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

Cuidados biomédicos de saúde em Angola e na Companhia de Diamantes de Angola, c. 1910-1970

Pretende-se caracterizar a prestação de cuidados biomédicos em Angola durante a atividade da Companhia de Diamantes de Angola. Uma análise comparativa de políticas e práticas de saúde pública de vários atores coloniais, como os serviços de saúde da Companhia, sua congénere do Estado e outras empresas coloniais, revelará diferenças de investimento na saúde, isto é, instalações e pessoal de saúde, e tratamentos. Este escrutínio bem como as condições de vida iluminarão o carácter idiossincrático e central dos serviços de saúde da Companhia em termos de morbimortalidade em Angola, e a centralidade destes para as representações de um império cuidador

Quantificação da morfologia de cristais de açucar e sua aplicação ao estudo das cinéticas de cristalização

Texte intégral accessible uniquement aux membres de l'Université de LorraineThe subject of the present thesis derives from problems related to the modelling and simulation of an industrial crystallisation unit for cane sugar production. The development of such a model raises issues related to the importance ofnucleation and agglomeration kinetics, whose knowledge should be improved. The first part describes the development of a image analysis-based tool that allows a better characterisation of the properties of crystals in terms of their size distribution but also their morphological properties, especially their degree of agglomeration. The second part describes the design and setting-up of a laboratory facility for sugar crystallisation. The experiments were conducted in pure sucrose/water systems - changing the supersaturation, temperature, agitation speed and seeding - and in systems where known amounts of chemical impurities, usually present in industrial solutions, were added. Finally, a model for the laboratory crystalliser was developed. It allows the simulation of the profile versus time of sucrose concentration in solution, of the crystal size distribution and of the agglomeration degree distribution. The model proved to be adequate to the case study particularly ,in describing properties closely related to agglomeration phenomena. The main difficulties had to do with the absence of experimental data concerning crystal size distribution and agglomeration degree distribution time trajectories. The main contribution or the present work was the development of image analysis tools that allow the quantification of sucrose crystals morphology, the introduction of the degree of agglomeration concept and the proposal of a model that allows, for the first time, the description of the degree agglomeration distribution as a function of crystal size.Le sujet de la thèse est lié aux problèmes rencontrés lors de la modélisation et la simulation d'un réacteur industriel de cristallisation du sucre de cane. Le développement d'un tel modèle met en exergue l'importance des cinétiques de nucléation et d'agglomération, que l'on doit chercher à mieux connaître. La première partie décrit le développement d'un outil basé sur l'analyse d'images et qui permet une meilleure caractérisation des cristaux en terme de leur distribution de taille mais aussi de leurs propriétés morphologiques, notamment de leur degré d'agglomération. La seconde partie décrit la conception d'un système de laboratoire pour la cristallisation du sucre. Les expériences ont été conduites dans des milieux sucre pur / eau - en changeant la sursaturation, la température, la vitesse d'agitation et l'ensemencement - et dans des milieux dans lesquels des quantités connues d'impuretés, usuelles en industrie sucrière, ont été ajoutées. Finalement un modèle du cristallisoir de laboratoire a été développé. Il permet la simulation de l'évolution en fonction du temps de la concentration en sucre dans la solution, de la distribution de taille des cristaux et de la celle du degré d'agglomération. Le modèle s'est révélé satisfaisant dans le cas présent pour décrire les propriétés liées au phénomène d'agglomération. Les difficultés principales rencontrées sont liées à l'absence de données expérimentales concernant les évolutions de la distribution de taille et du degré d'agglomération. La principale contribution de ce travail réside dans le développement des outils d'analyse d'images pour la quantification de la morphologie des cristaux de sucre, l'introduction du concept du degré d'agglomération et la proposition d'un modèle qui permet, pour la première fois, la description du degré d'agglomération en fonction de la taille du cristal

Quantificação da morfologia de cristais de açucar e sua aplicação ao estudo das cinéticas de cristalização

Texte intégral accessible uniquement aux membres de l'Université de LorraineThe subject of the present thesis derives from problems related to the modelling and simulation of an industrial crystallisation unit for cane sugar production. The development of such a model raises issues related to the importance ofnucleation and agglomeration kinetics, whose knowledge should be improved. The first part describes the development of a image analysis-based tool that allows a better characterisation of the properties of crystals in terms of their size distribution but also their morphological properties, especially their degree of agglomeration. The second part describes the design and setting-up of a laboratory facility for sugar crystallisation. The experiments were conducted in pure sucrose/water systems - changing the supersaturation, temperature, agitation speed and seeding - and in systems where known amounts of chemical impurities, usually present in industrial solutions, were added. Finally, a model for the laboratory crystalliser was developed. It allows the simulation of the profile versus time of sucrose concentration in solution, of the crystal size distribution and of the agglomeration degree distribution. The model proved to be adequate to the case study particularly ,in describing properties closely related to agglomeration phenomena. The main difficulties had to do with the absence of experimental data concerning crystal size distribution and agglomeration degree distribution time trajectories. The main contribution or the present work was the development of image analysis tools that allow the quantification of sucrose crystals morphology, the introduction of the degree of agglomeration concept and the proposal of a model that allows, for the first time, the description of the degree agglomeration distribution as a function of crystal size.Le sujet de la thèse est lié aux problèmes rencontrés lors de la modélisation et la simulation d'un réacteur industriel de cristallisation du sucre de cane. Le développement d'un tel modèle met en exergue l'importance des cinétiques de nucléation et d'agglomération, que l'on doit chercher à mieux connaître. La première partie décrit le développement d'un outil basé sur l'analyse d'images et qui permet une meilleure caractérisation des cristaux en terme de leur distribution de taille mais aussi de leurs propriétés morphologiques, notamment de leur degré d'agglomération. La seconde partie décrit la conception d'un système de laboratoire pour la cristallisation du sucre. Les expériences ont été conduites dans des milieux sucre pur / eau - en changeant la sursaturation, la température, la vitesse d'agitation et l'ensemencement - et dans des milieux dans lesquels des quantités connues d'impuretés, usuelles en industrie sucrière, ont été ajoutées. Finalement un modèle du cristallisoir de laboratoire a été développé. Il permet la simulation de l'évolution en fonction du temps de la concentration en sucre dans la solution, de la distribution de taille des cristaux et de la celle du degré d'agglomération. Le modèle s'est révélé satisfaisant dans le cas présent pour décrire les propriétés liées au phénomène d'agglomération. Les difficultés principales rencontrées sont liées à l'absence de données expérimentales concernant les évolutions de la distribution de taille et du degré d'agglomération. La principale contribution de ce travail réside dans le développement des outils d'analyse d'images pour la quantification de la morphologie des cristaux de sucre, l'introduction du concept du degré d'agglomération et la proposition d'un modèle qui permet, pour la première fois, la description du degré d'agglomération en fonction de la taille du cristal

Quantificação da morfologia de cristais de açúcar e sua aplicação ao estudo das cinéticas de cristalização

Dissertação apresentada para obtenção do grau de Doutor em Engenharia Química, na Faculdade de Engenharia da Universidade do Porto, sob a orientação do Prof. Doutor Sebastião Feyo de Azeved

Quantificação da morfologia de cristais de açucar e sua aplicação ao estudo das cinéticas de cristalização

NANCY/VANDOEUVRE-INPL (545472102) / SudocSudocFranceF

Submarine cables as precursors of persistent systems for large scale oceans monitoring and autonomous underwater vehicles operation

Long-term and reliable marine ecosystems monitoring is essential to address current environmental issues, including climate change and biodiversity threats. The existing oceans monitoring systems show clear data gaps, particularly when considering characteristics such as depth coverage or measured variables in deep and open seas. Over the last decades, the number of fixed and mobile platforms for in situ ocean data acquisition has increased significantly, covering all oceans' regions. However, these are largely dependent on satellite communications for data transmission, as well as on research cruises or opportunistic ship surveys, generally presenting a lag between data acquisition and availability. In this context, the creation of a widely distributed network of SMART cables (Science Monitoring And Reliable Telecommunications) - sensors attached to submarine telecommunication cables - appears as a promising solution to fill in the current ocean data gaps and ensure unprecedented oceans health continuous monitoring. The K2D (Knowledge and Data from the Deep to Space) project proposes the development of a persistent oceans monitoring network based on the use of telecommunications cables and Autonomous Underwater Vehicles (AUVs). The approach proposed includes several modules for navigation, communication and energy management, that enable the cost-effective gathering of extensive oceans data. These include physical, chemical, and biological variables, both registered with bottom fixed stations and AUVs operating in the water column. The data that can be gathered have multiple potential applications, including oceans health continuous monitoring and the enhancement of existing ocean models. The latter, in combination with geoinformatics and Artificial Intelligence, can create a continuum from the deep sea to near space, by integrating underwater remote sensing and satellite information to describe Earth systems in a holistic manner.POCI01-0247-FEDER-045941info:eu-repo/semantics/publishedVersio

Dynamics of Early Establishment of SARS-CoV-2 VOC Omicron Lineages in Minas Gerais, Brazil

Brazil is one of the nations most affected by Coronavirus disease 2019 (COVID-19). The introduction and establishment of new virus variants can be related to an increase in cases and fatalities. The emergence of Omicron, the most modified SARS-CoV-2 variant, caused alarm for the public health of Brazil. In this study, we examined the effects of the Omicron introduction in Minas Gerais (MG), the second-most populous state of Brazil. A total of 430 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples from November 2021 to June 2022 from Belo Horizonte (BH) city were sequenced. These newly sequenced genomes comprise 72% of all previously available SARS-CoV-2 genomes for the city. Evolutionary analysis of novel viral genomes reveals that a great diversity of Omicron sublineages have circulated in BH, a pattern in-keeping with observations across Brazil more generally. Bayesian phylogeographic reconstructions indicate that this diversity is a product of a large number of international and national importations. As observed previously, São Paulo state is shown as a significant hub for viral spread throughout the country, contributing to around 70% of all viral Omicron introductions detected in MG

Identification and microbial production of the raspberry phenol salidroside that is active against Huntington's disease

Sequence data from this article can be found in the GenBank/EMBL data libraries under accession numbers: KX262844.1 (RsUGT72B14, R. sachalinensis); AY547304.1 (RsUGT73B6. R. sachalinensis); NP_418458.1 (malE, E. coli); NP_415214.1 (pgm, E. coli); NP_415752.1 (galU, E. coli); NM_001180688.3 (aro10, S. cerevisiae), and NP_417484.1 (yqhD, E. coli).Edible berries are considered to be among nature's treasure chests as they contain a large number of (poly)phenols with potentially health-promoting properties. However, as berries contain complex (poly)phenol mixtures, it is challenging to associate any interesting pharmacological activity with a single compound. Thus, identification of pharmacologically interesting phenols requires systematic analyses of berry extracts. Here, raspberry (Rubus idaeus, var. Prestige) extracts were systematically analyzed to identify bioactive compounds against pathological processes of neurodegenerative diseases. Berry extracts were tested on different Saccharomyces cerevisiae strains expressing disease proteins associated with Alzheimer's, Parkinson's, or Huntington's disease or amyotrophic lateral sclerosis. After identifying bioactivity against Huntington's disease, the extract was fractionated and the obtained fractions were tested in the yeast model, which revealed that salidroside, a glycosylated phenol, displayed significant bioactivity. Subsequently, a metabolic route to salidroside was reconstructed in S. cerevisiae and Corynebacterium glutamicum. The best-performing S. cerevisiae strain was capable of producing 2.1 mM (640 mg L-1) salidroside from glucose in shake flasks, whereas an engineered C. glutamicum strain could efficiently convert the precursor tyrosol to salidroside, accumulating up to 32 mM (9,700 mg L-1) salidroside in bioreactor cultivations (yield: 0.81 mol mol-1). Targeted yeast assays verified that salidroside produced by both organisms has the same positive effects as salidroside of natural origin.We express our gratitude to Dr. Rute Neves (Chr. Hansen A/S, Denmark), Prof. Dr. Jochen Förster and Dr. Alexey Dudnik (The Nova Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark), who coordinated the BacHBerry project. We also thank Prof. Dr. Ian Macreadie (Centre of Excellence for Alzheimer’s Disease Research & Care, School of Exercise, Biomedical & Health Sciences, Edith Cowan University, WA, Australia) for providing p416_GPD-GFP_AB42; Prof. Dr. Tiago Outeiro (University Medical Center Gottingen, Department of Neurodegeneration and Restorative Research, Germany) for providing W303-1A_Syn and W303-1A TU; Prof. Dr. Flaviano Giorgini (Department of Genetics and Genome Biology, University of Leicester, UK) for providing p425GAL1_HTT103Q; and Prof. Dr. Greg Petsko (Department of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, U.S.) for providing pYES_GAL1pr-FUS-GFP and pYES_CT.info:eu-repo/semantics/publishedVersio

The National Student Survey: validation in Portuguese medical students

The UK National Student Survey (NSS) is a sound and widely used instrument for assessing students’ academic experiences. We aimed to translate the NSS for Portuguese students and to validate the instrument in a sample of medical undergraduates. The research team translated and adapted the NSS for Portuguese students (NSS-P). The survey was administered on an online platform to 1,256 final-year students at eight Portuguese medical schools. A total of 329 medical students (69.9% female) replied to the NSS-P, a response rate of 26.2%. Confirmatory factor analysis showed that the original six-factor structure had an adequate fit to the data. Adequate internal consistency was observed for all the subscales. Medium to large correlations were found among all the subscale scores and between the subscale scores and the students’ overall satisfaction. Multiple regression showed that the scores on the Teaching, Organization and Management and Personal Development subscales significantly predicted the students’ overall satisfaction. Approximately 64% of the students reported being satisfied with the quality of their courses. Significant differences among the medical schools in their NSS-P scores were found. The NSS-P is a valid and reliable measure for assessing medical students’ perceptions of academic quality