Visible Volume: a Robust Measure for Protein Structure Characterization

We propose a new characterization of protein structure based on the natural tetrahedral geometry of the β carbon and a new geometric measure of structural similarity, called visible volume. In our model, the side-chains are replaced by an ideal tetrahedron, the orientation of which is fixed with respect to the backbone and corresponds to the preferred rotamer directions. Visible volume is a measure of the non-occluded empty space surrounding each residue position after the side-chains have been removed. It is a robust, parameter-free, locally-computed quantity that accounts for many of the spatial constraints that are of relevance to the corresponding position in the native structure. When computing visible volume, we ignore the nature of both the residue observed at each site and the ones surrounding it. We focus instead on the space that, together, these residues could occupy. By doing so, we are able to quantify a new kind of invariance beyond the apparent variations in protein families, namely, the conservation of the physical space available at structurally equivalent positions for side-chain packing. Corresponding positions in native structures are likely to be of interest in protein structure prediction, protein design, and homology modeling. Visible volume is related to the degree of exposure of a residue position and to the actual rotamers in native proteins. In this article, we discuss the properties of this new measure, namely, its robustness with respect to both crystallographic uncertainties and naturally occurring variations in atomic coordinates, and the remarkable fact that it is essentially independent of the choice of the parameters used in calculating it. We also show how visible volume can be used to align protein structures, to identify structurally equivalent positions that are conserved in a family of proteins, and to single out positions in a protein that are likely to be of biological interest. These properties qualify visible volume as a powerful tool in a variety of applications, from the detailed analysis of protein structure to homology modeling, protein structural alignment, and the definition of better scoring functions for threading purposes.

A Spectrum of TCP-friendly Window-Based Congestion Control Algorithms

The increasing diversity of Internet application requirements has spurred recent interest in transport protocols with flexible transmission controls. In window-based congestion control schemes, increase rules determine how to probe available bandwidth, whereas decrease rules determine how to back off when losses due to congestion are detected. The control rules are parameterized so as to ensure that the resulting protocol is TCP-friendly in terms of the relationship between throughput and loss rate. This paper presents a comprehensive study of a new spectrum of window-based congestion controls, which are TCP-friendly as well as TCP-compatible under RED. Our controls utilize history information in their control rules. By doing so, they improve the transient behavior, compared to recently proposed slowly-responsive congestion controls such as general AIMD and binomial controls. Our controls can achieve better tradeoffs among smoothness, aggressiveness, and responsiveness, and they can achieve faster convergence. We demonstrate analytically and through extensive ns simulations the steady-state and transient behavior of several instances of this new spectrum.

Specification of optimum holistic building environmental and energy performance information to support informed decision making

Political drivers such as the Kyoto protocol, the EU Energy Performance of Buildings Directive and the Energy end use and Services Directive have been implemented in response to an identified need for a reduction in human related CO2 emissions. Buildings account for a significant portion of global CO2 emissions, approximately 25-30%, and it is widely acknowledged by industry and research organisations that they operate inefficiently. In parallel, unsatisfactory indoor environmental conditions have proven to negatively impact occupant productivity. Legislative drivers and client education are seen as the key motivating factors for an improvement in the holistic environmental and energy performance of a building. A symbiotic relationship exists between building indoor environmental conditions and building energy consumption. However traditional Building Management Systems and Energy Management Systems treat these separately. Conventional performance analysis compares building energy consumption with a previously recorded value or with the consumption of a similar building and does not recognise the fact that all buildings are unique. Therefore what is required is a new framework which incorporates performance comparison against a theoretical building specific ideal benchmark. Traditionally Energy Managers, who work at the operational level of organisations with respect to building performance, do not have access to ideal performance benchmark information and as a result cannot optimally operate buildings. This thesis systematically defines Holistic Environmental and Energy Management and specifies the Scenario Modelling Technique which in turn uses an ideal performance benchmark. The holistic technique uses quantified expressions of building performance and by doing so enables the profiled Energy Manager to visualise his actions and the downstream consequences of his actions in the context of overall building operation. The Ideal Building Framework facilitates the use of this technique by acting as a Building Life Cycle (BLC) data repository through which ideal building performance benchmarks are systematically structured and stored in parallel with actual performance data. The Ideal Building Framework utilises transformed data in the form of the Ideal Set of Performance Objectives and Metrics which are capable of defining the performance of any building at any stage of the BLC. It is proposed that the union of Scenario Models for an individual building would result in a building specific Combination of Performance Metrics which would in turn be stored in the BLC data repository. The Ideal Data Set underpins the Ideal Set of Performance Objectives and Metrics and is the set of measurements required to monitor the performance of the Ideal Building. A Model View describes the unique building specific data relevant to a particular project stakeholder. The energy management data and information exchange requirements that underlie a Model View implementation are detailed and incorporate traditional and proposed energy management. This thesis also specifies the Model View Methodology which complements the Ideal Building Framework. The developed Model View and Rule Set methodology process utilises stakeholder specific rule sets to define stakeholder pertinent environmental and energy performance data. This generic process further enables each stakeholder to define the resolution of data desired. For example, basic, intermediate or detailed. The Model View methodology is applicable for all project stakeholders, each requiring its own customised rule set. Two rule sets are defined in detail, the Energy Manager rule set and the LEED Accreditor rule set. This particular measurement generation process accompanied by defined View would filter and expedite data access for all stakeholders involved in building performance. Information presentation is critical for effective use of the data provided by the Ideal Building Framework and the Energy Management View definition. The specifications for a customised Information Delivery Tool account for the established profile of Energy Managers and best practice user interface design. Components of the developed tool could also be used by Facility Managers working at the tactical and strategic levels of organisations. Informed decision making is made possible through specified decision assistance processes which incorporate the Scenario Modelling and Benchmarking techniques, the Ideal Building Framework, the Energy Manager Model View, the Information Delivery Tool and the established profile of Energy Managers. The Model View and Rule Set Methodology is effectively demonstrated on an appropriate mixed use existing ‘green’ building, the Environmental Research Institute at University College Cork, using the Energy Management and LEED rule sets. Informed Decision Making is also demonstrated using a prototype scenario for the demonstration building.

Thomas Davis's education policies: theory and practice

This thesis explores the education policies of Thomas Davis. On the eve of the Great Famine Ireland was economically impoverished and politically dependent. The Irish people had a subservient mentality, were mainly uneducated and were unaware of their potential. He believed that education would develop a self-reliant, self-sufficient people; it would create a new generation of leaders and citizens necessary to transform Ireland into a prosperous, independent nation. This thesis explores his education philosophy which was political in orientation; he called for reform of university education so that it would educate leaders who were knowledgeable, patriotic and responsible. He formulated a curriculum which consisted of knowledge that would have direct use and application in public life; his curriculum included moral philosophy, oratory, philological studies and history. His contribution to the debate on the Queens Colleges bill, 1845, is explored including his public disagreement with Daniel O’Connell on the principle of multi-denominational education. This work also examines his policies on learning methodologies and teaching methods. It provides details of his thoughts on learning by experience, by observation, book learning and learning in the home. It focuses on the deficiencies evident in the system of teaching and learning that operated in Trinity College Dublin and it provides an analysis of his preferred method of instruction: Lyceum teaching. This thesis also explores his national curriculum in history and Irish culture which was designed to forge a sense of national identity, to win support for repeal and to develop the principle of nationality. He formulated a national curriculum to counteract the absence of national knowledge in the state schools, to provide the people with a positive self-image and ultimately to empower them to reclaim Ireland and to develop it. Davis knew the power of education and he used it as an instrument of political and social change.

Alcohol income and health: a complicated but desirable mix

The aim of this thesis is to examine if a difference exists in income for different categories of drinkers in Ireland using the 2007 Slán data set. The possible impact of alcohol consumption on health status and health care utilisation is also examined. Potential endogeneity and selection bias is accounted for throughout. Endogeneity is where an independent variable included in the model is determined within the context of the model (Chenhall and Moers, 2007). An endogenous relationship between income and alcohol and between health and alcohol is accounted for by the use of separate income equations and separate health status equations for each category of drinker similar to what was done in previous studies into the effects of alcohol on earnings (Hamilton and Hamilton, 1997; Barrett, 2002). Sample selection bias arises when a sector selection is non-random due to individuals choosing a particular sector because of their personal characteristics (Heckman, 1979; Zhang, 2004). In relation to alcohol consumption, selection bias may arise as people may select into a particular drinker group due to the fact that they know that by doing so it will not have a negative effect on their income or health (Hamilton and Hamilton, 1997; Di Pietro and Pedace, 2008; Barrett, 2002). Selection bias of alcohol consumption is accounted for by using the Multinomial Logit OLS Two Step Estimate as proposed by Lee (1982), which is an extension of the Heckman Probit OLS Two Step Estimate. Alcohol status as an ordered variable is examined and possible methods of estimation accounting for this ordinality while also accounting for selection bias are looked at. Limited Information Methods and Full Information Methods of estimation of simultaneous equations are assessed and compared. Findings show that in Ireland moderate drinkers have a higher income compared with abstainers or heavy drinkers. Some studies such as Barrett (2002) argue that this is as a consequence of alcohol improving ones health, which in turn can influence ones productivity which may ultimately be reflected in earnings, due to the fact that previous studies have found that moderate levels of alcohol consumption are beneficial towards ones health status. This study goes on to examine the relationship between health status and alcohol consumption and whether the correlation between income and the consumption of alcohol is similar in terms of sign and magnitude to the correlation between health status and the consumption of alcohol. Results indicate that moderate drinkers have a higher income than non or heavy drinkers, with the weekly household income of moderate drinkers being €660.10, non drinkers being €546.75 and heavy drinkers being €449.99. Moderate Drinkers also report having a better health status than non drinkers and a slightly better health status than heavy drinkers. More non-drinkers report poor health than either moderate or heavy drinkers. As part of the analysis into the effect of alcohol consumption on income and on health status, the relationship between other socio economic variables such as gender, age, education among others, with income, health and alcohol status is examined.

Leadership, fairness and gender: a practitioner's perspective

This Portfolio of Exploration outlines the course of learning by a practitioner on a personal leadership journey. It constructs a functional examination of ideas around leadership. It explores the belief system which underpins leadership practice and it also explores to what extent the increased participation of women can lead to a qualitatively different type of leadership. Different models of leadership are explored to find the model which can best fit with the author’s perception of leadership. The Women’s Intercultural Leadership Model is discussed. This model conceptualises leadership as the envisioning of oneself and others as potential leaders. It seeks to promote that recognition whilst at the same time encouraging personal transformation. The promotion of a values based leadership is examined. The value of fairness is examined as an element of functional leadership. The extent to which increasing the number of women in leadership can lead to a qualitatively different type of leadership is explored. Drucker’s assertion that every practice rests on theory is used to unearth the underlying assumptions of this reflective practitioner doctorate. Kegan’s Theory of Adult Mental Development and Subject-Object separation is used to explicitly examine knowledge construction. Myers Briggs Type Indicator (MBTI) and Assumption/Commitment/Behaviour/Outcome (ACBO) template are used to promote practice change.

Essays on Vietnam’s Financial Reforms: Foreign Exchange Statistics and Evidence of Long-Run Equilibrium

In this paper, we examine exchange rates in Vietnam’s transitional economy. Evidence of long-run equilibrium are established in most cases through a single co-integrating vector among endogenous variables that determine the real exchange rates. This supports relative PPP in which ECT of the system can be combined linearly into a stationary process, reducing deviation from PPP in the long run. Restricted coefficient vectors ß’ = (1, 1, -1) for real exchange rates of currencies in question are not rejected. This empirics of relative PPP adds to found evidences by many researchers, including Flre et al. (1999), Lee (1999), Johnson (1990), Culver and Papell (1999), Cuddington and Liang (2001). Instead of testing for different time series on a common base currency, we use different base currencies (USD, GBP, JPY and EUR). By doing so we want to know the whether theory may posit significant differences against one currency? We have found consensus, given inevitable technical differences, even with smallerdata sample for EUR. Speeds of convergence to PPP and adjustment are faster compared to results from other researches for developed economies, using both observed and bootstrapped HL measures. Perhaps, a better explanation is the adjustment from hyperinflation period, after which the theory indicates that adjusting process actually accelerates. We observe that deviation appears to have been large in early stages of the reform, mostly overvaluation. Over time, its correction took place leading significant deviations to gradually disappear.

Superoxide dismutase mimics: chemistry, pharmacology, and therapeutic potential.

Oxidative stress has become widely viewed as an underlying condition in a number of diseases, such as ischemia-reperfusion disorders, central nervous system disorders, cardiovascular conditions, cancer, and diabetes. Thus, natural and synthetic antioxidants have been actively sought. Superoxide dismutase is a first line of defense against oxidative stress under physiological and pathological conditions. Therefore, the development of therapeutics aimed at mimicking superoxide dismutase was a natural maneuver. Metalloporphyrins, as well as Mn cyclic polyamines, Mn salen derivatives and nitroxides were all originally developed as SOD mimics. The same thermodynamic and electrostatic properties that make them potent SOD mimics may allow them to reduce other reactive species such as peroxynitrite, peroxynitrite-derived CO(3)(*-), peroxyl radical, and less efficiently H(2)O(2). By doing so SOD mimics can decrease both primary and secondary oxidative events, the latter arising from the inhibition of cellular transcriptional activity. To better judge the therapeutic potential and the advantage of one over the other type of compound, comparative studies of different classes of drugs in the same cellular and/or animal models are needed. We here provide a comprehensive overview of the chemical properties and some in vivo effects observed with various classes of compounds with a special emphasis on porphyrin-based compounds.

C. G. Jung and literary theory: the challenge from fiction

C.G. Jung and Literary Theory remedies a significant omission in literary studies by doing for Jung and poststructuralist literary theories what has been done extensively for Freud, Lacan and post-Freudian psychoanalysis. This work represents a complete departure from traditional Jungian literary criticism. Instead, radically new Jungian literary theories are developed of deconstruction, feminist theory, gender and psyche, the body and sexuality, spirituality, postcolonialism, historicism and reader-response. As well as linking Jung to the work of Derrida, Kristeva and Irigaray, the book traces contentious occult, cultural and political narratives in Jung's career. It contains a chapter on Jung and fascism in a literary context. [From the Publisher]

Evaluation of extended training for general practice in Northern Ireland: qualitative study.

Objective To evaluate participants' perceptions of the impact on them of an additional six months' training beyond the standard 12 month general practice vocational training scheme. Design Qualitative study using focus groups. Setting General practice vocational training in Northern Ireland. Participants 13 general practitioner registrars, six of whom participated in the additional six months' training, and four trainers involved in the additional six months' training. Main outcome measures: Participants' views about their experiences in 18 month and 12 month courses. Results Participants reported that the 12 month course was generally positive but was too pressurised and focused on examinations, and also that it had a negative impact on self care. The nature of the learning and assessment was reported to have left participants feeling averse to further continuing education and lacking in confidence. In contrast, the extended six month component was reported to have restimulated learning by focusing more on patient care and promoting self directed learning. It developed confidence, promoted teamwork, and gave experience of two practice contexts, and was reported as valuable by both ex-registrars and trainers. However, both the 12 and 18 month courses left participants feeling underprepared for practice management and self care. Conclusions 12 months' training in general practice does not provide doctors with the necessary competencies and confidence to enter independent practice. The extended period was reported to promote greater professional development, critical evaluation skills, and orientation to lifelong learning but does not fill all the gaps.

Contratos públicos adjudicados a sociedades cooperativas en el País Vasco entre 2010 y 2012

La Contratación Pública constituye una fuente muy importante de la demanda de bienes y servicios, especialmente en la Comunidad Autónoma del País Vasco en donde el Gobierno Autonómico, también llamado la Administración General Vasca, desarrolla un papel capital como impulsor de dicha contratación pública. Por otro lado, la Economía Social, y especialmente el movimiento cooperativo, tiene en ese mismo ámbito geográfico un papel de gran peso en el conjunto de la Economía Vasca, por sus cifras de empleo y aportación al PIB, así como por tradición y arraigo social. Cabe preguntarse en tal caso, cuál es el papel que desempeñan las cooperativas en la Contratación Pública en aquella Comunidad Autónoma, cómo y cuáles son los contratos de los que resultan adjudicatarias, qué importes suponen esos contratos para las cuentas públicas y, en definitiva, si su papel de adjudicatarias se corresponde con el que desempeñan en el conjunto de la Economía Vasca. Del examen de los contratos publicados en el Perfil del Contratante del Gobierno Vasco, se obtienen datos suficientes que, una vez procesados y analizados, se visualizan en tablas y porcentajes que constituyen la base de un diagnóstico que responde a las preguntas planteadas y evidencia la situación de debilidad de las cooperativas en el campo de la contratación pública vasca.

Experiencia colaborativa de enseñanza y aprendizaje entre estudiantes de diferentes ámbitos universitarios. Narrativa en torno a los Desayunos Donostia-Barcelona

El texto presenta una experiencia socioconstruccionista que une el trabajo entre estudiantes de Bellas Artes de la Universidad de Barcelona y de Magisterio de la Universidad del País Vasco. Un trabajo colaborativo entre docentes y estudiantes que conllevó compartir conocimientos y saberes a través del uso de nuevas tecnologías de la información y la comunicación (Skype y Blogs). El foco del artículo está situado en las relaciones de enseñanza y aprendizaje propias y singulares de una experiencia concreta, y en lo que se deriva de ello en el desarrollo de identidades de discentes y docentes; en esta línea, surgieron temas vinculados con: las posicionamientos emergentes, los modos de colocarse en los espacios de aprendizaje, las formas de relacionarse con los conocimientos, resistencias y potenciales del uso de nuevas tecnologías, etc. El texto está articulado en dos partes: una primera en la que brevemente se muestra el anclaje teórico que sustentó el trabajo (la investigación narrativa, y el trabajo educativo basado en Leaning by Desing); y una segunda parte que, llevando por título Desayunos Donostia–Barcelona y con una retórica basada en la novela de ficción, presenta experiencias significativas que hablan de los encuentros entre estudiantes y docentes. Dichas experiencias se inscriben dentro de las actividades de los grupos de innovación docente Indaga-t (2010PID-UB/33) y Elkarrikertuz (IT433-10), y es el resultado de trabajos colaborativos entre docentes e investigadores miembros de los mismos.El texto, que parte de la relación entre los grupos de innovación Indaga-t (2010PID-UB/33) y Elkarrikertuz (IT433-10), muestra una experiencia de colaboración que permite a los estudiantes establecer puentes entre diferentes comunidades y entre dos lugares de aprendizaje supuestamente alejados como son las facultades de Bellas Artes y Magisterio. Además nos ha ofrecido la oportunidad de construir experiencias de aprendizaje donde hemos aprendido a trabajar de un modo colaborativo entre docentes y estudiantes.

Evidence That Interspecies Polymorphism in the Human and Rat Cholecystokinin Receptor-2 Affects Structure of the Binding Site for the Endogenous Agonist Cholecystokinin

The cholecystokinin (CCK) receptor-2 exerts very important central and peripheral functions by binding the neuropeptides cholecystokinin or gastrin. Because this receptor is a potential therapeutic target, great interest has been devoted to the identification of efficient antagonists. However, interspecies genetic polymorphism that does not alter cholecystokinin-induced signaling was shown to markedly affect activity of synthetic ligands. In this context, precise structural study of the agonist binding site on the human cholecystokinin receptor-2 is a prerequisite to elucidating the molecular basis for its activation and to optimizing properties of synthetic ligands. In this study, using site-directed mutagenesis and molecular modeling, we delineated the binding site for CCK on the human cholecystokinin receptor-2 by mutating amino acids corresponding to that of the rat homolog. By doing so, we demonstrated that, although resembling that of rat homolog, the human cholecystokinin receptor-2 binding site also displays important distinct structural features that were demonstrated by susceptibility to several point mutations (F120A, Y189A, H207A). Furthermore, docking of CCK in the human and rat cholecystokinin receptor-2, followed by dynamic simulations, allowed us to propose a plausible structural explanation of the experimentally observed difference between rat and human cholecystokinin-2 receptors.

Covenanter Politics: Evangelicalism, Political Liberalism and Ulster Presbyterians, 1798-1914

Historians of Ireland have devoted considerable attention to the Presbyterian origins of modern Irish republicanism in the 1790s and their overwhelming support for the Union with Great Britain in the 1880s. On the one hand, it has been argued that conservative politics came to dominate nineteenth-century Presbyterianism in the form of Henry Cooke who combined conservative evangelical religion with support for the established order. On the other hand, historians have long acknowledged the continued importance of liberal and radical impulses amongst Presbyterians. Few historians of the nineteenth century have attempted to bring these two stories together and to describe the relationship between the religion and politics of Presbyterians along the lines suggested by scholars of Presbyterian radicalism in the last quarter of the eighteenth century. This article argues that a distinctive form of Presbyterian evangelicalism developed in the nineteenth century that sought to bring the denomination back to the theological and spiritual priorities of seventeenth-century Scottish and Irish Presbyterianism. By doing so, it encouraged many Presbyterians to get involved in movements for reform and liberal politics. Supporters of ‘Covenanter Politics’ utilised their denominational principles and traditions as the basis for political involvement and as a rhetoric of opposition to Anglican privilege and Catholic tyranny. These could be the prime cause of Presbyterian opposition to the infringement of their rights, such as the marriage controversy and the Disruption of the Church of Scotland in the early 1840s, and they could also be employed as a language of opposition in response to broader social and political developments, such as the demands for land reform stimulated by the agricultural depression that accompanied the Famine. Despite their opposition to ascendancy, however, the Covenanter Politics of Presbyterian Liberals predisposed them towards pan-protestant unionism against the threat of ‘Rome Rule’.

Correlation Rotation Linear Precoding for MIMO Broadcast Communications

A simple linear precoding technique is proposed for multiple input multiple output (MIMO) broadcast systems using phase shift keying (PSK) modulation. The proposed technique is based on the fact that, on an instantaneous basis, the interference between spatial links in a MIMO system can be constructive and can contribute to the power of the useful signal to improve the performance of signal detection. In MIMO downlinks this co-channel interference (CCI) can be predicted and characterised prior to transmission. Contrary to common practice where knowledge of the interference is used to eliminate it, the main idea proposed here is to use this knowledge to influence the interference and benefit from it, thus gaining advantage from energy already existing in the communication system that is left unexploited otherwise. The proposed precoding aims at adaptively rotating, rather than zeroing, the correlation between the MIMO substreams depending on the transmitted data, so that the signal of interfering transmissions is aligned to the signal of interest at each receive antenna. By doing so, the CCI is always kept constructive and the received signal to interference-plus-noise ratio (SINR) delivered to the mobile units (MUs) is enhanced without the need to invest additional signal power per transmitted symbol at the MIMO base station (BS). It is shown by means of theoretical analysis and simulations that the proposed MIMO precoding technique offers significant performance and throughput gains compared to its conventional counterparts.