Modelação multiescala de qualidade do ar urbana para cidades mais saudáveis

Ambient air pollution is nowadays a serious public health problem worldwide, especially in urban areas due to high population density and intense anthropogenic activity. Among the main urban air pollution sources, the road traffic sector is one of the major concerns and the largest contributor to nitrogen dioxide (NO2) concentrations, though regional background chemical conditions must also be considered. In this context, the use of modelling tools is crucial to understand atmospheric and social dynamics in multiple scales, as well as to support in defining the best air quality improvement strategies. The main objective of this thesis is to develop and apply a multiscale modelling system able to simulate air quality and health impacts in cities. For this purpose, the modair4health multiscale air quality and health risk modelling system was developed and operationalized. It includes the online model WRF-Chem, which provides air quality and meteorological fields from regional to urban scales, and the Computational Fluid Dynamics (CFD) model VADIS, which uses the urban WRF-Chem outputs to calculate flows and dispersion of traffic emissions-related air pollutants in urban built-up areas. A health module, based on linear and non-linear World Health Organization approaches, was also integrated in modair4health to assess the health impacts resulting from air quality changes, and the overall health damage costs are calculated based on economic studies. The application and assessment of the modair4health system allowed to identify the most appropriate configurations and input data, which were used to apply the system over the case study testing air quality improvement scenarios. One of the busiest road traffic areas of the city of Coimbra (Fernão de Magalhães Avenue) in Portugal was selected as case study. The application considered a 4 domains setup: three nested domains (25, 5 and 1 km2 resolutions) for the WRF-Chem, and the 4th domain (4 m2 resolution) over the target local study area and NO2 for the VADIS. WRF-Chem was applied along the year 2015 and VADIS was simulating two particular periods: one week in winter and another one in summer. Short-term health impacts were estimated and the non-linear approach led to lower health outcomes that seem better adjusted to the local reality. Finally, to assess the modair4health capabilities for decision-making support, two traffic management scenarios were tested over the case study: replacement of 50% of the vehicle fleet below EURO 4 by electric vehicles (ELEC), and introduction of a Low Emission Zone (LEZ). Air quality and health positive impacts were higher for the ELEC scenario. This study represents a scientific advance in multiscale air quality and health modelling. The modair4health system can be easily adapted and applied to other simulation domains, providing urban air pollution levels and subsequent health impacts for different case studies and supporting the assessment of air pollution control policies.A poluição atmosférica é atualmente um sério problema mundial de saúde pública, especialmente em áreas urbanas, devido à elevada densidade populacional e intensa atividade antropogénica. O setor dos transportes rodoviários é uma das principais preocupações e o que mais contribui para concentrações de dióxido de azoto (NO2) na atmosfera, embora as condições químicas de fundo regional devam também ser consideradas. Neste contexto, a utilização de ferramentas de modelação é crucial para compreender a dinâmica atmosférica e humana a diferentes escalas, e apoiar na definição das melhores estratégias para melhoria da qualidade do ar (EMQA). Esta tese tem como objetivo principal o desenvolvimento e aplicação de um sistema de modelação multiescala que permita simular qualidade do ar e impactos na saúde em cidades. Para isso, foi desenvolvido e operacionalizado o sistema modair4health - multiscale air quality and health risk modelling. Este sistema inclui o modelo online WRF-Chem, que fornece campos meteorológicos e de qualidade do ar da escala regional à urbana, e o modelo CFD VADIS, que utiliza os resultados do WRF-Chem para calcular o impacto das emissões do tráfego rodoviário no escoamento e dispersão de poluentes em áreas urbanas. Para avaliar os impactos na saúde humana, foi também integrado um módulo baseado nas abordagens linear e não-linear da Organização Mundial de Saúde (OMS), e os custos são calculados com base em estudos económicos. A aplicação e avaliação do sistema modair4health permitiram identificar as configurações e dados de entrada mais apropriados, que foram posteriormente utilizados para testar EMQA sobre o caso de estudo, que corresponde a uma das áreas de maior tráfego rodoviário da cidade de Coimbra (Avenida Fernão de Magalhães). O WRF-Chem foi configurado com 3 domínios aninhados (resoluções de 25, 5 e 1 km2), simulados para o ano 2015; enquanto que para o VADIS, foi definido um quarto domínio (resolução de 4 m2) sobre o caso de estudo para simular concentrações de NO2 em dois períodos específicos: uma semana no inverno e outra no verão. Para quantificar os impactos na saúde, as duas abordagens da OMS foram aplicadas ao caso de estudo para avaliar efeitos a curto-prazo. A abordagem não-linear apresentou resultados de saúde mais baixos que aparentemente estão melhor ajustados à realidade local. Por fim, foram avaliadas as potencialidades do sistema no apoio à tomada de decisão, testando dois cenários de gestão do tráfego rodoviário: substituição de 50% da frota de veículos abaixo de EURO 4 por veículos elétricos (ELEC), e introdução de uma Zona de Emissões Reduzidas (LEZ). O cenário ELEC potencia melhorias mais significativas na qualidade do ar e saúde. Este estudo representa um avanço científico na modelação multiescala da qualidade do ar e saúde. O sistema modair4health pode ser facilmente adaptado e aplicado a outros casos de estudo para avaliar a qualidade do ar urbana e impactos na saúde, bem como para testar medidas de controlo da poluição atmosférica.Programa Doutoral em Ciências e Engenharia do Ambient

COPD at the Porto Metropolitan Area and the effect of heat and cold waves on this disease

Caracterizou-se a doença pulmonar obstrutiva crónica (DPOC) e os possíveis aspectos socioeconómicos associados à enfermidade e avaliaram-se os efeitos que as ondas de calor (OdC) e as ondas de frio (OdF) podem ter no aumento dos internamentos hospitalares nas pessoas residentes na Área Metropolitana do Porto (AMP) entre 2000 e 2015. Os efeitos das OdC e das OdF nas admissões hospitalares por DPOC foram investigados por meio da análise de regressão linear múltipla, com nível de significância de α = 5%. A análise estatística e cartográfica da distribuição geográfica dos internamentos hospitalares por DPOC, por grupos etários, por taxa de analfabetismo e por taxa de desemprego, à escala de freguesia, permitiu explicar os efeitos das OdC e das OdF no agravamento desta enfermidade. Do ponto de vista da caracterização das admissões por DPOC na AMP, concluiu-se que, em geral, esta doença está associada às freguesias com condições socioeconómicas mais precárias e com a população mais envelhecida. A intensidade e a duração, de acordo com o modelo utilizado, explicam o aumento nas taxas de admissões por DPOC durante os eventos de OdC e OdF. Todavia, a duração contribuiu mais nos eventos de calor e a intensidade nos eventos de frio. A severidade média foi o único parâmetro que não compôs o modelo.Chronic obstructive pulmonary disease (COPD) and the possible socioeconomic aspects associated with the disease were characterized and the effects that heat waves (HW) and cold waves (CW) can have on the increase of hospitalizations in people living in the Porto Metropolitan Area (PMA) between 2000 and 2015 were evaluated. The effects of HW and CW on hospital admissions for COPD were investigated by multiple linear regression analysis, with a significance level of α = 5%. Statistical and cartographic analysis of the geographic distribution of hospitalizations for COPD in the age groups, illiteracy rate and unemployment rate at the parish scale, explained the effects of HW and CW on the aggravation of this disease. From the point of view of the characterization of COPD admissions in PMA, it was concluded that, in general, this disease is associated with parishes with poorer socioeconomic conditions and the older population. Intensity and duration, according to the model used, explain the increase in COPD admission rates during the HW and CW events. However, duration contributed more in heat events and intensity in cold events. Average severity was the only parameter that did not make up the model

Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Geography and ecology shape the phylogenetic composition of Amazonian tree communities

Aim: Amazonia hosts more tree species from numerous evolutionary lineages, both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonized multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types. Location: Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods: Data for the abundance of 5082 tree species in 1989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran\u27s eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny. Results: In the terra firme and várzea forest types, the phylogenetic composition varies by geographic region, but the igapó and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R$^{2}$ = 19% overall for combined spatial/environmental effects). The phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R$^{2}$ = 28%). A greater number of lineages were significant indicators of geographic regions than forest types. Main Conclusion: Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization in specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions

Estimating the global conservation status of more than 15,000 Amazonian tree species

Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant species on Earth by 22%. We show that the trends observed in Amazonia apply to trees throughout the tropics, and we predict thatmost of the world’s >40,000 tropical tree species now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened species if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century

Geographic patterns of tree dispersal modes in Amazonia and their ecological correlates

Aim: To investigate the geographic patterns and ecological correlates in the geographic distribution of the most common tree dispersal modes in Amazonia (endozoochory, synzoochory, anemochory and hydrochory). We examined if the proportional abundance of these dispersal modes could be explained by the availability of dispersal agents (disperser-availability hypothesis) and/or the availability of resources for constructing zoochorous fruits (resource-availability hypothesis). Time period: Tree-inventory plots established between 1934 and 2019. Major taxa studied: Trees with a diameter at breast height (DBH) ≥ 9.55 cm. Location: Amazonia, here defined as the lowland rain forests of the Amazon River basin and the Guiana Shield. Methods: We assigned dispersal modes to a total of 5433 species and morphospecies within 1877 tree-inventory plots across terra-firme, seasonally flooded, and permanently flooded forests. We investigated geographic patterns in the proportional abundance of dispersal modes. We performed an abundance-weighted mean pairwise distance (MPD) test and fit generalized linear models (GLMs) to explain the geographic distribution of dispersal modes. Results: Anemochory was significantly, positively associated with mean annual wind speed, and hydrochory was significantly higher in flooded forests. Dispersal modes did not consistently show significant associations with the availability of resources for constructing zoochorous fruits. A lower dissimilarity in dispersal modes, resulting from a higher dominance of endozoochory, occurred in terra-firme forests (excluding podzols) compared to flooded forests. Main conclusions: The disperser-availability hypothesis was well supported for abiotic dispersal modes (anemochory and hydrochory). The availability of resources for constructing zoochorous fruits seems an unlikely explanation for the distribution of dispersal modes in Amazonia. The association between frugivores and the proportional abundance of zoochory requires further research, as tree recruitment not only depends on dispersal vectors but also on conditions that favour or limit seedling recruitment across forest types