Comparative analyses of classical phenotypic method and ribosomal RNA gene sequencing for identification of medically relevant Candida species

As the distribution of Candida species and their susceptibility to antifungal agents have changed, a new means of accurately and rapidly identifying these species is necessary for the successful early resolution of infection and the subsequent reduction of morbidity and mortality. The current work aimed to evaluate ribosomal RNA gene sequencing for the identification of medically relevant Candida species in comparison with a standard phenotypic method. Eighteen reference strains (RSs), 69 phenotypically identified isolates and 20 inconclusively identified isolates were examined. Internal transcribed spaces (ITSs) and D1/D2 of the 26S ribosomal RNA gene regions were used as targets for sequencing. Additionally, the sequences of the ITS regions were used to establish evolutionary relationships. The sequencing of the ITS regions was successful for 88% (94/107) of the RS and isolates, whereas 100% of the remaining 12% (13/107) of the samples were successfully analysed by sequencing the D1/D2 region. Similarly, genotypic analysis identified all of the RS and isolates, including the 20 isolates that were not phenotypically identified. Phenotypic analysis, however, misidentified 10% (7/69) of the isolates. Phylogenetic analysis allowed the confirmation of the relationships between evolutionarily close species. Currently, the use of genotypic methods is necessary for the correct identification of Candida species.

Design,implementation and use of an Internet kiosk as an an information system for CNC machinists

Tätä diplomityötä sponsoroi suuri Isobritannialainen lentokoneteollisuudessa toimiva yritys, joka huomasi että globaalin tuotantostrategian ollessa painopisteenä ja tietoteknisten järjestelmien kuten CAD/CAM ollessa merkittävänä osana tuotantoa, on löydettävä ymmärrys siitä, mitkä ovat tuotannon tietojärjestelmien tarpeet ja onko niiden kehittämisestä hyötyä yritykselle.Diplomityössä selitetään Internet teknologiaan perustuvan kioskin kehittämisestä tietotukijärjestelmäksi tuotanto-osastolle, jossa valmistetaan moottorin osia CNC-koneilla. Kioskeissa on piirteitä, jotka voisivat osoittautua hyödyllisiksi myös tuotantoympäristöissä ja siksi tässä työssä tutkitaan kioskiin perustuvaa lähestymistapaa tuotantoympäristöön sovellettuna.Diplomityö kuvaa informaatiokioskin kehittämistä alkaen alkuvaatimusten keruusta tietojärjestelmää varten, tietojärjestelmän suunnittelu- ja kehitysvaiheen sekä lopuksi analysoi kioskin onnistuneisuutta tuotantoympäristössä käytettävyystutkimuksen avulla, joka suoritettiin sen jälkeen kun kioski oli implementoitu tehtaassa.Johtopäätökset osoittavat, että kioski on hyvin implementoitavissa tuotantoympäristöön ja todistaa, että tuotantoinformaation jakelu sähköisessä muodossa on huomattavasti tehokkaampaa kuin paperilla. Käyttäjien kommentit osoittavat että kioski on sopiva heidän tietotarpeisiinsa ja siitä on hyötyä heidän työlleen. Kioski tarjoaa hyötyjä tuotantotason lisäksi myös johtotasolle.

International STakeholder NETwork (ISTNET): creating a developmental neurotoxicity (DNT) testing road map for regulatory purposes.

A major problem in developmental neurotoxicity (DNT) risk assessment is the lack of toxicological hazard information for most compounds. Therefore, new approaches are being considered to provide adequate experimental data that allow regulatory decisions. This process requires a matching of regulatory needs on the one hand and the opportunities provided by new test systems and methods on the other hand. Alignment of academically and industrially driven assay development with regulatory needs in the field of DNT is a core mission of the International STakeholder NETwork (ISTNET) in DNT testing. The first meeting of ISTNET was held in Zurich on 23-24 January 2014 in order to explore the concept of adverse outcome pathway (AOP) to practical DNT testing. AOPs were considered promising tools to promote test systems development according to regulatory needs. Moreover, the AOP concept was identified as an important guiding principle to assemble predictive integrated testing strategies (ITSs) for DNT. The recommendations on a road map towards AOP-based DNT testing is considered a stepwise approach, operating initially with incomplete AOPs for compound grouping, and focussing on key events of neurodevelopment. Next steps to be considered in follow-up activities are the use of case studies to further apply the AOP concept in regulatory DNT testing, making use of AOP intersections (common key events) for economic development of screening assays, and addressing the transition from qualitative descriptions to quantitative network modelling.

Évaluation formative du programme de santé sexuelle Chî kayeh sous l'angle de l'appréciation d'élèves de deux communautés cries

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Les campagnes sociales destinées aux jeunes adultes québécois sur Internet : pistes pour l'optimisation des sites Web

Avec la montée en popularité d’Internet et des médias sociaux, de plus en plus d’organismes sociaux et publics, notamment, intègrent des plateformes Web à leurs volets traditionnels. La question d’Internet demeure toutefois peu étudiée eu égard à la publicité sociale. Ce mémoire porte donc sur la question du Web en relation avec les campagnes sociales adressées aux jeunes Québécois de 18 à 25 ans, une population particulièrement réceptive aux nouvelles technologies. Plus exactement, dans cette étude, nous avons analysé trois sites Web rattachés à des campagnes sociales (La vitesse, ça coûte cher de la SAAQ, Les ITSS se propagent du MSSS et 50 000 adeptes, 5 000 toutous de la Fondation CHU Sainte-Justine) dans l’objectif de déterminer leurs forces et leurs faiblesses pour ensuite proposer des pistes pour leur optimisation. C’est à l’aide d’une analyse critique de contenu suivie d’entrevues et d’observations individuelles auprès de 19 participants que nous sommes parvenue à suggérer des pistes pour l’optimisation des sites Web de campagnes sociales destinées aux jeunes adultes québécois. Une des plus grandes difficultés en ce qui a trait à leur conception consiste à choisir les stratégies les plus appropriées pour provoquer un changement d’attitude ou de comportement, a fortiori chez ceux qui adoptent des comportements à risque (fumer, conduire en état d’ébriété, avoir des relations sexuelles non protégées); des stratégies qui, pour être plus efficaces, devraient être adaptées en fonction des caractéristiques propres aux publics cibles et aux médias de diffusion. Afin d’analyser adéquatement les campagnes sociales, nous avons fait appel aux théories de la persuasion et aux théories sur l’influence des médias jugées pertinentes dans notre contexte puisqu’elles sont propres à ce type d’étude. Ces approches combinées nous ont permis d’intégrer à l’analyse d’une campagne donnée les contextes qui l’entourent et les pratiques dans lesquelles elle s’inscrit. Cette étude nous a, entre autres, permis de démontrer qu’il existait d’importants écarts entre les attentes et les besoins des internautes et l’offre des sites Web étudiés.

Phylogenetic relationships among genera Eucalyptus and Corymbia species based on rnDNA internal transcribed spacers sequences

Phylogenetio relationships between Eucalyptus species, subgenus Symphyomyrtus (sections Adnataria, Exsertaria, Maldenaria, and Transversaria), and Corymbia species (sections Politaria and Ocharia) were established based on the sequence of Internal transcribed rDNA spacers (ITS1 and ITS2). The species analyzed were obtained from a collection kept in Brazil. Fragments obtained using primers ITS1 and ITS2 were sequenced and part of the sequence of ITS1 and ITS2 and the complete sequence of 5.8S rDNA were used in the analysis. ITSs and 5.8S rDNA sequences from E. globulus ssp. globulus and A. bakeri (Genus Angophora) were downloaded from the Genbank database and included in the analysis. Psidlum guajava was the selected outgroup used. The sequence alignment and a Neighbor-joining tree were obtained using Clustal X. Few variations were detected in the 5.8S rDNA sequences obtained, occurring mainly between Eucalyptus and Corymbia, thus defining these genera. Variations in ITS sequences occurred in all investigated species. Phylogenetic analysis showed a clear separation between the genera Corymbia and Eucalyptus. A bakeri was more closely related to species belonging to genus Corymbia. Regarding the subgenus Symphyomyrtus (Genus Eucalyptus), only species from section Maidenaria grouped together according to their common section. This could have been caused by the removal of natural reproductive barriers when these species were introduced In Brazil, with a consequent Increase in the rate of interspecific crossings and Introgression events.

Genetic Variability and Geographical Diversity of the Main Chagas' Disease Vector Panstrongylus megistus (Hemiptera: Triatominae) in Brazil Based on Ribosomal DNA Intergenic Sequences

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Extensive spreading of interstitial telomeric sites on the chromosomes of Characidium (Teleostei, Characiformes)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Phylogeographic Structure and Karyotypic Diversity of the Brazilian Shrew Mouse (Blarinomys breviceps, Sigmodontinae) in the Atlantic Forest

Blarinomys breviceps possesses cryptic and burrowing habits with poorly documented genetics and life history traits. Due to its rarity, only a few specimens and DNA sequences have been deposited in collections worldwide. Here, we present the most comprehensive cytogenetic and molecular characterization of this rare genus. Phylogenetic analyses based on partial cytochrome b sequences were performed, attempting to establish the relationships among individuals with distinct karyotypes along the geographic distribution of the genus in the Atlantic Forest. Classical and molecular cytogenetics, using banding patterns and FISH of telomeric and whole chromosome X-specific painting probes (obtained from the Akodontini Akodon cursor) were used to characterize and compare the chromosomal complements. Molecular phylogenetic analyses recovered 2 main geographically structured clades, northeastern and southeastern with pair-wise sequence divergences among specimens varying between 4.9 and 8.4%. Eight distinct karyomorphs are described: (A) 2n = 52 (50A, XX), (B) 2n = 52 (48A, XY+2Bs), (C) 2n = 45 (42A, XY+1B), (D) 2n = 43 (37A, XX+4Bs), (E) 2n = 37 (34A, XY+1B), (F) 2n = 34 (32A, XX), (G) 2n = 31 (27A, XX+2Bs), (H) 2n = 28 (26A, XY), all with the same number of autosomal arms (FNA = 50). Variation of 0-4 supernumerary chromosomes (Bs) presenting heterogeneity in morphology and distribution of interstitial telomeric sequences (ITSs) is reported. ITSs are also found in some metacentric autosomes. The phylogeographic separation between 2 major lineages with high levels of genetic divergence, and the wide karyotypic diversity indicate that B. breviceps is a diverse group that warrants taxonomic re-evaluation. Copyright (C) 2012 S. Karger AG, Basel

Integrated testing strategy (ITS) for bioaccumulation assessment under REACH

REACH (registration, evaluation, authorisation and restriction of chemicals) regulation requires that all the chemicals produced or imported in Europe above 1 tonne/year are registered. To register a chemical, physicochemical, toxicological and ecotoxicological information needs to be reported in a dossier. REACH promotes the use of alternative methods to replace, refine and reduce the use of animal (eco)toxicity testing. Within the EU OSIRIS project, integrated testing strategies (ITSs) have been developed for the rational use of non-animal testing approaches in chemical hazard assessment. Here we present an ITS for evaluating the bioaccumulation potential of organic chemicals. The scheme includes the use of all available data (also the non-optimal ones), waiving schemes, analysis of physicochemical properties related to the end point and alternative methods (both in silico and in vitro). In vivo methods are used only as last resort. Using the ITS, in vivo testing could be waived for about 67% of the examined compounds, but bioaccumulation potential could be estimated on the basis of non-animal methods. The presented ITS is freely available through a web tool.

Optimizing the aquatic toxicity assessment under REACH through an integrated testing strategy (ITS).

To satisfy REACH requirements a high number of data on chemical of interest should be supplied to the European Chemicals Agency. To organize the various kinds of information and help the registrants to choose the best strategy to obtain the needed information limiting at the minimum the use of animal testing, integrated testing strategies (ITSs) schemes can be used. The present work deals with regulatory data requirements for assessing the hazards of chemicals to the aquatic pelagic environment. We present an ITS scheme for organizing and using the complex existing data available for aquatic toxicity assessment. An ITS to optimize the choice of the correct prediction strategy for aquatic pelagic toxicity is described. All existing information (like physico-chemical information), and all the alternative methods (like in silico, in vitro or the acute-to-chronic ratio) are considered. Moreover the weight of evidence approach to combine the available data is included.

Una propuesta de modelado del estudiante basada en ontologías y diagnóstico pedagógico-cognitivo no monótono

Los recientes avances tecnológicos han encontrado un potencial campo de explotación en la educación asistida por computador. A finales de los años 90 surgió un nuevo campo de investigación denominado Entornos Virtuales Inteligentes para el Entrenamiento y/o Enseñanza (EVIEs), que combinan dos áreas de gran complejidad: Los Entornos Virtuales (EVs) y los Sistemas de Tutoría Inteligente (STIs). De este modo, los beneficios de los entornos 3D (simulación de entornos de alto riesgo o entornos de difícil uso, etc.) pueden combinarse con aquéllos de un STIs (personalización de materias y presentaciones, adaptación de la estrategia de tutoría a las necesidades del estudiante, etc.) para proporcionar soluciones educativas/de entrenamiento con valores añadidos. El Modelo del Estudiante, núcleo de un SIT, representa el conocimiento y características del estudiante, y refleja el proceso de razonamiento del estudiante. Su complejidad es incluso superior cuando los STIs se aplican a EVs porque las nuevas posibilidades de interacción proporcionadas por estos entornos deben considerarse como nuevos elementos de información clave para el modelado del estudiante, incidiendo en todo el proceso educativo: el camino seguido por el estudiante durante su navegación a través de escenarios 3D; el comportamiento no verbal tal como la dirección de la mirada; nuevos tipos de pistas e instrucciones que el módulo de tutoría puede proporcionar al estudiante; nuevos tipos de preguntas que el estudiante puede formular, etc. Por consiguiente, es necesario que la estructura de los STIs, embebida en el EVIE, se enriquezca con estos aspectos, mientras mantiene una estructura clara, estructurada, y bien definida. La mayoría de las aproximaciones al Modelo del Estudiante en STIs y en IVETs no consideran una taxonomía de posibles conocimientos acerca del estudiante suficientemente completa. Además, la mayoría de ellas sólo tienen validez en ciertos dominios o es difícil su adaptación a diferentes STIs. Para vencer estas limitaciones, hemos propuesto, en el marco de esta tesis doctoral, un nuevo mecanismo de Modelado del Estudiante basado en la Ingeniería Ontológica e inspirado en principios pedagógicos, con un modelo de datos sobre el estudiante amplio y flexible que facilita su adaptación y extensión para diferentes STIs y aplicaciones de aprendizaje, además de un método de diagnóstico con capacidades de razonamiento no monótono. El método de diagnóstico es capaz de inferir el estado de los objetivos de aprendizaje contenidos en el SIT y, a partir de él, el estado de los conocimientos del estudiante durante su proceso de aprendizaje. La aproximación almodelado del estudiante propuesta ha sido implementada e integrada en un agente software (el agente de modelado del estudiante) dentro de una plataforma software existente para el desarrollo de EVIEs denominadaMAEVIF. Esta plataforma ha sido diseñada para ser fácilmente configurable para diferentes aplicaciones de aprendizaje. El modelado del estudiante presentado ha sido implementado e instanciado para dos tipos de entornos de aprendizaje: uno para aprendizaje del uso de interfaces gráficas de usuario en una aplicación software y para un Entorno Virtual para entrenamiento procedimental. Además, se ha desarrollado una metodología para guiar en la aplicación del esta aproximación de modelado del estudiante a cada sistema concreto.---ABSTRACT---Recent technological advances have found a potential field of exploitation in computeraided education. At the end of the 90’s a new research field emerged, the so-called Intelligent Virtual Environments for Training and/or Education (IVETs), which combines two areas of great complexity: Virtual Environments (VE) and Intelligent Tutoring Systems (ITS). In this way, the benefits of 3D environments (simulation of high risk or difficult-to-use environments, etc.) may be combined with those of an ITS (content and presentation customization, adaptation of the tutoring strategy to the student requirements, etc.) in order to provide added value educational/training solutions. The StudentModel, core of an ITS, represents the student’s knowledge and characteristics, and reflects the student’s reasoning process. Its complexity is even higher when the ITSs are applied on VEs because the new interaction possibilities offered by these environments must be considered as new key information pieces for student modelling, impacting all the educational process: the path followed by the student during their navigation through 3D scenarios; non-verbal behavior such as gaze direction; new types of hints or instructions that the tutoring module can provide to the student; new question types that the student can ask, etc. Thus, it is necessary for the ITS structure, which is embedded in the IVET, to be enriched by these aspects, while keeping a clear, structured and well defined architecture. Most approaches to SM on ITSs and IVETs don’t consider a complete enough taxonomy of possible knowledge about the student. In addition, most of them have validity only in certain domains or they are hard to be adapted for different ITSs. In order to overcome these limitations, we have proposed, in the framework of this doctoral research project, a newStudentModeling mechanism that is based onOntological Engineering and inspired on pedagogical principles, with a wide and flexible data model about the student that facilitates its adaptation and extension to different ITSs and learning applications, as well as a rich diagnosis method with non-monotonic reasoning capacities. The diagnosis method is able to infer the state of the learning objectives encompassed by the ITS and, fromit, the student’s knowledge state during the student’s process of learning. The proposed student modelling approach has been implemented and integrated in a software agent (the student modeling agent) within an existing software platform for the development of IVETs called MAEVIF. This platform was designed to be easily configurable for different learning applications. The proposed student modeling has been implemented and it has been instantiated for two types of learning environments: one for learning to use the graphical user interface of a software application and a Virtual Environment for procedural training. In addition, a methodology to guide on the application of this student modeling approach to each specific system has been developed.

An iterative-style approach to constructing intelligent tutoring systems in mathematics

Mathematics is highly structured and also underpins most of science and engineering. For this reason, it has proved a very suitable domain for Intelligent Tutoring System (ITS) research, with the result that probably more tutoring systems have been constructed for the domain than any other. However, the literature reveals that there still exists no consensus on a credible approach or approaches for the design of such systems, despite numerous documented efforts. Current approaches to the construction of ITSs leave much to be desired. Consequently, existing ITSs in the domain suffer from a considerable number of shortcomings which render them 'unintelligent'. The thesis examines some of the reasons why this is the case. Following a critical review of existing ITSs in the domain, and some pilot studies, an alternative approach to their construction is proposed (the 'iterative-style' approach); this supports an iterative style, and also improves on at least some of the shortcomings of existing approaches. The thesis also presents an ITS for fractions which has been developed using this approach, and which has been evaluated in various ways. It has, demonstrably, improved on many of the limitations of existing ITSs; furthermore, it has been shown to be largely 'intelligent', at least more so than current tutors for the domain. Perhaps more significantly, the tutor has also been evaluated against real students with, so far, very encouraging results. The thesis thus concludes that the novel iterative-style approach is a more credible approach to the construction of ITSs in mathematics than existing techniques.

Comparing architectural styles for distributed expert knowledge modules in intelligent tutoring systems

Intelligent Tutoring Systems (ITSs) are computerized systems for learning-by-doing. These systems provide students with immediate and customized feedback on learning tasks. An ITS typically consists of several modules that are connected to each other. This research focuses on the distribution of the ITS module that provides expert knowledge services. For the distribution of such an expert knowledge module we need to use an architectural style because this gives a standard interface, which increases the reusability and operability of the expert knowledge module. To provide expert knowledge modules in a distributed way we need to answer the research question: ‘How can we compare and evaluate REST, Web services and Plug-in architectural styles for the distribution of the expert knowledge module in an intelligent tutoring system?’. We present an assessment method for selecting an architectural style. Using the assessment method on three architectural styles, we selected the REST architectural style as the style that best supports the distribution of expert knowledge modules. With this assessment method we also analyzed the trade-offs that come with selecting REST. We present a prototype and architectural views based on REST to demonstrate that the assessment method correctly scores REST as an appropriate architectural style for the distribution of expert knowledge modules.

Les technologies de l'information et de la télécommunication (TIC) pour la promotion de la santé sexuelle et reproductive (SSR) au sein des jeunes des Premières Nations du Québec : faisabilité et pistes d'intervention

La répartition des taux de prévalence des infections transmissibles sexuellement et par le sang (ITSS) et du VIH/SIDA au Canada présente de grandes inégalités entre les différents groupes socioculturels. Les Autochtones font partie des populations qui en payent le plus lourd tribut. Par rapport à cette situation, le plan directeur 2007-2017 de la commission de la santé et des services sociaux des Premières Nations du Québec et du Labrador (CSSSPNQL) identifie clairement le VIH/SIDA comme une problématique prioritaire de santé. La stratégie autochtone sur le VIH/SIDA estime que pour être efficaces, les interventions visant la prévention du VIH/SIDA doivent cibler divers groupes, au nombre desquels la jeunesse autochtone est une cible particulière. En ce sens, la familiarité des jeunes générations avec la technologie positionne l’utilisation des technologies de l’information et de la communication (TIC) comme une avenue fortement prometteuse dans le domaine de la prévention du VIH/SIDA chez les adolescents et jeunes adultes. Nous avons réalisé une synthèse des connaissances dans ce domaine novateur suivant une méthodologie suggérée par la Collaboration Cochrane dans le but de documenter l’efficacité et les facteurs d’adoption des interventions utilisant les TIC pour la prévention des ITSS/VIH/SIDA et la promotion de la santé sexuelle et reproductive auprès des adolescents et jeunes adultes. Les résultats de cette revue systématique ont permis d’élaborer et de mener, en partenariat avec la CSSSPNQL, un projet de recherche visant à évaluer la faisabilité de telles interventions au sein des adolescents et jeunes adultes de communautés des Premières Nations (PN) du Québec. En complément à cette étude de faisabilité et dans le but de formuler des recommandations en vue de la conception d’interventions utilisant les TIC et fondées autant sur les données probantes que sur les réalités des jeunes des PN, nous avons entrepris une dernière étude visant à identifier les facteurs sous-jacents du port du condom chez les 13-18 ans de communautés des Premières Nations du Québec. Nous avons discuté, dans la présente thèse, les résultats de ces études ainsi que divers enjeux du partenariat de recherche avec les parties prenantes des PN ayant participé à notre projet. Les implications pratiques de nos résultats, en matière de recherche et d’intervention, sont à discuter avec notre principale partenaire, la CSSSPNQL, afin d’en optimiser les retombées pour les populations des PN.