Predição de promotores de Bacillus subtilis usando técnicas de aprendizado de máquina

One of the most important goals of bioinformatics is the ability to identify genes in uncharacterized DNA sequences on world wide database. Gene expression on prokaryotes initiates when the RNA-polymerase enzyme interacts with DNA regions called promoters. In these regions are located the main regulatory elements of the transcription process. Despite the improvement of in vitro techniques for molecular biology analysis, characterizing and identifying a great number of promoters on a genome is a complex task. Nevertheless, the main drawback is the absence of a large set of promoters to identify conserved patterns among the species. Hence, a in silico method to predict them on any species is a challenge. Improved promoter prediction methods can be one step towards developing more reliable ab initio gene prediction methods. In this work, we present an empirical comparison of Machine Learning (ML) techniques such as Na¨ýve Bayes, Decision Trees, Support Vector Machines and Neural Networks, Voted Perceptron, PART, k-NN and and ensemble approaches (Bagging and Boosting) to the task of predicting Bacillus subtilis. In order to do so, we first built two data set of promoter and nonpromoter sequences for B. subtilis and a hybrid one. In order to evaluate of ML methods a cross-validation procedure is applied. Good results were obtained with methods of ML like SVM and Naïve Bayes using B. subtilis. However, we have not reached good results on hybrid database

Sistema inteligente para determinação das direções de chegada de múltiplos sinais em arranjos de antenas

This dissertation presents a new proposal for the Direction of Arrival (DOA) detection problem for more than one signal inciding simultaneously on an antennas array with linear or planar geometry by using intelligent algorithms. The DOA estimator is developed by using techniques of Conventional Beam-forming (CBF), Blind Source Separation (BSS), and the neural estimator MRBF (Modular Structure of Radial Basis Functions). The developed MRBF estimator has its capacity extended due to the interaction with the BSS technique. The BSS makes an estimation of the steering vectors of the multiple plane waves that reach the array in the same frequency, that means, obtains to separate mixed signals without information a priori. The technique developed in this work makes possible to identify the multiple sources directions and to identify and to exclude interference sources

Aplicação de técnicas de aprendizado de máquina no reconhecimento de classes estruturais de proteínas

Nowadays, classifying proteins in structural classes, which concerns the inference of patterns in their 3D conformation, is one of the most important open problems in Molecular Biology. The main reason for this is that the function of a protein is intrinsically related to its spatial conformation. However, such conformations are very difficult to be obtained experimentally in laboratory. Thus, this problem has drawn the attention of many researchers in Bioinformatics. Considering the great difference between the number of protein sequences already known and the number of three-dimensional structures determined experimentally, the demand of automated techniques for structural classification of proteins is very high. In this context, computational tools, especially Machine Learning (ML) techniques, have become essential to deal with this problem. In this work, ML techniques are used in the recognition of protein structural classes: Decision Trees, k-Nearest Neighbor, Naive Bayes, Support Vector Machine and Neural Networks. These methods have been chosen because they represent different paradigms of learning and have been widely used in the Bioinfornmatics literature. Aiming to obtain an improvment in the performance of these techniques (individual classifiers), homogeneous (Bagging and Boosting) and heterogeneous (Voting, Stacking and StackingC) multiclassification systems are used. Moreover, since the protein database used in this work presents the problem of imbalanced classes, artificial techniques for class balance (Undersampling Random, Tomek Links, CNN, NCL and OSS) are used to minimize such a problem. In order to evaluate the ML methods, a cross-validation procedure is applied, where the accuracy of the classifiers is measured using the mean of classification error rate, on independent test sets. These means are compared, two by two, by the hypothesis test aiming to evaluate if there is, statistically, a significant difference between them. With respect to the results obtained with the individual classifiers, Support Vector Machine presented the best accuracy. In terms of the multi-classification systems (homogeneous and heterogeneous), they showed, in general, a superior or similar performance when compared to the one achieved by the individual classifiers used - especially Boosting with Decision Tree and the StackingC with Linear Regression as meta classifier. The Voting method, despite of its simplicity, has shown to be adequate for solving the problem presented in this work. The techniques for class balance, on the other hand, have not produced a significant improvement in the global classification error. Nevertheless, the use of such techniques did improve the classification error for the minority class. In this context, the NCL technique has shown to be more appropriated

Plano Nacional de Saúde e o lugar social em disputa

O presente artigo apresenta uma análise do Plano Nacional de Saúde publicado em 2004. Este documento expressa um importante período de transição na gestão do SUS, uma vez que foi predecessor do Pacto pela Saúde. A partir de um estudo descritivo com base em procedimentos quantitativos e qualitativos, o objetivo foi compreender as ideias centrais do documento, identificando as conexões existentes entre seus princípios, objetivos e prioridades. O principal resultado do estudo foi a identificação da integralidade das ações, da capacitação dos recursos humanos e mudança do marco regulatório com base numa visão intersetorial como núcleo central do documento. Essas ideias, por sua vez, circulam pelo discurso das diretrizes do plano, fortalecendo os laços do eixo central do texto na reorganização da atenção ambulatorial e na qualificação profissional. Por fim, quando comparadas metas e ações previstas nas diretrizes, observa-se uma tensão entre o que foram denominados vetores da verticalidade e da horizontalidade, deixando em aberto o rumo do lugar social em disputa.

Análise da aceitação de aguardentes de cana por testes afetivos e mapa de preferência interno

A aceitação de 11 amostras de aguardentes de cana envelhecidas e não envelhecidas foi avaliada por testes sensoriais afetivos e análises estatísticas uni e multivariada. As aguardentes estudadas compreenderam seis amostras comerciais de diferentes marcas, (sendo três não envelhecidas e três envelhecidas) e ainda outras cinco amostras correspondentes a zero, 12, 24, 36 e 48 meses de envelhecimento em um tonel de carvalho de 200L. As amostras foram avaliadas por 100 provadores consumidores do produto, recrutados por questionário de avaliação quanto à afetividade. Para os testes afetivos foi utilizada escala hedônica não estruturada de 9cm, sendo os dados obtidos avaliados por dois métodos estatísticos distintos: o Mapa de Preferência Interno (MDPREF) e a análise de variância univariada (ANOVA) com comparação de médias pelo teste de Tukey e análise de correlação. As amostras de aguardente envelhecidas por 12, 36 e 48 meses obtiveram maior aceitação, com médias ao redor de 7,0 na escala hedônica. A amostra com menor aceitação foi a correspondente ao tempo zero de envelhecimento (controle). As demais amostras obtiveram aceitação intermediária. A análise por MDPREF gerou em espaço multidimensional (onde as variações com relação aos dados de preferência foram extraídas em eixos ortogonais e para cada dimensão de preferência), coordenadas relativas aos produtos, que foram geradas em função da resposta dos consumidores. Os dados de aceitação de cada provador foram utilizados para o desenvolvimento de vetores individuais de preferência, resultando na construção de um mapa mutidimensional das amostras, em função dos dados de aceitação. No presente estudo o MDPREF foi gerado pelas primeira e segunda dimensões de preferência, as quais explicaram em conjunto 89,83% das variações observadas entre as amostras com relação à aceitação. O MDPREF confirmou os resultados da ANOVA, indicando uma maior preferência dos provadores pelas amostras de aguardentes envelhecidas. Os resultados sugerem também que aguardentes envelhecidas por mais de 24 meses em tonel de carvalho de 200L são preferidas pelos consumidores, em detrimento das comerciais não envelhecidas e mesmo das comerciais envelhecidas, que podem ser adicionadas de aguardente não envelhecida (processo denominado corte) e também ter correção da cor, conforme permite a Legislação Brasileira. O conteúdo de polifenóis totais e a intensidade de cor também foram determinados, e ambos apresentaram correlação linear positiva significativa (p<=0,05) com o aumento do tempo de envelhecimento das amostras.

Monitoramento da suscetibilidade de populações de Triatoma sordida Stål, 1859 (Hemiptera: Reduviidae) ao inseticida deltametrina, na região Centro-Oeste do Brasil

INTRODUÇÃO: Populações de Triatoma sordida Stål, 1859 foram investigadas quanto à suscetibilidade à deltametrina. MÉTODOS: Análise por meio de bioensaios por aplicação tópica em 11 populações de T. sordida procedentes dos Estados de Goiás, Mato Grosso e Mato Grosso do Sul. RESULTADOS: As estimativas de DL50 e RR50 demonstraram elevados níveis de suscetibilidade (DL50 < 1 e RR50 < 2). Entretanto, as análises do coeficiente angular da curva dose resposta revelaram que as populações de triatomíneos dos municípios de Firminópolis/GO, Posse/GO, Poxoréu/MT, Douradina/MS e Aparecida do Taboado/MS apresentam maiores probabilidades de evolução de resistência, portanto, mais propícias a tolerar o tratamento com deltametrina. CONCLUSÕES: Detectaram-se pequenas alterações de suscetibilidade e baixos níveis de resistência, porém as alterações temporais de suscetibilidade deverão ser continuamente monitoradas, a fim de nortear adequadamente as ações de controle dos vetores da DC.

Ondas de spin em super-redes ferromagnéticas com campo de anisotropia

Conselho Nacional de Desenvolvimento Científico e Tecnológico

Propriedades físicas de bicamadas magnéticas

The magnetic order of bylayers composed by a ferromagnetic film (F) coupled with an antiferromagnetic film (AF) is studied. Piles of coupled monolayers describe the films and the interfilm coupling is described by an exchange interaction between the magnetic moments at the interface. The F has a cubic anisotropy while the AF has a uniaxial anisotropy. We analyze the effects of an external do magnetic field applied parallel to the interface. We consider the intralayer coupling is strong enough to keep parallel all moments of the monolayer an then they are described by one vector proportional to the magnetization of the layer. The interlayer coupling is represented by an exchange interaction between these vectors. The magnetic energy of the system is the sum of the exchange. Anisotropy and Zeeman energies and the equilibrium configuration is one that gives the absolute minimum of the total energy. The magnetization of the system is calculated and the influence of the external do field combined with the interfilm coupling and the unidirectional anisotropy is studied. Special attention is given to the region near of the transition fields. The torque equation is used to study dynamical behavior of these systems. We consider small oscillations around the equilibrium position and we negleet nonlinear terms to obtain the natural frequencies of the system. The dependence of the frequencies with the external do field and their behavior in the phase transition region is analized

Desenvolvimento de sistemas farmacêuticos emulsionados para veiculação gênica

Broadly speaking, the concept of gene therapy involves the transfer of a genetic material into a cell, tissue, or organ in order to cure a disease or at least improve the clinical status of a patient. Making it simple, gene therapy consists in the insertion of functional genes into cells containing defective genes by substituting, complementing or inhibiting them. The achievement of a foreigner DNA expression into a population of cells requires its transfer to the target. Therefore, it is a key issue to create systems able to transfer and protect the DNA until it reaches the target, the vectors. The disadvantages related to the use of viral vectors have encouraged efforts to develop emulsions as non-viral vectors. In fact, they are easily produced, present controllable stability and enable transfection. The aim of this work was to develop an emulsion for gene therapy and evaluate its ability to compact nucleic acids by the development of a complex with the plasmid pIRES2-EGFP. The first step was to determine the Hydrophilic Lipophilic Balance (HLB) of the Captex® 355 (oily internal phase of the emulsion) through long and short term stability assays. Based on the results, emulsions composed of Captex® 355, Tween 20® and Span 60® with 10.7 HLB were produced by three different methods: phase inversion, spontaneous emulsification and sonication. The results showed that the lowest diameter and best stability of the emulsions were achieved by the sonication method. The cationic emulsions were made by adding DOTAP to the basic emulsion. Its association with pIRES2-EGFP was evaluated by electrophoresis. Several rates of emulsion and DNA were evaluated and the results showed that 100% of the complex was formed when the rate DOTAP/DNA(nmol/µg) was 130. In conclusion, the overall results show the ability of the proposed emulsion to compact pIRES2-EGFP, which is a requirement to a successful transfection. Therefore, such formulation may be considered a promising candidate for gene therapy

Maus ares e malária: entre os pântanos de Natal e o feroz mosquito africano (1892-1932)

The development of epidemiological practices in the last years of the nineteenth and early twentieth century was characterized by both an influence of medical geography and the emergence of microbes and vectors of diseases. Both theories were used to explain outbreaks in Rio Grande do Norte specially in Natal. In this process were organized new institutions linked to public health, unhealthy spaces and prescribed hygiene measures. The redefinitions of the spaces were linked to updated elements of Hippocratic medicine such as aerism and emphasis on medical topography. How the physicians of the town were organized in the face of new meanings and fields of expertise in the demarcation of diseases and regulation of their own practices against the illegal medical practitioners? Likewise, the very occurrence of epidemics mobilized people, urban institutions and apparatuses. But how the Hippocratic legacy that leads to the idea of bad air originated by swamps from the eighteenth and nineteenth century has been linked to new microbial assumptions and disease vectors in the early twentieth century? How an invader from Africa, (the mosquito A. gambiae) mobilized transnational efforts to combat malaria and redefined the epidemiological practices? The aim of this work is to understand how epidemiological practices redefine the way we define spaces, practices and disease from both an approach influenced by a relational history of spaces and a theoretical synergy which includes topics in Science Studies, Post Structuralist Geography and some elements of Feminist Studies. Documentary research were surveyed in the reports of the provincial presidents, government posts to the Provincial Assembly, specialized medical articles and theses, and documents from the Rockefeller Foundation and national and international journals. In this regard shall be given to both material and discursive aspects of space-related practical epidemiological that Natal as much (in general) Rio Grande do Norte between bad air and malaria.

A dimensão sociocultural da reforma psiquiátrica: articulando redes para a consolidação da estratégia de atenção psicossocial

This thesis aims to discuss on articulations that have been produced on the socio-cultural field in the Psychiatric Reform process and its pertinence to the streghtening of Psychosocial Care Strategy (EAPS) in Fortaleza/CE. Such interest has been justified by the need to promote not only the production of these networks, but also interfaces to enable strategies of support and sociability from the perspective of deinstitutionalization of madness. We were inspired by the cartography perspective of Deleuze e Guattari, and determined as objectives: 1) to discuss the complexity of Psychiatric Reform process and analyze the EAPS as a model for the current Mental Health policy in the country; 2) to map socio-cultural strategies connected to the CAPS network in the city, investigating experiences that already exist or may be constituted as everyday social support networks; 3) from that mapping to start, define and discuss some aspects that converge to the accomplishment for this new mental health paradigm, drawing a cartography of the issues and movements in progress. The mapping was carried out in 2009 and consisted of semi-structured interviews with the coordinators of the 14 existent CAPS and with some people connected to the Coordination of Mental Health. Besides, during the whole development of the study, we have taken part in public events that brought us clues on the connection between mental health and culture. From the survey produced, we defined three vectors for discussion (Art, Labour and Partnership with Social Movements) which have been highlighted as effective possibilities of intervention in the socio-cultural field of Psychiatric Reform in Fortaleza and reveal important paths on the fulfillment process of a new pattern of care. For each of these axes, we chose a field of empirical research (Projeto Arte e Saúde, COOPCAPS e MSMCBJ) in which we could better understand their strengths and difficulties, starting from open interviews with some of their actors and the production of a diary of sensations in 2010. We have seen that they are articulated with the proposal of EAPS, being part of the concerns to the National Mental Health Policy and also the municipal administration. However, we have noticed to be necessary to promote those dimensions further, focusing on its complexity at the macro and micro policies, with the purpose of leading the Psychiatric Reform process

O Serviço Residencial Terapêutico: cartografias de um híbrido no contexto da desinstitucionalização em saúde mental

This thesis seeks to uphold the idea that the therapeutic residential service, as hybrid device and recent process of deinstitutionalization in mental health, works as a problem producer while it also indicates challenges and potentialities in this process, the attention on mental health and on its own care production. To that end, we work with the prospect map with which we approach reality as the subjectivities production field which transformations and intensities are the major thought propellants. From this perspective, it was possible to produce three "purpose maps" from meetings with actors and groups involved with the TRS and the theoretical study carried out. On the first map we mapped the conditions of possibility of this device and its design in the midst of the process of institutionalization and health policies. We indicate on it the TRS configuration as a hybrid and we hassled its proposition as a means of "social rehabilitation" that can work as a social homogeneity mechanism. On a second map, we cartographied mental captures through images and ways historically built from madness presented in the biopolitical contemporary game and we indicated that the resistance to such catches should be built on a politic daily basis as important vectors of the institutionalization process in mental health. Finally, on a third map we mapped the carefulness produced in the TRS, by analyzing the transition psychiatric hospital - TRS and the caregivers´ team work. On this mapping, the care, for the weakness in the coresponsibility field, is reveled crossed by mental, disciplinary and normality elements, but it is also built in resistance born from links in the intersubjective field of the caring work. We conclude, then, that the TRS power and the deinstitutionalization process itself were in building and strengthening affective labor micro political networks of life and liberty producers

Prova automática de satisfatibilidade módulo teoria aplicada ao método B

Este trabalho apresenta uma extensão do provador haRVey destinada à verificação de obrigações de prova originadas de acordo com o método B. O método B de desenvolvimento de software abrange as fases de especificação, projeto e implementação do ciclo de vida do software. No contexto da verificação, destacam-se as ferramentas de prova Prioni, Z/EVES e Atelier-B/Click n Prove. Elas descrevem formalismos com suporte à checagem satisfatibilidade de fórmulas da teoria axiomática dos conjuntos, ou seja, podem ser aplicadas ao método B. A checagem de SMT consiste na checagem de satisfatibilidade de fórmulas da lógica de primeira-ordem livre de quantificadores dada uma teoria decidível. A abordagem de checagem de SMT implementada pelo provador automático de teoremas haRVey é apresentada, adotando-se a teoria dos vetores que não permite expressar todas as construções necessárias às especificações baseadas em conjuntos. Assim, para estender a checagem de SMT para teorias dos conjuntos destacam-se as teorias dos conjuntos de Zermelo-Frankel (ZFC) e de von Neumann-Bernays-Gödel (NBG). Tendo em vista que a abordagem de checagem de SMT implementada no haRVey requer uma teoria finita e pode ser estendida para as teorias nãodecidíveis, a teoria NBG apresenta-se como uma opção adequada para a expansão da capacidade dedutiva do haRVey à teoria dos conjuntos. Assim, através do mapeamento dos operadores de conjunto fornecidos pela linguagem B a classes da teoria NBG, obtem-se uma abordagem alternativa para a checagem de SMT aplicada ao método B

Uma investigação de algoritmos exatos e metaheurísticos aplicados ao nonograma

Nonogram is a logical puzzle whose associated decision problem is NP-complete. It has applications in pattern recognition problems and data compression, among others. The puzzle consists in determining an assignment of colors to pixels distributed in a N  M matrix that satisfies line and column constraints. A Nonogram is encoded by a vector whose elements specify the number of pixels in each row and column of a figure without specifying their coordinates. This work presents exact and heuristic approaches to solve Nonograms. The depth first search was one of the chosen exact approaches because it is a typical example of brute search algorithm that is easy to implement. Another implemented exact approach was based on the Las Vegas algorithm, so that we intend to investigate whether the randomness introduce by the Las Vegas-based algorithm would be an advantage over the depth first search. The Nonogram is also transformed into a Constraint Satisfaction Problem. Three heuristics approaches are proposed: a Tabu Search and two memetic algorithms. A new function to calculate the objective function is proposed. The approaches are applied on 234 instances, the size of the instances ranging from 5 x 5 to 100 x 100 size, and including logical and random Nonograms

Algoritmo treansgenético na solução do problema do Caixeiro Viajante

The Traveling Purchaser Problem is a variant of the Traveling Salesman Problem, where there is a set of markets and a set of products. Each product is available on a subset of markets and its unit cost depends on the market where it is available. The objective is to buy all the products, departing and returning to a domicile, at the least possible cost defined as the summation of the weights of the edges in the tour and the cost paid to acquire the products. A Transgenetic Algorithm, an evolutionary algorithm with basis on endosymbiosis, is applied to the Capacited and Uncapacited versions of this problem. Evolution in Transgenetic Algorithms is simulated with the interaction and information sharing between populations of individuals from distinct species. The computational results show that this is a very effective approach for the TPP regarding solution quality and runtime. Seventeen and nine new best results are presented for instances of the capacited and uncapacited versions, respectively