Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis

The number of mammalian transcripts identified by full-length cDNA projects and genome sequencing projects is increasing remarkably. Clustering them into a strictly nonredundant and comprehensive set provides a platform for functional analysis of the transcriptome and proteome, but the quality of the clustering and predictive usefulness have previously required manual curation to identify truncated transcripts and inappropriate clustering of closely related sequences. A Representative Transcript and Protein Sets (RTPS) pipeline was previously designed to identify the nonredundant and comprehensive set of mouse transcripts based on clustering of a large mouse full-length cDNA set (FANTOM2). Here we propose an alternative method that is more robust, requires less manual curation, and is applicable to other organisms in addition to mouse. RTPSs of human, mouse, and rat have been produced by this method and used for validation. Their comprehensiveness and quality are discussed by comparison with other clustering approaches. The RTPSs are available at ftp://fantom2.gsc.riken.go.jp/RTPS/. (C). 2004 Elsevier Inc. All rights reserved.

An expert system for the development of a health and safety policy/risk assessment in the plastics industry

Health and safety policies may be regarded as the cornerstone for positive prevention of occupational accidents and diseases. The Health and Safety at Work, etc Act 1974 makes it a legal duty for employers to prepare and revise a written statement of a general policy with respect to the health and safety at work of employees as well as the organisation and arrangements for carrying out that policy. Despite their importance and the legal equipment to prepare them, health and safety policies have been found, in a large number of plastics processing companies (particularly small companies), to be poorly prepared, inadequately implemented and monitored. An important cause of these inadequacies is the lack of necessary health and safety knowledge and expertise to prepare, implement and monitor policies. One possible way of remedying this problem is to investigate the feasibility of using computers to develop expert system programs to simulate the health and safety (HS) experts' task of preparing the policies and assisting companies implement and monitor them. Such programs use artificial intelligence (AI) techniques to solve this sort of problems which are heuristic in nature and require symbolic reasoning. Expert systems have been used successfully in a variety of fields such as medicine and engineering. An important phase in the feasibility of development of such systems is the engineering of knowledge which consists of identifying the knowledge required, eliciting, structuring and representing it in an appropriate computer programming language.

Participation in a positive youth development program and multi -problem alternative high school students' transformative goals: An investigation of the theoretical and methodological utility and validity of the Transformative Goal Attainment (TGAS)

There is a growing body of literature that provides evidence for the efficacy of positive youth development programs in general and preliminary empirical support for the efficacy of the Changing Lives Program (CLP) in particular. This dissertation sought to extend previous efforts to develop and preliminarily examine the Transformative Goal Attainment Scale (TGAS) as a measure of participant empowerment in the promotion of positive development. Consistent with recent advances in the use of qualitative research methods, this dissertation sought to further investigate the utility of Relational Data Analysis (RDA) for providing categorizations of qualitative open-ended response data. In particular, a qualitative index of Transformative Goals, TG, was developed to complement the previously developed quantitative index of Transformative Goal Attainment (TGA), and RDA procedures for calculating reliability and content validity were refined. Second, as a Stage I pilot/feasibility study this study preliminarily examined the potentially mediating role of empowerment, as indexed by the TGAS, in the promotion of positive development. ^ Fifty-seven participants took part in this study, forty CLP intervention participants and seventeen control condition participants. All 57 participants were administered the study's measures just prior to and just following the fall 2003 semester. This study thus used a short-term longitudinal quasi-experimental research design with a comparison control group. ^ RDA procedures were refined and applied to the categorization of open-ended response data regarding participants' transformative goals (TG) and future possible selves (PSQ-QE). These analyses revealed relatively strong, indirect evidence for the construct validity of the categories as well as their theoretically meaningful structural organization, thereby providing sufficient support for the utility of RDA procedures in the categorization of qualitative open-ended response data. ^ In addition, transformative goals (TG) and future possible selves (PSQ-QE), and the quantitative index of perceived goal attainment (TGA) were evaluated as potential mediators of positive development by testing their relationships to other indices of positive intervention outcome within a four-step method involving both analysis of variance (ANOVA and RMANOVAs) and regression analysis. Though more limited in scope than the efforts at the development and refinement of the measures of these mediators, the results were also promising. ^

Multilevel Governance and Accountability: Does Decentralization Promote Good Governance?

Today, the trend towards decentralization is far-reaching. Proponents of decentralization have argued that decentralization promotes responsive and accountable local government by shortening the distance between local representatives and their constituency. However, in this paper, I focus on the countervailing effect of decentralization on the accountability mechanism, arguing that decentralization, which increases the number of actors eligible for policy making and implementation in governance as a whole, may blur lines of responsibility, thus weakening citizens’ ability to sanction government in election. By using the ordinary least squares (OLS) interaction model based on historical panel data for 78 countries in the 2002 – 2010 period, I test the hypothesis that as the number of government tiers increases, there will be a negative interaction between the number of government tiers and decentralization policies. The regression results show empirical evidence that decentralization policies, having a positive impact on governance under a relatively simple form of multilevel governance, have no more statistically significant effects as the complexity of government structure exceeds a certain degree. In particular, this paper found that the presence of intergovernmental meeting with legally binding authority have a negative impact on governance when the complexity of government structure reaches to the highest level.

Analysis of factors influencing the physical, chemical and sensorial properties of Serra da Estrela cheeses

The objective of this study was to evaluate the chemical, color, textural, and sensorial characteristics of Serra da Estrela cheese and also to identity the factors affecting these properties, namely thistle ecotype, place of production, dairy and maturation. The results demon- strated that the cheeses lost weight mostly during the first stage of maturation, which was negatively correlated with moisture content, being this also observed for fat and protein contents. During maturation the cheeses became darker and with a yellowish coloration. A strong corre- lation was found between ash and chlorides contents, being the last directly related to the added salt in the manufacturing process. The flesh firmness showed a strong positive correlation with the rind harness and the firmness of inner paste. Stickiness was strongly related with all the other textural properties being indicative of the creamy nature of the paste. Adhesiveness was posi- tively correlated with moisture content and negatively correlated with maturation time. The trained panelists liked the cheeses, giving high overall assessment scores, but these were not significantly correlated with the physicochemical properties. The salt differences between cheeses were not evident for the panelists, which was corroborated by the absence of correlation between the perception of saltiness and the analyzed chlorides con- tents. The Factorial Analysis of the chemical and physical properties evidenced that they could be explained by two factors, one associated to the texture and the color and the other associated with the chemical properties. Finally, there was a clear influence of the thistle ecotype, place of production and dairy factors in the analyzed properties.

Identification and analysis of business and software services : A consolidated approach

Although the benefits of service orientation are prevalent in literature, a review, analysis, and evaluation of the 30 existing service analysis approaches presented in this paper have shown that a comprehensive approach to the identification and analysis of both business and supporting software services is missing. Based on this evaluation of existing approaches and additional sources, we close this gap by proposing an integrated, consolidated approach to business and software service analysis that combines and extends the strengths of the examined methodologies.

Information and communication technologies : catalysts for sustainable development

The concept of sustainable urban development has been pushed to the forefront of policy-making and politics as the world wakes up to the impacts of climate change and the effects of modern urban lifestyles. Today, sustainable development has become a very prominent element in the day-to-day debate on urban policy and the expression of that policy in urban planning and development decisions. As a result of this, during the last few years, sustainable development automation applications such as sustainable urban development decision support systems have become popular tools as they offer new opportunities for local governments to realise their sustainable development agendas. This chapter explores a range of issues associated with the application of information and communication technologies and decision support systems in the process of underpinning sustainable urban development. The chapter considers how information and communication technologies can be applied to enhance urban planning, raise environmental awareness, share decisions and improve public participation. It introduces and explores three web-based geographical information systems projects as best practice. These systems are developed as support tools to include public opinion in the urban planning and development processes, and to provide planners with comprehensive tools for the analysis of sustainable urban development variants in order to prepare the best plans for constructing sustainable urban communities and futures.

An analysis of tax expenditure versus direct expenditure

Each financial year concessions, benefits and incentives are delivered to taxpayers via the tax system. These concessions, benefits and incentives, referred to as tax expenditure, differ from direct expenditure because of the recurring fiscal impact without regular scrutiny through the federal budget process. There are approximately 270 different tax expenditures existing within the current tax regime with total measured tax expenditures in the 2005-06 financial year estimated to be around $42.1 billion, increasing to $52.7 billion by 2009-10. Each year, new tax expenditures are introduced, while existing tax expenditures are modified and deleted. In recognition of some of the problems associated with tax expenditure, a Tax Expenditure Statement, as required by the Charter of Budget Honesty Act 1988, is produced annually by the Australian Federal Treasury. The Statement details the various expenditures and measures in the form of concessions, benefits and incentives provided to taxpayers by the Australian Government and calculates the tax expenditure in terms of revenue forgone. A similar approach to reporting tax expenditure, with such a report being a legal requirement, is followed by most OECD countries. The current Tax Expenditure Statement lists 270 tax expenditures and where it is able to, reports on the estimated pecuniary value of those expenditures. Apart from the annual Tax Expenditure Statement, there is very little other scrutiny of Australia’s Federal tax expenditure program. While there has been various academic analysis of tax expenditure in Australia, when compared to the North American literature, it is suggested that the Australian literature is still in its infancy. In fact, one academic author who has contributed to tax expenditure analysis recently noted that there is ‘remarkably little secondary literature which deals at any length with tax expenditures in the Australian context.’ Given this perceived gap in the secondary literature, this paper examines fundamental concept of tax expenditure and considers the role it plays in to the current tax regime as a whole, along with the effects of the introduction of new tax expenditures. In doing so, tax expenditure is contrasted with direct expenditure. An analysis of tax expenditure versus direct expenditure is already a sophisticated and comprehensive body of work stemming from the US over the last three decades. As such, the title of this paper is rather misleading. However, given the lack of analysis in Australia, it is appropriate that this paper undertakes a consideration of tax expenditure versus direct expenditure in an Australian context. Given this proposition, rather than purport to undertake a comprehensive analysis of tax expenditure which has already been done, this paper discusses the substantive considerations of any such analysis to enable further investigation into the tax expenditure regime both as a whole and into individual tax expenditure initiatives. While none of the propositions in this paper are new in a ‘tax expenditure analysis’ sense, this debate is a relatively new contribution to the Australian literature on the tax policy. Before the issues relating to tax expenditure can be determined, it is necessary to consider what is meant by ‘tax expenditure’. As such, part two if this paper defines ‘tax expenditure’. Part three determines the framework in which tax expenditure can be analysed. It is suggested that an analysis of tax expenditure must be evaluated within the framework of the design criteria of an income tax system with the key features of equity, efficiency, and simplicity. Tax expenditure analysis can then be applied to deviations from the ideal tax base. Once it is established what is meant by tax expenditure and the framework for evaluation is determined, it is possible to establish the substantive issues to be evaluated. This paper suggests that there are four broad areas worthy of investigation; economic efficiency, administrative efficiency, whether tax expenditure initiatives achieve their policy intent, and the impact on stakeholders. Given these areas of investigation, part four of this paper considers the issues relating to the economic efficiency of the tax expenditure regime, in particular, the effect on resource allocation, incentives for taxpayer behaviour and distortions created by tax expenditures. Part five examines the notion of administrative efficiency in light of the fact that most tax expenditures could simply be delivered as direct expenditures. Part six explores the notion of policy intent and considers the two questions that need to be asked; whether any tax expenditure initiative reaches its target group and whether the financial incentives are appropriate. Part seven examines the impact on stakeholders. Finally, part eight considers the future of tax expenditure analysis in Australia.

An analysis of holding cost impact on housing affordability in relation to midsized Greenfield residential property developments in South East Queensland

The position of housing demand and supply is not consistent. The Australian situation counters the experience demonstrated in many other parts of the world in the aftermath of the Global Financial Crisis, with residential housing prices proving particularly resilient. A seemingly inexorable housing demand remains a critical issue affecting the socio-economic landscape. Underpinned by high levels of population growth fuelled by immigration, and further buoyed by sustained historically low interest rates, increasing income levels, and increased government assistance for first home buyers, this strong housing demand level ensures problems related to housing affordability continue almost unabated. A significant, but less visible factor impacting housing affordability relates to holding costs. Although only one contributor in the housing affordability matrix, the nature and extent of holding cost impact requires elucidation: for example, the computation and methodology behind the calculation of holding costs varies widely - and in some instances completely ignored. In addition, ambiguity exists in terms of the inclusion of various elements that comprise holding costs, thereby affecting the assessment of their relative contribution. Such anomalies may be explained by considering that assessment is conducted over time in an ever-changing environment. A strong relationship with opportunity cost - in turn dependant inter alia upon prevailing inflation and / or interest rates - adds further complexity. By extending research in the general area of housing affordability, this thesis seeks to provide a detailed investigation of those elements related to holding costs specifically in the context of midsized (i.e. between 15-200 lots) greenfield residential property developments in South East Queensland. With the dimensions of holding costs and their influence over housing affordability determined, the null hypothesis H0 that holding costs are not passed on can be addressed. Arriving at these conclusions involves the development of robust economic and econometric models which seek to clarify the componentry impacts of holding cost elements. An explanatory sequential design research methodology has been adopted, whereby the compilation and analysis of quantitative data and the development of an economic model is informed by the subsequent collection and analysis of primarily qualitative data derived from surveying development related organisations. Ultimately, there are significant policy implications in relation to the framework used in Australian jurisdictions that promote, retain, or otherwise maximise, the opportunities for affordable housing.

Rethinking Youth Prostitution: National Provision at the Margins of Child Protection and Youth Justice

In March 2000, the Department of Health and the Home Office issued guidance fundamentally altering policy and practice with regard to young people in prostitution. 1 Instead of being arrested and punished for prostitution-related offences, those under 18 years old were to be thought of as children ‘in need’ and offered welfare-based interventions. The practice that has developed in the last three years has offered interventions that are located within both child protection and youth justice work. This article examines these changes in order to generate insights about the changing nature of youth justice. In particular, it is argued that the drive to manage the risks posed by young people in prostitution to specific organisations, takes precedence over either the desire to care for, or the demand to punish them. Through an analysis of how practitioners and policy makers responsible for implementing this new approach to youth prostitution talk about ‘risk’ and ‘responsibility’, ‘liability’, ‘protection’ and ‘punishment’, the article argues that the contradiction between care and control has been re-interpreted, such that there is noticeable blurring of the boundaries between welfare and punishment at the margins of youth justice work.

Content analysis of international research in geographical and environmental education : eighteen years of academic publishing

This paper examines the history of the IRGEE Journal in terms of its sustainable future. The development of geographical and environmental education is evaluated, as reflected from the articles published in the Journal “International Research in Geographical and Environmental Education” (IRGEE). A content analysis of all papers and forum sections which have appeared in the journal since Volume 1 Number 1 was published in 1992 has been conducted, examining the content of as many as 526 articles. The method was a content analysis, and revealed themes which have experienced an increasing or declining interest over the 18 years of publication of IRGEE (1992-2009), while other themes have remained current during this period. The main findings of this analysis are: a) the total number of articles has increased more than threefold, b) articles related to geographical education (sensu stricto) outweighed those related to environmental education, c) the themes “syllabi, textbooks, curricula” and “values, attitudes” attract the attention of researchers with increasing strength and d) emerging subjects, such as GIS and sustainability have appeared dynamically in the last years.

End-of-life care in the intensive care setting : a descriptive exploratory qualitative study of nurses' beliefs and practices

Background: End-of-life care is a significant component of work in intensive care. Limited research has been undertaken on the provision of end-of-life care by nurses in the intensive care setting. The purpose of this study was to explore the end-of-life care beliefs and practices of intensive care nurses. Methods: A descriptive exploratory qualitative research approach was used to invite a convenience sample of five intensive care nurses from one hospital to participate in a semi-structured interview. Interview transcripts were analysed using an inductive coding approach. Findings: Three major categories emerged from analysis of the interviews: beliefs about end-of-life care, end-of-life care in the intensive care context and facilitating end-of-life care. The first two categories incorporated factors contributing to the end-of-life care experiences and practices of intensive care nurses. The third category captured the nurses’ end-of-life care practices. Conclusions: Despite the uncertainty and ambiguity surrounding end-of-life care in this practice context, the intensive care setting presents unique opportunities for nurses to facilitate positive end-of-life experiences and nurses valued their participation in the provision of end-of-life care. Care of the family was at the core of nurses’ end-of-life care work and nurses play a pivotal role in supporting the patient and their family to have positive and meaningful experiences at the end-of-life.Variation in personal beliefs and organisational support may influence nurses’ experiences and the care provided to patients and their families. Strategies to promote an organisational culture supportive of quality end-of-life care practices, and to mentor and support nurses in the provision of this care are needed.

Critical success elements for the design and implementation of organisational e-learning

Organisations are engaging in e-learning as a mechanism for delivering flexible learning to meet the needs of individuals and organisations. In light of the increasing use and organisational investment in e-learning, the need for methods to evaluate the success of its design and implementation seems more important than ever. To date, developing a standard for the evaluation of e-learning appears to have eluded both academics and practitioners. The currently accepted evaluation methods for e-learning are traditional learning and development models, such as Kirkpatrick’s model (1976). Due to the technical nature of e-learning it is important to broaden the scope and consider other evaluation models or techniques, such as the DeLone and McLean Information Success Model, that may be applicable to the e-learning domain. Research into the use of e-learning courses has largely avoided considering the applicability of information systems research. Given this observation, it is reasonable to conclude that e-learning implementation decisions and practice could be overlooking useful or additional viewpoints. This research investigated how existing evaluation models apply in the context of organisational e-learning, and resulted in an Organisational E-learning success Framework, which identifies the critical elements for success in an e-learning environment. In particular this thesis highlights the critical importance of three e-learning system creation elements; system quality, information quality, and support quality. These elements were explored in depth and the nature of each element is described in detail. In addition, two further elements were identified as factors integral to the success of an e-learning system; learner preferences and change management. Overall, this research has demonstrated the need for a holistic approach to e-learning evaluation. Furthermore, it has shown that the application of both traditional training evaluation approaches and the D&M IS Success Model are appropriate to the organisational e-learning context, and when combined can provide this holistic approach. Practically, this thesis has reported the need for organisations to consider evaluation at all stages of e-learning from design through to implementation.

Some practical issues in the design and analysis of computer experiments

Deterministic computer simulations of physical experiments are now common techniques in science and engineering. Often, physical experiments are too time consuming, expensive or impossible to conduct. Complex computer models or codes, rather than physical experiments lead to the study of computer experiments, which are used to investigate many scientific phenomena of this nature. A computer experiment consists of a number of runs of the computer code with different input choices. The Design and Analysis of Computer Experiments is a rapidly growing technique in statistical experimental design. This thesis investigates some practical issues in the design and analysis of computer experiments and attempts to answer some of the questions faced by experimenters using computer experiments. In particular, the question of the number of computer experiments and how they should be augmented is studied and attention is given to when the response is a function over time.

Multiplexed tandem polymerase chain reaction identifies strong expression of oestrogen receptor and Her-2 from single, formalin-fixed, paraffin-embedded breast cancer sections

Aim To establish the suitability of multiplex tandem polymerase chain reaction (MT-PCR) for rapid identification of oestrogen receptor (ER) and Her-2 status using a single, formalin-fixed, paraffin-embedded (FFPE) breast tumour section. Methods Tissue sections from 29 breast tumours were analysed by immunohistochemistry (IHC) and fluorescence in situ hybridisation (FISH). RNA extracted from 10μm FFPE breast tumour sections from 24 of 29 tumours (14 ER positive and 5 Her-2 positive) was analysed by MT-PCR. After establishing a correlation between IHC and/or FISH and MT-PCR results, the ER/Her-2 status of a further 32 randomly selected, archival breast tumour specimens was established by MT-PCR in a blinded fashion, and compared to IHC/FISH results. Results MT-PCR levels of ER and Her-2 showed good concordance with IHC and FISH results. Furthermore, among the ER positive tumours, MT-PCR provided a quantitative score with a high dynamic range. Threshold values obtained from this data set applied to 32 archival tumour specimens showed that tumours strongly positive for ER and/or Her-2 expression were easily identified by MT-PCR. Conclusion MT-PCR can provide rapid, sensitive and cost-effective analysis of FFPE material and may prove useful as triage to identify patients suited to endocrine or trastuzumab (Herceptin) treatment.