Idiopathic pulmonary fibrosis--clinical presentation, outcome and baseline prognostic factors in a Portuguese cohort

Introduction: Idiopathic Pulmonary Fibrosis (IPF) is the most common disease in the subgroup of idiopathic interstitial pneumonias. It is inevitably associated to a bad prognosis, although assuming a highly variable clinical course. Methods: Patients with IPF, observed at Interstitial Lung Diseases outpatient clinic of Centro Hospitalar de São João – Porto, Portugal, were identified and clinical, functional, radiological and bronchoalveolar lavage (BAL) parameters were reviewed. Their clinical course and survival were analyzed in order to identify prognostic factors. Results: Eighty-one patients were included, with a mean age at diagnosis of 63.8 years old. At diagnosis, the main functional abnormalities were restrictive physiology, reduced lung diffusion and exercise capacity impairment. Clinical course was mainly slowly progressive (72.3%). Ten patients (13.2%) had a rapid progression and 11 (14.5%) patients had an acute exacerbation during the course of the disease. IPF's rapid progression was associated to a higher functional impairment at diagnosis, namely in what is related with Functional Vital Capacity (FVC) and Total Lung Capacity (TLC). Median survival was 36 months. A significant difference in survival was observed among different types of clinical course – 41 months for slow progressors and 9 months for rapid progressors. Lower levels of FVC, TLC, six-minute walk test (6MWT) distance and rest PaO2, and higher BAL neutrophil count were associated with poorer survival in univariate analysis. Conclusion: The analysis of this group of IPF patients confirms two clearly different phenotypes, slow and rapid progressors. Those phenotypes seem to have different presentations and a remarkably different natural history. These results could mean different physiopathologic pathways, which could implicate different therapeutic approaches

Combining geostatistical and biotic interaction modelling to predict amphibian refuges under crayfish invasion across dendritic stream networks

Biodiversity ResearchAim: Biological invasions are pervasive in freshwater ecosystems, often causing native species to contract into areas that remain largely free from invasive species impacts. Predicting the location of such ecological refuges is challenging, because they are shaped by the habitat requirements of native and invasive species, their biotic interactions, and the spatial and temporal invasion patterns. Here, we investigated the spatial distribution and environmental drivers of refuges from invasion in river systems, by considering biotic interactions in geostatistical models accounting for stream network topology. We focused on Mediterranean amphibians negatively impacted by the invasive crayfishes Procambarus clarkii and Pacifastacus leniusculus. Location: River Sabor, NE Portugal. Methods: We surveyed amphibians at 168 200-m stream stretches in 2015. Geostatistical models were used to relate the probabilities of occurrence of each species to environmental and biotic variables, while controlling for linear (Euclidean) and hydrologic spatial dependencies. Biotic interactions were specified using crayfish probabilities of occurrence extracted from previously developed geostatistical models. Models were used to map the distribution of potential refuges for the most common amphibian species, under current conditions and future scenarios of crayfish expansion. Results: Geostatistical models were produced for eight out of 10 species detected, of which five species were associated with lower stream orders and only one species with higher stream orders. Six species showed negative responses to one or both crayfish species, even after accounting for environmental effects and spatial dependencies. Most amphibian species were found to retain large expanses of potential habitat in stream headwaters, but current refuges will likely contract under plausible scenarios of crayfish expansion. Main conclusions: Incorporating biotic interactions in geostatistical modelling provides a practical and relatively simple approach to predict present and future distributions of refuges from biological invasion in stream networks. Using this approach, our study shows that stream headwaters are key amphibian refuges under invasion by alien crayfishinfo:eu-repo/semantics/publishedVersio

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

Metals impact into the Paranaguá Estuarine Complex (Brazil) during the exceptional flood of 2011

Abstract Particulate and dissolved metal concentrations were determined after the largest flood in the last 30 years on the east-west axis of the Paranaguá Estuarine Complex (PEC) and compared to the those of the dry period at two stations. Results confirmed that the flood greatly affected riverine outflows and the behavior of metals in the PEC. In particular, a sharp decrease in salinity was followed by extremely high SPM concentrations leading to a decrease in DO concentrations at both stations. For the dissolved phase, ANOSIM analysis showed a significant dissimilarity at each station between the sampled periods, whereas for the particulate phase this dissimilarity was found only for the samplings taken at the Antonina Station. KD values suggested dissolved Cu behavior was related to the presence of organic complexes and dissolved Mn had sediment resuspension of redox sediments and or/pore water injection as sources. Metal concentrations were lower than in polluted estuaries, though high enrichment factors found after the flood pointed to the influence of anthropogenic sources. In conclusion, the flood's influence was more evident at the Antonina Station, due to its location in the upper estuary, whereas in Paranaguá a high SPM content with low metal concentration was found, following the common pattern generally found in other marine systems subject to heavy rainfall events

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Currículo e Relações Étnico-Raciais: o Estado da Arte

Este artigo apresenta a sistematização e a análise dos 38 artigos, 13 teses e 50 dissertações da Categoria Currículo. Inicialmente, demonstraremos os resultados do exame das teses e das dissertações. Em seguida, refletiremos acerca dos artigos. Para a leitura e análise dos artigos e da produção discente, utilizamos como subsídio os referenciais da análise de conteúdo, por meio da análise categorial (BARDIN, 2008). Ao final, apresentaremos os caminhos abertos para pesquisas futuras e as recomendações da produção investigada para a implementação da Lei nº 10.639/2003

Preditores de conversão tardia dos exames micobacteriológicos direto e cultural de expetoração numa população portuguesa com tuberculose pulmonar

Resumo: Introdução: A ausência de conversão dos exames micobacteriológicos direto e/ou cultural de expetoração após 2 meses de tratamento para a tuberculose (TB) tem sido considerado um preditor do grau de infeciosidade do doente e de falência terapêutica. Os autores estabeleceram por objetivo a identificação dos fatores associados com a conversão tardia dos exames direto e cultural de expetoração num grupo de doentes com TB pulmonar sob tratamento antibacilar. Material e métodos: Coorte retrospetiva de 136 doentes adultos com TB pulmonar, confirmada por exame cultural de expetoração, referenciados a um Centro de Diagnóstico Pneumológico urbano. Foram analisadas variáveis sócio-demográficas, clínicas, radiológicas, microbiológicas e relacionadas com a terapêutica. Resultados: A mediana de idades foi 41,0 (intervalo interquartil [IIQ] 18,0) anos e 75,0% dos doentes eram do género masculino. A conversão tardia dos exames de expetoração direto e cultural ocorreu em 25,4% (30/118) e 27,2% (37/136) dos doentes, respetivamente. Pela análise multivariada, a idade ⥠50 anos (odds ratio [OR] 4,4, intervalo de confiança [IC] 95% 1,5-13,3), o género masculino (OR 10,8, IC 95% 1,3-91,1), e a carga bacilar > 1-9 bacilos álcool-ácido resistentes (BAAR)/campo (3+) (OR 11,7, IC 95% 1,4-100,6) estiveram significativamente associados com a positividade persistente do exame direto, após 2 meses de tratamento. O envolvimento radiológico bilateral (OR 3,7, IC 95% 1,5-9,0) e a contagem de colónias > 100 (3+) (OR 5,8, IC 95% 1,2-27,4) estiveram significativamente associados com a positividade persistente do exame cultural. Conclusões: A conversão tardia dos exames direto e cultural de expetoração ocorreu em cerca de um terço dos doentes. A idade mais avançada, o género masculino e a elevada carga bacilar estiveram independentemente associados com a conversão tardia do exame direto de expetoração. O envolvimento radiológico bilateral e a contagem de colónias mais elevada estiveram independentemente associados com a conversão tardia do exame cultural. Abstract: Introduction: Failure of sputum smear and/or culture conversion after 2 months of tuberculosis (TB) treatment has been considered a predictor of patient infectivity and treatment failure. We aimed to identify the factors associated with delayed sputum smear and culture conversion in patients with pulmonary TB who were given anti-TB treatment. Material and methods: Retrospective cohort of 136 adult patients with sputum culture-proven pulmonary TB referred to an urban Chest Disease Centre. Socio-demographic, clinical, radiological, microbiological, and therapeutic data were evaluated. Results: The median age was 41.0 (interquartile range [IQR] 18.0) years and 75.0% of patients were male. Delayed sputum smear and culture conversion occurred in 25.4% (30/118) and 27.2% (37/136) of patients, respectively. Multivariate analysis indicated that age ⥠50 years (odds ratio [OR] 4.4, 95% confidence interval [CI] 1.5-13.3), male gender (OR 10.8, 95% CI 1.3-91.1), and smear grade > 1-9 acid fast bacilli (AFB)/field (3+) (OR 11.7, 95% CI 1.4-100.6) were significantly associated with persistent smear positivity after 2 months of treatment. Bilateral radiological involvement (OR 3.7, 95% CI 1.5-9.0) and colony count > 100 (3+) (OR 5.8, 95% CI 1.2-27.4) were significantly associated with persistent culture positivity. Conclusions: Delayed sputum smear and culture conversion occurred in about one third of patients. Older age, male gender, and higher bacillary load were independently associated with delayed smear conversion. Bilateral radiological involvement and higher colony count were independently associated with delayed culture conversion. Palavras-chave: Tuberculose, Expetoração, Exame direto, Exame cultural, Conversão tardia, Keywords: Tuberculosis, Sputum, Smear, Culture, Delayed conversio

Predictors of delayed sputum smear and culture conversion among a Portuguese population with pulmonary tuberculosis

Introduction: Failure of sputum smear and/or culture conversion after 2 months of tuberculosis (TB) treatment has been considered a predictor of patient infectivity and treatment failure. We aimed to identify the factors associated with delayed sputum smear and culture conversion in patients with pulmonary TB who were given anti-TB treatment. Material and methods: Retrospective cohort of 136 adult patients with sputum culture-proven pulmonary TB referred to an urban Chest Disease Centre. Socio-demographic, clinical, radiological, microbiological, and therapeutic data were evaluated. Results: The median age was 41.0 (interquartile range [IQR] 18.0) years and 75.0% of patients were male. Delayed sputum smear and culture conversion occurred in 25.4% (30/118) and 27.2% (37/136) of patients, respectively. Multivariate analysis indicated that age â¥Â 50 years (odds ratio [OR] 4.4, 95% confidence interval [CI] 1.5â13.3), male gender (OR 10.8, 95% CI 1.3â91.1), and smear grade > 1â9 acid fast bacilli (AFB)/field (3+) (OR 11.7, 95% CI 1.4â100.6) were significantly associated with persistent smear positivity after 2 months of treatment. Bilateral radiological involvement (OR 3.7, 95% CI 1.5â9.0) and colony count > 100 (3+) (OR 5.8, 95% CI 1.2â27.4) were significantly associated with persistent culture positivity. Conclusions: Delayed sputum smear and culture conversion occurred in about one third of patients. Older age, male gender, and higher bacillary load were independently associated with delayed smear conversion. Bilateral radiological involvement and higher colony count were independently associated with delayed culture conversion. Resumo: Introdução: A ausência de conversão dos exames micobacteriológicos direto e/ou cultural de expetoração após 2 meses de tratamento para a tuberculose (TB) tem sido considerado um preditor do grau de infeciosidade do doente e de falência terapêutica. Os autores estabeleceram por objetivo a identificação dos fatores associados com a conversão tardia dos exames direto e cultural de expetoração num grupo de doentes com TB pulmonar sob tratamento antibacilar. Material e métodos: Coorte retrospetiva de 136 doentes adultos com TB pulmonar, confirmada por exame cultural de expetoração, referenciados a um Centro de Diagnóstico Pneumológico urbano. Foram analisadas variáveis sócio-demográficas, clínicas, radiológicas, microbiológicas e relacionadas com a terapêutica. Resultados: A mediana de idades foi 41,0 (intervalo interquartil [IIQ] 18,0) anos e 75,0% dos doentes eram do género masculino. A conversão tardia dos exames de expetoração direto e cultural ocorreu em 25,4% (30/118) e 27,2% (37/136) dos doentes, respetivamente. Pela análise multivariada, a idade â¥Â 50 anos (odds ratio [OR] 4,4, intervalo de confiança [IC] 95% 1,5â13,3), o género masculino (OR 10,8, IC 95% 1,3â91,1), e a carga bacilar > 1â9 bacilos álcool-ácido resistentes (BAAR)/campo (3+) (OR 11,7, IC 95% 1,4â100,6) estiveram significativamente associados com a positividade persistente do exame direto, após 2 meses de tratamento. O envolvimento radiológico bilateral (OR 3,7, IC 95% 1,5â9,0) e a contagem de colónias > 100 (3+) (OR 5,8, IC 95% 1,2â27,4) estiveram significativamente associados com a positividade persistente do exame cultural. Conclusões: A conversão tardia dos exames direto e cultural de expetoração ocorreu em cerca de um terço dos doentes. A idade mais avançada, o género masculino e a elevada carga bacilar estiveram independentemente associados com a conversão tardia do exame direto de expetoração. O envolvimento radiológico bilateral e a contagem de colónias mais elevada estiveram independentemente associados com a conversão tardia do exame cultural. Keywords: Tuberculosis, Sputum, Smear, Culture, Delayed conversion, Palavras-chave: Tuberculose, Expetoração, Exame direto, Exame cultural, Conversão tardi