undertaken by the student’s tutor/lecturer. - Student support services might be recommended to students once a poor grade has been given. Students can perceive this as remedial and a further sense of failure. - CRA sheet has a mark /grade attached to it. Stigma attached to low mark. Hard to focus on the CRA feedback with a poor mark etched next to it. - Limited opportunities for sessionals to access professional development to assist with engaging students and feedback. - FYE resources exist, however academic time is a factor in exploring and embedding these resources. Feedback is another area with differing expectations and understandings. Sadler (2009) contends that students are not equipped to decode the statements properly. For students to be able to apply feedback, they need to understand the meaning of the feedback statement. They also need to identify, the particular aspects of their work that need attention. The proposed Checklist/guide would be one page and submitted with each assessment piece thereby providing an interface to engage students and tutors in managing first year understandings and expectations around CRAs, feedback, and academic practice.

Australian data do not support current pharmaceutical benefits scheme criteria for use of tumour necrosis factor-α inhibitors in ankylosing spondylitis

On the basis of local data, we write in support of the conclusions of Smith and Ahern that current Pharmaceu- tical Benefits Scheme (PBS) criteria for tumour necrosis factor (TNF)-a inhibitors in ankylosing spondylitis (AS) are not evidence-based. 1 As a prerequisite to the appropriate use of biological therapy in AS, three aspects of the disease need to be defined: (i) diagnosis, (ii) activity and (iii) therapeutic failure (Table 1)....

An Explicit Guidance Scheme For A Low-Thrust Terminal Rendezvous

An explicit near-optimal guidance scheme is developed for a terminal rendezvous of a spacecraft with a passive target in circular orbit around the earth. The thrust angle versus time profile for the continuous-thrust, constant-acceleration maneuver is derived, based on the assumption that the components of inertial acceleration due to relative position and velocity are negligible on account of the close proximity between the two spacecraft. The control law is obtained as a ''bilinear tangent law'' and an analytic solution to the state differential equations is obtained by expanding a portion of the integrand as an infinite series in time. A differential corrector method is proposed, to obtain real-time updates to the guidance parameters at regular time intervals. Simulation of the guidance scheme is carried out using the Clohessy-Wiltshire equations of relative motion as well as the inverse-square two-body equations of motion. Results for typical examples are presented.

A frame-invariant scheme for the geometrically exact beam using rotation vector parametrization

While frame-invariant solutions for arbitrarily large rotational deformations have been reported through the orthogonal matrix parametrization, derivation of such solutions purely through a rotation vector parametrization, which uses only three parameters and provides a parsimonious storage of rotations, is novel and constitutes the subject of this paper. In particular, we employ interpolations of relative rotations and a new rotation vector update for a strain-objective finite element formulation in the material framework. We show that the update provides either the desired rotation vector or its complement. This rules out an additive interpolation of total rotation vectors at the nodes. Hence, interpolations of relative rotation vectors are used. Through numerical examples, we show that combining the proposed update with interpolations of relative rotations yields frame-invariant and path-independent numerical solutions. Advantages of the present approach vis-a-vis the updated Lagrangian formulation are also analyzed.

Scheme of squares: Part I. Systems formalism for potentiostatic studies

The so-called “Scheme of Squares”, displaying an interconnectivity of heterogeneous electron transfer and homogeneous (e.g., proton transfer) reactions, is analysed. Explicit expressions for the various partial currents under potentiostatic conditions are given. The formalism is applicable to several electrode geometries and models (e.g., semi-infinite linear diffusion, rotating disk electrodes, spherical or cylindrical systems) and the analysis is exact. The steady-state (t→∞) expressions for the current are directly given in terms of constant matrices whereas the transients are obtained as Laplace transforms that need to be inverted by approximation of numerical methods. The methodology employs a systems approach which replaces a system of partial differential equations (governing the concentrations of the several electroactive species) by an equivalent set of difference equations obeyed by the various partial currents.

Scheme of squares: Part II. Systems formalism for sinusoidal perturbations

We extend here the formalism developed in Part I (for the potentiostatic response) to the admittance analysis of the scheme of squares. The results are applicable, as before, to several configurations of the electrode such as the rotating disk or the planar. All that one has to do is “to plug in” the appropriate matrices relating the interfacial concentrations to the fluxes.

A Fuzzy Approximation Scheme for Sequential Learning in Pattern Recognition

An adaptive learning scheme, based on a fuzzy approximation to the gradient descent method for training a pattern classifier using unlabeled samples, is described. The objective function defined for the fuzzy ISODATA clustering procedure is used as the loss function for computing the gradient. Learning is based on simultaneous fuzzy decisionmaking and estimation. It uses conditional fuzzy measures on unlabeled samples. An exponential membership function is assumed for each class, and the parameters constituting these membership functions are estimated, using the gradient, in a recursive fashion. The induced possibility of occurrence of each class is useful for estimation and is computed using 1) the membership of the new sample in that class and 2) the previously computed average possibility of occurrence of the same class. An inductive entropy measure is defined in terms of induced possibility distribution to measure the extent of learning. The method is illustrated with relevant examples.