Enhanced Digital Breast Tomosynthesis diagnosis using 3D visualization and automatic classification of lesions

Breast cancer represents the main cause of cancer-related deaths in women. Nonetheless, the mortality rate of this disease has been decreasing over the last three decades, largely due to the screening programs for early detection. For many years, both screening and clinical diagnosis were mostly done through Digital Mammography (DM). Approved in 2011, Digital Breast Tomosynthesis (DBT) is similar to DM but it allows a 3D reconstruction of the breast tissue, which helps the diagnosis by reducing the tissue overlap. Currently, DBT is firmly established and is approved as a stand-alone modality to replace DM. The main objective of this thesis is to develop computational tools to improve the visualization and interpretation of DBT data. Several methods for an enhanced visualization of DBT data through volume rendering were studied and developed. Firstly, important rendering parameters were considered. A new approach for automatic generation of transfer functions was implemented and two other parameters that highly affect the quality of volume rendered images were explored: voxel size in Z direction and sampling distance. Next, new image processing methods that improve the rendering quality by considering the noise regularization and the reduction of out-of-plane artifacts were developed. The interpretation of DBT data with automatic detection of lesions was approached through artificial intelligence methods. Several deep learning Convolutional Neural Networks (CNNs) were implemented and trained to classify a complete DBT image for the presence or absence of microcalcification clusters (MCs). Then, a faster R-CNN (region-based CNN) was trained to detect and accurately locate the MCs in the DBT images. The detected MCs were rendered with the developed 3D rendering software, which provided an enhanced visualization of the volume of interest. The combination of volume visualization with lesion detection may, in the future, improve both diagnostic accuracy and also reduce analysis time. This thesis promotes the development of new computational imaging methods to increase the diagnostic value of DBT, with the aim of assisting radiologists in their task of analyzing DBT volumes and diagnosing breast cancer

Growth enhancement of benthic diatoms for industrial applications

Este resumo faz parte de: Book of abstracts of the Meeting of the Institute for Biotechnology and Bioengineering, 2, Braga, Portugal, 2010. A versão completa do livro de atas está disponível em: http://hdl.handle.net/1822/1096

Physiological responses of Tetrahymena pyriformis to copper, zinc, cycloheximide and Triton X-100

Protozoa, and particularly ciliates, are essential in aerobic purification processes of wastewaters and have proved to be very sensitive to environmental changes. The physiological response of the ciliate Tetrahymena pyriformis was assessed in terms of mortality, growth and grazing capacity after exposure to four toxicants: copper, zinc, cycloheximide and Triton X-100. In the ranges of concentrations used, mortality, inhibition of growth and inhibition of grazing were observed with all toxicants employed, but in different ways. Copper and zinc showed lower toxicity than observed in other studies with protozoa, though some of the present results are in accordance with those reported by other authors. This supports the importance of the organism tested and the experimental conditions of the bioassays.Instituto de Biotecnologia e Química Fina (IBQF).Fundação para a Ciência e a Tecnologia (FCT) - Praxis XXI - 2/2.1/BIO/1118/95, Praxis XXI - grant BD/5080/95

Trends in the use of protozoa in the assessment of wastewater treatment

Increasing environmental pollution and the continuous development of new chemicals and drugs has led to ever growing concern about the potential effects of these compounds directly or indirectly on human health. As concerns water pollution, protozoa seem to be an excellent tool to assess both toxicity and pollution: they are regarded as biological indicators of pollution when their presence or absence can be related to particular environmental conditions, and they are considered test organisms when a species or population is used to evaluate the toxicity of relevant toxic compounds. Thus, an integrated approach is being developed to assess how toxic compounds affect the different biological levels of organisation – from the community level to the species level – of ciliated protozoa. The present paper reports and discusses the current state of the art of this approach.Instituto de Biotecnologia e Química Fina (IBQF). Fundação para a Ciência e a Tecnologia - PRAXIS XXI-2/2.1/BIO/1118/95, PRAXIS XXI/BD/5080/95, PRAXIS XXI/BD/20328/99

Estudo da comunidade de protozoários exposta a tóxicos em estações de tratamentos de águas residuais

A importância e o papel dos protozoários nos processos de tratamento aeróbio de águas residuais são bem conhecidos, e constituem um valioso instrumento da avaliação do funcionamento das ETAR, por permitir relacionar a densidade, diversidade ou a ocorrência de determinadas espécies com a composição do esgoto ou com os factores físico-químicos prevalecentes no tanque de arejamento. No presente trabalho, duas estações de tratamento de águas residuais experimentais foram alimentadas com esgoto real e as lamas foram expostas a diversas concentrações de cobre, zinco e cicloheximida. Nestas condições, foi estudada a evolução da comunidade de protozoários, em termos de diversidade, de densidade e da sua estrutura, utilizando o Índice Biótico de Lamas, e relacionada esta evolução com a eficiência de remoção da CQO.Programa Praxi

Importância da identificação das espécies responsáveis pelo crescimento filamentoso nas ETARs

Para se ultrapassarem as situações de crescimento filamentoso exagerado, é necessário, antes de mais, identificar correctamente a espécie ou espécies responsáveis por esse crescimento. Após a correcta identificação dos microrganismos causadores do problema filamentoso poder-se-á então optar pelas medidas que incidam sobre as causas do fenómeno e não apenas sobre os efeitos. As acções sobre as causas podem ser complementadas por acções de remoção e/ou desinfecção, mas só quando se tornarem imprescindíveis e nunca substituindo as primeiras por estas. A identificação dos organismos filamentosos torna-se assim uma ferramenta essencial na gestão das estações de tratamento de águas residuais quando estiverem em causa problemas de bulking ou foaming. O presente trabalho avança algumas ideias sobre as principais causas do crescimento filamentoso, espécies ocorrentes e modos de resolução do crescimento filamentoso