Structural modeling of high-affinity thyroid receptor-ligand complexes

Understanding the molecular basis of the binding modes of natural and synthetic ligands to nuclear receptors is fundamental to our comprehension of the activation mechanism of this important class of hormone regulated transcription factors and to the development of new ligands. Thyroid hormone receptors (TR) are particularly important targets for pharmaceuticals development because TRs are associated with the regulation of metabolic rates, body weight, and circulating levels of cholesterol and triglycerides in humans. While several high-affinity ligands are known, structural information is only partially available. In this work we obtain structural models of several TR-ligand complexes with unknown structure by docking high affinity ligands to the receptors` ligand binding domain with subsequent relaxation by molecular dynamics simulations. The binding modes of these ligands are discussed providing novel insights into the development of TR ligands. The experimental binding free energies are reasonably well-reproduced from the proposed models using a simple linear interaction energy free-energy calculation scheme.

Building a Learning Architecture : e-Learning and e-Services

With the rapid advancement of the webtechnology, more and more educationalresources, including software applications forteaching/learning methods, are available acrossthe web, which enables learners to access thelearning materials and use various ways oflearning at any time and any place. Moreover,various web-based teaching/learning approacheshave been developed during the last decade toenhance the capability of both educators andlearners. Particularly, researchers from bothcomputer science and education are workingtogether, collaboratively focusing ondevelopment of pedagogically enablingtechnologies which are believed to improve theinfrastructure of education systems andprocesses, including curriculum developmentmodels, teaching/learning methods, managementof educational resources, systematic organizationof communication and dissemination ofknowledge and skills required by and adapted tousers. Despite of its fast development, however,there are still great gaps between learningintentions, organization of supporting resources,management of educational structures,knowledge points to be learned and interknowledgepoint relationships such as prerequisites,assessment of learning outcomes, andtechnical and pedagogic approaches. Moreconcretely, the issues have been widelyaddressed in literature include a) availability andusefulness of resources, b) smooth integration ofvarious resources and their presentation, c)learners’ requirements and supposed learningoutcomes, d) automation of learning process interms of its schedule and interaction, and e)customization of the resources and agilemanagement of the learning services for deliveryas well as necessary human interferences.Considering these problems and bearing in mindthe advanced web technology of which weshould make full use, in this report we willaddress the following two aspects of systematicarchitecture of learning/teaching systems: 1)learning objects – a semantic description andorganization of learning resources using the webservice models and methods, and 2) learningservices discovery and learning goals match foreducational coordination and learning serviceplanning.

Modeling and illustrating requirement prioritization in public e-service development from a value-based perspective

A major problem in e-service development is the prioritization of the requirements of different stakeholders. The main stakeholders are governments and their citizens, all of whom have different and sometimes conflicting requirements. In this paper, the prioritization problem is addressed by combining a value-based approach with an illustration technique. This paper examines the following research question: How can multiple stakeholder requirements be illustrated from a value-based perspective in order to be prioritizable? We used an e-service development case taken from a Swedish municipality to elaborate on our approach. Our contributions are: 1) a model of the relevant domains for requirement prioritization for government, citizens, technology, finances and laws and regulations; and 2) a requirement fulfillment analysis tool (RFA) that consists of a requirement-goal-value matrix (RGV), and a calculation and illustration module (CIM). The model reduces cognitive load, helps developers to focus on value fulfillment in e-service development and supports them in the formulation of requirements. It also offers an input to public policy makers, should they aim to target values in the design of e-services.

Radiation properties of coil-coated steel in building envelope surfaces and the influence on building thermal performance

Recent studies have shown that the optical properties of building exterior surfaces are important in terms of energy use and thermal comfort. While the majority of the studies are related to exterior surfaces, the radiation properties of interior surfaces are less thoroughly investigated. Development in the coil-coating industries has now made it possible to allocate different optical properties for both exterior and interior surfaces of steel-clad buildings. The aim of this thesis is to investigate the influence of surface radiation properties with the focus on the thermal emittance of the interior surfaces, the modeling approaches and their consequences in the context of the building energy performance and indoor thermal environment. The study consists of both numerical and experimental investigations. The experimental investigations include parallel field measurements on three similar test cabins with different interior and exterior surface radiation properties in Borlänge, Sweden, and two ice rink arenas with normal and low emissive ceiling in Luleå, Sweden. The numerical methods include comparative simulations by the use of dynamic heat flux models, Building Energy Simulation (BES), Computational Fluid Dynamics (CFD) and a coupled model for BES and CFD. Several parametric studies and thermal performance analyses were carried out in combination with the different numerical methods. The parallel field measurements on the test cabins include the air, surface and radiation temperatures and energy use during passive and active (heating and cooling) measurements. Both measurement and comparative simulation results indicate an improvement in the indoor thermal environment when the interior surfaces have low emittance. In the ice rink arenas, surface and radiation temperature measurements indicate a considerable reduction in the ceiling-to-ice radiation by the use of low emittance surfaces, in agreement with a ceiling-toice radiation model using schematic dynamic heat flux calculations. The measurements in the test cabins indicate that the use of low emittance surfaces can increase the vertical indoor air temperature gradients depending on the time of day and outdoor conditions. This is in agreement with the transient CFD simulations having the boundary condition assigned on the exterior surfaces. The sensitivity analyses have been performed under different outdoor conditions and surface thermal radiation properties. The spatially resolved simulations indicate an increase in the air and surface temperature gradients by the use of low emittance coatings. This can allow for lower air temperature at the occupied zone during the summer. The combined effect of interior and exterior reflective coatings in terms of energy use has been investigated by the use of building energy simulation for different climates and internal heat loads. The results indicate possible energy savings by the smart choice of optical properties on interior and exterior surfaces of the building. Overall, it is concluded that the interior reflective coatings can contribute to building energy savings and improvement of the indoor thermal environment. This can be numerically investigated by the choice of appropriate models with respect to the level of detail and computational load. This thesis includes comparative simulations at different levels of detail.

Combined Vertical And Lateral Channel Evolution Numerical Modeling

Vertical stream bed erosion has been studied routinely and its modeling is getting widespread acceptance. The same cannot be said with lateral stream bank erosion since its measurement or numerical modeling is very challenging. Bank erosion, however, can be important to channel morphology. It may contribute significantly to the overall sediment budget of a stream, is a leading cause of channel migration, and is the cause of major channel maintenance. However, combined vertical and lateral channel evolution is seldom addressed. In this study, a new geofluival numerical model is developed to simulate combined vertical and lateral channel evolution. Vertical erosion is predicted with a 2D depth-averaged model SRH-2D, while lateral erosion is simulated with a linear retreat bank erosion model developed in this study. SRH-2D and the bank erosion model are coupled together both spatially and temporally through a common mesh and the same time advancement. The new geofluvial model is first tested and verified using laboratory meander channels; good agreement are obtained between predicted bank retreat and measured data. The model is then applied to a 16-kilometer reach of Chosui River, Taiwan. Vertical and lateral channel evolution during a three-year period (2004 to 2007) is simulated and results are compared with the field data. It is shown that the geofluvial model correctly captures all major erosion and deposition patterns. The new model is shown to be useful for identifying potential erosion sites and providing information for river maintenance planning.

Business competition dynamics: agent-based modeling simulations of firms in search of economic performance

A intenção deste trabalho é explorar dinâmicas de competição por meio de “simulação baseada em agentes”. Apoiando-se em um crescente número de estudos no campo da estratégia e teoria das organizações que utilizam métodos de simulação, desenvolveu-se um modelo computacional para simular situações de competição entre empresas e observar a eficiência relativa dos métodos de busca de melhoria de desempenho teorizados. O estudo também explora possíveis explicações para a persistência de desempenho superior ou inferior das empresas, associados às condições de vantagem ou desvantagem competitiva

Alinhamento de expectativas e desempenho organizacional: um estudo sobre os métodos ágeis de gestão.

A adoção dos métodos ágeis de gestão do desenvolvimento de software tem sido uma tendência mundial, considerando-se as empresas do setor de tecnologia. Empresas brasileiras atuando neste mercado não estão apartadas deste quadro, uma vez que o objetivo desses métodos é endereçar um cenário comum a qualquer uma dessas organizações: lidar com a dificuldade de modelar adequadamente os problemas usualmente complexos que são objetivo da construção de um software e com a mudança constante de requisitos que esta situação representa, potencializada ainda mais pela dinâmica frenética da disseminação da informação no século XXI, além de modificar um quadro crônico de fracassos e falhas no setor, visando entregar produtos de qualidade aos seus clientes com o máximo de velocidade. Aspectos internos como o aumento de produtividade e a redução de retrabalho também fazem parte dos objetivos de adoção destas metodologias. O presente estudo visa avaliar os aspectos humanos e culturais envolvidos e identificar a convergência entre as expectativas da empresa e dos empregados quando da adoção de métodos ágeis de gestão, a partir de pesquisa de campo que capturou as reações de um grupo de entrevistados à implantação desses métodos na Módulo Security Solutions, empresa brasileira de tecnologia e serviços, após dois anos de uso interno abrangente. Os resultados apontam para o sucesso da implantação, com reação positiva dos empregados, a despeito da necessidade de endereçamento de aspectos humanos para ajuste do modelo e do impacto negativo da cultura local e organizacional terem sido amplamente percebidos.

Uma técnica para modelagem de cenários consistentes na previsão da demanda por energia elétrica

As técnicas qualitativas disponiveis para a modelagem de cenários têm sido reconhecidas pela extrema limitação, evidenciada no principio das atividades do processo, como a fase inicial de concepção. As principais restrições têm sido: • inexistência de uma ferramenta que teste a consistência estrutural interna do modelo, ou pela utilização de relações econômicas com fundamentação teórica mas sem interface perfeita com o ambiente, ou pela adoção de variações binárias para testes de validação; • fixação "a priori" dos possíveis cenários, geralmente classificados sob três adjetivos - otimista, mais provável e pessimista - enviesados exatamente pelos atributos das pessoas que fornecem esta informação. o trabalho trata da utilização de uma ferramenta para a interação entre uma técnica que auxilia a geração de modelos, suportada pela lógica relacional com variações a quatro valores e expectativas fundamentadas no conhecimento do decisor acerca do mundo real. Tem em vista a construção de um sistema qualitativo de previsão exploratória, no qual os cenários são obtidos por procedimento essencialmente intuitivo e descritivos, para a demanda regional por eletricidade. Este tipo de abordagem - apresentada por J. Gershuny - visa principalmente ao fornecimento de suporte metodológico para a consistência dos cenários gerados qualitativamente. Desenvolvimento e estruturação do modelo são realizados em etapas, partindo-se de uma relação simples e prosseguindo com a inclusão de variáveis e efeitos que melhoram a explicação do modelo. o trabalho apresenta um conjunto de relações para a demanda regional de eletricidade nos principais setores de consumo residencial, comercial e industrial bem como os cenários resultantes das variações mais prováveis das suas componentes exógenas. Ao final conclui-se que esta técnica é útil em modelos que: • incluem variáveis sociais relevantes e de dificil mensuração; • acreditam na importância da consistência externa entre os resultados gerados pelo modelo e aqueles esperados para a tomada de decisões; • atribuem ao decisor a responsabilidade de compreender a fundamentação da estrutura conceitual do modelo. Adotado este procedimento, o autor aqui recomenda que o modelo seja validado através de um procedimento iterativo de ajustes com a participação do decisor. As técnicas quantitativas poderão ser adotadas em seguida, tendo o modelo como elemento de consistência.

Analysis an development of a prototype based on media wiki and semantic media wiki integrated with a design modeling that allows modeling of organizations based on demo

In a world where organizations are ever more complex the need for the knowledge of the organizational self is a growing necessity. The DEMO methodology sets a goal in achieving the specification of the organizational self capturing the essence of the organization in way independent of its implementation and also coherent, consistent, complete, modular and objective. But having such organization self notion is of little meaning if this notion is not shared by the organization actors. To achieve this goal in a society that has grown attached to technology and where time is of utmost importance, using a tool such as a semantic Wikipedia may be the perfect way of making the information accessible. However, to establish DEMO methodology in such platform there is a need to create bridges between its modeling components and semantic Wikipedia. It’s in that aspect that our thesis focuses, trying to establish and implement, using a study case, the principles of a way of transforming the DEMO methodology diagrams in comprehensive pages on semantic Wikipedia but keeping them as abstract as possible to allow expansibility and generalization to all diagrams without losing any valuable information so that, if that is the wish, those diagrams may be recreated from the semantic pages and make this process a full cycle.

Transfer function-noise modeling and spatial interpolation to evaluate the risk of extreme (shallow) water-table levels in the Brazilian Cerrados

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Purification, characterization, crystallization and theoretical molecular modeling of gyroxin fraction from Crotalus durissus terrificus venom (Laurenti, 1768)

The venom of Crotalus durissus terrificus snakes presents various substances, including a serine protease with thrombin-like activity, called gyroxin, that clots plasmatic fibrinogen and promote the fibrin formation. The aim of this study was to purify and structurally characterize the gyroxin enzyme from Crotalus durissus terrificus venom. For isolation and purification, the following methods were employed: gel filtration on Sephadex G75 column and affinity chromatography on benzamidine Sepharose 6B; 12% SDS-PAGE under reducing conditions; N-terminal sequence analysis; cDNA cloning and expression through RT-PCR and crystallization tests. Theoretical molecular modeling was performed using bioinformatics tools based on comparative analysis of other serine proteases deposited in the NCBI (National Center for Biotechnology Information) database. Protein N-terminal sequencing produced a single chain with a molecular mass of similar to 30 kDa while its full-length cDNA had 714 bp which encoded a mature protein containing 238 amino acids. Crystals were obtained from the solutions 2 and 5 of the Crystal Screen Kit (R), two and one respectively, that reveal the protein constitution of the sample. For multiple sequence alignments of gyroxin-like B2.1 with six other serine proteases obtained from snake venoms (SVSPs), the preservation of cysteine residues and their main structural elements (alpha-helices, beta-barrel and loops) was indicated. The localization of the catalytic triad in His57, Asp102 and Ser198 as well as S1 and S2 specific activity sites in Thr193 and Gli215 amino acids was pointed. The area of recognition and cleavage of fibrinogen in SVSPs for modeling gyroxin B2.1 sequence was located at Arg60, Arg72, Gln75, Arg81, Arg82, Lis85, Glu86 and Lis87 residues. Theoretical modeling of gyroxin fraction generated a classical structure consisting of two alpha-helices, two beta-barrel structures, five disulfide bridges and loops in positions 37, 60, 70, 99, 148, 174 and 218. These results provided information about the functional structure of gyroxin allowing its application in the design of new drugs.

Extraction of Building Roof Contours From LiDAR Data Using a Markov-Random-Field-Based Approach

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

Predição de sombras de edifícios sobre vias urbanas com base em modelos digitais de elevações e dados de imagens aéreas de alta resolução

This research presents a methodology for prediction of building shadows cast on urban roads existing on high-resolution aerial imagery. Shadow elements can be used in the modeling of contextual information, whose use has become more and more common in image analysis complex processes. The proposed methodology consists in three sequential steps. First, the building roof contours are manually extracted from an intensity image generated by the transformation of a digital elevation model (DEM) obtained from airborne laser scanning data. In similarly, the roadside contours are extracted, now from the radiometric information of the laser scanning data. Second, the roof contour polygons are projected onto the adjacent roads by using the parallel projection straight lines, whose directions are computed from the solar ephemeris, which depends on the aerial image acquisition time. Finally, parts of shadow polygons that are free from building perspective obstructions are determined, given rise to new shadow polygons. The results obtained in the experimental evaluation of the methodology showed that the method works properly, since it allowed the prediction of shadow in high-resolution imagery with high accuracy and reliability.