Metabolic signature of lung cancer: a metabolomic study of human tissues and biofluids

This thesis reports the application of metabolomics to human tissues and biofluids (blood plasma and urine) to unveil the metabolic signature of primary lung cancer. In Chapter 1, a brief introduction on lung cancer epidemiology and pathogenesis, together with a review of the main metabolic dysregulations known to be associated with cancer, is presented. The metabolomics approach is also described, addressing the analytical and statistical methods employed, as well as the current state of the art on its application to clinical lung cancer studies. Chapter 2 provides the experimental details of this work, in regard to the subjects enrolled, sample collection and analysis, and data processing. In Chapter 3, the metabolic characterization of intact lung tissues (from 56 patients) by proton High Resolution Magic Angle Spinning (HRMAS) Nuclear Magnetic Resonance (NMR) spectroscopy is described. After careful assessment of acquisition conditions and thorough spectral assignment (over 50 metabolites identified), the metabolic profiles of tumour and adjacent control tissues were compared through multivariate analysis. The two tissue classes could be discriminated with 97% accuracy, with 13 metabolites significantly accounting for this discrimination: glucose and acetate (depleted in tumours), together with lactate, alanine, glutamate, GSH, taurine, creatine, phosphocholine, glycerophosphocholine, phosphoethanolamine, uracil nucleotides and peptides (increased in tumours). Some of these variations corroborated typical features of cancer metabolism (e.g., upregulated glycolysis and glutaminolysis), while others suggested less known pathways (e.g., antioxidant protection, protein degradation) to play important roles. Another major and novel finding described in this chapter was the dependence of this metabolic signature on tumour histological subtype. While main alterations in adenocarcinomas (AdC) related to phospholipid and protein metabolisms, squamous cell carcinomas (SqCC) were found to have stronger glycolytic and glutaminolytic profiles, making it possible to build a valid classification model to discriminate these two subtypes. Chapter 4 reports the NMR metabolomic study of blood plasma from over 100 patients and near 100 healthy controls, the multivariate model built having afforded a classification rate of 87%. The two groups were found to differ significantly in the levels of lactate, pyruvate, acetoacetate, LDL+VLDL lipoproteins and glycoproteins (increased in patients), together with glutamine, histidine, valine, methanol, HDL lipoproteins and two unassigned compounds (decreased in patients). Interestingly, these variations were detected from initial disease stages and the magnitude of some of them depended on the histological type, although not allowing AdC vs. SqCC discrimination. Moreover, it is shown in this chapter that age mismatch between control and cancer groups could not be ruled out as a possible confounding factor, and exploratory external validation afforded a classification rate of 85%. The NMR profiling of urine from lung cancer patients and healthy controls is presented in Chapter 5. Compared to plasma, the classification model built with urinary profiles resulted in a superior classification rate (97%). After careful assessment of possible bias from gender, age and smoking habits, a set of 19 metabolites was proposed to be cancer-related (out of which 3 were unknowns and 6 were partially identified as N-acetylated metabolites). As for plasma, these variations were detected regardless of disease stage and showed some dependency on histological subtype, the AdC vs. SqCC model built showing modest predictive power. In addition, preliminary external validation of the urine-based classification model afforded 100% sensitivity and 90% specificity, which are exciting results in terms of potential for future clinical application. Chapter 6 describes the analysis of urine from a subset of patients by a different profiling technique, namely, Ultra-Performance Liquid Chromatography coupled to Mass Spectrometry (UPLC-MS). Although the identification of discriminant metabolites was very limited, multivariate models showed high classification rate and predictive power, thus reinforcing the value of urine in the context of lung cancer diagnosis. Finally, the main conclusions of this thesis are presented in Chapter 7, highlighting the potential of integrated metabolomics of tissues and biofluids to improve current understanding of lung cancer altered metabolism and to reveal new marker profiles with diagnostic value.

Understanding and modelling hydrological and soil erosion processes in burnt forest catchments

Forest fires implications in overland flow and soil erosion have been researched for several years. Therefore, is widely known that fires enhance hydrological and geomorphological activity worldwide as also in Mediterranean areas. Soil burn severity has been widely used to describe the impacts of fire on soils, and has being recognized as a decisive factor controlling post-fire erosion rates. However, there is no unique definition of the term and the relationship between soil burn severity and post-fire hydrological and erosion response has not yet been fully established. Few studies have assessed post-fire erosion over multiple years, and the authors are aware of none which assess runoff. Small amount of studies concerning pre-fire management practices were also found. In the case of soil erosion models, the Revised Universal Soil Loss Equation (RUSLE) and the revised Morgan–Morgan–Finney (MMF) are well-known models, but not much information is available as regards their suitability in predicting post-fire soil erosion in forest soils. The lack of information is even more pronounced as regards post-fire rehabilitation treatments. The aim of the thesis was to perform an extensive research under the post fire hydrologic and erosive response subject. By understanding the effect of burn severity in ecosystems and its implications regarding post fire hydrological and erosive responses worldwide. Test the effect of different pre-fire land management practices (unplowed, downslope plowed and contour plowed) and time-since-fire, in the post fire hydrological and erosive response, between the two most common land uses in Portugal (pine and eucalypt). Assess the performance of two widely-known erosion models (RUSLE and Revised MMF), to predict soil erosion rates during first year following two wildfires of distinctive burn severity. Furthermore, to apply these two models considering different post-fire rehabilitation treatments in an area severely affected by fire. Improve model estimations of post-fire runoff and erosion rates in two different land uses (pine and eucalypt) using the revised MMF. To assess these improvements by comparing estimations and measurements of runoff and erosion, in two recently burned sites, as also with their post fire rehabilitation treatments. Model modifications involved: (1) focusing on intra-annual changes in parameters to incorporate seasonal differences in runoff and erosion; and (2) inclusion of soil water repellency in runoff predictions. Additionally, validate these improvements with the application of the model to other pine and eucalypt sites in Central Portugal. The review and meta-analysis showed that fire occurrence had a significant effect on the hydrological and erosive response. However, this effect was only significantly higher with increasing soil burn severity for inter-rill erosion, and not for runoff. This study furthermore highlighted the incoherencies between existing burn severity classifications, and proposed an unambiguous classification. In the case of the erosion plots with natural rainfall, land use factor affected annual runoff while land management affected both annual runoff and erosion amounts significantly. Time-since-fire had an important effect in erosion amounts among unplowed sites, while for eucalypt sites time affected both annual runoff and erosion amounts. At all studied sites runoff coefficients increase over the four years of monitoring. In the other hand, sediment concentration in the runoff, recorded a decrease during the same period. Reasons for divergence from the classic post-fire recovery model were also explored. Short fire recurrence intervals and forest management practices are viewed as the main reasons for the observed severe and continuing soil degradation. The revised MMF model presented reasonable accuracy in the predictions while the RUSLE clearly overestimated the observed erosion rates. After improvements: the revised model was able to predict first-year post-fire plot-scale runoff and erosion rates for both forest types, these predictions were improved both by the seasonal changes in the model parameters; and by considering the effect of soil water repellency on the runoff, individual seasonal predictions were considered accurate, and the inclusion of the soil water repellency in the model also improved the model at this base. The revised MMF model proved capable of providing a simple set of criteria for management decisions about runoff and erosion mitigation measures in burned areas. The erosion predictions at the validation sites attested both to the robustness of the model and of the calibration parameters, suggesting a potential wider application.

Channel modelling for MIMO systems

Systems equipped with multiple antennas at the transmitter and at the receiver, known as MIMO (Multiple Input Multiple Output) systems, offer higher capacities, allowing an efficient exploitation of the available spectrum and/or the employment of more demanding applications. It is well known that the radio channel is characterized by multipath propagation, a phenomenon deemed problematic and whose mitigation has been achieved through techniques such as diversity, beamforming or adaptive antennas. By exploring conveniently the spatial domain MIMO systems turn the characteristics of the multipath channel into an advantage and allow creating multiple parallel and independent virtual channels. However, the achievable benefits are constrained by the propagation channel’s characteristics, which may not always be ideal. This work focuses on the characterization of the MIMO radio channel. It begins with the presentation of the fundamental results from information theory that triggered the interest on these systems, including the discussion of some of their potential benefits and a review of the existing channel models for MIMO systems. The characterization of the MIMO channel developed in this work is based on experimental measurements of the double-directional channel. The measurement system is based on a vector network analyzer and a two-dimensional positioning platform, both controlled by a computer, allowing the measurement of the channel’s frequency response at the locations of a synthetic array. Data is then processed using the SAGE (Space-Alternating Expectation-Maximization) algorithm to obtain the parameters (delay, direction of arrival and complex amplitude) of the channel’s most relevant multipath components. Afterwards, using a clustering algorithm these data are grouped into clusters. Finally, statistical information is extracted allowing the characterization of the channel’s multipath components. The information about the multipath characteristics of the channel, induced by existing scatterers in the propagation scenario, enables the characterization of MIMO channel and thus to evaluate its performance. The method was finally validated using MIMO measurements.

Development of infrared spectroscopy for assessing bacterial quality in foods

Rapid and specific detection of foodborne bacteria that can cause food spoilage or illness associated to its consumption is an increasingly important task in food industry. Bacterial detection, identification, and classification are generally performed using traditional methods based on biochemical or serological tests and the molecular methods based on DNA or RNA fingerprints. However, these methodologies are expensive, time consuming and laborious. Infrared spectroscopy is a reliable, rapid, and economic technique which could be explored as a tool for bacterial analysis in the food industry. In this thesis it was evaluated the potential of IR spectroscopy to study the bacterial quality of foods. In Chapter 2, it was developed a calibration model that successfully allowed to predict the bacterial concentration of naturally contaminated cooked ham samples kept at refrigeration temperature during 8 days. In this part, it was developed the methodology that allowed the best reproducibility of spectra from bacteria colonies with minimal sample preparation, which was used in the subsequent work. Several attempts trying different resolutions and number of scans in the IR were made. A spectral resolution of 4 cm-1, with 32 scans were the settings that allowed the best results. Subsequently, in Chapter 3, it was made an attempt to identify 22 different foodborne bacterial genera/species using IR spectroscopy coupled with multivariate analysis. The principal component analysis, used as an exploratory technique, allowed to form distinct groups, each one corresponding to a different genus, in most of the cases. Then, a hierarchical cluster analysis was performed to further analyse the group formation and the possibility of distinction between species of the same bacterial genus. It was observed that IR spectroscopy not only is suitable to the distinction of the different genera, but also to differentiate species of the same genus, with the simultaneous use of principal component analysis and cluster analysis techniques. The utilization of IR spectroscopy and multivariate statistical analysis were also investigated in Chapter 4, in order to confirm the presence of Listeria monocytogenes and Salmonella spp. isolated from contaminated foods, after growth in selective medium. This would allow to substitute the traditional biochemical and serological methods that are used to confirm these pathogens and that delay the obtainment of the results up to 2 days. The obtained results allowed the distinction of 3 different Listeria species and the distinction of Salmonella spp. from other bacteria that can be mistaken with them. Finally, in chapter 5, high pressure processing, an emerging methodology that permits to produce microbiologically safe foods and extend their shelf-life, was applied to 12 foodborne bacteria to determine their resistance and the effects of pressure in cells. A treatment of 300 MPa, during 15 minutes at room temperature was applied. Gram-negative bacteria were inactivated to undetectable levels and Gram-positive showed different resistances. Bacillus cereus and Staphylococcus aureus decreased only 2 logs and Listeria innocua decreased about 5 logs. IR spectroscopy was performed in bacterial colonies before and after HPP in order to investigate the alterations of the cellular compounds. It was found that high pressure alters bands assigned to some cellular components as proteins, lipids, oligopolysaccharides, phosphate groups from the cell wall and nucleic acids, suggesting disruption of the cell envelopes. In this work, bacterial quantification and classification, as well as assessment of cellular compounds modification with high pressure processing were successfully performed. Taking this into account, it was showed that IR spectroscopy is a very promising technique to analyse bacteria in a simple and inexpensive manner.

Estudo da viabilidade da construção em alvenaria confinada no Algarve

Os sismos ocorridos nos últimos anos têm demonstrado um comportamento aceitável dos edifícios de pequeno porte, de alvenaria resistente confinada, que diversos estudos experimentais têm vindo a corroborar. No Algarve existe um tipo próprio de construção de pequeno porte, que embora constituindo uma profunda adulteração à construção vernacular, e tendo sido imposto por um impulso turístico pouco sustentado, se encontra abundantemente disseminado e que, por isso mesmo, constitui um conjunto suficientemente homogéneo para justificar uma análise de viabilidade de um processo construtivo. Neste trabalho, apresenta-se um estudo sobre a segurança estrutural de pequenas construções de alvenaria confinada, no enquadramento da referida tipologia e em conformidade com os materiais existentes na região. Procede-se a uma resumida caracterização tipológica dessas construções correntes e apresentam-se os resultados de alguns ensaios experimentais de alvenarias. Com base na tipologia construtiva e nos resultados experimentais, realizaram-se análises sísmicas (numéricas) de uma construção, tendo em vista a verificação da segurança no contexto dos Eurocódigos 6 e 8. Comparam-se, ainda, os resultados obtidos com alvenaria confinada (com elementos confinantes de betão armado), com os de estrutura reticulada em betão armado de baixa ductilidade (com alvenaria de preenchimento não resistente), para a mesma acção. Como consequência, alvitram-se algumas recomendações, visando a optimização dos processos construtivos, de que, eventualmente, as empresas regionais poderão usufruir, aquando da próxima entrada em vigor dos Eurocódigos Estruturais.

Application of LOICZ DPSIR framework to South asia Basins and developing typology for coastal vulnerability in South Asia

Dissertação de Mestrado, Gestão da Água e da Costa, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2007

Seasonal and storm induced morphological variations at praia de Faro, península do Ancão, southern Portugal

Dissertação de Mestrado, Estudos Marinhos e Costeiros, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2009

Aplicação de técnicas de vídeo subaquático na caracterização de biocenoses marinhas

Dissertação mest., Biologia Marinha - Ecologia e Conservação Marinha, Universidade do Algarve, 2008

Identificação das características dos clientes associadas ao risco de crédito

O processo da tomada de decisão sobre a avaliação de uma solicitação de crédito comercial é por vezes difícil para o julgamento humano, devido à imensidão de variáveis que estão em jogo e das suas inter- relações. Neste artigo propomo-nos identificar as características dos clientes associadas a alto e a baixo risco, com recurso a um modelo aplicacional. A partir de uma base de dados de um cartão de crédito, formada por variáveis de natureza qualitativa e quantitativa, ajustámos um modelo logit binário, com o objectivo de tornar o processo de decisão mais objectivo e quantificável. Em seguida, identificámos oito classes de risco através da aplicação de um método de classificação não hierárquica (K-means) sobre o vector da pontuação do modelo logit. Aferimos temporalmente o comportamento de cada classe de risco ao longo de 70 meses, verificando-se que probabilidades baixas de default estão associadas a classes de risco baixo. As características dos clientes tipicamente associadas ao risco de crédito foram identificadas através de uma Análise Factorial das Correspondências.

Da memória do povo - Recolha de literatura popular da tradição oral do Concelho de Portimão

Margarida Tengarrinha oferece - nos, nesta obra, um leque bastante diversificado do património, adentro das “artes da fala”, correndo nas memórias do povo do concelho de Portimão. O fruto da sua recolecção, os “textos” que recebeu, transcreveu e estudou, é aqui editado com uma valência, cremos,, primeiro que tudo pedagógica. Assim, os textos agrupam - se por “manchas de leitura” com uma coerência interna aglutinadora, aparecendo ordenados sob uma classificação entre formal — segundo os “géneros”, como “contos” , “lendas”, “romances”, “orações”, por exemplo — e temática — por “fundos de sentido” semantizados nas comunicações: “bruxas e bruxedos”, “benzeduras, mezinhas, maldições e superstições”, “poesias maliciosas”, por exemplo.

Spectral analysis of embolic signals

Tese de dout., Engenharia Electrónica e Computação, Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2005

Para uma teoria da anedota popular portuguesa

Corpo errático e volátil por excelência, a anedota constitui porventura o género do discurso através do qual uma comunidade (conceito, como se sabe, cada vez mais alargado) mais dinâmica e prontamente comenta os sentidos dos múltiplos fenómenos –éticos, culturais, filosóficos, pragmáticos, etc.– com que a cada passo se confronta e (re)constrói. Operando, antes de mais, em termos de uma concepção lúdica da vida, a anedota distende-se por múltiplas e versáteis conformações de natureza tipológica, tropológica e topológica.

Recuperação e valorização de lagoas em zonas húmidas: o caso da Lagoa dos Salgados

Dissertação de mest., Arquitectura Paisagista, Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2011

Contributo para o estudo da literatura oral no Algarve

Dissertação de mest., Promoção e Mediação da Leitura, Faculdade de Ciências Humanas e Sociais, Univ. do Algarve, 2012

Beach quality assessment and management in the Sotavento (Eastern) Algarve, Portugal

The purpose of this study on beach quality assessment and management was to evaluate the quality of five beaches in the Algarve Sotavento region of Portugal and to identify beach users’ preferences and priorities regarding their visit to a beach. The Algarve is one of the country’s most internationally known regions and it is generally perceived as a major tourist destination. Because of the increasing level of tourists, there is a specific need to address beach quality, as overcrowding can result in excessive litter, reduce water quality and consequently reduce the socio-economic value of the area. The main methodology for the evaluation of the beach quality in this pilot project was the Bathing Area Registration and Evaluation framework (BARE), which recognizes five beach types (rural, remote, resort, urban and village) through five main priority issues of concern to beach users (water quality, scenery, litter, safety, facilities) and evaluates the beach quality, ranging from one (low) to five (high) stars. After overall bathing area classification, Quarteira-Vilamoura, Ilha do Farol, Ilha Deserta and Ilha da Armona received three-star rating and Quinta do Lago site obtained a one-star rating. The quantitative research data on beach users’ preferences and priorities was obtained through administration of 50 questionnaires per beach and showed that beach users at all sites expressed the need for improved cleanliness, safety and facilities on the beach. The BARE framework, together with the questionnaire surveys, allowed the identification of management priorities required to improve the quality of individual beaches and therefore increase income from tourism.