A distributed platform for the volunteer execution of workflows on a local area network

Thesis submitted in fulfilment of the requirements for the Degree of Master of Science in Computer Science

Compact simulated countercurrent chromatography for downstream processing of (bio)pharmaceuticals

Dissertação para obtenção do Grau de Doutor em Engenharia Química e Bioquímica

Developing clinical trials in the portuguese family medicine : challenges and opportunities in the European context

RESUMO: Introdução: A hipótese colocada nesta tese é a de que poderia haver um número bastante mais elevado de ensaios clínicos na medicina familiar portuguesa se os obstáculos fossem removidos e as oportunidades exploradas de modo adequado. Contexto: Em Portugal existe uma nova geração de Médicos de Família que está a assumir postos de trabalho um pouco por todo o país e que é aceite como sendo a mais bem preparada geração de sempre. Métodos: Busca na MEDLINE. Leitura de artigos na única publicação científica dedicada à Medicina Geral e Familiar – RPMGF. Consulta em livros portugueses de política da saúde e acerca do Plano Nacional de Saúde. O INFARMED foi contactado e relatórios seus sobre ensaios clínicos foram analisados. Os Médicos de Família portugueses foram contactados e convidados a responder a questionários. Além disso, quinze personalidades da Medicina Portuguesa foram chamadas a sugerir soluções. Resultados: De acordo com dados do INFARMED, de 2006 a 2011 houve apenas quatro centros de saúde envolvidos em ensaios clínicos. Em Portugal: Existe um número pouco significativo de ensaios académicos; Praticamente não há infraestruturas de suporte ou treino; Os registos clínicos eletrónicos são usados de forma ineficiente; a investigação é fracamente ligada às carreiras médicas; há isolamento interno e externo; a já complexa regulamentação da União Europeia é complicada ainda mais; há um subfinanciamento da Investigação Clínica. Os Médicos de Família portugueses estão disponíveis para participar ativamente numa mudança. Discussão: Com os presentes resultados o diagnóstico para a presente situação é claramente negativo. Felizmente existem muito boas oportunidades para melhorar. Conclusão/Recomendações: Tempo, dinheiro e apoio têm de ser fornecidos aos Médicos de Família portugueses. É nesse sentido que são fornecidas vinte recomendações para obter uma verdadeira mudança no panorama dos Ensaios Clínicos na Medicina Familiar portuguesa.-------------ABSTRACT: Introduction: The hypothesis of this thesis is that there could be a much greater number of Clinical Trials in Portuguese Family Medicine if obstacles were removed and opportunities explored properly. Background: In Portugal there is a new generation of Family Doctors that is assuming permanent positions all over the country and is accepted to be the most well prepared generation ever. Methods: Search on MEDLINE. Relevant articles were also identified in the only jornal dedicated to Portuguese Family Medicine, RPMGF. A search was made on Portuguese health policy textbooks and national health plan policy. INFARMED was also contacted and their reports about Clinical Trials were analysed. Portuguese Family Doctors themselves were contacted and invited to answer questionnaires. Besides that, fifteen key opinion leaders related to Portuguese Medicine were approached for solutions. Results: According to INFARMED data, from 2006 to 2011 there were only four health centres involved in clinical trials. In Portugal there is: A negligible number of academic trials; almost no support infrastructures or training; inefficiently used electronic health records; a research weakly linked to medical careers; an uninformed isolation internally and externally; an already complex European Union regulation that is compounded even more; Scarce funding for clinical research. Portuguese Family Doctors are keen to actively participate in a change. Discussion: With the present results the diagnosis for the current situation is clearly negative. Fortunately there are very good opportunities to improve. Conclusion/Recommendations: Time, money and support must be given to Portuguese Family Doctors. In this context, twenty recommendations are provided intending to promote a true change in Portuguese Family Medicine Clinical Trials panorama.

Fractionation of hydro-ethanolic extracts from grape pomace through membrane processing: the effect of membrane and extracting media on process performance

The EM3E Master is an Education Programme supported by the European Commission, the European Membrane Society (EMS), the European Membrane House (EMH), and a large international network of industrial companies, research centers and universities

Ionic liquids as catalysts of lignocellulosic biomass processing

The present work is devoted to study the pre-treatment of lignocellulosic biomass, especially wheat straw, by the application of the acidic ionic liquid (IL) such as 1-butyl-3-methylimidazolium hydrogen sulphate. The ability of this IL to hydrolysis and conversion of biomass was scrutinised. The pre-treatment with hydrogen sulphate-based IL allowed to obtain a liquor rich in hemicellulosic sugars, furans and organic acids, and a solid fraction mainly constituted by cellulose and lignin. Quantitative and qualitative analyses of the produced liquors were made by capillary electrophoresis and high-performance liquid chromatography. Pre-treatment conditions were set to produce xylose or furfural. Specific range of temperatures from 70 to 175 °C and residence times from 20.0 to 163.3 min were studied by fixing parameters such as biomass/IL ratio (10 % (w/w)) and water content (1.25 % (w/w)) in the pre-treatment process. Statistical modelling was applied to maximise the xylose and furfural concentrations. For the purpose of reaction condition comparison the severity factor for studied ionic liquid was proposed and applied in this work. Optimum conditions for xylose production were identified to be at 125 °C and 82.1 min, at which 16.7 % (w/w) xylose yield was attained. Furfural was preferably formed at higher pre-treatment temperatures and longer reaction time (161 °C and 104.5 min) reaching 30.7 % (w/w) maximum yield. The influence of water content on the optimum xylose formation was also studied. Pre-treatments with 5 and 10 % (w/w) water content were performed and an increase of 100 % and 140 % of xylose yield was observed, respectively, while the conversion into furfural maintained unchanged.

Context-based identification of energy consumption in industrial plants

Nowadays, reducing energy consumption is one of the highest priorities and biggest challenges faced worldwide and in particular in the industrial sector. Given the increasing trend of consumption and the current economical crisis, identifying cost reductions on the most energy-intensive sectors has become one of the main concerns among companies and researchers. Particularly in industrial environments, energy consumption is affected by several factors, namely production factors(e.g. equipments), human (e.g. operators experience), environmental (e.g. temperature), among others, which influence the way of how energy is used across the plant. Therefore, several approaches for identifying consumption causes have been suggested and discussed. However, the existing methods only provide guidelines for energy consumption and have shown difficulties in explaining certain energy consumption patterns due to the lack of structure to incorporate context influence, hence are not able to track down the causes of consumption to a process level, where optimization measures can actually take place. This dissertation proposes a new approach to tackle this issue, by on-line estimation of context-based energy consumption models, which are able to map operating context to consumption patterns. Context identification is performed by regression tree algorithms. Energy consumption estimation is achieved by means of a multi-model architecture using multiple RLS algorithms, locally estimated for each operating context. Lastly, the proposed approach is applied to a real cement plant grinding circuit. Experimental results prove the viability of the overall system, regarding both automatic context identification and energy consumption estimation.

Towards an algorithmic skeleton framework for programming the Intel R Xeon PhiTM processor

The Intel R Xeon PhiTM is the first processor based on Intel’s MIC (Many Integrated Cores) architecture. It is a co-processor specially tailored for data-parallel computations, whose basic architectural design is similar to the ones of GPUs (Graphics Processing Units), leveraging the use of many integrated low computational cores to perform parallel computations. The main novelty of the MIC architecture, relatively to GPUs, is its compatibility with the Intel x86 architecture. This enables the use of many of the tools commonly available for the parallel programming of x86-based architectures, which may lead to a smaller learning curve. However, programming the Xeon Phi still entails aspects intrinsic to accelerator-based computing, in general, and to the MIC architecture, in particular. In this thesis we advocate the use of algorithmic skeletons for programming the Xeon Phi. Algorithmic skeletons abstract the complexity inherent to parallel programming, hiding details such as resource management, parallel decomposition, inter-execution flow communication, thus removing these concerns from the programmer’s mind. In this context, the goal of the thesis is to lay the foundations for the development of a simple but powerful and efficient skeleton framework for the programming of the Xeon Phi processor. For this purpose we build upon Marrow, an existing framework for the orchestration of OpenCLTM computations in multi-GPU and CPU environments. We extend Marrow to execute both OpenCL and C++ parallel computations on the Xeon Phi. We evaluate the newly developed framework, several well-known benchmarks, like Saxpy and N-Body, will be used to compare, not only its performance to the existing framework when executing on the co-processor, but also to assess the performance on the Xeon Phi versus a multi-GPU environment.

UAV - based imagery processing using structure from motion and remote sensing technology

With the recent advances in technology and miniaturization of devices such as GPS or IMU, Unmanned Aerial Vehicles became a feasible platform for a Remote Sensing applications. The use of UAVs compared to the conventional aerial platforms provides a set of advantages such as higher spatial resolution of the derived products. UAV - based imagery obtained by a user grade cameras introduces a set of problems which have to be solved, e. g. rotational or angular differences or unknown or insufficiently precise IO and EO camera parameters. In this work, UAV - based imagery of RGB and CIR type was processed using two different workflows based on PhotoScan and VisualSfM software solutions resulting in the DSM and orthophoto products. Feature detection and matching parameters influence on the result quality as well as a processing time was examined and the optimal parameter setup was presented. Products of the both workflows were compared in terms of a quality and a spatial accuracy. Both workflows were compared by presenting the processing times and quality of the results. Finally, the obtained products were used in order to demonstrate vegetation classification. Contribution of the IHS transformations was examined with respect to the classification accuracy.

Image processing for displacement measurements

Since the invention of photography humans have been using images to capture, store and analyse the act that they are interested in. With the developments in this field, assisted by better computers, it is possible to use image processing technology as an accurate method of analysis and measurement. Image processing's principal qualities are flexibility, adaptability and the ability to easily and quickly process a large amount of information. Successful examples of applications can be seen in several areas of human life, such as biomedical, industry, surveillance, military and mapping. This is so true that there are several Nobel prizes related to imaging. The accurate measurement of deformations, displacements, strain fields and surface defects are challenging in many material tests in Civil Engineering because traditionally these measurements require complex and expensive equipment, plus time consuming calibration. Image processing can be an inexpensive and effective tool for load displacement measurements. Using an adequate image acquisition system and taking advantage of the computation power of modern computers it is possible to accurately measure very small displacements with high precision. On the market there are already several commercial software packages. However they are commercialized at high cost. In this work block-matching algorithms will be used in order to compare the results from image processing with the data obtained with physical transducers during laboratory load tests. In order to test the proposed solutions several load tests were carried out in partnership with researchers from the Civil Engineering Department at Universidade Nova de Lisboa (UNL).

Context classification for service robots

This dissertation presents a solution for environment sensing using sensor fusion techniques and a context/environment classification of the surroundings in a service robot, so it could change his behavior according to the different rea-soning outputs. As an example, if a robot knows he is outdoors, in a field environment, there can be a sandy ground, in which it should slow down. Contrariwise in indoor environments, that situation is statistically unlikely to happen (sandy ground). This simple assumption denotes the importance of context-aware in automated guided vehicles.

Mobile image processing to support educational geometry games

The mobile IT era is here, it is still growing and expanding at a steady rate and, most of all, it is entertaining. Mobile devices are used for entertainment, whether social through the so-called social networks, or private through web browsing, video watching or gaming. Youngsters make heavy use of these devices, and even small children show impressive adaptability and skill. However not much attention is directed towards education, especially in the case of young children. Too much time is usually spent in games which only purpose is to keep children entertained, time that could be put to better use such as developing elementary geometric notions. Taking advantage of this pocket computer scenario, it is proposed an application geared towards small children in the 6 – 9 age group that allows them to consolidate knowledge regarding geometric shapes, forming a stepping stone that leads to some fundamental mathematical knowledge to be exercised later on. To achieve this goal, the application will detect simple geometric shapes like squares, circles and triangles using the device’s camera. The novelty of this application will be a core real-time detection system designed and developed from the ground up for mobile devices, taking into account their characteristic limitations such as reduced processing power, memory and battery. User feedback was be gathered, aggregated and studied to assess the educational factor of the application.

Improving downstream processing for viral vectors and viral vaccines

Viral vectors are playing an increasingly important role in the vaccine and gene therapy elds. The broad spectrum of potential applications, together with expanding medical markets, drives the e orts to improve the production processes for viral vaccines and viral vectors. Developing countries, in particular, are becoming the main vaccine market. It is thus critical to decrease the cost per dose, which is only achievable by improving the production process. In particular advances in the upstream processing have substantially increased bioreactor yields, shifting the bioprocess bottlenecks towards the downstream processing. The work presented in this thesis aimed to develop new processes for adenoviruses puri cation. The use of state-of-the-art technology combined with innovative continuous processes contributed to build robust and cost-e ective strategies for puri cation of complex biopharmaceuticals.(...)

Pedestrian Priority Zones in the Context of Urban Mobility and Valorization of Public Space

The second half of the XX century was marked by a great increase in the number of people living in cities. Urban agglomerations became poles of attraction for migration flows and these phenomena, coupled with growing car-ownership rates, resulted in the fact that modern transport systems are characterized by large number of users and traffic modes. The necessity to organize these complex systems and to provide space for different traffic modes changed the way cities look. Urban areas had to cope with traffic flows, and as a result nowadays typical street pattern consists of a road for motorized vehicles, a cycle lane (in some cases), pavement for pedestrians, parking and a range of crucial signage to facilitate navigation and make mobility more secure. However, this type of street organization may not be desirable in certain areas, more specifically, in the city centers. Downtown areas have always been places where economic, leisure, social and other types of facilities are concentrated, not surprisingly, they often attract large number of people and this frequently results in traffic jams, air and noise pollution, thus creating unpleasant environment. Besides, excessive traffic signage in central locations can harm the image and perception of a place, this relates in particular to historical centers with architectural heritage.

Rethinking the Portuguese banking sector in a post-crisis context

As the financial crisis hit the Portuguese banks, the profitability of the whole sector squeezed to historical minimums. Reinventing the banking business model in the post-crisis context is an overriding issue to achieve sustainable profits and a low cost-to-income ratio. We propose banks to adopt a true multichannel approach, proceeding to a branch network reformatting and a relocation of services to online channels; adopt a true customer-centric approach and reduce the product and services portfolio complexity; finally, industrialize operations and rationalize the structure. With these measures in place, Portuguese banks will become leaner and more efficient, aspiring to a cost-to-income ratio below 45%.

How Does Cultural Context Stimulate Creativity: A study of African Musicians in Lisbon, Portugal

The 21st century bodes an interesting time for companies and individuals alike with an increased focus on using creativity as a way to stimulate innovation to create competitive advantage. Several studies have looked at how creativity is stimulated within a corporate environment or how creativity is stimulated by people in a specific place. This study aimed to look at how the contextual environment fosters creativity in individuals and groups. With the increase in popularity of African and world music In Europe over the last ten years it was decided that the context of Lisbon, Portugal be used with a specific focus on African musicians living there and working in the Lisbon music scene. It became apparent themes of Creative crossovers, Geographical Location, a dynamic environment, Entrepreneurial encouragement and the presence of open-minded and flexible individual were involved in Lisbon’s ability to foster and empower creative individuals.