Predicting residue-wise contact orders in proteins by support vector regression

Background The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. Results We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. Conclusion The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.

ICU nurses' experiences and perspectives of caring for obstetric patients in intensive care: A qualitative study

Aims and objectives.  The aim of this study was to gain an understanding of the experiences and perspectives of intensive care nurses caring for critically ill obstetric patients. Background.  Current literature suggests critically ill obstetric patients need specialised, technically appropriate care to meet their specific needs with which many intensive care nurses are unfamiliar. Furthermore, there is little research and evidence to guide the care of this distinct patient group. Design.  This study used a descriptive qualitative design. Methods.  Two focus groups were used to collect data from 10 Australian intensive care units nurses in May 2007. Open-ended questions were used to guide the discussion. Latent content analysis was used to analyse the data set. Each interview lasted no longer than 60 minutes and was recorded using audio tape. The full interviews were transcribed prior to in-depth analysis to identify major themes. Results.  The themes identified from the focus group interviews were competence with knowledge and skills for managing obstetric patients in the intensive care unit, confidence in caring for obstetric patients admitted to the intensive care unit and acceptance of an expanded scope of practice perceived to include fundamental midwifery knowledge and skills. Conclusion.  The expressed lack of confidence and competence in meeting the obstetric and support needs of critically ill obstetric women indicates a clear need for greater assistance and education of intensive care nurses. This in turn may encourage critical care nurses to accept an expanded role of clinical practice in caring for critically ill obstetric patients. Relevance to clinical practice.  Recognition of the issues for nurses in successfully caring for obstetric patients admitted to an adult intensive care setting provides direction for designing education packages, ensuring specific carepaths and guidelines are in place and that support from a multidisciplinary team is available including midwifery staff.

A case study of how primary school teachers in Papua New Guinea understand outcomes-based education

This case study explored how a group of primary school teachers in Papua New Guinea (PNG) understood Outcomes-based Education (OBE). OBE measures students. learning against specific outcomes. These outcomes are derived from a country.s vision of the kind of citizen that the education system should produce. While countries such as Australia, South Africa, New Zealand and the United States have abandoned OBE, others such as PNG have adopted it in various ways. How teachers understand OBE in PNG is important because such understandings are likely to influence how they implement the OBE curriculum. There has been no research to date which has investigated PNG primary school teachers. understandings and experiences with OBE. This study used a single exploratory case study design to investigate how twenty primary school teachers from the National Capital District (NCD) in PNG understood OBE. The study, underpinned by an intepretivist paradigm, explored the research question: How do primary school teachers understand outcomes-based education in PNG? The data comprised surveys, in-depth interviews and documents. Data were analysed thematically and using explanation building techniques. The findings revealed that OBE is viewed by teachers as a way to equip them with additional strategies for planning and programming, teaching and learning, and assessment. Teachers also described how OBE enabled both students and teachers to become more engaged and develop positive attitudes towards teaching and learning. There was also a perception that OBE enhanced students. future life skills through increased local community support. While some teachers commented on how the OBE reforms provided them with increased professional development opportunities, the greatest impediment to implementing OBE was perceived to be a lack of sufficient teaching and learning resources. The process of planning and programming classroom activities was also regarded as onerous. Some teachers indicated that they had been required to implement OBE without adequate in-service training support. The social constructivist theory of knowledge which underpins OBE.s student-centred pedagogy can cause tensions within PNG.s cultural contexts of teaching and learning. Teachers need to be aware of these tensions when conducting peer or group learning under OBE in PNG. By exploring how these PNG primary teachers understood OBE, the study highlighted how teachers engaged with OBE concepts when interpreting syllabus documents and how they applied these concepts to curriculum. Identifying differences in teacher understanding of OBE provides guidance for both the design of materials to support the implementation of OBE and for the design of in-service training. Thus, the outcomes of this study will inform educators about the implementation of OBE in PNG. In addition, the outcomes will provide much needed insight into how a mandated curriculum and pedagogical reform impacts teachers‟ practices in PNG.

Factors influencing health promotion activities in midlife and older Australian women with a chronic disease

Background: Chronic diseases including type 2 diabetes are a leading cause of morbidity and mortality in midlife and older Australian women. There are a number of modifiable risk factors for type 2 diabetes and other chronic diseases including smoking, nutrition, physical activity and overweight and obesity. Little research has been conducted in the Australian context to explore the perceived barriers to health promotion activities in midlife and older Australian women with a chronic disease. Aims: The primary aim of this study was to explore women’s perceived barriers to health promotion activities to reduce modifiable risk factors, and the relationship of perceived barriers to smoking behaviour, fruit and vegetable intake, physical activity and body mass index. A secondary aim of this study was to investigate nurses’ perceptions of the barriers to action for women with a chronic disease, and to compare those perceptions with those of the women. Methods: The study was divided into two phases where Phase 1 was a cross sectional survey of women, aged over 45 years with type 2 diabetes who were attending Diabetes clinics in the Primary and Community Health Service of the Metro North Health Service District of Queensland Health (N = 22). The women were a subsample of women participating in a multi-model lifestyle intervention, the ‘Reducing Chronic Disease among Adult Australian Women’ project. Phase 2 of the study was a cross sectional online survey of nurses working in Primary and Community Health Service in the Metro North Health Service District of Queensland Health (N = 46). Pender’s health promotion model was used as the theoretical framework for this study. Results: Women in this study had an average total barriers score of 32.18 (SD = 9.52) which was similar to average scores reported in the literature for women with a range of physical disabilities and illnesses. The leading five barriers for this group of women were: concern about safety; too tired; not interested; lack of information about what to do; with lack of time and feeling I can’t do things correctly the equal fifth ranked barriers. In this study there was no statistically significant difference in average total barriers scores between women in the intervention group and those is the usual care group of the parent study. There was also no significant relationship between the women’s socio-demographic variables and lifestyle risk factors and their level of perceived barriers. Nurses in the study had an average total barriers score of 44.48 (SD = 6.24) which was higher than all other average scores reported in the literature. The leading five barriers that nurses perceived were an issue for women with a chronic disease were: lack of time and interferes with other responsibilities the leading barriers; embarrassment about appearance; lack of money; too tired and lack of support from family and friends. There was no significant relationship between the nurses’ sociodemographic and nursing variables and the level of perceived barriers. When comparing the results of women and nurses in the study there was a statistically significant difference in the median total barriers score between the groups (p < 0.001), where the nurses perceived the barriers to be higher (Md = 43) than the women (Md = 33). There was also a significant difference in the responses to the individual barriers items in fifteen of the eighteen items (p < 0.002). Conclusion: Although this study is limited by a small sample size, it contributes to understanding the perception of midlife and older women with a chronic disease and also the perception of nurses, about the barriers to healthy lifestyle activities that women face. The study provides some evidence that the perceptions of women and nurses may differ and argues that these differences may have significant implications for clinical practice. The study recommends a greater emphasis on assessing and managing perceived barriers to health promotion activities in health education and policy development and proposes a conceptual model for understanding perceived barriers to action.

Cultural support workers and long day care services

In Australia, eligible long day care services may apply for support at the state level to assist with the transition of children from culturally or linguistically diverse backgrounds into childcare settings. For staff in childcare services, this support comes in the form of a cultural support worker (CSW). The primary role of a CSW is to build capacity in childcare staff to support children and families as they enter the childcare program. This paper draws on interview data and documentation from multiple sources to report the perspectives of key stakeholders affiliated with a cultural support program in an Australian childcare setting. It concludes that a more flexible approach to policy that directs the work of CSWs is needed, as well as further research into ways to build capacity for cultural competence for both CSWs and childcare staff who work collaboratively to support young children as they transition to childcare.

Support teachers, learning difficulties and secondary school culture

This thesis will report on mixed method research which examined secondary Support Teachers Learning Difficulties (STLDs) and their modes of operation in New South Wales (NSW) government schools, Australia. Four modes of operation were identified in the literature as consultancy, team teaching, in-class support and withdrawal. An additional area of other duties was also included to examine the time when STLDs were not functioning in the four identified modes of operation. NSW government policy is in keeping with the literature as it recommends that STLDs should spend the majority of their time in consultancy and team teaching while in class with a minimum of withdrawal of students from their main classrooms for individual or small group instruction. STLDs, however, did not appear to be functioning in the recommended way. A number of factors identified in the literature, which may influence the modes of operation, can be grouped under the heading of school culture thus this research involved the examination of the effects of school culture on the modes of operation with the aim of expanding our understanding of the functioning of STLDs and providing suggestions for improvement. The theoretical base of social constructionism has informed this research which included survey and case study methods. Case studies of the STLDs in three secondary schools led to the conclusion that, in conjunction with factors such as flexibility and commitment, the involvement of the STLD in a sub-culture of learning support may lead to functioning in the recommended modes of operation.

A theory of waste behaviour in the construction industry

Levels of waste within the construction industry need to be reduced for environmental and economic reasons. Changing people's wasteful behaviour can make a significant contribution. This paper describes a research project that used Ajzen's 'theory of planned behaviour' to investigate the attitudinal forces that shape behaviour at the operative level. It concludes that operatives see waste as an inevitable by-product of construction activity. Attitudes towards waste management are not negative, although they are pragmatic and impeded by perceptions of a lack of managerial commitment. Waste management is perceived as a low project priority, and there is an absence of appropriate resources and incentives to support it. A theory of waste behaviour is proposed for the construction industry, and recommendations are made to help managers improve operatives' attitudes towards waste.

Exploring health behaviour determinants of ageing Australians with chronic diseases

Background: Chronic disease presents overwhelming challenges to elderly patients, their families, health care providers and the health care system. The aim of this study was to explore a theoretical model for effective management of chronic diseases, especially type 2 diabetes mellitus and/or cardiovascular disease. The assumed theoretical model considered the connections between physical function, mental health, social support and health behaviours. The study effort was to improve the quality of life for people with chronic diseases, especially type 2 diabetes and/or cardiovascular disease and to reduce health costs. Methods: A cross-sectional post questionnaire survey was conducted in early 2009 from a randomised sample of Australians aged 50 to 80 years. A total of 732 subjects were eligible for analysis. Firstly, factors influencing respondents‘ quality of life were investigated through bivariate and multivariate regression analysis. Secondly, the Theory of Planned Behaviour (TPB) model for regular physical activity, healthy eating and medication adherence behaviours was tested for all relevant respondents using regression analysis. Thirdly, TPB variable differences between respondents who have diabetes and/or cardiovascular disease and those without these diseases were compared. Finally, the TPB model for three behaviours including regular physical activity, healthy eating and medication adherence were tested in respondents with diabetes and/or cardiovascular diseases using Structure Equation Modelling (SEM). Results: This was the first study combining the three behaviours using a TPB model, while testing the influence of extra variables on the TPB model in one study. The results of this study provided evidence that the ageing process was a cumulative effect of biological change, socio-economic environment and lifelong behaviours. Health behaviours, especially physical activity and healthy eating were important modifiable factors influencing respondents‘ quality of life. Since over 80% of the respondents had at least one chronic disease, it was important to consider supporting older people‘s chronic disease self-management skills such as healthy diet, regular physical activity and medication adherence to improve their quality of life. Direct measurement of the TPB model was helpful in understanding respondents‘ intention and behaviour toward physical activity, healthy eating and medication adherence. In respondents with diabetes and/or cardiovascular disease, the TPB model predicted different proportions of intention toward three different health behaviours with 39% intending to engage in physical activity, 49% intending to engage in healthy eating and 47% intending to comply with medication adherence. Perceived behavioural control, which was proven to be the same as self-efficacy in measurement in this study, played an important role in predicting intention towards the three health behaviours. Also social norms played a slightly more important role than attitude for physical activity and medication adherence, while attitude and social norms had similar effects on healthy eating in respondents with diabetes and/or cardiovascular disease. Both perceived behavioural control and intention directly predicted recent actual behaviours. Physical activity was more a volitional control behaviour than healthy eating and medication adherence. Step by step goal setting and motivation was more important for physical activity, while accessibility, resources and other social environmental factors were necessary for improving healthy eating and medication adherence. The extra variables of age, waist circumference, health related quality of life and depression indirectly influenced intention towards the three behaviours mainly mediated through attitude and perceived behavioural control. Depression was a serious health problem that reduced the three health behaviours‘ motivation, mediated through decreased self-efficacy and negative attitude. This research provided evidence that self-efficacy is similar to perceived behavioural control in the TPB model and intention is a proximal goal toward a particular behaviour. Combining four sources of information in the self-efficacy model with the TPB model would improve chronic disease patients‘ self management behaviour and reach an improved long-term treatment outcome. Conclusion: Health intervention programs that target chronic disease management should focus on patients‘ self-efficacy. A holistic approach which is patient-centred and involves a multidisciplinary collaboration strategy would be effective. Supporting the socio-economic environment and the mental/ emotional environment for older people needs to be considered within an integrated health care system.

Towards a service framework for remote sales support via augmented reality

Real-time sales assistant service is a problematic component of remote delivery of sales support for customers. Solutions involving web pages, telephony and video support prove problematic when seeking to remotely guide customers in their sales processes, especially with transactions revolving around physically complex artefacts. This process involves a number of services that are often complex in nature, ranging from physical compatibility and configuration factors, to availability and credit services. We propose the application of a combination of virtual worlds and augmented reality to create synthetic environments suitable for remote sales of physical artefacts, right in the home of the purchaser. A high level description of the service structure involved is shown, along with a use case involving the sale of electronic goods and services within an example augmented reality application. We expect this work to have application in many sales domains involving physical objects needing to be sold over the Internet.

Under the carpet : the politics and trauma of patient harm

Few studies have investigated iatrogenic outcomes from the viewpoint of patient experience. To address this anomaly, the broad aim of this research is to explore the lived experience of patient harm. Patient harm is defined as major harm to the patient, either psychosocial or physical in nature, resulting from any aspect of health care. Utilising the method of Consensual Qualitative Research (CQR), in-depth interviews are conducted with twenty-four volunteer research participants who self-report having been severely harmed by an invasive medical procedure. A standardised measure of emotional distress, the Impact of Event Scale (IES), is additionally employed for purposes of triangulation. Thematic analysis of transcript data indicate numerous findings including: (i) difficulties regarding patients‘ prior understanding of risks involved with their medical procedure; (ii) the problematic response of the health system post-procedure; (iii) multiple adverse effects upon life functioning; (iv) limited recourse options for patients; and (v) the approach desired in terms of how patient harm should be systemically handled. In addition, IES results indicate a clinically significant level of distress in the sample as a whole. To discuss findings, a cross-disciplinary approach is adopted that draws upon sociology, medicine, medical anthropology, psychology, philosophy, history, ethics, law, and political theory. Furthermore, an overall explanatory framework is proposed in terms of the master themes of power and trauma. In terms of the theme of power, a postmodernist analysis explores the politics of patient harm, particularly the dynamics surrounding the politics of knowledge (e.g., notions of subjective versus objective knowledge, informed consent, and open disclosure). This analysis suggests that patient care is not the prime function of the health system, which appears more focussed upon serving the interests of those in the upper levels of its hierarchy. In terms of the master theme of trauma, current understandings of posttraumatic stress disorder (PTSD) are critiqued, and based on data from this research as well as the international literature, a new model of trauma is proposed. This model is based upon the principle of homeostasis observed in biology, whereby within every cell or organism a state of equilibrium is sought and maintained. The proposed model identifies several bio-psychosocial markers of trauma across its three main phases. These trauma markers include: (i) a profound sense of loss; (ii) a lack of perceived control; (iii) passive trauma processing responses; (iv) an identity crisis; (v) a quest to fully understand the trauma event; (vi) a need for social validation of the traumatic experience; and (vii) posttraumatic adaption with the possibility of positive change. To further explore the master themes of power and trauma, a natural group interview is carried out at a meeting of a patient support group for arachnoiditis. Observations at this meeting and members‘ stories in general support the homeostatic model of trauma, particularly the quest to find answers in the face of distressing experience, as well as the need for social recognition of that experience. In addition, the sociopolitical response to arachnoiditis highlights how public domains of knowledge are largely constructed and controlled by vested interests. Implications of the data overall are discussed in terms of a cultural revolution being needed in health care to position core values around a prime focus upon patients as human beings.

Grocery product pricing and Australian supermarket consumers : gender differences in perceived importance levels

Grocery shopping is an essential and routine activity. Although long regarded the responsibility of the female spouse, modern social and demographic shifts are causing men to become more engaged in this task. This is the first study to analyse gender differences with respect to the criterion of grocery product price within an Australian supermarket retail environment. A stratified sample of 140 male and 140 female grocery shoppers was surveyed. Results showed that men considered price attributes of products as being significantly lower in importance than did women. Additionally, men displayed lower levels of price nvolvement, reported referencing shelf price to a lesser extent, and gave lesser consideration to promotional tactics focusing on low price. Although men on average buy fewer items than do women, they spend more money for each item they purchase. This higher expenditure per item appears to be driven, at least in part, by a lack of price referencing. This research has implications for gender studies and consumer behaviour disciplines in relation to grocery shopping.

Supermarket consumers and gender differences relating to their perceived importance levels of store characteristics

Family grocery shopping is the accepted domain of women; however, modern social and demographic movements challenge traditional gender roles with in the family structure. Men now engage in grocery shopping more freely and frequently, yet the essence of male shopping behaviour and beliefs present an opportunity for examination. This research identifies specific store characteristics, investigates the perceived importance of those characteristics and explores gender, age and income differences that may exist. A random sample collection methodology involving 280 male and female grocery shoppers was selected. Results indicated significant statistical differences between genders based on perceptions of importance of most store characteristics. Overall, male grocery shoppers considered supermarket store characteristics less important than female shoppers. Income did not affect shoppers’ level of associated importance; however respondents’ age, education and occupation influenced perceptions of price, promotions and cleanliness.

Online geographic information systems for improving health planning practice : lessons learned from the case study of Logan-Beaudesert, Australia

This study examines the impact of utilising a Decision Support System (DSS) in a practical health planning study. Specifically, it presents a real-world case of a community-based initiative aiming to improve overall public health outcomes. Previous studies have emphasised that because of a lack of effective information, systems and an absence of frameworks for making informed decisions in health planning, it has become imperative to develop innovative approaches and methods in health planning practice. Online Geographical Information Systems (GIS) has been suggested as one of the innovative methods that will inform decision-makers and improve the overall health planning process. However, a number of gaps in knowledge have been identified within health planning practice: lack of methods to develop these tools in a collaborative manner; lack of capacity to use the GIS application among health decision-makers perspectives, and lack of understanding about the potential impact of such systems on users. This study addresses the abovementioned gaps and introduces an online GIS-based Health Decision Support System (HDSS), which has been developed to improve collaborative health planning in the Logan-Beaudesert region of Queensland, Australia. The study demonstrates a participatory and iterative approach undertaken to design and develop the HDSS. It then explores the perceived user satisfaction and impact of the tool on a selected group of health decision makers. Finally, it illustrates how decision-making processes have changed since its implementation. The overall findings suggest that the online GIS-based HDSS is an effective tool, which has the potential to play an important role in the future in terms of improving local community health planning practice. However, the findings also indicate that decision-making processes are not merely informed by using the HDSS tool. Instead, they seem to enhance the overall sense of collaboration in health planning practice. Thus, to support the Healthy Cities approach, communities will need to encourage decision-making based on the use of evidence, participation and consensus, which subsequently transfers into informed actions.

The PSS : From Flat Maps to Layered Perspectives - the contribution of the Airport Metropolis Planning Support System (PSS) to sub-regional planning in the Brisbane Airport case environment

Conventional planning and decision making, with its sectoral and territorial emphasis and flat-map based processes are no longer adequate or appropriate for the increased complexity confronting airport/city interfaces. These crowed and often contested governance spaces demand a more iterative and relational planning and decision-making approach. Emergent GIS based planning and decision-making tools provide a mechanism which integrate and visually display an array of complex data, frameworks and scenarios/expectations, often in ‘real time’ computations. In so doing, these mechanisms provide a common ground for decision making and facilitate a more ‘joined-up’ approach to airport/city planning. This paper analyses the contribution of the Airport Metropolis Planning Support System (PSS) to sub-regional planning in the Brisbane Airport case environment.