A performance focused, development friendly and model aided parallelization strategy for scientific applications

The amelioration of high performance computing platforms has provided unprecedented computing power with the evolution of multi-core CPUs, massively parallel architectures such as General Purpose Graphics Processing Units (GPGPUs) and Many Integrated Core (MIC) architectures such as Intel\u27s Xeon phi coprocessor. However, it is a great challenge to leverage capabilities of such advanced supercomputing hardware, as it requires efficient and effective parallelization of scientific applications. This task is difficult mainly due to complexity of scientific algorithms coupled with the variety of available hardware and disparate programming models. To address the aforementioned challenges, this thesis presents a parallelization strategy to accelerate scientific applications that maximizes the opportunities of achieving speedup while minimizing the development efforts. Parallelization is a three step process (1) choose a compatible combination of architecture and parallel programming language, (2) translate base code/algorithm to a parallel language and (3) optimize and tune the application. In this research, a quantitative comparison of run time for various implementations of k-means algorithm, is used to establish that native languages (OpenMP, MPI, CUDA) perform better on respective architectures as opposed to vendor-neutral languages such as OpenCL. A qualitative model is used to select an optimal architecture for a given application by aligning the capabilities of accelerators with characteristics of the application. Once the optimal architecture is chosen, the corresponding native language is employed. This approach provides the best performance with reasonable accuracy (78%) of predicting a fitting combination, while eliminating the need for exploring different architectures individually. It reduces the required development efforts considerably as the application need not be re-written in multiple languages. The focus can be solely on optimization and tuning to achieve the best performance on available architectures with minimized investment in terms of cost and efforts. To verify the prediction accuracy of the qualitative model, the OpenDwarfs benchmark suite, which implements the Berkeley\u27s dwarfs in OpenCL, is used. A dwarf is an algorithmic method that captures a pattern of computation and communication. For the purpose of this research, the focus is on 9 application from various algorithmic domains that cover the seven dwarfs of symbolic computation, which were identified by Phillip Colella, as omnipresent in scientific and engineering applications. To validate the parallelization strategy collectively, a case study is undertaken. This case study involves parallelization of the Lower Upper Decomposition for the Gaussian Elimination algorithm from the linear algebra domain, using conventional trial and error methods as well as the proposed \u27Architecture First, Language Later\u27\u27 strategy. The development efforts incurred are contrasted for both methods. The aforesaid proposed strategy is observed to reduce the development efforts by an average of 50%

Comparison of Post-Obturation Pain Following Single Visit and Multi Visit Root Canal Treatment in Diabetic and Non- Diabetic Patients with Irreversible Pulpitis: An In Vivo study

AIM OF THE STUDY: The Aim of this study is to evaluate and compare the pain following obturation in single visit and two-visit endodontic therapy in controlled Type II Diabetes Mellitus patients and Non-Diabetic individuals. MATERIALS AND METHODS: 90 patients with irreversible pulpitis [30 type II Diabetic (Group A) and 60 Non-Diabetic patients (Group B)] were included in this study. Each group was further subdivided into two subgroups; single visit (subgroup A) and two visit (subgroup B) by using a set of random numbers. The standard procedures performed for both the groups during the first visit included administration of local anesthesia, rubber dam isolation, and standard access cavity preparation. Canals were prepared using hand files (K files, Mani) and ProTaper (DENTSPLY) rotary Nitti files using the hybrid technique. Teeth in single visit group were obturated in the initial appointment using gutta-percha and ZOE sealer and those in two visit group were recalled for the second appointment one week later for obturation. The evaluation of post obturation pain was done with visual analogue scale (VAS) and converted to numerical rating scale. The results were statistically analyzed using chi-square test, Kolmogorov-Smirnovtest and Shapiro-Wilk tests. RESULTS: In controlled diabetic group, there was no significant difference in pain at any time interval between single visit and two-visit groups but the incidence of pain was high in single visit group in the first 24 hours which gradually reduced. Overall comparison of pain among diabetic and non-diabetic individuals following one-visit and two visit root canal therapy at various time intervals shows no significant difference. CONCLUSION: Within the limitations of the study, it can be concluded that type II controlled diabetic patients with irreversible pulpitis experienced more pain after single visit root canal treatment in the first 12 hours when compared to non-diabetic patients

Effect of Gsk3 inhibitor CHIR99021 on aneuploidy levels in rat embryonic stem cells

Germline competent embryonic stem (ES) cells can serve as a tool to create genetically engineered rat strains used to elucidate gene function or provide disease models. In optimum culture conditions, ES cells are able to retain their pluripotent state. The type of components present and their concentration in ES cell culture media greatly influences characteristics of ES cells including the ability to maintain the cells in a pluripotent state. We routinely use 2i media containing inhibitors CHIR99021 and PD0325901 to culture rat ES cells. CHIR99021 specifically inhibits the Gsk3β pathway. We have found that the vendor source of CHIR99021 has a measurable influence on the level of aneuploidy seen over time as rat ES cells are passaged. Karyotyping of three different rat ES cell lines passaged multiple times showed increased aneuploidy when CHIR99021 from source B was used. Mass spectrometry analysis of this inhibitor showed the presence of unexpected synthetic small molecules, which might directly or indirectly cause increases in chromosome instability. Identifying these molecules could further understanding of their influence on chromosome stability and indicate how to improve synthesis of this media component to prevent deleterious effects in culture

A novel Artificial Neural Network-based streamline tracing strategy applied to hypersonic waverider design

Streamline tracing in conical hypersonic flows is essential for designing high-performance waverider and intake. Conventionally, the streamline equations are solved after obtaining the velocity field from the solution of the axisymmetric conical flow field. The hypersonic waverider shape is generated from the base conical flow field by repeatedly applying the streamline tracing approach along several planes. When exploring the design space for optimization of the waverider, streamline tracing can be computationally expensive. We provide a novel strategy where first the Taylor-Maccoll equations for the inviscid axisymmetric conical flowfield and the streamlines from the shock are solved for a wide range of cone angle and Mach number conditions resulting in an extensive database. The streamlines are parametrized by a third-order polynomial, and an Artificial Neural Network (ANN) is trained to predict the coefficients of the polynomial for arbitrary inputs of Mach number, cone angle, and streamline originating location on the shock . We apply this strategy to design a cone derived waverider and compare the geometry obtained with the standard conical waverider design method and the simplified waverider design method. The ANN technique is highly accurate, with a difference of 0.68% with the standard in the coordinates of the waverider. RANS computations show that the ANN derived waverider does not indicate severe flow spillage at the leading edge, which is observed in the waverider generated from the simplified method. The new ANN-based approach is 20 times faster than the conventional method

A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses.

BACKGROUND: Sugar beet (Beta vulgaris sp. vulgaris) crops account for about 30% of world sugar. Sugar yield is compromised by reproductive growth hence crops must remain vegetative until harvest. Prolonged exposure to cold temperature (vernalization) in the range 6 °C to 12 °C induces reproductive growth, leading to bolting (rapid elongation of the main stem) and flowering. Spring cultivation of crops in cool temperate climates makes them vulnerable to vernalization and hence bolting, which is initiated in the apical shoot meristem in processes involving interaction between gibberellin (GA) hormones and vernalization. The underlying mechanisms are unknown and genome scale next generation sequencing approaches now offer comprehensive strategies to investigate them; enabling the identification of novel targets for bolting control in sugar beet crops. In this study, we demonstrate the application of an mRNA-Seq based strategy for this purpose. RESULTS: There is no sugar beet reference genome, or public expression array platforms. We therefore used RNA-Seq to generate the first reference transcriptome. We next performed digital gene expression profiling using shoot apex mRNA from two sugar beet cultivars with and without applied GA, and also a vernalized cultivar with and without applied GA. Subsequent bioinformatics analyses identified transcriptional changes associated with genotypic difference and experimental treatments. Analysis of expression profiles in response to vernalization and GA treatment suggested previously unsuspected roles for a RAV1-like AP2/B3 domain protein in vernalization and efflux transporters in the GA response. CONCLUSIONS: Next generation RNA-Seq enabled the generation of the first reference transcriptome for sugar beet and the study of global transcriptional responses in the shoot apex to vernalization and GA treatment, without the need for a reference genome or established array platforms. Comprehensive bioinformatic analysis identified transcriptional programmes associated with different sugar beet genotypes as well as biological treatments; thus providing important new opportunities for basic scientists and sugar beet breeders. Transcriptome-scale identification of agronomically important traits as used in this study should be widely applicable to all crop plants where genomic resources are limiting.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Effects of carbonated beverage and fruit juice on salivary pH among children in orphanage of Bareilly city: an in vivo study

Background: High degree of urbanization and economic development have resulted in rapid changes in diet and lifestyles, because of which there is a tremendous increase in prevalence of dental caries in developing countries. The aim of the study is to assess the acidogenic potential of commonly consumed carbonated beverage and commercially available fruit juice at various time intervals among orphan children. Methods: This is an in vivo study in which 60 orphan children were included. Two beverage groups (carbonated beverage and fruit juice) were tested for salivary pH before having respective drinks (baseline) and after having drinks at specific time intervals (immediately after, after 15 min and 30 min). Intra-group and inter-group comparisons were done using Friedman test and Mann Whitney U test. Results: Both the groups showed decrease in salivary pH after consumption and recovery of salivary pH to baseline value after 30 min. Conclusions: Beverages produce a remarkable drop in the salivary pH as they contain organic acids and sugars but saliva by virtue of its buffering capacity nullifies this effect and after some time it comes to normal

To evaluate and compare the efficacy of alcoholic and aqueous extract of Lagenaria siceraria in high fat diet model in wistar rats

Background: Obesity is not only affecting the affluent society but also affecting developing countries like India. The incidence of obesity is rapidly increasing throughout the world. However, the current anti-obesity drugs have numerous limitations.Methods: The obesity was induced in male wistar rats by giving high-fat diet over 12 weeks. The variables assessed were body weight, abdominal girth, blood triglyceride level, liver weight and fat mass and histopathology of liver. Aqueous and alcoholic extracts of Lagenaria siceraria (200mg/kg and 400mg/kg Doses) were compared to orlistat (treatment control) and high-fat diet group (disease control) for different variables.Results: Alcoholic and aqueous extracts high dose (400mg/kg) of Lagenaria siceraria significantly reduced total body weight (p<0.05), abdominal girth (p <0.05) at week 10 and 12 compared to high fat diet group. Alcoholic extract (400mg/kg) significantly reduced total blood triglyceride level (p <0.05) and total liver weight (p <0.05) compared to high-fat diet group. None of the study drugs reduced % liver weight. Alcoholic extract high dose (p <0.05) has shown improvement in histopathological score. Both aqueous and alcoholic extracts have shown reduced fat mass compared to high-fat diet group.Conclusions: The alcoholic extract (400mg/kg) of Lagenaria siceraria alleviated high fat diet induced obesity and dyslipidemic changes in rats. The alcoholic extract of Lagenaria siceraria is having better anti-obesity potential than aqueous extract