Evaluation of reference-based two-color methods for measurement of gene expression ratios using spotted cDNA microarrays

BACKGROUND: Spotted cDNA microarrays generally employ co-hybridization of fluorescently-labeled RNA targets to produce gene expression ratios for subsequent analysis. Direct comparison of two RNA samples in the same microarray provides the highest level of accuracy; however, due to the number of combinatorial pair-wise comparisons, the direct method is impractical for studies including large number of individual samples (e.g., tumor classification studies). For such studies, indirect comparisons using a common reference standard have been the preferred method. Here we evaluated the precision and accuracy of reconstructed ratios from three indirect methods relative to ratios obtained from direct hybridizations, herein considered as the gold-standard. RESULTS: We performed hybridizations using a fixed amount of Cy3-labeled reference oligonucleotide (RefOligo) against distinct Cy5-labeled targets from prostate, breast and kidney tumor samples. Reconstructed ratios between all tissue pairs were derived from ratios between each tissue sample and RefOligo. Reconstructed ratios were compared to (i) ratios obtained in parallel from direct pair-wise hybridizations of tissue samples, and to (ii) reconstructed ratios derived from hybridization of each tissue against a reference RNA pool (RefPool). To evaluate the effect of the external references, reconstructed ratios were also calculated directly from intensity values of single-channel (One-Color) measurements derived from tissue sample data collected in the RefOligo experiments. We show that the average coefficient of variation of ratios between intra- and inter-slide replicates derived from RefOligo, RefPool and One-Color were similar and 2 to 4-fold higher than ratios obtained in direct hybridizations. Correlation coefficients calculated for all three tissue comparisons were also similar. In addition, the performance of all indirect methods in terms of their robustness to identify genes deemed as differentially expressed based on direct hybridizations, as well as false-positive and false-negative rates, were found to be comparable. CONCLUSION: RefOligo produces ratios as precise and accurate as ratios reconstructed from a RNA pool, thus representing a reliable alternative in reference-based hybridization experiments. In addition, One-Color measurements alone can reconstruct expression ratios without loss in precision or accuracy. We conclude that both methods are adequate options in large-scale projects where the amount of a common reference RNA pool is usually restrictive

Análise da uniformidade de distribuição da água no sistema de irrigação por aspersão.

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Modelo matemático para determinar a uniformidade de distribuição da água no sistema de irrigação por aspersão.

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Correlating the properties of near-room-temperature first- and second-order magnetocaloric materials

Several magnetocaloric materials have been proposed since the discovery of the Giant Magnetocaloric Effect. Although some have great potential as magnetocaloric refrigerants or working materials in thermomagnetic motors/generators, only a few have been tested experimentally or had their properties incorporated into validated mathematical models. While experiments are limited by material costs and specialized equipment to determine magnetic field-dependent properties such as specific heat capacity and magnetization, the development of correlation methods must ensure data quality and resolution over a wide range of conditions to reduce interpolations errors. Aiming to keep the number of baseline experimental data points at a minimum, we propose a fitting procedure to correlate thermomagnetic quantities (i.e., isofield specific heat capacity, magnetization and isothermal entropy change) that is accurate at intermediate (i.e., not directly measured) temperatures and applied magnetic fields. The method has been applied to different first-order materials (La(Fe,Mn,Si) H and MnFeP As ) and second-order materials (Gd and Gd Y ) with a good reproducibility of the isofield specific heat capacity, entropy–temperature diagram, adiabatic temperature change and magnetization behavior around room temperature at applied fields between 0 and 2 T

Sex and body mass index impact on digit circumference for Leeds Dactylitis Index calculation

Objectives: To estimate digit circumference and the impact of sex and body mass index (BMI) for the calculation of the Leeds Dactylitis Index (LDI) in psoriatic arthritis (PsA) patients with bilateral dactylitis. Methods: Digit circumference of the hands and the foot were measured with a dactylometer and were studied according to sex and BMI (divided in 4 weight categories) in healthy Portuguese subjects, using Student's t-test and One-way ANOVA, respectively. The effect size of sex and BMI were calculated using Cohen's d test and Eta squared, respectively. Multiple linear regression was used to calculate the effect of sex and BMI, as well as their interaction, to create a formula to predict digit circumference. Results: Fifty-nine participants (33 women, 26 men) with a mean BMI of 24.8 were included. Men's mean digit circumferences were statistically higher than those of women (p<0.001), with a large sex effect size in most of the digits. Differences in the mean circumference between the four BMI categories were statistically significant (p<0.05) for all digits, with a large BMI effect size. Sex and BMI were independent variables to predict mean digit circumference (p<0.001). A new tool (based on regression analysis) allowing to estimate the circumference of digits for males and females of different BMIs is presented. Conclusions: Our data allows the calculation of digit circumference for males and females of different BMIs in the Portuguese population; and shows that BMI influences digital circumference supporting BMI inclusion in LDI references tablesinfo:eu-repo/semantics/publishedVersio

Inteligência territorial aplicada ao manejo de resíduos da pecuária.

Este estudo integra o projeto Tecnologias para Produção e Uso de Biogás e Fertilizantes a partir do Tratamento de Dejetos Animais no Âmbito do Plano ABC11, da Rede BiogásFert, que visa oferecer para a sociedade soluções tecnológicas para a produção e o uso integrado de biogás e biofertilizantes orgânicos e organominerais a partir de dejetos animais nos diferentes sistemas de produção agropecuários, visando estratégias de desenvolvimento sustentável com foco em agricultura de baixo carbono

Clinical Study The Bipolar Depression Electrical Treatment Trial (BETTER): Design, Rationale, and Objectives of a Randomized, Sham-Controlled Trial and Data from the Pilot Study Phase

Background. Bipolar depression (BD) is a prevalent condition, with poor therapeutic options and a high degree of refractoriness. This justifies the development of novel treatment strategies, such as transcranial direct current stimulation (tDCS) that showed promising results in unipolar depression. Methods. We describe a randomized, sham-controlled, double-blinded trial using tDCS for refractory, acutely symptomatic BD (the bipolar depression electrical treatment trial, BETTER). Sixty patients will be enrolled and assessed with clinical and neuropsychological tests. The primary outcome is change (over time and across groups) in the scores of the Hamilton Depression Rating Scale (17 items). Biological markers such as blood neurotrophins and interleukins, genetic polymorphisms, heart rate variability, and motor cortical excitability will be assessed. Twelve anodal-left/cathodal-right 2 mA tDCS sessions over the dorsolateral prefrontal cortex will be performed in 6 weeks. Results. In the pilot phase, five patients received active tDCS and were double-blindly assessed, two presenting clinical response. TDCS was well-tolerated, with no changes in cognitive scores. Conclusion. This upcoming clinical trial will address the efficacy of tDCS for BD on different degrees of refractoriness. The evaluation of biological markers will also help in understanding the pathophysiology of BD and the mechanisms of action of tDCS