All the World's a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health

The recent explosion of genetic and clinical data generated from tumor genome analysis presents an unparalleled opportunity to enhance our understanding of cancer, but this opportunity is compromised by the reluctance of many in the scientific community to share datasets and the lack of interoperability between different data platforms. The Global Alliance for Genomics and Health is addressing these barriers and challenges through a cooperative framework that encourages "team science" and responsible data sharing, complemented by the development of a series of application program interfaces that link different data platforms, thus breaking down traditional silos and liberating the data to enable new discoveries and ultimately benefit patients.

A revision of the polychaete family Nephtyidae, based on morphological and molecular data

A família Nephtyidae é uma das mais frequentes em habitats costeiros e marinhos de todo o mundo. São organismos errantes típicos de sedimentos arenosos e lodosos, ocorrendo frequentemente no domínio costeiro até 100 m de profundidade, e mais raramente em profundidades batiais e abissais. As primeiras espécies descritas foram o Nephtys caeca (Fabricius, 1780) e o N. ciliata (O. F. Müller, 1789), ambas atribuídas inicialmente ao género Nereis e posteriormente transferidas para o género Nephtys por Savigny, em 1818. A família Nephtyidae foi criada em 1851 por Grube para o género Nephtys Cuvier, 1817. No âmbito desta tese é feito um estudo taxonómico e filogenético da família Nephtyidae. O estudo filogenético inclui dados morfológicos e moleculares de 24 taxa representantes dos cinco géneros da família, Nephtys Cuvier, 1817, Aglaophamus Kinberg, 1866, Micronephthys (Friedrich, 1939), Inermonephtys Fauchald, 1967 e Dentinephtys Imajima e Takeda, 1987. A análise evidenciou dois grandes grupos correspondentes aos dois principais géneros, Aglaophamus e Nephtys. Duas espécies do género Nephtys (N. pulchra e N. australiensis) são transferidas para o género Aglaophamus, e consequentemente são propostas novas diagnoses para os géneros. O género Dentinephtys é sinonimizado com Nephtys e um novo género, Bipalponephtys, é descrito para acomodar as espécies Nephtys cornuta, N. danida e Micronephthys neotena. As relações filogenéticas entre os géneros são discutidas. Do estudo taxonómico resultou a revisão da família Nephtyidae para o Sul da Europa (entre o Canal da Mancha e o Mediterrâneo), com a descrição de uma nova espécie, Inermonephtys foretmontardoi. A espécie Micronephthys maryae é sinonimizada com M. stammeri. Para cada espécie são incluídas notas sobre a sua ecologia bem como a distribuição geográfica e batimétrica. São propostas novas diagnoses para os géneros do Sul da Europa bem como uma chave de identificação taxonómica para as espécies desta região. Após uma exaustiva revisão bibliográfica da família, e da observação de material museológico relativo a 44 espécies, foi compilada uma lista completa para a família de 128 espécies, distribuídas por cinco géneros (57 Nephtys, 53 Aglaophamus, sete Micronephthys, oito Inermonephtys e três Bipalponephtys), na qual são incluídas sinonímias e considerações taxonómicas para cada espécie. A espécie Nephtys serrata é sinonimizada com N. serratifolia. São apresentados as distribuições geográficas e batimétricas das diferentes espécies e notas sobre o seu habitat. São também incluídas tabelas de identificação com as principais características taxonómicas das espécies. O valor diagnóstico dos caracteres morfológicos é discutido. Vários problemas taxonómicos são realçados, indicando a necessidade de revisões adicionais para 23 espécies. Este trabalho realça a existência de vários problemas taxonómicos e filogenéticos dentro da família Nephtyidae, podendo ser considerado como a base para estudos futuros. Análises filogenéticas adicionais incluindo dados morfológicos e moleculares de um maior número de espécies vão certamente conduzir a uma melhor avaliação do estatuto e relações entre os géneros dentro da família.

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.

Hydrodynamic and sediment fluxes through the inlets of the Ria Formosa

Tese de dout., Ciências do Mar, da Terra e do Ambiente (Ciências do Mar-Oceanografia Física), Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2011

Exploring an uncommon host-parasite interaction to unveil the uniqueness of Perkinsus sp as a model organism

We report the exploration of some unique metabolic pathways in Perkinsus olseni a marine protist parasite, responsible to significant mortalities in mollusks, especially in bivalves all around the world. In Algarve, south of Portugal carpet shell clam Ruditapes decussatus mortalities can reach up to 70%, causing social and economic losses. The objective of studying those unique pathways, is finding new therapeutic strategies capable of controlling/eliminating P. olseni proliferation in clams. In that sense metabolic pathways, were explored, and drugs affecting these cycles were tested for activity. The first step involved the identification of the genes behind those pathways, the reconstitution of the main steps, and molecular characterization of those genes and later on, the identification of possible targets within the genes studied. Metabolic cycles were screened due to the fact of not being present in host or differ in a critical way, such as the following pathways: shikimate, MEP-­‐ isoprenoids, Leloir cycle for chitin production, purine biosynthesis (unique among protists), the de novo synthesis of folates (absent in metazoa) and some unique genes like, the alternative oxidase (a branch of respiratory chain) and the hypoxia sensor HPH. All those pathways were covered and possible chemical inhibition using therapeutic drugs was tested with positive results. The relation between the common host Ruditapes decussatus and P. olseni was also explored in a dimension not possible some years ago. With the accessibility to second generation sequencers and microarray analysis platforms, genes involved in host defense or parasite virulence and resistance to the host were deciphered, allowing aiming to new targets (mechanisms and pathways), offering new possibilities for the control of Perkinsus in close environments. The thousands of genes, generated by this work, sequenced and analyzed from this commercial valuable clam and for Perkinsus olseni will be an important and value tool for the scientific community, allowing a better understanding of host-­‐parasite interactions, promoting the usage of P. olseni as an emerging model for alveolata parasites.

Evaluation of the protective effect of Phlomis purpurea against Phytophthora cinnamomi in Fagaceae and of root metabolites involved

Tese de doutoramento, Ciências Agrárias (Proteção de Plantas), Faculdade de Ciência e Tecnologia, Universidade do Algarve, 2014

History of the World War due date card

This is a due date card for the book titled History of the World War, with stamped dates from 1939-1941.

Do Girls and Boys Perceive Themselves as Equally Engaged in School? The Results of an International Study from 12 Countries

This study examined gender differences in student engagement and academic performance in school. Participants included 3420 students (7th, 8th, and 9th graders) from Austria, Canada, China, Cyprus, Estonia, Greece, Malta, Portugal, Romania, South Korea, the United Kingdom, and the United States. The results indicated that, compared to boys, girls reported higher levels of engagement in school andwere rated higher by their teachers in academic performance. Student engagement accounted for gender differences in academic performance, but gender did not moderate the associations among student engagement, academic performance, or contextual supports. Analysis of multiple-group structural equation modeling revealed that perceptions of teacher support and parent support, but not peer support, were related indirectly to academic performance through student engagement. This partial mediation model was invariant across gender. The findings from this study enhance the understanding about the contextual and personal factors associated with girls' and boys' academic performance around the world.

Qualified exceptionalism: the US Congress in comparative perspective

The framers of the American Constitution devised a singular bicameral legislative body, which invested substantial power in both a broadly representative lower chamber and a second "deliberative" chamber that was both insulated from the voters and unrepresentative of the population as a whole. Until the early 20th Century, the singular U.S. Congress changed little, but with growing national responsibilities, it sought to construct organizational forms that could address a consistently stronger executive. Since the 1980s, the Congress has relied increasingly on stronger parties to organize its activities. This development, embraced in turn by Democrats and Republicans, has led to changes that have edged the Congress in the direction of parliamentary democracies. We conclude this analysis has real, but limited utility, as congressional party leaders continue to barter for votes and, in the context, of narrow chamber majorities, often rely heavily on presidential assistance on divisive issues that are important to their party brand. Yet, the traditional features of the American separated system - bicameralism, the committee systems, and the centrifugal forces emanating from diverse congressional districts, increasingly complex policy issues, and the fear of electoral retribution - also remain strong, and effectively constrain the influence of leaders.'Qualified exceptionalism' thus most aptly describes the contemporary American Congress, which remains 'exceptional,' but less than unique, as it responds to many of the same forces, in some of the same ways (e.g., strong parties), as do many other representative assemblies around the world.

Turning around the poorest neighbourhoods: learning the lessons from twenty years of neighbourhood-based regeneration strategies in England

In the past two decades governments in Britain have launched a series of initiatives designed to reduce the disparities between areas of affluence and deprivation. These initiatives were funded by central government and were delivered through a series of partnership boards operating at the neighbourhood level in areas with high levels of deprivation. Drawing on similar approaches in the US War on Poverty, the engagement of residents in the planning and delivery of projects was a major priority. This chapter draws on the national evaluations of three of these programmes in England: the Single Regeneration Budget, the New Deal for Communities and the Neighbourhood Management Pathfinders. The chapter begins by identifying the common characteristics of these programmes, known as area-based initiatives because they targeted areas of concentrated deprivation with a population of about 10,000 people each. It then goes on to discuss the three national programmes and summarises the main findings in relation to how far key indicators changed for the better. The final section sets out the ways in which policy objectives changed in 2010 after the election of a coalition government. This produced a shift to what was called the ‘Big Society’ where the rhetoric favoured a transfer of power away from central government towards the local, neighbourhood, level. This approach favoured self-help and a call to volunteering rather than channelling resources to the areas in greatest need. The chapter closes by reviewing the relatively modest achievements of this centralist, big-state approach to distressed neighbourhoods of 1990–2010.

The world without outside

The world is all that there is. In the world, ontology and epistemology coincide. The thing and the perspective are part of it, scale is ingested in its multiplicity, communication stops at the world's edge. By reading together Deleuze and Guattari's plane of immanence and Niklas Luhmann's proto-global concept of Weltgesellschaft (“world society”), I suggest a conceptualisation of the world as the materiality of the multiple spaces of creation in an insular, all-inclusive immanence. Deprived of an outside, the world pushes its own understanding of circumference through, first, the expansion of its own limits through the process of worlding, and, second, the multiplication of modes of material (self-)production through its process of othering. Thus, the world swells up from the inside and expands on both the material and the semantic level, producing a multiplicity of fractal microcosms. Issues of responsibility and justice arise that are intricately linked to the materiality of the world and take place in and between the various bodies and spaces of the world but without an overarching hierarchy or principle. This approach is a way of counteracting the all-pervasive Hegelian understanding of synthesis, arguing instead for a plenitude that brims with positivity and that can never become fully complete. The world remains its own infinite process of worlding.

Towards more sustainable urban forms in the city of Benghazi: a study of urban fragmentation at the neighbourhood level

Urban sprawl is a challenge to the sustainability of many cities around the world. Fragmented urban development and vacant land are widespread problems in many Arab cities (UN-Habitat, 2012) which are, according to Ben-Hamouch, mainly a result of inappropriate modern planning and poor land management (2013). This study addresses the problem of urban fragmentation at the neighbourhood level and examines to what extent the concept of compact urban form can contribute to the improvement of social and environmental sustainability in the Libyan city of Benghazi and Arab cities in general. The objectives and scope of the study have justified a morphological approach, where eleven case studies that present different urban typologies in the city have been investigated. The research strategy and selection of case studies were driven by the availability of data and meant to cover the main urban types and important issues defined within this context. This research, which has been conducted to explore and explain the relationships that exist between local urban forms and their performance in terms of sustainability, has produced valuable knowledge and helped to identify measures which target the improvement of people’s quality of life and environmental sustainability of the city. The research draws on the argument that adopting a type of human scale urban form, which is relatively compact and dense, well-connected and comfortably diverse, coupled with concepts of urban greening and flexible development relevant to the local context, would help to create a high quality urban form that is liveable and accessible, while causing minimum damage to the natural environment. This work is an attempt to respond and add to the ongoing debate on sustainable urban form in the developing countries (see: (Jenks, 2000)). The findings have contributed to the understanding of urban fragmentation and highlighted the relevance of the theory of compact city to sustainable development in Benghazi and the South in general. It is anticipated that this work would raise awareness on the impact of urban fragmentation on the sustainability of the built environment within this context and help to advance research on planning theory and practice based on real-life experience and responses to local circumstances.