The impacts of bus lanes on urban traffic environment

Tese de mestrado. Transportes. Faculdade de Engenharia. Universidade do Porto. 200

Integração de ferramentas de desenvolvimento no eclipse

Trabalho de projecto de mestrado em Engenharia Informática, apresentado à Universidade de Lisboa, através da Faculdade de Ciências, 2007Nos tempos que correm, são cada vez mais utilizadas ferramentas que facilitam o trabalho a quem desenvolve software. Isto acontece por razões óbvias, sendo a mais determinante a de permitir ao programador preocupar-se o menos possível, compormenores irrelevantes ao processo de criação de software, sejam eles inerentes à linguagem, o memorizar da totalidade das bibliotecas disponíveis ou o descobrir a localização de erros de sintaxe. O aparecimento deste tipo de ferramentas tem vindo a rentabilizar bastante o trabalho de quem as usa, não só em termos de velocidade mas, também de criatividade já que, menos interrupções ao raciocínio permitem ir mais longe em termos de abstracção e complexidade. Neste contexto, a plataforma de desenvolvimento Eclipse tem tomado uma posição dianteira face a outras por várias razões. Destacam-se a facilidade de utilização, o excelente apoio à linguagem Java, e talvez a mais relevante para o contexto deste projecto, a possibilidade de alterar funcionalidades já existentes e até a de criar outras novas, integrando-as na plataforma. Esta mais valia tem proporcionado, nos últimos tempos, uma adaptação da plataforma original aos objectivos, gostos e preferências dos elementos de várias empresas sendo mesmo, muitas vezes criada uma nova versão do Eclipse à medida de cada um. Este projecto tem como objectivo a integração de novas funcionalidades no Eclipse, entre as quais, um construtor específico para uma linguagem usada internamente, acompanhado de todas as funcionalidades que permitam e maximizem o seu uso. Tendo como objectivo principal o de rentabilizar e facilitar o desenvolvimento de software da empresa EF Tecnologias de Software, SA, este projecto foi elaborado no âmbito da disciplina de Projecto em Engenharia Informàtica, com uma duração de nove meses e com o objectivo de obter o grau de Mestre em Engenharia Informática.Nowadays we are witnessing a growing use of software development tools. The main objective of these tools is to allow the programmer to waste, as little time as possible, with irrelevant details to the process of software creation. Like errors inherent to the language nature, memorizing all of the available libraries or discovering the exact lines where syntax errors occur. The growing use of this type of tools has improved dramatically the work of whom uses them, not only at the level of creativity but also the development speed. This advantage allows the developer to focus on the real issue, reaching higher levels of abstraction and complexity. In this context, the development platform Eclipse has taken a lead position, among other platforms. It´s easy to use, it as excellent Java language support, and perhaps the most important feature for this project, the possibility to modify existing features and even to create new ones, integrating them in the platform. These features have allowed, in the last years, an evolution of the original platform to meet the users goals, tastes and preferences, sometimes even originating a new version of the Eclipse, built to meet specific needs. This project’s goal is the integration of new functionalities in the Eclipse platform. Among these tools, a builder for an internally used language, along with all the features that allow and maximize its use. To increase the productivity and ease up the work of the elements of the company EF Tecnologias de Software, SA is this application’s main goal. It was developed in the scope of project of Engineering Computer Sciences, with a duration of nine months and the goal of achieving the degree of Master in Engineering Computer Sciences

Compassion and extracurricular activities of Portuguese Health Sciences students in Portugal

Background Compassion, one of the items of empathy, is crucial in health care professions. So, the evaluation of the levels of compassion of Medicine, Dentistry and Pharmaceutical Sciences Master Degrees’ (M.D.) students of the public Colleges in Portugal according to the type of Master Degree and the participation in extracurricular activities (E.A.) was a task to be performed. Methods Cross-sectional study in 2020, applying an on-line questionnaire including the “Compassion” items of the Jefferson Medical Empathy Scale – Students’ version and questions about the participation in E.A. Results A sample of 901 students was studied. Its distribution by participation in E.A. did not differ significantly between M.D. (p = 0,854), most of the students participating in E.A. Using quartile distribution of compassion, the distribution of compassion levels was different among the three I.M. (p < 0.001), between Colleges (p < 0.001), and between curricular years (p < 0.001), with not different between genders (p = 0.036). For 56.4%, 74,6% and 69,5% of the respondents there was “medium-low” and “low” compassion for I.M. in Medicine, Pharmaceutical Sciences and Dentistry. These levels were also more prevalent among students in the 1st and 5th years. Levels of compassion were not different with the participation (p = 0,865), type (p = 0,177) and frequency of E.A. (p = 0,109). Conclusions For their importance in future health care professionals, compassion and their differences found among the M.Ds. of this area deserve future studies. Levels of compassion showed differences between the M.D. studied and academic years of frequency. There was no relationship between the participation, type, and frequency of E.A. and the students’ levels of compassion. The distribution of the level of compassion did not vary significantly with participation in E.A. (p = 0.865), with the type of E.A. (p = 0.177), with the frequency of E.A. (p = 0.109) or with the answer to the question “The practice of E.A. can make a person more compassionate?” (p = 0.503).info:eu-repo/semantics/publishedVersio

Genetic risk for covid-19 outcomes in COPD

There is strong individual variability in both susceptibility and clinical response to covid-19 infection. People with chronic obstructive pulmonary disease (COPD) constitute one of covid-19 risk groups for poor outcomes upon infection. This study contributes to unveil the underlying reasons for such outcomes by looking at the genetic background of people with COPD. 255 people with COPD (66±9y; 72%♂; FEV1 53.01±20.31pp) and 243 controls (67±10y; 80%♂; FEV1 100.46±19.19pp) were clinically characterized and genotyped using saliva samples. Covid-19 associated SNPs from the literature (susceptibility: rs286914/rs12329760; severity: rs657152/rs11385942) were assessed and their allelic frequencies used to calculate the probability of having multiple risk alleles in both groups. Polygenic risk analysis was also conducted. No differences in genetic risk for covid-19 susceptibility or severity were found between groups (all p-values > 0.01), either considering individual risk alleles, allelic combinations or polygenic risk scores (Fig. 1). These results suggest a low genetic contribution for the poor covid-19 outcomes observed in people with COPD.publishe

The worldwide covid-19 genetic risk scenario

Populations respond differently to the current global pandemic of covid-19. This study explores the role of individual factors in the differential response to covid-19, by looking at the genetic background of worldwide populations. Significant SNPs (susceptibility: rs286914/rs12329760; severity: rs657152/rs11385942) were selected from the literature and their allelic frequencies used to calculate the probability of having multiple risk alleles in each population. Portuguese (n=623), Spanish (n=9761) and Italian (n=6363) populations data are observed values, whereas data for world populations are estimations based on public information. All populations, even those with European ancestry (Portuguese/Spanish/Italian), were significantly different from the European population in both covid-19 susceptibility and severity (all p-values < 0.0001)(Fig. 1). Our study highlights a genetic heterogeneity across world populations, especially within European subpopulations. There is a need to build a European genetic map so that differences in the distribution of relevant alleles can be easily accessed and used to better manage the populations, ultimately, safeguarding those under higher genetic risk.publishe

Coronary X-ray angiography segmentation using Artificial Intelligence: a multicentric validation study of a deep learning model

© The Author(s) 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons. org/licenses/by/4.0/.Introduction: We previously developed an artificial intelligence (AI) model for automatic coronary angiography (CAG) segmentation, using deep learning. To validate this approach, the model was applied to a new dataset and results are reported. Methods: Retrospective selection of patients undergoing CAG and percutaneous coronary intervention or invasive physiology assessment over a one month period from four centers. A single frame was selected from images containing a lesion with a 50-99% stenosis (visual estimation). Automatic Quantitative Coronary Analysis (QCA) was performed with a validated software. Images were then segmented by the AI model. Lesion diameters, area overlap [based on true positive (TP) and true negative (TN) pixels] and a global segmentation score (GSS - 0 -100 points) - previously developed and published - were measured. Results: 123 regions of interest from 117 images across 90 patients were included. There were no significant differences between lesion diameter, percentage diameter stenosis and distal border diameter between the original/segmented images. There was a statistically significant albeit minor difference [0,19 mm (0,09-0,28)] regarding proximal border diameter. Overlap accuracy ((TP + TN)/(TP + TN + FP + FN)), sensitivity (TP / (TP + FN)) and Dice Score (2TP / (2TP + FN + FP)) between original/segmented images was 99,9%, 95,1% and 94,8%, respectively. The GSS was 92 (87-96), similar to the previously obtained value in the training dataset. Conclusion: the AI model was capable of accurate CAG segmentation across multiple performance metrics, when applied to a multicentric validation dataset. This paves the way for future research on its clinical uses.Open access funding provided by FCT|FCCN (b-on). Cardiovascular Center of the University of Lisbon, INESC-ID / Instituto Superior Técnico, University of Lisbon.info:eu-repo/semantics/publishedVersio

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

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

Pervasive gaps in Amazonian ecological research

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

Mitochondrial physiology

As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery