Compressão eficiente de sequências biológicas usando uma rede neuronal

Background: The increasing production of genomic data has led to an intensified need for models that can cope efficiently with the lossless compression of biosequences. Important applications include long-term storage and compression-based data analysis. In the literature, only a few recent articles propose the use of neural networks for biosequence compression. However, they fall short when compared with specific DNA compression tools, such as GeCo2. This limitation is due to the absence of models specifically designed for DNA sequences. In this work, we combine the power of neural networks with specific DNA and amino acids models. For this purpose, we created GeCo3 and AC2, two new biosequence compressors. Both use a neural network for mixing the opinions of multiple specific models. Findings: We benchmark GeCo3 as a reference-free DNA compressor in five datasets, including a balanced and comprehensive dataset of DNA sequences, the Y-chromosome and human mitogenome, two compilations of archaeal and virus genomes, four whole genomes, and two collections of FASTQ data of a human virome and ancient DNA. GeCo3 achieves a solid improvement in compression over the previous version (GeCo2) of 2:4%, 7:1%, 6:1%, 5:8%, and 6:0%, respectively. As a reference-based DNA compressor, we benchmark GeCo3 in four datasets constituted by the pairwise compression of the chromosomes of the genomes of several primates. GeCo3 improves the compression in 12:4%, 11:7%, 10:8% and 10:1% over the state-of-the-art. The cost of this compression improvement is some additional computational time (1:7_ to 3:0_ slower than GeCo2). The RAM is constant, and the tool scales efficiently, independently from the sequence size. Overall, these values outperform the state-of-the-art. For AC2 the improvements and costs over AC are similar, which allows the tool to also outperform the state-of-the-art. Conclusions: The GeCo3 and AC2 are biosequence compressors with a neural network mixing approach, that provides additional gains over top specific biocompressors. The proposed mixing method is portable, requiring only the probabilities of the models as inputs, providing easy adaptation to other data compressors or compression-based data analysis tools. GeCo3 and AC2 are released under GPLv3 and are available for free download at https://github.com/cobilab/geco3 and https://github.com/cobilab/ac2.Contexto: O aumento da produção de dados genómicos levou a uma maior necessidade de modelos que possam lidar de forma eficiente com a compressão sem perdas de biosequências. Aplicações importantes incluem armazenamento de longo prazo e análise de dados baseada em compressão. Na literatura, apenas alguns artigos recentes propõem o uso de uma rede neuronal para compressão de biosequências. No entanto, os resultados ficam aquém quando comparados com ferramentas de compressão de ADN específicas, como o GeCo2. Essa limitação deve-se à ausência de modelos específicos para sequências de ADN. Neste trabalho, combinamos o poder de uma rede neuronal com modelos específicos de ADN e aminoácidos. Para isso, criámos o GeCo3 e o AC2, dois novos compressores de biosequências. Ambos usam uma rede neuronal para combinar as opiniões de vários modelos específicos. Resultados: Comparamos o GeCo3 como um compressor de ADN sem referência em cinco conjuntos de dados, incluindo um conjunto de dados balanceado de sequências de ADN, o cromossoma Y e o mitogenoma humano, duas compilações de genomas de arqueas e vírus, quatro genomas inteiros e duas coleções de dados FASTQ de um viroma humano e ADN antigo. O GeCo3 atinge uma melhoria sólida na compressão em relação à versão anterior (GeCo2) de 2,4%, 7,1%, 6,1%, 5,8% e 6,0%, respectivamente. Como um compressor de ADN baseado em referência, comparamos o GeCo3 em quatro conjuntos de dados constituídos pela compressão aos pares dos cromossomas dos genomas de vários primatas. O GeCo3 melhora a compressão em 12,4%, 11,7%, 10,8% e 10,1% em relação ao estado da arte. O custo desta melhoria de compressão é algum tempo computacional adicional (1,7 _ a 3,0 _ mais lento do que GeCo2). A RAM é constante e a ferramenta escala de forma eficiente, independentemente do tamanho da sequência. De forma geral, os rácios de compressão superam o estado da arte. Para o AC2, as melhorias e custos em relação ao AC são semelhantes, o que permite que a ferramenta também supere o estado da arte. Conclusões: O GeCo3 e o AC2 são compressores de sequências biológicas com uma abordagem de mistura baseada numa rede neuronal, que fornece ganhos adicionais em relação aos biocompressores específicos de topo. O método de mistura proposto é portátil, exigindo apenas as probabilidades dos modelos como entradas, proporcionando uma fácil adaptação a outros compressores de dados ou ferramentas de análise baseadas em compressão. O GeCo3 e o AC2 são distribuídos sob GPLv3 e estão disponíveis para download gratuito em https://github.com/ cobilab/geco3 e https://github.com/cobilab/ac2.Mestrado em Engenharia de Computadores e Telemátic

ATLANTIC-CAMTRAPS: a dataset of medium and large terrestrial mammal communities in the Atlantic Forest of South America

Our understanding of mammal ecology has always been hindered by the difficulties of observing species in closed tropical forests. Camera trapping has become a major advance for monitoring terrestrial mammals in biodiversity rich ecosystems. Here we compiled one of the largest datasets of inventories of terrestrial mammal communities for the Neotropical region based on camera trapping studies. The dataset comprises 170 surveys of medium to large terrestrial mammals using camera traps conducted in 144 areas by 74 studies, covering six vegetation types of tropical and subtropical Atlantic Forest of South America (Brazil and Argentina), and present data on species composition and richness. The complete dataset comprises 53,438 independent records of 83 species of mammals, includes 10 species of marsupials, 15 rodents, 20 carnivores, eight ungulates and six armadillos. Species richness averaged 13 species (±6.07 SD) per site. Only six species occurred in more than 50% of the sites: the domestic dog Canis familiaris, crab-eating fox Cerdocyon thous, tayra Eira barbara, south American coati Nasua nasua, crab-eating raccoon Procyon cancrivorus and the nine-banded armadillo Dasypus novemcinctus. The information contained in this dataset can be used to understand macroecological patterns of biodiversity, community, and population structure, but also to evaluate the ecological consequences of fragmentation, defaunation, and trophic interactions. © 2017 by 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

Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference

Statins Increase Rifampin Mycobactericidal Effect

Made available in DSpace on 2015-06-26T13:04:35Z (GMT). No. of bitstreams: 2 license.txt: 1914 bytes, checksum: 7d48279ffeed55da8dfe2f8e81f3b81f (MD5) livia_lobatoetal_IOC_2014.pdf: 2385322 bytes, checksum: 5679c7e513bc97c5728fa40d92b3b46b (MD5) Previous issue date: 2014Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Microbiologia Celular. Rio de Janeiro, RJ, Brasil.Instituto Lauro de Souza Lima. Departamento de Biologia. Bauru, SP, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Microbiologia Celular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Microbiologia Celular. Rio de Janeiro, RJ, Brasil.Universidade Federal do Rio de Janeiro. Instituto de Microbiologia Professor Paulo de Góes. Laboratório de Microbactérias. Rio de Janeiro, RJ, Brasil.Instituto Lauro de Souza Lima. Departamento de Biologia. Bauru, SP, Brasil.Instituto Lauro de Souza Lima. Departamento de Biologia. Bauru, SP, Brasil.Instituto Lauro de Souza Lima. Departamento de Biologia. Bauru, SP, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Microbiologia Celular. Rio de Janeiro, RJ, Brasil.Instituto Lauro de Souza Lima. Departamento de Biologia. Bauru, SP, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Microbiologia Celular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto de Pesquisa Clínica Evandro Chgas. Centro de Pesquisa Clínica em HIV/AIDS. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Microbiologia Celular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Microbiologia Celular. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Microbiologia Celular. Rio de Janeiro, RJ, Brasil.niversidade Federal do Rio de Janeiro. Instituto de Microbiologia Professor Paulo de Góes. Laboratório de Microbactérias. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Microbiologia Celular. Rio de Janeiro, RJ, Brasil.Mycobacterium leprae and Mycobacterium tuberculosis antimicrobial resistance has been followed with great concern during the last years, while the need for new drugs able to control leprosy and tuberculosis, mainly due to extensively drug-resistant tuberculosis (XDR-TB), is pressing. Our group recently showed that M. leprae is able to induce lipid body biogenesis and cholesterol accumulation in macrophages and Schwann cells, facilitating its viability and replication. Considering these previous results, we investigated the efficacies of two statins on the intracellular viability of mycobacteria within the macrophage, as well as the effect of atorvastatin on M. leprae infections in BALB/c mice. We observed that intracellular mycobacteria viability decreased markedly after incubation with both statins, but atorvastatin showed the best inhibitory effect when combined with rifampin. Using Shepard’s model, we observed with atorvastatin an efficacy in controlling M. leprae and inflammatory infiltrate in the BALB/c footpad, in a serum cholesterol level-dependent way. We conclude that statins contribute to macrophage-bactericidal activity against Mycobacterium bovis, M. leprae, and M. tuberculosis. It is likely that the association of statins with the actual multidrug therapy effectively reduces mycobacterial viability and tissue lesion in leprosy and tuberculosis patients, although epidemiological studies are still needed for confirmation

Desempenho e rendimento de carcaça de bovinos mestiços alimentados com diferentes volumosos e fontes protéicas Performance and carcass dressing in crossbreed steers fed different forage and nitrogen sources

Quarenta bovinos machos, com 30 meses de idade e 371 kg, foram distribuídos em um delineamento em blocos casualizado com esquema fatorial 3 x 3, para avaliar o desempenho e rendimento de carcaça quando alimentados com diferentes fontes protéicas (Amiferm, uréia e farelo de soja) e volumosos (pastagem de capim-braquiária, cana-de-açúcar e silagem de milho). As dietas foram balanceadas para conterem níveis semelhantes de EM e PB. A interação volumoso x fonte de N não foi significativa para nenhum dos parâmetros estudados. O ganho de peso vivo diário (GPV/dia) dos animais alimentados com cana-de-açúcar (0,83 kg) não diferiu dos mantidos em pastagem (0,82 kg), mas ambos foram menores que dos animais alimentados com silagem de milho (1,09 kg). As diferentes fontes de N proporcionaram GPV/dia semelhantes, com valores de 0,94; 0,83 e 0,97 kg, para os animais que receberam uréia, Amiferm e farelo de soja, respectivamente. As dietas contendo farelo de soja proporcionaram maior ganho de carcaça diário (0,57 kg) em relação ao uso de Amiferm, não diferindo da uréia (0,55 kg). Não houve diferença entre volumosos e fontes nitrogenadas para rendimento de carcaça, rendimento de carcaça do corpo vazio, rendimento de carcaça do ganho de peso e espessura de gordura, com média de 51,03%, 54,49%, 60,10% e 8,5 mm, respectivamente. O uso de Amiferm proporcionou ganhos de peso e rendimento de carcaça semelhantes às demais fontes protéicas.<br>Forty steers averaging 371 kg BW were allotted to a randomized block design, in a factorial scheme 3 x 3 to evaluate the effect of feeding different protein sources (urea, amiferm, soybean meal) and forage (sugar cane, corn silage and pasture Bracharia brizantha) on performance and carcass dressing. Diets were formulated to contain similar ME and CP protein levels. Forage and nitrogen source interaction was not significant for all studied factors. Daily live weight (LWG/day) of animal fed sugar cane (0.83 kg) did not differ from those fed in pasture (0.82 kg), but both were different from corn silage (1.09 kg). The different protein sources resulted in similar LWG/day, with value of 0.94; 0.83 e 0.97 kg, for urea, Amiferm and soybean meal, respectively. Soybean meal diets showed higher daily carcass gain (0.57 kg) in relation to Amiferm (0.46 kg) but both nitrogen sources did not differ from urea (0.55 kg). There was no difference among forage and nitrogen sources for carcass dressing, carcass dressing in function of empty weight (%EBW), carcass yield of weight gain and fat layer, mean of 51.03%, 54.49%, 60.10% e 8.5 mm, respectively. The use of Amiferm provided weight gain and carcass dressing similar to the others nitrogen sources

Electrical Event Detection and Monitoring Data Storage from Wide Area Measurement System

Synchronized phasor measurement systems are being widely used around the world and have become essential elements in the evolution of the operation of large electrical power systems (EPS). These systems, called Phasor Measurement Units (PMUs), are capable of recording and communicating dynamic data from the EPSs in a synchronized way by GPS and with a high sampling rate, generate a huge set of data that, among many applications, has the capacity to detect events. In this way, this work presents a data management system architecture applied to a real PMU system located in the state of Paraná, Brazil that detects and storages events using principal component analysis and Pearson correlation. This method can detect and store electrical events that occurred during the operation of the national interconnected system of Brazil with good results

Electrical Event Detection and Monitoring Data Storage from Wide Area Measurement System

Synchronized phasor measurement systems are being widely used around the world and have become essential elements in the evolution of the operation of large electrical power systems (EPS). These systems, called Phasor Measurement Units (PMUs), are capable of recording and communicating dynamic data from the EPSs in a synchronized way by GPS and with a high sampling rate, generate a huge set of data that, among many applications, has the capacity to detect events. In this way, this work presents a data management system architecture applied to a real PMU system located in the state of Paran&aacute;, Brazil that detects and storages events using principal component analysis and Pearson correlation. This method can detect and store electrical events that occurred during the operation of the national interconnected system of Brazil with good results