Modelo integrado de fratura em modo misto para o dimensionamento de estruturas 2D em betão reforçado com fibras

Tese de doutoramento em Civil EngineeringThe research work presented in this Thesis aims at contributing to the field of numerical simulation and analysis of fibre reinforced concrete (FRC) structures by developing and implementing numerical tools in a computer code designated FEMIX, which is a general purpose finite element software. Initially, the existing multi-fixed smeared crack model approach in the FEMIX software is used in combination with the constitutive models currently available to conduct a set of numerical case studies of FRC elements failing in bending and shear to analyse the influence the fracture mode I/II parameters of the constitutive models. Subsequently, a generalised approach to compute the crack band width (CBW) is presented and its implementation in the FEMIX computer code is detailed. Furthermore, the extension of this approach to the integration point (IP) level was also conducted and its application made available for plane stress, shell and solid finite elements. The referred approach is analysed by means of a numerical case study where distinct mesh configurations are used to investigate the impact of the CBW in the results. Subsequently, an approach for deriving the fracture mode I parameters of FRC from experimental results of three-point notched beam bending test (3PNBBT) and round panel tests supported on three points (RPT-3PS) is proposed and implemented with C programming language. The developed inverse analysis (IA) approach is based on a nonlinear least squares algorithm coupled with an automatic parameter updating procedure in which the optimised variables are modified based on the deviation between numerical and experimental response. The numerical response is simulated by means of analytical models eliminating the need for a finite element (FE) model significantly reducing the computational time. The developed methodology provides very accurate predictions of the experimental responses both for 3PNBBT and RPT-3PS results. Furthermore, the automatic updating procedure of the input parameters ensures that the final results are practically insensitive to the initial guess of the variables provided by the user. Finally, the developed tool is used to derive the fracture mode I parameters of a real-scale fibre reinforced concrete (FRC) beam and the results are discussed. Finally, the development and implementation of a two dimensional mixedmode fracture smeared crack model (MMFSCM) in the FEMIX software is detailed. The model is based on the combination of the aggregate interlock and fibre pullout resisting mechanisms, using the rough crack model (RCM) and the contact density Model (CDM) for the aggregate interlock component, and the Pfyl, simplified diverse embeddment model (SDEM) and universal variable engagement model (UVEM) for simulating the fibre pullout contribution. The model is appraised by means of numerical case studies, addressing both mode I and mode II fracture dominant mechanisms. Furthermore, modifications to the original fibre pullout models formulation are proposed in order to enhance the predictive performance of the MMFSCM. The predictive performance of the MMFSCM is analysed and discussed by comparing numerical and experimental results gathered from the literature.O trabalho de investigação apresentado nesta Tese visa contribuir para a área da mecânica computacional e análise de estruturas em betão reforçado com fibras (BRF) através do desenvolvimento e implementação de ferramentas numéricas no software de elementos finitos designado FEMIX. Assim, analisam-se inicialmente um conjunto de casos de estudo numéricos de elementos em BRF cuja rotura se dá por flexão e por corte. Os casos apresentados são analisados através de modelos multifendas fixas de fendilhação distribuída disponíveis no FEMIX, sendo o impacto da variação dos parâmetros que simulam o modo I e II analisado através de um estudo paramétrico. Apresenta-se também neste trabalho uma abordagem genérica para o cálculo do comprimento característico (CC). A metodologia é aplicada ao nível do EF, usando a geometria de todo o elemento para efetuar o seu cálculo, tendo sido também estendida ao nível do PI, usando para o efeito a sua área tributária. Ambas as abordagens são implementadas no software FEMIX e a sua utilização analisada através de casos de estudo numéricos. A metodologia referida foi implementada para elementos de estado plano de tensão, elementos de casca e também elementos sólidos. Seguidamente é proposta uma nova metodologia de análise inversa (AI) para obtenção dos parâmetros de fratura em modo I de elementos em BRF tendo por base ensaios experimentais comummente utilizados nomeadamente ensaios de flexão sob três pontos de carga em vigas entalhadas e ensaios de painéis circulares apoiados em três pontos. A metodologia baseia-se num procedimento de regressão de mínimos quadrados não-linear acoplado a um processo automático de otimização das variáveis de entrada. A resposta numérica é calculada através de modelos analíticos em vez de modelos de EF, eliminando por um lado a necessidade de construção de um modelo de elementos finitos e por outro lado o custo computacional do cálculo da resposta numérica. A abordagem proposta é implementada na linguagem de programação C sendo o seu bom desempenho avaliada através de resultados numéricos e experimentais. Por fim, o desenvolvimento de um modelo integrado de fendilhação distribuída em modo de fratura misto é detalhado. O modelo proposto tem em consideração os mecanismos resistentes que se desenvolvem durante o processo de fendilhação de elementos em BRF, usando para o efeito modelos consitutivos de arrancamento das fibras e também modelos micromecânicos para simulação do efeito do embricamento dos agregados. São utilizados três modelos constitutivos para simular o arrancamento das fibras, nomeadamente o modelo proposto por Pfyl, o SDEM e o UVEM, e dois modelos para simulação do efeito de embricamento dos agregados, nomeadamente o RCM e CDM. O modelo integrado é implementado no software FEMIX, estudando-se por um lado o impacto das variáveis envolvidas na sua definição e por outro lado a sua capacidade preditiva, em roturas governadas pelo modo de fratura I e II. Para o efeito são levadas a cabo várias simulações numéricas utilizando o modelo proposto, e os resultados numéricos obtidos comparados com resultados experimentais encontrados na literatura.Fundação para Ciência e a Tecnologia (FCT) through the grants PD/BD/135174/2017 and COVID/BD/151997/2021

Logic-based schedulability analysis for compositional hard real-time embedded systems

This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in SIGBED Review, VOL.12, ISS.1, http://doi.acm.org/10.1145/2752801.2752808Over the past decades several approaches for schedu- lability analysis have been proposed for both uniprocessor and multi-processor real-time systems. Although different techniques are employed, very little has been put forward in using formal specifications, with the consequent possibility for misinterpretations or ambiguities in the problem statement. Using a logic based approach to schedulability analysis in the design of hard real-time systems eases the synthesis of correct-by- construction procedures for both static and dynamic verification processes. In this paper we propose a novel approach to schedulability analysis based on a timed temporal logic with time durations. Our approach subsumes classical methods for uniprocessor scheduling analysis over compositional resource models by providing the developer with counter-examples, and by ruling out schedules that cause unsafe violations on the system. We also provide an example showing the effectiveness of our proposal.This work was partially supported by National Funds through FCT (Portuguese Foundation for Science and Technology) and by ERDF (European Regional Development Fund) through COMPETE (Operational Programme ’Thematic Fac- tors of Competitiveness’), within projects Ref. FCOMP-01- 0124-FEDER-022701 (CISTER), FCOMP-01-0124-FEDER- 015006 (VIPCORE) and FCOMP-01-0124-FEDER-020486 (AVIACC)

The stress granule protein G3BP1 alleviates spinocerebellar ataxia-associated deficits

Koppenol et al. show that overexpression of G3BP1 in cell models of SCA2 and SCA3 leads to a reduction in ataxin-2 and ataxin-3 aggregation. G3BP1 lentiviral delivery reduces motor deficits and neuropathology in preclinical models, suggesting that G3BP1 may be a potential therapeutic target for polyQ disorders. Polyglutamine diseases are a group of neurodegenerative disorders caused by an abnormal expansion of CAG repeat tracts in the codifying regions of nine, otherwise unrelated, genes. While the protein products of these genes are suggested to play diverse cellular roles, the pathogenic mutant proteins bearing an expanded polyglutamine sequence share a tendency to self-assemble, aggregate and engage in abnormal molecular interactions. Understanding the shared paths that link polyglutamine protein expansion to the nervous system dysfunction and the degeneration that takes place in these disorders is instrumental to the identification of targets for therapeutic intervention. Among polyglutamine diseases, spinocerebellar ataxias (SCAs) share many common aspects, including the fact that they involve dysfunction of the cerebellum, resulting in ataxia. Our work aimed at exploring a putative new therapeutic target for the two forms of SCA with higher worldwide prevalence, SCA type 2 (SCA2) and type 3 (SCA3), which are caused by expanded forms of ataxin-2 (ATXN2) and ataxin-3 (ATXN3), respectively. The pathophysiology of polyglutamine diseases has been described to involve an inability to properly respond to cell stress. We evaluated the ability of GTPase-activating protein-binding protein 1 (G3BP1), an RNA-binding protein involved in RNA metabolism regulation and stress responses, to counteract SCA2 and SCA3 pathology, using both in vitro and in vivo disease models. Our results indicate that G3BP1 overexpression in cell models leads to a reduction of ATXN2 and ATXN3 aggregation, associated with a decrease in protein expression. This protective effect of G3BP1 against polyglutamine protein aggregation was reinforced by the fact that silencing G3bp1 in the mouse brain increases human expanded ATXN2 and ATXN3 aggregation. Moreover, a decrease of G3BP1 levels was detected in cells derived from patients with SCA2 and SCA3, suggesting that G3BP1 function is compromised in the context of these diseases. In lentiviral mouse models of SCA2 and SCA3, G3BP1 overexpression not only decreased protein aggregation but also contributed to the preservation of neuronal cells. Finally, in an SCA3 transgenic mouse model with a severe ataxic phenotype, G3BP1 lentiviral delivery to the cerebellum led to amelioration of several motor behavioural deficits. Overall, our results indicate that a decrease in G3BP1 levels may be a contributing factor to SCA2 and SCA3 pathophysiology, and that administration of this protein through viral vector-mediated delivery may constitute a putative approach to therapy for these diseases, and possibly other polyglutamine disorders.PPBI-POCI-01-0145-FEDER-022122info:eu-repo/semantics/publishedVersio

Arbustus unedo essence: morphological and genetic characterization of the strawberry tree of Castelo de Paiva

O medronheiro é um arbusto da região mediterrânica que pode ser encontrada por todo o país. Ao contrário do que verifica na região sul do país, no concelho de Castelo de Paiva é atribuída uma reduzida importância económica a esta espécie. Com o intuito de preservar e potenciar a produção desta espécie e contribuir para a dinamização da economia do concelho, procedeu-se à caracterização morfológica e genética de uma amostra da população de medronheiros de Castelo de Paiva. A caracterização morfológica e genética foi realizada para um total de 10 genótipos. Para tal recolheram-se 70 folhas aleatoriamente em cada árvore. Em 40 folhas mediu-se o comprimento, largura, comprimento do pedúnculo, peso fresco, peso seco e determinou-se a área foliar. Dos caracteres morfológicos analisados, aqueles que se revelaram mais úteis na distinção dos vários genótipos foram: comprimento do pedúnculo, peso fresco e peso seco. As restantes 30 folhas foram utilizadas para a caracterização genética. Esta caracterização foi realizada recorrendo a um marcador de DNA, ISSR. Os 5 primeiros exemplaresutilizados na técnica de ISSR demonstraram-se polimórficos. Os resultados da caracterização genética sugerem que a variabilidade genética na população é média a alta.The strawberry tree is a shrub native in the Mediterranean region and it can be found throughout Portugal. Unlike the case in the southern region of the country, in Castelo de Paiva a minor economic importance is given to this species. In order to preserve, to enhance the production of this species and to contribute to the boosting of the economy of the region, we proceeded to the characterization of a small sample population of this fruit tree of Castelo de Paiva in what concerns to its morphology and genetics. The morphological and genetic characterization was performed for a total of 10 genotypes. For this, 70 leaves were randomly collected from each tree. For 40 leaves, it was measured the length, the width, the peduncle length, the wet weight, the dry weight and determined the leaf area. Of the morphological characteristics analyzed, the ones that proved most useful in distinguishing the various genotypes were: the length peduncle, the wet weight and the dry weight. The remaining 30 leaves were used in the genetic characterization. This characterization was performed using a DNA marker, the ISSR. The 5 primers used in the ISSR technique proved to be polymorphic. The results from the genetic characterization suggest that variability in population genetics is medium to high

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

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

Unidad de excelencia María de Maeztu CEX2019-000940-MAim: 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

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