ENTRE SONHOS E DEVANEIOS: O ESPAÇO COMO COMPONENTE FUNDAMENTAL NAS NARRATIVAS FANTÁSTICAS

Este artigo objetiva analisar a importância do espaço na construção de sentidos na narrativa fantástica, tomando como exemplo o conto Onírico de Caio Fernando Abreu. A partir da análise desse conto, podemos ver como o autor transporta para o seu texto questões que afetam o sujeito pós-moderno, especialmente as relacionadas às relações humanas muitas vezes marcadas por laços frágeis e inconsistentes. Dessa forma, nesta narrativa, o fantástico e o insólito atuam para representar a realidade cotidiana e a fragilidade das relações humanas. Nosso suporte teórico será desenvolvido a partir das ideias de Roas (2012), Ceserani (2006), Gama-Khalil (2012), Borges Filho (2007), Brandão (2013), entre outros

Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics

Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomicand metatranscriptomic-based analyses of a large composting operation in the Sao Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 degrees C to 75 degrees C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem. The time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the processand that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin. Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Provost's Office for Research of the University of Sao PauloCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Univ Sao Paulo, Inst Quim, Dept Bioquim, Sao Paulo, BrazilUniv Sao Paulo, Programa Pos Graduacao Interunidades Bioinformat, Sao Paulo, BrazilUniv Sao Paulo, Escola Artes Ciencias & Humanidades, Sao Paulo, Brazil|Fundacao Parque Zool Sao Paulo, Sao Paulo, BrazilUniv Fed Sao Paulo, Dept Ciencias Biol, Sao Paulo, BrazilBiocomplex Inst Virginia, Blacksburg, VA USADepartamento de Ciências Biológicas, Universidade Federal de São Paulo, São Paulo, BrazilFAPESP: 2011/50870-6Web of Scienc

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

Familial hypercholesterolaemia in children and adolescents from 48 countries: a cross-sectional study

Background: Approximately 450 000 children are born with familial hypercholesterolaemia worldwide every year, yet only 2·1% of adults with familial hypercholesterolaemia were diagnosed before age 18 years via current diagnostic approaches, which are derived from observations in adults. We aimed to characterise children and adolescents with heterozygous familial hypercholesterolaemia (HeFH) and understand current approaches to the identification and management of familial hypercholesterolaemia to inform future public health strategies. Methods: For this cross-sectional study, we assessed children and adolescents younger than 18 years with a clinical or genetic diagnosis of HeFH at the time of entry into the Familial Hypercholesterolaemia Studies Collaboration (FHSC) registry between Oct 1, 2015, and Jan 31, 2021. Data in the registry were collected from 55 regional or national registries in 48 countries. Diagnoses relying on self-reported history of familial hypercholesterolaemia and suspected secondary hypercholesterolaemia were excluded from the registry; people with untreated LDL cholesterol (LDL-C) of at least 13·0 mmol/L were excluded from this study. Data were assessed overall and by WHO region, World Bank country income status, age, diagnostic criteria, and index-case status. The main outcome of this study was to assess current identification and management of children and adolescents with familial hypercholesterolaemia. Findings: Of 63 093 individuals in the FHSC registry, 11 848 (18·8%) were children or adolescents younger than 18 years with HeFH and were included in this study; 5756 (50·2%) of 11 476 included individuals were female and 5720 (49·8%) were male. Sex data were missing for 372 (3·1%) of 11 848 individuals. Median age at registry entry was 9·6 years (IQR 5·8-13·2). 10 099 (89·9%) of 11 235 included individuals had a final genetically confirmed diagnosis of familial hypercholesterolaemia and 1136 (10·1%) had a clinical diagnosis. Genetically confirmed diagnosis data or clinical diagnosis data were missing for 613 (5·2%) of 11 848 individuals. Genetic diagnosis was more common in children and adolescents from high-income countries (9427 [92·4%] of 10 202) than in children and adolescents from non-high-income countries (199 [48·0%] of 415). 3414 (31·6%) of 10 804 children or adolescents were index cases. Familial-hypercholesterolaemia-related physical signs, cardiovascular risk factors, and cardiovascular disease were uncommon, but were more common in non-high-income countries. 7557 (72·4%) of 10 428 included children or adolescents were not taking lipid-lowering medication (LLM) and had a median LDL-C of 5·00 mmol/L (IQR 4·05-6·08). Compared with genetic diagnosis, the use of unadapted clinical criteria intended for use in adults and reliant on more extreme phenotypes could result in 50-75% of children and adolescents with familial hypercholesterolaemia not being identified. Interpretation: Clinical characteristics observed in adults with familial hypercholesterolaemia are uncommon in children and adolescents with familial hypercholesterolaemia, hence detection in this age group relies on measurement of LDL-C and genetic confirmation. Where genetic testing is unavailable, increased availability and use of LDL-C measurements in the first few years of life could help reduce the current gap between prevalence and detection, enabling increased use of combination LLM to reach recommended LDL-C targets early in life

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

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

Identification of variants in the DNA sequence of patients deficient in DNA repair processes

Apesar de altamente estável, o DNA sofre milhares de alterações em sua estrutura diariamente, sejam essas espontâneas ou pela exposição a agentes mutagênicos. A maior parte dessas alterações é prontamente removida por um conjunto de eventos de reparo de DNA. A via de reparo por excisão de nucleotídeos (NER) é a mais versátil e flexível lidando com uma variedade de lesões que podem gerar distorções das hélices do DNA. Esses danos resultam em alterações características que, caso não reparadas, podem gerar mutações ou morte celular e, consequentemente, câncer e envelhecimento. Algumas síndromes, nas quais os pacientes são sensíveis à luz solar, estão relacionadas à deficiência no processo de NER, como a Xeroderma Pigmentosum (XP), síndrome de Cockayne (CS) e Tricotiodistrofia (TTD). Indivíduos brasileiros, incluindo pacientes com diagnóstico clínico de XP e membros das famílias, passaram por um processo in silico para a identificação variantes em genes relacionados aos processos de reparo do DNA após o sequenciamento do DNA por plataformas de nova geração (NGS: plataforma ABI 5500XL SOLiD e MiSeq Illumina) e análises de Bioinformática. Para cada paciente, foram selecionados os melhores valores de parâmetros para se realizar a busca por variantes considerando a qualidade de alinhamento e a taxa de cobertura das bases alvo. SNPs já depositados no banco de dados do projeto 1000genomes foram removidos de nossos dados. O restante das variantes foi analisado para encontrar potenciais candidatos que poderiam explicar o diagnóstico clínico do paciente. Em muitas amostras foi possível determinar pelo menos uma variante (mutação) com uma elevada possibilidade de ser responsável pelos sintomas XP. Para alguns pacientes, a má qualidade do sequenciamento ou eventos não esclarecidos durante este, dificultou a identificação de candidatos à mutação patogênica. Potenciais mutações não sinônimas foram analisadas com os programas SIFT e PROVEAN, que identificaram a potencial capacidade deletéria da alteração de aminoácido na proteína. Finalmente, foi desenvolvida uma interface de domínio público amigável, a Human Variantes do Finder Interface (http://www.varfinderhg.com.br), que visa facilitar a identificação de variantes em dados gerados por NGS.Although highly stable, DNA molecule undergoes thousands of damage in its structure every day, due to spontaneous lesions or exposure to various mutagens. Most of these lesions are readily removed by a number of cellular DNA repair processes. The process of nucleotide excision repair (NER) is the most versatile and flexible dealing with a variety of lesions that can lead to distortions of the DNA strands. Ultraviolet irradiation induced DNA damage are the main substrates for NER. These DNA damage, if not repaired, can generate mutations or cell death causing several diseases, including cancer and aging. Some syndromes, sensitive to sunlight, are related to deficiencies in the NER process, such as Xeroderma Pigmentosum (XP), Cockayne syndrome (CS) and Trichothiodystrophy (TTD). Brazilian individuals, including patients with clinical diagnosis of XP and family members, went through in silico process for the identification of variants in genes related to DNA repair processes after DNA sequencing by next generation sequencing (NGS in the platforms ABI 5500XL SOLiD and MiSeq Illumina) and dedicated Bioinformatics pipelines. For each patient the best search pattern of variant calling was used considering the alignment quality and coverage rate of bases in target. SNPs already deposited at the 1000genomes project database were removed from the data. The remaining variants were analyzed to find potential candidates that could explain the clinical diagnosis. In many samples, it was possible to determine at least one variant (mutation) with a high possibility of being responsible for the clinical XP. For some patients, the poor quality of the sequencing or unclear events during sequencing hampered the identification of clear mutation candidates. Potential nonsynonymous mutations were analyzed with SIFT and PROVEAN softwares, which identified the potential deleterious capacity of the amino acid change in the protein. Finally, we developed a user-friendly public domain interface, the Human Variants Finder Interface (http://www.varfinderhg.com.br), which, we expect, will facilitate the identification of variants in data generated by NGS

Recuperação de MAGs de alta qualidade em dados metagenômicos tempo seriado e desenvolvimento de FixAME: uma ferramenta auxiliar de curadoria de erros de montagem genômica

On a daily based, there is a huge amount of biological data being generated that brings deeper insight into our world. This exponential growth of information has brought many challenges, especially when dealing with metagenomic data. Thousands of metagenomic-assembled genomes (MAG) are recovered annually, and many methods try to achieve the best output possible through assembly and binning approaches. But the question that every time is more frequent is: Are these MAGs reliable? The importance of having good quality data is undeniable. Retrieving reliable and complete, or nearly-complete MAGs, provides important data for further analysis and research purposes. Within this scenario, we\'d like to know if it is possible to improve the MAGs metrics quality when compared to the state-of-the art in time series data. In addition, we\'d like to develop a tool capable of locating and fixing assembly errors, thereby assisting in genomic curation. Here, we describe an approach of MAGs recovery from time-serial data called the \"screening method\", drastically reducing the recovery from potentially unreliable MAGs. In addition, we present FixAME, a tool capable of helping curate assembled sequences of metagenome, single genome, a set of bins, phages, archaea, or any organism that contains single double-stranded DNA.Diariamente, há uma grande quantidade de dados biológicos sendo gerados que trazem uma visão mais profunda do nosso mundo. Esse crescimento exponencial de informações trouxe muitos desafios, principalmente quando se trata de dados metagenômicos. Milhares de genomas montados a partir de dados metagenômicos (MAG) são recuperados anualmente, e muitos métodos tentam alcançar o melhor resultado possível por meio de abordagens de montagem e binning. Mas a pergunta que cada vez é mais frequente é: esses MAGS são confiáveis? A importância de ter dados de boa qualidade é inegável. A recuperação de MAGs confiáveis e completos, ou quase completos, fornece dados importantes para análises futuras e propósitos de pesquisa. Dentro desse cenário, gostaríamos de saber se é possível melhorar a qualidade das métricas dos MAGs quando comparadas ao estado da arte em dados seriados no tempo. Além disso, gostaríamos de desenvolver uma ferramenta capaz de localizar e corrigir erros de montagem, dessa forma auxiliando na curadoria genômica. Aqui, nós descrevemos uma abordagem de MAGs recuperados de dados seriados no tempo chamado \"método de triagem\", reduzindo drasticamente a recuperação de MAGs potencialmente não confiáveis. Além disso, apresentamos FixAME, uma ferramenta capaz de auxiliar na curadoria de sequências montadas de metagenoma, genoma único, conjunto de bins, fagos, arqueias ou qualquer organismo que contenha DNA de fita simples