A Minimalist Model of Characteristic Earthquakes

In a spirit akin to the sandpile model of self-organized criticality, we present a simple statistical model of the cellular-automaton type which produces an avalanche spectrum similar to the characteristic-earthquake behavior of some seismic faults. This model, that has no parameter, is amenable to an algebraic description as a Markov Chain. This possibility illuminates some important results, obtained by Monte Carlo simulations, such as the earthquake size-frequency relation and the recurrence time of the characteristic earthquake.Comment: 9 pages, 4 figure

The impact of carbon source in Candida albicans virulence: participation of RLM1 in pathogen host interaction

Dissertação de mestrado em Genética MolecularThe survival of all microbes depends upon their ability to respond to environmental challenges. To establish infection, pathogens such as Candida albicans must support effective stress responses to counter host defenses while adapting to dynamic changes in nutrient status within host niches. Studies of C. albicans stress adaptation have generally been performed on glucose-grown cells, leaving the effects of alternative carbon sources upon stress resistance largely unexplored as well alterations in its virulence. In a previous work both copies of the RLM1 gene of C. albicans were deleted and phenotypic analysis of Δrlm1/Δrlm1 mutants showed typical cell wall weakening phenotypes, such as hypersensitivity to Congo Red, Calcofluor White and caspofungin, showing its involvement in the cell wall remodelling. To understand the role of RLM1 under the influence of different carbon source, phenotypic characterization against cell wall damaging stress agents, modulation of virulence factors as well as their involvement in host-pathogen interaction was preformed in the present work. Candida albicans Δrlm1/Δrlm1 mutant displayed phenotypes associated to cell wall deficiency such as, hypersensitivity to Congo red, caspofungin in glucose- and lactate- grown cells. However the RLM1 mutants were slight more resistant to Congo Red when grown in lactate. On the other hand lactate-grown cells were not able to growth al all in the presence of SDS and presented sensitivity to caffeine, in comparison with glucose-grown cells. The increased transcription of genes already reported to be involved in cell adhesion correlated well with adhesion and biofilm assays, in which RLM1 mutant presented greater biofilm formation than WT in both growth condition. However cell adapted to lactate adhered more and biofilm formation was more pronounced. The host-pathogen interaction was accessed by co-incubation with murine macrophages-like cell line (J774). In general, lactate-grown cells were less efficiently killed in comparison to glucose-grown cells. However the mutant presented distinct behaviors, they were more resistant when adapted to glucose than to lactate. The TNF-α and IL-10 were lower in response to Δrlm1/Δrlm1 mutant and the cellular toxicity, measured as extracellular lactate dehydrogenase activity, was significantly lower in comparison with the WT and complemented strains in glucose-grown cells. The effect observed before was reverted when C. albicans cells were grown on lactate. In conclusion, C. albicans cells adapted to different carbon sources behave differently, particularly in the interaction with macrophages, in which the RLM1 mutation plays a decisive effect since it affects the cell wall integrity.Os microrganismos para sobreviver dependem da capacidade de responder aos desafios apresentados pelo ambiente onde estão inseridos. O sucesso da infecção por parte dos agentes patogénicos, tais como Candida albicans, assenta na capacidade de responder eficazmente a stresses causados pelas defesas do hospedeiro e à adaptação a alterações constantes dos nutrientes no hospedeiro. Alguns estudos indicam que o crescimento em fontes de carbono alternativas tem influência na resistência ao stress e alteram a virulência de C. albicans. Em trabalhos anteriores, o gene RLM1 de C. albicans foi deletado e a análise fenotípica dos mutantes Δrlm1/Δrlm1 revelou que estes apresentam hipersensibilidade ao Congo Red, Calcofluor white e Caspofungina, fenótipos típicos de fragilidade na parede celular. De forma a perceber o papel de RLM1 em células adaptadas a diferentes fontes de carbono, foi feita uma caracterização fenotípica usando agentes que perturbam a parede celular, avaliada a modulação de alguns fatores de virulência, bem como a interação hospedeiro-patogéno. Os mutantes Δrlm1/Δrlm1 de Candida albicans crescidos em glucose e láctico exibiram fenótipos associados a deficiências na parede celular, tais como, hipersensibilidade ao Congo Red e Caspofungina. No entanto, estas revelaram ser ligeiramente mais resistentes ao Congo Red quando crescidas em láctico. Por outro lado, as células crescidas em ácido láctico apresentaram maior dificuldade em crescer na presença de cafeína, não tendo sido detectado crescimento em SDS, contrariamente às células crescidas em glucose que não apresentaram sensibilidade a estes stresses. O aumento da expressão de genes envolvidos na adesão célular correlacionou-se diretamente com os ensaios de adesão e biofilme, em que os mutantes Δrlm1/Δrlm1 apresentam uma maior formação de biofilme em comparação com a estirpe selvagem em ambas condições de crescimento. Contudo, células crescidas em ácido láctico aderiram mais e a formação de biofilme foi mais evidente. A interação Candida-hospedeiro foi avaliada através da co-incubação com a linha celular de macrófagos J774. Em geral, as células crescidas em ácido láctico foram fagocitadas de forma menos eficiente em comparação com células crescidas em glucose. As estirpes mutante Δrlm1/Δrlm1 apresentaram comportamentos distintos quando crescidas em diferentes fontes de carbono; em glucose os níveis de produção de TNF-α e IL-10 foram mais baixos e a toxicidade celular, avaliada pela atividade da lactato desidrogenase, foi significativamente mais baixa, em comparação com as estirpes selvagem e complementadas. O efeito anteriormente observado foi totalmente revertido quando o mutante foi crescido em meio com ácido láctico. Em conclusão, células de C. albicans a diferentes fontes de carbono apresentam comportamento diferentes, nomeadamente na interação com macrófagos, onde o gene RLM1 parece ter um papel decisivo pois afecta a integridade da parede celular

Meta-análise de metilação de DNA em invertebrados: tendências evolutivas e indicações para avaliação ambiental

The anthropogenic impact in a variety of ecosystems has been increasing significantly in recent decades. This anthropogenic pressure translates into globally spreading phenomena like habitat fragmentation, mass extinction or biodiversity decline, that threaten ecosystem services. The mitigation of such detrimental ecological impacts is largely dependent on our ability to properly assess effects of the pressures on biological systems, i.e., with sufficient resolution levels that allows establishing reliable cause-effect relationships. High-resolution tools to assess these effects have recently been emerging, e.g., tools based in gene expression and the epigenome. The latter is strongly influenced by environmental conditions, with consequences in gene expression. Thus, the epigenome constitutes a new opportunity for the mechanistic understanding of toxic effects of environmental contaminants and for the development of biomarkers of exposure and effect. In this context, the specific objectives of the present dissertation were as follows: (i) to collect reliable genomic data of various invertebrate species representing different environmental compartments; (ii) quantify the distribution of the potential for gene body methylation based on the prevalence of CpG dinucleotides in the genome of each species; (iii) elaborate on the differential ability of invertebrate species to respond or potentially adapt to challenging and/or highly fluctuating environments based on phenotypic plasticity mediated by DNA methylation and/or related mutations; (iv) conclude on the most favourable models to address gene body methylation within an ecotoxicological context. Among the set of 27 species with reliable genomic data publicly available selected for meta-analysis, 11 recorded an observed-to-expected CpG ratio distribution (CpG O/E) that suggest the existence of gene groups with high susceptibility to methylation, and 16 have distributions suggesting that the entire genome is little or very little susceptible to methylation. Patterns of reduced susceptibility to DNA methylation have been identified among phylogenetically closely related species, which supports the theory that DNA methylation may have played a relevant role in species adaptation to new ecological niches, e.g., during the colonization of terrestrial or freshwater environments from primitive marine environments. The concentration of CG dinucleotides in the analysed genomes also allowed to discuss the suitability of different model organisms used in ecotoxicology for the development of biomarkers of exposure or effect based on DNA methylation. In this context, the following species are noteworthy as those presenting higher relative levels of CG dinucleotides in their genome: N. vectensis and T. californicus in the marine environment; D. magna and D. polymorpha in freshwater ecosystems; I. scapularis and H. saltator in the soil compartment; A. albimanus, A. albopictus and N. vitripennis representing aerial species.O impacto humano no ambiente e nos ecossistemas tem aumentado, especialmente nas décadas mais recentes. Esta pressão antropogénica é traduzida em fenómenos que são globais, como fragmentação de habitat, extinção em massa ou declínio da biodiversidade, que ameaçam os serviços dos ecossistemas. A mitigação destes impactos negativos em diferentes ecossistemas é largamente dependente da nossa capacidade para avaliar os efeitos das pressões nos sistemas biológicos com resolução suficiente, permitindo estabelecer relações fidedignas de causa-efeito. Ferramentas de elevada resolução para avaliar estes efeitos têm emergido recentemente, por exemplo, as baseadas na expressão génica e no epigenoma. Este é fortemente influenciado pelas condições ambientais, com consequências na expressão génica. Assim, o epigenoma constitui uma nova oportunidade para a compreensão mecanicista dos efeitos tóxicos dos contaminantes ambientais e para o desenvolvimento de biomarcadores de exposição e efeito. Neste contexto, os objetivos específicos da presente Dissertação foram: (i) recolher dados genómicos relativos a várias espécies de invertebrados representantes de diferentes compartimentos ambientais; (ii) quantificar a distribuição do potencial para metilação de regiões genéticas codificantes nos genomas destes organismos, com base na prevalência de dinucleótidos citosina-guanina (CpG); (iii) elaborar sobre a capacidade diferencial das espécies de invertebrados para responderem ou potencialmente se adaptarem a pressões ou flutuações ambientais, com base na plasticidade fenotípica mediada pela metilação do DNA e/ou mutações relacionadas; (iv) concluir sobre as espécies-modelo mais favoráveis para abordar a metilação de regiões genéticas codificantes num contexto ecotoxicológico. De entre o conjunto de 27 espécies selecionadas para meta-análise com dados genómicos suficientes disponíveis, 11 apresentaram distribuições do rácio entre frequência de CpG observada e esperada (CpG O/E) que sugerem a existência de grupos de genes muito suscetíveis a metilação, e 16 apresentaram distribuições que sugerem que todo o genoma é pouco ou muito pouco suscetível a metilação. Padrões de redução de suscetibilidade à metilação do ADN foram identificados entre espécies filogeneticamente próximas, que apoiam a teoria de que a metilação do DNA poderá ter tido um papel relevante na adaptação das espécies a novos nichos ecológicos, p.ex. durante a colonização de ambientes terrestres ou dulçaquícolas a partir de ambientes primitivos marinhos. A concentração de dinucleótidos CG nos genomas analisados permitiu ainda discutir sobre a adequação de diferentes organismos-modelo usados em ecotoxicologia para o desenvolvimento de biomarcadores baseados na metilação do ADN. Neste contexto, destacam-se as seguintes espécies, como modelos com uma maior quantidade relativa de dinucleótidos CG: N. vectensis e T. californicus no ambiente marinho; D. magna e D. polymorpha em ecossistemas dulçaquícolas; I. scapularis e H. saltator no compartimento solo; A. albimanus, A. albopictus e N. vitripennis para representar espécies aéreas. Complementarmente a esta evidência, a escolha de organismos-modelo neste contexto deve ser guiada pela informação existente sobre as suas respostas ecotoxicológicas ao nível fenotípico.Mestrado em Biologia Aplicad

Monitoring Cities’ Environmental Sustainability : Lisbon’s Case Study

Pacheco, P. M. E., & Neto, M. D. C. (2022). Monitoring Cities’ Environmental Sustainability : Lisbon’s Case Study. In 2022 17th Iberian Conference on Information Systems and Technologies (CISTI): proceedings (pp. 1-7). (CISTI 2022. 17th Iberian Conference on Information Systems and Technologies, 22-25 June 2022, Madrid, Spain). IEEE. ISBN: 978-9-8933-3436-2. https://doi.org/10.23919/CISTI54924.2022.9820501------------------------FUNDING: Work developed as a contribution to Project C-TECH — Climate Driven Technologies for Low Carbon Cities (reference 045919), co-financed by the ERDF — European Regional Development Fund through the Operational Program for Competitiveness and Internationalisation — COMPETE 2020, the North Portugal Regional Operational Program — NORTE 2020 and by the Portuguese Foundation for Science and Technology — FCT under MIT Portugal.In a world of increasing urbanization and where climate change is a growing concern, data presents itself as way to measure the established efforts and forecast future needs and policies as Lisbon finds means to solve some of the major problems that come with being a large city such as air quality and pollution, waste management, mobility, and overall quality of life for its residents. As such, this project developed a dashboard in a BI visualization tool comprised of metrics and indicators based on a tailored framework from the city derived from pre-existing frameworks and conversations with Lisbon’s city experts. The result is a prototypical dashboard that can be built upon in the future, once the city invests in a stronger ICT infrastructure that allows for the collection of data to support a project of this nature, something that, currently, is lacking.authorsversionpublishe

An approach to the Contextual Design methodology in the context of Information

Based on an operative definition of Information Science (IS) as a study of the mediation aspects of the phenomena: data, information, knowledge and message, and their implementation in the cultural domain, the potential of Contextual Design (CD) as a methodology for the development of optimized interfaces between information resources and users is analyzed. The goals are (i) to identify papers that address or make use of the CD methodology in databases related to IS; (ii) to describe the approaches to the concept of CD in those papers; (iii) to point out the potentials and limitations of this methodology. We draw an exploratory / descriptive study based on a systematic review and categorical analysis. Eight papers were retrieved, being a possible indicator of the reduced use of the methodology, in the IS area, the same is essentially practical. Although the limitation of non-involvement of users throughout the design process is pointed out, the methodology shows the ability to collect implicit information through user activities and the possibility of shared systematization of complex data. These characteristics make CD a potential value for the development of appropriate interfaces between information resources and their users

Component-based software engineering: a quantitative approach

Dissertação apresentada para a obtenção do Grau de Doutor em Informática pela Universidade Nova de Lisboa, Faculdade de Ciências e TecnologiaBackground: Often, claims in Component-Based Development (CBD) are only supported by qualitative expert opinion, rather than by quantitative data. This contrasts with the normal practice in other sciences, where a sound experimental validation of claims is standard practice. Experimental Software Engineering (ESE) aims to bridge this gap. Unfortunately, it is common to find experimental validation efforts that are hard to replicate and compare, to build up the body of knowledge in CBD. Objectives: In this dissertation our goals are (i) to contribute to evolution of ESE, in what concerns the replicability and comparability of experimental work, and (ii) to apply our proposals to CBD, thus contributing to its deeper and sounder understanding. Techniques: We propose a process model for ESE, aligned with current experimental best practices, and combine this model with a measurement technique called Ontology-Driven Measurement (ODM). ODM is aimed at improving the state of practice in metrics definition and collection, by making metrics definitions formal and executable,without sacrificing their usability. ODM uses standard technologies that can be well adapted to current integrated development environments. Results: Our contributions include the definition and preliminary validation of a process model for ESE and the proposal of ODM for supporting metrics definition and collection in the context of CBD. We use both the process model and ODM to perform a series experimental works in CBD, including the cross-validation of a component metrics set for JavaBeans, a case study on the influence of practitioners expertise in a sub-process of component development (component code inspections), and an observational study on reusability patterns of pluggable components (Eclipse plug-ins). These experimental works implied proposing, adapting, or selecting adequate ontologies, as well as the formal definition of metrics upon each of those ontologies. Limitations: Although our experimental work covers a variety of component models and, orthogonally, both process and product, the plethora of opportunities for using our quantitative approach to CBD is far from exhausted. Conclusions: The main contribution of this dissertation is the illustration, through practical examples, of how we can combine our experimental process model with ODM to support the experimental validation of claims in the context of CBD, in a repeatable and comparable way. In addition, the techniques proposed in this dissertation are generic and can be applied to other software development paradigms.Departamento de Informática of the Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL); Centro de Informática e Tecnologias da Informação of the FCT/UNL; Fundação para a Ciência e Tecnologia through the STACOS project(POSI/CHS/48875/2002); The Experimental Software Engineering Network (ESERNET);Association Internationale pour les Technologies Objets (AITO); Association forComputing Machinery (ACM

Instrucción personalizada e instrucción tradicional

La presente investigación sobre la instrucción personalizada y la instrucción tradicional, trata de encontrar las ventajas y desventajas del Sistema de Instrucción Personalizada (SIP) con relación al Sistema de Instrucción Tradicional (SIT). La presente investigación permitirá apreciar la real eficiencia del SIP, en caso de confirmarse dará lugar a que se recomiende su aplicación en los diferentes niveles educacionales como primaria, secundaria y superior, la aplicación del SIP tendría implicancias en el desarrollo de la capacidad investigativa de los estudiantes y permitirá el desarrollo de la capacidad de análisis, síntesis, generalización y avstracción, etc