Monitoring coastal benthic colonization of artificial substrates with the support of DNA metabarcoding approaches

Tese de doutoramento em Biology (ramo do conhecimento em Integrated Management of the Sea)The aptitude and potential of DNA metabarcoding for high-throughput monitoring of marine macrozoobenthos has been recently demonstrated. However, there are still significant challenges retarding the widespread implementation of DNA-based monitoring strategies in coastal ecosystems. In this thesis, we tested a DNA metabarcoding-based system, coupled with artificial substrates, for monitoring marine macrozoobenthic communities. To this end, we a) assembled a comprehensive reference library of DNA barcodes for marine macroinvertebrate species of Atlantic Iberia, and evaluated gaps in species coverage, b) investigated the efficiency of different marker loci (COI and 18S) and primer-pairs in macrozoobenthos detection, c) compared the performance of DNA metabarcoding and morphology in species detection, d) compared the impact of artificial substrates, made of different materials (slate, PVC and granite) and shapes (ARMS and ASMS), on the patterns of colonization of macrozoobenthos, and e) investigated the temporal and regional variation in macrozoobentos from artificial substrates deployed in NW Atlantic Iberia. Through the compilation of a comprehensive reference library, we recorded a large portion of taxa pending barcode coverage (63%) and signaled a high proportion of species with significant intraspecific divergence (16%). The high complementary of species detection among primers and markers (maximum 13% overlap) indicated that no single marker or primer can provide a complete diagnosis of the macrozoobenthos diversity. Until more extensive monitoring data is available, DNA metabarcoding and morphology should be used in combination, to avoid missing relevant taxa and obtain abundance estimates. Unlike substrate materials,substrate shape strongly affected the colonization of species. Taxonomic diversity varied between substrates, especially when comparing ARMS and ASMS (maximum overlap 30%). Important fractions of diversity may be overlooked if only one substrate is used for monitoring. Substrate deployment periods also displayed a strong influence in the colonization of macrozoobenthos, signaling the importance of this factor for the monitoring design. We conclude that DNA metabarcoding combined with artificial substrates (especially through the combination of ARMS and ASMS) have great potential to be used in comprehensive coastal biomonitoring programs targeting macroinvertebrate biodiversity.A capacidade e o potencial do DNA metabarcoding para a monitorização de alto rendimento do macrozoobentos marinho têm sido demonstrados em estudos relativamente recentes. Contudo, existem ainda desafios significativos que têem retardado a sua implementação generalizada na monitorização de ecossistemas costeiros. Nesta tese, testamos uma abordagem de monitorização de comunidades macrozoobentónicas marinhas que conjuga DNA metabarcoding com substratos artificiais. Para esse feito, a) criámos uma biblioteca de referência de DNA barcodes para espécies macrozoobentónicas marinhas da Ibéria Atlântica, e avaliámos as lacunas na cobertura de espécies, b) investigámos a eficiência de diferentes marcadores moleculares (COI e 18S) e de primers na deteção de macrozoobentos, c) comparámos o desempenho entre morfologia e DNA metabarcoding na deteção de espécies, d) comparámos o impacto do material (ardósia, PVC e granito) e da forma (ARMS e ASMS) dos substratos artificiais nos padrões de colonização de macrozoobentos, e e) investigámos variações temporais e regionais na colonização de macrozoobentos em substratos artificiais implantados no noroeste Ibero Atlântico. Através da compilação da biblioteca de referência registou-se uma porção elevada de taxa sem DNA barcode (63%) e sinalizou-se uma grande proporção de espécies com divergência intraespecífica significativa (16%). A elevada complementaridade entre primers e marcadores na deteção de espécies (máximo 13% sobreposição), indicou que nenhum marcador ou primer consegue fornecer individualmente um diagnóstico completo da diversidade macrozoobentónica. Enquanto não estiveram disponíveis dados de monitorização mais sistematizados, tanto o DNA metabarcoding como a morfologia deverão ser utilizados, de modo a não discurar de taxa relevantes, e a obter estimativas de abundância. Contrariamente ao material, a forma dos substratos afetou fortemente a colonização de espécies. A diversidade taxonómica variou entre todos os substratos, especialmente ao comparar ARMS e ASMS (máximo 30% sobreposição). Frações importantes de diversidade poderão ser subestimadas se for apenas usado um substrato para monitorização. Os períodos de submersão dos substratos influenciaram fortemente na colonização de macrozoobenthos, evidenciando a importância deste fator no desenho da monitorização. Concluímos que o DNA metabarcoding conjugado com substratos artificiais (nomeadamente ARMS e ASMS) tem um potencial elevado para aplicação em programas de biomonitorização costeira que visem a biodiversidade de macroinvertebrados.I am grateful to the Portuguese Foundation for Science and Technology (FCT) for supporting my PhD grant PD/BD/127994/2016, hosted by the University of Minho (Portugal) and the University of Vigo (Spain), in the scope of the PhD programme in Marine Science Technology and Management (Do*Mar). I would also like to thank the project “The NextSea: Next generation monitoring of coastal ecosystems in a scenario of global change” (NORTE-01-0145-FEDER-000032), supported by NORTE 2020 (Norte Portugal Regional Operational Programme), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and the “Contrato-Programa” UIDB/04050/2020 funded by national funds through the FCT I.P. (Fundação para a Ciência e Tecnologia) for supporting this work

Catálogo Taxonômico da Fauna do Brasil: setting the baseline knowledge on the animal diversity in Brazil

The limited temporal completeness and taxonomic accuracy of species lists, made available in a traditional manner in scientific publications, has always represented a problem. These lists are invariably limited to a few taxonomic groups and do not represent up-to-date knowledge of all species and classifications. In this context, the Brazilian megadiverse fauna is no exception, and the Catálogo Taxonômico da Fauna do Brasil (CTFB) (http://fauna.jbrj.gov.br/), made public in 2015, represents a database on biodiversity anchored on a list of valid and expertly recognized scientific names of animals in Brazil. The CTFB is updated in near real time by a team of more than 800 specialists. By January 1, 2024, the CTFB compiled 133,691 nominal species, with 125,138 that were considered valid. Most of the valid species were arthropods (82.3%, with more than 102,000 species) and chordates (7.69%, with over 11,000 species). These taxa were followed by a cluster composed of Mollusca (3,567 species), Platyhelminthes (2,292 species), Annelida (1,833 species), and Nematoda (1,447 species). All remaining groups had less than 1,000 species reported in Brazil, with Cnidaria (831 species), Porifera (628 species), Rotifera (606 species), and Bryozoa (520 species) representing those with more than 500 species. Analysis of the CTFB database can facilitate and direct efforts towards the discovery of new species in Brazil, but it is also fundamental in providing the best available list of valid nominal species to users, including those in science, health, conservation efforts, and any initiative involving animals. The importance of the CTFB is evidenced by the elevated number of citations in the scientific literature in diverse areas of biology, law, anthropology, education, forensic science, and veterinary science, among others

Relações entre profissionais de saúde e usuários durante as práticas em saúde Relationships between health professionals and users throughout health care practices

Apresenta-se uma revisão integrativa sobre estudos que abordam as relações entre profissionais de saúde e usuários durante as práticas em saúde. Objetivou-se identificar os aspectos pesquisados no cotidiano dos serviços acerca dessas relações. A coleta foi realizada nas bases Lilacs e Pubmed segundo os descritores: acolhimento; relações profissional-família; relações profissional-paciente; humanização da assistência; e a palavra 'vínculo' associada ao descritor Sistema Único de Saúde. Selecionaram-se 290 estudos publicados entre 1990 e 2010. Por meio da análise temática, foram criados cinco núcleos de sentido: a relevância da confiança na relação profissional-usuário; sentimentos e sentidos na prática do cuidado; a importância da comunicação nos serviços de saúde; modo de organização das práticas em saúde; e (des)colonialismo. Identificou-se que as relações estabelecidas nas práticas de saúde têm uma dimensão transformadora. No entanto, permanece o desafio de humanizar os serviços de saúde. A enfermagem se destaca na produção do conhecimento nessa temática.<br>This article presents an integrative review about studies that address the relationships between health professionals and users in health care practices. It aimed to identify aspects that were researched on the daily life of the services concerning such relationships. Data were collected from the Lilacs and Pubmed databases based on these descriptors: user embracement; professionalfamily relations; professionalpatient relations; humanization of the care; and the bonding word associated to the Single Health System descriptor. Two hundred and ninety studies, published from 1990 to 2010, were selected. Through thematic analyses, five meaning cores were created: the relevance of the confidence in the professionaluser relationship; feelings and senses in the health care practice; the importance of communications in health care services; ways to organize health care practices and (de)colonialism. It was found that relationships established in health care practices have a transformative dimension. However, the challenge to humanize health care services remains. Nursing stands out in the production of knowledge on such theme

Núcleos de Ensino da Unesp: artigos 2007

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Brazilian Flora 2020: Leveraging the power of a collaborative scientific network

International audienceThe shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiversity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxonomic impediment to biodiversity research and conservation planning. The taxonomic impediment and the biodiversity crisis are widely recognized, highlighting the urgent need for reliable taxonomic data. Over the past decade, numerous countries worldwide have devoted considerable effort to Target 1 of the Global Strategy for Plant Conservation (GSPC), which called for the preparation of a working list of all known plant species by 2010 and an online world Flora by 2020. Brazil is a megadiverse country, home to more of the world's known plant species than any other country. Despite that, Flora Brasiliensis, concluded in 1906, was the last comprehensive treatment of the Brazilian flora. The lack of accurate estimates of the number of species of algae, fungi, and plants occurring in Brazil contributes to the prevailing taxonomic impediment and delays progress towards the GSPC targets. Over the past 12 years, a legion of taxonomists motivated to meet Target 1 of the GSPC, worked together to gather and integrate knowledge on the algal, plant, and fungal diversity of Brazil. Overall, a team of about 980 taxonomists joined efforts in a highly collaborative project that used cybertaxonomy to prepare an updated Flora of Brazil, showing the power of scientific collaboration to reach ambitious goals. This paper presents an overview of the Brazilian Flora 2020 and provides taxonomic and spatial updates on the algae, fungi, and plants found in one of the world's most biodiverse countries. We further identify collection gaps and summarize future goals that extend beyond 2020. Our results show that Brazil is home to 46,975 native species of algae, fungi, and plants, of which 19,669 are endemic to the country. The data compiled to date suggests that the Atlantic Rainforest might be the most diverse Brazilian domain for all plant groups except gymnosperms, which are most diverse in the Amazon. However, scientific knowledge of Brazilian diversity is still unequally distributed, with the Atlantic Rainforest and the Cerrado being the most intensively sampled and studied biomes in the country. In times of “scientific reductionism”, with botanical and mycological sciences suffering pervasive depreciation in recent decades, the first online Flora of Brazil 2020 significantly enhanced the quality and quantity of taxonomic data available for algae, fungi, and plants from Brazil. This project also made all the information freely available online, providing a firm foundation for future research and for the management, conservation, and sustainable use of the Brazilian funga and flora

Global variation in postoperative mortality and complications after cancer surgery: a multicentre, prospective cohort study in 82 countries

© 2021 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY-NC-ND 4.0 licenseBackground: 80% of individuals with cancer will require a surgical procedure, yet little comparative data exist on early outcomes in low-income and middle-income countries (LMICs). We compared postoperative outcomes in breast, colorectal, and gastric cancer surgery in hospitals worldwide, focusing on the effect of disease stage and complications on postoperative mortality. Methods: This was a multicentre, international prospective cohort study of consecutive adult patients undergoing surgery for primary breast, colorectal, or gastric cancer requiring a skin incision done under general or neuraxial anaesthesia. The primary outcome was death or major complication within 30 days of surgery. Multilevel logistic regression determined relationships within three-level nested models of patients within hospitals and countries. Hospital-level infrastructure effects were explored with three-way mediation analyses. This study was registered with ClinicalTrials.gov, NCT03471494. Findings: Between April 1, 2018, and Jan 31, 2019, we enrolled 15 958 patients from 428 hospitals in 82 countries (high income 9106 patients, 31 countries; upper-middle income 2721 patients, 23 countries; or lower-middle income 4131 patients, 28 countries). Patients in LMICs presented with more advanced disease compared with patients in high-income countries. 30-day mortality was higher for gastric cancer in low-income or lower-middle-income countries (adjusted odds ratio 3·72, 95% CI 1·70–8·16) and for colorectal cancer in low-income or lower-middle-income countries (4·59, 2·39–8·80) and upper-middle-income countries (2·06, 1·11–3·83). No difference in 30-day mortality was seen in breast cancer. The proportion of patients who died after a major complication was greatest in low-income or lower-middle-income countries (6·15, 3·26–11·59) and upper-middle-income countries (3·89, 2·08–7·29). Postoperative death after complications was partly explained by patient factors (60%) and partly by hospital or country (40%). The absence of consistently available postoperative care facilities was associated with seven to 10 more deaths per 100 major complications in LMICs. Cancer stage alone explained little of the early variation in mortality or postoperative complications. Interpretation: Higher levels of mortality after cancer surgery in LMICs was not fully explained by later presentation of disease. The capacity to rescue patients from surgical complications is a tangible opportunity for meaningful intervention. Early death after cancer surgery might be reduced by policies focusing on strengthening perioperative care systems to detect and intervene in common complications. Funding: National Institute for Health Research Global Health Research Unit

Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study

© 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 licenseBackground: Early death after cancer surgery is higher in low-income and middle-income countries (LMICs) compared with in high-income countries, yet the impact of facility characteristics on early postoperative outcomes is unknown. The aim of this study was to examine the association between hospital infrastructure, resource availability, and processes on early outcomes after cancer surgery worldwide. Methods: A multimethods analysis was performed as part of the GlobalSurg 3 study—a multicentre, international, prospective cohort study of patients who had surgery for breast, colorectal, or gastric cancer. The primary outcomes were 30-day mortality and 30-day major complication rates. Potentially beneficial hospital facilities were identified by variable selection to select those associated with 30-day mortality. Adjusted outcomes were determined using generalised estimating equations to account for patient characteristics and country-income group, with population stratification by hospital. Findings: Between April 1, 2018, and April 23, 2019, facility-level data were collected for 9685 patients across 238 hospitals in 66 countries (91 hospitals in 20 high-income countries; 57 hospitals in 19 upper-middle-income countries; and 90 hospitals in 27 low-income to lower-middle-income countries). The availability of five hospital facilities was inversely associated with mortality: ultrasound, CT scanner, critical care unit, opioid analgesia, and oncologist. After adjustment for case-mix and country income group, hospitals with three or fewer of these facilities (62 hospitals, 1294 patients) had higher mortality compared with those with four or five (adjusted odds ratio [OR] 3·85 [95% CI 2·58–5·75]; p<0·0001), with excess mortality predominantly explained by a limited capacity to rescue following the development of major complications (63·0% vs 82·7%; OR 0·35 [0·23–0·53]; p<0·0001). Across LMICs, improvements in hospital facilities would prevent one to three deaths for every 100 patients undergoing surgery for cancer. Interpretation: Hospitals with higher levels of infrastructure and resources have better outcomes after cancer surgery, independent of country income. Without urgent strengthening of hospital infrastructure and resources, the reductions in cancer-associated mortality associated with improved access will not be realised. Funding: National Institute for Health and Care Research