Project results presentation (deliverable D18)

This document is a report which collects together the CYCLOPS project results for dissemination to different interested audiences such as Grid communities and Civil Protection agencies. It also reports on national and international initiatives and projects, SMEs, training activities and related projects. The structure of this document shows the approach used in the project. Following an introduction, it describes a set of related projects, namely grid- based technologies/EGEE, risk management, and GMEs-based services. It then presents the business of Civil Protection and the use cases selected. These highlight the grid requirements for Grid-based CP applications. The research strategies and enhancements needed for the EGEE infra-structure are identified, based on the use cases. Dissemination of training and knowledge to different communities are also key points of the project.FP

Electrospun silk-elastin fibres functionalized with silver nanoparticles as antibacterial wound dressings

[Excerpt] Silk-elastin-like proteins (SELPs) are a class of bioinspired, genetically engineered block copolymers, composed of silk and elastin repeating units. As base materials for biomedical purposes, SELP nanofibre mats demonstrate potential to be applied as wound dressing materials [1]. The increasing antimicrobial resistance associated with the excessive and inappropriate use of antibiotics demands the research for new pathogen-free healthcare polymeric materials with enhanced biological performance. [...]This work was supported by the strategic programme UID/BIA/04050/2013 (POCI-01- 0145-FEDER- 007569) through FCT I.P. and by ERDF through COMPETE2020 - POCI. The authors are grateful for funding from FCT (project “FunBioPlas” ERA-IB-2-6/0004/2014) and a fellowship to RM (SFRH-BPD/86470/2012). The authors also thank support from the COST Action MP1206

Genetically engineered Silk-Elastin-Like Proteins as a versatile platform for the development of new biomaterials

[Excerpt] Throughout evolution nature created and refined proteins for a wide range of functions, working as structural components or as molecular motors. In this sense, the natural fibrous proteins represent the utmost case of function specialization and high performance materials. The remarkable mechanical properties of proteins like elastin or silk are founded on conservative blocks of amino acid sequences that propagate through the natural protein. These repetitive amino acid sequences are arranged in a way that creates flexible, rigid or tough domains, which are responsible for the physical and mechanical properties of the natural protein. Indeed, the recognition of the mechanics linking the nano- and micro-scale structure with the macromolecular assembly and organization, enabled molecular biologists to understand nature’s refined ways of creating high performance structural materials. Advances in synthetic protein biotechnology, emerging from the increase of knowledge in structural and molecular biology, combined with the use of recombinant DNA technology and biotechnology processes, made possible the advent of a new class of artificial biomacromolecules, the recombinant Protein-Based Polymers (rPBPs). This new class of protein-based materials, inspired in nature and with precisely controlled amino acid sequences, mimic the properties of their natural counterparts but can also combine in the same polypeptide chain the properties of two or more different proteins, creating copolymers with distinct properties from their native equivalents. Indeed, by recombinant DNA technology, it is possible to design and produce tailored synthetic genes, allowing for the creation of multifunctional complex PBPs with absolute control of its composition, structure and molecular weight. [...]This work is supported by the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569) funded by national funds through the FCT I.P. and by the ERDF through COMPETE2020 – Programa Operacional Competitividade e Internacionalização (POCI) and by the project EcoAgriFood (NORTE-01-0145-FEDER-000009), supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). It is also supported by FCT within the ERA-NET IB, project FunBioPlas with grant number ERA-IB-15-089 and FCT reference ERA-IB-2-6/0004/2014. AMPereira acknowledges DP_AEM and FCT for the PD/BD/113811/2015 grant

Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission

Funding: 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. This work is also a result of 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). This work was also supported by Fundos FEDER through the ProgramaOperacionalFactores de Competitividade–COMPETE and by FundosNacionais through the Fundação para a Ciência e a Tecnologia within the scope of the project UID/BIM/00009/2019 (Centre for Toxicogenomics and Human Health -ToxOmics).Dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions affects both patients and health-care workers (HCW), as well as the institutional capacity to provide essential health services. Here, we investigated an outbreak of SARS-CoV-2 in a "non-COVID-19" hospital ward unveiled by massive testing, which challenged the reconstruction of transmission chains. The contacts network during the 15-day period before the screening was investigated, and positive SARS-CoV-2 RNA samples were subjected to virus genome sequencing. Of the 245 tested individuals, 48 (21 patients and 27 HCWs) tested positive for SARS-CoV-2. HCWs were mostly asymptomatic, but the mortality among patients reached 57.1% (12/21). Phylogenetic reconstruction revealed that all cases were part of the same transmission chain. By combining contact tracing and genomic data, including analysis of emerging minor variants, we unveiled a scenario of silent SARS-CoV-2 dissemination, mostly driven by the close contact within the HCWs group and between HCWs and patients. This investigation triggered enhanced prevention and control measures, leading to more timely detection and containment of novel outbreaks. This study shows the benefit of combining genomic and epidemiological data for disclosing complex nosocomial outbreaks, and provides valuable data to prevent transmission of COVID-19 in healthcare facilities.publishersversionpublishe

Efeitos e aplicabilidade da terapia espelho na neurorreabilitação - revisão de literatura / Effects and applicability of mirror therapy in neurorehabilitation - literature review

Introdução: A Terapia Espelho (TE) foi originalmente desenvolvida na década de 90, pelo neurocientista indiano Ramachandran. A técnica utiliza um espelho posicionado no plano médio sagital, entre o membro afetado e o membro saudável, fornecendo feedback visual do membro saudável e gerando a sensação de dois membros móveis, como se o membro afetado estivesse realizando movimentos saudáveis no hemicampo negligenciado. Isso resulta na excitabilidade corticoespinhal e das áreas somatossensoriais, contribuindo para a recuperação motora. Objetivo: Identificar a aplicabilidade e os efeitos da Terapia Espelho como recurso da reabilitação neurológica.   Materiais e métodos: Trata-se de uma revisão de literatura, onde as bases de dados utilizadas foram Pedro, SciELO, PubMed e Lilacs, no período de Setembro de 2017 a Outubro de 2018. Utilizou-se como estratégia de pesquisa, nas bases de dados, a combinação dos descritores de acordo com o idioma. Além disso, foi realizada a busca manual na lista de referências dos artigos apresentados. Os estudos foram submetidos a uma avaliação da qualidade metodológica, utilizando-se a escala PeDro. Resultados: Foram encontrados 62 artigos, porém apenas 9 foram analisados. Eram compostos por amostras de indivíduos com diagnóstico de dor fantasma por amputação, Paralisia Cerebral (PC), lesão traumática cerebral ou Acidente Vascular Cerebral (AVC) em suas fases aguda, subaguda e crônica. Os instrumentos de avaliação variaram entre os estudos, assim como o modo de execução, a frequência e a duração do tratamento. Conclusão: A TE é benéfica para a recuperação motora de membros superiores e inferiores, função sensório-motora e para a diminuição da dor. Porém, a literatura voltada para o modo de execução da TE é muito escassa e existem muitas controvérsias em relação ao protocolo utilizado, tornando-se necessária a realização de novos estudos com maior número amostral, de modo que possam obter resultados mais significativos e amplos

Anomalia de Ebstein com comunicação interatrial em paciente gestante com pré-eclâmpsia: um raro relato de caso

A Anomalia de Ebstein (AE) é uma cardiopatia congênita rara, ocorre em apenas 1% das más formações cardíacas. É uma alteração da implantação dos folhetos da valva tricúspide, ocorre o aumento do volume do átrio direito e a atrialização do ventrículo direito. Geralmente, possui uma evolução clínica lenta, com sintomas aparecendo em idade avançada. A comunicação interatrial (CIA), também consiste em uma cardiopatia congênita, do tipo acianótica, comumente assintomática, com prevalência de 5 a 10% de todas as cardiopatias, mais comum em mulheres. Baseia-se na formação de um “shunt” esquerdo-direito, podendo causar hiperfluxo da veia pulmonar. Por outro lado, a pré-eclâmpsia é uma complicação gestacional detectada na vigésima semana. É uma disfunção materno/placentária responsável por elevação da pressão arterial (> 140/90 mmHg), associada a lesão de órgão alvo, proteinúria ou disfunção útero/placentária. Neste estudo, o objetivo é relatar as complicações desenvolvidas durante a gestação em paciente que possuía essa rara associação de comorbidades. Paciente feminina, 20 anos, primigesta com 30 semanas e 4 dias, vista em USG obstétrico, com descontrole pressórico desde de o início da gestação. Cardiopata, sem acompanhamento, apresentando EA e IA (diagnóstico em laudo de 2008). Foi admitida em Unidade de Terapia Intensiva (UTI) com dispneia, saturação de O2 de 91%, pressão de 150/100 mmHg. Após estabilização, solicitados pareceres para cardiologia, obstetrícia e risco anestésico. USG obstétrico mostrou compartimento fetal alterado e relação cérebro/placentária alterada. No 2º dia, após corticoterapia, paciente retorna do centro-cirúrgico após cesariana, acoplada à ventilação mecânica invasiva, devido à descompensação. Radiografia pós-cirurgia mostrou pequeno derrame pleural bilateral. Mantida Cefalotina por mais 2 dias. No dia 3, TC de tórax revelou derrame persistente e consolidações, iniciando Ceftriaxone e Clindamicina. Noradrenalina iniciada após descompensação hemodinâmica. No dia 6, após teste de respiração espontânea bem-sucedido, o ecocardiograma evidenciou AE, insuficiência tricúspide acentuada e mitral leve. Sem critérios graves, a paciente foi transferida para a enfermaria para seguimento e término da antibioticoterapia. A gestação pode agravar riscos em pacientes com comorbidades raras como anomalias cardíacas congênitas. O acompanhamento específico é crucial e, em casos graves, a gravidez deve ser evitada

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