BioPatML : pattern sharing for the genomic sciences

Computational biology increasingly demands the sharing of sophisticated data and annotations between research groups. Web 2.0 style sharing and publication requires that biological systems be described in well-defined, yet flexible and extensible formats which enhance exchange and re-use. In contrast to many of the standards for exchange in the genomic sciences, descriptions of biological sequences show a great diversity in format and function, impeding the definition and exchange of sequence patterns. In this presentation, we introduce BioPatML, an XML-based pattern description language that supports a wide range of patterns and allows the construction of complex, hierarchically structured patterns and pattern libraries. BioPatML unifies the diversity of current pattern description languages and fills a gap in the set of XML-based description languages for biological systems. We discuss the structure and elements of the language, and demonstrate its advantages on a series of applications, showing lightweight integration between the BioPatML parser and search engine, and the SilverGene genome browser. We conclude by describing our site to enable large scale pattern sharing, and our efforts to seed this repository.

Framework for investment decision-making under risk and uncertainty for infrastructure asset management

A study has been conducted to investigate current practices on decision-making under risk and uncertainty for infrastructure project investments. It was found that many European countries such as the UK, France, Germany including Australia use scenarios for the investigation of the effects of risk and uncertainty of project investments. Different alternative scenarios are mostly considered during the engineering economic cost-benefit analysis stage. For instance, the World Bank requires an analysis of risks in all project appraisals. Risk in economic evaluation needs to be addressed by calculating sensitivity of the rate of return for a number of events. Risks and uncertainties of project developments arise from various sources of errors including data, model and forecasting errors. It was found that the most influential factors affecting risk and uncertainty resulted from forecasting errors. Data errors and model errors have trivial effects. It was argued by many analysts that scenarios do not forecast what will happen but scenarios indicate only what can happen from given alternatives. It was suggested that the probability distributions of end-products of the project appraisal, such as cost-benefit ratios that take forecasting errors into account, are feasible decision tools for economic evaluation. Political, social, environmental as well as economic and other related risk issues have been addressed and included in decision-making frameworks, such as in a multi-criteria decisionmaking framework. But no suggestion has been made on how to incorporate risk into the investment decision-making process.

The journey to delivered value in Australian procurement

In line with developments overseas Australian clients are turning to considerations of value in project procurement. Until the 1980s the industry operated in a largely traditional manner however the extremely adversarial behaviour exhibited during towards the end of the decade led to a number of significant events and initiatives including the publication of “No Dispute”, the Gyles Royal Commission into the Building Industry, the Construction Industry Development Agency (CIDA) and the work of the Australian Procurement and Construction Council (APCC). A number of research projects in progress in the CRC for Construction Innovation (CRC CI) are focussing on the assessment of value and methodologies to support the delivery of value in the procurement and management of engineering and construction projects. This paper charts the emergence of several key drivers in the process and illustrates how they can be integrated into a comprehensive Decision Support System that balances value to stakeholders with project imperatives and incorporates a lessons learned data base which enriches the decision making process to optimise delivery method design and selection.

Reduction of Secondary Degeneration after Spinal Cord Injury by Acute Delivery of Proinflammatory Growth Factors

INTRODUCTION Inflammation is a protective attempt to facilitate the removal of damaged tissue and to initiate the healing response in other tissues. However, after spinal cord injury (SCI), this response is prolonged leading to secondary degeneration and glial scarring. Here, we investigate the potential of sustained delivery of pro-inflammatory factors vascular endothelial growth factor (VEGF) and platelet derived growth factor (PDGF) to increase early inflammatory events and promote inflammatory resolution. Method Animal ethics approval was obtained from the Queensland University of Technology. Adult Wistar-Kyoto rats (12-16 weeks old) were subjected to laminectomies and T10 hemisections. Animals were then randomised to treatment (implantation of osmotic pump (Alzet) loaded with 5ug VEGF & 5 ug PDGF) or control groups (lesion control or lesion plus pump delivering PBS). Rats were sacrificed at one month and the spinal cords were harvested and examined by immunohistology, using anti-neurofilament-200(NF200) and anti- ionized calcium binding adapter molecule 1 (Iba1). One way ANOVA was used for statistic analysis. Results At 1 month, active pump-treated cords showed a high level of axonal filament throughout the defects as compared to the control groups. The mean lesion size, as measured by NF200, was 0.47mm2 for the lesion control, 0.39mm2 for the vehicle control and 0.078mm2 for the active pump group. Significant differences were detected between the active pump group and the two control groups (AP vs LC p= 0.017 AG vs VC p= 0.004). Iba-1 staining also showed significant differences in the post-injury inflammatory response. Discussion We have shown that axons and activated microglia are co-located in the lesion of the treated cord. We hypothesise the delivery of VEGF/PDGF increases the local vessel permeability to inflammatory cells and activates these along with the resident microglia to threshold population, which ultimately resolved the prolonged inflammation. Here, we have shown that maintaining the inflammatory signals for at least 7 days improved the morphology of the injured cord. Conclusion This study has shown that boosting inflammation, by delivery VEGF/PDGF, in the early phase of SCI helps to reduce secondary degeneration and may promote inflammation resolution. This treatment may provide a platform for other neuro-regenrative therapies.

Conference Report of the First Meeting of the Native American and Indigenous Studies Association, 21-23 May 2009, Department of American Indian Studies, University of Minneapolis, Minesota, United States of America

Report provided back by Bronwyn Fredericks on her participation at the First Native American and Indigenous Studies Association Meeting held 21-23 May 2009 in Minnesota, United States of America.

Re-imagining and re-imaging the nation through the history curriculum.

Nationalism is not a naturally occurring sentiment, but rather needs to be carefully nurtured and sustained in the social imaginary through the production and circulation of unifying narratives that invoke the nation’s imagined community. The school curriculum is crucial in this process, legitimating and disseminating selected narratives while de-legitimating and marginalising other accounts and their voices. Certain watershed events in nations’ histories have always posed political problems in history curricula (Cajani & Ross, 2007) –however the pressures and concerns of current times now suggest political solutions in history curricula. This paper briefly examines recent political debates in Australia to argue that the school history curriculum has become a site of increasing interest for the exercise of official forms of nationalism and the production of a nostalgic, celebratory national biography. The public debates around school history curriculum are theorised as nostalgic re-nationalising efforts in response to the march of cultural globalisation and its attendant uncertainties.

Naming trouble in online internationalized education

This paper offers an analysis of cultural politics that emerged around naming practices in an ethnographic study of the interactions within an online MBA unit, offered by an Australian university to both ‘local’ Australian students and international students enrolled through a Malaysian partner institution. It became evident that names were doing important identity, textual and pedagogical work in these interactions and considerable interactive trouble arose over the social practices surrounding names. The analysis uses sociolinguistic concepts to analyse selected slices of the online texts and participants' interview accounts. The analysis shows how ethnocentric default settings in the courseware served to heighten and exacerbate cultural difference as a pedagogical problem. These events are related to the larger problematic of theorising the context of culture in times of globalisation and increasingly entangled educational routes, with implications for the enterprise of online internationalised education.

The ethical predisposition of university students in Western Australia : 1997 vs 2007

A sample of 285 Western Australian university students was used to assess the prevailing attitudes regarding potential breaches of ethical conduct on the part of business practitioners and organisations. The authors developed an ethical profile for the 2007 sample based on 14 scenarios used in the questionnaire. This profile was then compared to the results from data collected in 1997 using similar sampling and the same survey instrument. The prevailing predisposition is best viewed as centrist in nature, with a move to a more ethical stance in the last 10 years.

Embodied vulnerabilities : responding to violent encounters through installation practices

This practice-led research was initiated in response to a series of violent encounters that occurred between my fragile installations and viewers. The central focus of this study was to recuperate my installation practice in the wake of such events. This led to the development of a ‘responsive practice’ methodology, which reframed the installation process through an ethical lens developed from Emmanuel Levinas’ ethical phenomenology. The central propositions of this research are the reconceptualisation of ‘violent encounters’ in terms of difference whereby I accept viewers responses, even those which are violent, destructive or damaging, and secondly that the process operates as a generative excess for practice through which recuperative strategies can be found and implemented. By re-examining this process as it unfolded in the three phases of the practical component, I developed strategies whereby violated, destroyed or damaged works could be recuperated through the processes of reconfiguration, reparation and regeneration. Therefore my installations embody and articulate vulnerability but also demonstrate resilience and renewal.

Comparing the ethical predisposition of university students in five English-speaking countries : an examination of 14 questionable business practices

Recent years have seen intense scrutiny focused on the reported ethical breaches of enterprises across the globe. At the forefront of the accompanying criticism are the actions of giant American firms such as WorldCom, Arthur Anderson, and Enron. However, such deviations from acceptable standards of conduct have not been confined to the American market. Australia endured its era of “corporate excess” in the 1980s [Milton-Smith, 1997]. As a result, a spate of ethics-based research was undertaken in the early 1990s. More recently, China has been identified as a major venue for behavior deemed to be unacceptable, even unsafe. Issues such as counterfeit fashion items, software, and automobile parts have been a concern for several years [Gonzalez, 2007]. Perhaps more disconcerting are the recent recalls of children’s products, many of which were produced for leading toy companies such as Mattel and Fisher-Price, because of the use of dangerous lead-based paint. As one might anticipate, news reports and consumer protection agencies have been quick to condemn any action that falls within the “controversial” category. Indeed, many segments of society characterize such actions as unethical behavior. One result of this increased level of concern is the higher level of attention given to ethics in higher education programs. Even accreditation bodies such as AACSB have virtually mandated the integration of ethics into the curriculum. As a consequence, academicians have ramped up their ethics-based research agendas.

University-industry partnership for pedagogy : some principles for practice

Industries demand a closer alignment of university learning curriculum to real work tasks to better meet the needs of organizations and learners. Both, industries and learners prefer the learning challenges to be based on the exigencies of work to precisely reflect real work circumstances that overtly add to business outcomes. However, such alignment is often complicated and challenging for academics and workplace managers alike. It demands partnerships between universities and industries, similar to arrangements forged for the vocational education and training sector. Such partnerships should allow active participation by learners, academics, workplaces and university administrators to move beyond a teaching orientation to a demonstrably effective learning arrangement through work integrated learning. This paper draws on a case study that negotiated a partnership between a non-government organization and an Australian university to design and facilitate a boutique curriculum that met the needs of learners and their workplace. Data were collected from interviews with participants, a focus group of the interviewees, and feedback from university staff involved in the course delivery. The paper presents a set of principles for universities and industries for partnership to enhance the alignment of academic curriculum to meet organizational and individual learning needs through work integrated learning.

The inclusion of first aid in an injury prevention curriculum

Prompt first aid can have considerable benefits. The Skills for Preventing Injury in Youth (SPIY) program aims to teach, in part, first aid skills along with additional injury prevention strategies. The approach to including first aid is both as an injury prevention strategy and a way in which to reduce the severity of injuries once they occur. This paper outlines an implementation trial of the SPIY program with particular emphasis on the delivery and implementation of first aid skills. SPIY demonstrated effectiveness with regard to first aid knowledge and as an injury prevention program. SPIY is taught in the Year 9 Health curriculum by HPE teachers. Students and teachers who undergo or deliver such training offer important perspectives about implementation. In addition independent observation of delivery provides further information about the program. The research aimed to examine teachers‟ and students‟ experiences of first aid activities within a school-based injury prevention and control program and identify key issues in delivery from independent observation of the program. Focus groups were held with 8 teachers who delivered, and 70 students who participated in the SPIY curriculum program. Results showed favourable reports on the delivery of first aid material however teachers noted challenges in delivering practical activities. In sum, first aid can be effectively implemented within the high school setting and both students and teachers identified multiple benefits and positive experiences after undertaking first aid training.

Preventing physical activity induced heat illness in school settings

The climatic conditions of tropical and subtropical regions within Australia present, at times, extreme risk of physical activity induced heat illness. Many administrators and teachers in school settings are aware of the general risks of heat related illness. In the absence of reliable information applied at the local level, there is a risk that inappropriate decisions may be made concerning school events that incorporate opportunities to be physically active. Such events may be prematurely cancelled resulting in the loss of necessary time for physical activity. Under high or extremely high risk conditions however, the absence of appropriate modifications or continuation could place the health of students, staff and other parties at risk. School staff and other key stakeholders should understand the mechanisms of escalating risk and be supported to undertake action to reduce the level of risk through appropriate policies, procedures, resources and action plans.

Student success : the identification and support of first year university students at risk of attrition

The engagement behaviour of 1,524 student-enrolments (“students”) in five first year units was monitored and 608 (39.9%) were classified as “at risk” using the criterion of not submitting or failing their first assignment. Of these, 327 (53.8%) were successfully contacted (i.e., spoken to by phone) and provided with advice and/or referral to learning and personal support services while the remaining 281 (46.2%) could not be contacted. Nine hundred and sixteen students (60.1%) were classified as “not at risk.” Overall, the at risk group who were contacted achieved significantly higher end-of-semester final grades than, and persisted (completed the unit) at more than twice the rate of, the at risk group who were not contacted. There were variations among the units which were explained by the timing of the first assignment, specific teaching-learning processes and the structure of the curriculum. Implications for curriculum design and supporting first year students within a personal, social and academic framework are discussed.

Determining heavy vehicle suspension health from vibratory wheel loads

A low-cost test bed was made from a modified heavy vehicle (HV) brake tester. By rotating a test HV’s wheel on an eccentric roller, a known vibration was imparted to the wheel under test. A control case for dampers in good condition was compared with two test cases of ineffective shock absorbers. Measurement of the forces at the bearings of the roller provided an indication of the HV wheel-forces. Where the level of serviceability of the shock absorbers varied, differences in wheel load provided a quality indicator corresponding to a change of damper characteristic. Conclusions regarding the levels of damper maintenance beyond which HV suspensions cause road damage and dynamic wheel forces at the threshold of tyre wear at which HV shock absorbers are normally replaced are presented.