GPU Accelerated Discontinuous Galerkin Methods for Shallow Water Equations

We discuss the development, verification, and performance of a GPU accelerated discontinuous Galerkin method for the solutions of two dimensional nonlinear shallow water equations. The shallow water equations are hyperbolic partial differential equations and are widely used in the simulation of tsunami wave propagations. Our algorithms are tailored to take advantage of the single instruction multiple data (SIMD) architecture of graphic processing units. The time integration is accelerated by local time stepping based on a multi-rate Adams-Bashforth scheme. A total variational bounded limiter is adopted for nonlinear stability of the numerical scheme. This limiter is coupled with a mass and momentum conserving positivity preserving limiter for the special treatment of a dry or partially wet element in the triangulation. Accuracy, robustness and performance are demonstrated with the aid of test cases. We compare the performance of the kernels expressed in a portable threading language OCCA, when cross compiled with OpenCL, CUDA, and OpenMP at runtime.Comment: 26 pages, 51 figure

Interface Response Functions for multicomponent alloy solidification- An application to additive manufacturing

The near-rapid solidification conditions during additive manufacturing can lead to selection of non-equilibrium phases. Sharp interface models via interface response functions have been used earlier to explain the microstructure selection under such solidification conditions. However, most of the sharp interface models assume linear superposition of contributions of alloying elements without considering the non-linearity associated with the phase diagram. In this report, both planar and dendritic Calphad coupled sharp interface models have been implemented and used to explain the growth-controlled phase selection observed at high solidification velocities relevant to additive manufacturing. The implemented model predicted the growth-controlled phase selection in multicomponent alloys, which the other models with linear phase diagram could not. These models are calculated for steels and a Nickel-based superalloy and the results are compared with experimental observations.Comment: 33 pages, 11 figures, preprin

Biochemical Characterization of Kluyveromyces lactis Adenine Deaminase and Guanine Deaminase and Their Potential Application in Lowering Purine Content in Beer

Excess amounts of uric acid in humans leads to hyperuricemia, which is a biochemical precursor of gout and is also associated with various other disorders. Gout is termed as crystallization of uric acid, predominantly within joints. The burden of hyperuricemia and gout has increased worldwide due to lifestyle changes, obesity, and consumption of purine-rich foods, fructose-containing drinks, and alcoholic beverages. Some of the therapies available to cure gout are associated with unwanted side-effects and antigenicity. We propose an attractive and safe strategy to reduce purine content in beverages using enzymatic application of purine degrading enzymes such as adenine deaminase (ADA) and guanine deaminase (GDA) that convert adenine and guanine into hypoxanthine and xanthine, respectively. We cloned, expressed, purified, and biochemically characterized both adenine deaminase (ADA) and guanine deaminase (GDA) enzymes that play important roles in the purine degradation pathway of Kluyveromyces lactis, and demonstrate their application in lowering purine content in a beverage. The popular beverage beer has been selected as an experimental sample as it confers higher risks of hyperuricemia and gout. Quantification of purine content in 16 different beers from the Indian market showed varying concentrations of different purines. Enzymatic treatment of beer samples with ADA and GDA showed a reduction of adenine and guanine content, respectively. These enzymes in combination with other purine degrading enzymes showed marked reduction in purine content in beer samples. Both enzymes can work at 5.0–8.0 pH range and retain >50% activity at 40°C, making them good candidates for industrial applications

Study of prevalence of non alcoholic fatty liver disease in type 2 diabetes mellitus patients and variations in liver function tests, lipid profile and mean platelet volume in patients with fatty liver in comparison with patients without fatty liver

Background: Type 2 diabetes mellitus (T2DM) patients potentially are at risk of developing non-alcoholic fatty liver disease. The aim of the study is to determine the prevalence of NAFLD among T2DM patients, diagnosed by ultrasonography of liver, to study the age & sex incidence of NAFLD and to compare the liver function tests, lipid profile and mean platelet volume (MPV) between individuals with NAFLD and without NAFLD.Methods: Total of 97 type 2 diabetes mellitus ambulatory patients were selected for the study. Among them 62 were males (63.9%) and 35 were females (36%). 78 healthy subjects were selected as controls. Their age ranged between 27 to 75 years. Serum was used for the estimation of FBS, PPBS, total bilirubin, direct bilirubin, AST, ALT, ALP, GGT, total protein, albumin, total cholesterol, triglycerides, high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C). EDTA blood was used for the estimation of MPV. Fatty liver was diagnosed on ultrasound based on the echogenicity and size of the liver.Results: In this study, liver size & echotexture, liver enzymes such as AST, ALT, ALP and GGT, serum cholesterol, TGL and LDLC were found to be statistically significantly increased in T2DM patients when compared to controls. T2DM patients were divided in to two groups; group 1 included patients with NAFLD and group 2 included patients without NAFLD. Liver size, AST, ALT, ALP, GGT, Cholesterol and TGL were significantly increased in group 1 patients when compared to group 2 patients (P value<0.05). Elevation of MPV was found to be more in group 1 patients than group 2 patients ranging between 12.1±3.0 and 10.2±0.9 respectively.Conclusions: Early detection and optimum control of diabetes mellitus is important to minimize the effect of diabetes on liver. Hence, assay of serum levels of hepatic enzymes and USG abdomen to detect NAFLD should be done in all patients with T2DM as preliminary diagnostic tests.

Survey sequencing and in-silico development and validation of genomic SSR markers in Indian dill seed

Indian dill seed (Anethum sowa Roxb. ex Fleming) is an important member of family Apiaceae. It is a significant seed spice having many medicinal properties. But, this aromatic herb is still orphan from breeding and crop improvement perspective as no serious attention has been given by breeders. To swift the breeding program, molecular markers play the main role. But due to the paucity of markers, breeding is slower in dill seed. Therefore, an attempt was made to develop the genomic SSR markers in dill seed through next-generation sequencing. A total of 2119.51 Mbp of raw data were generated on the Miseq NGS platform during survey sequencing. In 2,25,956 contigs created by Spades assembler, a total 48,951 repeat motifs were identified. A set of 20,294 primer pairs (dimer to hexamer repeats) were produced. Among detected repeat motifs, 48.89% was mononucleotides. Of 12 primers, 10 (83%) primers could be successfully amplified in dill seed and produced 11 amplicons. During cross-genera amplification of markers, 9 out of 10 primers could be successfully amplified in related genera. Developed markers can also be used to initiate the molecular breeding program, association mapping and to assess the evolutionary relationship among seed spices

CYLD Inhibits Melanoma Growth and Progression through Suppression of the JNK/AP-1 and β1-Integrin Signaling Pathways

The molecular mechanisms mediating cylindromatosis (CYLD) tumor suppressor function appear to be manifold. Here, we demonstrate that, in contrast to the increased levels of phosphorylated c-Jun NH2-terminal kinase (pJNK), CYLD was decreased in a majority of the melanoma cell lines and tissues examined. Exogenous expression of CYLD but not its catalytically deficient mutant markedly inhibited melanoma cell proliferation and migration in vitro and subcutaneous tumor growth in vivo. In addition, the melanoma cells expressing exogenous CYLD were unable to form pulmonary tumor nodules following tail-vein injection. At the molecular level, CYLD decreased β1-integrin and inhibited pJNK induction by tumor necrosis factor-α or cell attachment to collagen IV. Moreover, CYLD induced an array of other molecular changes associated with modulation of the “malignant” phenotype, including a decreased expression of cyclin D1, N-cadherin, and nuclear Bcl3, and an increased expression of p53 and E-cadherin. Most interestingly, coexpression of the constitutively active MKK7 or c-Jun mutants with CYLD prevented the above molecular changes, and fully restored melanoma growth and metastatic potential in vivo. Our findings demonstrate that the JNK/activator protein 1 signaling pathway underlies the melanoma growth and metastasis that are associated with CYLD loss of function. Thus, restoration of CYLD and inhibition of JNK and β1-integrin function represent potential therapeutic strategies for treatment of malignant melanoma

Nitrogen Use Efficiency in Sorghum: Exploring Native Variability for Traits Under Variable N-Regimes

Exploring the natural genetic variability and its exploitation for improved Nitrogen Use Efficiency (NUE) in sorghum is one of the primary goals in the modern crop improvement programs. The integrated strategies include high-throughput phenotyping, next generation sequencing (NGS)-based genotyping technologies, and a priori selected candidate gene studies that help understand the detailed physiological and molecular mechanisms underpinning this complex trait. A set of sixty diverse sorghum genotypes was evaluated for different vegetative, reproductive, and yield traits related to NUE in the field (under three N regimes) for two seasons. Significant variations for different yield and related traits under 0 and 50% N confirmed the availability of native genetic variability in sorghum under low N regimes. Sorghum genotypes with distinct genetic background had interestingly similar NUE associated traits. The Genotyping- By-Sequencing based SNPs (>89 K) were used to study the population structure, and phylogenetic groupings identified three distinct groups. The information of grain N and stalk N content of the individuals covered on the phylogenetic groups indicated randomness in the distribution for adaptation under variable N regimes. This study identified promising sorghum genotypes with consistent performance under varying environments, with buffer capacity for yield under low N conditions. We also report better performing genotypes for varied production use—grain, stover, and dual-purpose sorghum having differential adaptation response to NUE traits. Expression profiling of NUE associated genes in shoot and root tissues of contrasting lines (PVK801 and HDW703) grown in varying N conditions revealed interesting outcomes. Root tissues of contrasting lines exhibited differential expression profiles for transporter genes [ammonium transporter (SbAMT), nitrate transporters (SbNRT)]; primary assimilatory (glutamine synthetase (SbGS), glutamate synthase (SbGOGAT[NADH], SbGOGAT[Fd]), assimilatory genes [nitrite reductase (SbNiR[NADH]3)]; and amino acid biosynthesis associated gene [glutamate dehydrogenase (SbGDH)]. Identification and expression profiling of contrasting sorghum genotypes in varying N dosages will provide new information to understand the response of NUE genes toward adaptation to the differential N regimes in sorghum. High NUE genotypes identified from this study could be potential candidates for in-depth molecular analysis and contribute toward the development of N efficient sorghum cultivars