Spectrum sensing through software defined radio

Dissertação apresentada para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Optimization of breast tomosynthesis image reconstruction using parallel computing

Breast cancer is the most common cancer among women, being a major public health problem. Worldwide, X-ray mammography is the current gold-standard for medical imaging of breast cancer. However, it has associated some well-known limitations. The false-negative rates, up to 66% in symptomatic women, and the false-positive rates, up to 60%, are a continued source of concern and debate. These drawbacks prompt the development of other imaging techniques for breast cancer detection, in which Digital Breast Tomosynthesis (DBT) is included. DBT is a 3D radiographic technique that reduces the obscuring effect of tissue overlap and appears to address both issues of false-negative and false-positive rates. The 3D images in DBT are only achieved through image reconstruction methods. These methods play an important role in a clinical setting since there is a need to implement a reconstruction process that is both accurate and fast. This dissertation deals with the optimization of iterative algorithms, with parallel computing through an implementation on Graphics Processing Units (GPUs) to make the 3D reconstruction faster using Compute Unified Device Architecture (CUDA). Iterative algorithms have shown to produce the highest quality DBT images, but since they are computationally intensive, their clinical use is currently rejected. These algorithms have the potential to reduce patient dose in DBT scans. A method of integrating CUDA in Interactive Data Language (IDL) is proposed in order to accelerate the DBT image reconstructions. This method has never been attempted before for DBT. In this work the system matrix calculation, the most computationally expensive part of iterative algorithms, is accelerated. A speedup of 1.6 is achieved proving the fact that GPUs can accelerate the IDL implementation.

Automatic delimitation of the clinical region of interest in ultra-wide field of view images of the retina

Retinal ultra-wide field of view images (fundus images) provides the visu-alization of a large part of the retina though, artifacts may appear in those images. Eyelashes and eyelids often cover the clinical region of interest and worse, eye-lashes can be mistaken with arteries and/or veins when those images are put through automatic diagnosis or segmentation software creating, in those cases, the appearance of false positives results. Correcting this problem, the first step in the development of qualified auto-matic diseases diagnosis programs can be done and in that way the development of an objective tool to assess diseases eradicating the human error from those processes can also be achieved. In this work the development of a tool that automatically delimitates the clinical region of interest is proposed by retrieving features from the images that will be analyzed by an automatic classifier. This automatic classifier will evaluate the information and will decide which part of the image is of interest and which part contains artifacts. The results were validated by implementing a software in C# language and validated through a statistical analysis. From those results it was confirmed that the methodology presented is capable of detecting artifacts and selecting the clin-ical region of interest in fundus images of the retina.

Characterization tests for insulation boards made from corn cob and natural glues

In recent years there has been a growing interest in developing news solutions for more ecologic and efficient construction, including natural, renewable and local materials, thus contributing in the search for more efficient, economic and environmentally friendly construction. Several authors have assessed the possibility of using various agricultural sub products or wastes, as part of the effort of the scientific community to find alternative and more ecologic construction materials. Corn cob is an agricultural waste from a very important worldwide crop. Natural glues are made from natural materials, non-mineral, that can be used as such or after some modifications to achieve the behaviour and performance required. Two examples of these natural glues are casein and wheat flour-based glues that were used in the present study. Boards with different compositions were manufactured, having as variables the type of glue, the dimension of the corn cob particles and the features of the pressing process. The tests boards were characterized with physical and mechanical tests, such as thermal conductivity (λ) with a ISOMET 2104 and 60 mm diameter contact probe, density (ρ) based on EN 1602:2013, surface hardness (SH) with a PCE Shore A durometer, surface resistance (SR) with a PROCEQ PT pendular sclerometer, bending behaviour (σ) based on EN 12089:2013, compression behaviour (σ10) based on EN 826:2013 and resilience (R) based on EN 1094-1:2008, with a Zwick Rowell bending equipment with 2 kN and 50 kN load cells (Fig. 1), dynamic modulus of elasticity (Ed) with a Zeus Resonance Meter equipment (Fig. 5) based on NP EN 14146:2006 and water vapour permeability (δ) based on EN 12086:2013. The various boards produced were characterized according to the tests and the ones with the best results were C8_c8 (casein glue, grain size 2,38-4,76 mm, cold pressing for 8 hours), C8_c4 (casein glue, grain size 2,38-4,76 mm, cold pressing for 4 hours), F8_h0.5 (wheat flour glue, grain size 2,38-4,76 mm, hot pressing for 0,5 hours), FEV8_h0.5 (wheat flour, egg white and vinegar glue, grain size 2,38-4,76 mm, hot pressing for 0,5 hours) and FEVH68_c4 (wheat flour, egg white, vinegar and 6 g of sodium hydroxide glue, grain size 2,38-4,76 mm, cold pressing for 4 hours). Taking into account the various boards produced and respective test results the type of glue and the pressure and pressing time are very important factors which strongly influence the final product. The results obtained confirmed the initial hypotheses that these boards have potential as a thermal and, eventually, acoustic insulation material, to use as coating or intermediate layer on walls, floors or false ceilings. This type of board has a high mechanical resistance when compared with traditional insulating materials.The integrity of these boards seems to be maintained even in higher humidity environments. However, due to biological susceptibility and sensitivity to water, they would be more adequate for application in dry interior conditions.

Towards modification of Medicago truncatula epigenome: genome editing with engineered nucleases

Periodic drought is the primary limitation of plant growth and crop yield. The rise of water demand caused by the increase in world population and climate change, leads to one of the biggest challenges of modern agriculture: to increase food and feed production. De novo DNA methylation is a process regulated by small interfering RNA (siRNAs), which play a role in plant response and adaptation to abiotic stress. In the particular case of water deficit, growing evidences suggest a link between the siRNA pathways and drought response in the model legume Medicago truncatula. As a first step to understand the role of DNA methylation under water stress, we have set up several bioinformatics and molecular methodologies allowing the design of Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 systems and the assembly of TALENs (transcription activator-like effector nucleases), to target both dicer-like 3 (MtDCL3) and RNA-Dependent RNA polymerase (MtRDR2), enzymes of the RNA-directed DNA methylation pathway. TALENs efficiency was evaluated prior to plant transformation by a yeast-based assay using two different strategies to test TALENs activity: Polyacrylamide gel electrophoresis (PAGE) and Single strand conformation polymorphisms (SSCP). In this assay, yeast cells triple transformation emerged as good and rapid alternative to laborious yeast mating strategies. PAGE analysis might be a valuable tool to test TALENs efficacy in vivo if we could increase TALENs activity. SSCP-based approach proved to be ineffective due to the generation of several false positives. TALENs and CRISPR/Cas9 system constructed and designed in this work will in the future certainly enable the successful disruption of DCL3 and RDR2 genes and shed the light on the relationship between plant stress resistance and epigenetic regulation mediated by siRNAs in M.truncatula.

Improving the early diagnostic of prostate cancer by multiple biomarker detection with new biosensing devices

Prostate cancer (PCa) is the most common form of cancer in men, in Europe (World Health Organization data). The most recent statistics, in Portuguese territory, confirm this scenario, which states that about 50% of Portuguese men may suffer from prostate cancer and 15% of these will die from this condition. Its early detection is therefore fundamental. This is currently being done by Prostate Specific Antigen (PSA) screening in urine but false positive and negative results are quite often obtained and many patients are sent to unnecessary biopsy procedures. This early detection protocol may be improved, by the development of point-of-care cancer detection devices, not only to PSA but also to other biomarkers recently identified. Thus, the present work aims to screen several biomarkers in cultured human prostate cell lines, serum and urine samples, developing low cost sensors based on new synthetic biomaterials. Biomarkers considered in this study are the following: prostate specific antigen (PSA), annexin A3 (ANXA3), microseminoprotein-beta (MSMB) and sarcosine (SAR). The biomarker recognition may occurs by means of molecularly imprinted polymers (MIP), which are a kind of plastic antibodies, and enzymatic approaches. The growth of a rigid polymer, chemically stable, using the biomarker as a template allows the synthesis of the plastic antibody. MIPs show high sensitivity/selectivity and present much longer stability and much lower price than natural antibodies. This nanostructured material was prepared on a carbon solid. The interaction between the biomarker and the sensing-material produces electrical signals generating quantitative or semi-quantitative data. These devices allow inexpensive and portable detection in point-of-care testing.

Efeito de um resultado falso positivo da leitura da mamografia na não participação no rastreio do cancro da mama : estudo de coorte histórico de um rastreio de base populacional da região de saúde do centro em Portugal

RESUMO - Introdução: O cancro da mama é uma das principais causas de mortalidade por doença oncológica. O rastreio contribui para o aumento da sobrevivência, mas apresenta riscos como a obtenção de um resultado falso positivo com efeitos controversos sobre a participação subsequente. Métodos: Realizou-se um estudo de coorte histórico (2006-2012) de 170.835 mulheres com 45-67 anos, elegíveis para o programa de rastreio do cancro da mama da ARSC,IP. Calcularam-se as medidas de efeito de um falso positivo da leitura na não participação na volta consecutiva de rastreio do cancro da mama, e a associação entre o evento em estudo e factores sociodemográficos, relacionados com o rastreio e com a anamnese, através de análise de regressão de Poisson. Resultados: A incidência de não participação foi 12,13%. A exposição a falso positivo da leitura aumentou 8,01% o risco absoluto de não participação. O falso positivo da leitura da mamografia revelou-se um factor de risco para a não participação (RRa=1,17; IC 1,10-1,25). O efeito protector da existência de participações anteriores foi superior ao efeito dos factores de risco identificados. Identificaram-se outros factores de risco e de protecção. Discussão: De acordo com os factores de risco e de protecção identificados recomendaram-se alterações à operacionalização do programa de rastreio, a manutenção das estatégias adequadas e a realização de estudos futuros para avaliar o efeito de outros factores não incluídos neste estudo. A comunicação do risco associado a um resultado anormal da mamografia é importante para diminuir a ansiedade consequente ao rastreio, devendo ser oferecidas intervenções que promovam a participação no rastreio.

A conspiracy theory for clefts : the syntax and interpretation of cleft constructions

O objetivo final deste estudo é contribuir para a discussão sobre qual a medida em que conceitos semânticos e discursivos estão sintaticamente codificados. Mais especificamente, investiga-se se existe alguma correlação consistente entre alguns aspetos interpretativos e sintáticos de quatro construções clivadas do Português Europeu, e como se deve dar conta teoricamente destas potenciais correlações. As clivadas consideradas são as clivadas canónicas, as pseudoclivadas, as clivadas de é que e as clivadas de SER. Sintaticamente podemos distinguir dois tipos: clivadas bioracionais (canónicas e pseudoclivadas) e clivadas mono-oracionais (clivadas de é que e de SER). Todas as estruturas têm um constituinte clivado focalizado que pode constituir tanto um foco informacional como um foco contrastivo, e uma oração clivada que introduz uma pressuposição existencial. Adicionalmente, o constituinte clivado identifica exaustivamente uma posição vazia na oração clivada. Adota-se a semântica alternativa para o foco (Rooth 1985), segundo a qual o foco entoacional contribui uniformemente um conjunto de alternativas na Forma Lógica. Regras pragmáticas operando neste conjunto dão origem a duas implicaturas que podem ser suspensas: pressuposição existencial e exaustividade. Dado que as clivadas de é que e as de SER têm a mesma interpretação que orações não-clivadas, conclui-se que a sua estrutura sintática particular não contribui para estas propriedades interpretativas. Em contrapartida, as clivadas bioracionais, que são orações copulativas especificacionais, têm uma presuposição existencial e uma interpretação exaustiva que não pode ser suspensa, tal como as orações especificacionais não-clivadas. Argumenta-se que isto se deve ao facto de o constituinte clivado identificar uma variável introduzida por uma descrição definida. Demonstra-se que a oração clivada, uma relativa em posição de complemento de um determinador definido nas clivadas canónicas e uma relativa livre nas pseudoclivadas, tem a mesma denotação que um DP definido, e portanto tem uma pressuposição existencial inerente. A interpretação exaustiva deve-se à relação identificacional entre o constituinte clivado e a descrição definida. Além disso, defende-se que em Português Europeu um traço de foco não desencadeia movimento-A’ para um FocP especializado. Os constituintes focalizados movem-se antes por razões independentes do foco. Isto é confirmado pelo facto de apenas o constituinte clivado das clivadas de é que ter propriedades de movimento A’, os outros parecem estar in situ. Propõe-se que o constituinte clivado das clivadas de é que é um tópico com um traço de foco que se move para um TopP. Esta análise dá conta da existência de restrições discursivas semelhantes para tópicos não focalizados e para o constituinte clivado das clivadas de é que. O traço quantificacional de foco arrastado pela topicalização dá origem a efeitos de intervenção, causando a não-recursividade do foco na periferia esquerda e a sua incompatibilidade com movimento de outros constituintes com traços quantificacionais. A análise prediz as restrições de encaixe observadas para as clivadas de é que. Finalmente, desenvolve-se uma análise sintática das clivadas de SER que aproxima estas estruturas das estruturas com partículas de foco. Propõe-se que a cópula é um operador sensível ao foco que é merged juntamente com o constituinte clivado. As restrições distribucionais da cópula devem-se a requisitos selecionais de núcleos.

Distributed solar micro generation

Taking into account the fact that the sun’s radiation is estimated to be enough to cover 10.000 times the world’s total energy needs (BRAKMANN & ARINGHOFF, 2003), it is difficult to understand how solar photovoltaic systems (PV) are still such a small part of the energy source matrix across the globe. Though there is an ongoing debate as to whether energy consumption leads to economic growth or whether it is the other way around, the two variables appear correlated and it is clear that ensuring the availability of energy to match a country’s growth targets is one of the prime concerns for any government. The topic of centralized vs distributed electricity generation is also approached, especially in what regards the latter fit to developing countries needs, namely the lack of investment capabilities and infrastructure, scattered population, and other factors. Finally, Brazil’s case is reviewed, showing that the current cost of electricity from the grid versus the cost from PV solutions still places an investment of this nature with 9 to 16 years to reach breakeven (from a 25 year panel lifespan), which is too high compared to the required 4 years for most Brazilians. Still, recently passed legislation opened the door, even if unknowingly, to the development of co-owned solar farms, which could reduce the implementation costs by as much as 20% and hence reduce the number of years to breakeven by 3 years.