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International Conference on Advances in Science, Engineering and Robotics Technology

作者： K. M. AzharulHasan MehnumaTabassum Omar RahatHaider Sk. Md. Masudul Ahsan Department of Computer Science and Engineering Khulna University of Engineering & Technology (KUET)

ISBN: (纸本)9781728134468

In recent years managing Big Data is a big challenge. Big data has huge volume, variety of format and its volume increases at a very high velocity. Traditional data structures fail to handle these types of data. Moreover Big Data storage scheme is very expensive. So some efficient scheme is needed. In this paper we show the application of dynamic Extendible array for Big data storage. It is an efficient scheme which has better performance over other approaches. We used MapReduce concept to distribute the data in heterogeneous environment. The data that belongs to different dimensions are distributed to different machines to do the operations efficiently. The basic operations including insertion, deletion, update and retrieval of various types namely point key query, single key query and range key query are performed. Moreover the dynamic extension of the structure without reorganizing the existing data is performed. Experimental results are well studied. We used cheap commodity machines for our implementation.

关键词： MapReduce Extendible array dynamic array storage Big data storage Future data maintanance big data dynamic array Data structures retrieval INDEL Mutation Volume

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dynamic FORMULATION OF CO-PRIME array FOR DOA ESTIMATION 50

DYNAMIC FORMULATION OF CO-PRIME ARRAY FOR DOA ESTIMATION

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50th Asilomar Conference on Signals, Systems, and Computers (ASILOMARSSC)

作者： Wang, Xiaomeng Wang, Xin SUNY Stony Brook Dept Elect & Comp Engn Stony Brook NY 11790 USA

ISBN: (纸本)9781538639542

Among various sparse array techniques, co-prime array is found to be more attractive because its higher DoF with a smaller number of sensing elements. However, because of its specific physical non-uniform linear structure, it would be inconvenient and costly to implement in the presence of varying detection scenarios. In this paper, we propose to exploit the current ULA to dynamically formulate a co-prime array structure, which takes advantage of the properties of co-prime array while reducing the energy consumption and operational cost. Rather than being constrained with the specific physical structure, our scheme can be cost effectively applied in existing systems.

关键词： Co-prime array dynamic array difference co-array DOA estimation

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High-throughput gene-expression quantification of grapevine defense responses in the field using microfluidic dynamic arrays

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BMC GENOMICS 2016年第1期17卷 1-20页

作者： Dufour, Marie-Cecile Magnin, Noel Dumas, Bernard Vergnes, Sophie Corio-Costet, Marie-France INRA ISW UMR Sante & Agroecol Vignoble SAVE 1065 CS 20032 F-33882 Villenave Dornon France Univ Toulouse UPS UMR 5546 Lab Rech Sci Vegetales BP 42617 F-31326 Castanet Tolosan France CNRS UMR 5546 BP 42617 F-31326 Castanet Tolosan France

Background: The fight against grapevine diseases due to biotrophic pathogens usually requires the massive use of chemical fungicides with harmful environmental effects. An alternative strategy could be the use of compounds able to stimulate plant immune responses which significantly limit the development of pathogens in laboratory conditions. However, the efficiency of this strategy in natura is still insufficient to be included in pest management programs. To understand and to improve the mode of action of plant defense stimulators in the field, it is essential to develop reliable tools that describe the resistance status of the plant upon treatment. Results: We have developed a pioneering tool ("NeoViGen96" chip) based on a microfluidic dynamic array platform allowing the expression profiling of 85 defense-related grapevine genes in 90 cDNA preparations in a 4 h single run. Two defense inducers, benzothiadiazole (BTH) and fosetyl-aluminum (FOS), have been tested in natura using the "NeoViGen96" chip as well as their efficacy against downy mildew. BTH-induced grapevine resistance is accompanied by the induction of PR protein genes (PR1, PR2 and PR3), genes coding key enzymes in the phenylpropanoid pathway (PAL and STS), a GST gene coding an enzyme involved in the redox status and an ACC gene involved in the ethylene pathway. FOS, a phosphonate known to possess a toxic activity against pathogens and an inducing effect on defense genes provided a better grapevine protection than BTH. Its mode of action was probably strictly due to its fungicide effect at high concentrations because treatment did not induce significant change in the expression level of selected defense-related genes. Conclusions: The NeoViGen96" chip assesses the effectiveness of plant defense inducers on grapevine in vineyard with an excellent reproducibility. A single run with this system (4 h and 1,500 (sic)), corresponds to 180 qPCR plates with conventional Q-PCR assays (Stragene system, 270 h and

关键词： BTH Defense responses dynamic array Elicitation Fosetyl Gene expression Grapevine Real-time qPCR Vineyard experiments Plasmopara viticola

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Quantitative miRNA Expression Analysis Using Fluidigm Microfluidics dynamic arrays

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BMC GENOMICS 2011年第1期12卷 144-144页

作者： Jang, Jin Sung Simon, Vernadette A. Feddersen, Rod M. Rakhshan, Fariborz Schultz, Debra A. Zschunke, Michael A. Lingle, Wilma L. Kolbert, Christopher P. Jen, Jin Dept Pulm & Crit Care Med Rochester MN 55905 USA Adv Genom Technol Ctr Rochester MN 55905 USA Mayo Clin Canc Ctr Rochester MN 55905 USA Dept Expt Pathol Rochester MN 55905 USA

Background: MicroRNAs (miRNAs) represent a growing class of small non-coding RNAs that are important regulators of gene expression in both plants and animals. Studies have shown that miRNAs play a critical role in human cancer and they can influence the level of cell proliferation and apoptosis by modulating gene expression. Currently, methods for the detection and measurement of miRNA expression include small and moderate-throughput technologies, such as standard quantitative PCR and microarray based analysis. However, these methods have several limitations when used in large clinical studies where a high-throughput and highly quantitative technology needed for the efficient characterization of a large number of miRNA transcripts in clinical samples. Furthermore, archival formalin fixed, paraffin embedded (FFPE) samples are increasingly becoming the primary resource for gene expression studies because fresh frozen (FF) samples are often difficult to obtain and requires special storage conditions. In this study, we evaluated the miRNA expression levels in FFPE and FF samples as well as several lung cancer cell lines employing a high throughput qPCR-based microfluidic technology. The results were compared to standard qPCR and hybridization-based microarray platforms using the same samples. Results: We demonstrated highly correlated Ct values between multiplex and singleplex RT reactions in standard qPCR assays for miRNA expression using total RNA from A549 (R = 0.98;p < 0.0001) and H1299 (R = 0.95;p < 0.0001) lung cancer cell lines. The Ct values generated by the microfluidic technology (Fluidigm 48.48 dynamic array systems) resulted in a left-shift toward lower Ct values compared to those observed by ABI 7900 HT (mean difference, 3.79), suggesting that the microfluidic technology exhibited a greater sensitivity. In addition, we show that as little as 10 ng total RNA can be used to reliably detect all 48 or 96 tested miRNAs using a 96-multiplexing RT reaction in both

关键词： miRNA Expression Reverse Transcription Reaction miRNA Expression Profile Microfluidic Technology dynamic array

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High-throughput single nucleotide polymorphism genotyping using nanofluidic dynamic arrays

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BMC GENOMICS 2009年第1期10卷 561-561页

作者： Wang, Jun Lin, Min Crenshaw, Andrew Hutchinson, Amy Hicks, Belynda Yeager, Meredith Berndt, Sonja Huang, Wen-Yi Hayes, Richard B. Chanock, Stephen J. Jones, Robert C. Ramakrishnan, Ramesh Fluidigm Corp San Francisco CA USA NCI Core Genotyping Facil SAIC Frederick Inc Adv Technol ProgramFCRDC Frederick MD 21701 USA NCI Div Canc Epidemiol & Genet NIH Bethesda MD 20892 USA

Background: Single nucleotide polymorphisms (SNPs) have emerged as the genetic marker of choice for mapping disease loci and candidate gene association studies, because of their high density and relatively even distribution in the human genomes. There is a need for systems allowing medium multiplexing (ten to hundreds of SNPs) with high throughput, which can efficiently and cost-effectively generate genotypes for a very large sample set (thousands of individuals). Methods that are flexible, fast, accurate and cost-effective are urgently needed. This is also important for those who work on high throughput genotyping in non-model systems where off-the-shelf assays are not available and a flexible platform is needed. Results: We demonstrate the use of a nanofluidic Integrated Fluidic Circuit (IFC) - based genotyping system for medium-throughput multiplexing known as the dynamic array, by genotyping 994 individual human DNA samples on 47 different SNP assays, using nanoliter volumes of reagents. Call rates of greater than 99.5% and call accuracies of greater than 99.8% were achieved from our study, which demonstrates that this is a formidable genotyping platform. The experimental set up is very simple, with a time-to-result for each sample of about 3 hours. Conclusion: Our results demonstrate that the dynamic array is an excellent genotyping system for medium-throughput multiplexing (30-300 SNPs), which is simple to use and combines rapid throughput with excellent call rates, high concordance and low cost. The exceptional call rates and call accuracy obtained may be of particular interest to those working on validation and replication of genome-wide-association (GWA) studies.

关键词： Reaction Chamber Call Rate Candidate Gene Association Study dynamic array HapMap Sample

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Direction of arrival estimation for more correlated sources than active sensors

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SIGNAL PROCESSING 2013年第12期93卷 3435-3448页

作者： Ariananda, Dyonisius Dony Leus, Geert Delft Univ Technol Fac Elect Engn Math & Comp Sci NL-2628 CD Delft Zuid Holland Netherlands

In this paper, a new direction of arrival (DOA) estimation method for more correlated sources than active receiving antennas is proposed. The trick to solve this problem using only second-order statistics is to consider a periodic scanning of an underlying uniform array, where a single scanning period contains several time slots and in different time slots different sets of antennas are activated leading to a dynamic non-uniform array with possibly less active antennas than sources in each time slot. We collect the spatial correlation matrices of the active antenna arrays for all time slots and are able to present them as a linear function of the spatial correlation matrix of the underlying array. We provide a necessary and sufficient condition for this system of equations to be full column-rank, which allows for a least squares (LS) reconstruction of the spatial correlation matrix of the underlying array. Some practical greedy algorithms are presented to design dynamic arrays satisfying this condition. In a second step, we use the resulting spatial correlation matrix of the underlying array to estimate the DOAs of the possibly correlated sources by spatial smoothing and MUSIC. Alternatively, we can express this matrix as a linear function of the correlation matrix of the sources (incoming signals) at a grid of investigated angles, and solve this system of equations using either LS or sparsity-regularized LS (possibly assisted by additional constraints), depending on the grid resolution compared to the number of antennas of the underlying array. (C) 2013 Elsevier B.V. All rights reserved.

关键词： dynamic array Periodic scanning More correlated sources than active sensors Underlying array Least squares Sparsity-regularized least squares Second-order statistics

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Engineering scalable, cache and space efficient tries for strings

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VLDB JOURNAL 2010年第5期19卷 633-660页

作者： Askitis, Nikolas Sinha, Ranjan Univ Melbourne Parkville Vic 3052 Australia

Storing and retrieving strings in main memory is a fundamental problem in computer science. The efficiency of string data structures used for this task is of paramount importance for applications such as in-memory databases, text-based search engines and dictionaries. The burst trie is a leading choice for such tasks, as it can provide fast sorted access to strings. The burst trie, however, uses linked lists as substructures which can result in poor use of CPU cache and main memory. Previous research addressed this issue by replacing linked lists with dynamic arrays forming a cache-conscious array burst trie. Though faster, this variant can incur high instruction costs which can hinder its efficiency. Thus, engineering a fast, compact, and scalable trie for strings remains an open problem. In this paper, we introduce a novel and practical solution that carefully combines a trie with a hash table, creating a variant of burst trie called HAT-trie. We provide a thorough experimental analysis which demonstrates that for large set of strings and on alternative computing architectures, the HAT-trie-and two novel variants engineered to achieve further space-efficiency-is currently the leading in-memory trie-based data structure offering rapid, compact, and scalable storage and retrieval of variable-length strings.

关键词： Cache-conscious hash table Burst trie Strings In-memory data structures Judy trie Space-efficient dynamic array Scalable

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Ultra-large Scale Molecular dynamics Simulation for Nano-engineering

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Chemical Research in Chinese Universities 2008年第3期24卷 367-370页

作者： ZHAO Jian-wei YIN Xing LIANG Shuai LIU Yun-hong WANG Dong-xu DENG Sheng-yuan HOU Jie School of Chemistry and Chemical Engineering Nanjing University Nanjing 210093 P. R. China

In light of the special need of nano-engineering, an ultra-large scale and high-performance molecular dynamics（MD） simulation program was implemented. In many nano-engineering processes, the free boundary condition should be adopted. To meet this particular requirement, a pointer link and dynamic array data structures were employed so that both reliability and accuracy of simulation could be ensured. Using this method, one could realize the MD simulation of the nano-engineering system consisting of several million atoms per single CPU.

关键词： Molecular dynamics Nano-engineering dynamic array Verlet table Cell list

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Evaluating the host defense responses in oil palm to complex biocontrol endophyte-pathogen-host plant interaction via Fluidigm® real-time polymerase chain reaction (RT-PCR)

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BIOLOGICAL CONTROL 2019年 129卷 148-157页

作者： Chow, Yiing Yng Rahman, Sadequr Ting, Adeline Su Yien Monash Univ Malaysia Sch Sci Jalan Lagoon Selatan Bandar Sunway 47500 Selangor Darul Malaysia

Induction of plant defense mechanisms by endophyte is an attractive biocontrol tool against plant pathogen in modern sustainable agricultural practices. However, knowledge on biochemical and genetic basis of defense responses due to plant-endophyte-pathogen interaction is still limited. This study aimed to determine the defense responses of oil palm to this complex interaction with respective endophytes (Diaporthe phaseolorum WAA02, Trichoderma asperellum T2, Penicillium citrinum BTF08) and pathogen (Ganoderma boninense). The defense responses were determined based on assays of the host-induced enzymes and further complemented with Fluidigm (R) real-time PCR (RT-PCR). Fluidigm (R) RT-PCR is a time-saving technique that allows the expression of multiple genes in multiple samples on a single chip array. Biochemical results showed that the levels of host defense enzymes (PO, PPO, PAL, TPC) were detected in co-inoculated plants, and these results were supported by RT-PCR. The Fluidigm (R) RT-PCR further revealed that of the 14 defense-related genes observed, induction of beta-1-3-glucanase (EgGLC), phenylalanine ammonia-lyase (PAL) and nitrate reductase (EgNR) were possibly responsible for the biochemical responses. This study highlights the use of Fluidigm (R) RT-PCR for the first time, to study defense responses elicited from the interaction of host plant with endophytes and pathogen.

关键词： Biocontrol dynamic array Endophyte Ganoderma boninense Gene expression Plant defense

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Proteomic and transcriptomic analysis of rice tranglutaminase and chloroplast-related proteins

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PLANT SCIENCE 2014年 229卷 142-153页

作者： Campos, N. Torne, J. M. Bleda, M. J. Manich, A. Urreta, I. Montalban, I. A. Castanon, S. Moncalean, P. Santos, M. CRAG Consorci CSIC IRTA UAB UB Dept Mol Genet Barcelona 08193 Spain CSIC Inst Adv Chem Catalonia IQAC ES-08034 Barcelona Spain CSIC Inst Adv Chem Catalonia IQAC Dept Chem & Surfactants Technol ES-08034 Barcelona Spain Neiker Tecnalia Arkaute Dept Biotechnol E-01080 Vitoria Araba Spain

The recently cloned rice transglutaminase gene (tgo) is the second plant transglutaminase identified to date (Campos et al. Plant Sci. 205-206 (2013) 97-110). Similarly to its counterpart in maize (t,gz), this rice TGase was localized in the chloroplast, although in this case not exclusively. To further characterise plastidial tgo functionality, proteomic and transcriptomic studies were carried out to identify possible TGO-related proteins. Some LHCII antenna proteins were identified as TGO related using an in vitro proteomic approach, as well as ATPase and some PSII core proteins by mass spectrometry. To study the relationship between TGO and other plastidial proteins, a transuiptomic in vivo dynamic array (FluidigmTM) was used to analyse the mRNA expression of 30 plastidial genes with respect to that of tgo, in rice plants subjected to different periods of continuous illumination. The results indicated a gene-dependent tendency in the expression pattern that was related to tgo expression and to the illumination cycle. For certain genes, including tgo, significant differences between treatments, principally at the initiation and/or at the end of the illumination period, connected with the day/night cycling of gene expression, were observed. The tgo expression was especially related to plastidial proteins involved in photoprotection and the thylakoid electrochemical gradient. (C) 2014 Elsevier Ireland Ltd. All rights reserved.

关键词： dynamic array Light dependence Photosynthesis-related proteins Relative mRNA gene expression Rice Transglutaminase

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