A web application to perform linkage disequilibrium and linkage analyses on a computational grid

Motivation: Unravelling the genetic architecture of complex traits requires large amounts of data, sophisticated models and large computational resources. The lack of user-friendly software incorporating all these requisites is delaying progress in the analysis of complex traits. Methods: Linkage disequilibrium and linkage analysis (LDLA) is a high-resolution gene mapping approach based on sophisticated mixed linear models, applicable to any population structure. LDLA can use population history information in addition to pedigree and molecular markers to decompose traits into genetic components. Analyses are distributed in parallel over a large public grid of computers in the UK. Results: We have proven the performance of LDLA with analyses of simulated data. There are real gains in statistical power to detect quantitative trait loci when using historical information compared with traditional linkage analysis. Moreover, the use of a grid of computers significantly increases computational speed, hence allowing analyses that would have been prohibitive on a single computer. © The Author 2009. Published by Oxford University Press. All rights reserved.

Higher degree research at Australian Universities : Responding to diversity in engineering and information technology

BACKGROUND There is increasing enrolment of international students in the Engineering and Information Technology disciplines and anecdotal evidence of a need for additional understanding and support for these students and their supervisors due to differences both in academic and social cultures. While there is a growing literature on supervisory styles and guidelines on effective supervision, there is little on discipline-specific, cross-cultural supervision responding to the growing diversity. In this paper, we report findings from a study of Engineering and Information technology Higher Degree Research (HDR)students and supervision in three Australian universities. PURPOSE The aim was to assess perceptions of students and supervisors of factors influencing success that are particular to international or culturally and linguistically diverse (CaLD) HDR students in Engineering and Information technology. DESIGN/METHOD Online survey and qualitative data was collected from international and CaLD HDR students and supervisors at the three universities. Bayesian network analysis, inferential statistics, and qualitative analysis provided the main findings. RESULTS Survey results indicate that both students and supervisors are positive about their experiences, and do not see language or culture as particularly problematic. The survey results also reveal strong consistency between the perceptions of students and supervisors on most factors influencing success. Qualitative analysis of critical supervision incidents has provided rich data that could help improve support services. CONCLUSIONS In contrast with anecdotal evidence, HDR completion data from the three universities reveal that international students, on average, complete in shorter time periods than domestic students. The analysis suggests that success is linked to a complex set of factors involving the student, supervision, the institution and broader community.

Exponential integrators and a dual-scale model for wood drying

For the timber industry, the ability to simulate the drying of wood is invaluable for manufacturing high quality wood products. Mathematically, however, modelling the drying of a wet porous material, such as wood, is a diffcult task due to its heterogeneous and anisotropic nature, and the complex geometry of the underlying pore structure. The well{ developed macroscopic modelling approach involves writing down classical conservation equations at a length scale where physical quantities (e.g., porosity) can be interpreted as averaged values over a small volume (typically containing hundreds or thousands of pores). This averaging procedure produces balance equations that resemble those of a continuum with the exception that effective coeffcients appear in their deffnitions. Exponential integrators are numerical schemes for initial value problems involving a system of ordinary differential equations. These methods differ from popular Newton{Krylov implicit methods (i.e., those based on the backward differentiation formulae (BDF)) in that they do not require the solution of a system of nonlinear equations at each time step but rather they require computation of matrix{vector products involving the exponential of the Jacobian matrix. Although originally appearing in the 1960s, exponential integrators have recently experienced a resurgence in interest due to a greater undertaking of research in Krylov subspace methods for matrix function approximation. One of the simplest examples of an exponential integrator is the exponential Euler method (EEM), which requires, at each time step, approximation of φ(A)b, where φ(z) = (ez - 1)/z, A E Rnxn and b E Rn. For drying in porous media, the most comprehensive macroscopic formulation is TransPore [Perre and Turner, Chem. Eng. J., 86: 117-131, 2002], which features three coupled, nonlinear partial differential equations. The focus of the first part of this thesis is the use of the exponential Euler method (EEM) for performing the time integration of the macroscopic set of equations featured in TransPore. In particular, a new variable{ stepsize algorithm for EEM is presented within a Krylov subspace framework, which allows control of the error during the integration process. The performance of the new algorithm highlights the great potential of exponential integrators not only for drying applications but across all disciplines of transport phenomena. For example, when applied to well{ known benchmark problems involving single{phase liquid ow in heterogeneous soils, the proposed algorithm requires half the number of function evaluations than that required for an equivalent (sophisticated) Newton{Krylov BDF implementation. Furthermore for all drying configurations tested, the new algorithm always produces, in less computational time, a solution of higher accuracy than the existing backward Euler module featured in TransPore. Some new results relating to Krylov subspace approximation of '(A)b are also developed in this thesis. Most notably, an alternative derivation of the approximation error estimate of Hochbruck, Lubich and Selhofer [SIAM J. Sci. Comput., 19(5): 1552{1574, 1998] is provided, which reveals why it performs well in the error control procedure. Two of the main drawbacks of the macroscopic approach outlined above include the effective coefficients must be supplied to the model, and it fails for some drying configurations, where typical dual{scale mechanisms occur. In the second part of this thesis, a new dual{scale approach for simulating wood drying is proposed that couples the porous medium (macroscale) with the underlying pore structure (microscale). The proposed model is applied to the convective drying of softwood at low temperatures and is valid in the so{called hygroscopic range, where hygroscopically held liquid water is present in the solid phase and water exits only as vapour in the pores. Coupling between scales is achieved by imposing the macroscopic gradient on the microscopic field using suitably defined periodic boundary conditions, which allows the macroscopic ux to be defined as an average of the microscopic ux over the unit cell. This formulation provides a first step for moving from the macroscopic formulation featured in TransPore to a comprehensive dual{scale formulation capable of addressing any drying configuration. Simulation results reported for a sample of spruce highlight the potential and flexibility of the new dual{scale approach. In particular, for a given unit cell configuration it is not necessary to supply the effective coefficients prior to each simulation.

Usability of small crisis data sets in the absence of big data

Big data is big news in almost every sector including crisis communication. However, not everyone has access to big data and even if we have access to big data, we often do not have necessary tools to analyze and cross reference such a large data set. Therefore this paper looks at patterns in small data sets that we have ability to collect with our current tools to understand if we can find actionable information from what we already have. We have analyzed 164390 tweets collected during 2011 earthquake to find out what type of location specific information people mention in their tweet and when do they talk about that. Based on our analysis we find that even a small data set that has far less data than a big data set can be useful to find priority disaster specific areas quickly.

Valid and reliable assessment of wellness among adolescents : do you know what you’re measuring?

Measuring wellness among adolescents is an emerging trend among professionals and researchers endeavouring to influence youth as they establish lifestyle patterns in this critical period of life. This discussion highlights instruments used to measure wellness among adolescents, and considers the empirical data supporting their validity and reliability amongst adolescents. In summary, Adolescent wellness is an important indicator of future health and lifestyle habits. There are a number of tools available to measure wellness, each with its own focus, depending on the definition or model from which it was developed. This may cause debate regarding the appropriateness of some instruments for evaluating wellness. The majority of wellness evaluation approaches reported among adolescents have less than ideal validation. A ‘gold standard’ definition could lead to the standardisation of a theoretical model against which wellness instruments could be validated. The absence of peer reviewed studies reporting psychometric testing for wellness evaluation instruments among adolescents is concerning given their growing popularity and highlights a priority area for future research in this field.

Optimized strategy for integrated traffic and transit signal control

This paper proposes a unique and innovative approach to integrate transit signal priority control into a traffic adaptive signal control strategy. The proposed strategy was named OSTRAC (Optimized Strategy for integrated TRAffic and TRAnsit signal Control). The cornerstones of OSTRAC include an online microscopic traffic f low prediction model and a Genetic Algorithm (GA) based traffic signal timing module. A sensitivity analysis was conducted to determine the critical GA parameters. The developed traffic f low model demonstrated reliable prediction results through a test. OSTRAC was evaluated by comparing its performance to three other signal control strategies. The evaluation results revealed that OSTRAC efficiently and effectively reduced delay time of general traffic and also transit vehicles.

Barriers to formal IT Governance practice - insights from a qualitative study

IT Governance (ITG) continues to be a top priority for organizations, public and non-public. While the level of awareness towards ITG is evident, it is hardly manifested in practice. The purpose of this study is to elicit factors that act as barriers to the adoption of formal ITG practice. This qualitative study consists of 9 semi-structured interviews with the key person in charge of ITG adoption and practice within their respective organizations. The interviews were analyzed using thematic content analysis, guided by themes previously obtained from the literature and from an earlier pilot study. Findings obtained supported previous findings and also reveal new factors noticeably absent from the ITG literature. The findings will provide useful input towards the development of a causal model on barriers to formal ITG practice

Comparing child product safety concerns with injury incidents : does the evidence support the response?

Background Efficient effective child product safety (PS) responses require data on hazards, injury severity and injury probability. PS responses in Australia largely rely on reports from manufacturers/retailers, other jurisdictions/regulators, or consumers. The extent to which reactive responses reflect actual child injury priorities is unknown. Aims/Objectives/Purpose This research compared PS issues for children identified using data compiled from PS regulatory data and data compiled from health data sources in Queensland, Australia. Methods PS regulatory documents describing issues affecting children in Queensland in 2008–2009 were compiled and analysed to identify frequent products and hazards. Three health data sources (ED, injury surveillance and hospital data) were analysed to identify frequent products and hazards. Results/Outcomes Projectile toys/squeeze toys were the priority products for PS regulators with these toys having the potential to release small parts presenting choking hazards. However, across all health datasets, falls were the most common mechanism of injury, and several of the products identified were not subject to a PS system response. While some incidents may not require a response, a manual review of injury description text identified child poisonings and burns as common mechanisms of injuries in the health data where there was substantial documentation of product-involvement, yet only 10% of PS system responses focused on these two mechanisms combined. Significance/contribution to the field Regulatory data focused on products that fail compliance checks with ‘potential’ to cause harm, and health data identified actual harm, resulting in different prioritisation of products/mechanisms. Work is needed to better integrate health data into PS responses in Australia.

State of multilevel research perspective in the information systems discipline

Existing distinctions among macro and micro approaches have been jeopardising the advances of Information Systems (IS) research. Both approaches have been criticized for explaining one level while neglecting the other; thereby, the current situation necessitates the application of multilevel research for revealing the deficiencies. Instead of studying single level (macro or micro), multilevel research entails more than one level of conceptualization and analysis, simultaneously. As the notion of multilevel is borrowed from reference disciplines, there tends to be confusions and inconsistencies within the IS discipline, which hinders the adoption of multilevel research. This paper speaks for the potential value of multilevel research, by investigating the current application status of multilevel research within the IS domain. A content analysis of multilevel research articles from major IS conferences and journals is presented. Analysis results suggest that IS scholars have applied multilevel research to produce high quality work ranging from a variety of topics. However, researchers have not yet been consistently defining “multilevel”, leading to idiosyncratic meanings of multilevel research, most often, in authors’ own interpretations. We argue that a rigorous definition of “multilevel research” needs to be explicated for consistencies in research community.

Healthcare teams : a practical framework for integration

Background: Delivering integrated team care is a major priority for many countries. In Australia this is a component of the GP Super Clinic Program but it is also a focus of the broader primary care sector. Explicit consideration of human dynamics and team process is often absent from the move to integrated team care. Objective: To provide a practical framework that will inform the development and evaluation of integrated healthcare teams. Discussion: The Team Focused and Clinical Content Framework is an approach to building integrated teams. This has the potential to be used to monitor and evaluate team development and functioning. Both the framework and clinical pathways provide practical tools for clinics to address the need to build integration into teams.

An informal community of practice : the case of the DEHub Virtual Worlds Working Group

The DEHub Virtual Worlds Working Group has an informal membership of nearly 200 members with an interest in education and virtual worlds within the Australian and New Zealand context. Members come from a variety of academic disciplines and may be teaching or research academics, Research Higher Degree candidates, project managers, virtual world builders and developers. The group acts as an informal Community of Practice, facilitating learning and the transfer of skills through social contact, opportunities to collaborate on projects and publications, and through the sharing of knowledge and experience. This poster provides a snapshot of the activity of this highly active group.

An evidence-informed strategy to prevent osteoporosis in Australia

Osteoporosis imposes a tremendous burden on Australia : 1.2 million Australians have osteoporosis and 6.3 million have Osteopenia. In the 2007-08 financial year, 82000 Australians suffered fragility fractures, of Which >17000 were hip fractures. In the 2000-01 financial year, direct costs were estimated at $1.9 billion per year and an additional $5.6 billion on indirect costs. Osteoporosis was designated a National Health Priority Area in 2002; however, implementation of national plans has not yet matched the rhetoric in terms of urgency. Building healthy bones throughout life, the Osteoporosis Australia strategy to prevent osteoporosis throughout the life cycle, presents an evidence-informed set of recommendations for consumers, health care professionals and policymakers. The strategy was adopted by consensus at the Osteoporosis Australia Summit in Sydney, 20 October 2011. Primary objectives throughout the life cycle are: to maximise peak bone mass during childhood and adolescence to prevent premature bone loss and improve or maintain muscle mass, strength and functional capacity in healthy adults to prevent and treat osteoporosis in order to minimise the risk of suffering fragility fractures, and reduce falls risk, in older people. The recommendations focus on three affordable and important interventions to ensure people have adequate calcium intake, vitamin D levels and appropriate, physical activity throughout their lives. Recommendations relevant to all stages of life include: daily dietary calcium intakes should be consistent with Australian and New Zealand guidelines serum levels of vitamin D in the general population should be above 50 nmol/L in winter or early spring for optimal bone health regular weight-bearing physical activity, Muscle strengthening exercises and challenging balance/ mobility activities should be conducted in a safe environment.

Towards a compendium of process technologies : the jBPT library for process model analysis

This paper presents the idea of a compendium of process technologies, i.e., a concise but comprehensive collection of techniques for process model analysis that support research on the design, execution, and evaluation of processes. The idea originated from observations on the evolution of process-related research disciplines. Based on these observations, we derive design goals for a compendium. Then, we present the jBPT library, which addresses these goals by means of an implementation of common analysis techniques in an open source codebase.

Rock, paper, scissors : reflective practice for design process in the novice landscape architect

We describe a pedagogical approach that addresses challenges in design education for novices. These include an inability to frame new problems and limited-to-no design capability or domain knowledge. Such challenges can reduce student engagement with design practice, cause derivative design solutions as well as the inappropriate simplification of design assignments and assessment criteria by educators. We argue that a curriculum that develops the student’s design process will enable them to deal with the uncertain and dynamic situations that characterise design. We describe how this may be achieved and explain our pedagogical approach in terms of methods from Reflective Practice and theories of abstraction and creativity. We present a landscape architecture unit, recently taught, as an example. It constitutes design exercises that require little domain or design expertise to support the development of conceptual thinking and a design rationale. We show how this approach (a) leveraged the novice’s existing spatial and thinking skills while (b) retaining contextually-rich design situations. Examples of the design exercises taught are described along with samples of student work. The assessment rationale is also presented and explained. Finally, we conclude by reflecting on how this approach relates to innovation, sustainability and other disciplines.

Guerrillas in the [urban] midst : Developing and using creative research methods - guerrilla research tactics

This paper explores what we are calling “Guerrilla Research Tactics” (GRT): research methods that exploit emerging mobile and cloud based digital technologies. We examine some case studies in the use of this technology to generate research data directly from the physical fabric and the people of the city. We argue that GRT is a new and novel way of engaging public participation in urban, place based research because it facilitates the co- creation of knowledge, with city inhabitants, ‘on the fly’. This paper discusses the potential of these new research techniques and what they have to offer researchers operating in the creative disciplines and beyond. This work builds on and extends Gauntlett’s “new creative methods” (2007) and contributes to the existing body of literature addressing creative and interactive approaches to data collection.