NGSPipes: from specification to automatic deployment of NGS pipelines

Biosciences have been revolutionized by next generation sequencing (NGS) technologies in last years, leading to new perspectives in medical, industrial and environmental applications. And although our motivation comes from biosciences, the following is true for many areas of science: published results are usually hard to reproduce either because data is not available or tools are not readily available, which delays the adoption of new methodologies and hinders innovation. Our focus is on tool readiness and pipelines availability. Even though most tools are freely available, pipelines are in general barely described and their configuration is far from trivial, with many parameters to be tuned.In this paper we discuss how to effectively build and use pipelines, relying on state of the art computing technologies to execute them without users need to configure, install and manage tools, servers and complex workflow management systems. A framework is also proposed showing that we can have public pipelines ready to process and analyse very high volume experimental data, produced for instance by high-throughput technologies, and that can be executed by users without effort. The NGSPipes framework and underlying architecture provides a major step towards open science and true collaboration in what concerns tools and pipelines among computational biology researchers and practitioners, which may share and replicate results in an easier and transparent way.info:eu-repo/semantics/publishedVersio

Electrocatalytic oxidation of hydrazine in alkaline media promoted by iron tetrapyridinoporphyrazine adsorbed on graphite surface

The electrocatalytic oxidation of hydrazine was studied using an ordinary pyrolytic graphite electrode modified with iron tetrapyridinoporphyrazine complex (FeTPyPz), employing cyclic voltammetry and rotating disk electrode techniques. Analyses of the voltammograms recorded at different potential scan rates and the polarization curves at different electrode rotation rates showed that the reaction of electrooxidation of hydrazine on FeTPyPz occurs via 4-electrons with the formation of N2 as main product. The kinetic parameters suggest that the second electron transfer step is rate controlling. The activity of FeTPyPz depends on its Fe(II)/Fe(I) formal potential and fits well in a volcano plot that includes several iron phthalocyanines, indicating that such formal potential is a good reactivity index for these complexes

Endonuclease IV Is the Main Base Excision Repair Enzyme Involved in DNA Damage Induced by UVA Radiation and Stannous Chloride

Stannous chloride (SnCl2) and UVA induce DNA lesions through ROS. The aim of this work was to study the toxicity induced by UVA preillumination, followed by SnCl2 treatment. E. coli BER mutants were used to identify genes which could play a role in DNA lesion repair generated by these agents. The survival assays showed (i) The nfo mutant was the most sensitive to SnCl2; (ii) lethal synergistic effect was observed after UVA pre-illumination, plus SnCl2 incubation, the nfo mutant being the most sensitive; (iii) wild type and nfo mutants, transformed with pBW21 plasmid (nfo+) had their survival increased following treatments. The alkaline agarose gel electrophoresis assays pointed that (i) UVA induced DNA breaks and fpg mutant was the most sensitive; (ii) SnCl2-induced DNA strand breaks were higher than those from UVA and nfo mutant had the slowest repair kinetics; (iii) UVA + SnCl2 promoted an increase in DNA breaks than SnCl2 and, again, nfo mutant displayed the slowest repair kinetics. In summary, Nfo protects E. coli cells against damage induced by SnCl2 and UVA + SnCl2

K+ channels expression in hypertension after arterial injury, and effect of selective Kv1.3 blockade with PAP-1 on intimal hyperplasia formation

Producción CientíficaK+ channels are central to vascular pathophysiology. Previous results demonstrated that phenotypic modulation associates with a change in Kv1.3 to Kv1.5 expression, and that Kv1.3 blockade inhibits proliferation of VSMCs cultures. Purpose: To explore whether the Kv1.3 to Kv1.5 switch could be a marker of the increased risk of intimal hyperplasia in essential hypertension and whether systemic treatment with Kv1.3 blockers can prevent intimal hyperplasia after endoluminal lesion . Methods: Morphometric and immunohistochemical analysis were performed in arterial segments following arterial injury and constant infusion of the Kv1.3 blocker PAP-1 during 28 days. Differential expression of K+ channel genes was studied in VSMC from hypertensive (BPH) and normotensive (BPN) mice, both in control and after endoluminal lesion. Finally, the migration and proliferation rate of BPN and BPH VSMCs was explored in vitro. Results: Changes in mRNA expression led to an increased Kv1.3/Kv1.5 ratio in BPH VSMC. Consistent with this, arterial injury in BPH mice induced a higher degree of luminal stenosis, (84±4 % vs. 70±5 % in BPN, p<0.01), although no differences in migration and proliferation rate were observed in cultured VSMCs. The in vivo proliferative lesions were significantly decreased upon PAP-1 systemic infusion (18± 6 % vs. 58±20 % with vehicle, p<0.05). Conclusions: Hypertension leads to a higher degree of luminal stenosis in our arterial injury model, that correlates with a decreased expression of Kv1.5 channels. Kv1.3 blockers decreased in vitro VSMCs proliferation, migration, and in vivo intimal hyperplasia formation, pointing to Kv1.3 channels as promising therapeutical targets against restenosis.La versión original del artículo contiene un error. El gráfico de la página 505 es incorrecto. La corrección del mismo se encuentra en el segundo fichero "Erratum to: K+ Channels Expression in Hypertension After Arterial Injury, and Effect of Selective Kv1.3 Blockade with PAP-1 on Intimal Hyperplasia Formation".Ministerio de Economía, Industria y Competitividad (project RD12/0042/0006)Fondo de Investigación en Salud - Instituto Carlos III (project PI11/00225)VALTEC 09-1-0042Ministerio de Ciencia, Innovación y Universidades (grant BFU2010-15898)Junta de Castilla y León (grant VA094A11-2

Foco de malária no Estado de São Paulo (Brasil)

The malaria focus which ocurred in the State of S.Paulo, Brazil, in the period from February to April 1984, is analysed. The transmission began at an unknown source of infection in an outlying area of Panorama county. Ten cases caused by Plasmodium falciparum were diagnosed. The interval between appearance of the symptoms and the diagnosis varied from 2 to as much as 22 days. Two species responsible for malaria transmission were found in the surveys: Anopheles (N.) darlingi and Anopheles (N.) albitarsis. The steps that led to the elimination of the focus are described, highlighting the detection of one case by means of the investigation slides (thick blood film) of 1,236 inhabitants of the area. The appearance of this focus was of great importance as a means of assessing the potential risk of the reintroduction of malaria into S.Paulo State. Epidemiological surveillance measures must be intensified in vulnerable/receptive areas.Assinala-se foco de malária instalado no período de fevereiro a abril de 1984, no Estado de São Paulo, Brasil. A transmissão teve início a partir de fonte de infecção desconhecida, em área periurbana do município de Panorama. Foram diagnosticados 10 casos, todos devidos a Plasmodium falciparum, variando o intervalo entre o aparecimento dos sintomas e o diagnóstico de 2 a 22 dias, tendo sido encontradas duas espécies transmissoras da malária: Anopheles (N) darlingi e Anopheles (N) albitarsis. São descritas a medidas que levaram à eliminação do foco destacando-se a detecção de um caso através da coleta de lâminas de investigação (gota espessa) entre 1236 moradores da área. O aparecimento desse foco permitiu avaliar o risco potencial da reintrodução da malária no Estado de São Paulo e intensificar as medidas de vigilância epidemiológica em áreas vulneráveis/receptivas

Rainfall Prediction in the State of Paraíba, Northeastern Brazil Using Generalized Additive Models

The state of Paraíba is part of the semi-arid region of Brazil, where severe droughts have occurred in recent years, resulting in significant socio-economic losses associated with climate variability. Thus, understanding to what extent precipitation can be influenced by sea surface temperature (SST) patterns in the tropical region can help, along with a monitoring system, to set up an early warning system, the first pillar in drought management. In this study, Generalized Additive Models for Location, Scale and Shape (GAMLSS) were used to filter climatic indices with higher predictive efficiency and, as a result, to perform rainfall predictions. The results show the persistent influence of tropical SST patterns in Paraíba rainfall, the tropical Atlantic Ocean impacting the rainfall distribution more effectively than the tropical Pacific Ocean. The GAMLSS model showed predictive capability during summer and southern autumn in Paraíba, highlighting the JFM (January, February and March), FMA (February, March and April), MAM (March, April and May), and AMJ (April, May and June) trimesters as those with the highest predictive potential. The methodology demonstrates the ability to be integrated with regional forecasting models (ensemble). Such information has the potential to inform decisions in multiple sectors, such as agriculture and water resources, aiming at the sustainable management of water resources and resilience to climate risk

Insulin resistance and carotid intima-media thickness mediate the association between resting-state heart rate variability and executive function: A path modelling study

Background: Research has linked high-frequency heart rate variability (HF-HRV) to cognitive function. The present study adopts a modern path modelling approach to understand potential causal pathways that may underpin this relationship. Methods: Here we examine the association between resting-state HF-HRV and executive function in a large sample of civil servants from Brazil (N = 8114) recruited for the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil). HF-HRV was calculated from 10-min resting-state electrocardiograms. Executive function was assessed using the trail-making test (version B). Results and conclusions: Insulin resistance (a marker of type 2 diabetes mellitus) and carotid intima-media thickness (subclinical atherosclerosis) mediated the relationship between HRV and executive function in seriatim. A limitation of the present study is its cross-sectional design; therefore, conclusions must be confirmed in longitudinal study. Nevertheless, findings support that possibility that HRV provides a 'spark' that initiates a cascade of adverse downstream effects that subsequently leads to cognitive impairment.Fil: Kemp, Andrew H.. University of Sydney; Australia. Universidade de Sao Paulo; BrasilFil: Rodríguez López, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones y Estudios sobre Cultura y Sociedad. Universidad Nacional de Córdoba. Centro de Investigaciones y Estudios sobre Cultura y Sociedad; Argentina. University of Sydney; Australia. Universidad Autónoma de Madrid; EspañaFil: Passos, Valeria M. A.. Universidade Federal de Minas Gerais; BrasilFil: Bittencourt, Marcio S.. Universidade de Sao Paulo; BrasilFil: Dantas, Eduardo M.. University of Vale do São Francisco; BrasilFil: Mill, José G.. Universidade Federal do Espírito Santo; BrasilFil: Ribeiro, Antonio L. P.. Universidade Federal de Minas Gerais; BrasilFil: Thayer, Julian F.. Ohio State University; Estados UnidosFil: Bensenor, Isabela M.. Universidade de Sao Paulo; BrasilFil: Lotufo, Paulo A.. Universidade de Sao Paulo; Brasi

Uso de dados potenciais de satélite (WGM2012 e EMAG2) para caracterização geotectônica do craton do São Francisco e regiões adjacentes / Use of satellite potential field data (WGM2012 and EMAG2) for geotectonic characterization of the São Francisco craton and neighboring regions

Dados potenciais oriundos de compilações de satélite têm sido usados na interpretação geofísica e geológica regional para a identificação, modelagem e dimensionamento de feições com assinaturas geofísicas regionais provenientes de fontes de baixa frequência que podem estar associadas a maiores profundidades. As informações desses dados são úteis para apresentar características da litosfera do Cráton do São Francisco e regiões limítrofes. A utilização desses dados possibilita a avaliação do contexto geotectônico e contribui com o conhecimento crustal da região.  O objetivo desta pesquisa é a interpretação geofísica com cunho geotectônico, de assinaturas gravimétricas e magnéticas presentes no Cráton do São Francisco e a obtenção de suas profundidades relativas na litosfera. Os dados foram compilados do World Gravity Map 2012 (WGM2012) e Earth Magnetic Anomaly Grid 2-arc min (EMAG2), oriundas dos satélites GRACE e CHAMP, respectivamente.  O produto gravimétrico Anomalia Bouguer indica a existência de fontes profundas com mais de 65 km de profundidade e o produto magnético Campo Magnético Anômalo apresenta fontes com profundidades maiores que 45 km, obtidas a partir da aplicação do Matched Filter sobre os dados base.  A remoção do efeito gravimétrico dos sedimentos foi aplicada ao produto Anomalia Bouguer o que permitiu isolar a assinatura gravimétrica dos terrenos tectônicos da área de pesquisa. Essas diferenças são caracterizadas pelo alto gravimétrico (-10 a 20 mGal) na porção que corresponde ao Arco Magmático de Goiás e Maciço de Goiás em contraste com o baixo gravimétrico (-95 a -65 mGal) relacionado à Zona Externa da Faixa Brasília, localizada no limite ocidental do Cráton do São Francisco. O produto também indicou uma região de alto gravimétrico (-35 a 5 mGal) no Cráton, em sua porção mais setentrional, em direção à Província Borborema e ao extremo sul da Bacia do Paranaíba. Os dados potenciais mostram uma feição circular que bordeja as regiões da Zona Externa da Faixa Brasília, Bacia do Paraná, Bacia do Parnaíba e Província Borborema, e pode estar relacionada ao limite da paleo placa Sanfraciscana, mais antiga e fria que os terrenos adjacentes, consequentemente caracterizada com assinaturas de baixas amplitudes gravimétricas (-128 a -50 mGal).  As informações gravimétricas e magnéticas são complementares para a descrição dos terrenos tectônicos da região. Assim, os dados potenciais de satélite possibilitam a obtenção de informações de fontes profundas, localizadas na base da litosfera, que trazem contribuições ao conhecimento geotectônico

Recomendações para o tratamento da crise migranosa - Um consenso brasileiro

In this article, a group of experts in headache management of the Brazilian Headache Society developed through a consensus strategic measurements to treat a migraine attack in both the child and the adult. Particular emphasis was laid on the treatment of migraine in women, including at pregnancy, lactation and perimenstrual period.Neste artigo um grupo de especialistas no tratamento de cefaleia da Sociedade Brasileira de Cefaleia através de um consenso elaborou medidas estratérgicas para tratar uma crise de migrânea tanto na criança como no adulto. Uma enfase particular foi dada no tratamento da migranea na mulher, incluindo gravidez, lactação e período perimenstrual.74326227