Phylogenetic analysis of the Monocotylidae (Monogenea) inferred from 28S rDNA sequences

The current classification of the Monocotylidae (Monogenea) is based on a phylogeny generated from morphological characters. The present study tests the morphological phylogenetic hypothesis using molecular methods. Sequences from domains C2 and D1 and the partial domains C1 and D2 from the 28S rDNA gene for 26 species of monocotylids from six of the seven subfamilies were used. Trees were generated using maximum parsimony, neighbour joining and maximum likelihood algorithms. The maximum parsimony tree, with branches showing less than 70% bootstrap support collapsed, had a topology identical to that obtained using the maximum likelihood analysis. The neighbour joining tree, with branches showing less than 70% support collapsed. differed only in its placement of Heterocotyle capricornensis as the sister group to the Decacotylinae clade. The molecular tree largely supports the subfamilies established using morphological characters. Differences are primarily how the subfamilies are related to each other. The monophyly of the Calicotylinae and Merizocotylinae and their sister group relationship is supported by high bootstrap values in all three methods, but relationships within the Merizocotylinae are unclear. Merizocotyle is paraphyletic and our data suggest that Mycteronastes and Thaumatocotyle, which were synonymized with Merizocotyle after the morphological cladistic analysis, should perhaps be resurrected as valid genera. The monophyly of the Monocotylinae and Decacotylinae is also supported by high bootstrap values. The Decacotylinae, which was considered previously to be the sister group to the Calicotylinae plus Merizocotylinae, is grouped in an unresolved polychotomy with the Monocotylinae and members of the Heterocotylinae. According to our molecular data, the Heterocotylinae is paraphyletic. Molecular data support a sister group relationship between Troglocephalus rhinobatidis and Neoheterocotyle rhinobatidis to the exclusion of the other species of Neoheterocotyle and recognition of Troglocephalus renders Neoheterocotyle,le paraphyletic. We propose Troglocephalus incertae sedis. An updated classification and full species list of the Monocotylidae is provided. (C) 2001 Australian Society for Parasitology Inc. Published by Elsevier Science Ltd. All rights reserved.

A monolithic smoothing-gap algorithm for contact-impact based on the signed distance function

A new algorithm has been developed for smoothing the surfaces in finite element formulations of contact-impact. A key feature of this method is that the smoothing is done implicitly by constructing smooth signed distance functions for the bodies. These functions are then employed for the computation of the gap and other variables needed for implementation of contact-impact. The smoothed signed distance functions are constructed by a moving least-squares approximation with a polynomial basis. Results show that when nodes are placed on a surface, the surface can be reproduced with an error of about one per cent or less with either a quadratic or a linear basis. With a quadratic basis, the method exactly reproduces a circle or a sphere even for coarse meshes. Results are presented for contact problems involving the contact of circular bodies. Copyright (C) 2002 John Wiley Sons, Ltd.

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.

Automatic segmentation and 3D feature extraction of protein aggregates in Caenorhabditis Elegans

In the last years, it has become increasingly clear that neurodegenerative diseases involve protein aggregation, a process often used as disease progression readout and to develop therapeutic strategies. This work presents an image processing tool to automatic segment, classify and quantify these aggregates and the whole 3D body of the nematode Caenorhabditis Elegans. A total of 150 data set images, containing different slices, were captured with a confocal microscope from animals of distinct genetic conditions. Because of the animals’ transparency, most of the slices pixels appeared dark, hampering their body volume direct reconstruction. Therefore, for each data set, all slices were stacked in one single 2D image in order to determine a volume approximation. The gradient of this image was input to an anisotropic diffusion algorithm that uses the Tukey’s biweight as edge-stopping function. The image histogram median of this outcome was used to dynamically determine a thresholding level, which allows the determination of a smoothed exterior contour of the worm and the medial axis of the worm body from thinning its skeleton. Based on this exterior contour diameter and the medial animal axis, random 3D points were then calculated to produce a volume mesh approximation. The protein aggregations were subsequently segmented based on an iso-value and blended with the resulting volume mesh. The results obtained were consistent with qualitative observations in literature, allowing non-biased, reliable and high throughput protein aggregates quantification. This may lead to a significant improvement on neurodegenerative diseases treatment planning and interventions prevention

Desigualdades sociodemográficas e suas conseqüências sobre o peso do recém-nascido

OBJETIVO: Analisar as desigualdades sociodemográficas, na assistência pré-natal e ao parto e suas conseqüências sobre o peso ao nascer. MÉTODOS: Estudo realizado em amostra de 10.072 puérperas atendidas em maternidades públicas, conveniadas com o Sistema Único de Saúde, e particulares do Município do Rio de Janeiro, no período de 1999-2001. Para verificar a associação entre peso ao nascer e características maternas, sociodemográficas, biológicas e da assistência pré-natal (índice de Kotelchuck modificado), realizaram-se regressões lineares múltiplas, estratificando as puérperas segundo nível de instrução. Foi utilizada a técnica de bootstrap com intervalos de confiança acurados para as estimativas dos efeitos. RESULTADOS: Na análise bivariada, para quase todas as variáveis estudadas, as médias de peso ao nascer foram menores entre as mães de escolaridade mais baixa. Na análise da regressão múltipla para o grupo de baixa escolaridade, o peso ao nascer associou-se diretamente com o índice de Kotelchuck modificado e a idade gestacional, e inversamente com as variáveis cor da pele preta, hábito de fumar e a experiência de filhos prematuros anteriores. Idade materna e paridade tiveram comportamentos distintos nos extremos e na faixa central dos dados. No grupo de maior escolaridade somente a paridade, a idade gestacional e o índice de Kotelchuck modificado foram significativos e se associaram diretamente com o peso ao nascer. Verificou-se o papel protetor da assistência pré-natal, assim como o efeito negativo do hábito de fumar independente do nível de escolaridade das mães. CONCLUSÕES: As variáveis que explicaram o peso ao nascer dos neonatos de mães com elevada escolaridade foram de natureza biológica, em contraste com os determinantes sociais encontrados no grupo de baixa escolaridade.

Azorean Agriculture Efficiency by PAR

Copyright © 2013 Springer Netherlands.

An evaluation of SAFIRE’s potential to reduce the dose received by paediatric patients undergoing CT: a narrative review

Introduction: The purpose of this review is to gather and analyse current research publications to evaluate Sinogram-Affirmed Iterative Reconstruction (SAFIRE). The aim of this review is to investigate whether this algorithm is capable of reducing the dose delivered during CT imaging while maintaining image quality. Recent research shows that children have a greater risk per unit dose due to increased radiosensitivity and longer life expectancies, which means it is particularly important to reduce the radiation dose received by children. Discussion: Recent publications suggest that SAFIRE is capable of reducing image noise in CT images, thereby enabling the potential to reduce dose. Some publications suggest a decrease in dose, by up to 64% compared to filtered back projection, can be accomplished without a change in image quality. However, literature suggests that using a higher SAFIRE strength may alter the image texture, creating an overly ‘smoothed’ image that lacks contrast. Some literature reports SAFIRE gives decreased low contrast detectability as well as spatial resolution. Publications tend to agree that SAFIRE strength three is optimal for an acceptable level of visual image quality, but more research is required. The importance of creating a balance between dose reduction and image quality is stressed. In this literature review most of the publications were completed using adults or phantoms, and a distinct lack of literature for paediatric patients is noted. Conclusion: It is necessary to find an optimal way to balance dose reduction and image quality. More research relating to SAFIRE and paediatric patients is required to fully investigate dose reduction potential in this population, for a range of different SAFIRE strengths.

F-LQE: a Fuzzy Link Quality Estimator for wireless sensor networks

Radio Link Quality Estimation (LQE) is a fundamental building block for Wireless Sensor Networks, namely for a reliable deployment, resource management and routing. Existing LQEs (e.g. PRR, ETX, Fourbit, and LQI ) are based on a single link property, thus leading to inaccurate estimation. In this paper, we propose F-LQE, that estimates link quality on the basis of four link quality properties: packet delivery, asymmetry, stability, and channel quality. Each of these properties is defined in linguistic terms, the natural language of Fuzzy Logic. The overall quality of the link is specified as a fuzzy rule whose evaluation returns the membership of the link in the fuzzy subset of good links. Values of the membership function are smoothed using EWMA filter to improve stability. An extensive experimental analysis shows that F-LQE outperforms existing estimators.

Improving accuracy for OTD based 3G geolocation in real urban/suburban environments

This paper presents the recent research results about the development of a Observed Time Difference (OTD) based geolocation algorithm based on network trace data, for a real Universal Mobile Telecommunication System (UMTS) Network. The initial results have been published in [1], the current paper focus on increasing the sample convergence rate, and introducing a new filtering approach based on a moving average spatial filter, to increase accuracy. Field tests have been carried out for two radio environments (urban and suburban) in the Lisbon area, Portugal. The new enhancements produced a geopositioning success rate of 47% and 31%, and a median accuracy of 151 m and 337 m, for the urban and suburban environments, respectively. The implemented filter produced a 16% and 20% increase on accuracy, when compared with the geopositioned raw data. The obtained results are rather promising in accuracy and geolocation success rate. OTD positioning smoothed by moving average spatial filtering reveals a strong approach for positioning trace extracted events, vital for boosting Self-Organizing Networks (SON) over a 3G network.

Spatial distribution and socioeconomic context of tuberculosis in Rio de Janeiro, Brazil

OBJECTIVE To analyze the spatial distribution of risk for tuberculosis and its socioeconomic determinants in the city of Rio de Janeiro, Brazil.METHODS An ecological study on the association between the mean incidence rate of tuberculosis from 2004 to 2006 and socioeconomic indicators of the Censo Demográfico (Demographic Census) of 2000. The unit of analysis was the home district registered in the Sistema de Informação de Agravos de Notificação (Notifiable Diseases Information System) of Rio de Janeiro, Southeastern Brazil. The rates were standardized by sex and age group, and smoothed by the empirical Bayes method. Spatial autocorrelation was evaluated by Moran’s I. Multiple linear regression models were studied and the appropriateness of incorporating the spatial component in modeling was evaluated.RESULTS We observed a higher risk of the disease in some neighborhoods of the port and north regions, as well as a high incidence in the slums of Rocinha and Vidigal, in the south region, and Cidade de Deus, in the west. The final model identified a positive association for the variables: percentage of permanent private households in which the head of the house earns three to five minimum wages; percentage of individual residents in the neighborhood; and percentage of people living in homes with more than two people per bedroom.CONCLUSIONS The spatial analysis identified areas of risk of tuberculosis incidence in the neighborhoods of the city of Rio de Janeiro and also found spatial dependence for the incidence of tuberculosis and some socioeconomic variables. However, the inclusion of the space component in the final model was not required during the modeling process.

Prognostic modelling of breast cancer patients: a benchmark of predictive models with external validation

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia Electrotécnica e de Computadores – Sistemas Digitais e Percepcionais pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Projecto solvência II - Modelação do risco de subscrição numa companhia de seguros não vida

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Matemática e Aplicações - Actuariado, Estatística e Investigação Operacional

Utilização da metodologia de bootstraap em inferência estatística

Neste artigo, apresentamos o bootstrap como metodologia de inferência estatística. Após apresentar o princípio teórico que fundamenta, analisamos as propriedades assimptóticas. São desenvolvidos também os vários métodos de cálculo de intervalos de confiança: método bootstrap -t, método dos percentis e métodos BCa e ABC.

Portfolio optimization with options

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Finance from the NOVA – School of Business and Economics

What is the best accounting policy for gains and losses in pensions?

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Finance from the NOVA – School of Business and Economics