Optimal Bayesian experimental design for models with intractable likelihoods using indirect inference applied to biological process models

This paper addresses the problem of determining optimal designs for biological process models with intractable likelihoods, with the goal of parameter inference. The Bayesian approach is to choose a design that maximises the mean of a utility, and the utility is a function of the posterior distribution. Therefore, its estimation requires likelihood evaluations. However, many problems in experimental design involve models with intractable likelihoods, that is, likelihoods that are neither analytic nor can be computed in a reasonable amount of time. We propose a novel solution using indirect inference (II), a well established method in the literature, and the Markov chain Monte Carlo (MCMC) algorithm of Müller et al. (2004). Indirect inference employs an auxiliary model with a tractable likelihood in conjunction with the generative model, the assumed true model of interest, which has an intractable likelihood. Our approach is to estimate a map between the parameters of the generative and auxiliary models, using simulations from the generative model. An II posterior distribution is formed to expedite utility estimation. We also present a modification to the utility that allows the Müller algorithm to sample from a substantially sharpened utility surface, with little computational effort. Unlike competing methods, the II approach can handle complex design problems for models with intractable likelihoods on a continuous design space, with possible extension to many observations. The methodology is demonstrated using two stochastic models; a simple tractable death process used to validate the approach, and a motivating stochastic model for the population evolution of macroparasites.

Surface science of plasma exposed surfaces : a challenge for applied plasma science

This article introduces a deterministic approach to using low-temperature, thermally non-equilibrium plasmas to synthesize delicate low-dimensional nanostructures of a small number of atoms on plasma exposed surfaces. This approach is based on a set of plasma-related strategies to control elementary surface processes, an area traditionally covered by surface science. Major issues related to balanced delivery and consumption of building units, appropriate choice of process conditions, and account of plasma-related electric fields, electric charges and polarization effects are identified and discussed in the quantum dot nanoarray context. Examples of a suitable plasma-aided nanofabrication facility and specific effects of a plasma-based environment on self-organized growth of size- and position-uniform nanodot arrays are shown. These results suggest a very positive outlook for using low-temperature plasma-based nanotools in high-precision nanofabrication of self-assembled nanostructures and elements of nanodevices, one of the areas of continuously rising demand from academia and industry.

A linear-elastic model of anisotropic tumour growth

This paper examines the effect of anisotropic growth on the evolution of mechanical stresses in a linear-elastic model of a growing, avascular tumour. This represents an important improvement on previous linear-elastic models of tissue growth since it has been shown recently that spatially-varying isotropic growth of linear-elastic tissues does not afford the necessary stress-relaxation for a steady-state stress distribution upon reaching a nutrient-regulated equilibrium size. Time-dependent numerical solutions are developed using a Lax-Wendroff scheme, which show the evolution of the tissue stress distributions over a period of growth until a steady-state is reached. These results are compared with the steady-state solutions predicted by the model equations, and key parameters influencing these steady-state distributions are identified. Recommendations for further extensions and applications of this model are proposed.

Training needs research applied to the development of a standardised incident investigator training framework

In response to the rail industry lacking a consistently accepted standard of minimal training to perform incident investigations, the Australasian rail industry requested the development of a unified approach to investigator training. This paper details how the findings from a training needs analysis were applied to inform the development of a standardised training package for rail incident investigators. Data from job descriptions, training documents and subject matter experts sourced from 17 Australasian organisations were analysed and refined to yield a draft set of 10 critical competencies. Finally the draft of critical competencies was reviewed by industry experts to verify the accuracy and completeness of the competency list and to consider the most appropriate level of qualification for training development. The competencies identified and the processes described to translate research into an applied training framework in this paper, can be generalised to assist practitioners and researchers in developing industry approved standardised training packages.

Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging

Cryo-electron tomography together with averaging of sub-tomograms containing identical particles can reveal the structure of proteins or protein complexes in their native environment. The resolution of this technique is limited by the contrast transfer function (CTF) of the microscope. The CTF is not routinely corrected in cryo-electron tomography because of difficulties including CTF detection, due to the low signal to noise ratio, and CTF correction, since images are characterised by a spatially variant CTF. Here we simulate the effects of the CTF on the resolution of the final reconstruction, before and after CTF correction, and consider the effect of errors and approximations in defocus determination. We show that errors in defocus determination are well tolerated when correcting a series of tomograms collected at a range of defocus values. We apply methods for determining the CTF parameters in low signal to noise images of tilted specimens, for monitoring defocus changes using observed magnification changes, and for correcting the CTF prior to reconstruction. Using bacteriophage PRDI as a test sample, we demonstrate that this approach gives an improvement in the structure obtained by sub-tomogram averaging from cryo-electron tomograms.

Performance psychology applied to dance

The recent interest in the area of performance psychology has included a focus on applied practice within the performing arts. The use of psychology within this field has been occurring for many years, although practice has been observed to originate primarily from within clinical psychology in dealing with ‘problems’ (e.g. eating disorders). During the past 15 years, increased interest and focus has come from the field of sport psychology and its application to fields such as dance. Experience with the application of sport psychology in the dance profession has shown that dancers identify primarily with the concept of performance psychology. The focus of applied performance psychology practice with dancers has been observed to incorporate principles from across sport, clinical and organisational psychology, yet packaged together in such a way that the focus is on performance enhancement – whether that be in terms of dance technique, artistry, creativity, or personal skill development both on and off the stage. This paper focuses upon sharing the practitioner’s experience of the delivery of performance psychology to dancers (both professionals and dancers-in-training), and discussion of the considerations related to this undertaking within this unique population.

Good choices, great future : an applied theatre prevention program to reduce alcohol-related risky behaviours during Schoolies

Introduction and Aims. The contextual and temporal factors of post-school celebratory events ('Schoolies') place young people at elevated risk of excessive drinking compared with other social occasions. This study investigates the impact of an applied theatre prevention program 'Choices' in reducing the risk of drinking and other risk behaviours during Schoolies celebrations. Design and Methods. Choices was delivered in the last term of Year 12 across 28 North Queensland schools. A total of 352 school leavers (43.1% male, mean age=17.14years) completed a questionnaire at Whitsunday Schoolies, Queensland, Australia on 23-24 November 2010. Nearly 49% of respondents had attended Choices. The survey included measures of alcohol use, illicit drug use and associated problems during Schoolies and a month prior to Schoolies. Results. After controlling for gender and pre-Schoolies drinking, school leavers who attended Choices were significantly less likely to report illicit drug use (OR=0.51, P<0.05) and problem behaviours (OR=0.40, P<0.01) than those who did not attend Choices. There was, however, no intervention effect in risky drinking (i.e. drank on 5 or more days, typical amount five or more standard drink and binge drank on 3 or more days) at Schoolies (OR=0.92, P=0.80). Discussion and Conclusions. Delivery of a youth-specific applied theatre prevention program employing a harm minimisation framework may be effective in reducing high-risk behaviours associated with alcohol consumption at celebratory events, even if young people expect to engage in excessive alcohol consumption. [Quek L-H, White A, Low C, Brown J, Dalton N, Dow D, Connor JP. Good choices, great future: An applied theatre prevention program to reduce alcohol-related risky behaviours during Schoolies. Drug Alcohol Rev 2012;31:897–902]

Physical mechanism of the compressive response of F-actin networks : significance of crosslinker unbinding events

A model of crosslinker unbinding is implemented in a highly coarsegrained granular model of F-actin cytoskeleton. We employ this specific granular model to study the mechanisms of the compressive responses of F-actin networks. It is found that the compressive response of F-actin cytoskeleton has dependency on the strain rate. The evolution of deformation energy in the network indicates that crosslinker unbinding events can induce the remodelling of F-actin cytoskeleton in response to external loadings. The internal stress in F-actin cytoskeleton can efficiently dissipate with the help of crosslinker unbinding, which could lead to the spontaneous relaxation of living cells.

An investigation of problem-solving support and relaxation motivations on e-WOM

As a consequence of greater computer-mediated consumer-to-consumer communication within the firm's marketing communications, there has been a growing need to understand these digital interactions more explicitly. That is, we still know little about the exact extrinsic and intrinsic motivations that drive electronic word-of-mouth. The purpose of the paper is to better understand why members within community-based websites develop a need to exchange and/or develop a social bond within the community. Questionnaire data were gathered from 147 members of an online beauty forum in Australia. The findings highlight that those members seeking problem-solving support in combination with elements of relaxation will be more inclined to exchange with other community members and develop a social bond within that community. Marketing managers can capitalise these findings by strengthening problem-solving support systems and creating environments where community members can also relax and unwind to increase the exchange between members and also increase the social bonds within the community.

Uncertainty quantification applied to the performance analysis of a conical diffuser

This paper offers an uncertainty quantification (UQ) study applied to the performance analysis of the ERCOFTAC conical diffuser. A deterministic CFD solver is coupled with a non-statistical generalised Polynomial Chaos(gPC)representation based on a pseudo-spectral projection method. Such approach has the advantage to not require any modification of the CFD code for the propagation of random disturbances in the aerodynamic field. The stochactic results highlihgt the importance of the inlet velocity uncertainties on the pressure recovery both alone and when coupled with a second uncertain variable. From a theoretical point of view, we investigate the possibility to build our gPC representation on arbitray grid, thus increasing the flexibility of the stochastic framework.

Effect of partial H2O-D2O replacement on the anisotropy of transverse proton spin relaxation in bovine articular cartilage

Anisotropy of transverse proton spin relaxation in collagen-rich tissues like cartilage and tendon is a well-known phenomenon that manifests itself as the "magic-angle" effect in magnetic resonance images of these tissues. It is usually attributed to the non-zero averaging of intra-molecular dipolar interactions in water molecules bound to oriented collagen fibers. One way to manipulate the contributions of these interactions to spin relaxation is by partially replacing the water in the cartilage sample with deuterium oxide. It is known that dipolar interactions in deuterated solutions are weaker, resulting in a decrease in proton relaxation rates. In this work, we investigate the effects of deuteration on the longitudinal and the isotropic and anisotropic contributions to transverse relaxation of water protons in bovine articular cartilage. We demonstrate that the anisotropy of transverse proton spin relaxation in articular cartilage is independent of the degree of deuteration, bringing into question some of the assumptions currently held over the origins of relaxation anisotropy in oriented tissues.

Creating new folk opera forms of applied theatre for HIV and AIDS education in Papua New Guinea

This research investigated the potential of folk opera as a tool for HIV and AIDS education in Papua New Guinea. It began with an investigation on the indigenous performativities and theatricalities of Papua New Guineans, conducting an audit of eight selected performance traditions in Papua New Guinea. These traditions were analysed, and five cultural forms and twenty performance elements were drawn out for further exploration. These elements were fused and combined with theatre techniques from western theatre traditions, through a script development process involving Australians, Papua New Guineans and international collaborators. The resulting folk opera, entitled Kumul, demonstrates what Murphy (2010) has termed story force, picture force, and feeling force, in the service of a story designed to educate Papua New Guinean audiences about HIV and the need to adopt safer sexual practices. Kumul is the story of a young man faced with decisions on whether or not to engage in risky sexual behaviours. Kumul's narrative is carefully framed within selected Papua New Guinean beliefs drawn from the audit to deliver HIV and AIDS messages using symbolic and metaphoric communication techniques without offending people. The folk opera Kumul was trialled in two communities in Papua New Guinea: a village community and an urban settlement area. Kumul is recognisable to Papua New Guinean audiences because it reflects their lifestyle and a worldview, which connects them to their beliefs and spirituality, and the larger cosmological order. Feedback from audience members indicated that the performance facilitated HIV and AIDS communication, increased people's awareness of HIV and AIDS, and encouraged behaviour change. Tellingly, in one performance venue, forty people queued for Voluntary Testing and Counseling immediately after the performance. Twenty of these people were tested on that night and the other twenty were tested the following day. Many of the volunteers were young men – a demographic historically difficult to engage in HIV testing. This encouraging result indicates that the Kumul folk opera form of applied theatre could be useful for facilitating communication and education regarding sexual health and safer sexual behaviours in Papua New Guinea. Feedback from participants, audience members and other research stakeholders suggests that the form might also be adapted to address other social and development issues, particularly in the areas of health and social justice.

Illuminative evaluation as a method applied to Australian Government policy borrowing and implementation in higher education

Any government deciding to invoke widespread change in its higher education sector through implementation of new policies impacts on every institution and all staff and students, often in both the time taken up and the heightened emotions caused. The central phenomenon that this study addresses is the process and consequences of policy changes in higher education in Australia. The aim of this article is to record the research design through the perspective (evaluation research), theoretical framework (program evaluation) and methods (content analysis, descriptive statistical analysis and bibliometric analysis) applied to the investigation of the 2003 federal government higher education reform package. This approach allows both the intended and unintended consequences arising from the policy implementation of three national initiatives focused on learning and teaching in higher education in Australia to surface. As a result, this program evaluation, also known in some disciplines as policy implementation analysis, will demonstrate the applicability of illuminative evaluation as a methodology and reinforce how program evaluation will assist and advise future government reform and policy implementation, and will serve as a legacy for future evaluative research.Any government deciding to invoke widespread change in its higher education sector through implementation of new policies impacts on every institution and all staff and students, often in both the time taken up and the heightened emotions caused. The central phenomenon that this study addresses is the process and consequences of policy changes in higher education in Australia. The aim of this article is to record the research design through the perspective (evaluation research), theoretical framework (program evaluation) and methods (content analysis, descriptive statistical analysis and bibliometric analysis) applied to the investigation of the 2003 federal government higher education reform package. This approach allows both the intended and unintended consequences arising from the policy implementation of three national initiatives focused on learning and teaching in higher education in Australia to surface. As a result, this program evaluation, also known in some disciplines as policy implementation analysis, will demonstrate the applicability of illuminative evaluation as a methodology and reinforce how program evaluation will assist and advise future government reform and policy implementation, and will serve as a legacy for future evaluative research.

Load applied on a bone-anchored transfemoral prosthesis: characterisation of a prosthesis : a pilot study

The objectives of this study were (A) to record the inner prosthesis loading during activities of daily living (ADL), (B) to present a set of variables comparing loading data, and (C) to provide an example of characterisation of two prostheses. The load was measured at 200 Hz using a multi-axial transducer mounted between the residuum and the knee of an individual with unilateral transfemoral amputation fitted with a bone-anchored prosthesis. The load was measured while using two different prostheses including a mechanically (PRO1) and a microprocessor controlled (PRO2) knee during six ADL. The characterisation of prosthesis was achieved using a set of variables split into four categories, including temporal characteristics, maximum loading, loading slopes and impulse. Approximately 360 gait cycles were analysed for each prosthesis. PRO1 showed a cadence improved by 19% and 7%, a maximum force on the long axis reduced by 11% and 19%, as well as an impulse reduced by 32% and 15% during descent of incline and stairs compared to PRO2, respectively. This work confirmed that the proposed apparatus and characterisation can reveal how changes of prosthetic components are translated into inner loading.