Managing memory and reducing I/O cost for correlation matrix calculation in bioinformatics

The generation of a correlation matrix from a large set of long gene sequences is a common requirement in many bioinformatics problems such as phylogenetic analysis. The generation is not only computationally intensive but also requires significant memory resources as, typically, few gene sequences can be simultaneously stored in primary memory. The standard practice in such computation is to use frequent input/output (I/O) operations. Therefore, minimizing the number of these operations will yield much faster run-times. This paper develops an approach for the faster and scalable computing of large-size correlation matrices through the full use of available memory and a reduced number of I/O operations. The approach is scalable in the sense that the same algorithms can be executed on different computing platforms with different amounts of memory and can be applied to different problems with different correlation matrix sizes. The significant performance improvement of the approach over the existing approaches is demonstrated through benchmark examples.

Narrative review of changing medical and feminist perspectives on menopause : from femininity and ageing to risk and choice

Meanings and descriptions of menopause have shifted focus over the past century and a half; more particularly the past sixty years has seen a shift from descriptions of hormone decline and its relation to ageing, femininity and symptoms of menopause since the 1960's to the possibility for preventive medicine afforded by menopause. Medicine is not a static field in its construction of menopause. It has changed, not least by its engagement (positively or negatively) with critique from both within (epidemiological) and without (feminist and social sciences). In this review we identify three recent changes: (1) Increasing concern with women's decision-making. (2) The emergence from within medicine of the rejection of the use of language which defines menopause as a condition of deficiency. (3) New insights from postmodern and poststructural analyses of menopause that examine the epistemological foundations of medical and feminist concepts of menopause and contest fixed descriptions of the experience of menopause. Key aspects of a ‘medical menopause’ nevertheless remain constant: menopause is a loss of hormones that results in predictable effects and risks and may be ameliorated by hormone replacement therapy. A question therefore emerges about how and to what effect medical practitioners have engaged with critiques of the medical menopause?

[Book Review] Urban Maps : Instruments of Narrative and Interpretation in the City by Richard Brook and Nick Dunn, Ashgate, Farham, United Kingdom, 2011, 250pp. ISBN 978-0-754676-5-77.

Urban maps discusses new ways and tools to read and navigate the contemporary city. Each chapter investigates a possible approach to unravel the complexity of contemporary urban forms. Each tool is first defined, introducing its philosophical background, and is then discussed with case studies, showing its relevance for the navigation of the built environment. Urbanism classics such as the work of Lynch, Jacobs, Venuti and Scott-Brown, Lefebrve and Walter Benjamin are fundamental in setting the framework of the volume. In the introduction cities and mapping are first discussed, the former are illustrated as ‘a composite of invisible networks devoid of landmarks and overrun by nodes’ (p. 3), and ‘a series of unbounded spaces where mass production and mass consumption reproduce a standardised quasi-global culture’ (p. 6).

Narrative, education policy and the newsprint media : A critical discourse analysis of the construction of young people's participation in education or employment

This thesis used Critical Discourse Analysis to investigate how a government policy and the newsprint media constructed discussion about young people’s participation in education or employment. The study found that a continuous narrative across both sites about government as a noble agent taking action to redress the social disruption caused by young people’s disengagement. Unlike the education policy, the newsprint media blamed young people who were disengaged and failed to recognise the barriers they often face. The study points to possibilities for utilising the power of narrative to build a more fair and rigorous discussion of issues in the public sphere.

Point of no return : exploring katabatic narrative and deterritorialisation in the Australian outback novel

This thesis consists of the novel Brolga and an exegesis examining in what ways the ideas of katabasis and deterritorialisation inform an understanding of descent narratives in contemporary Australian outback fiction. When writing the creative piece, it was observed that Joseph Campbell’s Hero’s Journey was an imprecise model for my manuscript and indeed for many of the contemporary novels I had read written in similar outback settings. On analysis a better fit lies in the idea of a heroic journey from which there is no clear return from the underworld. This narrative form is defined in this thesis as a katabatic narrative. To unpack this narrative trope, the inverse of territoriality, deterritorialisation, is used as a lens to examine the complex thematic and symbolic resonances of the outback in both Brolga and analogous works of contemporary outback fiction.

Tracing the influence of non-narrative film and expanded cinema sound on experimental music

This study surveys and interrogates key conceptual frameworks and artistic practises that flow through the distinct but interconnected traditions of non-narrative film and experimental music, and examines how these are articulated in my own creative sound practise.

Quality Assessment Matrix : A Collaborative Evaluation Using Multiple Lines of Evidence

Welcome to the Quality assessment matrix. This matrix is designed for highly qualified discipline experts to evaluate their course, major or unit in a systematic manner. The primary purpose of the Quality assessment matrix is to provide a tool that a group of academic staff at universities can collaboratively review the assessment within a course, major or unit annually. The annual review will result in you being read for an external curricula review at any point in time. This tool is designed for use in a workshop format with one, two or more academic staff, and will lead to an action plan for implementation.

Empathy : narrative empathy and children's literature

The term empathy has only existed in English for a little over a hundred years, but the idea of feeling with another person is an old one. Because of its perceived connection to moral behaviour, empathy and its development are of great interest to educators, policy makers, psychologists, and philosophers. Reading children’s literature is often considered important for developing (among other things) children’s ethical and empathic understandings of society and its people. However, claims as to the impact of reading on readers’ ability to become more empathic, tolerant, and better people are divided. While many readers may attribute positive influences that authors and texts have had on shaping their attitudes and actions, there is no guarantee that a desirable affective and cognitive response will follow the reading experience. The complexity of readers and texts refuses to be reduced to simple universal statements about the capacity of narrative empathy to create a particular kind of empathic reader or person: fiction that engages a reader with the emotional plight of a character does not necessarily translate into actions in the real world towards people who are similarly suffering, marginalized, or victimized. This chapter asks: Does children’s literature foster empathy? There are two implicit features of this question: one concerns narrative empathy; the other concerns empathic reader response. The discussion will focus on how a selection of ‘multicultural’ picture books attempts to create narrative empathy by focussing on cultural and spatial differences.

Ruptures in the heterosexual matrix through teenage flows and multiplicities

This article analyzes a series of stories and artworks that were produced in a collective biography workshop. It explores Judith Butler’s concept of the heterosexual matrix combined with a Deleuzian theoretical framework. The article begins with an overview of Butler’s concept of the heterosexual matrix and her theorizations on how it might be disrupted. It then suggests how a Deleuzian framework offers other tools for analyzing these ruptures at the micro level of girls’ everyday interactions.

Matrix metalloproteinase biosensor based on a porous silicon reflector

Matrix metalloproteinases (MMPs) are proteolytic enzymes important to wound healing. In non-healing wounds, it has been suggested that MMP levels become dysfunctional, hence it is of great interest to develop sensors to detect MMP biomarkers. This study presents the development of a label-free optical MMP biosensor based on a functionalised porous silicon (pSi) thin film. The biosensor is fabricated by immobilising a peptidomimetic MMP inhibitor in the porous layer using hydrosilylation followed by amide coupling. The binding of MMP to the immobilised inhibitor translates into a change of effective optical thickness (EOT) over the time. We investigate the effect of surface functionalisation on the stability of pSi surface and evaluate the sensing performance. We successfully demonstrate MMP detection in buffer solution and human wound fluid at physiologically relevant concentrations. This biosensor may find application as a point-of-care device that is prognostic of the healing trajectory of chronic wounds.

Development of a large scale flexible LED display matrix for the screen industry

This project addresses the viability of lightweight, low power consumption, flexible, large format LED screens. The investigation encompasses all aspects of the electrical and mechanical design, individually and as a system, and achieves a successful full scale prototype. The prototype implements novel techniques to achieve large displacement colour aliasing, a purely passive thermal management solution, a rapid deployment system, individual seven bit LED current control with two way display communication, auto-configuration and complete signal redundancy, all of which are in direct response to industry needs.

Malnutrition in the elderly : a narrative review

The focus of nutrition is often on healthy diets and exercise to minimise the risk of developing lifestyle diseases such as cancer, diabetes and cardiovascular disease. However, during the shift into older years often the nutrition priorities change towards meeting increased nutrient needs with less energy requirements and minimising lean muscle loss. There are several causes of general malnutrition in the elderly that lead to depletion of muscle including starvation (protein-energy malnutrition), sarcopenia and cachexia. The prevalence of protein-energy malnutrition increases with age and the number of comorbidities. A range of simple and validated screening tools can be used to identify malnutrition in older adults e.g. MST, MNA-SF and ‘MUST’. Older adults should be screened for nutritional issues at diagnosis, on admission to hospitals or care homes and during follow up at outpatient or General Practitioner clinics, at regular intervals depending on clinical status. Early identification and treatment of nutrition problems can lead to improved outcomes and better quality of life.

Matrix metalloproteinase localisation by in situ-RT-PCR in archival human breast biopsy material

Utilising archival human breast cancer biopsy material we examined the stromal/epithelial interactions of several matrix metalloproteinases (MMPs) using in situ-RT-PCR (IS-RT-PCR). In breast cancer, the stromal/epithelial interactions that occur, and the site of production of these proteases, are central to understanding their role in invasive and metastatic processes. We examined MT1-MMP (MMP-14, membrane type-1-MMP), MMP-1 (interstitial collagenase) and MMP-3 (stromelysin-1) for their localisation profile in progressive breast cancer biopsy material (poorly differentiated invasive breast carcinoma (PDIBC), invasive breast carcinomas (IBC) and lymph node metastases (LNM)). Expression of MT1-MMP, MMP-1 and MMP-3 was observed in both the tumour epithelial and surrounding stromal cells in most tissue sections examined. MT1-MMP expression was predominantly localised to the tumour component in the pre-invasive lesions. MMP-1 gene expression was relatively well distributed between both tissue compartments, while MMP-3 demonstrated highest expression levels in the stromal tissue surrounding the epithelial tumour cells. The results demonstrate the ability to distinguish compartmental gene expression profiles using IS-RT-PCR. Further, we suggest a role for MT1-MMP in early tumour progression, expression of MMP-1 during metastasis and focal expression pattern of MMP-3 in areas of expansion. These expression profiles may provide markers for early breast cancer diagnoses and present potential therapeutic targets.

Destination marketing organizations and destination marketing : a narrative analysis of the literature

This article presents the first narrative analysis of the areas of research that have developed within the destination marketing field since its commencement in 1973. Given the broad extent of the field, and the absence of any previous reviews in four decades, a key challenge is in providing a focus for such a disparate body of knowledge. The review is structured around one principal question: ‘To what extent is the Destination Marketing Organisation (DMO) responsible for the competitiveness of the destination’? In pursuit of this underlying question, we address a number of themes including nomenclature and the DMO, the evolution of the destination marketing literature, competitiveness as the DMO reason d’être, and DMO effectiveness including issues of branding and positioning, and future research themes in the field.

A matrix for appropriate assessment of workplace learning in stem disciplines

With increasing interest shown by Universities in workplace learning, especially in STEM disciplines, an issue has arisen amongst educators and industry partners regarding authentic assessment tasks for work integrated learning (WIL) subjects. This paper describes the use of a matrix, which is also available as a decision-tree, based on the features of the WIL experience, in order to facilitate the selection of appropriate assessment strategies. The matrix divides the WIL experiences into seven categories, based on such factors as: the extent to which the experience is compulsory, required for membership of a professional body or elective; whether the student is undertaking a project, or embedding in a professional culture; and other key aspects of the WIL experience. One important variable is linked to the fundamental purpose of the assessment. This question revolves around the focus of the assessment: whether on the person (student development); the process (professional conduct/language); or the product (project, assignment, literature review, report, software). The matrix has been trialed at QUT in the Faculty of Science and Technology, and also at the University of Surrey, UK, and has proven to have good applicability in both universities.