GEDI: a user-friendly toolbox for analysis of large-scale gene expression data

Abstract Background Several mathematical and statistical methods have been proposed in the last few years to analyze microarray data. Most of those methods involve complicated formulas, and software implementations that require advanced computer programming skills. Researchers from other areas may experience difficulties when they attempting to use those methods in their research. Here we present an user-friendly toolbox which allows large-scale gene expression analysis to be carried out by biomedical researchers with limited programming skills. Results Here, we introduce an user-friendly toolbox called GEDI (Gene Expression Data Interpreter), an extensible, open-source, and freely-available tool that we believe will be useful to a wide range of laboratories, and to researchers with no background in Mathematics and Computer Science, allowing them to analyze their own data by applying both classical and advanced approaches developed and recently published by Fujita et al. Conclusion GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us. It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations. Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology.

Risk factors for computer visual syndrome (CVS) among operators of two call centers in Sao Paulo, Brazil

The aims of this study were to investigate work conditions, to estimate the prevalence and to describe risk factors associated with Computer Vision Syndrome among two call centers' operators in Sao Paulo (n = 476). The methods include a quantitative cross-sectional observational study and an ergonomic work analysis, using work observation, interviews and questionnaires. The case definition was the presence of one or more specific ocular symptoms answered as always, often or sometimes. The multiple logistic regression model, were created using the stepwise forward likelihood method and remained the variables with levels below 5% (p < 0.05). The operators were mainly female and young (from 15 to 24 years old). The call center was opened 24 hours and the operators weekly hours were 36 hours with break time from 21 to 35 minutes per day. The symptoms reported were eye fatigue (73.9%), "weight" in the eyes (68.2%), "burning" eyes (54.6%), tearing (43.9%) and weakening of vision (43.5%). The prevalence of Computer Vision Syndrome was 54.6%. Associations verified were: being female (OR 2.6, 95% CI 1.6 to 4.1), lack of recognition at work (OR 1.4, 95% CI 1.1 to 1.8), organization of work in call center (OR 1.4, 95% CI 1.1 to 1.7) and high demand at work (OR 1.1, 95% CI 1.0 to 1.3). The organization and psychosocial factors at work should be included in prevention programs of visual syndrome among call centers' operators.

Maternal Melatonin Programs the Daily Pattern of Energy Metabolism in Adult Offspring

Background: Shift work was recently described as a factor that increases the risk of Type 2 diabetes mellitus. In addition, rats born to mothers subjected to a phase shift throughout pregnancy are glucose intolerant. However, the mechanism by which a phase shift transmits metabolic information to the offspring has not been determined. Among several endocrine secretions, phase shifts in the light/dark cycle were described as altering the circadian profile of melatonin production by the pineal gland. The present study addresses the importance of maternal melatonin for the metabolic programming of the offspring. Methodology/Principal Findings: Female Wistar rats were submitted to SHAM surgery or pinealectomy (PINX). The PINX rats were divided into two groups and received either melatonin (PM) or vehicle. The SHAM, the PINX vehicle and the PM females were housed with male Wistar rats. Rats were allowed to mate and after weaning, the male and female offspring were subjected to a glucose tolerance test (GTT), a pyruvate tolerance test (PTT) and an insulin tolerance test (ITT). Pancreatic islets were isolated for insulin secretion, and insulin signaling was assessed in the liver and in the skeletal muscle by western blots. We found that male and female rats born to PINX mothers display glucose intolerance at the end of the light phase of the light/dark cycle, but not at the beginning. We further demonstrate that impaired glucose-stimulated insulin secretion and hepatic insulin resistance are mechanisms that may contribute to glucose intolerance in the offspring of PINX mothers. The metabolic programming described here occurs due to an absence of maternal melatonin because the offspring born to PINX mothers treated with melatonin were not glucose intolerant. Conclusions/Significance: The present results support the novel concept that maternal melatonin is responsible for the programming of the daily pattern of energy metabolism in their offspring.

Availability of a rich source of sodium during the perinatal period programs the fluid balance restoration pattern in adult offspring

Osmoregulatory mechanisms can be vulnerable to electrolyte and/or endocrine environmental changes during the perinatal period, differentially programming the developing offspring and affecting them even in adulthood. The aim of this study was to evaluate whether availability of hypertonic sodium solution during the perinatal period may induce a differential programming in adult offspring osmoregulatory mechanisms. With this aim, we studied water and sodium intake after Furosemide-sodium depletion in adult offspring exposed to hypertonic sodium solution from 1 week before mating until postnatal day 28 of the offspring, used as a perinatal manipulation model [PM-Na group]. In these animals, we also identified the cell population groups in brain nuclei activated by Furosemide-sodium depletion treatment, analyzing the spatial patterns of Fos and Fos-vasopressin immunoreactivity. In sodium depleted rats, sodium and water intake were significantly lower in the PM-Na group vs. animals without access to hypertonic sodium solution [PM-Ctrol group]. Interestingly, when comparing the volumes consumed of both solutions in each PM group, our data show the expected significant differences between both solutions ingested in the PM-Ctrol group, which makes an isotonic cocktail: however, in the PM-Na group there were no significant differences in the volumes of both solutions consumed after Furosemide-sodium depletion, and therefore the sodium concentration of total fluid ingested by this group was significantly higher than that in the PM-Ctrol group. With regard to brain Fos immunoreactivity, we observed that Furosemide-sodium depletion in the PM-Na group induced a higher number of activated cells in the subfornical organ, ventral subdivision of the paraventricular nucleus and vasopressinergic neurons of the supraoptic nucleus than in the PM-Ctrol animals. Moreover, along the brainstem, we found a decreased number of sodium depletion-activated cells within the nucleus of the solitary tract of the PM-Na group. Our data indicate that early sodium availability induces a long-term effect on fluid drinking and on the cell activity of brain nuclei involved in the control of hydromineral balance. These results also suggest that availability of a rich source of sodium during the perinatal period may provoke a larger anticipatory response in the offspring, activating the vasopressinergic system and reducing thirst after water and sodium depletion, as a result of central osmosensitive mechanism alterations. (C) 2011 Elsevier Inc. All rights reserved.

LALP: a language to program custom FPGA-based acceleration engines

Field-Programmable Gate Arrays (FPGAs) are becoming increasingly important in embedded and high-performance computing systems. They allow performance levels close to the ones obtained with Application-Specific Integrated Circuits, while still keeping design and implementation flexibility. However, to efficiently program FPGAs, one needs the expertise of hardware developers in order to master hardware description languages (HDLs) such as VHDL or Verilog. Attempts to furnish a high-level compilation flow (e.g., from C programs) still have to address open issues before broader efficient results can be obtained. Bearing in mind an FPGA available resources, it has been developed LALP (Language for Aggressive Loop Pipelining), a novel language to program FPGA-based accelerators, and its compilation framework, including mapping capabilities. The main ideas behind LALP are to provide a higher abstraction level than HDLs, to exploit the intrinsic parallelism of hardware resources, and to allow the programmer to control execution stages whenever the compiler techniques are unable to generate efficient implementations. Those features are particularly useful to implement loop pipelining, a well regarded technique used to accelerate computations in several application domains. This paper describes LALP, and shows how it can be used to achieve high-performance computing solutions.