An open and parallel multiresolution framework using block-based adaptive grids

A numerical approach for solving evolutionary partial differential equations in two and three space dimensions on block-based adaptive grids is presented. The numerical discretization is based on high-order, central finite-differences and explicit time integration. Grid refinement and coarsening are triggered by multiresolution analysis, i.e. thresholding of wavelet coefficients, which allow controlling the precision of the adaptive approximation of the solution with respect to uniform grid computations. The implementation of the scheme is fully parallel using MPI with a hybrid data structure. Load balancing relies on space filling curves techniques. Validation tests for 2D advection equations allow to assess the precision and performance of the developed code. Computations of the compressible Navier-Stokes equations for a temporally developing 2D mixing layer illustrate the properties of the code for nonlinear multi-scale problems. The code is open source

Padrões micrometeorológicos da plantação de cana-de-açúcar.

A indústria do etanol e açúcar cresceu como uma atividade agrícola muito relevante no Brasil, especialmente no estado de São Paulo. Entender a variabilidade temporal de troca de água e calor sobre plantações de cana-de-açúcar tornou-se um assunto bastante importante no contexto de mudanças climáticas regionais e globais. Este trabalho pretende discutir a variabilidade dos fluxos de radiação e fluxos turbulentos de energia sobre 3 tipos de manejo de plantação de cana-de-açúcar, no estado de São Paulo, entre 1997 e 2007. Os agroecossistemas foram manejados com diferentes sistemas de colheita e com diferenças de solo entre dois deles. A variabilidade dos fluxos dependeu em primeiro lugar da variabilidade climática sazonal, e finalmente notou-se a caracterização de padrões que refletiram o tipo de manejo e por conseguinte os diferentes estágios fenológicos das plantas em cada um deles

Transcriptoma de frutos de Coffea arabica L. ao longo do seu desenvolvimento inicial.

Neste trabalho foi realizado o seqüenciamento de RNA em larga escala de 12 bibliotecas de Coffea arabica cv. IAPAR59: folha, flor, frutos ao longo do seu desenvolvimento e frutos tratados com o indutor de metabolismo secundário metiljasmonato. Foram gerados no total 84.798.835 sequências (Illumina, HiSeq2000), que foram montadas em 127.600 contigs com tamanho médio de 1264bp, dos quais 65480 foram considerados como variantes de splicing únicos (unigenes). Neste trabalho, reportamos a montagem de novo do transcriptoma realizada com as sequências destas bibliotecas e os dados preliminares de anotação funcional e categorização. Trata-se do primeiro trabalho de sequenciamento Illumina com frutos de cafeeiro, que pode trazer importantes informações sobre genes candidatos relacionados a produção de compostos-chave envolvidos na qualidade do café e maturação de frutos

Height-diameter allometry of tropical forest trees

Tropical tree height-diameter (H:D) relationships may vary by forest type and region making large-scale estimates of above-ground biomass subject to bias if they ignore these differences in stem allometry. We have therefore developed a new global tropical forest database consisting of 39 955 concurrent H and D measurements encompassing 283 sites in 22 tropical countries. Utilising this database, our objectives were: 1. to determine if H:D relationships differ by geographic region and forest type (wet to dry forests, including zones of tension where forest and savanna overlap). 2. to ascertain if the H:D relationship is modulated by climate and/or forest structural characteristics (e.g. stand-level basal area, A). 3. to develop H:D allometric equations and evaluate biases to reduce error in future local-to-global estimates of tropical forest biomass. Annual precipitation coefficient of variation (PV), dry season length (SD), and mean annual air temperature (TA) emerged as key drivers of variation in H:D relationships at the pantropical and region scales. Vegetation structure also played a role with trees in forests of a high A being, on average, taller at any given D. After the effects of environment and forest structure are taken into account, two main regional groups can be identified. Forests in Asia, Africa and the Guyana Shield all have, on average, similar H:D relationships, but with trees in the forests of much of the Amazon Basin and tropical Australia typically being shorter at any given D than their counterparts elsewhere. The region-environment-structure model with the lowest Akaike\u27s information criterion and lowest deviation estimated stand-level H across all plots to within amedian −2.7 to 0.9% of the true value. Some of the plot-to-plot variability in H:D relationships not accounted for by this model could be attributed to variations in soil physical conditions. Other things being equal, trees tend to be more slender in the absence of soil physical constraints, especially at smaller D. Pantropical and continental-level models provided less robust estimates of H, especially when the roles of climate and stand structure in modulating H:D allometry were not simultaneously taken into account

Exercise alters liver mitochondria phospholipidomic profile and mitochondrial activity in non-alcoholic steatohepatitis

Mitochondrial membrane lipid composition is a critical factor in non-alcoholic steatohepatitis (NASH). Exercise is the most prescribed therapeutic strategy against NASH and a potential modulator of lipid membrane. Thus, we aimed to analyze whether physical exercise exerted preventive (voluntary physical activity – VPA) and therapeutic (endurance training – ET) effect on NASH-induced mitochondrial membrane changes. Sprague-Dawley rats (n = 36) were divided into standard-diet sedentary (SS, n = 12), standard-diet VPA (SVPA, n = 6), high-fat diet sedentary (HS, n = 12) and high-fat diet VPA (HVPA, n = 6). After 9 weeks of diet-specific feeding, half of SS and HS group were engaged in an ET program for 8 weeks/5 day/week/1 h/day (SET, HET). Liver mitochondria were isolated for oxygen consumption and transmembrane-electric potential (ΔΨ) assays. Mitochondrial phospholipid classes and fatty acids were quantified through thin layer chromatography and gas chromatography, respectively, while cardiolipin (CL), phosphatidylcholine (PC) phosphatidylethanolamine (PE) and phosphatidylinositol (PI) molecular profile was determined by electrospray mass spectrometry. In parallel with histological signs of NASH, high-fat diet decreased PI, CL and PC/PE ratio, whereas PE and phosphatidic acid content increased in sedentary animals (HS vs. SS). Moreover, a decrease in linolelaidic, monounsaturated fatty acids content and an increase in saturated fatty acids (SFAS) were observed. Along with phospholipidomic alterations, HS animals showed a decrease in respiratory control ratio (RCR), ΔΨ and FCCP-induced uncoupling respiration (HS vs. SS). Both phospholipidomic (PC/PE, SFAS) and mitochondrial respiratory alterations were counteracted by exercise interventions. Exercise used as preventive (VPA) or therapeutic (ET) strategies preserved liver mitochondrial phospholipidomic profile and maintained mitochondrial function in a model of NASH