Search results for " array"
showing 10 items of 895 documents
Accelerating short read mapping on an FPGA (abstract only)
2012
The explosive growth of short read datasets produced by high throughput DNA sequencing technologies poses a challenge to the mapping of short reads to a reference genome in terms of sensitivity and execution speed. Existing methods often use a restrictive error model for computing the alignments to improve speed, whereas more flexible error models are generally too slow for large-scale applications. Although a number of short read mapping software tools have been proposed, designs based on hardware are relatively rare. In this paper, we present a hybrid system for short read mapping utilizing both software and field programmable gate array (FPGA)-based hardware. The compute intensive semi-g…
The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors.
2010
In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3'- and 5'-ends of 261 yeast genes by run-on. The results obtained indicate that the 3'/5' run-on ratio varies among the genes studied by over 12 log(2) units. This ratio seems to be an intrinsic characteristic of each transcriptional unit and does not significantly correlate with gene length, G + C content or level of expression. The correlation between the 3'/5' RNA polymerase II ratios measured by run-on and those obtained by chromatin immunoprecipitation is poor, although the genes encoding ribosomal proteins present exceptionally low ratios in …
Architecture of a digital PFM controller for IC implementation
2006
This paper presents a digital controller architecture oriented to IC implementation. The classical digital pulse width modulator (D-PWM), using digital analog converter (DAC), is replaced with a Sigma-Delta (/spl Sigma//spl Delta/) modulator based on pulse frequency modulator (PFM) technique. Results of an investigation from a prototype for DC-DC converter, in terms of simulated and experimental performances, are reported, together with harmonic frequency investigation. The control function design is implemented on a field programmable gate array (FPGA). As a consequence of good agreement between simulated and experimental results, the proposed architecture realizes a digital control loop w…
Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data
2016
International audience; Technical variation plays an important role in microarray-based gene expression studies, and batch effects explain a large proportion of this noise. It is therefore mandatory to eliminate technical variation while maintaining biological variability. Several strategies have been proposed for the removal of batch effects, although they have not been evaluated in large-scale longitudinal gene expression data. In this study, we aimed at identifying a suitable method for batch effect removal in a large study of microarray-based longitudinal gene expression. Monocytic gene expression was measured in 1092 participants of the Gutenberg Health Study at baseline and 5-year fol…
Large-Scale Gene-Centric Meta-Analysis across 39 Studies Identifies Type 2 Diabetes Loci
2012
To identify genetic factors contributing to type 2 diabetes (T2D), we performed large-scale meta-analyses by using a custom ∼50,000 SNP genotyping array (the ITMAT-Broad-CARe array) with ∼2000 candidate genes in 39 multiethnic population-based studies, case-control studies, and clinical trials totaling 17,418 cases and 70,298 controls. First, meta-analysis of 25 studies comprising 14,073 cases and 57,489 controls of European descent confirmed eight established T2D loci at genome-wide significance. In silico follow-up analysis of putative association signals found in independent genome-wide association studies (including 8,130 cases and 38,987 controls) performed by the DIAGRAM consortium id…
Concurrent Molecular Dynamics Simulation of ST2 Water on a Transputer Array
1988
Abstract A concurrent implementation of a Molecular Dynamics program for ST2 water molecules is presented, which exploits the great potentialities of the Transputer arrays for statistical mechanical calculations. High load-balance efficiency is obtained using a new task decomposition algorithm which evenly distributes particles and interaction calculations among the processors. This approach can also help to solve efficiently the more general problem of task distribution in parallel computing of symmetric pairwise system properties.
Pushing the Limit – MRI of the Lung Using Hyperpolarized 3-Helium in Conjunction with Parallel Imaging
2009
Imaging of the lung with hyperpolarized 3He became a well known technique in the last decade. Being able to image ventilation and the microstructure of the lung an increase of SNR and a shortage of scan time is eligible. By using a 32-channel phased array the sensitivity was increased dramatically. High resolution 2D-images with a resolution of 1 × 1 mm2 having a 3 mm slice was realized, showing highly detailed images of the lung. By applying parallel imaging techniques the SNR could be increased and scan time was reduced drastically by using a 2D acceleration of R = 4 × 2 with a 3D-protocol covering the whole lung.
Use of functional genes to quantify denitrifiers in the environment.
2006
During the last decade, application of molecular methods using cultivation-independent approaches has provided new insights into the composition and structure of denitrifying communities in various environments. However, little is known about their abundance, and quantification is still performed using cultivation-based approaches, which are not only biased by the inability to cultivate of many micro-organisms but also fastidious and time-consuming. Two types of cultivation-independent approaches have recently been developed to quantify denitrifiers. The first type, which is based on the hybridization technique, comprises the use of Southern hybridization and DNA arrays. The second type, ba…
Estradiol Stimulates Vasodilatory and Metabolic Pathways in Cultured Human Endothelial Cells
2009
Vascular effects of estradiol are being investigated because there are controversies among clinical and experimental studies. DNA microarrays were used to investigate global gene expression patterns in cultured human umbilical vein endothelial cells (HUVEC) exposed to 1 nmol/L estradiol for 24 hours. When compared to control, 187 genes were identified as differentially expressed with 1.9-fold change threshold. Supervised principal component analysis and hierarchical cluster analysis revealed the differences between control and estradiol-treated samples. Physiological concentrations of estradiol are sufficient to elicit significant changes in HUVEC gene expression. Notch signaling, actin cyt…
Proof of Concept of an Irradiance Estimation System for Reconfigurable Photovoltaic Arrays
2015
In order to reduce the mismatch effect caused by non-uniform shadows in PV arrays, reconfigurable interconnections approaches have been recently proposed in the literature. These systems usually require the knowledge of the solar radiation affecting every solar module. The aim of this work is to evaluate the effectiveness of three irradiance estimation approaches in order to define which can be well suited for reconfigurable PV arrays. It is presented a real-time solar irradiance estimation device (IrradEst), implementing the three different estimation methods. The proposed system is based on mathematical models of PV modules enabling to estimate irradiation values by sensing a combination …