Comparison of genomic DNA extraction techniques from whole blood samples : a time, cost and quality evaluation study

Genomic DNA obtained from patient whole blood samples is a key element for genomic research. Advantages and disadvantages, in terms of time-efficiency, cost-effectiveness and laboratory requirements, of procedures available to isolate nucleic acids need to be considered before choosing any particular method. These characteristics have not been fully evaluated for some laboratory techniques, such as the salting out method for DNA extraction, which has been excluded from comparison in different studies published to date. We compared three different protocols (a traditional salting out method, a modified salting out method and a commercially available kit method) to determine the most cost-effective and time-efficient method to extract DNA. We extracted genomic DNA from whole blood samples obtained from breast cancer patient volunteers and compared the results of the product obtained in terms of quantity (concentration of DNA extracted and DNA obtained per ml of blood used) and quality (260/280 ratio and polymerase chain reaction product amplification) of the obtained yield. On average, all three methods showed no statistically significant differences between the final result, but when we accounted for time and cost derived for each method, they showed very significant differences. The modified salting out method resulted in a seven- and twofold reduction in cost compared to the commercial kit and traditional salting out method, respectively and reduced time from 3 days to 1 hour compared to the traditional salting out method. This highlights a modified salting out method as a suitable choice to be used in laboratories and research centres, particularly when dealing with a large number of samples.

Longitudinal Evidence on Educational and Occupational Outcomes Amongst South Sudanese Men from Refugee Backgrounds Living in Urban and Regional Southeast Queensland

Australia has continued to benefit from the human, social and economic capital contributed by immigrant resettlement over many years. Humanitarian entrants have also made significant economic, social and civic contributions to the Australian society. Since 2000, approximately 160,000 people have entered Australia under the refugee and humanitarian resettlement program; around 15% have come from South Sudan and one third of these are adult males. In response to the 2003 evaluation of the Integrated Humanitarian Settlement Strategy (IHSS), which recommended to seek further opportunities to settle humanitarian entrants in regional Australia, the Department of Immigration and Citizenship (DIAC) has since encouraged regional settlement to “address the demand for less skilled labour in regional economies and to assist humanitarian entrants to achieve early employment”. There is evidence, however, of the many challenges faced by humanitarian arrivals living in regional areas. This chapter focuses on the educational and occupational outcomes among 117 South Sudanese adult men from refugee backgrounds. In particular, the chapter uses both cross-sectional (at first interview) and longitudinal data (four interviews with each participant at six-month intervals) to compares outcomes between men living in Brisbane and those living in the Toowoomba–Gatton region in Southeast Queensland.

Integrating Intangible Cultural Heritage elements and learning strategy : a case study

Tanzania has a rich and diverse cultural history based on community cultural life. However, at present, young people have limited opportunity to exploit this richness of creative expressions and engage in creative jobs as their future career. Hence, the significant challenge remains: how to integrate Intangible cultural heritage elements and learning strategy as a means of promoting creative jobs for youth. This paper presents a case study on 'Strategies for youth employment in Tanzania: A creative industries approach'. The case study employed mixed methods incorporating questionnaires, interviews and focus groups and was held in Dar-Es-Salaam, Mwanza, Dodoma, Lindi and Morogoro from July to October, 2012. This paper discusses some of the issues and argues that there is no virtual utilization of the intangible cultural heritage knowledge and skills in 'putting education to work' (UNESCO, 2012) for the better prospects of youth. Although the discussion is specific to Tanzania, the case may also apply to other developing countries.

Reflection as a dialogic strategy for developing a professional identity

The benefits of reflective practice have been well established in the literature (Rogers, 2001), as have models to embed reflective thinking in higher education curriculum (Ryan and Ryan, 2012). Reflection is commonly envisaged as a textual practice, through which students ‘reflect in and on action’ (Schön 1983), and articulate their experiences, learning and outcomes in written portfolios, journals, or blogs. While such approaches to individual written reflection are undoubtedly beneficial for deepening insight and self-criticality, reflection can also provide other benefits when approached as a collaborative, oral activity. This poster presents a dialogic model of reflective practice that affords the opportunity for developing presentation skills, critique, community and professional identity formation. This dialogic approach to reflection is illustrated by a first year subject (‘KIB101 Visual Communication’ at QUT), in which students apply visual theory (presented in lectures) to communication and graphic design problems in the studio. In regular (fortnightly) presentations, they critically reflect upon their work in progress by aligning it with the concepts, design principles and professional language of the lectures. This iterative process facilitates responsive peer feedback, similarly couched in the formal terms of the discipline. This ‘mirrored reflection’ not only provides opportunities to incrementally improve, it also sets designs in a theoretical frame; provides the opportunity for comparative analysis (to see design principles applied by peers in different ways); to practice formal design language and presentation techniques of the discipline and; because peer critique is framed as an act of generosity; it affords the development of a supportive community of practice. In these ways, dialogic reflection helps students develop a professional voice and identity from first year. Evidence of impact is provided by quantitative and qualitative student feedback over several years, as well as institutional feedback and recognition.

A pharmacogenomic evaluation of migraine therapy

Migraine is a common idiopathic primary headache disorder with significant mental, physical and social health implications. Accompanying an intense unilateral pulsating head pain other characteristic migraine symptoms include nausea, emesis, phonophobia, photophobia and in approximately 20-30% of migraine cases, neurologic disturbances associated with the aura phase. Although selective serotonin (5-HT) receptor agonists (i.e., 5-HT(1B/1D)) are successful in alleviating migrainous symptoms in < or = 70% of known sufferers, for the remaining 30%, additional migraine abortive medications remain unsuccessful, not tested or yet to be identified. Genetic characterization of the migrainous disorder is making steady progress with an increasing number of genomic susceptibility loci now identified on chromosomes 1q, 4q, 5q, 6p, 11q, 14q, 15q, 17p, 18q, 19p and Xq. The 4q, 5q, 17p and 18q loci involve endophenotypic susceptibility regions for various migrainous symptoms. In an effort to develop individualized pharmacotherapeutics, the identification of these migraine endophenotypic loci may well be the catalyst needed to aid in this goal. In this review the authors discuss the present treatment of migraine, known genomic susceptibility regions and results from migraine (genetic) association studies. The authors also discuss pharmacogenomic considerations for more individualized migraine prophylactic treatments.

The measurement of adenosine and estrogen receptor expression in rat brains following ovariectomy using quantitative PCR analysis

In our laboratory we have developed a quantitative-polymerase chain reaction (Q-PCR) strategy to examine the differential expression of adenosine receptor (ADOR), A(1), A(2A), A(2B) and A(3), and estrogen receptors (ER) alpha and beta. Brain and uterine mRNA were first used to optimise specific amplification conditions prior to SYBR Green I real time analysis of receptor subtype expression. SYBR Green I provided a convenient and sensitive means of examining specific PCR amplification product in real time, and allowed the generation of standard curves from which relative receptor abundance could be determined. Real time Q-PCR analysis was then performed, to examine changes in receptor expression levels in brains of adult female Wistar rats 3-month post ovariectomy. Comparison with sham-operated age-matched control rats demonstrated both comparative and absolute-copy number changes in receptor levels. Evaluation of both analytical methods investigated 18S rRNA as an internal reference for comparative gene expression analysis in the brain. The results of this study revealed preferential repression of ADORA(2A) (>4-fold down) and consistent (>2-fold) down-regulation of ADORA(1), ADORA(3), and ER-beta, following ovariectomy. No change was found in ADORA(2B) or ER-alpha. Analysis of absolute copy number in this study revealed a correlation between receptor expression in response to ovariectomy, and relative receptor subtype abundance in the brain.

Retrieval of health advice on the web: AEHRC at ShARe/CLEF eHealth Evaluation Lab Task 3

This paper details the participation of the Australian e- Health Research Centre (AEHRC) in the ShARe/CLEF 2013 eHealth Evaluation Lab { Task 3. This task aims to evaluate the use of information retrieval (IR) systems to aid consumers (e.g. patients and their relatives) in seeking health advice on the Web. Our submissions to the ShARe/CLEF challenge are based on language models generated from the web corpus provided by the organisers. Our baseline system is a standard Dirichlet smoothed language model. We enhance the baseline by identifying and correcting spelling mistakes in queries, as well as expanding acronyms using AEHRC's Medtex medical text analysis platform. We then consider the readability and the authoritativeness of web pages to further enhance the quality of the document ranking. Measures of readability are integrated in the language models used for retrieval via prior probabilities. Prior probabilities are also used to encode authoritativeness information derived from a list of top-100 consumer health websites. Empirical results show that correcting spelling mistakes and expanding acronyms found in queries signi cantly improves the e ectiveness of the language model baseline. Readability priors seem to increase retrieval e ectiveness for graded relevance at early ranks (nDCG@5, but not precision), but no improvements are found at later ranks and when considering binary relevance. The authoritativeness prior does not appear to provide retrieval gains over the baseline: this is likely to be because of the small overlap between websites in the corpus and those in the top-100 consumer-health websites we acquired.

Identify disorders in health records using Conditional Random Fields and Metamap: AEHRC at ShARe/CLEF 2013 eHealth Evaluation Lab Task 1

The Australian e-Health Research Centre (AEHRC) recently participated in the ShARe/CLEF eHealth Evaluation Lab Task 1. The goal of this task is to individuate mentions of disorders in free-text electronic health records and map disorders to SNOMED CT concepts in the UMLS metathesaurus. This paper details our participation to this ShARe/CLEF task. Our approaches are based on using the clinical natural language processing tool Metamap and Conditional Random Fields (CRF) to individuate mentions of disorders and then to map those to SNOMED CT concepts. Empirical results obtained on the 2013 ShARe/CLEF task highlight that our instance of Metamap (after ltering irrelevant semantic types), although achieving a high level of precision, is only able to identify a small amount of disorders (about 21% to 28%) from free-text health records. On the other hand, the addition of the CRF models allows for a much higher recall (57% to 79%) of disorders from free-text, without sensible detriment in precision. When evaluating the accuracy of the mapping of disorders to SNOMED CT concepts in the UMLS, we observe that the mapping obtained by our ltered instance of Metamap delivers state-of-the-art e ectiveness if only spans individuated by our system are considered (`relaxed' accuracy).

Empirical evaluation of public transport travel time variability

Although transit travel time variability is essential for understanding the deterioration of reliability, optimising transit schedule and route choice; it has not attracted enough attention from the literature. This paper proposes public transport-oriented definitions of travel time variability and explores the distributions of public transport travel time using the Transit Signal Priority data. First, definitions of public transport travel time variability are established by extending the common definitions of variability in the literature and by using route and services data of public transport vehicles. Second, the paper explores the distribution of public transport travel time. A new approach for analysing the distributions involving all transit vehicles as well as vehicles from a specific route is proposed. The Lognormal distribution is revealed as the descriptors for public transport travel time from the same route and service. The methods described in this study could be of interest for both traffic managers and transit operators for planning and managing the transit systems.

Empirical evaluation of brisbane macroscopic fundamental diagram

The Macroscopic Fundamental Diagram (MFD) relates space-mean density and flow, and the existence with dynamic features was confirmed in congested urban network with real data set from loop detectors and taxi probes. Since the MFD represents the area-wide network traffic performances, it gives foundations for perimeter control strategies and an area traffic state estimation enabling area-based network control. However, limited works have been reported on real world example from signalised arterial network. This paper fuses data from multiple sources (Bluetooth, Loops and Signals) and develops a framework for the development of the MFD for Brisbane. Existence of the MFD in Brisbane network is confirmed. Different MFDs (from whole network and several sub regions) are evaluated to discover the spatial partitioning in network performance representation.

Queensland police service : an evaluation of HealthStart 2012

The HS program consists of a voluntary health screening and personalised feedback (via a website) which incorporates physical measurements, psychological stress assessment and blood tests. The following report describes the results of a research project that evaluated the effectiveness of the QPS-HS program and examines the health benefits it offers its participants. This report has three main areas that correspond to the research questions and includes three primary aims: 1.Review the literature pertaining to the health, social and economic value of wellness programs in workplaces. In particular, we reviewed policing worksites and other safety sensitive workplaces, to understand best-practice wellness programming and return on investment, in terms of value to employees, social value to the community, and economic value to employers; 2.Evaluate health outcomes of participants in the HS program, including physical measurements, such as blood tests and psychological well-being. These measures were to form an outcome evaluation and assess the effectiveness of the HS program in positively impacting physical and psychological health of HS participants; and 3.Assess employee awareness and perceptions of the HS program for a process evaluation.

A systematic approach for selecting lean strategies and assessing leanness in manufacturing organizations

Lean strategies have been developed to eliminate or reduce manufacturing waste and thus improve operational efficiency in manufacturing processes. However, implementing lean strategies requires a large amount of resources and, in practice, manufacturers encounter difficulties in selecting appropriate lean strategies within their resource constraints. There is currently no systematic methodology available for selecting appropriate lean strategies within a manufacturer's resource constraints. In the lean transformation process, it is also critical to measure the current and desired leanness levels in order to clearly evaluate lean implementation efforts. Despite the fact that many lean strategies are utilized to reduce or eliminate manufacturing waste, little effort has been directed towards properly assessing the leanness of manufacturing organizations. In practice, a single or specific group of metrics (either qualitative or quantitative) will only partially measure the overall leanness. Existing leanness assessment methodologies do not offer a comprehensive evaluation method, integrating both quantitative and qualitative lean measures into a single quantitative value for measuring the overall leanness of an organization. This research aims to develop mathematical models and a systematic methodology for selecting appropriate lean strategies and evaluating the leanness levels in manufacturing organizations. Mathematical models were formulated and a methodology was developed for selecting appropriate lean strategies within manufacturers' limited amount of available resources to reduce their identified wastes. A leanness assessment model was developed by using the fuzzy concept to assess the leanness level and to recommend an optimum leanness value for a manufacturing organization. In the proposed leanness assessment model, both quantitative and qualitative input factors have been taken into account. Based on program developed in MATLAB and C#, a decision support tool (DST) was developed for decision makers to select lean strategies and evaluate the leanness value based on the proposed models and methodology hence sustain the lean implementation efforts. A case study was conducted to demonstrate the effectiveness of these proposed models and methodology. Case study results suggested that out of 10 wastes identified, the case organization (ABC Limited) is able to improve a maximum of six wastes from the selected workstation within their resource limitations. The selected wastes are: unnecessary motion, setup time, unnecessary transportation, inappropriate processing, work in process and raw material inventory and suggested lean strategies are: 5S, Just-In-Time, Kanban System, the Visual Management System (VMS), Cellular Manufacturing, Standard Work Process using method-time measurement (MTM), and Single Minute Exchange of Die (SMED). From the suggested lean strategies, the impact of 5S was demonstrated by measuring the leanness level of two different situations in ABC. After that, MTM was suggested as a standard work process for further improvement of the current leanness value. The initial status of the organization showed a leanness value of 0.12. By applying 5S, the leanness level significantly improved to reach 0.19 and the simulation of MTM as a standard work method shows the leanness value could be improved to 0.31. The optimum leanness value of ABC was calculated to be 0.64. These leanness values provided a quantitative indication of the impacts of improvement initiatives in terms of the overall leanness level to the case organization. Sensitivity analsysis and a t-test were also performed to validate the model proposed. This research advances the current knowledge base by developing mathematical models and methodologies to overcome lean strategy selection and leanness assessment problems. By selecting appropriate lean strategies, a manufacturer can better prioritize implementation efforts and resources to maximize the benefits of implementing lean strategies in their organization. The leanness index is used to evaluate an organization's current (before lean implementation) leanness state against the state after lean implementation and to establish benchmarking (the optimum leanness state). Hence, this research provides a continuous improvement tool for a lean manufacturing organization.

Heat-producing crust regulation of subsurface temperatures : a stochastic model re-evaluation of the geothermal potential in western Queensland, Australia

A large subsurface, elevated temperature anomaly is well documented in Central Australia. High Heat Producing Granites (HHPGs) intersected by drilling at Innamincka are often assumed to be the dominant cause of the elevated subsurface temperatures, although their presence in other parts of the temperature anomaly has not been confirmed. Geological controls on the temperature anomaly remain poorly understood. Additionally, methods previously used to predict temperature at 5 km depth in this area are simplistic and possibly do not give an accurate representation of the true distribution and magnitude of the temperature anomaly. Here we re-evaluate the geological controls on geothermal potential in the Queensland part of the temperature anomaly using a stochastic thermal model. The results illustrate that the temperature distribution is most sensitive to the thermal conductivity structure of the top 5 km. Furthermore, the results indicate the presence of silicic crust enriched in heat producing elements between and 40 km.

Formative evaluation for improving collaborative planning : a case study at the regional scale

In an earlier paper (Cameron & Johnson 2004) we introduced the idea of formative evaluation (or evaluation for development), the purpose of which is to provide information for improving planning programs and activities. This type of evaluation differs from the two other types: outcome evaluation which aims to judge the success or otherwise of a program; and evaluation for knowledge which seeks to contribute to theoretical work on planning processes and activities. In the earlier paper we also outlined the first stage of formative evaluation in the SEQ 2021 regional planning exercise showing how the process of planning for community engagement was modified in light of the evaluation findings. This current paper details the second stage of formative evaluation in which the collaborative planning component of SEQ 2021 was evaluated, as such it further demonstrates how formative evaluation can be used to improve planning programs. The evaluation findings also provide insights into strategies for more effective collaborative planning. We begin with an overview of collaborative approaches to regional planning, including the SEQ 2021 regional planning program. We then outline formal and informal evaluations of various collaborative regional planning exercises, including the predecessor of SEQ 2021 - SEQ 2001. This sets the scene for discussion of the approach used to evaluate the collaborative component of SEQ 2021. After outlining the main findings from the evaluation and the ways these findings were used to refine the collaborative planning process we conclude with a series of recommendations, relevant not only to SEQ 2021 but to other collaborative planning exercises

Reconstructing places and spaces in blended work integrated learning

This paper considers the emergence and ongoing development of an embedded, studentnegotiated work placement model of Work Integrated Learning (WIL) in the engineering and built environment disciplines at an Australian metropolitan university. The characteristics of the model and a continuous improvement strategy are provided. The model is characterised by large student cohorts independently sourcing and negotiating relevant work placements and completing at least one, mandatory credit-bearing WIL unit. Through ongoing analyses and evaluation of the model more experiential and collaborative learning approaches have been adopted. This has included the creation of blended learning spaces using technology. The paper focuses on the five year journey travelled by the teaching team as they embarked on ways to improve curriculum, pedagogy, administrative processes and assessment - effectively relocating much of their interaction with students online. The insights derived from this rich, single case study should be of interest to others considering alternative ways of responding to increasing student enrolments in WIL and the impact of blended learning in this context.