Repositório RCAAP

A mobilidade assume um papel fulcral na vida dos cidadãos e é necessário promover alternativas sustentáveis para atingir a neutralidade carbónica em 2050. As viagens realizadas diariamente, tal como as deslocações casa-trabalho, são ainda, em grande parte, realizadas através do veículo próprio, onde ocorre a combustão de combustíveis fósseis. Neste contexto, esta dissertação pretende avaliar os padrões de deslocação com a utilização da rede de bicicletas partilhadas de Lisboa, as GIRA, o efeito nas emissões dos gases com efeito de estufa (CO2eq) e no consumo de energia final. A análise cinge-se ao ano de 2018 e foi feita com os dados disponibilizados pelo LxDataLab através do protocolo existente com a Faculdade de Ciências da Universidade de Lisboa. Da análise aos padrões de utilização, nomeadamente nos períodos de janeiro a outubro, conclui-se que a maioria dos utilizadores prefere optar pelas bicicletas elétricas, contando as mesmas com 78,6% de utilização. Durante a semana os utilizadores deslocam-se, em média, 840 metros, as viagens têm uma duração média de 14 minutos e percorrem-se, em média, mais seis minutos e 20 metros, durante o fim de semana. No que toca aos pares de origem-destino mais utilizados são de destacar os pares: Alameda dos Oceanos- CC Vasco da Gama, CC Vasco da Gama- Alameda dos Oceanos, Avenida da RepúblicaAvenida Fontes Pereira de Melo, Rotunda dos Vice-Reis- CC Vasco da Gama e Avenida da RepúblicaCampo Grande/Museu da Cidade. Em termos de horas do dia preferenciais de utilização, durante a semana, a maioria das viagens ocorre entre as 8:00h e as 10:00h da manhã e entre as 18:00h e as 20:00h, coincidindo com os períodos de tráfego rodoviário, enquanto durante o fim de semana não se verificam muitas viagens realizadas durante a manhã e não se destaca a existência de um pico de utilização, mas sim de bastantes períodos de utilização entre as 16:00h e as 20:00h, principalmente. A variável climatérica precipitação é a que se comprovou ter maior influência no número médio de viagens, visto que os meses mais chuvosos são aqueles em que existe um menor número de viagens. Avaliaram-se dois cenários extremos: a utilização das bicicletas GIRA não alterou os padrões de utilização dos transportes rodoviários (o impacte traduz-se num aumento de consumo de energia elétrica da mobilidade e aumento de emissões de CO2eq, de acordo com a geração de energia elétrica) ou houve abandono do carro, substituindo-se o uso do mesmo pelo uso da bicicleta (o impacte traduz-se numa diminuição de consumo de energia final na mobilidade e numa diminuição de emissões de CO2eq). Os extremos revelam uma diminuição entre os 398 e os 472 GJ fóssil/ano de energia final ou um agravamento de 8 a 82 GJ elétricos/ano e uma diminuição de emissões de 30 a 36 toneladas de CO2eq/ano ou um agravamento de 0,7 a 7 toneladas CO2eq/ano.

The cosmological principle, which states that the Universe is homogeneous and isotropic, is the basis of modern cosmology. The upcoming ESA/Euclid satellite mission will test this paradigm over a wide range of scales allowing us to assess whether the non-homogeneous Lemaitre-Tolman-Bondi (LTB) models should be considered to accurately describe observations locally and at intermediate cosmological scales. The Euclid survey is expected to reveal/confirm more than 40 thousand new clusters in the optical and infrared bands, which represents a new era for cluster cosmology as well as for understanding the physical processes that govern the evolution of these structures. This project proposes to address the problem of modeling the galaxy cluster population in the context of LTB models, and the development of new numerical tools that may be used to provide ways of confronting model predictions with observations from galaxy surveys (e.g. Euclid) and the Cosmic Microwave Background (CMB) (such as Planck). The work of this thesis consists of gathering an in-depth knowledge of the machinery of the Planck Sky Model (PSM) code, identifying and modifying the key functions and procedures according to a LTB framework. More specifically, we employed the non-homogeneous isotropic Constrained Garcia-Bellido-Haugbølle (CGBH) model which is completely specified by the matter density profile of the large-scale void. Our focus is on the Delabrouille, Melin, Bartlett (DMB) method, implemented by the PSM, which we here modify to a LTB framework. This method computes the thermal and kinetic Sunyaev-Zel’dovich (SZ) components of the CMB, which are well-known and effective probes of structure formation. The dominant SZ effect is the thermal effect and is this component that we modified in this thesis to extend the DMB method in the PSM to LTB models. To assist our modified version of the DMB method we made use of the Bubble code which outputs the relativistic exact solutions in LTB framework. In a first stage, we changed only the PSM functions related to the background properties of the cosmos, and then in a second stage the same was undertook to include modifications in the functions concerning the mass function and the growth of perturbations. We named these two steps as "zero-order" and "first-order" modifications, respectively. The PSM then computes all-sky SZ effect maps, using the HEALPix tesselation tool, and galaxy cluster catalogues generated by our modified version of the DMB method. Having the maps, we were able to perform a fast statistical analysis obtaining the histogram of the distribution of pixels and its key (first four) moments, one of them being the mean SZ comptonization parameter ySZ that has been constrained by CMB satellite observations by the COBE-FIRAS experiment. We then explored the evolution of the power spectra, the thermal SZ maps and of the ySZ signal as the parameters of the CGBH model vary. We also compare our results to two different FLRW cosmologies: a critical and a ΛCDM "concordance" model. Finally, the code generated catalogues of galaxy clusters which allow to generate, for the first time, mock simulations of clusters. This is a crucial tool to characterise systematic effects and estimate covariance matrices for parameter inference with cluster observables in galaxy surveys. Having the catalogues and maps, the future steps would be to confront theoretical predictions against SZ (Planck) observations and optical catalogues from existing galaxy surveys (eg SDSS/MAXBSG). The study in this project is timely and innovative. This is the first time the galaxy cluster population is modelled in the LTB context with a set of new tools at the beginning of a new era for cluster cosmology with the ESA/Euclid satellite.

The spread of the coronavirus disease 2019 (COVID-19) has important links with population mobility. Social interaction is a known determinant of human-to-human transmission of infectious diseases and, in turn, population mobility as a proxy of interaction is of paramount importance to analyze COVID-19 diffusion. Using mobility data from Google’s Community Reports, this paper captures the association between changes in mobility patterns through time and the corresponding COVID-19 incidence at a multi-scalar approach applied to mainland Portugal. Results demonstrate a strong relationship between mobility data and COVID-19 incidence, suggesting that more mobility is associated with more COVID-19 cases. Methodological procedures can be summarized in a multiple linear regression with a time moving window. Model validation demonstrate good forecast accuracy, particularly when we consider the cumulative number of cases. Based on this premise, it is possible to estimate and predict future evolution of the number of COVID-19 cases using near real-time information of population mobility

Indirect resistance (IR) is a well documented polymicrobial interaction, defined as the protection of an antibiotic-sensitive strain by a neighboring resistant strain through the detoxification of the surrounding environment. It is typically observed as a consequence of antibiotic-based treatments, with a notable proclivity for β-lactam antibiotics. The large majority of IR occurrences involve cohabiting strains of diverging species. By comparison, examples of intra-species IR remain scarce. To explain this discrepancy, we propose that resource competition can counteract IR by rendering intra-species strain coexistence untenable. Likewise, inter-species IR can occur unimpeded as different strains can coexist by occuppying different metabolic niches, or even share metabolic by-products through cross-feeding. To test this hypothesis, we performed intra- and inter-species co-cultures of resistant and sensitive strains, in ampicillin-supplemented minimal media with competing and non-competing carbon sources. Also, cross-feeding was evaluated by performing co-cultures in media supplemented with carbon sources only consumable by one of the strains. While intra-species competition was invariable, interspecies competition was conditional of the carbon source. We found that sensitive strains exhibited significant growth reduction in intra-species co-culturing compared to when in mono-culture. By contrast, when paired with a resistant strain belonging to a different species, sensitive strains were able to match the growth observed in mono-culture. Co-cultures also showed potential cross-feeding interactions allowing the growth of both resistant and sensitive strains in the absence of their specific carbon source. Our results show that IR may be optimized in the absence of strain competition, which could potentially explain the lack of observable intra-species IR when compared to inter-species. Furthermore, we identified that cross-feeding mechanisms between strains might strenghten the cooperative nature of IR by permiting the growth of the resistant cells. Conversely, it may also extend the exploitation of the resistant strain to include metabolic nutrients in addition to antibiotic-disabling enzymes.

In recent years, several Earth-sized exoplanets have been detected in short-period orbits of a few Earth days, around low-mass stars. Despite their small size compared to gas giants, their close-in orbits, combined with the small radius of the host star compared to our Sun’s, make these worlds the best targets for atmospheric characterisation among rocky exoplanets. These worlds have stellar irradiation levels that can be several times that of the Earth, suggesting that a Venus-like climate is more likely. In this work, I use a Global Circulation Model (GCM), the Generic-GCM, to model a possible Venuslike atmosphere on TRAPPIST-1 c as a benchmark of highly-irradiated rocky exoplanets orbiting Mdwarf stars. The model has been developed at the Laboratoire de Météorologie Dynamique (LMD) for exoplanet and paleoclimate studies. It includes a 3D dynamical core common to all terrestrial planets and a planet-specific physical part. In addition, the Generic-GCM has a generalised radiative transfer routine for variable atmospheric compositions. The overarching goal is twofold: (1) to study the largescale atmospheric circulation of highly-irradiated rocky exoplanets; and (2) to address the observational prospects of this kind of planet by producing phase curves (reflection and emission) and transmission spectra to support future space missions (e.g., James Webb Space Telescope, JWST). I assumed that TRAPPIST-1 c is a synchronous rotator with zero eccentricity and obliquity. It has a Venus-like atmosphere, a 92 bar surface atmospheric pressure, and a radiatively active sulphuric acid prescribed global cloud cover. I run a test to assess the Generic-GCM representation of the large-scale atmospheric circulation on Venus, comparing the results with a Venus specific GCM: the IPSL-VGCM. First, the Generic-GCM reproduces the superrotation pressure range and high-latitudes jets observed in the IPSLVGCM. Second, the Generic-GCM responds well to decreasing insolation by reducing the zonal wind speeds. Third, superrotation is a robust dynamical feature present in the range of insolation explored. The results for TRAPPIST-1 c indicate a warmer atmosphere than that of Venus, possibly a consequence of carbon dioxide absorption of stellar radiation, which is strongest in the near-infrared. The day-night heat redistribution in the planet is done through eastward superrotation jets (equatorial and two high-latitudes) and meridional circulation. The latter comprises two large cells, one per hemisphere (northern and southern), crossing the pole. Heat transport is mainly explained by its mean meridional circulation component, with a minor poleward contribution of the stationary waves in the mid-latitudes. The cloud top temperature field shows a distinctive chevron-like pattern and an eastward shift of the peak thermal emission from the substellar point, suggesting an advection of warm air masses by the equatorial zonal superrotation jet. There is evidence for an equatorial wave (c¯ ∼ 130 m s−1 , Tw = 17.5 hours). The TRAPPIST-1 c reflection phase curves reach a maximum planet-to-star contrast on the order of 10−6 , confirming that high albedo sulphuric acid aerosols of Venus-like cloudy exoplanets may favour their detection by JWST and other future instruments. This work also shows that thermal phase curves can sound different atmospheric levels, depending on the spectral band: carbon dioxide absorption bands will sound mesospheric levels, while continuum bands will sound the cloud top. The simulated transmission spectrum of TRAPPIST-1 c is flattened by clouds, screening almost all but the strongest carbon dioxide absorption bands (e.g., 4.3 µm, 15 µm). Detection of weaker CO2 spectral lines might be possible, suggesting a higher abundance, Venus-like carbon dioxide atmosphere. In particular, the work shows that detecting the 4.8 µm CO2 spectral band might be possible, indicating a high-pressure atmosphere. The removal of Venus-like aerosols from simulations leads to a warmer deep atmosphere, including the development of polar warming. The parametric study reveals that larger exoplanets will have more intense zonal equatorial jets but a smaller eastward shift of the hotspot and larger planet-to-star contrast in the phase curves. The higher-order spin-orbit resonances will modulate the amplitude and peak emission of the thermal phase curve, suggesting that this observable can be used to constrain the rotation state.

No summary/description provided

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiological agent of paratuberculosis, a chronic infection affecting ruminants worldwide. In wildlife, MAP was first detected in the European rabbit and has since then been reported in a very broad host range. Information on the ecological factors that increase infection risk, as well as evidence for the transmission paths linking livestock, wildlife, and the environment, remain scarce. Thus, the objectives of this thesis included estimating MAP prevalence in the mammal community of a Mediterranean agro-forestry farmstead, the Companhia das Lezírias, through field and wet lab approaches, assessing MAP’s spatial distribution, determining which factors modulate exposure of wildlife to MAP, and predicting MAP risk within the study area. Using molecular detection of IS900 as a proxy, MAP was detected in ten wild mammal species, with emphasis on wild rabbit (19% overall prevalence), in cattle (54% individual prevalence and 100% herd prevalence) and in soil (44% prevalence). Wildlife diversity showed a positive influence on MAP presence in mammal feces, while wildlife abundance showed a negative influence. Land use variables showed distinct degrees of influence on MAP presence in feces of specific groups of mammals: mixed forest showed positive influence in carnivores, and shrubland showed positive influence in wild rabbit. The spatial prediction of MAP occurrence risk in wildlife generated two hotspots; however, model accuracy was low. In conclusion, the variables considered were insufficient to accurately predict MAP occurrence risk in mammals in our study area, showing the need for further studies. Increasing the number of samples and sampled species, as well as considering new variables, could improve prediction accuracy. Despite these limitations, this study represents a significant step forward in the knowledge of MAP occurrence at the livestock-wildlife interface in a Mediterranean agroecosystem.

Services of general interest (SGI) contribute to the European Union’s objectives, being fundamental to territorial cohesion and convergence, with a preeminent role in rural and peripheral territories. Hence, disparities in access to these services lead to critical regional disparities, impairing cohesion. It is in economic harsh times that SGI are preponderant, especially in more rural or peripheral regions and health services are one of the most impactful SGI, being an iconic representative of the Welfare State. Therefore, an assessment of regional health services must be developed in relation to Welfare State Regimes performance. This study is developed within this framework, with the objectives of understanding: how national and local expenditures in health are related to Welfare State Regimes; and how their expenses impact territorial cohesion through differentiated regional health service provision and population health status. The work was developed in two phases: one centred on the assessment of total and health expenditures made by national and local governments, discussed in the framework of distinct Welfare Regimes; another, that analyses regional health service provision and population health status, in their relationship with regional socio-economic characteristics and the framework of Welfare Regimes. Indicators regarding health expenditures countries' efforts, health status, and services at a regional scale were retrieved from Eurostat. Results confirm that the provision of services and health status differ among Welfare Regimes and territorial typologies. Urban regions showed better results than rural ones, with the Welfare Regime precluding this reality. We conclude that regional health disparities are a concerning factor that harms territorial cohesion.

Acute Respiratory Distress Syndrome (ARDS) is an inflammatory condition developed from parenchyma damage that ultimately leads to loss of aerated tissue. In the lung, the gas exchange occurs in the alveoli comprised by alveolar type (AT) 2 cells and AT1 cells. AT2 are known to be the alveolar stem cells as they can transdifferentiate into AT1 cells or dedifferentiate trough TGF-β driven epithelial-mesenchymal transition (EMT). In abnormal conditions, such as ARDS, the alveolar repair is impaired and both processes lead to a compromised parenchymal structure and gas exchange. For this reason, the mechanisms underlying the repair and differentiation should be further understood. Recent data suggest that epithelial CCR10 expression is not only associated with evolution towards fibrosis, but also with epithelial mobility. For this reason, we aimed to investigate the impact of different cytokines on CCR10 expression in alveolar epithelial cells in a wound healing assay. We used 7-day 2D cultures of the human A549 cell line, which are lung adenocarcinoma epithelial cells that resemble AT2 cells in vitro. After manual wound making, cells were exposed to IFNγ (type I), IL13 (type II), IL22 (type III), IL1β+IL6 (pro-inflammatory), TGFβ (EMT), GM-CSF and CCL28 (expressed by AT2 cells in demanding conditions). We found that CCL28, a CCR10 ligand, and IL13 increased the mean CCR10 expression by A549 cells. The levels of this chemokine receptor and frequency of KI-67+ cells were negatively correlated with percentage of wound closure, suggesting that like cell proliferation, CCR10 expression impacts wound repair. Interestingly, we observed that CCR10 highest mean expression was in cells in intermediate state, as we characterized in flow cytometry as Podoplanin+CD63+ . Using this same technique, we assessed A549 cell differentiation and observed that this process occurred in all conditions except for TGFβ and IFNγ, which were associated with an increase in Vimentin and decrease in E-cadherin levels, both characteristics of the EMT process. Despite the bigger frequency of AT2-like cells, neither TGFβ nor IFNγ had an effect on the production of pro-SFTPC, a marker of AT2 cell function, opposing CCL28 and GM-CSF that upregulated it. These results lead us to conclude that the CCL28/CCR10 axis may play a role in epithelial repair as CCL28 is a chemokine released by epithelial cells in pro-inflammatory/hypoxemic conditions as observed in ARDS. We propose that further studies should be done to assess the true function of this receptor in alveolar epithelial cells and intrinsic pathways that regulate CCR10 expression in a context of ARDS.

Bioinformatics aims to analyze and store complex biological datasets, which, due to the multidisciplinarity of the field, can be essential for finding meaning in biological systems, contributing to the modern life sciences knowledge. Transcriptomics is currently one of the areas if bioinformatics in greater expansion, namely through RNA sequencing (RNA-seq), which is an efficient transcriptome profiling approach. Its main application is the analysis of differentially expressed genes (DEGs), to assign biological meaning to specific tissues, environmental conditions, and other aspects. Reproductive strategies, resistance and stress responses can be evaluated through this technique, leading to a better understanding of the species fitness and survival. This thesis intended to detect and functionally annotate DEGs through the application of RNA seq pipelines. Moreover, since there’s still no gold standard for its best practices, this work mostly aimed to find the best suited tools and methods for each data type, such as length, depth and replicates, according to the research goals. Furthermore, it established a better understanding of the different expression profiles of species from three different genera, namely Casuarina, Coffea and Limonium. In general, the RNA-seq workflow was performed as follows: quality analysis, assembly (for non-model species), alignment, quantification, differential expression, and functional annotation. Since this project was developed as four separated analyses, each step and respective tools were evaluated according to each dataset features. The results of these analyses break the path for further studies and integration with other omics, which can help unravel relevant mechanism and pathways of the studied species. During the work of this thesis, a large set of scripts were developed to speed up and automatize the analysis, using Python and R languages, which have been made publicly available and can be applied by other users that work on similar studies.

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