Evaluating MPA effectiveness through inside and outside uses allowed : Portugal as a case study

Dissertação de Mestrado apresentada no ISPA – Instituto Universitário para obtenção de grau de Mestre na especialidade de Biologia Marinha e Conservação.As áreas marinhas protegidas (MPAs) são ferramentas de conservação mundial utilizadas para reduzir actividades humanas com impacto no meio marinho. No entanto, desenvolvimentos recentes colocam a sua validade em causa. A necessidade de avaliar a sua eficácia requer novas abordagens. Aqui, eu utilizo comparações dentro:fora de actividades que apresentam impacto potencial sobre a biodiversidade (pesca, aquacultura, exploração do fundo e actividades de recreio). As actividades foram recolhidas recorrendo às regulamentações em vigor em cada zona. Proponho relacionar cada redução de usos observada com o nível de proteção atribuído à MPA; e pela primeira vez, classificar o nível de proteção das zonas imediatamente fora usando um sistema de classificação baseado nos regulamentos para as MPAs. Todas as MPAs portuguesas efectivamente reduziram actividades extractivas e não-extractivas; enquanto, algumas MPAs não providenciaram proteção extra do exterior. Apenas áreas totalmente protegidas e áreas altamente protegidas reduziram/restringiram actividades extractivas. No geral, as MPAs portuguesas mostraram reduções de usos semelhantes com áreas moderamente protegidas; das quais 17 não aumentaram o nível de proteção observado. Novas medidas de gestão e conservação são urgentemente necessárias.Marine protected areas (MPAs) are world conservation tools to reduce human activities impacting the marine environment. However, recent developments place its validity in check. The need to assess their effectiveness calls for new approaches. Here, I use inside:outside comparisons of activities that have a potential impact on biodiversity (fishing, aquaculture, bottom exploitation, and recreational uses). The activities were collected using the regulations in force in each zone. I propose to relate each reduction of uses to the level of protection assigned; and, for the first time to evaluate the level of protection of outside zones, using a recent regulation-based classification system for MPAs. All Portuguese MPAs effectively reduce non-extractive and extractive activities, whereas some MPAs do not provide extra protection from outside. Only fully protected areas and highly protected areas reduce/restrict extractive uses. Overall, Portuguese MPAs show a similar reduction to moderately protected areas; of which 17 did not increase the protection level observed outside. New management and conservation measures are urgently needed

Interventions and outcomes in bronchiolitis clinical trials

Tese de doutoramento, Medicina (Pediatria), Universidade de Lisboa, Faculdade de Medicina, 2015Acute viral bronchiolitis is the most common acute infection of the lower respiratory tract during the first year of life. It is a major cause of clinical morbidity and financial health burden, and encompasses a spectrum of disease severity. This thesis addresses the uncertainties of current evidence on two widely used treatments for bronchiolitis, i.e. bronchodilators and corticosteroids, and how this evidence is limited by shortcomings in key areas of clinical trial design, namely disease definition and outcome selection and measurement. The thesis specific aims were: 1. to assess the comparative efficacy and safety of bronchodilators and corticosteroids, used alone or in combination; 2. to identify outcomes reported in previous clinical trials in bronchiolitis, and a. to assess which outcomes are considered most important to different physicians, and b. to study the measurement properties of two commonly used respiratory distress scales (Respiratory Distress Assessment Instrument - RDAI, and the Respiratory Assessment Change Score - RACS); and 3. to study how physicians define bronchiolitis. Chapter 1 presents an overview of relevant epidemiological, clinical and pathophysiological findings in bronchiolitis, preceded by a historical perspective. Chapter 2 describes the results of a comprehensive comparative effectiveness systematic review of bronchodilators and corticosteroids, including 48 trials (4897 patients and 13 comparisons), with network meta-analysis. Chapter 3.1 presents an exploratory study to identify outcome domains and measurement instruments reported in 90 clinical trials of bronchiolitis included in 11 Cochrane systematic reviews. In Chapter 3.2, we report on a measurement study which evaluates the validity, reliability and responsiveness of RDAI and RACS, including data from up to 1765 infants with bronchiolitis enrolled in pediatric emergency departments. Finally, in Chapter 4 we present results from a nationwide electronic survey of pediatricians and general practitioners, where we assessed physician perspectives on both definition of bronchiolitis, and relevant outcomes and outcome domains for future bronchiolitis trials.A bronquiolite aguda é a mais frequente infecção das vias aéreas inferiores durante o primeiro ano de vida, e tem um impacto clínico e económico substancial. Esta tese avalia a evidência actual sobre o uso de broncodilatadores e corticoesteróides, e de que forma essa evidência está limitada por dois aspectos metodológicos chave para o desenho de ensaios clínicos nesta área: a definição de bronquiolite, e a escolha e medição de “outcomes”. Os objectivos específicos incluem: 1. avaliar a eficácia e segurança comparativas de broncodilatadores e corticoesteróides, usados isoladamente ou em combinação; 2. identificar os “outcomes” reportados em ensaios clínicos de bronquiolite, e a. avaliar que “outcomes” são considerados mais relevantes por médicos, e b. estudar as propriedades de medida de duas escalas de dificuldade respiratória frequentemente usadas (Respiratory Distress Assessment Instrument - RDAI, e Respiratory Assessment Change Score - RACS); e 3. avaliar perspectivas médicas sobre a definição de bronquiolite. No Capítulo 1 revemos aspectos epidemiológicos, fisiopatológicos e clínicos da bronquiolite, enquadrados numa perspectiva histórica. No Capítulo 2 descrevemos os resultados de uma revisão sistemática comparativa sobre a eficácia e segurança de broncodilatadores e corticoesteróides, incluindo 48 ensaios (4897 doentes e 13 comparações), com meta-análise em rede. O Capítulo 3.1 apresenta um estudo exploratório que identifica domínios de “outcomes” e instrumentos de medida reportados em 90 ensaios clínicos de bronquiolite incluídos em 11 revisões sistemáticas Cochrane. No Capítulo 3.2 descrevemos um estudo de medição em que se avaliam a validade, fiabilidade e responsividade das escalas RDAI e RACS, incluindo dados de até 1765 crianças no contexto de bronquiolite na urgência pediátrica. Por fim, no Capítulo 4 apresentamos os resultados de um inquérito electrónico nacional a médicos pediatras e de medicina geral e familiar, avaliando as perspectivas médicas sobre definição de bronquiolite, e sobre quais os “outcomes” considerados relevantes para futuros ensaios clínicos nesta área

Simulation study

Publisher Copyright: © 2023 JMIR Publications Inc.. All rights reserved.Background: Contact tracing is a fundamental intervention in public health. When systematically applied, it enables the breaking of chains of transmission, which is important for controlling COVID-19 transmission. In theoretically perfect contact tracing, all new cases should occur among quarantined individuals, and an epidemic should vanish. However, the availability of resources influences the capacity to perform contact tracing. Therefore, it is necessary to estimate its effectiveness threshold. We propose that this effectiveness threshold may be indirectly estimated using the ratio of COVID-19 cases arising from quarantined high-risk contacts, where higher ratios indicate better control and, under a threshold, contact tracing may fail and other restrictions become necessary. Objective: This study assessed the ratio of COVID-19 cases in high-risk contacts quarantined through contact tracing and its potential use as an ancillary pandemic control indicator. Methods: We built a 6-compartment epidemiological model to emulate COVID-19 infection flow according to publicly available data from Portuguese authorities. Our model extended the usual susceptible-exposed-infected-recovered model by adding a compartment Q with individuals in mandated quarantine who could develop infection or return to the susceptible pool and a compartment P with individuals protected from infection because of vaccination. To model infection dynamics, data on SARS-CoV-2 infection risk (IR), time until infection, and vaccine efficacy were collected. Estimation was needed for vaccine data to reflect the timing of inoculation and booster efficacy. In total, 2 simulations were built: one adjusting for the presence and absence of variants or vaccination and another maximizing IR in quarantined individuals. Both simulations were based on a set of 100 unique parameterizations. The daily ratio of infected cases arising from high-risk contacts (q estimate) was calculated. A theoretical effectiveness threshold of contact tracing was defined for 14-day average q estimates based on the classification of COVID-19 daily cases according to the pandemic phases and was compared with the timing of population lockdowns in Portugal. A sensitivity analysis was performed to understand the relationship between different parameter values and the threshold obtained. Results: An inverse relationship was found between the q estimate and daily cases in both simulations (correlations >0.70). The theoretical effectiveness thresholds for both simulations attained an alert phase positive predictive value of >70% and could have anticipated the need for additional measures in at least 4 days for the second and fourth lockdowns. Sensitivity analysis showed that only the IR and booster dose efficacy at inoculation significantly affected the q estimates. Conclusions: We demonstrated the impact of applying an effectiveness threshold for contact tracing on decision-making. Although only theoretical thresholds could be provided, their relationship with the number of confirmed cases and the prediction of pandemic phases shows the role as an indirect indicator of the efficacy of contact tracing.publishe

Photodeposition of silver on Zinc/Calcium ferrite nanoparticles: A contribution to efficient effluent remediation and catalyst reutilization

The efficient photodegradation of textile dyes is still a challenge, especially considering resistant azo dyes. In this work, zinc/calcium mixed ferrite nanoparticles prepared by the sol-gel method were coupled with silver by a photodeposition method to enhance the photocatalytic potency. The obtained zinc/calcium ferrites are mainly cubic-shaped nanoparticles sized 15 ± 2 nm determined from TEM and XRD and an optical bandgap of 1.6 eV. Magnetic measurements indicate a superparamagnetic behavior with saturation magnetizations of 44.22 emu/g and 27.97 emu/g, respectively, for Zn/Ca ferrite and Zn/Ca ferrite with photodeposited silver. The zinc/calcium ferrite nanoparticles with photodeposited silver showed efficient photodegradation of the textile azo dyes C.I. Reactive Blue 250 and C.I. Reactive Yellow 145. Subsequent cycles of the use of the photocatalyst indicate the possibility of magnetic recovery and reutilization without a significant loss of efficiency.This work was supported by the Portuguese Foundation for Science and Technology (FCT) in the framework of the Strategic Funding of CF-UM-UP (UIDB/04650/2020) and research project PTDC/QUI-QFI/28020/2017 (POCI-01-0145-FEDER-028020) funded by FCT, FEDER, PORTUGAL2020, and COMPETE2020

Arbustus unedo essence: morphological and genetic characterization of the strawberry tree of Castelo de Paiva

O medronheiro é um arbusto da região mediterrânica que pode ser encontrada por todo o país. Ao contrário do que verifica na região sul do país, no concelho de Castelo de Paiva é atribuída uma reduzida importância económica a esta espécie. Com o intuito de preservar e potenciar a produção desta espécie e contribuir para a dinamização da economia do concelho, procedeu-se à caracterização morfológica e genética de uma amostra da população de medronheiros de Castelo de Paiva. A caracterização morfológica e genética foi realizada para um total de 10 genótipos. Para tal recolheram-se 70 folhas aleatoriamente em cada árvore. Em 40 folhas mediu-se o comprimento, largura, comprimento do pedúnculo, peso fresco, peso seco e determinou-se a área foliar. Dos caracteres morfológicos analisados, aqueles que se revelaram mais úteis na distinção dos vários genótipos foram: comprimento do pedúnculo, peso fresco e peso seco. As restantes 30 folhas foram utilizadas para a caracterização genética. Esta caracterização foi realizada recorrendo a um marcador de DNA, ISSR. Os 5 primeiros exemplaresutilizados na técnica de ISSR demonstraram-se polimórficos. Os resultados da caracterização genética sugerem que a variabilidade genética na população é média a alta.The strawberry tree is a shrub native in the Mediterranean region and it can be found throughout Portugal. Unlike the case in the southern region of the country, in Castelo de Paiva a minor economic importance is given to this species. In order to preserve, to enhance the production of this species and to contribute to the boosting of the economy of the region, we proceeded to the characterization of a small sample population of this fruit tree of Castelo de Paiva in what concerns to its morphology and genetics. The morphological and genetic characterization was performed for a total of 10 genotypes. For this, 70 leaves were randomly collected from each tree. For 40 leaves, it was measured the length, the width, the peduncle length, the wet weight, the dry weight and determined the leaf area. Of the morphological characteristics analyzed, the ones that proved most useful in distinguishing the various genotypes were: the length peduncle, the wet weight and the dry weight. The remaining 30 leaves were used in the genetic characterization. This characterization was performed using a DNA marker, the ISSR. The 5 primers used in the ISSR technique proved to be polymorphic. The results from the genetic characterization suggest that variability in population genetics is medium to high

Building a Portuguese Coalition for Biodiversity Genomics

The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic drivers, such as climate change, invasive species, land use changes, overexploitation or pathogen (re)emergence. The inventory, characterization and study of biodiversity at inter- and intra-specific levels using genomics is crucial to promote its preservation and recovery by informing biodiversity conservation policies, management measures and research. The participation of researchers from Portuguese institutions in the European Reference Genome Atlas (ERGA) initiative, and its pilot effort to generate reference genomes for European biodiversity, has reinforced the establishment of Biogenome Portugal. This nascent institutional network will connect the national community of researchers in genomics. Here, we describe the Portuguese contribution to ERGA’s pilot effort, which will generate high-quality reference genomes of six species from Portugal that are endemic, iconic and/or endangered, and include plants, insects and vertebrates (fish, birds and mammals) from mainland Portugal or the Azores islands. In addition, we outline the objectives of Biogenome Portugal, which aims to (i) promote scientific collaboration, (ii) contribute to advanced training, (iii) stimulate the participation of institutions and researchers based in Portugal in international biodiversity genomics initiatives, and (iv) contribute to the transfer of knowledge to stakeholders and engaging the public to preserve biodiversity. This initiative will strengthen biodiversity genomics research in Portugal and fuel the genomic inventory of Portuguese eukaryotic species. Such efforts will be critical to the conservation of the country’s rich biodiversity and will contribute to ERGA’s goal of generating reference genomes for European species.info:eu-repo/semantics/publishedVersio

Building a Portuguese coalition for biodiversity genomics

The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic drivers, such as climate change, invasive species, land use changes, overexploitation, or pathogen (re)emergence. The inventory, characterisation, and study of biodiversity at inter- and intra-specific levels using genomics is crucial to promote its preservation and recovery by informing biodiversity conservation policies, management measures, and research. The participation of researchers from Portuguese institutions in the European Reference Genome Atlas (ERGA) initiative and its pilot effort to generate reference genomes for European biodiversity has reinforced the establishment of Biogenome Portugal. This nascent institutional network will connect the national community of researchers in genomics. Here, we describe the Portuguese contribution to ERGA’s pilot effort, which will generate high-quality reference genomes of six species from Portugal that are endemic, iconic, and/or endangered and include plants, insects, and vertebrates (fish, birds, and mammals) from mainland Portugal or the Azores islands. In addition, we outline the objectives of Biogenome Portugal, which aims to (i) promote scientific collaboration, (ii) contribute to advanced training, (iii) stimulate the participation of institutions and researchers based in Portugal in international biodiversity genomics initiatives, and (iv) contribute to the transfer of knowledge to stakeholders and engaging the public to preserve biodiversity. This initiative will strengthen biodiversity genomics research in Portugal and fuel the genomic inventory of Portuguese eukaryotic species. Such efforts will be critical to the conservation of the country’s rich biodiversity and will contribute to ERGA’s goal of generating reference genomes for European species.info:eu-repo/semantics/publishedVersio

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio