ß-lactamases in the biochemistry and molecular biology laboratory

β-lactamases are hydrolytic enzymes that inactivate the β-lactam ring of antibiotics such as penicillins and cephalosporins. The major diversity of studies carried out until now have mainly focused on the characterization of β-lactamases recovered among clinical isolates of Gram-positive staphylococci and Gram-negative enterobacteria, amongst others. However, only some studies refer to the detection and development of β-lactamases carriers in healthy humans, sick animals, or even in strains isolated from environmental stocks such as food, water, or soils. Considering this, we proposed a 10-week laboratory programme for the Biochemistry and Molecular Biology laboratory for majors in the health, environmental, and agronomical sciences. During those weeks, students would be dealing with some basic techniques such as DNA extraction, bacterial transformation, polymerase chain reaction (PCR), gel electrophoresis, and the use of several bioinformatics tools. These laboratory exercises would be conducted as a mini research project in which all the classes would be connected with the previous ones. This curriculum was compared in an experiment involving two groups of students from two different majors. The new curriculum, with classes linked together as a mini research project, was taught to a major in Pharmacy and an old curriculum was taught to students from environmental health. The results showed that students who were enrolled in the new curriculum obtained better results in the final exam than the students who were enrolled in the former curriculum. Likewise, these students were found to be more enthusiastic during the laboratory classes than those from the former curriculum.

An ultrasound based computer-aided diagnosis tool for steatosis detection

Liver steatosis is a common disease usually associated with social and genetic factors. Early detection and quantification is important since it can evolve to cirrhosis. In this paper, a new computer-aided diagnosis (CAD) system for steatosis classification, in a local and global basis, is presented. Bayes factor is computed from objective ultrasound textural features extracted from the liver parenchyma. The goal is to develop a CAD screening tool, to help in the steatosis detection. Results showed an accuracy of 93.33%, with a sensitivity of 94.59% and specificity of 92.11%, using the Bayes classifier. The proposed CAD system is a suitable graphical display for steatosis classification.

First report of ciguatoxins in two starfish species : Ophidiaster ophidianus and Marthasterias glacialis

Ciguatera fish poisoning (CFP) is a syndrome caused by the ingestion of fish contaminated with Ciguatoxins (CTXs). These phycotoxins are produced mainly by dinoflagellates that belong to the genus Gambierdiscus that are transformed in more toxic forms in predatory fish guts, and are more present in the Indo-Pacific and Caribbean areas. It is estimated that CFP causes per year more than 10,000 intoxications worldwide. With the rise of water temperature and anthropogenic intervention, it is important to study the prevalence of CFP in more temperate waters. Through inter- and subtidal sampling, 22 species of organisms were collected, in Madeira and Azores archipelagos and in the northwestern Moroccan coast, during September of 2012 and June and July of 2013. A total of 94 samples of 22 different species of bivalves, gastropods, echinoderms and crustaceans where analyzed by Ultra Performance Liquid Chromatography-Mass Spectometry-Ion Trap-Time of Flight (UPLC-MS-IT-TOF) and Ultra Performance Chromatography- Mass Spectrometry (UPLC-MS). Our main aim was to detect new vectors and ascertain if there were some geographical differences. We detected for the first time putative CTXs in echinoderms, in two starfish species—M. glacialis and O. ophidianus. We detected differences regarding uptake values by organisms and geographical location. Toxin amounts were significant, showing the importance and the need for continuity of these studies to gain more knowledge about the prevalence of these toxins, in order to better access human health risk. In addition, we suggest monitoring of these toxins should be extended to other vectors, starfish being a good alternative for protecting and accessing human health risk.

Quantification of endocrine disruptors and pesticides in water by gas chromatography–tandem mass spectrometry. Method validation using weighted linear regression schemes

Amulti-residue methodology based on a solid phase extraction followed by gas chromatography–tandem mass spectrometry was developed for trace analysis of 32 compounds in water matrices, including estrogens and several pesticides from different chemical families, some of them with endocrine disrupting properties. Matrix standard calibration solutions were prepared by adding known amounts of the analytes to a residue-free sample to compensate matrix-induced chromatographic response enhancement observed for certain pesticides. Validation was done mainly according to the International Conference on Harmonisation recommendations, as well as some European and American validation guidelines with specifications for pesticides analysis and/or GC–MS methodology. As the assumption of homoscedasticity was not met for analytical data, weighted least squares linear regression procedure was applied as a simple and effective way to counteract the greater influence of the greater concentrations on the fitted regression line, improving accuracy at the lower end of the calibration curve. The method was considered validated for 31 compounds after consistent evaluation of the key analytical parameters: specificity, linearity, limit of detection and quantification, range, precision, accuracy, extraction efficiency, stability and robustness.

Spatial analysis of leprosy incidence and associated socioeconomic factors

OBJECTIVE: To identify clusters of the major occurrences of leprosy and their associated socioeconomic and demographic factors. METHODS: Cases of leprosy that occurred between 1998 and 2007 in São José do Rio Preto (southeastern Brazil) were geocodified and the incidence rates were calculated by census tract. A socioeconomic classification score was obtained using principal component analysis of socioeconomic variables. Thematic maps to visualize the spatial distribution of the incidence of leprosy with respect to socioeconomic levels and demographic density were constructed using geostatistics. RESULTS: While the incidence rate for the entire city was 10.4 cases per 100,000 inhabitants annually between 1998 and 2007, the incidence rates of individual census tracts were heterogeneous, with values that ranged from 0 to 26.9 cases per 100,000 inhabitants per year. Areas with a high leprosy incidence were associated with lower socioeconomic levels. There were identified clusters of leprosy cases, however there was no association between disease incidence and demographic density. There was a disparity between the places where the majority of ill people lived and the location of healthcare services. CONCLUSIONS: The spatial analysis techniques utilized identified the poorer neighborhoods of the city as the areas with the highest risk for the disease. These data show that health departments must prioritize politico-administrative policies to minimize the effects of social inequality and improve the standards of living, hygiene, and education of the population in order to reduce the incidence of leprosy.

Taxonomy of fundamental concepts of localization in cyber-physical and sensor networks

Localization is a fundamental task in Cyber-Physical Systems (CPS), where data is tightly coupled with the environment and the location where it is generated. The research literature on localization has reached a critical mass, and several surveys have also emerged. This review paper contributes on the state-of-the-art with the proposal of a new and holistic taxonomy of the fundamental concepts of localization in CPS, based on a comprehensive analysis of previous research works and surveys. The main objective is to pave the way towards a deep understanding of the main localization techniques, and unify their descriptions. Furthermore, this review paper provides a complete overview on the most relevant localization and geolocation techniques. Also, we present the most important metrics for measuring the accuracy of localization approaches, which is meant to be the gap between the real location and its estimate. Finally, we present open issues and research challenges pertaining to localization. We believe that this review paper will represent an important and complete reference of localization techniques in CPS for researchers and practitioners and will provide them with an added value as compared to previous surveys.

Aplicação de redes neuronais artificiais à deteção e isolamento de falhas em processos industriais

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Mecânica

Molecular diversity of bla genes in Klebsiella pneumoniae and Escherichia coli isolates

Dissertation presented to obtain a Ph.D. degree in Biology, speciality Microbiology, by Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Temporal trends in the prevalence of asthma and rhinoconjunctivitis in adolescents

ABSTRACT OBJECTIVE To analyze the temporal trend of asthma and rhinoconjunctivitis prevalences as well as their symptoms in adolescents. METHODS Two cross-sectional studies were conducted using the same methodology and questionnaire as was used for adolescents aged 12 to 14 years in the Brazilian city of Florianopolis, SC, Southern Brazil. Based on the international protocol of the International Study of Asthma and Allergies in Childhood (ISAAC) study, adolescents were evaluated in 2001 and 3,150 in 2012. The schools included in this study were the same as in the 2001 study. These schools were randomly selected after stratification by network (public and private) and geographic location. The total average percentage variation was estimated for the prevalence of asthma and rhinoconjunctivitis and their symptoms. RESULTS The prevalence of reported asthma was 10.9% in 2001 and 14.8% in 2012, with an average variation of 2.8% in the period. The highest average variation in the period was observed among female adolescents (4.1%). In parallel a significant increase occurred in reported physician-diagnosed asthma, 7.3% in 2001 and 11,1% in 2012, with an annual variation of 4.5%. The largest increases in reported physician-diagnosed asthma were seen in female (5.9%) and male (4.5%) public school pupils. In addition, a significant increase in reported rhinoconjunctivitis occurred, with the average variation in the period being 5.2%. Reports of severe asthma symptoms remained unchanged during the period, while the annual variation for reported current wheezing (-1.3%) and wheezing during exercise (-1.2%) decreased. CONCLUSIONS The results showed a significant increase in the annual average variation for asthma and rhinoconjunctivitis prevalence during the 2001 to 2012 period.

The 1998 Faial earthquake, Azores: Evidence for a transform fault associated with the Nubia-Eurasia plate boundary?

With very few exceptions, M > 4 tectonic earthquakes in the Azores show normal fault solution and occur away from the islands. Exceptionally, the 1998 shock was pure strike-slip and occurred within the northern edge of the Pico-Faial Ridge. Fault plane solutions show two possible planes of rupture striking ENE-WSW (dextral) and NNW-SSE (sinistral). The former has not been recognised in the Azores, but is parallel to the transform direction related to the relative motion between the Eurasia and Nubia plates. Therefore, the main question we address in the present study is: do transform faults related to the Eurasia/Nubia plate boundary exist in the Azores? Knowing that the main source of strain is related to plate kinematics, we conclude that the sinistral strike-slip NNW-SSE fault plane solution is not consistent with either the fault dip (ca. 65, which is typical of a normal fault) or the ca. ENE-WSW direction of maximum extension; both are consistent with a normal fault, as observed in most major earthquakes on faults striking around NNW-SSE in the Azores. In contrast, the dextral strike-slip ENE-WSW fault plane solution is consistent with the transform direction related to the anticlockwise rotation of Nubia relative to Eurasia. Altogether, tectonic data, measured ground motion, observed destruction, and modelling are consistent with a dextral strike-slip source fault striking ENE-WSW. Furthermore, the bulk clockwise rotation measured by GPS is typical of bookshelf block rotations observed at the termination of such master strike-slip faults. Therefore, we suggest that the 1998 earthquake can be related to the WSW termination of a transform (ENE-WSW fault plane solution) associated with the Nubia-Eurasia diffuse plate boundary. (C) 2014 Elsevier B.V. All rights reserved.

Real time fault injection using a modified debugging infrastructure

Dependability is a critical factor in computer systems, requiring high quality validation & verification procedures in the development stage. At the same time, digital devices are getting smaller and access to their internal signals and registers is increasingly complex, requiring innovative debugging methodologies. To address this issue, most recent microprocessors include an on-chip debug (OCD) infrastructure to facilitate common debugging operations. This paper proposes an enhanced OCD infrastructure with the objective of supporting the verification of fault-tolerant mechanisms through fault injection campaigns. This upgraded on-chip debug and fault injection (OCD-FI) infrastructure provides an efficient fault injection mechanism with improved capabilities and dynamic behavior. Preliminary results show that this solution provides flexibility in terms of fault triggering and allows high speed real-time fault injection in memory elements

Real time fault injection using enhanced OCD -- a performance analysis

Fault injection is frequently used for the verification and validation of dependable systems. When targeting real time microprocessor based systems the process becomes significantly more complex. This paper proposes two complementary solutions to improve real time fault injection campaign execution, both in terms of performance and capabilities. The methodology is based on the use of the on-chip debug mechanisms present in modern electronic devices. The main objective is the injection of faults in microprocessor memory elements with minimum delay and intrusiveness. Different configurations were implemented and compared in terms of performance gain and logic overhead.

Unified cooperative location system

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do Grau de Mestre em Engenharia Informática.

Hand gesture recognition system based in computer vision and machine learning : applications on human-machine interaction

Sendo uma forma natural de interação homem-máquina, o reconhecimento de gestos implica uma forte componente de investigação em áreas como a visão por computador e a aprendizagem computacional. O reconhecimento gestual é uma área com aplicações muito diversas, fornecendo aos utilizadores uma forma mais natural e mais simples de comunicar com sistemas baseados em computador, sem a necessidade de utilização de dispositivos extras. Assim, o objectivo principal da investigação na área de reconhecimento de gestos aplicada à interacção homemmáquina é o da criação de sistemas, que possam identificar gestos específicos e usálos para transmitir informações ou para controlar dispositivos. Para isso as interfaces baseados em visão para o reconhecimento de gestos, necessitam de detectar a mão de forma rápida e robusta e de serem capazes de efetuar o reconhecimento de gestos em tempo real. Hoje em dia, os sistemas de reconhecimento de gestos baseados em visão são capazes de trabalhar com soluções específicas, construídos para resolver um determinado problema e configurados para trabalhar de uma forma particular. Este projeto de investigação estudou e implementou soluções, suficientemente genéricas, com o recurso a algoritmos de aprendizagem computacional, permitindo a sua aplicação num conjunto alargado de sistemas de interface homem-máquina, para reconhecimento de gestos em tempo real. A solução proposta, Gesture Learning Module Architecture (GeLMA), permite de forma simples definir um conjunto de comandos que pode ser baseado em gestos estáticos e dinâmicos e que pode ser facilmente integrado e configurado para ser utilizado numa série de aplicações. É um sistema de baixo custo e fácil de treinar e usar, e uma vez que é construído unicamente com bibliotecas de código. As experiências realizadas permitiram mostrar que o sistema atingiu uma precisão de 99,2% em termos de reconhecimento de gestos estáticos e uma precisão média de 93,7% em termos de reconhecimento de gestos dinâmicos. Para validar a solução proposta, foram implementados dois sistemas completos. O primeiro é um sistema em tempo real capaz de ajudar um árbitro a arbitrar um jogo de futebol robótico. A solução proposta combina um sistema de reconhecimento de gestos baseada em visão com a definição de uma linguagem formal, o CommLang Referee, à qual demos a designação de Referee Command Language Interface System (ReCLIS). O sistema identifica os comandos baseados num conjunto de gestos estáticos e dinâmicos executados pelo árbitro, sendo este posteriormente enviado para um interface de computador que transmite a respectiva informação para os robôs. O segundo é um sistema em tempo real capaz de interpretar um subconjunto da Linguagem Gestual Portuguesa. As experiências demonstraram que o sistema foi capaz de reconhecer as vogais em tempo real de forma fiável. Embora a solução implementada apenas tenha sido treinada para reconhecer as cinco vogais, o sistema é facilmente extensível para reconhecer o resto do alfabeto. As experiências também permitiram mostrar que a base dos sistemas de interação baseados em visão pode ser a mesma para todas as aplicações e, deste modo facilitar a sua implementação. A solução proposta tem ainda a vantagem de ser suficientemente genérica e uma base sólida para o desenvolvimento de sistemas baseados em reconhecimento gestual que podem ser facilmente integrados com qualquer aplicação de interface homem-máquina. A linguagem formal de definição da interface pode ser redefinida e o sistema pode ser facilmente configurado e treinado com um conjunto de gestos diferentes de forma a serem integrados na solução final.

A self-healing real-time system based on run-time self-reconfiguration

The new generations of SRAM-based FPGA (field programmable gate array) devices are the preferred choice for the implementation of reconfigurable computing platforms intended to accelerate processing in real-time systems. However, FPGA's vulnerability to hard and soft errors is a major weakness to robust configurable system design. In this paper, a novel built-in self-healing (BISH) methodology, based on run-time self-reconfiguration, is proposed. A soft microprocessor core implemented in the FPGA is responsible for the management and execution of all the BISH procedures. Fault detection and diagnosis is followed by repairing actions, taking advantage of the dynamic reconfiguration features offered by new FPGA families. Meanwhile, modular redundancy assures that the system still works correctly