Transcriptome architecture across tissues in the pig

Background: Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues?Results: In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor - joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for similar to 11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes) and between sexes (19 genes). The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes.Conclusion: Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene x tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.

Market-driven security-constrained transmission network expansion planning

This paper presents a Bi-level Programming (BP) approach to solve the Transmission Network Expansion Planning (TNEP) problem. The proposed model is envisaged under a market environment and considers security constraints. The upper-level of the BP problem corresponds to the transmission planner which procures the minimization of the total investment and load shedding cost. This upper-level problem is constrained by a single lower-level optimization problem which models a market clearing mechanism that includes security constraints. Results on the Garver's 6-bus and IEEE 24-bus RTS test systems are presented and discussed. Finally, some conclusions are drawn. © 2011 IEEE.

The employment situation in Latin America and the Caribbean: Recovery of employment: towards a sustainable model

The adverse effects on Latin America and the Caribbean of the global economic and financial crisis, the worst since the 1930s, have been considerably less than was once feared. Although a run of growth was cut short in 2009 and regional output shrank by 1.9%, the impact of the crisis was limited by the application of countercyclical fiscal and monetary policies by many of the region’s governments. The recovery in the economies, particularly in South America, has gone hand-in-hand with the rapid resurgence of the emerging economies of Asia, with all the favourable consequences this has had for global trade. A similar pattern may be observed regarding the impact of the crisis on labour markets in Latin America and the Caribbean. Although millions of people lost their jobs or had to trade down to lower-quality work, levels of employment (including formal employment) fell by less than originally foreseen. At the same time, real wages rose slightly in a context of falling inflation. The labour market thus stabilized domestic demand, and this contributed to the recovery that began in many countries in late 2009. Improved international trade and financing conditions, and the pick-up in domestic demand driven by macroeconomic policies, have led different commentators to estimate growth in the region’s economy at some 6% in 2010. As detailed in the first part of this edition of the Bulletin, the upturn has been manifested at the regional level by the creation of formal employment, a rise in the employment rate, a decline in joblessness and a moderate increase in real wages. Specifically, it is estimatedthat the regional unemployment rate will have dropped by 0.6 percentage points, from 8.1% in 2009 to 7.5% in 2010. The performance of different countries and subregions has been very uneven, however. On the one hand, there is Brazil, where high economic growth has been accompanied by vigorous creation of formal jobs and the unemployment rate has dropped to levels not seen in a long time. Other countries in South America have benefited from strong demand for natural resources from the Asian countries. Combined with higher domestic demand, this has raised their economic growth rates and had a positive impact on employment indicators. On the other hand, the recovery is still very weak in certain countries and subregions, particularly in the Caribbean, with employment indicators continuing to worsen.Thus, the recovery in the region’s economy in 2010 may be characterized as dynamic but uneven. Growth estimates for 2011 are less favourable. The risks associated with the imbalances in the world economy and the withdrawal of countercyclical fiscal packages are likely to cause the region to grow more slowly in 2011. Accordingly, a small further reduction of between 0.2 and 0.4 percentage points in the unemployment rate is projected for 2011. However, these indicators of recovery do not guarantee growth with decent work in the long term. To bolster the improvement in labour market indicators and generate more productive employment and decent work, the region’s countries need to strengthen their macroeconomic policies, improve regional and global policy coordination, identify and remove bottlenecks in the labour market itself and enhance instruments designed to promote greater equality. Like the rest of the world, the Latin American and Caribbean region is also confronted with the challenge of transforming the way it produces so that its economies can develop along tracks that are sustainable in the long term. Climate change and the consequent challenge of developing and strengthening low-carbon production and consumption patterns will also affect the way people work. A great challenge ahead is to create green jobs that combine decent work with environmentally sustainable production patterns. From this perspective, the second part of this Bulletin discusses the green jobs approach, offering some information on the challenges and opportunities involved in moving towards a sustainable economy in the region and presenting a set of options for addressing environmental issues and the repercussions of climate change in the world of work. Although the debate about the green jobs concept is fairly new in the region, examples already exist and a number of countries have moved ahead with the application of policies and programmes in this area. Costa Rica has formulated a National Climate Change Strategy, for example, whose foremost achievements include professional training in natural-resource management. In Brazil, fuel production from biomass has increased and social housing with solar panelling is being built. A number of other countries in the region are making progress in areas such as ecotourism, sustainable agriculture and infrastructure for climate change adaptation, and in formalizing the work of people who recycle household waste. The shift towards a more environmentally sustainable economy may cause jobs to be destroyed in some economic sectors and created in others. The working world will inevitably undergo major changes. If the issue is approached by way of social dialogue and appropriate public policies, there is a chance to use this shift to create more decent jobs, thereby contributing to growth in the economy, the construction of higher levels of equality and protection for the environment.

Climate estimates for Eastern Amazon with OLAM model

O modelo OLAM tem como característica a vantagem de representar simultaneamente os fenômenos de escala global e regional através de um esquema de refinamento de grades. Durante o projeto REMAM o modelo foi aplicado para alguns estudos de caso com objetivo de avaliar o desempenho do modelo na estimativa do clima da região leste da Amazônia em períodos de El Niño e La Niña. Estudos de caso foram feitos para os períodos chuvosos dos anos 2010 e 2011que apresentaram condições oceânicas distintas. Inicialmente, os resultados do modelo foram comparados com dados observados da região de estudo. Os resultados mostraram que o modelo consegue representar bem os principais centros convectivos da região e adjacências, da evolução local do ciclo diurno de temperatura, e da dinâmica dos ventos. Posteriormente, a análise dos resultados mostrou que, se tivermos bons dados de condição inicial e boa representação da evolução das condições de temperatura da superfície do mar, o modelo consegue prever com antecedência de dois e três meses se uma estação chuvosa será mais seca ou úmida.

Effect of melatonin on tumor growth and angiogenesis in xenograft model of breast cancer

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Tunable Fermi acceleration in a nondissipative driven magnetic billiard

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Hymenaea stigonocarpa Mart. ex Hayne: A tropical medicinal plant with intestinal anti-inflammatory activity in TNBS model of intestinal inflammation in rats

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Bending of Layer-by-Layer Films Driven by an External Magnetic Field

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Deep learning architecture for gesture recognition

Pós-graduação em Engenharia Mecânica - FEG

A new probabilistic canopy dynamics model (SLCD) that is suitable for evergreen and deciduous forest ecosystems

There are strong uncertainties regarding LAI dynamics in forest ecosystems in response to climate change. While empirical growth & yield models (G&YMs) provide good estimations of tree growth at the stand level on a yearly to decennial scale, process-based models (PBMs) use LAI dynamics as a key variable for enabling the accurate prediction of tree growth over short time scales. Bridging the gap between PBMs and G&YMs could improve the prediction of forest growth and, therefore, carbon, water and nutrient fluxes by combining modeling approaches at the stand level.Our study aimed to estimate monthly changes of leaf area in response to climate variations from sparse measurements of foliage area and biomass. A leaf population probabilistic model (SLCD) was designed to simulate foliage renewal. The leaf population was distributed in monthly cohorts, and the total population size was limited depending on forest age and productivity. Foliage dynamics were driven by a foliation function and the probabilities ruling leaf aging or fall. Their formulation depends on the forest environment.The model was applied to three tree species growing under contrasting climates and soil types. In tropical Brazilian evergreen broadleaf eucalypt plantations, the phenology was described using 8 parameters. A multi-objective evolutionary algorithm method (MOEA) was used to fit the model parameters on litterfall and LAI data over an entire stand rotation. Field measurements from a second eucalypt stand were used to validate the model. Seasonal LAI changes were accurately rendered for both sites (R-2 = 0.898 adjustment, R-2 = 0.698 validation). Litterfall production was correctly simulated (R-2 = 0.562, R-2 = 0.4018 validation) and may be improved by using additional validation data in future work. In two French temperate deciduous forests (beech and oak), we adapted phenological sub-modules of the CASTANEA model to simulate canopy dynamics, and SLCD was validated using LAI measurements. The phenological patterns were simulated with good accuracy in the two cases studied. However, IA/max was not accurately simulated in the beech forest, and further improvement is required.Our probabilistic approach is expected to contribute to improving predictions of LAI dynamics. The model formalism is general and suitable to broadleaf forests for a large range of ecological conditions. (C) 2014 Elsevier B.V. All rights reserved.

Modelling the surface circulation and thermal structure of a tropical reservoir using three-dimensional hydrodynamic lake model and remote-sensing data

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Spatio-Temporal Event Model for Cyber-Physical Systems

The emerging Cyber-Physical Systems (CPSs) are envisioned to integrate computation, communication and control with the physical world. Therefore, CPS requires close interactions between the cyber and physical worlds both in time and space. These interactions are usually governed by events, which occur in the physical world and should autonomously be reflected in the cyber-world, and actions, which are taken by the CPS as a result of detection of events and certain decision mechanisms. Both event detection and action decision operations should be performed accurately and timely to guarantee temporal and spatial correctness. This calls for a flexible architecture and task representation framework to analyze CP operations. In this paper, we explore the temporal and spatial properties of events, define a novel CPS architecture, and develop a layered spatiotemporal event model for CPS. The event is represented as a function of attribute-based, temporal, and spatial event conditions. Moreover, logical operators are used to combine different types of event conditions to capture composite events. To the best of our knowledge, this is the first event model that captures the heterogeneous characteristics of CPS for formal temporal and spatial analysis.

A mixed model QTL analysis for sugarcane multiple-harvest-location trial data

Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane.

Antimicrobial effect of endodontic solutions used as final irrigants on a dentine biofilm model

Aim To evaluate the residual biovolume of live bacterial cells, the mean biofilm thickness and the substratum coverage found in mixed biofilms treated with different endodontic irrigant solutions. Methodology Twenty-five bovine dentine specimens were infected intraorally using a removable orthodontic device. Five samples were used for each irrigant solution: 2% chlorhexidine, 1% sodium hypochlorite (NaOCl), 10% citric acid, 17% EDTA and distilled water. The solutions were used for 5 min. The samples were stained using the Live/Dead technique and evaluated using a confocal microscope. Differences in the amount of total biovolume (mu m3), number of surviving cells (mu m3), mean biofilm thickness (mu m) and substratum coverage (%) of the treated biofilms were determined using nonparametric statistical tests (P < 0.05). Results Similar values of biovolume total, biovolume of live subpopulations and substratum coverage were found in 2% chlorhexidine, 10% citric acid, 17% EDTA and distilled water-treated biofilms (P > 0.05). The lower values of the studied parameters were found in 1% NaOCl-treated dentine (P < 0.05) with the exception of the mean biofilm height criteria that did not reveal significant differences amongst the irrigant solutions (P > 0.05). Conclusions One per cent sodium hypochlorite was the only irrigant that had a significant effect on biofilm viability and architecture.

Self-organized criticality in MHD driven plasma edge turbulence

We analyze long-range time correlations and self-similar characteristics of the electrostatic turbulence at the plasma edge and scrape-off layer in the Tokamak Chauffage Alfven Bresillien (TCABR), with low and high Magnetohydrodynamics (MHD) activity. We find evidence of self-organized criticality (SOC), mainly in the region near the tokamak limiter. Comparative analyses of data before and during the MHD activity reveals that during the high mHD activity the Hurst parameter decreases. Finally, we present a cellular automaton whose parameters are adjusted to simulate the analyzed turbulence SOC change with the MHD activity variation. (C) 2011 Published by Elsevier B.V.