Computational Methods for RNA Structure Validation and Improvement.

With increasing recognition of the roles RNA molecules and RNA/protein complexes play in an unexpected variety of biological processes, understanding of RNA structure-function relationships is of high current importance. To make clean biological interpretations from three-dimensional structures, it is imperative to have high-quality, accurate RNA crystal structures available, and the community has thoroughly embraced that goal. However, due to the many degrees of freedom inherent in RNA structure (especially for the backbone), it is a significant challenge to succeed in building accurate experimental models for RNA structures. This chapter describes the tools and techniques our research group and our collaborators have developed over the years to help RNA structural biologists both evaluate and achieve better accuracy. Expert analysis of large, high-resolution, quality-conscious RNA datasets provides the fundamental information that enables automated methods for robust and efficient error diagnosis in validating RNA structures at all resolutions. The even more crucial goal of correcting the diagnosed outliers has steadily developed toward highly effective, computationally based techniques. Automation enables solving complex issues in large RNA structures, but cannot circumvent the need for thoughtful examination of local details, and so we also provide some guidance for interpreting and acting on the results of current structure validation for RNA.

Venus infers

These poems mark the fault lines of myth, dream and memory, of a doubled identity emerging from the clash of war, desire and the cacophony of the city. 1974/Dead Sister , a narrative poem with a cast that includes Lewis Carroll’s Alice, Freud’s Dora, the Lady of Shalott, Ophelia, Esther, female cowboys and other deposed goddesses is ‘an autobiography’ of an imaginary dead twin. Alev Adil delineates the traces of a sense of displacement, but while the poems mark those frenetic uncertainties and erasures they celebrate the plenitude of new stories, epistemologies and possibilities born out of falling into fracture (the fracture of memory, gender, identity, culture) more than they mourn any loss. Venus Infers is haunted by the deities of ancient Greek myths and their contemporary manifestations. Eurydice is hiding out in Hackney, sometimes glimpsed on the Jubilee Line; Ariadne remembers her ancient palace as she prowls the endless corridors of a London hotel; Penelope still waits for peace in the ruins of Marash/Varosha. Cyprus often features in these poems, both as a landscape for myth and as a site for contemporary, and contested, memories. [From the Author]

Suez 1956: A European Intervention

This article does not analyse events in the Middle East. It is concerned with the structural background of the Suez Crisis. The Cold War bargain of 1949-50, and thus the Western bloc architecture, was challenged in 1956 and 1962-63. The Suez Crisis and the SKYBOLT Affair are classic examples of intra-bloc conflict. This article focuses on inter-allied conflict during the Suez Crisis. The crisis year 1956 witnessed a European challenge to the bipolar order of the Cold War. It is the hypothesis of this article that the mystique of the Suez Crisis unravels, if the events are interpreted as a clash of conflicting world views. The article attempts to enhance our understanding of the crisis by exploring the impact of the formation of a European core on the transatlantic pluralistic security community. The article will thus re-evaluate the architectural debate within the Western partial system. It is the aim to shed new light on the almost unexplored European foreign-policy co-operation within the Western European Union (WEU) in the crisis year 1956

A Sensitivity Approach for Eliminating Clashes from Computer Aided Design Model Assemblies

Clashes occur when components in an assembly unintentionally violate others. If clashes are not identified and designed out before manufacture, product function will be reduced or substantial cost will be incurred in rework. This paper introduces a novel approach for eliminating clashes by identifying which parameters defining the part features in a computer aided design (CAD) assembly need to change and by how much. Sensitivities are calculated for each parameter defining the part and the assembly as the change in clash volume due to a change in each parameter value. These sensitivities give an indication of important parameters and are used to predict the optimum combination of changes in each parameter to eliminate the clash. Consideration is given to the fact that it is sometimes preferable to modify some components in an assembly rather than others and that some components in an assembly cannot be modified as the designer does not have control over their shape. Successful elimination of clashes has been demonstrated in a number of example assemblies.

Proportionality in Age Discrimination Cases - a Model Suitable for Socially Embedded Rights

This chapter discusses the use of proportionality in age discrimination cases before the Court of Justice of the European Union. It argues that the Court does not use this concept systematically - indeed it exposes some contradiction that make the case law seem arbitrary - and proposes a more fruitful use of the principle, which is in line with a modern conception of human rights. The chapter argues that the principle of proportionality stems from the time when human rights served the recently liberated burgeois elite in guarding their rights to property and liberty against the state. Today, states not only respect human rights (which is fully sufficient for this elite, who can rely on their inherited wealth to fend for themselves). They also protect and promote human rights, and these activities are a precondition for human rights to be practically relevant for the whole population. This also means that state activity, which is experienced as a limitation of rights to property and liberty by some, may constitute a measure to promote and protect human rights of others. In employment law - the only field where the EU ban on age discrimination is applied - this is a typical situation. If such a situation occurs, the principle of proportionality must be applied in a bifurcated way.It is not sufficient that the limitation of property rights is proportionate for the achievement of a public policy aim. If the aim of public policy is to enable the effective use of human rights, the limitation of the state action must be proportionate to the protection and promotion of those human rights. It is argued that the principle of proportionality is superior to less structures balancing acts (e.g. the Wednesbury principle), if it is applied both ways. Going over to the field of age discrimination, the chapter identifies a number of potentially colliding aims pursued in this field. Banning age discrimination may relate to genuine aims of anti-discrimination law if bias against older or very young workers is addressed. However, the EU ban of discrimination against all ages also serves to restructure employment law and policy to the age of flexibilisation, replacing the synchronisation principle that has been predominant for the welfare states of the 20th century. The former aim is related to human rights protection, while the latter aim is not (at least not always). This has consequences for applying the proportionality test. The chapter proposes different ways to argue the most difficult age discrimination cases, where anti-discrimination rationales and flexibilisation rationales clash

The evaluative nature of the folk concepts of weakness and strength of will

This article examines the evaluative nature of the folk concepts of weakness and strength of will and hypothesizes that their evaluative nature is strongly connected to the folk concepts of blame and credit. We probed how people apply the concepts of weakness and strength of will to prototypical and non-prototypical scenarios. While regarding prototypical scenarios the great majority applied these concepts according to the predictions following from traditional philosophical analyses, when presented with non-prototypical scenarios, people were divided. Some, against traditional analyses, did not apply these concepts, which we explain in terms of a clash of evaluations involving different sorts of blame and credit. Others applied them according to traditional analyses, which we explain in terms of a disposition to be reflective and clearly set apart the different sorts of blame and credit involved. Still others applied them in an inverse way, seemingly bypassing the traditional components resolution and best judgment, which we explain in terms of a reinterpretation of the scenarios driven by an assumption that everyone knows deep inside that the best thing to do is to act morally. This division notwithstanding, we claim that our results are largely supportive of traditional analyses (qua analyses of folk concepts).

Religion, pragmatic fundamentalism and the transformation of the Northern Ireland conflict

Since 11 September 2001, the religious dimension of conflict has been the focus of increasing attention. In The Clash of Civilizations, Huntington has identified the West in religious-cultural terms, as Christian with a dominant democratic culture emphasizing tolerance, moderation and consensus. The persistence of conflict in Northern Ireland among 'White' Protestant and Catholic Christians undermines this simplistic argument and demands a more subtle understanding of the role of religion and fundamentalism in contemporary conflict. Modernization theory - which is echoed among some theorists of globalization - had predicted the declining importance of religion as the world became industrialized and increasingly interconnected. This is echoed by those who argue that the Northern Ireland conflict is 'ethno-national' and dismiss the role of religion. On the other hand, others have claimed that the conflict is religious and stress the role of Protestant fundamentalism. This article draws on new evidence from Northern Ireland of the complex and subtle ways in which religion impacts on the conflict there, incorporating insights about the pragmatism of fundamentalist Protestants and how religious actors are contributing to conflict transformation. This analysis leads to three broader conclusions about understanding conflicts with religious dimensions. First, the complexity of religion must be understood, and this includes a willingness to recognize the adaptability of fundamentalisms to particular contexts. Second, engaging with fundamentalists and taking their grievances seriously opens up possibilities for conflict transformation. Third, governments and religious actors within civil society can play complementary roles in constructing alternative (religious) ideologies and structures as part of a process of transformation. In a world in which the impact of religion is persistent, engaging with the religious dimension is a vital part of a broader-based strategy for dealing with conflict. © 2008 Journal of Peace Research.

Transnational Culture Wars

The well-known ‘culture wars’ clash in the United States between civil society actors has now gone transnational. Political science scholarship has long detailed how liberal human rights non-governmental organizations NGOs engage in extensive transnational activity in support of their ideals. More recently, US conservative groups (including faith-based NGOs) have begun to emulate these strategies, promoting their convictions by engaging in transnational advocacy. NGOs thus face off against each other politically across the globe. Less well known is the extent to which these culture wars are conducted in courts, using conflicting interpretations of human rights law. Many of the same protagonists, particularly NGOs that find themselves against each other in US courts, now find new litigation opportunities abroad in which to fight their battles. These developments, and their implications, are the focus of this article. In particular, the extent to which US faith-based NGOs have leveraged the experience gained transnationally to use international and foreign jurisprudence in interventions before the US Supreme Court is assessed.

Mixed Messages: American Correspondences in Visual and Verbal Practices

Mixed Messages presents and interrogates ten distinct moments from the arts of nineteenth, twentieth and twenty-first century America where visual and verbal forms blend and clash. Charting correspondences concerned with the expression and meaning of human experience, this volume moves beyond standard interdisciplinary theoretical approaches to consider the written and visual artwork in embodied, cognitive, and contextual terms.

Offering a genuinely interdisciplinary contribution to the intersecting fields of art history, avant-garde studies, word-image relations, and literary studies, Mixed Messages takes in architecture, notebooks, poetry, painting, conceptual art, contemporary art, comic books, photographs and installations, ending with a speculative conclusion on the role of the body in the experience of digital mixed media. Each of the ten case studies explores the juxtaposition of visual and verbal forms in a manner that moves away from treating verbal and visual symbols as operating in binary or oppositional systems, and towards a consideration of mixed media, multi-media and intermedia work as brought together in acts of creation, exhibition, reading, viewing, and immersion. The collection advances research into embodiment theory, affect, pragmatist aesthetics, as well as into the continuing legacy of romanticism and of dada, conceptual art and surrealism in an American context.

Reflectir e debater : a importância da problemática dos valores e da cultura para o processo de aprendizagem

Relatório da prática de ensino supervisionada, Mestrado em Ensino de Filosofia, Universidade de Lisboa, 2011

O tempo das reformas : o papel da companhia de Jesus no enfrentamento com ideais protestantes na Europa do Sul : uma proposta pedagógica

Relatório da prática de ensino supervisionada, Mestrado em Ensino da História e da Geografia no 3º Ciclo do Ensino Básico e no Ensino Secundário, Universidade de Lisboa, 2014

CNN Interactive just got more interactive

Interactive gallery installation which playfully re-contextualised online news feeds from CNN’s website with a soundtrack of found music in order to comment on an online environment where 'serious' news and trivial 'infotainment' often occupy the same space. ‘CNN Interactive just got more interactive’ aimed to investigate the balance between information and ‘info-tainment’ on the web. It demonstrated how the authority and presence of global news corporations online could be playfully subverted by enabling the audience to add a variety of emotively titled soundtracks to the monolithic CNN Interactive website. The project also explored how a work could exist dually as website and gallery installation. ‘CNN interactive’ contributes to the taxonomy of new media art as a new form of contemporary art. One of the first examples in the world of a gallery installation using live Internet data, it is also one of the first attempts in a new media art context to address how individuals respond to and comprehend the changed nature of the news as an immediate phenomenon as relayed by network communications systems. 'CNN interactive’ continues Craighead and Thomson’s research into how live digital networked information can be re-purposed as artistic material within gallery installation contexts but with specific reference to online-international news events, rather than arbitrary data sources (see e-poltergeist, output 1). ‘CNN Interactive’ was commissioned by Tate Britain for the exhibition ‘Art and Money Online’. This was the first gallery exhibition in Tate Britain featuring work that utilised and explored new media as an artistic area, and the first work commissioned by the Tate to operate simultaneously as an online gallery artwork. Selected reviews and citations include ‘Digital Art’ by Christiane Paul, 2003; ‘Internet Art: The Online Clash of Culture and Commerce’ by Julian Stallabrass. (2002); ‘Thomson & Craighead’ by Lisa Le Feuvre for Katalog Journal of Photography and Video, Denmark. All work is developed jointly and equally between Craighead and her collaborator, Jon Thomson, (Slade).

How Formal and Informal Institutions of Middle Eastern Countries Influence Managerial Discretion: An Empirical Investigation

Managerial discretion is the focal theme bridging the clash between two schools of thoughts; whether executives have greater influence on their firms’ outcomes or other factors restrain their actions (Hambrick & Finkelstein, 1987). It is argued that constraints come from inertial, normative and environmental forces (e.g. DiMaggio & Powell, 1983). Of these restraints is the institutional environment in which a firm is headquartered. Our paper falls within this research stream and provides an extension for Crossland and Hambrick (2007, 2011) work. We investigate the national level of discretion in new cross-cultural contexts, provide deeper understanding of its concept, and shed the light on undiscovered discretion’s antecedents and consequences. We adopt a quantitative approach in which questionnaires represent our data collection instrument. We anticipate that in high discretion countries firms tend to follow what Miles & Snow (1978) labeled ‘Prospector’ strategy as opposed to low discretion countries in which firms incline to implement a ‘Defender’ strategy.

Estudo do galgamento em estruturas marítimas verticais utilizando o modelo numérico AMAZON

O galgamento oceânico é um fenómeno associado à interação de ondas com estruturas marítimas. Nesta dissertação estudou-se o galgamento em estruturas marítimas verticais através da aplicação do modelo numérico AMAZON, que é um modelo bidimensional, baseado na resolução das equações não lineares de águas pouco profundas. Para validar a sua aplicação a estruturas marítimas verticais impermeáveis, os resultados de caudal médio galgado obtidos com o modelo AMAZON foram comparados com os resultados de ensaios em modelo físico bidimensional realizados anteriormente e disponíveis na base de dados do projeto europeu CLASH. Os resultados foram ainda comparados com os das fórmulas empíricas e semi-empíricas de Van der Meer & Bruce de 2014, de Goda de 2008 e de Hedges & Reis de 2015. Antes da sua validação, o modelo foi calibrado utilizando um dos ensaios do CLASH. Para tal, realizou-se uma análise de sensibilidade a alguns parâmetros do modelo, concretamente da dimensão mínima da malha, da escala de aplicação do AMAZOM (à escala reduzida ou à do protótipo), da forma de modelação da parede vertical, já que, dado este modelo ser integrado na vertical, não é possível considerar paredes verticais sem utilizar um artifício de cálculo, dos valores de alguns dos parâmetros de entrada do modelo (profundidade mínima molhada e a profundidade mínima de fricção) e da dimensão do domínio de cálculo. Os resultados da calibração do AMAZON mostram que, por causa da precisão do modelo para os menores caudais médios de galgamento, se deve aplicar o modelo à escala do protótipo. Para estruturas verticais, a aproximação que o modelo faz, por defeito, para a secção vertical da estrutura através de um talude fictício a 10:1 apresenta melhores resultados que a utilização de um talude a 20:1. Contudo, ambos requerem a adoção de uma dimensão da malha bastante reduzida nesta zona e na sua vizinhança (0.03 m). No caso em estudo, os dois parâmetros de entrada do modelo não têm impacto significativo nos resultados, ao contrário do domínio de cálculo que, tal como recomendado na literatura de referência, se deve iniciar (fronteira de entrada) a aproximadamente um comprimento de onda do pé da estrutura. Os resultados obtidos mostram que, em geral, o AMAZON subestima o valor medido do caudal médio galgado com erros relativos variáveis entre -91% e -49%; apenas para um caso o modelo sobrestima o caudal médio, com um erro relativo de 43%. Quando comparado com as formulações empíricas e semi-empíricas, a fórmula de Van der Meer & Bruce apresenta melhores aproximações aos caudais médios medidos que constam na base de dados do CLASH, seguida da fórmula de Goda e dos resultados do modelo AMAZON, embora estes dois últimos apresentem valores bastante próximos. Assim, uma vez que o modelo está em constante desenvolvimento, espera-se que no futuro seja uma ferramenta mais poderosa. Contudo, enquanto não se fizerem melhorias no modelo e/ou não se estender a outros ensaios a análise feita no âmbito desta dissertação, os resultados sugerem que não há vantagem na sua utilização face às formulações empíricas e semi-empíricas disponíveis, tendo também em conta o significativo tempo computacional exigido para executar o AMAZON com a dimensão da malha escolhida.

The human rights dilemma : an east-west encounter : Germany and China in 1996 /

Conflicts over human rights in relations between East Asia and the West have increased since the end of the Cold War. Western governments express concern about human rights standards in East Asian countries. In the East, these expressions have been perceived as interference in internal affairs. Due to dramatic economic development, East Asian nations recently have gained in pride and self-confidence as global actors. Such development is observed with suspicion in the West. Concerned about the decline of global U.S. influence, some American scholars have re-invented the notion of "culture" to point at an alleged East Asian threat. Also East Asian statesmen use the cultural argument by claiming the existence of so-called 'Asian values', which they allege are the key to Eastern economic success. This thesis argues that issues of human rights in East-West relations are not only a consequence of well-intended concern by Western governments regarding the human rights and welfare of the citizens of East Asian nations, but are in fact dominated by and used as a pawn in interplay with more complicated questions of global power and economic relations between East and West. The thesis reviews the relevance of culture in East-West relations. In the West, particularly Samuel P. Huntington with his prediction of the Clash of Civilizations stands out. Singapore's Lee Kuan Yew has been very vocal on the Eastern side. Whereas the West tries to cope with its decrease of global influence, after hundreds of years under Western hegemonism, the East believes in an Asian way of development without interference form the West. Most of this dispute revolves around the issue of human rights. The West claims the universality of rights which in fact emphasizes political and civil rights. Western countries critizise poor human rights standards in East Asia. The East, in return, accuses the West of hypocritical policies that seek global dominance. East Asian governments assert that due to a different stage of development they have to stress first their rights to development in order to assure stability. In particular, China argues this way. The country's leadership, however, shows concern about human rights and has already improved its human rights record over the past years. This thesis analyses the dispute over human rights in a case study on Germany and China. Both countries have a mutual interest in trade relations which has conflicted with Germany's criticism of China's problematic human rights record. In 1996, the two countries clashed after the German parliament passed a resolution condemning China's treatment of Tibet. This caused a lot of damage to the Chinese-German relationship which in the course of the year went back to normality. In the light of these frictions a German human rights policy that focuses on unspectacular grass-roots support of China, for example in strengthening China's legal system, would be preferable. Such co-operation must be based on mutual respect.