Circularidade e inovação nos projetos de arquitetura do setor da construção em Portugal

Mestrado Bolonha em Economia e Gestão de Ciência, Tecnologia e InovaçãoO setor da construção integra o grupo de setores com efeitos mais adversos para o ambiente, com uma utilização intensiva dos recursos naturais do planeta. A economia circular é vista como uma das abordagens mais viáveis de redução desses efeitos. Neste contexto, urge a necessidade de ação com vista a uma aplicação plena da economia circular no setor. A pressão internacional e europeia torna inevitável o rumo a seguir. A nível nacional, constituindo uma área ainda pouco explorada, há que avaliar qual o patamar de conhecimento e implementação dos princípios e práticas da economia circular no setor. Assumindo a relevância e potencial de influência da fase de design nas restantes fases do processo de construção, o presente estudo foca-se na análise das competências e práticas dos arquitetos, sobre a circularidade e a inovação no setor da construção, nos projetos que desenvolvem em Portugal. Os resultados obtidos revelam um limiar de conhecimento e implementação relativamente baixo em matéria de economia circular por parte dos arquitetos que desenvolvem projetos de arquitetura a nível nacional. Revelam ainda que, apesar de a inovação ser reconhecida como central para alcançar esses objetivos, a sua implementação prática apresenta fragilidades, nomeadamente a baixa familiaridade com conceitos e ferramentas eco-inovadoras consideradas facilitadoras da implementação da circularidade em projetos de arquitetura e o fraco nível de colaboração com Universidades e Centros de Investigação, que condicionam uma mais rápida evolução da integração dos princípios e práticas da economia circular no setor.The construction sector is one of the sectors with the most adverse effects on the environment, with an intensive use of the planet's natural resources. The circular economy is seen as one of the most viable approaches to reducing these effects. In this context, there is an urgent need for action to fully implement the circular economy in the sector. International and European pressure makes the way forward inevitable. At national level, as this is still an under-explored area, the level of knowledge and implementation of circular economy principles and practices in the sector must be assessed. Assuming the relevance and potential influence of the design phase on the other phases of the construction process, this study focuses on the analysis of architects’ skills and practices regarding circularity and innovation in the construction sector in the projects they develop in Portugal. The results show a relatively low threshold of knowledge and implementation of circular economy by architects developing architectural projects at national level. They also reveal that, despite innovation being recognized as central to achieving these goals, its practical implementation has weaknesses namely the low familiarity with eco-innovative concepts and tools that are considered to facilitate the implementation of circularity in architectural projects and the weak level of collaboration with Universities and Research Centres, which condition a faster evolution of the integration of circular economy principles and practices in the sector.info:eu-repo/semantics/publishedVersio

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data.

BACKGROUND: The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model. RESULTS: Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates. CONCLUSIONS: In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data

O Papel do Prestador De Cuidados na Prevenção de Úlceras por Pressão: Protocolo de Ensinos

Introdução: A DGS preconiza que a avaliação do risco de úlcera por pressão deve ser realizada em todos os Serviços de Internamento independentemente do diagnóstico e necessidades de cuidados (DGS, 2011). Segundo Gonçalves (2011), 55,5% dos cuidadores informais não sabem prevenir úlceras por pressão, evidenciado pelo contacto diário com a família em contexto de internamento de Medicina Interna onde os ensinos são realizados informalmente e sem registo em SClínico®. Surge a necessidade de implementar protocolos de atuação estruturada para ensinos ao prestador de cuidados acerca da prevenção de úlceras por pressão, para promover a continuidade de cuidados no domicílio e a educação dos familiares para melhorar indicadores de cuidados (DGS, 2011). Metodologia: Projeto de melhoria contínua para implementação num serviço de Medicina Interna de um protocolo de ensinos ao prestador de cuidados baseados na avaliação do risco de úlcera por pressão com recurso à Escala de Braden. Resultados: O levantamento dos dados num departamento de Medicina Interna demonstra uma baixa incidência de registos de enfermagem em SClínico® respeitante aos diagnósticos Potencial para melhorar o conhecimento/ capacidade do prestador de cuidados sobre prevenção de úlcera de pressão. Perante isto, criou-se um protocolo sob a forma de diagrama baseado na avaliação da interação social e do risco de úlcera por pressão pela Escala de Braden, dirigindo os ensinos de acordo com a probabilidade do risco. O protocolo a implementar permite a melhoria dos indicadores da qualidade dos cuidados e a uniformização de práticas, avaliadas por auditorias.info:eu-repo/semantics/publishedVersio

SV-Pop: population-based structural variant analysis and visualization.

BACKGROUND: Genetic structural variation underpins a multitude of phenotypes, with significant implications for a range of biological outcomes. Despite their crucial role, structural variants (SVs) are often neglected and overshadowed by single nucleotide polymorphisms (SNPs), which are used in large-scale analysis such as genome-wide association and population genetic studies. RESULTS: To facilitate the high-throughput analysis of structural variation we have developed an analytical pipeline and visualisation tool, called SV-Pop. The utility of this pipeline was then demonstrated through application with a large, multi-population P. falciparum dataset. CONCLUSIONS: Designed to facilitate downstream analysis and visualisation post-discovery, SV-Pop allows for straightforward integration of multi-population analysis, method and sample-based concordance metrics, and signals of selection

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

BAckground: Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing genomes or genomic regions with extremely biased base composition is still a great challenge to the currently available NGS platforms. The genomes of some important pathogenic organisms like Plasmodium falciparum (high AT content) and Mycobacterium tuberculosis (high GC content) display extremes of base composition. The standard library preparation procedures that employ PCR amplification have been shown to cause uneven read coverage particularly across AT and GC rich regions, leading to problems in genome assembly and variation analyses. Alternative library-preparation approaches that omit PCR amplification require large quantities of starting material and hence are not suitable for small amounts of DNA/RNA such as those from clinical isolates. We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences. Results: We have used our optimized conditions in parallel with standard methods to prepare Illumina sequencing libraries from a non-clinical and a clinical isolate (containing ~53% host contamination). By analyzing and comparing the quality of sequence data generated, we show that our optimized conditions that involve a PCR additive (TMAC), produces amplified libraries with improved coverage of extremely AT-rich regions and reduced bias toward GC neutral templates. Conclusion: We have developed a robust and optimized Next-Generation Sequencing library amplification method suitable for extremely AT-rich genomes. The new amplification conditions significantly reduce bias and retain the complexity of either extremes of base composition. This development will greatly benefit sequencing clinical samples that often require amplification due to low mass of DNA starting material

Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains

BACKGROUND: Klebsiella pneumoniae (Kp) Gram-negative bacteria cause nosocomial infections and rapidly acquire antimicrobial resistance (AMR), which makes it a global threat to human health. It also has a comparatively rare hypervirulent phenotype that can lead to severe disease in otherwise healthy individuals. Unlike classic Kp, canonical hypervirulent strains usually have limited AMR. However, after initial case reports in 2015, carbapenem-resistant hypervirulent Kp has increased in prevalence, including in China, but there is limited understanding of its burden  in other geographical regions. METHODS: Here, we examined the largest collection of publicly available sequenced Kp isolates (n=13,178), containing 1603 different sequence types (e.g. ST11 15.0%, ST258 9.5%), and 2174 (16.5%) hypervirulent strains. We analysed the plasmid replicons and carbapenemase and siderophore encoding genes to understand the movement of hypervirulence and AMR genes located on plasmids, and their convergence in carbapenem-resistant hypervirulent Kp. RESULTS: We identified and analysed 3034 unique plasmid replicons to inform the epidemiology and transmission dynamics of carbapenem-resistant hypervirulent Kp (n=1028, 7.8%). We found several outbreaks globally, including one involving ST11 strains in China and another of ST231 in Asia centred on India, Thailand, and Pakistan. There was evidence of global flow of Kp, including across multiple continents. In most cases, clusters of Kp isolates are the result of hypervirulence genes entering classic strains, instead of carbapenem resistance genes entering canonical hypervirulent ones. CONCLUSIONS: Our analysis demonstrates the importance of plasmid analysis in the monitoring of carbapenem-resistant and hypervirulent strains of Kp. With the growing adoption of omics-based technologies for clinical and surveillance applications, including in geographical regions with gaps in data and knowledge (e.g. sub-Saharan Africa), the identification of the spread of AMR will inform infection control globally

estMOI: estimating multiplicity of infection using parasite deep sequencing data.

Individuals living in endemic areas generally harbour multiple parasite strains. Multiplicity of infection (MOI) can be an indicator of immune status and transmission intensity. It has a potentially confounding effect on a number of population genetic analyses, which often assume isolates are clonal. Polymerase chain reaction-based approaches to estimate MOI can lack sensitivity. For example, in the human malaria parasite Plasmodium falciparum, genotyping of the merozoite surface protein (MSP1/2) genes is a standard method for assessing MOI, despite the apparent problem of underestimation. The availability of deep coverage data from massively parallizable sequencing technologies means that MOI can be detected genome wide by considering the abundance of heterozygous genotypes. Here, we present a method to estimate MOI, which considers unique combinations of polymorphisms from sequence reads. The method is implemented within the estMOI software. When applied to clinical P.falciparum isolates from three continents, we find that multiple infections are common, especially in regions with high transmission

Genomic analysis of hypervirulent Klebsiella pneumoniae reveals potential genetic markers for differentiation from classical strains.

The majority of Klebsiella pneumoniae (Kp) infections are nosocomial, but a growing number of community-acquired infections are caused by hypervirulent strains (hvKp) characterised by liver invasion and rapid metastasis. Unlike nosocomial Kp infections, hvKp are generally susceptible to antibiotics. Due to the rapid progression of hvKp infections, timely and accurate diagnosis is required for effective treatment. To identify potential drivers of the hypervirulent phenotype, we performed a genome-wide association study (GWAS) analysis on single nucleotide variants and accessory genome loci across 79 publicly available Kp isolates collected from patients' liver and a diverse global Kp dataset (n = 646). The GWAS analysis revealed 29 putative genes (P < 10-10) associated with higher risk of liver phenotype, including hypervirulence linked salmochelin iro (odds ratio (OR): 29.8) and aerobactin iuc (OR: 14.1) loci. A minority of liver isolates (n = 15, 19%) had neither of these siderophores nor any other shared biomarker, suggesting possible unknown drivers of hypervirulence and an intrinsic ability of Kp to invade the liver. Despite identifying potential novel loci linked to a liver invasive Kp phenotype, our work highlights the need for large-scale studies involving more sequence types to identify further hypervirulence biomarkers to assist clinical decision making

Association of common TMPRSS6 and TF gene variants with hepcidin and iron status in healthy rural Gambians.

Genome-wide association studies in Europeans and Asians have identified numerous variants in the transmembrane protease serine 6 (TMPRSS6) and transferrin (TF) genes that are associated with changes in iron status. We sought to investigate the effects of common TMPRSS6 and TF gene SNPs on iron status indicators in a cohort of healthy Africans from rural Gambia. We measured iron biomarkers and haematology traits on individuals participating in the Keneba Biobank with genotype data on TMPRSS6 (rs2235321, rs855791, rs4820268, rs2235324, rs2413450 and rs5756506) and TF (rs3811647 and rs1799852), n = 1316. After controlling for inflammation, age and sex, we analysed the effects of carrying either single or multiple iron-lowering alleles on iron status. TMPRSS6 rs2235321 significantly affected plasma hepcidin concentrations (AA genotypes having lower hepcidin levels; F ratio 3.7, P = 0.014) with greater impact in individuals with low haemoglobin or ferritin. No other TMPRSS6 variant affected hepcidin. None of the TMPRSS6 variants nor a TMPRSS6 allele risk score affected other iron biomarkers or haematological traits. TF rs3811647 AA carriers had 21% higher transferrin (F ratio 16.0, P < 0.0001), 24% higher unsaturated iron-binding capacity (F ratio 12.8, P < 0.0001) and 25% lower transferrin saturation (F ratio 4.3, P < 0.0001) compared to GG carriers. TF rs3811647 was strongly associated with transferrin, unsaturated iron-binding capacity (UIBC) and transferrin saturation (TSAT) with a single allele effect of 8-12%. There was no association between either TF SNP and any haematological traits or iron biomarkers. We identified meaningful associations between TMPRSS6 rs2235321 and hepcidin and replicated the previous findings on the effects of TF rs3811647 on transferrin and iron binding capacity. However, the effects are subtle and contribute little to population variance. Further genetic and functional studies, including polymorphisms frequent in Africa populations, are needed to identify markers for genetically stratified approaches to prevention or treatment of iron deficiency anaemia

A recall-by-genotype study on polymorphisms in the TMPRSS6 gene and oral iron absorption: a study protocol

Background: Oral iron supplementation is commonly used to treat and prevent anaemia. The transmembrane protease serine 6 gene (TMPRSS6), which encodes matriptase 2, is a negative regulator of hepcidin, the key controller of iron homeostasis. Genome-wide association studies (GWAS) have identified several single nucleotide polymorphisms (SNPs) in the TMPRSS6 gene that are associated with an increased risk of iron-deficiency anaemia.  We will investigate the in vivo effects of three previously reported TMPRSS6 variants (rs855791, rs4820268 and rs2235321) on oral iron absorption in non-anaemic volunteers in The Gambia. Methods: A recall-by-genotype study design will be employed. Pre-genotyped participants will be recruited from the West African BioResouce (WABR), which currently contains over 3000 genotyped individuals. Male and female volunteers will be selected based on polymorphisms (rs855791, rs4820268 and rs2235321) in the TMPRSS6 gene in the Gambian population. The effects of a single variant allele at one SNP and the additive effect of two or three variant alleles from either two or all three SNPs will be investigated. Study participants will be given a single oral dose of 400mg ferrous sulfate, and blood samples will be collected at baseline, two hours and five hours post supplementation. Differences in iron absorption between genotype groups will be assessed by measuring the increase in serum iron concentration at five hours post iron ingestion. Discussion: This study will increase understanding of the role of genetic variations in TMPRSS6 on oral iron absorption in subjects of West African origin. This will test for the biological basis for the association of each of the three TMPRSS6 variants with iron absorption. This may help in guiding future iron intervention strategies, particularly in populations with a high frequency of these SNPs and a high frequency of anaemia. Study registration: ClinicalTrials.gov NCT03341338 14/11/17.</ns4:p