Advanced image processing techniques for detection and quantification of drusen

Dissertation presented to obtain the degree of Doctor of Philosophy in Electrical Engineering, speciality on Perceptional Systems, by the Universidade Nova de Lisboa, Faculty of Sciences and Technology

Downstream processing development of enveloped viruses for clinical applications: innovative tools for rational process optimization

Dissertation presented to obtain a Ph.D. degree in Engineering and Technology Sciences, Biotechnology at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Using interval graphs in an order processing optimization problem

In this paper we address an order processing optimization problem known as minimization of open stacks (MOSP). We present an integer pro gramming model, based on the existence of a perfect elimination scheme in interval graphs, which finds an optimal sequence for the costumers orders.

Effects of storage, processing and proteolytic digestion on microcystin-LR concentration in edible clams

Accumulation of microcystin-LR (MC-LR) in edible aquatic organisms, particularly in bivalves, is widely documented. In this study, the effects of food storage and processing conditions on the free MC-LR concentration in clams (Corbicula fluminea) fed MC-LR-producing Microcystisaeruginosa (1 × 105 cell/mL) for four days, and the bioaccessibility of MC-LR after in vitro proteolytic digestion were investigated. The concentration of free MC-LR in clams decreased sequentially over the time with unrefrigerated and refrigerated storage and increased with freezing storage. Overall, cooking for short periods of time resulted in a significantly higher concentration (P < 0.05) of free MC-LR in clams, specifically microwave (MW) radiation treatment for 0.5 (57.5%) and 1 min (59%) and boiling treatment for 5 (163.4%) and 15 min (213.4%). The bioaccessibility of MC-LR after proteolytic digestion was reduced to 83%, potentially because of MC-LR degradation by pancreatic enzymes. Our results suggest that risk assessment based on direct comparison between MC-LR concentrations determined in raw food products and the tolerable daily intake (TDI) value set for the MC-LR might not be representative of true human exposure.

The Crystal Structure of the Escherichia coli Autoinducer-2 Processing Protein LsrF

PLOS ONE, 4(8):ARTe6820

Assessment of groundwater contamination in an agricultural peri-urban area (NW Portugal): an integrated approach

The excessive use of pesticides and fertilisers in agriculture has generated a decrease in groundwater and surface water quality in many regions of the EU, constituting a hazard for human health and the environment. Besides, on-site sewage disposal is an important source of groundwater contamination in urban and peri-urban areas. The assessment of groundwater vulnerability to contamination is an important tool to fulfil the demands of EU Directives. The purpose of this study is to assess the groundwater vulnerability to contamination related mainly to agricultural activities in a peri-urban area (Vila do Conde, NW Portugal). The hydrogeological framework is characterised mainly by fissured granitic basement and sedimentary cover. Water samples were collected and analysed for temperature, pH, electrical conductivity, chloride, phosphate, nitrate and nitrite. An evaluation of groundwater vulnerability to contamination was applied (GOD-S, Pesticide DRASTIC-Fm, SINTACS and SI) and the potential nitrate contamination risk was assessed, both on a hydrogeological GIS-based mapping. A principal component analysis was performed to characterised patterns of relationship among groundwater contamination, vulnerability, and the hydrogeological setting assessed. Levels of nitrate above legislation limits were detected in 75 % of the samples analysed. Alluvia units showed the highest nitrate concentrations and also the highest vulnerability and risk. Nitrate contamination is a serious problem affecting groundwater, particularly shallow aquifers, especially due to agriculture activities, livestock and cesspools. GIS-based cartography provided an accurate way to improve knowledge on water circulation models and global functioning of local aquifer systems. Finally, this study highlights the adequacy of an integrated approach, combining hydrogeochemical data, vulnerability assessments and multivariate analysis, to understand groundwater processes in peri-urban areas.

Effects of tissue handling and processing steps on PCR for detection of Mycobacterium tuberculosis in formalin-fixed paraffin-embedded samples

Development and standardization of reliable methods for detection of Mycobacterium tuberculosis in clinical samples is an important goal in laboratories throughout the world. In this work, lung and spleen fragments from a patient who died with the diagnosis of miliary tuberculosis were used to evaluate the influence of the type of fixative as well as the fixation and paraffin inclusion protocols on PCR performance in paraffin embedded specimens. Tissue fragments were fixed for four h to 48 h, using either 10% non-buffered or 10% buffered formalin, and embedded in pure paraffin or paraffin mixed with bee wax. Specimens were submitted to PCR for amplification of the human beta-actin gene and separately for amplification of the insertion sequence IS6110, specific from the M. tuberculosis complex. Amplification of the beta-actin gene was positive in all samples. No amplicons were generated by PCR-IS6110 when lung tissue fragments were fixed using 10% non-buffered formalin and were embedded in paraffin containing bee wax. In conclusion, combined inhibitory factors interfere in the detection of M. tuberculosis in stored material. It is important to control these inhibitory factors in order to implement molecular diagnosis in pathology laboratories.

Analysis of Natural and Artificial Phenomena Using Signal Processing and Fractional Calculus

In this paper we study several natural and man-made complex phenomena in the perspective of dynamical systems. For each class of phenomena, the system outputs are time-series records obtained in identical conditions. The time-series are viewed as manifestations of the system behavior and are processed for analyzing the system dynamics. First, we use the Fourier transform to process the data and we approximate the amplitude spectra by means of power law functions. We interpret the power law parameters as a phenomenological signature of the system dynamics. Second, we adopt the techniques of non-hierarchical clustering and multidimensional scaling to visualize hidden relationships between the complex phenomena. Third, we propose a vector field based analogy to interpret the patterns unveiled by the PL parameters.

Development and implementation of strategies for the incorporation of reinforcing elements in aluminium alloys by solid state processing

Dissertação para obtenção do Grau de Mestre em Engenharia Mecânica

Long-term biosignals visualization and processing

Thesis submitted in the fulfillment of the requirements for the Degree of Master in Biomedical Engineering

Parallel programming in biomedical signal processing

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Distributed processing of large remote sensing images using MapReduce - A case of Edge Detection

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Parallelization of web processing services on cloud computing: A case study of Geostatistical Methods

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Validating Regulatory Sensory Processing Disorders Using the Sensory Profile and Child Behavior Checklist (CBCL 1 –5)

The objective was to validate Regulatory Sensory Processing Disorders’ criteria (DC:0-3R, 2005) using empirical data on the presence and severity of sensory modulation deficits and specific psychiatric symptoms in clinical samples. Sixty toddlers who attended a child mental health unit were diagnosed by a clinical team. The following two groups were created: toddlers with RSPD(N = 14) and those with ‘‘other diagnoses in Axis I/II of the DC:0-3R00(OD3R) (N = 46). Independently of the clinical process, parents completed the Infant Toddler Sensory Profile (as a checklist for sensory symptoms) and the Achenbach Behavior Checklist for ages 1/2–5 (CBCL 1/2–5). The scores from the two groups were compared. The results showed the following for the RSPD group: a higher number of affected sensory areas and patterns than in the OD3R group; a higher percentage of sensory deficits in specific sensory categories; and a higher severity of behavioral symptoms such as withdrawal, inattention, other externalizing problems and pervasive developmental problems in CBCL 1/2–5. The results confirmed our hypotheses by indicating a higher severity of sensory symptoms and identifying specific behavioral problems in children with RSPD. The results revealed convergent validity between the instruments and the diagnostic criteria for RSPD and supported the validity of RSPD as a unique diagnosis. The findings also suggested the importance of identifying sensory modulation deficits in order to develop an early intervention to enhance the sensory capacities of children who do not fully satisfy the criteria for some DSM-IV-TR disorders.

Optimization of fMRI Processing Parameters for Simutaneous Acquisition of EEG/fMRI in Focal Epilepsy

In the context of focal epilepsy, the simultaneous combination of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) holds a great promise as a technique by which the hemodynamic correlates of interictal spikes detected on scalp EEG can be identified. The fact that traditional EEG recordings have not been able to overcome the difficulty in correlating the ictal clinical symptoms to the onset in particular areas of the lobes, brings the need of mapping with more precision the epileptogenic cortical regions. On the other hand, fMRI suggested localizations more consistent with the ictal clinical manifestations detected. This study was developed in order to improve the knowledge about the way parameters involved in the physical and mathematical data, produced by the EEG/fMRI technique processing, would influence the final results. The evaluation of the accuracy was made by comparing the BOLD results with: the high resolution EEG maps; the malformative lesions detected in the T1 weighted MR images; and the anatomical localizations of the diagnosed symptomatology of each studied patient. The optimization of the set of parameters used, will provide an important contribution to the diagnosis of epileptogenic focuses, in patients included on an epilepsy surgery evaluation program. The results obtained allowed us to conclude that: by associating the BOLD effect with interictal spikes, the epileptogenic areas are mapped to localizations different from those obtained by the EEG maps representing the electrical potential distribution across the scalp (EEG); there is an important and solid bond between the variation of particular parameters (manipulated during the fMRI data processing) and the optimization of the final results, from which smoothing, deleted volumes, HRF (used to convolve with the activation design), and the shape of the Gamma function can be certainly emphasized.