Structural and functional characterization of the gene products responsible for phototrophic iron oxidation by purple bacteria

Dissertação para a obtenção de grau de doutor em Bioquímica pelo Instituto de Tecnologia Química e Biológica. Universidade Nova de Lisboa

A flexible navigation system for autonomous robots operating in heterogeneous environments

Dissertação para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores

Data queries over heterogeneous sources

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

The Edges of Areal Units: a case study in the heterogeneous effects of assessment district edges

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies

Heterogeneous computing with an algorithmic skeleton framework

The Graphics Processing Unit (GPU) is present in almost every modern day personal computer. Despite its specific purpose design, they have been increasingly used for general computations with very good results. Hence, there is a growing effort from the community to seamlessly integrate this kind of devices in everyday computing. However, to fully exploit the potential of a system comprising GPUs and CPUs, these devices should be presented to the programmer as a single platform. The efficient combination of the power of CPU and GPU devices is highly dependent on each device’s characteristics, resulting in platform specific applications that cannot be ported to different systems. Also, the most efficient work balance among devices is highly dependable on the computations to be performed and respective data sizes. In this work, we propose a solution for heterogeneous environments based on the abstraction level provided by algorithmic skeletons. Our goal is to take full advantage of the power of all CPU and GPU devices present in a system, without the need for different kernel implementations nor explicit work-distribution.To that end, we extended Marrow, an algorithmic skeleton framework for multi-GPUs, to support CPU computations and efficiently balance the work-load between devices. Our approach is based on an offline training execution that identifies the ideal work balance and platform configurations for a given application and input data size. The evaluation of this work shows that the combination of CPU and GPU devices can significantly boost the performance of our benchmarks in the tested environments, when compared to GPU-only executions.

Biomimetic mineralization: encapsulation in calcium carbonate shells

Calcium carbonate biomineralization is a self-assembly process that has been studied to be applied in the biomedical field to encapsulate biomolecules. Advantages of engineering mineral capsules include improved drug loading efficiencies and protection against external environment. However, common production methods result in heterogeneous capsules and subject biomolecules to heat and vibration which cause irreversible damage. To overcome these issues, a microfluidic device was designed, manufactured and tested in terms of selectivity for water and oil to produce a W/O/W emulsion. During the development of this work there was one critical challenge: the selective functionalization in closed microfluidic channels. Wet chemical oxidation of PDMS with 1M NaOH, confirmed by FTIR, followed by adsorption of polyelectrolytes - PDADMAC/PSS - confirmed by UV-Vis and AFM results, render the surface of PDMS hydrophilic. UV-Vis spectroscopy also confirmed that this modification did not affect PDMS optical properties, making possible to monitor fluids and droplets. More important, with this approach PDMS remains hydrophilic over time. However, due to equipment constrains selectivity in microchannels was not achieved. Therefore, emulsion studies took place with conventional methods. Several systems were tried, with promising results achieved with CaCO3 in-situ precipitation, without the use of polymers or magnesium. This mineral stabilizes oil droplets in water, but not in air due to incomplete capsule formation.

Grafting of adipic anhydride to carbon nanotubes through a Diels-Alder cycloaddition/oxidation cascade reaction

Accepted Manuscript

Integrating data from heterogeneous DNA microarray platforms

DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests, reducing the data dimensionality problem. The integration of heterogeneous DNA microarray platforms comprehends a set of tasks that range from the re-annotation of the features used on gene expression, to data normalization and batch effect elimination. In this work, a complete methodology for gene expression data integration and application is proposed, which comprehends a transcript-based re-annotation process and several methods for batch effect attenuation. The integrated data will be used to select the best feature set and learning algorithm for a brain tumor classification case study. The integration will consider data from heterogeneous Agilent and Affymetrix platforms, collected from public gene expression databases, such as The Cancer Genome Atlas and Gene Expression Omnibus.

Degradação fotocatalítica de petróleo e seus derivados através da utilização de nanopartículas de dióxido de titânio puro e misturado com óxido de grafeno reduzido

Dissertação de mestrado integrado em Engenharia de Materiais

Remoção fotocatalítica de micropoluentes em meios porosos funcionalizados

Dissertação de mestrado integrado em Engenharia Civil

Anaerobic oxidation of methane associated with sulfate reduction in a natural freshwater gas source

The occurrence of anaerobic oxidation of methane (AOM) and trace methane oxidation (TMO) was investigated in a freshwater natural gas source. Sediment samples were taken and analyzed for potential electron acceptors coupled to AOM. Long-term incubations with 13C-labeled CH4 (13CH4) and different electron acceptors showed that both AOM and TMO occurred. In most conditions, 13C-labeled CO2 (13CO2) simultaneously increased with methane formation, which is typical for TMO. In the presence of nitrate, neither methane formation nor methane oxidation occurred. Net AOM was measured only with sulfate as electron acceptor. Here, sulfide production occurred simultaneously with 13CO2 production and no methanogenesis occurred, excluding TMO as a possible source for 13CO2 production from 13CH4. Archaeal 16S rRNA gene analysis showed the highest presence of ANME-2a/b (ANaerobic MEthane oxidizing archaea) and AAA (AOM Associated Archaea) sequences in the incubations with methane and sulfate as compared with only methane addition. Higher abundance of ANME-2a/b in incubations with methane and sulfate as compared with only sulfate addition was shown by qPCR analysis. Bacterial 16S rRNA gene analysis showed the presence of sulfate-reducing bacteria belonging to SEEP-SRB1. This is the first report that explicitly shows that AOM is associated with sulfate reduction in an enrichment culture of ANME-2a/b and AAA methanotrophs and SEEP-SRB1 sulfate reducers from a low-saline environment.

Comparison of the effect of two HMG CoA reductase inhibitors on LDL susceptibility to oxidation

OBJECTIVE: To study the differences between fluvastatin and pravastatin regarding LDL susceptibility to oxidation, plasma levels of total cholesterol (TC), HDL-C, LDL-C and triglycerides (TG) in hypercholesterolemic patients with established coronary heart disease (CHD). METHODS: A double-blind randomized parallel study was conducted that included 41 hypercholesterolemic outpatients with CHD treated at the Instituto de Cardiologia do Rio Grande do Sul. The inclusion criteria were LDL-C above 100 mg/dL and triglycerides below 400 mg/dL based on 2 measures. After 4 weeks on a low cholesterol diet, those patients that fullfilled the inclusion criteria were randomized into 2 groups: the fluvastatin group (fluvastatin 40 mg/day) and the pravastatin group (pravastatin 20 mg/day), for 24 weeks of treatment. LDL susceptibility to oxidation was analyzed with copper-induced production of conjugated dienes (Cu2+) and water-soluble free radical initiator azo-bis (2'-2'amidinopropanil) HCl (AAPH). Spectroscopy nuclear magnetic resonance was used for determination of lipids. RESULTS: After 24 weeks of drug therapy, fluvastatin and pravastatin significantly reduced LDL susceptibility to oxidation as demonstrated by the reduced rate of oxidation (azo and Cu) and by prolonged azo-induced lag time (azo lag). The TC, LDL-C, and TG reduced significantly and HDL-C increased significantly. No differences between the drugs were observed. CONCLUSION: In hypercholesterolemic patients with CHD, both fluvastatin and pravastatin reduced LDL susceptibility to oxidation.

Patrones dinámicos de abundancia y dispersión de una plaga en un paisaje heterogéneo. Dynamic patterns of abundance and dispersion of a pest in a heterogeneous landscape.

El desarrollo de conocimiento empírico sobre cómo la heterogeneidad espacial de un paisaje afecta los patrones de movimiento de una especie animal es considerado una prioridad para el manejo y la conservación de las especies y sus hábitats. En el caso de los insectos plaga, estos estudios resultan importantes ya que aportan las bases teóricas y empíricas fundamentales para su manejo. La persistencia de éstas especies en un paisaje modificado depende de la interrelación entre procesos ecológicos y la estructura del paisaje, tales como la interacción entre especies, la disponibilidad de parches hábitat y la influencia de las prácticas de manejo. El análisis de éstos procesos en un agroecosistema permite simplificar los modelos de heterogeneidad espacial, debido a que los lotes de cultivo son internamente homogéneos y los disturbios antropogénicos generalmente ocurren a la escala de parche, permitiendo determinar las respuestas de los insectos a dicha escala. La alfalfa (Medicago sativa) es un recurso fundamental para la producción agropecuaria y en Argentina, es el recurso forrajero más importante, constituyendo la base de la producción ganadera del país. Actualmente se cultivan alrededor de 5 millones de hectáreas, de las cuales un millón se siembran en la provincia de Córdoba. Además, cumple un rol importante en la sustentabilidad de los sistemas de producción por su función de recuperación de la fertilidad y estabilidad edáfica. La isoca de la alfalfa (Colias lesbia) es la plaga principal del cultivo, produciendo en promedio la pérdida de un corte por año. La hipótesis principal de nuestro trabajo es que los patrones de abundancia y movilidad de la isoca de la alfalfa son afectados por la estructura del paisaje y las prácticas de manejo. Los objetivos específicos del proyecto son: (a) Establecer el efecto de la estructura del paisaje y y el manejo del cultivo en la abundancia de los distintos estadios de Colias lesbia. (b) Determinar los patrones de dispersión de Colias lesbia en relación a la heterogeneidad espacial del paisaje (c) Generar un modelo predictivo de la abundancia de Colias lesbia según la estructura espacial del paisaje, el clima y el manejo del cultivo. (d) Desarrollar un conjunto de recomendaciones de manejo a escala regional para el control de la isoca de la alfalfa. Para ello se elegirán lotes de alfalfa en la región este de la provincia de Córdoba, en el departamento de San Justo, donde se realizará un relevamiento inicial del área de estudio y se dialogará con los productores. Paralelamente, se realizará una clasificación supervisada del área de estudio a partir de escenas de imágenes Landsat TM. En los parches seleccionados, durante 3 años y durante los meses de verano, se muestrearán quincenalmente los distintos estadios de Colias lesbia. Se realizarán análisis de correlación y regresión entre las variables independientes (métricas de la configuración y dinámica del paisaje) y las variables dependientes, (abundancia media de los diferentes estadios de las poblaciones). Asimismo, se realizarán experimentos de marcado-liberación-recaptura para determinar cómo el movimiento de la especie depende de la estructura del paisaje. Para modelar el movimiento inherente de la especie se combinará la información obtenida en el campo con un modelo de difusión utilizando métodos bayesianos. Se espera obtener modelos que permitan comprender los mecanismos que generan los patrones observados. Con esta información se propondrán lineamientos generales y específicos para un manejo de la isoca de la alfalfa a escala regional. En tal sentido, se espera aportar información para restringir la dispersión de la plaga, y reducir los costos y perjuicios del control químico que podrían evitarse con la aplicación de prácticas de manejo integrado y de "manejo de área" que minimicen el impacto de la plaga como también contribuir al conocimiento general de la ecología de insectos.

Experimental study on n-butane partial oxidation to maleic anhydride in a solid electrolyte membrane reactor

n-Butane, Partial oxidation, Maleic anhydride, electrochemical oxygen pumping, solid electrolyte membrane reactor

Spektroskopische in situ-Untersuchungen der katalytischen CO-Oxidation an oxidmodifizierten Platinmetalloberflächen

Magdeburg, Univ., Fak. für Verfahrens- und Systemtechnik, Diss., 2010