NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

Background: Shotgun metagenomes contain a sample of all the genomic material in an environment, allowing for the characterization of a microbial community. In order to understand these communities, bioinformatics methods are crucial. A common first step in processing metagenomes is to compute abundance estimates of different taxonomic or functional groups from the raw sequencing data. Given the breadth of the field, computational solutions need to be flexible and extensible, enabling the combination of different tools into a larger pipeline. Results: We present NGLess and NG-meta-profiler. NGLess is a domain specific language for describing next-generation sequence processing pipelines. It was developed with the goal of enabling user-friendly computational reproducibility. It provides built-in support for many common operations on sequencing data and is extensible with external tools with configuration files. Using this framework, we developed NG-meta-profiler, a fast profiler for metagenomes which performs sequence preprocessing, mapping to bundled databases, filtering of the mapping results, and profiling (taxonomic and functional). It is significantly faster than either MOCAT2 or htseq-count and (as it builds on NGLess) its results are perfectly reproducible. Conclusions: NG-meta-profiler is a high-performance solution for metagenomics processing built on NGLess. It can be used as-is to execute standard analyses or serve as the starting point for customization in a perfectly reproducible fashion. NGLess and NG-meta-profiler are open source software (under the liberal MIT license) and can be downloaded from https://ngless.embl.de or installed through bioconda

From Megawatts to Kilowatts: A Review of Small Wind Turbine Applications, Lessons From The US to Brazil

Increased use of fossil fuels has contributed to global warming due to greenhouse gas emissions, which has led countries to implement policies that favor the gradual replacement of their use with renewable energy sources. Wind expansion in Brazil is a success story, but its adherence to distributed generation is still a big challenge. In this context, the authors of this paper argue that the development of robust and viable distributed power grids will also depend in the future on improving small wind generation as an important alternative to the diversity of decentralized power grids. In this study, the authors present an overview of the small-sized Aeolic (or wind) energy market in Brazil, with the objective to support the debate regarding its expansion. Promoting the small wind market in Brazil is still a big challenge, but lessons can be learned from the United States. In this context, the article uses the United States learning curve, analyzing barriers that were found, as well as public policies implemented to overcome them. The lessons learned in the American market may guide public policies aimed at fostering this technology in Brazil. If technological improvements, certification and introduction of financial incentives were implemented in Brazil, the small wind industry chain could grow substantially, building a trajectory to promote the low carbon economy

Models for Synthetic Aperture Radar Image Analysis

After reviewing some classical statistical hypothesis commonly used in image processing and analysis, this paper presents some models that are useful in synthetic aperture radar (SAR) image analysis

Quem somos nós? Ou perfis da comunidade profissional arqueológica no Brasil: primeiras aproximações

WHO ARE WE? OR A PROFILE OF THE ARCHAEOLOGICAL PROFESSIONAL COMMUNITY IN BRAZIL: FIRST APPROACHESIn the last twenty years, archeological academic-scientific training has grown exponen-tially in Brazil, culminating in the recognition of the profession in 2018. However, little is known about the demographic profiles of people working in the area, as well as of students in the process of training, in undergraduate and graduate levels. By updating some data from previous studies, in this manuscript we present the results of an initial survey on the professional profile in Brazilian archeology, which includes information on the trajectory of education, gender, nationality and re-search themes. This initiative allows us to outline the challenges of inclusion and representativeness in the exercise of the profession, whose reflections will assist us in the conceiving of practical measures for a change in this situation in the future.Archaeology of the AmericasArchaeological Heritage Managemen

Características morfológicas e estudo da vascularização do corpo lúteo cíclico de cabras ao longo do ciclo estral

Corpus luteum is a temporary endocrine gland that regulates either the estrous cycle and pregnancy. It presents extreme dependency on the adequate blood supply. This work aims to evaluate goat corpus luteum (CL) vascular density (VD) over the estrous cycle. For that purpose, 20 females were submitted to estrus synchronization/ovulation treatment using a medroxyprogesterone intra-vaginal sponge as well as intramuscular (IM) application of cloprostenol and equine chorionic gonadotrophine (eCG). After sponge removal, estrus was identified at about 72hs. Once treatment was over, female goats were then subdivided into 4 groups (n=5 each) and slaughtered on days 2, 12, 16 and 22 after ovulation (p.o). Ovaries were collected, withdrawn and weighted. CL and ovaries had size and area recorded. Blood samples were collected and the plasma progesterone (P4) was measured through RIA commercial kits. The VD was 24.42±6.66, 36.26±5.61, 8.59±2.2 and 3.97±1.12 vessels/mm² for days 2, 12, 16 and 22 p.o, respectively. Progesterone plasma concentrations were 0.49±0.08, 2.63±0.66, 0.61±0.14 and 0.22±0.04ng/ml for days 2, 12, 16 e 22 p.o, respectively. Studied parameters were affected by the estrous cycle phase. Values greater than 12 p.o were observed. In the present work we observed that ovulation occurred predominantly in the right ovary (70% of the animals), which in turn presented bigger measures than the contra lateral one. There is a meaningful relationship between the weight and size of the ovary and these of CL (r=0.87, r=0.70, respectively, p<0.05). It is possible to conclude that morphology of goat's ovaries and plasma progesterone concentration changed according to estrous cycle stages. We propose these parameters can be used as indicators of CL functional activity.O corpo lúteo é uma glândula endócrina temporária que regula tanto o ciclo estral quanto a prenhez, apresentando extrema dependência de aporte sanguíneo adequado. Objetivaram-se avaliar mudanças morfométricas dos ovários e densidade vascular (DV) dos corpos lúteos (CL) de cabras ao longo do ciclo estral (AOLC). Vinte animais foram submetidos ao tratamento para indução/sincronização do estro, usando esponjas intravaginais commedroxiprogesterona, associadas a aplicações intramusculares de cloprostenol e gonadotrofina coriônica eqüina. Após remoção das esponjas, o estro foi identificado em aproximadamente de 72h. Concluído o tratamento, as cabras foram subdivididas em 4 grupos (n=5 cada) para abate nos dias 2, 12, 16 e 22 após ovulação (p.o.). Posteriormente, foram retirados os ovários e realizadas as mensurações de peso, tamanho e área do órgão e dos CL. Amostras de sangue foram coletadas e a progesterona sérica (P4) mensurada utilizando-se RIA convencional. A DV média dos CL AOLC foi 24,42±6,66; 36,26±5,61; 8,59±2,2 e 3,97±1,12 vasos/mm2 para os dias 2, 12, 16 e 22 p.o., respectivamente. A concentração média de P4 foi de 0,49±0,08; 2,63±0,66; 0,61±0,14 e 0,22±0,04ng/ml para os dias 2, 12, 16 e 22 p.o., respectivamente. Os parâmetros em estudo também se mostraram afetados pela fase do ciclo estral, sendo observados os maiores (p < 0,05) valores no dia 12 p.o. Neste experimento, a ovulação ocorreu predominantemente no ovário direito (70% dos animais), o qual apresentou medidas maiores que o contralateral. Observou-se ainda alta correlação significativa entre o peso do ovário e o do CL (r=0,87; p<0,05) e entre o tamanho destes órgãos (r=0,70; p<0,05). Conclui-se que, a morfologia dos ovários de cabras e a concentração sérica de progesterona variam em função da fase do ciclo estral e podem ser utilizadas como parâmetro na avaliação funcional do órgão