Metabonomic studies to assess beer quality and stability

The work reported in this thesis aimed at applying the methodology known as metabonomics to the detailed study of a particular type of beer and its quality control, with basis on the use of multivariate analysis (MVA) to extract meaningful information from given analytical data sets. In Chapter 1, a detailed description of beer is given considering the brewing process, main characteristics and typical composition of beer, beer stability and the commonly used analytical techniques for beer analysis. The fundamentals of the analytical methods employed here, namely nuclear magnetic resonance (NMR) spectroscopy, gas-chromatography-mass spectrometry (GC-MS) and mid-infrared (MIR) spectroscopy, together with the description of the metabonomics methodology are described shortly in Chapter 2. In Chapter 3, the application of high resolution NMR to characterize the chemical composition of a lager beer is described. The 1H NMR spectrum obtained by direct analysis of beer show a high degree of complexity, confirming the great potential of NMR spectroscopy for the detection of a wide variety of families of compounds, in a single run. Spectral assignment was carried out by 2D NMR, resulting in the identification of about 40 compounds, including alcohols, amino acids, organic acids, nucleosides and sugars. In a second part of Chapter 3, the compositional variability of beer was assessed. For that purpose, metabonomics was applied to 1H NMR data (NMR/MVA) to evaluate beer variability between beers from the same brand (lager), produced nationally but differing in brewing site and date of production. Differences between brewing sites and/or dates were observed, reflecting compositional differences related to particular processing steps, including mashing, fermentation and maturation. Chapter 4 describes the quantification of organic acids in beer by NMR, using different quantitative methods: direct integration of NMR signals (vs. internal reference or vs. an external electronic reference, ERETIC method) and by quantitative statistical methods (using the partial least squares (PLS) regression) were developed and compared. PLS1 regression models were built using different quantitative methods as reference: capillary electrophoresis with direct and indirect detection and enzymatic essays. It was found that NMR integration results generally agree with those obtained by the best performance PLS models, although some overestimation for malic and pyruvic acids and an apparent underestimation for citric acid were observed. Finally, Chapter 5 describes metabonomic studies performed to better understand the forced aging (18 days, at 45 ºC) beer process. The aging process of lager beer was followed by i) NMR, ii) GC-MS, and iii) MIR spectroscopy. MVA methods of each analytical data set revealed clear separation between different aging days for both NMR and GC-MS data, enabling the identification of compounds closely related with the aging process: 5-hydroxymethylfurfural (5-HMF), organic acids, γ-amino butyric acid (GABA), proline and the ratio linear/branched dextrins (NMR domain) and 5-HMF, furfural, diethyl succinate and phenylacetaldehyde (known aging markers) and, for the first time, 2,3-dihydro-3,5-dihydroxy-6-methyl-4(H)-pyran-4-one xii (DDMP) and maltoxazine (by GC-MS domain). For MIR/MVA, no aging trend could be measured, the results reflecting the need of further experimental optimizations. Data correlation between NMR and GC-MS data was performed by outer product analysis (OPA) and statistical heterospectroscopy (SHY) methodologies, enabling the identification of further compounds (11 compounds, 5 of each are still unassigned) highly related with the aging process. Data correlation between sensory characteristics and NMR and GC-MS was also assessed through PLS1 regression models using the sensory response as reference. The results obtained showed good relationships between analytical data response and sensory response, particularly for the aromatic region of the NMR spectra and for GC-MS data (r > 0.89). However, the prediction power of all built PLS1 regression models was relatively low, possibly reflecting the low number of samples/tasters employed, an aspect to improve in future studies.

O grau de investimento definido por um indicador económico e financeiro

No contexto econômico competitivo e globalizado no qual as corporações estão inseridas, emerge a necessidade de evolução constante para acompanhar as mudanças que o ambiente lhes impõe, visando a sustentabilidade e a perpetuidade. A evolução econômica e financeira das corporações pode promover o desenvolvimento de uma nação, mesmo que o aumento da concorrência no mercado obrigue-as a investirem em novas relações com o seu universo, buscando melhorar os seus níveis de desempenho mensurados por meio de novos instrumentos economicos e financeiros. Desta forma, o grau de investimento corporativo passa a ser relevante, pois pode gerar confiança em novos investimentos, sendo visto como sinônimo de economia forte. No concernente ao objetivo, esta tese teve como escopo o desenvolvimento de um indicador econômico e financeiro visando balizar o grau de credibilidade rating que as corporações apresentam em sua estrutura corporativa, por meio de um conjunto de índices econômicos e financeiros ligados à liquidez, à lucratividade, ao endividamento e à rentabilidade, provindos das demonstrações econômicas e financeiras das corporações estudadas. Este estudo caracteriza-se no contexto da tipologia aplicada, de objetivo descritivo com delineamento bibliográfico, na amplitude da problemática, caracteriza-se como quantitativo, compreendendo a população de 70 corporações brasileiras reconhecidas pelas certificadoras internacionais, Standard & Poor's, Moody's e Fitch Ratings, as quais detinham o grau de investimento corporativo no ano de 2008. Quanto aos métodos e procedimentos estatísticos, primeiramente utilizou-se a análise descritiva com vistas ao resumo dos dados, posteriormente foi feita a análise de correlação por meio do Coeficiente de Correlação Linear de Pearson, aplicando-se em seguida a análise de regressão. Em seguida para a confecção do modelo utilizou-se a análise fatorial e para testificar sua confiabilidade o Alfa de Cronbach, utilizou-se também a análise discriminante, para classificação dos quartis. As conclusões do estudo baseiamse nos resultados apresentados pela evolução do tratamento estatístico, que inicialmente apresentam uma correlação predominantemente fraca, no entanto isto não invalida a correlação de Pearson, pois todos os coeficientes apresentaram uma significância de (p<0,05). Na aplicação da análise de regressão, todos os modelos apresentaram resultados satisfatórios sendo perceptível a existência de uma forte correlação. A confiabilidade do modelo de grau de investimento corporativo provindo da análise fatorial foi testificada pelo coeficiente do Alpha de Cronbach, que apresentou valor de 0,768, o que indica consistência interna satisfatória ao estudo. O grau de investimento na base longitudinal de 2008 a 2010 apresenta variabilidade de 95,72% a 98,33% de acertividade. Portanto, conclui-se que o indicador criado por este estudo, possui condições de ser utilizado como base de definição do grau de investimento de corporações empresariais.

NMR in the characterization of heavy residual procedural streams

The main objective of this work was to monitor a set of physical-chemical properties of heavy oil procedural streams through nuclear magnetic resonance spectroscopy, in order to propose an analysis procedure and online data processing for process control. Different statistical methods which allow to relate the results obtained by nuclear magnetic resonance spectroscopy with the results obtained by the conventional standard methods during the characterization of the different streams, have been implemented in order to develop models for predicting these same properties. The real-time knowledge of these physical-chemical properties of petroleum fractions is very important for enhancing refinery operations, ensuring technically, economically and environmentally proper refinery operations. The first part of this work involved the determination of many physical-chemical properties, at Matosinhos refinery, by following some standard methods important to evaluate and characterize light vacuum gas oil, heavy vacuum gas oil and fuel oil fractions. Kinematic viscosity, density, sulfur content, flash point, carbon residue, P-value and atmospheric and vacuum distillations were the properties analysed. Besides the analysis by using the standard methods, the same samples were analysed by nuclear magnetic resonance spectroscopy. The second part of this work was related to the application of multivariate statistical methods, which correlate the physical-chemical properties with the quantitative information acquired by nuclear magnetic resonance spectroscopy. Several methods were applied, including principal component analysis, principal component regression, partial least squares and artificial neural networks. Principal component analysis was used to reduce the number of predictive variables and to transform them into new variables, the principal components. These principal components were used as inputs of the principal component regression and artificial neural networks models. For the partial least squares model, the original data was used as input. Taking into account the performance of the develop models, by analysing selected statistical performance indexes, it was possible to conclude that principal component regression lead to worse performances. When applying the partial least squares and artificial neural networks models better results were achieved. However, it was with the artificial neural networks model that better predictions were obtained for almost of the properties analysed. With reference to the results obtained, it was possible to conclude that nuclear magnetic resonance spectroscopy combined with multivariate statistical methods can be used to predict physical-chemical properties of petroleum fractions. It has been shown that this technique can be considered a potential alternative to the conventional standard methods having obtained very promising results.

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.

Organic contaminants in urban soils: major inputs and potential risks

Urban soil quality may be severely affected by hydrophobic organic contaminants (HOCs), impairing environmental quality and human health. A comprehensive study was conducted in two contrasting Portuguese urban areas (Lisbon and Viseu) in order to assess the levels and potential risks of these contaminants, to identify sources and study their behaviour in soils. The concentrations of HOCs were related to the size of the city, with much higher contamination levels observed in Lisbon urban area. Source apportionment was performed by studying the HOCs profiles, their relationship with potentially toxic elements and general characteristics of soil using multivariate statistical methods. Lisbon seems to be affected by nearby sources (traffic, industry and incineration processes) whereas in Viseu the atmospheric transport may be playing an important role. In a first tier of risk assessment (RA) it was possible to identify polycyclic aromatic hydrocarbons (PAHs) in Lisbon soils as a potential hazard. The levels of PAHs in street dusts were further studied and allowed to clarify that traffic, tire and pavement debris can be an important source of PAHs to urban soils. Street dusts were also identified as being a potential concern regarding human and environmental health, especially if reaching the nearby aquatic bodies. Geostatistical tools were also used and their usefulness in a RA analysis and urban planning was discussed. In order to obtain a more realistic assessment of risks of HOCs to environment and human health it is important to evaluate their available fraction, which is also the most accessible for organisms. Therefore, a review of the processes involved on the availability of PAHs was performed and the outputs produced by the different chemical methods were evaluated. The suitability of chemical methods to predict bioavailability of PAHs in dissimilar naturally contaminated soils has not been demonstrated, being especially difficult for high molecular weight compounds. No clear relationship between chemical and biological availability was found in this work. Yet, in spite of the very high total concentrations found in some Lisbon soils, both the water soluble fraction and the body residues resulting from bioaccumulation assays were generally very low, which may be due to aging phenomena. It was observed that the percentage of soluble fraction of PAHs in soils was found to be different among compounds and mostly regulated by soil properties. Regarding bioaccumulation assays, although no significant relationship was found between soil properties and bioavailability, it was verified that biota-to-soil bioaccumulation factors were sample dependent rather than compound dependent. In conclusion, once the compounds of potential concern are targeted, then performing a chemical screening as a first tier can be a simple and effective approach to start a RA. However, reliable data is still required to improve the existing models for risk characterization.

Ecological genetics in the North Atlantic: environmental gradients and adaptation at specific loci

The North Atlantic intertidal community provides a rich set of organismal and environmental material for the study of ecological genetics. Clearly defined environmental gradients exist at multiple spatial scales: there are broad latitudinal trends in temperature, meso-scale changes in salinity along estuaries, and smaller scale gradients in desiccation and temperature spanning the intertidal range. The geology and geography of the American and European coasts provide natural replication of these gradients, allowing for population genetic analyses of parallel adaptation to environmental stress and heterogeneity. Statistical methods have been developed that provide genomic neutrality tests of population differentiation and aid in the process of candidate gene identification. In this paper, we review studies of marine organisms that illustrate associations between an environmental gradient and specific genetic markers. Such highly differentiated markers become candidate genes for adaptation to the environmental factors in question, but the functional significance of genetic variants must be comprehensively evaluated. We present a set of predictions about locus-specific selection across latitudinal, estuarine, and intertidal gradients that are likely to exist in the North Atlantic. We further present new data and analyses that support and contradict these simple selection models. Some taxa show pronounced clinal variation at certain loci against a background of mild clinal variation at many loci. These cases illustrate the procedures necessary for distinguishing selection driven by internal genomic vs. external environmental factors. We suggest that the North Atlantic intertidal community provides a model system for identifying genes that matter in ecology due to the clarity of the environmental stresses and an extensive experimental literature on ecological function. While these organisms are typically poor genetic and genomic models, advances in comparative genomics have provided access to molecular tools that can now be applied to taxa with well-defined ecologies. As many of the organisms we discuss have tight physiological limits driven by climatic factors, this synthesis of molecular population genetics with marine ecology could provide a sensitive means of assessing evolutionary responses to climate change.

Contribuição da ecografia cerebral transfontanelar para a avaliação do crescimento cerebral do recém-nascido pré-termo

Tese de doutoramento, Medicina (Pediatria), Universidade de Lisboa, Faculdade de Medicina, 2013

Motorização de fármacos na água bruta e na água para consumo humano por cromatolografia líquida de ultra eficiência associada à espectrometria de massa tandem

Tese de doutoramento, Farmácia (Bromatologia), Universidade de Lisboa, Faculdade de Farmácia, 2014

Atmospheric Concentrations of Alternaria, Cladosporium, Ganoderma and Didymella Spores Monitored in Cork (Ireland) and Worcester (England) During the Summer of 2010

This study represents the first international intercomparison of fungal spore observations since 1990, focusing on atmospheric concentrations of Alternaria, Cladosporium, Ganoderma and Didymella spores. The campaigns were performed at sites located in Cork (Ireland) and Worcester (England) during summer 2010. Observations were made using Hirst-type volumetric spore traps and corresponding optical identification at the genus level by microscope. The measurements at both sites (including meteorological parameters) were compared and contrasted. The relationships between the fungal spore concentrations with selected meteorological parameters were investigated using statistical methods and multivariate regression trees (MRT). The results showed high correlations between the two sites with respect to daily variations. Statistically significant higher spore concentrations for Alternaria, Cladosporium and Ganoderma were monitored at the Worcester site. This result was most likely due to the differences in precipitation and local fungal spore sources at the two sites. Alternaria and Cladosporium reached their maxima a month earlier in Cork than in Worcester, and Didymella with Ganoderma peaked simultaneously with similar diurnal trends found for all the investigated spore types. MRT analysis helped to determine threshold values of the meteorological parameters that exerted most influence on the presence of spores: they were found to vary at the two sites. Our results suggest that the aeromycological profile is quite uniform over the British Isles, but a description of bioaerosols with respect to overall load and daily concentration can be quite diverse although the geographical difference between sites is relatively small. These variations in the concentrations therefore need to be explored at the national level

An Analysis of Local Wind and Air Mass Directions and Their Impact on Cladosporium Distribution Using HYSPLIT and Circular Statistics

Ecological studies that examine species-environment relationships are often limited to several meteorological parameters, i.e. mean air temperature, relative humidity, precipitation, vapour pressure deficit and solar radiation. The impact of local wind, its speed and direction are less commonly investigated in aerobiological surveys mainly due to difficulties related to the employment of specific analytical tools and interpretation of their outputs. Identification of inoculum sources of economically important plant pathogens, as well as highly allergenic bioaerosols like Cladosporium species, has not been yet explored with remote sensing data and atmospheric models such as Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT). We, therefore, performed an analysis of 24 h intra-diurnal cycle of Cladosporium spp. spores from an urban site in connection with both the local wind direction and overall air mass direction computed by HYSPLIT. The observational method was a volumetric air sampler of the Hirst design with 1 h time resolution and corresponding optical detection of fungal spores with light microscopy. The atmospheric modelling was done using the on-line data set from GDAS with 1° resolution and circular statistical methods. Our results showed stronger, statistically significant correlation (p ≤ 0.05) between high Cladosporium spp. spore concentration and air mass direction compared to the local wind direction. This suggested that a large fraction of the investigated fungal spores had a regional origin and must be located more than a few kilometers away from the sampling point.

Potencialidades e utilização do espaço recreio: um estudo desenvolvido em escolas do 1.º ciclo do ensino básico

Dissertação apresentada para a obtenção do grau de Mestre em Educação - Área de Especialização em Didática das Ciências

Digital Divide Across the European Union

Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação

Politicization of non-political events

Spatial analysis and social network analysis typically take into consideration social processes in specific contexts of geographical or network space. The research in political science increasingly strives to model heterogeneity and spatial dependence. To better understand and geographically model the relationship between “non-political” events, streaming data from social networks, and political climate was the primary objective of the current study. Geographic information systems (GIS) are useful tools in the organization and analysis of streaming data from social networks. In this study, geographical and statistical analysis were combined in order to define the temporal and spatial nature of the data eminating from the popular social network Twitter during the 2014 FIFA World Cup. The study spans the entire globe because Twitter’s geotagging function, the fundamental data that makes this study possible, is not limited to a geographic area. By examining the public reactions to an inherenlty non-political event, this study serves to illuminate broader questions about social behavior and spatial dependence. From a practical perspective, the analyses demonstrate how the discussion of political topics fluсtuate according to football matches. Tableau and Rapidminer, in addition to a set basic statistical methods, were applied to find patterns in the social behavior in space and time in different geographic regions. It was found some insight into the relationship between an ostensibly non-political event – the World Cup - and public opinion transmitted by social media. The methodology could serve as a prototype for future studies and guide policy makers in governmental and non-governmental organizations in gauging the public opinion in certain geographic locations.

Complete longitudinal analyses of the randomized, placebo-controlled, phase III trial of sunitinib in patients with gastrointestinal stromal tumor following imatinib failure.

PURPOSE: To analyze final long-term survival and clinical outcomes from the randomized phase III study of sunitinib in gastrointestinal stromal tumor patients after imatinib failure; to assess correlative angiogenesis biomarkers with patient outcomes. EXPERIMENTAL DESIGN: Blinded sunitinib or placebo was given daily on a 4-week-on/2-week-off treatment schedule. Placebo-assigned patients could cross over to sunitinib at disease progression/study unblinding. Overall survival (OS) was analyzed using conventional statistical methods and the rank-preserving structural failure time (RPSFT) method to explore cross-over impact. Circulating levels of angiogenesis biomarkers were analyzed. RESULTS: In total, 243 patients were randomized to receive sunitinib and 118 to placebo, 103 of whom crossed over to open-label sunitinib. Conventional statistical analysis showed that OS converged in the sunitinib and placebo arms (median 72.7 vs. 64.9 weeks; HR, 0.876; P = 0.306) as expected, given the cross-over design. RPSFT analysis estimated median OS for placebo of 39.0 weeks (HR, 0.505, 95% CI, 0.262-1.134; P = 0.306). No new safety concerns emerged with extended sunitinib treatment. No consistent associations were found between the pharmacodynamics of angiogenesis-related plasma proteins during sunitinib treatment and clinical outcome. CONCLUSIONS: The cross-over design provided evidence of sunitinib clinical benefit based on prolonged time to tumor progression during the double-blind phase of this trial. As expected, following cross-over, there was no statistical difference in OS. RPSFT analysis modeled the absence of cross-over, estimating a substantial sunitinib OS benefit relative to placebo. Long-term sunitinib treatment was tolerated without new adverse events.

Trophic ecology of jumbo squid and predatory fishes in the Northern Humboldt Current System

This work provides a contribution to a better understanding of the trophic ecology of important predators in the Northern Humboldt Current System, the jack mackerel (Trachurus murphyi), the chub mackerel (Scomber japonicus) and the jumbo squid (Dosidicus gigas) by the characterization of the highly variable feeding patterns of these species at different spatiotemporal scales. We provided new knowledge on the comparative trophic behaviour of these species, defined as opportunistic in previous investigations. For that purpose we applied a variety of statistical methods to an extensive dataset of 27,188 non-empty stomachs. We defined the spatial organization of the forage fauna of these predators and documented changes in prey composition according to predators’ size and spatiotemporal features of environment. Our results highligh the key role played by the dissolved oxygen. We also deciphered an important paradox on the jumbo squid diet: why do they hardly forage on the huge anchovy (Engraulis ringens) biomass distributed of coastal Peru? We showed that the shallow oxygen minimum zone present off coastal Peru could hamper the co-occurrence of jumbo squids and anchovies. In addition, we proposed a conceptual model on jumbo squid trophic ecology including the ontogenetic cycle, oxygen and prey availability. Moreover we showed that the trophic behaviour of jack mackerel and chub mackerel is adapted to forage on more accessible species such as for example the squat lobster Pleurocondes monodon and Zoea larvae. Besides, both predators present a trophic overlap. But jack mackerel was not as oracious as chub mackerel, contradictorily to what was observed by others authors. Fish diet presented a high spatiotemporal variability, and the shelf break appeared as a strong biogeographical frontier. Diet composition of our fish predators was not necessarily a consistent indicator of changes in prey biomass. El Niño events had a weak effect on the stomach fullness and diet composition of chub mackerel and jack mackerel. Moreover, decadal changes in diet diversity challenged the classic paradigm of positive correlation between species richness and temperature. Finally, the global patterns that we described in this work, illustrated the opportunistic foraging behaviour, life strategies and the high degree of plasticity of these species. Such behaviour allows adaptation to changes in the environment.