Diagnóstico molecular de cancros hereditários por sequenciação de nova geração: cancro da mama e cancro colorretal

O cancro da mama e o cancro colorretal constituem duas das principais causas de morte a nível mundial. Entre 5 a 10% destes casos estão associados a variantes germinais/hereditárias em genes de suscetibilidade para cancro. O objetivo deste trabalho consistiu em validar a utilização da sequenciação de nova geração (NGS) para identificar variantes previamente detetadas pelo método de Sanger em diversos genes de suscetibilidade para cancro da mama e colorretal. Foram sequenciadas por NGS 64 amostras de DNA de utentes com suspeita clínica de predisposição hereditária para cancro da mama ou colorretal, utilizando o painel de sequenciação TruSight Cancer e a plataforma MiSeq (Illumina). Estas amostras tinham sido previamente sequenciadas pelo método de Sanger para os genes BRCA1, BRCA2, TP53, APC, MUTYH, MLH1, MSH2 e STK11. A análise bioinformática dos resultados foi realizada com os softwares MiSeq Reporter, VariantStudio, Isaac Enrichment (Illumina) e Integrative Genomics Viewer (Broad Institute). A NGS demonstrou elevada sensibilidade e especificidade analíticas para a deteção de variantes de sequência em 8 genes de suscetibilidade para cancro colorretal e da mama, uma vez que permitiu identificar a totalidade das 412 variantes (93 únicas, incluindo 27 variantes patogénicas) previamente detetadas pelo método de Sanger. A utilização de painéis de sequenciação de genes de predisposição para cancro por NGS vem possibilitar um diagnóstico molecular mais abrangente, rápido e custo-eficiente, relativamente às metodologias convencionais.

Base molecular da hemocromatose hereditária não-clássica em Portugal

A Hemocromatose Hereditária (HH) é uma doença autossómica recessiva caracterizada pela absorção excessiva de ferro a nível intestinal e sua acumulação em órgãos vitais, podendo originar cardiomiopatia, cirrose e carcinoma hepatocelular. O correspondente diagnóstico molecular é obtido pela associação com genótipos específicos no gene HFE (homozigotia para p.Cys282Tyr ou heterozigotia composta p.Cys282Tyr/p.His63Asp). Contudo, nos países do sul da Europa, cerca de um terço dos doentes com diagnóstico clínico de HH não apresenta os referidos genótipos. Para identificar a base molecular da HH não-clássica em Portugal usaram-se metodologias de pesquisa geral de variantes genéticas (SSCP e dHPLC), Next-Generation Sequencing (NGS) e sequenciação de Sanger, cobrindo seis genes relacionados com o metabolismo do ferro em 303 doentes. Identificaram-se 69 variantes diferentes e de vários tipos, por ex. missense, nonsense, de splicing, que perturbam a transcrição do gene ou a regulação da tradução do mRNA. Seguidamente, realizaram-se estudos in silico e in vitro para esclarecer o significado etiológico de algumas das novas variantes. Concluiu-se que a base molecular desta patologia é bastante heterogénea e que a NGS é uma ferramenta adequada para efetuar a análise simultânea dos vários genes num grande número de amostras. Contudo, o estabelecimento da relevância clínica de algumas variantes requer a realização de estudos funcionais.

Elements of a methodology to assess the alignment of core-values in collaborative networks

Collaborative networks are typically formed by heterogeneous and autonomous entities, and thus it is natural that each member has its own set of core-values. Since these values somehow drive the behaviour of the involved entities, the ability to quickly identify partners with compatible or common core-values represents an important element for the success of collaborative networks. However, tools to assess or measure the level of alignment of core-values are lacking. Since the concept of 'alignment' in this context is still ill-defined and shows a multifaceted nature, three perspectives are discussed. The first one uses a causal maps approach in order to capture, structure, and represent the influence relationships among core-values. This representation provides the basis to measure the alignment in terms of the structural similarity and influence among value systems. The second perspective considers the compatibility and incompatibility among core-values in order to define the alignment level. Under this perspective we propose a fuzzy inference system to estimate the alignment level, since this approach allows dealing with variables that are vaguely defined, and whose inter-relationships are difficult to define. Another advantage provided by this method is the possibility to incorporate expert human judgment in the definition of the alignment level. The last perspective uses a belief Bayesian network method, and was selected in order to assess the alignment level based on members' past behaviour. An example of application is presented where the details of each method are discussed.

Geostatistical Mapping of Outfall Plume Dispersion Data gathered with an autonomous underwater vehicle

The main purpose of this study was to examine the applicability of geostatistical modeling to obtain valuable information for assessing the environmental impact of sewage outfall discharges. The data set used was obtained in a monitoring campaign to S. Jacinto outfall, located off the Portuguese west coast near Aveiro region, using an AUV. The Matheron’s classical estimator was used the compute the experimental semivariogram which was fitted to three theoretical models: spherical, exponential and gaussian. The cross-validation procedure suggested the best semivariogram model and ordinary kriging was used to obtain the predictions of salinity at unknown locations. The generated map shows clearly the plume dispersion in the studied area, indicating that the effluent does not reach the near by beaches. Our study suggests that an optimal design for the AUV sampling trajectory from a geostatistical prediction point of view, can help to compute more precise predictions and hence to quantify more accurately dilution. Moreover, since accurate measurements of plume’s dilution are rare, these studies might be very helpful in the future for validation of dispersion models.

Identificação do papilomavírus humano por biologia molecular em mulheres assintomáticas

OBJETIVO: Verificar a associação entre fatores epidemiológicos e infecção genital pelo papilomavírus humano (HPV). MÉTODOS: Realizou-se estudo transversal com 975 mulheres atendidas em um serviço público de rastreamento para o câncer cervical, em Porto Alegre, Brasil. As mulheres foram consideradas infectadas pelo HPV quando apresentaram o teste de DNA positivo para esse vírus, tanto pelo método de captura híbrida II (CH II) como pelo método de reação em cadeia da polimerase (PCR). Mulheres infectadas pelo HPV foram comparadas com mulheres não infectadas oriundas da mesma população. RESULTADOS: Foram estudadas 975 mulheres. A prevalência observada de HPV (pela combinação dos métodos de DNA) foi de 27%. Quando a análise de cada método de DNA foi feito isoladamente, a prevalência de HPV-DNA foi de 15% para a CH II e de 16% para PCR. Regressão logística múltipla incondicional foi utilizada na identificação dos fatores associados à infecção pelo HPV. Foi encontrada associação positiva com as seguintes variáveis: anos de escolaridade (11 anos: OR=2,05; IC95%=1,31; 3,20; referência: até oito anos de escolaridade); ser casada (OR=1,69; IC95%=0,78; 2,00; referência: ser solteira); parceiros sexuais ao longo da vida (dois parceiros: OR=1,67; IC95%=1,01; 2,77; quatro ou mais: OR=2,18; IC95%=1,15; 4,13; referência: um parceiro); idade da primeira relação sexual (15-16 anos: OR=4,05; IC95%=0,89; 18,29; referência: > ou = 22 anos). CONCLUSÕES: Vários fatores parecem estar associados à presença de infecção genital pelo HPV, especialmente aqueles referentes ao comportamento sexual (idade da primeira relação sexual, número de parceiros sexuais ao longo da vida e estado marital) e aqueles relacionados à situação socioeconômica (escolaridade).

Mapping atmospheric pollutants emissions in European countries

In this paper we present a methodology which enables the graphical representation, in a bi-dimensional Euclidean space, of atmospheric pollutants emissions in European countries. This approach relies on the use of Multidimensional Unfolding (MDU), an exploratory multivariate data analysis technique. This technique illustrates both the relationships between the emitted gases and the gases and their geographical origins. The main contribution of this work concerns the evaluation of MDU solutions. We use simulated data to define thresholds for the model fitting measures, allowing the MDU output quality evaluation. The quality assessment of the model adjustment is thus carried out as a step before interpretation of the gas types and geographical origins results. The MDU maps analysis generates useful insights, with an immediate substantive result and enables the formulation of hypotheses for further analysis and modeling.

Difusão molecular em ressonância magnética para estudo de lesões mamárias malignas

Objetivos – Com este estudo pretendeu-se i) avaliar o contributo da aplicação da sequência de difusão na caracterização das lesões mamárias malignas; ii) considerar se a sequência de difusão deve incorporar o protocolo standard em RM mamária e iii) correlacionar os resultados dos valores de coeficiente aparente de difusão (ADC) e os resultados histológicos. Metodologia – A amostra incluiu 18 pacientes do sexo feminino, com idades compreendidas entre 38 e 71 anos, que apresentavam lesões mamárias malignas confirmadas histologicamente. Foi adicionado ao protocolo de RM mamária a sequência de difusão, de modo a calcular os valores de ADC das lesões observadas. Resultados – Verificou-se que a range de valores de ADC para lesões malignas em ROI’s calculados no centro da lesão apresentavam uma média e desvio-padrão de (0,89 ± 0,14x10-3mm2/s). O método da utilização dos valores de ADC na caracterização de lesões mamárias malignas demonstrou uma sensibilidade de 100%. Conclusões – Neste estudo, com uma sensibilidade de 100%, a ponderação em difusão demonstrou ser uma técnica vantajosa na caracterização de lesões mamárias malignas pelo que se sugere a sua introdução no protocolo standard da RM mamária. ABSTRACT - Aims – The aim of this study was i) to evaluate the potential of the DWI sequence in the characterization of malignant breast lesions; ii) to verify if this sequence should incorporate the breast MRI protocol and iii) to correlate the apparent diffusion coefficients (ADC) values and histological results. Methodology – The sample includes 18 female patients between the ages of 38 and 71 years, who presented with malignant breast lesion confirmed by histology. The DWI sequence was added to the MRI standard protocol to calculate the ADC values. Results – In the results obtained we observed that the range of the ADC values calculated in the center of the malignant lesions, showed a mean and standard deviation of 0.89 ± 0.14 x10-3 mm2 / s. This method of using the ADC values for the detection of malignant lesions showed a sensitivity of 100%. Conclusion – The DWI technique proved to be a useful method in the characterization of malignant breast lesions, as it showed a sensitivity of 100%, so we suggest its inclusion in the Breast MR standard protocol.

Tuberculose resistente: revisão molecular

O progresso na compreensão dos mecanismos de resistência aos fármacos usados no tratamento da tuberculose tem permitido o desenvolvimento de novos métodos para a detecção da tuberculose resistente. A resistente aos fármacos representa uma ameaça para os programas de controle da tuberculose. Para tanto, é necessário conhecer o padrão de sensibilidade das linhagens para fornecer o tratamento adequado. Os estudos moleculares dos mecanismos de ação dos fármacos antituberculose têm elucidado as bases genéticas da resistência aos fármacos em Mycobacterium tuberculosis. Os mecanismos de resistência aos fármacos na tuberculose são causados por mutações cromossomais em diferentes genes da bactéria. Durante a exposição aos fármacos, há uma pressão seletiva favorecendo o desenvolvimento de linhagens resistentes. A tuberculose multirresistente é um problema nacional e internacional que traz sérias dificuldades para o controle global da doença. Realizou-se uma revisão sobre os mecanismos moleculares associados à resistência aos fármacos com ênfase nas novas perspectivas para detectar os isolados resistentes.

A Service Integration Platform for Collaborative Networks

Integrated manufacturing constitutes a complex system made of heterogeneous information and control subsystems. Those subsystems are not designed to the cooperation. Typically each subsystem automates specific processes, and establishes closed application domains, therefore it is very difficult to integrate it with other subsystems in order to respond to the needed process dynamics. Furthermore, to cope with ever growing marketcompetition and demands, it is necessary for manufacturing/enterprise systems to increase their responsiveness based on up-to-date knowledge and in-time data gathered from the diverse information and control systems. These have created new challenges for manufacturing sector, and even bigger challenges for collaborative manufacturing. The growing complexity of the information and communication technologies when coping with innovative business services based on collaborative contributions from multiple stakeholders, requires novel and multidisciplinary approaches. Service orientation is a strategic approach to deal with such complexity, and various stakeholders' information systems. Services or more precisely the autonomous computational agents implementing the services, provide an architectural pattern able to cope with the needs of integrated and distributed collaborative solutions. This paper proposes a service-oriented framework, aiming to support a virtual organizations breeding environment that is the basis for establishing short or long term goal-oriented virtual organizations. The notion of integrated business services, where customers receive some value developed through the contribution from a network of companies is a key element.

Short-term wind power forecasting in Portugal by neural networks and wavelet transform

This paper proposes artificial neural networks in combination with wavelet transform for short-term wind power forecasting in Portugal. The increased integration of wind power into the electric grid, as nowadays occurs in Portugal, poses new challenges due to its intermittency and volatility. Hence, good forecasting tools play a key role in tackling these challenges. Results from a real-world case study are presented. A comparison is carried out, taking into account the results obtained with other approaches. Finally, conclusions are duly drawn. (C) 2010 Elsevier Ltd. All rights reserved.

Scheduling maintenance activities of electric power transmission networks using an hybrid constraint method

In this paper we present a Constraint Logic Programming (CLP) based model, and hybrid solving method for the Scheduling of Maintenance Activities in the Power Transmission Network. The model distinguishes from others not only because of its completeness but also by the way it models and solves the Electric Constraints. Specifically we present a efficient filtering algorithm for the Electrical Constraints. Furthermore, the solving method improves the pure CLP methods efficiency by integrating a type of Local Search technique with CLP. To test the approach we compare the method results with another method using a 24 bus network, which considerers 42 tasks and 24 maintenance periods.

Symbolic Knowledge Extraction from Trained Neural Networks Governed by Lukasiewicz Logics

This work describes a methodology to extract symbolic rules from trained neural networks. In our approach, patterns on the network are codified using formulas on a Lukasiewicz logic. For this we take advantage of the fact that every connective in this multi-valued logic can be evaluated by a neuron in an artificial network having, by activation function the identity truncated to zero and one. This fact simplifies symbolic rule extraction and allows the easy injection of formulas into a network architecture. We trained this type of neural network using a back-propagation algorithm based on Levenderg-Marquardt algorithm, where in each learning iteration, we restricted the knowledge dissemination in the network structure. This makes the descriptive power of produced neural networks similar to the descriptive power of Lukasiewicz logic language, minimizing the information loss on the translation between connectionist and symbolic structures. To avoid redundance on the generated network, the method simplifies them in a pruning phase, using the "Optimal Brain Surgeon" algorithm. We tested this method on the task of finding the formula used on the generation of a given truth table. For real data tests, we selected the Mushrooms data set, available on the UCI Machine Learning Repository.

Syntheses, Molecular Structures, Electrochemical Behavior, Theoretical Study, and Antitumor Activities of Organotin(IV) Complexes Containing 1-(4-Chlorophenyl)-1-cyclopentanecarboxylato Ligands

The organotin(IV) compounds [Me2Sn(L)(2)] (1), [Et(2)sn(L)(2)] (2), [(Bu2Sn)-Bu-n(L)(2)] (3), [(n)Oct(2)Sn(L)(2)] (4), [Ph2Sn(L)(2)] (5), and [PhOSnL](6) (6) have been synthesized from the reactions of 1-(4-chlorophenyl)-1-cyclopentanecarboxylic acid (HL) with the corresponding diorganotin(IV) oxide or dichloride. They were characterized by IR and multinuclear NMR spectroscopies, elemental analysis, cyclic voltammetry, and, for 2, 3, 4 and 6, single crystal X-ray diffraction analysis. While 1-5 are mononuclear diorganotin (IV) compounds, the X-ray diffraction of 6 discloses a hexameric drumlike structure with a prismatic Sn6O6 core. All these complexes undergo irreversible reductions and were screened for their in vitro antitumor activities toward HL-60, BGC-823, Bel-7402, and KB human cancer cell lines. Within the mononuclear compounds, the most active ones (3, 5) are easiest to reduce (least cathodic reduction potentials), while the least active ones (1, 4) are the most difficult to reduce. Structural rearrangements (i.e., Sn-O bond cleavages and trans-to-cis isomerization) induced by reduction, which eventually can favor the bioactivity, are disclosed by theoretical/electrochemical studies.

An optimal scheduling problem in distribution networks considering V2G

This paper addresses the problem of energy resource scheduling. An aggregator will manage all distributed resources connected to its distribution network, including distributed generation based on renewable energy resources, demand response, storage systems, and electrical gridable vehicles. The use of gridable vehicles will have a significant impact on power systems management, especially in distribution networks. Therefore, the inclusion of vehicles in the optimal scheduling problem will be very important in future network management. The proposed particle swarm optimization approach is compared with a reference methodology based on mixed integer non-linear programming, implemented in GAMS, to evaluate the effectiveness of the proposed methodology. The paper includes a case study that consider a 32 bus distribution network with 66 distributed generators, 32 loads and 50 electric vehicles.

In vitro transference and molecular characterization of bla TEM genes in bacteria isolated from Portuguese ready-to-eat foods

The principal aim of this study was to investigate the possibility of transference to Escherichia coli of β-lactam resistance genes found in bacteria isolated from ready-to-eat (RTE) Portuguese traditional food. From previous screenings, 128 β-lactam resistant isolates (from different types of cheese and of delicatessen meats), largely from the Enterobacteriaceae family were selected and 31.3% of them proved to transfer resistance determinants in transconjugation assays. Multiplex PCR in donor and transconjugant isolates did not detect bla CTX, bla SHV and bla OXY, but bla TEM was present in 85% of them, while two new TEMs (TEM-179 and TEM-180) were identified in two isolates. The sequencing of these amplicons showed identity between donor and transconjugant genes indicating in vitro plasmid DNA transfer. These results suggest that if there is an exchange of genes in natural conditions, the consumption of RTE foods, particularly with high levels of Enterobacteriaceae, can contribute to the spread of antibiotic resistance.