Tensão interior e exterior. Regeneração a partir de um vazio.

Dissertação para obtenção do grau de Mestre em Arquitetura,A investigação incide sobre a temática dos vazios encerrados, degradados e abandonados do centro histórico que persistem no tecido da cidade antiga e estratégias de intervenção a partir de elementos indispensáveis ao pensamento arquitetónico como o pátio e o saguão. O vazio como consequência de um esquecimento e como sítio sobrante torna-se contido, sem carácter e desprovido de qualificação arquitetónica. A introdução ao tema, é estudado no Bairro Alto, património nacional, pela clareza e persistência do seu traçado antigo. Dada a dinâmica espacial reconhecida no bairro pretende-se encontrar um programa de unidade hoteleira digno e integrante na cidade de modo a promover relações entre a distinta população. O espaço vazio limitado por pré-existências, a Norte do Bairro Alto, delimitado pela Rua da Rosa, Rua São Boaventura e Pátio do Tijolo, foi em tempos uma litografia. Pretende-se explorar e propor uma intervenção com pátios e saguões, como elementos temáticos e fundamentais na arquitetura, de modo a promover o conforto, pela captação de luz e ventilação natural. A arquitetura distingue-se pelo seu carácter útil e objetivo, ao alcance de um destino, de um uso, de uma atmosfera memorável. Pretende-se a regeneração a partir de um vazio no centro histórico, através de uma estratégia de intervenção, de modo a reintegrar e conservar as fachadas pré-existentes do sítio, permitindo uma continuidade de expressões entre o antigo e o novo. Dada a proposta de intervenção pretende-se revitalizar o espaço a partir da importância da posição do arquiteto frente a pré-existências e fragmentos irregulares não integrados no tecido contínuo.ABSTRACT: The investigation shines on the theme of closed voids, degraded and abandoned in the historic center, that remain in the old city structure and intervention strategies from indispensable elements to architectural thinking like the Courtyard and the Lightwell. The void as the consequence of a forgetting and surplus place becomes absent, without character and lacking of architectonic qualification. The theme “Interior and Exterior Tension – Regeneration from a void” comes from the need to reoccupy these places of Bairro Alto, in a way to promote and enrich the old structure. Given the spatial dynamics recognized in the neighborhood it’s intended to find a hospitality unit program worthy and integrated in the city in a way to promote relations between distinct populations. The void of irregular configuration and limited by preexistences was at a time occupied by lithography. The investigation intends to explore and propose an intervention in a way to promote the comfort, by the capture of light and natural ventilation as well as reintegrating the facades with the pre-existing parts that encircle the place, allowing continuity between the old and new. The architecture distinguishes by its useful character and objective, within reach of a destiny, of a use, of a memorable atmosphere. Upon the place restrictions it becomes relevant to understand the adaptability of the space

Determinação da suscetibilidade à ocorrência de instabilidades em vertente à escala regional com métodos de base física

Tese de mestrado, Geologia do Ambiente, Riscos Geológicos e Ordenamento do Território, Universidade de Lisboa, Faculdade de Ciências, 2020Devido ao aumento do risco de movimentos em vertente inerente ao aumento populacional mundial, este fenómeno é cada vez mais estudado, com a intenção de proteger populações e infraestruturas. O presente estudo centra-se numa área correspondente a 8 sub-bacias hidrográficas, com uma área de 15.04 km2, que integra a bacia hidrográfica do Rio Grande da Pipa, localizada a cerca de 25 km a Norte de Lisboa. O desenvolvimento da presente dissertação tem como objetivos principais a aplicação de modelos de base física estático, recorrendo ao software Shalstab e consequente aplicação do método do Talude Infinito, e modelos de base física dinâmico, aplicando o software TRIGRS, na área em estudo. No decorrer dos trabalhos verificou-se a necessidade de proceder à atualização do inventário de movimentos existente, datados de 1967 a 2013, através da observação de fotografias aéreas de 2004. A este inventário apenas foram adicionados 5 movimentos, tratando-se de reativações de deslizamentos anteriores, aparentando sempre a mesma geometria e mesmo eixo de translação. Foi necessário, ainda, a realização de melhorias na cartografia lito-estratigráfica existente, tendo sido modificadas as posições e limites das unidades litológicas, assim como, acrescentadas outras, inexistentes na carta original, com isto, propõe-se uma coluna lito-estratigráfica para a área de estudo. De forma a proceder a uma correta e ampla calibração dos modelos de espessura de solo potencialmente instável, foram estabelecidos três modelos como hipóteses para área de estudo, para a determinação dos valores de m (razão entre a espessura de solo saturado e espessura de solo potencialmente instável) e do Fator de segurança, que correspondem às hipóteses A (modelo proposto por Catani et al, 2010), B (modelo proposto por Saulnier, 1997, tendo como base a carta de declives da área em estudo) e C (modelo proposto por Saulnier, 1997, tendo por base as elevações presentes na área em estudo). Para uma determinação correta do fator de segurança para cada uma das hipóteses propostas, verificou-se a necessidade de calibrar os parâmetros geotécnicos e hidrogeológicos, tendo como base a bibliografia adequada. Foi ainda utilizado um software que permite uma visualização dinâmica, ao longo de um espaço de tempo pré-definido pelo utilizador, o TRIGRS, para análise da suscetibilidade à ocorrência de instabilidade em vertente na área de estudo. Este software foi utilizado para todas as hipóteses de espessura de solo potencialmente instável propostas. Recorrendo à determinação das curvas ROC cuja capacidade preditiva corresponde à área abaixo da curva, para a aplicação do método do Talude Infinito, conclui-se que todos os modelos das hipóteses utilizadas podem ser considerados bons para utilização na área de estudo, ainda assim, o que menos se enquadra é o modelo relativo à hipótese A, porque os resultados foram ligeiramente mais baixos. Relativamente aos resultados obtidos por aplicação dos modelos no TRIGRS, conclui-se que, para a área de estudo, o modelo proposto mais adequado é o relativo à hipótese C.Due to the increased risk of movements inherent in world population growth, this phenomenon is increasingly studied with the intention of protecting populations and infrastructures. This study focuses on an area corresponding to 8 sub-basins, with an area of 15.04 km2, which integrates the Rio Grande da Pipa river basin, located about 25 km north of Lisbon. The development of this dissertation has as main objectives the application of static physics-based models, using the Shalstab software and consequent application of the Infinite Slope method, and dynamic physics-based models, applying the TRIGRS software, in the area under study. During the work it was necessary to update the existing inventory of movements, dated from 1967 to 2013, through the observation of aerial photographs from 2004. Only 5 movements were added to this inventory, being the reactivation of previous slides, always appearing the same geometry and same axis of translation. It was also necessary to improve the existing litho-stratigraphic cartography, having been modified the positions and limits of the lithological units, as well as adding others, non-existent in the original chart, with this, we propose a litho-stratigraphic column for the study area. In order to perform a correct and broad calibration of the models of potentially unstable soil thickness, three models were established as hypotheses for the study area, to determine the values of m (ratio of saturated soil thickness to potentially unstable soil thickness) and the Safety Factor, which correspond to hypotheses A (model proposed by Catani et al, 2010), B (model proposed by Saulnier, 1997, based on the slope chart of the study area) and C (model proposed by Saulnier, 1997, based on the elevations present in the study area). For a correct determination of the safety factor for each of the proposed hypotheses, it was necessary to calibrate the geotechnical and hydrogeological parameters, based on the appropriate bibliography. It was also used a software that allows a dynamic visualization, over a pre-defined time space by the user, the TRIGRS, for the analysis of the susceptibility to the occurrence of instability in the study area. This software was used for all the proposed assumptions of potentially unstable soil thickness. Using the ROC curves whose predictive capacity corresponds to the area below the curve, for the application of the Infinite Slope method, it is concluded that all models of the hypotheses used can be considered good for use in the study area, even so, the model relative to hypothesis A is the least fitting, because the results were slightly lower. Regarding the results obtained by applying the models in TRIGRS, it is concluded that, for the study area, the most appropriate model proposed is the one concerning hypothesis C

A resource for sustainable management:<i>De novo</i> assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, <i>Scomber colias</i>

Mackerels represent a valuable fishery worldwide. Their ample geographic distribution and capture levels make them an insightful model to address stock management strategies in the context of global changes. Yet, and despite recent impressive genome and transcriptome sequencing efforts from teleost species, available resources from the Scombridae family are comparatively scarce. Here, we generated the first high-quality de novo assembly of the liver transcriptome of the Atlantic chub mackerel (Scomber colias). Through the use of RNA-Seq Illumina technology, 111,124,228 clean reads were obtained for the liver transcriptome. De novo assembly resulted in 93,731 transcripts with an N50 of 1462 bp. This dataset provides an important insight into the context of fisheries management. Keywords: RNA-Seq, Scombridae, Stock management, Atlantic chub mackerel, Live

A propósito de um caso partilhado com estudantes de Medicina da Universidade da Beira Interior

Introdução: A eutanásia constitui um problema ético. A educação médica e experiência clínica influenciam a capacidade deliberativa. À semelhança da Europa, a aceitação social da eutanásia tem aumentado em Portugal. Importa compreender a atitude dos médicos do futuro relativamente à eutanásia uma vez que a sua prática clínica poderá ser confrontada com eventuais alterações da legislação. Objetivo: Observar a compreensão dos estudantes em questões de fim de vida relacionadas com a eutanásia, comparando entre dois grupos – em início e no final da formação pré-graduada, respetivamente. Material e métodos: Este é um estudo descritivo e transversal. A população alvo constitui os alunos do 1º e 6º ano do Mestrado Integrado em Medicina da Universidade da Beira Interior ao ano letivo 2019/20; composta por 330 alunos. Por metodologia Delphi, contrui-se um questionário de 7 perguntas. Questionou-se se o caso Vincent Lambert se tratava de eutanásia. Pesquisou-se a concordância relativamente à remoção das medidas de suporte de vida. Sondou-se a opinião sobre o impacto dos estágios curriculares e formação em ética na preparação para gerir decisões de fim de vida. Posteriormente, procedeu-se à análise estatística, através do programa Statistical Package for Social Sciences® versão 26, utilizando-se o teste Qui-quadrado, teste Mann-Whitney e teste exato de Fisher. Resultados: Dos 101 alunos que integraram o estudo, a maioria (65,3%) considerou o caso eutanásia, opção concordante entre os dois anos (p=0,398), classificada mais frequentemente como passiva (63,1%). A maioria dos participantes (61,4%) manifestou-se a favor da remoção das medidas de suporte de vida, sobretudo os alunos de 1º ano (71,2% contra 51,0% do 6º ano, p=0,038). Os alunos finalistas mostraram-se mais discordantes (65,3%) da capacidade formativa do estágio na preparação para gerir dilemas de fim de vida. Os alunos de 1ºe 6º ano revelaram-se satisfeitos com a capacitação adquirida pela formação curricular em ética (61,5% e 59,2%, respetivamente). Conclusão: A maioria dos alunos em estudo considera o caso apresentado como eutanásia, revelando que não distinguem moralmente entre eutanásia e ortotanásia. Recomenda-se a dinamização de estratégicas formativas com um enfoque mais prático no ensino da ética médica.Introduction: Euthanasia is an ethical issue. Medical education and clinical experience influence ethical reasoning. Like in other European countries, social acceptance of euthanasia has increased in Portugal. It is important to understand future doctors’ attitude towards euthanasia since during their clinical practice they may face eventual modifications to legislation. Aim: This study seeks to observe students’ understanding of end of life matters related to euthanasia, comparing between two groups - one at the beginning and the other at the end of undergraduate education. Materials and methods: This is an observational cross-seccional study. The target population were first and sixth-year medical students of the Master’s Degree in Medicine of the University of Beira Interior, academic year 2019/20; it was composed of 330 elements. A 7-question questionnaire was constructed through Delphi method. It was asked if the Vincent Lambert case was considered euthanasia. Acceptance of the withdrawal of life-sustaining treatment was searched. Students’ opinions about curricular residences and teaching of ethics on the preparation to decision making regarding end-oflife dilemmas was inquired. Afterwards, statistical analysis was carried out using the Statistical Package for Social Sciences® version 26, using the following tests: Chi-square test, Mann Whitney test and Fisher’s exact test. Results: Of the 101 students who integrated the study, the majority (65,3%) classified the case as euthanasia, this option was concordant between the two curricular years (p=0,398), most often as passive euthanasia (63,1%). Most students (61,4%) were in favour of withdrawing the life-sustaining measures, especially first year medical students (71,2% against 51,0% of sixth year, p=0,038). Final year students disagreed the most (65,3%) of the curricular residences’ formative capacity on the preparation to manage endof-life dilemmas. Both first and final year undergraduates expressed satisfaction regarding attainment of knowledge in end-of-life decisions through curricular training in ethics (61,5% and 59,2%, respectively). Conclusion: Most students thought the presented case was considered euthanasia, suggesting they do not distinguish between euthanasia and orthothanasia. It is argued that a more practical formative approach should be considered in medical ethics teaching

A solidão existencial do doente com necessidades paliativas : tradução e validação para português da escala EDSOL Versão 2

Tese de mestrado, Cuidados Paliativos, 2021, Faculdade de Medicina, Universidade de LisboaIntrodução: O envelhecimento da população é uma realidade cada vez mais evidente na sociedade portuguesa. O processo de envelhecimento está associado a várias perdas, nomeadamente a perda de papéis sociais, a perda de familiares e amigos, a perda de hábitos, a perda do lar e a perda de contextos de socialização, aumentando, assim, a probabilidade de isolamento e sentimento de solidão. Os instrumentos de avaliação da solidão são escassos, existindo apenas UCLA validada para a população portuguesa. Contudo, a UCLA avalia a solidão no geral, não existindo nenhum instrumento validado para avaliar a solidão existencial. Objetivos: Traduzir e validar a escala EDSOL V2 para a população portuguesa e avaliar se existem diferenças na solidão existencial em função do género, da idade, do diagnóstico e se possui o estatuto de adulto acompanhado. Método: Participaram 40 utentes de uma estrutura residencial para idosos, com doença avançada, progressiva e crónica, com necessidades paliativas. Para determinar a validade convergente e a confiabilidade da escala da deteção da solidão existencial (EDSOL V2), foi calculada a consistencia interna e a análise factorial exploratória. Para a recolha de dados, utilizou-se as seguintes escalas: a Supportive and palliative care indicators toll (SPICT™), a escala de ansiedade e depressão hospitalar (HADS), e a escala de avaliação de mal-estar emocional (AME). Resultados: A escala EDSOL V2 apresenta uma excelente fiabilidade e validade que foi medida através do alfa Cronbach (0.87) e uma variância explicada de 88.54%. O teste Keiser-Meyer-Olkin foi de 0.50 e a sua saturação do item no fator foi de 0.94. A solidão existencial apresentou correlações positivas e significativas com a ansiedade (r = .51; p = .001) e com o mal-estar emocional (r = .46; p = .003). A depressão correlacionou-se significativamente com o mal-estar emocional (r = .56; p < .001). Os participantes do género masculino apresentam níveis mais baixos de solidão existencial comparativamente as mulheres. Conclusão: A escala EDSOL V2 apresenta boas propriedades psicométricas, é fiável e válida para a avaliação da solidão existencial em doentes com doenças avançadas, progressivas e crónicas com necessidades paliativas.Introduction: Population aging is an increasingly evident reality in Portuguese society. The aging process is associated with several losses, including the loss of social roles, the loss of family and friends, the loss of habits, the loss of home and the loss of socialization contexts, thus increasing the probability of isolation and feeling of loneliness. Loneliness assessment instruments are scarce, with only UCLA validated for the Portuguese population. However, UCLA assesses loneliness in general, and there is no validated instrument to assess existential loneliness. Objectives: To translate and validate the EDSOL V2 scale for the Portuguese population and to assess whether there are differences in existential loneliness depending on gender, age, diagnosis, and whether they have the status of accompanied adult. Method: 40 users of a residential structure for the elderly, with advanced, progressive and chronic illness, with palliative needs, participated. To determine the convergent validity and reliability of the existential loneliness detection scale (EDSOL V2), internal consistency and exploratory factor analysis were calculated. For data collection, the following scales were used: The Supportive and palliative care indicators toll (SPICT™), the hospital anxiety and depression scale (HADS), and the emotional distress assessment scale (AME). Results: The EDSOL V2 scale has an excellent reliability and validity that was measured using the Cronbach alpha (0.87) and an explained variance of 88.54%. The Keiser-Meyer-Olkin test was 0.50 and its item saturation in the factor was 0.94. Existential loneliness showed positive and significant correlations with anxiety (r = .51; p = .001) and with emotional distress (r = .46; p = .003). Depression was significantly correlated with emotional distress (r = .56; p < .001). Male participants have lower levels of existential loneliness compared to women. Conclusion: The EDSOL V2 scale has good psychometric properties, is reliable and valid for the assessment of existential loneliness in patients with advanced, progressive and chronic diseases with palliative needs

The elusive nature of adaptive mitochondrial DNA evolution of an Arctic lineage prone to frequent introgression

Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process, but its direct role in adaptation remains far from understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because 1) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and 2) mtDNA introgression from arctic into temperate species is widespread. Here, we analyzed the sequences of 11 complete mitogenomes (ten newly obtained) of hares of temperate and arctic origins (including two of arctic origin introgressed into temperate species). The analysis of patterns of codon substitutions along the reconstructed phylogeny showed evidence for positive selection in several codons in genes of the OXPHOS complexes, most notably affecting the arctic lineage. However, using theoretical models, no predictable effect of these differences was found on the structure and physicochemical properties of the encoded proteins, suggesting that the focus of selection may lie on complex interactions with nuclear encoded peptides. Also, a cloverleaf structure was detected in the control region only from the arctic mtDNA lineage, which may influence mtDNA replication and transcription. These results suggest that adaptation impacted the evolution of hare mtDNA and may have influenced the occurrence and consequences of the many reported cases of massive mtDNA introgression. However, the origin of adaptation remains elusive

Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases

<p>Abstract</p> <p>Background</p> <p>Cytosolic glutathione transferases (cGST) are a large group of ubiquitous enzymes involved in detoxification and are well known for their undesired side effects during chemotherapy. In this work we have performed thorough phylogenetic analyses to understand the various aspects of the evolution and functional diversification of cGSTs. Furthermore, we assessed plausible correlations between gene duplication and substrate specificity of gene paralogs in humans and selected species, notably in mammalian enzymes and their natural substrates.</p> <p>Results</p> <p>We present a molecular phylogeny of cytosolic GSTs that shows that several classes of cGSTs are more ubiquitous and thus have an older ancestry than previously thought. Furthermore, we found that positive selection is implicated in the diversification of cGSTs. The number of duplicate genes per class is generally higher for groups of enzymes that metabolize products of oxidative damage.</p> <p>Conclusions</p> <p>1) Protection against oxidative stress seems to be the major driver of positive selection in mammalian cGSTs, explaining the overall expansion pattern of this subfamily;</p> <p>2) Given the functional redundancy of GSTs that metabolize xenobiotic chemicals, we would expect the loss of gene duplicates, but by contrast we observed a gene expansion of this family, which likely has been favored by: i) the diversification of endogenous substrates; ii) differential tissue expression; and iii) increased specificity for a particular molecule;</p> <p>3) The increased availability of sequence data from diversified taxa is likely to continue to improve our understanding of the early origin of the different cGST classes.</p

DivA:detection of non-homologous and very divergent regions in protein sequence alignments

BACKGROUND: Sequence alignments are used to find evidence of homology but sometimes contain regions that are difficult to align which can interfere with the quality of the subsequent analyses. Although it is possible to remove problematic regions manually, this is non-practical in large genome scale studies, and the results suffer from irreproducibility arising from subjectivity. Some automated alignment trimming methods have been developed to remove problematic regions in alignments but these mostly act by removing complete columns or complete sequences from the MSA, discarding a lot of informative sites. FINDINGS: Here we present a tool that identifies Divergent windows in protein sequence Alignments (DivA). DivA makes no assumptions on evolutionary models, and it is ideal for detecting incorrectly annotated segments within individual gene sequences. DivA works with a sliding-window approach to estimate four divergence-based parameters and their outlier values. It then classifies a window of a sequence of an alignment as very divergent (potentially non-homologous) if it presents a combination of outlier values for the four parameters it calculates. The windows classified as very divergent can optionally be masked in the alignment. CONCLUSIONS: DivA automatically identifies very divergent and incorrectly annotated genic regions in MSAs avoiding the subjective and time-consuming problem of manual annotation. The output is clear to interpret and allows the user to take more informed decisions for reducing the amount of sequence discarded but still finding the potentially erroneous and non-homologous regions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1756-0500-7-806) contains supplementary material, which is available to authorized users

The adaptive evolution of the mammalian mitochondrial genome

<p>Abstract</p> <p>Background</p> <p>The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures.</p> <p>Results</p> <p>Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome <it>b </it>in species with more-specialized metabolic requirements (such as adaptation to low energy diet <it>or </it>large body size, such as in elephant, dugong, sloth, and pangolin, and adaptation to unusual oxygen requirements, for example diving in cetaceans, flying in bats, and living at high altitudes in alpacas). Signatures of adaptive variation in the NADH dehydrogenase complex were restricted to the loop regions of the transmembrane units which likely function as protons pumps. Evidence of adaptive variation in the cytochrome <it>c </it>oxidase complex was observed mostly at the interface between the mitochondrial and nuclear-encoded subunits, perhaps evidence of co-evolution. The ATP8 subunit, which has an important role in the assembly of F₀, exhibited the highest signal of adaptive variation. ATP6, which has an essential role in rotor performance, showed a high adaptive variation in predicted loop areas.</p> <p>Conclusion</p> <p>Our study provides insight into the adaptive evolution of the mtDNA genome in mammals and its implications for the molecular mechanism of oxidative phosphorylation. We present a framework for future experimental characterization of the impact of specific mutations in the function, physiology, and interactions of the mtDNA encoded proteins involved in oxidative phosphorylation.</p