Xenome--a tool for classifying reads from xenograft samples

Motivation Shotgun sequence read data derived from xenograft material contains a mixture of reads arising from the host and reads arising from the graft. Classifying the read mixture to separate the two allows for more precise analysis to be performed. Results We present a technique, with an associated tool Xenome, which performs fast, accurate and specific classification of xenograft-derived sequence read data. We have evaluated it on RNA-Seq data from human, mouse and human-in-mouse xenograft datasets.

Connecting the person with dementia and family : a feasibility study of a telepresence robot

Background Maintenance of communication is important for people with dementia living in long-term care. The purpose of this study was to assess the feasibility of using “Giraff”, a telepresence robot to enhance engagement between family and a person with dementia living in long-term care. Methods A mixed-methods approach involving semi-structured interviews, call records and video observational data was used. Five people with dementia and their family member participated in a discussion via the Giraff robot for a minimum of six times over a six-week period. A feasibility framework was used to assess feasibility and included video analysis of emotional response and engagement. Results Twenty-six calls with an average duration of 23 mins took place. Residents showed a general state of positive emotions across the calls with a high level of engagement and a minimal level of negative emotions. Participants enjoyed the experience and families reported that the Giraff robot offered the opportunity to reduce social isolation. A number of software and hardware challenges were encountered. Conclusions Participants perceived this novel approach to engage families and people with dementia as a feasible option. Participants were observed and also reported to enjoy the experience. The technical challenges identified have been improved in a newer version of the robot. Future research should include a feasibility trial of longer duration, with a larger sample and a cost analysis.

Small and medium enterprises using software as a service : exploring the different roles of intermediaries

Software as a Service (SaaS) can provide significant benefits to small and medium enterprises (SMEs) due to advantages like ease of access, 7*24 availability, and utility pricing. However, underlying the SaaS delivery model is often the assumption that SMEs will directly interact with the SaaS vendor and use a self-service approach. In practice, we see the rise of SaaS intermediaries who can support SMEs with sourcing and leveraging SaaS. This paper reports on the roles of intermediaries and how they support SMEs with using SaaS. We conducted an empirical study of two SaaS intermediaries and analysed their business models, in particular their value propositions. We identified orientation (technology or customer) and alignment (operational or strategic) as themes for understanding their roles. The contributions of this paper include: (1) the identification and description of SaaS intermediaries for SMEs based on an empirical study and (2) understanding the different roles of SaaS intermediaries, in particular a more basic role based on technology orientation and operational alignment and a more value adding role based on customer orientation and strategic alignment. We propose that SaaS intermediaries can address SaaS adoption and implementation challenges of SMEs by playing a basic role and can also aim to support SMEs in creating business value with SaaS based solutions by playing an added value role.

Use of contract models to improve environmental outcomes in transport infrastructure construction

The type of contract model may have a significant influence on achieving project objectives, including environmental and climate change goals. This research investigates non-standard contract models impacting greenhouse gas emissions (GHG) in transport infrastructure construction in Australia. The research is based on the analysis of two case studies: an Early Contractor Involvement (ECI) contract and a Design and Construct (D&C) contract with GHG reduction requirements embedded in the contractor selection. Main findings support the use of ECIs for better integrating decisions made during the planning phase with the construction activities, and improve environmental outcomes while achieving financial and time savings. Key words: greenhouse gases reduction; road construction; contracting; ECI; D&C

Insurance and transport law : controlling insurance contract terms : Section 54 of the Insurance Contracts Act – compliance, recovery and accountability

Commonwealth legislation covering insurance contracts contains numerous provisions designed to control the operation and effect of terms in life and general insurance contracts. For example, the Life Insurance Act 1995 (Cth) contains provisions regulating the consequences attendant upon incorrect statements in proposals [1] and non-payment of premiums, [2] provides that an insurer may only exclude liability in the case of suicide if it has made express provision for such contingency in its policy, [3] and severely restricts the efficacy of conditions as to war risks. [4] The Insurance Contracts Act 1984 (Cth) is even more intrusive and has a major impact upon contractual provisions in the general insurance field. It is beyond the scope of this note to explore all of these provisions in any detail but examples of controls and constraints imposed upon the operation and effect of contractual provisions include the following. A party is precluded from relying upon a provision in a contract of insurance if such reliance would amount to a failure to act with the utmost good faith. [5] Similarly, a policy provision which requires differences or disputes arising out of the insurance to be submitted to arbitration is void, [6] unless the insurance is a genuine cover for excess of loss over and above another specified insurance. [7] Similarly clause such as conciliation clauses, [8] average clauses, [9] and unusual terms [10] are given qualified operation. [11] However the provision in the Insurance Contracts Act that has the greatest impact upon, and application to, a wide range of insurance clauses and claims is s 54. This section has already generated a significant volume of case law and is the focus of this note. In particular this note examines two recent cases. The first, Johnson v Triple C Furniture and Electrical Pty Ltd [2012] 2 Qd R 337, (hereafter the Triple C case), is a decision of the Queensland Court of Appeal; and the second, Matthew Maxwell v Highway Hauliers Pty Ltd [2013] WASCA 115, (hereafter the Highway Hauliers case), is a decision of the Court of Appeal in Western Australia. This latter decision is on appeal to the High Court of Australia. The note considers too the decision of the New South Wales Court of Appeal in Prepaid Services Pty Ltd v Atradius Credit Insurance NV [2013] NSWCA 252 (hereafter the Prepaid Services case).These cases serve to highlight the complex nature of s 54 and its application, as well as the difficulty in achieving a balance between an insurer and an insured's reasonable expectations.

Sustainable innovation for Queensland’s housing design : a case study

This research provides an assessment tool that assists the selection process of sustainability in detached suburban housing. It investigates the implications of using different design and construction methods including architecturally designed houses, developer housing and prefabricated houses. The study simulates one example of the three types of houses that have been chosen to fulfil a real client brief on a real site on the Sunshine Coast, Queensland Australia. Criteria for sustainability assessment are formulated based on literature reviews, exemplar designs and similar research projects for which the houses can be adequately evaluated. This criterion covers aspects including energy use, materials and thermal performance. The data is collected using computer models and sustainability assessment software to compare and draw conclusions on the success of each house. Our study indicates that architecturally designed housing with prefabricated building techniques are a better alternative to generic developer style housing. Our research provides an insight into the implications of three key elements of sustainability including energy use, materials and thermal performance. Designers, builders, developers and home-buyers are given an insight into some options currently available on the housing market and how the choices made during early design stages can provide a more positive environmental impact.

Meta-analysis of prevalence

Meta-analysis is a method to obtain a weighted average of results from various studies. In addition to pooling effect sizes, meta-analysis can also be used to estimate disease frequencies, such as incidence and prevalence. In this article we present methods for the meta-analysis of prevalence. We discuss the logit and double arcsine transformations to stabilise the variance. We note the special situation of multiple category prevalence, and propose solutions to the problems that arise. We describe the implementation of these methods in the MetaXL software, and present a simulation study and the example of multiple sclerosis from the Global Burden of Disease 2010 project. We conclude that the double arcsine transformation is preferred over the logit, and that the MetaXL implementation of multiple category prevalence is an improvement in the methodology of the meta-analysis of prevalence.

Veracity of the archive : a research approach to the collection and verification of urban morphological records using qualitative data analysis software

Critical to the research of urban morphologists is the availability of historical records that document the urban transformation of the study area. However, thus far little work has been done towards an empirical approach to the validation of archival data in this field. Outlined in this paper, therefore, is a new methodology for validating the accuracy of archival records and mapping data, accrued through the process of urban morphological research, so as to establish a reliable platform from which analysis can proceed. The paper particularly addresses the problems of inaccuracies in existing curated historical information, as well as errors in archival research by student assistants, which together give rise to unacceptable levels of uncertainty in the documentation. The paper discusses the problems relating to the reliability of historical information, demonstrates the importance of data verification in urban morphological research, and proposes a rigorous method for objective testing of collected archival data through the use of qualitative data analysis software.

Creating a legal framework for copyright management of open access within the Australian academic and research sector

This chapter analyses the copyright law framework needed to ensure open access to outputs of the Australian academic and research sector such as journal articles and theses. It overviews the new knowledge landscape, the principles of copyright law, the concept of open access to knowledge, the recently developed open content models of copyright licensing and the challenges faced in providing greater access to knowledge and research outputs.

Understanding Formal and Informal Governance on Infrastructure Projects - Literature Review [industry report]

In Australia, collaborative contracts have been increasingly used to govern infrastructure projects. These contracts combine formal and informal mechanisms to manage project delivery. Formal mechanisms (e.g. financial risk sharing) are specified in the contract, while informal mechanisms (e.g. integrated team) are not. The paper reports on a literature review to operationalise the concepts of formal and informal governance, as the literature contains a multiplicity of, often un-testable, definitions. This work is the first phase of a study that will examine the optimal balance of formal and informal governance structures. Desk-top review of leading journals in the areas of construction management and business management, as well as recent government documents and industry guidelines, was undertaken to to conceptualise and operatinalise formal and informal governance mechanisms. The study primarily draws on transaction-cost economics (e.g. Williamson 1979; 1991), relational contract theory (Feinman 2000; Macneil 2000) and social psychology theory (e.g. Gulati 1995). Content analysis of the literature was undertaken to identify key governance mechanisms. Content analysis is a commonly used methodology in the social sciences area. It provides rich data through the systematic and objective review of literature (Krippendorff 2004). NVivo 9, a qualitative data analysis software package, was used to assist in this process. Formal governance mechanisms were found to be usefully broken down into four measurable categories: (1) target cost arrangement (2) financial risk and reward sharing regime (3) transparent financials and (4) collaborative multi-party agreement Informal governance mechanisms were found to be usefully broken down into three measurable categories: (1) leadership structure (2) integrated team (3) joint management system We expect these categories to effectively capture the key governance drivers of outcomes on infrastructure projects. These categories will be further refined and broken down into individual governance mechanisms for assessment through a large-scale Australian survey planned for late 2012. These individual mechanisms will feature in the questionnaire that QUT will deliver to AAA in October 2012.

FaceXpress : an integrated software suite for facial emotion stimulus manipulation and facial measurement

The characterisation of facial expression through landmark-based analysis methods such as FACEM (Pilowsky & Katsikitis, 1994) has a variety of uses in psychiatric and psychological research. In these systems, important structural relationships are extracted from images of facial expressions by the analysis of a pre-defined set of feature points. These relationship measures may then be used, for instance, to assess the degree of variability and similarity between different facial expressions of emotion. FaceXpress is a multimedia software suite that provides a generalised workbench for landmark-based facial emotion analysis and stimulus manipulation. It is a flexible tool that is designed to be specialised at runtime by the user. While FaceXpress has been used to implement the FACEM process, it can also be configured to support any other similar, arbitrary system for quantifying human facial emotion. FaceXpress also implements an integrated set of image processing tools and specialised tools for facial expression stimulus production including facial morphing routines and the generation of expression-representative line drawings from photographs.

Multi-level neural modelling : an application of object-oriented software engineering

Neu-Model, an ongoing project aimed at developing a neural simulation environment that is extremely computationally powerful and flexible, is described. It is shown that the use of good Software Engineering techniques in Neu-Model’s design and implementation is resulting in a high performance system that is powerful and flexible enough to allow rigorous exploration of brain function at a variety of conceptual levels.