A nanopore-based stochastic detection method: Single molecule characterisation of nanoparticles using ()- hemolysin

Dissertation presented to obtain the Ph.D degree in Chemistry.

A volumetric hybrid representation for obstacle detection in all-terrain robots

This dissertation presents an approach aimed at three-dimensional perception’s obstacle detection on all-terrain robots. Given the huge amount of acquired information, the adversities such environments present to an autonomous system and the swiftness, thus required, from each of its navigation decisions, it becomes imperative that the 3-D perceptional system to be able to map obstacles and passageways in the most swift and detailed manner. In this document, a hybrid approach is presented bringing the best of several methods together, combining the lightness of lesser meticulous analyses with the detail brought by more thorough ones. Realizing the former, a terrain’s slope mapping system upon a low resolute volumetric representation of the surrounding occupancy. For the latter’s detailed evaluation, two novel metrics were conceived to discriminate the little depth discrepancies found in between range scanner’s beam distance measurements. The hybrid solution resulting from the conjunction of these two representations provides a reliable answer to traversability mapping and a robust discrimination of penetrable vegetation from that constituting real obstructions. Two distinct robotic platforms offered the possibility to test the hybrid approach on very different applications: a boat, under an European project, the ECHORD Riverwatch, and a terrestrial four-wheeled robot for a national project, the Introsys Robot.

As atitudes face à doença no Portugal dos séculos XIV e XV: a lepra, os leprosos e as leprosarias

A doença como tópico de reflexão historiográfica encontra-se relativamente ausente do actual rol de interesses da medievística portuguesa. Apesar de lhe ser feita referência em vários artigos de pequena e média dimensão – publicados, sobretudo, nas décadas de 80 e 90 do século passado -, a enfermidade aparece, por norma, como subtema de problemáticas maiores como a assistência ou a pobreza, não tendo merecido ainda estudos de grande profundidade. Num sentido inverso, a historiografia internacional, com particular destaque para a francesa e inglesa, tem vindo a desenvolver interessantes e renovadas perspectivas de análise que incidem não só sobre as percepções medievais da doença mas também sobre as atitudes dos indivíduos face aos seus congéneres enfermos. O presente artigo segue algumas destas linhas de investigação recentemente propostas, procurando aplicá-las ao caso português nas centúrias de Quatrocentos e Quinhentos. Em concreto, interessa-nos avaliar a validade e/ou utilidade das equações “lepra = medo do contágio”, “leproso = pobre e marginal”, “leprosaria = segregação social”. Para tal, começaremos por discutir o conceito de doença, avançando, depois, para a análise das fontes recolhidas, privilegiando o caso de Lisboa mas sem esquecer outros núcleos urbanos como o Porto, Coimbra, Évora e Santarém. Aqui serão explorados problemas na linha dos que se seguem: Era comum, em contexto urbano, a noção de contágio da lepra? Em sendo, as atitudes face aos leprosos respondiam apenas a essa ideia ou devem ser tidos em conta outros factores? Qual a pertinência de uma abordagem genera-lista em relação à suposta posição marginalizada dos leprosos? Que diferenças existiam entre os “lázaros andantes ao mundo”, os residentes nas leprosarias e os lázaros domésticos? Devem entender-se as gafarias meramente como mecanismos profilácticos e como espaços de exclusão social ou há que ter em consideração ainda o papel que desempenhavam na integração dos enfermos?

A semi-automatic approach to code smells detection

Eradication of code smells is often pointed out as a way to improve readability, extensibility and design in existing software. However, code smell detection remains time consuming and error-prone, partly due to the inherent subjectivity of the detection processes presently available. In view of mitigating the subjectivity problem, this dissertation presents a tool that automates a technique for the detection and assessment of code smells in Java source code, developed as an Eclipse plugin. The technique is based upon a Binary Logistic Regression model that uses complexity metrics as independent variables and is calibrated by expert‟s knowledge. An overview of the technique is provided, the tool is described and validated by an example case study.

Transimpedance amplifier for early detection of breast cancer

Breast cancer is the most common type of cancer worldwide. The effectiveness of its treatment depends on early stage detection, as well as on the accuracy of its diagnosis. Recently, diagnosis techniques have been submitted to relevant breakthroughs with the upcoming of Magnetic Resonance Imaging, Ultrasound Sonograms and Positron Emission Tomography (PET) scans, among others. The work presented here is focused on studying the application of a PET system to a Positron Emission Mammography (PEM) system. A PET/PEM system works under the principle that a scintillating crystal will detect a gamma-ray pulse, originated at the cancerous cells, converting it into a correspondent visible light pulse. The latter must then be converted into an electrical current pulse by means of a Photo- -Sensitive Device (PSD). After the PSD there must be a Transimpedance Amplifier (TIA) in order to convert the current pulse into a suitable output voltage, in a time period lower than 40 ns. In this Thesis, the PSD considered is a Silicon Photo-Multiplier (SiPM). The usage of this recently developed type of PSD is impracticable with the conventional TIA topologies, as it will be proven. Therefore, the usage of the Regulated Common-Gate (RCG) topology will be studied in the design of the amplifier. There will be also presented two RCG variations, comprising a noise response improvement and differential operation of the circuit. The mentioned topology will also be tested in a Radio-Frequency front-end, showing the versatility of the RCG. A study comprising a low-voltage self-biasing feedback TIA will also be shown. The proposed circuits will be simulated with standard CMOS technology (UMC 130 nm), using a 1.2 V power supply. A power consumption of 0.34 mW with a signal-to-noise ratio of 43 dB was achieved.

Amorphous silicon e 3D sensors applied to object detection

Nowadays, existing 3D scanning cameras and microscopes in the market use digital or discrete sensors, such as CCDs or CMOS for object detection applications. However, these combined systems are not fast enough for some application scenarios since they require large data processing resources and can be cumbersome. Thereby, there is a clear interest in exploring the possibilities and performances of analogue sensors such as arrays of position sensitive detectors with the final goal of integrating them in 3D scanning cameras or microscopes for object detection purposes. The work performed in this thesis deals with the implementation of prototype systems in order to explore the application of object detection using amorphous silicon position sensors of 32 and 128 lines which were produced in the clean room at CENIMAT-CEMOP. During the first phase of this work, the fabrication and the study of the static and dynamic specifications of the sensors as well as their conditioning in relation to the existing scientific and technological knowledge became a starting point. Subsequently, relevant data acquisition and suitable signal processing electronics were assembled. Various prototypes were developed for the 32 and 128 array PSD sensors. Appropriate optical solutions were integrated to work together with the constructed prototypes, allowing the required experiments to be carried out and allowing the achievement of the results presented in this thesis. All control, data acquisition and 3D rendering platform software was implemented for the existing systems. All these components were combined together to form several integrated systems for the 32 and 128 line PSD 3D sensors. The performance of the 32 PSD array sensor and system was evaluated for machine vision applications such as for example 3D object rendering as well as for microscopy applications such as for example micro object movement detection. Trials were also performed involving the 128 array PSD sensor systems. Sensor channel non-linearities of approximately 4 to 7% were obtained. Overall results obtained show the possibility of using a linear array of 32/128 1D line sensors based on the amorphous silicon technology to render 3D profiles of objects. The system and setup presented allows 3D rendering at high speeds and at high frame rates. The minimum detail or gap that can be detected by the sensor system is approximately 350 μm when using this current setup. It is also possible to render an object in 3D within a scanning angle range of 15º to 85º and identify its real height as a function of the scanning angle and the image displacement distance on the sensor. Simple and not so simple objects, such as a rubber and a plastic fork, can be rendered in 3D properly and accurately also at high resolution, using this sensor and system platform. The nip structure sensor system can detect primary and even derived colors of objects by a proper adjustment of the integration time of the system and by combining white, red, green and blue (RGB) light sources. A mean colorimetric error of 25.7 was obtained. It is also possible to detect the movement of micrometer objects using the 32 PSD sensor system. This kind of setup offers the possibility to detect if a micro object is moving, what are its dimensions and what is its position in two dimensions, even at high speeds. Results show a non-linearity of about 3% and a spatial resolution of < 2µm.

Immunohistochemistry detection of putative miR-200c and miR-203 targets in breast cancer patients

Part of this thesis will be published in the following: Gomes, B.C., Santos, B. 2015. Methods for studying microRNAs expression and their targets in formalin-fixed, paraffin-embedded (FFPE) breast cancer tissues. In Methods in Molecular Biology: Cancer Drug Resistance (Rueff, J. & Rodrigues, A.S. eds), Springer Protocols.

Gold nanoparticles for the detection of DNA adducts as biomarkers of exposure to acrylamide

The main objective of this thesis was the development of a gold nanoparticle-based methodology for detection of DNA adducts as biomarkers, to try and overcome existing drawbacks in currently employed techniques. For this objective to be achieved, the experimental work was divided in three components: sample preparation, method of detection and development of a model for exposure to acrylamide. Different techniques were employed and combined for de-complexation and purification of DNA samples (including ultrasonic energy, nuclease digestion and chromatography), resulting in a complete protocol for sample treatment, prior to detection. The detection of alkylated nucleotides using gold nanoparticles was performed by two distinct methodologies: mass spectrometry and colorimetric detection. In mass spectrometry, gold nanoparticles were employed for laser desorption/ionisation instead of the organic matrix. Identification of nucleotides was possible by fingerprint, however no specific mass signals were denoted when using gold nanoparticles to analyse biological samples. An alternate method using the colorimetric properties of gold nanoparticles was employed for detection. This method inspired in the non-cross-linking assay allowed the identification of glycidamide-guanine adducts and DNA adducts generated in vitro. For the development of a model of exposure, two different aquatic organisms were studies: a goldfish and a mussel. Organisms were exposed to waterborne acrylamide, after which mortality was recorded and effect concentrations were estimated. In goldfish, both genotoxicity and metabolic alterations were assessed and revealed dose-effect relationships of acrylamide. Histopathological alterations were verified primarily in pancreatic cells, but also in hepatocytes. Mussels showed higher effect concentrations than goldfish. Biomarkers of oxidative stress, biotransformation and neurotoxicity were analysed after prolonged exposure, showing mild oxidative stress in mussel cells, and induction of enzymes involved in detoxification of oxygen radicals. A qualitative histopathological screening revealed gonadotoxicity in female mussels, which may present some risk to population equilibrium.

State detection in a financial portfolio: a self-organizing maps approach for financial time series

This study analyses financial data using the result characterization of a self-organized neural network model. The goal was prototyping a tool that may help an economist or a market analyst to analyse stock market series. To reach this goal, the tool shows economic dependencies and statistics measures over stock market series. The neural network SOM (self-organizing maps) model was used to ex-tract behavioural patterns of the data analysed. Based on this model, it was de-veloped an application to analyse financial data. This application uses a portfo-lio of correlated markets or inverse-correlated markets as input. After the anal-ysis with SOM, the result is represented by micro clusters that are organized by its behaviour tendency. During the study appeared the need of a better analysis for SOM algo-rithm results. This problem was solved with a cluster solution technique, which groups the micro clusters from SOM U-Matrix analyses. The study showed that the correlation and inverse-correlation markets projects multiple clusters of data. These clusters represent multiple trend states that may be useful for technical professionals.

Avaliação de necessidades das pessoas idosas em Medicina Geral e Familiar: um estudo de exequibilidade

RESUMO: Os médicos de família devem participar na detecção precoce dos factores de risco que favorecem o declínio funcional nas pessoas idosas. A avaliação estruturada das suas necessidades poderá contribuir para identificar os problemas de saúde que traduzam deterioração funcional. O objectivo deste trabalho foi avaliar a exequibilidade da implementação de um processo de avaliação de necessidades de cuidados em saúde das pessoas idosas na consulta de MGF.Seleccionou-se uma amostra não aleatória de pacientes com 65 ou mais anos de idade, na consulta médica de uma Unidade de Saúde Familiar da região de Lisboa. A avaliação de necessidades foi realizada, pelos médicos, com cinco itens da entrevista Camberwell Assessment of Need for the Elderly (CANE-5). Avaliou-se a percepção dos médicos e dos pacientes sobre este processo de avaliação de necessidades mediante um questionário escrito e entrevistas individuais, respectivamente. Identificaram-se necessidades em 38 (75%) dos 51 pacientes avaliados. Do total das 83 necessidades identificadas, 17 não estavam cobertas. O sofrimento psicológico foi a necessidade não coberta mais frequente. A comparação das avaliações do médico com as do paciente mostrou concordância razoável ou boa nas cinco áreas avaliadas. Esta avaliação foi bem aceite e considerada útil na perspectiva dos médicos e dos pacientes. A principal dificuldade identificada pelos médicos foi o tempo despendido na avaliação face à duração da consulta. Este estudo aponta para a exequibilidade da utilização da entrevista CANE-5 na prática clínica de MGF. No entanto, será importante alargar este estudo a amostras de maior dimensão e avaliar a utilidade da entrevista em intervenções sobre a funcionalidade dos pacientes idosos.----------ABSTRACT: General practitioners (GP) should participate in the early detection of risk factors for fuctional disability in elderly people. Structured needs assessments may contribute to a better identification of health problems that are linked to functional decline. The aim of this study was to assess the feasibility of a structured assessment of needs in the elderly, in the context of opportunistic screening in primary care. A convenience sample was selected of patients aged 65 years and over with scheduled appointments in one general practice in the Lisbon region. The assessment of needs was done by their GPs, using five items of the Camberwell Assessment of Need for the Elderly (CANE-5). Perceptions of GPs and patients about this process of needs assessment were ev+aluated by means of a written questionnaire and individual interviews, respectively. Needs were identified in 38 (75%) of 51 patients. Seventeen unmet needs were identified, out of a total number of 83 needs. Psychological distress was the most frequent unmet need. GP’s and patients’ assessments showed moderate or good agreement in all five areas. This needs’ assessment process was well accepted and considered useful by both GPs and patients. The main difficulty, according to the views of GPs, was the time consumed in this process, given the length of consultation. This study suggests the feasibility of using the CANE-5 interview in clinical practice in primary care settings. However it is important to replicate this study in larger samples and to evaluate the usefulness of the interview regarding interventions related to functionality in elderly patients.

Modelação do risco de incêndio florestal à escala municipal com recurso a dados de detecção remota

Neste projecto é testada uma metodologia para actualização de mapas de ocupação do solo já existentes, derivados de fotografia aérea, usando uma imagem satélite para posterior modelação com vista à obtenção da cartografia do risco de incêndio actualizada. Os diferentes passos metodológicos na fase da actualização dos mapas de ocupação de solo são: Classificação digital das novas ocupações, Produção do mapa de alterações, Integração de informação auxiliar, Actualização da Cartografia Temática. Para a produção do mapa de alterações a detecção de alterações foi efectuada através de expressões de Álgebra de Mapas. A classificação digital foi realizada com um classificador assistido - Classificador da Máxima Verosimilhança. A integração de informação auxiliar serviu para melhorar os resultados da classificação digital, nomeadamente em termos das áreas ardidas permitindo uma resolução temática mais detalhada. A actualização resultou da sobreposição do mapa das áreas alteradas classificadas com o mapa desactualizado. Como produto obteve-se a Carta de Alterações da Ocupação do Solo com Potencial Influência no Risco de Incêndio actualizada para 2008, base para a fase da Modelação do Risco. A metodologia foi testada no concelho de Viseu, Centro de Portugal. A Carta de Uso e Ocupação do Solo de Portugal Continental para 2007 (COS2007) foi utilizada como carta de referência. A nova carta actualizada para 2008, no concelho de Viseu, apresenta 103 classes temáticas, 1ha de unidade mínima e 90% de precisão global. A modelação do risco de incêndio geralmente é feita através de índices que variam, de forma geral, numa escala qualitativa, tendo como fim possibilitar a definição de acções de planeamento e ordenamento florestal no âmbito da defesa da floresta contra incêndios. Desta forma, as cartas de risco são indicadas para acções de prevenção, devendo ser utilizadas em conjunto com a carta da perigosidade que juntas podem ser utilizadas em acções de planeamento, em acções de combate e supressão. A metodologia testada, neste projecto, para elaboração de cartografia de risco foi, a proposta por Verde (2008) e adoptada pela AFN (2012). Os resultados apresentados vão precisamente ao encontro do que diz respeito no Guia Técnico para Plano Municipal de Defesa da Floresta Contra Incêndios, "O mapa de Risco combina as componentes do mapa de perigosidade com as componentes do dano potencial (vulnerabilidade e valor) para indicar qual o potencial de perda face ao incêndio florestal".

Design of a CMOS amplifier for breast cancer detection

A transimpedance amplifier (TIA) is used, in radiation detectors like the positron emission tomography(PET), to transform the current pulse produced by a photo-sensitive device into an output voltage pulse with a desired amplitude and shape. The TIA must have the lowest noise possible to maximize the output. To achieve a low noise, a circuit topology is proposed where an auxiliary path is added to the feedback TIA input, In this auxiliary path a differential transconductance block is used to transform the node voltage in to a current, this current is then converted to a voltage pulse by a second feedback TIA complementary to the first one, with the same amplitude but 180º out of phase with the first feedback TIA. With this circuit the input signal of the TIA appears differential at the output, this is used to try an reduced the circuit noise. The circuit is tested with two different devices, the Avalanche photodiodes (APD) and the Silicon photomultiplier (SIPMs). From the simulations we find that when using s SIPM with Rx=20kΩ and Cx=50fF the signal to noise ratio is increased from 59 when using only one feedback TIA to 68.3 when we use an auxiliary path in conjunction with the feedback TIA. This values where achieved with a total power consumption of 4.82mv. While the signal to noise ratio in the case of the SIPM is increased with some penalty in power consumption.

Land cover mapping analysis and urban growth modeling using remote sensing techniques

The rapid growth of big cities has been noticed since 1950s when the majority of world population turned to live in urban areas rather than villages, seeking better job opportunities and higher quality of services and lifestyle circumstances. This demographic transition from rural to urban is expected to have a continuous increase. Governments, especially in less developed countries, are going to face more challenges in different sectors, raising the essence of understanding the spatial pattern of the growth for an effective urban planning. The study aimed to detect, analyse and model the urban growth in Greater Cairo Region (GCR) as one of the fast growing mega cities in the world using remote sensing data. Knowing the current and estimated urbanization situation in GCR will help decision makers in Egypt to adjust their plans and develop new ones. These plans should focus on resources reallocation to overcome the problems arising in the future and to achieve a sustainable development of urban areas, especially after the high percentage of illegal settlements which took place in the last decades. The study focused on a period of 30 years; from 1984 to 2014, and the major transitions to urban were modelled to predict the future scenarios in 2025. Three satellite images of different time stamps (1984, 2003 and 2014) were classified using Support Vector Machines (SVM) classifier, then the land cover changes were detected by applying a high level mapping technique. Later the results were analyzed for higher accurate estimations of the urban growth in the future in 2025 using Land Change Modeler (LCM) embedded in IDRISI software. Moreover, the spatial and temporal urban growth patterns were analyzed using statistical metrics developed in FRAGSTATS software. The study resulted in an overall classification accuracy of 96%, 97.3% and 96.3% for 1984, 2003 and 2014’s map, respectively. Between 1984 and 2003, 19 179 hectares of vegetation and 21 417 hectares of desert changed to urban, while from 2003 to 2014, the transitions to urban from both land cover classes were found to be 16 486 and 31 045 hectares, respectively. The model results indicated that 14% of the vegetation and 4% of the desert in 2014 will turn into urban in 2025, representing 16 512 and 24 687 hectares, respectively.

Methodological framework for detection of harmonisation breaking in service environments

As the complexity of markets and the dynamicity of systems evolve, the need for interoperable systems capable of strengthening enterprise communication effectiveness increases. This is particularly significant when it comes to collaborative enterprise networks, like manufacturing supply chains, where several companies work, communicate, and depend on each other, in order to achieve a specific goal. Once interoperability is achieved, that is once all network parties are able to communicate with and understand each other, organisations are able to exchange information along a stable environment that follows agreed laws. However, as markets adapt to new requirements and demands, an evolutionary behaviour is triggered giving space to interoperability problems, thus disrupting the sustainability of interoperability and raising the need to develop monitoring activities capable of detecting and preventing unexpected behaviour. This work seeks to contribute to the development of monitoring techniques for interoperable SOA-based enterprise networks. It focuses on the automatic detection of harmonisation breaking events during real-time communications, and strives to develop and propose a methodological approach to handle these disruptions with minimal or no human intervention, hence providing existing service-based networks with the ability to detect and promptly react to interoperability issues.

Posicionamento do Brasil face aos países mais avançados em cloud computing

This study discusses some fundamental issues so that the development and diffusion of services based in cloud computing happen positively in several countries. For exposure of this subject is discusses public initiatives by the most advanced countries in terms of cloud computing application and the brazilin position in this context. Based on presented evidences here it appears that the essential elements for the development and diffusion of cloud computing in Brazil made important steps and show evidence of maturity, as the cybercrime legislation. However, other elements still require analysis and specifically adaptations for the cloud computing case, such as the Intellectual Property Rights. Despite showing broadband services still lacking, one cannot disregard the government effort to facilitate access for all society. In contrast, the large volume of the Brazilian IT market is an interest factor for companies seeking to invest in the country.