Candidate disease gene prediction using Gentrepid: application to a genome-wide association study on coronary artery disease

Current single-locus-based analyses and candidate disease gene prediction methodologies used in genome-wide association studies (GWAS) do not capitalize on the wealth of the underlying genetic data, nor functional data available from molecular biology. Here, we analyzed GWAS data from the Wellcome Trust Case Control Consortium (WTCCC) on coronary artery disease (CAD). Gentrepid uses a multiple-locus-based approach, drawing on protein pathway- or domain-based data to make predictions. Known disease genes may be used as additional information (seeded method) or predictions can be based entirely on GWAS single nucleotide polymorphisms (SNPs) (ab initio method). We looked in detail at specific predictions made by Gentrepid for CAD and compared these with known genetic data and the scientific literature. Gentrepid was able to extract known disease genes from the candidate search space and predict plausible novel disease genes from both known and novel WTCCC-implicated loci. The disease gene candidates are consistent with known biological information. The results demonstrate that this computational approach is feasible and a valuable discovery tool for geneticists.

Firsts: performing ways first year teachers experience identity transformation

This thesis reports on research showing the survival discourse of beginning teaching has shifted from sink or swim metaphors to describe surviving transition shock and classroom management concerns to surviving contract employment. Beginning teachers are neither sinking nor swimming in this liminal state. Rather, it is as though they are on a lifeboat where they cannot feel like a ‘real’ teacher until they can operate with certainty.

Interrogating the experiences of beginning teachers, and the transformation of their identity in their first year (1yr) of teaching, the thesis explores research participants’ firsts as epiphanic or revelatory moments of identity transformation. Participants were followed for three years from upon completion of their teacher education, through their first year of teaching, up to the beginning of their third year in the profession. The major finding was that while contemporary understandings of professional identity highlight the transformative nature of the phenomenon,  contract employment had the most impact on these teachers’ identity transformation.

Teachers’ perceptions of their own professional identity affect their efficacy and professional development as well as their ability and willingness to cope with educational change (Beijaard, Verloop & Vermunt 2000). It has been reported by the Australian Education Union (AEU) and in the Victorian media in recent years that up to 50% of beginning teachers are leaving the profession within their first five years. The reasons given for this level of
attrition include workload, pay, and behaviour management, among the top concerns of beginning teachers. These categories have positioned beginning teachers in a survival discourse for many years, yet there is more to beginning teachers’ intentions to leave than their struggles to survive in the classroom. More recently in Victoria what it means to ‘survive’ has shifted to surviving the pervasive contractual nature of beginning teachers’
employment conditions.

This qualitative study seeks to question what remains concealed with regard to beginning teachers’ experiences through an investigation of the differences between and within individuals, allowing categories of description to emerge from the data rather than pre-determining categories of investigation. Data was collected from twelve participants through individual semi-structured interviews and written communication. A theatre-based research approach to representing the participants’ experiences was employed, culminating in a performance titled ‘The First Time’. The processes of scripting, rehearsing, and performing, were utilised to analyse and represent the data to expert audiences. In an aim to uncover questions that have been buried by answers, the research is oriented as a
phenomenographic inquiry. This mode of inquiry seeks to describe, analyse, and understand (Marton 1981) the qualitatively different experiences 1yr teachers undergo in their identity formation and transformation.

The results of this research reveal the destabilising effect of short-term contracts so prevalent in the current context; that status and belonging are central to 1yr teachers’ identity work. Status and belonging are positioned within survival, liminal, and hegemonic discourses; and expressed through artefacts as symbols of belonging. The low status ascribed to contractual work has a clear impact on beginning teachers’ commitment to the profession.

Introduction: of turtles, dining and the importance of history in food, food in history

Feasting on North American moose or Caribbean turtle in Renaissance Italy, Ancient Rome, or the colonial working-class pub, is Social and Cultural history in a new and exciting form. Dining on Turtles traverses time and place to open up food and drink as a new field of historical enquiry. In chapters covering the heritage landscapes of sugar canefields, the reform of popular drinking customs, the importance of eating and drinking culture to Olympic Games planning, and the significance of cookbooks to civic society, historians here break new ground in locating food's importance. From the exploration of French tavern rituals, Scottish feasting on haggis, and memories of food traditions in Cyprus come themes of identity and nationalism, change and continuity.

Context matters: SETE mapping of teacher education in diverse contexts

The Studying the Effectiveness of Teacher Education (SETE) project (2010- ) investigates, as a priority, how well equipped teacher education graduates are to meet the requirements of diverse school settings. This paper outlines notions of diversity as reflected in large-scale longitudinal data sets including quantitative teacher and principal surveys (n=5,000+), national audit of teacher education programs (n=500+), and analysis of data from intensive case studies which track 170 graduate teachers through the first three years of their teaching career.

Navigating teacher education: mapping the terrain, surveying the landscape

While there are many small-scale case studies that investigate specific teacher education practices, large scale longitudinal studies designed to provide rich and comprehensive data about the effectiveness of teacher education, are limited (Cochran-Smith & Zeichner, 2005). The Studying the Effectiveness of Teacher Education (SETE) project aims to address this gap by investigating the effectiveness of teacher education programs in preparing teachers for the variety of school settings in which they begin their careers. This three-year study utilises large-scale surveys and case studies, and includes a comprehensive mapping of teacher education programs across Australia. It tracks all 2010/2011 teacher education graduates in Queensland and Victoria to investigate the effectiveness of particular characteristics of their teacher education programs in equipping them with the capacity to meet the learning needs of young people in a diverse range of Australian school settings.

This paper presents the findings from the mapping exercise and the surveys of teachers and principals, and the problematics and possibilities of reading across the data sets. The SETE mapping exercise used publicly available online information to examine the characteristics of initial teacher education programs accredited by the Victorian Institute of Teaching (VIT) and the Queensland College of Teachers (QCT). Preliminary results address, inter alia, the length, content and delivery of programs and critical issues of the development of pedagogical and assessment expertise and preparation to teach in diverse contexts. The paper also presents findings from the first of a series of online surveys completed by teacher education graduates in Queensland and Victoria. Beginning teachers’ responses are mapped against key characteristics of participants' pre-service programs and framed in relation to the key themes of curriculum, pedagogy, assessment, behaviour management, and engagement with school stakeholders and local community.

Investigating the effectiveness of teacher education for early career teachers in diverse settings: analysis of large-scale survey data

‘As researchers and practitioners in the field of teacher education, we seem ill prepared to respond to critics who question the value of professional education for teachers with evidence of our effectiveness’ (Grossman, 2008, p.13). While there are many small-scale, nuanced case studies that speak about the particularities of specific teacher education practices, large scale, systematic, longitudinal studies that can provide rich and comprehensive data about the effectiveness of teacher education are limited (Cochran-Smith & Zeichner, 2005). In Australia, the Studying the Effectiveness of Teacher Education (SETE) project is addressing this gap by investigating the effectiveness of teacher education programs in preparing teachers for the variety of school settings in which they begin their careers. This three-year study utilises large-scale surveys and case studies to construct a deeper understanding of early career teachers’ experiences. It tracks all 2010/2011 teacher education graduates in Queensland and Victoria to investigate the effectiveness of particular characteristics of their teacher education programs in equipping them with the capacity to meet the learning needs of young people in a diverse range of Australian school settings.

This paper will discuss findings from the first of a series of online surveys completed by teacher education graduates in Queensland and Victoria (March-April 2012). Survey data includes teacher demographic information which form independent variables to inform inferential statistical analysis. Beginning teacher responses are mapped against key characteristics of participants' pre-service programs and framed in relation to the key themes of curriculum, pedagogy, assessment, behaviour management, and engagement with school stakeholders and local community. The findings will assist teacher educators design teacher education programs for effective beginning teaching in diverse settings and will also provide an evidentiary basis for policy decisions regarding teacher education and beginning teaching.

Building an effective school-university partnership : a cluster approach

Deakin University has introduced a new Master of Teaching course incorporating a new form school-university partnership that we refer to as the ‘cluster approach’. In addition to responding to recent state and National reports on teacher education (e.g. House of Representatives Standing Committee on Education and Vocational Training, 2007; Kruger et al., 2009; Parliament of Victoria Education and Training Committee, 2005), this cluster approach aims to respond directly to recommendations from the Australian Teaching and Learning Council funded project into practicum partnerships (Ure, 2009), and focuses specifically on one of the reform agendas of the National Partnership Agreement on Improving Teacher Quality, that of ‘improving the quality and consistency of teacher training in partnership with universities’ (see http://smarterschools.gov.au/nationalpartnerships/Pages/ImprovingTeacherQuality.aspx)
Learning to teach is a continuum whereby teachers create new understandings and build professional knowledge and practice in collaboration with colleagues during their pre-service teacher education and then during their careers as teachers (Fieman-Nemser 2001). Learning to teach is not a sole learning activity; rather teachers learn in communities and in collaboration with colleagues. Moreover, teachers are always balancing ‘being the teacher’ while at the same time ‘becoming a teacher’ (e.g. Britzman, 2003). Thus, they balance the notion of ‘doing teaching’ while at the same time ‘learning teaching’, and this is nowhere more evident than during the professional experience component of teacher education. This cluster approach is based on these premises.
The work of Le Cornu (2004), Le Cornu and Ewing (2008) and Little (2001) also informed aspects of the approach, which is predicated on ‘reciprocal relationships’ amongst pre-service teachers, and between pre-service teachers and experienced teachers both in schools and in universities. It frames teachers as cultural producers of knowledge, pre-service teachers as new resources bringing different ideas and practices into schools and schools as knowledge building communities (Little 2001, Nias 1998, Retallick et al 1999, Veugelers & O’Hair 2005).