Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.

Model-based clustering in gene expression microarrays: An application to breast cancer data

In microarray studies, the application of clustering techniques is often used to derive meaningful insights into the data. In the past, hierarchical methods have been the primary clustering tool employed to perform this task. The hierarchical algorithms have been mainly applied heuristically to these cluster analysis problems. Further, a major limitation of these methods is their inability to determine the number of clusters. Thus there is a need for a model-based approach to these. clustering problems. To this end, McLachlan et al. [7] developed a mixture model-based algorithm (EMMIX-GENE) for the clustering of tissue samples. To further investigate the EMMIX-GENE procedure as a model-based -approach, we present a case study involving the application of EMMIX-GENE to the breast cancer data as studied recently in van 't Veer et al. [10]. Our analysis considers the problem of clustering the tissue samples on the basis of the genes which is a non-standard problem because the number of genes greatly exceed the number of tissue samples. We demonstrate how EMMIX-GENE can be useful in reducing the initial set of genes down to a more computationally manageable size. The results from this analysis also emphasise the difficulty associated with the task of separating two tissue groups on the basis of a particular subset of genes. These results also shed light on why supervised methods have such a high misallocation error rate for the breast cancer data.

Gest??o por compet??ncias: m??todos e t??cnicas para mapeamento de compet??ncias

A gest??o por compet??ncias tem sido apontada como alternativa aos modelos gerenciais tradicionalmente utilizados pelas organiza????es. Prop??e-se a orientar esfor??os para planejar, captar, desenvolver e avaliar, nos diferentes n??veis da organiza????o, as compet??ncias necess??rias ?? consecu????o de seus objetivos. Uma das principais etapas desse processo constitui o denominado mapeamento de compet??ncias. Este artigo objetiva apresentar m??todos, t??cnicas e instrumentos utilizados para mapeamento de compet??ncias em organiza????es p??blicas e privadas. Para isso, fazem-se uma revis??o da literatura sobre o conceito de compet??ncia, o mapeamento de compet??ncias e a gest??o por compet??ncias, discutindo-se seus pressupostos e suas aplica????es. Ao final, s??o levantadas as implica????es desse modelo de gest??o para o setor p??blico e s??o apresentadas recomenda????es pr??ticas.

Tecnologias e metodologias na ensinagem de inglês no século XXI : elaboração e análise de webquests

Este trabalho tem como objetivo geral apresentar mecanismos de análise e validação de propostas de material didático na forma de Webquests e, com base nesses mecanismos, elaborar e validar três propostas de material didático em forma de WebQuests criticamente situados para a ensinagem de inglês como língua adicional. As WebQuests elaboradas visam priorizar o desenvolvimento do letramento digital crítico e da competência comunicativa em inglês como língua adicional do aprendiz. A WebQuest se insere na perspectiva de uma metodologia que tem esse mesmo nome e consiste na proposta de uma pesquisa orientada e organizada em etapas em que toda ou grande parte do conteúdo a ser acessado e necessário para a realização da(s) tarefa(s) encontra-se disponível online (DODGE, 1995). A metodologia deste estudo é de cunho qualitativo e também se insere na perspectiva da metodologia de desenvolvimento. O design metodológico dessa investigação foi organizado em três etapas, quais sejam, a análise de necessidades, a elaboração de três WebQuests e a análise das WebQuests elaboradas a partir de uma rubrica. A revisão de literatura, que constituiu parte da análise de necessidades, sugere que as demandas do século XXI exigem maior atenção e investimento para o desenvolvimento de letramentos múltiplos e críticos, de competências comunicativas e interacionais e de formação de cidadania. A análise de WebQuests disponíveis para ensinagem de inglês no principal sítio brasileiro de WebQuests, que compôs a segunda parte da análise de necessidades desse estudo, evidenciou a escassez de WebQuests que abordam de forma significativa tanto as questões do letramento digital crítico quanto os aspectos da competência comunicativa na língua adicional do indivíduo. A análise de necessidades como um todo forneceu subsídios relevantes para o processo de elaboração das WebQuests propostas neste estudo, que também se embasou nas diretrizes e princípios do modelo WebQuest e em grande parte do seu embasamento teórico. Como fase final deste estudo, as três WebQuests elaboradas foram submetidas à validação a partir de uma rubrica criada especialmente para esse propósito. Os resultados das análises de validação das três WebQuests elaboradas sugerem que a proposta desses materiais é válida sob o ponto de vista teórico, pois mostram que as ferramentas criadas vão ao encontro da proposta do modelo WebQuests de Dodge (1995, 2001) e das recomendações de qualidade sugeridas por Bottentuit Junior e Coutinho (2008a, 2012), bem como estão ancoradas na teoria sócio-construtivista e do ensino situado e nos princípios metodológicos da abordagem de ensino baseada em tarefas e da abordagem de ensino de conteúdos diversos por meio da língua (CLIL). Concluímos que as três WebQuests são materiais de ensinagem de inglês que fogem do enfoque tradicional conteudista historicamente voltado para o ensino de vocabulário e gramática na língua-alvo, extrapolando os objetivos linguísticos para alcançar também objetivos sociais e culturais da ensinagem de inglês como língua adicional, na medida em que se trabalha paralelamente (e intencionalmente, por entender que ambos se complementam) o desenvolvimento da competência comunicativa e do letramento digital crítico do indivíduo, contribuindo, assim, para a sua formação cidadã e colaborando para a “inclusão” do aprendiz no mundo social e digital.

Criteria for ERP selection using an AHP approach

Information systems are a foundation key element of modern organizations. Quite often, chief executive officers and managers have to decide about the acquisition of new software solution based in an appropriated set of criteria. Analytic Hierarchy Process (AHP) is one technique used to support that kind of decisions. This paper proposes the application of AHP method to the selection of ERP (Enterprise Resource Planning) systems, identifying the set of criteria to be used. A set of criteria was retrieved from the scientific literature and validated through a survey-based approach.

The rights approach to local public management: experiences from Brazil

The Fundação Getulio Vargas, São Paulo, Public Management and Citizenship Program was set up in 1996 with Ford Foundation support to identify and disseminate Brazilian subnational government initiatives in service provision that have a direct effect on citizenship. Already, the program has 2,500 different experiences in its data bank, the results of four annual cycles. The article draws some initial conclusions about the possibilities of a rights-based approach to public management and about the engagement of other agencies and civil society organizations.

Overview of the tuning template for radiography in Europe

HENRE II (Higher Education Network for Radiography in Europe)

ANN-Based LMP forecasting in a distribution network with large penetration of DG

In recent years, power systems have experienced many changes in their paradigm. The introduction of new players in the management of distributed generation leads to the decentralization of control and decision-making, so that each player is able to play in the market environment. In the new context, it will be very relevant that aggregator players allow midsize, small and micro players to act in a competitive environment. In order to achieve their objectives, virtual power players and single players are required to optimize their energy resource management process. To achieve this, it is essential to have financial resources capable of providing access to appropriate decision support tools. As small players have difficulties in having access to such tools, it is necessary that these players can benefit from alternative methodologies to support their decisions. This paper presents a methodology, based on Artificial Neural Networks (ANN), and intended to support smaller players. In this case the present methodology uses a training set that is created using energy resource scheduling solutions obtained using a mixed-integer linear programming (MIP) approach as the reference optimization methodology. The trained network is used to obtain locational marginal prices in a distribution network. The main goal of the paper is to verify the accuracy of the ANN based approach. Moreover, the use of a single ANN is compared with the use of two or more ANN to forecast the locational marginal price.

A decision-support system based on particle swarm optimization for multiperiod hedging in electricity markets

This paper proposes a particle swarm optimization (PSO) approach to support electricity producers for multiperiod optimal contract allocation. The producer risk preference is stated by a utility function (U) expressing the tradeoff between the expectation and variance of the return. Variance estimation and expected return are based on a forecasted scenario interval determined by a price range forecasting model developed by the authors. A certain confidence level is associated to each forecasted scenario interval. The proposed model makes use of contracts with physical (spot and forward) and financial (options) settlement. PSO performance was evaluated by comparing it with a genetic algorithm-based approach. This model can be used by producers in deregulated electricity markets but can easily be adapted to load serving entities and retailers. Moreover, it can easily be adapted to the use of other type of contracts.

An integrated approach for distributed energy resource short term scheduling in smart grids considering realistic power system simulation

The large increase of distributed energy resources, including distributed generation, storage systems and demand response, especially in distribution networks, makes the management of the available resources a more complex and crucial process. With wind based generation gaining relevance, in terms of the generation mix, the fact that wind forecasting accuracy rapidly drops with the increase of the forecast anticipation time requires to undertake short-term and very short-term re-scheduling so the final implemented solution enables the lowest possible operation costs. This paper proposes a methodology for energy resource scheduling in smart grids, considering day ahead, hour ahead and five minutes ahead scheduling. The short-term scheduling, undertaken five minutes ahead, takes advantage of the high accuracy of the very-short term wind forecasting providing the user with more efficient scheduling solutions. The proposed method uses a Genetic Algorithm based approach for optimization that is able to cope with the hard execution time constraint of short-term scheduling. Realistic power system simulation, based on PSCAD , is used to validate the obtained solutions. The paper includes a case study with a 33 bus distribution network with high penetration of distributed energy resources implemented in PSCAD .

Case-based reasoning for meta-heuristics self-parameterization in a multi-agent scheduling system

A novel agent-based approach to Meta-Heuristics self-configuration is proposed in this work. Meta-heuristics are examples of algorithms where parameters need to be set up as efficient as possible in order to unsure its performance. This paper presents a learning module for self-parameterization of Meta-heuristics (MHs) in a Multi-Agent System (MAS) for resolution of scheduling problems. The learning is based on Case-based Reasoning (CBR) and two different integration approaches are proposed. A computational study is made for comparing the two CBR integration perspectives. In the end, some conclusions are reached and future work outlined.

Profibus protocol extensions for enabling inter-cell mobility in bridge-based hybrid wired/wireless networks

Future industrial control/multimedia applications will increasingly impose or benefit from wireless and mobile communications. Therefore, there is an enormous eagerness for extending currently available industrial communications networks with wireless and mobility capabilities. The RFieldbus European project is just one example, where a PROFIBUS-based hybrid (wired/wireless) architecture was specified and implemented. In the RFieldbus architecture, interoperability between wired and wireless components is achieved by the use specific intermediate networking systems operating at the physical layer level, i.e. operating as repeaters. Instead, in this paper we will focus on a bridge-based approach, which presents several advantages. This concept was introduced in (Ferreira, et al., 2002), where a bridge-based approach was briefly outlined. Then, a specific Inter-Domain Protocol (IDP) was proposed to handle the Inter-Domain transactions in such a bridge-based approach (Ferreira, et al., 2003a). The major contribution of this paper is in extending these previous works by describing the protocol extensions to support inter-cell mobility in such a bridge-based hybrid wired/wireless PROFIBUS networks.

Task-based occupational exposure assessment and particle number concentration: two important data resources to perform risk assessment for occupational exposure to particles

Environment monitoring has an important role in occupational exposure assessment. However, due to several factors is done with insufficient frequency and normally don´t give the necessary information to choose the most adequate safety measures to avoid or control exposure. Identifying all the tasks developed in each workplace and conducting a task-based exposure assessment help to refine the exposure characterization and reduce assessment errors. A task-based assessment can provide also a better evaluation of exposure variability, instead of assessing personal exposures using continuous 8-hour time weighted average measurements. Health effects related with exposure to particles have mainly been investigated with mass-measuring instruments or gravimetric analysis. However, more recently, there are some studies that support that size distribution and particle number concentration may have advantages over particle mass concentration for assessing the health effects of airborne particles. Several exposure assessments were performed in different occupational settings (bakery, grill house, cork industry and horse stable) and were applied these two resources: task-based exposure assessment and particle number concentration by size. The results showed interesting results: task-based approach applied permitted to identify the tasks with higher exposure to the smaller particles (0.3 μm) in the different occupational settings. The data obtained allow more concrete and effective risk assessment and the identification of priorities for safety investments.

Repeater-based hybrid wired/wireless PROFIBUS network simulator

This technical report describes the Repeater-Based Hybrid Wired/Wireless PROFIBUS Network Simulator that implements a simulation model of the repeater-based approach. This approach defines the mechanism to extend the PROFIBUS protocol to supprot wireless communication, in which the interconnection of the wired and wireless segments is done by a intermediate system operating at Physical Layer, as repeater.

Meta-heuristics self-parameterization in a multi-agent scheduling system using case-based reasoning

This paper proposes a novel agent-based approach to Meta-Heuristics self-configuration. Meta-heuristics are algorithms with parameters which need to be set up as efficient as possible in order to unsure its performance. A learning module for self-parameterization of Meta-heuristics (MH) in a Multi-Agent System (MAS) for resolution of scheduling problems is proposed in this work. The learning module is based on Case-based Reasoning (CBR) and two different integration approaches are proposed. A computational study is made for comparing the two CBR integration perspectives. Finally, some conclusions are reached and future work outlined.