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

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

ATLANTIC-PRIMATES: a dataset of communities and occurrences of primates in the Atlantic Forests of South America

Primates play an important role in ecosystem functioning and offer critical insights into human evolution, biology, behavior, and emerging infectious diseases. There are 26 primate species in the Atlantic Forests of South America, 19 of them endemic. We compiled a dataset of 5,472 georeferenced locations of 26 native and 1 introduced primate species, as hybrids in the genera Callithrix and Alouatta. The dataset includes 700 primate communities, 8,121 single species occurrences and 714 estimates of primate population sizes, covering most natural forest types of the tropical and subtropical Atlantic Forest of Brazil, Paraguay and Argentina and some other biomes. On average, primate communities of the Atlantic Forest harbor 2 ± 1 species (range = 1–6). However, about 40% of primate communities contain only one species. Alouatta guariba (N = 2,188 records) and Sapajus nigritus (N = 1,127) were the species with the most records. Callicebus barbarabrownae (N = 35), Leontopithecus caissara (N = 38), and Sapajus libidinosus (N = 41) were the species with the least records. Recorded primate densities varied from 0.004 individuals/km 2 (Alouatta guariba at Fragmento do Bugre, Paraná, Brazil) to 400 individuals/km 2 (Alouatta caraya in Santiago, Rio Grande do Sul, Brazil). Our dataset reflects disparity between the numerous primate census conducted in the Atlantic Forest, in contrast to the scarcity of estimates of population sizes and densities. With these data, researchers can develop different macroecological and regional level studies, focusing on communities, populations, species co-occurrence and distribution patterns. Moreover, the data can also be used to assess the consequences of fragmentation, defaunation, and disease outbreaks on different ecological processes, such as trophic cascades, species invasion or extinction, and community dynamics. There are no copyright restrictions. Please cite this Data Paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data. © 2018 by the The Authors. Ecology © 2018 The Ecological Society of Americ

ATLANTIC EPIPHYTES: a data set of vascular and non-vascular epiphyte plants and lichens from the Atlantic Forest

Epiphytes are hyper-diverse and one of the frequently undervalued life forms in plant surveys and biodiversity inventories. Epiphytes of the Atlantic Forest, one of the most endangered ecosystems in the world, have high endemism and radiated recently in the Pliocene. We aimed to (1) compile an extensive Atlantic Forest data set on vascular, non-vascular plants (including hemiepiphytes), and lichen epiphyte species occurrence and abundance; (2) describe the epiphyte distribution in the Atlantic Forest, in order to indicate future sampling efforts. Our work presents the first epiphyte data set with information on abundance and occurrence of epiphyte phorophyte species. All data compiled here come from three main sources provided by the authors: published sources (comprising peer-reviewed articles, books, and theses), unpublished data, and herbarium data. We compiled a data set composed of 2,095 species, from 89,270 holo/hemiepiphyte records, in the Atlantic Forest of Brazil, Argentina, Paraguay, and Uruguay, recorded from 1824 to early 2018. Most of the records were from qualitative data (occurrence only, 88%), well distributed throughout the Atlantic Forest. For quantitative records, the most common sampling method was individual trees (71%), followed by plot sampling (19%), and transect sampling (10%). Angiosperms (81%) were the most frequently registered group, and Bromeliaceae and Orchidaceae were the families with the greatest number of records (27,272 and 21,945, respectively). Ferns and Lycophytes presented fewer records than Angiosperms, and Polypodiaceae were the most recorded family, and more concentrated in the Southern and Southeastern regions. Data on non-vascular plants and lichens were scarce, with a few disjunct records concentrated in the Northeastern region of the Atlantic Forest. For all non-vascular plant records, Lejeuneaceae, a family of liverworts, was the most recorded family. We hope that our effort to organize scattered epiphyte data help advance the knowledge of epiphyte ecology, as well as our understanding of macroecological and biogeographical patterns in the Atlantic Forest. No copyright restrictions are associated with the data set. Please cite this Ecology Data Paper if the data are used in publication and teaching events. © 2019 The Authors. Ecology © 2019 The Ecological Society of Americ

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 understanding 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,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 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 underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities 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 organism 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 neglected 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 lost

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Disinfection of intermediate level of rigid endoscope through prior cleaning with detergent followed by ethyl alcohol 70% w/v: standard operating protocol

INTRODUÇÃO: A limpeza prévia de endoscópios rígidos (ER) seguida de desinfecção de nível intermediário com álcool etílico a 70% p/v após o exame de endoscopia nasal é uma prática adotada em muitos serviços de otorrinolaringologia. A literatura atual, no entanto, recomenda a esterilização ou desinfecção de alto nível como o método de descontaminação mais aceito para produtos para saúde classificados como semicríticos. No entanto, há que se fazer distinção entre equipamentos de alta complexidade e sua invasividade como os endoscópios flexíveis com lumens longos e estreitos utilizados na endoscopia digestiva, daqueles de conformação simples sem lumens de baixa invasividade como os endoscópios rígidos utilizados em otorrinolaringologia. OBJETIVO: Avaliar a segurança da desinfecção de nível intermediário com álcool etílico 70% p/v, após limpeza prévia dos endoscópios rígidos utilizados em procedimentos clínicos de endoscopia nasal considerando a carga microbiológica recuperada após o uso. MÉTODO: Imediatamente após a realização do exame, uma gaze úmida foi utilizada para o arraste da carga biológica do endoscópio rígido, gerando as amostras do Controle Positivo e, após a aplicação do POP, um novo arraste para constituir as amostras do Grupo Experimental. Estas gazes foram inicialmente submetidas à sonicação e agitação imersas em soro fisiológico e em seguida a solução foi submetida a uma técnica de extração de carga microbiológica por filtragem por meio de uma Membrana de Celulose de 0,22um de poro que foi, em seguida, semeada nos meios de ágar Sangue, Chocolate, Sabouraud, Löwenstein-Jensen e Tioglicolato. Estes meios ficaram incubados em estufa a 37ºC ± 2ºC e avaliados, no máximo, até por 60 dias conforme o perfil de crescimento dos diferentes microrganismos de interesse; foram analisados de maneira quantitativa e qualitativa para identificação e classificação dos micro-organismos recuperados após as semeaduras. RESULTADO: Os resultados da análise estatística evidenciaram diferença significativa entre Controle Positivo e Grupo Experimental quando comparados em relação à presença de Streptococcus coagulase negativa (p < 0,001), Bacillus spp (p < 0,001) e Staphylococcus aureus (p=0,001). No Controle Positivo, foram encontradas presença desses micro-organismos respectivamente na seguinte frequência: 63,2%, 28,9% e 28,9%, enquanto que, no Grupo Experimental, não foi houve recuperação microbiana alguma. CONCLUSÃO: Os resultados desta pesquisa demonstram a eficiência, na prática diária, da desinfecção de nível intermediário dos endoscópios utilizados na otorrinolaringologia por meio da fricção com álcool etílico 70% p/v por 90 segundos, com protocolo de limpeza préviaINTRODUCTION: Prior cleaning of rigid endoscopes (REs) followed by intermediate-level disinfection with 70% ethyl alcohol (w/v) after nasal endoscopy is a common practice in many otolaryngology services. Current literature, in turn, recommends high-level sterilization or disinfection as the most accepted decontamination method for health products classified as semi-critical. However, it is necessary to distinguish highly complex equipment according to their invasiveness, e.g., flexible endoscopes with long and narrow lumens used in digestive endoscopy and those with a simple conformation without lumens of low invasiveness, such as rigid endoscopes used in otorhinolaryngology. OBJECTIVE: To evaluate the safety of intermediate-level disinfection with 70% ethyl alcohol (w/v) after cleaning of REs used in clinical procedures of nasal endoscopy considering the microbiological load recovered after use. METHOD: Immediately after the test, a wet gauze was used to drag the biological load from the RE, generating positive control samples; after applying POP, dragging was carried out again to generate samples of the experimental group. These gasses were initially subjected to sonication and shaking while immersed in physiological saline; the solution was then subjected to the microbiological loading technique by filtration through a 0.22-um pore cellulose membrane and then cultivated on blood, chocolate, Sabouraud, Löwenstein-Jensen, and thioglycolate agar media. These media were incubated at 37ºC ± 2ºC and evaluated for up to 60 days, according to the growth profile of the different microorganisms of interest. A quantitative and qualitative analysis was performed for the identification and classification of microorganisms recovered after cultivation. RESULTS: The results of statistical analysis showed a significant difference between the positive control and experimental groups for the presence of coagulase-negative Streptococcus (p < 0.001), Bacillus spp (p < 0.001), and Staphylococcus aureus (p=0.001). In the positive control group, these microorganisms were found in the following proportions: 63.2%, 28.9%, and 28.9%, respectively, whereas in the experimental group, no microorganisms were recovered. CONCLUSION: The results of this study demonstrate the efficiency of the daily practice of intermediate-level disinfection of endoscopes used in otorhinolaryngology by means of treatment with 70% ethyl alcohol (w/v) for 90 seconds, using a previous cleaning protoco

Growth dynamics of young trees of Araucaria angustifolia and Pinus taeda Dinâmica de crescimento de plantios jovens de Araucaria angustifolia e Pinus taeda

&lt;p&gt;Este estudo objetivou investigar o ritmo de crescimento mensal de plantios jovens de Araucaria angustifolia (Bert.) O. Kuntze e Pinus taeda L., ao longo do ano vegetativo, e estabelecer suas correlações com variáveis climáticas. Foram feitas medições mensais de diâmetro e altura total em dois plantios de P. taeda e um de A. angustifolia. Matrizes de correlação entre os incrementos correntes mensais e as variáveis climáticas indicaram que o fotoperíodo e as temperaturas mínima, média e máxima são as que mais afetaram o desenvolvimento de P. taeda, enquanto que temperaturas mínima e média foram as que exerceram maior efeito sobre o crescimento de A. angustifolia.&lt;/p&gt;&lt;p&gt; &lt;/p&gt;&lt;p&gt;doi: 10.4336/2010.pfb.30.62.165&lt;/p&gt;&lt;p&gt;The objective of this research was to investigate the monthly growth rhythm of young trees of Araucaria angustifolia and Pinus taeda throughout the vegetative year and to establish its correlation with climatic variables. Monthly measurements of diameter and total height were carried out in one stand of A. angustifolia and two of Pinus taeda. Correlation matrices among the current monthly increments and the climatic variables indicated that the development of Pinus taeda is mostly affected by photoperiod and by minimum, average, and maximum temperatures, while A. angustifolia growth is affected mostly by minimum and average temperatures.&lt;/p&gt;&lt;p&gt; &lt;/p&gt;&lt;p&gt;doi: 10.4336/2010.pfb.30.62.165&lt;/p&gt