Free fatty acid receptors:structural models and elucidation of ligand binding interactions

BACKGROUND: The free fatty acid receptors (FFAs), including FFA1 (orphan name: GPR40), FFA2 (GPR43) and FFA3 (GPR41) are G protein-coupled receptors (GPCRs) involved in energy and metabolic homeostasis. Understanding the structural basis of ligand binding at FFAs is an essential step toward designing potent and selective small molecule modulators.

RESULTS: We analyse earlier homology models of FFAs in light of the newly published FFA1 crystal structure co-crystallized with TAK-875, an ago-allosteric ligand, focusing on the architecture of the extracellular binding cavity and agonist-receptor interactions. The previous low-resolution homology models of FFAs were helpful in highlighting the location of the ligand binding site and the key residues for ligand anchoring. However, homology models were not accurate in establishing the nature of all ligand-receptor contacts and the precise ligand-binding mode. From analysis of structural models and mutagenesis, it appears that the position of helices 3, 4 and 5 is crucial in ligand docking. The FFA1-based homology models of FFA2 and FFA3 were constructed and used to compare the FFA subtypes. From docking studies we propose an alternative binding mode for orthosteric agonists at FFA1 and FFA2, involving the interhelical space between helices 4 and 5. This binding mode can explain mutagenesis results for residues at positions 4.56 and 5.42. The novel FFAs structural models highlight higher aromaticity of the FFA2 binding cavity and higher hydrophilicity of the FFA3 binding cavity. The role of the residues at the second extracellular loop used in mutagenesis is reanalysed. The third positively-charged residue in the binding cavity of FFAs, located in helix 2, is identified and predicted to coordinate allosteric modulators.

CONCLUSIONS: The novel structural models of FFAs provide information on specific modes of ligand binding at FFA subtypes and new suggestions for mutagenesis and ligand modification, guiding the development of novel orthosteric and allosteric chemical probes to validate the importance of FFAs in metabolic and inflammatory conditions. Using our FFA homology modelling experience, a strategy to model a GPCR, which is phylogenetically distant from GPCRs with the available crystal structures, is discussed.

Symposium - Organisational transformation in policing: Leadership and change in extreme contexts

Nearly 4000 people died in Northern Ireland’s long running conflict, 314 of them police officers (Brewer and Magee 1991, Brewer 1996, Hennessey 1999, Guelke and Milton-Edwards 2000). The republican and loyalist ceasefires of 1994 were the first significant signal that NI society was moving beyond the ‘troubles’ and towards a normalised political environment. The Belfast (Good Friday) Agreement of 1998 cemented that movement (Hennessey 1999). Policing was a key and seemingly unresolvable element of the conflict, seen as unrepresentative and partisan. Its reform or ‘recasting’ in a new dispensation was an integral part of the conflict transformation endeavour(Ellison 2010). As one of the most controversial elements of the conflicted past, it had remained outside the Agreement and was subject to a specific commission of interest (1999), generally known as the Patten Commission. The Commission’s far reaching proposals included a change of name, badge and uniform, the introduction of 50/50 recruitment (50% Roman Catholic and 50% other), a new focus on human rights, a new district command and headquarter structure, a review of ‘Special Branch’ and covert techniques, a concern for ‘policing with the community’ and a significant voluntary severance process to make room for new recruits, unconnected with the past history of the organisation(Murphy 2013).

This paper reflects upon the first data collection phase of a long term processual study of organisational change within the Royal Ulster Constabulary / Police Service of Northern Ireland. This phase (1996-2002) covers early organisational change initiation (including the pre-change period) and implementation including the instigation of symbolic changes (name, badge, and crest) and structural changes (new HQ structure and District Command structure). It utilises internal documentation including messages from the organisations leaders, interviews with forty key informants (identified through a combination of snow-balling from referrals by initial contacts, and key interviews with significant individuals), as well as external documentation and commentary on public perceptions of the change. Using a processual lens (Langley, Smallman et al. 2013) it seeks to understand this initial change phase and its relative success in a highly politicised environment.

By engaging key individuals internally and externally, setting up a dedicated change team, adopting a non normative, non urgent, calming approach to dissent, communicating in orthodox and unorthodox ways with members, acknowledging the huge emotional strain of letting go of the organisation’s name and all it embodied, and re-emphasising the role of officers as ‘police first’, rather than ‘RUC first’, the organisations leadership remained in control of a volatile and unhappy organisational body and succeeded in moving it on through this initial phase, even while much of the political establishment lambasted them externally. Three years into this change process the organisation had a new name, a new crest, new structures, procedures and was deeply engaged in embedding the joint principles of human rights and community policing within its re-woven fabric. While significant problems remained, the new Police Service of Northern Ireland had successfully begun a long journey to full community acceptance in a post conflict context.

This case illustrates the significant challenges of leading change under political pressure, with external oversight and no space for failure(Hannah, Uhl-Bien et al. 2009). It empirically reflects the reality of change implementation as messy, disruptive and unpredictable and highlights the significance of political skill and contextual understanding to success in the early stages(Buchanan and Boddy 1992). The implications of this for change theory and the practice of change implementation are explored (Eisenhardt and Graebner 2007) and some conclusions drawn about what such an extreme case tells us about change generally and change implementation under pressure.

Navigating the Borderlands: Brian McGilloway as Contemporary Cartographer of the Liminal in the Ulster Landscape

Set in the borderlands between Letterkenny and Derry-Londonderry, a landscape scarred by geological fold, river and cartographer’s pen, the Ulster crime novelist Brian McGilloway chronicles the hopes and fears of a contemporary society unable to escape a complicated history, redolent and entwined with the voices of its ‘ghosts of its past.’ Through his choice of chief protagonist, An Garda Síochána officer Benedict Devlin, McGilloway turns detective to critically investigate the both the seemingly straightforward and the unseen dwelling in the rural Ulster landscape. Following in the footsteps of Nordic and Tartan Noir in making commentary on current societ,y McGilloway recognises the importance of the past in trying to reach an understanding of the present. His critique however goes beyond criminal behaviour motivated primarily by politics or religion, allowing a deeper and more meaningful diagnosis of the ‘state of the nation’. Place, name and event become especially important in contextualising the liminality of McGilloway’s real rural border settings. In doing so, McGilloway continues in the rich tradition of Ulster poet such as Heaney, MacNiece, Muldoon and Hewitt in trying to rationalise the man-made amidst the elemental in the land of both the ‘Planter & The Gael.’ History, language, tradition and the sacral are all instruments of investigation in helping McGilloway present a revealing pathology and atlas of our times to his readers. Turning literary investigator, the author contends that there is much to learn from this physiography, not just for the borderlands region, but for the wider countryside and society beyond. Keywords Cultural Atlas, Crime Fiction, Place, Poetry, Rural.

Conversations with the Future: Creativity, Aesthetics and Industry Application in Anthropological Practice

This article presents a series of conversations with anthropologists working in collaborative, interdisciplinary settings and projects. It examines the changing role and place of anthropology on the island of Ireland, particular for early career anthropologists. With anthropologists now working in settings as diverse as business schools, health, music, documentary making and industry (to name but a few), early career researchers are now dealing with new challenges. In this piece, we map out a number of these debates and show how a multiplicity of anthropologies and practices are emerging on the island.

LL-37 quantification in gingival crevicular fluid (GCF) from periodontitis patients

Background: LL-37, an anti-microbial peptide belonging to the cathelicidin family, derives its name from two N-terminal leucine residues and the 37 amino acids comprising the peptide. LL-37 is the only known cathelicidin to exist in humans. It exhibits both anti-bacterial and immunomodulatory properties. Objectives: In the current study, LL-37 was quantified in GCF from periodontitis patients. Previous studies have relied on qualitative results from Western blotting to detect LL-37 in GCF. This study aims to quantitatively determine LL-37 levels in GCF. Methods: GCF and bacterial plaque samples, pre- and post non-surgical periodontal treatment, were collected from 4 sites in 12 patients presenting with advanced periodontitis. Plaque samples were analysed by QPCR for the presence or absence of the periodontopathic bacterium Porphyromonas gingivalis (P. gingivalis). The concentrations of LL-37 in patient samples pre- and post-treatment were deduced by indirect enzyme linked immunosorbent assay (ELISA). Results: Concentrations of LL-37 in samples varied between a minimum and maximum of 1 and 40 ng/ml. LL-37 levels were shown, pre-treatment, to be higher in deep pockets (6-9 mm) compared with shallower pockets (3-5 mm) and highest in those sites which were positive for P. gingivalis. Non-surgical therapy resulted in a significant improvement in clinical indices while expression levels of P. gingivalis were reduced. Following treatment, LL-37 levels in GCF decreased from an average of 6.5 ± 1 - 5.8 ± 1.2 ng/ml. The most interesting observation however was the reduction in LL-37 levels, from an average of 7 ± 1.3 – 2.5 ± 1.1 ng/ml in those sites where P. gingivalis infection was eradicated post-treatment. Conclusions: LL-37 levels are increased at sites showing advanced periodontal disease, reduce following treatment and appear to be linked to the presence of P. gingivalis. This study will further our knowledge of host defence in chronic diseases such as periodontitis.

Molecular phylogenetic analysis of a known and a new hydrothermal vent octopod:Their relationships with the genus Benthoctopus (Cephalopoda: Octopodidae)

The resolution of evolutionary relationships among deep-sea incirrate octopuses has been hindered by the paucity of individuals available for morphological studies and by the lack of tissue samples preserved using fixatives compatible with simple DNA extraction techniques. Evolutionary relationships from 11 species of deep-sea incirrate octopuses were investigated using 2392 base pairs (bp) of DNA from four mitochondrial genes (12S rDNA, 16S rDNA, cytochrome c oxidase subunit III, and cytochrome b) and the nuclear gene, rhodopsin. Morphological examination of these species was also undertaken. Molecular analyses distinguish a species of octopus from hydrothermal vents at Manus Basin from the vent octopodid Vulcanoctopus hydrothermalis known from vents on the East Pacific Rise. Both are herein considered members of the clade currently assigned the name Benthoctopus, although taxonomic implications preclude formally naming Vulcanoctopus as a junior synonym. Morphological investigations led to the conclusion that Benthoctopus macrophallus is a junior synonym of Benthoctopus yaquinae. An amended diagnosis of Benthoctopus is provided with additional information on male reproductive characteristics. Copyright © 2009 · Magnolia Press.

Wavelet entropy of Doppler ultrasound blood velocity flow waveforms distinguishes nitric oxide-modulated states

Wavelet entropy assesses the degree of order or disorder in signals and presents this complex information in a simple metric. Relative wavelet entropy assesses the similarity between the spectral distributions of two signals, again in a simple metric. Wavelet entropy is therefore potentially a very attractive tool for waveform analysis. The ability of this method to track the effects of pharmacologic modulation of vascular function on Doppler blood velocity waveforms was assessed. Waveforms were captured from ophthalmic arteries of 10 healthy subjects at baseline, after the administration of glyceryl trinitrate (GTN) and after two doses of N(G)-nitro-L-arginine-methyl ester (L-NAME) to produce vasodilation and vasoconstriction, respectively. Wavelet entropy had a tendency to decrease from baseline in response to GTN, but significantly increased after the administration of L-NAME (mean: 1.60 ± 0.07 after 0.25 mg/kg and 1.72 ± 0.13 after 0.5 mg/kg vs. 1.50 ± 0.10 at baseline, p < 0.05). Relative wavelet entropy had a spectral distribution from increasing doses of L-NAME comparable to baseline, 0.07 ± 0.04 and 0.08 ± 0.03, respectively, whereas GTN had the most dissimilar spectral distribution compared with baseline (0.17 ± 0.08, p = 0.002). Wavelet entropy can detect subtle changes in Doppler blood velocity waveform structure in response to nitric-oxide-mediated changes in arteriolar smooth muscle tone.

Italian Canzone d'autore and Greek Entechno tragoudi: a comparative overview

‘Canzone d’autore’ is the name that a vast community of Italian music critics, authors, per-formers, producers agreed upon in the mid-1970s, to describe the Italian singer-songwriter genre. Singer-songwriters, who had been missing from Italian popular music – with very few exceptions – until the late 1950s, had become increasingly popular after 1958, and were dubbed ‘cantautori’ in 1960. The term, which propagated to Spain, Catalonia, and Latin Amer-ica, is still in use, but ‘canzone d’autore’ superseded it as a genre label, highlighting the con-nections between authorship and artistic value, implied in the already established notion of ‘Cinéma d’auteur’ from which it was derived.

The expression ‘entechno laiko tragoudi’ (‘art-folk song’) was coined in Greece by Mikis The-odorakis in the 1950s, to describe a new music genre combining the urban-folk musical idi-om with lyrics coming from high-art poetry. Although the origins of the genre are tied to the work of composers like Theodorakis and Hatzidakis who did not perform as singers, from the 1970s onwards entechno became the privileged field of new generations of Greek singer-songwriters. Dropping ‘laiko’ (folk) from its label, entechno expanded its musical influences outside the urban-folk repertory and transformed into the more all-encompassing contempo-rary ‘art song’.

The Pine Wood Nematode: a personal view

The first report of the disease (“pine wilt disease”) associated with the pinewood nematode, goes back to 1905, when Yano reported an unusual decline of pines from Nagasaki. For a long time thereafter, the cause of he disease was sought, but without success. Because of the large number of insect species that were usually seen around and on infected trees, it had always been assumed that the causal agent would prove to be one of these. However, in 1971, Kiyohara and Tokushike found a nematode of the genus Bursaphelenchus in infected trees. The nematode found was multiplied on fungal culture, inoculated into healthy trees and then re-isolated from the resulting wilted trees. The subsequent published reports were impressive: this Bursaphelenchus species could kill fully-grown trees within a few months in the warmer areas of Japan, and could destroy complete forests of susceptible pine species within a few years. Pinus densiflora, P. thunbergii und P. luchuensis were particularly affected. In 1972, Mamiya and Kiyohara described the new species of nematode extracted from the wood of diseased pines; it was a named Bursaphelenchus lignicolus. Since 1975, the species has spread to the north of Japan, with the exception of the most northerly prefectures. In 1977, the loss of wood in the west of the country reached 80%. Probably as a result of unusually high summer temperatures and reduced rainfall in the years 1978 and 1979, the losses were more than 2 million m3 per year. From the beginning, B. lignicolus was always considered by Japanese scientists to be an exotic pest. But where did it come from? That this nematode could also cause damage in the USA became clear in 1979 when B. lignicolus was isolated in great numbers from wood of a 39 year-old pine tree (Pinus nigra) in Missouri which had suddenly died after the colour of its needles changed to a reddish-brown colour (Dropkin und Foudin, 2 1979). In 1981, B. lignicolus was synonymised by Nickle et al. with B. xylophilus which had been found for the first time in the USA as far back as 1929, and reported by Steiner and Buhrer in 1934. It had originally been named Aphelenchoides xylophilus, the wood-inhabiting Aphelenchoides but was recognised by Nickle, in 1970,to belong in the genus Bursaphelenchus. Its common name in the USA was the "pine wood nematode" (PWN. After its detection in Missouri, it became known that B. xylophilus was widespread throughout the USA and Canada. It occurred there on native species of conifers where, as a rule, it did not show the symptoms of pine wilt disease unless susceptible species were stressed eg., by high temperature. This fact was an illuminating piece of evidence that North America could be the homeland of PWN. Dwinell (1993) later reported the presence of B. xylophilus in Mexico. The main vector of the PWN in Japan was shown to be the long-horned beetle Monochamus alternatus, belonging to the family Cerambycidae. This beetle lays its eggs in dead or dying trees where the developing larvae then feed in the cambium layer. It was already known in Japan in the 19th century but in the 1930s, it was said to be present in most areas of Japan, but was generally uncommon. However, with the spread of the pine wilt disease, and the resulting increase of weakened trees that could act as breeding sites for beetles, the populations of Monochamus spp. increased significantly In North America, other Monochamus species transmit PWN, and the main vector is M. carolinensis. In Japan, there are also other, less efficient vectors in the genus Monochamus. Possibly, all Monochamus species that breed in conifers can transmit the PWN. The occasional transmission by less efficient species of Monochamus or by some of the many other beetle genera in the bark or wood is of little significance. In Europe, M. galloprovincialis and M. sutor transmits the closely related species B. mucronatus. Some speculate that these two insect species are “standing by” and waiting for the arrival of B. xylophilus. In 1982, the nematode was detected and China. It was first found in dead pines near the Zhongshan Monument of Nanjing (CHENG et. al. 1983); 265 trees were then killed by pine wilt disease. Despite great efforts at eradication in China, the nematode spread further and pine wilt disease has been 3 reported from parts of the provinces of Jiangsu, Anhui, Guangdong, Shandong, Zhejiang and Hubei (YANG, 2003). In 1986, the spread of the PWN to Taiwan was discovered and in 1989, the nematode was reported to be present in the Republic of Korea where it had first been detected in Pinus thunbergii and P. densiflora. It was though to have been introduced with packing material from Japan. PWN was advancing. In 1984, B. xylophilus was found in wood chips imported into Finland from the USA and Canada, and this was the impetus to establish phytosanitary measures to prevent any possible spread into Europe. Finland prohibited the import of coniferous wood chips from these sources, and the other Nordic countries soon followed suit. EPPO (the European and Mediterranean Plant Protection Organization) made a recommendation to its member countries in 1986 to refuse wood imports from infested countries. With its Directive of 1989 (77/93 EEC), the European Community (later called the European Union or EU) recognised the potential danger of B. xylophilus for European forests and imposed restrictions on imports into the Europe. PWN was placed on the quarantine list of the EU and also of other European countries. Later, in 1991, a dispensation was allowed by the Commission of the EU(92/13 EEC) for coniferous wood from North America provided that certain specified requirements were fulfilled that would prevent introduction.

Taxonomic databases for Bursaphelenchus and other aphelenchoid nematodes

Nematodes are the most abundant metazoans, comprising more than 80% of all animals alive today. Since 1743, when Needham (Needham, 1743) described the first nematode, approximately 20,000 - 30,000 species have been named, with estimates of species remaining to be described ranging from 100,000 to 1 million (Blaxter, 2004; De Ley, 2000). Unfortunately, the taxonomic community is woefully inadequate for this task. The number of taxonomists currently describing new species of nematodes around the world is less than 100, and significant increases are not expected. If each of these taxonomists were able to describe 10 new species every year, it would take between 100 to 1,000 years to name these yet to be described species.

Web 2.0, PC e EFA: impactes de uma oficina de formação de professores

As competências em Tecnologia da Informação e Comunicação (TIC) e o Pensamento Crítico (PC) são duas das linhas orientadoras da Aprendizagem ao Longo da Vida (ALV) que reconhecendo que todos os contextos (informais, não-formais e formais) podem ser de aprendizagem, assumiram no quadro da Educação e Formação de Adultos (EFA), em Portugal, uma expressividade plasmada no Referencial de Competências-Chave de Educação e Formação de Adultos, nível secundário (EFA-NS). Contudo a orientação PC/TIC não tem sido explicitamente conciliada nas práticas de educação e formação de adultos. Neste contexto desenvolveu-se uma Oficina de Formação para professores/formadores de cursos EFA-NS, na qual se trabalhou a integração de ferramentas da Web 2.0 com a infusão de PC em materiais/atividades para cursos EFA-NS. No desenvolvimento da Oficina foram consideradas três vertentes. Primeira, conceções dos professores sobre EFA/TIC e EFA/PC. Segunda, a formação sobre PC/TIC. Terceira, produção e implementação de materiais/atividades com orientação PC/TIC. A componente de trabalho autónomo da Oficina passou essencialmente pela dinâmica de uma comunidade online de nome EF@. O grupo de formação era constituído por 17 professores do ensino secundário, e pela investigadora/formadora, autora deste estudo. Acrescente-se que no conjunto das 10 sessões de trabalho presencial a investigadora/formadora foi coadjuvada por mais três formadores. Estudar os impactes da Oficina no desenvolvimento profissional dos professores, conjuntamente com a avaliação da influência dos materiais/atividades produzidos (na Oficina) no nível de PC dos alunos, assumiram-se como as duas questões de investigação a que este estudo pretendeu dar resposta. Neste sentido estudámos o grupo de professores em formação – estudo de caso – e o grupo de alunos – plano quasi experimental do tipo grupo de controlo/experimental, pré/pós-teste, pelo que o enquadramento da metodologia num estudo misto, predominantemente de natureza qualitativa, foi a adotada. A recolha e o tratamento de dados foram feitos mediante várias técnicas – observação, inquérito, análise e testagem – associadas a diferentes instrumentos: dois questionários, diário de investigador e Teste de Pensamento Crítico – Cornell (Nível X). A análise dos dados recolhidos possibilitou a compreensão de como a Oficina contribui para a reflexão: (i) nas práticas anteriores dos professores; (ii) nas competências adquiridas na Oficina e (iii) nas práticas implementadas. Ao nível do PC dos alunos, podemos dizer que os materiais/atividades produzidos na Oficina influenciaram o nível de PC dos alunos, já que os resultados da média do PC do pós-teste foram estatisticamente significativos para o grupo experimental, quando comparado com a média do PC no grupo de controlo.

Caracterização experimental e modelação numérica de espumas metálicas

As espumas de alumínio são materiais ultraleves, o que as torna atractivas para um largo espectro de aplicações comerciais na área da defesa, na indústria automóvel e aeroespacial, entre outras. Actualmente, há um grande interesse na utilização de espumas de alumínio em componentes estruturais ultraleves, incorporados em sistemas de absorção de energia para protecção contra o impacto. O recurso à simulação numérica para resolver problemas de engenharia em várias áreas é cada vez mais comum. A modelação numérica dos materiais assume vital importância quando o problema envolve a análise de processos tecnológicos como, por exemplo, a conformação plástica de materiais, ou a análise de estruturas. Deste modo, torna-se imprescindível garantir que a modelação dos materiais é de tal forma rigorosa que permite simular o melhor possível o seu comportamento real nas condições concretas da análise a realizar. A forma mais comum de garantir o rigor dos modelos utilizados é a validação dos modelos numéricos tendo por base resultados experimentais. Neste trabalho, fez-se a caracterização do comportamento mecânico das espumas de alumínio com nome comercial ALPORAS!, obtidas pelo processo de fabrico denominado expansão directa do metal fundido por adição de um agente expansor. Esta caracterização consistiu num conjunto de ensaios experimentais quer no regime quasi-estático, quer no regime dinâmico. No regime quasi-estático realizaram-se ensaios de compressão uniaxial e de compressão multiaxial. Para a caracterização no regime dinâmico foram realizados ensaios em barras de Hopkinson de polimetil-metacrilato (PMMA). Com base nos resultados experimentais obtidos determinaram-se os parâmetros dos dois modelos constitutivos para espumas metálicas implementados no programa comercial Abaqus™/Explicit. Estes modelos, e os respectivos parâmetros determinados, foram validados reproduzindo numericamente alguns ensaios experimentais quasi-estáticos e dinâmicos. Assim, verificou-se a adequabilidade dos modelos em diversas condições quer em termos de esforços quer em termos de regime de taxa de deformação Por último, desenvolveu-se uma estrutura inovadora para absorção de energia durante um impacto, constituída por componentes perfilados em liga de alumínio e por componentes em espumas de alumínio. Esta estrutura foi testada exclusivamente com recurso à simulação numérica, utilizando os modelos constitutivos validados anteriormente.

Mining biomedical information from scientific literature

The rapid evolution and proliferation of a world-wide computerized network, the Internet, resulted in an overwhelming and constantly growing amount of publicly available data and information, a fact that was also verified in biomedicine. However, the lack of structure of textual data inhibits its direct processing by computational solutions. Information extraction is the task of text mining that intends to automatically collect information from unstructured text data sources. The goal of the work described in this thesis was to build innovative solutions for biomedical information extraction from scientific literature, through the development of simple software artifacts for developers and biocurators, delivering more accurate, usable and faster results. We started by tackling named entity recognition - a crucial initial task - with the development of Gimli, a machine-learning-based solution that follows an incremental approach to optimize extracted linguistic characteristics for each concept type. Afterwards, Totum was built to harmonize concept names provided by heterogeneous systems, delivering a robust solution with improved performance results. Such approach takes advantage of heterogenous corpora to deliver cross-corpus harmonization that is not constrained to specific characteristics. Since previous solutions do not provide links to knowledge bases, Neji was built to streamline the development of complex and custom solutions for biomedical concept name recognition and normalization. This was achieved through a modular and flexible framework focused on speed and performance, integrating a large amount of processing modules optimized for the biomedical domain. To offer on-demand heterogenous biomedical concept identification, we developed BeCAS, a web application, service and widget. We also tackled relation mining by developing TrigNER, a machine-learning-based solution for biomedical event trigger recognition, which applies an automatic algorithm to obtain the best linguistic features and model parameters for each event type. Finally, in order to assist biocurators, Egas was developed to support rapid, interactive and real-time collaborative curation of biomedical documents, through manual and automatic in-line annotation of concepts and relations. Overall, the research work presented in this thesis contributed to a more accurate update of current biomedical knowledge bases, towards improved hypothesis generation and knowledge discovery.

Partial Secrets

The ability and right to have secrets may be a condition of social ethics (Derrida, A Taste for the Secret), but at the same time the nature of secrets is that they undermine themselves. Once told, secrets are no longer secret but are known. Even to name them as possibilities is to bring them into view as objects of knowledge. Secrets are thus always in some ways partial secrets, but their “openness” also connotes the lack of certainty of any knowledge about them, their evasiveness, their lack of fixity, and hence, their partial character and openness to change. In this article, I explore partial secrets in relation to a 2011 interview study of HIV support in the United Kingdom, where HIV’s relatively low prevalence and high treatment access tends toward its invisibilization. I suggest that in this context, HIV is positioned ambiguously, as a “partial secret,” in an ongoing and precarious tension between public knowledge and acceptance of HIV, HIV’s constitution as a condition of citizenship attended by full human rights, and HIV’s being resecreted through ongoing illness, constrained resources, citizenly exclusion, and the psychological and social isolation of those affected.

Chemical and microbial changes during the natural fermentation of strawberry tree (Arbutus unedo L.) fruits

Aguardente de medronho is the name given in Portugal to a spirit made from the fermented fruit of Arbutus unedo (strawberry tree), a plant grown in the Mediterranean region. In order to gain a better understanding of the fermentation process, as it is performed in the farms, a natural fermentation with wild microbiota was carried out during 36 days, and some physicochemical and microbiological parameters were studied. The microbial parameters analyzed were total viable, lactic and acetic acids bacteria, and yeast counts. The physicochemical parameters monitored were sugars, minerals, ethanol, organic acids and pH. Yeasts were the main responsible for the fermentation of the fruits, as the lactic and acetic acids bacteria are absent. As the fermentation progressed, the sugars increased during the first 2 days and gradually decreased along the fermentation period. Maintaining the good quality of the product could contribute to the preservation and valorization of traditional resources that are of great importance to prevent their disappearance.