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.

An old language for a new landscape

Because aesthetics can have a profound effect upon the human relationship to the non-human environment the importance of aesthetics to ecologically sustainable designed landscapes has been acknowledged. However, in recognition that the physical forms of designed landscapes are an expression of the social values of the time, some design professionals have called for a new aesthetic ― one that reflects these current ecological concerns. To address this, some authors have suggested various theoretical design frameworks upon which such an aesthetic could be based. Within these frameworks there is an underlying theme that the patterns and processes of natural systems have the potential to form a new aesthetic for landscape design —an aesthetic based on fractal rather than Euclidean geometry. Perry, Reeves and Sim (2008) have shown that it is possible to differentiate between different landscape forms by fractal analysis. However, this research also shows that individual scenes from within very different landscape forms can possess the same fractal properties. Early data, revealed by transforming landscape images from the spatial to the frequency domain, using the fast Fourier transform, suggest that fractal patterning can have a significant effect within the landscape. In fact, it may be argued that any landscape design that includes living processes will include some design element whose ultimate form can only be expressed through the mathematics of fractal geometry. This paper will present ongoing research into the potential role of fractal geometry as a basis for a new form language – a language that may articulate an aesthetic for landscape design that echoes our ecological awakening.

Validation of an Australian sign language instrument of outcome measurement for adults in mental health settings

Objective: There are currently no adult mental health outcome measures that have been translated into Australian sign language (Auslan). Without a valid and reliable Auslan outcome measure, empirical research into the efficacy of mental health interventions for sign language users is unattainable. To address this research problem the Outcome Rating Scale (ORS), a measure of general functioning, was translated into Auslan and recorded on to digital video disk for use in clinical settings. The purpose of the present study was therefore to examine the reliability, validity and acceptability of an Auslan version of the ORS (ORS-Auslan). Method: The ORS-Auslan was administered to 44 deaf people who use Auslan as their first language and who identify as members of a deaf community (termed ‘Deaf’ people) on their first presentation to a mental health or counselling facility and to 55 Deaf people in the general community. The community sample also completed an Auslan version of the Depression Anxiety Stress Scale-21 (DASS-21). Results: t-Tests indicated significant differences between the mean scores for the clinical and community sample. Internal consistency was acceptable given the low number of items in the ORS-Auslan. Construct validity was established by significant correlations between total scores on the DASS-21-Auslan and ORS-Auslan. Acceptability of ORS-Auslan was evident in the completion rate of 93% compared with 63% for DASS-21-Auslan. Conclusions: This is the only Auslan outcome measure available that can be used across a wide variety of mental health and clinical settings. The ORS-Auslan provides mental health clinicians with a reliable and valid, brief measure of general functioning that can significantly distinguish between clinical and non-clinical presentations for members of the Deaf community.

Values, wellness and the social sciences curriculum

Recent initiatives in values education in Australia emphasise the importance of the process of valuing and general methodologies that foster this in the classroom. Although a range of strategies are available, this chapter argues that inquiry-based approaches in the Social Sciences play a significant role in linking valuing processes with decision making skills. Collectively, these approaches prompt the development of reasoning and self awareness which also impact on student wellness. This chapter proposes some curriculum approaches to foreground values education in the Australian Social Sciences classroom. It argues that valuing is an important life skill that can be cultivated in the classroom through specific valuing strategies. It contends that the development of the capacity to make informed value choices is a critical factor in promoting wellness and resilience in students and in preparing them for the decision making skills required for effective participation in society.

Embedding values through global education in social sciences pre-service teacher education : linking the head and heart

This chapter aims to situate values education as a core component of social science pre-service teacher education. In particular, it reflects on an experiment in embedding a values laden Global Education perspective in a fourth year social science curriculum method unit. This unit was designed and taught by the researcher on the assumption that beginning social science teachers need to be empowered with pedagogical skills and new dispositions to deal with value laden emerging global and regional concerns in their secondary school classrooms. Moreover, it was assumed that when pre-service teachers engage in dynamic and interactive learning experiences in their curriculum unit, they commence the process of ‘capacity building’ those skills which prepare them for their own lifelong professional learning. This approach to values education also aimed at providing pre-service teachers with opportunities to ‘create deep understandings of teaching and learning’ (Barnes, 1989, p. 17) by reflecting on the ways in which ‘pedagogy can be transformative’ (Lovat and Toomey, 2011 add page no from Chapter One). It was assumed that this tertiary experience would foster the sine qua non of teaching – a commitment to students and their learning. Central to fostering new ‘dispositions’ through this approach, was the belief in the power of pedagogy to make the difference in enhancing student participation and learning. In this sense, this experiment in values education in secondary social science pre-service teacher education aligns with the Troika metaphor for a paradigm change, articulated by Lovat and Toomey (2009) in Chapter One.

Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

Background The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

Enhancing foreign language learning through listening strategy delivered in L1: an experimental study

Listening used in language teaching refers to a complex process that allows us to understand spoken language. The current study, conducted in Iran with an experimental design, investigated the effectiveness of teaching listening strategies delivered in L1 (Persian) and its effect on listening comprehension in L2. Five listening strategies: Guessing, making inferences, identifying topics, repetition, and note-taking were taught over 14 weeks during a semester. Sixty lower intermediate female participants came from two EFL classrooms in an English language institute. The experimental class (n = 30) who listened to their classroom activities performed better (t value = 10.083) than the control class using a methodology that led learners through five listening strategies in Persian. The same teacher taught the students in the control class (n = 30), who listened to the same classroom listening activities without any of the above listening strategies. A pre and post listening test made by a group of experts in the language institute assessed the effect of teaching listening strategies delivered in L1. Results gathered on the post intervention listening test revealed that listening strategies delivered in L1 led to a statistically significant improvement in their discrete listening scores compared with the control group.

The ethnographer as community manager : language translation and user negotiation

This article investigates the ethnographic methodological question of how the researcher observes objectively while being part of the problem they are observing. It uses a case study of ABC Pool to argue a cooperative approach that combines the roles of the ethnographer with that of a community manager who assists in constructing a true representation of the researched environment. By using reflexivity as a research tool, the ethnographer engages in a process to self-check their personal presumptions and prejudices, and to strengthen the constructed representation of the researched environment. This article also suggests combining management and expertise research from the social sciences with ethnography, to understand and engage with the research field participants more intimately - which, ultimately, assists in gathering and analysing richer qualitative data.

Language and utilisation of emergency care in Queensland

Objective: To compare access and utilisation of EDs in Queensland public hospitals between people who speak only English at home and those who speak another language at home. Methods: A retrospective analysis of a Queensland statewide hospital ED dataset (ED Information System) from 1 January 2008 to 31 December 2010 was conducted. Access to ED care was measured by the proportion of the state’s population attending EDs. Logistic regression analyses were performed to determine the relationships between ambulance use and language, and between hospital admission and language, both after adjusting for age, sex and triage category. Results: The ED utilisation rate was highest in English only speakers (290 per 1000 population), followed by Arabic speakers (105), and lowest among German speakers (30). Compared with English speakers, there were lower rates of ambulance use in Chinese (odds ratio 0.50, 95% confidence interval, 0.47–0.54), Vietnamese (0.87, 0.79–0.95), Arabic (0.87, 0.78–0.97), Spanish (0.56, 0.50–0.62), Italian (0.88, 0.80–0.96), Hindi (0.61, 0.53–0.70) and German (0.87, 0.79–0.90) speakers. Compared with English speakers, German speakers had higher admission rates (odds ratio 1.17, 95% confidence interval, 1.02–1.34), whereas there were lower admission rates in Chinese (0.90, 0.86–0.99), Arabic (0.76, 0.67–0.85) and Spanish (0.83, 0.75–0.93) speakers. Conclusion: This study showed that there was a significant association between lower utilisation of emergency care and speaking languages other than English at home. Further researches are needed using in-depth methodology to investigate if there are language barriers in accessing emergency care in Queensland.

Language affects length of stay in emergency departments in Queensland public hospitals

BACKGROUND: A long length of stay (LOS) in the emergency department (ED) associated with overcrowding has been found to adversely affect the quality of ED care. The objective of this study is to determine whether patients who speak a language other than English at home have a longer LOS in EDs compared to those whose speak only English at home. METHODS: A secondary data analysis of a Queensland state-wide hospital EDs dataset (Emergency Department Information System) was conducted for the period, 1 January 2008 to 31 December 2010. RESULTS: The interpreter requirement was the highest among Vietnamese speakers (23.1%) followed by Chinese (19.8%) and Arabic speakers (18.7%). There were significant differences in the distributions of the departure statuses among the language groups (Chi-squared=3236.88, P<0.001). Compared with English speakers, the Beta coeffi cient for the LOS in the EDs measured in minutes was among Vietnamese, 26.3 (95%CI: 22.1–30.5); Arabic, 10.3 (95%CI: 7.3–13.2); Spanish, 9.4 (95%CI: 7.1–11.7); Chinese, 8.6 (95%CI: 2.6–14.6); Hindi, 4.0 (95%CI: 2.2–5.7); Italian, 3.5 (95%CI: 1.6–5.4); and German, 2.7 (95%CI: 1.0–4.4). The fi nal regression model explained 17% of the variability in LOS. CONCLUSION: There is a close relationship between the language spoken at home and the LOS at EDs, indicating that language could be an important predictor of prolonged LOS in EDs and improving language services might reduce LOS and ease overcrowding in EDs in Queensland's public hospitals.

English language teacher education in Cuba : context, pedagogy and identity

In this study, I investigate the model of English language teacher education developed in Cuba. It includes features that would be considered innovative, contemporary, good practice anywhere in the Western world, as well as having distinctly Cuban elements. English is widely taught in Cuba in the education system and on television by Cuban teachers who are prepared in five-year courses at pedagogical universities by bilingual Cuban teacher educators. This case study explores the identity and pedagogy of six English language teacher educators at Cuba’s largest university of pedagogical sciences. Postcolonial theory provides a framework for examining how the Cuban pedagogy of English language teacher education resists the negative representation of Cuba in hegemonic Western discourse; and challenges neoliberal Western dogma. Postcolonial concepts of representation, resistance and hybridity are used in this examination. Cuban teacher education features a distinctive ‘pedagogy of tenderness’. Teacher educators build on caring relationships and institutionalised values of solidarity, collectivism and collaboration. Communicative English language teaching strategies are contextualised to enhance the pedagogical and communicative competence of student teachers, and intercultural intelligibility is emphasised. The collaborative pedagogy of Cuban English language teacher education features peer observation, mentoring and continuing professional development; as well as extensive pre-service classroom teaching and research skill development for student teachers. Being Cuban and bilingual are significant aspects of the professional identity of case members, who regard their profession as a vocation and who are committed to preparing good English language teachers.