Supplementary Information : Hogan, Holland, Holloway, Petit and Read : Read Classification for Next Generation Sequencing, ESANN 2013, April 2013

This item provides supplementary materials for the paper mentioned in the title, specifically a range of organisms used in the study. The full abstract for the main paper is as follows: Next Generation Sequencing (NGS) technologies have revolutionised molecular biology, allowing clinical sequencing to become a matter of routine. NGS data sets consist of short sequence reads obtained from the machine, given context and meaning through downstream assembly and annotation. For these techniques to operate successfully, the collected reads must be consistent with the assumed species or species group, and not corrupted in some way. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans,with some strains exhibiting antibiotic resistance. In this paper, we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from alternative pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

Uncertainty analysis of pollutant build-up modelling based on a Bayesian Weighted Least Squares approach

Reliable pollutant build-up prediction plays a critical role in the accuracy of urban stormwater quality modelling outcomes. However, water quality data collection is resource demanding compared to streamflow data monitoring, where a greater quantity of data is generally available. Consequently, available water quality data sets span only relatively short time scales unlike water quantity data. Therefore, the ability to take due consideration of the variability associated with pollutant processes and natural phenomena is constrained. This in turn gives rise to uncertainty in the modelling outcomes as research has shown that pollutant loadings on catchment surfaces and rainfall within an area can vary considerably over space and time scales. Therefore, the assessment of model uncertainty is an essential element of informed decision making in urban stormwater management. This paper presents the application of a range of regression approaches such as ordinary least squares regression, weighted least squares Regression and Bayesian Weighted Least Squares Regression for the estimation of uncertainty associated with pollutant build-up prediction using limited data sets. The study outcomes confirmed that the use of ordinary least squares regression with fixed model inputs and limited observational data may not provide realistic estimates. The stochastic nature of the dependent and independent variables need to be taken into consideration in pollutant build-up prediction. It was found that the use of the Bayesian approach along with the Monte Carlo simulation technique provides a powerful tool, which attempts to make the best use of the available knowledge in the prediction and thereby presents a practical solution to counteract the limitations which are otherwise imposed on water quality modelling.

'Going live' : establishing the creative attributes of the live multi-camera television professional

In my capacity as a television professional and teacher specialising in multi-camera live television production for over 40 years, I was drawn to the conclusion that opaque or inadequately formed understandings of how creativity applies to the field of live television, have impeded the development of pedagogies suitable to the teaching of live television in universities. In the pursuit of this hypothesis, the thesis shows that television degrees were born out of film studies degrees, where intellectual creativity was aligned to single camera production, and the 'creative roles' of producers, directors and scriptwriters. At the same time, multi-camera live television production was subsumed under the 'mass communication' banner, leading to an understanding that roles other than producer and director are simply technical, and bereft of creative intent or acumen. The thesis goes on to show that this attitude to other television production personnel, for example, the vision mixer, videotape operator and camera operator, relegates their roles to that of 'button pusher'. This has resulted in university teaching models with inappropriate resources and unsuitable teaching practices. As a result, the industry is struggling to find people with the skills to fill the demands of the multi-camera live television sector. In specific terms the central hypothesis is pursued through the following sequenced approach. Firstly, the thesis sets out to outline the problems, and traces the origins of the misconceptions that hold with the notion that intellectual creativity does not exist in live multi-camera television. Secondly, this more adequately conceptualised rendition, of the origins particular to the misconceptions of live television and creativity, is then anchored to the field of examination by presentation of the foundations of the roles involved in making live television programs, using multicamera production techniques. Thirdly, this more nuanced rendition of the field sets the stage for a thorough analysis of education and training in the industry, and teaching models at Australian universities. The findings clearly establish that the pedagogical models are aimed at single camera production, a position that deemphasises the creative aspects of multi-camera live television production. Informed by an examination of theories of learning, qualitative interviews, professional reflective practice and observations, the roles of four multi-camera live production crewmembers (camera operator, vision mixer, EVS/videotape operator and director's assistant), demonstrate the existence of intellectual creativity during live production. Finally, supported by the theories of learning, and the development and explication of a successful teaching model, a new approach to teaching students how to work in live television is proposed and substantiated.

Using 3D visualisation to understand human articular cartilage deterioration

Understanding complex systems within the human body presents a unique challenge for medical engineers and health practitioners. One significant issue is the ability to communicate their research findings to audiences with limited medical knowledge or understanding of the behaviour and composition of such structures. Much of what is known about the human body is currently communicated through abstract representations which include raw data sets, hand drawn illustrations or cellular automata. The development of 3D Computer Graphics Animation has provided a new medium for communicating these abstract concepts to audiences in new ways. This paper presents an approach for the visualisation of human articular cartilage deterioration using 3D Computer Graphics Animation. The animated outcome of this research introduces the complex interior structure of human cartilage to audiences with limited medical engineering knowledge.

Using a pharmacokinetic model to interpret biomonitoring data of PBDEs in the Australian population

From human biomonitoring data that are increasingly collected in the United States, Australia, and in other countries from large-scale field studies, we obtain snap-shots of concentration levels of various persistent organic pollutants (POPs) within a cross section of the population at different times. Not only can we observe the trends within this population with time, but we can also gain information going beyond the obvious time trends. By combining the biomonitoring data with pharmacokinetic modeling, we can re-construct the time-variant exposure to individual POPs, determine their intrinsic elimination half-lives in the human body, and predict future levels of POPs in the population. Different approaches have been employed to extract information from human biomonitoring data. Pharmacokinetic (PK) models were combined with longitudinal data1, with single2 or multiple3 average concentrations of a cross-sectional data (CSD), or finally with multiple CSD with or without empirical exposure data4. In the latter study, for the first time, the authors based their modeling outputs on two sets of CSD and empirical exposure data, which made it possible that their model outputs were further constrained due to the extensive body of empirical measurements. Here we use a PK model to analyze recent levels of PBDE concentrations measured in the Australian population. In this study, we are able to base our model results on four sets5-7 of CSD; we focus on two PBDE congeners that have been shown3,5,8-9 to differ in intake rates and half-lives with BDE-47 being associated with high intake rates and a short half-life and BDE-153 with lower intake rates and a longer half-life. By fitting the model to PBDE levels measured in different age groups in different years, we determine the level of intake of BDE-47 and BDE-153, as well as the half-lives of these two chemicals in the Australian population.

Psychology students’ beliefs about integrating Complementary and Alternative Therapy (CAT) into their future psychology practice

We investigated whether belief-based differences exist between students who have strong and weak intentions to integrate complementary and alternative therapy (CAT) into future psychology practice by recommending CAT or specific CAT practitioners to clients. A cross-sectional methodology was used. Psychology undergraduate students (N = 106) participated in a paper-based questionnaire design to explore their underlying beliefs related to CAT integration. The study was undertaken at a major university in Queensland, Australia. The theory of planned behaviour belief-based framework guided the study. Multivariate analyses of variance examined the influence of behavioural, normative, and control beliefs on the strong and weak intention groups. A multiple regression analysis investigated the relative importance of these belief sets for predicting intentions. We found that clear differences emerged between strong and weak intenders on behavioural and normative beliefs, but not control beliefs. Strong intenders perceived the positive outcomes of integrating CAT, such as being able to offer clients a more holistic practice and having confidence in the practitioners/practices, as more likely to occur than weak intenders, and perceived the negative outcome of compromising my professional practice as less likely. Strong in-tenders were more likely than weak intenders to perceive that a range of important referents (e.g., clients) would think they should integrate CAT. Results of the regression analysis revealed the same pattern of results in that behavioural and normative beliefs, but not control beliefs, significantly predicted intentions. The findings from this study can be used to inform policy and educational initiatives that aim to encourage CAT use in psychology practice.