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.

Working in groups

This chapter is a condensation of a guide written by the chapter authors for both university teachers and students (Fowler et al., 2006). All page references given in this chapter are to this guide, unless otherwise stated. University students often work in groups. It may be a formal group (i.e. one that has been formed for a group presentation, writing a report, or completing a project) or an informal group (i.e. some students have decided to form a study group or undertake research together). Whether formal or informal, this chapter aims to make working in groups easier for you. Health care professionals also often work in groups. Yes, working in groups will extend well beyond your time at university. In fact, the skills and abilities to work effectively in groups are some of the most sought-after attributes in health care professionals. It seems obvious, then, that taking the opportunity to develop and enhance your skills and abilities for working in groups is a wise choice.

A comparison of the hazard perception ability of matched groups of healthy drivers aged 35 to 55, 65 to 74, and 75 to 84 years

We examined differences in response latencies obtained during a validated video-based hazard perception driving test between three healthy, community-dwelling groups: 22 mid-aged (35-55 years), 34 young-old (65-74 years), and 23 old-old (75-84 years) current drivers, matched for gender, education level, and vocabulary. We found no significant difference in performance between mid-aged and young-old groups, but the old-old group was significantly slower than the other two groups. The differences between the old-old group and the other groups combined were independently mediated by useful field of view (UFOV), contrast sensitivity, and simple reaction time measures. Given that hazard perception latency has been linked with increased crash risk, these results are consistent with the idea that increased crash risk in older adults could be a function of poorer hazard perception, though this decline does not appear to manifest until age 75+ in healthy drivers.

Utilisation of seed resources by small mammals : a two-way interaction

Within the Australian wet tropics bioregion, only 900 000 hectares of once continuous rainforest habitat between Townsville and Cooktown now remains. While on the Atherton Tableland, only 4% of the rainforest that once occurred there remains today with remnant vegetation now forming a matrix of rainforest dispersed within agricultural land (sugarcane, banana, orchard crops, townships and pastoral land). Some biologists have suggested that remnants often support both faunal and floral communities that differ significantly from remaining continuous forest. Australian tropical forests possess a relatively high diversity of native small mammal species particularly rodents, which unlike larger mammalian and avian frugivores elsewhere, have been shown to be resilient to the effects of fragmentation, patch isolation and reduction in patch size. While small mammals often become the dominant mammalian frugivores, in terms of their relative abundance, the relationship that exists between habitat diversity and structure, and the impacts of small mammal foraging within fragmented habitat patches in Australia, is still poorly understood. The relationship between foraging behaviour and demography of two small mammal species, Rattus fuscipes and Melomys cervinipes, and food resources in fragmented rainforest sites, were investigated in the current study. Population densities of both species were strongly related with overall density of seed resources in all rainforest fragments. The distribution of both mammal species however, was found to be independent of the distribution of seed resources. Seed utilisation trials indicated that M.cervinipes and R.fuscipes had less impact on seed resources (extent of seed harvesting) than did other rainforest frugivores. Experimental feeding trials demonstrated that in 85% of fruit species tested, rodent feeding increased seed germination by a factor of 3.5 suggesting that in Australian tropical rainforest remnants, small mammals may play a significant role in enhancing germination of large seeded fruits. This study has emphasised the role of small mammals in tropical rainforest systems in north eastern Australia, in particular, the role that they play within isolated forest fragments where larger frugivorous species may be absent.

Demographic category membership and leadership in small groups : a social identity analysis

Developing the social identity theory of leadership (e.g., [Hogg, M. A. (2001). A social identity theory of leadership. Personality and Social Psychology Review, 5, 184–200]), an experiment (N=257) tested the hypothesis that as group members identify more strongly with their group (salience) their evaluations of leadership effectiveness become more strongly influenced by the extent to which their demographic stereotype-based impressions of their leader match the norm of the group (prototypicality). Participants, with more or less traditional gender attitudes (orientation), were members, under high or low group salience conditions (salience), of non-interactive laboratory groups that had “instrumental” or “expressive” group norms (norm), and a male or female leader (leader gender). As predicted, these four variables interacted significantly to affect perceptions of leadership effectiveness. Reconfiguration of the eight conditions formed by orientation, norm and leader gender produced a single prototypicality variable. Irrespective of participant gender, prototypical leaders were considered more effective in high then low salience groups, and in high salience groups prototypical leaders were more effective than less prototypical leaders. Alternative explanations based on status characteristics and role incongruity theory do not account well for the findings. Implications of these results for the glass ceiling effect and for a wider social identity analysis of the impact of demographic group membership on leadership in small groups are discussed.

Critique groups : a technique for the author’s toolbox?

With a lack of places to gain an education in the craft of romance writing, novelists have few places to turn to gain real feedback. This paper investigates an alternative to textbooks, conferences, and workshops through an examination of the role provided to the writer by critique groups. How these groups work, how they benefit an author, and the critique groups as a whole are discussed. This work studies the form of Peer Assessment and Learning (PAL) and compares the technique used by educational institutions all over the world with the practice of author groups critiquing their own work. The research shows how a critique group can assist a writer to learn, grow and develop, helping to enhance the writer’s skills through constructive feedback, which gives them confidence to sell their work.

Survey of eResearch practices and skills at QUT, Australia

Queensland University of Technology (QUT) is a multidisciplinary university in Brisbane, Queensland, Australia, and has 40,000 students and 1,700 researchers. Notable eResearch infrastructure includes the QUT ePrints repository, Microsoft QUT Research Centre, the OAK (Open Access to Knowledge) Law Project, Cambia and leading research institutes. ---------- The Australian Government, via the Australian National Data Service (ANDS), is funding institutions to identify and describe their research datasets, to develop and populate data repositories and collaborative infrastructure, and to seed the Australian Research Data Commons. QUT is currently broadening its range of research support services, including those to support the management of research data, in recognition of the value of these datasets as products of the research process, and in order to maximize the potential for reuse. QUT is integrating Library and High Performance Computing (HPC) services to achieve its research support goals. ---------- The Library and HPC released an online survey using Key Survey to 1,700 researchers in September 2009. A comprehensive range of eResearch practices and skills was presented for response, and grouped into areas of scholarly communication and open access publishing, using collaborative technologies, data management, data collection and management, computation and visualization tools. Researchers were asked to rate their skill level on each practice. 254 responses were received over two weeks. Eight focus groups were also held with 35 higher degree research (HDR) students and staff to provide additional qualitative feedback. A similar survey was released to 100 support staff and 73 responses were received.---------- Preliminary results from the researcher survey and focus groups indicate a gap between current eResearch practices, and the potential for researchers to engage in eResearch practices. Researchers are more likely to seek advice from their peers, than from support staff. HDR students are more positive about eResearch practices and are more willing to learn new ways of conducting research. An account of the survey methodology, the results obtained, and proposed strategies to embed eResearch practices and skills across and within the research disciplines will be provided.

Indigenous men's support groups and social and emotional wellbeing : a meta-synthesis of the evidence

Indigenous men’s support groups are designed to empower men to take greater control and responsibility for their health and wellbeing. They provide health education sessions, counselling, men’s health clinics, diversionary programs for men facing criminal charges, cultural activities, drug- and alcohol-free social events, and advocacy for resources. Despite there being ~100 such groups across Australia, there is a dearth of literature on their strategies and outcomes. This paper is based on participatory action research involving two north Queensland groups which were the subject of a series of five ‘phased’ evaluative reports between 2002 and 2007. By applying ‘meta-ethnography’ to the five studies, we identified four themes which provide new interpretations of the data. Self-reported benefits included improved social and emotional wellbeing, modest lifestyle modifications and willingness to change current notions of ‘gendered’ roles within the home, such as sharing housework. Our qualitative research to date suggests that through promoting empowerment, wellbeing and social cohesion for men and their families, men’s support groups may be saving costs through reduced expenditure on health care, welfare, and criminal justice costs, and higher earnings. Future research needs to demonstrate this empirically.