A machine learning based framework to identify and classify long terminal repeat retrotransposons

Transposable elements (TEs) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes. They can move and duplicate within a genome, increasing genome size and contributing to genetic diversity within and across species. Accurate identification and classification of TEs present in a genome is an important step towards understanding their effects on genes and their role in genome evolution. We introduce TE-LEARNER, a framework based on machine learning that automatically identifies TEs in a given genome and assigns a classification to them. We present an implementation of our framework towards LTR retrotransposons, a particular type of TEs characterized by having long terminal repeats (LTRs) at their boundaries. We evaluate the predictive performance of our framework on the well-annotated genomes of Drosophila melanogaster and Arabidopsis thaliana and we compare our results for three LTR retrotransposon superfamilies with the results of three widely used methods for TE identification or classification: REPEATMASKER, CENSOR and LTRDIGEST. In contrast to these methods, TE-LEARNER is the first to incorporate machine learning techniques, outperforming these methods in terms of predictive performance , while able to learn models and make predictions efficiently. Moreover, we show that our method was able to identify TEs that none of the above method could find, and we investigated TE-LEARNER'S predictions which did not correspond to an official annotation. It turns out that many of these predictions are in fact strongly homologous to a known TE

Neural networks and genetic algorithms for hierarchical multi-label classification problems

In conventional classification problems, each instance of a dataset is associated with just one among two or more classes. However, there are more complex classification problems where instances can be simultaneously classified into classes belonging to two or more paths of a hierarchy. Such a hierarchy can be structured as a tree or a directed acyclic graph. These problems are known in the machine learning literature as hierarchical multi-label classification (HMC) problems. In this\ud Thesis, two methods for hierarchical multi-label classification are proposed and investigated. The first one associates a Multi-Layer Perceptron (MLP) to each hierarchical level, being each MLP responsible for the predictions in its associated level. The method is called HMC-LMLP. The second method induces hierarchical multi-label classification rules using a Genetic Algorithm. The method is called HMC-GA. Experiments using hierarchies structured as trees showed that HMC-LMLP obtained classification performances superior to the state-of-the-art method in the literature, and superior or competitive performances when using graph-structured hierarchies. The HMC-GA method obtained\ud competitive results with other methods of the literature in both tree and graph-structured hierarchies, being able of inducing, in many cases, smaller and in less quantity rules.FAPESP (grant 2009/17401-2)CNP

The role of magnetic resonance imaging in the postoperative management of cholesteatomas

A tomografia computadorizada e ressonância magnética (RM) com seqüências convencionais têm baixa especificidade para a diferenciação entre tecido de granulação e recidiva de colesteatoma. OBJETIVO: Avaliar a aplicação da RM com sequência de difusão e pós-contraste T1 tardio na detecção de recidiva de colesteatoma. MATERIAL E MÉTODO: Realizado estudo transversal prospectivo de dezessete pacientes estudados no pós-operatório de colesteatoma utilizando RM de 1.5 T com seqüência difusão, T1, T2 e pós-contraste T1 tardio nos planos coronal e axial. Dois radiologistas avaliaram e decidiram em consenso a presença de foco de hipersinal na difusão e T2, iso/hipossinal em T1 e ausência de impregnação pelo contraste como suspeitos de recidiva de colesteatoma. Os achados da revisão cirúrgica foram comparados com o resultado da RM. RESULTADOS: Onze dos doze casos de recidiva de colesteatoma apresentaram hipersinal na difusão. Todos os pacientes com tecido de granulação na cavidade cirúrgica não apresentaram alteração de sinal na difusão. Um paciente com abscesso no conduto auditivo interno também apresentou hipersinal na difusão. A sensibilidade, especificidade, valor preditivo positivo e negativo foram respectivamente 91,6%, 60%, 84,6% e 75%. CONCLUSÃO: A seqüência de difusão combinada com pós-contraste tardio pode ser útil na diferenciação entre tecido de granulação e recidiva de colesteatoma.Conventional CT and MRI scans have low specificity when it comes to differentiating granulation tissue from relapsing cholesteatoma. AIM: this paper aims to analyze the use of DWI and delayed post-contrast T1-weighed imaging in the detection of recurring cholesteatomas. MATERIALS AND METHOD: this is a cross-sectional prospective study that looked at 17 cholesteatoma patients postoperatively. All patients underwent diffusion magnetic resonance imaging at 1.5T, T1, T2, and delayed post-contrast T1 and images were produced from both coronal and axial planes. Two radiologists assessed the images and decided consensually that the presence of hyperintensive signal in DWI on T2, iso/hypointensive signal on T1, and absence of contrast uptake were indicative of relapsing cholesteatoma. Surgical review findings were compared to DWI scans. RESULTS: eleven of the twelve cases of recurring cholesteatoma presented hyperintensive signal in the DWI scans. None of the patients with granulation tissue in the surgical wound presented hyperintensive signal in the DWI scans. A patient with an abscess in the internal acoustic meatus also presented a hyperintensive signal in the DWI scans. Sensibility, specificity, positive predictive value and negative predictive value were 91.6%, 60.0%, 84.6%, and 75.0%, respectively. CONCLUSION: DWI combined with delayed post-contrast T1 SE sequence proved to be useful in the differential diagnosis of granulation tissue and recurring cholesteatoma

Gestão de projectos no âmbito da construção sustentável

A indústria da construção, nomeadamente no sector da edificação, baseia-se essencialmente em métodos de construção tradicional. Esta indústria é caracterizada pelo consumo excessivo de matérias-primas, de recursos energéticos não renováveis e pela elevada produção de resíduos. Esta realidade é de todo incompatível com os desígnios do desenvolvimento sustentável, nos quais se procura a conveniência harmoniosa entre as dimensões ambiental, social e económica. O desafio da sustentabilidade, colocado à actividade da construção, tem motivado abordagens distintas, não só por parte das várias especialidades da engenharia, como também da arquitectura. É nesta perspectiva, que o presente modelo pretende ser um contributo para uma abordagem inovadora, introduzindo linhas de intervenção e de orientação, para apoiar e estimular o desenvolvimento de soluções sustentáveis em edifícios habitacionais, em qualquer fase do ciclo de evolução de um projecto e das várias especialidades do mesmo. Assim, no sentido de optimizar os recursos envolvidos no projecto são expostas estratégias de intervenção, com os seguintes objectivos: optimização do potencial do local, preservação da identidade regional e cultural, minimização do consumo de energia, utilização de materiais e produtos de baixo impacto ambiental, redução do consumo de água, redução da produção de emissões, resíduos e outros poluentes, adequada qualidade do ambiente interior e optimização das fases de operação e manutenção. A ferramenta apresentada surge como um instrumento facilitador para a equipa de projectistas, e que se esta adaptada para o desenvolvimento de projectos de edifícios de habitação, dada a génese dos métodos utilizados. As soluções de sustentabilidade apresentadas neste manual emanam dos sistemas de certificação LíderA, LEED, BREEAM e SBToolpt. O modelo encontra-se estruturado, no que às fases de projecto diz respeito, de acordo com os requisitos expressos na Portaria 701-H/2008 de 29 de Julho, tendo sido igualmente seguido o descrito para os respectivos intervenientes.The construction industry, particularly the building sector, is based mainly on traditional construction methods. This industry is characterized by excessive consumption of raw materials, non-renewable energy resources and high production of waste. This reality is entirely incompatible with the aims of sustainable development, which require a “harmonious convergence” between the environmental, social and economic dimensions. It is therefore necessary to change attitudes and proceedings in a responsible and intelligent way. The sustainability challenge faced by the construction activity has motivated different approaches, not only by the various engineering specialties, but also by the architecture. It is with this background that this document is intended as a contribution to an innovative approach by introducing lines of action and guidance to support and encourage the development of sustainable solutions in residential buildings at any stage of a project and its different specialties. Therefore, in order to optimize the resources involved in the project, are exposed intervention strategies, with the following main objectives: optimizing the potential of the site, preservation of cultural and regional identity, minimize energy consumption, use of materials and products with low environmental impact, reducing the water consumption, reducing the production of emissions, waste and other pollutants, adequate indoor environmental quality and optimization of the operation and maintenance phases. This tool emerges as a facilitator for the design team and is adapted to the development of residential building projects, given the genesis of the methods used. The sustainability solutions presented in this document are based on the certification systems LíderA, LEED, BREEAM and SBToolpt. The manual is structured, in the phases of the project concerns, according to the requirements stated in “Portaria 701-H/2008 de 29 de Julho”

Efeito da continuidade da fisioterapia respiratória até a alta hospitalar na incidência de complicações pulmonares após esofagectomia por câncer

This study assessed the effects of chest physical therapy all through hospital stay until discharge onto the incidence of pulmonary complications in patients having undergone esophagectomy for cancer. Medical records of esophagectomy patients were examined and 40 subsequent ones selected (none excluded), and divided into two groups: one having received chest physiotherapy only in the intensive care unit (ICUg, n=20) and the other having received it during full hospital stay (DISg, n=20). Information concerning pre-, peri- and postoperative periods were drawn from patients' records. Results show that ICUg and DISg were similar (mean±sd) concerning age (55.5±9.9 vs 57.1±10.8 years old), BMI (22.5±3.3 vs 18±4 kg/m²), operating time (400±103.8 vs 408.5±142 min), anesthesia time (498.3±107.3 vs 516±148.9 min) and number of chest physical therapy sessions in the ICU (9.6±14.9 vs 8.3±7.6 sessions). Despite the fact that DISg patients had higher tobacco consumption than ICUg ones (35.7±17.6 vs 26.1±18.4 packs-year, pO presente estudo avaliou os efeitos na incidência de complicações pulmonares do cuidado contínuo de fisioterapia respiratória no pós-operatório de esofagectomia, até a alta hospitalar. Examinaram-se retrospectivamente 40 prontuários de pacientes de esofagectomia consecutivos (nenhuma exclusão), que foram divididos em dois grupos: um dos que receberam fisioterapia respiratória apenas na unidade de tratamento intensivo (gUTI, n=20) e outro dos que a receberam até a alta hospitalar (gALTA, n=20). Foram coletadas informações referentes ao pré, intra e pós-operatório. Os resultados mostram que gUTI e gALTA, respectivamente, apresentaram-se similares (média±dp) quanto a idade (55,5±9,9 e 57,1±10,8 anos), IMC (22,5±3,3 e 18±4 kg/m²), tempo de cirurgia (400±103,8 e 408,5±142 min), tempo de anestesia (498,3±107,3 e 516±148,9 min) e número de atendimentos de fisioterapia na UTI (9,6±14,9 e 8,3±7,6). Apesar de o gALTA apresentar história de tabagismo superior (35,7±17,6 vs 26,1±18,4 maços-ano,

Constraints on the χ_(c1) versus χ_(c2) polarizations in proton-proton collisions at √s = 8 TeV

The polarizations of promptly produced χ_(c1) and χ_(c2) mesons are studied using data collected by the CMS experiment at the LHC, in proton-proton collisions at √s=8  TeV. The χ_c states are reconstructed via their radiative decays χ_c → J/ψγ, with the photons being measured through conversions to e⁺e⁻, which allows the two states to be well resolved. The polarizations are measured in the helicity frame, through the analysis of the χ_(c2) to χ_(c1) yield ratio as a function of the polar or azimuthal angle of the positive muon emitted in the J/ψ → μ⁺μ⁻ decay, in three bins of J/ψ transverse momentum. While no differences are seen between the two states in terms of azimuthal decay angle distributions, they are observed to have significantly different polar anisotropies. The measurement favors a scenario where at least one of the two states is strongly polarized along the helicity quantization axis, in agreement with nonrelativistic quantum chromodynamics predictions. This is the first measurement of significantly polarized quarkonia produced at high transverse momentum