Epidemics in networks of spatially correlated three-dimensional root-branching structures

Using digitized images of the three-dimensional, branching structures for root systems of bean seedlings, together with analytical and numerical methods that map a common susceptible-infected- recovered (`SIR`) epidemiological model onto the bond percolation problem, we show how the spatially correlated branching structures of plant roots affect transmission efficiencies, and hence the invasion criterion, for a soil-borne pathogen as it spreads through ensembles of morphologically complex hosts. We conclude that the inherent heterogeneities in transmissibilities arising from correlations in the degrees of overlap between neighbouring plants render a population of root systems less susceptible to epidemic invasion than a corresponding homogeneous system. Several components of morphological complexity are analysed that contribute to disorder and heterogeneities in the transmissibility of infection. Anisotropy in root shape is shown to increase resilience to epidemic invasion, while increasing the degree of branching enhances the spread of epidemics in the population of roots. Some extension of the methods for other epidemiological systems are discussed.

One, two or no record of late neoproterozoic glaciation in South-East Cameroon?

Severe climate changes culminating in at least three major glacial events have been recognized in the Neoproterozoic sedimentary record from many parts of the world Supportive to the global nature of these climatic shifts a considerable amount of data have been acquired from deposits exposed in Pan-African orogenic belts in southwestern and western Africa By comparison published data from the Pan-African belts in Central Africa are scarce We report here evidence of possibly two glacial events recorded in the Mintom Formation that is located on the margin of the Pan-African orogenic Yaounde belt in South-East Cameroon In the absence of reliable radiometric data only maximum and minimum age limits of 640 and 580 Ma respectively can at present be applied to the Mintom Formation The formation consists of two lithostratigraphic ensembles each subdivided in two members (i e in ascending stratigraphic order the Kol Metou Momibole and Atog Adjap Members) The basal ensemble exhibits a typical glacial to post-glacial succession It includes diamictites comprising cobbles and boulders in a massive argillaceous siltstone matrix and laminated siltstones followed by in sharp contact a 2 m-thick massive dolostone that yielded negative delta(13)C values (<-3 parts per thousand. V-PDB) similar to those reported for Marinoan cap carbonates elsewhere However uncertainty remains regarding the glacial influence on the siliciclastic facies because the diamictite is better explained as a mass-flow deposit and diagnostic features such as dropstones have not been seen in the overlying siltstones The Mintom Formation may thus provide an example of an unusual succession of non-glacial diamictite overlain by a truly glacial melt-related cap-carbonate We also report the recent discovery of ice-striated pavements on the structural surface cut in the Mintom Formation suggesting that glaciers developed after the latter had been deposited and deformed during the Pan-African orogeny Striations which consistently exhibit two principal orientations (N60 and N110) were identified in two different localities in the west of the study area on siltstones of the Kol Member and in the east on limestones of the Atog Adjap Member respectively N60-oriented striae indicate ice flow towards the WSW Assigning an age to these features remains problematical because they were not found associated with glaciogenic deposits Two hypotheses can equally be envisaged e either the striated surfaces are correlated (1) to the Gaskiers (or Neoproterozoic post-Gaskiers) glaciation and represent the youngest Ediacaran glacial event documented in the southern Yaounde belt or (2) to the Late Ordovician Hirnantian (Saharan) glaciation thereby providing new data about Hirnantian ice flows in Central Africa (C) 2010 Elsevier Ltd 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.

Model Configuration And Data Management In The Short-Term Water Information Forecasting Tools

The Short-term Water Information and Forecasting Tools (SWIFT) is a suite of tools for flood and short-term streamflow forecasting, consisting of a collection of hydrologic model components and utilities. Catchments are modeled using conceptual subareas and a node-link structure for channel routing. The tools comprise modules for calibration, model state updating, output error correction, ensemble runs and data assimilation. Given the combinatorial nature of the modelling experiments and the sub-daily time steps typically used for simulations, the volume of model configurations and time series data is substantial and its management is not trivial. SWIFT is currently used mostly for research purposes but has also been used operationally, with intersecting but significantly different requirements. Early versions of SWIFT used mostly ad-hoc text files handled via Fortran code, with limited use of netCDF for time series data. The configuration and data handling modules have since been redesigned. The model configuration now follows a design where the data model is decoupled from the on-disk persistence mechanism. For research purposes the preferred on-disk format is JSON, to leverage numerous software libraries in a variety of languages, while retaining the legacy option of custom tab-separated text formats when it is a preferred access arrangement for the researcher. By decoupling data model and data persistence, it is much easier to interchangeably use for instance relational databases to provide stricter provenance and audit trail capabilities in an operational flood forecasting context. For the time series data, given the volume and required throughput, text based formats are usually inadequate. A schema derived from CF conventions has been designed to efficiently handle time series for SWIFT.

Aspects de la syntaxe, de la semantique et de la morphologie des verbes a trait de /complexite/

Cette dissertation porte sur l’analyse syntactico-sémantique des verbes à trait de complexité. Le trait de complexité (Blanche-Benveniste et al. 1984) réunit une classe de verbes connue comme verbes ‘symétriques’, ‘réciproques’ ou ‘collectifs’ sans toutefois se limiter à ces ensembles (cf. grouiller, collectionner, amonceler, scinder, etc.). Ce trait induit une lecture ‘plurielle’ à l’entité formée du lexème verbal et de ses arguments et qui se traduit, sur le plan morphosyntaxique, par deux propriétés: sélection obligatoire d’une position syntaxique (sujet ou objet) au pluriel; en absence de ce pluriel morphologique, le trait de complexité se réalise par la sélection d’un complément prépositionnel correlié à une position syntaxique (sujet ou objet) et l’interprétation de ‘pluriel’ des deux éléments correliés. L’hypothèse générale, et point de départ de cette dissertation, consiste à préciser l’interprétation de ‘pluralité inhérente’ des verbes à trait de complexité comme étant de type ‘collectif’, défini comme désignant du ‘plus d’un en un’ (Jespersen, 1971). La notion de ‘collectif’ est à distinguer de la notion de ‘pluriel’ (Gillon, 1992) et permet d’expliquer le lien entre les deux propriétés morphosyntaxiques présentées. Cette hypothèse générale s’appuie sur la sélection d’un ensemble d’outils d’analyse. Un premier outil vise à rendre compte, du point de vue formel, des réseaux syntactico-sémantiques, par une représentation abstraite de la syntaxe verbale, conçue comme une ‘syntaxe de position’ et où sont délimitées, autour du noyau verbal, deux zones syntaxiques (zone SUJET et zone OBJET) constituées de points d’ancrage du trait de complexité. En tenant compte de la spécificité du ‘collectif’ par rapport à la ‘pluralité’, le recours au concept d’opérateurs de complexité, entendus comme des opérateurs du trait [+discret] (Doetjes, 1999), permet de mieux définir la notion du ‘collectif’ appliquée au domaine verbal. Les différents opérateurs – affixes dérivationnels, constructions prépositionnelles, constructions en SE - se situent à différents niveaux de structuration. L’analyse par ‘opérateurs de complexité’ ([+discret]) présuppose également la prise en compte de la fonction quantitative. Dans cette perspective, ces opérateurs induisent différents degrés de l‘individuation’ des constituants du ‘collectif’ dénoté par la sémantique des verbes à trait de complexité. Les échelles de gradation de [+discret] rendent compte de cette propriété. Les valeurs de ‘plus d’un’ et ‘en un’ dénotées par les expressions verbales à trait de complexité sont interprétées comme faisant partie d’une structure conceptuelle de type ‘tout-intégré’ d’après l’approche lexicale et multidimensionnelle de la sémantique conceptuelle des relations parties/tout de Moltmann (1997).

Implementação de classificador de tarefas mentais baseado em EEG

BARBOSA, André F. ; SOUZA, Bryan C. ; PEREIRA JUNIOR, Antônio ; MEDEIROS, Adelardo A. D.de, . Implementação de Classificador de Tarefas Mentais Baseado em EEG. In: CONGRESSO BRASILEIRO DE REDES NEURAIS, 9., 2009, Ouro Preto, MG. Anais... Ouro Preto, MG, 2009

An investigation of Hebbian phase sequences as assembly graphs

Hebb proposed that synapses between neurons that fire synchronously are strengthened, forming cell assemblies and phase sequences. The former, on a shorter scale, are ensembles of synchronized cells that function transiently as a closed processing system; the latter, on a larger scale, correspond to the sequential activation of cell assemblies able to represent percepts and behaviors. Nowadays, the recording of large neuronal populations allows for the detection of multiple cell assemblies. Within Hebb's theory, the next logical step is the analysis of phase sequences. Here we detected phase sequences as consecutive assembly activation patterns, and then analyzed their graph attributes in relation to behavior. We investigated action potentials recorded from the adult rat hippocampus and neocortex before, during and after novel object exploration (experimental periods). Within assembly graphs, each assembly corresponded to a node, and each edge corresponded to the temporal sequence of consecutive node activations. The sum of all assembly activations was proportional to firing rates, but the activity of individual assemblies was not. Assembly repertoire was stable across experimental periods, suggesting that novel experience does not create new assemblies in the adult rat. Assembly graph attributes, on the other hand, varied significantly across behavioral states and experimental periods, and were separable enough to correctly classify experimental periods (Naïve Bayes classifier; maximum AUROCs ranging from 0.55 to 0.99) and behavioral states (waking, slow wave sleep, and rapid eye movement sleep; maximum AUROCs ranging from 0.64 to 0.98). Our findings agree with Hebb's view that assemblies correspond to primitive building blocks of representation, nearly unchanged in the adult, while phase sequences are labile across behavioral states and change after novel experience. The results are compatible with a role for phase sequences in behavior and cognition.

Projeto em Áreas Consolidadas de Patrimônio Cultural: Propostas para a Construção de uma Metodologia de Ensino

Le thème du patrimoine culturel architectural et urbain continue d avoir une place importante dans le milieu technique et scientifique. Le concept s est élargi et aujourd hui comprend différentes procédures de projets d intervention. L importance accordée au thème amène à l inclusion de la matière de techniques rétrospectives et aux contenus qui en sont liés: conservation, restauration, restructuration et reconstruction d édifices et ensembles urbains, dans les parcours des cours d architecture et d urbanisme au Brésil établies par le Ministère de l Education Nationale (MEC) dans les années quatre-vingt-dix, postérieurement incorporés dans les directrices disciplinaires nationales. Nous partons des discussions théoriques et conceptuelles du Domaine du Patrimoine Culturel, ainsi que des principales théories pédagogiques d enseignements et d apprentissage articulées au projet. Dans ce contexte les objectifs principaux de cette thèse consistent à systématiser et à analyser les principales procédures méthodologiques contribuant pour la construction de méthodes d enseignement tournée vers des activités pratiques dans ce domaine. Pour cela, la recherche a été systématisée dans une approche à deux niveaux. En ce qui concerne le premier, basé sur des données secondaires, neuf cours d architecture et urbanisme ont étés identifiés entre institutions publiques d enseignement supérieur dont huit brésiliennes et une française, considérées représentatives en ce qui concerne les pratiques d enseignement de projet et de patrimoine culturel. Trente disciplines dédiées à la matière ont été également reconnues initialement, et postérieurement, cinq disciplines qui possèdent un emploi du temps dédié à la pratique de projet ont aussi été reconnues. Dans le deuxième cas, basée sur des données primaires, ont étés analysées les méthodologies et les stratégies d enseignement de projet basées sur les définitions des matières et des autres éléments des plans de travail avec des observations, des entrevues et des questionnaires en trois ateliers. Par rapport aux résultats nous avons constaté que toutes les écoles possèdent les contenus de la matière, mais peu d entre elles privilégient la relation du projet appliqué au patrimoine culturel. Nous avons constaté que les questions des projets dans ce contexte, même s elles sont considérées complexes, ont privilégié le listage et l analyse du site. L atelier qui intègre les fondements des théories de préservation, l histoire de l architecture et urbanisme et techniques anciennes et actuelles, est mis en valeur comme un modèle cohérent avec les propositions d intégration des connaissances théoriques et pratiques du projet appliqué à la discipline. Basé sur ces constatations il est possible de démontrer quatre étapes du projet appliqué au patrimoine culturel: 1ª) les fondements généraux qui concernent les bases théoriques sur la préservation, histoire et technique rétrospective, par exemple, l appropriation de lois et normes et la sensibilisation de l élève sur les questions de patrimoine culturel; 2ª) le contacte avec la réalité qui inclut l appropriation du problème à partir de ces acteurs, de ces échelles, de cette lecture de site et l analyse de l objet d étude; 3ª) le développement de la proposition qui inclut programmes (fonctions existantes et propositions), définitions du partit (types d intervention), conception (hypothèse et discussion) et définition de proposition; 4ª) la finalisation du projet qui consiste à développer la proposition avec sa représentation graphique et sa présentation finale. Nous concluons que le projet en Domaine du Patrimoine Culturel demande une attention spéciale et doit être présent dans les cursus considérant les principes généraux nécessaires à la formation de l élève. Le binôme projet / patrimoine signifie avoir dans le cursus universitaire les contenus et questions nécessaires les connaissances, les variables et possibilités existantes dans le projet appliqué au patrimoine culturel de façon à ce que ces connaissances soient incorporées dans l exercice de projet et n apparaissent pas comme un simple contenu théorique sans articulation avec la pratique. Naturellement ces conclusions n épuisent pas la réflexion sur la question. Nous espérons que les analyses faites contribuent à définir des méthodologies d enseignements capables d êtres vérifiées et testées dans la pratique en salle de cours, et puisse collaborer avec les nouvelles recherches surtout celles qui ont pour but des nouvelles théories pédagogiques d enseignement apprentissage du projet en Domaine du Patrimoine Culturel

Interesses da habitação social : políticas e processos no Rio Grande do Norte

En 2003, le gouvernement brésilien (gestion Lula) a initié une nouvelle phase dans son histoire de l habitation, en intensifiant les constructions de logements sociaux au Brésil. Un tel accroissement a eut des répercussions tant en ville comme à la campagne, et fût marqué dans le Rio Grande do Norte, par la production a grande échelle d ensembles d habitations, dans les programmes de Gouvernement. Afin de viabiliser ces transformations, des instruments politiques, financiers et de gestion ont étés articulés conjointement, utilisant la répétition d une typologie d édification, comme modèle, accompagnée de la reproduction d une morphologie dans les constructions de logements sociaux. Afin de comprendre ce processus nous introduisons une recherche urbanistique et socio-économique du problème du logement social au Brésil, en cherchant à mettre en relation les aspects techniques avec les questions historique, professionnelles et culturelles, éléments complémentaires. Notre analyse cherche a identifier comment les politiques de gestion et financement officielles (administrées dans sa grande majorité par la Caisse Économique Fédérale -CEF-), influencent le processus de conception de projets, en provoquant les répétitions de type/morphologiques, déjà citées. Basée sur l observation directe au cour de deux expériences différenciées pour du logement social en milieu rural, au Rio Grande do Norte, nous montrerons aussi certaines limitations et possibilités des acteurs sociaux, face aux agents et politiques officielles pour le logement social au Brésil, proposant des solutions alternatives standardisées qui caractérisent le résultat des projets financées et gérés par la CEF. Nos principales références théoriques et méthodologiques sont Nabil Bonduki (1998), David Harvey (2009,1982), Henry Lefèbvre (1970), Ermínia Maricato (2010, 2009, 2000, 1987) et Raquel Rolnik (2010, 2009, 2008, 1997)

Classificação de padrões através de um comitê de máquinas aprimorado por aprendizagem por reforço

Reinforcement learning is a machine learning technique that, although finding a large number of applications, maybe is yet to reach its full potential. One of the inadequately tested possibilities is the use of reinforcement learning in combination with other methods for the solution of pattern classification problems. It is well documented in the literature the problems that support vector machine ensembles face in terms of generalization capacity. Algorithms such as Adaboost do not deal appropriately with the imbalances that arise in those situations. Several alternatives have been proposed, with varying degrees of success. This dissertation presents a new approach to building committees of support vector machines. The presented algorithm combines Adaboost algorithm with a layer of reinforcement learning to adjust committee parameters in order to avoid that imbalances on the committee components affect the generalization performance of the final hypothesis. Comparisons were made with ensembles using and not using the reinforcement learning layer, testing benchmark data sets widely known in area of pattern classification

Algoritmos genéticos aplicados a um comitê de LS-SVM em problemas de classificação

The pattern classification is one of the machine learning subareas that has the most outstanding. Among the various approaches to solve pattern classification problems, the Support Vector Machines (SVM) receive great emphasis, due to its ease of use and good generalization performance. The Least Squares formulation of SVM (LS-SVM) finds the solution by solving a set of linear equations instead of quadratic programming implemented in SVM. The LS-SVMs provide some free parameters that have to be correctly chosen to achieve satisfactory results in a given task. Despite the LS-SVMs having high performance, lots of tools have been developed to improve them, mainly the development of new classifying methods and the employment of ensembles, in other words, a combination of several classifiers. In this work, our proposal is to use an ensemble and a Genetic Algorithm (GA), search algorithm based on the evolution of species, to enhance the LSSVM classification. In the construction of this ensemble, we use a random selection of attributes of the original problem, which it splits the original problem into smaller ones where each classifier will act. So, we apply a genetic algorithm to find effective values of the LS-SVM parameters and also to find a weight vector, measuring the importance of each machine in the final classification. Finally, the final classification is obtained by a linear combination of the decision values of the LS-SVMs with the weight vector. We used several classification problems, taken as benchmarks to evaluate the performance of the algorithm and compared the results with other classifiers

Conceitos e técnicas da mecânica estatística e termodinâmica aplicados ao estudo dos grafos aleatórios

This dissertation briefly presents the random graphs and the main quantities calculated from them. At the same time, basic thermodynamics quantities such as energy and temperature are associated with some of their characteristics. Approaches commonly used in Statistical Mechanics are employed and rules that describe a time evolution for the graphs are proposed in order to study their ergodicity and a possible thermal equilibrium between them

Otimização em comitês de classificadores: uma abordagem baseada em filtro para seleção de subconjuntos de atributos

Traditional applications of feature selection in areas such as data mining, machine learning and pattern recognition aim to improve the accuracy and to reduce the computational cost of the model. It is done through the removal of redundant, irrelevant or noisy data, finding a representative subset of data that reduces its dimensionality without loss of performance. With the development of research in ensemble of classifiers and the verification that this type of model has better performance than the individual models, if the base classifiers are diverse, comes a new field of application to the research of feature selection. In this new field, it is desired to find diverse subsets of features for the construction of base classifiers for the ensemble systems. This work proposes an approach that maximizes the diversity of the ensembles by selecting subsets of features using a model independent of the learning algorithm and with low computational cost. This is done using bio-inspired metaheuristics with evaluation filter-based criteria

Utilizando Pesos estáticos e dinâmicos em sistemas multi-classificadores com diferentes níveis de diversidade

Although some individual techniques of supervised Machine Learning (ML), also known as classifiers, or algorithms of classification, to supply solutions that, most of the time, are considered efficient, have experimental results gotten with the use of large sets of pattern and/or that they have a expressive amount of irrelevant data or incomplete characteristic, that show a decrease in the efficiency of the precision of these techniques. In other words, such techniques can t do an recognition of patterns of an efficient form in complex problems. With the intention to get better performance and efficiency of these ML techniques, were thought about the idea to using some types of LM algorithms work jointly, thus origin to the term Multi-Classifier System (MCS). The MCS s presents, as component, different of LM algorithms, called of base classifiers, and realized a combination of results gotten for these algorithms to reach the final result. So that the MCS has a better performance that the base classifiers, the results gotten for each base classifier must present an certain diversity, in other words, a difference between the results gotten for each classifier that compose the system. It can be said that it does not make signification to have MCS s whose base classifiers have identical answers to the sames patterns. Although the MCS s present better results that the individually systems, has always the search to improve the results gotten for this type of system. Aim at this improvement and a better consistency in the results, as well as a larger diversity of the classifiers of a MCS, comes being recently searched methodologies that present as characteristic the use of weights, or confidence values. These weights can describe the importance that certain classifier supplied when associating with each pattern to a determined class. These weights still are used, in associate with the exits of the classifiers, during the process of recognition (use) of the MCS s. Exist different ways of calculating these weights and can be divided in two categories: the static weights and the dynamic weights. The first category of weights is characterizes for not having the modification of its values during the classification process, different it occurs with the second category, where the values suffers modifications during the classification process. In this work an analysis will be made to verify if the use of the weights, statics as much as dynamics, they can increase the perfomance of the MCS s in comparison with the individually systems. Moreover, will be made an analysis in the diversity gotten for the MCS s, for this mode verify if it has some relation between the use of the weights in the MCS s with different levels of diversity

Uma Análise Comparativa entre Sistemas de Combinação de Classificadores com Distribuição Vertical dos Dados

In systems that combine the outputs of classification methods (combination systems), such as ensembles and multi-agent systems, one of the main constraints is that the base components (classifiers or agents) should be diverse among themselves. In other words, there is clearly no accuracy gain in a system that is composed of a set of identical base components. One way of increasing diversity is through the use of feature selection or data distribution methods in combination systems. In this work, an investigation of the impact of using data distribution methods among the components of combination systems will be performed. In this investigation, different methods of data distribution will be used and an analysis of the combination systems, using several different configurations, will be performed. As a result of this analysis, it is aimed to detect which combination systems are more suitable to use feature distribution among the components