Augmenting Numerical Stability of the Galerkin Finite Element Formulation for Electromagnetic Flowmeter Analysis

The magnetic flow meter is one of the best possible choice for the measurement of flow rate of liquid metals in fast breeder reactors. Due to the associated complexities in the measuring environment, theoretical evaluation of their sensitivity is always preferred. In order to consider the 3D nature of the problem and the general flow patterns, numerical field computational approach is inevitable. When classical Galerkin's finite element formulation is employed for the solution, it is known to introduce numerical oscillations at high flow rates. The magnetic field produced by the flow induced currents circulate within the fluid and forms the source of this numerical problem. To overcome this, modified methods like stream-line upwind Petrov-Galerkin schemes are generally suggested in the allied areas like fluid dynamics, in which a similar dominance of advective (curl or circulation) component occurs over diffusion (divergence) component. After a careful analysis of the numerical instability through a reduced one dimensional problem, an elegant stable approach is devised. In this scheme, a pole-zero cancellation approach is adopted. The proposed scheme is shown to be absolutely stable. However, at lower flow rates numerical results exhibits small oscillation, which can be controlled by reducing the element size. The source of stability at higher flow rates, as well as, oscillations at lower flow rates are analysed using analytical solution of the associated difference equation. Finally the proposed approach is applied to the original flow meter problem and the solution is shown to be stable.Comment: IET Science, Measurement & Technology, 201

The plasma nitric oxide and homocysteine levels and their association with insulin resistance in South Indian women with polycystic ovary syndrome

Background: Women with polycystic ovary syndrome (PCOS) exhibit features of the metabolic syndrome apart from low-grade chronic inflammation and endothelial dysfunction and may be at increased risk for cardiovascular disease (CVD). The Nitric oxide (NO) and Homocysteine (Hcy) are important plasma markers of endothelial dysfunction, an early marker of atherosclerosis. There are no Indian studies on NO and Hcy levels in women with PCOS and their association with Insulin Resistance (IR). Therefore the present study is to estimate plasma levels of NO and Hcy in south Indian women with PCOS and association with insulin resistance.Methods: 104 women with PCOS and 95 healthy age matched control subject were enrolled in the study. Standard physical methods and Chemiluminescent Immunoassay technique were employed for estimation of Anthropometric parameter and plasma sex hormones respectively. Fasting insulin, glucose, NO and Hcy were measured by standard methods. Insulin resistance was evaluated by using Homeostasis Model Assessment for Insulin Resistance (HOMA- IR)Results: Women with PCOS had significantly higher insulin resistance (P<0.01), Hcy (p<0.05) and lower NO levels (P<0.05), IR was positively correlated with Hcy (r= 0.610, p<0.01) and negatively correlated with NO (r= -0.285; p<0.01)Conclusions: Our data revealed that South Indian women with PCOS had elevated IR and homocyeteine and lowered NO levels

Discovery of active enhancers through bidirectional expression of short transcripts

Abstract Background Long-range regulatory elements, such as enhancers, exert substantial control over tissue-specific gene expression patterns. Genome-wide discovery of functional enhancers in different cell types is important for our understanding of genome function as well as human disease etiology. Results In this study, we developed an in silico approach to model the previously reported phenomenon of transcriptional pausing, accompanied by divergent transcription, at active promoters. We then used this model for large-scale prediction of non-promoter-associated bidirectional expression of short transcripts. Our predictions were significantly enriched for DNase hypersensitive sites, histone H3 lysine 27 acetylation (H3K27ac), and other chromatin marks associated with active rather than poised or repressed enhancers. We also detected modest bidirectional expression at binding sites of the CCCTC-factor (CTCF) genome-wide, particularly those that overlap H3K27ac. Conclusions Our findings indicate that the signature of bidirectional expression of short transcripts, learned from promoter-proximal transcriptional pausing, can be used to predict active long-range regulatory elements genome-wide, likely due in part to specific association of RNA polymerase with enhancer regions

Techniques, Tricks and Algorithms for Efficient GPU-Based Processing of Higher Order Hyperbolic PDEs

GPU computing is expected to play an integral part in all modern Exascale supercomputers. It is also expected that higher order Godunov schemes will make up about a significant fraction of the application mix on such supercomputers. It is, therefore, very important to prepare the community of users of higher order schemes for hyperbolic PDEs for this emerging opportunity. We focus on three broad and high-impact areas where higher order Godunov schemes are used. The first area is computational fluid dynamics (CFD). The second is computational magnetohydrodynamics (MHD) which has an involution constraint that has to be mimetically preserved. The third is computational electrodynamics (CED) which has involution constraints and also extremely stiff source terms. Together, these three diverse uses of higher order Godunov methodology, cover many of the most important applications areas. In all three cases, we show that the optimal use of algorithms, techniques and tricks, along with the use of OpenACC, yields superlative speedups on GPUs! As a bonus, we find a most remarkable and desirable result: some higher order schemes, with their larger operations count per zone, show better speedup than lower order schemes on GPUs. In other words, the GPU is an optimal stratagem for overcoming the higher computational complexities of higher order schemes! Several avenues for future improvement have also been identified. A scalability study is presented for a real-world application using GPUs and comparable numbers of high-end multicore CPUs. It is found that GPUs offer a substantial performance benefit over comparable number of CPUs, especially when all the methods designed in this paper are used.Comment: 73 pages, 17 figure

Evaluation of fatty acid profile with special reference to hypertension intake from marine edible fishes

The present study describes the changes in fatty acid profile in hypertension patients by up taking the marine edible fishes Elutherenema tetradactylum, Sphyraena obtusata and Siganus javus because these marine edible fishes are rich in ? –fatty acids.  In this study the total cholesterol, HDL and LDL were significantly decreased from 211.9 – 202.1 mg/dl, 177-159.6 mg/dl. The palmitic acid (C16:0) was found significantly higher in all of peoples compared with other SFAs. This study revealed that the most abundant in individual FAs 16:0,18:0,18:1 n9 and 20:2 n6 were present in blood in both before and after dietary intake. The minimal changes of SFAs levels were decreased averagely from 59.2 to 52.2%. In addition to above PUFAs also increased from 27.7-30.5%. The essential FAs like ALA (C18:3n3), EPA (C20:5n3) and DHA (C22:6n3) were accounting in the range of 2.64-2.92%, 3.67-3.94% and 3.65-4.38%. Omega – 6/3 ratio were recorded from 1.77-2.45%. This study proves the marine edible fishes reduce the hypertension of the patients. Keywords: Edible fishes, ? –fatty acids, SFAs, HDL and LD

Genome-Wide Analysis of Natural Selection on Human Cis-Elements

Background: It has been speculated that the polymorphisms in the non-coding portion of the human genome underlie much of the phenotypic variability among humans and between humans and other primates. If so, these genomic regions may be undergoing rapid evolutionary change, due in part to natural selection. However, the non-coding region is a heterogeneous mix of functional and non-functional regions. Furthermore, the functional regions are comprised of a variety of different types of elements, each under potentially different selection regimes. Findings and Conclusions: Using the HapMap and Perlegen polymorphism data that map to a stringent set of putative binding sites in human proximal promoters, we apply the Derived Allele Frequency distribution test of neutrality to provide evidence that many human-specific and primate-specific binding sites are likely evolving under positive selection. We also discuss inherent limitations of publicly available human SNP datasets that complicate the inference of selection pressures. Finally, we show that the genes whose proximal binding sites contain high frequency derived alleles are enriched for positive regulation of protein metabolism and developmental processes. Thus our genome-scale investigation provide

Differential impact of glucose administered intravenously and orally on circulating mir-375 levels in human subjects

Background: To date, numerous nucleic acid species have been detected in the systemic circulation including microRNAs (miRNAs); however their functional role in this compartment remains unclear. Objective: The aim of this study was to determine whether systemic levels of miRNAs abundant in blood, including the neuroendocrine tissue-enriched miR-375, are altered in response to a glucose challenge. Design: Twelve healthy males were recruited for an acute cross-over study which consisted of two tests each following an eight-hour fasting period. An oral glucose tolerance test (OGTT) was performed and blood samples were collected over a 3-hour period. Following a period of at least one week, the same participants were administered an isoglycemic intravenous glucose infusion (IIGI) with the same blood collection protocol. Results: The glucose response curve following the IIGI mimicked that obtained after the OGTT, but as expected systemic insulin levels were lower during the IIGI compared to the OGTT (P<0.05). MiR-375 levels in circulation were increased only in response to an OGTT and not during an IIGI. In addition, the response to the OGTT also coincided with the transient increase of circulating glucagon-like peptide-1 (GLP-1), glucagon-like peptide-2 (GLP-2), and glucose-dependent insulinotropic polypeptide (GIP). Conclusions: The present findings show levels of miR-375 increase following administration of an OGTT and in light of its enrichment in cells of the gut, suggest that the gastrointestinal tract may play a significant role to the abundance and function of this microRNA in the blood

A Systematic Mapping Approach of 16q12.2/FTO and BMI in More Than 20,000 African Americans Narrows in on the Underlying Functional Variation: Results from the Population Architecture using Genomics and Epidemiology (PAGE) Study

Genetic variants in intron 1 of the fat mass- and obesity-associated (FTO) gene have been consistently associated with body mass index (BMI) in Europeans. However, follow-up studies in African Americans (AA) have shown no support for some of the most consistently BMI-associated FTO index single nucleotide polymorphisms (SNPs). This is most likely explained by different race-specific linkage disequilibrium (LD) patterns and lower correlation overall in AA, which provides the opportunity to fine-map this region and narrow in on the functional variant. To comprehensively explore the 16q12.2/FTO locus and to search for second independent signals in the broader region, we fine-mapped a 646-kb region, encompassing the large FTO gene and the flanking gene RPGRIP1L by investigating a total of 3,756 variants (1,529 genotyped and 2,227 imputed variants) in 20,488 AAs across five studies. We observed associations between BMI and variants in the known FTO intron 1 locus: the SNP with the most significant p-value, rs56137030 (8.3×10-6) had not been highlighted in previous studies. While rs56137030was correlated at r2>0.5 with 103 SNPs in Europeans (including the GWAS index SNPs), this number was reduced to 28 SNPs in AA. Among rs56137030 and the 28 correlated SNPs, six were located within candidate intronic regulatory elements, including rs1421085, for which we predicted allele-specific binding affinity for the transcription factor CUX1, which has recently been implicated in the regulation of FTO. We did not find strong evidence for a second independent signal in the broader region. In summary, this large fine-mapping study in AA has substantially reduced the number of common alleles that are likely to be functional candidates of the known FTO locus. Importantly our study demonstrated that comprehensive fine-mapping in AA provides a powerful approach to narrow in on the functional candidate(s) underlying the initial GWAS findings in European populations