Detection and identification of dengue virus isolates from Brazil by a simplified reverse transcription - polymerase chain reaction (RT-PCR) method

We show here a simplified RT-PCR for identification of dengue virus types 1 and 2. Five dengue virus strains, isolated from Brazilian patients, and yellow fever vaccine 17DD as a negative control, were used in this study. C6/36 cells were infected and supernatants were collected after 7 days. The RT-PCR, done in a single reaction vessel, was carried out following a 1/10 dilution of virus in distilled water or in a detergent mixture containing Nonidet P40. The 50 µl assay reaction mixture included 50 pmol of specific primers amplifying a 482 base pair sequence for dengue type 1 and 210 base pair sequence for dengue type 2. In other assays, we used dengue virus consensus primers having maximum sequence similarity to the four serotypes, amplifying a 511 base pair sequence. The reaction mixture also contained 0.1 mM of the four deoxynucleoside triphosphates, 7.5 U of reverse transcriptase, 1U of thermostable Taq DNA polymerase. The mixture was incubated for 5 minutes at 37ºC for reverse transcription followed by 30 cycles of two-step PCR amplification (92ºC for 60 seconds, 53ºC for 60 seconds) with slow temperature increment. The PCR products were subjected to 1.7% agarose gel electrophoresis and visualized by UV light after staining with ethidium bromide solution. Low virus titer around 10 3, 6 TCID50/ml was detected by RT-PCR for dengue type 1. Specific DNA amplification was observed with all the Brazilian dengue strains by using dengue virus consensus primers. As compared to other RT-PCRs, this assay is less laborious, done in a shorter time, and has reduced risk of contamination

Algorithms for time series clustering applied to biomedical signals

Thesis submitted in the fulfillment of the requirements for the Degree of Master in Biomedical Engineering

Trypanosoma cruzi: chemotherapy with benznidazole in mice inoculated with strains from Paraná State and from different endemic areas of Brazil

Strains of Trypanosoma cruzi from different geographical areas have shown different levels of susceptibility to trypanocidal drugs. The susceptibility in vivo to benznidazole was investigated in eighteen strains of T. cruzi. Twelve were isolated from chronic chagasic patients from different Chagas’ disease endemic areas. The other six strains were isolated from the northwestern region of Paraná state; two of them from patients three from triatomines (Triatoma sordida) and one from wild reservoir (Didelphis sp.). To test drug the infected mice were divided into two groups of twenty. One group was treated with benznidazole for twenty consecutive days and the other group was used as untreated control. The treatment began after detection of the infection by direct blood examination or haemoculture. The control of cure was done through haemoculture and indirect immunofluorescence test. The drug eliminated the inflammatory lesions of the skeletal muscle of mice considered cured and from the heart of most of them. Moreover, the inflammatory lesions were reduced in treated but not cured animals. The T. cruzi strains studied showed a gradient of drug susceptibility that varied from 0% to 100%. Ten strains were considered sensitive to the treatment (61 to 100% of cure), one strain was partially sensitive (50% of cure) and seven strains were considered resistant to the treatment (0 to 40% of cure). This variation was observed both in strains of T. cruzi isolated from domestic and sylvatic cycles

Análise estatística do preço da energia elétrica em mercado livre - Uma aplicação ao caso português

Neste relatório apresentam-se resultados de um estudo estatístico que procura contribuir para um melhor entendimento da problemática inerente à liberalização do setor elétrico em Portugal e dos desafios que esta liberalização, existente desde meados de 2007, trás aos seus intervenientes. Iniciam-se os trabalhos com um estudo que pretende avaliar a existência de relação entre o Preço de Mercado da eletricidade e um conjunto de variáveis potencialmente explicativas/condicionantes do Preço de Mercado. Neste estudo consideram-se duas abordagens. A primeira usa a função de correlação cruzada para avaliar a existência de relação do tipo linear entre pares de variáveis. A segunda considera o teste causalidade de Granger na avaliação de uma relação de causa e efeito entre esses pares. Este estudo avaliou a relação entre o Preço de Mercado da eletricidade e 19 variáveis ditas condicionantes distribuídas por três categorias distintas (consumo e produção de eletricidade; indicadores climáticos; e energias primárias). O intervalo de tempo em estudo cinge-se ao biénio 2012-2103. Durante este período avaliam-se as relações entre as variáveis em diversos sub-períodos de tempo em ciclos de consumo representativos do consumo em baixa (fim de semana) e de consumo mais elevado (fora de vazio) com os valores observados de cada uma das variáveis tratados com uma base horária e diária (média). Os resultados obtidos mostram a existência relação linear entre algumas das variáveis em estudo e o preço da eletricidade em regime de mercado liberalizado, mas raramente é possível identificar precedência temporal entre as variáveis. Considerando os resultados da análise de correlação e causalidade, apresenta-se ainda um modelo de previsão do Preço de Mercado para o curto e médio prazo em horas de período fora de vazio.

Crystallographic and biochemical studies on dissimilatory sulfite reductases

Thesis dissertation presented to obtain a PhD degree in Biochemistry at Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Exploring distributed computing tools through data mining tasks

Harnessing idle PCs CPU cycles, storage space and other resources of networked computers to collaborative are mainly fixated on for all major grid computing research projects. Most of the university computers labs are occupied with the high puissant desktop PC nowadays. It is plausible to notice that most of the time machines are lying idle or wasting their computing power without utilizing in felicitous ways. However, for intricate quandaries and for analyzing astronomically immense amounts of data, sizably voluminous computational resources are required. For such quandaries, one may run the analysis algorithms in very puissant and expensive computers, which reduces the number of users that can afford such data analysis tasks. Instead of utilizing single expensive machines, distributed computing systems, offers the possibility of utilizing a set of much less expensive machines to do the same task. BOINC and Condor projects have been prosperously utilized for solving authentic scientific research works around the world at a low cost. In this work the main goal is to explore both distributed computing to implement, Condor and BOINC, and utilize their potency to harness the ideal PCs resources for the academic researchers to utilize in their research work. In this thesis, Data mining tasks have been performed in implementation of several machine learning algorithms on the distributed computing environment.

A process-based control for evolvable production systems

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores

Avaliação do padrão de participação em atividades de lazer de crianças e jovens com e sem incapacidade nos seus contextos imediatos

O objetivo deste estudo foi avaliar o padrão de participação em atividades de lazer, formais e informais, de crianças e jovens com e sem incapacidade nos seus contextos imediatos – em casa, “fora de casa”, e na escola. Usamos uma adaptação do instrumento CAPE - Children’s Assessment of Participation and Enjoyment e CAP - Preferences for Activities of Children, originalmente desenvolvido no Canadá por King e seus colaboradores (2004). Participaram neste estudo 56 alunos – 19 com incapacidades e 37 sem incapacidades – de dez turmas dos três ciclos de educação básica com idades compreendidas entre os 7 e 16 anos de idade. Os resultados deste estudo revelaram que, ao nível da diversidade, apenas no contexto “fora de casa” existem diferenças significativas, isto é, as crianças/jovens com incapacidade participam em menos atividades – no total, em atividades formais, em atividades físicas e de autoaperfeiçoamento. Também se verificou existência de diferenças no padrão de participação ao nível da intensidade, com as crianças e jovens com incapacidades a reportarem uma participação mais limitada mas maiores índices nos contextos em casa e na escola. No contexto “escola”, os alunos com incapacidades participam em atividades com significativa menor dimensão social. No entanto, em relação ao nível de satisfação, verificámos que não existem diferenças. No que diz respeito à dimensão preferência verificamos que está positivamente relacionada com o padrão de participação. A consideração de outras características pessoais como a idade e o sexo poderá enriquecer este estudo, bem como a aplicação deste estudo a amostras mais representativas.

Archaeometallurgical study of artefacts from Castro de Vila Nova de São Pedro (Azambuja, Portugal)

Dissertação para obtenção do Grau de Mestre em Conservação e Restauro

Projecto de Expansão do ContiSeal

Com o crescente aumento na procura de pneus com maior capacidade de mobilidade, como é caso dos pneus ContiSeal, a Continental AG iniciou um projecto de expansão da unidade industrial portuguesa onde a tecnologia ContiSeal é aplicada, projecto esse a ser desenvolvido pela Continental Mabor. Na prossecução deste projecto são necessárias diversas áreas de conhecimento da gestão industrial, nomeadamente: a análise dos fluxos produtivos, o cálculo de capacidade e respectiva análise de tempos perdidos, análise e projecto de layouts e a produção de propostas de optimização tanto ao nível de equipamentos como do fluxo produtivo. Na realização deste projecto foi necessário estudar profundamente a unidade produtiva em questão. O estudo foi realizado aos diversos subprocessos do ContiSeal, na qual a recolha e análise de dados estão fundamentadas através de extensos levantamentos obtidos por amostragem. Estes dados são vitais para uma correcta análise de custos de investimento na aquisição de novos equipamentos, sendo estes necessários para o cumprimento dos objectivos propostos para a expansão do ContiSeal. O início do projecto incidiu no estudo detalhado sobre os ciclos produtivos dos equipamentos e no levantamento e registo dos tempos perdidos da unidade industrial, que permitiu a análise das capacidades instaladas dos vários subprocessos. Após o levantamento das capacidades foram determinadas as necessidades relativas à aquisição de novos equipamentos. De notar que alguns protótipos de equipamentos necessários foram desenvolvidos em parceria com fornecedores seleccionados, assim como foram apresentadas propostas de melhoria aos equipamentos já existentes. Uma vez aprovada a aquisição dos novos equipamentos pela Continental AG, deu-se início ao desenvolvimento da expansão do layout do ContiSeal, tanto ao nível do edifício como de novos equipamentos e ainda do fluxo dos pneus com vista à sua optimização.

Antigenic typing of brazilian rabies virus samples isolated from animals and humans, 1989-2000

Animal and human rabies samples isolated between 1989 and 2000 were typified by means of a monoclonal antibody panel against the viral nucleoprotein. The panel had been previously established to study the molecular epidemiology of rabies virus in the Americas. Samples were isolated in the Diagnostic Laboratory of the Pasteur Institute and in other rabies diagnostic centers in Brazil. In addition to the fixed virus samples CVS-31/96-IP, preserved in mouse brain, and PV-BHK/97, preserved in cell culture, a total of 330 rabies virus samples were isolated from dogs, cats, cattle, horses, bats, sheep, goat, swine, foxes, marmosets, coati and humans. Six antigenic variants that were compatible with the pre-established monoclonal antibodies panel were defined: numbers 2 (dog), 3 (Desmodus rotundus), 4 (Tadarida brasiliensis), 5 (vampire bat from Venezuela), 6 (Lasiurus cinereus) and Lab (reacted to all used antibodies). Six unknown profiles, not compatible with the panel, were also found. Samples isolated from insectivore bats showed the greatest variability and the most commonly isolated variant was variant-3 (Desmodus rotundus). These findings may be related to the existence of multiple independent transmission cycles, involving different bat species.

Oral transmission of Chagas disease: importance of Trypanosoma cruzi biodeme in the intragastric experimental infection

Oral transmission of Trypanosoma cruzi has been suspected when epidemic episodes of acute infection were observed in areas devoid of domiciled insect vectors. Considering that the distribution of T. cruzi biodemes differs in sylvatic and domestic cycles, results of studies on biodemes can be of interest regarding oral transmission. The infectivity of T. cruzi strains of different biodemes was tested in mice subjected to infection by the digestive route (gavage). Swiss mice were infected either with the Peruvian strain (Biodeme Type I, Z2b) or the Colombian strain (Biodeme Type III, Z1, or T. cruzi I); for control, intraperitoneal inoculation was performed in a group of mice. The Colombian strain revealed a similar high infectivity and pathogenicity when either route of infection was used. However, the Peruvian strain showed contrasting levels of infectivity and pathogenicity, being high by intraperitoneal inoculation and low when the gastric route was used. The higher infectivity of the Colombian strain (Biodeme Type III) by gastric inoculation is in keeping with its role in the epidemic episodes of acute Chagas disease registered in the literature, since strains belonging to Biodeme III are most often found in sylvatic hosts.

Aquaponics System - An EPS@ISEP 2014 Spring Project

The goal of this project, one of the proposals of the EPS@ISEP 2014 Spring, was to develop an Aquaponics System. Over recent years Aquaponics systems have received increased attention due to its possibilities in helping reduce strain on resources within 1st and 3rd world countries. Aquaponics is the combination of Hydroponics and Aquaculture and mimics a natural environment in order to successfully apply and enhance the understanding of natural cycles within an indoor process. By using this knowledge of natural cycles it was possible to create a system with the capabilities similar to that of a natural environment with the benefits of electronic adaptions to enhance the overall efficiency of the system. The multinational team involved in its development was composed of five students, from five countries and fields of study. This paper covers their solution, involving overall design, the technology involved and the benefits it could bring to the current market. The team was able to achieve the final rendered Computer Aided Design (CAD) drawings, successfully performed all the electronic testing, and designed a solution under budget. Furthermore, the solution presented was deeply studied from the sustainability viewpoint and the team also developed a product specific marketing plan. Finally, the students involved in this project obtained new knowledge and skills.

A novel antibody-like material for breast cancer antigen CA15-3, used to track breast cancer by potentiometric transduction

This work presents the development of a low cost sensor device for the diagnosis of breast cancer in point-of-care, made with new synthetic biomimetic materials inside plasticized poly(vinyl chloride), PVC, membranes, for subsequent potentiometric detection. This concept was applied to target a conventional biomarker in breast cancer: Breast Cancer Antigen (CA15-3). The new biomimetic material was obtained by molecularly-imprinted technology. In this, a plastic antibody was obtained by polymerizing around the biomarker that acted as an obstacle to the growth of the polymeric matrix. The imprinted polymer was specifically synthetized by electropolymerization on an FTO conductive glass, by using cyclic voltammetry, including 40 cycles within -0.2 and 1.0 V. The reaction used for the polymerization included monomer (pyrrol, 5.0×10-3 mol/L) and protein (CA15-3, 100U/mL), all prepared in phosphate buffer saline (PBS), with a pH of 7.2 and 1% of ethylene glycol. The biomarker was removed from the imprinted sites by proteolytic action of proteinase K. The biomimetic material was employed in the construction of potentiometric sensors and tested with regard to its affinity and selectivity for binding CA15-3, by checking the analytical performance of the obtained electrodes. For this purpose, the biomimetic material was dispersed in plasticized PVC membranes, including or not a lipophilic ionic additive, and applied on a solid conductive support of graphite. The analytical behaviour was evaluated in buffer and in synthetic serum, with regard to linear range, limit of detection, repeatability, and reproducibility. This antibody-like material was tested in synthetic serum, and good results were obtained. The best devices were able to detect 5 times less CA15-3 than that required in clinical use. Selectivity assays were also performed, showing that the various serum components did not interfere with this biomarker. Overall, the potentiometric-based methods showed several advantages compared to other methods reported in the literature. The analytical process was simple, providing fast responses for a reduced amount of analyte, with low cost and feasible miniaturization. It also allowed the detection of a wide range of concentrations, diminishing the required efforts in previous sample pre-treating stages.

Fractional order describing functions

This paper addresses limit cycles and signal propagation in dynamical systems with backlash. The study follows the describing function (DF) method for approximate analysis of nonlinearities and generalizes it in the perspective of the fractional calculus. The concept of fractional order describing function (FDF) is illustrated and the results for several numerical experiments are analysed. FDF leads to a novel viewpoint for limit cycle signal propagation as time-space waves within system structure.