A new pentameric structure of rotavirus NSP4 revealed by molecular replacement

The region spanning residues 95-146 of the rotavirus nonstructural protein NSP4 from the asymptomatic human strain ST3 has been purified and crystallized and diffraction data have been collected to a resolution of 2.6 angstrom. Several attempts to solve the structure by the molecular-replacement method using the available tetrameric structures of this domain were unsuccessful despite a sequence identity of 73% to the already known structures. A more systematic approach with a dimer as the search model led to an unexpected pentameric structure using the program Phaser. The various steps involved in arriving at this molecular-replacement solution, which unravelled a case of subtle variation between different oligomeric states unknown at the time of solving the structure, are presented in this paper.

Severe diffraction anisotropy, rotational pseudosymmetry and twinning complicate the refinement of a pentameric coiled-coil structure of NSP4 of rotavirus

The crystal structure of the region spanning residues 95-146 of the rotavirus nonstructural protein NSP4 from the asymptomatic human strain ST3 was determined at a resolution of 2.5 angstrom. Severe diffraction anisotropy, rotational pseudo-symmetry and twinning complicated the refinement of this structure. A systematic explanation confirming the crystal pathologies and describing how the structure was successfully refined is given in this report.

Los buques públicos y el derecho internacional contemporáneo : el caso de la “Fragata ARA Libertad”

Resumen: El Derecho del Mar constituye, históricamente, uno de los puntos sobresalientes en la evolución y actualidad del Derecho Internacional ya que, incluso, su aparición y gestación precede a los mismos Estados. En ese sentido, a partir de la denominada “batalla de los libros”, el mar ha sido objeto de arduos y permanentes debates que pueden reflejarse, casi en su totalidad, en la Tercera Conferencia de las Naciones Unidas sobre el Derecho del Mar, realizada entre 1973 y 1982. Sobre estas consideraciones, la propuesta del presente trabajo es analizar una de ellas, como lo es la inmunidad de los buques de guerra extranjeros durante su estadía en puertos de otros Estados. Si bien a priori la cuestión no se manifiesta como compleja, lo cierto es que a 200 años del Schooner Exchange, su debate ha reaparecido, especialmente, a partir del caso de la Fragata ARA Libertad. En razón de lo expuesto, comenzaremos con una breve conceptualización jurídica de los buques y su clasificación, para luego examinar el régimen de inmunidad que poseen los buques de guerra extranjeros y las características que presenta la relación entre éste y el Estado ribereño local. Posteriormente, consideraremos estos aspectos a la luz del caso referido para, finalmente, formular algunas reflexiones considerando todo lo analizado en su conjunto.

Obasan, by Joy Kogawa, and Alias Grace, by Margaret Atwood: fictional representations of Canadian identity and History

Esta dissertação investiga de que maneiras a representação do sujeito canadense pode ser encontrada em dois romances representativos da literatura canadense contemporânea: Obasan, de Joy Kogawa, e Alias Grace, de Margaret Atwood. Esta investigação também demonstra que a busca pela definição da identidade canadense tem sido tema constante e relevante da cultura deste país. A indefinição quanto ao que significa ser canadense também tem permeado a literatura canadense ao longo dos séculos, notadamente desde o século XIX. A fim de observar a representação literária da busca pela definição da identidade canadense, esta investigação aborda os conceitos relativos à representação de grupos subalternos tradicionalmente silenciados. A análise comparativa dos romances citados contempla a relação entre memória e trauma autobiográficos, assim como as semelhanças narrativas entre ficção e história. Esta investigação também verifica de que maneiras a literatura pós-moderna emprega documentação oficial, relatos históricos e dados (auto) biográficos a serviço da reescrita da história através da metaficção historiográfica

An assessment of scup (Stenotomus chrysops) and black sea bass (Centropristas striata) discards in the directed otter trawl fisheries in the Mid-Atlantic Bight

This study was undertaken to re-assess the level of scup (Stenotomus chrysops) discards by weight and to evaluate the effect of various codend mesh sizes on the level of scup discards in the winter-trawl scup fishery. Scup discards were high in directed scup tows regardless of codend mesh — typically one to five times the weight of landings. The weight of scup discards in the present study did not differ significantly from that recorded in scup-targeted tows in the NMFS observer database. Most discards were required as such by the 22.86 cm TL (total length) fish-size limit for catches. Mesh sizes ≤12.7 cm, including the current legal mesh size (11.43 cm) did not adequately filter out scup smaller than 22.86 cm. The median length of scup discards was about 19.83 cm TL. Lowering the legal size for scup from 22.86 to 19.83 cm TL would greatly reduce discard mortality. Scup discards were a small fraction (0.4%) of black sea bass (Centropristis striata) landings in blacksea-bass−targeted tows. The black sea bass fishery is currently regulated under the small-mesh fishery gearrestricted area plan in which fishing is prohibited in some areas to reduce scup mortality. Our study found no evidence to support the efficacy of this management approach. The expectations that discarding would increase disproportionately as the trip limit (limit [in kilograms] on catch for a species) was reached towards the end of the trip and that discards would increase when the trip limit was reduced from 4536 kg to 454 kg at the end of the directed fishing season were not supported. Trip limits did not significantly affect discard mortality.

Bottom simulating reflector and gas seepage in Okinawa Trough: Evidence of gas hydrate in an active back-arc basin

To look for gas hydrate, 22 multi-channel and 3 single-channel seismic lines on the East China Sea (ECS) shelf slope and at the bottom of the Okinawa Trough were examined. It was found that there was indeed bottom simulating reflector (BSR) occurrence, but it is very rare. Besides several BSRs, a gas seepage was also found. As shown by the data, both the BSR and gas seepage are all related with local geological structures, such as mud diapir, anticline, and fault-controlled graben-like structure. However, similar structural "anomalies" are quite common in the tectonically very active Okinawa Trough region, but very few of them have developed BSR or gas seepage. The article points out that the main reason is probably the low concentration of organic carbon of the sediment in this area. It was speculated that the rare occurrence of gas hydrates in this region is governed by structure-controlled fluid flow. Numerous faults and fractures form a network of high-permeability channels in the sediment and highly fractured igneous basement to allow fluid circulation and ventilation. Fluid flow in this tectonic environment is driven primarily by thermal buoyancy and takes place on a wide range of spatial scales. The fluid flow may play two roles to facilitate hydrate formation: to help gather enough methane into a small area and to modulate the thermal regime.

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.

Reasoning about trust, entrepreneurial services, and the virtual team

This Portfolio of Exploration (PoE) tracks a transformative learning developmental journey that is directed at changing meaning making structures and mental models within an innovation practice. The explicit purpose of the Portfolio is to develop new and different perspectives that enable the handling of new and more complex phenomena through self transformation and increased emotional intelligence development. The Portfolio provides a response to the question: ‘What are the key determinants that enable a Virtual Team (VT) to flourish where flourishing means developing and delivering on the firm’s innovative imperatives?’ Furthermore, the PoE is structured as an investigation into how higher order meaning making promotes ‘entrepreneurial services’ within an intra-firm virtual team, with a secondary aim to identify how reasoning about trust influence KGPs to exchange knowledge. I have developed a framework which specifically focuses on the effectiveness of any firms’ Virtual Team (VT) through transforming the meaning making of the VT participants. I hypothesized it is the way KGPs make meaning (reasoning about trust) which differentiates the firm as a growing firm in the sense of Penrosean resources: ‘inducement to expand and a limit of expansion’ (1959). Reasoning about trust is used as a higher order meaning-making concept in line with Kegan’s (1994) conception of complex meaning making, which is the combining of ideas and data in ways that transform meaning and implicates participants to find new ways of knowledge generation. Simply, it is the VT participants who develop higher order meaning making that hold the capabilities to transform the firm from within, providing a unique competitive advantage that enables the firm to grow.

Explorations in a meaning making system: Kerry as an entrepreneurial platform and the equine sector as a cluster

This Portfolio is about the changes that can be supported and achieved through transformational education that impacts on personal, professional and organisational levels. Having lived through an era of tremendous change over the second half of the twentieth century and into the twenty-first the author has a great drawing board to contemplate in the context of professional career experience as an engineer. The ability to engage in ‘subject-object’ separation is the means by which Kegan (1994, 2009) explains that transformation takes place and the Essays in this Portfolio aim to support and bring about such change. Exploration of aspects of ‘Kerry’ is the material selected to both challenge support change in the way of knowing from being subject to certain information and knowledge that to being able to consider it more objectively. The task of being able to distance judgement about the economy and economic development of Kerry was facilitated by various readings around of a number of key thinkers including Kegan, Drucker, Porter and Penrose. The central themes of Kerry or the potential for economic development are built into each Essay. Essay One focuses on reflections of Kerry life - on Kerry people within and without Kerry - and events as they affected understandings of how people related to and worked with one another. These reflections formed the basis for transformational goals identified which required a shift from an engineering mindset to encompass an economics-based view. In Essay Two knowledge of economic concepts is developed by exploring the writings of Drucker, Penrose, and Porter with pertinence to considering economic development generally, and for Kerry in particular in the form of an ‘entrepreneurial platform’. The concepts and theories were the basis of explorations presented in Essays Three and Four. Essay Three focuses on Kerry’s potential for economic development give its current economic profile and includes results from interviews with selected businesses. Essay Four is an exercise in the application of Porter’s ‘Cluster’ concept to the equine sector.

Inquiring into perspective transformation in university education

My Portfolio of Exploration tackles the difficult question as to whether adult mental development can be accelerated and if so how. Rooted in constructive-developmental ideas, adult mental development is explained as an evolutionary unfolding of human capability. Going beyond this I look at the possibility of advancing development as transformational growth in adulthood in the belief that a broader perspective leads to increased effectiveness in professional life. Initially I explored my own meaning making, to make sense of my experiences, knowledge, relationships and my own motivations. This exploration has provided me with a ‘developmental bridge’ between my current way of knowing and a new more enlightened way. I have come to view my way of making meaning in the world as an evolving and progressive sequence of emotional and cognitive development. Through the formation of new stretching experiences, increased self - awareness and reflection my previous perspective has been overtaken by a more complex form of being aware of myself, others and the world. I refer to this process of growth as transformation. As part of my own transformational work I have conducted an inquiry into transformational growth and learning in the early academic life of university undergraduates. The result shows how accelerated adult mental development can be achieved in an academic environment ably preparing students for the workplace. This new model of education is part of a truly unique and exciting model signalling ground-breaking change for the undergraduate experience. The overhaul of a traditional BA degree in Economics into a world-class transformational programme is discussed through-out my Portfolio. Central to my broadening awareness is the challenge and nurturing required to awaken the student’s ‘internal authority’ . This involves stimulating students to take ownership for their own thinking, steering them away from the passivity and complacency of thinking through the minds of others. In doing so, the ultimate aim of renewing the BA is to narrow the developmental ‘mismatch’ which exists for m any college students between them and the world of work, by encouraging and inviting them to take on the challenge of thinking independently. Mindfulness, awareness, and personal authority are treated with reverence throughout the exploration as I consider them core parts of the students engaging with development. Engagement is construed as an active and open-minded process of awareness involving planning and reviewing one’s own goals and performance, engaging in constructive feedback, reflection and new action. I conclude with a view that the journey of adult mental development is relentless and that undergraduate education represents a crucial beginning. The value and relevance of transformational education rooted in developmental principles provides a significant opportunity in advancing development and perspectives at the start of adult life.

Reflections on the transformation of my meaning making to support the organic growth of a firm

The objective of my Portfolio is to explore the working hypothesis that the organic growth of a firm is governed by the perspectives of individuals and such perspectives are governed by their meaning-making. The Portfolio presents explorations of the transformation of my meaning making and in adopting new practices to support the organic growth of a firm. I use the work of other theorists to transition my understanding of how the world works. This transition process is an essential tool to engage with and understand the perspectives of others and develop a mental capacity to “train one’s imagination to go visiting” (Arendt, 1982; p.43). The Portfolio, therefore, is primarily located in reflective research. Using Kegan’s (1994) approach to Adult Mental Development, and Sowell’s (2007) understanding of the visions which silently shape our thoughts I organise the developments of my meaning making around three transformation pillars of change. In pillar one I seek to transform an unthinking respect for authority and break down a blind pervasiveness of thought within my reasoning process arising from an instinct for attachment and support from others whom I trust. In pillar two I seek to discontinue using autocratic leadership and learn to use the thoughts and contributions of a wider team to make improved choices about uncertain future events. In pillar three I explore the use of a more reflective thinking framework to test the accuracy of my perceptions and apply a high level of integrity in my reasoning process. The transformation of my meaning making has changed my perspectives and in turn my preferred practices to support the organic growth of a firm. I identify from practice that a transformative form of leadership is far more effective that a transactional form of leadership to stimulate the trust and teamwork required to sustain the growth a firm. Creating an environment where one feels free to share thoughts and feelings with others is an essential tool to build a team to critique the thoughts of one other. Furthermore, the entrepreneurial wisdom to grow a firm must come from a wider team, located both inside and outside the boundaries of a firm. No individual or small team has the mental capacity to provide the entrepreneurship required to drive the organic growth of a firm. I address my Portfolio to leaders in organisations who have no considered framework on the best practices required to lead a social organisation. These individuals may have no sense of what they implicitly believe drives social causation and they may have no understanding if their meaning making supports or curtails the practices required to grow a firm. They may have a very limited capacity to think in a logical manner, with the result they are using guesses from their ‘gut’ to make poor judgements in the management of a firm.

The political and economic context of Keynes’s 1933 Finlay lecture: transforming a business practitioner’s ways of knowing

This thesis is structured in the format of a three part Portfolio of Exploration to facilitate transformation in my ways of knowing to enhance an experienced business practitioner’s capabilities and effectiveness. A key factor in my ways of knowing, as opposed to what I know, is my exploration of context and assumptions. By interacting with my cultural, intellectual, economic, and social history, I seek to become critically aware of the biographical, historical, and cultural context of my beliefs and feelings about myself. This Portfolio is not exclusively for historians of economics or historians of ideas but also for those interested in becoming more aware of how these culturally assimilated frames of reference and bundles of assumptions that influence the way they perceive, think, decide, feel and interpret their experiences in order to operate more effectively in their professional and organisational lives. In the first part of my Portfolio, I outline and reflect upon my Portfolio’s overarching theory of adult development; the writings of Harvard’s Robert Kegan and Columbia University’s Jack Mezirow. The second part delves further into how meaning-making, the activity of how one organises and makes sense of the world and how meaning-making evolves to different levels of complexity. I explore how past experience and our interpretations of history influences our understandings since all perception is inevitably tinged with bias and entrenched ‘theory-laden’ assumptions. In my third part, I explore the 1933 inaugural University College Dublin Finlay Lecture delivered by economist John Maynard Keynes. My findings provide a new perspective and understanding of Keynes’s 1933 lecture by not solely reading or relying upon the text of the three contextualised essay versions of his lecture. The purpose and context of Keynes’s original longer lecture version was quite different to the three shorter essay versions published for the American, British and German audiences.

A study of diet and health in the elderly; the gut microbiota as a source of bioactive agents

The global proportion of older persons is increasing rapidly. Diet and the intestinal microbiota independently and jointly contribute to health in the elderly. The habitual dietary patterns and functional microbiota components of elderly subjects were investigated in order to identify specific effector mechanisms. A study of the dietary intake of Irish community-dwelling elderly subjects showed that the consumption of foods high in fat and/or sugar was excessive, while consumption of dairy foods was inadequate. Elderly females typically had a more nutrient- dense diet than males and a considerable proportion of subjects, particularly males, had inadequate intakes of calcium, magnesium, vitamin D, folate, zinc and vitamin C. The association between dietary patterns, glycaemic index and cognitive function was also investigated. Elderly subjects consuming ‘prudent’ dietary patterns had better cognitive function compared to those consuming ‘Western’ dietary patterns. Furthermore, fully-adjusted regression models revealed that a high glycaemic diet was associated with poor cognitive function, demonstrating a new link between nutrition and cognition. An extensive screening study of the elderly faecal-derived microbiota was also undertaken to examine the prevalence of antimicrobial production by intestinal bacteria. A number of previously characterised bacteriocins were isolated (gassericin T, ABP-118, mutacin II, enterocin L-50 and enterocin P) in this study. Interestingly, a Lactobacillus crispatus strain was found to produce a potentially novel antimicrobial compound. Full genome sequencing of this strain revealed the presence of three loci which exhibited varying degrees of homology with the genes responsible for helveticin J production in Lb. helveticus. An additional study comparing the immunomodulatory capacity of ‘viable’ and ‘non-viable’ Bifidobacterium strains found that Bifidobacterium-fermented milks (BFMs) containing ‘non-viable’ cells could stimulate levels of IL-10 and TNF-α in a manner similar to those stimulated by BFMs containing ‘viable’ cells in vitro.

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.

Evolving perspectives on business and books: practitioner implications

The research subject of this Portfolio of Essays is my ‘apparatus of thought’ in the context of my professional development. I have examined theory and the application of theory to a professional life. I analyse how my use of theory has changed and enabled my professional development. Each of the three Essays takes a different perspective and applies the theories of adult mental development, business and firm growth as an analytical framework. Using Kegan’s theories of Adult Mental Development as an ‘apparatus of thought’, Essay One is my reflection on my professional development in the light of my training, education, and development. I describe how changes in my ‘apparatus of thought’, my meaning-making system, have enabled me to develop my professional practice. Exposure to the theories of Adult Mental Development have also enabled me to understand how my development has precipitated and necessitated my career changes. In Essay Two, moving from military aviation to book publishing was a major career change for me, enabled by a change in my meaning-making system. In the context of my professional development, I sought to change my practice so that I could make a more meaningful contribution to the firm. To achieve this, I directed my reading towards a deeper understanding of the nature of the firm and the impact of industrial change on the firm. Using the context of my professional environment in Essay Three, I show how my use of theory has developed. I describe how I sought to change working practices in the firm and discuss the impact this initiative had on my professional self. I use the ‘data of my experience’ to examine my theory of the business from a Penrosian perspective. The Penrosian perspective coupled with my exposure to theories of Adult Mental Development and the effects of a transformational education process enabled me to transition to a leadership role with an international online publisher.