Análise do grau de conservação de resíduos em proteínas com estrutura 3D resolvida utilizando o SMS.

HSSP e entropia relativa. Módulos do SMS para análise de conservação. Discussão e trabalhos futuros.

Confirmação do modelo da estrutura 3D do vale inferior do Tejo a partir de dados de ruído sísmico ambiente

Ao longo de sua história a região do Vale Inferior do Tejo VIT foi abalada por vários sismos consideravelmente destrutivas, tendo alguns deles produzido significativas deformações nas estruturas marítimas localizadas no litoral a sudoeste do território Português; outros, moderados, foram produzidos por fontes locais, como os de 1344, 1531 e 1909. Nos últimos anos, devido à melhoria dos modelos de estrutura 3D e o desenvolvimento dos métodos numéricos, foram elaborados vários estudos de síntese de movimento forte do solo para a região do Baixo Tejo utilizando o método de diferenças finitas. Para confirmar o modelo de velocidades desta bacia usámos medidas de ruído sísmico, aplicámos um método baseado na razão espectral H/V, e, a partir destas curvas, por inversão, obtivemos um modelo de velocidades para a região estudada. Os resultados revelam uma boa concordância entre o modelo obtido e os dados geofísicos e geológicos recolhidos na mesma área._ ABSTRACT: Along his history the Lower Tagus Valley (LTV) area was shaken by several earthquakes. The largest reported had their origin in the southwestern part of Iberia. Other moderate earthquakes were produced by local sources such as the 1344, 1531 and the 1909. ln the last years, due to 3D structural model improvement and development in numerical methods, several studies have successful obtained strong-ground motion synthesis for the LVT region using finite difference method. To confirm the velocity model of the LTV sedimentary basin obtained by geophysical and geological data, we use broad-band microtremor measurements and application of the horizontal to vertical (H/V) spectral ratio method. We have obtained a velocity model for the studied region by inversion of the H/V curve. The results have good agreement geological and geophysical data.

Purification, characterization and structural determination of chitinases produced by Moniliophthora perniciosa

The enzyme chitinase from Moniliophthora perniciosa the causative agent of the witches' broom disease in Theobroma cacao, was partially purified with ammonium sulfate and filtration by Sephacryl S-200 using sodium phosphate as an extraction buffer. Response surface methodology (RSM) was used to determine the optimum pH and temperature conditions. Four different isoenzymes were obtained: ChitMp I, ChitMp II, ChitMp III and ChitMp IV. ChitMp I had an optimum temperature at 44-73ºC and an optimum pH at 7.0-8.4. ChitMp II had an optimum temperature at 45-73ºC and an optimum pH at 7.0-8.4. ChitMp III had an optimum temperature at 54-67ºC and an optimum pH at 7.3-8.8. ChitMp IV had an optimum temperature at 60ºC and an optimum pH at 7.0. For the computational biology, the primary sequence was determined in silico from the database of the Genome/Proteome Project of M. perniciosa, yielding a sequence with 564 bp and 188 amino acids that was used for the three-dimensional design in a comparative modeling methodology. The generated models were submitted to validation using Procheck 3.0 and ANOLEA. The model proposed for the chitinase was subjected to a dynamic analysis over a 1 ns interval, resulting in a model with 91.7% of the residues occupying favorable places on the Ramachandran plot and an RMS of 2.68.

Investigação da microarquitetura óssea através de microtomografia 3D

A microtomografia computadorizada (uCT) é uma técnica de ensaio não destrutivo, frequentemente utilizada no estudo da estrutura interna de ossos, com uma resolução espacial da ordem de mícrons. Neste trabalho, seis pares de amostras ósseas (fêmur de rato) foram estudados através da uCT. Os ensaios foram conduzidos na presença ou não de filtros de alumínio (espessura de 0,25; 0,50 e 0,75 mm), utilizando-se três níveis de resolução (33,3; 15,0 e 9,5 um). Os parâmetros de arquitetura óssea BS (área óssea da amostra), BV (volume ósseo da amostra), TS (área superficial da amostra), TV (volume da amostra), BV/TV (razão entre o volume ósseo e o volume da amostra), BS/BV (razão entre a área óssea da amostra e o volume ósseo da amostra), Tb.N (densidade trabecular), Tb.Th (espaçamento entre as trabéculas), Tb.Sp (separação trabecular), conectividade e anisotropia foram determinados através das análises em duas (2D) e/ou três (3D) dimensões. A comparação entre os valores dos parâmetros obtidos através dessas análises foi realizada através do teste t pareado e da correlação de Pearson. Com base nos resultados, foi possível determinar a influência da resolução da imagem na qualidade dos parâmetros da arquitetura óssea obtidos através das análises 2D e/ou 3D. Os dados mostram que a presença de filtro de alumínio também afeta a qualidade desses parâmetros. Assim, os melhores resultados são obtidos com resolução máxima e filtro de alumínio com espessura de 0,25 ou 0,50 mm.

Visualização interativa e manipulação de imagens 3D em tempo real usando métodos baseados na GPU

Este trabalho apresenta um conjunto de ferramentas que exploram as capacidades recentes das placas gráficas de computadores pessoais para prover a visualização e a interação com volumes de dados. O objetivo é oferecer ao usuário ferramentas que permitam a remoção interativa de partes não relevantes do volume. Assim, o usuário é capaz de selecionar um volume de interesse, o que pode tanto facilitar a compreensão da sua estrutura quanto a sua relação com os volumes circundantes. A técnica de visualização direta de volumes através do mapeamento de texturas é explorada para desenvolver estas ferramentas. O controle programável dos cálculos realizados pelo hardware gráfico para gerar a aparência de cada pixel na tela é usado para resolver a visibilidade de cada ponto do volume em tempo real. As ferramentas propostas permitem a modificação da visibilidade de cada ponto dentro do hardware gráfico, estendendo o benefício da visualização acelerada por hardware. Três ferramentas de interação são propostas: uma ferramenta de recorte planar que permite a seleção de um volume de interesse convexo; uma ferramenta do tipo “borracha”, para eliminar partes não relevantes da imagem; e uma ferramenta do tipo “escavadeira”, para remover camadas do volume Estas ferramentas exploram partes distintas do fluxo de visualização por texturas, onde é possível tomar a decisão sobre a visibilidade de cada ponto do volume. Cada ferramenta vem para resolver uma deficiência da ferramenta anterior. Com o recorte planar, o usuário aproxima grosseiramente o volume de interesse; com a borracha, ele refina o volume selecionado que, finalmente, é terminado com a escavadeira. Para aplicar as ferramentas propostas ao volume visualizado, são usadas técnicas de interação conhecidas, comuns nos sistemas de visualização 2D. Isto permite minimizar os esforços do usuário no treinamento do uso das ferramentas. Finalmente, são ilustradas as aplicações potenciais das ferramentas propostas para o estudo da anatomia do fígado humano. Nestas aplicações foi possível identificar algumas necessidades do usuário na visualização interativa de conjuntos de dados médicos. A partir destas observações, são propostas também novas ferramentas de interação, baseadas em modificações nas ferramentas propostas.

Impressoras 3D: o direito da propriedade intelectual precisará alcançar novas dimensões?

A presente monografia tem como objeto a análise dos possíveis impactos causados no campo da Propriedade Intelectual oriundos do desenvolvimento da tecnologia de impressão 3D. Este trabalho se estrutura em torno de três grandes seções. A primeira visa à apresentação das impressoras 3D ao leitor, descrevendo um pouco de sua história e, também, suas aplicações. A segunda expõe os principais contornos jurídicos que caracterizam a Propriedade Intelectual e os direitos dela decorrentes, relacionando-os com a impressão 3D. Na última seção, por fim, realiza-se uma reflexão quanto aos desafios apresentados no decorrer do texto e, também, a apresentação de situações que indicam possíveis rumos para a interação entre a tecnologia em questão e a Propriedade Intelectual.

Laboratório - estrutura física

Este item é parte de um conjunto de modelos produzido pela equipe do Laboratório de Objetos de Apredizagem (LOA)/UFSCar para o jogo LabTecA

Simulação computacional da interação fluido-estrutura em bombas de cavidades progressivas

The pumping through progressing cavities system has been more and more employed in the petroleum industry. This occurs because of its capacity of elevation of highly viscous oils or fluids with great concentration of sand or other solid particles. A Progressing Cavity Pump (PCP) consists, basically, of a rotor - a metallic device similar to an eccentric screw, and a stator - a steel tube internally covered by a double helix, which may be rigid or deformable/elastomeric. In general, it is submitted to a combination of well pressure with the pressure generated by the pumping process itself. In elastomeric PCPs, this combined effort compresses the stator and generates, or enlarges, the clearance existing between the rotor and the stator, thus reducing the closing effect between their cavities. Such opening of the sealing region produces what is known as fluid slip or slippage, reducing the efficiency of the PCP pumping system. Therefore, this research aims to develop a transient three-dimensional computational model that, based on single-lobe PCP kinematics, is able to simulate the fluid-structure interaction that occurs in the interior of metallic and elastomeric PCPs. The main goal is to evaluate the dynamic characteristics of PCP s efficiency based on detailed and instantaneous information of velocity, pressure and deformation fields in their interior. To reach these goals (development and use of the model), it was also necessary the development of a methodology for generation of dynamic, mobile and deformable, computational meshes representing fluid and structural regions of a PCP. This additional intermediary step has been characterized as the biggest challenge for the elaboration and running of the computational model due to the complex kinematic and critical geometry of this type of pump (different helix angles between rotor and stator as well as large length scale aspect ratios). The processes of dynamic generation of meshes and of simultaneous evaluation of the deformations suffered by the elastomer are fulfilled through subroutines written in Fortan 90 language that dynamically interact with the CFX/ANSYS fluid dynamic software. Since a structural elastic linear model is employed to evaluate elastomer deformations, it is not necessary to use any CAE package for structural analysis. However, an initial proposal for dynamic simulation using hyperelastic models through ANSYS software is also presented in this research. Validation of the results produced with the present methodology (mesh generation, flow simulation in metallic PCPs and simulation of fluid-structure interaction in elastomeric PCPs) is obtained through comparison with experimental results reported by the literature. It is expected that the development and application of such a computational model may provide better details of the dynamics of the flow within metallic and elastomeric PCPs, so that better control systems may be implemented in the artificial elevation area by PCP

Análises estratigráfica e estrutural da Seção Rifte (Valanginiano ao Barremiano) na área do levantamento sísmico 3D de baixo vermelho, Bacia Potiguar emersa

Baixo Vermelho area, situated on the northern portion of Umbuzeiro Graben (onshore Potiguar Basin), represents a typical example of a rift basin, characterized, in subsurface, by the sedimentary rift sequence, correlated to Pendência Formation (Valanginian-Barremian), and by the Carnaubais fault system. In this context, two main goals, the stratigraphic and the structural analysis, had guided the research. For this purpose, it was used the 3D seismic volume and eight wells located in the study area and adjacencies. The stratigraphic analysis of the Valanginian-Barremian interval was carried through in two distinct phases, 1D and 2D, in which the basic concepts of the sequence stratigraphy had been adapted. In these phases, the individual analysis of each well and the correlation between them, allowed to recognize the main lithofacies, to interpret the effective depositional systems and to identify the genetic units and key-surfaces of chronostratigraphic character. The analyzed lithofacies are represented predominantly by conglomerates, sandstones, siltites and shales, with carbonate rocks and marls occurring subordinately. According to these lithofacies associations, it is possible to interpret the following depositional systems: alluvial fan, fluvio-deltaic and lacustrine depositional systems. The alluvial fan system is mainly composed by conglomerates deposits, which had developed, preferentially in the south portion of the area, being directly associated to Carnaubais fault system. The fluvial-deltaic system, in turn, was mainly developed in the northwest portion of the area, at the flexural edge, being characterized by coarse sandstones with shales and siltites intercalated. On the other hand, the lacustrine system, the most dominant one in the study area, is formed mainly by shales that could occur intercalated with thin layers of fine to very fine sandstones, interpreted as turbidite deposits. The recognized sequence stratigraphy units in the wells are represented by parasequence sets, systems tracts and depositional sequences. The parasequence sets, which are progradational or retrogradational, had been grouped and related to the systems tracts. The predominance of the progradation parasequence sets (general trend with coarsening-upward) characterizes the Regressive Systems Tract, while the occurrence, more frequently, of the retrogradation parasequence sets (general trend with finning-upward) represents the Transgressive System Tract. In the seismic stratigraphic analysis, the lithofacies described in the wells had been related to chaotic, progradational and parallel/subparallel seismic facies, which are associated, frequently, to the alluvial fans, fluvial-deltaic and lacustrine depositional systems, respectively. In this analysis, it was possible to recognize fifteen seismic horizons that correspond to sequence boundaries and to maximum flooding surfaces, which separates Transgressive to Regressive systems tracts. The recognition of transgressive-regressive cycles allowed to identify nine, possibly, 3a order deposicional sequences, related to the tectonic-sedimentary cycles. The structural analysis, in turn, was done at Baixo Vermelho seismic volume, which shows, clearly, the structural complexity printed in the area, mainly related to Carnaubais fault system, acting as an important fault system of the rift edge. This fault system is characterized by a main arrangement of normal faults with trend NE-SO, where Carnaubais Fault represents the maximum expression of these lineations. Carnaubais Fault corresponds to a fault with typically listric geometry, with general trend N70°E, dipping to northwest. It is observed, throughout all the seismic volume, with variations in its surface, which had conditioned, in its evolutive stages, the formation of innumerable structural features that normally are identified in Pendencia Formation. In this unit, part of these features is related to the formation of longitudinal foldings (rollover structures and distentional folding associated), originated by the displacement of the main fault plan, propitiating variations in geometry and thickness of the adjacent layers, which had been deposited at the same time. Other structural features are related to the secondary faultings, which could be synthetic or antithetic to Carnaubais Fault. In a general way, these faults have limited lateral continuity, with listric planar format and, apparently, they play the role of the accomodation of the distentional deformation printed in the area. Thus, the interaction between the stratigraphic and structural analysis, based on an excellent quality of the used data, allowed to get one better agreement on the tectonicsedimentary evolution of the Valanginian-Barremian interval (Pendência Formation) in the studied area

Interpretação sísmica e análise de atributos - área do levantamento sísmico 3D de siririzinho (Bacia Sergipe-Alagoas, NE do Brasil)

The main objective of the present thesis was the seismic interpretation and seismic attribute analysis of the 3D seismic data from the Siririzinho high, located in the Sergipe Sub-basin (southern portion of Sergipe-Alagoas Basin). This study has enabled a better understanding of the stratigraphy and structure that the Siririzinho high experienced during its development. In a first analysis, we used two types of filters: the dip-steered median filter, was used to remove random noise and increase the lateral continuity of reflections, and fault-enhancement filter was applied to enhance the reflection discontinuities. After this filtering step similarity and curvature attributes were applied in order to identify and enhance the distribution of faults and fractures. The use of attributes and filtering greatly contributed to the identification and enhancement of continuity of faults. Besides the application of typical attributes (similarity and curvature) neural network and fingerprint techniques were also used, which generate meta-attributes, also aiming to highlight the faults; however, the results were not satisfactory. In a subsequent step, well log and seismic data analysis were performed, which allowed the understanding of the distribution and arrangement of sequences that occur in the Siririzinho high, as well as an understanding of how these units are affected by main structures in the region. The Siririzinho high comprises an elongated structure elongated in the NS direction, capped by four seismo-sequences (informally named, from bottom to top, the sequences I to IV, plus the top of the basement). It was possible to recognize the main NS-oriented faults, which especially affect the sequences I and II, and faults oriented NE-SW, that reach the younger sequences, III and IV. Finally, with the interpretation of seismic horizons corresponding to each of these sequences, it was possible to define a better understanding of geometry, deposition and structural relations in the area.

Representação e armazenamento de dados cadastrais 3D em banco de dados geográficos

Pós-graduação em Ciências Cartográficas - FCT

Expansão ex vivo de células uroteliais em scaffolds 3D

Malformations and possible damages to the urogenital system can be originated in the embryonic period. Moreover, fire guns, knives and accidents, where there is the disruption of the urethra, also cause these lesions. The objective was to analyze the contribution of tissue engineering in the construction of neo-urethra, developed by bioengineering. We performed an urothelial ex vivo expansion of cells in 3D scaffolds (platelet gel matrix and acellular porcine aorta) to assess the contribution of this technique in the construction of a neo-urethra. Mechanical dissociation was made of the inner wall of 10 North Folk rabbit’s bladder, weighing 2.5 to 3.0 kg. After dissociation the cell content was centrifuged and obtained a pellet of urothelial cells. The pellet was ressuspended in culture medium DMEM F12 and cells were maintained in culture for 15 days. Immunohistochemical analysis characterized the urothelial culture. The cells were then implanted in the scaffold - platelet gel. In a second experiment using aortic porcine acellular matrix were implanted urothelial cells alone and urothelial cells on platelet gel, on the inner wall of the scaffold - aorta, with space for setting bordered by a urethral probe. The complex probe - cells - aorta and probe - cells in platelet gel - aorta, were sealed with suture material and culture were maintained in a humidified 37ºC incubator with 5% CO2 in air for 12 days to subsequent histological analysis of urothelium cell adhesion to the scaffolds. By observation under an optical microscope, we could see the growth of cells in the scaffold platelet gel, from a monolayer in to a three-dimensional structure. In the acellular porcine aortic matrix containing the platelet gel, we could observe a few quantity of urothelial cells adhered. However with the acellular porcine aortic matrix in which was implanted only the urothelial cells, we have obtained adhesion to the wall

Sistema computacional com geração de dados e visualização de resultados para estrutura de edifícios

Este trabalho trata do desenvolvimento de um sistema computacional, para a geração de dados e apresentação de resultados, específico para as estruturas de edifícios. As rotinas desenvolvidas devem trabalhar em conjunto com um sistema computacional para análise de estruturas com base no Método dos Elementos Finitos, contemplando tanto as estruturas de pavimentos; com a utilização de elementos de barra, placa/casca e molas; como as estruturas de contraventamento; com a utilização de elementos de barra tridimensional e recursos especiais como nó mestre e trechos rígidos. A linguagem computacional adotada para a elaboração das rotinas mencionadas é o Object Pascal do DELPHI, um ambiente de programação visual estruturado na programação orientada a objetos do Object Pascal. Essa escolha tem como objetivo, conseguir um sistema computacional onde alterações e adições de funções possam ser realizadas com facilidade, sem que todo o conjunto de programas precise ser analisado e modificado. Por fim, o programa deve servir como um verdadeiro ambiente para análise de estruturas de edifícios, controlando através de uma interface amigável com o usuário uma série de outros programas já desenvolvidos em FORTRAN, como por exemplo o dimensionamento de vigas, pilares, etc.