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.

"I drove after drinking alcohol" and other risky driving behaviours reported by young novice drivers

Background Volitional risky driving behaviours including drink- and drug-driving and speeding contribute to the overrepresentation of young novice drivers in road crash fatalities, and crash risk is greatest during the first year of independent driving in particular. Aims To compare: 1) the self-reported compliance of drivers with road rules relating to substance-impaired driving and other risky driving behaviours including speeding and driving tired, one year after progression from a Learner to a Provisional (intermediate) licence; and 2) the interrelationships between substance-impaired driving and other risky driving behaviours (crashes, offences, and Police avoidance). Methods 1268 drivers (373 males) aged 17-26 years were surveyed regarding their sociodemographics (age, gender) and self-reported driving behaviours including crashes, offences, Police-avoidance, and driving intentions. Results A relatively small proportion of participants reported driving after taking drugs (5.9% males, 1.3% females) and drinking alcohol (19.3% males, 11.6% females). In comparison, a considerable proportion of participants reported at least occasionally exceeding speed limits (85.7% novices) and driving when tired (82.7% novices). Substance-impaired driving was associated with avoiding Police, speeding, risky driving intentions, and self reported crashes and offences. Forty-four percent of illicit-drug drivers also reported alcohol-impaired driving. Discussion and conclusions The low self-reported prevalence of substance-impaired driving suggests official enforcement measures play a role in promoting compliance, in addition to social influences such as the broader community and the young novice drivers’ social networks including friends and family. Conversely, the prevalence of speeding appears to reflect the pervasive cultural acceptance of this behaviour. Given the interrelationships between the risky driving behaviours, a deeper understanding of influential factors is required to inform targeted and general countermeasure implementation and evaluation during this critical driving period.

Performance of elite seated discus throwers in F30s classes : part I: does whole body positioning matter?

Background: Studies on the relationship between performance and design of the throwing frame have been limited and therefore require further investigation. Objectives: The specific objectives were to provide benchmark information about performance and whole body positioning of male athletes in F30s classes. Study Design: Descriptive analysis. Methods: A total of 48 attempts performed by 12 stationary discus throwers in F33 and F34 classes during seated discus throwing event of 2002 International Paralympic Committee Athletics World Championships were analysed in this study. The whole body positioning included overall throwing posture (i.e. number of points of contact between the thrower and the frame, body position, throwing orientation and throwing side) and lower limb placements (i.e. seating arrangements, points of contact on the both feet, type of attachment of both legs and feet). Results: Three (25%), five (42%), one (8%) and three (25%) athletes used from three to six points of contact, respectively. Seven (58%) and five (42%) athletes threw from a standing or a seated position, respectively. A straddle, a stool or a chair was used by six (50%), four (33%) or two (17%) throwers, respectively. Conclusions: This study provides key information for a better understanding of the interaction between throwing technique of elite seated throwers and their throwing frame.

I dress therefore I am

This paper examines the fashion of the post-punk era in London through the work of British Photographer, Derek Ridgers.

An overview of level I evidence for the management of radiation dermatitis literature

Background: Despite the technologic advances, radiation dermatitis is still a prevalent and distressing symptom in patients with cancer undergoing radiotherapy. Systematic reviews (SRs) are regarded as level I evidence providing direction for clinical practice and guidelines. This overview aims to provide a critical appraisal of SRs published on interventions for the prevention/management of radiation dermatitis. Methodology: We searched the following electronic databases: MEDLINE, CINAHL, EMBASE, and the Cochrane Library (up to Feb 2012). We also hand-searched reference lists of potentially eligible articles and a number of key journals in the area. Two authors screened all potential articles and included eligible SRs. Two authors critically appraised and extracted key findings from the included reviews using the “A Measurement Tool to Assess Systematic Reviews” (AMSTAR). Results: Of 1837 potential titles, six SRs were included. A number of interventions have been reported to be potentially beneficial for managing radiation dermatitis. Interventions evaluated in these reviews included skin care advice, steroidal/non-steroidal topical agents, systematic therapies, modes of radiation delivery, and dressings. However, all the included SRs reported that there is insufficient evidence supporting any single effective intervention. The methodological quality of the included studies varied, and methodological shortfalls in these reviews may create biases to the overall results or recommendations for clinical practice. Conclusions and implications: An up-to-date high quality SR in preventing/managing radiation dermatitis is needed to guide practice and direction for future research. Clinicians or guideline developers are recommended to critically evaluate the information of SRs in their decision making.

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.

P.I.C.U., H.D.U., A.O.A. What treatment do we provide?: Current descriptions of the function of intensive care for inpatient Psychiatric Health Care.

Purpose – This paper adds to growing research of psychiatric intensive care units (PICU) by recounting descriptions of psychiatric intensive care settings and discusses the perceptions held by nurses of the organisational interfaces, arrangements and provisions of care in these settings. Design/methodology/approach – Data gathered from focus groups held with nurses from two PICUs was used to establish terminology, defining attributes, related concepts, antecedents, values, processes and concepts related to current practices. A literature search was conducted to permit a review of the conceptual arrangements and contemporary understanding of intensive care for people experiencing acute psychiatric illness based on the perspectives held by the nurses from the focus groups. Findings – Dissonance between service needs and the needs and management of individual patients overshadow strategies to implement comprehensive recovery-oriented approaches. Three factors are reported in this paper that influence standards and procedural practice in PICU; organisational structures; physical structures; and subtype nomenclature. Practical implications – Acute inpatient care is an important part of a comprehensive approach to mental health services. Commonly intensive acute care is delivered in specialised wards or units co-located with acute mental health inpatient units mostly known as PICU. Evidence of the most effective treatment and approaches in intensive care settings that support comprehensive recovery for improved outcomes is nascent. Originality/value – Current descriptions from nurses substantiate wide variations in the provisions, design and classifications of psychiatric intensive care. Idiosyncratic and localised conceptions of psychiatric intensive care are not adequately entailing effective treatment and methods in support of recovery principles for improved and comprehensive outcomes. The authors suggest that more concrete descriptions, guidelines, training and policies for provision of intensive psychiatric health care encompassing the perspective of nursing professionals, would reinforce conceptual construction and thus optimum treatments within a comprehensive, recovery-oriented approach to mental health services.

Taka 'i fonua mahu : being Tongan; second generation Tongan migrants

Taka ‘i fonua mahu is a Tongan proverb, which means: "Going about or living in a fruitful land". This thesis analyses the experiences and impacts on migration on being Tongan, particularly Tongan youth in an adopted fruitful land, South East Queensland. The thesis argues that being Tongan in Tonga, has new meaning in the diaspora because of remittances, job prospects, educational opportunity, adapting to a multicultural society, and social justice. These issues are revealed by comparisons made with the experiences of the first generation Tongan migrants, and second generation Tongan migrants, as well as those in New Zealand and America. It argues that the Church, the family and kainga (extended family) impact on the anga fakatonga (Tongan way) and the essence of community as experienced by the first and second generation Tongan migrants. The framework for this analysis is a study of transnationalism, and being Tongan as it is maintained and changed in the diaspora.

Use of thermal imaging in sports medicine research : a short report

The assessment of skin temperature (Tsk) in athletic therapy and sports medicine research is an extremely important physiological outcome measure.Various methodsof recording Tsk, including thermistors, thermocouples and thermocrons are currently being used for research purposes. These techniques are constrained by their wires limiting the freedom of the subject, slow response times, and/or sensors falling off. Furthermore, as these products typically are directly attached to the skin and cover the measurement site, their validity may be questionable.This manuscript addresses the use and potential benefits of using thermal imaging (TI) in sport medicine research.Non-contact infrared TI offers a quick, non-invasive, portable and athlete-friendly method of assessing Tsk. TI is a useful Tsk diagnostic tool that has potential to be an integral part of sport medicine research in the future. Furthermore, as the technique is non-contact it has several advantages over existing methods of recording skin temperature

“If I were a community leader”: knowing the world by changing it

Education Queensland teachers Gael Wilson and Tracey Herslet, and the principal of Waterford West State School, Di Carter, were proud as they watched the screening of their year five students’ movies at the national Building Child Friendly Communities Conference, held in Logan, Queensland in November 2011.

Differences in Epidural and Analgesic Use in Patients with Apparent Stage I Endometrial Cancer treated by open versus laparoscopic surgery: results from the randomised LACE trial

Objectives: We compared post-operative analgesic requirements between women with early stage endometrial cancer treated by total abdominal hysterectomy (TAH) or total laparoscopic hysterectomy (TLH). Methods: 760 patients with apparent stage I endometrial cancer were treated in the international, multicentre, prospective randomised trial (LACE) by TAH (n=353) or TLH (n=407) (2005-2010). Epidural, opioid and non-opioid analgesic requirements were collected until ten months after surgery. Results: Baseline demographics and analgesic use were comparable between treatment arms. TAH patients were more likely to receive epidural analgesia than TLH patients (33% vs 0.5%, p<0.001) during the early postoperative phase. Although opioid use was comparable in the TAH vs TLH groups during postoperative 0-2 days (99.7% vs 98.5%, p 0.09), a significantly higher proportion of TAH patients required opioids 3-5 days (70% vs 22%, p<0.0001), 6-14 days (35% vs 15%, p<0.0001), and 15-60 days (15% vs 9%, p 0.02) post-surgery. Mean pain scores were significantly higher in the TAH versus TLH group one (2.48 vs 1.62, p<0.0001) and four weeks (0.89 vs 0.63, p 0.01) following surgery. Conclusion: Treatment of early stage endometrial cancer with TLH is associated with less frequent use of epidural, lower post-operative opioid requirements and better pain scores than TAH.

What should I say?: Qualitative findings on dilemmas in palliative care nursing

The nursing literature suggests that talking and listening to patients about issues associated with death and dying, is both important and difficult, and may be improved with training. This discussion presents the results of recent nursing research to confirm, and elaborate on, this theme. In this research participants touched on many central issues in communicating with patients that included articulating a sense of discomfort and inadequacy about the whole process, detailing the innumerable blocks to open communication [e.g., interference, denial, unrealistic optimism, resistance, collusion and anger] and sharing their sense of success and failure. The insights of nurses who participated in this research testify to the ongoing need to prioritize the development of nursing skills and support in this challenging but important area.

A study of post diagnosis breast cancer concerns for women living in rural and remote Queensland. Part I : Personal concerns

The findings presented in this paper are part of a research project designed to provide a preliminary indication of the support needs of postdiagnosis women with breast cancer in remote and isolated areas in Queensland. This discussion will present data that focuses on the women’s expressed personal concerns. For participants in this research a diagnosis of breast cancer involves a confrontation with their own mortality and the possibility of a reduced life span. This is a definite life crisis, creating shock and needing considerable adjustment. Along with these generic issues the participants also articulated significant issues in relation to their experience as women in a rural setting. These concerns centred around worries about how their partner and families cope during their absences for treatment, the additional burden on the family of having to cope with running the property or farm during the participant’s absence or illness, added financial strain brought about by the cost of travel for treatment, maintenance of properties during absences, and problems created by time off from properties or self-employment. These findings accord with other reports of health and welfare services for rural Australian and the generic literature on psycho-oncology studies of breast cancer.

Investigations Into the Significance of Lysine Residues in IGF-I

This PhD thesis presents novel and original research in the field of Insulin-like Growth Factor-I (or IGF-I) biology. IGF-I plays an essential role in promoting normal human growth and development; it also represents both a target and treatment for various diseases. This thesis provides interesting insights into previously uncharacterised mechanisms of action that underlie IGF-I biology. Such findings may lead to improved and novel treatments across a broad range of medical conditions.

A combined environmental scanning electron microscopy and Raman microscopy study of methanol oxidation on silver(I) oxide

The techniques of environmental scanning electron microscopy (ESEM) and Raman microscopy have been used to respectively elucidate the morphological changes and nature of the adsorbed species on silver(I) oxide powder, during methanol oxidation conditions. Heating Ag2O in either water vapour or oxygen resulted firstly in the decomposition of silver(I) oxide to polycrystalline silver at 578 K followed by sintering of the particles at higher temperature. Raman spectroscopy revealed the presence of subsurface oxygen and hydroxyl species in addition to surface hydroxyl groups after interaction with water vapour. Similar species were identified following exposure to oxygen in an ambient atmosphere. This behaviour indicated that the polycrystalline silver formed from Ag2O decomposition was substantially more reactive than silver produced by electrochemical methods. The interaction of water at elevated temperatures subsequent to heating silver(I) oxide in oxygen resulted in a significantly enhanced concentration of subsurface hydroxyl species. The reaction of methanol with Ag2O at high temperatures was interesting in that an inhibition in silver grain growth was noted. Substantial structural modification of the silver(I) oxide material was induced by catalytic etching in a methanol/air mixture. In particular, "pin-hole" formation was observed to occur at temperatures in excess of 773 K, and it was also recorded that these "pin- holes" coalesced to form large-scale defects under typical industrial reaction conditions. Raman spectroscopy revealed that the working surface consisted mainly of subsurface oxygen and surface Ag=O species. The relative lack of sub-surface hydroxyl species suggested that it was the desorption of such moieties which was the cause of the "pin-hole" formation.