999 resultados para Code validation


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Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schrödinger equation for low-dimensionality systems.

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The genetic code establishes the rules that govern gene translation into proteins. It was established more than 3.5 billion years ago and it is one of the most conserved features of life. Despite this, several alterations to the standard genetic code have been discovered in both prokaryotes and eukaryotes, namely in the fungal CTG clade where a unique seryl transfer RNA (tRNACAG Ser) decodes leucine CUG codons as serine. This tRNACAG Ser appeared 272±25 million years ago through insertion of an adenosine in the middle position of the anticodon of a tRNACGA Ser gene, which changed its anticodon from 5´-CGA-3´ to 5´-CAG-3´. This most dramatic genetic event restructured the proteome of the CTG clade species, but it is not yet clear how and why such deleterious genetic event was selected and became fixed in those fungal genomes. In this study we have attempted to shed new light on the evolution of this fungal genetic code alteration by reconstructing its evolutionary pathway in vivo in the yeast Saccharomyces cerevisiae. For this, we have expressed wild type and mutant versions of the C. albicans tRNACGA Ser gene into S. cerevisiae and evaluated the impact of the mutant tRNACGA Ser on fitness, tRNA stability, translation efficiency and aminoacylation kinetics. Our data demonstrate that these mutants are expressed and misincorporate Ser at CUGs, but their expression is repressed through an unknown molecular mechanism. We further demonstrate, using in vivo forced evolution methodologies, that the tRNACAG Ser can be easily inactivated through natural mutations that prevent its recognition by the seryl-tRNA synthetase. The overall data show that repression of expression of the mistranslating tRNACAG Ser played a critical role on the evolution of CUG reassignment from Leu to Ser. In order to better understand the evolution of natural genetic code alterations, we have also engineered partial reassignment of various codons in yeast. The data confirmed that genetic code ambiguity affects fitness, induces protein aggregation, interferes with the cell cycle and results in nuclear and morphologic alterations, genome instability and gene expression deregulation. Interestingly, it also generates phenotypic variability and phenotypes that confer growth advantages in certain environmental conditions. This study provides strong evidence for direct and critical roles of the environment on the evolution of genetic code alterations.

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Ria deAveiro is a very complex shallow water coastal lagoon located on the northwest of Portugal. Important issues would be left unanswered without a good understanding of hydrodynamic and transport processes occurring in the lagoon. Calibration and validation of hydrodynamic, salt and heat transport models for Ria de Aveiro lagoon are presented. The calibration of the hydrodynamic model was performed adjusting the bottom friction coefficient, through the comparison between measured and predicted time series of sea surface elevation for 22 stations. Harmonic analysis was performed in order to evaluate the model's accuracy. To validate the hydrodynamic model measured and predicted SSE values were compared for 11 stations, as well as main flow direction velocities for 10 stations. The salt and heat transport models were calibrated comparing measured and predicted time series of salinity and water temperature for 7 stations, and the RMS of the difference between the series was determined. These models were validated comparing the model results with an independent field data set. The hydrodynamic and the salt and heat transport models for Ria de Aveiro were successfully calibrated and validated. They reproduce accurately the barotropic flows and can therefore adequately represent the salt and heat transport and the heat transfer processes occurring in Ria deAveiro.

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The genetic code is not universal. Alterations to its standard form have been discovered in both prokaryotes and eukaryotes and demolished the dogma of an immutable code. For instance, several Candida species translate the standard leucine CUG codon as serine. In the case of the human pathogen Candida albicans, a serine tRNA (tRNACAGSer) incorporates in vivo 97% of serine and 3% of leucine in proteins at CUG sites. Such ambiguity is flexible and the level of leucine incorporation increases significantly in response to environmental stress. To elucidate the function of such ambiguity and clarify whether the identity of the CUG codon could be reverted from serine back to leucine, we have developed a forced evolution strategy to increase leucine incorporation at CUGs and a fluorescent reporter system to monitor such incorporation in vivo. Leucine misincorporation increased from 3% up to nearly 100%, reverting CUG identity from serine back to leucine. Growth assays showed that increasing leucine incorporation produced impressive arrays of phenotypes of high adaptive potential. In particular, strains with high levels of leucine misincorporation exhibited novel phenotypes and high level of tolerance to antifungals. Whole genome re-sequencing revealed that increasing levels of leucine incorporation were associated with accumulation of single nucleotide polymorphisms (SNPs) and loss of heterozygozity (LOH) in the higher misincorporating strains. SNPs accumulated preferentially in genes involved in cell adhesion, filamentous growth and biofilm formation, indicating that C. albicans uses its natural CUG ambiguity to increase genetic diversity in pathogenesis and drug resistance related processes. The overall data provided evidence for unantecipated flexibility of the C. albicans genetic code and highlighted new roles of codon ambiguity on the evolution of genetic and phenotypic diversity.

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Although the genetic code is generally viewed as immutable, alterations to its standard form occur in the three domains of life. A remarkable alteration to the standard genetic code occurs in many fungi of the Saccharomycotina CTG clade where the Leucine CUG codon has been reassigned to Serine by a novel transfer RNA (Ser-tRNACAG). The host laboratory made a major breakthrough by reversing this atypical genetic code alteration in the human pathogen Candida albicans using a combination of tRNA engineering, gene recombination and forced evolution. These results raised the hypothesis that synthetic codon ambiguities combined with experimental evolution may release codons from their frozen state. In this thesis we tested this hypothesis using S. cerevisiae as a model system. We generated ambiguity at specific codons in a two-step approach, involving deletion of tRNA genes followed by expression of non-cognate tRNAs that are able to compensate the deleted tRNA. Driven by the notion that rare codons are more susceptible to reassignment than those that are frequently used, we used two deletion strains where there is no cognate tRNA to decode the rare CUC-Leu codon and AGG-Arg codon. We exploited the vulnerability of the latter by engineering mutant tRNAs that misincorporate Ser at these sites. These recombinant strains were evolved over time using experimental evolution. Although there was a strong negative impact on the growth rate of strains expressing mutant tRNAs at high level, such expression at low level had little effect on cell fitness. We found that not only codon ambiguity, but also destabilization of the endogenous tRNA pool has a strong negative impact in growth rate. After evolution, strains expressing the mutant tRNA at high level recovered significantly in several growth parameters, showing that these strains adapt and exhibit higher tolerance to codon ambiguity. A fluorescent reporter system allowing the monitoring of Ser misincorporation showed that serine was indeed incorporated and possibly codon reassignment was achieved. Beside the overall negative consequences of codon ambiguity, we demonstrated that codons that tolerate the loss of their cognate tRNA can also tolerate high Ser misincorporation. This raises the hypothesis that these codons can be reassigned to standard and eventually to new amino acids for the production of proteins with novel properties, contributing to the field of synthetic biology and biotechnology.

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A three-dimensional primitive equation model and its application to a tidal estuary is described. The model solves the primitive equations for incompressible fluids with Boussinesq and hydrostatic approximations. The discretization is based on the finite volume method and allows a general vertical coordinate. The computational code is implemented in such a way that different vertical coordinates can be used in different parts of the domain. The model was designed to be able to simulate the flow both in the open ocean and in coastal and estuarine zones and can be coupled in a simple way to ecological models. The model was implemented successfully in several estuarine and coastal areas. Results are show for the Sado estuary in Portugal to illustrate model accuracy and potential. Quantitative validation is based on field data (water levels and velocities) while qualitative verification is based on the analysis of secondary flows.

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Dissolved oxygen (DO) is one of the most important environmental variables of water quality, especially for marine life. Consequently, oxygen is one of the Chemical Quality Elements required for the implementation of European Union Water Framework Directive. This study uses the example of the Ria Formosa, a meso-tidal lagoon on the south coast of Portugal to demonstrate how monitoring of water quality for coastal waters must be well designed to identify symptoms of episodic hypoxia. New data from the western end of the Ria Formosa were compared to values in a database of historical data and in the published literature to identify long-term trends. The dissolved oxygen concentration values in the database and in the literature were generally higher than those found in this study, where episodic hypoxia was observed during the summer. Analysis of the database showed that the discrepancy was probably related with the time and the sites where the samples had been collected, rather than a long-term trend. The most problematic situations were within the inner lagoon near the city of Faro, where episodic hypoxia (<2 mg dm3 DO) occurred regularly in the early morning. These results emphasise the need for a balanced sampling strategy for oxygen monitoring which includes all periods of the day and night, as well as a representative range of sites throughout the lagoon. Such a strategy would provide adequate data to apply management measures to reduce the risk of more persistent hypoxia that would impact on the ecological, important natural resource. economic and leisure uses of this important natural resource.

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La Bibliothèque du Code civil de Charles-Chamilly de Lorimier et Charles-Albert Vilbon, parue au cours de la seconde moitié du XIXe siècle, demeure un des ouvrages de référence marquants de la production juridique québécoise. Les artisans de cet ouvrage présentent le droit civil comme un héritage du passé. L’oeuvre, par sa valorisation des anciens auteurs, propose une lecture du Code civil qui s’inscrit dans la tradition. En même temps, elle se révèle un outil adapté à la transformation que connaît alors la pratique du droit. La Bibliothèque constitue un témoin éloquent de l’évolution de la culture juridique québécoise.

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Cet essai présente les résultats d'une recherche expérimentation en vue de valider un modèle de formation en ligne auprès des diététistes. Les besoins accrus de formation suscités par le nouveau cadre normatif amènent l'Ordre professionnel des diététistes du Québec (OPDQ) à développer différents moyens de perfectionnement pour ses membres. Bien que les moyens actuellement disponibles soient assez diversifiés, il importe de pouvoir offrir au plus grand nombre possible une offre de formation de haut niveau afin d'assurer e développement des compétences des diététistes. Comme l'OPDQ n'a pas les effectifs nécessaires pour former rapidement un grand nombre de personnes dispersées géographiquement, il devient intéressant d'explorer des moyens de formation complémentaires et d'envisager exploiter les possibilités offertes par la formation en ligne. C'est ainsi que l'auteure de cette recherche a constaté que l'ajout d'une offre complémentaire de formation en ligne pourrait grandement profiter aux diététistes afin de les aider à mieux répondre à l'obligation de mise à jour de leurs connaissances. Une enquête réalisée à l'été 2006 auprès des membres de l'OPDQ confirmait l'intérêt des répondantes pour ce type de formation ainsi que la présence des habiletés technologiques nécessaires. Les données alors recueillies ont permis de cibler une compétence à développer et d'expérimenter, auprès des diététistes, un modèle de formation en ligne portant sur le choix de la voie d'alimentation appropriée. Les objectifs spécifiques de la recherche expérimentation consistaient à élaborer un modèle de formation en ligne pour ensuite l'expérimenter auprès d'un groupe pilote de diététistes en exercice afin d'en évaluer le potentiel. Ce modèle identifiait les dimensions à considérer en ce qui concerne les apprenantes et les apprenants, leur accompagnement, le choix de la compétence et l'élaboration du système d'apprentissage.

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Tese de doutoramento, Bioquimica, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

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Dissertação de mestrado, Qualidade em Análises, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

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Dissertação de Mestrado, Qualidade em Análises, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

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Wir beschreiben und belegen anhand eines Pilotprojekts in einer zweiten Grundschulklasse, dass Informatik in der Grundschule das Potential hat, fächerübergreifend Kompetenzen in fast allen Fächern des Grundschulkanons zu fördern. Wir erläutern mehrere Unterrichtseinheiten eines ScratchJr-Einsatzes und dokumentieren positive Wirkungen auf vielfältige Kompetenzen, die Kinder im Grundschulalter erwerben sollen. Der Beitrag stellt einen Erfahrungsbericht und qualitative Ergebnisse zur Verfügung. Eingesetzte Arbeitsmaterialien werden online zur Verfügung gestellt. Die bisherigen positiven Erfahrungen haben uns veranlasst, die Arbeit mit ScratchJr in der Pilotklasse auf mehrere Monate auszudehnen.

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Tese de doutoramento, Geografia (Geografia Física), Universidade de Lisboa, Instituto de Geografia e Ordenamento do Território, 2014

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Tese de mestrado. Biologia (Biologia Humana e Ambiente). Universidade de Lisboa, Faculdade de Ciências, 2014