Masa-StarPU : estratégia com múltiplas políticas de escalonamento de tarefas para alinhamento de sequências com pruning

Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Exatas, Departamento de Ciência da Computação, 2020.A comparação de sequências biológicas é uma tarefa importante executada com frequência na análise genética de organismos. Algoritmos que realizam este procedimento utilizando um método exato possuem complexidade quadrática de tempo, demandando alto poder computacional e uso de técnicas de paralelização. Muitas soluções têm sido propostas para tratar este problema utilizam aceleradores como GPUs e FPGAs, porém poucas soluções utilizam apenas CPUs. O MASA é uma ferramenta multiplataforma específica para realizar a comparação de sequências biológicas. Uma de suas maiores virtudes é a otimização block pruning que realiza a poda da matriz de programação dinâmica em tempo de execução acelerando o processamento, porém introduzindo um problema de desbalanceamento de carga. O StarPU é uma ferramenta de programação paralela que possui implementações de diversas políticas de escalonamento dinâmico de tarefas. Neste trabalho, propomos e avaliamos o MASA-StarPU, uma ferramenta que utiliza a estrutura do MASA para realizar a comparação de sequências biológicas e as políticas do StarPU adequadas ao block pruning com o objetivo de eliminar o problema de desbalanceamento de carga. O MASA-StarPU foi testado em dois ambientes, avaliando pares de sequências de DNA cujos tamanhos variam entre 10 KBP (milhares de pares de bases) e 47 MBP (milhões de pares de bases), e as políticas de escalonamento de tarefas foram avaliadas em diferentes casos. Quando comparado com outras soluções da literatura que utilizam apenas CPU, o MASA-StarPU obteve o melhor resultado para todas as comparações. O MASA-StarPU atingiu o máximo de 18,4 GCUPS (bilhões de células atualizadas por segundo).The comparison of biological sequences is an important task performed frequently in the genetic analysis of organisms. Algorithms that perform this procedure using an exact method have quadratic time complexity, demanding high computational power and, consequently parallelization techniques. Many solutions have been proposed to address this problem using accelerators such as GPUs and FPGAs, but few solutions use only CPUs. MASA is a domain-specific platform for performing biological sequence comparison. One of its greatest virtues is the optimization block pruning. Which prunes the dynamic programming matrix at run time introducing load imbalance. StarPU is a generic parallel programming tool that provides several dynamic task scheduling policies. In this work, we propose and evaluate MASA-StarPU, a tool that uses the MASA structure to carry out the comparison of biological sequences and uses the StarPU policies to accelerate the computation. MASA-StarPU was tested in two environments, evaluating pairs of DNA sequences whose sizes vary between 10 KBP (thousands of base pairs) and 47 MBP (millions of pairs of bases), and multiple task scheduling policies were evaluated in different cases. When compared to other solutions in the literature that use only CPU, MASA-StarPU obtained the best result for all comparisons and reached a maximum of 18.4 GCUPS (billions of cells updated by second)

A influência da suplementação de coenzima Q10 sobre o esquema de tratamento medicamentoso de Hipertensão Arterial Sistêmica

Objetivo: Avaliar, através de revisão de literatura, qual o efeito do uso de CoQ10 sobre a dose dos medicamentos hipotensores, quando usados em conjunto. Método: Trata-se de um estudo de revisão da literatura. A busca de artigos foi realizada na base de dados Medline entre os meses de janeiro a março de 2023. Foram utilizados na pesquisa os descritores “hypertension” e “coenzyme Q10”. Resultados: Foram encontrados 17 estudos, mas atenderam aos critérios da pesquisa apenas 2 estudos; em uma publicação os autores descreveram o resultado da administração de CoQ10 a pacientes hipertensos e em outra compilou várias intervenções feitas com o uso de CoQ10 em diferentes cardiopatias. Conclusão: Os estudos que avaliaram a influência da CoQ10 na dose de anti-hipertensivos quando associada ao tratamento padrão mostraram necessidade de menor dose ou de menos medicamentos para controle pressórico

Development and validation of the MMCD score to predict kidney replacement therapy in COVID-19 patients

Abstract Background Acute kidney injury (AKI) is frequently associated with COVID-19, and the need for kidney replacement therapy (KRT) is considered an indicator of disease severity. This study aimed to develop a prognostic score for predicting the need for KRT in hospitalised COVID-19 patients, and to assess the incidence of AKI and KRT requirement. Methods This study is part of a multicentre cohort, the Brazilian COVID-19 Registry. A total of 5212 adult COVID-19 patients were included between March/2020 and September/2020. Variable selection was performed using generalised additive models (GAM), and least absolute shrinkage and selection operator (LASSO) regression was used for score derivation. Accuracy was assessed using the area under the receiver operating characteristic curve (AUC-ROC). Results The median age of the model-derivation cohort was 59 (IQR 47–70) years, 54.5% were men, 34.3% required ICU admission, 20.9% evolved with AKI, 9.3% required KRT, and 15.1% died during hospitalisation. The temporal validation cohort had similar age, sex, ICU admission, AKI, required KRT distribution and in-hospital mortality. The geographic validation cohort had similar age and sex; however, this cohort had higher rates of ICU admission, AKI, need for KRT and in-hospital mortality. Four predictors of the need for KRT were identified using GAM: need for mechanical ventilation, male sex, higher creatinine at hospital presentation and diabetes. The MMCD score had excellent discrimination in derivation (AUROC 0.929, 95% CI 0.918–0.939) and validation (temporal AUROC 0.927, 95% CI 0.911–0.941; geographic AUROC 0.819, 95% CI 0.792–0.845) cohorts and good overall performance (Brier score: 0.057, 0.056 and 0.122, respectively). The score is implemented in a freely available online risk calculator ( https://www.mmcdscore.com/ ). Conclusions The use of the MMCD score to predict the need for KRT may assist healthcare workers in identifying hospitalised COVID-19 patients who may require more intensive monitoring, and can be useful for resource allocation

12,500+ and counting: biodiversity of the Brazilian Pampa

Knowledge on biodiversity is fundamental for conservation strategies. The Brazilian Pampa region, located in subtropical southern Brazil, is neglected in terms of conservation, and knowledge of its biodiversity is fragmented. We aim to answer the question: how many, and which, species occur in the Brazilian Pampa? In a collaborative effort, we built species lists for plants, animals, bacteria, and fungi that occur in the Brazilian Pampa. We included information on distribution patterns, main habitat types, and conservation status. Our study resulted in referenced lists totaling 12,503 species (12,854 taxa, when considering infraspecific taxonomic categories [or units]). Vascular plants amount to 3,642 species (including 165 Pteridophytes), while algae have 2,046 species (2,378 taxa) and bryophytes 316 species (318 taxa). Fungi (incl. lichenized fungi) contains 1,141 species (1,144 taxa). Animals total 5,358 species (5,372 taxa). Among the latter, vertebrates comprise 1,136 species, while invertebrates are represented by 4,222 species. Our data indicate that, according to current knowledge, the Pampa holds approximately 9% of the Brazilian biodiversity in an area of little more than 2% of Brazil’s total land. The proportion of species restricted to the Brazilian Pampa is low (with few groups as exceptions), as it is part of a larger grassland ecoregion and in a transitional climatic setting. Our study yielded considerably higher species numbers than previously known for many species groups; for some, it provides the first published compilation. Further efforts are needed to increase knowledge in the Pampa and other regions of Brazil. Considering the strategic importance of biodiversity and its conservation, appropriate government policies are needed to fund studies on biodiversity, create accessible and constantly updated biodiversity databases, and consider biodiversity in school curricula and other outreach activities

AMAZONIA CAMTRAP: A data set of mammal, bird, and reptile species recorded with camera traps in the Amazon forest

The Amazon forest has the highest biodiversity on Earth. However, information on Amazonian vertebrate diversity is still deficient and scattered across the published, peer-reviewed, and gray literature and in unpublished raw data. Camera traps are an effective non-invasive method of surveying vertebrates, applicable to different scales of time and space. In this study, we organized and standardized camera trap records from different Amazon regions to compile the most extensive data set of inventories of mammal, bird, and reptile species ever assembled for the area. The complete data set comprises 154,123 records of 317 species (185 birds, 119 mammals, and 13 reptiles) gathered from surveys from the Amazonian portion of eight countries (Brazil, Bolivia, Colombia, Ecuador, French Guiana, Peru, Suriname, and Venezuela). The most frequently recorded species per taxa were: mammals: Cuniculus paca (11,907 records); birds: Pauxi tuberosa (3713 records); and reptiles: Tupinambis teguixin (716 records). The information detailed in this data paper opens up opportunities for new ecological studies at different spatial and temporal scales, allowing for a more accurate evaluation of the effects of habitat loss, fragmentation, climate change, and other human-mediated defaunation processes in one of the most important and threatened tropical environments in the world. The data set is not copyright restricted; please cite this data paper when using its data in publications and we also request that researchers and educators inform us of how they are using these data

NEOTROPICAL ALIEN MAMMALS: a data set of occurrence and abundance of alien mammals in the Neotropics

Biological invasion is one of the main threats to native biodiversity. For a species to become invasive, it must be voluntarily or involuntarily introduced by humans into a nonnative habitat. Mammals were among first taxa to be introduced worldwide for game, meat, and labor, yet the number of species introduced in the Neotropics remains unknown. In this data set, we make available occurrence and abundance data on mammal species that (1) transposed a geographical barrier and (2) were voluntarily or involuntarily introduced by humans into the Neotropics. Our data set is composed of 73,738 historical and current georeferenced records on alien mammal species of which around 96% correspond to occurrence data on 77 species belonging to eight orders and 26 families. Data cover 26 continental countries in the Neotropics, ranging from Mexico and its frontier regions (southern Florida and coastal-central Florida in the southeast United States) to Argentina, Paraguay, Chile, and Uruguay, and the 13 countries of Caribbean islands. Our data set also includes neotropical species (e.g., Callithrix sp., Myocastor coypus, Nasua nasua) considered alien in particular areas of Neotropics. The most numerous species in terms of records are from Bos sp. (n = 37,782), Sus scrofa (n = 6,730), and Canis familiaris (n = 10,084); 17 species were represented by only one record (e.g., Syncerus caffer, Cervus timorensis, Cervus unicolor, Canis latrans). Primates have the highest number of species in the data set (n = 20 species), partly because of uncertainties regarding taxonomic identification of the genera Callithrix, which includes the species Callithrix aurita, Callithrix flaviceps, Callithrix geoffroyi, Callithrix jacchus, Callithrix kuhlii, Callithrix penicillata, and their hybrids. This unique data set will be a valuable source of information on invasion risk assessments, biodiversity redistribution and conservation-related research. There are no copyright restrictions. Please cite this data paper when using the data in publications. We also request that researchers and teachers inform us on how they are using the data

NEOTROPICAL CARNIVORES: a data set on carnivore distribution in the Neotropics

Mammalian carnivores are considered a key group in maintaining ecological health and can indicate potential ecological integrity in landscapes where they occur. Carnivores also hold high conservation value and their habitat requirements can guide management and conservation plans. The order Carnivora has 84 species from 8 families in the Neotropical region: Canidae; Felidae; Mephitidae; Mustelidae; Otariidae; Phocidae; Procyonidae; and Ursidae. Herein, we include published and unpublished data on native terrestrial Neotropical carnivores (Canidae; Felidae; Mephitidae; Mustelidae; Procyonidae; and Ursidae). NEOTROPICAL CARNIVORES is a publicly available data set that includes 99,605 data entries from 35,511 unique georeferenced coordinates. Detection/non-detection and quantitative data were obtained from 1818 to 2018 by researchers, governmental agencies, non-governmental organizations, and private consultants. Data were collected using several methods including camera trapping, museum collections, roadkill, line transect, and opportunistic records. Literature (peer-reviewed and grey literature) from Portuguese, Spanish and English were incorporated in this compilation. Most of the data set consists of detection data entries (n = 79,343; 79.7%) but also includes non-detection data (n = 20,262; 20.3%). Of those, 43.3% also include count data (n = 43,151). The information available in NEOTROPICAL CARNIVORES will contribute to macroecological, ecological, and conservation questions in multiple spatio-temporal perspectives. As carnivores play key roles in trophic interactions, a better understanding of their distribution and habitat requirements are essential to establish conservation management plans and safeguard the future ecological health of Neotropical ecosystems. Our data paper, combined with other large-scale data sets, has great potential to clarify species distribution and related ecological processes within the Neotropics. There are no copyright restrictions and no restriction for using data from this data paper, as long as the data paper is cited as the source of the information used. We also request that users inform us of how they intend to use the data

NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics

Xenarthrans—anteaters, sloths, and armadillos—have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, 10 anteaters, and 6 sloths. Our data set includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the southern United States, Mexico, and Caribbean countries at the northern portion of the Neotropics, to the austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n = 5,941), and Cyclopes sp. have the fewest (n = 240). The armadillo species with the most data is Dasypus novemcinctus (n = 11,588), and the fewest data are recorded for Calyptophractus retusus (n = 33). With regard to sloth species, Bradypus variegatus has the most records (n = 962), and Bradypus pygmaeus has the fewest (n = 12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other data sets of Neotropical Series that will become available very soon (i.e., Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans data set. Please cite this data paper when using its data in publications. We also request that researchers and teachers inform us of how they are using these data

The surgical safety checklist and patient outcomes after surgery: a prospective observational cohort study, systematic review and meta-analysis

© 2017 British Journal of Anaesthesia Background: The surgical safety checklist is widely used to improve the quality of perioperative care. However, clinicians continue to debate the clinical effectiveness of this tool. Methods: Prospective analysis of data from the International Surgical Outcomes Study (ISOS), an international observational study of elective in-patient surgery, accompanied by a systematic review and meta-analysis of published literature. The exposure was surgical safety checklist use. The primary outcome was in-hospital mortality and the secondary outcome was postoperative complications. In the ISOS cohort, a multivariable multi-level generalized linear model was used to test associations. To further contextualise these findings, we included the results from the ISOS cohort in a meta-analysis. Results are reported as odds ratios (OR) with 95% confidence intervals. Results: We included 44 814 patients from 497 hospitals in 27 countries in the ISOS analysis. There were 40 245 (89.8%) patients exposed to the checklist, whilst 7508 (16.8%) sustained ≥1 postoperative complications and 207 (0.5%) died before hospital discharge. Checklist exposure was associated with reduced mortality [odds ratio (OR) 0.49 (0.32–0.77); P\u3c0.01], but no difference in complication rates [OR 1.02 (0.88–1.19); P=0.75]. In a systematic review, we screened 3732 records and identified 11 eligible studies of 453 292 patients including the ISOS cohort. Checklist exposure was associated with both reduced postoperative mortality [OR 0.75 (0.62–0.92); P\u3c0.01; I2=87%] and reduced complication rates [OR 0.73 (0.61–0.88); P\u3c0.01; I2=89%). Conclusions: Patients exposed to a surgical safety checklist experience better postoperative outcomes, but this could simply reflect wider quality of care in hospitals where checklist use is routine