Approximating the Set of Local Minima in Partial RNA Folding Landscapes

Motivation: We study a stochastic method for approximating the set of local minima in partial RNA folding landscapes associated with a bounded-distance neighbourhood of folding conformations. The conformations are limited to RNA secondary structures without pseudoknots. The method aims at exploring partial energy landscapes pL induced by folding simulations and their underlying neighbourhood relations. It combines an approximation of the number of local optima devised by Garnier and Kallel (2002) with a run-time estimation for identifying sets of local optima established by Reeves and Eremeev (2004).

Results: The method is tested on nine sequences of length between 50 nt and 400 nt, which allows us to compare the results with data generated by RNAsubopt and subsequent barrier tree calculations. On the nine sequences, the method captures on average 92% of local minima with settings designed for a target of 95%. The run-time of the heuristic can be estimated by O(n2D?ln?), where n is the sequence length, ? is the number of local minima in the partial landscape pL under consideration and D is the maximum number of steepest descent steps in attraction basins associated with pL.

Europeanization of Inequality and Europeanization of Reference Groups

In this article we take advantage of the availability of European Union Statistics on Income and Living Conditions (EU-SILC) data to address both weak and strong versions of the Europeanization of reference groups thesis. The former proposes that common standards of evaluation emerge as a consequence of knowledge of conditions in other societies. The latter argues that people increasingly perceive themselves as part of a larger European stratification system. Our analysis leads us to reject both versions of the thesis. Material deprivation rather than having a uniform effect is highly dependent on national context. If a process of convergence is underway, it is one that as yet has had a limited impact. In circumstances where the Europeanization of inequality is raising issues relating to both national and transnational forms of legitimacy, it is important to understand that there is no necessary relationship between such Europeanization and the Europeanization of reference groups.

Material Deprivation, Economic Stress, and Reference Groups in Europe: An Analysis of EU-SILC 2009

In this article, we take advantage of the recent availability of data from the special module on material deprivation in the 2009 European Union Statistics on Income and Living Conditions to develop a more comprehensive understanding of the relationship between material deprivation and economic stress, the mediating and moderating roles played by cross-national differences in levels of income and income inequality, and the implications for competing perspectives on the nature of reference groups in Europe. The article establishes the critical role of basic deprivation, relating to inability to enjoy customary standards of living, in influencing economic stress levels. National income levels and inequality had no direct influence on economic stress. However, the impact of basic deprivation was stronger in countries with higher levels of income, indicating the crucial role of national reference groups. An interaction between basic deprivation and income inequality was also observed. However, contrary to the expectation that experiencing basic deprivation in a national context of high income inequality is likely to be particularly stressful, the consequences of such deprivation were most negative in low inequality countries. Experiencing basic deprivation where high income levels and lower inequality would lead to the expectation that such deprivation is eminently avoidable exacerbates its impact. © The Author 2013.

The experiences of palliative care health service provision for people with non-malignant respiratory disease and their caregivers: an all-Ireland study

Aim: To explore the perception of palliative care provision for people with non-malignant respiratory disease from the perspective of bereaved caregivers.

Background: It is recognized that the majority of patients diagnosed with a malignant disease will have access to palliative care provision. However, it is less clear if the same standards of palliative care are available to those with non-malignant respiratory disease in Northern Ireland and the Republic of Ireland.

Design: A qualitative study based on broad interpretivism.

Methods: This research is a PhD study funded by the Department of Education and Learning in Northern Ireland (awarded February 2011). Data collection will consist of two stages; interviews with 20 bereaved caregivers of people who have died 3–18 months previously with a diagnosis of non-malignant respiratory disease and four focus groups with healthcare professionals involved in the care of this client group. This study will be carried out at four healthcare sites across the Island of Ireland. The data will be analysed using thematic content analysis. Research Ethics committee approval was obtained (March 2012).

Discussion: This research will explore the experiences of patients with Chronic Obstructive Pulmonary Disease, Interstitial Lung Disease and Bronchiectasis and their caregivers from the perspective of the bereaved caregiver. The outcomes of this study will provide a critical first step in the development of more responsive palliative care for this client group and have important implications for future practice and policy in the palliative care provided to this client group.

The quality of reporting of diagnostic accuracy studies published in ophthalmic journals

Aim: To evaluate the quality of reporting of all diagnostic studies published in five major ophthalmic journals in the year 2002 using the Standards for Reporting of Diagnostic Accuracy (STARD) initiative parameters. Methods: Manual searching was used to identify diagnostic studies published in 2002 in five leading ophthalmic journals, the American Journal of Ophthalmology (AJO), Archives of Ophthalmology (Archives), British Journal of Ophthalmology (BJO), Investigative Ophthalmology and Visual Science (IOVS), and Ophthalmology. The STARD checklist of 25 items and flow chart was used to evaluate the quality of each publication. Results: A total of 16 publications were included (AJO = 5, Archives = 1, BJO = 2, IOVS = 2, and Ophthalmology = 6). More than half of the studies (n = 9) were related to glaucoma diagnosis. Other specialties included retina (n = 4) cornea (n = 2), and neuro-ophthalmology (n = 1). The most common description of diagnostic accuracy was sensitivity and specificity values, published in 13 articles. The number of fully reported items in evaluated studies ranged from eight to 19. Seven studies reported more than 50% of the STARD items. Conclusions: The current standards of reporting of diagnostic accuracy tests are highly variable. The STARD initiative may be a useful tool for appraising the strengths and weaknesses of diagnostic accuracy studies.

Effectiveness of the Construction Management Courses

This research assesses the effectiveness of current MSc. Construction Project Management programmes within the UK and Ireland. A review of published prospectuses is used to create questionnaires for universities, graduates and employers. Responses provide an insight into programme creation and their relative success in addressing the needs of industry and in achieving other educational objectives. Since the majority of learning institutions have attained professional accreditation, it is useful to review these awards and to assess their potential value to both graduates and industry alike. Interviews are conducted with representatives from the main professional accrediting bodies to understand their procedures and rigour in enforcing standards of education and training. The results show that project management education could be further enhanced by the inclusion of more practical learning and that current programmes place greater emphasis on hard skills at the expense of the softer human skills. There is clearly a need for a closer working relationship between academics and practitioners to tackle the perceived gap between theoretical learning and construction practice. Learning institutions can use the findings to improve their programmes and address the education deficiencies identified by the industry, by the professional institutions and by graduates.

Navigating Risk: Understanding the Impact of the Conflict on Children and Young People in Northern Ireland:Special Issue: Northern Ireland: 20 Years After the Cease-Fires

Twenty years on from the 1994 cease-fires, Northern Ireland is a markedly safer place for children and young people to grow up. However, for a significant number, growing up in post-conflict Northern Ireland has brought with it continued risks and high levels of marginalization. Many young people growing up on the sharp edge of the transition have continued to experience troubling levels of poverty, lower educational attainment, poor standards of childhood health, and sustained exposure to risk-laden environments. Reflecting on interdisciplinary research carried out since the start of the “transition” to peace, this article emphasizes the impact that embedded structural inequalities continue to have on the social, physical, mental, and emotional well-being of many children and young people. In shining a light on the enduring legacy of the conflict, this article moves to argue that greater attention needs to be given to the ongoing socioeconomic factors that result in limited lifetime opportunities, marginalization, and sustained poverty for many young people growing up in “peacetime” Northern Ireland.

Pre-intravitrael injection preparation: endophthalmitis prevention and the importance of povidone-iodine

Despite adherence to strict standards of care in preparation for intravitreal injections, endophthalmitis can still occur. This article focuses on endophthalmitis and the importance of povidone-iodine in pre-procedure antisepsis. An overview of endophthalmitis and an examination of the benefits of povidone-iodine in ocular aseptic technique for the prevention of post-procedure endophthalmitis are provided. The misconceptions that patients and health practitioners may have in relation to povidone-iodine hypersensitivity are also explored.

Evaluation of a partnership between primary and secondary care providing an accessible Level 1 sexual health service in the community

Comprehensive testing for asymptomatic sexually transmitted infections in Northern Ireland has traditionally been provided by genitourinary medicine clinics. As patient demand for services has increased while budgets have remained limited, there has been increasing difficulty in accommodating this demand. In May 2013, the newly commissioned specialist Sexual Health service in the South Eastern Trust sought to pilot a new model of care working alongside a GP partnership of 12 practices. A training programme to enable GPs and practice nurses to deliver Level 1 sexual health care to heterosexual patients aged >16 years, in accordance with the standards of BASHH, was developed. A comprehensive care pathway and dedicated community health advisor supported this new model with close liaison between primary and secondary care. Testing for Chlamydia, gonorrhoea, HIV and syphilis was offered. The aims of the pilot were achieved, namely to provide accessible, cost-effective sexual health care within a framework of robust clinical governance. Furthermore, it uncovered a high positivity rate for Chlamydia, especially in young men attending their general practice, and demonstrated a high level of patient satisfaction. Moreover the capacity of secondary care to deliver Levels 2 and 3 services was increased.

What is being taught in Religious Education classes in Northern Ireland and to what extent should states be concerned about regulation, quality and control of the subject?

This paper reports on a research project designed to discover what schools are teaching in Religious Education in Northern Ireland and what procedures are in place to maintain standards in the delivery of the subject. A search through literature shows that little research has been carried out to determine what is being taught in Religious Education in Northern Ireland. It also indicates that there are very weak systems of control to measure the effectiveness or quality of what is delivered. A survey of the websites of all Post-Primary schools in the region was used to provide some answers to the basic question of what is being taught in RE. Using content and discourse analysis of these alongside supporting documentary sources (textbooks and exam specifications), it is possible to get a clearer picture of how the Northern Ireland Core Syllabus for Religious Education and any additional curricular elements are delivered in schools. The findings show that a significant minority of schools do not publicly articulate what pupils do in religious education. In situations where the content of religious education is made clear, some definite trends are evident. Despite the existence of a statutory core syllabus, there is significant variation in what is taught in schools. The content is most divergent from the syllabus in relation to the teaching of World Religions at Key Stage 3 and at Key Stage 4 whole elements of the syllabus are neglected due to limited conformity between the syllabus and exam specifications. These results raise important questions about the systems of regulation and control of the subject in the region. In law the subject is exempt from formal inspection by the local inspection authority; instead, a form of inspection is allowed for by the Christian churches who design the syllabus, but it is a process that is either entirely neglected or entirely unreported in situations where it does occur. It is argued that these findings raise questions of more general concern for this and other regions in Europe where the teaching of religious education is largely unregulated. For example, to what extent should states take an interest in what is taught in religious education, how it is delivered, what values it promotes and how standards of teaching and learning in the subject are upheld?

Food fraud and consumers' choices in the wake of the horsemeat scandal

Purpose – In 2012, the European food industry was hit by a food fraud: horsemeat was found in
pre-prepared foods, without any declaration on the package. This is commonly referred to as the
“horsemeat scandal”. The purpose of this paper is to investigate consumers’ preferences across
Europe for a selected ready meal, ready to heat (RTH) fresh lasagne, to consider whether the effects of
potential food frauds on consumers’ choices can be mitigated by introducing enhanced standards of
RTH products.
Design/methodology/approach – An online survey was administered to 4,598 consumers of RTH
lasagne in six European countries (Republic of Ireland, France, Italy, Spain, Germany and Norway),
applying discrete choice experiments to estimate consumers’ willingness to pay for enhanced food
safety standards and highlight differences between countries.
Findings – Many similarities across countries emerged, as well as some differences. Consumers in
Europe are highly concerned with the authenticity of the meat in ready meals and strongly prefer to
know that ingredients are nationally sourced. Strong regional differences in price premiums exist for
enhanced food safety standards.
Originality/value – This research adds relevant insights in the analysis of consumers’ reaction to
food fraud, providing practical guidelines on the most appropriate practices that producers should
adopt and on the information to reduce food risk perception among consumers. This would prove
beneficial for the food processing industry and the European Union. The survey is based on a
representative sample of European consumers making this the largest cross-country study of this kind.

Production of biodiesel from the resources endogeneous of Timor Leste

Os biocombustíveis têm estado na linha da frente das políticas energéticas mundiais visto que as suas vantagens conseguem colmatar as incertezas e resolver alguns dos problemas associados aos combustíveis fósseis. O biodiesel tem provado ser um combustível muito fiável, alternativo ao petrodiesel. É uma mistura de ésteres alquílicos produzidos a partir de óleos vegetais e gorduras animais através de uma reacção de transesterificação. Como combustível, o biodiesel é economicamente viável, socialmente responsável, tecnicamente compatível e ambientalmente amigável. O principal desafio associado ao seu desenvolvimento tem a ver com a escolha de matéria-prima para a sua produção. Nos países do terceiro mundo, óleos alimentares são mais importantes para alimentar pessoas do que fazer funcionar carros. Esta tese tem como objectivos produzir/processar biodiesel a partir de recursos endógenos de Timor-Leste e medir/prever as propriedades termodinâmicas do biodiesel, a partir das dos esteres alquílicos. A síntese do biodiesel a partir dos óleos de Aleurites moluccana, Jatropha curcas e borras de café foram aqui estudados. As propriedades termodinâmicas como densidade, viscosidade, tensão superficial, volatilidade e velocidade do som também foram medidas e estimadas usando modelos preditivos disponíveis na literatura, incluindo as equações de estado CPA e soft-SAFT. Timor-Leste é um país muito rico em recursos naturais, mas a maioria da população ainda vive na pobreza e na privação de acesso a serviços básicos e condições de vida decentes. A exploração de petróleo e gás no mar de Timor tem sido controlado pelo Fundo Petrolífero. O país ainda carece de electricidade e combustíveis que são cruciais para materializar as políticas de redução da pobreza. Como solução, o governo timorense criou recentemente o Plano Estratégico de Desenvolvimento a 20 anos cujas prioridades incluem trazer o desenvolvimento do petróleo do mar para a costa sul de Timor-Leste e desenvolver as energias renováveis. É neste último contexto que o biodiesel se insere. O seu desenvolvimento no país poderá ser uma solução para o fornecimento de electricidade, a criação de empregos e sobretudo o combate contra a pobreza e a privação. Para ser usado como combustível, no entanto, o biodiesel deve possuir propriedades termodinâmicas coerentes com as especificadas nas normas da ASTM D6751 (nos Estados Unidos) ou EN 14214 (na Europa) para garantir uma adequada ignição, atomização e combustão do biodiesel no motor.

Phylogenetic insights of Avena genus based on genomic analysis of 45S rDNA molecular organization

Tese de mestrado. Biologia (Biologia Molecular e Genética). Universidade de Lisboa, Faculdade de Ciências, 2014

The Personal and Professional Selves of Teachers: Stable and Unstable Identities

In much educational literature it is recognised that the broader social conditions in which teachers live and work, and the personal and professional elements of teachers' lives, experiences, beliefs and practices are integral to one another, and that there are often tensions between these which impact to a greater or lesser extent upon teachers' sense of self or identity. If identity is a key influencing factor on teachers' sense of purpose, self‐efficacy, motivation, commitment, job satisfaction and effectiveness, then investigation of those factors which influence positively and negatively, the contexts in which these occur and the consequences for practice, is essential. Surprisingly, although notions of ‘self’ and personal identity are much used in educational research and theory, critical engagement with individual teachers' cognitive and emotional ‘selves’ has been relatively rare. Yet such engagement is important to all with an interest in raising and sustaining standards of teaching, particularly in centralist reform contexts which threaten to destabilise long‐held beliefs and practices. This article addresses the issue of teacher identities by drawing together research which examines the nature of the relationships between social structures and individual agency; between notions of a socially constructed, and therefore contingent and ever‐remade, ‘self’, and a ‘self’ with dispositions, attitudes and behavioural responses which are durable and relatively stable; and between cognitive and emotional identities. Drawing upon existing research literature and findings from a four‐year Department for Education and Skills funded project with 300 teachers in 100 schools which investigated variations in teachers' work and lives and their effects on pupils (VITAE), it finds that identities are neither intrinsically stable nor intrinsically fragmented, as earlier literature suggests. Rather, teacher identities may be more, or less, stable and more or less fragmented at different times and in different ways according to a number of life, career and situational factors.

Survival or Sustainability? Contributions of Innovatively-Managed News Ventures to the Future of Egyptian Journalism

In the repressive political climate prevailing in Egypt in 2013-15, news ventures aspiring to high standards of reporting were forced to innovate. This paper analyses three Egyptian start-ups that experimented with novel revenue streams and news services during that period, to gain insights into their approaches to managing journalism. In the process it compares different criteria for assessing sustainability and concludes that, in adverse political environments, narrow economic measures of profitability and survival may give a misleading picture as to the sustainability of the kind of journalism conducive to democratic practice. Operating collaboratively, transparently and ethically may slow productivity and profitability in the short term while laying stronger foundations for durable relations among media teams, as well as with readers and advertisers, in the long run.