Modelling tools to predict potential distribution of forest species : using Pico Island and the Azores as study case

Tese de Doutoramento, Biologia, 16 de novembro de 2018, Universidade dos Açores.Os modelos de distribuição de espécies (SDMs) têm sido aplicados em diferentes áreas da ecologia, nomeadamente para modelar a distribuição potencial de espécies invasoras, para avaliar espécies prioritárias no âmbito da conservação e para apoiar o planeamento florestal. Um SDM é uma descrição matemática da distribuição de uma espécie no espaço ambiental, a qual pode ser utilizada para prever a distribuição da espécie no espaço geográfico. O avanço ao nível da capacidade computacional disponibilizou uma diversidade de métodos estatísticos, que anteriormente não era possível utilizar. Esta diversidade de métodos reflete-se num número crescente de publicações direcionadas ao estudo e aplicação dos SDMs e também numa variedade crescente de métodos de modelação. Nos Açores, a abundância crescente de dados corológicos, a diversidade geomorfológica do arquipélago e os diferentes padrões espaciais que é possível encontrar em diferentes ilhas e em diferentes espécies, contribuem para que o arquipélago seja um bom modelo para a comparação de diferentes abordagens de modelação, bem como para testar possíveis constrangimentos inerentes ao processo de modelação. As perguntas de investigação a que pretendemos responder nesta tese foram as seguintes: (i) As abordagens de modelação, baseadas em diferentes fundamentos teóricos, originam resultados semelhantes, ao nível da distribuição potencial das espécies florestais estudadas? (ii) Existe alguma diferença relevante, entre o cálculo de Modelos Lineares Generalizados (GLMs) usando métodos de máxima verossimilhança ou métodos bayesianos? (iii) Existe alguma vantagem, no uso de um campo aleatório relativo à estrutura espacial dos dados, em comparação com os modelos que incluem apenas os efeitos fixos das variáveis ambientais? (iv) As diferentes abordagens de modelação originam resultados consistentes, em particular quando o número de variáveis ambientais utilizadas na modelação é reduzido? (v) As diferentes técnicas de modelação são afetadas de um modo relevante pela dimensão da amostra, pelo tipo de distribuição da espécie e pelas alterações no uso do solo? Para responder a estas questões, foram desenvolvidos três exercícios de modelação: (i) Uma comparação da Análise Fatorial do Nicho Ecológico (ENFA) e da modelação baseada na Máxima Entropia (MaxEnt), utilizando dados relativos à presença de três espécies (Pittosporum undulatum, Acacia melanoxylon e Morella faya) em três ilhas (Pico, Terceira e São Miguel), e incluindo o efeito da redução da dimensão da amostra; (ii) A comparação de modelos com efeitos fixos ou mistos, utilizando a plataforma R para o cálculo de GLMs e da aproximação de Laplace (INLA), permitindo o cálculo da estrutura espacial dos dados (função de covariância de Matérn), baseada em dados de duas ilhas (Pico e São Miguel) para duas espécies (P. undulatum e M. faya), e incluindo o efeito da redução da dimensão da amostra; e (iii) A comparação de GLMs e de uma seleção de algoritmos de autoaprendizagem (Machine Learning), usados para modelar as possíveis alterações nas áreas de distribuição de P. undulatum, A. melanoxylon e M. faya nas três ilhas, resultantes das alterações climáticas previstas para 2100. Em relação ao primeiro exercício, ambas as abordagens originaram cenários semelhantes, particularmente quando a quantidade de informação explicada pela ENFA era elevada; os resultados da modelação foram afetados pela redução do tamanho da amostra; os modelos com melhor capacidade de previsão incluíam um conjunto variado de variáveis ambientais (topográficas, climáticas e de uso do solo); e os modelos eram afetados pela transferência para um novo habitat (i.e. ilha). Os resultados do segundo exercício de modelação indicaram que os GLMs, calculados através de métodos de máxima verossimilhança ou métodos bayesianos originaram resultados similares, mesmo nos casos em que a dimensão da amostra era reduzida; e que a adição de um campo aleatório aumentou o ajustamento dos modelos, particularmente para a árvore menos abundante, M. faya, embora a estrutura do campo aleatório fosse claramente afetada pela dimensão da amostra. O terceiro exercício de modelação revelou que existem várias limitações quando se modela o efeito das alterações climáticas na distribuição das espécies, uma vez que os melhores modelos incluíram variáveis topográficas, demonstrando que a modelação baseada somente no clima poderá não ser fiável; verificou-se igualmente que o ajuste dos modelos variava de forma relevante entre as diferentes abordagens de modelação, e que o algoritmo Random Forest apresentou, em geral, os melhores resultados. De uma forma geral, os resultados desta investigação poderão ser aplicados como forma de apoio à gestão da floresta açoriana. Poderão ser replicados em outros sistemas insulares e noutras regiões florestais, não somente em projetos direcionados para a ecologia das espécies florestais, mas também em questões de investigação relacionadas com a previsão do sucesso e expansão das plantas invasoras, a deteção de áreas adequadas para projetos de restauro, a modelação baseada em dados de deteção remota e a modelação do efeito potencial das alterações climáticas.ABSTRACT: Species distribution models (SDMs) have been used in different areas within ecology, namely to model the potential spread of invasive species, to evaluate and manage priority species for conservation and to support forest management. An SDM is a mathematical description of the species distribution in the environmental space that can be used to predict the distribution of the species in the geographic space. The advances in computational capabilities have provided increasingly greater and more intensive statistical algorithms than was previously possible, as reflected by the increasing number of publications addressing SDMs and also the growing variety of modelling approaches. In the Azores, the growing abundance of the species distribution data, the diversity on island size and morphology, and the different spatial patterns that are possible among islands and species, make the archipelago a good model for the comparison of different modelling approaches and to test possible modelling constraints. Overall, the results of this research can be expanded to support Azorean forestry management, and could be replicated in other island systems and forest regions, not only in projects addressing the ecology of particular forest species, but also when handling research questions related with the prediction of plant invader success and expansion, the detection of areas potentially suited for restoration projects, modelling based on remote sense data, and modelling of the potential effect of climate change

The Educated Russian's Curse: Returns to Education in the Russian Federation.

This paper uses the only representative sample of the Russian Federation, the Russian Longitudinal Monitoring Survey, to estimate the returns to education in this ex-communist country. This is one of the first studies to tackle this classic issue in labor economics with the realistic expectation of obtaining results for Russia comparable in quality and reliability to those available in developed countries and other economies in transition. Using standard regression techniques we find that the returns to education in Russia are quite low compared with those reported in the literature on countries throughout the world, in almost no specification reaching higher than 5\%. Moreover, there is virtually no improvement in returns to education in the 1992-99 period, a result somewhat at odds with the suggestion of several studies using Russian data from the early 1990s. When we instrument our main regressor using policy experiments from the 1960s, we find comparable results. We also perform a selectivity correction and discover even lower returns to education for men, although they become slightly higher for women. Additionally, we find extremely low returns to tenure, which can even become negative in certain specifications. These results present a bleak perspective for educated Russians, with negative implications for investments in education at all levels, auguring the imminent erosion of one of Russia's few assets not yet completely devalued, the human capital of its citizens.Returns to Education, Russia, Economic Transition, Instrumental Variables, Selectivity Correction

Past expectations as a determinant of equilibrium prices - hysteresis in a simple economy

We give an illustration of hysteresis (path-dependence) in a simple economy. In the presence of multiple possible equilibrium prices, we find that past expectations determine present prices. This phenomenon of path-dependence is robust under perturbations of the economy.Hysteresis, Path-dependence, Tatônnement, Equilibrium selection

An experiment about the impact of social influence on the wisdom of the crowds' effect

Groups have the impressive ability to perform better collectively than the best of its individuals. Galton observed this first in 1907 in his ox weight experiment, but the term wisdom of the crowds (WoC) was coined only later in 2004 by Surowiecki. Cognitive diversity at the individual level enables groups to produce differentiated solutions that ultimately cluster near the true value. By cancelling out the wrongs, the aggregation method exposes the convergence of multiple local optima solutions into one, typically an averaged value that comes incredibly close to the truth-value of what is being estimating. Some accounts suggest that social influence hinders the WoC effect because it diminishes the group diversity resulting in biased outcomes. However, social influence is a naturally occurring phenomenon and it is hardly determinable the extent to which individuals are biased or independent given the complexity of the social interactions. We investigated the impact of social influence on the WoC effect by comparing the collective predictions of 4 groups regarding the number of jellybeans in a jar. We demonstrate that the group disclosing full information performs nearly as well as the control group, where no information was shared. The aggregation method to converge the estimates was the arithmetic mean showing that both groups predicted by approximately 7% the correct number. Statistical analysis has shown that diversity is not affected significantly in the social groups. We conclude that the WoC is not affected by social influence but by the degree of aggregation of the social information shared.Um grupo de pessoas tem a impressionante capacidade de obter melhores resultados a resolver problemas como colectivo do que o mais capaz dos seus indivíduos. Galton observou este fenómeno pela primeira vez na experiência que levou a cabo em 1907 num concurso sobre o peso de um boi, embora o termo wisdom of the crowds (WoC) só viesse a ser popularizado mais tarde, em 2004, por Surowiecki. A diversidade cognitiva a nível individual possibilita a criação de uma variedade de soluções ao nível colectivo que acaba por gravitar em torno do valor real uma vez que os valores errados se cancelam mutuamente quando é aplicado um método agregador, normalmente a média. Alguns autores sugerem que a influência social dificulta o efeito de WoC porque diminui a diversidade dos grupos e por conseguinte produz resultados tendenciosos. No entanto a influência é um fenómeno que ocorre naturalmente e é difícil determinar o grau de influência individual devido à complexidade de interações sociais. Investigámos o impacto da influência social sobre o efeito de WoC comparando as estimativas colectivas de 4 grupos relativamente ao número de doces num jarro. Demonstrámos que o grupo que mostra informação colectiva total obtém resultados semelhantes ao grupo de controlo onde nenhuma informação é partilhada. Usando a média aritmética, os dois grupos previram com uma eficácia aproximada de 7% o número correto de doces no jarro. Testes estatísticos revelaram que a diversidade nos grupos sob influência social não foi significativamente diferente da do grupo de controlo. Concluímos que a influência social não interfere com a diversidade dos grupos se se manifestar de forma integral incluindo toda a informação das estimativas anteriores sem haver convergência de valores

O efeito da indução miofascial suboccipital no sistema nervoso autónomo

Projeto de Graduação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Licenciada em FisioterapiaIntrodução: Com a prática baseada na evidência a ser cada vez mais valorizada é premente comprovar a eficácia das técnicas manuais.A modulação do sistema nervoso autónomo (SNA) é cada vez mais importante na prevenção/tratamento de doenças pela manutenção/restabelecimento da homeostasia corporal.Objectivo:Averiguar qual o efeito das técnicas miofasciais no SNA.Métodos:Foram avaliadas as variáveis da variabilidade da frequência cardíaca (VFC) e a pressão arterial (PA) de 30 indivíduos (idade média=23,50±4,02 anos),utilizando um protocolo onde os indivíduos deveriam respirar a um ritmo de 15cpm, durante 15 minutos sendo realizada no grupo experimental(GE) a indução miofascial suboccipital nos 5 minutos intermédios.Resultados:Com a aplicação da técnica obteve-se um aumento do RMSSD e diminuição da frequência cardíaca média no GE, ainda que se verifique uma leve tendência para aumento SDNN, pNN50, HF e diminuição da razão LF/HF.Houve também uma diminuição da PA Sistólica (PAS).Conclusão:As técnicas miofasciais causam o aumento da actividade do sistema nervoso parassimpático(SNP), podendo ser úteis em diversas áreas desde a prevenção de doenças cardiovasculares à intervenção em geriatria/desporto. prove the effect of manual techniques.Autonomous nervous system (ANS) modulation takes its place as a tool for diseases’ treatment and prevention by maintenance/reestablishment of body homeostasis.Aim:Understand the effect of myofascial techniques on ANS.Methods: Heart rate and blood pressure data from 30 subjects (mean age=23,50±4,02 years-old) were evaluated,using a protocol were they should breath at a pre-determinate rate (15cpm), during 15 minutes.In the experimental group (EG) the technique (suboccipital induction) was performed on the 5 central minutes.Results:With the application of the technique in the EG there was a significant increase of RMSSD and decrease on average HR,with a light tendency to increased SDNN,pNN50,HF and decreased LF/HF ratio.It was also visible a decrease in Systolic BP.Conclusion:Myofascial techniques caused an increase in parasympathetic nervous system,being therefor useful in several areas since heart disease prevention to geriatric/sports intervention

Efficient Haplotype Inference with Pseudo-Boolean Optimization

Abstract. Haplotype inference from genotype data is a key computational problem in bioinformatics, since retrieving directly haplotype information from DNA samples is not feasible using existing technology. One of the methods for solving this problem uses the pure parsimony criterion, an approach known as Haplotype Inference by Pure Parsimony (HIPP). Initial work in this area was based on a number of different Integer Linear Programming (ILP) models and branch and bound algorithms. Recent work has shown that the utilization of a Boolean Satisfiability (SAT) formulation and state of the art SAT solvers represents the most efficient approach for solving the HIPP problem. Motivated by the promising results obtained using SAT techniques, this paper investigates the utilization of modern Pseudo-Boolean Optimization (PBO) algorithms for solving the HIPP problem. The paper starts by applying PBO to existing ILP models. The results are promising, and motivate the development of a new PBO model (RPoly) for the HIPP problem, which has a compact representation and eliminates key symmetries. Experimental results indicate that RPoly outperforms the SAT-based approach on most problem instances, being, in general, significantly more efficient

VCAM1 modulation on endothelial cells – implications for vasculopathy in sickle cell anemia

Sickle cell anemia (SCA) is a highly heterogeneous and multifactorial-like monogenic disease that arises from homozygosity for the c.20A>T mutation in the HBB gene. Vascular disease is systemic in SCA, with profound effects in organs like the brain, where stroke is the most severe end of the cerebral vasculopathy (CVA) spectrum. Endothelial dysfunction plays a major role in vasculopathy with several adhesion molecules, such as VCAM1, being produced by the endothelium altered as a response to inflammatory cytokine (e.g., TNF-α) signalling. In previous association studies, we found positive associations between the presence of four specific VCAM1 gene promoter haplotypes and i) high blood flow velocities in the median cerebral artery, and ii) a chronic hemolysis biochemical marker. In this study, we aimed to assess the functional role of those VCAM1 promoter haplotypes in endothelial cell response following endothelial activation through TNF-α stimulation. After molecular cloning of 3 haplotype constructs, using a pGL4 promoterless vector, haplotype sequence was confirmed, by Sanger sequencing, prior to transfection. We used EAhy926, HUVEC and HBEC as different endothelial cell models, and performed transfection experiments for each construct, with and without TNF-α stimulation. Differences in promoter activity were assessed by luciferase reporter assay. All haplotypes showed differences in promoter activity, after TNF-α stimulation, in all cell models. Haplotype 1 showed decreased promoter activity, while haplotypes 7 and 8 showed increased activity after TNF-α stimulation, in all cell models. These results are consistent with lower VCAM1 expression due to haplotype 1, and therefore a protective effect. Conversely, a higher expression due to haplotypes 7 and 8, suggests an increased vasculopathy risk, in a pro-inflammatory milieu. The association between specific haplotypes and endothelial cell response further enhances the modifier effect of VCAM1 on endothelial dysfunction and its impact in SCA pathophysiology, as well as its potential role as a biomarker of SCA vasculopathy risk, severity and prognosis.This work was partially supported by INSA_202DGH720 project.info:eu-repo/semantics/publishedVersio

Dissecting the molecular mechanism of developmental macular dystrophies

North Carolina macular dystrophy (NCMD) and Progressive bifocal chorioretinal atrophy (PBCRA) are a rare set of dominantly inherited disorders that affect central vision from birth. Two linked loci had been previously identified at 5p21 and 6q16. Whole-genome sequencing (WGS) analysis of our cohort of 92 affected individuals has identified 3 novel causative structural variants (SVs) on 5p21 in 13 NCMD families, and 2 novel noncoding single nucleotide variants on 6q16 upstream of the promoter of PRDM13 in three PBCRA families. Combined, the rearrangements in 5p21 have a shared duplicated region of 39kb, located in a gene desert downstream of IRX1 and upstream of ADAMTS16. DNAse-seq data publicly available for human fetal retina identified active open chromatin sites at both loci at restricted times during retinal development. To dissect the molecular mechanism of the identified variants, skin-derived fibroblasts lines from selected patients were established; CRISPR-CAS9 technology was used to recreate the patient variants in a mouse model; and candidate genes expression profile was assessed in three stages of human fetal retina tissue. Additionally, chromosome conformation capture technology was performed in patient fibroblasts and in mouse developing tissue to characterise the genomic landscape of the locus and assess the effect of structural variants. Genome-wide analysis of chromosome occupancy was also performed for the architectural protein CTCF and for histone modifications relevant for identification of cis-acting elements. Expression studies showed altered expression of IRX genes and ADAMTS16 in mutant lines. Together with evidence from human retinal tissue immunohistochemistry and in situ expression data, these genes are suggested to be miss-expressed and/or ectopically expressed during macular development, with involvement of PRDM13, FGF8 and FGF10, which were also found miss-expressed in mutant lines . This work provides novel insight into the gene regulation landscape involved in human macular development and prognostic information for affected families

Parliamentary online public engagement in the 21st Century : A comparative perspective with a focus on Austria and Portugal

This thesis concerns how parliaments, as institutions, utilise the Internet (and ICTs) to reach and engage citizen. It is structured around the concept of parliamentary (online) public engagement, which has only recently gained some attention in the research agendas of political science and legislative studies. This concept covers a very wide range of outlets and activities offered by parliaments, which can have different purposes and can assume both passive and active forms of engaging with citizens. This thesis focuses on a comparative study of PWs in 21 countries in Europe, and it is complemented by multiple case studies. A mixed method approach was applied, relying on both quantitative and qualitative data and methods. First, the measurement and description of parliamentary online public engagement activities and tools in 21 European parliaments was undergone. Then, it proceeded to a qualitative strand, first assessing the causal conditions necessary and/or sufficient for explaining the results from the quantitative strand and second studying in two case studies in depth – Portugal and Austria – in order to understand the relevant mechanisms, processes and critical actors behind parliaments’ online public engagement strategies over time. Empirically, the study finds that parliaments are selective in their strategies for engaging with the public. In their selectivity, most parliaments choose to invest largely in information provision, leaving other activities of public engagement as secondary. This means that most parliaments have not yet implemented activities and tools to truly engage with their citizens. Additionally, some of the examples found are of an experimental nature or are still in their infancy. Furthermore, parliaments still have a long way to go in pursuing the way they delivery public engagement activities to their audiences. Descriptive results also show that parliaments are cautious when it comes to citizen’s actual participation in the policymaking and prefer to convert conventional forms of participation to digital versions instead of creating innovative democratic instruments. From the explanatory analysis it was possible to conclude that besides parliamentary resources, a committed leadership and political will from key critical actors are also important when it comes to changing the way parliaments engage with citizens through digital media. Additionally, these institutions are mimicking other parliaments that are perceived as successful in using ICTs to communicate and engage with citizens as a response to environmental uncertainty. Finally, it seems that inter-parliamentary cooperation, i.e. learning mechanisms, are increasingly relevant for parliaments on these matters