Nanopore sequencing in human genetic studies: application to structural variant detection

Background: Nanopore sequencing is a recent technology which allows direct real-time sequencing of DNA or RNA molecules and production of read lengths as long as the size of the original fragments. It is based on the application of an ionic current to move DNA strands through an array of nanopores embedded in an electrically-resistant membrane. An ASIC chip placed below this membrane is responsible for recording signal changes in the nanopore, which are then translated into a specific base sequence. Although major improvements have been made in the genomic short-read sequencing technologies, structural variants (SV) detection still stands as a challenge. The characteristics of nanopore sequencing make it well suited for whole genome sequencing and as a preferential tool to identify SV, namely those associated with tumours. In this work we present a complete workflow to detect SV in tumour samples using nanopore sequencing. Methods: We used a test tumour sample to prepare DNA libraries using the rapid sequencing kit (Oxford Nanopore Technologies-ONT) and sequenced those in a single R9.4 flow cell on the MinION device (ONT). We implemented a pipeline for SV detection using multiple bioinformatics tools: MinKNOW software (ONT) (run set up and data acquisition), Albacore pipeline (ONT) (basecalling), LAST aligner (mapping) and Picky (SV detection and analysis). Results: The use of the rapid sequencing kit allowed a fast preparation of sequencing libraries when compared with standard library preparation procedures. The MinION generated a total of 2.34 Gb of DNA. The highest number of reads were obtained during the first 8-10h of the sequencing run. Overall, 87.8% of reads had a quality (Q) value >7 (quality threshold) and 54.2% had a Q value >10. The longest read obtained had 74369 bases and the mean read length was of 4508 bases. All reads with a length >50 kb had Q values >= 7. A total of 3470 SV were identified, including deletions, duplications, translocations, insertions and inversions. Conclusions: Long-read sequencing technology is becoming an important tool as it poses itself as a powerful complementary method that suppresses the inherent limitations of other technologies. Nanopore sequencing is a fast and sensitive approach of great potential for human genomics research and for use in a clinical perspective, namely in the detection of SV in the human genome. A critical issue in nanopore sequencing is DNA quality and integrity because longer size reads make it easier to detect large SV.This work was supported by Toxomics (Centre for Toxicogenomics and Human Health), Nova Medical School and is 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).info:eu-repo/semantics/publishedVersio

Chamberlain on Product Differentiation, Market Structure and Competition: An essay

In the 1930s the imperfect competition - monopolistic competition debate took new approaches to the analysis of economic equilibrium with two main works which derived independently came published almost simultaneously in time: Mrs. Robinson’s Economics of Imperfect Competition [1933] and Chamberlin’s Theory of Monopolistic Competition [1933]. They face the competitive structure in completely different ways in aim, methodology and content. His work can be considered revolutionary in the sense that he consideres a market structure characterized by both competitive and monopoly elements and this is the “little” difference that made his work so important to the modern microeconomic theory with so important concepts such as product differentiation, the role of advertising and the randomness associated to the choice process: with Chamberlin, advertizing and product differentiation lead to new market structures, opening up field of industrial organization. Two dimensions are enormously relevant: product differentiation linked to selling costs (advertising, non-price competition, etc.) and numbers (includes oligopoly and competition linked to large numbers, even if demand curves not horizontal).oligopoly, monopolistic and imperfect competition, product and price differentiation, selling costs, advertising, demand curves.

Integral Representation of Generalized Grey Brownian Motion

In this paper we investigate the representation of a class of non Gaussian processes, namely generalized grey Brownian motion, in terms of a weighted integral of a stochastic process which is a solution of a certain stochastic differential equation. In particular the underlying process can be seen as a non Gaussian extension of the Ornstein-Uhlenbeck process, hence generalizing the representation results of Muravlev as well as Harms and Stefanovits to the non Gaussian case.Comment: arXiv admin note: text overlap with arXiv:1708.06784, arXiv:1807.0786

Poderá a valorização energética da biomassa contribuir para a contenção das plantas exóticas invasoras?

A secção Biologia é coordenada pelo Professor Universitário Armindo Rodrigues.Recentemente foi publicado o Regulamento (UE) N.º 1143/2014 do Parlamento Europeu e do Conselho, relativo à problemática das espécies exóticas invasoras. Espécie exótica é qualquer espécime vivo, introduzido fora da sua área de distribuição natural, incluindo quaisquer partes (ovos, sementes) que possam sobreviver e posteriormente reproduzir-se. Exemplos bem conhecidos nos Açores incluem o rato ou o coelho, assim como a criptoméria. O regulamento da EU considera que as espécies exóticas invasoras representam uma ameaça à biodiversidade, especialmente em ecossistemas isolados, como as ilhas, podendo os seus impactes intensificar-se devido à expansão do comércio, dos transportes, do turismo e das alterações climáticas. Excluindo as espécies cultivadas, nos Açores existem cerca de 700 espécies vegetais naturalizadas. As espécies indígenas ou nativas, que terão chegado às ilhas antes do povoamento humano, correspondem apenas a numero inferior a 300. […].info:eu-repo/semantics/publishedVersio

Sustentabilidade da Frota DHC1 CHIPMUNK

O sistema de armas Chipmunk está ao serviço da Força Aérea Portuguesa desde 1951. Desde essa altura, já comportou diversas modificações, tendo procurado manter-se a aeronave operacional e o mais adequada possível à missão e aos padrões de segurança dos nossos dias. Há já 14 anos que a aeronave foi remotorizada, com um novo motor mais potente, tendo sido introduzida ao serviço da Academia da Força Aérea para efetuar a atividade aérea curricular com os alunos daquele estabelecimento de ensino militar. A frota aproxima-se do fim de vida de muitos dos seus componentes, pelo que importa medir se é praticável continuar a modificar e modernizar a aeronave a fim de garantir uma operação sustentada por mais dez anos. Este trabalho de investigação centrou-se nesta questão, tendo provado que tal investimento não é aconselhável, visto que a frota e toda a sua estrutura de apoio logístico sofrem grandes óbices, muitas das vezes difíceis de quantificar. Provamos neste trabalho a insustentabilidade do sistema de armas Chipmunk, mas como garantido desde o início da investigação propomos também uma alternativa que não acarreta um acréscimo de custos para a organização. Conseguimos provar que não existe, ao serviço da Força Aérea, um sistema de armas com as características necessárias para absorver a missão do Chipmunk, tendo patente que a solução mais adequada e aceitável para a sua substituição é a contratualização da missão do Centro de Atividades Aéreas a uma empresa civil. Demonstrámos que os custos desta opção são muito próximos daqueles que a organização tem atualmente com a frota Chipmunk e que com este cenário conseguimos garantir uma aeronave capaz de satisfazer os requisitos da missão em questão. Para tal foi efetuado o estudo de duas empresas civis, a título de exemplo, tendo sido estudadas as características de duas aeronaves distintas e colhida a vasta experiencia de instrução de ambas as empresas. Abstract: The Chipmunk aircraft is on duty since 1951. Since then it has experience several modifications in a continuous process of approaching to the modern days safety standards. It has passed already 14 years since the re-engine process that the fleet was forced to do. After this modification the aircraft was introduced in the syllabus flying activity of the Portuguese Air Force Academy. The fleet is approaching the end of life of many components, and for that, is important to determine if it is practical to continue modifying and to continue the process of modernization of the fleet, in order to guaranty its sustainability for the next ten years. This investigation has centered in this question, and we have demonstrated that it is not advisable to invest more on modernization of the fleet, since the logistic chain has enormous problems, concerning mainly spare parts. We have proven that the Chipmunk is not sustainable for the next ten years to come, but we, like advertised in the beginning of the investigation, have manage to find a solution that fits the demands of the academy flying activity and keeping the size of the budget for that. It is also demonstrated, in this investigation, that there isn’t another aircraft, in service, that can take over the Chipmunk mission. So the best scenario for the replacement of this aircraft is the outsourcing of the mission of the Aerial Activity Center of the academy. We were able to demonstrate that the costs are very similar to the current ones, with the Chipmunk, and that the outsourcing scenario is able to provide an aircraft with the desired performance and able to comply with the requisites of the mission in question. For this we have studied two civilian companies, equipped with different aircrafts, where we studied the performances of the two aircrafts and we collected the vast experience of the companies in the flying instruction

Adoption of renewable energy innovations among hoteliers in Portugal

UIDB/04038/2020 UIDP/04038/2020 CEECIND/01814/2017This article examines the owners' and/or managers' perceptions and attitudes towards the adoption of renewable energy innovations in hotels in Portugal, as well as the factors that affect the adoption. The study is based on an e-mail-based survey conducted with hoteliers in 2022 (n = 208). First, the results demonstrate that despite the respondents' positive perceptions of renewable energy, the adoption level of renewable energy innovations in hotels is low. Second, the reasons given for this gap relate mainly to unfavourable market factors. Third, market factors have a statistically significant influence on adoption. In contrast, the characteristics of the hotels and hoteliers, their opinion about the need to cut the carbon footprint of tourist accommodations and the type of hotel ownership have no significant influence. Este artigo analisa as perceções e atitudes dos proprietários e/ou gestores relativamente à adoção de inovações de energias renováveis nos hotéis em Portugal, bem como os fatores que influenciam a adoção. O estudo baseia-se num inquérito aos hoteleiros realizado por e-mail em 2022 (n = 208). Os resultados demonstram, em primeiro lugar, que apesar das perceções positivas dos inquiridos sobre as energias renováveis, o nível de adoção de inovações em energias renováveis é baixo. Em segundo lugar, as razões apresentadas para este diferencial relacionam-se principalmente com fatores de mercado desfavoráveis. Em terceiro lugar, os fatores de mercado têm uma influência estatisticamente significativa na adoção, enquanto as características dos hotéis e dos hoteleiros, a opinião destes sobre a necessidade de reduzir a pegada de carbono e o tipo de propriedade do hotel não têm influência significativa.publishersversionpublishe

Wind and Power in the Anthropocene, de Cymene Howe

CEECIND/01814/2017 UIDB/04038/2020 UIDP/04038/2020publishersversionpublishe