The use of non-standard CT conversion ramps for Monte Carlo verification of 6 MV prostate IMRT plans

Monte Carlo (MC) dose calculation algorithms have been widely used to verify the accuracy of intensity-modulated radiotherapy (IMRT) dose distributions computed by conventional algorithms due to the ability to precisely account for the effects of tissue inhomogeneities and multileaf collimator characteristics. Both algorithms present, however, a particular difference in terms of dose calculation and report. Whereas dose from conventional methods is traditionally computed and reported as the water-equivalent dose (Dw), MC dose algorithms calculate and report dose to medium (Dm). In order to compare consistently both methods, the conversion of MC Dm into Dw is therefore necessary. This study aims to assess the effect of applying the conversion of MC-based Dm distributions to Dw for prostate IMRT plans generated for 6 MV photon beams. MC phantoms were created from the patient CT images using three different ramps to convert CT numbers into material and mass density: a conventional four material ramp (CTCREATE) and two simplified CT conversion ramps: (1) air and water with variable densities and (2) air and water with unit density. MC simulations were performed using the BEAMnrc code for the treatment head simulation and the DOSXYZnrc code for the patient dose calculation. The conversion of Dm to Dw by scaling with the stopping power ratios of water to medium was also performed in a post-MC calculation process. The comparison of MC dose distributions calculated in conventional and simplified (water with variable densities) phantoms showed that the effect of material composition on dose-volume histograms (DVH) was less than 1% for soft tissue and about 2.5% near and inside bone structures. The effect of material density on DVH was less than 1% for all tissues through the comparison of MC distributions performed in the two simplified phantoms considering water. Additionally, MC dose distributions were compared with the predictions from an Eclipse treatment planning system (TPS), which employed a pencil beam convolution (PBC) algorithm with Modified Batho Power Law heterogeneity correction. Eclipse PBC and MC calculations (conventional and simplified phantoms) agreed well (<1%) for soft tissues. For femoral heads, differences up to 3% were observed between the DVH for Eclipse PBC and MC calculated in conventional phantoms. The use of the CT conversion ramp of water with variable densities for MC simulations showed no dose discrepancies (0.5%) with the PBC algorithm. Moreover, converting Dm to Dw using mass stopping power ratios resulted in a significant shift (up to 6%) in the DVH for the femoral heads compared to the Eclipse PBC one. Our results show that, for prostate IMRT plans delivered with 6 MV photon beams, no conversion of MC dose from medium to water using stopping power ratio is needed. In contrast, MC dose calculations using water with variable density may be a simple way to solve the problem found using the dose conversion method based on the stopping power ratio.

Mould and yeast identification in archival settings: preliminary results on the use of traditional methods and molecular biology options in Portuguese archives

This project was developed to fully assess the indoor air quality in archives and libraries from a fungal flora point of view. It uses classical methodologies such as traditional culture media – for the viable fungi – and modern molecular biology protocols, especially relevant to assess the non-viable fraction of the biological contaminants. Denaturing high-performance liquid chromatography (DHPLC) has emerged as an alternative to denaturing gradient gel electrophoresis (DGGE) and has already been applied to the study of a few bacterial communities. We propose the application of DHPLC to the study of fungal colonization on paper-based archive materials. This technology allows for the identification of each component of a mixture of fungi based on their genetic variation. In a highly complex mixture of microbial DNA this method can be used simply to study the population dynamics, and it also allows for sample fraction collection, which can, in many cases, be immediately sequenced, circumventing the need for cloning. Some examples of the methodological application are shown. Also applied is fragment length analysis for the study of mixed Candida samples. Both of these methods can later be applied in various fields, such as clinical and sand sample analysis. So far, the environmental analyses have been extremely useful to determine potentially pathogenic/toxinogenic fungi such as Stachybotrys sp., Aspergillus niger, Aspergillus fumigatus, and Fusarium sp. This work will hopefully lead to more accurate evaluation of environmental conditions for both human health and the preservation of documents.

A biosignal embedded system for physiological computing

Thesis submitted in the fulfilment of the requirements for the Degree of Master in Electronic and Telecomunications Engineering

Complementarity of conventional and molecular methods in the assessment of fungal contamination caused by Aspergillus fumigatus complex in one Portuguese composting plant

The handling of waste and compost that occurs frequently in composting plants (compost turning, shredding, and screening) has been shown to be responsible for the release of dust and air borne microorganisms and their compounds in the air. Thermophilic fungi, such as A. fumigatus, have been reported and this kind of contamination in composting facilities has been associated with increased respiratory symptoms among compost workers. This study intended to characterize fungal contamination in a totally indoor composting plant located in Portugal. Besides conventional methods, molecular biology was also applied to overcome eventual limitations.

Auditoria dos sistemas de informação das instituições financeiras

Mestrado em Contabilidade e Gestão das Instituições Financeiras

Parallel implementation of vertex component analysis for hyperspectral endmember extraction

International Conference with Peer Review 2012 IEEE International Conference in Geoscience and Remote Sensing Symposium (IGARSS), 22-27 July 2012, Munich, Germany

BIT: Biosignal Igniter Toolkit

The study of biosignals has had a transforming role in multiple aspects of our society, which go well beyond the health sciences domains to which they were traditionally associated with. While biomedical engineering is a classical discipline where the topic is amply covered, today biosignals are a matter of interest for students, researchers and hobbyists in areas including computer science, informatics, electrical engineering, among others. Regardless of the context, the use of biosignals in experimental activities and practical projects is heavily bounded by the cost, and limited access to adequate support materials. In this paper we present an accessible, albeit versatile toolkit, composed of low-cost hardware and software, which was created to reinforce the engagement of different people in the field of biosignals. The hardware consists of a modular wireless biosignal acquisition system that can be used to support classroom activities, interface with other devices, or perform rapid prototyping of end-user applications. The software comprehends a set of programming APIs, a biosignal processing toolbox, and a framework for real time data acquisition and postprocessing. (C) 2014 Elsevier Ireland Ltd. All rights reserved.

Arrow plot and CA maps on microarray preprocessing methods

Microarray allow to monitoring simultaneously thousands of genes, where the abundance of the transcripts under a same experimental condition at the same time can be quantified. Among various available array technologies, double channel cDNA microarray experiments have arisen in numerous technical protocols associated to genomic studies, which is the focus of this work. Microarray experiments involve many steps and each one can affect the quality of raw data. Background correction and normalization are preprocessing techniques to clean and correct the raw data when undesirable fluctuations arise from technical factors. Several recent studies showed that there is no preprocessing strategy that outperforms others in all circumstances and thus it seems difficult to provide general recommendations. In this work, it is proposed to use exploratory techniques to visualize the effects of preprocessing methods on statistical analysis of cancer two-channel microarray data sets, where the cancer types (classes) are known. For selecting differential expressed genes the arrow plot was used and the graph of profiles resultant from the correspondence analysis for visualizing the results. It was used 6 background methods and 6 normalization methods, performing 36 pre-processing methods and it was analyzed in a published cDNA microarray database (Liver) available at http://genome-www5.stanford.edu/ which microarrays were already classified by cancer type. All statistical analyses were performed using the R statistical software.

Workplace aggression in organizational changing processes: The mediation role of leader political (soft and hard) behavior

One of the main trends in workplace aggression research is studying its antecedents. But the literature also reveals that some predictors remain understudied, like organizational change [1]. Additionally, possible mediators of this relationship were not investigated. The main objective of this research is studding the mediating effect of the leader political behavior (soft and hard version) on the relationship between organizational change and workplace aggression. Participants representing a wide variety of jobs across many organizations were surveyed. The measures used in this research are an Organizational Change Questionnaire climate of change, processes, and readiness [2], a Workplace Aggression Scale [e.g. 3, 4] and a Political Behavior Questionnaire [5]. The results of the study and its theoretical and practical implications will be presented and discussed.

Controladores linguísticos Fuzzy

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

Teacher placement report: investigation: action research project investigating methods for promoting creativity in double bass students attending a portuguese music school

The investigation which employed the action research method (qualitative analysis)was divided into four fases. In phases 1-3 the participants were six double bass students at Nossa Senhora do Cabo Music School. Pilot exercises in creativity were followed by broader and more ambitious projects. In phase 4 the techniques were tested and amplified during a summer course for twelve double bass students at Santa Cecilia College.

Influência dos métodos de correção de atenuação na quantificação da função renal relativa em cintigrafia renal com 99mTc-DMSA

Introdução – A estimativa da função renal relativa (FRR) através de cintigrafia renal (CR) com ácido dimercaptossuccínico marcado com tecnécio-99 metaestável (99mTc-DMSA) pode ser influenciada pela profundidade renal (PR), atendendo ao efeito de atenuação por parte dos tecidos moles que envolvem os rins. Dado que raramente é conhecida esta mesma PR, diferentes métodos de correção de atenuação (CA) foram desenvolvidos, nomeadamente os que utilizam fórmulas empíricas, como os de Raynaud, de Taylor ou de Tonnesen, ou recorrendo à aplicação direta da média geométrica (MG). Objetivos – Identificar a influência dos diferentes métodos de CA na quantificação da função renal relativa através da CR com 99mTc-DMSA e avaliar a respetiva variabilidade dos resultados de PR. Metodologia – Trinta e um pacientes com indicação para realização de CR com 99mTc-DMSA foram submetidos ao mesmo protocolo de aquisição. O processamento foi efetuado por dois operadores independentes, três vezes por exame, variando para o mesmo processamento o método de determinação da FRR: Raynaud, Taylor, Tonnesen, MG ou sem correção de atenuação (SCA). Aplicou-se o teste de Friedman para o estudo da influência dos diferentes métodos de CA e a correlação de Pearson para a associação e significância dos valores de PR com as variáveis idade, peso e altura. Resultados – Da aplicação do teste de Friedman verificaram-se diferenças estatisticamente significativas entre os vários métodos (p=0,000), excetuando as comparações SCA/Raynaud, Tonnesen/MG e Taylor/MG (p=1,000) para ambos os rins. A correlação de Pearson demonstra que a variável peso apresenta uma correlação forte positiva com todos os métodos de cálculo da PR. Conclusões – O método de Taylor, entre os três métodos de cálculo de PR, é o que apresenta valores de FRR mais próximos da MG. A escolha do método de CA influencia significativamente os parâmetros quantitativos de FRR.

Mobile collaborative cloudless computing

Although the computational power of mobile devices has been increasing, it is still not enough for some classes of applications. In the present, these applications delegate the computing power burden on servers located on the Internet. This model assumes an always-on Internet connectivity and implies a non-negligible latency. The thesis addresses the challenges and contributions posed to the application of a mobile collaborative computing environment concept to wireless networks. The goal is to define a reference architecture for high performance mobile applications. Current work is focused on efficient data dissemination on a highly transitive environment, suitable to many mobile applications and also to the reputation and incentive system available on this mobile collaborative computing environment. For this we are improving our already published reputation/incentive algorithm with knowledge from the usage pattern from the eduroam wireless network in the Lisbon area.

Parallel hyperspectral unmixing on GPUs

This letter presents a new parallel method for hyperspectral unmixing composed by the efficient combination of two popular methods: vertex component analysis (VCA) and sparse unmixing by variable splitting and augmented Lagrangian (SUNSAL). First, VCA extracts the endmember signatures, and then, SUNSAL is used to estimate the abundance fractions. Both techniques are highly parallelizable, which significantly reduces the computing time. A design for the commodity graphics processing units of the two methods is presented and evaluated. Experimental results obtained for simulated and real hyperspectral data sets reveal speedups up to 100 times, which grants real-time response required by many remotely sensed hyperspectral applications.

BITalino: a novel hardware framework for physiological computing

Physical computing has spun a true global revolution in the way in which the digital interfaces with the real world. From bicycle jackets with turn signal lights to twitter-controlled christmas trees, the Do-it-Yourself (DiY) hardware movement has been driving endless innovations and stimulating an age of creative engineering. This ongoing (r)evolution has been led by popular electronics platforms such as the Arduino, the Lilypad, or the Raspberry Pi, however, these are not designed taking into account the specific requirements of biosignal acquisition. To date, the physiological computing community has been severely lacking a parallel to that found in the DiY electronics realm, especially in what concerns suitable hardware frameworks. In this paper, we build on previous work developed within our group, focusing on an all-in-one, low-cost, and modular biosignal acquisition hardware platform, that makes it quicker and easier to build biomedical devices. We describe the main design considerations, experimental evaluation and circuit characterization results, together with the results from a usability study performed with volunteers from multiple target user groups, namely health sciences and electrical, biomedical, and computer engineering. Copyright © 2014 SCITEPRESS - Science and Technology Publications. All rights reserved.