Stochastic models and simulation of ion channel dynamics

The behaviour of ion channels within cardiac and neuronal cells is intrinsically stochastic in nature. When the number of channels is small this stochastic noise is large and can have an impact on the dynamics of the system which is potentially an issue when modelling small neurons and drug block in cardiac cells. While exact methods correctly capture the stochastic dynamics of a system they are computationally expensive, restricting their inclusion into tissue level models and so approximations to exact methods are often used instead. The other issue in modelling ion channel dynamics is that the transition rates are voltage dependent, adding a level of complexity as the channel dynamics are coupled to the membrane potential. By assuming that such transition rates are constant over each time step, it is possible to derive a stochastic differential equation (SDE), in the same manner as for biochemical reaction networks, that describes the stochastic dynamics of ion channels. While such a model is more computationally efficient than exact methods we show that there are analytical problems with the resulting SDE as well as issues in using current numerical schemes to solve such an equation. We therefore make two contributions: develop a different model to describe the stochastic ion channel dynamics that analytically behaves in the correct manner and also discuss numerical methods that preserve the analytical properties of the model.

From concept to capability : developing design thinking within a professional services firm

Corporate business and management are embracing design thinking for its potential to deliver competitive advantage through helping them be more innovative, differentiate their brands, and bring more customer centric products and services to market (Brown, 2008). As consumers continue to expect more personalisation and customisation from their service providers, the use of design thinking for innovation within organisations is a logical progression. To date however, there is little empirical literature discussing how organisations are setting about integrating design thinking into their culture and innovation practices. This paper is a first step in initiating a scholarly discussion on the integration of design thinking within organisational culture. Deloitte Australia is a large professional services firm employing over 5700 staff in 12 offices across Australia. The company provides a range of services to clients in the areas of audit, tax, financial advisory and consulting. In early 2011 the company made a strategic commitment to introducing design thinking into the organisation’s practices. While it already maintains a strong innovation culture, to date it had largely been operating within an analytical business environment. For Deloitte, design thinking is an opportunity to create better outcomes for the people they serve – both internal and external stakeholders (Brown and Wyatt, 2010). Research was conducted using case study methodology and ethnographic methods from June to September 2011 at the Melbourne Deloitte office. It involved three methods of data collection: semi structured interviews, participant observation and artifact analysis. This paper presents preliminary case study findings of Deloitte’s approach to building awareness and a consistent understanding of design thinking, as well as large scale capability, across the firm. Deloitte’s commitment to transforming its culture to one of design thinking poses significant potential for understanding how design thinking is comprehended, enabled and integrated within a complex organisational environment.

Peer review of teaching practice and resources : exploring new spaces to embrace cultural change

The implementation of systematic peer review as a professional development activity, and as a support for educational design activities is under-utilised in many Australian higher education institutions. This case study reports on the first stages of planning and implementation of an institution-wide project to enhance teaching and learning quality at a remote and regional university, where one of the major strategies for improvement is peer review. Through a systematic process of staff engagement in peer review, within and from outside the organisation, a substantial change in flexible learning is envisaged. A mix of new and different learning spaces are to be used in the project, including blended learning spaces for academic development. This paper describes the research framework that will guide the peer review process and examines the early findings of the design-based research. Leadership, awareness raising and development of a supportive community of inquiry are seen as key components for successful implementation of peer review. In addition, unique contextual elements add to the complexity of designing for transformative change within such a relatively new organization.

Comparison of high level FPGA hardware design for solving tri-diagonal linear systems

Reconfigurable computing devices can increase the performance of compute intensive algorithms by implementing application specific co-processor architectures. The power cost for this performance gain is often an order of magnitude less than that of modern CPUs and GPUs. Exploiting the potential of reconfigurable devices such as Field-Programmable Gate Arrays (FPGAs) is typically a complex and tedious hardware engineering task. Re- cently the major FPGA vendors (Altera, and Xilinx) have released their own high-level design tools, which have great potential for rapid development of FPGA based custom accelerators. In this paper, we will evaluate Altera’s OpenCL Software Development Kit, and Xilinx’s Vivado High Level Sythesis tool. These tools will be compared for their per- formance, logic utilisation, and ease of development for the test case of a Tri-diagonal linear system solver.

Computation of ECG signal features using MCMC modelling in software and FPGA reconfigurable hardware

Computational optimisation of clinically important electrocardiogram signal features, within a single heart beat, using a Markov-chain Monte Carlo (MCMC) method is undertaken. A detailed, efficient data-driven software implementation of an MCMC algorithm has been shown. Initially software parallelisation is explored and has been shown that despite the large amount of model parameter inter-dependency that parallelisation is possible. Also, an initial reconfigurable hardware approach is explored for future applicability to real-time computation on a portable ECG device, under continuous extended use.

Computational science for undergraduate biologists via QUT.Bio.Excel

Molecular biology is a scientific discipline which has changed fundamentally in character over the past decade to rely on large scale datasets – public and locally generated - and their computational analysis and annotation. Undergraduate education of biologists must increasingly couple this domain context with a data-driven computational scientific method. Yet modern programming and scripting languages and rich computational environments such as R and MATLAB present significant barriers to those with limited exposure to computer science, and may require substantial tutorial assistance over an extended period if progress is to be made. In this paper we report our experience of undergraduate bioinformatics education using the familiar, ubiquitous spreadsheet environment of Microsoft Excel. We describe a configurable extension called QUT.Bio.Excel, a custom ribbon, supporting a rich set of data sources, external tools and interactive processing within the spreadsheet, and a range of problems to demonstrate its utility and success in addressing the needs of students over their studies.

Dielectric performance of polymer nanocomposites synthesized by atmospheric-pressure plasma-treated silica nanoparticles

In this study, atmospheric-pressure plasmas were applied to modify the surface of silane-coated silica nanoparticles. Subsequently nanocomposites were synthesized by incorporating plasma-treated nanoparticles into an epoxy resin matrix. Electrical testing showed that such novel dielectric materials obtained high partial discharge resistance, high dielectric breakdown strength, and enhanced endurance under highly stressed electric field. Through spectroscopic and microscopic analysis, we found surface groups of nanoparticles were activated and radicals were created after the plasma treatment. Moreover, a uniform dispersion of nanoparticles in nanocomposites was observed. It was expected that the improved dielectric performance of the nanocomposites can attribute to stronger chemical bonds formed between surface groups of plasma-treated nanoparticles and molecules in the matrix. This simple yet effective and environmentally friendly approach aims to synthesize the next generation of high-performance nanocomposite dielectric insulation materials for applications in high-voltage power systems.

Visualization of long-duration acoustic recordings of the environment

Acoustic recordings of the environment are an important aid to ecologists monitoring biodiversity and environmental health. However, rapid advances in recording technology, storage and computing make it possible to accumulate thousands of hours of recordings, of which, ecologists can only listen to a small fraction. The big-data challenge addressed in this paper is to visualize the content of long-duration audio recordings on multiple scales, from hours, days, months to years. The visualization should facilitate navigation and yield ecologically meaningful information. Our approach is to extract (at one minute resolution) acoustic indices which reflect content of ecological interest. An acoustic index is a statistic that summarizes some aspect of the distribution of acoustic energy in a recording. We combine indices to produce false-color images that reveal acoustic content and facilitate navigation through recordings that are months or even years in duration.

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.

Clustering acoustic events in environmental recordings for species richness surveys

Environmental acoustic recordings can be used to perform avian species richness surveys, whereby a trained ornithologist can observe the species present by listening to the recording. This could be made more efficient by using computational methods for iteratively selecting the richest parts of a long recording for the human observer to listen to, a process known as “smart sampling”. This allows scaling up to much larger ecological datasets. In this paper we explore computational approaches based on information and diversity of selected samples. We propose to use an event detection algorithm to estimate the amount of information present in each sample. We further propose to cluster the detected events for a better estimate of this amount of information. Additionally, we present a time dispersal approach to estimating diversity between iteratively selected samples. Combinations of approaches were evaluated on seven 24-hour recordings that have been manually labeled by bird watchers. The results show that on average all the methods we have explored would allow annotators to observe more new species in fewer minutes compared to a baseline of random sampling at dawn.

Populations of models, experimental designs and coverage of parameter space by Latin Hypercube and Orthogonal Sampling

In this paper we have used simulations to make a conjecture about the coverage of a t-dimensional subspace of a d-dimensional parameter space of size n when performing k trials of Latin Hypercube sampling. This takes the form P(k,n,d,t) = 1 - e^(-k/n^(t-1)). We suggest that this coverage formula is independent of d and this allows us to make connections between building Populations of Models and Experimental Designs. We also show that Orthogonal sampling is superior to Latin Hypercube sampling in terms of allowing a more uniform coverage of the t-dimensional subspace at the sub-block size level. These ideas have particular relevance when attempting to perform uncertainty quantification and sensitivity analyses.

R U there yet? using virtual classrooms to transform teaching practice

Access to quality higher education is challenging for many Western Australians that live outside the metropolitan area. In 2010, the School of Education moved to flexible delivery of a fully online Bachelor of Education degree for their non -metropolitan students. The new model of delivery allows access for students from any location provided they have a computer and an internet connection. A number of academic staff had previously used an asynchronous environment to deliver learning modules housed within a learning management system (LMS) but had not used synchronous software with their students. To enhance the learning environment and to provide high quality learning experiences to students learning at a distance, the adoption of synchronous software (Elluminate Live) was introduced. This software is a real-time virtual classroom environment that allows for communication through Voice over Internet Protocol (VoIP) and videoconferencing, along with a large number of collaboration tools to engage learners. This research paper reports on the integration of a live e-learning solution into the current LMS environment. Qualitative data were collected from academic staff through informal interviews and participant observation. The findings discuss (i) perceived level of support; (ii) identification of strategies used to create an effective online teacher presence; (iii) the perceived impact on the students' learning outcomes; and (iv) guidelines for professional development to enhance pedagogy within the live e-learning environment.

Domestic violence on #qanda: The “Man” question in live Twitter discussion on the Australian Broadcasting Corporation's Q&A

Domestic violence is currently undergoing a period of heightened visibility in Australia. This article uses social media to analyze public discussions about this violence with respect to a specific theoretical frame, which Adrian Howe has called the “Man” question: where and how are men visible or invisible in narratives about their violence against women? The article presents a qualitative study of the Twitter conversation surrounding a special episode of the Australian Broadcasting Corporation's television program Q&A, themed around family violence, which aired in February 2015. We found that the place of men in this conversation was contested. Some tweets privileged men's voices and concerns, as did the organization and production of the program. However, feminist voices were also highly visible via presenting facts, legitimating survivor voices, and recuperating anti-feminist memes to challenge hegemonic patriarchal discourses on men's violence against women. La violence conjugale connait actuellement une visibilité accrue en Australie. Les auteures du présent article utilisent les réseaux sociaux pour analyser les débats publics sur cette violence selon un cadre théorique précis, qu'Adrian Howe a appelé la question de « l'homme » : où et comment les hommes sont-ils visibles ou invisibles dans les récits de leur violence envers les femmes? L'article présente une étude qualitative d'une conversation sur Twitter au sujet d'un épisode axé sur la famille diffusé en février 2015 dans le cadre de l'émission Q & A, à la télévision nationale d'Australie. Nous avons remarqué que dans cette conversation la place des hommes était remise en question. Certains tweets privilégiaient les voix et les craintes des hommes, comme l'ont fait les organisateurs et les producteurs de l'émission. Cependant, il y avait une forte présence de voix féministes dans la présentation des faits, légitimant le point de vue des survivantes et relevant des éléments culturels antiféministes afin de défier les discours hégémoniques et patriarcaux sur la violence des hommes envers les femmes.

Warfare in stingless bees

Bees are well known for being industrious pollinators. Some species, however, have taken to invading the nests of other colonies to steal food, nest material or the nest site itself. Despite the potential mortality costs due to fighting with an aggressive opponent, the prospects of a large bounty can be worth the risk. In this review, we aim to bring together current knowledge on intercolony fighting with a view to better understand the evolution of warfare in bees and identify avenues for future research. A review of literature reveals that at least 60 species of stingless bees are involved in heterospecific conflicts, either as attacking or victim colonies. The threat of invasion has led to the evolution of architectural, behavioural and morphological adaptations, such as narrow entrance tunnels, mud balls to block the entrance, decoy nests that direct invaders away from the brood chamber, fighting swarms, and soldiers that are skilled at immobilising attackers. Little is known about how victim colonies are selected, but a phylogenetically controlled analysis suggests that the notorious robber bee Lestrimelitta preferentially attacks colonies of species with more concentrated honey. Warfare among bees poses many interesting questions, including why species differ so greatly in their response to attacks and how these alternative strategies of obtaining food or new nest sites have evolved.