52 research outputs found
Performance analysis of machine learning applications on rapid: a highly parallel computer architecture
No full textOver the past few years, the interest and application of machine learning algorithms has risen exponentially. Machine learning has found extensive use in diverse fields like self-driving cars, speech recognition, image processing, computer vision, molecular biology, security etc. A lot of recent research involves evaluation of machine learning applications on different architectures. In this thesis, we evaluate the performance of six common machine learning algorithms: K-Means, K-Nearest Neighbors, Linear Regression, Latent Dirichlet Allocation, Deep Neural Network, and Radix Sort on RAPID. RAPID is a highly parallel computer architecture developed at Oracle Labs for accelerating and improving the performance of database analytic workloads. We find that the RAPID platform performs well on the performance-per-watt metric i.e. it is a power-efficient architecture. Moreover, the machine learning applications can be easily scaled to hundreds of nodes of the RAPID architecture, thereby making it suitable for distributed machine learning applications. However, we find certain bottlenecks in the micro-architecture, memory system and network of the RAPID architecture and propose optimizations to make it a more performance efficient architecture for machine learning applications.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2019-05-01The student, Aakash Modi, accepted the attached license on 2017-04-26 at 12:22.The student, Aakash Modi, submitted this Thesis for approval on 2017-04-26 at 12:30.This Thesis was approved for publication on 2017-04-26 at 16:22.DSpace SAF Submission Ingestion Package generated from Vireo submission #11087 on 2017-08-10 at 14:32:41Made available in DSpace on 2017-08-10T19:52:24Z (GMT). No. of bitstreams: 2
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Previous issue date: 2017-04-26Embargo set by: Colleen Fallaw for item 102690
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An intelligent spectrum handover scheme for cognitive radio Ad hoc networks Using ANFIS With ANN
No full text
Multi-SUs interference avoidance spectrum handover algorithm using ant colony method in cognitive radio networks
No full text<span style="font-size:11.0pt;mso-bidi-font-size: 10.0pt;font-family:"Times New Roman";mso-fareast-font-family:"Times New Roman"; mso-bidi-font-family:"Times New Roman";text-transform:uppercase;mso-ansi-language: EN-GB;mso-fareast-language:EN-US;mso-bidi-language:AR-SA" lang="EN-GB">D<span style="font-size:11.0pt;mso-bidi-font-size:10.0pt;font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman"; mso-ansi-language:EN-GB;mso-fareast-language:EN-US;mso-bidi-language:AR-SA" lang="EN-GB">evelopment of ‘Assam’ type tea specific scar marker from RAPD products</span></span>
No full text376-380Tea is one of the most important plantation
crop in India, accounting for two-third of global tea production. However, the
genetic diversity of tea is narrowing down because of the large-scale use of vegetatively
propagated clones and massive uprooting of age-old bushes. The present study
was carried out to develop DNA based marker for characterization of tea
germplasms. A RAPD marker (811 base pair) putatively specific to ‘Assam’ type
tea was identified and converted to sequenced characterized amplified region
(SCAR) marker by cloning and sequencing the specific RAPD product. A pair of
primers from SCAR marker so produced amplified a 640 bp product specifically
identifying the ‘Assam’ type tea clones from others. The marker was validated
and found to be useful for identifying the ‘Assam’ type tea clones easily and
economically
The involvement of secondary signaling molecules in cytochrome P-450 1A1-mediated inducible nitric oxide synthase expression in benzo(a)pyrene-treated rat polymorphonuclear leukocytes
No full textComparative transcriptome profiling reveals differential defense responses among Alternaria brassicicola resistant Sinapis alba and susceptible Brassica rapa
No full textAlternaria blight is a devastating disease that causes significant crop losses in oilseed Brassicas every year. Adoption of conventional breeding to generate disease-resistant varieties has so far been unsuccessful due to the lack of suitable resistant source germplasms of cultivated Brassica spp. A thorough understanding of the molecular basis of resistance, as well as the identification of defense-related genes involved in resistance responses in closely related wild germplasms, would substantially aid in disease management. In the current study, a comparative transcriptome profiling was performed using Illumina based RNA-seq to detect differentially expressed genes (DEGs) specifically modulated in response to Alternaria brassicicola infection in resistant Sinapis alba, a close relative of Brassicas, and the highly susceptible Brassica rapa. The analysis revealed that, at 48 hpi (hours post inoculation), 3396 genes were upregulated and 23239 were downregulated, whereas at 72 hpi, 4023 genes were upregulated and 21116 were downregulated. Furthermore, a large number of defense response genes were detected to be specifically regulated as a result of Alternaria infection. The transcriptome data was validated using qPCR-based expression profiling for selected defense-related DEGs, that revealed significantly higher fold change in gene expression in S. alba when compared to B. rapa. Expression of most of the selected genes was elevated across all the time points under study with significantly higher expression towards the later time point of 72 hpi in the resistant germplasm. S. alba activates a stronger defense response reaction against the disease by deploying an array of genes and transcription factors involved in a wide range of biological processes such as pathogen recognition, signal transduction, cell wall modification, antioxidation, transcription regulation, etc. Overall, the study provides new insights on resistance of S. alba against A. brassicicola, which will aid in devising strategies for breeding resistant varieties of oilseed Brassica
Novel insights into structure–function mechanism and tissue-specific expression profiling of full-length dxr gene from Cymbopogon winterianus
No full textAbstractThe 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR; EC1.1.1.267), an NADPH-dependent reductase, plays a pivotal role in the methylerythritol 4-phosphate pathway (MEP), in the conversion of 1-deoxy-d-xylulose-5-phosphate (DXP) into MEP. The sheath and leaf of citronella (Cymbopogon winterianus) accumulates large amount of terpenes and sesquiterpenes with proven medicinal value and economic uses. Thus, sequencing of full length dxr gene and its characterization seems to be a valuable resource in metabolic engineering to alter the flux of isoprenoid active ingredients in plants. In this study, full length DXR from citronella was characterized through in silico and tissue-specific expression studies to explain its structure–function mechanism, mode of cofactor recognition and differential expression. The modelled DXR has a three-domain architecture and its active site comprised of a cofactor (NADPH) binding pocket and the substrate-binding pocket. Molecular dynamics simulation studies indicated that DXR model retained most of its secondary structure during 10ns simulation in aqueous solution. The modelled DXR superimposes well with its closest structural homolog but subtle variations in the charge distribution over the cofactor recognition site were noticed. Molecular docking study revealed critical residues aiding tight anchoring NADPH within the active pocket of DXR. Tissue-specific differential expression analysis using semi-quantitative RT-PCR and qRT-PCR in various tissues of citronella plant revealed distinct differential expression of DXR. To our knowledge, this is the first ever report on DXR from the important medicinal plant citronella and further characterization of this gene will open up better avenues for metabolic engineering of secondary metabolite pathway genes from medicinal plants in the near future
Insights into the mode of flavin mononucleotide binding and catalytic mechanism of bacterial chromate reductases: A molecular dynamics simulation study
No full textEnzymes from natural sources protect the environment via complex biological mechanisms, which aid in reductive immobilization of toxic metals including chromium. Nevertheless, progress was being made in elucidating high-resolution crystal structures of reductases and their binding with flavin mononucleotide (FMN) to understand the underlying mechanism of chromate reduction. Therefore, herein, we employed molecular dynamics (MD) simulations, principal component analysis (PCA), and binding free energy calculations to understand the dynamics behavior of these enzymes with FMN. Six representative chromate reductases in monomeric and dimeric forms were selected to study the mode, dynamics, and energetic component that drive the FMN binding process. As evidenced by MD simulation, FMN prefers to bind the cervix formed between the catalytic domain surrounded by strong conserved hydrogen bonding, electrostatic, and hydrophobic contacts. The slight movement and reorientation of FMN resulted in breakage of some crucial H-bonds and other nonbonded contacts, which were well compensated with newly formed H-bonds, electrostatic, and hydrophobic interactions. The critical residues aiding in tight anchoring of FMN within dimer were found to be strongly conserved in the bacterial system. The molecular mechanics combined with the Poisson-Boltzmann surface area binding free energy of the monomer portrayed that the van der Waals and electrostatic energy contribute significantly to the total free energy, where, the polar solvation energy opposes the binding of FMN. The proposed proximity relationships between enzyme and FMN binding site presented in this study will open up better avenues to engineer enzymes with optimized chromate reductase activity for sustainable bioremediation of heavy metals.</p
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