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)

A construção estilística das identidades poéticas da cidade de Natal: um olhar bakhtiniano

The purpose of this work is to bring forward cultural identities of the city of Natal that are built upon representations contained in the work of Twentieth-Century Potiguar1 poets. We started out with the premise that the urban tissue owes its formation to the effect of the feelings produced and to the individuals that give shape to them, thus causing the city to abound with feelings and meanings that are relevant for both society and the individual. As cities and their identities may be studied and interpreted from different viewpoints, we have used in this study poetic discourse that functions as a memory to the city and takes shape out of a set of historically established social practices. Our research is situated within the area of Applied Linguistics, an area of knowledge focused mainly in language that is increasingly expanding its investigation limits in an interdisciplinary way. Therefore, this study is based on a social and historical model of language, with language construed as a discourse practice (Bakhtin and Circle), and presents an interface with cultural studies (Hall, Canclini), taking into account the fact that culture builds up values and brings forth differences in respect of the conditions under which such values and differences are produced. In this sense, we have tried to ―listen‖ to what the poets say, by understanding and interpreting the meanings produced by their discourse, in order to identify the formation of the identities of the city that arise out of distinct points of view and diverse stylistic marks. Analysis of these poetic utterances lead to multifold cultural identities of the city, ranging from a naive and multicolored Natal to a city that builds itself on its characters and on to an insurgent, usurped Natal

Effects of intra-hippocampal infusion of WAY-100635 on plus-maze behavior in mice - Influence of site of injection and prior test experience

The positive profile of systemically-administered 5-HT(1A) receptor antagonists in several rodent models of anxiolytic activity suggests an important role for postsynaptic 5-HT(1A) receptor mechanisms in anxiety. To test this hypothesis, we investigated the effects of WAY-100635 microinfusions (0, 0.1, 1.0 or 3.0 mug in 0.2 mul) into the dorsal (DH) or ventral (VH) hippocampus an behaviours displayed by male Swiss-Webster mice in the elevated plus-maze. As prior experience is known to modify pharmacological responses in this test, the effects of intra-hippocampal infusions were examined both in maze-naive and maze-experienced subjects. Test videotapes were scored for conventional indices of anxiety (% open arm entries/time) and locomotor activity (closed arm entries), as well as a range of ethological measures (e.g. risk assessment). In maze-naive mice, intra-VH (but not intra-M) infusions of WAY-100635 (3.0 mug but not lower doses) increased open arm exploration and reduced risk assessment. These effects were observed in the absence of significant changes in locomotor activity. In contrast, neither intra-VH nor intra-DH infusions of WAY-100635 altered the behaviour of maze-experienced mice. These Findings suggest that postsynaptic 5-HT(1A) receptors in the ventral (but not dorsal) hippocampus play a significant role both in the mediation of plus-maze anxiety in mice and in experientially-induced alterations in responses to this test. (C) 2002 Elsevier B.V. BY All rights reserved.

Concurrent nociceptive stimulation impairs the anxiolytic effect of midazolam injected into the periaqueductal gray in mice

This study investigated whether the opportunity to avoid or escape the open arms of an elevated plus-maze (EPM) affects the antinociceptive response observed when mice are subjected to open arm confinement. Furthermore, in order to better characterize the relationship between emotion and antinociception in the EPM, we examined the behavioral effects of midazolam injection into the midbrain periaqueductal gray matter (PAG). As our main aim was to evaluate the relevance of different levels of approach-avoid conflict (i.e. The presence of open and closed arms) to maze-induced antinociception, mice were exposed to one of three types of EPM-a standard EPM (sEPM), an open EPM (oEPM: four open arms) or, as a control condition, an enclosed EPM (eEPM: four enclosed arms). Nociception was assessed using the formalin test. Twenty minutes after formalin injection (50 mu l, 2.5% formalin) into the dorsal right hind paw, mice received an intra-PAG injection of saline or midazolam (10-20 nmol). Five minutes later, they were individually exposed to one of the mazes for 10 min (25-35 min after formalin injection). Videotapes of the test sessions were scored for a variety of behavioral measures including time spent licking the formalin-injected paw. To examine whether the effects of midazolam on anxiety-like behavior may have been influenced by concurrent nociceptive stimulation (i.e. formalin pretreatment), naive mice were submitted to a similar procedure to that described above for the sEPM test but without formalin pretreatment. Results showed that mice exposed to the oEPM spent significantly less time licking the injected paw compared to groups exposed to either the sEPM or eEPM. Although exposure to the sEPM induced anxiety-like behaviors (i.e. open arm avoidance), it did not result in antinociception. Intra-PAG infusions of midazolam failed to block oEPM-induced antinociception or to alter sEPM-induced anxiety in mice that had received formalin injection. However, under normal test conditions (i.e. in the absence of formalin-induced nociceptive stimulation), intra-PAG midazolam produced clear anti-anxiety effects in mice exposed to the sEPM. Findings are discussed in terms of different emotional states induced by the oEPM and sEPM and the influence of concurrent nociceptive stimulation on the anti-anxiety effect of intra-PAG midazolam. (c) 2005 Elsevier B.V. All rights reserved.

Anxiolytic-like effect of way-100635 microinfusions into the median (but not dorsal) raphe nucleus in mice exposed to the plus-maze: influence of prior test experience

Studies in several laboratories have confirmed the anxiolytic potential of a wide range of 5-HT1A receptor antagonists in rats and mice, with recent evidence pointing to a postsynaptic site of action in the ventral hippocampus. It would, therefore, be predicted that blockade of 5-HT1A somatodendritic autoreceptors in the midbrain raphe nuclei should produce anxiogenic-like effects. To test this hypothesis, we investigated the effects of WAY-100635 microinfusions (0, 1.0 or 3.0 mug in 0.1 mul) into the dorsal (DRN) or median (MRN) raphe nuclei on behaviours displayed by male Swiss-Webster mice in the elevated plus-maze. As this test is sensitive to prior experience. The effects of intra-raphe infusions were examined both in maze-naive and maze-experienced subjects. Sessions, were videotaped and subsequently scored for conventional indices of anxiety (open arm avoidance) and locomotor activity (closed arm entries), as well as a range of ethological measures (e.g. risk assessment). In maze-naive mice, intra-MRN (but not intra-DRN) infusions of WAY-100635 (3.0 mug) increased open arm exploration and reduced risk assessment. Importantly, these effects could not be attributed to a general reduction in locomotor activity. A similar, though somewhat weaker, pattern of behavioural change was observed in maze-experienced animals. This unexpected anxiolytic effect of 5-HT1A autoreceptor blockade in the MRN cannot be accounted fur by a disinhibition of 5-HT release in forebrain targets (e.g. hippocampus and amygdala), where stimulation of postsynaptic 5-HT1A receptors enhances anxiety-like responses. However, as the MRN also projects to the periaqueductal gray matter (PAG), an area known to be sensitive to the anti-aversive effects or 5-HT, it is argued that present results may reflect increased 5-HT release at this crucial midbrain locus within the neural circuitry of defense. (C) 2002 Elsevier B.V. B.V. All rights reserved.

Blockade of fear-induced antinociception with intra-amygdala infusion of midazolam: Influence of prior test experience

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

Spin-1 duality in D dimensions

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Uma Análise de métodos de distriubuição de atributos em comitês de classificadores

The objective of the researches in artificial intelligence is to qualify the computer to execute functions that are performed by humans using knowledge and reasoning. This work was developed in the area of machine learning, that it s the study branch of artificial intelligence, being related to the project and development of algorithms and techniques capable to allow the computational learning. The objective of this work is analyzing a feature selection method for ensemble systems. The proposed method is inserted into the filter approach of feature selection method, it s using the variance and Spearman correlation to rank the feature and using the reward and punishment strategies to measure the feature importance for the identification of the classes. For each ensemble, several different configuration were used, which varied from hybrid (homogeneous) to non-hybrid (heterogeneous) structures of ensemble. They were submitted to five combining methods (voting, sum, sum weight, multiLayer Perceptron and naïve Bayes) which were applied in six distinct database (real and artificial). The classifiers applied during the experiments were k- nearest neighbor, multiLayer Perceptron, naïve Bayes and decision tree. Finally, the performance of ensemble was analyzed comparatively, using none feature selection method, using a filter approach (original) feature selection method and the proposed method. To do this comparison, a statistical test was applied, which demonstrate that there was a significant improvement in the precision of the ensembles

Nitric oxide synthase activity in tissues of the blowfly Chrysomya megacephala (Fabricius, 1794)

Although insects lack the adaptive immune response of the mammalians, they manifest effective innate immune responses, which include both cellular and Immoral components. Cellular responses are mediated by hemocytes, and Immoral responses include the activation of proteolytic cascades that initiate many events, including NO production. In mammals, nitric oxide synthases (NOSs) are also present in the endothelium, the brain, the adrenal glands, and the platelets. Studies on the distribution of NO-producing systems in invertebrates have revealed functional similarities between NOS in this group and vertebrates. We attempted to localize NOS activity in tissues of naive (UIL), yeast-injected (YIL), and saline-injected (SIL) larvae of the blowfly Chrysomya megacephala, using the NADPH diaphorase technique. Our findings revealed similar levels of NOS activity in muscle, fat body, Malpighian tubule, gut, and brain, suggesting that NO synthesis may not be involved in the immune response of these larval systems. These results were compared to many studies that recorded the involvement of NO in various physiological functions of insects.

mRNA profile of Nellore calves after primary infection with Haemonchus placei

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Repeated unrewarded scent exposure influences the food choice of stingless bee foragers, Melipona scutellaris

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Unpalatability of Hyla semilineata tadpoles (Anura) to captive and free-ranging vertebrate predators

This study examines the unpalatability of Hyla semilineata tadpoles, relating this possible defence mechanism to their black, presumably aposematic, colouration. Bullfrog tadpoles (Rana catesbeiana), similar in size to the H. semilineata larvae, were used as controls in the experiments. The palatability of H. semilineata tadpoles was tested by offering the tadpoles to Fish (Hoplias malabaricus), free-ranging passerine birds (Pitangus sulphuratus) and hawks (Buteo magnirostris), and domestic chickens (Gallus domesticus). All predators showed a significant preference towards the control R. catesbeiana tadpoles. However, in experiments with fish, this preference was not significant for tadpole capture, only for their ingestion, suggesting that the fish could not distinguish between the two species before tasting them. Although great kiskadees (P. sulphuratus) preferred the control R. catesbeiana tadpoles, they promptly ingested more than half of the test H. semilineata tadpoles when these were offered alone. The chickens, used as naive predators, clearly learned to avoid the black H. semilineata tadpoles after a few trials. The conspicuous colouration and unpalatability of H. semilineata tadpoles may benefit the individual as well as the group, depending on the predator involved.

Effect of exogenous galectin-1 on leukocyte migration: modulation of cytokine levels and adhesion molecules

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

Complementarity of eastern and western hemisphere long-baseline neutrino oscillation experiments

We present a general formalism for extracting information on the fundamental parameters associated with neutrino masses and mixings from two or more long baseline neutrino oscillation experiments. This formalism is then applied to the current most likely experiments using neutrino beams from the Japan Hadron Facility (JHF) and Fermilab's NuMI beamline. Different combinations of muon neutrino or muon anti-neutrino running are considered. The type of neutrino mass hierarchy is extracted using the effects of matter on neutrino propogation. Contrary to naive expectation, we find that both beams using neutrinos is more suitable for determining the hierarchy provided that the neutrino energy divided by baseline (E/L) for NuMI is smaller than or equal to that of JHF, whereas to determine the small mixing angle, theta(13), and the CP or T violating phase delta, one neutrino and the other anti-neutrino are most suitable. We make extensive use of bi-probability diagrams for both understanding and extracting the physics involved in such comparisons.