Estimation and dynamics of above ground biomass with very high resolution satellite images in Pinus pinaster stands

Biomass estimation is a tool for evaluating stands and forest dynamics. Traditional indirect methods use forest inventories and allometric functions at tree level to evaluate biomass at plot level, and an extrapolation method to assess an area. The goal of this study was the development of allometric functions for Pinus pinaster with crown horizontal projection derived from very high spatial resolution satellite images as an independent variable, as well as their application to the analysis of above ground biomass dynamics. The fitted functions show a good performance. The function used to estimate the above ground biomass per grid in 2004, 2007 and 2011 for the study area enable the evaluation of their temporal dynamics. From 2004 to 2007 it decreased in 90.5% of the study area, due to forest fires and cuts to control the pinewood nematode; from 2007 to 2011 increased in 45.6% and decreased in 51.6%, the latter corresponding to cuts to control the aforementioned disease. In 76.4% of the burnt areas, natural regeneration resulted in an increase of above ground biomass. The method's main advantages are the simultaneous evaluation of small or large areas and, when implemented in a GIS, it allows straightforward monitoring over a short period of time

Effects of Forest Stand Structure in Biomass and Carbon

Biomass has been gaining an increased interest due to its importance in sustainable forest management and in carbon sequestration. Biomass in each forest stand varies according to its structure and influences not only the biomass per area unit but also its distribution in space and time. The structure analysis with absolute stand density measures and structure and diversity measures and indices for the number of trees and basal area does not always reflect the above-ground biomass distribution and variability. The use of above-ground biomass as an absolute density measure and the development of diversity measures and indices derived from it enable further details in the stand structure characterisation. The results of this study highlighted the differences between pure even-aged, pure multiaged, mixed even-aged and mixed multiaged structures. The measures and indices of above-ground biomass are considered primordial as they integrate the horizontal and the vertical distribution, thus enabling a more detailed evaluation of biomass and carbon stocks

Multi-Species Stand Classification: Definition and Perspectives

The increasing demands for products and services from forests enhanced new approaches to stand composition, structure, and management, which encompass multiple use systems, frequently mixed either even aged or uneven aged. Stand classification is frequently based on one density measure (number of trees, basal area, volume or crown cover). As no standard criteria exist, the direct comparison between the different stand classifications is difficult. This created a need for a stand classification that incorporates not only the forest species and composition but also their horizontal and vertical arrangements. The four criteria stand classification incorporates the number of species and their proportion, their horizontal and vertical distribution. The application of this methodology enables an integrated approach, bridging the gap between composition and stand structure. Its use in the National Forest Inventories and in research studies is simple, as shown in the two cases of study presented. It also allows the evaluation of stands in a certain moment in time and their dynamics

Avaliação de desempenho de fundos de obrigações com base em modelos não condicionais versus modelos condicionais : evidência para o mercado Norte Americano

Dissertação de mestrado em FinançasOs métodos de avaliação do desempenho de fundos de investimento têm sido alvo de bastante discussão na literatura financeira, que advém da incerteza que caracteriza os mercados financeiros e da necessidade de estes incorporem essa incerteza, de forma a obter estimativas de desempenho o mais fiáveis possível. Ao longo desta tese proponho-me avaliar o desempenho de fundos de obrigações “Corporate” Norte Americanos, confrontando os resultados obtidos através das metodologias tradicionais (não condicionais) com aqueles obtidos com a aplicação de metodologias condicionais de avaliação de desempenho. Proponho-me ainda apresentar e discutir as metodologias de avaliação de desempenho, desde a mais tradicional com base num modelo de um fator (medida de Jensen, 1968), a metodologias condicionais que incorporam variáveis de informação pública com o objectivo de captar a variabilidade do risco. Aplicando a medida de Jensen (1968) bem como o modelo de Ferson e Schadt (1996), à amostra de fundos para o período de janeiro de 1999 a junho de 2009, observamos resultados semelhantes aos já anteriormente obtidos noutros estudos, na medida em que os gestores dos fundos de investimento não conseguem superar o desempenho de mercado, obtendo maioritariamente desempenhos neutros ou negativos. Com a aplicação da metodologia condicional de avaliação de desempenho, observa-se uma diminuição da penalização do desempenho negativo dos gestores dos fundos de investimento. O modelo condicional apresenta ainda um maior poder explicativo do desempenho dos fundos. Foi observada evidência de risco variável ao longo do tempo, em particular em função da variável taxa de crescimento dos dividendos do índice de mercado.Performance evaluation of investment funds has been the subject of an intense debate in the financial literature. The uncertainty surrounding financial markets and the need to incorporate this uncertainty in the performance evaluation models, in order to obtain the most reliable performance estimates possible, has been pointed out as a major issue in this area. The purpose of this thesis is to evaluate the performance of "Corporate" North American bond funds, comparing the results obtained through unconditional models and conditional models of performance evaluation. We propose present and discuss performance evaluation methodologies, from traditional models based on a single factor (Jensen’s alpha), conditional models that incorporates public information variables in order to account for time-varying risk. Applying both measures to the sample of bond funds over the period from january 1999 to june 2009, we found evidence that is in line with previous studies, in the sense that mutual funds do not outperform the market, showing mostly neutral and negative performance. When the conditional model is applied, there is light reduction of the negative performance. Also the conditional model has greater explanatory power. Finally, there seems that risk is time-varying and dependent on the dividend yield of the market index

A computational pipeline to identify phenotypic manifestations related to genes

Tese de Mestrado, Bioinformática e Biologia computacional, 2022, Universidade de Lisboa, Faculdade de CiênciasUma proporção de pacientes com doenças de neuro desenvolvimento, tem uma mutação genética diretamente ligada à sua doença. A Perturbação do Espectro do Autismo (PEA) é uma patologia de neuro desenvolvimento com apresentação clínica muito heterogênea (Cummings et al., 2005). PEA é caracterizada por ter padrões de ações ou interesses repetitivos, dificuldades/limitações em interações sociais e comunicação que se manifestam desde a infância. Estes sintomas afetam mais homens que mulheres e podem variar em severidade. Talvez o maior avanço em perceber a fisiopatologia do PEA é ter sido reconhecido a contribuição genética para a etiologia do PEA com a ajuda do aparecimento de métodos NGS e WES (Daniel H. Geschwind, 2011; Asif et al., 2018). Há vários genes e mutações associados com o PEA o que aponta a uma origem heterogenia da doença. A combinação de uma arquitetura genética complexa e pouco compreendida, heterogeneidade fenotípica e o envolvimento de múltiplos loci que interagem entre si dificulta a descoberta dos genes com mutações específicas que levam ao PEA. Consequentemente, a etiologia genética dos distúrbios relacionados ao PEA permanece em grande parte desconhecida (Gupta et al., 2006). Vários estudos demonstraram que duplicações ou deleções de segmentos do genoma denominados de Variantes de Número de Cópias (CNVs), polimorfismos de nucleotídeo único (SNPs) e variantes de nucleotídeo único (SNVs) provavelmente têm um papel causal na PEA (Chang et al., 2014; Soler et al., 2018). O estabelecimento da relação entre os diferentes genes com as variantes do fenótipo do PEA pode facilitar o diagnóstico dos pacientes e, assim, possibilitar que os pacientes obtenham o tratamento mais eficiente e específico numa idade mais jovem. Devido aos recentes avanços nas tecnologias genómicas, os estudos genéticos em larga escala estão a revelar um grande número de variantes genéticas que potencialmente contribuem para o risco de doenças. O objetivo global deste trabalho foi propor um pipeline para identificar a manifestação fenotípica de variantes genéticas putativas causadoras de doenças. Para isso, foram estabelecidos dois objetivos específicos: • Identificação de clusters de genes funcionalmente semelhantes; • Inferir o fenótipo da doença para cada cluster separadamente. Para alcançar estes objetivos, neste estudo foi usado um dataset que contem 3707 genes de pacientes diagnosticados com PEA. A este dataset são aplicadas ferramenta como o DishIn e GoSemSim para calcular o valor da semelhança semântica em pares de genes, obtendo no fim uma matriz quadrada de semelhança semântica. Este valor é obtido pelas ferramentas ao quantificar a informação partilhada entre dois termos GO, associados a cada gene, como o conteúdo de informação do ancestral comum mais informativo de dois termos. As medidas para calcular a semelhança semântica do conteúdo de informação usadas neste trabalho são Lin, Jiang & Conrath e Rel. Através da matriz de semelhança semântica é calculada a matriz de distâncias à qual são aplicados os algoritmos de clustering DBSCAN, Kmeans e hierárquico, de modo a obter grupos de genes que sejam funcionalmente semelhantes. Após a análise dos resultados, foi possível concluir que variantes genéticas podem ser agrupados usando cálculos de semelhança semântica. Demonstrou-se que os genes que foram agrupados são funcionalmente semelhantes, estavam inseridos em redes de interação genética e podem levar a diferentes grupos de fenótipos de PEA. Os genes agrupados foram enriquecidos para diferentes pathways e sub fenótipos relacionados ao PEA.In most neurodevelopmental diseases, a proportion of patients carries a known gene mutation directly linked to their illness. Autism Spectrum Disorder (ASD) is a neurodevelopmental pathology with very heterogeneous clinical presentation (Cummings et al., 2005). ASD is characterized by symptoms of repetitive patterns of actions or interests, difficulties/limitations in social interactions and communication that appear since childhood. These symptoms affect more men than women and can vary in severity. Perhaps the greatest advance in understanding the pathophysiology of ASD is the recognition of the genetic contribution to the etiology of ASD with the help of the emergence of NGS and WES methods (Daniel H. Geschwind, 2011; Asif et al., 2018). There are several genes and mutations associated with ASD which point to a heterogeneous origin of the disease. A combination of a complex and poorly understood genetic architecture, phenotypic heterogeneity and the involvement of multiple loci interacting with one another hinder efforts to discover the genes with specific mutations that lead to ASD. Consequently, the genetic etiology of disorders related to ASD remains largely unknown (Gupta et al., 2006). Several studies demonstrated that duplications or deletions of genome segments called Copy Number Variants (CNVs), single nucleotide polymorphisms (SNPs) and single nucleotide variants (SNVs) are likely to have a causal role in ASD (Chang et al., 2014; Soler et al., 2018). The establishment of the relationship between different genes to the ASD phenotype variants may facilitate the diagnosis of patients and thus enable patients to obtain the correct treatment at a younger age. Due to recent advances in genomic technologies, the large-scale genetic studies are unraveling large numbers of genetic variants potentially contributing to disease risk. The global objective of this work was to propose a pipeline to identify the phenotypic manifestation of putative disease-causing genetic variants. For this purpose, two specific objectives were pursued: • Identification of clusters of functionally similar genes; • Inferring the disease phenotype for each cluster separately. To achieve these goals in this study, a dataset containing 3707 genes from patients diagnosed with ASD was used. Tools such as DishIn and GoSemSim are applied to this dataset to calculate the value of semantic similarity in pairs of genes, obtaining in the end a square matrix of semantic similarity. This value is obtained by the tools by quantifying the pairwise GO term semantic similarity through the amount of information shared between two terms, such as the information content of the most informative common ancestor of two terms. The measures to calculate the similarity of information content used in this work are Lin, Jiang & Conrath and Rel. Through the matrix of the semantic similarity matrix, the distance matrix is calculated to which the DBSCAN, Kmeans and hierarchical clustering algorithms are applied, to obtain functionally similar clusters of genes. After analyzing the results, it was possible to conclude that genes that were disrupted by genetic variants in patients can be clustered using semantic similarity measures. Clustered genes were functionally similar, also indicated by gene interaction networks and can lead to different ASD sub-phenotype. Genes clusters were enriched for different pathways and phenotype that were related to ASD subtypes

Influence of umbrella pine (Pinus pinea L.) stand type and tree characteristics on cone production

Most umbrella pine (Pinus pinea L.) stands are managed as agroforestry systems, whose main production is fruit, due to the edible and highly nutritious kernels, and are frequently associated to natural or seeded pastures and grazing. The stands have low density, in order to enhance crown growth and fruit production. Nevertheless, cone production, both with regard to number and weight, varies greatly between stands, trees and years. In this study were selected three agroforestry systems, representative of umbrella pine stands whose main production is fruit, and one stand representative of the timber production system, where fruit is the secondary production. It was evaluated the variability in cone production as a function of the tree’s diameter at breast height and crown diameter and the individual tree’s competition status. The results indicate that stands managed in agroforestry systems with lower competition and individuals with larger diameter at breast height and crown diameter tend to produce more and heavier cones per tree. The first two principal components of the principal component analysis explain 84 % of the variance in cone production, trees’ dimensions and competition index. Tree competition status has a negative impact on production per tree

Eucalyptus globulus coppices in Portugal: influence of site and percentage of residues collected for energy

Studies that quantify forest bioenergy potentials hardly address the questions of site quality, proportion and type of residues removed from the stands, and environmental impacts of those removals. However, those factors are important for energy-potential results and forest sustainability. This study compares, in terms of residual biomass availability for energy production and of sustainability, different locations, site indices, and forest management strategies in Eucalyptus globulus stands for pulp and paper in northern and central Portugal. A growth and production simulator was used to calculate the availability of residues and the area needed to supply a biomass-fired power plant under a variety of scenarios. Regions with more rainfall generate more residues, but site index and quantity and type of residues harvested are the most important factors. Under the different scenarios analyzed, the amount of residues potentially harvested range from 0.7 to 4.3 Mg ha−1 a−1, the upper bound corresponding to a scenario where stumps are valorized. The maximization of residue removal maximizes the bioenergy produced but has to be considered prudently. Studies indicate that stump removal has limited effect on Eucalyptus globulus stand productivity, diversity, and system sustainability, but impacts of residue removals increase with a decrease in site index

The Fire in the Mediterranean Region: A Case Study of Forest Fires in Portugal

Forest fires are a common disturbance in many forest systems in the world and in particular in the Mediterranean region. Their origins can be either natural or anthropogenic. The effects in regard to the time trends, vegetation, and soil will be reflected in the species distribution, forest composition, and soil potential productivity. In general, it can be said that the larger the fire and the shorter the time between two consecutive occurrences, the higher the probability to originate shifts in vegetation and soil degradation. In the Mediterranean region, the number of fire ignitions does not reflect the burnt area due to the occurrence of very large fires. The latter occur in a very small proportion of the number of ignitions, but result in very large burnt areas. Also there seems to be an increasing trend toward larger fires in the Mediterranean region due mainly to climatic and land use changes. This case study highlights the importance of vegetation regrowth a short time after the fire to maintain both forest systems and soil conservation

Relationship between Portuguese consumer preferences and textural properties, chemical composition and nutritional value of beef

Tese de Doutoramento em Ciências Veterinárias. Especialidade de Produção AnimalBeef is a nutritionally rich product with a high economic value. However in the last decades beef has been target of negative publicity by the media, mainly due to the high content of cholesterol as well as saturated and trans fatty acids (FA). The increasing number of food scares across the Europe over the last years has increased even more consumers’ concerns about beef quality and safety. Despite the health concerns beef sensory properties still remain the main purchasing and repeat purchasing criteria for the consumers. Tenderness has been considered the major palatability characteristic of beef and defines its commercial value. However, tenderness variability has been considered a major problem to the beef industry. In this context, the aim of this proposal was to ascertain the organoleptic properties and lipid nutritional value of beef and to relate them with the Portuguese consumer` preferences. The experimental work was divided in two trials. In the first trial, the meat quality and lipid nutritional value from “Vitela Tradicional do Montado”-PGI veal, Mertolenga-PDO veal and Mertolenga-PDO beef were studied. The results suggested that the three products are not very different, but the two veal types are more alike, which means that age had a more powerful effect than the crossbred or gender. Nevertheless, despite the similarity in FA profile and of the production systems of the animals sampled, it was possible to discriminate the meat types. Moreover, the PGI veal seems to have higher variability than the other two meat types studied. In the second trial, three beef types from the Portuguese market place, Carnalentejana-PDO, imported from Brazil and national undifferentiated beef, were studied and compared to characterise nutritional value and variability of beef lipids as well as the organoleptic properties and their variability. We also intended to relate the sensory attributes with instrumental measurements in order to realise if it is possible to predict sensory evaluation through instrumental measurements. Brazilian beef had the highest lipid nutritional value and lipid stability as this beef presented higher contents of α-tocopherol, β-carotene, CLA and PUFA. The data indicated that all beef types seem to have α-tocopherol values high enough to inhibit lipid oxidation and discoloration. Energy intake was calculated for the main FA and compared with the recommended daily intake. All beef types seem to have low cholesterol and SFA contents. Concerning the relation between the sensory attributes and the instrumental measurement, sensory tenderness was correlated with WBSF but not with TPA hardness. Nevertheless, TPA chewiness was well correlated with sensory tenderness indicating TPA usefulness to give addicional information of beef texture. Off-flavour was the ix main determinant of overall acceptability and Brazilian beef presented the highest and lowest values, respectively. Brazilian beef also had the lowest juiciness score, indicating that this beef type despite having the best lipid nutritional value can be rejected due to it sensory attributes. All beef types were considered slightly to moderately tender regarding WBSF and sensory tenderness mean values. National undifferentiated beef seem to have higher variability in the colour measurements, whilst Carnalentejana-PDO seems to depicted higher tenderness variability. Despite having mean values in the aforementioned attributes that indicates a consumer high acceptability, the high variability in both cases can be detrimental in the moment of sale.RESUMO - Relação entre as preferências do consumidor português e a textura, composição química e valor nutricional da carne de bovino - A carne bovina é um produto nutricionalmente rico e de elevado valor económico. No entanto, nos últimos anos tem sido alvo de publicidade negativa por parte da comunicação social devido ao seu conteúdo em colesterol e em ácidos gordos saturados e trans. O crescente número de surtos alimentares na Europa aumentou a preocupação dos consumidores quanto à segurança e qualidade alimentar. No entanto, apesar das referidas preocupações, os atributos sensoriais ainda permanecem a principal razão que leva os consumidores a comprar e a repetir a compra de carne de bovino. A tenrura tem sido considerada o atributo mais importante da carne bovina e define o seu valor comercial, mas a sua variabilidade tem representado um problema para a indústria. Neste contexto, o objectivo deste trabalho foi determinar as propriedades organolépticas e o valor nutricional da fracção lipídica da carne bovina e relacioná-las com as preferências dos consumidores. O trabalho experimental consistiu em dois ensaios. No primeiro ensaio foram estudados a qualidade organoléptica e o valor nutricional da fracção lipídica da carne de vitela “Vitela Tradicional do Montado”-IGP e Mertolenga-DOP e do novilho Mertolenga-DOP. Os resultados sugerem que as duas vitelas têm composições similares, o que pode significar que o efeito da idade foi maior do que o efeito da raça ou género. Apesar das semelhanças do sistema de produção e no perfil lipídico as três carnes foram bem discriminadas. No segundo ensaio foram estudados a qualidade organoléptica e o valor nutricional dos lípidos das carnes de bovino Carnalentejana-DOP, importada do Brasil e nacional indiferenciada. Também aqui se pretendeu prever a qualidade sensorial das carnes com base nas medições instrumentais. Todos os tipos de carne apresentaram baixo teor em colesterol, e teor em α-tocoferol suficiente para inibir a oxidação lipídica e a descoloração. A carne Brasileira apresentou o melhor valor nutricional do perfil lipídico e potencial anti-oxidante, visto ter apresentado conteúdos superiores em α-tocoferol, β-caroteno, CLA e ácidos gordos poliinsaturados. A ingestão de energia foi calculada para os ácidos gordos mais importantes e comparada com as recomendações de ingestão diárias. Todos os tipos de carne apresentaram baixo conteúdo em colesterol e ácidos gordos saturados. Os atributos sensoriais apresentaram correlações baixas com os parâmetros instrumentais, e apenas a força de corte se correlacionou com a tenrura sensorial. No entanto, a tenrura sensorial correlacionou-se com a mastigabilidade indicando que o TPA pode ser útil, dando informação adicional sobre a textura da carne. O off-flavour foi o principal determinante da xi aceitabilidade da carne, apresentando a carne Brasileira os valores mais e menos elevados, respectivamente. A carne Brasileira foi também a menos suculenta, indicando que apesar de apresentar o melhor valor lipídico pode, no entanto, ser rejeitada pelas suas características sensoriais. Todas as carnes foram consideradas ligeira a moderadamente tenras, tendo em conta os seus valores de força de corte e de tenrura sensorial avaliada pelo painel de provadores. As carnes nacionais apresentaram heterogeneidade da sua composição química, a Carnalentejana-DOP na tenrura e a nacional indiferenciada na cor, o que é indesejável e pode condicionar a sua comercialização, pelo que este aspecto deve ser melhorado

Brucellosis: an emerging disease in Portugal

Human brucellosis is one of the most common zoonosis worldwide. In Portugal, brucellosis is a notifiable disease in humans and the casuistic puts it among the three zoonosis with the highest incidence. Despite this, studies on prevalence of brucellosis in Portugal are scarce. The present study intends to evaluate the epidemiological situation of human brucellosis in Portugal and to identify the species associated with human cases. It also intend to investigate the origin of infection in humans using molecular typing studies and whole genome sequencing approaches. In this work, we propose study the genetic polymorphism of several virulence factors in Brucella spp. Our results showed that Brucella melitensis is the main species associated to human brucellosis and that there is a strong epidemiological link between many cases studies, whose originated small clusters and may even correspond to small outbreaks. In this study, it was possible to verify a strong phylogenetic proximity between isolated strains in the Mediterranean area (Spain, Greece and Italy) probably due to geographical, cultural and type of food proximity. In this work, using an advanced approach, new generation sequencing methodologies, we were able to validate the use of MLVA - 16, the gold standard for typing Brucella spp., using in silico extraction. Globally, the findings presented in this PhD thesis contribute for better understanding of the brucellosis situation in Portugal. The results may contribute to the implementation of a new laboratory tool to improve the epidemiological surveillance of brucellosis. Furthermore, is providing more accurate and quick information to the decision makers with responsibilities in the area of the implementation of measures of prevention and control of this disease in our Country, both in human and veterinary health, in line with the One Health approach