Remote Monitoring of Fish in Small Streams: A Unified Approach Using Pit Tags

Accurate assessments of fish populations are often limited by re-observation or recapture events. Since the early 1990s, passive integrated transponders (PIT tags) have been used to understand the biology of many fish species. Until recently, PIT applications in small streams have been limited to physical recapture events. To maximize recapture probability, we constructed PIT antenna arrays in small streams to remotely detect individual fish. Experiences from two different laboratories (three case studies) allowed us to develop a unified approach to applying PIT technology for enhancing data assessments. Information on equipment, its installation, tag considerations, and array construction is provided. Theoretical and practical definitions are introduced to standardize metrics for assessing detection efficiency. We demonstrate how certain conditions (stream discharge, vibration, and ambient radio frequency noise) affect the detection efficiency and suggest that by monitoring these conditions, expectations of efficiency can be modified. We emphasize the importance of consistently estimating detection efficiency for fisheries applications.

Validation of an instrument for assessing the medicolegal death investigation system: A public health approach

Background. This study validated the content of an instrument designed to assess the performance of the medicolegal death investigation system. The instrument was modified from Version 2.0 of the Local Public Health System Performance Assessment Instrument (CDC) and is based on the 10 Essential Public Health Services. ^ Aims. The aims were to employ a cognitive testing process to interview a randomized sample of medicolegal death investigation office leaders, qualitatively describe the results, and revise the instrument accordingly. ^ Methods. A cognitive testing process was used to validate the survey instrument's content in terms of the how well participants could respond to and interpret the questions. Twelve randomly selected medicolegal death investigation chiefs (or equivalent) that represented the seven types of medicolegal death investigation systems and six different state mandates were interviewed by telephone. The respondents also were representative of the educational diversity within medicolegal death investigation leadership. Based on respondent comments, themes were identified that permitted improvement of the instrument toward collecting valid and reliable information when ultimately used in a field survey format. ^ Results. Responses were coded and classified, which permitted the identification of themes related to Comprehension/Interpretation, Retrieval, Estimate/Judgment, and Response. The majority of respondent comments related to Comprehension/Interpretation of the questions. Respondents identified 67 questions and 6 section explanations that merited rephrasing, adding, or deleting examples or words. In addition, five questions were added based on respondent comments. ^ Conclusion. The content of the instrument was validated by cognitive testing method design. The respondents agreed that the instrument would be a useful and relevant tool for assessing system performance. ^

A matrix pencil approach to the existence of compactly supported reconstruction functions in average sampling

The aim of this work is to solve a question raised for average sampling in shift-invariant spaces by using the well-known matrix pencil theory. In many common situations in sampling theory, the available data are samples of some convolution operator acting on the function itself: this leads to the problem of average sampling, also known as generalized sampling. In this paper we deal with the existence of a sampling formula involving these samples and having reconstruction functions with compact support. Thus, low computational complexity is involved and truncation errors are avoided. In practice, it is accomplished by means of a FIR filter bank. An answer is given in the light of the generalized sampling theory by using the oversampling technique: more samples than strictly necessary are used. The original problem reduces to finding a polynomial left inverse of a polynomial matrix intimately related to the sampling problem which, for a suitable choice of the sampling period, becomes a matrix pencil. This matrix pencil approach allows us to obtain a practical method for computing the compactly supported reconstruction functions for the important case where the oversampling rate is minimum. Moreover, the optimality of the obtained solution is established.

The estimation of truncation error by tau-estimation revisited

The aim of this paper was to accurately estimate the local truncation error of partial differential equations, that are numerically solved using a finite difference or finite volume approach on structured and unstructured meshes. In this work, we approximated the local truncation error using the @t-estimation procedure, which aims to compare the residuals on a sequence of grids with different spacing. First, we focused the analysis on one-dimensional scalar linear and non-linear test cases to examine the accuracy of the estimation of the truncation error for both finite difference and finite volume approaches on different grid topologies. Then, we extended the analysis to two-dimensional problems: first on linear and non-linear scalar equations and finally on the Euler equations. We demonstrated that this approach yields a highly accurate estimation of the truncation error if some conditions are fulfilled. These conditions are related to the accuracy of the restriction operators, the choice of the boundary conditions, the distortion of the grids and the magnitude of the iteration error.

Artificial cognitive control system based on the shared circuits model of sociocognitive capacities. A first approach

sharedcircuitmodels is presented in this work. The sharedcircuitsmodelapproach of sociocognitivecapacities recently proposed by Hurley in The sharedcircuitsmodel (SCM): how control, mirroring, and simulation can enable imitation, deliberation, and mindreading. Behavioral and Brain Sciences 31(1) (2008) 1–22 is enriched and improved in this work. A five-layer computational architecture for designing artificialcognitivecontrolsystems is proposed on the basis of a modified sharedcircuitsmodel for emulating sociocognitive experiences such as imitation, deliberation, and mindreading. In order to show the enormous potential of this approach, a simplified implementation is applied to a case study. An artificialcognitivecontrolsystem is applied for controlling force in a manufacturing process that demonstrates the suitability of the suggested approach

Comparison of Mesh Adaptation Using the Adjoint Methodology and Truncation Error Estimates

Mesh adaptation based on error estimation has become a key technique to improve th eaccuracy o fcomputational-fluid-dynamics computations. The adjoint-based approach for error estimation is one of the most promising techniques for computational-fluid-dynamics applications. Nevertheless, the level of implementation of this technique in the aeronautical industrial environment is still low because it is a computationally expensive method. In the present investigation, a new mesh refinement method based on estimation of truncation error is presented in the context of finite-volume discretization. The estimation method uses auxiliary coarser meshes to estimate the local truncation error, which can be used for driving an adaptation algorithm. The method is demonstrated in the context of two-dimensional NACA0012 and three-dimensional ONERA M6 wing inviscid flows, and the results are compared against the adjoint-based approach and physical sensors based on features of the flow field.

Efficient adaptive methods based on adjoint equations and truncation error estimation for unstructured grids

El propósito de esta tesis es la implementación de métodos eficientes de adaptación de mallas basados en ecuaciones adjuntas en el marco de discretizaciones de volúmenes finitos para mallas no estructuradas. La metodología basada en ecuaciones adjuntas optimiza la malla refinándola adecuadamente con el objetivo de mejorar la precisión de cálculo de un funcional de salida dado. El funcional suele ser una magnitud escalar de interés ingenieril obtenida por post-proceso de la solución, como por ejemplo, la resistencia o la sustentación aerodinámica. Usualmente, el método de adaptación adjunta está basado en una estimación a posteriori del error del funcional de salida mediante un promediado del residuo numérico con las variables adjuntas, “Dual Weighted Residual method” (DWR). Estas variables se obtienen de la solución del problema adjunto para el funcional seleccionado. El procedimiento habitual para introducir este método en códigos basados en discretizaciones de volúmenes finitos involucra la utilización de una malla auxiliar embebida obtenida por refinamiento uniforme de la malla inicial. El uso de esta malla implica un aumento significativo de los recursos computacionales (por ejemplo, en casos 3D el aumento de memoria requerida respecto a la que necesita el problema fluido inicial puede llegar a ser de un orden de magnitud). En esta tesis se propone un método alternativo basado en reformular la estimación del error del funcional en una malla auxiliar más basta y utilizar una técnica de estimación del error de truncación, denominada _ -estimation, para estimar los residuos que intervienen en el método DWR. Utilizando esta estimación del error se diseña un algoritmo de adaptación de mallas que conserva los ingredientes básicos de la adaptación adjunta estándar pero con un coste computacional asociado sensiblemente menor. La metodología de adaptación adjunta estándar y la propuesta en la tesis han sido introducidas en un código de volúmenes finitos utilizado habitualmente en la industria aeronáutica Europea. Se ha investigado la influencia de distintos parámetros numéricos que intervienen en el algoritmo. Finalmente, el método propuesto se compara con otras metodologías de adaptación de mallas y su eficiencia computacional se demuestra en una serie de casos representativos de interés aeronáutico. ABSTRACT The purpose of this thesis is the implementation of efficient grid adaptation methods based on the adjoint equations within the framework of finite volume methods (FVM) for unstructured grid solvers. The adjoint-based methodology aims at adapting grids to improve the accuracy of a functional output of interest, as for example, the aerodynamic drag or lift. The adjoint methodology is based on the a posteriori functional error estimation using the adjoint/dual-weighted residual method (DWR). In this method the error in a functional output can be directly related to local residual errors of the primal solution through the adjoint variables. These variables are obtained by solving the corresponding adjoint problem for the chosen functional. The common approach to introduce the DWR method within the FVM framework involves the use of an auxiliary embedded grid. The storage of this mesh demands high computational resources, i.e. over one order of magnitude increase in memory relative to the initial problem for 3D cases. In this thesis, an alternative methodology for adapting the grid is proposed. Specifically, the DWR approach for error estimation is re-formulated on a coarser mesh level using the _ -estimation method to approximate the truncation error. Then, an output-based adaptive algorithm is designed in such way that the basic ingredients of the standard adjoint method are retained but the computational cost is significantly reduced. The standard and the new proposed adjoint-based adaptive methodologies have been incorporated into a flow solver commonly used in the EU aeronautical industry. The influence of different numerical settings has been investigated. The proposed method has been compared against different grid adaptation approaches and the computational efficiency of the new method has been demonstrated on some representative aeronautical test cases.

A swarm intelligence approach based on coupled oscillators: an application in demand side management with photovoltaic distributed generation

Esta Tesis aborda los problemas de eficiencia de las redes eléctrica desde el punto de vista del consumo. En particular, dicha eficiencia es mejorada mediante el suavizado de la curva de consumo agregado. Este objetivo de suavizado de consumo implica dos grandes mejoras en el uso de las redes eléctricas: i) a corto plazo, un mejor uso de la infraestructura existente y ii) a largo plazo, la reducción de la infraestructura necesaria para suplir las mismas necesidades energéticas. Además, esta Tesis se enfrenta a un nuevo paradigma energético, donde la presencia de generación distribuida está muy extendida en las redes eléctricas, en particular, la generación fotovoltaica (FV). Este tipo de fuente energética afecta al funcionamiento de la red, incrementando su variabilidad. Esto implica que altas tasas de penetración de electricidad de origen fotovoltaico es perjudicial para la estabilidad de la red eléctrica. Esta Tesis trata de suavizar la curva de consumo agregado considerando esta fuente energética. Por lo tanto, no sólo se mejora la eficiencia de la red eléctrica, sino que también puede ser aumentada la penetración de electricidad de origen fotovoltaico en la red. Esta propuesta conlleva grandes beneficios en los campos económicos, social y ambiental. Las acciones que influyen en el modo en que los consumidores hacen uso de la electricidad con el objetivo producir un ahorro energético o un aumento de eficiencia son llamadas Gestión de la Demanda Eléctrica (GDE). Esta Tesis propone dos algoritmos de GDE diferentes para cumplir con el objetivo de suavizado de la curva de consumo agregado. La diferencia entre ambos algoritmos de GDE reside en el marco en el cual estos tienen lugar: el marco local y el marco de red. Dependiendo de este marco de GDE, el objetivo energético y la forma en la que se alcanza este objetivo son diferentes. En el marco local, el algoritmo de GDE sólo usa información local. Este no tiene en cuenta a otros consumidores o a la curva de consumo agregado de la red eléctrica. Aunque esta afirmación pueda diferir de la definición general de GDE, esta vuelve a tomar sentido en instalaciones locales equipadas con Recursos Energéticos Distribuidos (REDs). En este caso, la GDE está enfocada en la maximización del uso de la energía local, reduciéndose la dependencia con la red. El algoritmo de GDE propuesto mejora significativamente el auto-consumo del generador FV local. Experimentos simulados y reales muestran que el auto-consumo es una importante estrategia de gestión energética, reduciendo el transporte de electricidad y alentando al usuario a controlar su comportamiento energético. Sin embargo, a pesar de todas las ventajas del aumento de auto-consumo, éstas no contribuyen al suavizado del consumo agregado. Se han estudiado los efectos de las instalaciones locales en la red eléctrica cuando el algoritmo de GDE está enfocado en el aumento del auto-consumo. Este enfoque puede tener efectos no deseados, incrementando la variabilidad en el consumo agregado en vez de reducirlo. Este efecto se produce porque el algoritmo de GDE sólo considera variables locales en el marco local. Los resultados sugieren que se requiere una coordinación entre las instalaciones. A través de esta coordinación, el consumo debe ser modificado teniendo en cuenta otros elementos de la red y buscando el suavizado del consumo agregado. En el marco de la red, el algoritmo de GDE tiene en cuenta tanto información local como de la red eléctrica. En esta Tesis se ha desarrollado un algoritmo autoorganizado para controlar el consumo de la red eléctrica de manera distribuida. El objetivo de este algoritmo es el suavizado del consumo agregado, como en las implementaciones clásicas de GDE. El enfoque distribuido significa que la GDE se realiza desde el lado de los consumidores sin seguir órdenes directas emitidas por una entidad central. Por lo tanto, esta Tesis propone una estructura de gestión paralela en lugar de una jerárquica como en las redes eléctricas clásicas. Esto implica que se requiere un mecanismo de coordinación entre instalaciones. Esta Tesis pretende minimizar la cantidad de información necesaria para esta coordinación. Para lograr este objetivo, se han utilizado dos técnicas de coordinación colectiva: osciladores acoplados e inteligencia de enjambre. La combinación de estas técnicas para llevar a cabo la coordinación de un sistema con las características de la red eléctrica es en sí mismo un enfoque novedoso. Por lo tanto, este objetivo de coordinación no es sólo una contribución en el campo de la gestión energética, sino también en el campo de los sistemas colectivos. Los resultados muestran que el algoritmo de GDE propuesto reduce la diferencia entre máximos y mínimos de la red eléctrica en proporción a la cantidad de energía controlada por el algoritmo. Por lo tanto, conforme mayor es la cantidad de energía controlada por el algoritmo, mayor es la mejora de eficiencia en la red eléctrica. Además de las ventajas resultantes del suavizado del consumo agregado, otras ventajas surgen de la solución distribuida seguida en esta Tesis. Estas ventajas se resumen en las siguientes características del algoritmo de GDE propuesto: • Robustez: en un sistema centralizado, un fallo o rotura del nodo central provoca un mal funcionamiento de todo el sistema. La gestión de una red desde un punto de vista distribuido implica que no existe un nodo de control central. Un fallo en cualquier instalación no afecta el funcionamiento global de la red. • Privacidad de datos: el uso de una topología distribuida causa de que no hay un nodo central con información sensible de todos los consumidores. Esta Tesis va más allá y el algoritmo propuesto de GDE no utiliza información específica acerca de los comportamientos de los consumidores, siendo la coordinación entre las instalaciones completamente anónimos. • Escalabilidad: el algoritmo propuesto de GDE opera con cualquier número de instalaciones. Esto implica que se permite la incorporación de nuevas instalaciones sin afectar a su funcionamiento. • Bajo coste: el algoritmo de GDE propuesto se adapta a las redes actuales sin requisitos topológicos. Además, todas las instalaciones calculan su propia gestión con un bajo requerimiento computacional. Por lo tanto, no se requiere un nodo central con un alto poder de cómputo. • Rápido despliegue: las características de escalabilidad y bajo coste de los algoritmos de GDE propuestos permiten una implementación rápida. No se requiere una planificación compleja para el despliegue de este sistema. ABSTRACT This Thesis addresses the efficiency problems of the electrical grids from the consumption point of view. In particular, such efficiency is improved by means of the aggregated consumption smoothing. This objective of consumption smoothing entails two major improvements in the use of electrical grids: i) in the short term, a better use of the existing infrastructure and ii) in long term, the reduction of the required infrastructure to supply the same energy needs. In addition, this Thesis faces a new energy paradigm, where the presence of distributed generation is widespread over the electrical grids, in particular, the Photovoltaic (PV) generation. This kind of energy source affects to the operation of the grid by increasing its variability. This implies that a high penetration rate of photovoltaic electricity is pernicious for the electrical grid stability. This Thesis seeks to smooth the aggregated consumption considering this energy source. Therefore, not only the efficiency of the electrical grid is improved, but also the penetration of photovoltaic electricity into the grid can be increased. This proposal brings great benefits in the economic, social and environmental fields. The actions that influence the way that consumers use electricity in order to achieve energy savings or higher efficiency in energy use are called Demand-Side Management (DSM). This Thesis proposes two different DSM algorithms to meet the aggregated consumption smoothing objective. The difference between both DSM algorithms lie in the framework in which they take place: the local framework and the grid framework. Depending on the DSM framework, the energy goal and the procedure to reach this goal are different. In the local framework, the DSM algorithm only uses local information. It does not take into account other consumers or the aggregated consumption of the electrical grid. Although this statement may differ from the general definition of DSM, it makes sense in local facilities equipped with Distributed Energy Resources (DERs). In this case, the DSM is focused on the maximization of the local energy use, reducing the grid dependence. The proposed DSM algorithm significantly improves the self-consumption of the local PV generator. Simulated and real experiments show that self-consumption serves as an important energy management strategy, reducing the electricity transport and encouraging the user to control his energy behavior. However, despite all the advantages of the self-consumption increase, they do not contribute to the smooth of the aggregated consumption. The effects of the local facilities on the electrical grid are studied when the DSM algorithm is focused on self-consumption maximization. This approach may have undesirable effects, increasing the variability in the aggregated consumption instead of reducing it. This effect occurs because the algorithm only considers local variables in the local framework. The results suggest that coordination between these facilities is required. Through this coordination, the consumption should be modified by taking into account other elements of the grid and seeking for an aggregated consumption smoothing. In the grid framework, the DSM algorithm takes into account both local and grid information. This Thesis develops a self-organized algorithm to manage the consumption of an electrical grid in a distributed way. The goal of this algorithm is the aggregated consumption smoothing, as the classical DSM implementations. The distributed approach means that the DSM is performed from the consumers side without following direct commands issued by a central entity. Therefore, this Thesis proposes a parallel management structure rather than a hierarchical one as in the classical electrical grids. This implies that a coordination mechanism between facilities is required. This Thesis seeks for minimizing the amount of information necessary for this coordination. To achieve this objective, two collective coordination techniques have been used: coupled oscillators and swarm intelligence. The combination of these techniques to perform the coordination of a system with the characteristics of the electric grid is itself a novel approach. Therefore, this coordination objective is not only a contribution in the energy management field, but in the collective systems too. Results show that the proposed DSM algorithm reduces the difference between the maximums and minimums of the electrical grid proportionally to the amount of energy controlled by the system. Thus, the greater the amount of energy controlled by the algorithm, the greater the improvement of the efficiency of the electrical grid. In addition to the advantages resulting from the smoothing of the aggregated consumption, other advantages arise from the distributed approach followed in this Thesis. These advantages are summarized in the following features of the proposed DSM algorithm: • Robustness: in a centralized system, a failure or breakage of the central node causes a malfunction of the whole system. The management of a grid from a distributed point of view implies that there is not a central control node. A failure in any facility does not affect the overall operation of the grid. • Data privacy: the use of a distributed topology causes that there is not a central node with sensitive information of all consumers. This Thesis goes a step further and the proposed DSM algorithm does not use specific information about the consumer behaviors, being the coordination between facilities completely anonymous. • Scalability: the proposed DSM algorithm operates with any number of facilities. This implies that it allows the incorporation of new facilities without affecting its operation. • Low cost: the proposed DSM algorithm adapts to the current grids without any topological requirements. In addition, every facility calculates its own management with low computational requirements. Thus, a central computational node with a high computational power is not required. • Quick deployment: the scalability and low cost features of the proposed DSM algorithms allow a quick deployment. A complex schedule of the deployment of this system is not required.

Truncation error estimation in the Discontinuous Galerkin Spectral Element Method

En esta tesis, el método de estimación de error de truncación conocido como restimation ha sido extendido de esquemas de bajo orden a esquemas de alto orden. La mayoría de los trabajos en la bibliografía utilizan soluciones convergidas en mallas de distinto refinamiento para realizar la estimación. En este trabajo se utiliza una solución en una única malla con distintos órdenes polinómicos. Además, no se requiere que esta solución esté completamente convergida, resultando en el método conocido como quasi-a priori T-estimation. La aproximación quasi-a priori estima el error mientras el residuo del método iterativo no es despreciable. En este trabajo se demuestra que algunas de las hipótesis fundamentales sobre el comportamiento del error, establecidas para métodos de bajo orden, dejan de ser válidas en esquemas de alto orden, haciendo necesaria una revisión completa del comportamiento del error antes de redefinir el algoritmo. Para facilitar esta tarea, en una primera etapa se considera el método conocido como Chebyshev Collocation, limitando la aplicación a geometrías simples. La extensión al método Discontinuouos Galerkin Spectral Element Method presenta dificultades adicionales para la definición precisa y la estimación del error, debidos a la formulación débil, la discretización multidominio y la formulación discontinua. En primer lugar, el análisis se enfoca en leyes de conservación escalares para examinar la precisión de la estimación del error de truncación. Después, la validez del análisis se demuestra para las ecuaciones incompresibles y compresibles de Euler y Navier Stokes. El método de aproximación quasi-a priori r-estimation permite desacoplar las contribuciones superficiales y volumétricas del error de truncación, proveyendo información sobre la anisotropía de las soluciones así como su ratio de convergencia con el orden polinómico. Se demuestra que esta aproximación quasi-a priori produce estimaciones del error de truncación con precisión espectral. ABSTRACT In this thesis, the τ-estimation method to estimate the truncation error is extended from low order to spectral methods. While most works in the literature rely on fully time-converged solutions on grids with different spacing to perform the estimation, only one grid with different polynomial orders is used in this work. Furthermore, a non timeconverged solution is used resulting in the quasi-a priori τ-estimation method. The quasi-a priori approach estimates the error when the residual of the time-iterative method is not negligible. It is shown in this work that some of the fundamental assumptions about error tendency, well established for low order methods, are no longer valid in high order schemes, making necessary a complete revision of the error behavior before redefining the algorithm. To facilitate this task, the Chebyshev Collocation Method is considered as a first step, limiting their application to simple geometries. The extension to the Discontinuous Galerkin Spectral Element Method introduces additional features to the accurate definition and estimation of the error due to the weak formulation, multidomain discretization and the discontinuous formulation. First, the analysis focuses on scalar conservation laws to examine the accuracy of the estimation of the truncation error. Then, the validity of the analysis is shown for the incompressible and compressible Euler and Navier Stokes equations. The developed quasi-a priori τ-estimation method permits one to decouple the interfacial and the interior contributions of the truncation error in the Discontinuous Galerkin Spectral Element Method, and provides information about the anisotropy of the solution, as well as its rate of convergence in polynomial order. It is demonstrated here that this quasi-a priori approach yields a spectrally accurate estimate of the truncation error.

Adaptation Strategies for Discontinuous Galerkin Spectral Element Methods by means of Truncation Error Estimations

In this work a p-adaptation (modification of the polynomial order) strategy based on the minimization of the truncation error is developed for high order discontinuous Galerkin methods. The truncation error is approximated by means of a truncation error estimation procedure and enables the identification of mesh regions that require adaptation. Three truncation error estimation approaches are developed and termed a posteriori, quasi-a priori and quasi-a priori corrected. Fine solutions, which are obtained by enriching the polynomial order, are required to solve the numerical problem with adequate accuracy. For the three truncation error estimation methods the former needs time converged solutions, while the last two rely on non-converged solutions, which lead to faster computations. Based on these truncation error estimation methods, algorithms for mesh adaptation were designed and tested. Firstly, an isotropic adaptation approach is presented, which leads to equally distributed polynomial orders in different coordinate directions. This first implementation is improved by incorporating a method to extrapolate the truncation error. This results in a significant reduction of computational cost. Secondly, the employed high order method permits the spatial decoupling of the estimated errors and enables anisotropic p-adaptation. The incorporation of anisotropic features leads to meshes with different polynomial orders in the different coordinate directions such that flow-features related to the geometry are resolved in a better manner. These adaptations result in a significant reduction of degrees of freedom and computational cost, while the amount of improvement depends on the test-case. Finally, this anisotropic approach is extended by using error extrapolation which leads to an even higher reduction in computational cost. These strategies are verified and compared in terms of accuracy and computational cost for the Euler and the compressible Navier-Stokes equations. The main result is that the two quasi-a priori methods achieve a significant reduction in computational cost when compared to a uniform polynomial enrichment. Namely, for a viscous boundary layer flow, we obtain a speedup of a factor of 6.6 and 7.6 for the quasi-a priori and quasi-a priori corrected approaches, respectively. RESUMEN En este trabajo se ha desarrollado una estrategia de adaptación-p (modificación del orden polinómico) para métodos Galerkin discontinuo de alto orden basada en la minimización del error de truncación. El error de truncación se estima utilizando el método tau-estimation. El estimador permite la identificación de zonas de la malla que requieren adaptación. Se distinguen tres técnicas de estimación: a posteriori, quasi a priori y quasi a priori con correción. Todas las estrategias requieren una solución obtenida en una malla fina, la cual es obtenida aumentando de manera uniforme el orden polinómico. Sin embargo, mientras que el primero requiere que esta solución esté convergida temporalmente, el resto utiliza soluciones no convergidas, lo que se traduce en un menor coste computacional. En este trabajo se han diseñado y probado algoritmos de adaptación de malla basados en métodos tau-estimation. En primer lugar, se presenta un algoritmo de adaptacin isótropo, que conduce a discretizaciones con el mismo orden polinómico en todas las direcciones espaciales. Esta primera implementación se mejora incluyendo un método para extrapolar el error de truncación. Esto resulta en una reducción significativa del coste computacional. En segundo lugar, el método de alto orden permite el desacoplamiento espacial de los errores estimados, permitiendo la adaptación anisotropica. Las mallas obtenidas mediante esta técnica tienen distintos órdenes polinómicos en cada una de las direcciones espaciales. La malla final tiene una distribución óptima de órdenes polinómicos, los cuales guardan relación con las características del flujo que, a su vez, depenen de la geometría. Estas técnicas de adaptación reducen de manera significativa los grados de libertad y el coste computacional. Por último, esta aproximación anisotropica se extiende usando extrapolación del error de truncación, lo que conlleva un coste computational aún menor. Las estrategias se verifican y se comparan en téminors de precisión y coste computacional utilizando las ecuaciones de Euler y Navier Stokes. Los dos métodos quasi a priori consiguen una reducción significativa del coste computacional en comparación con aumento uniforme del orden polinómico. En concreto, para una capa límite viscosa, obtenemos una mejora en tiempo de computación de 6.6 y 7.6 respectivamente, para las aproximaciones quasi-a priori y quasi-a priori con corrección.

Phenotypic knockout of HIV type 1 chemokine coreceptor CCR-5 by intrakines as potential therapeutic approach for HIV-1 infection

A genetic defect in a CC-chemokine receptor (CCR)-5, the principal coreceptor for the macrophage-tropic HIV type 1 (HIV-1), recently was found to naturally protect CCR-5-defective, but healthy, individuals from HIV-1 infection. In this study, we mimic the natural resistance of the CCR-5-defective individuals by designing a strategy to phenotypically knock out CCR-5. The inactivation of the CCR-5 coreceptor is accomplished by targeting a modified CC-chemokine to the endoplasmic reticulum to block the surface expression of newly synthesized CCR-5. The lymphocytes transduced to express the intracellular chemokine, termed “intrakine,” were found to be viable and resistant to macrophage-tropic HIV-1 infection. Thus, this gene-based intrakine strategy targeted at the conserved cellular receptor for the prevention of HIV-1 entry should have significant advantages over currently described approaches for HIV-1 therapy.

Sustained delivery of erythropoietin in mice by genetically modified skin fibroblasts.

We have examined whether the secretion of erythropoietin (Epo) from genetically modified cells could represent an alternative to repeated injections of the recombinant hormone for treating chronic anemias responsive to Epo. Primary mouse skin fibroblasts were transduced with a retroviral vector in which the murine Epo cDNA is expressed under the control of the murine phosphoglycerate kinase promoter. "Neo-organs" containing the genetically modified fibroblasts embedded into collagen lattices were implanted into the peritoneal cavity of mice. Increased hematocrit (> 80%) and elevated serum Epo concentration (ranging from 60 to 408 milliunits/ml) were observed in recipient animals over a 10-month observation period. Hematocrit values measured in recipient mice varied according to the number of implanted Epo-secreting fibroblasts (ranging from 2.5 to 20 x 10(6)). The implantation of neo-organs containing Epo-secreting fibroblasts appeared, therefore, as a convenient method to achieve permanent in vivo delivery of the hormone. We estimated that the biological efficacy of the approach may be relevant for the treatment of human hemoglobinopathies.

Nutraceutical approach to the modulation of cholesterol metabolism: in vitro and in vivo studies

Negli ultimi anni, si sono diffusi nuove strategie per il trattamento delle malattie cardiovascolari, che possano supportare una terapia medica, o in alcuni casi, sostituirla. Infatti, l’abbandono delle terapie è il più importante problema di salute pubblica del mondo occidentale, soprattutto per le malattie croniche. Ciò è dovuto alla complessità delle terapie farmacologiche e ai numerosi e in alcuni casi gravi effetti collaterali dei farmaci somministrati. Di conseguenza, una riduzione di questi effetti migliorerebbe le condizioni di vita del paziente e quindi diminuirebbe il rischio di abbandono della terapia. Per ottenere ciò, è possibile affiancare al trattamento farmacologico una terapia nutraceutica, consistente nella somministrazione di complessi molecolari o microorganismi, provenienti da piante, latte o cibi funzionali. Lo scopo generale di questo studio è indagare le attività ipolipidemizzanti di un composto nutraceutico e di un ceppo batterio specifico nel modello animale che presenta elevati alti livelli plasmatici di colesterolo. Inoltre, sono stati analizzati gli effetti del trattamento nutraceutico sui meccanismi fisiologici che contrastano la creazione della placca aterosclerotica come l’efflusso di colesterolo dalle “foam cells” presenti nell’ateroma, o la riduzione dell’assorbimento intestinale di colesterolo. La presente tesi è divisa in due parti. Nella prima parte, abbiamo analizzato la capacità dei Bifidobacteria di ridurre i livelli di colesterolo nel medium di crescita. Dall’analisi, si è osservato che vari ceppi del genere Bifidobacteria presentano un’ampia capacità di assimilazione del colesterolo all’interno della cellula batterica, in particolare il Bifidobacterium bifidum PRL2010. Le analisi di trascrittomica del Bb PRL2010 incubato in presenza di colesterolo, hanno rivelato un significativo aumento dei livelli di trascrizione di geni codificanti trasportatori e riduttasi, responsabili del meccanismo di accumulo all’interno della cellula batterica e della conversione del colesterolo in coprostanolo. L’attività ipolipidemizzante del Bb PRL2010 è stata poi valutata nel modello murino, mostrando la modificazione del microbiota dei topi trattati dopo somministrazione del batterio in questione. Nella seconda parte del progetto di ricerca, abbiamo indagato sugli effetti di un composto coperto da brevetto, chiamato “Ola”, sull’efflusso di colesterolo di criceti trattati con questo composto nutraceutico. L’efflusso di colesterolo è il primo step del meccanismo fisiologico noto come Trasporto Inverso del Colesterolo, che consente l’eliminazione del colesterolo dalle placche aterosclerotiche, attraverso l’interazione fra le HDL, presenti nella circolazione sanguigna, e specifici trasportatori delle foam cells, come ABCA1/G1 e SR-BI. In seguito, le lipoproteine rilasciano il colesterolo alle cellule epatiche, dove è metabolizzato ed escreto attraverso le feci. Per valutare l’effetto dell’Ola sul profilo lipidico dei criceti, sono state condotte analisi in vitro. I risultati mostrano un aumento dell’efflusso di colesterolo in cellule che esprimono il trasportatore ABCA1, comparato con il gruppo controllo. Questi due studi mostrano come l’approccio nutraceutico può essere un importante modo per contrastare l’aterosclerosi. Come mostrato in letteratura, gli effetti dei composti nutraceutici sull’aterosclerosi e su altre malattie croniche, hanno portato a un ampio uso come supporto alle terapie farmacologiche, ed in alcuni casi hanno rimpiazzato la terapia farmacologica stessa.

Haloferax mediterranei GlnK proteins are post-translationally modified by uridylylation

In this work we report for the first time a post-translational modification of PII homologues from the Archaea Domain. Haloferax mediterranei is the first haloarchaea whose PII proteins have been studied, it possesses two of them (GlnK1 and GlnK2), both encoded adjacent to a gene for the ammonia transporter Amt. An approach based on 2DE, anti-GlnK immunoblot and peptide mass fingerprint (MALDI-TOF-MS) of the reactive spots showed that GlnK proteins in H. mediterranei are post-translationally uridylylated. A third spot with lower pI suggests the existence of a non-descript post-translational modification in this protein family.

How can an invasive grass affect fire behavior in a tropical savanna? A community and individual plant level approach

Some invasive grasses have been reported to change fire behavior in invaded plant communities. Urochloa brizantha is an aggressive invasive grass in the Brazilian Cerrado, an ecosystem where fire is a common disturbance. We investigated the effects of U. brizantha on fire behavior in an open Cerrado physiognomy in Central Brazil. Using experimental burnings we compared fire behavior at both the community and the individual plant level in invaded (UJ) and non-invaded (NJ) areas burned in July. We also assessed the effect of fire season in invaded areas by comparing July (UJ) and October (UO) burnings. We evaluated the following variables: fuel load, fuel moisture, combustion efficiency, maximum fire temperature, flame height, and fire intensity. Additionally, we evaluated the temperatures reached under invasive and native grass tussocks in both seasons. Fuel load, combustion efficiency, and fire intensity were higher in NJ than in UJ, whilst flame height showed the opposite trend. Fuel amount and fire intensity were higher in October than in July. At the individual plant level, U. brizantha moisture was higher than that of native species, however, temperatures reaching ≥600 °C at ground level were more frequent under U. brizantha tussocks than under native grasses. At the community level, the invasive grass modified fire behavior towards lower intensity, lower burning efficiency, and higher flame height. These results provide essential information for the planning of prescribed burnings in invaded Cerrado areas.