Code: Aplicació per a la revisió d'activitats

Code és una aplicaicó web per a permetre el comentari remot d'activitats de programació. La interfície web està desenvolupada usat el Google Web Toolkit (GWT) per aconseguir un alt nivell d'interactivitat.

Uso de injerto dermo-graso para el tratamiento de la exposición del implante orbitario

La utilización de un implante orbitario es imprescindible para restaurar el volumen tras la evisceración o enucleación del globo ocular. Dicho volumen en la cavidad anoftálmica permitirá la utilización de una cascarilla que dará al paciente una mejor apariencia y simetría tras la pérdida del globo ocular. La exposición del implante orbitario es una de las complicaciones más frecuentes que nos encontramos tras evisceración o enucleación con la utilización de implante orbitario. Hay diferentes factores reconocidos que propiciarán dicha exposición, entre los que se encuentran la colonización del implante, escasez de mucosa conjuntival, tamaño y composición del implante, etc... Hay diferentes opciones de tratamiento de la exposición del implante orbitario que incluyen la utilización de tejidos por medio de injerto o flap o bien la extracción del propio implante con la consecuente afectación en la apariencia del paciente. El uso de injerto dermo-graso ha sido descrito con anterioridad, pero no hemos encontrado un estudio de una serie de casos que demuestre su utilidad. Nuestro objetivo es determinar la efectividad del injerto dermo-graso en el tratamiento de la exposición del implante orbitario en la cavidad anoftálmica. Para ello estudiamos la evolución de 15 pacientes que presentaron exposición de implante orbitario, tras enucleación o evisceración, y a los que se les ha tratado dicha exposición con un injerto dermo-graso. Se evaluan clínicamente los resultados de dicha técnica en estos pacientes, en algún caso hasta 22 meses tras la intervención.

Draft genome of the red harvester ant Pogonomyrmex barbatus.

We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps in parallel with the development of the North American deserts.

Dispositius de control a la web: una topologia dels llocs webs a l'Estat Espanyol

Navegar per la World Wide Web és avui una acció rutinària per milions de persones arreu del globus terraqui. En el transcurs d'aquesta activitat cada individu deixa traces digitals a mesura que es va relacionant amb cada un dels elements que integren la Web. Aquest treball de recerca es proposa analitzar el codi font de llocs web per trobar evidències d'aquest procés latent de recollida de dades i, en la mesura del possible (i també del factible), identificar actors, establir usos potencials i cartografiar els espais de la web tenint en compte el grau de monitorització al que està sotmès l'usuari quan els visita.

Pre-procés i segmentació en imatges d’ultrasons 2D i 3D de la pròstata

Aquest projecte s'ha dut a terme amb el Grup de visió per computador del departamentd'Arquitectura i Tecnologia de Computadors (ATC) de la Universitat de Girona. Està enfocat a l'anàlisi d'imatges mèdiques, en concret s'analitzaran imatges de pròstata en relació a desenvolupaments que s'estan realitzant en el grup de visió esmentat. Els objectius fixats per aquest projecte són desenvolupar dos mòduls de processamentm d'imatges els quals afrontaran dos blocs important en el tractament d'imatges, aquests dos mòduls seran un pre-processat d'imatges, que constarà de tres filtres i un bloc de segmentació per tal de cercar la pròstata dintre de les imatges a tractar. En el projecte es treballarà amb el llenguatge de programació C++, concretament amb unes llibreries que es denominen ITK (Insight Toolkit ) i són open source enfocades al tractament d'imatges mèdiques. A part d'aquesta eina s'utilitzaran d'altres com les Qt que és una biblioteca d'eines per crear entorns gràfics

Ontology Mapping Evolution

Introdução Hoje em dia, o conceito de ontologia (Especificação explícita de uma conceptualização [Gruber, 1993]) é um conceito chave em sistemas baseados em conhecimento em geral e na Web Semântica em particular. Entretanto, os agentes de software nem sempre concordam com a mesma conceptualização, justificando assim a existência de diversas ontologias, mesmo que tratando o mesmo domínio de discurso. Para resolver/minimizar o problema de interoperabilidade entre estes agentes, o mapeamento de ontologias provou ser uma boa solução. O mapeamento de ontologias é o processo onde são especificadas relações semânticas entre entidades da ontologia origem e destino ao nível conceptual, e que por sua vez podem ser utilizados para transformar instâncias baseadas na ontologia origem em instâncias baseadas na ontologia destino. Motivação Num ambiente dinâmico como a Web Semântica, os agentes alteram não só os seus dados mas também a sua estrutura e semântica (ontologias). Este processo, denominado evolução de ontologias, pode ser definido como uma adaptação temporal da ontologia através de alterações que surgem no domínio ou nos objectivos da própria ontologia, e da gestão consistente dessas alterações [Stojanovic, 2004], podendo por vezes deixar o documento de mapeamento inconsistente. Em ambientes heterogéneos onde a interoperabilidade entre sistemas depende do documento de mapeamento, este deve reflectir as alterações efectuadas nas ontologias, existindo neste caso duas soluções: (i) gerar um novo documento de mapeamento (processo exigente em termos de tempo e recursos computacionais) ou (ii) adaptar o documento de mapeamento, corrigindo relações semânticas inválidas e criar novas relações se forem necessárias (processo menos existente em termos de tempo e recursos computacionais, mas muito dependente da informação sobre as alterações efectuadas). O principal objectivo deste trabalho é a análise, especificação e desenvolvimento do processo de evolução do documento de mapeamento de forma a reflectir as alterações efectuadas durante o processo de evolução de ontologias. Contexto Este trabalho foi desenvolvido no contexto do MAFRA Toolkit1. O MAFRA (MApping FRAmework) Toolkit é uma aplicação desenvolvida no GECAD2 que permite a especificação declarativa de relações semânticas entre entidades de uma ontologia origem e outra de destino, utilizando os seguintes componentes principais: Concept Bridge – Representa uma relação semântica entre um conceito de origem e um de destino; Property Bridge – Representa uma relação semântica entre uma ou mais propriedades de origem e uma ou mais propriedades de destino; Service – São aplicados às Semantic Bridges (Property e Concept Bridges) definindo como as instâncias origem devem ser transformadas em instâncias de destino. Estes conceitos estão especificados na ontologia SBO (Semantic Bridge Ontology) [Silva, 2004]. No contexto deste trabalho, um documento de mapeamento é uma instanciação do SBO, contendo relações semânticas entre entidades da ontologia de origem e da ontologia de destino. Processo de evolução do mapeamento O processo de evolução de mapeamento é o processo onde as entidades do documento de mapeamento são adaptadas, reflectindo eventuais alterações nas ontologias mapeadas, tentando o quanto possível preservar a semântica das relações semântica especificadas. Se as ontologias origem e/ou destino sofrerem alterações, algumas relações semânticas podem tornar-se inválidas, ou novas relações serão necessárias, sendo por isso este processo composto por dois sub-processos: (i) correcção de relações semânticas e (ii) processamento de novas entidades das ontologias. O processamento de novas entidades das ontologias requer a descoberta e cálculo de semelhanças entre entidades e a especificação de relações de acordo com a ontologia/linguagem SBO. Estas fases (“similarity measure” e “semantic bridging”) são implementadas no MAFRA Toolkit, sendo o processo (semi-) automático de mapeamento de ontologias descrito em [Silva, 2004]. O processo de correcção de entidades SBO inválidas requer um bom conhecimento da ontologia/linguagem SBO, das suas entidades e relações, e de todas as suas restrições, i.e. da sua estrutura e semântica. Este procedimento consiste em (i) identificar as entidades SBO inválidas, (ii) a causa da sua invalidez e (iii) corrigi-las da melhor forma possível. Nesta fase foi utilizada informação vinda do processo de evolução das ontologias com o objectivo de melhorar a qualidade de todo o processo. Conclusões Para além do processo de evolução do mapeamento desenvolvido, um dos pontos mais importantes deste trabalho foi a aquisição de um conhecimento mais profundo sobre ontologias, processo de evolução de ontologias, mapeamento etc., expansão dos horizontes de conhecimento, adquirindo ainda mais a consciência da complexidade do problema em questão, o que permite antever e perspectivar novos desafios para o futuro.

Differential transgene expression profiles in rat brain, using rAAV2/1 vectors with tetracycline-inducible and cytomegalovirus promoters.

The biodistribution of transgene expression in the CNS after localized stereotaxic vector delivery is an important issue for the safety of gene therapy for neurological diseases. The cellular specificity of transgene expression from rAAV2/1 vectors (recombinant adeno-associated viral vectors pseudotyped with viral capsids from serotype 1) using the tetracycline-inducible (TetON) expression cassette in comparison with the cytomegalovirus (CMV) promoter was investigated in the rat nigrostriatal pathway. After intrastriatal injection, although green fluorescent protein (GFP) was expressed mainly in neurons with both vectors, the relative proportions of DARPP-32-positive projection neurons and parvalbumin-positive interneurons were, respectively, 13:1 and 2:1 for the CMV and TetON vectors. DARP32-positive neurons projecting to the globus pallidus were strongly GFP positive with both vectors, whereas those projecting to the substantia nigra pars reticulata (SNpr) were efficiently labeled by the CMV vector but poorly by the TetON vector. Numerous GFP-positive cells were evidenced in the subventricular zone with both vectors. However, in the olfactory bulb (OB), GFP-positive neurons were observed with the CMV vector but not the TetON vector. We conclude that the absence of significant amounts of transgene product in distant regions (SN and OB) constitutes a safety advantage of the AAV2/1-TetON vector for striatal gene therapy. Midbrain injections resulted in selective GFP expression in tyrosine hydroxylase-positive neurons by the TetON vector whereas with the CMV vector, GFP-positive cells covered a widespread area of the midbrain. The biodistribution of GFP protein corresponded to that of the transcripts and not of the viral genomes. We conclude that the rAAV2/1-TetON vector constitutes an interesting tool for specific transgene expression in midbrain dopaminergic neurons.

Efficiency and safety of bilateral contemporaneous pallidal stimulation (deep brain stimulation) in levodopa-responsive patients with Parkinson's disease with severe motor fluctuations: a 2-year follow-up review.

OBJECT: The aim of this study was to evaluate the long-term safety and efficacy of bilateral contemporaneous deep brain stimulation (DBS) in patients who have levodopa-responsive parkinsonism with untreatable motor fluctuations. Bilateral pallidotomy carries a high risk of corticobulbar and cognitive dysfunction. Deep brain stimulation offers new alternatives with major advantages such as reversibility of effects, minimal permanent lesions, and adaptability to individual needs, changes in medication, side effects, and evolution of the disease. METHODS: Patients in whom levodopa-responsive parkinsonism with untreatable severe motor fluctuations has been clinically diagnosed underwent bilateral pallidal magnetic resonance image-guided electrode implantation while receiving a local anesthetic. Pre- and postoperative evaluations at 3-month intervals included Unified Parkinson's Disease Rating Scale (UPDRS) scoring, Hoehn and Yahr staging, 24-hour self-assessments, and neuropsychological examinations. Six patients with a mean age of 55 years (mean 42-67 years), a mean duration of disease of 15.5 years (range 12-21 years), a mean "on/off' Hoehn and Yahr stage score of 3/4.2 (range 3-5), and a mean "off' time of 40% (range 20-50%) underwent bilateral contemporaneous pallidal DBS, with a minimum follow-up period lasting 24 months (range 24-30 months). The mean dose of levodopa in these patients could not be changed significantly after the procedure and pergolide was added after 12 months in five patients because of recurring fluctuations despite adjustments in stimulation parameters. All but two patients had no fluctuations until 9 months. Two of the patients reported barely perceptible fluctuations at 12 months and two at 15 months; however, two patients remain without fluctuations at 2 years. The mean improvements in the UPDRS motor score in the off time and the activities of daily living (ADL) score were more than 50%; the mean off time decreased from 40 to 10%, and the mean dyskinesia and complication of treatment scores were reduced to one-third until pergolide was introduced at 12 months. No significant improvement in "on" scores was observed. A slight worsening after 1 year was observed and three patients developed levodopa- and stimulation-resistant gait ignition failure and minimal fluctuations at 1 year. Side effects, which were controlled by modulation of stimulation, included dysarthria, dystonia, and confusion. CONCLUSIONS: Bilateral pallidal DBS is safe and efficient in patients who have levodopa-responsive parkinsonism with severe fluctuations. Major improvements in motor score, ADL score, and off time persisted beyond 2 years after the operation, but signs of decreased efficacy started to be seen after 12 months.

Littératie en santé : élaboration d'un outil de dépistage pour les médecins de famille

La littératie en santé est un concept prenant en compte les compétences et les ressources que chacun doit posséder pour gérer l'information nécessaire au maintien d'un bon état de santé. Néanmoins, il n'y pas de consensus sur une définition unique, ce qui complique une intégration adéquate de cette thématique dans le domaine de la santé. Un faible niveau de littératie en santé est un problème fréquent et concernerait près de 50% de la population Suisse (OCDE 2005). Cette problématique est d'une importance majeure car les individus avec un niveau de littératie insuffisant sont plus à risque d'un mauvais état de santé (AMA 1999) et ce phénomène représenterait 3 à 6% des coûts de la santé en Suisse selon une estimation basée sur les chiffres d'études américaines. (Spycher 2006). Les médecins de famille, considérés comme l'une des principales sources d'information en santé pour la population en Suisse, jouent un rôle central dans la promotion d'un bon niveau de santé. L'idée de ce travail vient à la suite des résultats du travail de Maîtrise de de Lara Van Leckwyck qui s'est intéressée à la perception que les médecins de famille de la région lausannoise ont du niveau de littératie de leurs patients. Ces derniers considèrent posséder les ressources nécessaires pour prendre en charge leurs patients avec un faible niveau de littératie mais ils sont ouverts à de nouveaux outils. Nous avons alors voulu tenter l'expérience et créer un outil sous la forme d'une brochure A6 contenant quatre faces dans le but d'aider ces médecins. Les objectifs sont les suivants : 1) sensibiliser et informer les médecins de famille à la problématique de la littératie en santé ; 2) offrir une aide au dépistage du niveau de littératie en santé de leurs patients ; 3) proposer une aide à la prise en charge des patients avec un faible niveau de littératie en fournissant une liste de moyens pratiques basés sur une revue de la littérature pour aider les médecins généralistes internistes dans leur prise en charge et 4) proposer une sélection d'adresses internet utiles en lien avec la problématique de la littératie en santé. Cet outil a été présenté à 15 assistants et chefs de clinique de la Policlinique médicale universitaire (PMU) de Lausanne ainsi qu'à 30 médecins internistes généralistes installés dans la région de Lausanne qui évalueront son utilité dans le cadre d'un prochain travail de Maîtrise. Les limites principales concernant un tel projet sont le format choisi pour l'outil et le fait de récolter et de transcrire des informations sur un sujet principalement étudié dans les pays anglo-saxons. Nous pouvons déjà prévoir que des adaptations sur la traduction de certains éléments de l'outil (notamment les questions de dépistage) seront certainement relevées par les médecins qui auront testé l'outil. Un travail supplémentaire mené de manière différente pourra également faire l'objet d'un futur travail.

Improved segmentation of deep brain grey matter structures using magnetization transfer (MT) parameter maps.

Basal ganglia and brain stem nuclei are involved in the pathophysiology of various neurological and neuropsychiatric disorders. Currently available structural T1-weighted (T1w) magnetic resonance images do not provide sufficient contrast for reliable automated segmentation of various subcortical grey matter structures. We use a novel, semi-quantitative magnetization transfer (MT) imaging protocol that overcomes limitations in T1w images, which are mainly due to their sensitivity to the high iron content in subcortical grey matter. We demonstrate improved automated segmentation of putamen, pallidum, pulvinar and substantia nigra using MT images. A comparison with segmentation of high-quality T1w images was performed in 49 healthy subjects. Our results show that MT maps are highly suitable for automated segmentation, and so for multi-subject morphometric studies with a focus on subcortical structures.

Beyond the 'dyad': a qualitative re-evaluation of the changing clinical consultation.

OBJECTIVE: To identify characteristics of consultations that do not conform to the traditionally understood communication 'dyad', in order to highlight implications for medical education and develop a reflective 'toolkit' for use by medical practitioners and educators in the analysis of consultations. DESIGN: A series of interdisciplinary research workshops spanning 12 months explored the social impact of globalisation and computerisation on the clinical consultation, focusing specifically on contemporary challenges to the clinician-patient dyad. Researchers presented detailed case studies of consultations, taken from their recent research projects. Drawing on concepts from applied sociolinguistics, further analysis of selected case studies prompted the identification of key emergent themes. SETTING: University departments in the UK and Switzerland. PARTICIPANTS: Six researchers with backgrounds in medicine, applied linguistics, sociolinguistics and medical education. One workshop was also attended by PhD students conducting research on healthcare interactions. RESULTS: The contemporary consultation is characterised by a multiplicity of voices. Incorporation of additional voices in the consultation creates new forms of order (and disorder) in the interaction. The roles 'clinician' and 'patient' are blurred as they become increasingly distributed between different participants. These new consultation arrangements make new demands on clinicians, which lie beyond the scope of most educational programmes for clinical communication. CONCLUSIONS: The consultation is changing. Traditional consultation models that assume a 'dyadic' consultation do not adequately incorporate the realities of many contemporary consultations. A paradox emerges between the need to manage consultations in a 'super-diverse' multilingual society, while also attending to increasing requirements for standardised protocol-driven approaches to care prompted by computer use. The tension between standardisation and flexibility requires addressing in educational contexts. Drawing on concepts from applied sociolinguistics and the findings of these research observations, the authors offer a reflective 'toolkit' of questions to ask of the consultation in the context of enquiry-based learning.

The Brazilian electronic theses and dissertations digital library: providing open access for scholarly information

This paper describes a project led by the Instituto Brasileiro de Informações em Ciência e Tecnologia (Ibict), a government institution, to build a national digital library for electronic theses and dissertations - Bibliteca Digital de Teses e Dissertações (BDTD). The project has been a collaborative effort among Ibict, universities and other research centers in Brazil. The developers adopted a system architecture based on the Open Archives Initiative (OAI) in which universities and research centers act as data providers and Ibict as a service provider. A Brazilian metadata standard for electronic theses and dissertations was developed for the digital library. A toolkit including open source package was also developed by Ibict to be distributed to potential data providers. BDTD has been integrated with the international initiative: the Networked Digital Library of Thesis and Dissertation (NDLTD). Discussions in the paper address various issues related to project design, development and management as well as the role played by Ibict. Conclusions highlight some important lessons learned to date and challenges for the future in expanding the BDTD project.

Challenges to the implementation of behavioural survellance for HIV/STI in Europe

Background: Well-conducted behavioural surveillance (BS) is essential for policy planning and evaluation. Data should be comparable across countries. In 2008, the European Centre for Disease Prevention and Control (ECDC) began a programme to support Member States in the implementation of BS for Second Generation Surveillance. Methods: Data from a mapping exercise on current BS activities in EU/EFTA countries led to recommendations for establishing national BS systems and international coordination, and the definition of a set of core and transversal (UNGASS-Dublin compatible) indicators for BS in the general and eight specific populations. A toolkit for establishing BS has been developed and a BS needs-assessment survey has been launched in 30 countries. Tools for BS self-assessment and planning are currently being tested during interactive workshops with country representatives. Results: The mapping exercise revealed extreme diversity between countries. Around half had established a BS system, but this did not always correspond to the epidemiological situation. Challenges to implementation and harmonisation at all levels emerged from survey findings and workshop feedback. These include: absence of synergy between biological and behavioural surveillance and of actors having an overall view of all system elements; lack of awareness of the relevance of BS and of coordination between agencies; insufficient use of available data; financial constraints; poor sustainability, data quality and access to certain key populations; unfavourable legislative environments. Conclusions: There is widespread need in the region not only for technical support but also for BS advocacy: BS remains the neglected partner of second generation surveillance and requires increased political support and capacity-building in order to become effective. Dissemination of validated tools for BS, developed in interaction with country experts, proves feasible and acceptable.

C19orf12 mutation leads to a pallido-pyramidal syndrome.

Pallido-pyramidal syndromes combine dystonia with or without parkinsonism and spasticity as part of a mixed neurodegenerative disorder. Several causative genes have been shown to lead to pallido-pyramidal syndromes, including FBXO7, ATP13A2, PLA2G6, PRKN and SPG11. Among these, ATP13A2 and PLA2G6 are inconsistently associated with brain iron deposition. Using homozygosity mapping and direct sequencing in a multiplex consanguineous Saudi Arabian family with a pallido-pyramidal syndrome, iron deposition and cerebellar atrophy, we identified a homozygous p.G53R mutation in C19orf12. Our findings add to the phenotypic spectrum associated with C19orf12 mutations.

INdividual SUrveys in RAllies (INSURA), A new tool for exploring transnational activism?

Prior the middle of the 90', interviewing participants in protest events was quiet rare. INdividual SUrveys in RAllies (INSURA) did enter the social researcher's usual toolkit only in the following decade after Favre, Fillieule and Mayer (1997) conducted such a survey with as a primary ambition to build a solid methodological framework that could be subsequently applied by other researchers. After some years of intensive use of INSURA, one is entitled to wonder whether that technique has fulfilled social researchers' hopes or not. In that paper, results of a collective work on alter-global rallies in Evian and Saint- Denis are used to answer three interrelated questions. Firstly, some basic methodological questions about how to collect data on crowds are adressed. What are the specific constraints of interviewing people at the very moment they are "expressing" a political opinion? What specific constraints result from the morphology of the covered events, that is to say, how to build a valid sampling frame? The authors then turn to a more general point about the questions that can be solved, or not, using that technique. Secondly it is the strenghts and weaknesses of INSURA in exploring the transnational dimension of alter global protests that is adressed. The authors show that INSURA is certainly well suited to explore the demographics of alter-global events, as well as relational networks of individuals and multiple belongings. On the contrary, it is assumed that organization networks and movement's boundaries are far more difficult to explore through that method, a fact that seriously limits international cross comparisons of events and movements based on that tool.