Read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molec- ular biology, allowing routine clinical sequencing. NGS data consists of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans, with some strains exhibiting antibiotic resistance. Here we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from other pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

The next generation health intervention tool - Can smart phone applications help young people track and moderate alcohol use and potential harms?

Whilst alcohol is a common feature of many social gatherings, there are numerous immediate and long-term health and social harms associated with its abuse. Alcohol consumption is the world’s third largest risk factor for disease and disability with almost 4% of all deaths worldwide attributed to alcohol. Not surprisingly, alcohol use and binge drinking by young people is of particular concern with Australian data reporting that 39% of young people (18-19yrs) admitted drinking at least weekly and 32% drank to levels that put them at risk of alcohol-related harm. The growing market penetration and connectivity of smartphones may be an opportunities for innovation in promoting health-related self-management of substance use. However, little is known about how best to harness and optimise this technology for health-related intervention and behaviour change. This paper explores the utility and interface of smartphone technology as a health intervention tool to monitor and moderate alcohol use. A review of the psychological health applications of this technology will be presented along with the findings of a series of focus groups, surveys and behavioural field trials of several drink-monitoring applications. Qualitative and quantitative data will be presented on the perceptions, preferences and utility of the design, usability and functionality of smartphone apps to monitoring and moderate alcohol use. How these findings have shaped the development and evolution of the OnTrack app will be specifically discussed, along with future directions and applications of this technology in health intervention, prevention and promotion.

Isolation and characterization of 21 polymorphic microsatellite loci in the iconic Australian lungfish, Neoceratodus forsteri, using the Ion Torrent next-generation sequencing platform

We isolated and characterized 21 microsatellite loci in the vulnerable and iconic Australian lungfish, Neoceratodus forsteri. Loci were screened across eight individuals from the Burnett River and 40 individuals from the Pine River. Genetic diversity was low with between one and six alleles per locus within populations and a maximum expected heterozygosity of 0.774. These loci will now be available to assess effective population sizes and genetic structure in N. forsteri across its natural range in South East Queensland, Australia.

Two-stage power network reconfiguration strategy considering node importance and restored generation capacity

Network reconfiguration after complete blackout of a power system is an essential step for power system restoration. A new node importance evaluation method is presented based on the concept of regret, and maximisation of the average importance of a path is employed as the objective of finding the optimal restoration path. Then, a two-stage method is presented to optimise the network reconfiguration strategy. Specifically, the restoration sequence of generating units is first optimised so as to maximise the restored generation capacity, then the optimal restoration path is selected to restore the generating nodes concerned and the issues of selecting a serial or parallel restoration mode and the reconnecting failure of a transmission line are next considered. Both the restoration path selection and skeleton-network determination are implemented together in the proposed method, which overcomes the shortcoming of separate decision-making in the existing methods. Finally, the New England 10-unit 39-bus power system and the Guangzhou power system in South China are employed to demonstrate the basic features of the proposed method.

Digital PWM waveform generation using adders, not counters

An alternative approach to digital PWM generation using an adder rather than a counter is presented. This offers several advantages. The resolution and gain of the pulse width modulator remain constant regardless of the module clock frequency and PWM output frequency. The PWM resolution also becomes fixed at the register width. Even at high PWM frequencies, the resolution remains high when averaged over a number of PWM cycles. An inherent dithering of the PWM waveform introduced over successive cycles blurs the switching spectra without distorting the modulating waveform. The technique also lends itself to easily generating several phase shifted PWM waveforms suitable for multilevel converter modulation.

Migrating to a sustainable energy system : distributed generation and storage, fuel cells and hypercars

This paper examines a number of issues in sustainable energy generation and distribution, and explores avenues that are available for integration of our society’s energy supplies. In particular, the paper presents a way in which transport vehicle energy supplies could be integrated with distributed generation schemes to achieve synergistic and beneficial outcomes. The worldwide energy system contains fundamental problems that result directly from the use of unsustainable fuels and a lack of energy system integration. There is a need to adopt an integrated, sustainable energy system for our society. The adoption of distributed generation could result in beneficial restructuring of the energy trade, and a change in the role of energy providers. Inherent benefits in distributed generation schemes would directly combat barriers to installation of renewable generation facilities, which might prove distributed renewable energy sources to be more feasible. The presence of fuel cells, batteries, power electronic inverters and intelligent controls in vehicles of the future provides many opportunities for the integration of vehicle energy supplies into a distributed generation scheme. In such a system, vehicles could play a major role in power generation and storage.

Migrating to a sustainable energy system : distributed generation and storage, fuel cells and hypercars

This paper examines a number of issues in sustainable energy generation and distribution, and explores avenues that are available for integration of our society’s energy supplies. In particular, the paper presents a way in which transport vehicle energy supplies could be integrated with distributed generation schemes to achieve synergistic and beneficial outcomes. The worldwide energy system contains fundamental problems that result directly from the use of unsustainable fuels and a lack of energy system integration. There is a need to adopt an integrated, sustainable energy system for our society. The adoption of distributed generation could result in beneficial restructuring of the energy trade, and a change in the role of energy providers. Inherent benefits in distributed generation schemes would directly combat barriers to installation of renewable generation facilities, which might prove distributed renewable energy sources to be more feasible. The presence of fuel cells, batteries, power electronic inverters and intelligent controls in vehicles of the future provides many opportunities for the integration of vehicle energy supplies into a distributed generation scheme. In such a system, vehicles could play a major role in power generation and storage.

Towards a dignified and sustainable electricity generation sector in Australia : a comparative review of three models

Electricity is the cornerstone of modern life. It is essential to economic stability and growth, jobs and improved living standards. Electricity is also the fundamental ingredient for a dignified life; it is the source of such basic human requirements as cooked food, a comfortable living temperature and essential health care. For these reasons, it is unimaginable that today's economies could function without electricity and the modern energy services that it delivers. Somewhat ironically, however, the current approach to electricity generation also contributes to two of the gravest and most persistent problems threatening the livelihood of humans. These problems are anthropogenic climate change and sustained human poverty. To address these challenges, the global electricity sector must reduce its reliance on fossil fuel sources. In this context, the object of this research is twofold. Initially it is to consider the design of the Renewable Energy (Electricity) Act 2000 (Cth) (Renewable Electricity Act), which represents Australia's primary regulatory approach to increase the production of renewable sourced electricity. This analysis is conducted by reference to the regulatory models that exist in Germany and Great Britain. Within this context, this thesis then evaluates whether the Renewable Electricity Act is designed effectively to contribute to a more sustainable and dignified electricity generation sector in Australia. On the basis of the appraisal of the Renewable Electricity Act, this thesis contends that while certain aspects of the regulatory regime have merit, ultimately its design does not represent an effective and coherent regulatory approach to increase the production of renewable sourced electricity. In this regard, this thesis proposes a number of recommendations to reform the existing regime. These recommendations are not intended to provide instantaneous or simple solutions to the current regulatory regime. Instead, the purpose of these recommendations is to establish the legal foundations for an effective regulatory regime that is designed to increase the production of renewable sourced electricity in Australia in order to contribute to a more sustainable and dignified approach to electricity production.

Generation of active surface states of gold and the role of such states in electrocatalysis

The cyclic voltammetry behaviour of gold in aqueous media is often regarded in very simple terms as a combination of two distinct processes, double layer charging/discharging and monolayer oxide formation/removal. This view is questioned here on the basis of both the present results and earlier independent data by other authors. It was demonstrated in the present case that both severe cathodization or thermal pretreatment of polycrystalline gold in acid solution resulted in the appearance of substantial Faradaic responses in the double layer region. Such anamolous behaviour, as outlined recently also for other metals, is rationalized in terms of the presence of active metal atoms (which undergo premonolayer oxidation) at the electrode surface. Such behaviour, which is also assumed to correspond to that of active sites on conventional gold surfaces, is assumed to be of vital importance in electrocatalysis; in many instances the latter process is also quite marked in the double layer region.

Electrochemically-induced TCNQ/Mn TCNQ 2 (H2O) 2 (TCNQ= 7, 7, 8, 8-Tetracyanoquinodimethane) solid-solid interconversion : two voltammetrically distinct processes that allow selective generation of nanofiber or nanorod network morphologies

Unlike the case with other divalent transition metal M\[TCNQ](2)(H(2)O)(2) (M = Fe, Co, Ni) analogues, the electrochemically induced solid-solid phase interconversion of TCNQ microcrystals (TCNQ = 7,7,8,8-tetracyanoquinodimethane) to Mn\[TCNQ](2)(H(2)O)(2) occurs via two voltammetrically distinct, time dependent processes that generate the coordination polymer in nanofiber or rod-like morphologies. Careful manipulation of the voltammetric scan rate, electrolysis time, Mn(2+)((aq)) concentration, and the method of electrode modification with solid TCNQ allows selective generation of either morphology. Detailed ex situ spectroscopic (IR, Raman), scanning electron microscopy (SEM), and X-ray powder diffraction (XRD) characterization clearly establish that differences in the electrochemically synthesized Mn-TCNQ material are confined to morphology. Generation of the nanofiber form is proposed to take place rapidly via formation and reduction of a Mn-stabilized anionic dimer intermediate, \[(Mn(2+))(TCNQ-TCNQ)(2)(*-)], formed as a result of radical-substrate coupling between TCNQ(*-) and neutral TCNQ, accompanied by ingress of Mn(2+) ions from the aqueous solution at the triple phase TCNQ/electrode/electrolyte boundary. In contrast, formation of the nanorod form is much slower and is postulated to arise from disproportionation of the \[(Mn(2+))(TCNQ-TCNQ)(*-)(2)] intermediate. Thus, identification of the time dependent pathways via the solid-solid state electrochemical approach allows the crystal size of the Mn\[TCNQ](2)(H(2)O)(2) material to be tuned and provides new mechanistic insights into the formation of different morphologies.

Indirect message injection for MAC generation

This paper presents a model for the generation of a MAC tag using a stream cipher. The input message is used indirectly to control segments of the keystream that form the MAC tag. Several recent proposals can be considered as instances of this general model, as they all perform message accumulation in this way. However, they use slightly different processes in the message preparation and finalisation phases. We examine the security of this model for different options and against different types of attack, and conclude that the indirect injection model can be used to generate MAC tags securely for certain combinations of options. Careful consideration is required at the design stage to avoid combinations of options that result in susceptibility to forgery attacks. Additionally, some implementations may be vulnerable to side-channel attacks if used in Authenticated Encryption (AE) algorithms. We give design recommendations to provide resistance to these attacks for proposals following this model.

Made by motion, Series one

“Made by Motion” is a collaboration between digital artist Paul Van Opdenbosch and performer and choreographer Elise May; a series of studies on captured motion data used to generating experimental visual forms that reverberate in space and time. The project investigates the invisible forces generated by and influencing the movement of a dancer. Along with how the forces can be captured and applied to generating visual outcomes that surpass simple data visualisation, projecting the intent of the performer’s movements. The source or ‘seed’ comes from using an Xsens MVN - Inertial Motion Capture system to capture spontaneous dance movements, with the visual generation conducted through a customised dynamics simulation. In this first series the visual investigation focused on manipulating the movement date at the instance of capture, capture been the recording of three-dimensional movement as ‘seen’ by the hardware and ‘understood’ through the calibration of software. By repositioning the capture hardware on the body we can effectively change how the same sequence of movements is ‘seen’ by the motion capture system thus generating a different visual result from effetely identical movement. The outcomes from the experiments clearly demonstrates the effectiveness of using motion capture hardware as a creative tool to manipulate the perception of the capture subject, in this case been a sequence of dance movements. The creative work exhibited is a cross-section of the experiments conducted in practice with the first animated work (Movement A - Control) using the motion capture hardware in its default ‘normal’ configuration. Following this is the lower body moved to the upper body (Lb-Ub), right arm moved onto the left arm (Ra-La), right leg moved onto the left leg (Rl-Ll) and finally the left leg moved onto a object that is then held in the left hand (Ll-Pf (Lh)).

Experimental arts practice incorporating motion capture

My practice-led research explores and maps workflows for generating experimental creative work involving inertia based motion capture technology. Motion capture has often been used as a way to bridge animation and dance resulting in abstracted visuals outcomes. In early works this process was largely done by rotoscoping, reference footage and mechanical forms of motion capture. With the evolution of technology, optical and inertial forms of motion capture are now more accessible and able to accurately capture a larger range of complex movements. Made by Motion is a collaboration between digital artist Paul Van Opdenbosch and performer and choreographer Elise May; a series of studies on captured motion data used to generate experimental visual forms that reverberate in space and time. The project investigates the invisible forces generated by and influencing the movement of a dancer. Along with how the forces can be captured and applied to generating visual outcomes that surpass simple data visualisation, projecting the intent of the performer’s movements. The source or ‘seed’ comes from using an Xsens MVN – Inertial Motion Capture system to capture spontaneous dance movements, with the visual generation conducted through a customised dynamics simulation. In my presentation I will be displaying and discussing a selected creative works from the project along with the process and considerations behind the work.

Next generation filmmaking and media arts in the Australian curriculum

Media education has been included as a mandatory component of the Arts within the new Australian national curriculum, which purports to set out a framework that encompasses core knowledge, understanding and skills critical to twenty-first century learning. This will position Australia as the only country to require media education as a compulsory aspect of Arts education and one of the first to implement a sequenced national media education curriculum from pre-school to year 12. A broad framework has been outlined for what the Media Arts curriculum will encompass and in this article we investigate the extent to which this framework is likely to provide media educators the opportunity to broaden the scope of established media education to effectively educate students about the ever-changing nature of media ecologies. The article outlines significant shifts occurring in the film and television industries to identify the types of knowledge students may need to understand these changes. This is followed by an analysis of existing state-based media curricula offered at years 11 and 12 in Australia to demonstrate that the concepts of institutions and audiences are not currently approached in ways that reflect contemporary media ecologies.

Evaluation of two-view geometry methods with automatic ground-truth generation

A large number of methods have been published that aim to evaluate various components of multi-view geometry systems. Most of these have focused on the feature extraction, description and matching stages (the visual front end), since geometry computation can be evaluated through simulation. Many data sets are constrained to small scale scenes or planar scenes that are not challenging to new algorithms, or require special equipment. This paper presents a method for automatically generating geometry ground truth and challenging test cases from high spatio-temporal resolution video. The objective of the system is to enable data collection at any physical scale, in any location and in various parts of the electromagnetic spectrum. The data generation process consists of collecting high resolution video, computing accurate sparse 3D reconstruction, video frame culling and down sampling, and test case selection. The evaluation process consists of applying a test 2-view geometry method to every test case and comparing the results to the ground truth. This system facilitates the evaluation of the whole geometry computation process or any part thereof against data compatible with a realistic application. A collection of example data sets and evaluations is included to demonstrate the range of applications of the proposed system.