Cluster-based network model for time-course gene expression data

We propose a model-based approach to unify clustering and network modeling using time-course gene expression data. Specifically, our approach uses a mixture model to cluster genes. Genes within the same cluster share a similar expression profile. The network is built over cluster-specific expression profiles using state-space models. We discuss the application of our model to simulated data as well as to time-course gene expression data arising from animal models on prostate cancer progression. The latter application shows that with a combined statistical/bioinformatics analyses, we are able to extract gene-to-gene relationships supported by the literature as well as new plausible relationships.

Thinking Collaboratively about the Peer-Review Process for Journal- Article Publication

In this conversation, Kevin K. Kumashiro shares his reflections on challenges to publishing anti-oppressive research in educational journals. He then invites eight current and former editors of leading educational research journals--William F. Pinar, Elizabeth Graue, Carl A. Grant, Maenette K. P. Benham, Ronald H. Heck, James Joseph Scheurich, Allan Luke, and Carmen Luke--to critique and expand on his analysis. Kumashiro begins the conversation by describing his own experiences submitting manuscripts to educational research journals and receiving comments by anonymous reviewers and journal editors. He suggests three ways to rethink the collaborative potential of the peer-review process: as constructive, as multilensed, and as situated. The eight current and former editors of leading educational research journals then critique and expand Kumashiro's analysis. Kumashiro concludes the conversation with additional reflections on barriers and contradictions involved in advancing anti-oppressive educational research in educational journals. (Contains 3 notes.)

Work-related driving safety in light vehicle fleets : a review of past research and the development of an intervention framework

This paper presents a critical review of past research in the work-related driving field in light vehicle fleets (e.g., vehicles < 4.5 tonnes) and an intervention framework that provides future direction for practitioners and researchers. Although work-related driving crashes have become the most common cause of death, injury, and absence from work in Australia and overseas, very limited research has progressed in establishing effective strategies to improve safety outcomes. In particular, the majority of past research has been data-driven, and therefore, limited attention has been given to theoretical development in establishing the behavioural mechanism underlying driving behaviour. As such, this paper argues that to move forward in the field of work-related driving safety, practitioners and researchers need to gain a better understanding of the individual and organisational factors influencing safety through adopting relevant theoretical frameworks, which in turn will inform the development of specifically targeted theory-driven interventions. This paper presents an intervention framework that is based on relevant theoretical frameworks and sound methodological design, incorporating interventions that can be directed at the appropriate level, individual and driving target group.

Transit users' route-choice modelling in transit assignment : a review

This paper reviews the main studies on transit users’ route choice in thecontext of transit assignment. The studies are categorized into three groups: static transit assignment, within-day dynamic transit assignment, and emerging approaches. The motivations and behavioural assumptions of these approaches are re-examined. The first group includes shortest-path heuristics in all-or-nothing assignment, random utility maximization route-choice models in stochastic assignment, and user equilibrium based assignment. The second group covers within-day dynamics in transit users’ route choice, transit network formulations, and dynamic transit assignment. The third group introduces the emerging studies on behavioural complexities, day-to-day dynamics, and real-time dynamics in transit users’ route choice. Future research directions are also discussed.

A systematic review of the association between physical activity and colorectal cancer risk

This review evaluated the strength of the evidence for a causal relationship between physical activity (PA) and colorectal cancer (CRC). A systematic review of databases through February 2008 was conducted to identify studies that assessed the association between total or recreational PA and incidence or mortality of CRC (including CRC, rectal cancer, colon cancer, and proximal or distal colon cancer). Studies were evaluated for significant associations between PA and risk of CRC endpoints and for evidence of dose–response relationships in the highest quality studies. Twenty cohort studies were evaluated; 11 were high-quality. Fifty percent of all studies and 64%of highest quality studies reported at least one significant association between PA and risk of a CRC endpoint (Po0.05).However, only 28%of all analyses (31% of analyses of highest quality studies) were significant (Po0.05). Only 40% of analyses of highest quality studies resulted in a significant P for trend (Po0.05); however, a non-significant inverse linear association between PA and colon cancer riskwas apparent.Heterogeneity in the evidence from all studies and from the highest quality studies was evident. Evidence from cohort studies is not sufficient to claim a convincing relationship exists between PA and CRC risk.

Exercise and cancer rehabilitation : a systematic review

Introduction: Cancer is increasingly being viewed as a chronic illness requiring long-term management, and there is a growing need for evidence-based rehabilitation interventions for cancer survivors. Previous reviews have evaluated the benefits of exercise interventions for patients undergoing cancer treatment and long-term survivors, but none have investigated the role of exercise during cancer rehabilitation, the period immediately following cancer treatment completion. This systematic review summarises the literature on the health effects of exercise during cancer rehabilitation and evaluates the methodological rigour of studies in this area to date.----------- Methods: Relevant studies were identified through a systematic search of PubMed and Embase to April 2009. Data on study design, recruitment strategy, participants, exercise intervention, adherence rates, and outcomes were extracted. Methodological rigour was assessed using a structured rating system.---------- Results: Ten studies were included. Breast cancer patients were the predominate patient group represented. Most interventions were aerobic or resistance-training exercise programmes, and exercise type, frequency, duration and intensity varied across studies. Improvements in physical functioning, strength, physical activity levels, quality of life, fatigue, immune function, haemoglobin concentrations, potential markers of recurrence, and body composition were reported. However, all studies were limited by incomplete reporting and methodological limitations.---------- Conclusions: Although the methodological limitations of studies in this new field must be acknowledged, initial evidence indicates that exercise is feasible and may provide physiological and psychological benefits for cancer survivors during the rehabilitation period. Future studies with rigorous study designs are now required to advance the field.

Informed consent : the review of the law of negligence and the utility of reference to NHMRC guidelines

Although rarely referred to in litigation in the years that have followed the Ipp Review Report, there may well be some merit in more frequent judicial reference to the NHMRC guidelines for medical practitioners on providing information to patients 2004.

What's cooking for dietetics? A review of the literature

Aim: There has been no systematic research on the role of cooking skills for improving dietary intakes in Australia. Cooking skills are proposed to be declining and/or being devalued. If cooking skills have been devalued and declining, then what evidence is there for this decline and what impact might this have on dietary intakes? The aim of the present paper is to explore these assumptions with particular reference to Australia. The objectives of the present paper are to define the terms cooking and cooking skills, discuss evidence on levels of cooking skills in Australia and describe the evidence linking cooking skills to dietary intakes.---------- Methods: A review of the peer-reviewed literature using multiple databases from 1990 to September 2009.---------- Results: Cooking skills are complex and require a range of processes for people to develop efficiency or confidence in food preparation. There is little evidence on the level of cooking skills in the Australian population and how this relates to dietary intakes. The Australian Bureau of Statistic’s latest Time Use Survey and Household Expenditure Survey suggest that cooking is still a gendered activity and that the time devoted to cooking has changed little in the past 15 years, but there is an increasing use of foods prepared outside the home.---------- Conclusion: Further research is required to examine the prevalence of different types and levels of cooking skills in Australia as well as their potential effects on dietary intakes. Dietitians need evidence about the level of cooking skills people require for healthy dietary intakes.

Research and application of Building Information Modelling (BIM) in the Architecture, Engineering and Construction (AEC) industry : a review and direction for future research

With an increasing level of collaboration amongst researchers, software developers and industry practitioners in the past three decades, building information modelling (BIM) is now recognized as an emerging technological and procedural shift within the architect, engineering and construction (AEC) industry. BIM is not only considered as a way to make a profound impact on the professions of AEC, but is also regarded as an approach to assist the industry to develop new ways of thinking and practice. Despite the widespread development and recognition of BIM, a succinct and systematic review of the existing BIM research and achievement is scarce. It is also necessary to take stock on existing applications and have a fresh look at where BIM should be heading and how it can benefit from the advances being made. This paper first presents a review of BIM research and achievement in AEC industry. A number of suggestions are then made for future research in BIM. This paper maintains that the value of BIM during design and construction phases is well documented over the last decade, and new research needs to expand the level of development and analysis from design/build stage to postconstruction and facility asset management. New research in BIM could also move beyond the traditional building type to managing the broader range of facilities and built assets and providing preventative maintenance schedules for sustainable and intelligent buildings

Case management educational intervention with public health nurses : cluster randomized controlled trial

Aim: This paper is a report of a study conducted to determine the effectiveness of a community case management collaborative education intervention in terms of satisfaction, learning and performance among public health nurses. Background: Previous evaluation studies of case management continuing professional education often failed to demonstrate effectiveness across a range of outcomes and had methodological weaknesses such as small convenience samples and lack of control groups. Method: A cluster randomised controlled trial was conducted between September 2005 and February 2006. Ten health centre clusters (5 control, 5 intervention) recruited 163 public health nurses in Taiwan to the trial. After pre-tests for baseline measurements, public health nurses in intervention centres received an educational intervention of four half-day workshops. Post-tests for both groups were conducted after the intervention. Two-way repeated measures analysis of variance was performed to evaluate the effect of the intervention on target outcomes. Results: A total of 161 participants completed the pre- and post-intervention measurements. This was almost a 99% response rate. Results revealed that 97% of those in the experimental group were satisfied with the programme. There were statistically significant differences between the two groups in knowledge (p = 0.001), confidence in case management skills (p = 0.001), preparedness for case manager role activities (p = 0.001), self-reported frequency in using skills (p = 0.001), and role activities (p = 0.004). Conclusion: Collaboration between academic and clinical nurses is an effective strategy to prepare nurses for rapidly-changing roles.

Improving road safety through deterrence-based initiatives : a review of research

The efficacy of road safety countermeasures to deter motorists from engaging in illegal behaviours is extremely important when considering the personal and economic impact of road accidents on the community. Within many countries, deterrence theory has remained a cornerstone to criminology and criminal justice policy, particularly within the field of road safety, as policy makers and enforcement agencies attempt to increase perceptions regarding the certainty, severity and swiftness of sanctions for those who engage in illegal motoring behaviours. Using the Australian experience (particularly the tremendous amount of research into drink driving), the current paper reviews the principles underpinning deterrence theory, the utilisation of the approach within some contemporary road safety initiatives (e.g., Random Breath Testing) as well as highlights some methods to enhance a deterrent effect. The paper also provides direction for future deterrence-based research, in particular, considering the powerful impact of non-legal sanctions, punishment avoidance as well as creating culturally embedded behavioural change.

Accelerated Partial Breast Irradiation (APBI) : a review of available techniques

Breast conservation therapy (BCT) is the procedure of choice for the management of the early stage breast cancer. However, its utilization has not been maximized because of logistics issues associated with the protracted treatment involved with the radiation treatment. Accelerated Partial Breast Irradiation (APBI) is an approach that treats only the lumpectomy bed plus a 1-2 cm margin, rather than the whole breast. Hence because of the small volume of irradiation a higher dose can be delivered in a shorter period of time. There has been growing interest for APBI and various approaches have been developed under phase I-III clinical studies; these include multicatheter interstitial brachytherapy, balloon catheter brachytherapy, conformal external beam radiation therapy and intra-operative radiation therapy (IORT). Balloon-based brachytherapy approaches include Mammosite, Axxent electronic brachytherapy and Contura, Hybrid brachytherapy devices include SAVI and ClearPath. This paper reviews the different techniques, identifying the weaknesses and strength of each approach and proposes a direction for future research and development. It is evident that APBI will play a role in the management of a selected group of early breast cancer. However, the relative role of the different techniques is yet to be clearly identified.

Old Brisbane Botanic Gardens: Conservation Plan Review 2005, Report of Stage 1 Heritage Significance and Conservation Policies

Report for City Design, for Environment and Parks, within the Brisbane City Council. Context of this Project A Conservation Study for the Old Brisbane Botanic Gardens, formerly called the Brisbane City Botanic Gardens, was finalised in 1995 and prepared by Jeannie Sim for the Landscape Section of Brisbane City Council, the same author of the present report. This unpublished report was the first conservation plan prepared for the place and it was recommended that it be reviewed in five years time. That time has arrived finally with the preparation of the 2005 Review. The present project was commissioned by City Design on behalf of Environment and Parks Section of Brisbane City Council. The author has purposely chosen to call the study site the 'Old Brisbane Botanic Gardens' (OBBG) to differentiate it from the Brisbane Botanic Gardens, Mt. Coot-tha (BBG-MC), and to maintain the claim for this original garden to remain as a botanic garden for Brisbane. This name immediately brings to mind an association with history, as in the precedent set by the naming of the nearby 'Old Government House' at Gardens Point.

Public participation, values and interests in the procurement of infrastructure projects in Australia : a review and future research direction

In many countries, the main providers for major infrastructure projects are government or public agencies. Public infrastructure projects includes economic and social infrastructure such as transportation, education and health facilities. Most decision-making models for delivery of public infrastructure projects are heavily weighted towards financial/economic factors. In Australia, public participation is an essential instrument in the procurement of infrastructure and development within Australia. This study reviews the public participation, values and interests in the procurement of infrastructure projects in Australia, and identifies the research direction in this research area in order to improve the decision-making models that capture stakeholder social, economical and environmental concerns in infrastructure projects.