Biomarkers in Solea Senegalensis Kaup, 1858 exposed to contaminated estuarine sediments: a multi-level approach

Thesis submitted to the Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia for the degree of Doctor of Philosophy in Environmental Sciences

Multi-scale vegetation classification using earth observation data of the Sundarban mangrove forest, Bangladesh.

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies.

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

Identification of Toxoplasma gondii antigens involved in the IgM AND IgG indirect hemagglutination tests for the diagnosis of toxoplasmosis

Crude Toxoplasma gondii antigens represent raw material used to prepare reagents to be employed in different serologic tests for the diagnosis of toxoplasmosis, including the IgM and IgG indirect hemagglutination (IgG-HA and IgM-HA) tests. So far, the actual antigenic molecules of the parasite involved in the interaction with agglutinating anti-T. gondii antibodies in these tests are unknown. The absorption process of serum samples from toxoplasmosis patients with the IgG-HA reagent (G-toxo-HA) demonstrated that red cells from this reagent were coated with T. gondii antigens with Mr of 39, 35, 30, 27, 22 and 14 kDa. The immune-absorption process with the IgM-HA reagent (M-toxo-HA), in turn, provided antibody eluates which recognized antigenic bands of the parasite corresponding to Mr of 54, 35 and 30 kDa, implying that these antigens are coating red cells from this reagent. The identification of most relevant antigens for each type of HA reagent seems to be useful for the inspection of the raw antigenic material, as well as of reagent batches routinely produced. Moreover the present findings can be used to modify these reagents in order to improve the performance of HA tests for the diagnosis of toxoplasmosis

Multi-agent Simulation of Bilateral Contracting in Competitive Electricity Markets

Traditional vertically integrated power utilities around the world have evolved from monopoly structures to open markets that promote competition among suppliers and provide consumers with a choice of services. Market forces drive the price of electricity and reduce the net cost through increased competition. Electricity can be traded in both organized markets or using forward bilateral contracts. This article focuses on bilateral contracts and describes some important features of an agent-based system for bilateral trading in competitive markets. Special attention is devoted to the negotiation process, demand response in bilateral contracting, and risk management. The article also presents a case study on forward bilateral contracting: a retailer agent and a customer agent negotiate a 24h-rate tariff.

Realistic Multi-Agent Simulation of Competitive Electricity Markets

The dynamism and ongoing changes that the electricity markets sector is constantly suffering, enhanced by the huge increase in competitiveness, create the need of using simulation platforms to support operators, regulators, and the involved players in understanding and dealing with this complex environment. This paper presents an enhanced electricity market simulator, based on multi-agent technology, which provides an advanced simulation framework for the study of real electricity markets operation, and the interactions between the involved players. MASCEM (Multi-Agent Simulator of Competitive Electricity Markets) uses real data for the creation of realistic simulation scenarios, which allow the study of the impacts and implications that electricity markets transformations bring to different countries. Also, the development of an upper-ontology to support the communication between participating agents, provides the means for the integration of this simulator with other frameworks, such as MAN-REM (Multi-Agent Negotiation and Risk Management in Electricity Markets). A case study using the enhanced simulation platform that results from the integration of several systems and different tools is presented, with a scenario based on real data, simulating the MIBEL electricity market environment, and comparing the simulation performance with the real electricity market results.

Data Mining Approach to support the Generation of Realistic Scenarios for Multi-Agent simulation of Electricity Markets

This paper presents the Realistic Scenarios Generator (RealScen), a tool that processes data from real electricity markets to generate realistic scenarios that enable the modeling of electricity market players’ characteristics and strategic behavior. The proposed tool provides significant advantages to the decision making process in an electricity market environment, especially when coupled with a multi-agent electricity markets simulator. The generation of realistic scenarios is performed using mechanisms for intelligent data analysis, which are based on artificial intelligence and data mining algorithms. These techniques allow the study of realistic scenarios, adapted to the existing markets, and improve the representation of market entities as software agents, enabling a detailed modeling of their profiles and strategies. This work contributes significantly to the understanding of the interactions between the entities acting in electricity markets by increasing the capability and realism of market simulations.

Distributed Intelligent Management of Microgrids using a Multi-Agent Simulation Platform

Multi-agent approaches have been widely used to model complex systems of distributed nature with a large amount of interactions between the involved entities. Power systems are a reference case, mainly due to the increasing use of distributed energy sources, largely based on renewable sources, which have potentiated huge changes in the power systems’ sector. Dealing with such a large scale integration of intermittent generation sources led to the emergence of several new players, as well as the development of new paradigms, such as the microgrid concept, and the evolution of demand response programs, which potentiate the active participation of consumers. This paper presents a multi-agent based simulation platform which models a microgrid environment, considering several different types of simulated players. These players interact with real physical installations, creating a realistic simulation environment with results that can be observed directly in the reality. A case study is presented considering players’ responses to a demand response event, resulting in an intelligent increase of consumption in order to face the wind generation surplus.

PCR in the First Oropharynx Aspirate of the Newborn: A Possible Source for Identification of Congenital Infection Agents

We present a case of prenatal diagnosis of congenital rubella. After birth, in addition to traditional serologic and clinical examinations to confirm the infection, we could identify the virus in the "first fluid aspirated from the oropharynx of the newborn", using polimerase chain reaction (PCR). We propose that this first oropharynx fluid (collected routinely immediately after birth) could be used as a source for identification of various congenital infection agents, which may not always be easily identified by current methods

Sistema de apoio à navegação baseado em automatic identification system

Dissertação de Mestrado Integrado em Engenharia Electrotécnica e Computadores

Diagnosis of plague and identification of virulence markers in Yersinia pestis by multiplex-PCR

We have developed a procedure for the rapid diagnosis of plague that also allows the identification of prominent virulence markers of Y. pestis strains. This procedure is based upon the use of a single polymerase chain reaction with multiple pairs of primers directed at genes present in the three virulence plasmids as well as in the chromosomal pathogenicity island of the bacterium. The technique allowed the discrimination of strains which lacked one or more of the known pathogenic loci, using as template total DNA obtained from bacterial cultures and from simulated blood cultures containing diluted concentration of bacteria. It also proved effective in confirming the disease in a blood culture from a plague suspected patient. As the results are obtained in a few hours this technique will be useful in the methodology of the Plague Control Program.

Identification of risk factors for death from tetanus in Pernambuco, Brazil: a case-control study

A case-control study was conducted to identify risk factors for death from tetanus in the State of Pernambuco, Brazil. Information was obtained from medical records of 152 cases and 152 controls, admitted to the tetanus unit in the State University Hospital, in Recife, from 1990 to 1995. Variables were grouped in three different sets. Crude and adjusted odds ratios, p-values and 95% confidence intervals were estimated. Variables selected in the multivariate analysis in each set were controlled for the effect of those selected in the others. All factors related to the disease progression - incubation period, time elapsed between the occurrence of the first tetanus symptom and admission, and period of onset - showed a statistically significant association with death from tetanus. Similarly, signs and/or symptoms occurring on admission or in the following 24 hours (second set): reflex spasms, neck stiffness, respiratory signs/symptoms and respiratory failure requiring artificial ventilation (third set) were associated with death from tetanus even when adjusted for the effect of the others.

hsp65 PCR-restriction enzyme analysis (PRA) for identification of mycobacteria in the clinical laboratory

More than 70 species of mycobacteria have been defined, and some can cause disease in humans, especially in immunocompromised patients. Species identification in most clinical laboratories is based on phenotypic characteristics and biochemical tests and final results are obtained only after two to four weeks. Quick identification methods, by reducing time for diagnosis, could expedite institution of specific treatment, increasing chances of success. PCR restriction-enzyme analysis (PRA) of the hsp65 gene was used as a rapid method for identification of 103 clinical isolates. Band patterns were interpreted by comparison with published tables and patterns available at an Internet site (http://www.hospvd.ch:8005). Concordant results of PRA and biochemical identification were obtained in 76 out of 83 isolates (91.5%). Results from 20 isolates could not be compared due to inconclusive PRA or biochemical identification. The results of this work showed that PRA could improve identification of mycobacteria in a routine setting because it is accurate, fast, and cheaper than conventional phenotypic identification.

Análise de Integridade Estrutural de uma Flare Industrial

Para garantir que um equipamento opere com segurança e fiabilidade durante o seu ciclo de vida, desde a sua instalação ao desmantelamento, devem ser realizadas inspeções e/ou monitorizações que, dependendo dos dados recolhidos, podem implicar avaliações Fitness- For-Service (FFS) que definirão a necessidade de reparação ou alteração do equipamento ou das condições processuais. A combinação de inspeção ou monitorização com os melhores procedimentos e técnicas de avaliação atuais fazem sobressair insuficiências dos procedimentos mais antigos. Usando métodos mais avançados de avaliação, validados e suportados através de uma vasta experiência de campo, pode-se agora avaliar defeitos nos ativos (equipamentos) e determinar a adequação ao serviço com uma análise FFS. As análises FFS tornaram-se cada vez mais aceites em toda a indústria ao longo dos últimos anos. A norma API 579 - 1/ASME FFS-1: 2007 fornece diretrizes para avaliar os tipos de danos que afetam os equipamentos processuais e a norma API RP 571: 2011 descreve os mecanismos de degradação que afetam os equipamentos nas petroquímicas e refinarias, que incluem os danos por corrosão, desalinhamentos, deformações plásticas, laminações, fissuras, entre outros. Este trabalho consiste na análise de Integridade Estrutural de uma Flare Industrial que surgiu da necessidade real de análise do equipamento no âmbito da atividade profissional do candidato. O estudo realizado a nível profissional é de grande abrangência, incluindo a inspeção do equipamento, identificação da falha ou dano, recolha e registo de dados, definição de estratégia de atuação e seleção de técnicas de avaliação da condição para posterior alteração, reparação ou desmantelamento. Na presente dissertação de mestrado em Engenharia Mecânica, Ramo Construções Mecânicas, pretende-se efetuar o estudo aprofundado de uma das etapas de projeto, nomeadamente estudar a causa, avaliar a falha e implicações estruturais ou processuais devido à degradação interior do riser de uma flare, com base numa análise FFS, assumindo a operabilidade em segurança e garantindo resolutas condições de funcionamento. A presente análise FFS tem como finalidade validar ou não a integridade atual (avaliação técnica quantitativa) de modo a conhecer se o item em questão é seguro e confiável para continuar a operar em condições específicas durante um período de tempo determinado, tendo em consideração as condições verificadas no ato de inspeção e especificações de projeto, segundo os itens de verificação de segurança estabelecidos na norma EN 1990:2002/A1:2005/AC:2010 e com base na norma API 579-1/ASME FFS-1: 2007. No âmbito do presente trabalho foram realizadas as seguintes tarefas: - Identificar e analisar os mecanismos de degradação com base na norma API RP 571: 2011, face às condições processuais e geométricas que o equipamento em análise está sujeito de modo a perceber a evolução da degradação estrutural e quais as implicações na sua longevidade. - Avaliar e propor soluções de reparação e ou alterações processuais e ou geométricas do equipamento em análise de modo a permitir a continuidade em funcionamento sem afetar as condições de segurança e por conseguinte minimizar ou evitar o elevado custo económico associado a um novo equipamento e tempo de paragem processual. - Assumir limites estruturais face às condições processuais e ações externas ou adjacentes. - Garantir a segurança e qualidade da vida humana ou meio que o rodeia, do equipamento, das instalações, das infraestruturas envolventes e evitar o colapso económico, quer por motivos processuais, quer indeminizações ou agravamento do prémio do seguro. Verificou-se que os resultados serão a base para as alterações inerentes, tais como reforço estrutural, alteração da geometria do defletor, ajuste no tensionamento dos cabos e controlo da espessura mínima, de modo a alargar o período de vida útil da flare com segurança.