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

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

Aquatic weed automatic classification using machine learning techniques

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

Euler e os números pentagonais

The present investigation includes a study of Leonhard Euler and the pentagonal numbers is his article Mirabilibus Proprietatibus Numerorum Pentagonalium - E524. After a brief review of the life and work of Euler, we analyze the mathematical concepts covered in that article as well as its historical context. For this purpose, we explain the concept of figurate numbers, showing its mode of generation, as well as its geometric and algebraic representations. Then, we present a brief history of the search for the Eulerian pentagonal number theorem, based on his correspondence on the subject with Daniel Bernoulli, Nikolaus Bernoulli, Christian Goldbach and Jean Le Rond d'Alembert. At first, Euler states the theorem, but admits that he doesn t know to prove it. Finally, in a letter to Goldbach in 1750, he presents a demonstration, which is published in E541, along with an alternative proof. The expansion of the concept of pentagonal number is then explained and justified by compare the geometric and algebraic representations of the new pentagonal numbers pentagonal numbers with those of traditional pentagonal numbers. Then we explain to the pentagonal number theorem, that is, the fact that the infinite product(1 x)(1 xx)(1 x3)(1 x4)(1 x5)(1 x6)(1 x7)... is equal to the infinite series 1 x1 x2+x5+x7 x12 x15+x22+x26 ..., where the exponents are given by the pentagonal numbers (expanded) and the sign is determined by whether as more or less as the exponent is pentagonal number (traditional or expanded). We also mention that Euler relates the pentagonal number theorem to other parts of mathematics, such as the concept of partitions, generating functions, the theory of infinite products and the sum of divisors. We end with an explanation of Euler s demonstration pentagonal number theorem

Estimates for the Poisson kernel and Hardy spaces on compact manifolds

We study Hardy spaces on the boundary of a smooth open subset or R-n and prove that they can be defined either through the intrinsic maximal function or through Poisson integrals, yielding identical spaces. This extends to any smooth open subset of R-n results already known for the unit ball. As an application, a characterization of the weak boundary values of functions that belong to holomorphic Hardy spaces is given, which implies an F. and M. Riesz type theorem. (C) 2004 Elsevier B.V. All rights reserved.

PERIODIC PERTURBATION of QUADRATIC SYSTEMS WITH TWO INFINITE HETEROCLINIC CYCLES

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Time-periodic perturbation of a Lienard equation with an unbounded homoclinic loop

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Periodic perturbations of quadratic planar polynomial vector fields

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Condições de energia de hawking e ellis e a equação de raychaudhuri

In the Einstein s theory of General Relativity the field equations relate the geometry of space-time with the content of matter and energy, sources of the gravitational field. This content is described by a second order tensor, known as energy-momentum tensor. On the other hand, the energy-momentum tensors that have physical meaning are not specified by this theory. In the 700s, Hawking and Ellis set a couple of conditions, considered feasible from a physical point of view, in order to limit the arbitrariness of these tensors. These conditions, which became known as Hawking-Ellis energy conditions, play important roles in the gravitation scenario. They are widely used as powerful tools for analysis; from the demonstration of important theorems concerning to the behavior of gravitational fields and geometries associated, the gravity quantum behavior, to the analysis of cosmological models. In this dissertation we present a rigorous deduction of the several energy conditions currently in vogue in the scientific literature, such as: the Null Energy Condition (NEC), Weak Energy Condition (WEC), the Strong Energy Condition (SEC), the Dominant Energy Condition (DEC) and Null Dominant Energy Condition (NDEC). Bearing in mind the most trivial applications in Cosmology and Gravitation, the deductions were initially made for an energy-momentum tensor of a generalized perfect fluid and then extended to scalar fields with minimal and non-minimal coupling to the gravitational field. We also present a study about the possible violations of some of these energy conditions. Aiming the study of the single nature of some exact solutions of Einstein s General Relativity, in 1955 the Indian physicist Raychaudhuri derived an equation that is today considered fundamental to the study of the gravitational attraction of matter, which became known as the Raychaudhuri equation. This famous equation is fundamental for to understanding of gravitational attraction in Astrophysics and Cosmology and for the comprehension of the singularity theorems, such as, the Hawking and Penrose theorem about the singularity of the gravitational collapse. In this dissertation we derive the Raychaudhuri equation, the Frobenius theorem and the Focusing theorem for congruences time-like and null congruences of a pseudo-riemannian manifold. We discuss the geometric and physical meaning of this equation, its connections with the energy conditions, and some of its several aplications.

Teoria cinética não extensiva: efeitos físicos em gases e plasmas

The standard kinetic theory for a nonrelativistic diluted gas is generalized in the spirit of the nonextensive statistic distribution introduced by Tsallis. The new formalism depends on an arbitrary q parameter measuring the degree of nonextensivity. In the limit q = 1, the extensive Maxwell-Boltzmann theory is recovered. Starting from a purely kinetic deduction of the velocity q-distribution function, the Boltzmann H-teorem is generalized for including the possibility of nonextensive out of equilibrium effects. Based on this investigation, it is proved that Tsallis' distribution is the necessary and sufficient condition defining a thermodynamic equilibrium state in the nonextensive context. This result follows naturally from the generalized transport equation and also from the extended H-theorem. Two physical applications of the nonextensive effects have been considered. Closed analytic expressions were obtained for the Doppler broadening of spectral lines from an excited gas, as well as, for the dispersion relations describing the eletrostatic oscillations in a diluted electronic plasma. In the later case, a comparison with the experimental results strongly suggests a Tsallis distribution with the q parameter smaller than unity. A complementary study is related to the thermodynamic behavior of a relativistic imperfect simple fluid. Using nonequilibrium thermodynamics, we show how the basic primary variables, namely: the energy momentum tensor, the particle and entropy fluxes depend on the several dissipative processes present in the fluid. The temperature variation law for this moving imperfect fluid is also obtained, and the Eckart and Landau-Lifshitz formulations are recovered as particular cases

Evolução do reparo por excisão de nucleotídeo

The phylogeny is one of the main activities of the modern taxonomists and a way to reconstruct the history of the life through comparative analysis of these sequences stored in their genomes aimed find any justification for the origin or evolution of them. Among the sequences with a high level of conservation are the genes of repair because it is important for the conservation and maintenance of genetic stability. Hence, variations in repair genes, as the genes of the nucleotide excision repair (NER), may indicate a possible gene transfer between species. This study aimed to examine the evolutionary history of the components of the NER. For this, sequences of UVRA, UVRB, UVRC and XPB were obtained from GenBank by Blast-p, considering 10-15 as cutoff to create a database. Phylogenetic studies were done using algorithms in PAUP programs, BAYES and PHYLIP package. Phylogenetic trees were build with protein sequences and with sequences of 16S ribosomal RNA for comparative analysis by the methods of parsimony, likelihood and Bayesian. The XPB tree shows that archaeal´s XPB helicases are similar to eukaryotic helicases. According to this data, we infer that the eukaryote nucleotide excision repair system had appeared in Archaea. At UVRA, UVRB and UVRC trees was found a monophyletic group formed by three species of epsilonproteobacterias class, three species of mollicutes class and archaeabacterias of Methanobacteria and Methanococci classes. This information is supported by a tree obtained with the proteins, UVRA, UVRB and UVRC concatenated. Thus, although there are arguments in the literature defending the horizontal transfer of the system uvrABC of bacteria to archaeabacterias, the analysis made in this study suggests that occurred a vertical transfer, from archaeabacteria, of both the NER genes: uvrABC and XPs. According the parsimony, this is the best way because of the occurrence of monophyletic groups, the time of divergence of classes and number of archaeabacterias species with uvrABC system

On extension theorems for holomorphic generalized functions

We present two extension theorems for holomorphic generalized functions. The first one is a version of the classic Hartogs extension theorem. In this, we start from a holomorphic generalized function on an open neighbourhood of the bounded open boundary, extending it, holomorphically, to a full open. In the second theorem a generalized version of a classic result is obtained, done independently, in 1943, by Bochner and Severi. For this theorem, we start from a function that is holomorphic generalized and has a holomorphic representative on the bounded domain boundary, we extend it holomorphically the function, for the whole domain.

O papel das rotas e da obtenção de informações sobre a eficiência no forrageio de dinoponera quadriceps em ambiente natural

In this study, we investigated the role of routes and information attainment for the queenless ant species Dinoponera quadriceps foraging efficiency. Two queenless ant colonies were observed in an area of Atlantic secondary Forest at the FLONA-ICMBio of Nisia Floresta, in the state of Rio Grande do Norte, northeastern Brazil, at least once a week. In the first stage of the study, we observed the workers, from leaving until returning to the colony. In the second stage, we introduced a acrylic plate (100 x 30 x 0,8 cm) on a selected entrance of the nest early in the morning before the ants left the nest. All behavioral recordings were done through focal time and all occurence samplings. The recording windows were of 15 minutes with 1 minute interval, and 5 minute intervals between each observation window. Foraging was the main activity when the workers were outside the nest. There was a positive correlation between time outside the nest and distance travelled by the ants. These variables influenced the proportion of resource that was taken to the nest, that is, the bigger its proportion, the longer the time outside and distance travelled during the search. That proportion also influenced the time the worker remained in the nest before a new trip, the bigger the proportion of the item, the shorter was the time in the nest. During all the study, workers showed fidelity to the route and to the sectors in the home range, even when the screen was in the ant´s way, once they deviated and kept the route. The features of foraging concerning time, distance, route and flexibility to go astray by the workers indicate that decisions are made by each individual and are optimal in terms of a cost-benefit relation. The strategy chosen by queenless ants fits the central place foraging and marginal value theorem theories and demonstrate its flexibility to new informations. This indicates that the workers can learn new environmental landmarks to guide their routes

Attitude stability of artificial satellites subject to gravity gradient torque

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Study of Stability of Rotational Motion of Spacecraft with Canonical Variables

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)