Rqc: a bioconductor package for quality control of high-throughput sequencing data

FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOAs sequencing costs drop with the constant improvements in the field, next-generation sequencing becomes one of the most used technologies in biological research. Sequencing technology allows the detailed characterization of events at the molecular level,87CN2114FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO2013/24801-2sem informaçã

Abordagem Multidisciplinar do Primeiro Caso Autóctone de Tularémia Notificado em Portugal

Case ReportFrancisella tularensis, a Gram-negative coccobacillus, is a highly virulent pathogen responsible for several zoonotic outbreaks in Europe in the last few decades. The authors report the case of a 46-year-old male who developed fever, myalgias and headache a week after having contact with animal feed contaminated by rodents. Serological tests were positive for Francisella tularensis. This first case of autochthonous tularemia in Portugal led to an intensive investigation involving several healthcare services and national governmental authorities. The authors address the possible underdiagnosis of this infection in the country.Francisella tularensis, um cocobacilo Gram-negativo, é um microrganismo infecioso altamente virulento, responsável por vários surtos de doença na Europa nas últimas décadas. Os autores apresentam o caso de um homem de 46 anos com febre, mialgias e cefa- leias cerca de uma semana após contacto com ração de animais contaminada por roedores. O estudo serológico foi positivo para Francisella tularensis. Este caso, o primeiro caso de tularémia autóctone notificado em Portugal, originou uma intensa investigação envolvendo diversas autoridades de saúde e governamentais portuguesas. Os autores alertam para a possibilidade de subdiagnóstico desta doença no país.info:eu-repo/semantics/publishedVersio

Lyme Borreliosis as a Cause of Myocarditis in Pediatric Age

Lyme borreliosis with myocarditis is rare in pediatrics and diagnosis requires a high index of suspicion. We present an adolescent with myocarditis, depressed left ventricular function, and evidence of Lyme borreliosis infection. Early recognition and treatment of Lyme disease can help to avoid serious complications.info:eu-repo/semantics/publishedVersio

Meningomyeloradiculitis as an Unusual Presentation of Neuroborreliosis in Childhood

We report a pediatric case of Lyme neuroborreliosis-associated meningomyeloradiculitis with atypical manifestations and negative initial cerebrospinal fluid borrelial antibodies. Transverse myelitis and painful radiculoneuritis have rarely been described in pediatric neuroborreliosis. Clinical manifestations are wide ranging and nonspecific, and the serologic diagnosis is often delayed in the acute phase.info:eu-repo/semantics/publishedVersio

Rock Powder Can Improve Vermicompost Chemical Properties and Plant Nutrition: an On-farm Experiment

Together with farmers, we evaluated nutrient availability from vermicomposted gneiss powder, assessed its influence on growth promotion, nutrition and heavy metal accumulation in maize plants and the effect on soil chemical properties in the field. Three soil treatments were applied: fertilization with vermicompost with gneiss powder, fertilization with vermicompost without gneiss powder, and soil without fertilization (control), in a randomized block design with five replicates. The dry weight of shoots and the concentrations of potassium, calcium, magnesium, manganese, nickel, chrome and lead in the dry matter of maize were higher with vermicompost with gneiss powder. In the soil, the potential of hydrogen and phosphorus, potassium and calcium concentrations were higher with vermicompost with gneiss. There were no detectable levels of heavy metal wastes in the soil after the experiment. We conclude that vermicomposted gneiss powder has potential for use in agriculture as a nutrient source and can improve soil chemical properties

External application of dsRNA targeting a Phakopsora pachyrhizi effector candidate attenuated fungal pathogenicity.

PLANT AND ANIMAL GENOME XXV CONFERENCE - INTLPAG, 2017

Automatic learning of pre-miRNAs from different species.

Discovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complicate this task. To accommodate the peculiarities of plant and animal miRNAs systems, tools for both systems have evolved differently. However, these tools are biased towards the species for which they were primarily developed and, consequently, their predictive performance on data sets from other species of the same kingdom might be lower. While these biases are intrinsic to the species, their characterization can lead to computational approaches capable of diminishing their negative effect on the accuracy of pre-miRNAs predictive models. We investigate in this study how 45 predictive models induced for data sets from 45 species, distributed in eight subphyla/classes, perform when applied to a species different from the species used in its induction. Results: Our computational experiments show that the separability of pre-miRNAs and pseudo pre-miRNAs instances is species-dependent and no feature set performs well for all species, even within the same subphylum/class. Mitigating this species dependency, we show that an ensemble of classifiers reduced the classification errors for all 45 species. As the ensemble members were obtained using meaningful, and yet computationally viable feature sets, the ensembles also have a lower computational cost than individual classifiers that rely on energy stability parameters, which are of prohibitive computational cost in large scale applications. Conclusion: In this study, the combination of multiple pre-miRNAs feature sets and multiple learning biases enhanced the predictive accuracy of pre-miRNAs classifiers of 45 species. This is certainly a promising approach to be incorporated in miRNA discovery tools towards more accurate and less species-dependent tools

Controle genético do comprimento do pedúnculo em feijão-caupi.

O estudo da herança do caráter comprimento do pedúnculo em feijão-caupi foi realizado através de estimativas dos parâmetros genéticos, baseando-se em médias e variâncias, a partir do cruzamento entre genótipos parentais TVx-5058-09C de pedúnculo curto e TR 96-282-22G de pedúnculo longo. Estes genótipos e as gerações F1, F2, RC1 (P1 x F1) e RC2 (P2 x F1) foram avaliados quanto ao caráter citado, num experimento de blocos casualizados com quatro repetições. Foram estimados valores para as variâncias fenotípica, genotípica, ambiental, aditiva, e devido à dominância; herdabilidades no sentido amplo e restrito; grau médio de dominância e número mínimo de genes determinando o caráter. O modelo aditivo-dominante foi suficiente para explicar a variação observada, o efeito gênico aditivo foi o mais importante no controle do caráter em estudo, sendo este controlado por cinco genes. O alto valor da herdabilidade no sentido restrito permite a seleção precoce para o comprimento do pedúnculo

Reação à murcha bacteriana (Ralstonia pseudosolanacearum) em linhagens do programa de melhoramento de seis grupos de pimentas Capsicum.

Neste trabalho, avaliou-se a resistência de linhagens dos grupos de pimenta cumari-do-Pará, de-cheiro, murupi, habanero, cayenne e jalapeño do programa de melhoramento de Capsicum da Embrapa Hortaliças a R. pseudosolanacearum.bitstream/item/223236/1/BPD-221-.pd