Protein folding, metal ions and conformational states: the case of a di-cluster ferredoxin

Dissertation presented to obtain the PhD degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Towards high-available and energy-efficient virtual computing environments in the cloud

Empowered by virtualisation technology, cloud infrastructures enable the construction of flexi- ble and elastic computing environments, providing an opportunity for energy and resource cost optimisation while enhancing system availability and achieving high performance. A crucial re- quirement for effective consolidation is the ability to efficiently utilise system resources for high- availability computing and energy-efficiency optimisation to reduce operational costs and carbon footprints in the environment. Additionally, failures in highly networked computing systems can negatively impact system performance substantially, prohibiting the system from achieving its initial objectives. In this paper, we propose algorithms to dynamically construct and readjust vir- tual clusters to enable the execution of users’ jobs. Allied with an energy optimising mechanism to detect and mitigate energy inefficiencies, our decision-making algorithms leverage virtuali- sation tools to provide proactive fault-tolerance and energy-efficiency to virtual clusters. We conducted simulations by injecting random synthetic jobs and jobs using the latest version of the Google cloud tracelogs. The results indicate that our strategy improves the work per Joule ratio by approximately 12.9% and the working efficiency by almost 15.9% compared with other state-of-the-art algorithms.

The impact of the 2008 and 2010 financial crises on international stock markets : contagion and long memory

Nesta tese estudamos os efeitos de contágio financeiro e de memória longa causados pelas crises financeiras de 2008 e 2010 em alguns mercados acionistas internacionais. A tese é composta por três ensaios interligados. No Ensaio 1, recorremos à teoria das cópulas para testar a existência de contágio e revelar os canais “investor induced” de transmissão da crise de 2008 aos mercados da Bélgica, França, Holanda e Portugal (grupo NYSE Euronext). Concluímos que existe contágio nestes mercados, que o canal “portfolio rebalancing” é o mecanismo mais importante de transmissão da crise, e que o fenómeno “flight to quality” está presente nos mercados. No Ensaio 2, usando novamente modelos de cópulas, avaliamos os efeitos de contágio provocados pelo mercado acionista grego nos mercados do grupo NYSE Euronext, no contexto da crise de 2010. Os resultados obtidos sugerem que durante a crise de 2010 apenas o mercado português foi objeto de contágio; além disso, conclui-se que os efeitos de contágio provocados pela crise de 2008 são claramente superiores aos efeitos provocados pela crise de 2010. No Ensaio 3, abordamos o tema da memória longa através do estudo do expoente de Hurst dos mercados acionistas da Bélgica, E.U.A., França, Grécia, Holanda, Japão, Reino Unido e Portugal. Verificamos que as propriedades de memória longa dos mercados foram afetadas pelas crises, especialmente a de 2008 – que aumentou a memória longa dos mercados e tornou-os mais persistentes. Finalmente, usando cópulas mais uma vez, verificamos que as crises provocaram, em geral, um aumento na correlação entre os expoentes de Hurst locais dos mercados foco das crises (E.U.A. e Grécia) e os expoentes de Hurst locais dos outros mercados da amostra, sugerindo que o expoente de Hurst pode ser utilizado para detetar efeitos de contágio financeiro. Em síntese, os resultados desta tese sugerem que comparativamente com períodos de acalmia, os períodos de crises financeiras tendem a provocar ineficiência nos mercados acionistas e a conduzi-los na direção da persistência e do contágio financeiro.

Prescribed burning impact on forest soil properties – a fuzzy boolean nets approach

The Portuguese northern forests are often and severely affected by wildfires during the Summer season. These occurrences significantly affect and negatively impact all ecosystems, namely soil, fauna and flora. In order to reduce the occurrences of natural wildfires, some measures to control the availability of fuel mass are regularly implemented. Those preventive actions concern mainly prescribed burnings and vegetation pruning. This work reports on the impact of a prescribed burning on several forest soil properties, namely pH, soil moisture, organic matter content and iron content, by monitoring the soil self-recovery capabilities during a one year span. The experiments were carried out in soil cover over a natural site of Andaluzitic schist, in Gramelas, Caminha, Portugal, which was kept intact from prescribed burnings during a period of four years. Soil samples were collected from five plots at three different layers (0–3, 3–6 and 6–18) 1 day before prescribed fire and at regular intervals after the prescribed fire. This paper presents an approach where Fuzzy Boolean Nets (FBN) and Fuzzy reasoning are used to extract qualitative knowledge regarding the effect of prescribed fire burning on soil properties. FBN were chosen due to the scarcity on available quantitative data. The results showed that soil properties were affected by prescribed burning practice and were unable to recover their initial values after one year.

Psychological impact of diagnostic exams

Introduction: Anxiety is a common problem in primary care and specialty medical settings. Treating an anxious patient takes more time and adds stress to staff. Unrecognized anxiety may lead to exam repetition, and impedance of exam performance. Objective: The aim of the study was to examine the anxiety levels of patients who are to undergo diagnostic exams related to cancer diagnostic: PET/CT and mammography. Methods: Two hundred and thirty two patients who undergo PET/CT and one hundred thirteen women who undergo mammography filled out one questionnaire after the procedure to determine their concerns, expectations and perceptions of anxiety. Results: Our results show that the main causes of anxiety in patients who are having a PET/CT is the fear of the procedure itself and fear of the results. Patients who suffered from greater anxiety were those who were scanned during the initial stage of an oncological disease. On the other hand, the diagnostic is the main cause of anxiety in women who are requiring a mammography. 28% of the women reported having experienced pain or intense pain. Conclusions: The performance of diagnostic exams related to cancer diagnostic like a PET/CT and a mammography are important and statistically generators of anxiety. Patients are often poorly informed and present with a range of anxieties that may ultimately affect examination quality. These results provide expertise that can be used in the development of future training programs to integrate post-graduate courses of health professionals.

10 kVp rule - An anthropomorphic pelvis phantom imaging study using a CR system: impact on image quality and effective dose using AEC and manual mode

Purpose: This study aims to investigate the influence of tube potential (kVp) variation in relation to perceptual image quality and effective dose for pelvis using automatic exposure control (AEC) and non-AEC in a computed radiography (CR) system. Methods and Materials: To determine the effects of using AEC and non-AEC by applying the 10 kVp rule in two experiments using an anthropomorphic pelvis phantom. Images were acquired using 10 kVp increments (60-120 kVp) for both experiments. The first experiment, based on seven AEC combinations, produced 49 images. The mean mAs from each kVp increment were used as a baseline for the second experiment producing 35 images. A total of 84 images were produced and a panel of 5 experienced observers participated for the image scoring using the 2 AFC visual grading software. PCXMC software was used to estimate the effective dose. Results: A decrease in perceptual image quality as the kVp increases was observed both in non-AEC and AEC experiments, however no significant statistical differences (p> 0.05) were found. Image quality scores from all observers at 10 kVp increments for all mAs values using non-AEC mode demonstrates a better score up to 90 kVp. Effective dose results show a statistical significant decrease (p=0.000) on the 75th quartile from 0.3 mSv at 60 kVp to 0.1 mSv at 120 kVp when applying the 10 kVp rule in non-AEC mode. Conclusion: No significant reduction in perceptual image quality is observed when increasing kVp whilst a marked and significant effective dose reduction is observed.

Radiological impact associated to Technologically Enhanced Naturally Occurring Radioactive Materials (TENORM) from coal-fired power plants emissions

Certain materials used and produced in a wide range of non-nuclear industries contain enhanced activity concentrations of natural radionuclides. In particular, electricity production from coal is one of the major sources of increased human exposure to naturally occurring radioactive materials. A methodology was developed to assess the radiological impact due to natural radiation background. The developed research was applied to a specific case study, the Sines coal-fired power plant, located in the southwest coastline of Portugal. Gamma radiation measurements were carried out with two different instruments: a sodium iodide scintillation detector counter (SPP2 NF, Saphymo) and a gamma ray spectrometer with energy discrimination (Falcon 5000, Canberra). Two circular survey areas were defined within 20 km of the power plant. Forty relevant measurements points were established within the sampling area: 15 urban and 25 suburban locations. Additionally, ten more measurements points were defined, mostly at the 20-km area. The registered gamma radiation varies from 20 to 98.33 counts per seconds (c.p.s.) corresponding to an external gamma exposure rate variable between 87.70 and 431.19 nGy/h. The highest values were measured at locations near the power plant and those located in an area within the 6 and 20 km from the stacks. In situ gamma radiation measurements with energy discrimination identified natural emitting nuclides as well as their decay products (Pb-212, Pb-2142, Ra-226, Th-232, Ac-228, Th-234, Pa-234, U- 235, etc.). According to the results, an influence from the stacks emissions has been identified both qualitatively and quantitatively. The developed methodology accomplished the lack of data in what concerns to radiation rate in the vicinity of Sines coal-fired power plant and consequently the resulting exposure to the nearby population.

Impact of prescribed fire on the chemical properties of soil

Prescribed fire is a common forest management tool used in Portugal to reduce the fuel load availability and minimize the occurrence of wildfires. In addition, the use of this technique also causes an impact to ecosystems. In this presentation we propose to illustrate some results of our project in two forest sites, both located in Northwest Portugal, where the effect of prescribed fire on soil properties were recorded during a period of 6 months. Changes in soil moisture, organic matter, soil pH and iron, were examined by Principal Component Analysis multivariate statistics technique in order to determine impact of prescribed fire on these soil properties in these two different types of soils and determine the period of time that these forest soils need to recover to their pre-fire conditions, if they can indeed recover. Although the time allocated to this study does not allow for a widespread conclusion, the data analysis clearly indicates that the pH values are positively correlated with iron values at both sites. In addition, geomorphologic differences between both sampling sites, Gramelas and Anjos, are relevant as the soils’ properties considered have shown different performances in time. The use of prescribed fire produced a lower impact in soils originated from more amended bedrock and therefore with a ticker humus covering (Gramelas) than in more rocky soils with less litter covering (Anjos) after six months after the prescribed fire occurrence.

Impact of the Meteorology Conditions on the Particulate Matter Dispersion from an Industrial Complex into Urban and Suburban Areas

The aim of this work was to assess the influence of meteorological conditions on the dispersion of particulate matter from an industrial zone into urban and suburban areas. The particulate matter concentration was related to the most important meteorological variables such as wind direction, velocity and frequency. A coal-fired power plant was considered to be the main emission source with two stacks of 225 m height. A middle point between the two stacks was taken as the centre of two concentric circles with 6 and 20 km radius delimiting the sampling area. About 40 sampling collectors were placed within this area. Meteorological data was obtained from a portable meteorological station placed at approximately 1.7 km to SE from the stacks. Additional data was obtained from the electrical company that runs the coal power plant. These data covers the years from 2006 to the present. A detailed statistical analysis was performed to identify the most frequent meteorological conditions concerning mainly wind speed and direction. This analysis revealed that the most frequent wind blows from Northwest and North and the strongest winds blow from Northwest. Particulate matter deposition was obtained in two sampling campaigns carried out in summer and in spring. For the first campaign the monthly average flux deposition was 1.90 g/m2 and for the second campaign this value was 0.79 g/m2. Wind dispersion occurred predominantly from North to South, away from the nearest residential area, located at about 6 km to Northwest from the stacks. Nevertheless, the higher deposition fluxes occurred in the NW/N and NE/E quadrants. This study was conducted considering only the contribution of particulate matter from coal combustion, however, others sources may be present as well, such as road traffic. Additional chemical analyses and microanalysis are needed to identify the source linkage to flux deposition levels.

Impact of Social Responsibility Programmes in Stakeholder Satisfaction: An Empirical Study of Portuguese Managers’ Perceptions

Investigação no âmbito do Projeto de Doutoramento(PhD), especialidade de Gestão Global, Estratégia e Desenvolvimento Empresarial (ISCTE-IUL - 2012, classificação de “Aprovado com Muito Bom”).

Schistosomiasis mansoni in an area of low transmission: I. impact of control measures

This work was undertaken in the municipality of Pedro de Toledo (São Paulo State, Brazil) in 1987, to clarify aspects related to the transmission levels of Schistosoma mansoni in a human population where the snail host is Biomphalaria tenagophila. Since 1980 a control programme has been undertaken in this municipality. Urban and rural populations (4,719 subjects) were submitted to faecal examinations (Kato-Katz method). The overall prevalence rate was 4.8% being higher in males (6.2%) and also in the rural zone (5.8%). The geometric mean of S. mansoni eggs was 35.1 eggs per gramme of faeces (epg). Approximately 80.0% of the carriers presented less than 100 epg and only 20 individuals (9.0%) eliminated more than half of total eggs. The highest index of potencial contamination (IPC) was in the age group of 5 to 20 years (57.6%). Two thirds of the investigated patients (207) were autochthonous of Pedro de Toledo. The geographical distribution of the carriers showed a clear aggregation of the autochthonous cases and a close association between human contact sites and breeding places of B. tenagophila. This study shows that schistosomiasis subjects were not randomly aggregated, the youngsters should be the main target in the prophylaxis, and the efficacy of the control programme.

The impact of driving styles on fuel consumption: a data-warehouse-and-data-mining-based discovery process

This paper discusses the results of applied research on the eco-driving domain based on a huge data set produced from a fleet of Lisbon's public transportation buses for a three-year period. This data set is based on events automatically extracted from the control area network bus and enriched with GPS coordinates, weather conditions, and road information. We apply online analytical processing (OLAP) and knowledge discovery (KD) techniques to deal with the high volume of this data set and to determine the major factors that influence the average fuel consumption, and then classify the drivers involved according to their driving efficiency. Consequently, we identify the most appropriate driving practices and styles. Our findings show that introducing simple practices, such as optimal clutch, engine rotation, and engine running in idle, can reduce fuel consumption on average from 3 to 5l/100 km, meaning a saving of 30 l per bus on one day. These findings have been strongly considered in the drivers' training sessions.

On performance of distributed model predictive control in power system frequency regulation

This paper describes the implementation of a distributed model predictive approach for automatic generation control. Performance results are discussed by comparing classical techniques (based on integral control) with model predictive control solutions (centralized and distributed) for different operational scenarios with two interconnected networks. These scenarios include variable load levels (ranging from a small to a large unbalance generated power to power consumption ratio) and simultaneously variable distance between the interconnected networks systems. For the two networks the paper also examines the impact of load variation in an island context (a network isolated from each other).

The impact of CdSe/ZnS Quantum Dots in cells of Medicago sativa in suspension culture

Abstract Background: Nanotechnology has the potential to provide agriculture with new tools that may be used in the rapid detection and molecular treatment of diseases and enhancement of plant ability to absorb nutrients, among others. Data on nanoparticle toxicity in plants is largely heterogeneous with a diversity of physicochemical parameters reported, which difficult generalizations. Here a cell biology approach was used to evaluate the impact of Quantum Dots (QDs) nanocrystals on plant cells, including their effect on cell growth, cell viability, oxidative stress and ROS accumulation, besides their cytomobility. Results: A plant cell suspension culture of Medicago sativa was settled for the assessment of the impact of the addition of mercaptopropanoic acid coated CdSe/ZnS QDs. Cell growth was significantly reduced when 100 mM of mercaptopropanoic acid -QDs was added during the exponential growth phase, with less than 50% of the cells viable 72 hours after mercaptopropanoic acid -QDs addition. They were up taken by Medicago sativa cells and accumulated in the cytoplasm and nucleus as revealed by optical thin confocal imaging. As part of the cellular response to internalization, Medicago sativa cells were found to increase the production of Reactive Oxygen Species (ROS) in a dose and time dependent manner. Using the fluorescent dye H2DCFDA it was observable that mercaptopropanoic acid-QDs concentrations between 5-180 nM led to a progressive and linear increase of ROS accumulation. Conclusions: Our results showed that the extent of mercaptopropanoic acid coated CdSe/ZnS QDs cytotoxicity in plant cells is dependent upon a number of factors including QDs properties, dose and the environmental conditions of administration and that, for Medicago sativa cells, a safe range of 1-5 nM should not be exceeded for biological applications.

Sub-notificação de reacções adversas medicamentosas : um problema com solução? : contribuição para o conhecimento da sub-notificação de RAMs em Portugal e implementação de medidas minimizadoras do impacte

RESUMO - Introdução: As Reacções Adversas Medicamentosas (RAMs) constituem um grave problema de Saúde Pública em termos da mortalidade e morbilidade provocadas, tendo também um impacto económico considerável nos Sistemas de Saúde. Os Sistemas de Notificacão Espontânea de RAMs são considerados como o método de vigilância de medicamentos mais eficaz, sendo a sub-notificação de RAMs uma das suas maiores limitações. Em termos globais, foi estimado que apenas 6% de todas as reacções adversas são notificadas. Portugal apresenta uma taxa de notificação de RAMs relativamente baixa quando comparada com os países mais notificadores da Europa. São objectivos deste estudo: 1) caracterizar as atitudes e os comportamentos dos médicos, dos farmacêuticos e dos enfermeiros em Portugal Continental relativamente à notificação de RAMs; e 2) caracterizar a efectividade de intervenções educacionais destinadas a reduzir a sub-notificação de RAMs. Métodos: Numa primeira fase será efectuado um estudo de caso-controlo em médicos, farmacêuticos e enfermeiros de Portugal Continental, a exercer actividade no Servico Nacional de Saúde (SNS), de modo a caracterizar as suas atitudes e comportamentos relativamente à notificação de RAMs. Como casos serão considerados os Profissionais de Saúde que notificaram pelo menos uma RAM num determinado período e os controlos os Profissionais de Saúde que não notificaram qualquer RAM nesse mesmo período, sendo estes útimos seleccionados aleatoriamente. O estudo será conduzido através de um questionário de auto-resposta, em que as questões relativas às atitudes e comportamentos são baseadas nos “sete pecados mortais” de Inman. Será utilizada uma Escala Visual Analógica para registar as respostas, podendo estas ir de zero (totalmente em desacordo) até 10 (totalmente de acordo). Será utilizada uma análise de regressão logística para determinar o odds ratio ajustado (ORadj) da notificação de RAMs para uma mudança de exposição correspondente ao range interquartil para cada atitude. Numa segunda fase, será efectuado ensaio aleatorizado controlado de cluster, para caracterizar a efectividade das intervenções educacionais realizadas sobre as causas identificadas na primeira parte do trabalho, com o intuito de reduzir a sub-notificação de RAMs. Com base em informacão de 2007 foram identificados 43 clusters dispersos pelas várias Regiões de Saúde. As intervenções educacionais são compostas por uma apresentação com uma hora de duração complementada por um folheto recordatório. Serão ainda realizados dois sub-estudos, em que o V1.0, Final 28Set09 viii Sub-notificação de RAMs em Portugal – Um problema com solução ? primeiro tentará caracterizar o efeito de contaminação entre Profissionais de Saúde e o segundo pretende caracterizar a duração do efeito das intervenções educacionais. Resultados a atingir: Pretende-se, com a implementação deste projecto, aumentar o número de notificações de RAMs pelos médicos, farmacêuticos e enfermeiros em cerca de 110%, de modo a atingir-se uma taxa de notificação de aproximadamente 300 notificações por milhão de habitantes por ano (i.e., multiplicar por 2,1 o número notificações existentes). -------------------ABSTRACT - Introduction: The Adverse Drug Reactions (ADRs) are a serious Public Health problem in terms of mortality and morbidity caused, being also an economic burden for the health systems. The Spontaneous Adverse Event Reporting Systems are considered as the most effective drug surveillance methods, in which the ADR under-reporting represents one of its biggest limitations. It was estimated that only 6% of all adverse reactions are notified globally. When comparing with high ADR reporting rate countries Portugal shows a low ADR reporting rate. This study aims to: 1) characterize the physicians, pharmacists and nurses attitudes and behaviours related to ADR under-reporting; 2) characterize the educational interventions effectiveness to decrease the ADRs under-reporting. Methods: During a first phase a case-control study will be conducted in physicians, pharmacists and nurses in Continental Portugal working in the National Health System (NHS) in order to characterize their attitudes and behaviours related to ADR reporting. The Healthcare Professionals that have reported at least one ADR during a determined period will be considered as the cases and those that have not reported any ADR during the same period will be considered as the controls. The controls will be randomly selected. The study will be conducted through a self-administered questionnaire in which the questions related to the attitudes and behaviours are based in the Inmans’s “seven mortal sins”. A Visual Analogue Scale will be used to record the responses. The responses can range from 0 (totally disagree) to 10 (totally agree). Logistic regression will be used to determine the ADR reporting adjusted odds ratio (ORadj) for a change in the exposure corresponding to the interquartile range for each attitude. In the second phase of the study a cluster-randomized controlled trial will be conducted to characterize the educational interventions effectiveness focused on the first phase identified causes with the aim to decrease the ADRs under-reporting. Based in 2007’s information 43 clusters have been identified throughout the several Health Regions. The educational interventions are composed of one hour presentation complemented by an informational leaflet. Two sub-studies will be also conducted in which the first one will try to characterize the contamination effect between the Healthcare Professionals and the second to characterize the educational interventions effect duration. V1.0, Final 28Set09 x Sub-notificação de RAMs em Portugal – Um problema com solução ? Outcome: With the project implementation an increase of the ADR notifications performed by the physicians, pharmacists and nurses by 110% is aimed in order to obtain approximately 300 notifications per million habitants per year (i.e., multiply by 2,1 the existent notifications).