Neural Network and Bioinformatic Methods for Predicting HIV-1 Protease Inhibitor Resistance

This article presents a new method for predicting viral resistance to seven protease inhibitors from the HIV-1 genotype, and for identifying the positions in the protease gene at which the specific nature of the mutation affects resistance. The neural network Analog ARTMAP predicts protease inhibitor resistance from viral genotypes. A feature selection method detects genetic positions that contribute to resistance both alone and through interactions with other positions. This method has identified positions 35, 37, 62, and 77, where traditional feature selection methods have not detected a contribution to resistance. At several positions in the protease gene, mutations confer differing degress of resistance, depending on the specific amino acid to which the sequence has mutated. To find these positions, an Amino Acid Space is introduced to represent genes in a vector space that captures the functional similarity between amino acid pairs. Feature selection identifies several new positions, including 36, 37, and 43, with amino acid-specific contributions to resistance. Analog ARTMAP networks applied to inputs that represent specific amino acids at these positions perform better than networks that use only mutation locations.

Becoming a CEO: an exploration of the theory and practice of effective organisational leadership

This Thesis is an exploration of potential enhancement in effectiveness, personally, professionally and organisationally through the use of Theory as an Apparatus of Thought. Enhanced effectiveness was sought by the practitioner (Subject), while in transition to becoming Chief Executive of his organization. The introduction outlines the content and the structure of the University College Cork DBA. Essay One outlines what Theory is, what Adult Mental Development is and an exploration of Theories held in the Authors past professional practice. Immunity to change is also reflected on. Essay Two looks at the construct of the key Theories used in the Thesis. Prof. Robert Kegan’s Theory of Adult Mental Development was used to aid the generation of insight. The other key Theories used were The Theory of The Business, Theory of the Co‐operative and a Theory of Organisational Leadership. Essay Three explores the application of the key Theories in a professional setting. The findings of the Thesis were that the subject was capable of dealing with increased environmental complexity and uncertainty by using Theory as an Apparatus of Thought, which in turn enhanced personal, professional and organisational effectiveness. This was achieved by becoming more aware of the Theories held by the practitioner, the experiences from the application of those Theories, which then led to greater insight. The author also found that a detailed understanding of the Theory of the Business and a Theory of Leadership would support any new CEO in the challenging early part of their tenure.

On classical and other methods of discriminant analysis and estimation of log-odds

For two multinormal populations with equal covariance matrices the likelihood ratio discriminant function, an alternative allocation rule to the sample linear discriminant function when n1 ≠ n2 ,is studied analytically. With the assumption of a known covariance matrix its distribution is derived and the expectation of its actual and apparent error rates evaluated and compared with those of the sample linear discriminant function. This comparison indicates that the likelihood ratio allocation rule is robust to unequal sample sizes. The quadratic discriminant function is studied, its distribution reviewed and evaluation of its probabilities of misclassification discussed. For known covariance matrices the distribution of the sample quadratic discriminant function is derived. When the known covariance matrices are proportional exact expressions for the expectation of its actual and apparent error rates are obtained and evaluated. The effectiveness of the sample linear discriminant function for this case is also considered. Estimation of true log-odds for two multinormal populations with equal or unequal covariance matrices is studied. The estimative, Bayesian predictive and a kernel method are compared by evaluating their biases and mean square errors. Some algebraic expressions for these quantities are derived. With equal covariance matrices the predictive method is preferable. Where it derives this superiority is investigated by considering its performance for various levels of fixed true log-odds. It is also shown that the predictive method is sensitive to n1 ≠ n2. For unequal but proportional covariance matrices the unbiased estimative method is preferred. Product Normal kernel density estimates are used to give a kernel estimator of true log-odds. The effect of correlation in the variables with product kernels is considered. With equal covariance matrices the kernel and parametric estimators are compared by simulation. For moderately correlated variables and large dimension sizes the product kernel method is a good estimator of true log-odds.

Language legislation in Ireland and the United Kingdom: Exploring the gaps between theory and practice

The central objective in this thesis is to explore the gaps between the normative justifications advanced for language rights and language legislative protection and the effective realisation of those rights and legislative provisions in practice. This objective is achieved by examining the scope and application of language rights and legislative provisions within language legislation in Ireland and the United Kingdom. Drawing on Canadian jurisprudence advocating for language rights to be recognised as “purposeful”, the thesis considers the extent to which Ireland and the United Kingdom have limited the acceptance of positive obligations as they relate to the provision of language services in the public sphere. In arguing that language rights are distinct in nature, the thesis suggests that in order for language rights to be effectively realised, an approach to language rights and language legislation more generally must be underpinned by a substantive vision of equality, otherwise language rights and legislative provisions merely amount to symbolic recognition and vacuous rhetoric as opposed to being substantive and enabling rights and provisions. Having said that, the thesis also recognises and elucidates the practical difficulties that arise in the realisation of language rights and language legislative provisions and in doing so seeks to stimulate further dialogue about the nature and limits of language rights and language legislation.

Non-product related environmental process and production methods (NPR-PPMs): a view from international trade law and international environmental governance

The primary aim of this thesis is to analyse legal and governance issues in the use of Environmental NPR-PPMs, particularly those aiming to promote sustainable practices or to protect natural resources. NPR-PPMs have traditionally been thought of as being incompatible with the rules of the World Trade Organization (WTO). However, the issue remains untouched by WTO adjudicatory bodies. One can suggest that WTO adjudicatory bodies may want to leave this issue to the Members, but the analysis of the case law also seems to indicate that the question of legality of NPR-PPMs has not been brought ‘as such’ in dispute settlement. This thesis advances the argument that despite the fact that the legal status of NPR-PPMs remains unsettled, during the last decades adjudicatory bodies have been scrutinising environmental measures based on NPR-PPMs just as another expression of the regulatory autonomy of the Members. Though NPR-PPMs are regulatory choices associated with a wide range of environmental concerns, trade disputes giving rise to questions related to the legality of process-based measures have been mainly associated with the protection of marine wildlife (i.e., fishing techniques threatening or affecting animal species). This thesis argues that environmental objectives articulated as NPR-PPMs can indeed qualify as legitimate objectives both under the GATT and the TBT Agreement. However, an important challenge for the their compatibility with WTO law relate to aspects associated with arbitrary or unjustifiable discrimination. In the assessment of discrimination procedural issues play an important role. This thesis also elucidates other important dimensions to the issue from the perspective of global governance. One of the arguments advanced in this thesis is that a comprehensive analysis of environmental NPR-PPMs should consider not only their role in what is regarded as trade barriers (governmental and market-driven), but also their significance in global objectives such as the transition towards a green economy and sustainable patterns of consumption and production.

Modulational instabilities in passive cavities: theory and experiment

Les Houches workshop, September 28-October 2, 1998.

Economic theory and environmental sciences, a historic review : from physiocrats to institutionalists

p.57-70

Economic theory and environmental sciences, a historic review : from physiocrats to institutionalists

p.57-70

A survey of teaching and assessment methods employed in UK higher education programmes for HCI course

A survey of teaching and assessment methods employed in UK Higher Education programmes for Human-Computer Interaction (HCI) courses was conducted in April 2003. The findings from this survey are presented, and conclusions drawn.

Information Visualisation Theory and Practice

Participation in European Union research projects now requires the setting-up of a project website. This paper discusses the creation of the "Matrix" to facilitate the information visualisation of a project; experiments, data, and results, etc, i.e. information far beyond the promotional details of the website. The paper describes the theory of such an endeavour before proceeding to discuss the practical realities for this case study project. Finally, we consider any lessons that can be learnt from this real-world application.

Theory and practice of manual blood pressure management

This article outlines the process of taking a manual blood pressure measurement. The author suggests that it is a skill that nursing students should be using in clinical practice rather than relying on automated monitors.