Using gap-crossing capacity to evaluate functional connectivity of two Atlantic rainforest birds and their response to fragmentation

One of the main consequences of habitat loss and fragmentation is the increase in patch isolation and the consequent decrease in landscape connectivity. In this context, species persistence depends on their responses to this new landscape configuration, particularly on their capacity to move through the interhabitat matrix. Here, we aimed first to determine gap-crossing probabilities related to different gap widths for two forest birds (Thamnophilus caerulescens, Thamnophilidae, and Basileuterus culicivorus, Parulidae) from the Brazilian Atlantic rainforest. These values were defined with a playback technique and then used in analyses based on graph theory to determine functional connections among forest patches. Both species were capable of crossing forest gaps between patches, and these movements were related to gap width. The probability of crossing 40 m gaps was 50% for both species. This probability falls to 10% when the gaps are 60 m (for B. culicivorus) or 80 m (for T caerulescens). Actually, birds responded to stimulation about two times more distant inside forest trials (control) than in gap-crossing trials. Models that included gap-crossing capacity improved the explanatory power of species abundance variation in comparison to strictly structural models based merely on patch area and distance measurements. These results highlighted that even very simple functional connectivity measurements related to gap-crossing capacity can improve the understanding of the effect of habitat fragmentation on bird occurrence and abundance.

Expression and purification of human respiratory syncytial virus recombinant fusion protein

The Human Respiratory Syncytial Virus (HRSV) fusion protein (F) was expressed in Escherichia call BL21A using the pET28a vector at 37 degrees C. The protein was purified from the soluble fraction using affinity resin. The structural quality of the recombinant fusion protein and the estimation of its secondary structure were obtained by circular dichroism. Structural models of the fusion protein presented 46% of the helices in agreement with the spectra by circular dichroism analysis. There are only few studies that succeeded in expressing the HRSV fusion protein in bacteria. This is a report on human fusion protein expression in E. call and structure analysis, representing a step forward in the development of fusion protein F inhibitors and the production of antibodies. (c) 2008 Elsevier Inc. All rights reserved.

Flexibility and inhibitor binding in Cdc25 phosphatases

Cdc25 phosphatases involved in cell cycle checkpoints are now active targets for the development of anti-cancer therapies. Rational drug design would certainly benefit from detailed structural information for Cdc25s. However, only apo- or sulfate-bound crystal structures of the Cdc25 catalytic domain have been described so far. Together with previously available crystalographic data, results from molecular dynamics simulations, bioinformatic analysis, and computer-generated conformational ensembles shown here indicate that the last 30-40 residues in the C-terminus of Cdc25B are partially unfolded or disordered in solution. The effect of C-terminal flexibility upon binding of two potent small molecule inhibitors to Cdc25B is then analyzed by using three structural models with variable levels of flexibility, including an equilibrium distributed ensemble of Cdc25B backbone conformations. The three Cdc25B structural models are used in combination with flexible docking, clustering, and calculation of binding free energies by the linear interaction energy approximation to construct and validate Cdc25B-inhibitor complexes. Two binding sites are identified on top and beside the Cdc25B active site. The diversity of interaction modes found increases with receptor flexibility. Backbone flexibility allows the formation of transient cavities or compact hydrophobic units on the surface of the stable, folded protein core that are unexposed or unavailable for ligand binding in rigid and densely packed crystal structures. The present results may help to speculate on the mechanisms of small molecule complexation to partially unfolded or locally disordered proteins.

Modelagem de previsões econômicas em cenários prospectivos

A estabilidade econômica que o Brasil atualmente experimenta permite resgatar a tradição de construção e análises prospectivas de médio e longo prazos. Isto remete à necessidade de se pensar mais profundamente acerca da possível evolução da economia brasileira, sendo mister o conhecimento de ferramentas de previsão. O objetivo deste trabalho é contribuir com este propósito. Avanços significativos têm sido observados na modelagem de previsões macro econômicas. Para se avaliar como os modelos de previsão estarão se desenvolvendo no futuro próximo, é necessário entender a evolução das abordagens dos modelos de previsão não-estruturais e estruturais. Como dependem da teoria econômica, os modelos estruturais ganham importância e descaso na medida em que a teoria evolui e cai em desuso. A marca registrada das previsões macroeconômicas nos próximos anos será o casamento das melhores abordagens estruturais e não-estruturais, facilitadas por avanços em técnicas numéricas e de simulação. Para ilustrar o trabalho de forma empírica, três cenários para a economia brasileira foram desenvolvidos, utilizando-se como base o arcabouço teórico resumido em uma das seções deste trabalho. Cenários potencialmente têm um valor muito grande na gestão de uma empresa ou de uma instituição. Cenários são a oitava ferramenta gerencial mais utilizada nas empresas em todo o mundo1 e esta dissertação é mais uma contribuição para este rico campo.

A Framework supporting collaboration on the distributed design of integrated systems

The work described in this thesis aims to support the distributed design of integrated systems and considers specifically the need for collaborative interaction among designers. Particular emphasis was given to issues which were only marginally considered in previous approaches, such as the abstraction of the distribution of design automation resources over the network, the possibility of both synchronous and asynchronous interaction among designers and the support for extensible design data models. Such issues demand a rather complex software infrastructure, as possible solutions must encompass a wide range of software modules: from user interfaces to middleware to databases. To build such structure, several engineering techniques were employed and some original solutions were devised. The core of the proposed solution is based in the joint application of two homonymic technologies: CAD Frameworks and object-oriented frameworks. The former concept was coined in the late 80's within the electronic design automation community and comprehends a layered software environment which aims to support CAD tool developers, CAD administrators/integrators and designers. The latter, developed during the last decade by the software engineering community, is a software architecture model to build extensible and reusable object-oriented software subsystems. In this work, we proposed to create an object-oriented framework which includes extensible sets of design data primitives and design tool building blocks. Such object-oriented framework is included within a CAD Framework, where it plays important roles on typical CAD Framework services such as design data representation and management, versioning, user interfaces, design management and tool integration. The implemented CAD Framework - named Cave2 - followed the classical layered architecture presented by Barnes, Harrison, Newton and Spickelmier, but the possibilities granted by the use of the object-oriented framework foundations allowed a series of improvements which were not available in previous approaches: - object-oriented frameworks are extensible by design, thus this should be also true regarding the implemented sets of design data primitives and design tool building blocks. This means that both the design representation model and the software modules dealing with it can be upgraded or adapted to a particular design methodology, and that such extensions and adaptations will still inherit the architectural and functional aspects implemented in the object-oriented framework foundation; - the design semantics and the design visualization are both part of the object-oriented framework, but in clearly separated models. This allows for different visualization strategies for a given design data set, which gives collaborating parties the flexibility to choose individual visualization settings; - the control of the consistency between semantics and visualization - a particularly important issue in a design environment with multiple views of a single design - is also included in the foundations of the object-oriented framework. Such mechanism is generic enough to be also used by further extensions of the design data model, as it is based on the inversion of control between view and semantics. The view receives the user input and propagates such event to the semantic model, which evaluates if a state change is possible. If positive, it triggers the change of state of both semantics and view. Our approach took advantage of such inversion of control and included an layer between semantics and view to take into account the possibility of multi-view consistency; - to optimize the consistency control mechanism between views and semantics, we propose an event-based approach that captures each discrete interaction of a designer with his/her respective design views. The information about each interaction is encapsulated inside an event object, which may be propagated to the design semantics - and thus to other possible views - according to the consistency policy which is being used. Furthermore, the use of event pools allows for a late synchronization between view and semantics in case of unavailability of a network connection between them; - the use of proxy objects raised significantly the abstraction of the integration of design automation resources, as either remote or local tools and services are accessed through method calls in a local object. The connection to remote tools and services using a look-up protocol also abstracted completely the network location of such resources, allowing for resource addition and removal during runtime; - the implemented CAD Framework is completely based on Java technology, so it relies on the Java Virtual Machine as the layer which grants the independence between the CAD Framework and the operating system. All such improvements contributed to a higher abstraction on the distribution of design automation resources and also introduced a new paradigm for the remote interaction between designers. The resulting CAD Framework is able to support fine-grained collaboration based on events, so every single design update performed by a designer can be propagated to the rest of the design team regardless of their location in the distributed environment. This can increase the group awareness and allow a richer transfer of experiences among them, improving significantly the collaboration potential when compared to previously proposed file-based or record-based approaches. Three different case studies were conducted to validate the proposed approach, each one focusing one a subset of the contributions of this thesis. The first one uses the proxy-based resource distribution architecture to implement a prototyping platform using reconfigurable hardware modules. The second one extends the foundations of the implemented object-oriented framework to support interface-based design. Such extensions - design representation primitives and tool blocks - are used to implement a design entry tool named IBlaDe, which allows the collaborative creation of functional and structural models of integrated systems. The third case study regards the possibility of integration of multimedia metadata to the design data model. Such possibility is explored in the frame of an online educational and training platform.

Previsão de preços de ativos usando restrições do modelo de valor presente

Motivados pelo debate envolvendo modelos estruturais e na forma reduzida, propomos nesse artigo uma abordagem empírica com o objetivo de ver se a imposição de restrições estruturais melhoram o poder de previsibilade vis-a-vis modelos irrestritos ou parcialmente restritos. Para respondermos nossa pergunta, realizamos previsões utilizando dados agregados de preços e dividendos de ações dos EUA. Nesse intuito, exploramos as restrições de cointegração, de ciclo comum em sua forma fraca e sobre os parâmetros do VECM impostas pelo modelo de Valor Presente. Utilizamos o teste de igualdade condicional de habilidade de previsão de Giacomini e White (2006) para comparar as previsões feitas por esse modelo com outros menos restritos. No geral, encontramos que os modelos com restrições parciais apresentaram os melhores resultados, enquanto o modelo totalmente restrito de VP não obteve o mesmo sucesso.

Forecasting Brazilian inflation by its aggregate and disaggregated data: a test of predictive power by forecast horizon

This work aims to compare the forecast efficiency of different types of methodologies applied to Brazilian Consumer inflation (IPCA). We will compare forecasting models using disaggregated and aggregated data over twelve months ahead. The disaggregated models were estimated by SARIMA and will have different levels of disaggregation. Aggregated models will be estimated by time series techniques such as SARIMA, state-space structural models and Markov-switching. The forecasting accuracy comparison will be made by the selection model procedure known as Model Confidence Set and by Diebold-Mariano procedure. We were able to find evidence of forecast accuracy gains in models using more disaggregated data

Previsão de inflação utilizando modelos de séries temporais

Este trabalho compara modelos de séries temporais para a projeção de curto prazo da inflação brasileira, medida pelo Índice de Preços ao Consumidor Amplo (IPCA). Foram considerados modelos SARIMA de Box e Jenkins e modelos estruturais em espaço de estados, estimados pelo filtro de Kalman. Para a estimação dos modelos, foi utilizada a série do IPCA na base mensal, de março de 2003 a março de 2012. Os modelos SARIMA foram estimados no EVIEWS e os modelos estruturais no STAMP. Para a validação dos modelos para fora da amostra, foram consideradas as previsões 1 passo à frente para o período de abril de 2012 a março de 2013, tomando como base os principais critérios de avaliação de capacidade preditiva propostos na literatura. A conclusão do trabalho é que, embora o modelo estrutural permita, decompor a série em componentes com interpretação direta e estudá-las separadamente, além de incorporar variáveis explicativas de forma simples, o desempenho do modelo SARIMA para prever a inflação brasileira foi superior, no período e horizonte considerados. Outro importante aspecto positivo é que a implementação de um modelo SARIMA é imediata, e previsões a partir dele são obtidas de forma simples e direta.

Comparação de previsões para a produção industrial brasileira considerando efeitos calendário e modelos agregados e desagregados

O trabalho tem como objetivo verificar a existência e a relevância dos Efeitos Calendário em indicadores industriais. São explorados modelos univariados lineares para o indicador mensal da produção industrial brasileira e alguns de seus componentes. Inicialmente é realizada uma análise dentro da amostra valendo-se de modelos estruturais de espaço-estado e do algoritmo de seleção Autometrics, a qual aponta efeito significante da maioria das variáveis relacionadas ao calendário. Em seguida, através do procedimento de Diebold-Mariano (1995) e do Model Confidence Set, proposto por Hansen, Lunde e Nason (2011), são realizadas comparações de previsões de modelos derivados do Autometrics com um dispositivo simples de Dupla Diferença para um horizonte de até 24 meses à frente. Em geral, os modelos Autometrics que consideram as variáveis de calendário se mostram superiores nas projeções de 1 a 2 meses adiante e superam o modelo simples em todos os horizontes. Quando se agrega os componentes de categoria de uso para formar o índice industrial total, há evidências de ganhos nas projeções de prazo mais curto.

Estudo do genoma do vírus causador da mionecrose infecciosa em camarões e desenvolvimento de métodos para detecção de diferentes variantes

Shrimp farming is one of the activities that contribute most to the growth of global aquaculture. However, this business has undergone significant economic losses due to the onset of viral diseases such as Infectious Myonecrosis (IMN). The IMN is already widespread throughout Northeastern Brazil and affects other countries such as Indonesia, Thailand and China. The main symptom of disease is myonecrosis, which consists of necrosis of striated muscles of the abdomen and cephalothorax of shrimp. The IMN is caused by infectious myonecrosis virus (IMNV), a non-enveloped virus which has protrusions along its capsid. The viral genome consists of a single molecule of double-stranded RNA and has two Open Reading Frames (ORFs). The ORF1 encodes the major capsid protein (MCP) and a potential RNA binding protein (RBP). ORF2 encodes a probable RNA-dependent RNA polymerase (RdRp) and classifies IMNV in Totiviridae family. Thus, the objective of this research was study the IMNV complete genome and encoded proteins in order to develop a system differentiate virus isolates based on polymorphisms presence. The phylogenetic relationship among some totivirus was investigated and showed a new group to IMNV within Totiviridae family. Two new genomes were sequenced, analyzed and compared to two other genomes already deposited in GenBank. The new genomes were more similar to each other than those already described. Conserved and variable regions of the genome were identified through similarity graphs and alignments using the four IMNV sequences. This analyze allowed mapping of polymorphic sites and revealed that the most variable region of the genome is in the first half of ORF1, which coincides with the regions that possibly encode the viral protrusion, while the most stable regions of the genome were found in conserved domains of proteins that interact with RNA. Moreover, secondary structures were predicted for all proteins using various softwares and protein structural models were calculated using threading and ab initio modeling approaches. From these analyses was possible to observe that the IMNV proteins have motifs and shapes similar to proteins of other totiviruses and new possible protein functions have been proposed. The genome and proteins study was essential for development of a PCR-based detection system able to discriminate the four IMNV isolates based on the presence of polymorphic sites

Expression, purification, and circular dichroism analysis of human CDK9

The human cyclin-dependent kinase 9 (CDK9) protein was expressed in E coli BL21 using the pET23a vector at 30 degrees C. Several milligrams of protein were purified from soluble fraction using ionic exchange and ATP-affinity chromatography. The structural quality of recombinant CDK9 and the estimation of its secondary structure were obtained by circular dichroism. Structural models of CDK9 presented 26% of helices in agreement with the spectra by circular dichroism analysis. This is the first report on human CDK9 expression in Escherichia coli and structure analysis and provides the first step for the development of CDK9 inhibitors. (c) 2006 Elsevier B.V. All rights reserved.

Hierarquia de dominância durante a obtenção de Alimento em cebus apella e cebus libidinosus em Cativeiro

The analysis of the index of hierarchy and structural models of the formation of groups allowed to establish the hierarchical position of members of two groups of the genus Cebus. By the analyses of the hierarchical positions and the application of tests to obtain a food resource (TORA), we know the difference between these groups and groups in the wild. The results show a high ranking for both Cebus apella, as well as Cebus libidinosus. The results have enabled us to establish that the hierarchical structure in groups of Cebus in captivity: a) can be fixed and rigid different from highly flexible hierarchical structure studied in groups of wild b) even which similar hierarchy indices, there are differences in the hierarchical structure presents between C. apella and C. libidinosus in captivity c) hierarchy directly influence the behavioral patterns of obtaining food in Cebus

Expression and purification of human respiratory syncytial virus recombinant fusion protein

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

Molecular modeling and small angle X-ray scattering studies of Hoplosternum littorale cathodic haemoglobin

Considerable interest is currently focused on fish haemoglobins in order to identify the structural basis for their diversity of functional behavior. Hoplosternum littorale is a catfish that presents bimodal gill (water)/gut (air) -breathing, which allows this species to survive in waters with low oxygen content. The hemolysate of this fish showed the presence of two main haemoglobins, cathodic and anodic. This work describes structural features analyzed here by integration of molecular modeling with small angle X-ray scattering. Here is described a molecular model for the cathodic haemoglobin in the unliganded and liganded states. The models were determined by molecular modeling based on the high-resolution crystal structure of fish haemoglobins. The structural models for both forms of H. littorale haemoglobin were compared to human haemoglobin. (C) 2004 Elsevier B.V. All rights reserved.