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

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held in conjunction with the 30th Annual International ACM SIGIR Conferenc

Tokenization and Proper Noun Recognition for Information Retrieval

In this paper we consider a set of natural language processing techniques that can be used to analyze large amounts of texts, focusing on the advanced tokenizer which accounts for a number of complex linguistic phenomena, as well as for pre-tagging tasks such as proper noun recognition. We also show the results of several experiments performed in order to study the impact of the strategy chosen for the recognition of proper nouns

Improving Non-English Web Searching (iNEWS07)

This workshop attempted to promote the discussion and the research on non-English Web searching. Most search engines were first built for English. They do not take full account of inflectional semantics nor, for example, diacritics or the use of capitals. Our main aim was to discuss the additional problems faced in non-English Web queries and to suggest techniques to improve the response of searching systems. Papers related to Arabic, Basque, Farsi (Persian), Greek, Spanish, Swedish, Hindi, Bengali and other south asian languages were accepted. Conclusions were that search engines would be more effective if they took more account of the properties of individual languages, and that there is a need for more studies of real user behaviour in practical situations

COLE Experiments at CLEF 2003 - Spanish Monolingual Track

In this our second participation in the CLEF Spanish monolingual track, we have continued applying Natural Language Processing techniques for single word and multi-word term con- ation. Two dierent conation approaches have been tested. The rst approach is based on the lemmatization of the text in order to avoid inectional variation. Our second approach consists of the employment of syntactic dependencies as complex index terms, in an attempt to solve the problems derived from syntactic variation and, in this way, to obtain more precise terms. Such dependencies are obtained through a shallow parser based on cascades of nitestate transducers

Boas práticas no tratamento da disfagia em doentes com AVC: consenso de peritos portugueses

Dysphagia is frequent after stroke, and it increases the risk of respiratory infection, dehydration and malnutrition, resulting in worse outcomes. Different clinical guidelines present recommendations for the assessment and management of dysphagia in stroke patients in a scattered way. These best practice recommendations address seven clinical questions on the assessment and management of dysphagia in stroke patients, gathering the best-updated evidence. A systematic literature review using the PICO strategy was performed. The recommendations draft was then appraised by a multidisciplinary panel of experts (nutritionists, physiatrists, speechlanguage pathologists and rehabilitation nurses) in a total of 3 Delphi rounds. A minimum of 80% consensus was established, and the final version offers a total of 21 recommendations for use in clinical practice for stroke patients. These clinical recommendations are an overview of the most recent evidence combined with experts’ consensus and translated into clinically relevant statements. In implementing recommendations at the local level, health professionals should identify facilitators and barriers to evidence-based practice within their contexts and determine the best strategies to address local needs. Where the change is needed, initial and continuing training on all recommendations is essential and relevant.A disfagia é frequente após o acidente vascular cerebral e aumenta o risco de infecção respiratória, desidratação e desnutrição, resultando em piores resultados em saúde. Diferentes diretrizes clínicas apresentam recomendações para a avaliação e tratamento da disfagia em doentes com acidente vascular cerebral de forma dispersa. Estas recomendações de melhores práticas abordam sete questões clínicas sobre avaliação e tratamento da disfagia em doentes com acidente vascular cerebral, reunindo a evidência mais atualizada. Para responder a estas questões foi realizada uma revisão sistemática da literatura usando a estratégia PICO. O projeto de recomendações foi então submetido à apreciação de um painel multidisciplinar de peritos (nutricionistas, fisiatras, terapeutas da fala e enfermeiros especialistas em enfermagem de reabilitação) num total de três rondas Delphi. Foi estabelecido um consenso mínimo de 80% e a versão final apresenta um total de 21 recomendações para uso na prática clínica para doentes com acidente vascular cerebral. Estas recomendações clínicas são uma visão geral da evidência mais recente combinada com o consenso de peritos e traduzidas em declarações clinicamente relevantes. Ao implementar as recomendações ao nível local, os profissionais de saúde devem identificar facilitadores e barreiras para a prática baseada na evidências em seus próprios contextos e determinar quais as melhores estratégias para responder às necessidades locais. Onde a mudança é necessária, a formação inicial e contínua em todas as recomendações é essencial e relevante