GeNS : the genomic name server

Mestrado em Engenharia de Computadores e TelemáticaOs desenvolvimentos científicos vindo do campo da biologia molecular dependem em grande parte da capacidade de análise de resultados laboratoriais por parte de aplicações informáticas. Uma análise completa de uma experiência requer, tipicamente, o estudo simultâneo dos resultados obtidos a par com dados disponíveis em várias bases de dados públicas. Fornecer uma visão unificada deste tipo de dados tem sido um problema fundamental na investigação ao nível de bases de dados desde o aparecimento da Bioinformática. Esta dissertação apresenta o GeNS, um data warehouse híbrido com uma abordagem simples e inovadora que pretende resolver diversos problemas de integração de dados biológicos. ABSTRACT: The scientific achievements coming from molecular biology depend greatly on the capability of computational applications to analyze the laboratorial results. A comprehensive analysis of an experiment requires, typically, the simultaneous study of the obtained results with data that is available from distinct public databases. Being able to provide a unified view of this data has been a fundamental problem in database research since the dawn of Bioinformatics. This dissertation introduces GeNS, a hybrid data warehouse that presents a simple, yet innovative approach to address several biological data integration issues

Composição de serviços para aplicações biomédicas

Doutoramento em Engenharia InformáticaA exigente inovação na área das aplicações biomédicas tem guiado a evolução das tecnologias de informação nas últimas décadas. Os desafios associados a uma gestão, integração, análise e interpretação eficientes dos dados provenientes das mais modernas tecnologias de hardware e software requerem um esforço concertado. Desde hardware para sequenciação de genes a registos electrónicos de paciente, passando por pesquisa de fármacos, a possibilidade de explorar com precisão os dados destes ambientes é vital para a compreensão da saúde humana. Esta tese engloba a discussão e o desenvolvimento de melhores estratégias informáticas para ultrapassar estes desafios, principalmente no contexto da composição de serviços, incluindo técnicas flexíveis de integração de dados, como warehousing ou federação, e técnicas avançadas de interoperabilidade, como serviços web ou LinkedData. A composição de serviços é apresentada como um ideal genérico, direcionado para a integração de dados e para a interoperabilidade de software. Relativamente a esta última, esta investigação debruçou-se sobre o campo da farmacovigilância, no contexto do projeto Europeu EU-ADR. As contribuições para este projeto, um novo standard de interoperabilidade e um motor de execução de workflows, sustentam a sucesso da EU-ADR Web Platform, uma plataforma para realizar estudos avançados de farmacovigilância. No contexto do projeto Europeu GEN2PHEN, esta investigação visou ultrapassar os desafios associados à integração de dados distribuídos e heterogéneos no campo do varíoma humano. Foi criada uma nova solução, WAVe - Web Analyses of the Variome, que fornece uma coleção rica de dados de variação genética através de uma interface Web inovadora e de uma API avançada. O desenvolvimento destas estratégias evidenciou duas oportunidades claras na área de software biomédico: melhorar o processo de implementação de software através do recurso a técnicas de desenvolvimento rápidas e aperfeiçoar a qualidade e disponibilidade dos dados através da adopção do paradigma de web semântica. A plataforma COEUS atravessa as fronteiras de integração e interoperabilidade, fornecendo metodologias para a aquisição e tradução flexíveis de dados, bem como uma camada de serviços interoperáveis para explorar semanticamente os dados agregados. Combinando as técnicas de desenvolvimento rápidas com a riqueza da perspectiva "Semantic Web in a box", a plataforma COEUS é uma aproximação pioneira, permitindo o desenvolvimento da próxima geração de aplicações biomédicas.The demand for innovation in the biomedical software domain has been an information technologies evolution driver over the last decades. The challenges associated with the effective management, integration, analyses and interpretation of the wealth of life sciences information stemming from modern hardware and software technologies require concerted efforts. From gene sequencing hardware to pharmacology research up to patient electronic health records, the ability to accurately explore data from these environments is vital to further improve our understanding of human health. This thesis encloses the discussion on building better informatics strategies to address these challenges, primarily in the context of service composition, including warehousing and federation strategies for resource integration, as well as web services or LinkedData for software interoperability. Service composition is introduced as a general principle, geared towards data integration and software interoperability. Concerning the latter, this research covers the service composition requirements within the pharmacovigilance field, namely on the European EU-ADR project. The contributions to this area, the definition of a new interoperability standard and the creation of a new workflow-wrapping engine, are behind the successful construction of the EUADR Web Platform, a workspace for delivering advanced pharmacovigilance studies. In the context of the European GEN2PHEN project, this research tackles the challenges associated with the integration of heterogeneous and distributed data in the human variome field. For this matter, a new lightweight solution was created: WAVe, Web Analysis of the Variome, provides a rich collection of genetic variation data through an innovative portal and an advanced API. The development of the strategies underlying these products highlighted clear opportunities in the biomedical software field: enhancing the software implementation process with rapid application development approaches and improving the quality and availability of data with the adoption of the Semantic Web paradigm. COEUS crosses the boundaries of integration and interoperability as it provides a framework for the flexible acquisition and translation of data into a semantic knowledge base, as well as a comprehensive set of interoperability services, from REST to LinkedData, to fully exploit gathered data semantically. By combining the lightness of rapid application development strategies with the richness of its "Semantic Web in a box" approach, COEUS is a pioneering framework to enhance the development of the next generation of biomedical applications

18th-20th Century British Literature

Openly licensed anthology focused on the theme of 18th-20th Century British Literature. Contains Persuasion by Jane Austen; Wuthering Heights by Emily Brontë; Lady Audley’s Secret by M.E. Braddon; Middlemarch by George Eliot; A Passage to India by E.M. Forster; Jude the Obscure by Thomas Hardy; Pamela by Samuel Richardson; Carmilla by Joseph Sheridan Le Fanu

Functional biogeography: evaluating community assemblage patterns and ecosystem functioning in intertidal systems using trait-based approaches

Analyses of taxonomic diversity patterns within coastal systems has been critical in the development of the theory of biogeography. Increasing evidence, however, shows that the variety of functions that species perform in ecosystems (rather than their taxonomic identity) is a better predictor of the influence of the environment on the species. This information has been useful in predictive ecology leading to the development of trait-based approaches (TBA). Until the late 1970s, however, limited effort (particularly in marine systems) was channeled towards patterns in functional species traits and how they may be affected by changes in environmental gradients. Here, I mapped the functional biogeography of the South African coastline based on a suite of species' reproduction and development traits. Because species composition is one of the key tools used by zoogeographers to map species distribution patterns, I expected lower variability in trait composition within main biogeographic regions than in intervening transition zones based on the habitat templet theory and following the biomass ratio and limiting similarity hypotheses. In brief, the habitat templet theory proposes that “the habitat provides a templet upon which evolution forges species characteristics”, while the biomass ratio hypothesis assumes that the most abundant species traits determine ecosystem functioning. The limiting similarity hypothesis also sometimes referred to as the niche complementarity hypothesis, however, predicts that species can coexist if their niches complement one another. In light of the habitat being an evolutionary templet, abiotic and biotic habitat patterns were measured as nearshore SST and chlorophyll-a gradients, respectively. I expected the SST gradient to act as the stronger key filter of trait diversification because temperature is often considered the most influential environmental factor affecting species survival with seasonality of SST affecting the timing of spawning and along with food availability, possibly influencing fecundity. Functional trait data were thus compiled for macroinvertebrate species collected from fifty-two rocky shore sites from three main bioregions (east, south, and west) and two transition zones (south-west and south-east). Biological trait analysis and functional diversity indices were used to evaluate how traits related to species development and reproduction respond to temperature and chlorophyll -a (used as a proxy for food availability) gradients along the coastline. GLMM and hierarchical cluster analyses showed distinct patterns/shifts in SST and chlorophyll-a gradients across bioregions, with two main breaks in SST separating the east and south-east overlap (SEO) bioregions from the south, south-west overlap (SWO) and west bioregions. In contrast, chlorophyll-a exhibited three major breaks with the east, SEO–south–SWO, and west clustering independently of each other. The RLQ analysis (a type of co-inertia analysis) which simultaneously ordinates 3-matrix datasets [i.e., (environment × site[R]), (species × site[L]) and (species × traits [Q])] showed that the higher SST gradient on the east and SEO promoted higher abundance and biomass of simultaneous hermaphrodites while higher chlorophyll-a gradients on the SWO and west coasts strongly promoted reproductive maturity at larger-sizes. The combined fourth-corner analyses showed that the modalities within the development trait domain responding to chlorophyll-a gradients primarily included filter feeders, sessile and swimming species and also species living on the infratidal zone. In addition, the reproduction trait domain showed higher sensitivity and association to differences in chlorophyll-a and SST gradients than development traits. Overall, SST and chlorophyll-a gradients influenced the distribution of the most dominant traits as indicated by shifts in community-weighted mean trait values across bioregions. This suggests the importance of habitat filtering on coastal species reproduction. A separate study evaluating the influence of large-scale biogeographic effects vs the micro-scale biogenic habitat structure offered by coralline seaweeds across 24 sites revealed some notable effects of both factors on the diversity and abundance of macroalgal epifauna. There was a notable biogeographic influence on epifauna, with the SEO recording the highest epifaunal species richness and abundance, followed by the south coast, then the SWO and lastly the west coast. In addition, the total biomass gradient of the corallines followed a similar trend. The epifauna however, showed no host-specificity, illustrating that epifauna may not be species–centric as commonly assumed, and the higher diversity of epifaunal diversity may well be simply because those corallines are the available habitat within the sampled part of the coastline. Lastly, macroinvertebrate trait distribution on the South African coastline confirms that the habitat, particularly the biotic filter (in this case chl-a) provides a templet upon which evolution forges species traits. However, since temperature is a proxy for nutrient availability (cold upwelling brings nutrients), then temperature drives chlorophyll-a. Subsequently this means the abiotic component indirectly drives trait distribution by influencing the biotic environment (chl-a). For epifauna species, also, the coralline diversity and composition can also be regarded as a biotic filter influencing the epifaunal abundances and composition across different bioregions. Moreover, since temperature is regarded as a conservative trait in seaweeds, temperature tolerance defines the biogeographical boundaries of seaweeds, therefore temperature may be indirectly affecting epifauna abundances through coralline species diversity and biomass. In summary, considering the deterministic processes governing ecosystem functioning and community assemblage, the mass ratio and limiting similarity hypotheses showed complementary effects. Different bioregions provided variable support for these two hypotheses, but overall, the mass ratio hypothesis (weighted by species biomass) received stronger support and may be more meaningful to the interpretation of ecosystem functioning and persistence within rocky shore systems. Lastly, although, the SWO showed some of the characteristics of a subtraction zone based on the relatively low abundance, diversity, and biomass measures. Nonetheless, there was evidence of high functional redundancy across all other four bioregions. This suggests that in the context of development and reproduction traits, the rocky shore ecosystem along the SA coastline may be functionally stable at this stage.Thesis (PhD) -- Faculty of Science, Zoology and Entomology, 202

The use of law in feminist activism: a governmentality analysis of the legal answers to problems of transactional sex

In several forms of contemporary feminist discourse, the law is presented as both a vital and useful response to problems associated with transactional sex. Several critics have argued that this emphasis on the law as a useful response is theoretically naive and disconnected from the lived realities of sex workers. Such research has contended that, as a result of its over-reliance on the law, feminist activism has had deleterious effects and been co-opted by projects of (neo)liberal governmentality. This thesis aims to develop and complicate these insights. It investigates how feminist relationships with the use of law regulates the possibilities of its activism. The thesis specifically asks: How is the law rationalised to be useful by feminist activists? Do these rationalisations of law's utility affect the subjectivities, practices, and political objectives of feminist activism itself? Deploying a methodology based on Michel Foucault's governmentality and Sara Ahmed's recent work on 'use' the thesis analyses a diverse range of feminist activist writing over the past 50 years. Case studies considered by this research include: the feminist publication and collective Spare Rib; online expression from (neo)abolitionist feminist communities; and, the contrasting engagements with the use of human rights law by Sisters Uncut and Reclaim These Streets. This analysis finds that the use of law plays a key role in facilitating contemporary associations that are important to feminist practices. Specifically, it demonstrates how these relationships have encouraged the emergence of feminist expertise and practices of servile virtuosity, whereby activists display willingness to be governed and assessed as compatible with parochial standards of gender and sexual performance. As a result, relationships with the use of law are found to have extensively regulated and sustained limited forms of activism, that have historically closed off meaningful critique, disobedience, and the possibility of other socialities. However, the thesis also contends that alternative futures are actively pursued and made possible through recognising the importance of law’s use in efforts to be governed differently

Patchwork Someone: A Memoir, and Religious Memoir in a Secular Age: Critical Commentary

This thesis in Creative Writing comprises two parts. The memoir, Patchwork Someone, is a ‘coming of faith’ story that deals with themes of religious certainty and mental illness. It is set primarily in Hong Kong, in the period encompassing the region’s handover from British sovereignty back to China. The memoir recounts how, as a teenager engaged in a search for belonging, I encountered Evangelical Christianity, and found an allure in the church that was juxtaposed against the instability of mentally ill family members and my own experimentation with drugs. The memoir then describes a mental health crisis that followed more than a decade later, when, as a committed believer and church member, I had a serious incident of self-harming. Recovery follows, but the book departs from the classic conversion arc because it lacks an explicit conclusion and alludes, instead, to the value of negative capability. The accompanying critical work, Religious Memoir in a Secular Age, is a study of the influence of the Confessions of Saint Augustine on apparently non- religious contemporary life-writing. Although the Confessions is regularly cited as the first example of autobiographical writing, there has been little investigation into it by the creative writing community. This critical commentary seeks to address the shortage, and analyses how religious memoirists who strive for diverse audiences can gain insight from a close reading of the Confessions. It offers a brief history of religion in self-life writing, and identifies written forms of religious practices that are evidenced in the Confessions, namely prayer, confession, reflection and testimony. Contemporary articulations of these practices are identified in eight memoirs published between 1985 and 2016 for comparison. Regardless of the changing influence of religion in society, the urges that first prompted Augustine to write his memoir prevail, and continue to be expressed in contemporary literature

Abstracts from the 25th Fungal Genetics Conference

Abstracts from the 25th Fungal Genetics Conferenc

Christian Progress and American Myth: A Deep Cultural Analysis of Spatiality and Exceptionalism in Struggles over American Indian Lands

Although typically characterized in politico-economic, social, and environmental terms, land struggles involving American Indian communities can be more accurately and valuably characterized as deep culture conflicts over the problem of space. As scholars like Vine Deloria Jr. and Tink Tinker contend, a significant distinction can be noted between the traditional American Indian and White Western approaches to this problem regarding how human communities should relate to particular spatial locations. In short, while Indian peoples tend to situate their identities relative to clearly defined places or lands, individuals of European descent are inclined to subordinate spatial relations to temporal concerns. Considering this distinction in light of the United States’ particular context of power, this dissertation explores the connection between spatiality and faith in American Exceptionalism. I argue that the widespread Exceptionalist faith depends profoundly upon the perpetuation of a fundamental disorientation to space deep within the dominant culture. American Exceptionalism, as a particular discursive formation within the master narrative about America, functions to prevent local communities from meaningfully and relationally engaging the spaces in which they exist. It does so in part by shaping thought about American identity and history through a deceptive set of images of the land. Conversely, the cultural influence of a deeply embedded disorientation to space ensures that only those types of behavior which support Exceptionalism can be deemed logically acceptable and ethically proper. This largely unconscious cognitive-behavioral approach legitimizes and extends politico-economic hegemony, creating an oppressive feedback loop of privilege into which only those individuals deemed “American-enough” are enabled to enter. The feedback loop is sustained both deliberately and implicitly, as the privileged seek to protect their advantage and the marginalized are socialized not to question the claims of the master narrative. The illicit bond between spatial disorientation and Exceptionalist faith touches nearly every corner of American life. However, its complex nature is exposed perhaps most explicitly and thoroughly through struggles over American Indian lands, which demonstrate the intimate interconnection between environmental exploitation and the exploitation of those types of beings (both human and non-human) habitually classified as “Other.” Based firmly in the disciplinary realm of cultural studies and utilizing discursivesemiotic analysis as a primary methodological tool, the dissertation is advanced through a theoretical synthesis which illustrates the enduring influence of Western cultural mores and Christian theological values. The synthesis is built upon a two-level deconstruction of deep cultural symbols related to space. First, spatial cognition is considered in light of four well-known yet deceptive images which index how the land should be conceptualized. These four images include promised land, terra nullius (“uninhabited land”), frontier wilderness, and city upon a hill. Next, spatial behavior is investigated in relation to four broadly accepted themes which signify how the land should be treated. These themes are categorized as privilege, property, positivism, and progress. Finally, the theoretical synthesis is evaluated in light of three distinctive responses to the natural world present and active within the dominant culture–dominion, stewardship, and deep ecology–and three case studies involving historical struggles over Indian lands: Newe Sogobia (“Land of the People”) and the Western Shoshone of the Nevada region, Crandon Mine and the Sokaogon Ojibwe of northern Wisconsin, and the “Save San Onofre” campaign and the Acjachemen of southern California