WorldWideScience

Sample records for gene array studies

  1. Liver steatosis study_PFAA treated mouse gene array data

    Data.gov (United States)

    U.S. Environmental Protection Agency — This file contains a link for Gene Expression Omnibus and the GSE designations for the publicly available gene expression data used in the study and reflected in...

  2. HuMiChip: Development of a Functional Gene Array for the Study of Human Microbiomes

    Energy Technology Data Exchange (ETDEWEB)

    Tu, Q.; Deng, Ye; Lin, Lu; Hemme, Chris L.; He, Zhili; Zhou, Jizhong

    2010-05-17

    Microbiomes play very important roles in terms of nutrition, health and disease by interacting with their hosts. Based on sequence data currently available in public domains, we have developed a functional gene array to monitor both organismal and functional gene profiles of normal microbiota in human and mouse hosts, and such an array is called human and mouse microbiota array, HMM-Chip. First, seed sequences were identified from KEGG databases, and used to construct a seed database (seedDB) containing 136 gene families in 19 metabolic pathways closely related to human and mouse microbiomes. Second, a mother database (motherDB) was constructed with 81 genomes of bacterial strains with 54 from gut and 27 from oral environments, and 16 metagenomes, and used for selection of genes and probe design. Gene prediction was performed by Glimmer3 for bacterial genomes, and by the Metagene program for metagenomes. In total, 228,240 and 801,599 genes were identified for bacterial genomes and metagenomes, respectively. Then the motherDB was searched against the seedDB using the HMMer program, and gene sequences in the motherDB that were highly homologous with seed sequences in the seedDB were used for probe design by the CommOligo software. Different degrees of specific probes, including gene-specific, inclusive and exclusive group-specific probes were selected. All candidate probes were checked against the motherDB and NCBI databases for specificity. Finally, 7,763 probes covering 91.2percent (12,601 out of 13,814) HMMer confirmed sequences from 75 bacterial genomes and 16 metagenomes were selected. This developed HMM-Chip is able to detect the diversity and abundance of functional genes, the gene expression of microbial communities, and potentially, the interactions of microorganisms and their hosts.

  3. Evolution of orthologous tandemly arrayed gene clusters

    Directory of Open Access Journals (Sweden)

    Bertrand Denis

    2011-10-01

    Full Text Available Abstract Background Tandemly Arrayed Gene (TAG clusters are groups of paralogous genes that are found adjacent on a chromosome. TAGs represent an important repertoire of genes in eukaryotes. In addition to tandem duplication events, TAG clusters are affected during their evolution by other mechanisms, such as inversion and deletion events, that affect the order and orientation of genes. The DILTAG algorithm developed in 1 makes it possible to infer a set of optimal evolutionary histories explaining the evolution of a single TAG cluster, from an ancestral single gene, through tandem duplications (simple or multiple, direct or inverted, deletions and inversion events. Results We present a general methodology, which is an extension of DILTAG, for the study of the evolutionary history of a set of orthologous TAG clusters in multiple species. In addition to the speciation events reflected by the phylogenetic tree of the considered species, the evolutionary events that are taken into account are simple or multiple tandem duplications, direct or inverted, simple or multiple deletions, and inversions. We analysed the performance of our algorithm on simulated data sets and we applied it to the protocadherin gene clusters of human, chimpanzee, mouse and rat. Conclusions Our results obtained on simulated data sets showed a good performance in inferring the total number and size distribution of duplication events. A limitation of the algorithm is however in dealing with multiple gene deletions, as the algorithm is highly exponential in this case, and becomes quickly intractable.

  4. Tandemly Arrayed Genes in Vertebrate Genomes

    Directory of Open Access Journals (Sweden)

    Deng Pan

    2008-01-01

    Full Text Available Tandemly arrayed genes (TAGs are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72–94% have parallel transcription orientation (i.e., they are encoded on the same strand in contrast to the genome, which has about 50% of its genes in parallel transcription orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our recent finding that tandem duplication played a more important role than retroposition in large families, this fact suggests that among all types of duplication mechanisms, tandem duplication is the predominant mechanism of duplication, especially in large families. Finally, several species have a higher proportion of large tandem arrays that are species-specific than random expectation.

  5. Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies.

    Directory of Open Access Journals (Sweden)

    Brendan J Keating

    Full Text Available A wealth of genetic associations for cardiovascular and metabolic phenotypes in humans has been accumulating over the last decade, in particular a large number of loci derived from recent genome wide association studies (GWAS. True complex disease-associated loci often exert modest effects, so their delineation currently requires integration of diverse phenotypic data from large studies to ensure robust meta-analyses. We have designed a gene-centric 50 K single nucleotide polymorphism (SNP array to assess potentially relevant loci across a range of cardiovascular, metabolic and inflammatory syndromes. The array utilizes a "cosmopolitan" tagging approach to capture the genetic diversity across approximately 2,000 loci in populations represented in the HapMap and SeattleSNPs projects. The array content is informed by GWAS of vascular and inflammatory disease, expression quantitative trait loci implicated in atherosclerosis, pathway based approaches and comprehensive literature searching. The custom flexibility of the array platform facilitated interrogation of loci at differing stringencies, according to a gene prioritization strategy that allows saturation of high priority loci with a greater density of markers than the existing GWAS tools, particularly in African HapMap samples. We also demonstrate that the IBC array can be used to complement GWAS, increasing coverage in high priority CVD-related loci across all major HapMap populations. DNA from over 200,000 extensively phenotyped individuals will be genotyped with this array with a significant portion of the generated data being released into the academic domain facilitating in silico replication attempts, analyses of rare variants and cross-cohort meta-analyses in diverse populations. These datasets will also facilitate more robust secondary analyses, such as explorations with alternative genetic models, epistasis and gene-environment interactions.

  6. Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variation

    Directory of Open Access Journals (Sweden)

    Coulombe-Huntington Jasmin

    2009-11-01

    Full Text Available Abstract Background The emergence of isoform-sensitive microarrays has helped fuel in-depth studies of the human transcriptome. The Affymetrix GeneChip Human Exon 1.0 ST Array (Exon Array has been previously shown to be effective in profiling gene expression at the isoform level. More recently, the Affymetrix GeneChip Human Gene 1.0 ST Array (Gene Array has been released for measuring gene expression and interestingly contains a large subset of probes from the Exon Array. Here, we explore the potential of using Gene Array probes to assess expression variation at the sub-transcript level. Utilizing datasets of the high quality Microarray Quality Control (MAQC RNA samples previously assayed on the Exon Array and Gene Array, we compare the expression measurements of the two platforms to determine the performance of the Gene Array in detecting isoform variations. Results Overall, we show that the Gene Array is comparable to the Exon Array in making gene expression calls. Moreover, to examine expression of different isoforms, we modify the Gene Array probe set definition file to enable summarization of probe intensity values at the exon level and show that the expression profiles between the two platforms are also highly correlated. Next, expression calls of previously known differentially spliced genes were compared and also show concordant results. Splicing index analysis, representing estimates of exon inclusion levels, shows a lower but good correlation between platforms. As the Gene Array contains a significant subset of probes from the Exon Array, we note that, in comparison, the Gene Array overlaps with fewer but still a high proportion of splicing events annotated in the Known Alt Events UCSC track, with abundant coverage of cassette exons. We discuss the ability of the Gene Array to detect alternative splicing and isoform variation and address its limitations. Conclusion The Gene Array is an effective expression profiling tool at gene and

  7. Some statistical properties of gene expression clustering for array data

    DEFF Research Database (Denmark)

    Abreu, G C G; Pinheiro, A; Drummond, R D;

    2010-01-01

    DNA array data without a corresponding statistical error measure. We propose an easy-to-implement and simple-to-use technique that uses bootstrap re-sampling to evaluate the statistical error of the nodes provided by SOM-based clustering. Comparisons between SOM and parametric clustering are presented......DNA arrays have been a rich source of data for the study of genomic expression of a wide variety of biological systems. Gene clustering is one of the paradigms quite used to assess the significance of a gene (or group of genes). However, most of the gene clustering techniques are applied to c...... for simulated as well as for two real data sets. We also implement a bootstrap-based pre-processing procedure for SOM, that improves the false discovery ratio of differentially expressed genes. Code in Matlab is freely available, as well as some supplementary material, at the following address: https...

  8. Studying Genes

    Science.gov (United States)

    ... NIGMS NIGMS Home > Science Education > Studying Genes Studying Genes Tagline (Optional) Middle/Main Content Area Other Fact Sheets What are genes? Genes are segments of DNA that contain instructions ...

  9. A Brassica exon array for whole-transcript gene expression profiling.

    Directory of Open Access Journals (Sweden)

    Christopher G Love

    Full Text Available Affymetrix GeneChip® arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip® arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip® arrays whose probes are localised primarily in 3' exons. Plant whole-transcript (WT GeneChip® arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip® Brassica Exon 1.0 ST Array is a 5 µM feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E(-5, with ≤98% sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18, and categorisation by Gene Ontologies (GO based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at http://www.brassica.info/BrassEnsembl/index.html.

  10. Array data extractor (ADE): a LabVIEW program to extract and merge gene array data.

    Science.gov (United States)

    Kurtenbach, Stefan; Kurtenbach, Sarah; Zoidl, Georg

    2013-12-01

    Large data sets from gene expression array studies are publicly available offering information highly valuable for research across many disciplines ranging from fundamental to clinical research. Highly advanced bioinformatics tools have been made available to researchers, but a demand for user-friendly software allowing researchers to quickly extract expression information for multiple genes from multiple studies persists. Here, we present a user-friendly LabVIEW program to automatically extract gene expression data for a list of genes from multiple normalized microarray datasets. Functionality was tested for 288 class A G protein-coupled receptors (GPCRs) and expression data from 12 studies comparing normal and diseased human hearts. Results confirmed known regulation of a beta 1 adrenergic receptor and further indicate novel research targets. Although existing software allows for complex data analyses, the LabVIEW based program presented here, "Array Data Extractor (ADE)", provides users with a tool to retrieve meaningful information from multiple normalized gene expression datasets in a fast and easy way. Further, the graphical programming language used in LabVIEW allows applying changes to the program without the need of advanced programming knowledge.

  11. Gene cassette transcription in a large integron-associated array

    Directory of Open Access Journals (Sweden)

    Michael Carolyn A

    2010-09-01

    Full Text Available Abstract Background The integron/gene cassette system is a diverse and effective adaptive resource for prokaryotes. Short cassette arrays, with less than 10 cassettes adjacent to an integron, provide this resource through the expression of cassette-associated genes by an integron-borne promoter. However, the advantage provided by large arrays containing hundreds of cassettes is less obvious. In this work, using the 116-cassette array of Vibrio sp. DAT722 as a model, we investigated the theory that the majority of genes contained within large cassette arrays are widely expressed by intra-array promoters in addition to the integron-borne promoter. Results We demonstrated that the majority of the cassette-associated genes in the subject array were expressed. We further showed that cassette expression was conditional and that the conditionality varied across the array. We finally showed that this expression was mediated by a diversity of cassette-borne promoters within the array capable of responding to environmental stressors. Conclusions Widespread expression within large gene cassette arrays could provide an adaptive advantage to the host in proportion to the size of the array. Our findings explained the existence and maintenance of large cassette arrays within many prokaryotes. Further, we suggested that repeated rearrangement of cassettes containing genes and/or promoters within large arrays could result in the assembly of operon-like groups of co-expressed cassettes within an array. These findings add to our understanding of the adaptive repertoire of the integron/gene cassette system in prokaryotes and consequently, the evolutionary impact of this system.

  12. Microfluidic gene arrays for rapid genomic profiling

    Science.gov (United States)

    West, Jay A.; Hukari, Kyle W.; Hux, Gary A.; Shepodd, Timothy J.

    2004-12-01

    Genomic analysis tools have recently become an indispensable tool for the evaluation of gene expression in a variety of experiment protocols. Two of the main drawbacks to this technology are the labor and time intensive process for sample preparation and the relatively long times required for target/probe hybridization. In order to overcome these two technological barriers we have developed a microfluidic chip to perform on chip sample purification and labeling, integrated with a high density genearray. Sample purification was performed using a porous polymer monolithic material functionalized with an oligo dT nucleotide sequence for the isolation of high purity mRNA. These purified mRNA"s can then rapidly labeled using a covalent fluorescent molecule which forms a selective covalent bond at the N7 position of guanine residues. These labeled mRNA"s can then released from the polymer monolith to allow for direct hybridization with oligonucletide probes deposited in microfluidic channel. To allow for rapid target/probe hybridization high density microarray were printed in microchannels. The channels can accommodate array densities as high as 4000 probes. When oligonucleotide deposition is complete, these channels are sealed using a polymer film which forms a pressure tight seal to allow sample reagent flow to the arrayed probes. This process will allow for real time target to probe hybridization monitoring using a top mounted CCD fiber bundle combination. Using this process we have been able to perform a multi-step sample preparation to labeled target/probe hybridization in less than 30 minutes. These results demonstrate the capability to perform rapid genomic screening on a high density microfluidic microarray of oligonucleotides.

  13. Use of functional gene arrays for elucidating in situ biodegradation

    Directory of Open Access Journals (Sweden)

    Joy D. Van Nostrand

    2012-09-01

    Full Text Available Microarrays have revolutionized the study of microbiology by providing a high-throughput method for examining thousands of genes with a single test and overcome the limitations of many culture-independent approaches. Functional gene arrays (FGA probe a wide range of genes involved in a variety of functions of interest to microbial ecology (e.g., carbon degradation, N-fixation, metal resistance from many different microorganisms, cultured and uncultured. The most comprehensive FGA to date is the GeoChip array, which targets tens of thousands of genes involved in the geochemical cycling of carbon, nitrogen, phosphorus, and sulphur, metal resistance and reduction, energy processing, antibiotic resistance and contaminant degradation as well as phylogenetic information (gyrB. Since the development of GeoChips, many studies have been performed using this FGA and have shown it to be a powerful tool for rapid, sensitive and specific examination of microbial communities in a high-throughput manner. As such, the GeoChip is well-suited for linking geochemical processes with microbial community function and structure. This technology has been used successfully to examine microbial communities before, during and after in situ bioremediation at a variety of contaminated sites. These studies have expanded our understanding of biodegradation and bioremediation processes and the associated microorganisms and environmental conditions responsible. This review provides an overview of FGA development with a focus on the GeoChip and highlights specific GeoChip studies involving in situ bioremediation.

  14. Cross-platform comparison of SYBR® Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC study

    Directory of Open Access Journals (Sweden)

    Dial Stacey L

    2008-07-01

    Full Text Available Abstract Background The MicroArray Quality Control (MAQC project evaluated the inter- and intra-platform reproducibility of seven microarray platforms and three quantitative gene expression assays in profiling the expression of two commercially available Reference RNA samples (Nat Biotechnol 24:1115-22, 2006. The tested microarrays were the platforms from Affymetrix, Agilent Technologies, Applied Biosystems, GE Healthcare, Illumina, Eppendorf and the National Cancer Institute, and quantitative gene expression assays included TaqMan® Gene Expression PCR Assay, Standardized (Sta RT-PCR™ and QuantiGene®. The data showed great consistency in gene expression measurements across different microarray platforms, different technologies and test sites. However, SYBR® Green real-time PCR, another common technique utilized by half of all real-time PCR users for gene expression measurement, was not addressed in the MAQC study. In the present study, we compared the performance of SYBR Green PCR with TaqMan PCR, microarrays and other quantitative technologies using the same two Reference RNA samples as the MAQC project. We assessed SYBR Green real-time PCR using commercially available RT2 Profiler™ PCR Arrays from SuperArray, containing primer pairs that have been experimentally validated to ensure gene-specificity and high amplification efficiency. Results The SYBR Green PCR Arrays exhibit good reproducibility among different users, PCR instruments and test sites. In addition, the SYBR Green PCR Arrays have the highest concordance with TaqMan PCR, and a high level of concordance with other quantitative methods and microarrays that were evaluated in this study in terms of fold-change correlation and overlap of lists of differentially expressed genes. Conclusion These data demonstrate that SYBR Green real-time PCR delivers highly comparable results in gene expression measurement with TaqMan PCR and other high-density microarrays.

  15. Expression Divergence of Tandemly Arrayed Genes in Human and Mouse

    Directory of Open Access Journals (Sweden)

    Valia Shoja

    2007-01-01

    Full Text Available Tandemly arrayed genes (TAGs account for about one third of the duplicated genes in eukaryotic genomes, yet there has not been any systematic study of their gene expression patterns. Taking advantage of recently published large-scale microarray data sets, we studied the expression divergence of 361 two-member TAGs in human and 212 two-member TAGs in mouse and examined the effect of sequence divergence, gene orientation, and chromosomal proximity on the divergence of TAG expression patterns. Our results show that there is a weak negative correlation between sequence divergence of TAG members and their expression similarity. There is also a weak negative correlation between chromosomal proximity of TAG members and their expression similarity. We did not detect any significant relationship between gene orientation and expression similarity. We also found that downstream TAG members do not show significantly narrower expression breadth than upstream members, contrary to what we predict based on TAG expression divergence hypothesis that we propose. Finally, we show that both chromosomal proximity and expression correlation in TAGs do not differ significantly from their neighboring non-TAG gene pairs, suggesting that tandem duplication is unlikely to be the cause for the higher-than-random expression association between neighboring genes on a chromosome in human and mouse.

  16. Human transcriptome array for high-throughput clinical studies.

    Science.gov (United States)

    Xu, Weihong; Seok, Junhee; Mindrinos, Michael N; Schweitzer, Anthony C; Jiang, Hui; Wilhelmy, Julie; Clark, Tyson A; Kapur, Karen; Xing, Yi; Faham, Malek; Storey, John D; Moldawer, Lyle L; Maier, Ronald V; Tompkins, Ronald G; Wong, Wing Hung; Davis, Ronald W; Xiao, Wenzhong

    2011-03-01

    A 6.9 million-feature oligonucleotide array of the human transcriptome [Glue Grant human transcriptome (GG-H array)] has been developed for high-throughput and cost-effective analyses in clinical studies. This array allows comprehensive examination of gene expression and genome-wide identification of alternative splicing as well as detection of coding SNPs and noncoding transcripts. The performance of the array was examined and compared with mRNA sequencing (RNA-Seq) results over multiple independent replicates of liver and muscle samples. Compared with RNA-Seq of 46 million uniquely mappable reads per replicate, the GG-H array is highly reproducible in estimating gene and exon abundance. Although both platforms detect similar expression changes at the gene level, the GG-H array is more sensitive at the exon level. Deeper sequencing is required to adequately cover low-abundance transcripts. The array has been implemented in a multicenter clinical program and has generated high-quality, reproducible data. Considering the clinical trial requirements of cost, sample availability, and throughput, the GG-H array has a wide range of applications. An emerging approach for large-scale clinical genomic studies is to first use RNA-Seq to the sufficient depth for the discovery of transcriptome elements relevant to the disease process followed by high-throughput and reliable screening of these elements on thousands of patient samples using custom-designed arrays.

  17. A functional gene array for detection of bacterial virulence elements

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, C

    2007-11-01

    We report our development of the first of a series of microarrays designed to detect pathogens with known mechanisms of virulence and antibiotic resistance. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples. To validate our approach, we developed a first generation array targeting genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for microorganism detection and discrimination, measured the required target concentration, and assessed tolerance for mismatches between probe and target sequences. Mismatch tolerance is a priority for this application, due to DNA sequence variability among members of gene families. Arrays were created using the NimbleGen Maskless Array Synthesizer at Lawrence Livermore National Laboratory. Purified genomic DNA from combinations of one or more of the four target organisms, pure cultures of four related organisms, and environmental aerosol samples with spiked-in genomic DNA were hybridized to the arrays. Based on the success of this prototype, we plan to design further arrays in this series, with the goal of detecting all known virulence and antibiotic resistance gene families in a greatly expanded set of organisms.

  18. Study of stacked microstrip phased arrays

    Science.gov (United States)

    Arts, M. J.; Smolders, A. B.

    1993-06-01

    Two theoretical methods for studying stacked-patch microstrip phased arrays are compared: (1) the element-by-element approach (finite array approach) of Pozar (1986) and Smolders (1992); and (2) the infinite approach of Pozar and Shaubert (1984) and Liu et al. (1988). Both theories were found to give almost the same results for a 7 x 7 stacked microstrip antenna, except for edge array elements and for large scan angles. Edge array elements could only be analyzed properly by using a finite array approach. Coupling measurements were made on a 7 x 7 array with a single patch layer, and the results agreed well with calculations.

  19. A functional gene array for detection of bacterial virulence elements.

    Directory of Open Access Journals (Sweden)

    Crystal Jaing

    Full Text Available Emerging known and unknown pathogens create profound threats to public health. Platforms for rapid detection and characterization of microbial agents are critically needed to prevent and respond to disease outbreaks. Available detection technologies cannot provide broad functional information about known or novel organisms. As a step toward developing such a system, we have produced and tested a series of high-density functional gene arrays to detect elements of virulence and antibiotic resistance mechanisms. Our first generation array targets genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for gene family detection and discrimination. When tested with organisms at varying phylogenetic distances from the four target strains, the array detected orthologs for the majority of targeted gene families present in bacteria belonging to the same taxonomic family. In combination with whole-genome amplification, the array detects femtogram concentrations of purified DNA, either spiked in to an aerosol sample background, or in combinations from one or more of the four target organisms. This is the first report of a high density NimbleGen microarray system targeting microbial antibiotic resistance and virulence mechanisms. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples.

  20. FGX : a frequentist gene expression index for Affymetrix arrays

    NARCIS (Netherlands)

    Purutçuoğlu, Vilda; Wit, Ernst

    2007-01-01

    We consider a new frequentist gene expression index for Affymetrix oligonucleotide DNA arrays, using a similar probe intensity model as suggested previously, called the Bayesian gene expression index (BGX). According to this model, the perfect match and mismatch values are assumed to be correlated a

  1. NORMAL NASAL GENE EXPRESSION LEVELS USING CDNA ARRAY TECHNOLOGY

    Science.gov (United States)

    Normal Nasal Gene Expression Levels Using cDNA Array Technology. The nasal epithelium is a target site for chemically-induced toxicity and carcinogenicity. To detect and analyze genetic events which contribute to nasal tumor development, we first defined the gene expressi...

  2. Explorative study to identify novel candidate genes related to oxaliplatin efficacy and toxicity using a DNA repair array.

    NARCIS (Netherlands)

    Kweekel, D.M.; Antonini, N.F.; Nortier, J.W.; Punt, C.J.A.; Gelderblom, H.; Guchelaar, H.J.

    2009-01-01

    PURPOSE: To identify new polymorphisms (single nucleotide polymorphisms, SNPs) in DNA repair pathways that are associated with efficacy and toxicity in patients receiving oxaliplatin and capecitabine for advanced colorectal cancer (ACC). METHODS: We studied progression-free survival (PFS) in 91 ACC

  3. INDUCIBLE RNAi-MEDIATED GENE SILENCING USING NANOSTRUCTURED GENE DELIVERY ARRAYS

    Energy Technology Data Exchange (ETDEWEB)

    Mann, David George James [ORNL; McKnight, Timothy E [ORNL; Mcpherson, Jackson [University of Tennessee, Knoxville (UTK); Hoyt, Peter R [ORNL; Melechko, Anatoli Vasilievich [ORNL; Simpson, Michael L [ORNL; Sayler, Gary Steven [ORNL

    2008-01-01

    RNA interference has become a powerful biological tool over the last decade. In this study, a tetracycline-inducible shRNA vector system was designed for silencing CFP expression and introduced alongside the yfp marker gene into Chinese hamster ovary cells using spatially indexed vertically aligned carbon nanofiber arrays (VACNFs) in a gene delivery process termed impalefection. The VACNF architecture provided simultaneous delivery of multiple genes, subsequent adherence and proliferation of interfaced cells, and repeated monitoring of single cells over time. 24 hours after nanofiber-mediated delivery, 53.1% 10.4% of the cells that expressed the yfp marker gene were also fully silenced by the inducible CFP-silencing shRNA vector. Additionally, efficient CFP-silencing was observed in single cells among a population of cells that remained CFP-expressing. This effective transient expression system enables rapid analysis of gene silencing effects using RNAi in single cells and cell populations.

  4. Blood pressure loci identified with a gene-centric array.

    Science.gov (United States)

    Johnson, Toby; Gaunt, Tom R; Newhouse, Stephen J; Padmanabhan, Sandosh; Tomaszewski, Maciej; Kumari, Meena; Morris, Richard W; Tzoulaki, Ioanna; O'Brien, Eoin T; Poulter, Neil R; Sever, Peter; Shields, Denis C; Thom, Simon; Wannamethee, Sasiwarang G; Whincup, Peter H; Brown, Morris J; Connell, John M; Dobson, Richard J; Howard, Philip J; Mein, Charles A; Onipinla, Abiodun; Shaw-Hawkins, Sue; Zhang, Yun; Davey Smith, George; Day, Ian N M; Lawlor, Debbie A; Goodall, Alison H; Fowkes, F Gerald; Abecasis, Gonçalo R; Elliott, Paul; Gateva, Vesela; Braund, Peter S; Burton, Paul R; Nelson, Christopher P; Tobin, Martin D; van der Harst, Pim; Glorioso, Nicola; Neuvrith, Hani; Salvi, Erika; Staessen, Jan A; Stucchi, Andrea; Devos, Nabila; Jeunemaitre, Xavier; Plouin, Pierre-François; Tichet, Jean; Juhanson, Peeter; Org, Elin; Putku, Margus; Sõber, Siim; Veldre, Gudrun; Viigimaa, Margus; Levinsson, Anna; Rosengren, Annika; Thelle, Dag S; Hastie, Claire E; Hedner, Thomas; Lee, Wai K; Melander, Olle; Wahlstrand, Björn; Hardy, Rebecca; Wong, Andrew; Cooper, Jackie A; Palmen, Jutta; Chen, Li; Stewart, Alexandre F R; Wells, George A; Westra, Harm-Jan; Wolfs, Marcel G M; Clarke, Robert; Franzosi, Maria Grazia; Goel, Anuj; Hamsten, Anders; Lathrop, Mark; Peden, John F; Seedorf, Udo; Watkins, Hugh; Ouwehand, Willem H; Sambrook, Jennifer; Stephens, Jonathan; Casas, Juan-Pablo; Drenos, Fotios; Holmes, Michael V; Kivimaki, Mika; Shah, Sonia; Shah, Tina; Talmud, Philippa J; Whittaker, John; Wallace, Chris; Delles, Christian; Laan, Maris; Kuh, Diana; Humphries, Steve E; Nyberg, Fredrik; Cusi, Daniele; Roberts, Robert; Newton-Cheh, Christopher; Franke, Lude; Stanton, Alice V; Dominiczak, Anna F; Farrall, Martin; Hingorani, Aroon D; Samani, Nilesh J; Caulfield, Mark J; Munroe, Patricia B

    2011-12-09

    Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a bespoke gene-centric array to genotype an independent discovery sample of 25,118 individuals that combined hypertensive case-control and general population samples. We followed up four SNPs associated with BP at our p < 8.56 × 10(-7) study-specific significance threshold and six suggestively associated SNPs in a further 59,349 individuals. We identified and replicated a SNP at LSP1/TNNT3, a SNP at MTHFR-NPPB independent (r(2) = 0.33) of previous reports, and replicated SNPs at AGT and ATP2B1 reported previously. An analysis of combined discovery and follow-up data identified SNPs significantly associated with BP at p < 8.56 × 10(-7) at four further loci (NPR3, HFE, NOS3, and SOX6). The high number of discoveries made with modest genotyping effort can be attributed to using a large-scale yet targeted genotyping array and to the development of a weighting scheme that maximized power when meta-analyzing results from samples ascertained with extreme phenotypes, in combination with results from nonascertained or population samples. Chromatin immunoprecipitation and transcript expression data highlight potential gene regulatory mechanisms at the MTHFR and NOS3 loci. These results provide candidates for further study to help dissect mechanisms affecting BP and highlight the utility of studying SNPs and samples that are independent of those studied previously even when the sample size is smaller than that in previous studies.

  5. INDUCIBLE RNAi-MEDIATED GENE SILENCING USING NANOSTRUCTURED GENE DELIVERY ARRAYS

    Energy Technology Data Exchange (ETDEWEB)

    Mann, David George James [ORNL; McKnight, Timothy E [ORNL; Mcpherson, Jackson [University of Tennessee, Knoxville (UTK); Hoyt, Peter R [ORNL; Melechko, Anatoli Vasilievich [ORNL; Simpson, Michael L [ORNL; Sayler, Gary Steven [ORNL

    2008-01-01

    RNA interference has become a powerful biological tool over the last decade. In this study, a tetracycline-inducible shRNA vector system was designed for silencing CFP expression and delivered alongside the yfp marker gene into Chinese hamster ovary cells using impalefection on spatially indexed vertically aligned carbon nanofiber arrays (VACNFs). The VACNF architecture provided simultaneous delivery of multiple genes, subsequent adherence and proliferation of interfaced cells, and repeated monitoring of single cells over time. Following impalefection and tetracycline induction, 53.1% 10.4% of impalefected cells were fully silenced by the inducible CFP-silencing shRNA vector. Additionally, efficient CFP-silencing was observed in single cells among a population of cells that remained CFP-expressing. This effective transient expression system enables rapid analysis of gene silencing effects using RNAi in single cells and cell populations.

  6. Significance of RNA reference in tumour-related gene expression analyses by cDNA array.

    Science.gov (United States)

    Laytragoon-Lewin, Nongnit; Lagerlund, Magnus; Lundgren, Jan; Nordlander, Britt; Elmberger, Göran; Södergren, Towe; Lagerros, Christofer; Rutqvist, Lars Erik; Lewin, Freddi

    2005-01-01

    The cDNA array technique is an efficient approach for studying the expression of a large number of genes in a single experiment. The cDNA array analysis indicates the relative level of corresponding gene expression from a specimen and a reference. Our investigation was performed to address the significance of reference RNA on the outcome of the cancer-related gene expression profile obtained from cDNA array analysis. Human head and neck squamous cell carcinoma (HNSCC) biopsies and 5 sources of RNA reference were used for this purpose. In these biopsies, each individual patient expressed a unique set of genes both in normal and tumour tissue. It is important to note that 5 striking patterns of tumour-related gene expression were obtained according to the 5 references used. Significant differences in 60%, 16%, 15% and 15% of the genes expressed were shown when autologous normal matched tissue biopsy references were compared to pooled cell lines, allogenic normal mixed cell types, tumours or allogenic normal matched cell type references, respectively. Thus, theoretically and our study suggested that patient autologous normal cells matching with the tumour type should be the most suitable reference in cDNA array for the identification of individual tumour gene profiles with clinical purpose.

  7. Combining gene expression data from different generations of oligonucleotide arrays

    Directory of Open Access Journals (Sweden)

    Kong Sek

    2004-10-01

    Full Text Available Abstract Background One of the important challenges in microarray analysis is to take full advantage of previously accumulated data, both from one's own laboratory and from public repositories. Through a comparative analysis on a variety of datasets, a more comprehensive view of the underlying mechanism or structure can be obtained. However, as we discover in this work, continual changes in genomic sequence annotations and probe design criteria make it difficult to compare gene expression data even from different generations of the same microarray platform. Results We first describe the extent of discordance between the results derived from two generations of Affymetrix oligonucleotide arrays, as revealed in cluster analysis and in identification of differentially expressed genes. We then propose a method for increasing comparability. The dataset we use consists of a set of 14 human muscle biopsy samples from patients with inflammatory myopathies that were hybridized on both HG-U95Av2 and HG-U133A human arrays. We find that the use of the probe set matching table for comparative analysis provided by Affymetrix produces better results than matching by UniGene or LocusLink identifiers but still remains inadequate. Rescaling of expression values for each gene across samples and data filtering by expression values enhance comparability but only for few specific analyses. As a generic method for improving comparability, we select a subset of probes with overlapping sequence segments in the two array types and recalculate expression values based only on the selected probes. We show that this filtering of probes significantly improves the comparability while retaining a sufficient number of probe sets for further analysis. Conclusions Compatibility between high-density oligonucleotide arrays is significantly affected by probe-level sequence information. With a careful filtering of the probes based on their sequence overlaps, data from different

  8. Identification of SNP-containing regulatory motifs in the myelodysplastic syndromes model using SNP arrays and gene expression arrays

    Institute of Scientific and Technical Information of China (English)

    Jing Fan; Jennifer G.Dy; Chung-Che Chang; Xiaobo Zhou

    2013-01-01

    Myelodysplastic syndromes have increased in frequency and incidence in the American population,but patient prognosis has not significantly improved over the last decade.Such improvements could be realized if biomarkers for accurate diagnosis and prognostic stratification were successfully identified.In this study,we propose a method that associates two state-of-the-art array technologies-single nucleotide polymorphism (SNP) array and gene expression array-with gene motifs considered transcription factor-binding sites (TFBS).We are particularly interested in SNP-containing motifs introduced by genetic variation and mutation as TFBS.The potential regulation of SNP-containing motifs affects only when certain mutations occur.These motifs can be identified from a group of co-expressed genes with copy number variation.Then,we used a sliding window to identify motif candidates near SNPs on gene sequences.The candidates were filtered by coarse thresholding and fine statistical testing.Using the regression-based LARS-EN algorithm and a level-wise sequence combination procedure,we identified 28 SNP-containing motifs as candidate TFBS.We confirmed 21 of the 28 motifs with ChIP-chip fragments in the TRANSFAC database.Another six motifs were validated by TRANSFAC via searching binding fragments on coregulated genes.The identified motifs and their location genes can be considered potential biomarkers for myelodysplastic syndromes.Thus,our proposed method,a novel strategy for associating two data categories,is capable of integrating information from different sources to identify reliable candidate regulatory SNP-containing motifs introduced by genetic variation and mutation.

  9. Breast Carcinoma Cells in Primary Tumors and Effusions Have Different Gene Array Profiles

    Directory of Open Access Journals (Sweden)

    Sophya Konstantinovsky

    2010-01-01

    Full Text Available The detection of breast carcinoma cells in effusions is associated with rapidly fatal outcome, but these cells are poorly characterized at the molecular level. This study compared the gene array signatures of breast carcinoma cells in primary carcinomas and effusions. The genetic signature of 10 primary tumors and 10 effusions was analyzed using the Array-Ready Oligo set for the Human Genome platform. Results for selected genes were validated using PCR, Western blotting, and immunohistochemistry. Array analysis identified 255 significantly downregulated and 96 upregulated genes in the effusion samples. The majority of differentially expressed genes were part of pathways involved in focal adhesion, extracellular matrix-cell interaction, and the regulation of the actin cytoskeleton. Genes that were upregulated in effusions included KRT8, BCAR1, CLDN4, VIL2, while DCN, CLDN19, ITGA7, and ITGA5 were downregulated at this anatomic site. PCR, Western blotting, and immunohistochemistry confirmed the array findings for BCAR1, CLDN4, VIL2, and DCN. Our data show that breast carcinoma cells in primary carcinomas and effusions have different gene expression signatures, and differentially express a large number of molecules related to adhesion, motility, and metastasis. These differences may have a critical role in designing therapy and in prognostication for patients with metastatic disease localized to the serosal cavities.

  10. Cloning chromosome specific genes by reciprocal probing of arrayed cDNA and cosmid libraries

    Energy Technology Data Exchange (ETDEWEB)

    Yazdani, A.; Lee, C.C.; Wehnert, M. [Baylor College of Medicine, Houston, TX (United States)] [and others

    1994-09-01

    A human gene map will greatly facilitate the association of genes to single locus diseases and provide candidates for genes involved in complex genetic traits. Given the estimated 100,000 human genes an integrated strategy with a high throughput approach for isolation and mapping of expressed sequences is needed to create such a gene map. We have developed an approach that allows high throughput gene isolation and mapping using arrayed genomic and cDNA lambda libraries. Reciprocal probing of the arrayed genomic and cDNA cosmic libraries can rapidly establish cDNA-cosmid associations. Fluorescence in situ hybridization (FISH) chromosomal mapping and expressed sequence tag/sequence tag site (EST/STS) primers generated from DNA sequence of PCR-based mapping using somatic hybrid cell line mapping panels were utilized to characterize further the hybridization-based cDNA cosmid association. We have applied this approach to chromosome 17 using a placental cDNA library and have identified a total of 30 genes out of which 11 are novel. Furthermore seven cDNAs were mapped to 17q21 in this study, providing novel candidate genes for BRCA-1 gene for early onset breast cancer. The results of our study clearly show that an integration of an expression map into physical and genetic maps can provide candidate genes for human diseases that have been mapped to specific regions. This approach combined with the current physical mapping efforts could efficiently provide a detailed human gene map.

  11. Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.

    Directory of Open Access Journals (Sweden)

    Ki-Hong Jung

    Full Text Available Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa. We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org. The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics.

  12. Analyzing the gene expression profile of pediatric acute myeloid leukemia with real-time PCR arrays

    Directory of Open Access Journals (Sweden)

    Yan-Fang Tao

    2012-09-01

    Full Text Available Abstract Background The Real-time PCR Array System is the ideal tool for analyzing the expression of a focused panel of genes. In this study, we will analyze the gene expression profile of pediatric acute myeloid leukemia with real-time PCR arrays. Methods Real-time PCR array was designed and tested firstly. Then gene expression profile of 11 pediatric AML and 10 normal controls was analyzed with real-time PCR arrays. We analyzed the expression data with MEV (Multi Experiment View cluster software. Datasets representing genes with altered expression profile derived from cluster analyses were imported into the Ingenuity Pathway Analysis Tool. Results We designed and tested 88 real-time PCR primer pairs for a quantitative gene expression analysis of key genes involved in pediatric AML. The gene expression profile of pediatric AML is significantly different from normal control; there are 19 genes up-regulated and 25 genes down-regulated in pediatric AML. To investigate possible biological interactions of differently regulated genes, datasets representing genes with altered expression profile were imported into the Ingenuity Pathway Analysis Tool. The results revealed 12 significant networks. Of these networks, Cellular Development, Cellular Growth and Proliferation, Tumor Morphology was the highest rated network with 36 focus molecules and the significance score of 41. The IPA analysis also groups the differentially expressed genes into biological mechanisms that are related to hematological disease, cell death, cell growth and hematological system development. In the top canonical pathways, p53 and Huntington’s disease signaling came out to be the top two most significant pathways with a p value of 1.5E-8 and2.95E-7, respectively. Conclusions The present study demonstrates the gene expression profile of pediatric AML is significantly different from normal control; there are 19 genes up-regulated and 25 genes down-regulated in pediatric AML. We

  13. Some statistical properties of gene expression clustering for array data

    DEFF Research Database (Denmark)

    Abreu, G C G; Pinheiro, A; Drummond, R D

    2010-01-01

    DNA array data without a corresponding statistical error measure. We propose an easy-to-implement and simple-to-use technique that uses bootstrap re-sampling to evaluate the statistical error of the nodes provided by SOM-based clustering. Comparisons between SOM and parametric clustering are presented...... for simulated as well as for two real data sets. We also implement a bootstrap-based pre-processing procedure for SOM, that improves the false discovery ratio of differentially expressed genes. Code in Matlab is freely available, as well as some supplementary material, at the following address: https...

  14. Gene chip array for differentiation of mycobacterial species and detection of drug resistance

    Institute of Scientific and Technical Information of China (English)

    SHI Xiao-chun; LIU Xiao-qing; XIE Xiu-li; XU Ying-chun; ZHAO Zhi-xian

    2012-01-01

    Background Gene chip array can differentiate isolated mycobacterial strains using vadous mycobacterium specific probes simultaneously.Gene chip array can evaluate drug resistance to isoniazid and rifampin of tuberculosis strains by detecting drug resistance related gene mutation.This technique has great potential for clinical application.We performed a retrospective study to investigate the capability of gene chip array in the rapid differentiation of species and detection of drug resistance in mycobacterium,and to evaluate its clinical efficacy.Methods We selected 39 patients (54 clinical mycobacterium isolates),used gene chip array to identify the species of these isolates and detect drug resistance to isoniazid and rifampin in Mycobacterium tuberculosis isolates.Meanwhile,these patients' clinical data were analyzed retrospectively.Results Among these 39 patients whose mycopacterium culture were positive,32 patients' isolates were identified as Mycobacterium tubercu/osis, all of them were clinical infection. Seven patients' isolates were identified as non-tuberculosis mycobacterium.Analyzed with their clinical data,only two patients were considered as clinical infection,both of them were diagnosed as hematogenous disseminated Mycobacterium introcellulare infection.The other five patients' isolates were of no clinical significance; their clinical samples were all respiratory specimens.Clinical manifestations of tuberculosis and non-tuberculous mycobacterial infections were similar.Isoniazid resistance was detected in two tuberculosis patients,while rifampin resistance was detected in one tuberculosis patient; there was another patient whose Mycobacterium tuberculosis isolate was resistant to both isoniazid and rifampin (belongs to multidrug resistance tuberculosis).The fact that this patient did not respond to routine anti-tuberculosis chemotherapy also confirmed this result.Conclusions Gene chip array may be a simple,rapid,and reliable method for the

  15. miRSNPs of miR1274 and miR3202 Genes that Target MeCP2 and DNMT3b Are Associated with Lung Cancer Risk: A Study Conducted on MassARRAY Genotyping.

    Science.gov (United States)

    Ozbayer, Cansu; Degirmenci, Irfan; Ustuner, Derya; Ak, Guntulu; Saydam, Faruk; Colak, Ertugrul; Gunes, Hasan Veysi; Metintas, Muzaffer

    2016-01-01

    Genetic variants of miRNAs that target DNMTs and MBDs involved in DNA methylation were scanned with current databases, and 35 miRSNPs in 22 miRNA genes were identified. The aim of the study was to determine the association between these variants of miRNA genes and lung cancer (LC). DNA samples were isolated from blood samples and genotyped using a Sequenom MassARRAY System. An association between the rs188912830 gene variant of miR3202 that targets the MeCP2 protein and LC was indicated in both subtypes. The presence of the C-allele in patients with LC and its subtypes was significantly lower, and the absence of the C-allele was determined to increase the risk of LC by 7,429-times compared to the presence (p=0,010). The rs318039 gene variant of miR1274 that targets DNMT3b was found to be associated with LC subtypes. When allele distributions were compared, the numbers of individuals with the C-allele were significantly lower in the NSCLC and SCLC groups. No significant associations were found for the rs72563729 variant of the miR200b gene that targets DNMT3a or for the rs145416750 variant of the miR513c gene that targets TRDMT1. The other 33 variants were found to be ancestral genotypes. Consequently, rs188912830 and rs318039 variations were associated with LC subtypes. Importantly, this study is the first to indicate the functional characterisation of miRSNPs of genes that target DNA methylation.

  16. X chromosome array-CGH for the identification of novel X-linked mental retardation genes.

    Science.gov (United States)

    Bauters, Marijke; Van Esch, Hilde; Marynen, Peter; Froyen, Guy

    2005-01-01

    Array-CGH technology for the detection of submicroscopic copy number changes in the genome has recently been developed for the identification of novel disease-associated genes. It has been estimated that submicroscopic genomic deletions or duplications will be present in 5-7% of patients with idiopathic mental retardation (MR). Since 30% more males than females are diagnosed with MR, we have developed a full coverage X chromosome array-CGH with a theoretical resolution of 82 kb, for the detection of copy number alterations in patients with suspected X-linked mental retardation (XLMR). First, we have validated the genomic location of X-derived clones through male versus female hybridisations. Next, we validated our array for efficient and reproducible detection of known alterations in XLMR patients. In all cases, we were able to detect the deletions and duplications in males as well as females. Due to the high resolution of our X-array, the boundaries of the genomic aberrations could clearly be identified making genotype-phenotype studies more reliable. Here, we describe the production and validation of a full coverage X-array-CGH, which will allow for fast and easy screening of submicroscopic copy number alterations in XLMR patients with the aim to identify novel MR genes or mechanisms involved in a deranged cognitive development.

  17. Evaluation of low density array technology for quantitative parallel measurement of multiple genes in human tissue

    Directory of Open Access Journals (Sweden)

    Harmer Daniel W

    2006-02-01

    Full Text Available Abstract Background Low density arrays (LDAs have recently been introduced as a novel approach to gene expression profiling. Based on real time quantitative RT-PCR (QRT-PCR, these arrays enable a more focused and sensitive approach to the study of gene expression than gene chips, while offering higher throughput than more established approaches to QRT-PCR. We have now evaluated LDAs as a means of determining the expression of multiple genes simultaneously in human tissues and cells. Results Comparisons between LDAs reveal low variability, with correlation coefficients close to 1. By performing 2-fold and 10-fold serial dilutions of cDNA samples in the LDAs we determined a clear linear relationship between the gene expression data points over 5 orders of magnitude. We also showed that it is possible to use LDAs to accurately and quantitatively detect 2-fold changes in target copy number as well as measuring genes that are expressed with low and high copy numbers in the range of 1 × 102 – 1 × 106 copies. Furthermore, the data generated by the LDA from a cell based pharmacological study were comparable to data generated by conventional QRT-PCR. Conclusion LDAs represent a valuable new approach for sensitive and quantitative gene expression profiling.

  18. Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression

    Directory of Open Access Journals (Sweden)

    Eichner Lillian J

    2005-07-01

    Full Text Available Abstract Background Affymetrix GeneChip Array and Massively Parallel Signature Sequencing (MPSS are two high throughput methodologies used to profile transcriptomes. Each method has certain strengths and weaknesses; however, no comparison has been made between the data derived from Affymetrix arrays and MPSS. In this study, two lineage-related prostate cancer cell lines, LNCaP and C4-2, were used for transcriptome analysis with the aim of identifying genes associated with prostate cancer progression. Methods Affymetrix GeneChip array and MPSS analyses were performed. Data was analyzed with GeneSpring 6.2 and in-house perl scripts. Expression array results were verified with RT-PCR. Results Comparison of the data revealed that both technologies detected genes the other did not. In LNCaP, 3,180 genes were only detected by Affymetrix and 1,169 genes were only detected by MPSS. Similarly, in C4-2, 4,121 genes were only detected by Affymetrix and 1,014 genes were only detected by MPSS. Analysis of the combined transcriptomes identified 66 genes unique to LNCaP cells and 33 genes unique to C4-2 cells. Expression analysis of these genes in prostate cancer specimens showed CA1 to be highly expressed in bone metastasis but not expressed in primary tumor and EPHA7 to be expressed in normal prostate and primary tumor but not bone metastasis. Conclusion Our data indicates that transcriptome profiling with a single methodology will not fully assess the expression of all genes in a cell line. A combination of transcription profiling technologies such as DNA array and MPSS provides a more robust means to assess the expression profile of an RNA sample. Finally, genes that were differentially expressed in cell lines were also differentially expressed in primary prostate cancer and its metastases.

  19. Spallation reactions studied with 4-detector arrays

    Indian Academy of Sciences (India)

    J Galin

    2001-07-01

    Recently there has been a renewed interest in the study of spallation reactions in basic nuclear physics as well as in potential applications. Spallation reactions induced by light projectiles (protons, antiprotons, pions, etc.) in the GeV range allow the formation of hot nuclei which do not suffer the collective excitations (compression, rotation, deformation) unavoidable when using massive projectiles. Such nuclei provide an ideal testbench for probing their decay as a function of excitation energy. In these investigations, 4-detector arrays for charged particles and neutrons play a major role in the event-by-event sorting according to the excitation energy of the nucleus. Spallation reactions induced on heavy nuclei allow the conversion of the incident GeV proton into several tens of evaporated neutrons. The neutron production in thick targets has been investigated in great detail thanks to the use of high efficiency neutron detector arrays. When scattered on samples of inert or biological materials, these neutrons can be used to study details of the material structure. They could also be utilized for the transmutation of long-lived nuclear wastes or for the feeding of sub-critical nuclear reactors. The role of different types of multi-detector arrays is highlighted in this paper. Several references are also given for different uses of high efficiency neutron detectors in other contexts.

  20. Studies on coaxial circular array for underwater transducer applications

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, B.

    This thesis presents analytical methods to study important aspects of a coaxial circular array for wideband underwater transducer application. It begins with detailed theoretical study of a coaxial circular array of three turns and an analysis...

  1. Tandem gene arrays in Trypanosoma brucei: Comparative phylogenomic analysis of duplicate sequence variation

    Directory of Open Access Journals (Sweden)

    Jackson Andrew P

    2007-04-01

    Full Text Available Abstract Background The genome sequence of the protistan parasite Trypanosoma brucei contains many tandem gene arrays. Gene duplicates are created through tandem duplication and are expressed through polycistronic transcription, suggesting that the primary purpose of long, tandem arrays is to increase gene dosage in an environment where individual gene promoters are absent. This report presents the first account of the tandem gene arrays in the T. brucei genome, employing several related genome sequences to establish how variation is created and removed. Results A systematic survey of tandem gene arrays showed that substantial sequence variation existed across the genome; variation from different regions of an array often produced inconsistent phylogenetic affinities. Phylogenetic relationships of gene duplicates were consistent with concerted evolution being a widespread homogenising force. However, tandem duplicates were not usually identical; therefore, any homogenising effect was coincident with divergence among duplicates. Allelic gene conversion was detected using various criteria and was apparently able to both remove and introduce sequence variation. Tandem arrays containing structural heterogeneity demonstrated how sequence homogenisation and differentiation can occur within a single locus. Conclusion The use of multiple genome sequences in a comparative analysis of tandem gene arrays identified substantial sequence variation among gene duplicates. The distribution of sequence variation is determined by a dynamic balance of conservative and innovative evolutionary forces. Gene trees from various species showed that intraspecific duplicates evolve in concert, perhaps through frequent gene conversion, although this does not prevent sequence divergence, especially where structural heterogeneity physically separates a duplicate from its neighbours. In describing dynamics of sequence variation that have consequences beyond gene dosage, this

  2. HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data

    Directory of Open Access Journals (Sweden)

    Wouters Bas J

    2010-05-01

    Full Text Available Abstract Background Tiling-arrays are applicable to multiple types of biological research questions. Due to its advantages (high sensitivity, resolution, unbiased, the technology is often employed in genome-wide investigations. A major challenge in the analysis of tiling-array data is to define regions-of-interest, i.e., contiguous probes with increased signal intensity (as a result of hybridization of labeled DNA in a region. Currently, no standard criteria are available to define these regions-of-interest as there is no single probe intensity cut-off level, different regions-of-interest can contain various numbers of probes, and can vary in genomic width. Furthermore, the chromosomal distance between neighboring probes can vary across the genome among different arrays. Results We have developed Hypergeometric Analysis of Tiling-arrays (HAT, and first evaluated its performance for tiling-array datasets from a Chromatin Immunoprecipitation study on chip (ChIP-on-chip for the identification of genome-wide DNA binding profiles of transcription factor Cebpa (used for method comparison. Using this assay, we can refine the detection of regions-of-interest by illustrating that regions detected by HAT are more highly enriched for expected motifs in comparison with an alternative detection method (MAT. Subsequently, data from a retroviral insertional mutagenesis screen were used to examine the performance of HAT among different applications of tiling-array datasets. In both studies, detected regions-of-interest have been validated with (qPCR. Conclusions We demonstrate that HAT has increased specificity for analysis of tiling-array data in comparison with the alternative method, and that it accurately detects regions-of-interest in two different applications of tiling-arrays. HAT has several advantages over previous methods: i as there is no single cut-off level for probe-intensity, HAT can detect regions-of-interest at various thresholds, ii it can

  3. Array2BIO: from microarray expression data to functional annotation of co-regulated genes

    Directory of Open Access Journals (Sweden)

    Rasley Amy

    2006-06-01

    Full Text Available Abstract Background There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility. Results Array2BIO converts raw intensities into probe expression values, automatically maps those to genes, and subsequently identifies groups of co-expressed genes using two complementary approaches: (1 comparative analysis of signal versus control and (2 clustering analysis of gene expression across different conditions. The identified genes are assigned to functional categories based on Gene Ontology classification and KEGG protein interaction pathways. Array2BIO reliably handles low-expressor genes and provides a set of statistical methods for quantifying expression levels, including Benjamini-Hochberg and Bonferroni multiple testing corrections. An automated interface with the ECR Browser provides evolutionary conservation analysis for the identified gene loci while the interconnection with Crème allows prediction of gene regulatory elements that underlie observed expression patterns. Conclusion We have developed Array2BIO – a web based tool for rapid comprehensive analysis of Affymetrix microarray expression data, which also allows users to link expression data to Dcode.org comparative genomics tools and integrates a system for translating co-expression data into mechanisms of gene co-regulation. Array2BIO is publicly available at http://array2bio.dcode.org.

  4. Integrated strain array for cellular mechanobiology studies

    Science.gov (United States)

    Simmons, C. S.; Sim, J. Y.; Baechtold, P.; Gonzalez, A.; Chung, C.; Borghi, N.; Pruitt, B. L.

    2011-05-01

    We have developed an integrated strain array for cell culture enabling high-throughput mechano-transduction studies. Biocompatible cell culture chambers were integrated with an acrylic pneumatic compartment and microprocessor-based control system. Each element of the array consists of a deformable membrane supported by a cylindrical pillar within a well. For user-prescribed waveforms, the annular region of the deformable membrane is pulled into the well around the pillar under vacuum, causing the pillar-supported region with cultured cells to be stretched biaxially. The optically clear device and pillar-based mechanism of operation enables imaging on standard laboratory microscopes. Straightforward fabrication utilizes off-the-shelf components, soft lithography techniques in polydimethylsiloxane and laser ablation of acrylic sheets. Proof of compatibility with basic biological assays and standard imaging equipment were accomplished by straining C2C12 skeletal myoblasts on the device for 6 h. At higher strains, cells and actin stress fibers realign with a circumferential preference.

  5. A Study of End-Fed Arrays

    CERN Document Server

    Kondylis, Konstantinos; Zimourtopoulos, Petros

    2010-01-01

    This paper presents a general analysis of end-fed space arrays with application to self-standing linear arrays of parallel dipoles. A number of test array models were simulated, constructed and their radiation pattern was then measured. The experimental and computational results were found to be in good agreement. The developed software applications are available through the Internet as FLOSS Free Libre Open Source Software.

  6. Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio

    Directory of Open Access Journals (Sweden)

    Gillings Michael R

    2006-01-01

    Full Text Available Abstract Background Integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene cassettes. Gene cassettes generally consist of a promoterless gene associated with a recombination site known as a 59-base element (59-be. Multiple insertion events can lead to the assembly of large integron-associated cassette arrays. The most striking examples are found in Vibrio, where such cassette arrays are widespread and can range from 30 kb to 150 kb. Besides those found in completely sequenced genomes, no such array has yet been recovered in its entirety. We describe an approach to systematically isolate, sequence and annotate large integron gene cassette arrays from bacterial strains. Results The complete Vibrio sp. DAT722 integron cassette array was determined through the streamlined approach described here. To place it in an evolutionary context, we compare the DAT722 array to known vibrio arrays and performed phylogenetic analyses for all of its components (integrase, 59-be sites, gene cassette encoded genes. It differs extensively in terms of genomic context as well as gene cassette content and organization. The phylogenetic tree of the 59-be sites collectively found in the Vibrio gene cassette pool suggests frequent transfer of cassettes within and between Vibrio species, with slower transfer rates between more phylogenetically distant relatives. We also identify multiple cases where non-integron chromosomal genes seem to have been assembled into gene cassettes and others where cassettes have been inserted into chromosomal locations outside integrons. Conclusion Our systematic approach greatly facilitates the isolation and annotation of large integrons gene cassette arrays. Comparative analysis of the Vibrio sp. DAT722 integron obtained through this approach to those found in other vibrios confirms the role of this genetic element in promoting lateral gene transfer and suggests a high rate of gene

  7. Development and application of functional gene arrays for microbial community analysis

    Institute of Scientific and Technical Information of China (English)

    Z.L.HE; J.D.VAN NOSTRAND; L.Y.WU; J.Z.ZHOU

    2008-01-01

    Functional gene markers can provide important information about functional gene diversity and potential activity of microbial communities.Although microarray technology has been successfully applied to study gene expression for pure cultures,simple,and artificial microbial communities,adapting such a technology to analyze complex microbial communities still presents a lot of challenges in terms of design,sample preparation,and data analysis.This work is focused on the development and application of functional gene arrays (FGAs) to target key functional gene markers for microbial community studies.A few key issues specifically related to FGAs,such as oligonucleotide probe design,nucleic acid extraction and purification,data analysis,specificity,sensitivity,and quantitative capability are discussed in detail.Recent studies have demonstrated that FGAs can provide specific,sensitive,and potentially quantitative information about microbial communities from a variety of natural environments and controlled ecosystems.This technology is expected to revolutionize the analysis of microbial communities,and link microbial structure to ecosystem functioning.

  8. Analysis of gene expression patterns with cDNA micro-array during late stage of spermatogenesis in mice

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The differentiation process of round spermatids to spermatozoa during the late stage of spermatogenesis is called spermiogenesis. To explore spermiogenesis-related genes, cDNA microarray was used to study expression patterns of 1176 genes in pachytene spermatocytes, round spermatids and elongating spermatids of Balb/c mice. The results showed that 208 genes were detected in all the three cell types. Most of them were down-regulated from pachytene spermatocytes to round spermatids and elongating spermatids. However, up-regulation of 7 genes expression in round spermatids and 3 genes in elongating spermatids were found. Expression of 7 differentially expressed genes in cDNA arrays was further confirmed by semi-quantitative RT-PCR study. The RT-PCR results indicated that the expression of 6 genes was consistent with that in cDNA arrays, only one gene did not show differential expression by RT-PCR. These results may provide important clues for studying of expression, regulation, and function of spermiogenesis-related genes.

  9. Altered expression of mitochondrial related genes in the native Tibetan placents by mitochondrial cDNA array analysis

    Institute of Scientific and Technical Information of China (English)

    Luo Yongjun; Gao Wenxiang; Zhao Xiuxin; Suo Lang; Chen Li; Liu Fuyu; Song Tonglin; Chen Jian; Gao Yuqi

    2009-01-01

    Objective: To explore the mechanism of native Tibetan fetuses adaptation to hypoxia, we tried to find the different expression genes about mitochondrial function in the native Tibetan placents. Methods: In this study, the placents of native Tibetan and the high-altitude Han (ha-Han) were collected. After the total RNA extraction, the finally synthesized cDNAs were hybridized to mitochondrial array to find the altered expression genes between them. Then, the cytochrome c oxidase 17 (Coxl7), dynactin 2 (DCTN2, also known as p50), and vascular endothelial growth factor receptor (VEGFR, also known as KDR) were chosen from the altered expression genes to further verify the array results using the SYBR Green real-time PCR. Because the altered expression genes (such as Cybb and Coxl 7) in the array results related to the activities of COXI and COXIV, the placental mitochondria activities of COXI and COXIV were measured to find their changes in the hypoxia. Results: By a standard of >1.5 or <0.67, there were 24 different expressed genes between the native Tibetan and the ha-Han placents, including 3 up-regulated genes and 21 down-regulated genes. These genes were related to energy metabolism, signal transduction, cell proliferation, electron transport, cell adhesion, nucleotide-excision repair. The array results of Coxl7, DCTN2 and KDR were further verified by the real-time RT-PCR. Through the mitochondria respiration measurements, the activity of COXI in the native Tibetan placents were higher than that of ha-Han, there was no difference in COXIV activity between them. Conclusion: The altered mitochondrial related genes in the native Tibetan placents may have a role in the high altitude adaptation for fetuses through changing the activity of mitochondrial COX.

  10. Combustion of Interacting Droplet Arrays Being Studied

    Science.gov (United States)

    Dietrich, Daniel L.

    2002-01-01

    The combustion of liquid fuels is a major source of energy in the world today, and the majority of these fuels are burned in the form of a spray. This droplet combustion project at the NASA Glenn Research Center has the overall goal of providing a better understanding of spray combustion by extending existing studies of single droplets to a regime where droplet interactions are important (as occurs in a practical spray). The Combustion of Interacting Droplet Arrays is a collaborative effort between Glenn and the National Center for Microgravity Research. The group at Glenn also collaborates with scientists at the National Institute of Advanced Industrial Science and Technology in Hokkaido, Japan. The project is studying the combustion of a small number of droplets suspended on small quartz fibers in a 0.1-atm combustion chamber. Data consist primarily of video images of the flames and droplets. The tests are being conducted in Glenn's reduced-gravity facilities (2.2-sec and 5.2-sec drop towers) and in the Japan Microgravity Center's 10-sec drop tower (JAMIC).

  11. Identification of brassinosteroid responsive genes in Arabidopsis by cDNA array

    Institute of Scientific and Technical Information of China (English)

    胡玉欣; 汪政科; 王永红; 包方; 李凝; 彭镇华; 李家洋

    2001-01-01

    We have systematically monitored brassinosteroid (BR) responsive genes in a BR-deficient mutant det2 suspension culture of Arabidopsis by using a cDNA array approach. Among 13000 cDNA clones arrayed on filters, 53 BR responsive clones were identified and designated BRR1-BRR53. Sequence analysis of 43 clones showed that 19 clones are novel genes, 3 clones are genes involved in the control of cell division, 4 clones are genes related to plant stress responses, 4 clones are transcriptional factor or signal transduction component genes, and 3 clones are genes involved in RNA splicing or structure forming. In addition, we also found that BR regulated the transcription of genes related to many physiological processes, such as photoreaction, ion transportation and some metabolic processes. These findings present molecular evidence that BR plays an essential role in plant growth and development.

  12. Sensivity studies for the Cherenkov Telescope Array

    Science.gov (United States)

    Collado, Tarek Hassan

    2015-06-01

    Since the creation of the first telescope in the 17th century, every major discovery in astrophysics has been the direct consequence of the development of novel observation techniques, opening new windows in the electromagnetic spectrum. After Karl Jansky discovered serendipitously the first radio source in 1933, Grote Reber built the first parabolic radio telescope in his backyard, planting the seed of a whole new field in astronomy. Similarly, new technologies in the 1950s allowed the establishment of other fields, such as the infrared, ultraviolet or the X-rays. The highest energy end of the electromagnetic spectrum, the γ-ray range, represents the last unexplored window for astronomers and should reveal the most extreme phenomena that take place in the Universe. Given the technical complexity of γ-ray detection and the extremely relative low fluxes, γ-ray astronomy has undergone a slower development compared to other wavelengths. Nowadays, the great success of consecutive space missions together with the development and refinement of new detection techniques from the ground, has allowed outstanding scientific results and has brought gamma-ray astronomy to a worthy level in par with other astronomy fields. This work is devoted to the study and improvement of the future Cherenkov Telescope Array (CTA), the next generation of ground based γ-ray detectors, designed to observe photons with the highest energies ever observed from cosmic sources.

  13. Mapping of bionic array electric field focusing in plasmid DNA-based gene electrotransfer.

    Science.gov (United States)

    Browne, C J; Pinyon, J L; Housley, D M; Crawford, E N; Lovell, N H; Klugmann, M; Housley, G D

    2016-04-01

    Molecular medicine through gene therapy is challenged to achieve targeted action. This is now possible utilizing bionic electrode arrays for focal delivery of naked (plasmid) DNA via gene electrotransfer. Here, we establish the properties of array-based electroporation affecting targeted gene delivery. An array with eight 300 μm platinum ring electrodes configured as a cochlear implant bionic interface was used to transduce HEK293 cell monolayers with a plasmid-DNA green fluorescent protein (GFP) reporter gene construct. Electroporation parameters were pulse intensity, number, duration, separation and electrode configuration. The latter determined the shape of the electric fields, which were mapped using a voltage probe. Electrode array-based electroporation was found to require ~100 × lower applied voltages for cell transduction than conventional electroporation. This was found to be due to compression of the field lines orthogonal to the array. A circular area of GFP-positive cells was created when the electrodes were ganged together as four adjacent anodes and four cathodes, whereas alternating electrode polarity created a linear area of GFP-positive cells. The refinement of gene delivery parameters was validated in vivo in the guinea pig cochlea. These findings have significant clinical ramifications, where spatiotemporal control of gene expression can be predicted by manipulation of the electric field via current steering at a cellular level.

  14. Gene expression profiles in squamous cell cervical carcinoma using array-based comparative genomic hybridization analysis.

    Science.gov (United States)

    Choi, Y-W; Bae, S M; Kim, Y-W; Lee, H N; Kim, Y W; Park, T C; Ro, D Y; Shin, J C; Shin, S J; Seo, J-S; Ahn, W S

    2007-01-01

    Our aim was to identify novel genomic regions of interest and provide highly dynamic range information on correlation between squamous cell cervical carcinoma and its related gene expression patterns by a genome-wide array-based comparative genomic hybridization (array-CGH). We analyzed 15 cases of cervical cancer from KangNam St Mary's Hospital of the Catholic University of Korea. Microdissection assay was performed to obtain DNA samples from paraffin-embedded cervical tissues of cancer as well as of the adjacent normal tissues. The bacterial artificial chromosome (BAC) array used in this study consisted of 1440 human BACs and the space among the clones was 2.08 Mb. All the 15 cases of cervical cancer showed the differential changes of the cervical cancer-associated genetic alterations. The analysis limit of average gains and losses was 53%. A significant positive correlation was found in 8q24.3, 1p36.32, 3q27.1, 7p21.1, 11q13.1, and 3p14.2 changes through the cervical carcinogenesis. The regions of high level of gain were 1p36.33-1p36.32, 8q24.3, 16p13.3, 1p36.33, 3q27.1, and 7p21.1. And the regions of homozygous loss were 2q12.1, 22q11.21, 3p14.2, 6q24.3, 7p15.2, and 11q25. In the high level of gain regions, GSDMDC1, RECQL4, TP73, ABCF3, ALG3, HDAC9, ESRRA, and RPS6KA4 were significantly correlated with cervical cancer. The genes encoded by frequently lost clones were PTPRG, GRM7, ZDHHC3, EXOSC7, LRP1B, and NR3C2. Therefore, array-CGH analyses showed that specific genomic alterations were maintained in cervical cancer that were critical to the malignant phenotype and may give a chance to find out possible target genes present in the gained or lost clones.

  15. Hybrid Enrichment Verification Array: Module Characterization Studies

    Energy Technology Data Exchange (ETDEWEB)

    Zalavadia, Mital A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Smith, Leon E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); McDonald, Benjamin S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kulisek, Jonathan A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mace, Emily K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Deshmukh, Nikhil S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-03-01

    The work presented in this report is focused on the characterization and refinement of the Hybrid Enrichment Verification Array (HEVA) approach, which combines the traditional 186-keV 235U signature with high-energy prompt gamma rays from neutron capture in the detector and surrounding collimator material, to determine the relative enrichment and 235U mass of the cylinder. The design of the HEVA modules (hardware and software) deployed in the current field trial builds on over seven years of study and evolution by PNNL, and consists of a ø3''×3'' NaI(Tl) scintillator coupled to an Osprey digital multi-channel analyzer tube base from Canberra. The core of the HEVA methodology, the high-energy prompt gamma-ray signature, serves as an indirect method for the measurement of total neutron emission from the cylinder. A method for measuring the intrinsic efficiency of this “non-traditional” neutron signature and the results from a benchmark experiment are presented. Also discussed are potential perturbing effects on the non-traditional signature, including short-lived activation of materials in the HEVA module. Modeling and empirical results are presented to demonstrate that such effects are expected to be negligible for the envisioned implementation scenario. In comparison to previous versions, the new design boosts the high-energy prompt gamma-ray signature, provides more flexible and effective collimation, and improves count-rate management via commercially available pulse-processing electronics with a special modification prompted by PNNL.

  16. Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression.

    Science.gov (United States)

    Kadam, Anagha; Janto, Benjamin; Eutsey, Rory; Earl, Joshua P; Powell, Evan; Dahlgren, Margaret E; Hu, Fen Z; Ehrlich, Garth D; Hiller, N Luisa

    2015-02-02

    There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome.

  17. Heteroduplex analysis by capillary array electrophoresis for rapid mutation detection in large multiexon genes.

    Science.gov (United States)

    Velasco, Eladio; Infante, Mar; Durán, Mercedes; Pérez-Cabornero, Lucía; Sanz, David J; Esteban-Cardeñosa, Eva; Miner, Cristina

    2007-01-01

    Heteroduplex analysis (HA) has proven to be a robust tool for mutation detection. HA by capillary array electrophoresis (HA-CAE) was developed to increase throughput and allow the scanning of large multiexon genes in multicapillary DNA sequencers. HA-CAE is a straightforward and high-throughput technique to detect both known and novel DNA variants with a high level of sensitivity and specificity. It consists of only three steps: multiplex-PCR using fluorescently labeled primers, heteroduplex formation and electrophoresis in a multicapillary DNA sequencer. It allows, e.g., the complete coding and flanking intronic sequences of BRCA1 and BRCA2 genes from two patients (approximately 25 kb each) to be scanned in a single run of a 16-capillary sequencer, and has enabled us to detect 150 different mutations to date (both single nucleotide substitutions, or SNSs, and small insertions/deletions). Here, we describe the protocol developed in our laboratory to scan BRCA1, BRCA2, MLH1, MSH2 and MSH6 genes using an ABI3130XL sequencer. This protocol could be adapted to other instruments or to the study of other large multiexon genes and can be completed in 7-8 h.

  18. Using Antenna Arrays to Motivate the Study of Sinusoids

    Science.gov (United States)

    Becker, J. P.

    2010-01-01

    Educational activities involving antenna arrays to motivate the study of sinusoids are described. Specifically, using fundamental concepts related to phase and simple geometric arguments, students are asked to predict the location of interference nulls in the radiation pattern of two-element phased array antennas. The location of the radiation…

  19. Using Antenna Arrays to Motivate the Study of Sinusoids

    Science.gov (United States)

    Becker, J. P.

    2010-01-01

    Educational activities involving antenna arrays to motivate the study of sinusoids are described. Specifically, using fundamental concepts related to phase and simple geometric arguments, students are asked to predict the location of interference nulls in the radiation pattern of two-element phased array antennas. The location of the radiation…

  20. Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes

    DEFF Research Database (Denmark)

    Weile, Christian; Gardner, Paul P; Hedegaard, Mads M

    2007-01-01

    BACKGROUND: Within the last decade a large number of noncoding RNA genes have been identified, but this may only be the tip of the iceberg. Using comparative genomics a large number of sequences that have signals concordant with conserved RNA secondary structures have been discovered in the human...... genome. Moreover, genome wide transcription profiling with tiling arrays indicate that the majority of the genome is transcribed. RESULTS: We have combined tiling array data with genome wide structural RNA predictions to search for novel noncoding and structural RNA genes that are expressed in the human...... of 3 of the hairpin structures and 3 out of 9 high covariance structures in SK-N-AS cells. CONCLUSION: Our results demonstrate that many human noncoding, structured and conserved RNA genes remain to be discovered and that tissue specific tiling array data can be used in combination with computational...

  1. GENE EXPRESSION PROFILING OF GANGLIOGLIOMA MALIGNANT PROGRESSION BY cDNA ARRAY

    Institute of Scientific and Technical Information of China (English)

    ZHANG Quan-bin; HUANG Qiang; DONG Jun; WANG Ai-dong; SUN Ji-yong; LAN Qing; HU Geng-xi

    2005-01-01

    Objective: To establish gene expression profiles associated with malignant progression of ganglioglioma. Methods: The primary and two recurrent glioma specimens were collected intraoperatively from the same patient who experienced tumor transformation into anaplastic astrocytoma and glioblastoma multiform for the first and second recurrence respectively. Gene expression was assayed through cDNA array and bioinformatics analysis. Results: A total of 197 differentially expressed genes with differential ratio value more than 3 compared with normal brain tissue were obtained. Among 109 functionally denned genes, those associated with development ranked the first by frequency, followed by genes associated with metabolism, differentiation, signal transduction and so on. As a result of cluster analysis among 368 genes, eleven genes were up regulated with malignant progression, while six genes were down regulated. Conclusion: Gene expression profiles associated with malignant progression of glioma were successfully established, which provides a powerful tool for research on molecular mechanisms of malignant progression of gliomas.

  2. Evaluating methods for ranking differentially expressed genes applied to microArray quality control data

    Directory of Open Access Journals (Sweden)

    Shimizu Kentaro

    2011-06-01

    Full Text Available Abstract Background Statistical methods for ranking differentially expressed genes (DEGs from gene expression data should be evaluated with regard to high sensitivity, specificity, and reproducibility. In our previous studies, we evaluated eight gene ranking methods applied to only Affymetrix GeneChip data. A more general evaluation that also includes other microarray platforms, such as the Agilent or Illumina systems, is desirable for determining which methods are suitable for each platform and which method has better inter-platform reproducibility. Results We compared the eight gene ranking methods using the MicroArray Quality Control (MAQC datasets produced by five manufacturers: Affymetrix, Applied Biosystems, Agilent, GE Healthcare, and Illumina. The area under the curve (AUC was used as a measure for both sensitivity and specificity. Although the highest AUC values can vary with the definition of "true" DEGs, the best methods were, in most cases, either the weighted average difference (WAD, rank products (RP, or intensity-based moderated t statistic (ibmT. The percentages of overlapping genes (POGs across different test sites were mainly evaluated as a measure for both intra- and inter-platform reproducibility. The POG values for WAD were the highest overall, irrespective of the choice of microarray platform. The high intra- and inter-platform reproducibility of WAD was also observed at a higher biological function level. Conclusion These results for the five microarray platforms were consistent with our previous ones based on 36 real experimental datasets measured using the Affymetrix platform. Thus, recommendations made using the MAQC benchmark data might be universally applicable.

  3. Array gain for a conformal acoustic vector sensor array: An experimental study

    Science.gov (United States)

    Wang, Yong; Yang, Yi-Xin; He, Zheng-Yao; Lei, Bo; Sun, Chao; Ma, Yuan-Liang

    2016-12-01

    An acoustic vector sensor can measure the components of particle velocity and the acoustic pressure at the same point simultaneously, which provides a larger array gain against the ambient noise and a higher angular resolution than the omnidirectional pressure sensor. This paper presents an experimental study of array gain for a conformal acoustic vector sensor array in a practical environment. First, the manifold vector is calculated using the real measured data so that the effects of array mismatches can be minimized. Second, an optimal beamformer with a specific spatial response on the basis of the stable directivity of the ambient noise is designed, which can effectively suppress the ambient noise. Experimental results show that this beamformer for the conformal acoustic vector sensor array provides good signal-to-noise ratio enhancement and is more advantageous than the delay-and-sum and minimum variance distortionless response beamformers. Project supported by the China Postdoctoral Science Foundation (Grant No. 2016M592782) and the National Natural Science Foundation of China (Grant Nos. 11274253 and 11604259).

  4. Obtaining Relevant Genes by Analysis of Expression Arrays with a Multi-Agent System

    Directory of Open Access Journals (Sweden)

    Alfonso GONZÁLEZ

    2015-05-01

    Full Text Available Triple negative breast cancer (TNBC is an aggressive form of breast cancer. Despite treatment with chemotherapy, relapses are frequent and response to these treatments is not the same in younger women as in older women. Therefore, the identification of genes that provoke this disease is required, as well as the identification of therapeutic targets.There are currently different hybridization techniques, such as expression ar-rays, which measure the signal expression of both the genomic and tran-scriptomic levels of thousands of genes of a given sample. Probesets of Gene 1.0 ST GeneChip arrays provide the ultimate genome transcript coverage, providing a measurement of the expression level of the sample.This paper proposes a multi-agent system to manage information of expres-sion arrays, with the goal of providing an intuitive system that is also extensible to analyze and interpret the results.The roles of agent integrate different types of techniques, from statistical and data mining techniques that select a set of genes, to search techniques that find pathways in which such genes participate, and information extraction techniques that apply a CBR system to check if these genes are involved in the disease.

  5. A pilot trial assessing urinary gene expression profiling with an mRNA array for diabetic nephropathy.

    Directory of Open Access Journals (Sweden)

    Min Zheng

    Full Text Available BACKGROUND: The initiation and progression of diabetic nephropathy (DN is complex. Quantification of mRNA expression in urinary sediment has emerged as a novel strategy for studying renal diseases. Considering the numerous molecules involved in DN development, a high-throughput platform with parallel detection of multiple mRNAs is needed. In this study, we constructed a self-assembling mRNA array to analyze urinary mRNAs in DN patients with aims to reveal its potential in searching novel biomarkers. METHODS: mRNA array containing 88 genes were fabricated and its performance was evaluated. A pilot study with 9 subjects including 6 DN patients and 3 normal controls were studied with the array. DN patients were assigned into two groups according to their estimate glomerular rate (eGFR: DNI group (eGFR>60 ml/min/1.73 m(2, n = 3 and DNII group (eGFR<60 ml/min/1.73 m(2, n = 3. Urinary cell pellet was collected from each study participant. Relative abundance of these target mRNAs from urinary pellet was quantified with the array. RESULTS: The array we fabricated displayed high sensitivity and specificity. Moreover, the Cts of Positive PCR Controls in our experiments were 24±0.5 which indicated high repeatability of the array. A total of 29 mRNAs were significantly increased in DN patients compared with controls (p<0.05. Among these genes, α-actinin4, CDH2, ACE, FAT1, synaptopodin, COL4α, twist, NOTCH3 mRNA expression were 15-fold higher than those in normal controls. In contrast, urinary TIMP-1 mRNA was significantly decreased in DN patients (p<0.05. It was shown that CTGF, MCP-1, PAI-1, ACE, CDH1, CDH2 mRNA varied significantly among the 3 study groups, and their mRNA levels increased with DN progression (p<0.05. CONCLUSION: Our pilot study demonstrated that mRNA array might serve as a high-throughput and sensitive tool for detecting mRNA expression in urinary sediment. Thus, this primary study indicated that mRNA array probably could be a

  6. Ranking: a closer look on globalisation methods for normalisation of gene expression arrays

    Science.gov (United States)

    Kroll, Torsten C.; Wölfl, Stefan

    2002-01-01

    Data from gene expression arrays are influenced by many experimental parameters that lead to variations not simply accessible by standard quantification methods. To compare measurements from gene expression array experiments, quantitative data are commonly normalised using reference genes or global normalisation methods based on mean or median values. These methods are based on the assumption that (i) selected reference genes are expressed at a standard level in all experiments or (ii) that mean or median signal of expression will give a quantitative reference for each individual experiment. We introduce here a new ranking diagram, with which we can show how the different normalisation methods compare, and how they are influenced by variations in measurements (noise) that occur in every experiment. Furthermore, we show that an upper trimmed mean provides a simple and robust method for normalisation of larger sets of experiments by comparative analysis. PMID:12034851

  7. A new method of preparing fiber-optic DNA biosensor and its array for gene detection

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A new method of preparing fiber-optic DNA biosensor and its arrayfor the simultaneous detection of multiple genes is described. The optical fibers were first treated with poly-l-lysine, and then were made into fiber-optic DNA biosensors by adsorbing and immobilizing the oligonucleotide probe on its end. By assembling the fiber-optic DNA biosensors in a bundle in which each fiber carried a different DNA probe, the fiber-optic DNA biosensor array was well prepared. Hybridization of fluorescent- labeled cDNA of p53 gene, N-ras gene and Rb1 gene to the DNA array was monitored by CCD camera. A good result was achieved.

  8. Experimental Study of Fully Developed Wind Turbine Array Boundary Layer

    Science.gov (United States)

    Turner v, John; Wosnik, Martin

    2014-11-01

    Results from an experimental study of an array of up to 100 model wind turbines with 0.25 m diameter, conducted in the turbulent boundary layer of the 6.0 m wide × 2.7 m tall × 72.0 m long test section of the UNH Flow Physics Facility, are reported. The study aims to address two questions. First, for a given configuration (turbine spacing, initial conditions, etc.), when will the model wind farm reach a ``fully developed'' condition, in which turbulence statistics remain the same from one row to the next within and above the wind turbine array. Second, how is kinetic energy transported in the wind turbine array boundary layer (WTABL). Measurements in the fully developed WTABL can provide valuable insight to the optimization of wind farm energy production. Previous experimental studies with smaller model wind farms were unable to reach the fully developed condition. Due to the size of the UNH facility and the current model array, the fully developed WTABL condition can be achieved. The wind turbine array was simulated by a combination of drag-matched porous disks, used in the upstream part of the array, and by a smaller array of realistic, scaled 3-bladed wind turbines immediately upstream of the measurement location.

  9. Vaginal microbiome and epithelial gene array in post-menopausal women with moderate to severe dryness.

    Science.gov (United States)

    Hummelen, Ruben; Macklaim, Jean M; Bisanz, Jordan E; Hammond, Jo-Anne; McMillan, Amy; Vongsa, Rebecca; Koenig, David; Gloor, Gregory B; Reid, Gregor

    2011-01-01

    After menopause, many women experience vaginal dryness and atrophy of tissue, often attributed to the loss of estrogen. An understudied aspect of vaginal health in women who experience dryness due to atrophy is the role of the resident microbes. It is known that the microbiota has an important role in healthy vaginal homeostasis, including maintaining the pH balance and excluding pathogens. The objectives of this study were twofold: first to identify the microbiome of post-menopausal women with and without vaginal dryness and symptoms of atrophy; and secondly to examine any differences in epithelial gene expression associated with atrophy. The vaginal microbiome of 32 post-menopausal women was profiled using Illumina sequencing of the V6 region of the 16S rRNA gene. Sixteen subjects were selected for follow-up sampling every two weeks for 10 weeks. In addition, 10 epithelial RNA samples (6 healthy and 4 experiencing vaginal dryness) were acquired for gene expression analysis by Affymetrix Human Gene array. The microbiota abundance profiles were relatively stable over 10 weeks compared to previously published data on premenopausal women. There was an inverse correlation between Lactobacillus ratio and dryness and an increased bacterial diversity in women experiencing moderate to severe vaginal dryness. In healthy participants, Lactobacillus iners and L. crispatus were generally the most abundant, countering the long-held view that lactobacilli are absent or depleted in menopause. Vaginal dryness and atrophy were associated with down-regulation of human genes involved in maintenance of epithelial structure and barrier function, while those associated with inflammation were up-regulated consistent with the adverse clinical presentation.

  10. Vaginal microbiome and epithelial gene array in post-menopausal women with moderate to severe dryness.

    Directory of Open Access Journals (Sweden)

    Ruben Hummelen

    Full Text Available After menopause, many women experience vaginal dryness and atrophy of tissue, often attributed to the loss of estrogen. An understudied aspect of vaginal health in women who experience dryness due to atrophy is the role of the resident microbes. It is known that the microbiota has an important role in healthy vaginal homeostasis, including maintaining the pH balance and excluding pathogens. The objectives of this study were twofold: first to identify the microbiome of post-menopausal women with and without vaginal dryness and symptoms of atrophy; and secondly to examine any differences in epithelial gene expression associated with atrophy. The vaginal microbiome of 32 post-menopausal women was profiled using Illumina sequencing of the V6 region of the 16S rRNA gene. Sixteen subjects were selected for follow-up sampling every two weeks for 10 weeks. In addition, 10 epithelial RNA samples (6 healthy and 4 experiencing vaginal dryness were acquired for gene expression analysis by Affymetrix Human Gene array. The microbiota abundance profiles were relatively stable over 10 weeks compared to previously published data on premenopausal women. There was an inverse correlation between Lactobacillus ratio and dryness and an increased bacterial diversity in women experiencing moderate to severe vaginal dryness. In healthy participants, Lactobacillus iners and L. crispatus were generally the most abundant, countering the long-held view that lactobacilli are absent or depleted in menopause. Vaginal dryness and atrophy were associated with down-regulation of human genes involved in maintenance of epithelial structure and barrier function, while those associated with inflammation were up-regulated consistent with the adverse clinical presentation.

  11. A systemic lupus erythematosus gene expression array in disease diagnosis and classification: a preliminary report.

    Science.gov (United States)

    Juang, Y-T; Peoples, C; Kafri, R; Kyttaris, V C; Sunahori, K; Kis-Toth, K; Fitzgerald, L; Ergin, S; Finnell, M; Tsokos, G C

    2011-03-01

    Systemic lupus erythematosus (SLE) is a clinically heterogeneous disease diagnosed on the presence of a constellation of clinical and laboratory findings. At the pathogenetic level, multiple factors using diverse biochemical and molecular pathways have been recognized. Succinct recognition and classification of clinical disease subsets, as well as the availability of disease biomarkers, remains largely unsolved. Based on information produced by the present authors' and other laboratories, a lupus gene expression array consisting of 30 genes, previously claimed to contribute to aberrant function of T cells, was developed. An additional eight genes were included as controls. Peripheral blood was obtained from 10 patients (19 samples) with SLE and six patients with rheumatoid arthritis (RA) as well as 19 healthy controls. T cell mRNA was subjected to reverse transcription and PCR, and the gene expression levels were measured. Conventional statistical analysis was performed along with principal component analysis (PCA) to capture the contribution of all genes to disease diagnosis and clinical parameters. The lupus gene expression array faithfully informed on the expression levels of genes. The recorded changes in expression reflect those reported in the literature by using a relatively small (5 ml) amount of peripheral blood. PCA of gene expression levels placed SLE samples apart from normal and RA samples regardless of disease activity. Individual principal components tended to define specific disease manifestations such as arthritis and proteinuria. Thus, a lupus gene expression array based on genes previously claimed to contribute to immune pathogenesis of SLE may define the disease, and principal components of the expression of 30 genes may define patients with specific disease manifestations.

  12. Experimental design, analysis of variance and slide quality assessment in gene expression arrays.

    Science.gov (United States)

    Draghici, S; Kuklin, A; Hoff, B; Shams, S

    2001-05-01

    A microarray experiment is a sequence of complicated molecular biology procedures relying on various laboratory tools, instrumentation and experimenter's skills. This paper discusses statistical models for distinguishing small changes in gene expression from the noise in the system. It describes methods for assigning statistical confidence to gene expression values derived from a single array slide. Some of the theory is discussed in the context of practical applications via software usage.

  13. Microwell Arrays for Studying Many Individual Cells

    Science.gov (United States)

    Folch, Albert; Kosar, Turgut Fettah

    2009-01-01

    "Laboratory-on-a-chip" devices that enable the simultaneous culturing and interrogation of many individual living cells have been invented. Each such device includes a silicon nitride-coated silicon chip containing an array of micromachined wells sized so that each well can contain one cell in contact or proximity with a patch clamp or other suitable single-cell-interrogating device. At the bottom of each well is a hole, typically 0.5 m wide, that connects the well with one of many channels in a microfluidic network formed in a layer of poly(dimethylsiloxane) on the underside of the chip. The microfluidic network makes it possible to address wells (and, thus, cells) individually to supply them with selected biochemicals. The microfluidic channels also provide electrical contact to the bottoms of the wells.

  14. Study on the Beam Quality of Uncoupled Laser Diode Arrays

    Institute of Scientific and Technical Information of China (English)

    GAO Chunqing; WEI Guanghui

    2001-01-01

    The beam quality of uncoupled laser diode array is studied theoretically and experimentally. By calculating the second order moments of the beam emitted from the laser diode array, the dependence of the M2-factor of the laser diode array on the M2-factor of the single emitter, the ratio of the emitting region to the non-emitting space, and the number of emitters, has been deduced. From the measurement of the beam propagation the M2-factor of a laser diode bar is experimentally determined. The measured M2-factor of the laser diode bar agrees with the theoretical prediction.

  15. Development of a cDNA array for chicken gene expression analysis

    Directory of Open Access Journals (Sweden)

    Burt David

    2005-02-01

    Full Text Available Abstract Background The application of microarray technology to functional genomic analysis in the chicken has been limited by the lack of arrays containing large numbers of genes. Results We have produced cDNA arrays using chicken EST collections generated by BBSRC, University of Delaware and the Fred Hutchinson Cancer Research Center. From a total of 363,838 chicken ESTs representing 24 different adult or embryonic tissues, a set of 11,447 non-redundant ESTs were selected and added to an existing collection of clones (4,162 from immune tissues and a chicken bursal cell line (DT40. Quality control analysis indicates there are 13,007 useable features on the array, including 160 control spots. The array provides broad coverage of mRNAs expressed in many tissues; in addition, clones with expression unique to various tissues can be detected. Conclusions A chicken multi-tissue cDNA microarray with 13,007 features is now available to academic researchers from genomics@fhcrc.org. Sequence information for all features on the array is in GenBank, and clones can be readily obtained. Targeted users include researchers in comparative and developmental biology, immunology, vaccine and agricultural technology. These arrays will be an important resource for the entire research community using the chicken as a model.

  16. Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays

    Directory of Open Access Journals (Sweden)

    Aramburu Ander

    2010-11-01

    Full Text Available Abstract Background Exon arrays provide a way to measure the expression of different isoforms of genes in an organism. Most of the procedures to deal with these arrays are focused on gene expression or on exon expression. Although the only biological analytes that can be properly assigned a concentration are transcripts, there are very few algorithms that focus on them. The reason is that previously developed summarization methods do not work well if applied to transcripts. In addition, gene structure prediction, i.e., the correspondence between probes and novel isoforms, is a field which is still unexplored. Results We have modified and adapted a previous algorithm to take advantage of the special characteristics of the Affymetrix exon arrays. The structure and concentration of transcripts -some of them possibly unknown- in microarray experiments were predicted using this algorithm. Simulations showed that the suggested modifications improved both specificity (SP and sensitivity (ST of the predictions. The algorithm was also applied to different real datasets showing its effectiveness and the concordance with PCR validated results. Conclusions The proposed algorithm shows a substantial improvement in the performance over the previous version. This improvement is mainly due to the exploitation of the redundancy of the Affymetrix exon arrays. An R-Package of SPACE with the updated algorithms have been developed and is freely available.

  17. Exome sequencing and arrayCGH detection of gene sequence and copy number variation between ILS and ISS mouse strains.

    Science.gov (United States)

    Dumas, Laura; Dickens, C Michael; Anderson, Nathan; Davis, Jonathan; Bennett, Beth; Radcliffe, Richard A; Sikela, James M

    2014-06-01

    It has been well documented that genetic factors can influence predisposition to develop alcoholism. While the underlying genomic changes may be of several types, two of the most common and disease associated are copy number variations (CNVs) and sequence alterations of protein coding regions. The goal of this study was to identify CNVs and single-nucleotide polymorphisms that occur in gene coding regions that may play a role in influencing the risk of an individual developing alcoholism. Toward this end, two mouse strains were used that have been selectively bred based on their differential sensitivity to alcohol: the Inbred long sleep (ILS) and Inbred short sleep (ISS) mouse strains. Differences in initial response to alcohol have been linked to risk for alcoholism, and the ILS/ISS strains are used to investigate the genetics of initial sensitivity to alcohol. Array comparative genomic hybridization (arrayCGH) and exome sequencing were conducted to identify CNVs and gene coding sequence differences, respectively, between ILS and ISS mice. Mouse arrayCGH was performed using catalog Agilent 1 × 244 k mouse arrays. Subsequently, exome sequencing was carried out using an Illumina HiSeq 2000 instrument. ArrayCGH detected 74 CNVs that were strain-specific (38 ILS/36 ISS), including several ISS-specific deletions that contained genes implicated in brain function and neurotransmitter release. Among several interesting coding variations detected by exome sequencing was the gain of a premature stop codon in the alpha-amylase 2B (AMY2B) gene specifically in the ILS strain. In total, exome sequencing detected 2,597 and 1,768 strain-specific exonic gene variants in the ILS and ISS mice, respectively. This study represents the most comprehensive and detailed genomic comparison of ILS and ISS mouse strains to date. The two complementary genome-wide approaches identified strain-specific CNVs and gene coding sequence variations that should provide strong candidates to

  18. Study of intrinsic localized vibrational modes in micromechanical oscillator arrays.

    Science.gov (United States)

    Sato, M; Hubbard, B E; English, L Q; Sievers, A J; Ilic, B; Czaplewski, D A; Craighead, H G

    2003-06-01

    Intrinsic localized modes (ILMs) have been observed in micromechanical cantilever arrays, and their creation, locking, interaction, and relaxation dynamics in the presence of a driver have been studied. The micromechanical array is fabricated in a 300 nm thick silicon-nitride film on a silicon substrate, and consists of up to 248 cantilevers of two alternating lengths. To observe the ILMs in this experimental system a line-shaped laser beam is focused on the 1D cantilever array, and the reflected beam is captured with a fast charge coupled device camera. The array is driven near its highest frequency mode with a piezoelectric transducer. Numerical simulations of the nonlinear Klein-Gordon lattice have been carried out to assist with the detailed interpretation of the experimental results. These include pinning and locking of the ILMs when the driver is on, collisions between ILMs, low frequency excitation modes of the locked ILMs and their relaxation behavior after the driver is turned off.

  19. Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity

    Directory of Open Access Journals (Sweden)

    Viljoen Katie S

    2013-01-01

    Full Text Available Abstract Background RNA and microarray quality assessment form an integral part of gene expression analysis and, although methods such as the RNA integrity number (RIN algorithm reliably asses RNA integrity, the relevance of RNA integrity in gene expression analysis as well as analysis methods to accommodate the possible effects of degradation requires further investigation. We investigated the relationship between RNA integrity and array quality on the commonly used Affymetrix Gene 1.0 ST array platform using reliable within-array and between-array quality assessment measures. The possibility of a transcript specific bias in the apparent effect of RNA degradation on the measured gene expression signal was evaluated after either excluding quality-flagged arrays or compensation for RNA degradation at different steps in the analysis. Results Using probe-level and inter-array quality metrics to assess 34 Gene 1.0 ST array datasets derived from historical, paired tumour and normal primary colorectal cancer samples, 7 arrays (20.6%, with a mean sample RIN of 3.2 (SD = 0.42, were flagged during array quality assessment while 10 arrays from samples with RINs Conclusions Here, we demonstrate an effective array-quality assessment strategy, which will allow the user to recognize lower quality arrays that can be included in the analysis once appropriate measures are applied to account for known or unknown sources of variation, such as array quality- and batch- effects, by implementing ComBat or Surrogate Variable Analysis. This approach of quality control and analysis will be especially useful for clinical samples with variable and low RNA qualities, with RIN scores ≥ 2.

  20. Gene expression array analyses predict increased proto-oncogene expression in MMTV induced mammary tumors.

    Science.gov (United States)

    Popken-Harris, Pamela; Kirchhof, Nicole; Harrison, Ben; Harris, Lester F

    2006-08-01

    Exogenous infection by milk-borne mouse mammary tumor viruses (MMTV) typically induce mouse mammary tumors in genetically susceptible mice at a rate of 90-95% by 1 year of age. In contrast to other transforming retroviruses, MMTV acts as an insertional mutagen and under the influence of steroid hormones induces oncogenic transformation after insertion into the host genome. As these events correspond with increases in adjacent proto-oncogene transcription, we used expression array profiling to determine which commonly associated MMTV insertion site proto-oncogenes were transcriptionally active in MMTV induced mouse mammary tumors. To verify our gene expression array results we developed real-time quantitative RT-PCR assays for the common MMTV insertion site genes found in RIII/Sa mice (int-1/wnt-1, int-2/fgf-3, int-3/Notch 4, and fgf8/AIGF) as well as two genes that were consistently up regulated (CCND1, and MAT-8) and two genes that were consistently down regulated (FN1 and MAT-8) in the MMTV induced tumors as compared to normal mammary gland. Finally, each tumor was also examined histopathologically. Our expression array findings support a model whereby just one or a few common MMTV insertions into the host genome sets up a dominant cascade of events that leave a characteristic molecular signature.

  1. Quantitative analysis of EDC-condensed DNA on vertically aligned carbon nanofiber gene delivery arrays

    Energy Technology Data Exchange (ETDEWEB)

    Mann, David G. J. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology; McKnight, Timothy E. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Engineering Science and Technology Division; Melechko, Anatoli V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science (CNMS); Simpson, Michael L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science (CNMS); Sayler, Gary S. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology

    2006-12-08

    Vertically aligned carbon nanofibers (VACNFs) with immobilized DNA have been developed as a novel tool for direct physical introduction and expression of exogenous genes in mammalian cells. Immobilization of DNA base amines to the carboxylic acids on nanofibers can influence the accessibility and transcriptional activity of the DNA template, making it necessary to determine the number of accessible gene copies on nanofiber arrays. We used polymerase chain reaction (PCR) and in vitro transcription (IVT) to investigate the transcriptional accessibility of DNA tethered to VACNFs by correlating the yields of both IVT and PCR to that of non-tethered, free DNA. Yields of the promoter region and promoter/gene region of bound DNA plasmid were high. Amplification using primers designed to cover 80% of the plasmid failed to yield any product. These results are consistent with tethered, longer DNA sequences having a higher probability of interfering with the activity of DNA and RNA polymerases. Quantitative PCR (qPCR) was used to quantify the number of accessible gene copies tethered to nanofiber arrays. Copy numbers of promoters and reporter genes were quantified and compared to non-tethered DNA controls. In subsequent reactions of the same nanofiber arrays, DNA yields decreased dramatically in the non-tethered control, while the majority of tethered DNA was retained on the arrays. This decrease could be explained by the presence of DNA which is non-tethered to all samples and released during the assay. In conclusion,this investigation shows the applicability of these methods for monitoring DNA immobilization techniques.

  2. Array CGH improves detection of mutations in the GALC gene associated with Krabbe disease

    Directory of Open Access Journals (Sweden)

    Tanner Alice K

    2012-06-01

    Full Text Available Abstract Background Krabbe disease is an autosomal recessive lysosomal storage disorder caused by mutations in the GALC gene. The most common mutation in the Caucasian population is a 30-kb deletion of exons 11 through 17. There are few other reports of intragenic GALC deletions or duplications, due in part to difficulties detecting them. Methods and results We used gene-targeted array comparative genomic hybridization (CGH to analyze the GALC gene in individuals with Krabbe disease in whom sequence analysis with 30-kb deletion analysis identified only one mutation. In our sample of 33 cases, traditional approaches failed to identify two pathogenic mutations in five (15.2% individuals with confirmed Krabbe disease. The addition of array CGH deletion/duplication analysis to the genetic testing strategy led to the identification of a second pathogenic mutation in three (9.1% of these five individuals. In all three cases, the deletion or duplication identified through array CGH was a novel GALC mutation, including the only reported duplication in the GALC gene, which would have been missed by traditional testing methodologies. We report these three cases in detail. The second mutation remains unknown in the remaining two individuals (6.1%, despite our full battery of testing. Conclusions Analysis of the GALC gene using array CGH deletion/duplication testing increased the two-mutation detection rate from 84.8% to 93.9% in affected individuals. Better mutation detection rates are important for improving molecular diagnosis of Krabbe disease, as well as for providing prenatal and carrier testing in family members.

  3. Identification of auxin responsive genes in Arabidopsis by cDNA array

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The plant hormone auxin influences a variety of developmental and physiological processes. But the mechanism of its action is quite unclear. In order to identify and analyze the expression of auxin responsive genes, a cDNA array approach was used to screen for genes with altered expression from Arabidopsis suspension culture after IAA treatment and was identified 50 differentially expressed genes from 13824 cDNA clones. These genes were related to signal transduction, stress responses, senescence, photosynthesis, protein biosynthesis and transportation. The results provide the molecular evidence that auxin influences a variety of physiological processes and pave a way for further investigation of the mechanism of auxin action. Furthermore,we found that the expression of a ClpC (regulation subunit of Clp protease) was repressed by exogenous auxin, but increased in dark-induced senescing leaves. This suggests that ClpC may be a senescence-associated gene and can be regulated by auxin.

  4. Blood Pressure Loci Identified with a Gene-Centric Array

    NARCIS (Netherlands)

    Johnson, Toby; Gaunt, Tom R.; Newhouse, Stephen J.; Padmanabhan, Sandosh; Tomaszewski, Maciej; Kumari, Meena; Morris, Richard W.; Tzoulaki, Ioanna; O'Brien, Eoin T.; Poulter, Neil R.; Sever, Peter; Shields, Denis C.; Thom, Simon; Wannamethee, Sasiwarang G.; Whincup, Peter H.; Brown, Morris J.; Connell, John M.; Dobson, Richard J.; Howard, Philip J.; Mein, Charles A.; Onipinla, Abiodun; Shaw-Hawkins, Sue; Zhang, Yun; Smith, George Davey; Day, Ian N. M.; Lawlor, Debbie A.; Goodall, Alison H.; Fowkes, F. Gerald; Abecasis, Goncalo R.; Elliott, Paul; Gateva, Vesela; Braund, Peter S.; Burton, Paul R.; Nelson, Christopher P.; Tobin, Martin D.; van der Harst, Pim; Glorioso, Nicola; Neuvrith, Hani; Salvi, Erika; Staessen, Jan A.; Stucchi, Andrea; Devos, Nabila; Jeunemaitre, Xavier; Plouin, Pierre-Francois; Tichet, Jean; Juhanson, Peeter; Org, Elin; Putku, Margus; Sober, Siim; Veldre, Gudrun; Viigimaa, Margus; Levinsson, Anna; Rosengren, Annika; Thelle, Dag S.; Hastie, Claire E.; Hedner, Thomas; Lee, Wai K.; Melander, Olle; Wahlstrand, Bjoern; Hardy, Rebecca; Wong, Andrew; Cooper, Jackie A.; Palmen, Jutta; Chen, Li; Stewart, Alexandre F. R.; Wells, George A.; Westra, Harm-Jan; Wolfs, Marcel G. M.; Clarke, Robert; Franzosi, Maria Grazia; Goel, Anuj; Hamsten, Anders; Lathrop, Mark; Peden, John F.; Seedorf, Udo; Watkins, Hugh; Ouwehand, Willem H.; Sambrook, Jennifer; Stephens, Jonathan; Casas, Juan-Pablo; Drenos, Fotios; Holmes, Michael V.; Kivimaki, Mika; Shah, Sonia; Shah, Tina; Talmud, Philippa J.; Whittaker, John; Wallace, Chris; Delles, Christian; Laan, Mans; Kuh, Diana; Humphries, Steve E.; Nyberg, Fredrik; Cusi, Daniele; Roberts, Robert; Newton-Cheh, Christopher; Franke, Lude; Stanton, Alice V.; Dominiczak, Anna F.; Farrall, Martin; Hingorani, Aroon D.; Samani, Nilesh J.; Caulfield, Mark J.; Munroe, Patricia B.

    2011-01-01

    Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a

  5. Blood Pressure Loci Identified with a Gene-Centric Array

    NARCIS (Netherlands)

    Johnson, Toby; Gaunt, Tom R.; Newhouse, Stephen J.; Padmanabhan, Sandosh; Tomaszewski, Maciej; Kumari, Meena; Morris, Richard W.; Tzoulaki, Ioanna; O'Brien, Eoin T.; Poulter, Neil R.; Sever, Peter; Shields, Denis C.; Thom, Simon; Wannamethee, Sasiwarang G.; Whincup, Peter H.; Brown, Morris J.; Connell, John M.; Dobson, Richard J.; Howard, Philip J.; Mein, Charles A.; Onipinla, Abiodun; Shaw-Hawkins, Sue; Zhang, Yun; Smith, George Davey; Day, Ian N. M.; Lawlor, Debbie A.; Goodall, Alison H.; Fowkes, F. Gerald; Abecasis, Goncalo R.; Elliott, Paul; Gateva, Vesela; Braund, Peter S.; Burton, Paul R.; Nelson, Christopher P.; Tobin, Martin D.; van der Harst, Pim; Glorioso, Nicola; Neuvrith, Hani; Salvi, Erika; Staessen, Jan A.; Stucchi, Andrea; Devos, Nabila; Jeunemaitre, Xavier; Plouin, Pierre-Francois; Tichet, Jean; Juhanson, Peeter; Org, Elin; Putku, Margus; Sober, Siim; Veldre, Gudrun; Viigimaa, Margus; Levinsson, Anna; Rosengren, Annika; Thelle, Dag S.; Hastie, Claire E.; Hedner, Thomas; Lee, Wai K.; Melander, Olle; Wahlstrand, Bjoern; Hardy, Rebecca; Wong, Andrew; Cooper, Jackie A.; Palmen, Jutta; Chen, Li; Stewart, Alexandre F. R.; Wells, George A.; Westra, Harm-Jan; Wolfs, Marcel G. M.; Clarke, Robert; Franzosi, Maria Grazia; Goel, Anuj; Hamsten, Anders; Lathrop, Mark; Peden, John F.; Seedorf, Udo; Watkins, Hugh; Ouwehand, Willem H.; Sambrook, Jennifer; Stephens, Jonathan; Casas, Juan-Pablo; Drenos, Fotios; Holmes, Michael V.; Kivimaki, Mika; Shah, Sonia; Shah, Tina; Talmud, Philippa J.; Whittaker, John; Wallace, Chris; Delles, Christian; Laan, Mans; Kuh, Diana; Humphries, Steve E.; Nyberg, Fredrik; Cusi, Daniele; Roberts, Robert; Newton-Cheh, Christopher; Franke, Lude; Stanton, Alice V.; Dominiczak, Anna F.; Farrall, Martin; Hingorani, Aroon D.; Samani, Nilesh J.; Caulfield, Mark J.; Munroe, Patricia B.

    2011-01-01

    Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a besp

  6. Identification of Novel Stress-responsive Transcription Factor Genes in Rice by cDNA Array Analysis

    Institute of Scientific and Technical Information of China (English)

    Cong-Qing Wu; Hong-Hong Hu; Ya Zeng; Da-Cheng Liang; Ka-Bin Xie; Jian-Wei Zhang; Zhao-Hui Chu; Li-Zhong Xiong

    2006-01-01

    Numerous studies have shown that array of transcription factors has a role in regulating plant responses to environmental stresses. Only a small portion of them however, have been identified or characterized.More than 2 300 putative transcription factors were predicted in the rice genome and more than half of them were supported by expressed sequences. With an attempt to identify novel transcription factors involved in the stress responses, a cDNA array containing 753 putative rice transcription factors was generated to analyze the transcript profiles of these genes under drought and salinity stresses and abscisic acid treatment at seedling stage of rice. About 80% of these transcription factors showed detectable levels of transcript in seedling leaves. A total of 18 up-regulated transcription factors and 29 down-regulated transcription factors were detected with the folds of changes from 2.0 to 20.5 in at least one stress treatment.Most of these stress-responsive genes have not been reported and the expression patterns for five genes under stress conditions were further analyzed by RNA gel blot analysis. These novel stress-responsive transcription factors provide new opportunities to study the regulation of gene expression in plants under stress conditions.

  7. The Array for Nuclear Astrophysics Studies with Exotic Nuclei (anasen)

    Science.gov (United States)

    Matos, M.; Blackmon, J. C.; Gardiner, H. E.; Linhardt, L. E.; Macon, K. T.; Mondello, L. L.; Baby, L.; Johnson, E.; Koshchiy, E.; Rogachev, G.; Wiedenhöver, I.; Bardayan, D. W.

    2013-03-01

    Experimental information about most reactions involving short-lived nuclei is limited. New facilities aim to provide wider access to unstable isotopes, but the limited intensities require more efficient and selective techniques and devices. The Array for Nuclear Astrophysics Studies with Exotic Nuclei (ANASEN) is a charged-particle detector array designed primarily for studies of reactions important in the αp- and rp- processes with proton-rich exotic nuclei. The array consists of 40 silicon-strip detectors backed with CsI scintillators. The detectors cover an area of about 1300 cm2 providing essentially complete solid angle coverage for the reactions of interest with good energy and position resolution. ANASEN also includes a position-sensitive annular gas proportional counter that allows it to be used as an active gas target/detector. ANASEN is designed for direct measurement of (α,p) re-actions in inverse kinematics as well as for studies of proton elastic and inelastic scattering, (p, γ) reactions and transfer reactions. The array is being developed by Louisiana State University and Florida State University. Presently it is located at the RESOLUT radioacitve ion beam facility at FSU, where the first experiments are being performed. In the future, the array will be used at the ReA3 facility at the National Superconducting Cyclotron Laboratory.

  8. Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

    Directory of Open Access Journals (Sweden)

    Settles Matthew L

    2009-05-01

    Full Text Available Abstract Background Natural antisense transcripts (NATs are transcripts of the opposite DNA strand to the sense-strand either at the same locus (cis-encoded or a different locus (trans-encoded. They can affect gene expression at multiple stages including transcription, RNA processing and transport, and translation. NATs give rise to sense-antisense transcript pairs and the number of these identified has escalated greatly with the availability of DNA sequencing resources and public databases. Traditionally, NATs were identified by the alignment of full-length cDNAs or expressed sequence tags to genome sequences, but an alternative method for large-scale detection of sense-antisense transcript pairs involves the use of microarrays. In this study we developed a novel protocol to assay sense- and antisense-strand transcription on the 55 K Affymetrix GeneChip Wheat Genome Array, which is a 3' in vitro transcription (3'IVT expression array. We selected five different tissue types for assay to enable maximum discovery, and used the 'Chinese Spring' wheat genotype because most of the wheat GeneChip probe sequences were based on its genomic sequence. This study is the first report of using a 3'IVT expression array to discover the expression of natural sense-antisense transcript pairs, and may be considered as proof-of-concept. Results By using alternative target preparation schemes, both the sense- and antisense-strand derived transcripts were labeled and hybridized to the Wheat GeneChip. Quality assurance verified that successful hybridization did occur in the antisense-strand assay. A stringent threshold for positive hybridization was applied, which resulted in the identification of 110 sense-antisense transcript pairs, as well as 80 potentially antisense-specific transcripts. Strand-specific RT-PCR validated the microarray observations, and showed that antisense transcription is likely to be tissue specific. For the annotated sense

  9. Sequential displacement of Type VI Secretion System effector genes leads to evolution of diverse immunity gene arrays in Vibrio cholerae

    Science.gov (United States)

    Kirchberger, Paul C.; Unterweger, Daniel; Provenzano, Daniele; Pukatzki, Stefan; Boucher, Yan

    2017-01-01

    Type VI secretion systems (T6SS) enable bacteria to engage neighboring cells in contact-dependent competition. In Vibrio cholerae, three chromosomal clusters each encode a pair of effector and immunity genes downstream of those encoding the T6SS structural machinery for effector delivery. Different combinations of effector-immunity proteins lead to competition between strains of V. cholerae, which are thought to be protected only from the toxicity of their own effectors. Screening of all publically available V. cholerae genomes showed that numerous strains possess long arrays of orphan immunity genes encoded in the 3′ region of their T6SS clusters. Phylogenetic analysis reveals that these genes are highly similar to those found in the effector-immunity pairs of other strains, indicating acquisition by horizontal gene transfer. Extensive genomic comparisons also suggest that successive addition of effector-immunity gene pairs replaces ancestral effectors, yet retains the cognate immunity genes. The retention of old immunity genes perhaps provides protection against nearby kin bacteria in which the old effector was not replaced. This mechanism, combined with frequent homologous recombination, is likely responsible for the high diversity of T6SS effector-immunity gene profiles observed for V. cholerae and closely related species. PMID:28327641

  10. A Study on TOFD Inspection Using Phased Array Ultrasonic Technique

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Byung Sik; Kim, Yong Sik; Lee, Hee Jong [Korea Electric Power Research Institute, Daejeon (Korea, Republic of); Lee, Young Ho [Chungnam National University, Daejeon (Korea, Republic of)

    2005-08-15

    The techniques in order to measure the depth of defect in weldment and structure accurately have been developed. Many researches have made efforts to develop the methods for the accurate depth sizing of defect. TOFD is known as the most accurate method of various methods for measuring depth sizing. However, there is a possibility to miss defects because of the limitation of beam coverage for the ultrasound incident angle. In this study, the results for detectability and depth sizing using phased array ultrasonic technique for thick body were compared with those of conventional TOFD technique. It was experimentally confirmed that the phased array ultrasonic TOFD technique gives good detectability and accurate depth measurement for the various types of defects. The phased array ultrasonic TOFD technique developed in this study will contribute to increase the inspection reliability in thick component such as the pressure vessel of power generation industry

  11. Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels

    Energy Technology Data Exchange (ETDEWEB)

    Waldron, P.J.; Wu, L.; Van Nostrand, J.D.; Schadt, C.W.; Watson, D.B.; Jardine, P.M.; Palumbo, A.V.; Hazen, T.C.; Zhou, J.

    2009-06-15

    To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity but greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17-70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination.

  12. Assessing Apoptosis Gene Expression Profiling with a PCR Array in the Hippocampus of Ts65Dn Mice

    Directory of Open Access Journals (Sweden)

    Bin Yu

    2015-01-01

    Full Text Available It is well known that Down syndrome (DS is a condition in which extra genetic material causes delays in the way a child develops, both mentally and physically. Intellectual disability is the foremost and most debilitating trait, which caused loss of cognitive abilities and the development of early onset Alzheimer’s disease (AD. Ts65Dn mice were used in this study. We isolated the hippocampus. First, we used transmission scanning electron microscopy to directly observe the hippocampus and confirm if apoptosis had occurred. Second, we customized a PCR array with 53 genes, including several important genes related to cell apoptosis. Gene expression was detected by RT-PCR. There were varying degrees of changes characteristic of apoptosis in the hippocampus of Ts65Dn mice, which mainly included the following: nuclear membrane thinning, unevenly distributed chromosomes, the production of chromatin crescents, and pyknosis of the nuclei with some nuclear fragmentation. Meanwhile, three genes (API5, AIFM1, and NFκB1 showed changes of expression in the hippocampus of Ts65Dn mice compared with normal mice. Only NFκB1 expression was significantly increased, while the expressions of API5 and AIFM1 were notably decreased. The fold changes in the expression of API5, AIFM1, and NFκB1 were 11.55, 5.94, and 3.11, respectively. However, some well-known genes related to cell apoptosis, such as the caspase family, Bcl-2, Bad, Bid, Fas, and TNF, did not show changes in expression levels. The genes we found which were differentially expressed in the hippocampus of Ts65Dn mice may be closely related to cell apoptosis. PCR array technology can assist in the screening and identification of genes involved in apoptosis.

  13. ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics.

    Science.gov (United States)

    Chung, Hee-Joon; Kim, Mingoo; Park, Chan Hee; Kim, Jihoon; Kim, Ju Han

    2004-07-01

    Biological pathways can provide key information on the organization of biological systems. ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG). By integrating major bio-databases and searching pathway resources, ArrayXPath automatically maps different types of identifiers from microarray probes and pathway elements. When one inputs gene-expression clusters, ArrayXPath produces a list of the best matching pathways for each cluster. We applied Fisher's exact test and the false discovery rate (FDR) to evaluate the statistical significance of the association between a cluster and a pathway while correcting the multiple-comparison problem. ArrayXPath produces Javascript-enabled SVGs for web-enabled interactive visualization of pathways integrated with gene-expression profiles.

  14. Design of a microchannel-nanochannel-microchannel array based nanoelectroporation system for precise gene transfection.

    Science.gov (United States)

    Gao, Keliang; Li, Lei; He, Lingna; Hinkle, Kevin; Wu, Yun; Ma, Junyu; Chang, Lingqian; Zhao, Xi; Perez, Daniel Gallego; Eckardt, Sigrid; McLaughlin, John; Liu, Boyu; Farson, Dave F; Lee, L James

    2014-03-12

    A micro/nano-fabrication process of a nanochannel electroporation (NEP) array and its application for precise delivery of plasmid for non-viral gene transfection is described. A dip-combing device is optimized to produce DNA nanowires across a microridge array patterned on the polydimethylsiloxane (PDMS) surface with a yield up to 95%. Molecular imprinting based on a low viscosity resin, 1,4-butanediol diacrylate (1,4-BDDA), adopted to convert the microridge-nanowire-microridge array into a microchannel-nanochannel-microchannel (MNM) array. Secondary machining by femtosecond laser ablation is applied to shorten one side of microchannels from 3000 to 50 μm to facilitate cell loading and unloading. The biochip is then sealed in a packaging case with reservoirs and microfluidic channels to enable cell and plasmid loading, and to protect the biochip from leakage and contamination. The package case can be opened for cell unloading after NEP to allow for the follow-up cell culture and analysis. These NEP cases can be placed in a spinning disc and up to ten discs can be piled together for spinning. The resulting centrifugal force can simultaneously manipulate hundreds or thousands of cells into microchannels of NEP arrays within 3 minutes. To demonstrate its application, a 13 kbp OSKM plasmid of induced pluripotent stem cell (iPSC) is injected into mouse embryonic fibroblasts cells (MEFCs). Fluorescence detection of transfected cells within the NEP biochips shows that the delivered dosage is high and much more uniform compared with similar gene transfection carried out by the conventional bulk electroporation (BEP) method.

  15. Profiling of differentially expressed chemotactic-related genes in MCP-1 treated macrophage cell line using human cDNA arrays

    Institute of Scientific and Technical Information of China (English)

    Guang-Xing Bian; Hong Miao; Lei Qiu; Dong-Mei Cao; Bao-Yu Guo

    2005-01-01

    AIM: To study the global gene expression of chemotactic genes in macrophage line U937 treated with human monocyte chemoattractant protein-1 (MCP-1) through the use of ExpreeChipTMHO2 cDNA array.METHODS: Total RNA was extracted from MCP-1 treated macrophage line U937 and normal U937 cells, reversely transcribed to cDNA, and then screened in parallel with HO2 human cDNA array chip. The scanned result was additionally validated using RT-PCR.RESULTS: The result of cDNA array showed that one chemotactic-related gene was up-regulated more than two-fold (RANTES) and seven chemotactic-related genes were down-regulated more than two-fold (CCR1, CCR5,ccl16, GROβ, GROγ, IL-8 and granulocyte chemotactic protein 2) in MCP-1 treated U937 cells at mRNA level.RT-PCR analysis of four of these differentially expressed genes gave results consistent with cDNA array findings.CONCLUSION: MCP-1 could influence some chemokine and receptor expressions in macrophages in vitro. MCP-1mainly down-regulates the expression of chemotactic genes influencing neutrophilic granulocyte expression (GROβ, GROγ, IL-8 and granulocyte chemotactic protein 2), and the mRNA level of CCR5, which plays a critical role in many disorders and illnesses.

  16. Development of a coral cDNA array to examine gene expression profiles in Montastraea faveolata exposed to environmental stress.

    Science.gov (United States)

    Edge, Sara E; Morgan, Michael B; Gleason, Daniel F; Snell, Terry W

    2005-01-01

    The development of a cDNA array of coral genes and its application to investigate changes in coral gene expression associated with stressful conditions is described. The array includes both well-characterized and previously unidentified coral genes from Acropora cervicornis and Montastraea faveolata. Corals were exposed to either natural or anthropogenic stressors to elicit the expression of stress genes for isolation and incorporation onto the array. A total of 32 genes involved in protein synthesis, apoptosis, cell signaling, metabolism, cellular defense and inflammation were included on the array. Labeled cDNA from coral (Montastraea faveolata) exposed to elevated seawater temperature, salinity and ultraviolet light was tested against the microarray to determine patterns of gene expression associated with each stressor. Carbonic anhydrase, thioredoxin, a urokinase plasminogen activator receptor (uPAR) and three ribosomal genes demonstrated differential expression across all replicates on the array and between replicate colonies. Specific gene expression patterns produced in response to different stressors demonstrate the potential for gene expression profiling in characterizing the coral stress response.

  17. Characterization of the chicken GCAP gene array and analyses of GCAP1, GCAP2, and GC1 gene expression in normal and rd chicken pineal.

    Science.gov (United States)

    Semple-Rowland, S L; Larkin, P; Bronson, J D; Nykamp, K; Streit, W J; Baehr, W

    1999-07-28

    This study had three objectives: (1) to characterize the structures of the chicken GCAP1 and GCAP2 genes; (2) to determine if GCAP1, GCAP2, and GC1 genes are expressed in chicken pineal gland; (3) if GC1 is expressed in chicken pineal, to determine if the GC1 null mutation carried by the retinal degeneration (rd) chicken is associated with degenerative changes within the pineal glands of these animals. GCAP1 and GCAP2 gene structures were determined by analyses of chicken cosmid and cDNA clones. The putative transcription start points for these genes were determined using 5'-RACE. GCAP1, GCAP2 and GC1 transcripts were analyzed using Northern blot and RT-PCR. Routine light microscopy was used to examine pineal morphology. Chicken GCAP1 and GCAP2 genes are arranged in a tail-to-tail array. Each protein is encoded by 4 exons that are interrupted by 3 introns of variable length, the positions of which are identical within each gene. The putative transcription start points for GCAP1 and GCAP2 are 314 and 243 bases upstream of the translation start codons of these genes, respectively. As in retina, GCAP1, GCAP2 and GC1 genes are expressed in the chicken pineal. Although the GC1 null mutation is present in both the retina and pineal of the rd chicken, only the retina appears to undergo degeneration. The identical arrangement of chicken, human, and mouse GCAP1/2 genes suggests that these genes originated from an ancient gene duplication/inversion event that occurred during evolution prior to vertebrate diversification. The expression of GC1, GCAP1, and GCAP2 in chicken pineal is consistent with the hypothesis that chicken pineal contains a functional phototransduction cascade. The absence of cellular degeneration in the rd pineal gland suggests that GC1 is not critical for pineal cell survival.

  18. Gene expression and single nucleotide polymorphism array analyses of spindle cell lipomas and conventional lipomas with 13q14 deletion.

    Science.gov (United States)

    Bartuma, Hammurabi; Nord, Karolin H; Macchia, Gemma; Isaksson, Margareth; Nilsson, Jenny; Domanski, Henryk A; Mandahl, Nils; Mertens, Fredrik

    2011-08-01

    Spindle cell lipomas (SCL) are circumscribed, usually s.c. tumors that typically occur on the posterior neck, shoulder, and back of middle aged men. Cytogenetically, almost all SCL are characterized by deletions of chromosome arm 13q, often in combination with loss of 16q. Deletions of 13q are seen also in approximately 15% of conventional lipomas. Through single nucleotide polymorphism (SNP) array analyses, we identified two minimal deleted regions (MDR) in 13q14 in SCL. In MDR1, four genes were located, including the tumor suppressor gene RB1. MDR1 in SCL overlapped with the MDR detected in conventional lipomas with 13q14 deletion. In MDR2 in SCL there were 34 genes and the two microRNA (miRNA) genes miR-15a and miR-16-1. Global gene expression analysis was used to study the impact of the deletions on genes mapping to the two SCL-associated MDR. Five genes (C13orf1, DHRS12, ATP7B, ALG11, and VPS36) in SCL and one gene (C13orf1) in conventional lipomas with 13q-deletions were found to be significantly underexpressed compared with control tissues. Quantitative real-time PCR showed that miR-16-1 was expressed at lower levels in SCL than in the control samples. No mutations were found at sequencing of RB1, miR-15a, and miR-16-1. Our findings further delineate the target region for the 13q deletion in SCL and conventional lipomas and show that the deletions are associated with down-regulated expression of several genes, notably C13orf1, which was the only gene to be significantly down-regulated in both tumor types. Copyright © 2011 Wiley-Liss, Inc.

  19. Identification of Differentially Expressed Genes During Anther Abortion of Taigu Genic Male Sterile Wheat by Combining Suppression Subtractive Hybridization and cDNA Array

    Institute of Scientific and Technical Information of China (English)

    Qing-Shan Chang; Rong-Hua Zhou; Xiu-Ying Kong; Zeng-Liang Yu; Ji-Zeng Jia

    2006-01-01

    Taigu Genic Male Sterile Wheat (TGMSW; Triticum aestivum L.), a dominant genic male sterile germplasm, is of considerable value in the genetic improvement of wheat because of its stable inherence, complete male abortion, and high cross-fertilization rate. To identify specially transcribed genes in sterile anther, a suppression subtractive hybridization (SSH) library was constructed with sterile anther as the tester and fertile anther as the driver. A total of 2 304 SSH inserts amplified by polymerase chain reaction were arrayed using robotic printing. The cDNA arrays were hybridized with 32P-labeled probes prepared from the RNA of forward- and reverse-subtracted anthers. Ninety-six clones were scored as upregulated in sterile anthers compared with the corresponding fertile anthers and some clones were selected for sequencing and analysis in GenBank. Based on their putative functions, 87 non-redundant clones were classified into the following groups: (i) eight genes involved in metabolic processes; (ii) four material transportation genes;(iii) three signal transduction-associated genes; (iv) four stress response and senescence-associated protein genes; (v) seven other functional protein genes; (vi) five genes with no known function; and (vii)another 56 genes with no match to the databases. To test the hybridization efficiency, eight genes were selected and analyzed by Northern blot. The results of the present study provide a comprehensive overview of the genes and gene products involved in anther abortion in TGMSW.

  20. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

    Directory of Open Access Journals (Sweden)

    Sugnet Charles

    2006-12-01

    Full Text Available Abstract Background Alternative splicing is a mechanism for increasing protein diversity by excluding or including exons during post-transcriptional processing. Alternatively spliced proteins are particularly relevant in oncology since they may contribute to the etiology of cancer, provide selective drug targets, or serve as a marker set for cancer diagnosis. While conventional identification of splice variants generally targets individual genes, we present here a new exon-centric array (GeneChip Human Exon 1.0 ST that allows genome-wide identification of differential splice variation, and concurrently provides a flexible and inclusive analysis of gene expression. Results We analyzed 20 paired tumor-normal colon cancer samples using a microarray designed to detect over one million putative exons that can be virtually assembled into potential gene-level transcripts according to various levels of prior supporting evidence. Analysis of high confidence (empirically supported transcripts identified 160 differentially expressed genes, with 42 genes occupying a network impacting cell proliferation and another twenty nine genes with unknown functions. A more speculative analysis, including transcripts based solely on computational prediction, produced another 160 differentially expressed genes, three-fourths of which have no previous annotation. We also present a comparison of gene signal estimations from the Exon 1.0 ST and the U133 Plus 2.0 arrays. Novel splicing events were predicted by experimental algorithms that compare the relative contribution of each exon to the cognate transcript intensity in each tissue. The resulting candidate splice variants were validated with RT-PCR. We found nine genes that were differentially spliced between colon tumors and normal colon tissues, several of which have not been previously implicated in cancer. Top scoring candidates from our analysis were also found to substantially overlap with EST-based bioinformatic

  1. Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array

    Directory of Open Access Journals (Sweden)

    Yick Ching Wong

    2014-11-01

    Full Text Available Gene expression changes that occur during mesocarp development are a major research focus in oil palm research due to the economic importance of this tissue and the relatively rapid increase in lipid content to very high levels at fruit ripeness. Here, we report the development of a transcriptome-based 105,000-probe oil palm mesocarp microarray. The expression of genes involved in fatty acid (FA and triacylglycerol (TAG assembly, along with the tricarboxylic acid cycle (TCA and glycolysis pathway at 16 Weeks After Anthesis (WAA exhibited significantly higher signals compared to those obtained from a cross-species hybridization to the Arabidopsis (p-value < 0.01, and rice (p-value < 0.01 arrays. The oil palm microarray data also showed comparable correlation of expression (r2 = 0.569, p < 0.01 throughout mesocarp development to transcriptome (RNA sequencing data, and improved correlation over quantitative real-time PCR (qPCR (r2 = 0.721, p < 0.01 of the same RNA samples. The results confirm the advantage of the custom microarray over commercially available arrays derived from model species. We demonstrate the utility of this custom microarray to gain a better understanding of gene expression patterns in the oil palm mesocarp that may lead to increasing future oil yield.

  2. Close-field electroporation gene delivery using the cochlear implant electrode array enhances the bionic ear.

    Science.gov (United States)

    Pinyon, Jeremy L; Tadros, Sherif F; Froud, Kristina E; Y Wong, Ann C; Tompson, Isabella T; Crawford, Edward N; Ko, Myungseo; Morris, Renée; Klugmann, Matthias; Housley, Gary D

    2014-04-23

    The cochlear implant is the most successful bionic prosthesis and has transformed the lives of people with profound hearing loss. However, the performance of the "bionic ear" is still largely constrained by the neural interface itself. Current spread inherent to broad monopolar stimulation of the spiral ganglion neuron somata obviates the intrinsic tonotopic mapping of the cochlear nerve. We show in the guinea pig that neurotrophin gene therapy integrated into the cochlear implant improves its performance by stimulating spiral ganglion neurite regeneration. We used the cochlear implant electrode array for novel "close-field" electroporation to transduce mesenchymal cells lining the cochlear perilymphatic canals with a naked complementary DNA gene construct driving expression of brain-derived neurotrophic factor (BDNF) and a green fluorescent protein (GFP) reporter. The focusing of electric fields by particular cochlear implant electrode configurations led to surprisingly efficient gene delivery to adjacent mesenchymal cells. The resulting BDNF expression stimulated regeneration of spiral ganglion neurites, which had atrophied 2 weeks after ototoxic treatment, in a bilateral sensorineural deafness model. In this model, delivery of a control GFP-only vector failed to restore neuron structure, with atrophied neurons indistinguishable from unimplanted cochleae. With BDNF therapy, the regenerated spiral ganglion neurites extended close to the cochlear implant electrodes, with localized ectopic branching. This neural remodeling enabled bipolar stimulation via the cochlear implant array, with low stimulus thresholds and expanded dynamic range of the cochlear nerve, determined via electrically evoked auditory brainstem responses. This development may broadly improve neural interfaces and extend molecular medicine applications.

  3. Correlation of Dynamic PET and Gene Array Data in Patients with Gastrointestinal Stromal Tumors

    Directory of Open Access Journals (Sweden)

    Ludwig G. Strauss

    2012-01-01

    Full Text Available Introduction. The results obtained with dynamic PET (dPET were compared to gene expression data obtained in patients with gastrointestinal stromal tumors (GIST. The primary aim was to assess the association of the dPET results and gene expression data. Material and Methods. dPET was performed following the injection of F-18-fluorodeoxyglucose (FDG in 22 patients with GIST. All patients were examined prior to surgery for staging purpose. Compartment and noncompartment models were used for the quantitative evaluation of the dPET examinations. Gene array data were based on tumor specimen obtained by surgery after the PET examinations. Results. The data analysis revealed significant correlations for the dPET parameters and the expression of zinc finger genes (znf43, znf85, znf91, znf189. Furthermore, the transport of FDG (k1 was associated with VEGF-A. The cell cycle gene cyclin-dependent kinase inhibitor 1C was correlated with the maximum tracer uptake (SUVmax in the tumors. Conclusions. The data demonstrate a dependency of the tracer kinetics on genes associated with prognosis in GIST. Furthermore, angiogenesis and cell proliferation have an impact on the tracer uptake.

  4. Identification of genes differentially expressed in monocyte-derived dendritic cells with 1α,25-dihydroxyvitamin D3 using cDNA arrays

    Institute of Scientific and Technical Information of China (English)

    沈倩云; 郑树森

    2004-01-01

    In order to study the molecular mechanism of the inhibitory effect of 1,25-dihydroxyvitamin D3 on dendritic cells,experiments were performed using Atlas cDNA expression arrays from Clonetech to identify the differentially expressed genes of dendritic cells by 1,25-dihydroxyvitamin D3. Analysis ofcDNA arrays revealed changes in the expression of 9 genes,including those involved in DNA binding and transcription, extracellular cell signaling and communication, intracellular transducers, as well as cell adhesions. The results indicated that a multiple molecular network is involved in the inhibitory role of 1,25-dihydroxyvitamin D3 on dendritic cells. The Atlas Array technology may facilitate the elucidation of complex pharmacological process of 1,25-dihydroxyvitamin D3 on dendritic cells.

  5. Identification of genes differentially expressed in monocyte-deriveddendritic cells with 1α,25-dihydroxyvitamin D3 using cDNA arrays

    Institute of Scientific and Technical Information of China (English)

    沈倩云; 郑树森

    2004-01-01

    In order to study the molecular mechanism of the inhibitory effect of 1,25-dihydroxyvitamin D3 on dendritic cells, experiments were performed using Atlas cDNA expression arrays from Clonetech to identify the differentially expressed genes of dendritic cells by 1,25-dihydroxyvitamin D3. Analysis of cDNA arrays revealed changes in the expression of 9 genes, including those involved in DNA binding and transcription, extracellular cell signaling and communication, intracellular transducers, as well as cell adhesions. The results indicated that a multiple molecular network is involved in the inhibitory role of 1,25-dihydroxyvitamin D3 on dendritic cells. The Atlas Array technology may facilitate the elucidation of complex pharmacological nrocess of 1.25-dihvdroxvvitamin D3 on dondritie cells.

  6. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.

    Science.gov (United States)

    Edgar, Ron; Domrachev, Michael; Lash, Alex E

    2002-01-01

    The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. GEO is not intended to replace in house gene expression databases that benefit from coherent data sets, and which are constructed to facilitate a particular analytic method, but rather complement these by acting as a tertiary, central data distribution hub. The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. A platform is, essentially, a list of probes that define what set of molecules may be detected. A sample describes the set of molecules that are being probed and references a single platform used to generate its molecular abundance data. A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.

  7. A Study of Filled and Sparse Line Array Beamformers.

    Science.gov (United States)

    1980-09-01

    RESOLUTION TESI CHART NAIII NAt RItRI Al SI 1TANT ART 1161 A - LEVEL($ 0met 0o 1 A STUDY OF FILLED AND SPARSE LINE ARRAY BEAMFORMERS y! C- I L1 0___...8217 deviennent importantes . L’auteur d~montre que le PSB posse~de des avantages par rapport au CB pour produire le diagraune de directiviteA. Toutefois

  8. Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons

    Directory of Open Access Journals (Sweden)

    De Paepe Anne

    2004-02-01

    Full Text Available Abstract Background Activation of proto-oncogenes by DNA amplification is an important mechanism in the development and maintenance of cancer cells. Until recently, identification of the targeted genes relied on labour intensive and time consuming positional cloning methods. In this study, we outline a straightforward and efficient strategy for fast and comprehensive cloning of amplified and overexpressed genes. Results As a proof of principle, we analyzed neuroblastoma cell line IMR-32, with at least two amplification sites along the short arm of chromosome 2. In a first step, overexpressed cDNA clones were isolated using a PCR based subtractive cloning method. Subsequent deposition of these clones on a custom microarray and hybridization with IMR-32 DNA, resulted in the identification of clones that were overexpressed due to gene amplification. Using this approach, amplification of all previously reported amplified genes in this cell line was detected. Furthermore, four additional clones were found to be amplified, including the TEM8 gene on 2p13.3, two anonymous transcripts, and a fusion transcript, resulting from 2p13.3 and 2p24.3 fused sequences. Conclusions The combinatorial strategy of subtractive cDNA cloning and array CGH analysis allows comprehensive amplicon dissection, which opens perspectives for improved identification of hitherto unknown targeted oncogenes in cancer cells.

  9. Validation of RNAi Silencing Efficiency Using Gene Array Data shows 18.5% Failure Rate across 429 Independent Experiments

    Directory of Open Access Journals (Sweden)

    Gyöngyi Munkácsy

    2016-01-01

    Full Text Available No independent cross-validation of success rate for studies utilizing small interfering RNA (siRNA for gene silencing has been completed before. To assess the influence of experimental parameters like cell line, transfection technique, validation method, and type of control, we have to validate these in a large set of studies. We utilized gene chip data published for siRNA experiments to assess success rate and to compare methods used in these experiments. We searched NCBI GEO for samples with whole transcriptome analysis before and after gene silencing and evaluated the efficiency for the target and off-target genes using the array-based expression data. Wilcoxon signed-rank test was used to assess silencing efficacy and Kruskal–Wallis tests and Spearman rank correlation were used to evaluate study parameters. All together 1,643 samples representing 429 experiments published in 207 studies were evaluated. The fold change (FC of down-regulation of the target gene was above 0.7 in 18.5% and was above 0.5 in 38.7% of experiments. Silencing efficiency was lowest in MCF7 and highest in SW480 cells (FC = 0.59 and FC = 0.30, respectively, P = 9.3E−06. Studies utilizing Western blot for validation performed better than those with quantitative polymerase chain reaction (qPCR or microarray (FC = 0.43, FC = 0.47, and FC = 0.55, respectively, P = 2.8E−04. There was no correlation between type of control, transfection method, publication year, and silencing efficiency. Although gene silencing is a robust feature successfully cross-validated in the majority of experiments, efficiency remained insufficient in a significant proportion of studies. Selection of cell line model and validation method had the highest influence on silencing proficiency.

  10. DNA micro-array-based identification of bile-responsive genes in Lactobacillus plantarum

    NARCIS (Netherlands)

    Bron, P.A.; Molenaar, D.; Vos, de W.M.; Kleerebezem, M.

    2006-01-01

    The purpose of this study was to determine the global transcriptional response in a food-associated lactic acid bacterium during bile stress. Methods and Results:¿ Clone-based DNA micro-arrays were employed to describe the global transcriptional response of Lactobacillus plantarum WCFS1 towards 0·1%

  11. Genome Fusion Detection: a novel method to detect fusion genes from SNP-array data.

    Science.gov (United States)

    Thieme, Sebastian; Groth, Philip

    2013-03-15

    Fusion genes result from genomic rearrangements, such as deletions, amplifications and translocations. Such rearrangements can also frequently be observed in cancer and have been postulated as driving event in cancer development. to detect them, one needs to analyze the transition region of two segments with different copy number, the location where fusions are known to occur. Finding fusion genes is essential to understanding cancer development and may lead to new therapeutic approaches. Here we present a novel method, the Genomic Fusion Detection algorithm, to predict fusion genes on a genomic level based on SNP-array data. This algorithm detects genes at the transition region of segments with copy number variation. With the application of defined constraints, certain properties of the detected genes are evaluated to predict whether they may be fused. We evaluated our prediction by calculating the observed frequency of known fusions in both primary cancers and cell lines. We tested a set of cell lines positive for the BCR-ABL1 fusion and prostate cancers positive for the TMPRSS2-ERG fusion. We could detect the fusions in all positive cell lines, but not in the negative controls.

  12. Study of the plasma interference with high voltage electrode array for space power application

    OpenAIRE

    Iwasa, Minoru; TANAKA, KOJI; Sasaki, Susumu; ODAWARA, OSAMU; 岩佐 稔; 田中 孝治; 佐々木 進; 小田原 修

    2005-01-01

    We are studying the problems associated with high voltage power systems in space. Especially we are interested in the potential distribution of the solar array that is resistant to the electrical discharge. We have carried out experiments on the interaction between the high voltage solar array and the ambient plasma. In the experiment, an array of electrodes distributed on the insulation panel was used to simulate the inter-connectors of the solar array. An electrode array without the insulat...

  13. AnovArray: a set of SAS macros for the analysis of variance of gene expression data

    Directory of Open Access Journals (Sweden)

    Renard Jean-Paul

    2005-06-01

    Full Text Available Abstract Background Analysis of variance is a powerful approach to identify differentially expressed genes in a complex experimental design for microarray and macroarray data. The advantage of the anova model is the possibility to evaluate multiple sources of variation in an experiment. Results AnovArray is a package implementing ANOVA for gene expression data using SAS® statistical software. The originality of the package is 1 to quantify the different sources of variation on all genes together, 2 to provide a quality control of the model, 3 to propose two models for a gene's variance estimation and to perform a correction for multiple comparisons. Conclusion AnovArray is freely available at http://www-mig.jouy.inra.fr/stat/AnovArray and requires only SAS® statistical software.

  14. Experimental study on silicon micro-heat pipe arrays

    Energy Technology Data Exchange (ETDEWEB)

    Launay, S.; Sartre, V.; Lallemand, M. [Institut National des Sciences Appliquees, Villeurbanne (France). Centre de Thermique

    2004-02-01

    In this study, micro-heat pipe arrays etched into silicon wafers have been investigated for electronic cooling purposes. Micro-heat pipes of triangular cross-section and with liquid arteries were fabricated by wet anisotropic etching with a KOH solution. The microchannels (230 {mu}m wide) are closed by molecular bonding of a plain wafer with the grooved one. A test bench was developed for the micro-heat pipe filling and the thermal characterisation. The temperature profile on the silicon surface is deduced from experimental measurements. The results show that with the artery micro-heat pipe array, filled with methanol, the effective thermal conductivity of the silicon wafer is significantly improved compared to massive silicon. (author)

  15. Study of LCP based flexible patch antenna array

    KAUST Repository

    Ghaffar, Farhan A.

    2012-07-01

    Wrapping of a two element LCP based patch antenna array is studied in this work. For the first time, the designed array is bent in both E and H planes to observe the effect on the radiation and impedance performance of the antenna. The 38 GHz simulation results reveal better performance for H plane bending as compared to E plane bending. A 100 um thick substrate is used for the design which is best suited for flexible antenna applications. Gain variations of 1.1 dB and 1.4 dB are observed for the two orientations while a significantly increased impedance bandwidth of 3 % is obtained with H plane wrapping. The design is highly suitable for broadband micro-cellular backhaul applications. © 2012 IEEE.

  16. Lentivirus Live Cell Array for Quantitative Assessment of Gene and Pathway Activation during Myogenic Differentiation of Mesenchymal Stem Cells.

    Directory of Open Access Journals (Sweden)

    Janhavi Moharil

    Full Text Available Stem cell differentiation involves multiple cascades of transcriptional regulation that govern the cell fate. To study the real-time dynamics of this complex process, quantitative and high throughput live cell assays are required. Herein, we developed a lentiviral library of promoters and transcription factor binding sites to quantitatively capture the gene expression dynamics over a period of several days during myogenic differentiation of human mesenchymal stem cells (MSCs harvested from two different anatomic locations, bone marrow and hair follicle. Our results enabled us to monitor the sequential activation of signaling pathways and myogenic gene promoters at various stages of differentiation. In conjunction with chemical inhibitors, the lentiviral array (LVA results also revealed the relative contribution of key signaling pathways that regulate the myogenic differentiation. Our study demonstrates the potential of LVA to monitor the dynamics of gene and pathway activation during MSC differentiation as well as serve as a platform for discovery of novel molecules, genes and pathways that promote or inhibit complex biological processes.

  17. Array configuration studies for the Square Kilometre Array - Implementation of figures of merit based on spatial dynamic range

    CERN Document Server

    Lal, Dharam Vir; Jiménez-Monferrer, Sergio

    2010-01-01

    The Square Kilometre Array (SKA) will be operating at the time when several new large optical, X-ray and Gamma-ray facilities are expected to be working. To make SKA both competitive and complementary to these large facilities, thorough design studies are needed, focused in particular on imaging performance of the array. One of the crucial aspects of such studies is the choice of the array configuration, which affects substantially the resolution, rms noise, sidelobe level and dynamic range achievable with the SKA. We present here a quantitative assessment of the effect of the array configuration on imaging performance of the SKA, introducing the spatial dynamic range (SDR) and a measure of incompleteness of the Fourier domain coverage ($\\Delta u/u$) as prime figures of merit.

  18. A 220 GHz reflection-type phased array concept study

    Science.gov (United States)

    Hedden, Abigail S.; Dietlein, Charles R.; Wikner, David A.

    2011-05-01

    The goal of this project is to enable light-weight, durable, and portable systems capable of performing standoff detection of person-borne improvised explosive devices (PB-IEDs) through the development of millimeter-wave reflection-type phased arrays. Electronic beam steering eliminates the need for complex mechanical scanners that are commonly implemented with millimeter-wave imaging systems and would reduce overall system size and weight. We present a concept study of a 220 GHz reflection-type phased array for the purpose of performing beam scanning of a confocal reflector system. Requirements for effective imaging of the desired target region are established, including spatial resolution, total scan angle, and number of image pixels achievable. We examine the effects of array architecture on beam characteristics as it is scanned off broadside, including Gaussicity and encircled energy. Benchmark requirements are determined and compared with the capabilities of several potential phase shifter technologies, including MEMS-based variable capacitor phase shifters, switches, and varactor diode-based phase shifters.

  19. An infrasound array study of Mount St. Helens

    Science.gov (United States)

    Matoza, Robin S.; Hedlin, Michael A. H.; Garcés, Milton A.

    2007-02-01

    The ongoing activity of Mount St. Helens provides an opportunity to study the infrasonic wavefield produced by an active, silica-rich volcano. In late October 2004, as a pilot experiment for the Acoustic Surveillance for Hazardous Eruptions (ASHE) project, we deployed two infrasound arrays, each co-located with a broadband seismometer and weather station, to continuously record seismo-acoustic signals from Mount St. Helens. The nearest array, Coldwater, was deployed on the northern flank of the volcano, ˜ 13 km from the summit. The second array, Sacajawea, was deployed ˜ 250 km east of the volcano, at a distance where stratospherically ducted acoustic waves may be expected during the winter. This paper presents an overview of the experimental setup, and preliminary results from this unique data set. Eruptions on January 16th 2005 and March 9th 2005 produced strong infrasonic signals. The aseismic January 16th eruption signal lasted ˜ 9.4 min beginning at ˜ 11:20:44 01/16/05 UTC, while the March 9th eruption signal lasted ˜ 52.8 min beginning at ˜ 01:26:17 03/09/05 UTC, with the main steam and ash venting stage probably lasting ˜ 7.2 min. The March 9th signal was an order of magnitude larger than the January 16th signal, and was clearly recorded 250 km east at the Sacajawea array. Infrasonic expressions of long period (LP) seismic events ('drumbeats') have also been intermittently observed, and are recorded as acoustic waves mimicking the waveform and temporal sequence of their seismic counterparts. These acoustic observations provide important constraints for source models of long period events and eruptions.

  20. Global analysis of candidate genes important for fitness in a competitive biofilm using DNA-array-based transposon mapping.

    Science.gov (United States)

    Junker, Lauren M; Peters, Joseph E; Hay, Anthony G

    2006-08-01

    Escherichia coli strain PHL628 was subjected to saturating Tn5 transposon mutagenesis and then grown under competitive planktonic or biofilm conditions. The locations of transposon insertions from the remaining cells were then mapped on a gene array. The results from the array mapping indicated that 4.5 % of the E. coli genome was important under these conditions. Specifically, 114 genes were identified as important for the biofilm lifestyle, whereas 80 genes were important for the planktonic lifestyle. Four broad functional categories were identified as biofilm-important. These included genes encoding cell structures, small-molecule transport, energy metabolism and regulatory functions. For one of these genes, arcA, an insertion mutant was generated and its biofilm-related phenotype was examined. Results from both the transposon array and insertion mutagenesis indicated that arcA, which is known to be a negative response regulator of genes in aerobic pathways, was important for competitiveness in E. coli PHL628 biofilms. This work also demonstrated that ligation-mediated PCR, coupled with array-based transposon mapping, was an effective tool for identifying a large variety of candidate genes that are important for biofilm fitness.

  1. Gene electrotransfer into skin using noninvasive multi-electrode array for vaccination and wound healing.

    Science.gov (United States)

    Kos, Spela; Vanvarenberg, Kevin; Dolinsek, Tanja; Cemazar, Maja; Jelenc, Jure; Préat, Véronique; Sersa, Gregor; Vandermeulen, Gaëlle

    2017-04-01

    Skin is an attractive target for gene electrotransfer due to its easy accessibility and its interesting immune properties. Since electrodes are often invasive and frequently induce discomfort during pulse application, there is a fundamental need for non-invasive electrodes for skin delivery. We developed circular pin non-invasive multi-electrode array (MEA), suitable for different clinical applications. MEA was first employed to deliver a luciferase reporter gene. Then, it was used to deliver a DNA vaccine coding for ovalbumin or a plasmid encoding hCAP-18/LL-37 for promoting wound healing. The results demonstrated a strong gene expression and an efficient delivery of both, DNA vaccine and wound healing agent, dependent on the pulses applied. The use of MEA to deliver the ovalbumin plasmid demonstrated a strong immune response, as evidenced by the presence of antibodies in sera, the IFN-gamma response and the delayed tumor growth when the mice were subsequently challenged with B16-OVA cells. The delivery of a plasmid encoding hCAP-18/LL-37 significantly accelerated wound closure. The easy applicability and non-invasiveness of MEA make it suitable for various clinical applications that require gene electrotransfer to skin. Specifically, by adapting electric pulses to the expected action of a transgene, non-invasive MEA can be employed either for vaccination or for wound healing.

  2. A pulmonary rat gene array for screening altered expression profiles in air pollutant-induced lung injury.

    Science.gov (United States)

    Nadadur, S S; Schladweiler, M C; Kodavanti, U P

    2000-12-01

    Pulmonary tissue injury and repair processes involve complex and coordinated cellular events such as necrosis, inflammation, cell growth/differentiation, apoptosis, and remodeling of extracellular matrix. These processes are regulated by expression of multiple mediator genes. Commercially available microarray blots and slides allow screening of hundreds to thousands of genes in a given tissue or cell preparation. However, often these blots do not contain cDNAs of one's interest and are difficult to interpret. In order to analyze the tissue expression profile of a large number of genes involved in pulmonary injury and pathology, we developed a rat gene array filter using array technology. This array consisted of 27 genes representing inflammatory and anti-inflammatory cytokines, growth factors, adhesion molecules, stress proteins, transcription factors and antioxidant enzymes; 3 negative controls, and 2 blank spots. Using rat gene-specific polymerase chain reaction (PCR) primer pairs, cDNAs for these genes were amplified and cloned into a TA vector. Plasmids with recombinant cDNA inserts were purified and blotted onto a nylon membrane. Lung total RNA was isolated at 3 or 24 h following intratracheal (IT) exposure of male Sprague Dawley rats to either saline (control), residual oil fly ash (ROFA; 3.3 mg/kg) or metals found in one instillate of ROFA: nickel (NiSO(4); 1. 3 micromol/kg) or vanadium (VSO(4); 2.2 micromol/kg). (32)P-Labeled cDNA was generated from RNA samples in a reverse transcriptase reaction and subsequently hybridized to array blots. Densitometric scans of array blots revealed a twofold induction of interleukin (IL)-6 and TIMP-1 at 24 h post ROFA or Ni exposure. The pulmonary expressions of cellular fibronectin (cFn-EIIIA), ICAM-1, IL-1beta, and iNOS genes were also increased 24 h post ROFA-, V-, or Ni-exposure. Consistent hybridization of beta-actin in all array blots and absence of hybridization signals in negative controls indicated gene specific

  3. Rapid mutation detection in complex genes by heteroduplex analysis with capillary array electrophoresis.

    Science.gov (United States)

    Velasco, Eladio; Infante, Mar; Durán, Mercedes; Esteban-Cardeñosa, Eva; Lastra, Enrique; García-Girón, Carlos; Miner, Cristina

    2005-06-01

    Mutational analysis of large multiexon genes without prevalent mutations is a laborious undertaking that requires the use of a high-throughput scanning technique. The Human Genome Project has enabled the development of powerful techniques for mutation detection in large multiexon genes. We have transferred heteroduplex analysis (HA) by conformation-sensitive gel electrophoresis of the two major breast cancer (BC) predisposing genes, BRCA1 and BRCA2, to a multicapillary DNA sequencer in order to increase the throughput of this technique. This new method that we have called heteroduplex analysis by capillary array electrophoresis (HA-CAE) is based on the use of multiplex-polymerase chain reaction (PCR), different fluorescent labels and HA in a 16-capillary DNA sequencer. To date, a total of 114 different DNA sequence variants (19 insertions/deletions and 95 single-nucleotide substitutions - SNS) of BRCA1 and BRCA2 from 431 unrelated BC families have been successfully detected by HA-CAE. In addition, we have optimized the multiplex-PCR conditions for the colorectal cancer genes MLH1 and MSH2 in order to analyze them by HA-CAE. Both genes have been amplified in 13 multiplex groups, which contain the 35 exons, and their corresponding flanking intronic sequences. MLH1 and MSH2 have been analyzed in nine hereditary nonpolyposis colorectal cancer patients, and we have found six different DNA changes: one complex deletion/insertion mutation in MLH1 exon 19 and another five SNS. Only the complex mutation and one SNS may be classified as cancer-prone mutations. Our experience has revealed that HA-CAE is a simple, fast, reproducible and sensitive method to scan the sequences of complex genes.

  4. Studying Functions of All Yeast Genes Simultaneously

    Science.gov (United States)

    Stolc, Viktor; Eason, Robert G.; Poumand, Nader; Herman, Zelek S.; Davis, Ronald W.; Anthony Kevin; Jejelowo, Olufisayo

    2006-01-01

    A method of studying the functions of all the genes of a given species of microorganism simultaneously has been developed in experiments on Saccharomyces cerevisiae (commonly known as baker's or brewer's yeast). It is already known that many yeast genes perform functions similar to those of corresponding human genes; therefore, by facilitating understanding of yeast genes, the method may ultimately also contribute to the knowledge needed to treat some diseases in humans. Because of the complexity of the method and the highly specialized nature of the underlying knowledge, it is possible to give only a brief and sketchy summary here. The method involves the use of unique synthetic deoxyribonucleic acid (DNA) sequences that are denoted as DNA bar codes because of their utility as molecular labels. The method also involves the disruption of gene functions through deletion of genes. Saccharomyces cerevisiae is a particularly powerful experimental system in that multiple deletion strains easily can be pooled for parallel growth assays. Individual deletion strains recently have been created for 5,918 open reading frames, representing nearly all of the estimated 6,000 genetic loci of Saccharomyces cerevisiae. Tagging of each deletion strain with one or two unique 20-nucleotide sequences enables identification of genes affected by specific growth conditions, without prior knowledge of gene functions. Hybridization of bar-code DNA to oligonucleotide arrays can be used to measure the growth rate of each strain over several cell-division generations. The growth rate thus measured serves as an index of the fitness of the strain.

  5. Studying the Complex Expression Dependences between Sets of Coexpressed Genes

    Directory of Open Access Journals (Sweden)

    Mario Huerta

    2014-01-01

    Full Text Available Organisms simplify the orchestration of gene expression by coregulating genes whose products function together in the cell. The use of clustering methods to obtain sets of coexpressed genes from expression arrays is very common; nevertheless there are no appropriate tools to study the expression networks among these sets of coexpressed genes. The aim of the developed tools is to allow studying the complex expression dependences that exist between sets of coexpressed genes. For this purpose, we start detecting the nonlinear expression relationships between pairs of genes, plus the coexpressed genes. Next, we form networks among sets of coexpressed genes that maintain nonlinear expression dependences between all of them. The expression relationship between the sets of coexpressed genes is defined by the expression relationship between the skeletons of these sets, where this skeleton represents the coexpressed genes with a well-defined nonlinear expression relationship with the skeleton of the other sets. As a result, we can study the nonlinear expression relationships between a target gene and other sets of coexpressed genes, or start the study from the skeleton of the sets, to study the complex relationships of activation and deactivation between the sets of coexpressed genes that carry out the different cellular processes present in the expression experiments.

  6. Antibodies against Human Cytomegalovirus in the Pathogenesis of Systemic Sclerosis: A Gene Array Approach.

    Directory of Open Access Journals (Sweden)

    2005-12-01

    Full Text Available BACKGROUND: Systemic sclerosis is an autoimmune disease characterized by immunological abnormalities, vascular damage, and fibroblast proliferation. We have previously shown that a molecular mimicry mechanism links antibodies against the human-cytomegalovirus-derived protein UL94 to the pathogenesis of systemic sclerosis. The UL94 epitope shows homology with NAG-2, a surface molecule highly expressed on endothelial cells. Anti-UL94 peptide antibodies purified from patients' sera induce apoptosis of endothelial cells upon engagement of the NAG-2-integrin complex. METHODS AND FINDINGS: We show here that NAG-2 is expressed on dermal fibroblasts and that anti-UL94 antibodies bind to fibroblasts. We have used the gene array strategy (Affimetrix oligonucleotide microarrays to analyze the transcriptional profile in response to a 4-h and an 8-h treatment with antibodies against the UL94 peptide in endothelial cells and dermal fibroblasts. Exposure of endothelial cells to anti-UL94 antibodies had a profound impact on gene expression, resulting in the upregulation of 1,645 transcripts. Several gene clusters were upregulated including genes encoding adhesion molecules, chemokines, colony-stimulating factors (CSFs, growth factors, and molecules involved in apoptosis. Following antibody stimulation, dermal fibroblasts showed an upregulation of 989 transcripts and acquired a "scleroderma-like" phenotype. Indeed, genes involved in extracellular matrix deposition, growth factors, chemokines, and cytokines were upregulated. We confirmed the microarray results by real-time quantitative polymerase chain reaction and by measuring some of the corresponding proteins with ELISA and Western blotting. CONCLUSION: Our results show that anti-human-cytomegalovirus antibodies may be linked to the pathogenesis of systemic sclerosis not only by inducing endothelial cell activation and apoptosis but also by causing activation of fibroblasts, one of the hallmarks of the disease.

  7. Antibodies against human cytomegalovirus in the pathogenesis of systemic sclerosis: a gene array approach.

    Directory of Open Access Journals (Sweden)

    Claudio Lunardi

    2006-01-01

    Full Text Available BACKGROUND: Systemic sclerosis is an autoimmune disease characterized by immunological abnormalities, vascular damage, and fibroblast proliferation. We have previously shown that a molecular mimicry mechanism links antibodies against the human-cytomegalovirus-derived protein UL94 to the pathogenesis of systemic sclerosis. The UL94 epitope shows homology with NAG-2, a surface molecule highly expressed on endothelial cells. Anti-UL94 peptide antibodies purified from patients' sera induce apoptosis of endothelial cells upon engagement of the NAG-2-integrin complex. METHODS AND FINDINGS: We show here that NAG-2 is expressed on dermal fibroblasts and that anti-UL94 antibodies bind to fibroblasts. We have used the gene array strategy (Affimetrix oligonucleotide microarrays to analyze the transcriptional profile in response to a 4-h and an 8-h treatment with antibodies against the UL94 peptide in endothelial cells and dermal fibroblasts. Exposure of endothelial cells to anti-UL94 antibodies had a profound impact on gene expression, resulting in the upregulation of 1,645 transcripts. Several gene clusters were upregulated including genes encoding adhesion molecules, chemokines, colony-stimulating factors (CSFs, growth factors, and molecules involved in apoptosis. Following antibody stimulation, dermal fibroblasts showed an upregulation of 989 transcripts and acquired a "scleroderma-like" phenotype. Indeed, genes involved in extracellular matrix deposition, growth factors, chemokines, and cytokines were upregulated. We confirmed the microarray results by real-time quantitative polymerase chain reaction and by measuring some of the corresponding proteins with ELISA and Western blotting. CONCLUSION: Our results show that anti-human-cytomegalovirus antibodies may be linked to the pathogenesis of systemic sclerosis not only by inducing endothelial cell activation and apoptosis but also by causing activation of fibroblasts, one of the hallmarks of the disease.

  8. A Customized Pigmentation SNP Array Identifies a Novel SNP Associated with Melanoma Predisposition in the SLC45A2 Gene

    Science.gov (United States)

    Alonso, Santos; Boyano, M. Dolores; Peña-Chilet, Maria; Pita, Guillermo; Aviles, Jose A.; Mayor, Matias; Gomez-Fernandez, Cristina; Casado, Beatriz; Martin-Gonzalez, Manuel; Izagirre, Neskuts; De la Rua, Concepcion; Asumendi, Aintzane; Perez-Yarza, Gorka; Arroyo-Berdugo, Yoana; Boldo, Enrique; Lozoya, Rafael; Torrijos-Aguilar, Arantxa; Pitarch, Ana; Pitarch, Gerard; Sanchez-Motilla, Jose M.; Valcuende-Cavero, Francisca; Tomas-Cabedo, Gloria; Perez-Pastor, Gemma; Diaz-Perez, Jose L.; Gardeazabal, Jesus; de Lizarduy, Iñigo Martinez; Sanchez-Diez, Ana; Valdes, Carlos; Pizarro, Angel; Casado, Mariano; Carretero, Gregorio; Botella-Estrada, Rafael; Nagore, Eduardo; Lazaro, Pablo; Lluch, Ana; Benitez, Javier; Martinez-Cadenas, Conrado; Ribas, Gloria

    2011-01-01

    As the incidence of Malignant Melanoma (MM) reflects an interaction between skin colour and UV exposure, variations in genes implicated in pigmentation and tanning response to UV may be associated with susceptibility to MM. In this study, 363 SNPs in 65 gene regions belonging to the pigmentation pathway have been successfully genotyped using a SNP array. Five hundred and ninety MM cases and 507 controls were analyzed in a discovery phase I. Ten candidate SNPs based on a p-value threshold of 0.01 were identified. Two of them, rs35414 (SLC45A2) and rs2069398 (SILV/CKD2), were statistically significant after conservative Bonferroni correction. The best six SNPs were further tested in an independent Spanish series (624 MM cases and 789 controls). A novel SNP located on the SLC45A2 gene (rs35414) was found to be significantly associated with melanoma in both phase I and phase II (P<0.0001). None of the other five SNPs were replicated in this second phase of the study. However, three SNPs in TYR, SILV/CDK2 and ADAMTS20 genes (rs17793678, rs2069398 and rs1510521 respectively) had an overall p-value<0.05 when considering the whole DNA collection (1214 MM cases and 1296 controls). Both the SLC45A2 and the SILV/CDK2 variants behave as protective alleles, while the TYR and ADAMTS20 variants seem to function as risk alleles. Cumulative effects were detected when these four variants were considered together. Furthermore, individuals carrying two or more mutations in MC1R, a well-known low penetrance melanoma-predisposing gene, had a decreased MM risk if concurrently bearing the SLC45A2 protective variant. To our knowledge, this is the largest study on Spanish sporadic MM cases to date. PMID:21559390

  9. A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.

    Directory of Open Access Journals (Sweden)

    Maider Ibarrola-Villava

    Full Text Available As the incidence of Malignant Melanoma (MM reflects an interaction between skin colour and UV exposure, variations in genes implicated in pigmentation and tanning response to UV may be associated with susceptibility to MM. In this study, 363 SNPs in 65 gene regions belonging to the pigmentation pathway have been successfully genotyped using a SNP array. Five hundred and ninety MM cases and 507 controls were analyzed in a discovery phase I. Ten candidate SNPs based on a p-value threshold of 0.01 were identified. Two of them, rs35414 (SLC45A2 and rs2069398 (SILV/CKD2, were statistically significant after conservative Bonferroni correction. The best six SNPs were further tested in an independent Spanish series (624 MM cases and 789 controls. A novel SNP located on the SLC45A2 gene (rs35414 was found to be significantly associated with melanoma in both phase I and phase II (P<0.0001. None of the other five SNPs were replicated in this second phase of the study. However, three SNPs in TYR, SILV/CDK2 and ADAMTS20 genes (rs17793678, rs2069398 and rs1510521 respectively had an overall p-value<0.05 when considering the whole DNA collection (1214 MM cases and 1296 controls. Both the SLC45A2 and the SILV/CDK2 variants behave as protective alleles, while the TYR and ADAMTS20 variants seem to function as risk alleles. Cumulative effects were detected when these four variants were considered together. Furthermore, individuals carrying two or more mutations in MC1R, a well-known low penetrance melanoma-predisposing gene, had a decreased MM risk if concurrently bearing the SLC45A2 protective variant. To our knowledge, this is the largest study on Spanish sporadic MM cases to date.

  10. Applications of the theory of Gr?bner bases to the study of linear recurring arrays

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This is a small survey of applications of the theory of Gr?bner bases to the study of linear recurring arrays. It applies some properties of Gr?bner bases to studying linear recurring arrays and contains recent new results on linear recurring arrays.

  11. The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization

    Directory of Open Access Journals (Sweden)

    Lo Fang-Yi

    2012-06-01

    Full Text Available Abstract Background Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Methods Array-comparative genomic hybridization (array-CGH was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR, chromogenic in situ hybridization (CISH, reverse transcriptase-qPCR (RT-qPCR, and immunohistochemistry (IHC in more patients. Results We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1 functioning in Rho activity control, FRAT2 (10q24.1 involved in Wnt signaling, PAFAH1B1 (17p13.3 functioning in motility control, and ZNF322A (6p22.1 involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (PP=0.06. In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of

  12. Feasibility study of patient motion monitoring using tactile array sensor

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tae Ho; Kang, Seong Hee; Kim, Dong Su; Cho, Min Seok; Kim, Kyeong Hyeon; Suh, Tae Suk [Dept. of Biomedical Engineering, Research Institute of Biomedical Engineering, the Catholic University of Korea, Seoul (Korea, Republic of); Kim, Si Yong [Dept. of Radiation Oncology, Virginia Commonwealth University, Richmond (United States)

    2014-11-15

    The aim of this study is to evaluate patient pretreatment set-up error and intra-fraction motion using the tactile array sensors (Pressure Profile Systems Inc, Los Angeles, CA) which could measure distributed pressure profiles along the contacting surface and to check a feasibility of the sensor (tactile array sensor) in the patient motion monitoring. Laser alignment and optical camera based monitoring system are very useful for reduce patient set-up error but these systems could not monitor the blind area like patient's back position. Actually after patient alignment using laser or optical monitoring system, it was assumed that there is no error in the patient's back position (pressure profile distribution). But if an error occurs in the patient's back position, it will affect the radiation therapy accuracy. In spite of optical motion monitoring or using the immobilization tool, distributed pressure profiles of patient's back position was changed during inter and intra-fraction. For more accurate patient set-up, blind area (patient's back) monitoring was necessary. We expect that the proposed method will be very useful for make up for the weakness of optical monitoring method.

  13. Profile of muscle tissue gene expression specific to water buffalo: Comparison with domestic cattle by genome array.

    Science.gov (United States)

    Zhang, Yingying; Wang, Hongbao; Gui, Linsheng; Wang, Hongcheng; Mei, Chugang; Zhang, Yaran; Xu, Huaichao; Jia, Cunlin; Zan, Linsen

    2016-02-10

    In contrast with the past, the water buffalo is now not only a draft animal, but also an important food source of milk and meat. It is increasingly apparent that the water buffalo have huge potential for meat production, but its breeding needs to be investigated. Regarding the molecular mechanisms involved in the meat quality difference between the buffalo (Bubalus bulabis) and yellow cattle (Bos taurus), 12 chemical-physical characteristics related to the meat quality of longissimus thoracis muscles (LTM) have been compared at the age of 36 months. Intramuscular lipid and b* (yellowness) were greater in cattle than the buffalo, whereas a* (redness) was greater in the buffalo. Gene expression profiles were constructed by bovine genome array. A total of 8884 and 10,960 probes were detected in buffalo and cattle, respectively, with 1580 genes being differentially expressed. Over 400 probes were upregulated and nearly 1200 were downregulated in LTM of the buffalo, most being involved in ribosomal RNA (rRNA) processing, cholesterol homeostasis, regulation of transcription, response to hypoxia, and glycolysis. Quantitative real-time PCR was used to validate the microarray data. Enriched GO analyses of highly expressed genes in LTM showed that protein biosynthesis, striated muscle contraction, iron homeostasis, iron transport, glycolysis and glucose metabolism were similar between the buffalo and cattle. High protein content, low fat content and deep meat color of buffalo LTM may be closely associated with the increased expression of genes involved in cholesterol and iron homeostasis, while also reducing the expression of genes involved in ubiquitin-mediated proteolysis and protein oxidative phosphorylation. These results establish the groundwork for further studies on buffalo meat quality and will be beneficial in improving water buffalo breeding by molecular biotechnology.

  14. Proof of principle study of ultrasonic particle manipulation by a circular array device

    OpenAIRE

    Grinenko, Alon; Wilcox, Paul D.; Courtney, Charles R. P.; Drinkwater, Bruce W.

    2012-01-01

    A feasibility study of a circular ultrasonic array device for acoustic particle manipulation is presented. A general approach based on Green's function is developed to analyse the underlying properties of a circular acoustic array. It allows the size of a controllable device area as a function of the number of array elements to be established and the array excitation required to produce a desired field distribution to be determined. A set of quantitative parameters characterizing the complexi...

  15. Study of the interaction between space plasma and high voltage solar array

    OpenAIRE

    Iwasa, Minoru; TANAKA, KOJI; Sasaki, Susumu; ODAWARA, OSAMU; 岩佐 稔; 田中 孝治; 佐々木 進; 小田原 修

    2006-01-01

    We are studying the problems associated with high voltage power systems in space. Especially we are interested in the potential distribution of the solar array that is resistant to the electrical discharge. We have carried out experiment on the interaction between the space plasma and the high voltage solar array. An array of electrodes distributed on a dielectric material was used to simulate the inter-connectors of the solar array panel in space environment. One of major concerns in the usa...

  16. Gene array analysis of adrenal glands in broiler chickens following ACTH treatment

    Directory of Open Access Journals (Sweden)

    Guémené Daniel

    2009-09-01

    Full Text Available Abstract Background Difference in adaptability responses to stress has been observed amongst bird species, strains, and individuals. Components of the HPA axis, one of the internal systems involved in homeostasis re-establishment following stress, could play a role in this variability of responses. The aim of the present study was 1 to identify genes involved in the regulation of adrenal activity following ACTH stimulation and 2 to examine adrenal genes differentially expressed in individuals with high and low plasma corticosterone response following ACTH treatment. Results Analysis with 21 K poultry oligo microarrays indicated that ACTH treatment affected the expression of 134 genes. Several transcripts assigned to genes involved in the adrenal ACTH signaling pathway and steroidogenic enzymes were identified as differentially expressed by ACTH treatment. Real-time PCR on 18 selected genes confirmed changes in transcript levels of 11 genes, including MC2R, CREM, Cry, Bmal1, Sqle, Prax1, and StAR. Only 4 genes revealed to be differentially expressed between higher and lower adrenal responders to ACTH treatment. Conclusion The results from the present study reveal putative candidate genes; their role in regulation of adrenal functions and adaptability to stress should be further investigated.

  17. Single strand conformation polymorphism analysis of candidate genes for reliable identification of alleles by capillary array electrophoresis.

    Science.gov (United States)

    We investigated the reliability of capillary array electrophoresis-SSCP to determine if it can be used to identify novel alleles of candidate genes in a germplasm collection. Both strands of three different size fragments (160 bp, 245 pb and 437 bp) that differed by one or more nucleotides in sequen...

  18. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis

    NARCIS (Netherlands)

    Greshock, J; Naylor, TL; Margolin, A; Diskin, S; Cleaver, SH; Futreal, PA; deJong, PJ; Zhao, SY; Liebman, M; Weber, BL

    2004-01-01

    Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for disease-gene discovery in cancer and developmental disorders as well as numerous other applications. However, w

  19. A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays

    NARCIS (Netherlands)

    Alberts, Rudi; Terpstra, Peter; Bystrykh, Leonid V.; Haan, Gerald de; Jansen, Ritsert C.

    2005-01-01

    Short-oligonucleotide arrays typically contain multiple probes per gene. In genetical genomics applications a statistical model for the individual probe signals can help in separating ‘‘true’’ differential mRNA expression from ‘‘ghost’’ effects caused by polymorphisms, misdesigned probes, and batch

  20. Commercial/industrial photovoltaic module and array requirement study. Low-cost solar array project engineering area

    Science.gov (United States)

    1981-01-01

    Design requirements for photovoltaic modules and arrays used in commercial and industrial applications were identified. Building codes and referenced standards were reviewed for their applicability to commercial and industrial photovoltaic array installation. Four general installation types were identified - integral (replaces roofing), direct (mounted on top of roofing), stand-off (mounted away from roofing), and rack (for flat or low slope roofs, or ground mounted). Each of the generic mounting types can be used in vertical wall mounting systems. This implies eight mounting types exist in the commercial/industrial sector. Installation costs were developed for these mounting types as a function of panel/module size. Cost drivers were identified. Studies were performed to identify optimum module shapes and sizes and operating voltage cost drivers. The general conclusion is that there are no perceived major obstacles to the use of photovoltaic modules in commercial/industrial arrays.

  1. Global Identification of Significantly Expressed Genes in Developing Endosperm of Rice by Expression Sequence Tags and cDNA Array Approaches

    Institute of Scientific and Technical Information of China (English)

    Qichao Tu; Haitao Dong; Haigen Yao; Yongqi Fang; Cheng'en Dai; Hongmei Luo; Jian Yao; Dong Zhao; Debao Li

    2008-01-01

    Rice endosperm plays a very important role in seedling germination and determines the qualities of fice grain.Although studies on specific gene categories in endosperm have been carried out,global view of gene expression at a transcription level in rice endosperm is still limited.To gain a better understanding of the global and tissue-specific gene expression profiles in rice endosperm,a cDNA library from rice endosperm of immature seeds was sequenced.A cDNA array was constructed based on the tentative unique transcripts derived from expression sequence tag (EST) assembling results and then hybridized with cONAs from five different tissues or organs including endosperm,embryo,leaf,stem and root of rice.Significant redundancy was found for genes encoding prolamin,glutelin,allergen,and starch synthesis proteins,accounting for~34% of the total ESTs obtained.The cDNA array revealed 87 significantly expressed genes in endosperm compared with the other four organs or tissues.These genes included 13 prolamin family proteins,17 glutelin family proteins,12 binding proteins,nine catalytic proteins and four ribosomal proteins,indicating a complicated biological processing in rice endosperm.In addition,Northern verification of 1,4-alpha-glucan branching enzyme detected two isoforms in rice endosperm,the larger one of which only existed in endosperm.

  2. Mechanistic study of ZnO nanorod array electrodeposition

    Energy Technology Data Exchange (ETDEWEB)

    El Belghiti, H.; Pauporte, T.; Lincot, D. [Laboratoire d' Electrochimie et Chimie Analytique, UMR7575, Ecole Nationale Superieure de Chimie de Paris-Universite Paris 6 (France)

    2008-10-15

    The growth of ZnO nanorods by electrodeposition from oxygenated aqueous mixture of zinc chloride and potassium chloride is studied experimentally as a function of the deposition time, zinc concentration and the substrate. These parameters influence markedly the characteristics of the deposits (rod density, aspect ratio, orientation). A mechanistic model is presented in order to explain the formation of ZnO nanorod arrays by electrodeposition. The model is based on the effect of zinc concentration on the interfacial pH at the electrode surface and then on the charged stable zinc species able to react with the growing film. The charge of the complex seems to be the key parameter which stops the lateral growth and then significantly increases the aspect ratio of the single crystalline nanorods. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  3. Studying protein-protein interactions using peptide arrays

    NARCIS (Netherlands)

    Katz, C.; Levy-Beladev, L.; Rotem-Bamberger, S.; Rito, T.; Rudiger, S.G.D.; Friedler, A.

    2010-01-01

    Screening of arrays and libraries of compounds is well-established as a high-throughput method for detecting and analyzing interactions in both biological and chemical systems. Arrays and libraries can be composed from various types of molecules, ranging from small organic compounds to DNA, proteins

  4. Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood

    Directory of Open Access Journals (Sweden)

    Turner Renee J

    2009-08-01

    Full Text Available Abstract Background Gene expression studies require appropriate normalization methods. One such method uses stably expressed reference genes. Since suitable reference genes appear to be unique for each tissue, we have identified an optimal set of the most stably expressed genes in human blood that can be used for normalization. Methods Whole-genome Affymetrix Human 2.0 Plus arrays were examined from 526 samples of males and females ages 2 to 78, including control subjects and patients with Tourette syndrome, stroke, migraine, muscular dystrophy, and autism. The top 100 most stably expressed genes with a broad range of expression levels were identified. To validate the best candidate genes, we performed quantitative RT-PCR on a subset of 10 genes (TRAP1, DECR1, FPGS, FARP1, MAPRE2, PEX16, GINS2, CRY2, CSNK1G2 and A4GALT, 4 commonly employed reference genes (GAPDH, ACTB, B2M and HMBS and PPIB, previously reported to be stably expressed in blood. Expression stability and ranking analysis were performed using GeNorm and NormFinder algorithms. Results Reference genes were ranked based on their expression stability and the minimum number of genes needed for nomalization as calculated using GeNorm showed that the fewest, most stably expressed genes needed for acurate normalization in RNA expression studies of human whole blood is a combination of TRAP1, FPGS, DECR1 and PPIB. We confirmed the ranking of the best candidate control genes by using an alternative algorithm (NormFinder. Conclusion The reference genes identified in this study are stably expressed in whole blood of humans of both genders with multiple disease conditions and ages 2 to 78. Importantly, they also have different functions within cells and thus should be expressed independently of each other. These genes should be useful as normalization genes for microarray and RT-PCR whole blood studies of human physiology, metabolism and disease.

  5. [Subchromosomal microdeletion identified by molecular karyotyping using DNA microarrays (array CGH) in Rett syndrome girls negative for MECP2 gene mutations].

    Science.gov (United States)

    Vorsanova, S G; Iurov, I Iu; Voinova, V Iu; Kurinnaia, O S; Zelenova, M A; Demidova, I A; Ulas, E V; Iurov, Iu B

    2013-01-01

    Molecular karyotyping using DNA microarrays (array CGH) was applied for identification of subchromosomal microdeletions in a cohort of 12 girls with clinical features of RETT syndrome, but negative for MECP2 gene mutations. Recurrent microdeletions of MECP2 gene in chromosome X (locus Xq28) were identified in 5 girls of 12 studied. Probably RTT girls with subchromosomic microdeletions in Xq28 could represent a special subtype of the disease, which appears as clinically milder than the classic form of disease. In one case, an atypical form of RTT was associated with genomic abnormalities affecting CDKL5 gene and region critical for microdeletion Prader-Willi and Angelman syndromes (15q11.2). In addition, data are presented for the first time that genetic variation in regions 3p13, 3q27.1, and 1q21.1-1q21.2 could associate with RTT-like clinical manifestations. Without application of molecular karyotyping technology and bioinformatic method of assessing the pathogenic significance of genomic rearrangements these RTT-like girls negative for MECP2 gene mutations were considered as cases of idiopathic mental retardation associated with autism. It should be noted that absence of intragenic mutations in MECP2 gene is not sufficient criteria to reject the clinical diagnosis of RTT. To avoid errors in the genetic diagnosis of this genetically heterogeneous brain disease molecular cytogenetic studies using high resolution oligonucleotide array CGH (molecular karyotyping) are needed.

  6. How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results

    Directory of Open Access Journals (Sweden)

    Voesenek Laurentius ACJ

    2006-03-01

    Full Text Available Abstract Background Short oligonucleotide arrays for transcript profiling have been available for several years. Generally, raw data from these arrays are analysed with the aid of the Microarray Analysis Suite or GeneChip Operating Software (MAS or GCOS from Affymetrix. Recently, more methods to analyse the raw data have become available. Ideally all these methods should come up with more or less the same results. We set out to evaluate the different methods and include work on our own data set, in order to test which method gives the most reliable results. Results Calculating gene expression with 6 different algorithms (MAS5, dChip PMMM, dChip PM, RMA, GC-RMA and PDNN using the same (Arabidopsis data, results in different calculated gene expression levels. Consequently, depending on the method used, different genes will be identified as differentially regulated. Surprisingly, there was only 27 to 36% overlap between the different methods. Furthermore, 47.5% of the genes/probe sets showed good correlation between the mismatch and perfect match intensities. Conclusion After comparing six algorithms, RMA gave the most reproducible results and showed the highest correlation coefficients with Real Time RT-PCR data on genes identified as differentially expressed by all methods. However, we were not able to verify, by Real Time RT-PCR, the microarray results for most genes that were solely calculated by RMA. Furthermore, we conclude that subtraction of the mismatch intensity from the perfect match intensity results most likely in a significant underestimation for at least 47.5% of the expression values. Not one algorithm produced significant expression values for genes present in quantities below 1 pmol. If the only purpose of the microarray experiment is to find new candidate genes, and too many genes are found, then mutual exclusion of the genes predicted by contrasting methods can be used to narrow down the list of new candidate genes by 64 to 73%.

  7. Space solar array reliability: A study and recommendations

    Science.gov (United States)

    Brandhorst, Henry W., Jr.; Rodiek, Julie A.

    2008-12-01

    Providing reliable power over the anticipated mission life is critical to all satellites; therefore solar arrays are one of the most vital links to satellite mission success. Furthermore, solar arrays are exposed to the harshest environment of virtually any satellite component. In the past 10 years 117 satellite solar array anomalies have been recorded with 12 resulting in total satellite failure. Through an in-depth analysis of satellite anomalies listed in the Airclaim's Ascend SpaceTrak database, it is clear that solar array reliability is a serious, industry-wide issue. Solar array reliability directly affects the cost of future satellites through increased insurance premiums and a lack of confidence by investors. Recommendations for improving reliability through careful ground testing, standardization of testing procedures such as the emerging AIAA standards, and data sharing across the industry will be discussed. The benefits of creating a certified module and array testing facility that would certify in-space reliability will also be briefly examined. Solar array reliability is an issue that must be addressed to both reduce costs and ensure continued viability of the commercial and government assets on orbit.

  8. Polymer nanopillar-gold arrays as surface-enhanced Raman spectroscopy substrate for the simultaneous detection of multiple genes.

    Science.gov (United States)

    Picciolini, Silvia; Mehn, Dora; Morasso, Carlo; Vanna, Renzo; Bedoni, Marzia; Pellacani, Paola; Marchesini, Gerardo; Valsesia, Andrea; Prosperi, Davide; Tresoldi, Cristina; Ciceri, Fabio; Gramatica, Furio

    2014-10-28

    In our study, 2D nanopillar arrays with plasmonic crystal properties are optimized for surface-enhanced Raman spectroscopy (SERS) application and tested in a biochemical assay for the simultaneous detection of multiple genetic leukemia biomarkers. The special fabrication process combining soft lithography and plasma deposition techniques allows tailoring of the structural and chemical parameters of the crystal surfaces. In this way, it has been possible to tune the plasmonic resonance spectral position close to the excitation wavelength of the monochromatic laser light source in order to maximize the enhancing properties of the substrate. Samples are characterized by scanning electron microscopy and reflectance measurements and tested for SERS activity using malachite green. Besides, as the developed substrate had been prepared on a simple glass slide, SERS detection from the support side is also demonstrated. The optimized substrate is functionalized with thiol-modified capture oligonucleotides, and concentration-dependent signal of the target nucleotide is detected in a sandwich assay with labeled gold nanoparticles. Gold nanoparticles functionalized with different DNA and various Raman reporters are applied in a microarray-based assay recognizing a disease biomarker (Wilms tumor gene) and housekeeping gene expressions in the same time on spatially separated microspots. The multiplexing performance of the SERS-based bioassay is illustrated by distinguishing Raman dyes based on their complex spectral fingerprints.

  9. Trophic actions of extracellular ATP: gene expression profiling by DNA array analysis.

    Science.gov (United States)

    Neary, J T

    2000-07-01

    In addition to Professor Burnstock's work on the short-term signaling actions of extracellular nucleotides and nucleosides, Geoff has had a long-standing interest in trophic actions of purines in development and in pathophysiological conditions which has been instrumental in encouraging my work in this area. The trophic actions of extracellular ATP, alone or in combination with polypeptide growth factors, may play an important role in brain development and may contribute to the reactive gliosis that accompanies brain injury and neurodegeneration. P2Y receptors in astrocytes are coupled to the ERK/MAPK cascade, a signal transduction mechanism crucial for cellular proliferation and differentiation. The mitogenic signaling pathway from P2Y receptors to ERK involves phospholipase D and a calcium-independent PKC isoform, PKCdelta. DNA array analysis reveals a number of changes in gene expression after P2Y receptor occupancy, indicating that this methodology will be a powerful tool in understanding the mechanisms underlying the trophic actions of extracellular nucleotides and nucleosides.

  10. Identification of a novel gene by whole human genome tiling array.

    Science.gov (United States)

    Ishida, Hirokazu; Yagi, Tomohito; Tanaka, Masami; Tokuda, Yuichi; Kamoi, Kazumi; Hongo, Fumiya; Kawauchi, Akihiro; Nakano, Masakazu; Miki, Tsuneharu; Tashiro, Kei

    2013-03-01

    When the whole human genome sequence was determined by the Human Genome Project, the number of identified genes was fewer than expected. However, recent studies suggest that undiscovered transcripts still exist in the human genome. Furthermore, a new technology, the DNA microarray, which can simultaneously characterize huge amounts of genome sequence data, has become a useful tool for analyzing genetic changes in various diseases. A version of this tool, the tiling DNA microarray, was designed to search all the transcripts of the entire human genome, and provides huge amounts of data, including both exon and intron sequences, by a simple process. Although some previous studies using tiling DNA microarray analysis have indicated that numerous novel transcripts can be found in the human genome, none of them has reported any novel full-length human genes. Here, to find novel genes, we analyzed all the transcripts expressed in normal human prostate cells using this microarray. Because the optimal analytical parameters for using tiling DNA microarray data for this purpose had not been established, we established parameters for extracting the most likely regions for novel transcripts. The three parameters we optimized were the threshold for positive signal intensity, the Max gap, and the Min run, which we set to detect all transcriptional regions that were above the average length of known exons and had a signal intensity in the top 5%. We succeeded in obtaining the full-length sequence of one novel gene, located on chromosome 12q24.13. We named the novel gene "POTAGE". Its 5841-bp mRNA consists of 26 exons. We detected part of exon 2 in the tiling data analysis. The full-length sequence was then obtained by RT-PCR and RACE. Although the function of POTAGE is unclear, its sequence showed high homology with genes in other species, suggesting it might have an important or essential function. This study demonstrates that the tiling DNA microarray can be useful for

  11. An array-based study of increased system lifetime probability

    DEFF Research Database (Denmark)

    Nesgaard, Carsten

    2003-01-01

    Society's increased dependence on electronic systems calls for highly reliable power supplies comprised of multiple converters working in parallel. This paper describes a redundancy control scheme, based on the array technology that increases the overall reliability quite considerably and thereby...

  12. Preliminary experimental study of a carbon fiber array cathode

    Science.gov (United States)

    Li, An-kun; Fan, Yu-wei

    2016-08-01

    The preliminary experimental results of a carbon fiber array cathode for the magnetically insulated transmission line oscillator (MILO) operations are reported. When the diode voltage and diode current were 480 kV and 44 kA, respectively, high-power microwaves with a peak power of about 3 GW and a pulse duration of about 60 ns were obtained in a MILO device with the carbon fiber array cathode. The preliminary experimental results show that the shot-to-shot reproducibility of the diode current and the microwave power is stable until 700 shots. No obvious damage or deterioration can be observed in the carbon fiber surface morphology after 700 shots. Moreover, the cathode performance has no observable deterioration after 700 shots. In conclusion, the maintain-free lifetime of the carbon fiber array cathode is more than 700 shots. In this way, this carbon fiber array cathode offers a potential replacement for the existing velvet cathode.

  13. A Study of Lane Differentiation Using An Array of Detectors.

    Energy Technology Data Exchange (ETDEWEB)

    McKigney E. A. (Edward A.); Gholkar, R. V. (Rohun V.); Vega, D. A. (Daniel A.)

    2004-01-01

    The authors discuss a method for locating a radioactive source in the context of determining which lane a source is in on a roadway. This method is appropriate for use over a large range of source velocities, and could provide an advance alarm prior to a vehicle passing a portal monitor. This is a novel method which uses data from the entire array simultaneously to locate the source, rather than relying on only one or two sensors. A description of the underlying method will be given, along with results from five and six detector arrays. The five detector array was used mainly for static tests. The six detector array was used for dynamic tests, including slow movement of a source in a vehicle.

  14. EMAT phased array: A feasibility study of surface crack detection.

    Science.gov (United States)

    Isla, J; Cegla, F

    2017-02-14

    Electromagnetic-acoustic transducers (EMATs) consist of a magnet and a coil. They are advantageous in some non-destructive evaluation (NDE) applications because no direct contact with the specimen is needed to send and receive ultrasonic waves. However, EMATs commonly require excitation peak powers greater than 1kW and therefore the driving electronics and the EMAT coils have to be bulky. This has hindered the development of EMAT phased arrays with characteristics similar to those of conventional piezoelectric phased arrays. Phased arrays are widely used in NDE because they offer superior defect characterization in comparison to single-element transducers. In this paper, we report a series of novel techniques and design elements that make it possible to construct an EMAT phased array that performs similarly to conventional piezoelectric arrays used in NDE. One of the key enabling features is the use of coded excitation to reduce the excitation peak power to less than 4.8W (24 Vpp and 200mA) so that racetrack coils with dimensions 3.2×18mm(2) can be employed. Moreover, these racetrack coils are laid out along their shortest dimension so that 1/3 of their area is overlapped. This helps to reduce the crosstalk between the coils, i.e., the array elements, to less than -15dB. We show that an 8-element EMAT phased array operating at a central frequency of 1MHz can be used to detect defects which have a width and a depth of 0.2 and 0.8mm respectively and are located on the surface opposite to the array.

  15. A Comparative Study of Inspection Techniques for Array Packages

    Science.gov (United States)

    Mohammed, Jelila; Green, Christopher

    2008-01-01

    This viewgraph presentation reviews the inspection techniques for Column Grid Array (CGA) packages. The CGA is a method of chip scale packaging using high temperature solder columns to attach part to board. It is becoming more popular over other techniques (i.e. quad flat pack (QFP) or ball grid array (BGA)). However there are environmental stresses and workmanship challenges that require good inspection techniques for these packages.

  16. Residential photovoltaic module and array requirement study. Low-Cost Solar Array Project engineering area. Final report appendices

    Energy Technology Data Exchange (ETDEWEB)

    1979-06-01

    This volume contains the appendices to a study to identify design requirements for photovoltaic modules and arrays used in residential applications. Appendices include: (1) codes, standards, and manuals of accepted practice-definition and importance; (2) regional code variations-impact; (3) model and city codes-review; (4) National Electric Code (NEC)-review; (5) types of standards-definition and importance; (6) federal standards-review; (7) standards review method; (8) manuals of accepted practice; (9) codes and referenced standards-summary; (10) public safety testing laboratories; (11) insurance review; (12) studies approach; (13) mounting configurations; (14) module/panel size and shape cost analysis; (15) grounding, wiring, terminal and voltage studies; (16) array installation cost summary; (17) photovoltaic shingle/module comparison; (18) retrofit application; (19) residential photovoltaic module performance criteria; (20) critique of JPL's solar cell module design and test specifications for residential applications; and (21) CSI format specification. (WHK)

  17. Sex-linked pheromone receptor genes of the European corn borer, Ostrinia nubilalis, are in tandem arrays.

    Directory of Open Access Journals (Sweden)

    Yuji Yasukochi

    Full Text Available BACKGROUND: Tuning of the olfactory system of male moths to conspecific female sex pheromones is crucial for correct species recognition; however, little is known about the genetic changes that drive speciation in this system. Moths of the genus Ostrinia are good models to elucidate this question, since significant differences in pheromone blends are observed within and among species. Odorant receptors (ORs play a critical role in recognition of female sex pheromones; eight types of OR genes expressed in male antennae were previously reported in Ostrinia moths. METHODOLOGY/PRINCIPAL FINDINGS: We screened an O. nubilalis bacterial artificial chromosome (BAC library by PCR, and constructed three contigs from isolated clones containing the reported OR genes. Fluorescence in situ hybridization (FISH analysis using these clones as probes demonstrated that the largest contig, which contained eight OR genes, was located on the Z chromosome; two others harboring two and one OR genes were found on two autosomes. Sequence determination of BAC clones revealed the Z-linked OR genes were closely related and tandemly arrayed; moreover, four of them shared 181-bp direct repeats spanning exon 7 and intron 7. CONCLUSIONS/SIGNIFICANCE: This is the first report of tandemly arrayed sex pheromone receptor genes in Lepidoptera. The localization of an OR gene cluster on the Z chromosome agrees with previous findings for a Z-linked locus responsible for O. nubilalis male behavioral response to sex pheromone. The 181-bp direct repeats might enhance gene duplications by unequal crossovers. An autosomal locus responsible for male response to sex pheromone in Heliothis virescens and H. subflexa was recently reported to contain at least four OR genes. Taken together, these findings support the hypothesis that generation of additional copies of OR genes can increase the potential for male moths to acquire altered specificity for pheromone components, and accordingly

  18. Ultrasound cylindrical phased array for transoesophageal thermal therapy: initial studies

    Energy Technology Data Exchange (ETDEWEB)

    Melodelima, David [INSERM, Unite 556, 151 Cours Albert Thomas, 69424 Lyon (France); Lafon, Cyril [INSERM, Unite 556, 151 Cours Albert Thomas, 69424 Lyon (France); Prat, Frederic [Centre Hospitalier Bicetre, 78 Avenue General Leclerc, 94275 Le Kremlin Bicetre (France); Birer, Alain [INSERM, Unite 556, 151 Cours Albert Thomas, 69424 Lyon (France); Cathignol, Dominique [INSERM, Unite 556, 151 Cours Albert Thomas, 69424 Lyon (France)

    2002-12-07

    This work was undertaken to investigate the feasibility of constructing a cylindrical phased array composed of 64 elements spread around the periphery (OD 10.6 mm) for transoesophageal ultrasound thermotherapy. The underlying operating principle of this applicator is to rotate a plane ultrasound beam electronically. For this purpose, eight adjacent transducers were successively excited with appropriate delay times so as to generate a plane wave. The exposure direction was changed by exciting a different set of eight elements. For these feasibility studies, we used a cylindrical prototype (OD 10.6 mm) composed of 16 elementary transducers distributed over a quarter of the cylinder, all operating at 4.55 MHz. The active part was mechanically reinforced by a rigid damper structure behind the transducers. It was shown that an ultrasound field similar to that emitted by a plane transducer could be generated. Ex vivo experiments on pig's liver demonstrated that the ultrasound beam could be accurately rotated to generate sector-based lesions to a suitable depth (up to 19 mm). Throughout these experiments, exposures lasting 20 s were delivered at an acoustic intensity of 17 W cm{sup -2}. By varying the power from exposure to exposure, the depth of the lesion at different angles could be controlled.

  19. Nanoparticle-lipid bilayer interactions studied with lipid bilayer arrays

    Science.gov (United States)

    Lu, Bin; Smith, Tyler; Schmidt, Jacob J.

    2015-04-01

    The widespread environmental presence and commercial use of nanoparticles have raised significant health concerns as a result of many in vitro and in vivo assays indicating toxicity of a wide range of nanoparticle species. Many of these assays have identified the ability of nanoparticles to damage cell membranes. These interactions can be studied in detail using artificial lipid bilayers, which can provide insight into the nature of the particle-membrane interaction through variation of membrane and solution properties not possible with cell-based assays. However, the scope of these studies can be limited because of the low throughput characteristic of lipid bilayer platforms. We have recently described an easy to use, parallel lipid bilayer platform which we have used to electrically investigate the activity of 60 nm diameter amine and carboxyl modified polystyrene nanoparticles (NH2-NP and COOH-NP) with over 1000 lipid bilayers while varying lipid composition, bilayer charge, ionic strength, pH, voltage, serum, particle concentration, and particle charge. Our results confirm recent studies finding activity of NH2-NP but not COOH-NP. Detailed analysis shows that NH2-NP formed pores 0.3-2.3 nm in radius, dependent on bilayer and solution composition. These interactions appear to be electrostatic, as they are regulated by NH2-NP surface charge, solution ionic strength, and bilayer charge. The ability to rapidly measure a large number of nanoparticle and membrane parameters indicates strong potential of this bilayer array platform for additional nanoparticle bilayer studies.The widespread environmental presence and commercial use of nanoparticles have raised significant health concerns as a result of many in vitro and in vivo assays indicating toxicity of a wide range of nanoparticle species. Many of these assays have identified the ability of nanoparticles to damage cell membranes. These interactions can be studied in detail using artificial lipid bilayers, which

  20. Excitation of ultrasonic Lamb waves using a phased array system with two array probes: phantom and in vitro bone studies.

    Science.gov (United States)

    Nguyen, Kim-Cuong T; Le, Lawrence H; Tran, Tho N H T; Sacchi, Mauricio D; Lou, Edmond H M

    2014-07-01

    Long bones are good waveguides to support the propagation of ultrasonic guided waves. The low-order guided waves have been consistently observed in quantitative ultrasound bone studies. Selective excitation of these low-order guided modes requires oblique incidence of the ultrasound beam using a transducer-wedge system. It is generally assumed that an angle of incidence, θi, generates a specific phase velocity of interest, co, via Snell's law, θi=sin(-1)(vw/co) where vw is the velocity of the coupling medium. In this study, we investigated the excitation of guided waves within a 6.3-mm thick brass plate and a 6.5-mm thick bovine bone plate using an ultrasound phased array system with two 0.75-mm-pitch array probes. Arranging five elements as a group, the first group of a 16-element probe was used as a transmitter and a 64-element probe was a receiver array. The beam was steered for six angles (0°, 20°, 30°, 40°, 50°, and 60°) with a 1.6-MHz source signal. An adjoint Radon transform algorithm mapped the time-offset matrix into the frequency-phase velocity dispersion panels. The imaged Lamb plate modes were identified by the theoretical dispersion curves. The results show that the 0° excitation generated many modes with no modal discrimination and the oblique beam excited a spectrum of phase velocities spread asymmetrically about co. The width of the excitation region decreased as the steering angle increased, rendering modal selectivity at large angles. The phenomena were well predicted by the excitation function of the source influence theory. The low-order modes were better imaged at steering angle ⩾30° for both plates. The study has also demonstrated the feasibility of using the two-probe phased array system for future in vivo study.

  1. Study on failure analysis of array chip components in IRFPA

    Science.gov (United States)

    Zhang, Xiaonan; He, Yingjie; Li, Jinping

    2016-10-01

    Infrared focal plane array detector has advantages of strong anti-interference ability and high sensitivity. Its size, weight and power dissipation has been noticeably decreased compared to the conventional infrared imaging system. With the development of the detector manufacture technology and the cost reduction, IRFPA detector has been widely used in the military and commercial fields. Due to the restricting of array chip manufacturing process and material defects, the fault phenomenon such as cracking, bad pixel and abnormal output was showed during the test, which restricts the performance of the infrared detector imaging system, and these effects are gradually intensified with the expanding of the focal plane array size and the shrinking of the pixel size. Based on the analysis of the test results for the infrared detector array chip components, the fault phenomenon was classified. The main cause of the chip component failure is chip cracking, bad pixel and abnormal output. The reason of the failure has been analyzed deeply. According to analyze the mechanism of the failure, a series of measures which contain filtrating materials and optimizing the manufacturing process of array chip components were used to improve the performance of the chip components and the test pass rate, which is used to meet the needs of the detector performance.

  2. Monte Carlo design studies for the Cherenkov Telescope Array

    CERN Document Server

    Bernlöhr, K; Becherini, Y; Bigas, O Blanch; Carmona, E; Colin, P; Decerprit, G; Di Pierro, F; Dubois, F; Farnier, C; Funk, S; Hermann, G; Hinton, J A; Humensky, T B; Khélifi, B; Kihm, T; Komin, N; Lenain, J -P; Maier, G; Mazin, D; Medina, M C; Moralejo, A; Nolan, S J; Ohm, S; Wilhelmi, E de Oña; Parsons, R D; Arribas, M Paz; Pedaletti, G; Pita, S; Prokoph, H; Rulten, C B; Schwanke, U; Shayduk, M; Stamatescu, V; Vallania, P; Vorobiov, S; Wischnewski, R; Yoshikoshi, T; Zech, A

    2012-01-01

    The Cherenkov Telescopes Array (CTA) is planned as the future instrument for very-high-energy (VHE) gamma-ray astronomy with a wide energy range of four orders of magnitude and an improvement in sensitivity compared to current instruments of about an order of magnitude. Monte Carlo simulations are a crucial tool in the design of CTA. The ultimate goal of these simulations is to find the most cost-effective solution for given physics goals and thus sensitivity goals or to find, for a given cost, the solution best suited for different types of targets with CTA. Apart from uncertain component cost estimates, the main problem in this procedure is the dependence on a huge number of configuration parameters, both in specifications of individual telescope types and in the array layout. This is addressed by simulation of a huge array intended as a superset of many different realistic array layouts, and also by simulation of array subsets for different telescope parameters. Different analysis methods -- in use with cu...

  3. Polycistronic transcription of fused cassettes and identification of translation initiation signals in an unusual gene cassette array from Pseudomonas aeruginosa [version 3; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Érica L. Fonseca

    2015-11-01

    Full Text Available The gene cassettes found in class 1 integrons are generally promoterless units composed by an open reading frame (ORF, a short 5’ untranslated region (UTR and a 3’ recombination site (attC. Fused gene cassettes are generated by partial or total loss of the attC from the first cassette in an array, creating, in some cases, a fusion with the ORF from the next cassette. These structures are rare and little is known about their mechanisms of mobilization and expression. The aim of this study was to evaluate the dynamic of mobilization and transcription of the gcu14-blaGES-1/aacA4 gene cassette array, which harbours a fused gene cassette represented by blaGES-1/aacA4. The cassette array was analyzed by Northern blot and real-time reverse transcription-polymerase chain reaction (RT-PCR in order to assess the transcription mechanism of blaGES-1/aacA4 fused cassette. Also, inverse polymerase chain reactions (PCR were performed to detect the free circular forms of gcu14, blaGES-1 and aacA4. The Northern blot and real time RT-PCR revealed a polycistronic transcription, in which the fused cassette blaGES-1/aacA4 is transcribed as a unique gene, while gcu14 (with a canonical attC recombination site has a monocistronic transcription. The gcu14 cassette, closer to the weak configuration of cassette promoter (PcW, had a higher transcription level than blaGES-1/aacA4, indicating that the cassette position affects the transcript amounts. The presence of ORF-11 at attI1, immediately preceding gcu14, and of a Shine-Dalgarno sequence upstream blaGES-1/aacA4 composes a scenario for the occurrence of array translation. Inverse PCR generated amplicons corresponding to gcu14, gcu14-aacA4 and gcu14-blaGES-1/aacA4 free circular forms, but not to blaGES-1 and aacA4 alone, indicating that the GES-1 truncated attC is not substrate of integrase activity and that these genes are mobilized together as a unique cassette. This study was original in showing the transcription

  4. The Comprehensive Study of Electrical Faults in PV Arrays

    Directory of Open Access Journals (Sweden)

    M. Sabbaghpur Arani

    2016-01-01

    Full Text Available The rapid growth of the solar industry over the past several years has expanded the significance of photovoltaic (PV systems. Fault analysis in solar photovoltaic (PV arrays is a fundamental task to increase reliability, efficiency, and safety in PV systems and, if not detected, may not only reduce power generation and accelerated system aging but also threaten the availability of the whole system. Due to the current-limiting nature and nonlinear output characteristics of PV arrays, faults in PV arrays may not be detected. In this paper, all possible faults that happen in the PV system have been classified and six common faults (shading condition, open-circuit fault, degradation fault, line-to-line fault, bypass diode fault, and bridging fault have been implemented in 7.5 KW PV farm. Based on the simulation results, both normal operational curves and fault curves have been compared.

  5. Study of ultrasonic phased array inspection imaging technology for NDT

    Institute of Scientific and Technical Information of China (English)

    Shan Baohua; Duan Zhongdong; Ou Jinping

    2006-01-01

    A research about the ultrasonic phased array imaging principle from A-scan signal to B-scan image for nondestructive testing (NDT) was conducted in this paper, the ultrasonic phased array inspection imaging system used in industrial field was developed and the experiment was performed on the steel testing block by the system with 64 elements, 5MHz phased array transducer.Experimental results show that the flaws could be accurately detected and the flaws size could be estimated from the B-scan images, and the B-scan images could clearly show the location of the flaws, but the quality of Bscan images needs to be enhanced by digital signal processing and controlling dynamic focusing for improving the image resolution.

  6. A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species.

    Science.gov (United States)

    Geraldes, A; Difazio, S P; Slavov, G T; Ranjan, P; Muchero, W; Hannemann, J; Gunter, L E; Wymore, A M; Grassa, C J; Farzaneh, N; Porth, I; McKown, A D; Skyba, O; Li, E; Fujita, M; Klápště, J; Martin, J; Schackwitz, W; Pennacchio, C; Rokhsar, D; Friedmann, M C; Wasteneys, G O; Guy, R D; El-Kassaby, Y A; Mansfield, S D; Cronk, Q C B; Ehlting, J; Douglas, C J; Tuskan, G A

    2013-03-01

    Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.

  7. Study of Far—Field Directivity Pattern for Linear Arrays

    Science.gov (United States)

    Ana-Maria, Chiselev; Luminita, Moraru; Laura, Onose

    2011-10-01

    A model to calculate directivity pattern in far field is developed in this paper. Based on this model, the three-dimensional beam pattern is introduced and analyzed in order to investigate geometric parameters of linear arrays and their influences on the directivity pattern. Simulations in azimuthal plane are made to highlight the influence of transducers parameters, including number of elements and inter-element spacing. It is true that these parameters are important factors that influence the directivity pattern and the appearance of side-lobes for linear arrays.

  8. Clinical array-based karyotyping of breast cancer with equivocal HER2 status resolves gene copy number and reveals chromosome 17 complexity

    Directory of Open Access Journals (Sweden)

    Zadeh Soheila

    2010-07-01

    Full Text Available Abstract Background HER2 gene copy status, and concomitant administration of trastuzumab (Herceptin, remains one of the best examples of targeted cancer therapy based on understanding the genomic etiology of disease. However, newly diagnosed breast cancer cases with equivocal HER2 results present a challenge for the oncologist who must make treatment decisions despite the patient's unresolved HER2 status. In some cases both immunohistochemistry (IHC and fluorescence in situ hybridization (FISH are reported as equivocal, whereas in other cases IHC results and FISH are discordant for positive versus negative results. The recent validation of array-based, molecular karyotyping for clinical oncology testing provides an alternative method for determination of HER2 gene copy number status in cases remaining unresolved by traditional methods. Methods In the current study, DNA extracted from 20 formalin fixed paraffin embedded (FFPE tissue samples from newly diagnosed cases of invasive ductal carcinoma referred to our laboratory with unresolved HER2 status, were analyzed using a clinically validated genomic array containing 127 probes covering the HER2 amplicon, the pericentromeric regions, and both chromosome 17 arms. Results Array-based comparative genomic hybridization (array CGH analysis of chromosome 17 resolved HER2 gene status in [20/20] (100% of cases and revealed additional chromosome 17 copy number changes in [18/20] (90% of cases. Array CGH analysis also revealed two false positives and one false negative by FISH due to "ratio skewing" caused by chromosomal gains and losses in the centromeric region. All cases with complex rearrangements of chromosome 17 showed genome-wide chromosomal instability. Conclusions These results illustrate the analytical power of array-based genomic analysis as a clinical laboratory technique for resolution of HER2 status in breast cancer cases with equivocal results. The frequency of complex chromosome 17

  9. Responses of murine and human macrophages to leptospiral infection: a study using comparative array analysis.

    Directory of Open Access Journals (Sweden)

    Feng Xue

    Full Text Available Leptospirosis is a re-emerging tropical infectious disease caused by pathogenic Leptospira spp. The different host innate immune responses are partially related to the different severities of leptospirosis. In this study, we employed transcriptomics and cytokine arrays to comparatively calculate the responses of murine peritoneal macrophages (MPMs and human peripheral blood monocytes (HBMs to leptospiral infection. We uncovered a series of different expression profiles of these two immune cells. The percentages of regulated genes in several biological processes of MPMs, such as antigen processing and presentation, membrane potential regulation, and the innate immune response, etc., were much greater than those of HBMs (>2-fold. In MPMs and HBMs, the caspase-8 and Fas-associated protein with death domain (FADD-like apoptosis regulator genes were significantly up-regulated, which supported previous results that the caspase-8 and caspase-3 pathways play an important role in macrophage apoptosis during leptospiral infection. In addition, the key component of the complement pathway, C3, was only up-regulated in MPMs. Furthermore, several cytokines, e.g. interleukin 10 (IL-10 and tumor necrosis factor alpha (TNF-alpha, were differentially expressed at both mRNA and protein levels in MPMs and HBMs. Some of the differential expressions were proved to be pathogenic Leptospira-specific regulations at mRNA level or protein level. Though it is still unclear why some animals are resistant and others are susceptible to leptospiral infection, this comparative study based on transcriptomics and cytokine arrays partially uncovered the differences of murine resistance and human susceptibility to leptospirosis. Taken together, these findings will facilitate further molecular studies on the innate immune response to leptospiral infection.

  10. Identification of salt-stress responsive genes in rice (Oryza sativa L.) by cDNA array

    Institute of Scientific and Technical Information of China (English)

    何新建; 陈建权; 张志刚; 张劲松; 陈受宜

    2002-01-01

    To identify salt stress-responsive genes, we constructed a cDNA library with the salt-tolerant rice cultivar, Lansheng. About 15000 plasmids were extracted and dotted on filters with Biomeck 2000 HDRT system or by hand. Thirty genes were identified to display altered expression levels responding to 150 mmol/L NaCl. Among them eighteen genes were up-regulated and the remainders down-regulated. Twenty-seven genes have their homologous genes in GenBank Databases. The expression of twelve genes was studied by Northern analysis. Based on the functions, these genes can be classified into five categories, including photosynthesis-related gene, transport-related gene, metabolism-related gene, stress- or resistance-related gene and the others with various functions. The results showed that salt stress influenced many aspects of rice growth. Some of these genes may play important roles in plant salt tolerance.

  11. Proof of principle study of ultrasonic particle manipulation by a circular array device

    Science.gov (United States)

    Grinenko, Alon; Wilcox, Paul D.; Courtney, Charles R. P.; Drinkwater, Bruce W.

    2012-01-01

    A feasibility study of a circular ultrasonic array device for acoustic particle manipulation is presented. A general approach based on Green's function is developed to analyse the underlying properties of a circular acoustic array. It allows the size of a controllable device area as a function of the number of array elements to be established and the array excitation required to produce a desired field distribution to be determined. A set of quantitative parameters characterizing the complexity of the pressure landscape is suggested, and relation to the number of array elements is found. Next, a finite-element model of a physically realizable circular piezo-acoustic array device is employed to demonstrate that the trapping capability can be achieved in practice. PMID:23197936

  12. Effect of Selenium-Enriched Agaricus bisporus (Higher Basidiomycetes) Extracts, Obtained by Pressurized Water Extraction, on the Expression of Cholesterol Homeostasis Related Genes by Low-Density Array.

    Science.gov (United States)

    Gil-Ramírez, Alicia; Soler-Rivas, Cristina; Rodriguez-Casado, Arantxa; Ruiz-Rodríguez, Alejandro; Reglero, Guillermo; Marín, Francisco Ramón

    2015-01-01

    Culinary-medicinal mushrooms are able to lower blood cholesterol levels in animal models by different mechanisms. They might impair the endogenous cholesterol synthesis and exogenous cholesterol absorption during digestion. Mushroom extracts, obtained using pressurized water extractions (PWE) from Agaricus bisporus basidiomes, supplemented or not supplemented with selenium, were applied to HepG2 cell cultures to study the expression of 19 genes related to cholesterol homeostasis by low-density arrays (LDA). Only the PWE fractions obtained at 25°C showed 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) inhibitory activity. Besides the enzymatic inhibition, PWE extracts may downregulate some of the key genes involved in the cholesterol homeostasis, such as the squalene synthase gene (FDFT1), since its mRNA expression falls by one third of its initial value. In summary, A. bisporus extracts may also modulate biological cholesterol levels by molecular mechanisms further than the enzymatic way previously reported.

  13. Gene array and real time PCR analysis of the adrenal sensitivity to adrenocorticotropic hormone in pig

    Directory of Open Access Journals (Sweden)

    SanCristobal Magali

    2008-02-01

    Full Text Available Abstract Background Variability in hypothalamic-pituitary-adrenal (HPA axis activity has been shown to be influenced by genetic factors and related to great metabolic differences such as obesity. The aim of this study was to investigate molecular bases of genetic variability of the adrenal sensitivity to ACTH, a major source of variability, in Meishan (MS and Large White (LW pigs, MS being reported to exhibit higher basal cortisol levels, response to ACTH and fatness than LW. A pig cDNA microarray was used to identify changes in gene expression in basal conditions and in response to ACTH stimulation. Results Genotype and/or ACTH affected the expression of 211 genes related to transcription, cell growth/maintenance, signal transduction, cell structure/adhesion/extra cellular matrix and protein kinase/phosphatase activity. No change in the expression of known key regulator proteins of the ACTH signaling pathway or of steroidogenic enzymes was found. However, Mdh2, Sdha, Suclg2, genes involved in the tricarboxylic acid (TCA pathway, were over-expressed in MS pigs. Higher TCA cycle activity in MS than in LW may thus result in higher steroidogenic activity and thus explain the typically higher cortisol levels in MS compared to LW. Moreover, up-regulation of Star and Ldlr genes in MS and/or in response to ACTH suggest that differences in the adrenal function between MS and LW may also involve mechanisms requisite for cholesterol supply to steroidogenesis. Conclusion The present study provides new potential candidate genes to explain genetic variations in the adrenal sensitivity to ACTH and better understand relationship between HPA axis activity and obesity.

  14. Study of the characteristics of reconfigurable plasma antenna array

    Energy Technology Data Exchange (ETDEWEB)

    Alias, Nur Salihah; Dagang, Ahmad Nazri [School of Ocean Engineering, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu (Malaysia); Ali, Mohd Tarmizi [Microwave Technology Centre, Faculty of Electrical Engineering, Universiti Teknologi Mara Shah Alam 40450 Shah Alam, Selangor (Malaysia)

    2015-04-24

    This paper presents a design and simulation of a reconfigurable array of plasma antenna. The plasma column is used as radiating elements instead of metal to create an antenna. The advantages of the plasma antenna over the conventional antenna are its possible to change the operating parameters, such as the working pressure, input power, radius of the discharge tube, resonant frequency, and length of the plasma column. In addition, plasma antenna can be reconfigurable with respect to shape, frequency and radiation parameters in a very short time. The plasma discharge tube was designed with a length of 200 mm, the radius of the plasma column was 2.5 mm and the coupling sleeve was connected to the SMA as the ground. This simulation was performed by using the simulation software Computer Simulation Technology (CST). The frequency is set in the range of 1 GHz to 10 GHz. The performance of the designed antenna was analyzed in term of return loss, gain and radiation pattern. For reconfigurable plasma antenna array, it shows that the gain is increase when the number of antenna element is increase. The combination of the discharge tube and metal rod as an antenna array has been done, and the result shows that an array with the plasma element can achieve higher gain.

  15. High-Throughput DNA Array for SNP Detection of KRAS Gene Using a Centrifugal Microfluidic Device.

    Science.gov (United States)

    Sedighi, Abootaleb; Li, Paul C H

    2016-01-01

    Here, we describe detection of single nucleotide polymorphism (SNP) in genomic DNA samples using a NanoBioArray (NBA) chip. Fast DNA hybridization is achieved in the chip when target DNAs are introduced to the surface-arrayed probes using centrifugal force. Gold nanoparticles (AuNPs) are used to assist SNP detection at room temperature. The parallel setting of sample introduction in the spiral channels of the NBA chip enables multiple analyses on many samples, resulting in a technique appropriate for high-throughput SNP detection. The experimental procedure, including chip fabrication, probe array printing, DNA amplification, hybridization, signal detection, and data analysis, is described in detail.

  16. An experimental burn wound-healing study of non-thermal atmospheric pressure microplasma jet arrays.

    Science.gov (United States)

    Lee, Ok Joo; Ju, Hyung Woo; Khang, Gilson; Sun, Peter P; Rivera, Jose; Cho, Jin Hoon; Park, Sung-Jin; Eden, J Gary; Park, Chan Hum

    2016-04-01

    In contrast with a thermal plasma surgical instrument based on coagulative and ablative properties, low-temperature (non-thermal) non-equilibrium plasmas are known for novel medicinal effects on exposed tissue while minimizing undesirable tissue damage. In this study we demonstrated that arrays of non-thermal microplasma jet devices fabricated from a transparent polymer can efficiently inactivate fungi (Candida albicans) as well as bacteria (Escherichia coli), both in vitro and in vivo, and that this leads to a significant wound-healing effect. Microplasma jet arrays offer several advantages over conventional single-jet devices, including superior packing density, inherent scalability for larger treatment areas, unprecedented material flexibility in a plasma jet device, and the selective generation of medically relevant reactive species at higher plasma densities. The therapeutic effects of our multi-jet device were verified on second-degree burns in animal rat models. Reduction of the wound area and the histology of the wound after treatment have been investigated, and expression of interleukin (IL)-1α, -6 and -10 was verified to evaluate the healing effects. The consistent effectiveness of non-thermal plasma treatment has been observed especially in decreasing wound size and promoting re-epithelialization through collagen arrangement and the regulation of expression of inflammatory genes.

  17. Identification of brassinosteroid responsive genes in Arabidopsis by cDNA array

    Institute of Scientific and Technical Information of China (English)

    HU; Yuxin; (

    2001-01-01

    [1]Grove, M. D., Spencer, G. F., Rohwedder, W. K. et al., Brassinolide, a plant growth-promoting steroid isolated from Brassica napus pollen, Nature, 1979, 281: 216-217.[2]Mandava, N. B., Plant growth-promoting brassinosteroids, Annu. Rev. Plant Physiol. Plant Mol. Biol., 1988, 39: 23-52.[3]Clouse, S. D., Sasse, J. M., Brassinosteroids: essential regulators of plant growth and development, Annu. Rev. Plant Physiol. Plant Mol. Biol., 1998, 49: 427-451.[4]Altmann, T., Recent advances in brassinosteroid molecular genetics, Curr. Opin. Plant Biol., 1998, 1: 378-383.[5]Aharoni, A., Keizer, L. C. P., Bouwmeester, H. J. et al., Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarray, Plant Cell, 2000, 12: 647-661.[6]Reymond, P., Weber, H., Damond, M. et al., Differential gene expression in response to mechanical wounding and insect feeding in Arabidopsis, Plant Cell, 2000, 12: 707-719.[7]Hu, Y., Han, C., Mou, Z. et al., Monitoring gene expression by cDNA array, Chin. Sci. Bull., 1999, 44: 441-444.[8]Fujioka, S., Li, J., Choi, Y. H. et al., The Arabidopsis deetiolated2 mutant is blocked early in brassinosteroid biosynthesis, Plant Cell, 1997, 9: 1951-1962.[9]Wadsworth, G. J., Redinbaugh, M. G., Scandalios, J. G., A procedure for small-scale isolation of plant RNA suitable for RNA blot analysis, Anal. Biochem., 1988, 172: 279-283.[10]Church, G. M., Gilbert, W., Genomic sequencing, Proc. Natl. Acad. Sci. USA, 1984, 81: 1991-1995.[11]Huntley, R. P., Murray, J. A. H., The plant cell cycle, Curr. Opin. Plant Biol., 1999, 2: 440-446.[12]Riou-Khamlichi, C., Huntley, R., Jacqmard, A. et al., Cytokinin activation of Arabidopsis cell division through a D-type cyclin, Science, 1999, 283: 1541-1544.[13]Hu, Y., Bao, F., Li, J., Promotive effect of brassinosteroids on cell division involves a distinct CycD3-induction pathway, Plant J., 2000, 24: 693-701.[14]Hirayama, T., Shinozaki, K., A

  18. High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array.

    Directory of Open Access Journals (Sweden)

    Guy C J Abell

    Full Text Available Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively, combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.

  19. Novel Genomic Aberrations in Testicular Germ Cell Tumors by Array-CGH, and Associated Gene Expression Changes

    Directory of Open Access Journals (Sweden)

    Rolf I. Skotheim

    2006-01-01

    Full Text Available Introduction: Testicular germ cell tumors of adolescent and young adult men (TGCTs generally have near triploid and complex karyotypes. The actual genes driving the tumorigenesis remain essentially to be identified. Materials and Methods: To determine the detailed DNA copy number changes, and investigate their impact on gene expression levels, we performed an integrated microarray profiling of TGCT genomes and transcriptomes. We analyzed 17 TGCTs, three precursor lesions, and the embryonal carcinoma cell lines, NTERA2 and 2102Ep, by comparative genomic hybridization microarrays (array-CGH, and integrated the data with transcriptome profiles of the same samples. Results: The gain of chromosome arm 12p was, as expected, the most common aberration, and we found CCND2, CD9, GAPD, GDF3, NANOG, and TEAD4 to be the therein most highly over-expressed genes. Additional frequent genomic aberrations revealed some shorter chromosomal segments, which are novel to TGCT, as well as known aberrations for which we here refined boundaries. These include gains from 7p15.2 and 21q22.2, and losses of 4p16.3 and 22q13.3. Integration of DNA copy number information to gene expression profiles identified that BRCC3, FOS, MLLT11, NES, and RAC1 may act as novel oncogenes in TGCT. Similarly, DDX26, ERCC5, FZD4, NME4, OPTN, and RB1 were both lost and under-expressed genes, and are thus putative TGCT suppressor genes. Conclusion: This first genome-wide integrated array-CGH and gene expression profiling of TGCT provides novel insights into the genome biology underlying testicular tumorigenesis.

  20. Study of the Gene Expression Profile of Human Ovarian Carcinoma by a Gene Chip

    Institute of Scientific and Technical Information of China (English)

    Shenhua Xu; Hanzhou Mou; Chihong Zhu; Lijuan Qian; Zhengyan Yang; Ye Ying; Xianglin Liu

    2005-01-01

    OBJECTIVE To study the difference in gene expression between human ovarian carcinoma and normal ovarian tissues, and screen the novel associated genes by cDNA microarrays.METHODS Total RNA from 10 cases of ovarian cancer and from normal ovarian tissues were extracted by a single step method. The cDNA was retro-transcribed from an equal quantity of mRNA derived from the 10 cases of ovarian carcinoma and normal ovarian tissues, followed by labeling the cDNA strands with Cy5 and Cy3 fluorescence as probes. The mixed probes were hybridized with BiostarH 8464 dot human somatic cell genes.Fluorescence signals were assessed by a ScanArray 4000 laser scanner and the images analyzed by Gene Pix Pro 3.0 software with a digital computer.RESULTS By applying the cDNA microarray we found a total of 185 genes for which expression levels differed more than 5 times comparing human ovarian carcinoma with normal ovarian epithelium. Among these genes 86 were up-regulated >5 times and 99 were down regulated <0.2.CONCLUSION The cDNA microarray technique is effective in screening the differential gene expression between human ovarian cancers and normal ovarian epithelium. It is suggested that these genes identified are related to the genesis and development of ovarian carcinoma.

  1. Large-Scale Gene-Centric Meta-Analysis across 39 Studies Identifies Type 2 Diabetes Loci

    NARCIS (Netherlands)

    Saxena, Richa; Elbers, Clara C.; Guo, Yiran; Peter, Inga; Gaunt, Tom R.; Mega, Jessica L.; Lanktree, Matthew B.; Tare, Archana; Almoguera Castillo, Berta; Li, Yun R.; Johnson, Toby; Bruinenberg, Marcel; Gilbert-Diamond, Diane; Rajagopalan, Ramakrishnan; Voight, Benjamin F.; Balasubramanyam, Ashok; Barnard, John; Bauer, Florianne; Baumert, Jens; Bhangale, Tushar; Boehm, Bernhard O.; Braund, Peter S.; Burton, Paul R.; Chandrupatla, Hareesh R.; Clarke, Robert; Cooper-DeHoff, Rhonda M.; Crook, Errol D.; Davey-Smith, George; Day, Ian N.; de Boer, Anthonius; de Groot, Mark C. H.; Drenos, Fotios; Ferguson, Jane; Fox, Caroline S.; Furlong, Clement E.; Gibson, Quince; Gieger, Christian; Gilhuijs-Pederson, Lisa A.; Glessner, Joseph T.; Goel, Anuj; Gong, Yan; Grant, Struan F. A.; Grobbee, Diederick E.; Hastie, Claire; Humphries, Steve E.; Kim, Cecilia E.; Kivimaki, Mika; Kleber, Marcus; Meisinger, Christa; Kumari, Meena; Langaee, Taimour Y.; Lawlor, Debbie A.; Li, Mingyao; Lobmeyer, Maximilian T.; Maitland-van der Zee, Anke-Hilse; Meijs, Matthijs F. L.; Molony, Cliona M.; Morrow, David A.; Murugesan, Gurunathan; Musani, Solomon K.; Nelson, Christopher P.; Newhouse, Stephen J.; O'Connell, Jeffery R.; Padmanabhan, Sandosh; Palmen, Jutta; Patel, Sanjey R.; Pepine, Carl J.; Pettinger, Mary; Price, Thomas S.; Rafelt, Suzanne; Ranchalis, Jane; Rasheed, Asif; Rosenthal, Elisabeth; Ruczinski, Ingo; Shah, Sonia; Shen, Haiqing; Silbernagel, Guenther; Smith, Erin N.; Spijkerman, Annemieke W. M.; Stanton, Alice; Steffes, Michael W.; Thorand, Barbara; Trip, Mieke; van der Harst, Pim; van der A, Daphne L.; van Iperen, Erik P. A.; van Setten, Jessica; van Vliet-Ostaptchouk, Jana V.; Verweij, Niek; Wolffenbuttel, Bruce H. R.; Young, Taylor; Zafarmand, M. Hadi; Zmuda, Joseph M.; Boehnke, Michael; Altshuler, David; McCarthy, Mark; Kao, W. H. Linda; Pankow, James S.; Cappola, Thomas P.; Sever, Peter; Poulter, Neil; Caulfield, Mark; Dominiczak, Anna; Shields, Denis C.; Bhatt, Deepak L.; Zhang, Li; Curtis, Sean P.; Danesh, John; Casas, Juan P.; van der Schouw, Yvonne T.; Onland-Moret, N. Charlotte; Doevendans, Pieter A.; Dorn, Gerald W.; Farrall, Martin; FitzGerald, Garret A.; Hamsten, Anders; Hegele, Robert; Hingorani, Aroon D.; Hofker, Marten H.; Huggins, Gordon S.; Illig, Thomas; Jarvik, Gail P.; Johnson, Julie A.; Klungel, Olaf H.; Knowler, William C.; Koenig, Wolfgang; Maerz, Winfried; Meigs, James B.; Melander, Olle; Munroe, Patricia B.; Mitchell, Braxton D.; Bielinski, Susan J.; Rader, Daniel J.; Reilly, Muredach P.; Rich, Stephen S.; Rotter, Jerome I.; Saleheen, Danish; Samani, Nilesh J.; Schadt, Eric E.; Shuldiner, Alan R.; Silverstein, Roy; Kottke-Marchant, Kandice; Talmud, Philippa J.; Watkins, Hugh; Asselbergs, Folkert W.; de Bakker, Paul I. W.; McCaffery, Jeanne; Wijmenga, Cisca; Sabatine, Marc S.; Wilson, James G.; Reiner, Alex; Bowden, Donald W.; Hakonarson, Hakon; Siscovick, David S.; Keating, Brendan J.

    2012-01-01

    To identify genetic factors contributing to type 2 diabetes (T2D), we performed large-scale meta-analyses by using a custom similar to 50,000 SNP genotyping array (the ITMAT-Broad-CARe array) with similar to 2000 candidate genes in 39 multiethnic population-based studies, case-control studies, and c

  2. Numerical study of the properties of optical vortex array laser tweezers.

    Science.gov (United States)

    Kuo, Chun-Fu; Chu, Shu-Chun

    2013-11-01

    Chu et al. constructed a kind of Ince-Gaussian modes (IGM)-based vortex array laser beams consisting of p x p embedded optical vortexes from Ince-Gaussian modes, IG(e)(p,p) modes [Opt. Express 16, 19934 (2008)]. Such an IGM-based vortex array laser beams maintains its vortex array profile during both propagation and focusing, and is applicable to optical tweezers. This study uses the discrete dipole approximation (DDA) method to study the properties of the IGM-based vortex array laser tweezers while it traps dielectric particles. This study calculates the resultant force exerted on the spherical dielectric particles of different sizes situated at the IGM-based vortex array laser beam waist. Numerical results show that the number of trapping spots of a structure light (i.e. IGM-based vortex laser beam), is depended on the relation between the trapped particle size and the structure light beam size. While the trapped particle is small comparing to the beam size of the IGM-based vortex array laser beams, the IGM-based vortex array laser beams tweezers are suitable for multiple traps. Conversely, the tweezers is suitable for single traps. The results of this study is useful to the future development of the vortex array laser tweezers applications.

  3. Microcavity arrays for X-ray diffraction studies of ordering phenomena in confined colloid solutions

    NARCIS (Netherlands)

    Diaz, A.; David, C.; Guo, H.; Keymeulen, H.; Pfeiffer, F.; Wegdam, G.; Weitkamp, T.; van der Veen, J.F.

    2005-01-01

    We present a way to fabricate high-aspect-ratio silicon microcavity arrays which can be used for the investigation of confinement-induced ordering phenomena within colloid solutions. In these studies, the microcavity arrays serve as containers for confinement of the colloid. X-ray diffraction measur

  4. An exome array study of the plasma metabolome

    Science.gov (United States)

    Rhee, Eugene P.; Yang, Qiong; Yu, Bing; Liu, Xuan; Cheng, Susan; Deik, Amy; Pierce, Kerry A.; Bullock, Kevin; Ho, Jennifer E.; Levy, Daniel; Florez, Jose C.; Kathiresan, Sek; Larson, Martin G.; Vasan, Ramachandran S.; Clish, Clary B.; Wang, Thomas J.; Boerwinkle, Eric; O'Donnell, Christopher J.; Gerszten, Robert E.

    2016-01-01

    The study of rare variants may enhance our understanding of the genetic determinants of the metabolome. Here, we analyze the association between 217 plasma metabolites and exome variants on the Illumina HumanExome Beadchip in 2,076 participants in the Framingham Heart Study, with replication in 1,528 participants of the Atherosclerosis Risk in Communities Study. We identify an association between GMPS and xanthosine using single variant analysis and associations between HAL and histidine, PAH and phenylalanine, and UPB1 and ureidopropionate using gene-based tests (P<5 × 10−8 in meta-analysis), highlighting novel coding variants that may underlie inborn errors of metabolism. Further, we show how an examination of variants across the spectrum of allele frequency highlights independent association signals at select loci and generates a more integrated view of metabolite heritability. These studies build on prior metabolomics genome wide association studies to provide a more complete picture of the genetic architecture of the plasma metabolome. PMID:27453504

  5. Meta-GWAS and Meta-Analysis of Exome Array Studies Do Not Reveal Genetic Determinants of Serum Hepcidin

    Science.gov (United States)

    Galesloot, Tessel E.; van Dijk, Freerk; Geurts-Moespot, Anneke J.; Girelli, Domenico; Kiemeney, Lambertus A. L. M.; Sweep, Fred C. G. J.; Swertz, Morris A.; van der Meer, Peter; Camaschella, Clara; Toniolo, Daniela; Vermeulen, Sita H.; van der Harst, Pim; Swinkels, Dorine W.

    2016-01-01

    Serum hepcidin concentration is regulated by iron status, inflammation, erythropoiesis and numerous other factors, but underlying processes are incompletely understood. We studied the association of common and rare single nucleotide variants (SNVs) with serum hepcidin in one Italian study and two large Dutch population-based studies. We genotyped common SNVs with genome-wide association study (GWAS) arrays and subsequently performed imputation using the 1000 Genomes reference panel. Cohort-specific GWAS were performed for log-transformed serum hepcidin, adjusted for age and gender, and results were combined in a fixed-effects meta-analysis (total N 6,096). Six top SNVs (p<5x10-6) were genotyped in 3,821 additional samples, but associations were not replicated. Furthermore, we meta-analyzed cohort-specific exome array association results of rare SNVs with serum hepcidin that were available for two of the three cohorts (total N 3,226), but no exome-wide significant signal (p<1.4x10-6) was identified. Gene-based meta-analyses revealed 19 genes that showed significant association with hepcidin. Our results suggest the absence of common SNVs and rare exonic SNVs explaining a large proportion of phenotypic variation in serum hepcidin. We recommend extension of our study once additional substantial cohorts with hepcidin measurements, GWAS and/or exome array data become available in order to increase power to identify variants that explain a smaller proportion of hepcidin variation. In addition, we encourage follow-up of the potentially interesting genes that resulted from the gene-based analysis of low-frequency and rare variants. PMID:27846281

  6. Study on electrothermally actuated cantilever array for nanolithography

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Nanolithography is a patterning technique for the fabrication of nano-scale structures.A promising method of nanolithography known as scanning probe lithography has particularly extensive applications for its high resolution,high reliability,and simple operation.In this paper,a novel electrothermally actuated cantilever with integrated heater,thermal conductor and actuator for scanning probe lithography is proposed.Cantilevers are designed in an 8×4 array.Analytical models are presented to simulate the temperature distribution,deflection and thermal crosstalk of the cantilever array.This structure is successfully fabricated.It is demonstrated that this structure can produce a tip deflection of 16.9 μm at an actuation current of 5.5 mA and the thermal crosstalk between the cantilevers is neglected.

  7. A full optically operated magnetometer array: an experimental study.

    Science.gov (United States)

    Ijsselsteijn, R; Kielpinski, M; Woetzel, S; Scholtes, T; Kessler, E; Stolz, R; Schultze, V; Meyer, H-G

    2012-11-01

    We show the operation of an optically pumped magnetometer array in a 50 μT magnetic field. The various components for a fully optical and non-magnetic detector unit were constructed and evaluated, from which a prototype unit was assembled with fiber coupled electronics. In this unit the magnetometers were operated using the intensity modulated method and heated with an off-resonant laser. Calculations on the temperature distribution were used to design the magnetometer array. Different magnetometers in such a detector unit were characterized and showed identical performance. Without applying noise reduction schemes, the obtained magnetic field resolution is a factor 2.5 above the shot noise level down to frequencies of about 7 Hz.

  8. A study into the design of steerable microphone arrays

    CERN Document Server

    Lai, Chiong Ching; Leung, Yee Hong

    2017-01-01

    The book covers the design formulations for broadband beamformer targeting nearfield and farfield sources. The book content includes background information on the acoustic environment, including propagation medium, the array geometries, signal models and basic beamformer designs. Subsequently it introduces design formulation for nearfield, farfield and mixed nearfield-farfield beamformers and extends the design formulation into electronically steerable beamformers. In addition, a robust formulation is introduced for all the designs mentioned.

  9. Comparative study by simulation of photovoltaic pumping systems with stationary and polar tracking arrays

    Energy Technology Data Exchange (ETDEWEB)

    Illanes, R.; De Francisco, A. [Universidad Politecnica de Madrid, E.T.S.I. de Montes, Madrid (Spain); Torres, J.L.; De Blas, M. [Universidad Publica de Navarra, Dept. Proyectos e Ingenieria Rural, Navarra (Spain); Appelbaum, J. [Tel Aviv Univ., Faculty of Engineering, Tel Aviv (Israel)

    2003-07-01

    Using mathematical models for the different components of the photovoltaic pumping system: generator, inverter (if applicable), motors, pumps and piping, we have developed a computer program that, for given irradiance and temperature data, calculates the flow of water pumped at any given time. The program has been applied to study the hourly and yearly water flow pumped by a photovoltaic pumping system located in Madrid, employing centrifugal pumps powered by AC motors. The photovoltaic generator consists of, in one case, a stationary array and in the second case a polar tracking array. The hourly radiation data were estimated from the distribution of the atmospheric clearness coefficients and the monthly average daily radiation on a horizontal surface. The results of this study show that the use of a polar tracking array increases the average yearly water flow compared with the stationary array more than the corresponding increase of the incident radiation on the arrays. (Author)

  10. Study on Clutter Model and Characteristics of Airborne Radar with Parabolic Conformal Phased Array

    Institute of Scientific and Technical Information of China (English)

    Hao Jiang; Nini Rao; Xingbo Chen; Jiabin Zhou; Chaoyang Qiu; Wen Zhai; Zhimei Hao

    2016-01-01

    The studies on clutter modeling and suppression of airborne radar with a parabolic conformal array are uncommon due to the complexity of this type of antenna array configuration. The correct understanding of clutter characteristics for airborne radar with a parabolic conformal antenna array is the prerequisite and foundation of optimal suppression of this type of clutter. This paper establishes the model of clutter echo of airborne parabolic conformal phased array radar and analyzes the structure characteristics and the distribution features of this type of clutter. The simulation results show that this type of clutter has the following characteristics: 1) The main lobe on the azimuth is seriously broadened, 2) the power spectrum presents strong heterogeneity, and 3) the freedom degrees are high. Based on the existing related clutter suppression methods, we verified the correctness of the constructed clutter model. This work has an important guidance to further study on clutter suppression methods in airborne parabolic conformal array radar.

  11. Tissue array for Tp53, C-myc, CCND1 gene over-expression in different tumors

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    AIM: To rapidly detect molecular alterations in different malignancies and investigate the possible role of Tp53, C-myc, and CCND1 genes in development of tumors in human organs and their adjacent normal tissues, as well as the possible relation between well- and poorly-differentiated tumors. METHODS: A tissue array consisting of seven different tumors was generated. The tissue array included 120 points of esophagus, 120 points of stomach, 80 points of rectum, 60 points of thyroid gland, 100 points of mammary gland, 80 points ofliver, and 80 points of colon. Expressions of Tp53, C-myc, and CCND1 were determined by RNA in situ hybridization. 3' terminal digoxin-labeled anti-sense single stranded oligonucleotide and locked nucleic acid modifying probe were used.RESULTS: The expression level of Tp53 gene was higher in six different carcinoma tissue samples than in paracancerous tissue samples with the exception in colon carcinoma tissue samples (P < 0.05). The expression level of CCND1 gene was significantly different in different carcinoma tissue samples with the exception in esophagus and colon carcinoma tissue samples. The expression level of C-myc gene was different in esophagus carcinoma tissue samples (x2 = 18.495, P = 0.000), stomach carcinoma tissue samples (x2 = 23.750, P = 0.000), and thyroid gland tissue samples (x2 = 10.999, P = 0.004). The intensity of signals was also different in different carcinoma tissue samples and paracancerous tissue samples.CONCLUSION: Over-expression of the Tp53, CCND1, and C-myc genes appears to play a role in development of human cancer by regulating the expression of mRNA. Tp53, CCND1 and C-myc genes are significantly correlated with the development of different carcinomas.

  12. ExonMiner: Web service for analysis of GeneChip Exon array data

    Directory of Open Access Journals (Sweden)

    Imoto Seiya

    2008-11-01

    Full Text Available Abstract Background Some splicing isoform-specific transcriptional regulations are related to disease. Therefore, detection of disease specific splice variations is the first step for finding disease specific transcriptional regulations. Affymetrix Human Exon 1.0 ST Array can measure exon-level expression profiles that are suitable to find differentially expressed exons in genome-wide scale. However, exon array produces massive datasets that are more than we can handle and analyze on personal computer. Results We have developed ExonMiner that is the first all-in-one web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells. ExonMiner can perform the following analyses: (1 data normalization, (2 statistical analysis based on two-way ANOVA, (3 finding transcripts with significantly different splice patterns, (4 efficient visualization based on heatmaps and barplots, and (5 meta-analysis to detect exon level biomarkers. We implemented ExonMiner on a supercomputer system in order to perform genome-wide analysis for more than 300,000 transcripts in exon array data, which has the potential to reveal the aberrant splice variations in cancer cells as exon level biomarkers. Conclusion ExonMiner is well suited for analysis of exon array data and does not require any installation of software except for internet browsers. What all users need to do is to access the ExonMiner URL http://ae.hgc.jp/exonminer. Users can analyze full dataset of exon array data within hours by high-level statistical analysis with sound theoretical basis that finds aberrant splice variants as biomarkers.

  13. ExonMiner: Web service for analysis of GeneChip Exon array data

    Science.gov (United States)

    Numata, Kazuyuki; Yoshida, Ryo; Nagasaki, Masao; Saito, Ayumu; Imoto, Seiya; Miyano, Satoru

    2008-01-01

    Background Some splicing isoform-specific transcriptional regulations are related to disease. Therefore, detection of disease specific splice variations is the first step for finding disease specific transcriptional regulations. Affymetrix Human Exon 1.0 ST Array can measure exon-level expression profiles that are suitable to find differentially expressed exons in genome-wide scale. However, exon array produces massive datasets that are more than we can handle and analyze on personal computer. Results We have developed ExonMiner that is the first all-in-one web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells. ExonMiner can perform the following analyses: (1) data normalization, (2) statistical analysis based on two-way ANOVA, (3) finding transcripts with significantly different splice patterns, (4) efficient visualization based on heatmaps and barplots, and (5) meta-analysis to detect exon level biomarkers. We implemented ExonMiner on a supercomputer system in order to perform genome-wide analysis for more than 300,000 transcripts in exon array data, which has the potential to reveal the aberrant splice variations in cancer cells as exon level biomarkers. Conclusion ExonMiner is well suited for analysis of exon array data and does not require any installation of software except for internet browsers. What all users need to do is to access the ExonMiner URL . Users can analyze full dataset of exon array data within hours by high-level statistical analysis with sound theoretical basis that finds aberrant splice variants as biomarkers. PMID:19036125

  14. Study of acoustic signal in the process of resistance spot welding based on array sensor system

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    This investigation was performed to study acoustic field signal in order to improve RSW quality. Researchers firstly built an acoustic array sensor system, which included 8 MPA-416 acoustic sensors, data acquisition card and LabVIEW. The system obtained the acoustic field information in the process of nugget growing. Due to the nonlinearity field signal, array sensor algorithm was utilized to quantitatively analyze the characteristics of acoustic field and reduced noise. The experiment and calculation results show that array sensor system can acquire acoustic field signal of nugget growing in the RSW process and array processing algorithm based on acoustic field can extract characteristic parameters to evaluate RSW quality. It was concluded that the acoustic array sensor system offers a new methodology for RSW quality inspection.

  15. Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products.

    Science.gov (United States)

    Owen, Jeremy G; Reddy, Boojala Vijay B; Ternei, Melinda A; Charlop-Powers, Zachary; Calle, Paula Y; Kim, Jeffrey H; Brady, Sean F

    2013-07-16

    Complex microbial ecosystems contain large reservoirs of unexplored biosynthetic diversity. Here we provide an experimental framework and data analysis tool to facilitate the targeted discovery of natural-product biosynthetic gene clusters from the environment. Multiplex sequencing of barcoded PCR amplicons is followed by sequence similarity directed data parsing to identify sequences bearing close resemblance to biosynthetically or biomedically interesting gene clusters. Amplicons are then mapped onto arrayed metagenomic libraries to guide the recovery of targeted gene clusters. When applied to adenylation- and ketosynthase-domain amplicons derived from saturating soil DNA libraries, our analysis pipeline led to the recovery of biosynthetic clusters predicted to encode for previously uncharacterized glycopeptide- and lipopeptide-like antibiotics; thiocoraline-, azinomycin-, and bleomycin-like antitumor agents; and a rapamycin-like immunosuppressant. The utility of the approach is demonstrated by using recovered eDNA sequences to generate glycopeptide derivatives. The experiments described here constitute a systematic interrogation of a soil metagenome for gene clusters capable of encoding naturally occurring derivatives of biomedically relevant natural products. Our results show that previously undetected biosynthetic gene clusters with potential biomedical relevance are very common in the environment. This general process should permit the routine screening of environmental samples for gene clusters capable of encoding the systematic expansion of the structural diversity seen in biomedically relevant families of natural products.

  16. Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array

    NARCIS (Netherlands)

    Zetsche, Bernd; Heidenreich, Matthias; Mohanraju, Prarthana; Fedorova, Iana; Kneppers, Jeroen; Degennaro, Ellen M.; Winblad, Nerges; Choudhury, Sourav R.; Abudayyeh, Omar O.; Wu, Wen Y.; Oost, van der John

    2017-01-01

    Targeting of multiple genomic loci with Cas9 is limited by the need for multiple or large expression constructs. Here we show that the ability of Cpf1 to process its own CRISPR RNA (crRNA) can be used to simplify multiplexed genome editing. Using a single customized CRISPR array, we edit up to fo

  17. A Study of the Broadband Parametric Acoustic Array

    Science.gov (United States)

    1982-01-04

    parametric array 141 *0 Ia 0 oC ) 0 0 CO U,. U, 4 , a o o co~ cc I U.W D w 0L 0 0 td ~ v*V) - NX ALU AS00 161 JM ZG 142R 6.65 8 00 wo E - rii C 4 Ci ZU Z...sufficiently low that the relative 184 Lim"" 00 d 0C 0000 0~0 aj 0i0 0 c 00 0 CL z1 cV 0> 0 ao - - (L gp-~~~ ccMK iSd ARL:U AS4 9108 VMH cA 185~~ 6.69

  18. Empirical study of supervised gene screening

    Directory of Open Access Journals (Sweden)

    Ma Shuangge

    2006-12-01

    Full Text Available Abstract Background Microarray studies provide a way of linking variations of phenotypes with their genetic causations. Constructing predictive models using high dimensional microarray measurements usually consists of three steps: (1 unsupervised gene screening; (2 supervised gene screening; and (3 statistical model building. Supervised gene screening based on marginal gene ranking is commonly used to reduce the number of genes in the model building. Various simple statistics, such as t-statistic or signal to noise ratio, have been used to rank genes in the supervised screening. Despite of its extensive usage, statistical study of supervised gene screening remains scarce. Our study is partly motivated by the differences in gene discovery results caused by using different supervised gene screening methods. Results We investigate concordance and reproducibility of supervised gene screening based on eight commonly used marginal statistics. Concordance is assessed by the relative fractions of overlaps between top ranked genes screened using different marginal statistics. We propose a Bootstrap Reproducibility Index, which measures reproducibility of individual genes under the supervised screening. Empirical studies are based on four public microarray data. We consider the cases where the top 20%, 40% and 60% genes are screened. Conclusion From a gene discovery point of view, the effect of supervised gene screening based on different marginal statistics cannot be ignored. Empirical studies show that (1 genes passed different supervised screenings may be considerably different; (2 concordance may vary, depending on the underlying data structure and percentage of selected genes; (3 evaluated with the Bootstrap Reproducibility Index, genes passed supervised screenings are only moderately reproducible; and (4 concordance cannot be improved by supervised screening based on reproducibility.

  19. Analysis of immune system gene expression in small rheumatoid arthritis biopsies using a combination of subtractive hybridization and high-density cDNA arrays.

    Science.gov (United States)

    Zanders, E D; Goulden, M G; Kennedy, T C; Kempsell, K E

    2000-01-13

    Subtractive hybridization of cDNAs generated from synovial RNA which had been isolated from patients with rheumatoid arthritis (RA) or normal controls was used in conjunction with high-density array hybridization to identify genes of immunological interest. The method was designed to detect gene expression in small needle biopsy specimens by means of a prior amplification of nanogram amounts of total RNA to full-length cDNA using PCR. The latter was cut with Rsa I, ligated with adapters, hybridized with unmodified driver cDNA, and subjected to suppression subtraction PCR. Differentially expressed products were cloned into E. coli and picked into 384 well plates. Inserts were obtained by PCR across the multiple cloning site, and the products arrayed at high density on nylon filters. The subtracted cDNAs were also labelled by random priming for use as probes for library screening. The libraries chosen were the subtracted one described above and a set of 45,000 ESTs from the I.M. A.G.E consortium. Clones showing positive hybridization were identified by sequence analysis and homology searching. The results showed that the subtracted hybridization approach could identify many gene fragments expressed at different levels, the most abundant being immunoglobulins and HLA-DR. The expression profile was characteristic of macrophage, B cell and plasma cell infiltration with evidence of interferon induction. In addition, a significant number of sequences without matches in the nucleotide databases were obtained, this demonstrates the utility of the method in finding novel gene fragments for further characterisation as potential members of the immune system. Although RA was studied here, the technology is applicable to any disease process even in cases where amounts of tissue may be limited.

  20. Gene expression arrays reveal a rapid return to normal homeostasis in immunologically-challenged trophoblast-like JAR cells.

    Science.gov (United States)

    Jarvis, James N; Dozmorov, Igor; Jiang, Kaiyu; Chen, Yanmin; Frank, Mark Barton; Cadwell, Craig; Turner, Sean; Centola, Michael

    2004-04-01

    The immunologic adaptations of pregnancy have come under increasing scrutiny in the past 15 years. Existing experimental evidence clearly demonstrates that placental trophoblasts play an important role in regulating immunologic/inflammatory responses at the maternal-fetal interface. We used a well-developed gene expression array to examine in greater detail the physiologic response of trophoblast-like choriocarcinoma cells to a model immunologic 'challenge.' We co-cultured PHA-activated or resting peripheral blood mononuclear cells (PBMC) with the human choriocarcinoma cell line JAR for time periods ranging from 2 to 18 h. Messenger RNA expression in the JAR cells was then assessed using a 21,329-gene microarray and novel biostatistical analyses that we have previously published. Patterns of differential gene expression were assessed using a commercial pathway analysis software program. Differences in gene expression between JAR cells cultured with activated PBMC (experimental samples) and JAR cells cultured with resting PBMC (control samples) were seen only at the 2h time point. That is, multiple genes were transcribed in JAR cells in response to activated PBMC, but expression levels of the genes had all returned to baseline by 6h. Molecular modeling demonstrated that the differentially expressed genes were largely associated with cell growth and differentiation. This model was confirmed by noting a two-fold increase in CD10/neutral endopeptidase expression (a marker for cell differentiation) in JAR cells incubated with media from activated PBMC compared with JAR cells incubated with resting PBMC. These findings support the hypothesis that there is a delicate immunologic milieu at the maternal-fetal interface that must be maintained. Immunologic/inflammatory challenge at the maternal-fetal interface is compensated by cellular mechanisms that work to reduce inflammation and rapidly restore immunologic balance.

  1. Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes

    Directory of Open Access Journals (Sweden)

    Streelman J Todd

    2011-05-01

    Full Text Available Abstract Background Divergence within cis-regulatory sequences may contribute to the adaptive evolution of gene expression, but functional alleles in these regions are difficult to identify without abundant genomic resources. Among African cichlid fishes, the differential expression of seven opsin genes has produced adaptive differences in visual sensitivity. Quantitative genetic analysis suggests that cis-regulatory alleles near the SWS2-LWS opsins may contribute to this variation. Here, we sequence BACs containing the opsin genes of two cichlids, Oreochromis niloticus and Metriaclima zebra. We use phylogenetic footprinting and shadowing to examine divergence in conserved non-coding elements, promoter sequences, and 3'-UTRs surrounding each opsin in search of candidate cis-regulatory sequences that influence cichlid opsin expression. Results We identified 20 conserved non-coding elements surrounding the opsins of cichlids and other teleosts, including one known enhancer and a retinal microRNA. Most conserved elements contained computationally-predicted binding sites that correspond to transcription factors that function in vertebrate opsin expression; O. niloticus and M. zebra were significantly divergent in two of these. Similarly, we found a large number of relevant transcription factor binding sites within each opsin's proximal promoter, and identified five opsins that were considerably divergent in both expression and the number of transcription factor binding sites shared between O. niloticus and M. zebra. We also found several microRNA target sites within the 3'-UTR of each opsin, including two 3'-UTRs that differ significantly between O. niloticus and M. zebra. Finally, we examined interspecific divergence among 18 phenotypically diverse cichlids from Lake Malawi for one conserved non-coding element, two 3'-UTRs, and five opsin proximal promoters. We found that all regions were highly conserved with some evidence of CRX transcription

  2. Comparative Transcriptomic Profiling of Vitis vinifera Under High Light Using a Custom-Made Array and the Affymetrix GeneChip

    Institute of Scientific and Technical Information of China (English)

    Luisa C. Carvalho; Belmiro J. Vilela; Phil M. Mullineaux; Sara Am(a)ncio

    2011-01-01

    Understanding abiotic stress responses is one of the most important issues in plant research nowadays.Abiotic stress,including excess light,can promote the onset of oxidative stress through the accumulation of reactive oxygen species.Oxidative stress also arises when in vitro propagated plants are exposed to high light upon transfer to ex vitro.To determine whether the underlying pathways activated at the transfer of in vitro grapevine to ex vitro conditions reflect the processes occurring upon light stress,we used Vitis vinifera Affymetrix GeneChip (VvGA) and a custom array of genes responsive to light stress (LSCA) detected by real-time reverse transcriptase PCR (qRT-PCR).When gene-expression profiles were compared,‘protein metabolism and modification',‘signaling',and ‘anti-oxidative' genes were more represented in LSCA,while,in VvGA,‘cell wall metabolism' and ‘secondary metabolism' were the categories in which gene expression varied more significantly.The above functional categories confirm previous studies involving other types of abiotic stresses,enhancing the common attributes of abiotic stress defense pathways.The LSCA analysis of our experimental system detected strong response of heat shock genes,particularly the protein rescuing mechanism involving the cooperation of two ATP-dependent chaperone systems,Hsp100 and Hsp70,which showed an unusually late response during the recovery period,of extreme relevance to remove non-functional,potentially harmful polypeptides arising from misfolding,denaturation,or aggregation brought about by stress.The success of LSCA also proves the feasibility of a custommade qRT-PCR approach,particularly for species for which no GeneChip is available and for researchers dealing with a specific and focused problem.

  3. A novel field emission microscopy method to study field emission characteristics of freestanding carbon nanotube arrays

    Science.gov (United States)

    Li, Yunhan; Sun, Yonghai; Jaffray, David A.; Yeow, John T. W.

    2017-04-01

    Field emission (FE) uniformity and the mechanism of emitter failure of freestanding carbon nanotube (CNT) arrays have not been well studied due to the difficulty of observing and quantifying FE performance of each emitter in CNT arrays. Herein a field emission microscopy (FEM) method based on poly(methyl methacrylate) (PMMA) thin film is proposed to study the FE uniformity and CNT emitter failure of freestanding CNT arrays. FE uniformity of freestanding CNT arrays and different levels of FE current contributions from each emitter in the arrays are recorded and visualized. FEM patterns on the PMMA thin film contain the details of the CNT emitter tip shape and whether multiple CNT emitters occur at an emission site. Observation of real-time FE performance and the CNT emitter failure process in freestanding CNT arrays are successfully achieved using a microscopic camera. High emission currents through CNT emitters causes Joule heating and light emission followed by an explosion of the CNTs. The proposed approach is capable of resolving the major challenge of building the relationship between FE performance and CNT morphologies, which can significantly facilitate the study of FE non-uniformity, the emitter failure mechanism and the development of stable and reliable FE devices in practical applications.

  4. Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array

    Directory of Open Access Journals (Sweden)

    Kaltenboeck Ludmilla

    2011-01-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs have become the marker of choice for genome-wide association studies. In order to provide the best genome coverage for the analysis of performance and production traits, a large number of relatively evenly distributed SNPs are needed. Gene-associated SNPs may fulfill these requirements of large numbers and genome wide distribution. In addition, gene-associated SNPs could themselves be causative SNPs for traits. The objective of this project was to identify large numbers of gene-associated SNPs using high-throughput next generation sequencing. Results Transcriptome sequencing was conducted for channel catfish and blue catfish using Illumina next generation sequencing technology. Approximately 220 million reads (15.6 Gb for channel catfish and 280 million reads (19.6 Gb for blue catfish were obtained by sequencing gene transcripts derived from various tissues of multiple individuals from a diverse genetic background. A total of over 35 billion base pairs of expressed short read sequences were generated. Over two million putative SNPs were identified from channel catfish and almost 2.5 million putative SNPs were identified from blue catfish. Of these putative SNPs, a set of filtered SNPs were identified including 342,104 intra-specific SNPs for channel catfish, 366,269 intra-specific SNPs for blue catfish, and 420,727 inter-specific SNPs between channel catfish and blue catfish. These filtered SNPs are distributed within 16,562 unique genes in channel catfish and 17,423 unique genes in blue catfish. Conclusions For aquaculture species, transcriptome analysis of pooled RNA samples from multiple individuals using Illumina sequencing technology is both technically efficient and cost-effective for generating expressed sequences. Such an approach is most effective when coupled to existing EST resources generated using traditional sequencing approaches because the reference ESTs facilitate

  5. Exclusion of APC and VHL gene deletions by array-based comparative hybridization in two patients with microscopically visible chromosomal aberrations.

    Science.gov (United States)

    Wallerstein, Robert J; Brooks, Susan Sklower; Streck, Deanna L; Kurvathi, Rohini; Toruner, Gokce A

    2007-10-15

    Karyotyping is a major component of the genetic work-up of patients with dysmorphism. Cytogenetic aberrations close to a known tumor suppressor gene raise important clinical issues because deletion of that tumor suppressor gene can cause genetic predisposition to cancer. We present two cancer-free dysmorphic patients with karyotypes of 46,XX,del(5)(q15q22.3) and 46,XX,del(3)(p25.2~pter). These deletions are close to the APC and VHL genes that confer susceptibility to familial Adenomatous polyposis (OMIM #17510) and von-Hippel-Lindau syndrome (OMIM #193300), respectively. The array-based comparative genomic hybridization (array-CGH) analysis using a custom Agilent 44K oligonucleotide array demonstrated an interstitial 20.7-megabase (Mb) deletion on 5q (chr5: 89,725,638-110,491,345) and a terminal 9.45-Mb deletion on 3p (chr3:pter-9,450,984). According to the March 2006 human reference sequence, the APC gene is located at chr5: 112,101,483-112,209,835 and the VHL gene is located at chr3: 10,158,319-10,168,746. These results indicate that the APC gene is 2,300 kilobases (kb) and the VHL gene is 700 kb away from deleted regions. Southern blot analysis for APC and VHL genes were negative, consistent with array-CGH findings. These results demonstrate the power of array-CCH to assess potential tumor suppressor gene involvement and cancer risk in patients with microscopically visible deletions in areas near tumor suppressors.

  6. Data Mining of Gene Arrays for Biomarkers of Survival in Ovarian Cancer

    Directory of Open Access Journals (Sweden)

    Clare Coveney

    2015-07-01

    Full Text Available The expected five-year survival rate from a stage III ovarian cancer diagnosis is a mere 22%; this applies to the 7000 new cases diagnosed yearly in the UK. Stratification of patients with this heterogeneous disease, based on active molecular pathways, would aid a targeted treatment improving the prognosis for many cases. While hundreds of genes have been associated with ovarian cancer, few have yet been verified by peer research for clinical significance. Here, a meta-analysis approach was applied to two carefully selected gene expression microarray datasets. Artificial neural networks, Cox univariate survival analyses and T-tests identified genes whose expression was consistently and significantly associated with patient survival. The rigor of this experimental design increases confidence in the genes found to be of interest. A list of 56 genes were distilled from a potential 37,000 to be significantly related to survival in both datasets with a FDR of 1.39859 × 10−11, the identities of which both verify genes already implicated with this disease and provide novel genes and pathways to pursue. Further investigation and validation of these may lead to clinical insights and have potential to predict a patient’s response to treatment or be used as a novel target for therapy.

  7. Data Mining of Gene Arrays for Biomarkers of Survival in Ovarian Cancer.

    Science.gov (United States)

    Coveney, Clare; Boocock, David J; Rees, Robert C; Deen, Suha; Ball, Graham R

    2015-07-17

    The expected five-year survival rate from a stage III ovarian cancer diagnosis is a mere 22%; this applies to the 7000 new cases diagnosed yearly in the UK. Stratification of patients with this heterogeneous disease, based on active molecular pathways, would aid a targeted treatment improving the prognosis for many cases. While hundreds of genes have been associated with ovarian cancer, few have yet been verified by peer research for clinical significance. Here, a meta-analysis approach was applied to two carefully selected gene expression microarray datasets. Artificial neural networks, Cox univariate survival analyses and T-tests identified genes whose expression was consistently and significantly associated with patient survival. The rigor of this experimental design increases confidence in the genes found to be of interest. A list of 56 genes were distilled from a potential 37,000 to be significantly related to survival in both datasets with a FDR of 1.39859 × 10(-11), the identities of which both verify genes already implicated with this disease and provide novel genes and pathways to pursue. Further investigation and validation of these may lead to clinical insights and have potential to predict a patient's response to treatment or be used as a novel target for therapy.

  8. Selection of reliable biomarkers from PCR array analyses using relative distance computational model: methodology and proof-of-concept study.

    Directory of Open Access Journals (Sweden)

    Chunsheng Liu

    Full Text Available It is increasingly evident about the difficulty to monitor chemical exposure through biomarkers as almost all the biomarkers so far proposed are not specific for any individual chemical. In this proof-of-concept study, adult male zebrafish (Danio rerio were exposed to 5 or 25 µg/L 17β-estradiol (E2, 100 µg/L lindane, 5 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD or 15 mg/L arsenic for 96 h, and the expression profiles of 59 genes involved in 7 pathways plus 2 well characterized biomarker genes, vtg1 (vitellogenin1 and cyp1a1 (cytochrome P450 1A1, were examined. Relative distance (RD computational model was developed to screen favorable genes and generate appropriate gene sets for the differentiation of chemicals/concentrations selected. Our results demonstrated that the known biomarker genes were not always good candidates for the differentiation of pair of chemicals/concentrations, and other genes had higher potentials in some cases. Furthermore, the differentiation of 5 chemicals/concentrations examined were attainable using expression data of various gene sets, and the best combination was the set consisting of 50 genes; however, as few as two genes (e.g. vtg1 and hspa5 [heat shock protein 5] were sufficient to differentiate the five chemical/concentration groups in the present test. These observations suggest that multi-parameter arrays should be more reliable for biomonitoring of chemical exposure than traditional biomarkers, and the RD computational model provides an effective tool for the selection of parameters and generation of parameter sets.

  9. Selection of reliable biomarkers from PCR array analyses using relative distance computational model: methodology and proof-of-concept study.

    Science.gov (United States)

    Liu, Chunsheng; Xu, Hongyan; Lam, Siew Hong; Gong, Zhiyuan

    2013-01-01

    It is increasingly evident about the difficulty to monitor chemical exposure through biomarkers as almost all the biomarkers so far proposed are not specific for any individual chemical. In this proof-of-concept study, adult male zebrafish (Danio rerio) were exposed to 5 or 25 µg/L 17β-estradiol (E2), 100 µg/L lindane, 5 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) or 15 mg/L arsenic for 96 h, and the expression profiles of 59 genes involved in 7 pathways plus 2 well characterized biomarker genes, vtg1 (vitellogenin1) and cyp1a1 (cytochrome P450 1A1), were examined. Relative distance (RD) computational model was developed to screen favorable genes and generate appropriate gene sets for the differentiation of chemicals/concentrations selected. Our results demonstrated that the known biomarker genes were not always good candidates for the differentiation of pair of chemicals/concentrations, and other genes had higher potentials in some cases. Furthermore, the differentiation of 5 chemicals/concentrations examined were attainable using expression data of various gene sets, and the best combination was the set consisting of 50 genes; however, as few as two genes (e.g. vtg1 and hspa5 [heat shock protein 5]) were sufficient to differentiate the five chemical/concentration groups in the present test. These observations suggest that multi-parameter arrays should be more reliable for biomonitoring of chemical exposure than traditional biomarkers, and the RD computational model provides an effective tool for the selection of parameters and generation of parameter sets.

  10. Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses

    Directory of Open Access Journals (Sweden)

    van Wieringen Wessel N

    2012-05-01

    Full Text Available Abstract Background An increasing number of genomic studies interrogating more than one molecular level is published. Bioinformatics follows biological practice, and recent years have seen a surge in methodology for the integrative analysis of genomic data. Often such analyses require knowledge of which elements of one platform link to those of another. Although important, many integrative analyses do not or insufficiently detail the matching of the platforms. Results We describe, illustrate and discuss six matching procedures. They are implemented in the R-package sigaR (available from Bioconductor. The principles underlying the presented matching procedures are generic, and can be combined to form new matching approaches or be applied to the matching of other platforms. Illustration of the matching procedures on a variety of data sets reveals how the procedures differ in the use of the available data, and may even lead to different results for individual genes. Conclusions Matching of data from multiple genomics platforms is an important preprocessing step for many integrative bioinformatic analysis, for which we present six generic procedures, both old and new. They have been implemented in the R-package sigaR, available from Bioconductor.

  11. Application of conformal map theory for design of 2-D ultrasonic array structure for NDT imaging application: a feasibility study.

    Science.gov (United States)

    Ramadas, Sivaram N; Jackson, Joseph C; Dziewierz, Jerzy; O'Leary, Richard; Gachagan, Anthony

    2014-03-01

    Two-dimensional ultrasonic phased arrays are becoming increasingly popular in nondestructive evaluation (NDE). Sparse array element configurations are required to fully exploit the potential benefits of 2-D phased arrays. This paper applies the conformal mapping technique as a means of designing sparse 2-D array layouts for NDE applications. Modeling using both Huygens' field prediction theory and 2-D fast Fourier transformation is employed to study the resulting new structure. A conformal power map was used that, for fixed beam width, was shown in simulations to have a greater contrast than rectangular or random arrays. A prototype aperiodic 2-D array configuration for direct contact operation in steel, with operational frequency ~3 MHz, was designed using the array design principle described in this paper. Experimental results demonstrate a working sparse-array transducer capable of performing volumetric imaging.

  12. A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species

    Energy Technology Data Exchange (ETDEWEB)

    Geraldes, Armando [University of British Columbia, Vancouver; Hannemann, Jan [University of Victoria, Canada; Grassa, Chris [University of British Columbia, Vancouver; Farzaneh, Nima [University of British Columbia, Vancouver; Porth, Ilga [University of British Columbia, Vancouver; McKown, Athena [University of British Columbia, Vancouver; Skyba, Oleksandr [University of British Columbia, Vancouver; Li, Eryang [University of British Columbia, Vancouver; Mike, Fujita [University of British Columbia, Vancouver; Friedmann, Michael [University of British Columbia, Vancouver; Wasteneys, Geoffrey [University of British Columbia, Vancouver; Guy, Robert [University of British Columbia, Vancouver; El-Kassaby, Yousry [University of British Columbia, Vancouver; Mansfield, Shawn [University of British Columbia, Vancouver; Cronk, Quentin [University of British Columbia, Vancouver; Ehlting, Juergen [University of Victoria, Canada; Douglas, Carl [University of British Columbia, Vancouver; DiFazio, Stephen P [West Virginia University, Morgantown; Slavov, Gancho [West Virginia University, Morgantown; Ranjan, Priya [ORNL; Muchero, Wellington [ORNL; Gunter, Lee E [ORNL; Wymore, Ann [ORNL; Tuskan, Gerald A [ORNL; Martin, Joel [U.S. Department of Energy, Joint Genome Institute; Schackwitz, Wendy [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Christa [U.S. Department of Energy, Joint Genome Institute; Rokhsar, Daniel [U.S. Department of Energy, Joint Genome Institute

    2013-01-01

    Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. Despite the declining costs of genotyping by sequencing, for most studies, the use of large SNP genotyping arrays still offers the most cost-effective solution for large-scale targeted genotyping. Here we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species range. Due to the rapid decay of linkage disequilibrium in P. trichocarpa we adopted a candidate gene approach to the array design that resulted in the selection of 34,131 SNPs, the majority of which are located in, or within 2 kb, of 3,543 candidate genes. A subset of the SNPs (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%, indicating that high-quality data are generated with this array. We demonstrate that even among small numbers of samples (n=10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that due to ascertainment bias the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca (P. balsamifera and P. angustifolia). Finally, we provide evidence for the utility of the array for intraspecific studies of genetic differentiation and for species assignment and the detection of natural hybrids.

  13. Mission-Oriented Sensor Arrays and UAVs - a Case Study on Environmental Monitoring

    Science.gov (United States)

    Figueira, N. M.; Freire, I. L.; Trindade, O.; Simões, E.

    2015-08-01

    This paper presents a new concept of UAV mission design in geomatics, applied to the generation of thematic maps for a multitude of civilian and military applications. We discuss the architecture of Mission-Oriented Sensors Arrays (MOSA), proposed in Figueira et Al. (2013), aimed at splitting and decoupling the mission-oriented part of the system (non safety-critical hardware and software) from the aircraft control systems (safety-critical). As a case study, we present an environmental monitoring application for the automatic generation of thematic maps to track gunshot activity in conservation areas. The MOSA modeled for this application integrates information from a thermal camera and an on-the-ground microphone array. The use of microphone arrays technology is of particular interest in this paper. These arrays allow estimation of the direction-of-arrival (DOA) of the incoming sound waves. Information about events of interest is obtained by the fusion of the data provided by the microphone array, captured by the UAV, fused with information from the termal image processing. Preliminary results show the feasibility of the on-the-ground sound processing array and the simulation of the main processing module, to be embedded into an UAV in a future work. The main contributions of this paper are the proposed MOSA system, including concepts, models and architecture.

  14. MISSION-ORIENTED SENSOR ARRAYS AND UAVs – A CASE STUDY ON ENVIRONMENTAL MONITORING

    Directory of Open Access Journals (Sweden)

    N. M. Figueira

    2015-08-01

    Full Text Available This paper presents a new concept of UAV mission design in geomatics, applied to the generation of thematic maps for a multitude of civilian and military applications. We discuss the architecture of Mission-Oriented Sensors Arrays (MOSA, proposed in Figueira et Al. (2013, aimed at splitting and decoupling the mission-oriented part of the system (non safety-critical hardware and software from the aircraft control systems (safety-critical. As a case study, we present an environmental monitoring application for the automatic generation of thematic maps to track gunshot activity in conservation areas. The MOSA modeled for this application integrates information from a thermal camera and an on-the-ground microphone array. The use of microphone arrays technology is of particular interest in this paper. These arrays allow estimation of the direction-of-arrival (DOA of the incoming sound waves. Information about events of interest is obtained by the fusion of the data provided by the microphone array, captured by the UAV, fused with information from the termal image processing. Preliminary results show the feasibility of the on-the-ground sound processing array and the simulation of the main processing module, to be embedded into an UAV in a future work. The main contributions of this paper are the proposed MOSA system, including concepts, models and architecture.

  15. An array microscope for ultrarapid virtual slide processing and telepathology. Design, fabrication, and validation study.

    Science.gov (United States)

    Weinstein, Ronald S; Descour, Michael R; Liang, Chen; Barker, Gail; Scott, Katherine M; Richter, Lynne; Krupinski, Elizabeth A; Bhattacharyya, Achyut K; Davis, John R; Graham, Anna R; Rennels, Margaret; Russum, William C; Goodall, James F; Zhou, Pixuan; Olszak, Artur G; Williams, Bruce H; Wyant, James C; Bartels, Peter H

    2004-11-01

    This paper describes the design and fabrication of a novel array microscope for the first ultrarapid virtual slide processor (DMetrix DX-40 digital slide scanner). The array microscope optics consists of a stack of three 80-element 10 x 8-lenslet arrays, constituting a "lenslet array ensemble." The lenslet array ensemble is positioned over a glass slide. Uniquely shaped lenses in each of the lenslet arrays, arranged perpendicular to the glass slide constitute a single "miniaturized microscope." A high-pixel-density image sensor is attached to the top of the lenslet array ensemble. In operation, the lenslet array ensemble is transported by a motorized mechanism relative to the long axis of a glass slide. Each of the 80 miniaturized microscopes has a lateral field of view of 250 microns. The microscopes of each row of the array are offset from the microscopes in other rows. Scanning a glass slide with the array microscope produces seamless two-dimensional image data of the entire slide, that is, a virtual slide. The optical system has a numerical aperture of N.A.= 0.65, scans slides at a rate of 3 mm per second, and accrues up to 3,000 images per second from each of the 80 miniaturized microscopes. In the ultrarapid virtual slide processing cycle, the time for image acquisition takes 58 seconds for a 2.25 cm2 tissue section. An automatic slide loader enables the scanner to process up to 40 slides per hour without operator intervention. Slide scanning and image processing are done concurrently so that post-scan processing is eliminated. A virtual slide can be viewed over the Internet immediately after the scanning is complete. A validation study compared the diagnostic accuracy of pathologist case readers using array microscopy (with images viewed as virtual slides) and conventional light microscopy. Four senior pathologists diagnosed 30 breast surgical pathology cases each using both imaging modes, but on separate occasions. Of 120 case reads by array microscopy

  16. Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India

    Directory of Open Access Journals (Sweden)

    Johan eBengtsson-Palme

    2014-12-01

    Full Text Available There is increasing evidence for an environmental origin of many antibiotic resistance genes. Consequently, it is important to identify environments of particular risk for selecting and maintaining such resistance factors. In this study, we described the diversity of antibiotic resistance genes in an Indian lake subjected to industrial pollution with fluoroquinolone antibiotics. We also assessed the genetic context of the identified resistance genes, to try to predict their genetic transferability. The lake harbored a wide range of resistance genes (81 identified gene types against essentially every major class of antibiotics, as well as genes responsible for mobilization of genetic material. Resistance genes were estimated to be 7000 times more abundant than in a Swedish lake included for comparison, where only eight resistance genes were found. The sul2 and qnrD genes were the most common resistance genes in the Indian lake. Twenty-six known and twenty-one putative novel plasmids were recovered in the Indian lake metagenome, which, together with the genes found, indicate a large potential for horizontal gene transfer through conjugation. Interestingly, the microbial community of the lake still included a wide range of taxa, suggesting that, across most phyla, bacteria has adapted relatively well to this highly polluted environment. Based on the wide range and high abundance of known resistance factors we have detected, it is plausible that yet unrecognized resistance genes are also present in the lake. Thus, we conclude that environments polluted with waste from antibiotic manufacturing could be important reservoirs for mobile antibiotic resistance genes.

  17. Using macro-arrays to study routes of infection of Helicobacter pylori in three families.

    Directory of Open Access Journals (Sweden)

    Josette Raymond

    Full Text Available BACKGROUND: Analysis of the evolutionary dynamics of Helicobacter pylori allowed tracing the spread of infection through populations on different continents but transmission pathways between individual humans have not been clearly described. MATERIALS AND METHODS: To investigate person-to-person transmission, we studied three families each including one child with persistence of symptoms after antibiotic treatment. Ten isolates from the antrum and corpus of stomach of each family member were analyzed both by sequencing of two housekeeping genes and macroarray tests. RESULTS: A total of 134 (8.4% out of the 1590 coding sequences (CDSs tested, including cag PAI and insertion sequences, were present in some but not all isolates (and are therefore defined as variable CDSs. Most of the variable CDSs encoded proteins of unknown function (76/134 or were selfish DNA including that encoding restriction/modification enzymes (13/134. Isolates colonizing the stomach of one individual can vary by point mutations, as seen in hspA, or by the gain or loss of one to five CDSs. They were considered as (genetic variants. The phylogenetic clustering of gene profiles obtained on macro-arrays allowed identifying the different strains infecting families. Two to five strains circulated within a family. Identical strains were present in at least two members of all three families supporting the accepted model of intrafamilial transmission. Surprisingly, the mother was not implicated in the transmission of H. pylori in the two French families. Sibling-to-sibling transmission and acquisition of H. pylori from outside the family appeared to be probable in the transmission pathways. CONCLUSION: Macroarray analysis based on previously selected CDSs gives a comprehensive view of the genome diversity of a pathogen. This approach combined with information on the origin of the hspA and glmM alleles revealed that Helicobacter pylori infection may be acquired by more diverse routes

  18. Molecular Studies on Preproinsulin Gene

    Directory of Open Access Journals (Sweden)

    Sabir Sarah

    2016-01-01

    Full Text Available Insulin plays an important role in maintaining the blood glucose level of the body. The β-cells of pancreas produce insulin in the form of precursor that is preproinsulin. The gene of preproinsulin provides an interesting system for addressing question related to molecular evolution. Recombinant DNA technology has made it possible to isolate and sequence the chromosomal genes coding for unique protein products. Although preproinsulin of various organism has been isolated and cloned, but there is no report from buffalo (Bubalus bubalis that is our major livestock. The genomic DNA of buffalo was isolated using Laura-Lee-Boodram method. The part of preproinsulin gene (596bp and 520bp using BPPI-UPS and bpiful_F as forward and BC1-C as reverse primer was amplified. Cloning of amplified fragments of gene were performed in pCR 2.1 vector. Positive clones were screened on the basis of blue white selection. The band obtained on 596bp and 520bp after colony PCR confirmed the successful cloning of preproinsulin gene in pCR 2.1 vector.

  19. Genomic analysis of lung cell lines exposures to space radiation and the effect of lunar dust on selected fibrosis gene using RT2 PCR Array

    Science.gov (United States)

    Yeshitla, Samrawit

    In the United States (U.S.), lung cancer is the number one cause of cancer death among men and women. Previous studies on human and animal epithelial lung cells showed that ionizing radiation and certain environmental pollutants are carcinogens. The surface area of the lungs and the slow turnover rate of the epithelial cells are suggested to play a role in the vulnerability of the cells, which lead to increase in the progenitor cell of the lung. It has been proposed that these progenitor cells, when exposed to radiation undergo multiple alterations that cause the cells to become cancerous. The current thought is that the lungs contain several facultative progenitor cells that are situated throughout the lung epithelium and are regionally restricted in their regenerative capacity. In this study, normal Human Bronchial Epithelial Cells (HBECs) were immortalized through the expression of Cdk4 and hTERT and evaluated for the effects radiation using in vitro study. The HBECs retained its novel multipotent capacity in vitro and represented unrestricted progenitor cells of the adult lungs, which resemble an embryonic progenitor. Analysis of the transformed clones of human bronchial epithelial cell line, HEBC3KT exposed to Fe ions and gamma rays revealed chromosomal abnormality, which was detected with the Multi-color Fluorescent In Situ Hybridization (mFish). In Part two of this study the F344 rats exposed to lunar dust, for 4 weeks (6h/d; 5d/wk.) in nose-only inhalation chambers at concentrations of 0 (control air), 2.1, 6.8, 20.8, and 61 mg/m3 of lunar dust, were used to determine the lunar dust toxicity on the lung tissues and total RNA were prepared from the tissues and used for gene expression. Analysis of gene expression data using Ingenuity Pathway Analysis tool identified multiple pathways of which fibrosis was one of the pathways. The Rat Fibrosis RT 2 Profile PCR Array was used to profile the expression of 84 genes that are relevant to fibrosis in the lung

  20. Bioinformatics study of the mangrove actin genes

    Science.gov (United States)

    Basyuni, M.; Wasilah, M.; Sumardi

    2017-01-01

    This study describes the bioinformatics methods to analyze eight actin genes from mangrove plants on DDBJ/EMBL/GenBank as well as predicted the structure, composition, subcellular localization, similarity, and phylogenetic. The physical and chemical properties of eight mangroves showed variation among the genes. The percentage of the secondary structure of eight mangrove actin genes followed the order of a helix > random coil > extended chain structure for BgActl, KcActl, RsActl, and A. corniculatum Act. In contrast to this observation, the remaining actin genes were random coil > extended chain structure > a helix. This study, therefore, shown the prediction of secondary structure was performed for necessary structural information. The values of chloroplast or signal peptide or mitochondrial target were too small, indicated that no chloroplast or mitochondrial transit peptide or signal peptide of secretion pathway in mangrove actin genes. These results suggested the importance of understanding the diversity and functional of properties of the different amino acids in mangrove actin genes. To clarify the relationship among the mangrove actin gene, a phylogenetic tree was constructed. Three groups of mangrove actin genes were formed, the first group contains B. gymnorrhiza BgAct and R. stylosa RsActl. The second cluster which consists of 5 actin genes the largest group, and the last branch consist of one gene, B. sexagula Act. The present study, therefore, supported the previous results that plant actin genes form distinct clusters in the tree.

  1. National Array of Neutron Detectors (NAND): A versatile tool for nuclear reaction studies

    Energy Technology Data Exchange (ETDEWEB)

    Golda, K.S., E-mail: goldaks@gmail.com [Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi 110067 (India); Jhingan, A.; Sugathan, P. [Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi 110067 (India); Singh, Hardev [Department of Physics, Kurukshetra University, Kurukshetra 136119 (India); Singh, R.P. [Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi 110067 (India); Behera, B.R. [Department of Physics, Panjab University, Chandigarh 160014 (India); Mandal, S. [Department of Physics and Astrophysics, Delhi University, New Delhi 110007 (India); Kothari, A.; Gupta, Arti; Zacharias, J.; Archunan, M.; Barua, P.; Venkataramanan, S.; Bhowmik, R.K. [Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi 110067 (India); Govil, I.M. [Department of Physics, Panjab University, Chandigarh 160014 (India); Datta, S.K.; Chatterjee, M.B. [Inter University Accelerator Centre, Aruna Asaf Ali Marg, New Delhi 110067 (India)

    2014-11-01

    The first phase of the National Array of Neutron Detectors (NAND) consisting of 26 neutron detectors has been commissioned at the Inter University Accelerator Centre (IUAC), New Delhi. The motivation behind setting up of such a detector system is the need for more accurate and efficient study of reaction mechanisms in the projectile energy range of 5–8 MeV/n using heavy ion beams from a 15 UD Pelletron and an upgraded LINAC booster facility at IUAC. The above detector array can be used for inclusive as well as exclusive measurements of reaction products of which at least one product is a neutron. While inclusive measurements can be made using only the neutron detectors along with the time of flight technique and a pulsed beam, exclusive measurements can be performed by detecting neutrons in coincidence with charged particles and/or fission fragments detected with ancillary detectors. The array can also be used for neutron tagged gamma-ray spectroscopy in (HI, xn) reactions by detecting gamma-rays in coincidence with the neutrons in a compact geometrical configuration. The various features and the performance of the different aspects of the array are described in the present paper. -- Highlights: •We report the design, fabrication and installation of a 26 element modular neutron detection system (NAND). •The array has been designed for the fusion–fission studies at near and above the barrier energies. •The relevant characteristics of the array are studied exhaustively and reported. •The efficiency of the detectors are measured and compared with the monte carlo simulations. •The second phase of the array will be augmented with 80 more neutron detectors which will enable the system to measure the neutron multiplicity distribution.

  2. Single-strand conformation polymorphism analysis of candidate genes for reliable identification of alleles by capillary array electrophoresis.

    Science.gov (United States)

    Kuhn, David N; Borrone, James; Meerow, Alan W; Motamayor, Juan C; Brown, J Steven; Schnell, Raymond J

    2005-01-01

    We investigated the reliability of capillary array electrophoresis-single strand conformation polymorphism (CAE-SSCP) to determine if it can be used to identify novel alleles of candidate genes in a germplasm collection. Both strands of three different size fragments (160, 245 and 437 bp) that differed by one or more nucleotides in sequence were analyzed at four different temperatures (18 degrees C, 25 degrees C, 30 degrees C, and 35 degrees C). Mixtures of amplified fragments of either the intron interrupting the C-terminal WRKY domain of the Tc10 locus or the NBS domain of the TcRGH1 locus of Theobroma cacao were electroinjected into all 16 capillaries of an ABI 3100 Genetic Analyzer and analyzed three times at each temperature. Multiplexing of samples of different size range is possible, as intermediate and large fragments were analyzed simultaneously in these experiments. A statistical analysis of the means of the fragment mobilities demonstrated that single-stranded conformers of the fragments could be reliably identified by their mobility at all temperatures and size classes. The order of elution of fragments was not consistent over strands or temperatures for the intermediate and large fragments. If samples are only run once at a single temperature, small fragments could be identified from a single strand at a single temperature. A combination of data from both strands of a single run was needed to identify correctly all four of the intermediate fragments and no combination of data from strands or temperatures would allow the correct identification of two large fragments that differed by only a single single-nucleotide polymorphism (SNP) from a single run. Thus, to adequately assess alleles at a candidate gene locus using SSCP on a capillary array, fragments should be strands and both temperatures, and undenatured double-stranded (ds)DNA molecular weight standards, such as ROX 2500, should be included as internal standards.

  3. A Novel Acousto-Electric Levitator for Studies of Drop and Particle Clusters and Arrays

    Science.gov (United States)

    Tian, Yuren; Apfel, Robert E.; Zheng, Yibing

    1999-01-01

    A novel and compact instrumentation for studying the behavior of drop sprays and of clusters of drops now permits fundamental research into the behavior of reacting and non-reacting fluid and solid species. The new capability is made possible by simultaneous acousto-electric levitation and charging of "seed" droplets (10-30 microns in diameter) which come together in 2-D clusters (with up to 300 droplets). These clusters are interesting in their own right because of their crystalline and quasi-crystalline forms, which depend on the acoustic and electric field parameters. By varying the electric and acoustic field intensities, one can cause a cluster of droplets to condense into larger drops (e.g. 50-300 microns) which, because of their charge, form uniformly spaced 2-D arrays of monodispersed drops (e.g. 30-40 array drops in preliminary experiments). One or more layers of these 2-D arrays can form in the acoustic standing wave. Such a configuration permits a wide range of fundamental studies of drop evaporation, combustion, and nucleation. The drops can be single or multicomponent. Therefore, fundamental materials studies can also be performed. Using this same Cluster and Array Generation (CAG) instrumentation, it has been also possible in preliminary experiments to demonstrate the clustering and arraying of solid particles, both coated with an electrically conducting layer and uncoated, and both charged and uncharged.

  4. Gene expression studies using microarrays

    NARCIS (Netherlands)

    Burgess, Janette

    2001-01-01

    1. The rapid progression of the collaborative sequencing programmes that are unravelling the complete genome sequences of many organisms are opening pathways for new approaches to gene analysis. As the sequence data become available, the bottleneck in biological research will shift to understanding

  5. Reducing crosstalk in array structures by controlling the excitation voltage of individual elements: a feasibility study.

    Science.gov (United States)

    Bybi, A; Grondel, S; Assaad, J; Hladky-Hennion, A-C; Granger, C; Rguiti, M

    2013-08-01

    This paper describes a procedure to minimize crosstalk between the individual elements of a piezoelectric transducer array. A two-dimensional finite elements model was developed and the excitation voltages predicted by the model were applied to the array prototypes made of PZT 27 ceramic. Symmetric and asymmetric linear phased arrays operating at approximately 450 kHz were tested in the feasibility study. The studies were carried out at low frequency to facilitate the fabrication of the transducer arrays and to check the feasibility in this case. The novelty of our approach is to offer active cancellation of crosstalk in transducer arrays generating continuous waves, even in the presence of fabrication defects. The experimental results showed the validity of the approach and demonstrated that crosstalk can be reduced by about 6-10 dB. In ultrasonic imaging systems, this method could be introduced by using a multichannel generator providing electrical signals containing both phased signals required to focalize and deflect the acoustic beam associated with the correction signals.

  6. Numerical hydrodynamics study around turbine array of tidal stream farm in Zhoushan, China

    Science.gov (United States)

    Yu, Zhiwen; Zhang, Jisheng; Zhai, Yanyan; Zhang, Tiantian; Zheng, Jinhai

    2017-08-01

    In recent decades, great efforts have been made to efficiently explore tidal stream energy due to its unique advantages of easy prediction and great potential. China recently launched a national tidal stream farm demonstration project in the waterway between Putuoshan and Hulu Islands in the Zhoushan area. Before deployment of the turbine array, it is necessary to understand the hydrodynamic changes associated with the construction of a turbine array. In this study, we developed a depth-averaged hydrodynamics model that solves the shallow water governing equations to simulate the tidal hydrodynamics around the Zhoushan Archipelago. The simulation results agree with field data in terms of the water elevation and stream velocity. We considered two types of turbine arrays in this study and investigated their impacts on the local hydrodynamics. In general, the stream velocity in the northern and southern areas is reduced due to the power take-off of the turbine array, whereas stream velocity in the western and eastern areas is slightly increased due to the blockage impact of the turbine array.

  7. Design of a HIFU array for the treatment of deep venous thrombosis: a simulation study

    Science.gov (United States)

    Smirnov, Petr; Hynynen, Kullervo

    2017-08-01

    Deep venous thrombosis of the iliofemoral veins is a common and morbid disease, with the recommended interventional treatment carrying a high risk of hemorrhaging and complications. High intensity focused ultrasound delivered with a single element transducer has been shown to successfully precipitate thrombolysis non-invasively in vitro and in vivo. However, in all previous studies damage to the veins or surrounding tissue has been observed. Using a simulation model of the human thigh, this study investigated whether a phased array device could overcome the large focal region limitations faced by single transducer treatment devices. Effects of the size, shape and frequency of the array on its focal region were considered. It was found that a λ/2 spaced array of 7680 elements operating at 500 kHz could consistently focus to a region fully contained within the femoral vein. Furthermore, it is possible to reduce the number of elements required by building arrays operating at lower frequencies. The results suggest that phased transducer arrays hold potential for developing a safe, non-invasive treatment of thrombolysis.

  8. Parametric study of radiative heat transfer in arrays of fixed discrete surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Antoniak, Z.I.; Palmer, B.J.; Drost, M.K. [Pacific Northwest Lab., Richland, WA (United States); Welty, J.R. [Oregon State Univ., Corvallis, OR (United States)

    1996-02-01

    The parameter space for study of radiative transfer in and through arrays of regular elements is extremely large. The present study has developed a number of correlations, based on MCLITE code results for simple geometric elements. These correlations can guide a designer of heat exchangers in optimizing performance. When the incident radiation is diffuse, these correlations are fairly accurate. When the incident radiation is collimated, and strikes the array at some arbitrary angle, the correlations are less accurate. For detailed analysis of heat exchanger performance there is no substitute for exercising a code such as MCLITE. 4 refs., 3 figs., 3 tabs.

  9. The european FAZIA initiative: a high-performance digital telescope array for heavy-ion studies

    CERN Document Server

    Casini, G; Pasquali, G; Pastore, G; Bini, M; Carboni, S; Olmi, A; Piantelli, S; Poggi, G; Stefanini, A; Valdre', S; Bonnet, E; Borderie, B; Bougault, R; Bruno, M; Chbihi, A; Cinausero, M; Degerlier, M; Edelbruck, P; Frankland, J D; Gramegna, F; Gruyer, D; Guerzoni, M; Kordjasz, A; Kozik, T; Neindre, N Le; Lopez, O; Marchi, T; Marini, P; Morelli, L; Ordine, A; Parlog, M; Rivet, M F; Rosato, E; Salomon, F; Spadaccini, G; Twarog, T; Vient, E; Vigilante, M

    2013-01-01

    The european Fazia collaboration aims at building a new modular array for charged product identification to be employed for heavy-ion studies. The elementary module of the array is a Silicon-Silicon-CsI telescope, optimized for ion identification also via pulse shape analysis. The achievement of top performances imposes specific electronics which has been developed by FAZIA and features high quality charge and current preamplifiers, coupled to fully digital front-end. During the initial R&D phase, original and novel solutions have been tested in prototypes, obtaining unprecedented ion identification capabilities. FAZIA is now constructing a demonstrator array consisting of about two hundreds telescopes arranged in a compact and transportable configuration. In this contribution, we mainly summarize some aspects studied by FAZIA to improve the ion identification. Then we will briefly discuss the FAZIA program centered on experiments to be done with the demonstrator. First results on the isospin dynamics obt...

  10. Exon Array Analysis using re-defined probe sets results in reliable identification of alternatively spliced genes in non-small cell lung cancer

    Directory of Open Access Journals (Sweden)

    Gröne Jörn

    2010-11-01

    Full Text Available Abstract Background Treatment of non-small cell lung cancer with novel targeted therapies is a major unmet clinical need. Alternative splicing is a mechanism which generates diverse protein products and is of functional relevance in cancer. Results In this study, a genome-wide analysis of the alteration of splicing patterns between lung cancer and normal lung tissue was performed. We generated an exon array data set derived from matched pairs of lung cancer and normal lung tissue including both the adenocarcinoma and the squamous cell carcinoma subtypes. An enhanced workflow was developed to reliably detect differential splicing in an exon array data set. In total, 330 genes were found to be differentially spliced in non-small cell lung cancer compared to normal lung tissue. Microarray findings were validated with independent laboratory methods for CLSTN1, FN1, KIAA1217, MYO18A, NCOR2, NUMB, SLK, SYNE2, TPM1, (in total, 10 events and ADD3, which was analysed in depth. We achieved a high validation rate of 69%. Evidence was found that the activity of FOX2, the splicing factor shown to cause cancer-specific splicing patterns in breast and ovarian cancer, is not altered at the transcript level in several cancer types including lung cancer. Conclusions This study demonstrates how alternatively spliced genes can reliably be identified in a cancer data set. Our findings underline that key processes of cancer progression in NSCLC are affected by alternative splicing, which can be exploited in the search for novel targeted therapies.

  11. Arrays in rays: terminal addition in echinoderms and its correlation with gene expression.

    Science.gov (United States)

    Mooi, Rich; David, Bruno; Wray, Gregory A

    2005-01-01

    The echinoderms are deuterostomes that superimpose radial symmetry upon bilateral larval morphology. Consequently, they are not the first animals that come to mind when the concepts of segmentation and terminal addition are being discussed. However, it has long been recognized that echinoderms have serial elements along their radii formed in accordance with the ocular plate rule (OPR). The OPR is a special case of terminal growth, forming elements of the ambulacra that define the rays in echinoderms. New elements are added at the terminus of the ray, which may or may not be marked by a calcified element called the terminal plate (the "ocular" of sea urchins). The OPR operates in every echinoderm, from the occasionally bizarre fossils of the Cambrian to the most familiar extant taxa. Using the OPR and other criteria of recognition, echinoderm body wall can be divided into two main regions: extraxial components are associated with the somatocoels, axial components (formed in accordance with the OPR) with the hydrocoel. We compare patterns of development in axial regions of echinoderms with those found in the anterior-posterior axes of the earliest echinoderms as well as other invertebrates. Although axial and extraxial skeletons appear to be composed of the same biomineral matrix, the genes involved in patterning these two skeletal components are likely distinct. During development of the axial skeleton, for instance, the genes engrailed and orthodenticle are expressed in spatial and temporal patterns consistent with the OPR. Other genes such as distal-less seem to demarcate early ontogenetic boundaries between the axial rudiment and the extraxial larval body. There is a complex and pervasive reorganization of gene expression domains to produce the highly divergent morphologies seen in the Echinodermata. We integrate morphological and genetic information, particularly with respect to the origins of radial symmetry in the rudiment, and the concomitant development of

  12. Recent advances in theoretical and numerical studies of wire array Z-pinch in the IAPCM

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Ning, E-mail: ding-ning@iapcm.ac.cn; Zhang, Yang, E-mail: ding-ning@iapcm.ac.cn; Xiao, Delong, E-mail: ding-ning@iapcm.ac.cn; Wu, Jiming, E-mail: ding-ning@iapcm.ac.cn; Huang, Jun, E-mail: ding-ning@iapcm.ac.cn; Yin, Li, E-mail: ding-ning@iapcm.ac.cn; Sun, Shunkai, E-mail: ding-ning@iapcm.ac.cn; Xue, Chuang, E-mail: ding-ning@iapcm.ac.cn; Dai, Zihuan, E-mail: ding-ning@iapcm.ac.cn; Ning, Cheng, E-mail: ding-ning@iapcm.ac.cn; Shu, Xiaojian, E-mail: ding-ning@iapcm.ac.cn; Wang, Jianguo, E-mail: ding-ning@iapcm.ac.cn; Li, Hua, E-mail: ding-ning@iapcm.ac.cn [Institute of Applied Physics and Computational Mathematics, Beijing 100088 (China)

    2014-12-15

    Fast Z-pinch has produced the most powerful X-ray radiation source in laboratory and also shows the possibility to drive inertial confinement fusion (ICF). Recent advances in wire-array Z-pinch researches at the Institute of Applied Physics and Computational Mathematics are presented in this paper. A typical wire array Z-pinch process has three phases: wire plasma formation and ablation, implosion and the MRT instability development, stagnation and radiation. A mass injection model with azimuthal modulation coefficient is used to describe the wire initiation, and the dynamics of ablated plasmas of wire-array Z-pinches in (r, θ) geometry is numerically studied. In the implosion phase, a two-dimensional(r, z) three temperature radiation MHD code MARED has been developed to investigate the development of the Magneto-Rayleigh-Taylor(MRT) instability. We also analyze the implosion modes of nested wire-array and find that the inner wire-array is hardly affected before the impaction of the outer wire-array. While the plasma accelerated to high speed in the implosion stage stagnates on the axis, abundant x-ray radiation is produced. The energy spectrum of the radiation and the production mechanism are investigated. The computational x-ray pulse shows a reasonable agreement with the experimental result. We also suggest that using alloyed wire-arrays can increase multi-keV K-shell yield by decreasing the opacity of K-shell lines. In addition, we use a detailed circuit model to study the energy coupling between the generator and the Z-pinch implosion. Recently, we are concentrating on the problems of Z-pinch driven ICF, such as dynamic hohlraum and capsule implosions. Our numerical investigations on the interaction of wire-array Z-pinches on foam convertors show qualitative agreements with experimental results on the “Qiangguang I” facility. An integrated two-dimensional simulation of dynamic hohlraum driven capsule implosion provides us the physical insights of wire-array

  13. Recent advances in theoretical and numerical studies of wire array Z-pinch in the IAPCM

    Science.gov (United States)

    Ding, Ning; Zhang, Yang; Xiao, Delong; Wu, Jiming; Huang, Jun; Yin, Li; Sun, Shunkai; Xue, Chuang; Dai, Zihuan; Ning, Cheng; Shu, Xiaojian; Wang, Jianguo; Li, Hua

    2014-12-01

    Fast Z-pinch has produced the most powerful X-ray radiation source in laboratory and also shows the possibility to drive inertial confinement fusion (ICF). Recent advances in wire-array Z-pinch researches at the Institute of Applied Physics and Computational Mathematics are presented in this paper. A typical wire array Z-pinch process has three phases: wire plasma formation and ablation, implosion and the MRT instability development, stagnation and radiation. A mass injection model with azimuthal modulation coefficient is used to describe the wire initiation, and the dynamics of ablated plasmas of wire-array Z-pinches in (r, θ) geometry is numerically studied. In the implosion phase, a two-dimensional(r, z) three temperature radiation MHD code MARED has been developed to investigate the development of the Magneto-Rayleigh-Taylor(MRT) instability. We also analyze the implosion modes of nested wire-array and find that the inner wire-array is hardly affected before the impaction of the outer wire-array. While the plasma accelerated to high speed in the implosion stage stagnates on the axis, abundant x-ray radiation is produced. The energy spectrum of the radiation and the production mechanism are investigated. The computational x-ray pulse shows a reasonable agreement with the experimental result. We also suggest that using alloyed wire-arrays can increase multi-keV K-shell yield by decreasing the opacity of K-shell lines. In addition, we use a detailed circuit model to study the energy coupling between the generator and the Z-pinch implosion. Recently, we are concentrating on the problems of Z-pinch driven ICF, such as dynamic hohlraum and capsule implosions. Our numerical investigations on the interaction of wire-array Z-pinches on foam convertors show qualitative agreements with experimental results on the "Qiangguang I" facility. An integrated two-dimensional simulation of dynamic hohlraum driven capsule implosion provides us the physical insights of wire-array

  14. A new method of preparing fiber-optic DNA biosensor and its array for gene detection

    Institute of Scientific and Technical Information of China (English)

    JIANG; Guangfen; (

    2001-01-01

    , 1146(1): 136.[12] Howlett, N. G., Avery, S. V., Relationship between cadmium sensitivity and degree of plasma membrane fatty acid unsatu-ration in Saccharomyces cerevisiae, Appl. Microbiol. Biotechnol., 1997, 48(4): 539.[13] Petriz, J., Oconnor, J. E., Carmona, M. et al., Is Rhodamine-123 an appropriate fluorescent probe to assess P-glycoprotein mediated multidrug resistance in vinblastine-resistant CHO cells? Analytical Cellular Pathology, 1997, 14(3): 129.[14] Leonce, S., Burbridge, M., Flow cytometry: a useful technique in the study of multidrug resistance, J. Bio. Cell, 1993, 78(1-2): 63.[15] Le Moyec, L., Tatoud, R., Degorges, A. et al., Proton nuclear magnetic resonance spectroscopy reveals cellular lipids in-volved in resistance to Adriamycin and Taxol by the K562 Leukemia cell line, Cancer Res., 1996, 56: 3461.[16] Callaghan, R., Stafford, A., Epand, R. M., Increased accumulation of drugs in a multidrug resistant cell line by alteration of membrane biophysical properties, Biochim. Biophys. Acta, 1993, 1175(3): 277.[17] Sinicrope, F. A., Dudeia, P. K., Bissommette, B. M. et al., Modulation of P-glycoprotein-mediated drug transport by al-terations in lipid fluidity of rat liver canlicular membrane vesicles, J. Biol. Chem., 1992, 267(35): 24995.[18] Romsicki, Y., Sharom, F. J., The membrane lipid environment modulates drug interactions with the P-glycoprotein multi-drug transporter, Biochemistry, 1999, 38(21): 6887.[19] Garel, O., Lecureur, V., Guillouzo, A., The P-glycoprotein multidrug transporter, Gen. Pharmacol., 1996, 27(8): 1283.[20] Aran, J. M., Pastan, I., Gottesman, M. M., Therapeutic strategies involving the multidrug resistance phenotype: the MDR1 gene as target, chemoprotectant, and selectable marker in gene therapy, Adv. Pharmacol., 1999, 46: 1.[21] Zaman, G. J., Flens, M. J., Vanleusden, M. R. et al., The human multidrug resistance-associated protein (MRP) is a plasma membrane drug efflux pump, Proc. Natl. Acad

  15. Theoretical study of acoustic field patterns of 2-D ultrasound phased arrays for hyperthermia therapy

    Institute of Scientific and Technical Information of China (English)

    HUO Jian; ZHANG Wei; SHI Keren

    2005-01-01

    Acoustic field patterns of 2-D ultrasound phased arrays for the high intensity focused ultrasound (HIFU) hyperthermia therapy are studied, and controlling algorithms of field patterns are provided. The 2-D phased array using the conventional single-focus scanning pattern can exactly control the focal distance and the steering direction of the beam, but in general produce a single focus. Extremely high intensity levels will be needed when this pattern is used to treat large tumors. However, a direct synthesis method of the acoustic field based on the pseudo-inverse matrix can produce the multiple-focus field pattern. The rectangular radiator method of the acoustic field was used to simulate the single-focus scanning pattern and the multiple-focus pattern which are produced by a 2-D phased array consisting of 20×20 elements,and simulation results show that the 2-D array using the multiple-focus pattern can produce several foci with lower intensity levels simultaneously. Furthermore, the improved eigenvector algorithm was used to optimize the intensity gain of the multiple-focus pattern. It is shown to increase the power deposition in the target volume and eliminate the undesired interference.And the multiple-focus pattern also allows the complex excitation vector to be weighted to increase the array excitation efficiency, and therefore we can only control the phase distribution of the excitation vector to realize the phase-only multiple-focus pattern synthesis.

  16. Dual Langmuir-probe array for 3D plasma studies in TORPEX

    Science.gov (United States)

    Baquero-Ruiz, M.; Avino, F.; Chellai, O.; Fasoli, A.; Furno, I.; Jacquier, R.; Manke, F.; Patrick, S.

    2016-11-01

    We have designed and installed a new Langmuir-probe (LP) array diagnostic to determine basic three-dimensional (3D) features of plasmas in TORPEX. The diagnostic consists of two identical LP arrays, placed on opposite sides of the apparatus, which provide comprehensive coverage of the poloidal cross section at the two different toroidal locations. Cross correlation studies of signals from the arrays provide a basic way to extract 3D information from the plasmas, as experiments show. Moreover, the remarkable signal-to-noise performance of the front-end electronics allows us to follow a different approach in which we combine information from all probes in both arrays to reconstruct elementary 3D plasma structures at each acquisition time step. Then, through data analysis, we track the structures as they evolve in time. The LP arrays include a linear-motion mechanism that can displace radially the probes located on the low field side for experiments that require fine-tuning of the probe locations, and for operational compatibility with the recently installed in-vessel toroidal conductor.

  17. Transcriptome sequencing study implicates immune-related genes differentially expressed in schizophrenia: new data and a meta-analysis

    Science.gov (United States)

    Sanders, A R; Drigalenko, E I; Duan, J; Moy, W; Freda, J; Göring, H H H; Gejman, P V

    2017-01-01

    We undertook an RNA sequencing (RNAseq)-based transcriptomic profiling study on lymphoblastoid cell lines of a European ancestry sample of 529 schizophrenia cases and 660 controls, and found 1058 genes to be differentially expressed by affection status. These differentially expressed genes were enriched for involvement in immunity, especially the 697 genes with higher expression in cases. Comparing the current RNAseq transcriptomic profiling to our previous findings in an array-based study of 268 schizophrenia cases and 446 controls showed a highly significant positive correlation over all genes. Fifteen (18%) of the 84 genes with significant (false discovery rateRNAseq and array data sets (797 cases and 1106 controls) showed 169 additional genes (besides those found in the primary RNAseq-based analysis) to be differentially expressed, and provided further evidence of immune gene enrichment. In addition to strengthening our previous array-based gene expression differences in schizophrenia cases versus controls and providing transcriptomic support for some genes implicated by other approaches for schizophrenia, our study detected new genes differentially expressed in schizophrenia. We highlight RNAseq-based differential expression of various genes involved in neurodevelopment and/or neuronal function, and discuss caveats of the approach. PMID:28418402

  18. Hygroscopic particle behavior studied by interdigitated array microelectrode impedance sensors.

    Science.gov (United States)

    Schindelholz, Eric; Tsui, Lok-kun; Kelly, Robert G

    2014-01-09

    The hygroscopic behavior of soluble salts bears importance in many research fields including atmospheric sciences, corrosion, porous building materials, and pharmaceuticals. Several methods have been used to study deliquescence (solid to liquid) and efflorescence (liquid to solid) phase transitions of these salts. In this study, we measured the deliquescence and efflorescence RH values of single salt microparticles deposited on an interdigitated microelectrode sensor via electrical impedance. The salts examined were NaCl, LiCl, NaBr, KCl, and MgCl2. Measured values were in agreement with in situ optical microscopic observations and, with the exception of MgCl2, literature values. In the case of MgCl2, deliquescence occurred at 33% RH and 12-15% RH, with the latter range being previously unreported. The depressed deliquescence RH was hypothesized to be a result of the formation of a metastable MgCl2 hydrate. Incomplete efflorescence of MgCl2 was also observed after exposure to <1.5% RH for up to 22 h due to formation of solid shells which trapped fluid. The phenomena elucidated by these results provide an explanation for the anomalous water retention and uptake behavior of MgCl2 below 33% RH reported elsewhere in the literature. The results presented in this study validate the use of this method as an alternative or complementary method for study of bulk-phase transitions of substrate-deposited particles across a broad RH range. These findings also demonstrate the utility of this method for detection of fluid trapping which cannot be directly ascertained by gravimetric and line-of-sight techniques commonly used in the study of hygroscopic particles.

  19. Numerical study of jets produced by conical wire arrays on the Magpie pulsed power generator

    Science.gov (United States)

    Bocchi, M.; Chittenden, J. P.; Ciardi, A.; Suzuki-Vidal, F.; Hall, G. N.; de Grouchy, P.; Lebedev, S. V.; Bott, S. C.

    2011-11-01

    The aim of this work is to model the jets produced by conical wire arrays on the MAGPIE generator, and to design and test new setups to strengthen the link between laboratory and astrophysical jets. We performed the modelling with direct three-dimensional magneto-hydro-dynamic numerical simulations using the code GORGON. We applied our code to the typical MAGPIE setup and we successfully reproduced the experiments. We found that a minimum resolution of ˜100 μm is required to retrieve the unstable character of the jet. We investigated the effect of changing the number of wires and found that arrays with less wires produce more unstable jets, and that this effect has magnetic origin. Finally, we studied the behaviour of the conical array together with a conical shield on top of it to reduce the presence of unwanted low density plasma flows. The resulting jet is shorter and less dense.

  20. Online charge calibration of LHAASO-WCDA---a study with the engineering array

    CERN Document Server

    Bo, Gao; Ming-Hao, Gu; Xin-Jun, Hao; Hui-Cai, Li; Han-Rong, Wu; Zhi-Guo, Yao; Xiao-Hao, You

    2013-01-01

    LHAASO-WCDA is a large ground-based water Cherenkov detector array planned to be built at Shangri-La, Yunnan Province, China. As a major component of LHAASO project, the main purpose of LHAASO-WCDA is to survey the northern sky for very-high-energy (above 100 GeV) gamma ray sources. To gain full knowledge of water Cherenkov technique and to well investigate engineering issues, a 9-cell detector array has been built at Yang-Ba-Jing site, neighboring to the ARGO-YBJ experiment. With the array, charge calibration methods for low and high ranges of the PMT readout are studied, whose result shows that a very high precision at several percentages can be reached. These calibration methods are proposed to be applied in the future LHAASO-WCDA project.

  1. Numerical study of jets produced by conical wire arrays on the Magpie pulsed power generator

    CERN Document Server

    Bocchi, M; Ciardi, A; Suzuki-Vidal, F; Hall, G N; de Grouchy, P; Lebedev, S V; Bott, S C

    2011-01-01

    The aim of this work is to model the jets produced by conical wire arrays on the MAGPIE generator, and to design and test new setups to strengthen the link between laboratory and astrophysical jets. We performed the modelling with direct three-dimensional magneto-hydro-dynamic numerical simulations using the code GORGON. We applied our code to the typical MAGPIE setup and we successfully reproduced the experiments. We found that a minimum resolution of approximately 100 is required to retrieve the unstable character of the jet. We investigated the effect of changing the number of wires and found that arrays with less wires produce more unstable jets, and that this effect has magnetic origin. Finally, we studied the behaviour of the conical array together with a conical shield on top of it to reduce the presence of unwanted low density plasma flows. The resulting jet is shorter and less dense.

  2. A 91 kb microdeletion at Xq26.2 involving the GPC3 gene in a female fetus with Simpson-Golabi-Behmel syndrome detected by prenatal arrayCGH

    DEFF Research Database (Denmark)

    Ramsing, Mette; Becher, Naja Helene; Christensen, Rikke

    A 91 kb microdeletion at Xq26.2 involving the GPC3 gene in a female fetus with Simpson-Golabi-Behmel syndrome detected by prenatal arrayCGH......A 91 kb microdeletion at Xq26.2 involving the GPC3 gene in a female fetus with Simpson-Golabi-Behmel syndrome detected by prenatal arrayCGH...

  3. Advanced studies on human gene ZNF322

    Institute of Scientific and Technical Information of China (English)

    LI Yongqing; WANG Yuequn; YUAN Wuzhou; DENG Yun; ZHU Chuanbing; WU Xiushan

    2007-01-01

    The human novel gene of ZNF322 is cloned from human fetal eDNA library using the primers on the basis of the ZNF322 sequence analyzed with computer.The gene is located on Chromosome 6p22.1,and encodes a protein consisting of 402 amino acid residues and containing nine tandem C2H2-type zinc-finger motifs.Northern blot result shows that the gene is expressed in all examined adult tissues.Subcellular location study indicates that ZNF322-EGFP fusion protein is distributed in the nucleus and cytoplasm.Reporter gene assays show that ZNF322 is a potential transcriptional activator.

  4. STUDIES OF FCC HEISENBERG ANTIFERROMAGNETS BY MONTE CARLO SIMULATION ON LARGE SPIN ARRAYS

    OpenAIRE

    Minor, W.; Giebultowicz, T.

    1988-01-01

    We report Monte Carlo studies of fcc Heisenberg antiferromagnets carried out on arrays with 108,000 spins. A lattice with only JNN ≠ 0 was found to exhibit a Type I AF order despite the disordered nature of its ground state. Contrary to previous reports, our data indicate in this case a first order phase transition.

  5. Field Study on the Effects of Waves and Currents on a Distributed Explosive Array

    Science.gov (United States)

    1993-12-01

    taken during each deployment. Table 1 Summary of Video Camera Resources Used During Study Camra ID [LoGato Formal Availabilty BWTEL Top of tower Black... usage . First, the offshore-flowing current would help extend the array seaward from the rocket anchors while reducing the longshore deformation

  6. Synthesis Study of a 6-Element Non-Uniform Array with Tilted Elements for CLARREO Project

    Science.gov (United States)

    Jamnejad, Vahraz; Hoorfar, Ahmad

    2012-01-01

    This paper presents the results of a preliminary study of the gain/pattern properties of a 6-element Radio Occultation (RO) array for the proposed CLARREO (Climate Absolute Radiance and Refractivity Observatory (CLARREO) Project. CLARREO is one of the 4 highest priority missions recommended in the National Research Council Earth Science Decadal Survey.

  7. Hybrid Enrichment Verification Array: Module Characterization Studies Version 2

    Energy Technology Data Exchange (ETDEWEB)

    Zalavadia, Mital A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Smith, Leon E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); McDonald, Benjamin S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kulisek, Jonathan A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mace, Emily K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Deshmukh, Nikhil S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-12-01

    The work presented in this report is focused on the characterization and refinement of the HEVA approach, which combines the traditional 186-keV 235U signature with high-energy prompt gamma rays from neutron capture in the detector and surrounding collimator material, to determine the relative enrichment and 235U mass of the cylinder. The design of the HEVA modules (hardware and software) deployed in the current field trial builds on over seven years of study and evolution by PNNL and consists of a ø3''×3'' NaI(Tl) scintillator coupled to an Osprey digital multi-channel analyzer tube base from Canberra. In comparison to previous versions, the new design boosts the high energy prompt gamma-ray signature, provides more flexible and effective collimation, and improves count-rate management via commercially available pulse-processing electronics with a special modification prompted by PNNL.

  8. Parametric Studies Of Lightweight Reflectors Supported On Linear Actuator Arrays

    Science.gov (United States)

    Seibert, George E.

    1987-10-01

    This paper presents the results of numerous design studies carried out at Perkin-Elmer in support of the design of large diameter controllable mirrors for use in laser beam control, surveillance, and astronomy programs. The results include relationships between actuator location and spacing and the associated degree of correctability attainable for a variety of faceplate configurations subjected to typical disturbance environments. Normalizations and design curves obtained from closed-form equations based on thin shallow shell theory and computer based finite-element analyses are presented for use in preliminary design estimates of actuator count, faceplate structural properties, system performance prediction and weight assessments. The results of the analyses were obtained from a very wide range of mirror configurations, including both continuous and segmented mirror geometries. Typically, the designs consisted of a thin facesheet controlled by point force actuators which in turn were mounted on a structurally efficient base panel, or "reaction structure". The faceplate materials considered were fused silica, ULE fused silica, Zerodur, aluminum and beryllium. Thin solid faceplates as well as rib-reinforced cross-sections were treated, with a wide variation in thickness and/or rib patterns. The magnitude and spatial frequency distribution of the residual or uncorrected errors were related to the input error functions for mirrors of many different diameters and focal ratios. The error functions include simple sphere-to-sphere corrections, "parabolization" of spheres, and higher spatial frequency input error maps ranging from 0.5 to 7.5 cycles per diameter. The parameter which dominates all of the results obtained to date, is a structural descriptor of thin shell behavior called the characteristic length. This parameter is a function of the shell's radius of curvature, thickness, and Poisson's ratio of the material used. The value of this constant, in itself

  9. Human cell-based micro electrode array platform for studying neurotoxicity

    Directory of Open Access Journals (Sweden)

    Laura eYlä-Outinen

    2010-09-01

    Full Text Available At present, most of the neurotoxicological analyses are based on in vitro and in vivo models utilizing animal cells or animal models. In addition, the used in vitro models are mostly based on molecular biological end-point analyses. Thus, for neurotoxicological screening, human cell-based analysis platforms in which the functional neuronal networks responses for various neurotoxicants can be also detected real-time are highly needed. Microelectrode array (MEA is a method which enables the measurement of functional activity of neuronal cell networks in vitro for long periods of time. Here, we utilize MEA to study the neurotoxicity of methyl mercury chloride (MeHgCl, concentrations 0.5-500 nM to human embryonic stem cell (hESC-derived neuronal cell networks exhibiting spontaneous electrical activity. The neuronal cell cultures were matured on MEAs into networks expressing spontaneous spike train-like activity before exposing the cells to MeHgCl for 72 hours. MEA measurements were performed acutely and 24, 48, and 72 hours after the onset of the exposure. Finally, exposed cells were analyzed with traditional molecular biological methods for cell proliferation, cell survival, and gene and protein expression. Our results show that 500 nM MeHgCl decreases the electrical signaling and alters the pharmacologic response of hESC-derived neuronal networks in delayed manner whereas effects can not be detected with qRT-PCR, immunostainings, or proliferation measurements. Thus, we conclude that human cell-based MEA-platform is a sensitive online method for neurotoxicological screening.

  10. High-resolution array CGH profiling identifies Na/K transporting ATPase interacting 2 (NKAIN2 as a predisposing candidate gene in neuroblastoma.

    Directory of Open Access Journals (Sweden)

    Paolo Romania

    Full Text Available Neuroblastoma (NB, the most common solid cancer in early childhood, usually occurs sporadically but also its familial occurance is known in 1-2% of NB patients. Germline mutations in the ALK and PHOX2B genes have been found in a subset of familial NBs. However, because some individuals harbouring mutations in these genes do not develop this tumor, additional genetic alterations appear to be required for NB pathogenesis. Herein, we studied an Italian family with three NB patients, two siblings and a first cousin, carrying an ALK germline-activating mutation R1192P, that was inherited from their unaffected mothers and with no mutations in the PHOX2B gene. A comparison between somatic and germline DNA copy number changes in the two affected siblings by a high resolution array-based Comparative Genomic Hybridization (CGH analysis revealed a germline gain at NKAIN2 (Na/K transporting ATPase interacting 2 locus in one of the sibling, that was inherited from the parent who does not carry the ALK mutation. Surprisingly, NKAIN2 was expressed at high levels also in the affected sibling that lacks the genomic gain at this locus, clearly suggesting the existance of other regulatory mechanisms. High levels of NKAIN2 were detected in the MYCN-amplified NB cell lines and in the most aggressive NB lesions as well as in the peripheral blood of a large cohort of NB patients. Consistent with a role of NKAIN2 in NB development, NKAIN2 was down-regulated during all-trans retinoic acid differentiation in two NB cell lines. Taken together, these data indicate a potential role of NKAIN2 gene in NB growth and differentiation.

  11. A statistical study of traveling convection vortices using the Magnetometer Array for Cusp and Cleft Studies

    Science.gov (United States)

    Zesta, E.; Hughes, W. J.; Engebretson, M. J.

    2002-10-01

    The Magnetometer Array for Cusp and Cleft Studies (MACCS) is primarily a longitudinal magnetometer array located in the eastern Canadian arctic at cusp latitudes. We present a statistical study of traveling convection vortices (TCVs) as observed by MACCS from the first year of operations, August 1992 to July 1993. For this period, data are routinely available from three stations, extending more than 2 hours in magnetic local time (MLT) and located roughly on a line of constant geomagnetic latitude at 75°. With the selection criteria used, we find an average of 38 TCV events per month. We characterize the events as "isolated" and "nonisolated". The isolated events have the typical, accepted signature of a TCV while the nonisolated ones are events that satisfy the selection criteria but occur among relatively strong magnetic activity. The diurnal distribution of these events shows a prenoon-afternoon asymmetry, but the distribution has a single peak at 10 MLT and then falls off smoothly in the afternoon hours. It does not show the previously reported minimum of event occurrence around magnetic local noon except for isolated events occurring during higher Kp values. The most likely explanation for this discrepancy is the wide longitudinal extent of MACCS. The majority of the events have propagation velocities between 3 and 11 km/s, which can be a factor of 2 larger than the events reported in previous studies. The majority of the events move away from noon, as is expected, with a small fraction moving toward noon. Most (80%) of the studied events exhibit all the characteristics of a typical TCV, while the remaining 20% show some form of irregularity. We find four different types of irregularities. The isolated and nonisolated events have many similar morphological and propagation characteristics. However, quantitative comparison of the statistical distributions of the two types of TCVs indicates that they belong to different populations. We also find that nonisolated

  12. Study of the characteristics of a scintillation array and single pixels for nuclear medicine imaging applications

    Institute of Scientific and Technical Information of China (English)

    ZHU Jie; MA Hong-Guang; MA Wen-Yan; ZENG Hui; WANG Zhao-Min; XU Zi-Zong

    2009-01-01

    By using a pixelized Nal(T1) crystal array coupled to a R2486 PSPMT, the characteristics of the array and of a single pixel, such as the light output, energy resolution, peak-to-valley ratio (P/V) and imaging performance of the detector were studied. The pixel size of the NaI(TI) scintillation pixel array is 2 min×2 mm×5 mm. There are in total 484 pixels in a 22~22 matrix. In the pixel spectrum an average peak-to-valley ratio (P/V) of 16 was obtained. In the image of all the pixels, good values for the Peak-to-Valley ratios could be achieved, namely a mean of 17, a maximum of 45 and the average peak FWHM (the average value of intrinsic spatial resolution) of 2.3 mm. However, the PSPMT non-uniform response and the scintillation pixels array inhomogeneities degrade the imaging performance of the detector.

  13. hsp70 genes in the human genome: Conservation and differentiation patterns predict a wide array of overlapping and specialized functions

    Directory of Open Access Journals (Sweden)

    Macario Alberto JL

    2008-01-01

    Full Text Available Abstract Background Hsp70 chaperones are required for key cellular processes and response to environmental changes and survival but they have not been fully characterized yet. The human hsp70-gene family has an unknown number of members (eleven counted over ten years ago; some have been described but the information is incomplete and inconsistent. A coherent body of knowledge encompassing all family components that would facilitate their study individually and as a group is lacking. Nowadays, the study of chaperone genes benefits from the availability of genome sequences and a new protocol, chaperonomics, which we applied to elucidate the human hsp70 family. Results We identified 47 hsp70 sequences, 17 genes and 30 pseudogenes. The genes distributed into seven evolutionarily distinct groups with distinguishable subgroups according to phylogenetic and other data, such as exon-intron and protein features. The N-terminal ATP-binding domain (ABD was conserved at least partially in the majority of the proteins but the C-terminal substrate-binding domain (SBD was not. Nine proteins were typical Hsp70s (65–80 kDa with ABD and SBD, two were lighter lacking partly or totally the SBD, and six were heavier (>80 kDa with divergent C-terminal domains. We also analyzed exon-intron features, transcriptional variants and protein structure and isoforms, and modality and patterns of expression in various tissues and developmental stages. Evolutionary analyses, including human hsp70 genes and pseudogenes, and other eukaryotic hsp70 genes, showed that six human genes encoding cytosolic Hsp70s and 27 pseudogenes originated from retro-transposition of HSPA8, a gene highly expressed in most tissues and developmental stages. Conclusion The human hsp70-gene family is characterized by a remarkable evolutionary diversity that mainly resulted from multiple duplications and retrotranspositions of a highly expressed gene, HSPA8. Human Hsp70 proteins are clustered into

  14. Study on the characteristics of novel optical phase array based on waveguide

    Science.gov (United States)

    Li, Li-jing; Ye, Jia-Yu; Chen, Wen

    2016-10-01

    A novel scheme of optical phase array(OPA) based on wave-guide is represented in this paper. Fiber paths is main design of system, the single mode fibers are used as transmission paths, photonic crystal fibers(PCF) are adopted as the output array, LiNbO3 wave-guide is used as the phase modulator. The system configuration have been given in the paper, performance of main device such as LiNbO3 wave-guide and PCF array are analyzed. According to the theory of OPA and electro-optical effect of LiNbO3 wave-guide, the feasibility of system have been demonstrated. By adjusting the phase shift of each LiNbO3 wave-guide, the beam deflection have been observed. Simulation experiments have been implemented to study the influence of its structure parameter on output diffraction characteristics. The results show that the inter-elements distance, the quantity of fiber core and arrangement of fiber core affect the beam steering quality including full width at half-maximum(FWHM), output intensity distribution and normalized amplitude distribution. The grating lobes can be suppressed by smaller distance, the beam scanning accuracy is improved by more units of fiber core. Then two-dimension arrangements of fiber core is analyzed. By adjusting the arrangements of the fiber core, the coupling coefficient and the coupling length between two fiber core in the PCF array are changed, which conduct the different output amplitude distribution. So the structure parameter of PCF array is main factor to the beam steering. With the development of craft for PCF, the research result will provide assistance for the design of OPA in the future.

  15. cDNA array analysis of stress-induced gene expression in barley androgenesis

    NARCIS (Netherlands)

    Maraschin, S.D.F.; Caspers, M.; Potokina, E.; Wülfert, F.; Graner, A.; Spaink, H.P.; Wang, M.

    2006-01-01

    Different aspects of androgenesis induction have been studied in detail, but little is known about the molecular mechanisms associated with this developmental switch. We have employed macroarrays containing 1421 expressed sequence tags covering the early stages of barley zygotic embryogenesis to com

  16. Hox genes and study of Hox genes in crustacean

    Institute of Scientific and Technical Information of China (English)

    HOU Lin; CHEN Zhijuan; XU Mingyu; LIN Shengguo; WANG Lu

    2004-01-01

    Homeobox genes have been discovered in many species. These genes are known to play a major role in specifying regional identity along the anterior-posterior axis of animals from a wide range of phyla.The products of the homeotic genes are a set of evolutionarily conserved transcription factors that control elaborate developmental processes and specify cell fates in metazoans. Crustacean, presenting a variety of body plans not encountered in any other class or phylum of the Metazoa, has been shown to possess a single set of homologous Hox genes like insect. The ancestral crustacean Hox gene complex comprised ten genes: eight homologous to the hometic Hox genes and two related to nonhomeotic genes presented within the insect Hox complexes. The crustacean in particular exhibits an abundant diversity segment specialization and tagmosis. This morphological diversity relates to the Hox genes. In crustacean body plan, different Hox genes control different segments and tagmosis.

  17. The utility of sparse 2D fully electronically steerable focused ultrasound phased arrays for thermal surgery: a simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Ellens, Nicholas; Pulkkinen, Aki; Song Junho; Hynynen, Kullervo, E-mail: nicholas.ellens@utoronto.ca [Department of Imaging Research, Sunnybrook Research Institute, Toronto (Canada)

    2011-08-07

    Sparse arrays are widely used in diagnostic ultrasound for their strong performance and relative technical simplicity. This simulation study assessed the efficacy of phased arrays of varied sparseness for thermal surgery, especially with regard to power consumption and near-field heating. It employs a linear ultrasound propagation model and a semi-analytical solution to the Pennes' bioheat transfer equation. The basic design had 4912 cylindrical transducers (500 kHz) arranged on a flat 12 cm disk (1.5 mm spacing). This array was compared to randomly-thinned sparse arrays with 75%, 50% and 25% populations. Temperature elevations of 60 and 70 deg. C were induced in sonication times of 5-20 s, at foci spanning depths of 50-150 mm and radii of 0-60 mm. The sparse arrays produced nearly indistinguishable focal patterns but, averaged across the foci, required 132%, 200% and 393% of the power of the full array, respectively, applied through fewer transducer elements. Comparable results were found at 1 MHz from equivalent arrays. Simulated lesions were formed (thermal dose {>=} 240 equivalent minutes at 43 deg. C (T{sub 43})) and 'transition' and 'unsafe' regions (both defined as 5 min < T{sub 43} < 240 min) were identified, the former immediately surrounding the lesion and the latter anywhere else. At a depth of 100 mm, sparse arrays were found to produce comparable lesions to the full array at the focus, but 'unsafe', over-heated near-field regions after some ablated lesion volume: about 12 mL for the 25% array, around 100 mL for the 50% array, while the 75% and full arrays produced 150 mL lesions safely.

  18. Gene set analysis for interpreting genetic studies

    DEFF Research Database (Denmark)

    Pers, Tune H

    2016-01-01

    Interpretation of genome-wide association study (GWAS) results is lacking behind the discovery of new genetic associations. Consequently, there is an urgent need for data-driven methods for interpreting genetic association studies. Gene set analysis (GSA) can identify aetiologic pathways and func......Interpretation of genome-wide association study (GWAS) results is lacking behind the discovery of new genetic associations. Consequently, there is an urgent need for data-driven methods for interpreting genetic association studies. Gene set analysis (GSA) can identify aetiologic pathways...

  19. Study of the Interaction User Head-Ultrawideband MIMO Antenna Array for Mobile Terminals

    DEFF Research Database (Denmark)

    Zhekov, Stanislav Stefanov; Tatomirescu, Alexandru; Franek, Ondrej

    2016-01-01

    aspects of the interaction are considered: 1) the influence of the user head on the antenna operation, and 2) the exposure of the human head tissue to antenna electromagnetic radiation. The first aspect is related to the degradation of the antenna performance in a proximity to the user which is evaluated......This paper presents a numerical study of the interaction between the user head and MIMO antenna array for mobile phones. The antenna array is composed of two identical antennas and covers the frequency ranges 698-990 MHz and 1710-5530 MHz with a good radiation efficiency in free space. The two...... by the reduction of the antenna radiation efficiency. The second aspect refers to the antenna operation effect on the human and the exposure of the user head is studied by Specific Absorption Ratio (SAR)....

  20. Numerical study of rotating detonation engine with an array of injection holes

    Science.gov (United States)

    Yao, S.; Han, X.; Liu, Y.; Wang, J.

    2017-05-01

    This paper aims to adopt the method of injection via an array of holes in three-dimensional numerical simulations of a rotating detonation engine (RDE). The calculation is based on the Euler equations coupled with a one-step Arrhenius chemistry model. A pre-mixed stoichiometric hydrogen-air mixture is used. The present study uses a more practical fuel injection method in RDE simulations, injection via an array of holes, which is different from the previous conventional simulations where a relatively simple full injection method is usually adopted. The computational results capture some important experimental observations and a transient period after initiation. These phenomena are usually absent in conventional RDE simulations due to the use of an idealistic injection approximation. The results are compared with those obtained from other numerical studies and experiments with RDEs.

  1. Study of the Interaction User Head-Ultrawideband MIMO Antenna Array for Mobile Terminals

    DEFF Research Database (Denmark)

    Zhekov, Stanislav Stefanov; Tatomirescu, Alexandru; Franek, Ondrej;

    2016-01-01

    This paper presents a numerical study of the interaction between the user head and MIMO antenna array for mobile phones. The antenna array is composed of two identical antennas and covers the frequency ranges 698-990 MHz and 1710-5530 MHz with a good radiation efficiency in free space. The two...... aspects of the interaction are considered: 1) the influence of the user head on the antenna operation, and 2) the exposure of the human head tissue to antenna electromagnetic radiation. The first aspect is related to the degradation of the antenna performance in a proximity to the user which is evaluated...... by the reduction of the antenna radiation efficiency. The second aspect refers to the antenna operation effect on the human and the exposure of the user head is studied by Specific Absorption Ratio (SAR)....

  2. BRB-ArrayTools Data Archive for Human Cancer Gene Expression: A Unique and Efficient Data Sharing Resource

    Directory of Open Access Journals (Sweden)

    Richard Simon

    2008-01-01

    Full Text Available The explosion of available microarray data on human cancer increases the urgency for developing methods for effectively sharing this data among clinical cancer investigators. Lack of a smooth interface between the databases and statistical analysis tools limits the potential benefits of sharing the publicly available microarray data. To facilitate the efficient sharing and use of publicly available microarray data among cancer investigators, we have built a BRB-ArrayTools Data Archive including over one hundred human cancer microarray projects for 28 cancer types. Expression array data and clinical descriptors have been imported into BRB-ArrayTools and are stored as BRB-ArrayTools project folders on the archive. The data archive can be accessed from: http://linus.nci.nih.gov/~brb/DataArchive.html Our BRB-ArrayTools data archive and GEO importer represent ongoing efforts to provide effective tools for efficiently sharing and utilizing human cancer microarray data.

  3. Monte Carlo Studies of medium-size telescope designs for the Cherenkov Telescope Array

    CERN Document Server

    Wood, M; Dumm, J; Funk, S

    2015-01-01

    We present studies for optimizing the next generation of ground-based imaging atmospheric Cherenkov telescopes (IACTs). Results focus on mid-sized telescopes (MSTs) for CTA, detecting very high energy gamma rays in the energy range from a few hundred GeV to a few tens of TeV. We describe a novel, flexible detector Monte Carlo package, FAST (FAst Simulation for imaging air cherenkov Telescopes), that we use to simulate different array and telescope designs. The simulation is somewhat simplified to allow for efficient exploration over a large telescope design parameter space. We investigate a wide range of telescope performance parameters including optical resolution, camera pixel size, and light collection area. In order to ensure a comparison of the arrays at their maximum sensitivity, we analyze the simulations with the most sensitive techniques used in the field, such as maximum likelihood template reconstruction and boosted decision trees for background rejection. Choosing telescope design parameters repre...

  4. Musett: A segmented Si array for Recoil-Decay-Tagging studies at VAMOS

    Energy Technology Data Exchange (ETDEWEB)

    Theisen, Ch., E-mail: christophe.theisen@cea.fr [CEA, Centre de Saclay, IRFU, F-91191 Gif-sur-Yvette (France); Jeanneau, F.; Sulignano, B.; Druillole, F. [CEA, Centre de Saclay, IRFU, F-91191 Gif-sur-Yvette (France); Ljungvall, J. [CSNSM, F-91405 Orsay Campus (France); Paul, B.; Virique, E.; Baron, P.; Bervas, H. [CEA, Centre de Saclay, IRFU, F-91191 Gif-sur-Yvette (France); Clément, E. [GANIL, Boulevard Henri Becquerel, BP 55027 – F-14076 CAEN Cedex 05 (France); Delagnes, E. [CEA, Centre de Saclay, IRFU, F-91191 Gif-sur-Yvette (France); Dijon, A. [GANIL, Boulevard Henri Becquerel, BP 55027 – F-14076 CAEN Cedex 05 (France); Dossat, E.; Drouart, A. [CEA, Centre de Saclay, IRFU, F-91191 Gif-sur-Yvette (France); Farget, F. [GANIL, Boulevard Henri Becquerel, BP 55027 – F-14076 CAEN Cedex 05 (France); Flouzat, Ch. [CEA, Centre de Saclay, IRFU, F-91191 Gif-sur-Yvette (France); De France, G. [GANIL, Boulevard Henri Becquerel, BP 55027 – F-14076 CAEN Cedex 05 (France); Görgen, A. [CEA, Centre de Saclay, IRFU, F-91191 Gif-sur-Yvette (France); Houarner, Ch.; Jacquot, B. [GANIL, Boulevard Henri Becquerel, BP 55027 – F-14076 CAEN Cedex 05 (France); and others

    2014-05-21

    A new segmented silicon-array called MUSETT has been built for the study of heavy elements using the Recoil-Decay-Tagging technique. MUSETT is located at the focal plane of the VAMOS spectrometer at GANIL and is used in conjunction with a γ-ray array at the target position. This paper describes the device, which consists of four 10×10 cm{sup 2} Si detectors and its associated front-end electronics based on highly integrated ASICs electronics. The triggerless readout electronics, the data acquisition and the analysis tools developed for its characterization are presented. This device was commissioned at GANIL with the EXOGAM γ-ray spectrometer using the fusion–evaporation reaction {sup 197}Au({sup 22}Ne,5n){sup 214}Ac. Additionally, the performance of the VAMOS Wien filter used during the in-beam commissioning is also reported.

  5. Cross-flow turbines: physical and numerical model studies towards improved array simulations

    Science.gov (United States)

    Wosnik, M.; Bachant, P.

    2015-12-01

    Cross-flow, or vertical-axis turbines, show potential in marine hydrokinetic (MHK) and wind energy applications. As turbine designs mature, the research focus is shifting from individual devices towards improving turbine array layouts for maximizing overall power output, i.e., minimizing wake interference for axial-flow turbines, or taking advantage of constructive wake interaction for cross-flow turbines. Numerical simulations are generally better suited to explore the turbine array design parameter space, as physical model studies of large arrays at large model scale would be expensive. However, since the computing power available today is not sufficient to conduct simulations of the flow in and around large arrays of turbines with fully resolved turbine geometries, the turbines' interaction with the energy resource needs to be parameterized, or modeled. Most models in use today, e.g. actuator disk, are not able to predict the unique wake structure generated by cross-flow turbines. Experiments were carried out using a high-resolution turbine test bed in a large cross-section tow tank, designed to achieve sufficiently high Reynolds numbers for the results to be Reynolds number independent with respect to turbine performance and wake statistics, such that they can be reliably extrapolated to full scale and used for model validation. To improve parameterization in array simulations, an actuator line model (ALM) was developed to provide a computationally feasible method for simulating full turbine arrays inside Navier--Stokes models. The ALM predicts turbine loading with the blade element method combined with sub-models for dynamic stall and flow curvature. The open-source software is written as an extension library for the OpenFOAM CFD package, which allows the ALM body force to be applied to their standard RANS and LES solvers. Turbine forcing is also applied to volume of fluid (VOF) models, e.g., for predicting free surface effects on submerged MHK devices. An

  6. Beta-delayed neutron emission studies with a C7LYC array at CARIBU

    Science.gov (United States)

    Wilson, Gemma; Chowdhury, Partha; Lister, Christopher; Brown, Tristan; Carpenter, Michael; Chillery, Thomas; Copp, Patrick; Doucet, Emery; Mitchell, Alan; Savard, Guy; Zhu, Shaofei

    2016-09-01

    This work is a study of β-delayed neutron and γ emission from 94Rb at CARIBU. Beta-delayed neutron emission studies are important in the astrophysical r-process, nuclear structure and for nuclear reactor safety and design. Approximately 150 γ rays are known in the daughter 94Sr, many of which are unplaced. An estimated 26% of γ rays are thought to be missing. The probability of β-delayed neutron emission in 94Sr is 10.2(2)%. Recently, substantial γ-decay from above the neutron separation energy in 94Rb has been reported. This research is aimed at understanding this high-lying γ-strength. The experiment employed the X-Array (a high efficiency HPGe clover array), SCANS (Small CLYC Array for Neutron Scattering) and the SATURN decay station (Scintillator And Tape Using Radioactive Nuclei) for γ, fast neutron and β-particle detection, respectively. Data were collected in a triggerless digital data acquisition system, with detected β , n , and γ events correlated offline. Techniques, analysis and first results will be discussed. Supported by the NNSA Stewardship Science Academic Alliance Program under Grant DE-NA00013008, and by US DoE, Office of Nuclear Physics, under DE-FG02-94ER40848.

  7. The european FAZIA initiative: a high-performance digital telescope array for heavy-ion studies

    Science.gov (United States)

    Casini, G.; Barlini, S.; Pasquali, G.; Pastore, G.; Bini, M.; Carboni, S.; Olmi, A.; Piantelli, S.; Poggi, G.; Stefanini, A.; Valdré, S.; Bonnet, E.; Borderie, B.; Bougault, R.; Bruno, M.; Chbihi, A.; Cinausero, M.; Degerlier, M.; Edelbruck, P.; Frankland, J. D.; Gramegna, F.; Gruyer, D.; Guerzoni, M.; Kordjasz, A.; Kozik, T.; Le Neindre, N.; Lopez, O.; Marchi, T.; Marini, P.; Morelli, L.; Ordine, A.; Pârlog, M.; Rivet, M. F.; Rosato, E.; Salomon, F.; Spadaccini, G.; Twaróg, T.; Vient, E.; Vigilante, M.

    2014-03-01

    The european Fazia collaboration aims at building a new modular array for charged product identification to be employed for heavy-ion studies. The elementary module of the array is a Silicon-Silicon-CsI telescope, optimized for ion identification including pulse shape analysis, too. The achievement of top performances imposes specific electronics which has been developed by the FAZIA collaboration and includes high quality charge and current preamplifiers, coupled to fully digital front-end. During the initial R&D phase, original and novel solutions have been tested in prototypes, obtaining unprecedented ion identification capabilities. FAZIA is now constructing a demonstrator array consisting of about two hundreds telescopes arranged in a compact and transportable configuration. In this contribution, we mainly summarize some aspects studied by FAZIA to improve the ion identification. Then we will briefly discuss the FAZIA program focused on experiments to be done with the demonstrator. First results on the isospin dynamics obtained with a reduced set-up demonstrate well the performance of the telescope and represent a good starting point towards future investigations with both stable and exotic beams.

  8. The european FAZIA initiative: a high-performance digital telescope array for heavy-ion studies

    Directory of Open Access Journals (Sweden)

    Casini G.

    2014-03-01

    Full Text Available The european Fazia collaboration aims at building a new modular array for charged product identification to be employed for heavy-ion studies. The elementary module of the array is a Silicon-Silicon-CsI telescope, optimized for ion identification including pulse shape analysis, too. The achievement of top performances imposes specific electronics which has been developed by the FAZIA collaboration and includes high quality charge and current preamplifiers, coupled to fully digital front-end. During the initial R&D phase, original and novel solutions have been tested in prototypes, obtaining unprecedented ion identification capabilities. FAZIA is now constructing a demonstrator array consisting of about two hundreds telescopes arranged in a compact and transportable configuration. In this contribution, we mainly summarize some aspects studied by FAZIA to improve the ion identification. Then we will briefly discuss the FAZIA program focused on experiments to be done with the demonstrator. First results on the isospin dynamics obtained with a reduced set-up demonstrate well the performance of the telescope and represent a good starting point towards future investigations with both stable and exotic beams.

  9. A case study on the identification of confounding factors for gene disease association analysis.

    Science.gov (United States)

    Han, Bin; Xie, Ruifei; Wu, Shixiu; Li, Lihua; Zhu, Lei

    2015-01-01

    Variation in the expression of genes arises from a variety of sources. It is important to remove sources of variation between arrays of non-biological origin. Non-biological variation, caused by lurking confounding factors, usually attracts little attention, although it may substantially influence the expression profile of genes. In this study, we proposed a method which is able to identify the potential confounding factors and highlight the non-biological variations. We also developed methods and statistical tests to study the confounding factors and their influence on the homogeneity of microarray data, gene selection, and disease classification. We explored an ovarian cancer gene expression profile and showed that data batches and arraying conditions are two confounding factors. Their influence on the homogeneity of data, gene selection, and disease classification are statistically analyzed. Experiments showed that after normalization, their influences were removed. Comparative studies further showed that the data became more homogeneous and the classification quality was improved. This research demonstrated that identifying and reducing the impact of confounding factors is paramount in making sense of gene-disease association analysis.

  10. A ChIP-on-chip tiling array approach detects functional histone-free regions associated with boundaries at vertebrate HOX genes

    Directory of Open Access Journals (Sweden)

    Surabhi Srivastava

    2014-12-01

    Full Text Available Hox genes impart segment identity to body structures along the anterior–posterior axis and are crucial for proper development. A unique feature of the Hox loci is the collinearity between the gene position within the cluster and its spatial expression pattern along the body axis. However, the mechanisms that regulate collinear patterns of Hox gene expression remain unclear, especially in higher vertebrates. We recently identified novel histone-free regions (HFRs that can act as chromatin boundary elements demarcating successive murine Hox genes and help regulate their precise expression domains (Srivastava et al., 2013. In this report, we describe in detail the ChIP-chip analysis strategy associated with the identification of these HFRs. We also provide the Perl scripts for HFR extraction and quality control analysis for this custom designed tiling array dataset.

  11. A ChIP-on-chip tiling array approach detects functional histone-free regions associated with boundaries at vertebrate HOX genes.

    Science.gov (United States)

    Srivastava, Surabhi; Sowpati, Divya Tej; Garapati, Hita Sony; Puri, Deepika; Dhawan, Jyotsna; Mishra, Rakesh K

    2014-12-01

    Hox genes impart segment identity to body structures along the anterior-posterior axis and are crucial for proper development. A unique feature of the Hox loci is the collinearity between the gene position within the cluster and its spatial expression pattern along the body axis. However, the mechanisms that regulate collinear patterns of Hox gene expression remain unclear, especially in higher vertebrates. We recently identified novel histone-free regions (HFRs) that can act as chromatin boundary elements demarcating successive murine Hox genes and help regulate their precise expression domains (Srivastava et al., 2013). In this report, we describe in detail the ChIP-chip analysis strategy associated with the identification of these HFRs. We also provide the Perl scripts for HFR extraction and quality control analysis for this custom designed tiling array dataset.

  12. A study of bacterial gene regulatory mechanisms

    DEFF Research Database (Denmark)

    Hansen, Sabine

    the different regulatory mechanisms affect system dynamics. We have designed a synthetic gene regulatory network (GRN) in bacterial cells that enables us to study the dynamics of GRNs. The results presented in this PhD thesis show that model equations based on the established mechanisms of action of each...... of a particular type of regulatory mechanism. The synthetic system presented in this thesis is, to our knowledge, the first of its kind to allow a direct comparison of the dynamic behaviors of gene regulatory networks that employ different mechanisms of regulation. In addition to studying the dynamic behavior...... of GRNs this thesis also provided the first evidence of the sensor histidine kinase VC1831 being an additional player in the Vibrio cholerae quorum sensing (QS) GRN. Bacteria use a process of cell-cell communication called QS which enable the bacterial cells to collectively control their gene expression...

  13. MEGHNAD – A multi element detector array for heavy ion collision studies

    Indian Academy of Sciences (India)

    Satyajit Saha

    2001-07-01

    In the coming decade, the expanding field of experimental nuclear physics in our country is going to see a quantum leap in research and developmental activities with new accelerator facilities like the variable energy cyclotron with ECR heavy ion source, the upcoming K-500 superconducting cyclotron, both at VECC, Calcutta, and the superconducting linac boosters at both the Pelletron Accelerator Facilities at TIFR, Mumbai and NSC, New Delhi. When heavy ion beam available from such machines fall on a target and undergo collision, very rich and often pristine fields of research open up. In order to carry on such activities, we have taken up a project to build a multi element gamma, heavy ion and neutron array of detectors (MEGHNAD) to detect and study the properties of a wide variety of particles like neutrons, protons, light mass clusters, massive ejected fragments, and gamma rays with good solid angle coverage and efficiency. Design of the detector array, performance of the prototype detector and brief outline of the research programme to be undertaken with the detector array will be discussed.

  14. Study of micro-pinches in wire-array Z pinches

    Energy Technology Data Exchange (ETDEWEB)

    Ivanov, V. V.; Papp, D.; Anderson, A. A.; Talbot, B. R.; Astanovitskiy, A. L.; Nalajala, V.; Dmitriev, O. [Department of Physics, University of Nevada, Reno, Nevada 89557 (United States); Chittenden, J. P.; Niasse, N. [Blackett Laboratory, Imperial College, London SW7 2BZ (United Kingdom); Pikuz, S. A.; Shelkovenko, T. A. [P.N. Lebedev Physical Institute, Moscow 119991 (Russian Federation)

    2013-11-15

    Bright and hot areas with a high plasma density and temperature are observed in all kinds of Z pinches. We studied bright radiating spots produced by micro-pinches in cylindrical and planar wire-arrays at the 1 MA Zebra pulsed power generator using an x-ray streak camera synchronized with laser diagnostics, x-ray time-gated pinhole camera, and spectroscopy. Hot spots with extremely dense and relatively hot plasma arise during the collapse of the micro-pinches. These hot spots radiate a continuum spectrum with energy >2.5 keV. Typical micro-pinches in Al wire arrays generate x-ray bursts with durations of 0.4–1 ns in the soft x-ray range and 0.1–0.4 ns in the keV range. UV two-frame shadowgraphy shows spatial correlation of hot spots with the collapse and explosion of micro-pinches. Micro-pinches typically occur at the necks of the Z pinch, but can demonstrate a variety of parameters and different dynamics. An analysis of x-ray streak images shows that micro-pinches can generate >20% of the x-ray energy in some types of wire-array Z pinches.

  15. Study of 1 MW PV array at the Kennedy Space Center

    Science.gov (United States)

    Dhere, Neelkanth G.; Schneller, Eric; Martin, Wayne R.; Dhere, Ramesh G.

    2016-09-01

    FP and L has deployed a 1 MW c-Si in a fenced compound at the Kennedy Space Center. Two 500 kW inverters located in an elevated and air-conditioned enclosure convert direct current (DC) to alternating current (AC). The generated power, DC and AC voltages and currents are measured and recorded. Charts of variation of PV parameters are generated for analyses. The generated power is also tabulated and reported on periodic basis. Infrared and visual images of the array, sections of the array, and of individual modules from the front and back are recorded periodically. Any interruption of power generation are recorded. The dust and corrosion on screws and frame were observed in a few modules. The temperature of active area of module is higher than that of metallic support and frame probably because of conduction of the heat by the heavy metallic structure. The 1-MW PV array is operating normally without signs of excessive degradation except for collection of dust towards the bottom of a few modules. Since these modules were not washed periodically and any cleaning was by rain. Thus the collection of dust towards the bottom of modules can be understood and does not pose a serious problem. Corrosion on screws and frame were observed in a few modules. This study if continued over a long time, will serve to follow the behavior of this reasonable size PV Plant.

  16. Study of the Photon Strength Functions for Gadolinium Isotopes with the DANCE Array

    Science.gov (United States)

    Dashdorj, D.; Mitchell, G. E.; Baramsai, B.; Chankova, R.; Chyzh, A.; Walker, C.; Agvaanluvsan, U.; Becker, J. A.; Parker, W.; Sleaford, B.; Wu, C. Y.; Bredeweg, T. A.; Couture, A.; Haight, R. C.; Jandel, M.; Rundberg, R. S.; Ullmann, J. L.; Vieira, D. J.; Wouters, J. M.; Krtička, M.; Bečvář, F.

    2009-03-01

    The gadolinium isotopes are interesting for reactor applications as well as for medicine and astrophysics. The gadolinium isotopes have some of the largest neutron capture cross sections. As a consequence they are used in the control rod in reactor fuel assembly. From the basic science point of view, there are seven stable isotopes of gadolinium with varying degrees of deformation. Therefore they provide a good testing ground for the study of deformation dependent structure such as the scissors mode. Decay gamma rays following neutron capture on Gd isotopes are detected by the DANCE array, which is located at flight path 14 at the Lujan Neutron Scattering Center at Los Alamos National Laboratory. The high segmentation and close packing of the detector array enable gamma-ray multiplicity measurements. The calorimetric properties of the DANCE array coupled with the neutron time-of-flight technique enables one to gate on a specific resonance of a specific isotope in the time-of-flight spectrum and obtain the summed energy spectrum for that isotope. The singles gamma-ray spectrum for each multiplicity can be separated by their DANCE cluster multiplicity. Various photon strength function models are used for comparison with experimentally measured DANCE data and provide insight for understanding the statistical decay properties of deformed nuclei.

  17. A study of response of a LuYAP:Ce array with innovative assembling for PET

    Energy Technology Data Exchange (ETDEWEB)

    Pani, Roberto [Department of Sciences and Medical and Surgical Biotechnology, Sapienza University of Rome, Rome (Italy); Cinti, Maria Nerina, E-mail: marianerina.cinti@uniroma1.it [Department of Molecular Medicine, Sapienza University of Rome, Rome (Italy); Scafè, Raffaele [Department of Molecular Medicine, Sapienza University of Rome, Rome (Italy); Bennati, Paolo [Department of Medical Engineering, Royal Institute of Technology (KTH), Stockholm (Sweden); Lo Meo, Sergio [ENEA, Ezio Clementel Research Center, Bologna (Italy); Preziosi, Enrico [Department of Molecular Medicine, Sapienza University of Rome, Rome (Italy); Morphofunctional Sciences – Biophysics, Doctorate School of Biology and Molecular Medicine – SAIMLAL Department, Sapienza University of Rome, Rome (Italy); Pellegrini, Rosanna [Department of Molecular Medicine, Sapienza University of Rome, Rome (Italy); De Vincentis, Giuseppe [Department of Radiological Sciences, Oncology and Anatomical Pathology, Sapienza University of Rome, Rome (Italy); Sacco, Donatella [INAIL, DIPIA, Monteporzio, Rome (Italy); Fabbri, Andrea [Department of Molecular Medicine, Sapienza University of Rome, Rome (Italy)

    2015-09-21

    We propose the characterization of a first array of 10×10 Lutetium Yttrium Orthoaluminate Perovskite (LuYAP:Ce) crystals, 2 mm×2 mm×10 mm pixel size, with an innovative assembling designed to enhance light output, uniformity and detection efficiency. The innovation consists of the use of 0.015 mm thick dielectric coating as inter-pixel light-insulators, manufactured by Crytur (Czech Republic) intended to improve crystal insulation and then light collection. Respect to the traditional treatment with 0.2 mm of white epoxy, a thinner pixel gap enhances packing fraction up to 98% with a consequent improvement of detection efficiency. Spectroscopic characterization of the array was performed by a Hamamatsu R6231 photomultiplier tube. A pixel-by-pixel scanning with a collimated {sup 99m}Tc radioisotope (140 keV photon energy) highlighted a deviation in pulse height close to 3.5% respect to the overall mean value. Meanwhile, in term of energy resolution a difference between the response of single pixel and the array of about 10% was measured. Results were also supported and validated by Monte Carlo simulations performed with GEANT4. Although the dielectric coating pixel insulator cannot overcome the inherent limitations of LuYAP crystal due to its self-absorption of light (still present), this study demonstrated that the new coating treatment allows better light collection (nearly close to the expected one) with in addition a very good uniformity between different pixels. These results confirm the high potentiality of this coating for any other crystal array suited for imaging application and new expectations for the use of LuYAP for PET systems.

  18. Development of a human mitochondrial oligonucleotide microarray (h-MitoArray and gene expression analysis of fibroblast cell lines from 13 patients with isolated F1Fo ATP synthase deficiency

    Directory of Open Access Journals (Sweden)

    Hansíková Hana

    2008-01-01

    Full Text Available Abstract Background To strengthen research and differential diagnostics of mitochondrial disorders, we constructed and validated an oligonucleotide microarray (h-MitoArray allowing expression analysis of 1632 human genes involved in mitochondrial biology, cell cycle regulation, signal transduction and apoptosis. Using h-MitoArray we analyzed gene expression profiles in 9 control and 13 fibroblast cell lines from patients with F1Fo ATP synthase deficiency consisting of 2 patients with mt9205ΔTA microdeletion and a genetically heterogeneous group of 11 patients with not yet characterized nuclear defects. Analysing gene expression profiles, we attempted to classify patients into expected defect specific subgroups, and subsequently reveal group specific compensatory changes, identify potential phenotype causing pathways and define candidate disease causing genes. Results Molecular studies, in combination with unsupervised clustering methods, defined three subgroups of patient cell lines – M group with mtDNA mutation and N1 and N2 groups with nuclear defect. Comparison of expression profiles and functional annotation, gene enrichment and pathway analyses of differentially expressed genes revealed in the M group a transcription profile suggestive of synchronized suppression of mitochondrial biogenesis and G1/S arrest. The N1 group showed elevated expression of complex I and reduced expression of complexes III, V, and V-type ATP synthase subunit genes, reduced expression of genes involved in phosphorylation dependent signaling along MAPK, Jak-STAT, JNK, and p38 MAP kinase pathways, signs of activated apoptosis and oxidative stress resembling phenotype of premature senescent fibroblasts. No specific functionally meaningful changes, except of signs of activated apoptosis, were detected in the N2 group. Evaluation of individual gene expression profiles confirmed already known ATP6/ATP8 defect in patients from the M group and indicated several candidate

  19. Detection of gene x gene interactions in genome-wide association studies of human population data

    National Research Council Canada - National Science Library

    Musani, Solomon K; Shriner, Daniel; Liu, Nianjun; Feng, Rui; Coffey, Christopher S; Yi, Nengjun; Tiwari, Hemant K; Allison, David B

    2007-01-01

    Empirical evidence supporting the commonality of gene x gene interactions, coupled with frequent failure to replicate results from previous association studies, has prompted statisticians to develop...

  20. Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling

    Directory of Open Access Journals (Sweden)

    Beuf Kristof

    2012-09-01

    Full Text Available Abstract Background Existing statistical methods for tiling array transcriptome data either focus on transcript discovery in one biological or experimental condition or on the detection of differential expression between two conditions. Increasingly often, however, biologists are interested in time-course studies, studies with more than two conditions or even multiple-factor studies. As these studies are currently analyzed with the traditional microarray analysis techniques, they do not exploit the genome-wide nature of tiling array data to its full potential. Results We present an R Bioconductor package, waveTiling, which implements a wavelet-based model for analyzing transcriptome data and extends it towards more complex experimental designs. With waveTiling the user is able to discover (1 group-wise expressed regions, (2 differentially expressed regions between any two groups in single-factor studies and in (3 multifactorial designs. Moreover, for time-course experiments it is also possible to detect (4 linear time effects and (5 a circadian rhythm of transcripts. By considering the expression values of the individual tiling probes as a function of genomic position, effect regions can be detected regardless of existing annotation. Three case studies with different experimental set-ups illustrate the use and the flexibility of the model-based transcriptome analysis. Conclusions The waveTiling package provides the user with a convenient tool for the analysis of tiling array trancriptome data for a multitude of experimental set-ups. Regardless of the study design, the probe-wise analysis allows for the detection of transcriptional effects in both exonic, intronic and intergenic regions, without prior consultation of existing annotation.

  1. Study of atmospheric gravity waves and infrasonic sources using the USArray Transportable Array pressure data

    Science.gov (United States)

    Hedlin, Michael; de Groot-Hedlin, Catherine; Hoffmann, Lars; Alexander, M. Joan; Stephan, Claudia

    2016-04-01

    The upgrade of the USArray Transportable Array (TA) with microbarometers and infrasound microphones has created an opportunity for a broad range of new studies of atmospheric sources and the large- and small-scale atmospheric structure through which signals from these events propagate. These studies are akin to early studies of seismic events and the Earth's interior structure that were made possible by the first seismic networks. In one early study with the new dataset we use the method of de Groot-Hedlin and Hedlin (2015) to recast the TA as a massive collection of 3-element arrays to detect and locate large infrasonic events. Over 2,000 events have been detected in 2013. The events cluster in highly active regions on land and offshore. Stratospherically ducted signals from some of these events have been recorded more than 2,000 km from the source and clearly show dispersion due to propagation through atmospheric gravity waves. Modeling of these signals has been used to test statistical models of atmospheric gravity waves. The network is also useful for making direct observations of gravity waves. We are currently studying TA and satellite observations of gravity waves from singular events to better understand how the waves near ground level relate to those observed aloft. We are also studying the long-term statistics of these waves from the beginning of 2010 through 2014. Early work using data bandpass filtered from 1-6 hr shows that both the TA and satellite data reveal highly active source regions, such as near the Great Lakes. de Groot-Hedlin and Hedlin, 2015, A method for detecting and locating geophysical events using clusters of arrays, Geophysical Journal International, v203, p960-971, doi: 10.1093/gji/ggv345.

  2. Improved SNR of phased-array PERES coils via simulation study

    Energy Technology Data Exchange (ETDEWEB)

    RodrIguez, Alfredo O [Centro de Investigacion en Imagenologia e Instrumentacion Medica, Universidad Autonoma Metropolitana Iztapalapa, Av. San Rafael Atlixco 186, Mexico, DF, 09340 (Mexico); Medina, LucIa [DISCA, Instituto de Investigacion en Matematicas Aplicadas y Sistemas, Universidad Nacional Autonoma de Mexico, AP 20-728, Admo. No. 20, 01000 Mexico, DF (Mexico); Facultad de Ciencias, Universidad Nacional Autonoma de Mexico, Ciudad Universitaria, 04510 Mexico, DF (Mexico)

    2005-09-21

    A computational comparison of signal-to-noise ratio (SNR) was performed between a conventional phased array of two circular-shaped coils and a petal resonator surface array. The quasi-static model and phased-array optimum SNR were combined to derive an SNR formula for each array. Analysis of mutual inductance between coil petals was carried out to compute the optimal coil separation and optimum number of petal coils. Mutual interaction between coil arrays was not included in the model because this does not drastically affect coil performance. Phased arrays of PERES coils show a 114% improvement in SNR over that of the simplest circular configuration. (note)

  3. Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

    Directory of Open Access Journals (Sweden)

    Muehlbauer Gary J

    2010-12-01

    Full Text Available Abstract Background Considerations in applying association mapping (AM to plant breeding are population structure and size: not accounting for structure and/or using small populations can lead to elevated false-positive rates. The principal determinants of population structure in cultivated barley are growth habit and inflorescence type. Both are under complex genetic control: growth habit is controlled by the epistatic interactions of several genes. For inflorescence type, multiple loss-of-function alleles in one gene lead to the same phenotype. We used these two traits as models for assessing the effectiveness of AM. This research was initiated using the CAP Core germplasm array (n = 102 assembled at the start of the Barley Coordinated Agricultural Project (CAP. This array was genotyped with 4,608 SNPs and we re-sequenced genes involved in morphology, growth and development. Larger arrays of breeding germplasm were subsequently genotyped and phenotyped under the auspices of the CAP project. This provided sets of 247 accessions phenotyped for growth habit and 2,473 accessions phenotyped for inflorescence type. Each of the larger populations was genotyped with 3,072 SNPs derived from the original set of 4,608. Results Significant associations with SNPs located in the vicinity of the loci involved in growth habit and inflorescence type were found in the CAP Core. Differentiation of true and spurious associations was not possible without a priori knowledge of the candidate genes, based on re-sequencing. The re-sequencing data were used to define allele types of the determinant genes based on functional polymorphisms. In a second round of association mapping, these synthetic markers based on allele types gave the most significant associations. When the synthetic markers were used as anchor points for analysis of interactions, we detected other known-function genes and candidate loci involved in the control of growth habit and inflorescence type. We

  4. Gene expression arrays as a tool to unravel mechanisms of normal tissue radiation injury and prediction of response

    Institute of Scientific and Technical Information of China (English)

    Jacqueline JCM Kruse; Fiona A Stewart

    2007-01-01

    Over the past 5 years there has been a rapid increase in the use of microarray technology in the field of cancer research. The majority of studies use microarray analysis of tumor biopsies for profiling of molecular characteristics in an attempt to produce robust classifiers for prognosis. There are now several published gene sets that have been shown to predict for aggressive forms of breast cancer, where patients are most likely to benefit from adjuvant chemotherapy and tumors most likely to develop distant metastases, or be resistant to treatment. The number of publications relating to the use of microarrays for analysis of normal tissue damage, after cancer treatment or genotoxic exposure, is much more limited. A PubMed literature search was conducted using the following keywords and combination of terms: radiation, normal tissue, microarray, gene expression profiling, prediction. With respect to normal tissue radiation injury, microarrays have been used in three ways: (1) to generate gene signatures to identify sensitive and resistant populations (prognosis); (2) to identify sets of biomarker genes for estimating radiation exposure, either accidental or as a result of terrorist attack (diagnosis); (3) to identify genes and pathways involved in tissue response to injury (mechanistic). In this article we will review all (relevant) papers that covered our literature search criteria on microarray technology as it has been applied to normal tissue radiation biology and discuss how successful this has been in defining predisposition markers for radiation sensitivity or how it has helped us to unravel molecular mechanisms leading to acute and late tissue toxicity. We also discuss some of the problems and limitations in application and interpretation of such data.

  5. Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array

    Directory of Open Access Journals (Sweden)

    Goldstein Alisa M

    2006-11-01

    Full Text Available Abstract Background Esophageal squamous cell carcinoma (ESCC is a common malignancy worldwide. Comprehensive genomic characterization of ESCC will further our understanding of the carcinogenesis process in this disease. Results Genome-wide detection of chromosomal changes was performed using the Affymetrix GeneChip 10 K single nucleotide polymorphism (SNP array, including loss of heterozygosity (LOH and copy number alterations (CNA, for 26 pairs of matched germ-line and micro-dissected tumor DNA samples. LOH regions were identified by two methods – using Affymetrix's genotype call software and using Affymetrix's copy number alteration tool (CNAT software – and both approaches yielded similar results. Non-random LOH regions were found on 10 chromosomal arms (in decreasing order of frequency: 17p, 9p, 9q, 13q, 17q, 4q, 4p, 3p, 15q, and 5q, including 20 novel LOH regions (10 kb to 4.26 Mb. Fifteen CNA-loss regions (200 kb to 4.3 Mb and 36 CNA-gain regions (200 kb to 9.3 Mb were also identified. Conclusion These studies demonstrate that the Affymetrix 10 K SNP chip is a valid platform to integrate analyses of LOH and CNA. The comprehensive knowledge gained from this analysis will enable improved strategies to prevent, diagnose, and treat ESCC.

  6. Array based detection of antibiotic resistance genes in Gram negative bacteria isolated from retail poultry meat in the UK and Ireland.

    Science.gov (United States)

    McNeece, Grainne; Naughton, Violetta; Woodward, Martin J; Dooley, James S G; Naughton, Patrick J

    2014-06-02

    The use of antibiotics in birds and animals intended for human consumption within the European Union (EU) and elsewhere has been subject to regulation prohibiting the use of antimicrobials as growth promoters and the use of last resort antibiotics in an attempt to reduce the spread of multi-resistant Gram negative bacteria. Given the inexorable spread of antibiotic resistance there is an increasing need for improved monitoring of our food. Using selective media, Gram negative bacteria were isolated from retail chicken of UK-Intensively reared (n=27), Irish-Intensively reared (n=19) and UK-Free range (n=30) origin and subjected to an oligonucleotide based array system for the detection of 47 clinically relevant antibiotic resistance genes (ARGs) and two integrase genes. High incidences of β-lactamase genes were noted in all sample types, acc (67%), cmy (80%), fox (55%) and tem (40%) while chloramphenicol resistant determinants were detected in bacteria from the UK poultry portions and were absent in bacteria from the Irish samples. Denaturing Gradient Gel Electrophoresis (DGGE) was used to qualitatively analyse the Gram negative population in the samples and showed the expected diversity based on band stabbing and DNA sequencing. The array system proved to be a quick method for the detection of antibiotic resistance gene (ARG) burden within a mixed Gram negative bacterial population.

  7. Optimized in situ construction of oligomers on an array surface

    Science.gov (United States)

    Tolonen, Andrew C.; Albeanu, Dinu F.; Corbett, Julia F.; Handley, Heather; Henson, Charlotte; Malik, Pratap

    2002-01-01

    Oligonucleotide arrays are powerful tools to study changes in gene expression for whole genomes. These arrays can be synthesized by adapting photolithographic techniques used in microelectronics. Using this method, oligonucleotides are built base by base directly on the array surface by numerous cycles of photodeprotection and nucleotide addition. In this paper we examine strategies to reduce the number of synthesis cycles required to construct oligonucleotide arrays. By computer modeling oligonucleotide synthesis, we found that the number of required synthesis cycles could be significantly reduced by focusing upon how oligonucleotides are chosen from within genes and upon the order in which nucleotides are deposited on the array. The methods described here could provide a more efficient strategy to produce oligonucleotide arrays. PMID:12384609

  8. Clinical applications of BAC array-CGH to the study of diffuse large B-cell lymphomas.

    Science.gov (United States)

    Robledo, Cristina; García, Juan Luis; Hernández, Jesús M

    2013-01-01

    BAC array-CGH is a powerful method to identify DNA copy number changes (gains, amplifications and deletions) on a genome-wide scale, and to map these changes to genomic sequence. It is based on the analysis of genomic DNA isolated from test and reference cell populations, the differential labelling with fluorescent dyes and the co-hybridization with a genomic array. BAC array-CGH has proven to be a specific, sensitive, and reliable technique, with considerable advantages compared to other methods used for the analysis of DNA copy number changes. The application of genome scanning technologies and the recent advances in bioinformatics tools that enable us to perform a robust and highly sensitive analysis of array-CGH data, useful not only for genome scanning of tumor cells but also in the identification of novel cancer related genes, oncogenes and suppressor genes. Cytogenetic analysis provides essential information for diagnosis and prognosis in patients with hematologic malignancies such as lymphomas. However, the chromosomal interpretation in non-Hodgkin lymphoma (NHL) is sometimes inconclusive. Copy number aberrations identified by BAC array-CGH analyses could be a complementary methodology to chromosomal analysis. In NHL the genomic imbalances might have a prognostic rather than a diagnostic value. In fact, the diagnosis of NHL is based on pathological and molecular cytogenetics data. Furthermore genetic variations and their association with specific types of lymphoma development, and elucidation of the variable genetic pathways leading to lymphoma development, are important directions for future cancer research. Array-CGH, along with FISH and PCR, will be used for routine diagnostic purposes in near future.

  9. A Study on Genes of Bayanbulak Sheep

    Directory of Open Access Journals (Sweden)

    Beiyao Zuo

    2013-01-01

    Full Text Available The average twin lambing rate of Bayanbulak sheep is 2% to 3%. However, a flock of sheep with a close genetic relationship and an average of 2 to 3 lambs per birth has been found recently. To determine the major genes controlling the prolificacy of the flock in the present study, the flock was designated A while 100 normal Bayanbulak sheep were randomly selected to comprise the control flock B. Ligase detection reaction method was applied to detect and analyze the 10 mutational loci of the 3 candidate prolificacy genes including bone morphogenetic protein type I receptors, bone morphogenetic protein 15, and growth differentiation factor 9. The 10 mutational loci are as follows: FecB locus of the BMPR-IB gene; FecXI, FecXB, FecXL, FecXH, FecXG, and FecXR of the BMP15 gene; and G1, G8, and FecTT of the GDF9 gene. Two mutations including BMPR-IB/FecB and GDF9/G1 were found in Bayanbulak sheep. Independence test results of the two flocks demonstrate that the FecB locus has a significant effect on the lambing number of Bayanbulak sheep. However, the mutation frequency of the G1 locus in GDF9 is very low. Independence test results demonstrate that the GDF9 locus does not have a significant impact on the lambing performance of Bayanbulak sheep. Among the 10 detected loci, BMPR-IB/FecB is the major gene that influences the high lambing rate of Bayanbulak sheep.

  10. Study of heat transfer in the bubble meniscus with an array of temperature micro-sensors

    Directory of Open Access Journals (Sweden)

    Orlik Evgeniy

    2016-01-01

    Full Text Available Experimental setup has been designed and manufactured to study the evaporation processes in the bubble meniscus. New method for accurate measurements of local heat transfer has been proposed in collaboration with Kyushu University. Two side transparent coatings (thin film uniform heater and an array of temperature micro-sensors are developed on sapphire substrates. Application of such substrate allows one to investigate heat transfer in the vicinity of the contact line. The shadow technique is used to define shape and contact angles of bubble.

  11. The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits.

    Directory of Open Access Journals (Sweden)

    Benjamin F Voight

    Full Text Available Genome-wide association studies have identified hundreds of loci for type 2 diabetes, coronary artery disease and myocardial infarction, as well as for related traits such as body mass index, glucose and insulin levels, lipid levels, and blood pressure. These studies also have pointed to thousands of loci with promising but not yet compelling association evidence. To establish association at additional loci and to characterize the genome-wide significant loci by fine-mapping, we designed the "Metabochip," a custom genotyping array that assays nearly 200,000 SNP markers. Here, we describe the Metabochip and its component SNP sets, evaluate its performance in capturing variation across the allele-frequency spectrum, describe solutions to methodological challenges commonly encountered in its analysis, and evaluate its performance as a platform for genotype imputation. The metabochip achieves dramatic cost efficiencies compared to designing single-trait follow-up reagents, and provides the opportunity to compare results across a range of related traits. The metabochip and similar custom genotyping arrays offer a powerful and cost-effective approach to follow-up large-scale genotyping and sequencing studies and advance our understanding of the genetic basis of complex human diseases and traits.

  12. An IB-LBM study of continuous cell sorting in deterministic lateral displacement arrays

    Science.gov (United States)

    Wei, Qiang; Xu, Yuan-Qing; Tang, Xiao-Ying; Tian, Fang-Bao

    2016-12-01

    The deterministic lateral displacement (DLD) is an important method used to sort particles and cells of different sizes. In this paper, the flexible cell sorting with the DLD method is studied by using a numerical model based on the immersed boundary-lattice Boltzmann method (IB-LBM). In this model, the fluid motion is solved by the LBM, and the cell membrane-fluid interaction is modeled with the LBM. The proposed model is validated by simulating the rigid particle sorted with the DLD method, and the results are found in good agreement with those measured in experiments. We first study the effect of flexibility on a single cell and multiple cells continuously going through a DLD device. It is found that the cell flexibility can significantly affect the cell path, which means the flexibility could have significant effects on the continuous cell sorting by the DLD method. The sorting characteristics of white blood cells and red blood cells are further studied by varying the spatial distribution of cylinder arrays and the initial cell-cell distance. The numerical results indicate that a well concentrated cell sorting can be obtained under a proper arrangement of cylinder arrays and a large enough initial cell-cell distance.

  13. cDNA Array Analysis of the Differential Expression Change in Virulence-related Genes During the Development of Resistance in Candida albicans

    Institute of Scientific and Technical Information of China (English)

    Zheng XU; Yuan-Ying JIANG; Yong-Bing CAO; Jun-Dong ZHANG; Ying-Ying CAO; Ping-Hui GAO; De-Jun WANG; Xu-Ping FU; Kang YING; Wan-Sheng CHEN

    2005-01-01

    Candida albicans is the most frequently isolated fungus in immunocompromised patients associated with mucosal and deep-tissue infections. To investigate the correlation between virulence and resistance on a gene expression profile in C. albicans, we examined the changes in virulence-related genes during the development of resistance in C. albicans from bone marrow transplant patients using a constructed cDNA array representing 3096 unigenes. In addition to the genes known to be associated with azole resistance,16 virulence-related genes were identified, whose differential expressions were newly found to be associated with the resistant phenotype. Differential expressions for these genes were confirmed by RT-PCR independently. Furthermore, the up-regulation of EFG1, CPH2, TEC1, CDC24, SAP10, ALS9, SNF1, SPO72 and BDF1, and the down-regulation of RAD32, IPF3636 and UBI4 resulted in stronger virulence and invasiveness in the resistant isolates compared with susceptible ones. These findings provide a link between the expression of virulence genes and development of resistance during C. albicans infection in bone marrow transplant (BMT) patients, where C. albicans induces hyphal formation and expression change in multiple virulence factors.

  14. Impact of cigarette smoke on the human and mouse lungs: a gene-expression comparison study.

    Directory of Open Access Journals (Sweden)

    Mathieu C Morissette

    Full Text Available Cigarette smoke is well known for its adverse effects on human health, especially on the lungs. Basic research is essential to identify the mechanisms involved in the development of cigarette smoke-related diseases, but translation of new findings from pre-clinical models to the clinic remains difficult. In the present study, we aimed at comparing the gene expression signature between the lungs of human smokers and mice exposed to cigarette smoke to identify the similarities and differences. Using human and mouse whole-genome gene expression arrays, changes in gene expression, signaling pathways and biological functions were assessed. We found that genes significantly modulated by cigarette smoke in humans were enriched for genes modulated by cigarette smoke in mice, suggesting a similar response of both species. Sixteen smoking-induced genes were in common between humans and mice including six newly reported to be modulated by cigarette smoke. In addition, we identified a new conserved pulmonary response to cigarette smoke in the induction of phospholipid metabolism/degradation pathways. Finally, the majority of biological functions modulated by cigarette smoke in humans were also affected in mice. Altogether, the present study provides information on similarities and differences in lung gene expression response to cigarette smoke that exist between human and mouse. Our results foster the idea that animal models should be used to study the involvement of pathways rather than single genes in human diseases.

  15. Curvilinear 3-D Imaging Using Row--Column-Addressed 2-D Arrays with a Diverging Lens: Feasibility Study

    DEFF Research Database (Denmark)

    Bouzari, Hamed; Engholm, Mathias; Beers, Christopher

    2017-01-01

    Constructing a double-curved row–columnaddressed (RCA) 2-D array or applying a diverging lens over the flat RCA 2-D array can extend the imaging field-of-view (FOV) to a curvilinear volume without increasing the aperture size, which is necessary for applications such as abdominal and cardiac imag...... of this study demonstrate that the proposed beamforming approach is accurate for achieving correct time-of-flight calculations, and hence avoids geometrical distortions....

  16. Study of High-Energy Particles Correlated with Lightning at Utah's Telescope Array Cosmic Ray Observatory

    Science.gov (United States)

    Belz, John

    2016-03-01

    It is known that x-ray and gamma radiation is emitted by lightning. This phenomenon has been observed by both ground-based and spaced-based detectors. Recently, cosmic ray physicists studying data collected by the 700 square-kilometer Telescope Array Surface Detector (TASD) have observed energetic elementary particles in coincidence with lightning strikes. A subset of these events contain reconstructable ``showers'' which point back to the particles' origin in the Earth's atmosphere. This implies that the energetic radiation may for the first time be traced to its source within the lightning strike. The Lightning Mapping Array (LMA) pioneered at Langmuir Laboratories is the ideal instrument to couple with the TASD in order to perform these studies. These LMA's consist of roughly ten VHF detectors spread over hundreds of square kilometers, and detect impulsive radiation from lightning. The sources of these impulses may be reconstructed and used to create a 3-dimensional GPS-timed reconstruction of a lightning strike. The merger of TA and LMA is also the ideal instrument to search for evidence of a more speculative - but more profound - connection between particle astrophysics and climate: The seeding of lightning strikes by cosmic ray air showers.

  17. The Study of a Beam Profile Monitor based on Faraday Cup Array

    Energy Technology Data Exchange (ETDEWEB)

    Park, K. M.; Park, S. H.; Kim, S. G.; Kwon, H. J.; Cho, Y. S. [KAERI, Daejeon (Korea, Republic of)

    2015-05-15

    The metal can then be discharged to measure a small current equivalent to the number of impinging ions. The beam current can be measured and used to determine the number of ions or electrons hitting the cup. Recently, beam profile monitor (BPM) based on Faraday cup array (FCA), which represented beam position through the spatial and temporal distribution of the beam current, has been studied due to advantages of measure of wide-range ion beam current. FCA system is divided into a FC, an electrical circuit and display parts. We have studied FCA to monitor beam profile on an electrostatic accelerator with wide-range ion current. In this paper, we represented basic characteristics and designs for the fabricated FCA. FCA system, which consisted of FC system, electronic readout system, and output display, was suggested to measure ion beam current, efficiently. FC system consisted of a collimator, suppressor, tiny FC, insulator frame, and circuit board divided into elec PCB, cap PCB, and con PCB. FC size was 4 mm diameters and FCA system was considered as 8 x 8 array and whole size of 8 x 8 mm''2. FCA system was set-up in vacuum chamber and an integrator and output display parts were formed out of chamber to minimize number of feed-through.

  18. Use of intein-mediated phosphoprotein arrays to study substrate specificity of protein phosphatases.

    Science.gov (United States)

    Kochinyan, Samvel; Sun, Luo; Ghosh, Inca; Barshevsky, Tanya; Xu, Jie; Xu, Ming-Qun

    2007-01-01

    Synthetic peptides incorporating various chemical moieties, for example, phosphate groups, are convenient tools for investigating protein modification enzymes, such as protein phosphatases (PPs). However, short peptides are sometimes poor substrates, and their binding to commonly used matrices is unpredictable and variable. In general, protein substrates for PPs are superior for enzymatic assays, binding to various matrices, and Western blot analysis. The preparation and characterization of phosphoproteins, however can be difficult and technically demanding. In this study, the intein-mediated protein ligation (IPL) technique was used to readily generate phosphorylated protein substrates by ligating a synthetic phosphopeptide to an intein-generated carrier protein (CP) possessing a carboxyl-terminal thioester with a one-to-one stoichiometry. The ligated phosphoprotein (LPP) substrate was treated with a PP and subsequently subjected to array or Western blot analysis with a phospho-specific antibody. This approach is highly effective in producing arrays of protein substrates containing phosphorylated amino acid residues and has been applied for screening of PPs with specificity toward phosphorylated tyrosine, serine, or threonine residues, resulting in an approximately 240-fold increase in sensitivity in dot blot analysis compared with the use of synthetic peptides. The IPL technique overcomes the disadvantages of current methods and is a versatile system for the facile production of protein substrates containing well-defined structural motifs for the study of protein modification enzymes.

  19. Study of transition mechanisms induced by an array of roughness elements

    Science.gov (United States)

    Shrestha, Prakash; Candler, Graham V.; Computational Hypersonics Research Lab Team

    2016-11-01

    We study transition mechanisms of a Mach 5.92 laminar boundary layer due to an array of prismatic roughness elements using large-scale direct numerical simulations (DNS). We simulate a boundary layer tripped by arrays of different numbers of roughness elements, corresponding to experiments conducted at the Texas A & M University Actively Controlled Experimental (ACE) facility. We obtain solutions using a high-order, low-dissipation scheme for the convection terms in the Navier-Stokes equations. We perform separate 2D and 3D simulations. Flow parallel inflow acoustic disturbances are implemented in the 2D domain. We then interpolate spectral content obtained at 30 mm from the leading edge of the 2D domain to the inflow of the 3D domain. In the 3D domain, we compute optimal modes of pressure using dynamic mode decomposition (DMD). Using sparsity-promoting dynamic mode decomposition (SPDMD), we select the dominant modes to study the transition mechanisms. Recirculating vortices upstream and separated shear layers downstream of the roughness elements are observed to be the most dominant modes of transition. We compare streamwise mean mass flux and energy spectral densities at different streamwise locations to validate our simulations. Office of Naval Research.

  20. With Reference to Reference Genes: A Systematic Review of Endogenous Controls in Gene Expression Studies.

    Science.gov (United States)

    Chapman, Joanne R; Waldenström, Jonas

    2015-01-01

    The choice of reference genes that are stably expressed amongst treatment groups is a crucial step in real-time quantitative PCR gene expression studies. Recent guidelines have specified that a minimum of two validated reference genes should be used for normalisation. However, a quantitative review of the literature showed that the average number of reference genes used across all studies was 1.2. Thus, the vast majority of studies continue to use a single gene, with β-actin (ACTB) and/or glyceraldehyde 3-phosphate dehydrogenase (GAPDH) being commonly selected in studies of vertebrate gene expression. Few studies (15%) tested a panel of potential reference genes for stability of expression before using them to normalise data. Amongst studies specifically testing reference gene stability, few found ACTB or GAPDH to be optimal, whereby these genes were significantly less likely to be chosen when larger panels of potential reference genes were screened. Fewer reference genes were tested for stability in non-model organisms, presumably owing to a dearth of available primers in less well characterised species. Furthermore, the experimental conditions under which real-time quantitative PCR analyses were conducted had a large influence on the choice of reference genes, whereby different studies of rat brain tissue showed different reference genes to be the most stable. These results highlight the importance of validating the choice of normalising reference genes before conducting gene expression studies.

  1. Theoretical study of 2 × 2 element planar array of equilateral triangular patch microstrip antenna in plasma medium

    Indian Academy of Sciences (India)

    K K Verma; K R Soni

    2005-01-01

    The radiation properties of 2 × 2 element planar array of equilateral triangular patch microstrip antenna in plasma medium are studied. The array factor and far-zone EM-mode and P-mode radiation fields of the array geometry are derived using vector wave function techniques and pattern multiplication approaches. The total field patterns and various characteristics of pattern such as half power beam width (HPBW), first null beam width (FNBW) and direction of maximum radiation are computed for two different values of progressive phase excitation difference between the elements. The results of this array geometry are obtained both in plasma medium and in free space and compared with those of single element equilateral triangular patch microstrip antenna.

  2. Long-term study of Mkn 421 with the HAGAR Array of Telescopes

    CERN Document Server

    Sinha, Atreyee; Saha, Lab; Acharya, B S; Anupama, G C; Bhattacharya, P; Britto, R J; Chitnis, V R; Prabhu, T P; Singh, B B; Vishwanath, P R

    2016-01-01

    Context:The HAGAR Telescope Array at Hanle, Ladakh has been regularly monitoring the nearby blazar Mkn 421 for the past 7yrs. Aims: Blazars show flux variability in all timescales across the electromagnetic spectrum. While there is abundant literature characterizing the short term flares from different blazars, comparatively little work has been done to study the long term variability. We aim to study the long term temporal and spectral variability in the radiation from Mkn 421 during 2009-2015. Methods: We quantify the variability and lognormality from the radio to the VHE bands, and compute the correlations between the various wavebands using the z-transformed discrete correlation function. We construct the Spectral Energy Distribution (SED) contemporaneous with HAGAR observation seasons and fit it with a one zone synchrotron self Compton model to study the spectral variability. Results: The flux is found to be highly variable across all time scales. The variability is energy dependant, and is maximum in th...

  3. Recurrent chromosomal aberrations in intravenous leiomyomatosis of the uterus: high-resolution array comparative genomic hybridization study.

    Science.gov (United States)

    Buza, Natalia; Xu, Fang; Wu, Weiqing; Carr, Ryan J; Li, Peining; Hui, Pei

    2014-09-01

    Uterine intravenous leiomyomatosis (IVL) is a distinct smooth muscle neoplasm with a potential of clinical aggressiveness due to its ability to extend into intrauterine and extrauterine vasculature. In this study, chromosomal alterations analyzed by oligonucleotide array comparative genomic hybridization were performed in 9 cases of IVL. The analysis was informative in all cases with multiple copy number losses and/or gains observed in each tumor. The most frequent recurrent loss of 22q12.3-q13.1 was observed in 6 tumors (66.7%), followed by losses of 22q11.23-q13.31, 1p36.13-p33, 2p25.3-p23.3, and 2q24.2-q32.2 and gains of 6p22.2, 2q37.3 and 10q22.2-q22.3, in decreasing order of frequency. Copy number variants were identified at 14q11.2, 15q11.1-q11.2, and 15q26.2. Genes mapping to the regions of loss include CHEK2, EWS, NF2, PDGFB, and MAP3K7IP1 on chromosome 22q, HEI10 on chromosome 14q, and succinate dehydrogenase subunit B, E2F2, ARID1A KPNA6, EIF3S2 , PTCH2, and PIK3R3 on chromosome 1p. Regional losses on chromosomes 22q and 1p and gains on chromosomes 12q showed overlaps with those previously observed in uterine leiomyosarcomas. In addition, presence of multiple chromosomal aberrations implies a higher level of genetic instability. Follow-up polymerase chain reaction (PCR) sequencing analysis of MED12 gene revealed absence of G> A transition at nucleotides c.130 or c.131 in all 9 cases, a frequent mutation found in uterine leiomyoma and its variants. In conclusion, this is the first report of high-resolution, genome-wide investigation of IVL by oligonucleotide array comparative genomic hybridization. The presence of high frequencies of recurrent regional loss involving several chromosomes is an important finding and likely related to the pathogenesis of the disease.

  4. A compact array calibrator to study the feasibility of acoustic neutrino detection

    Directory of Open Access Journals (Sweden)

    Ardid M.

    2016-01-01

    Full Text Available Underwater acoustic detection of ultra-high-energy neutrinos was proposed already in 1950s: when a neutrino interacts with a nucleus in water, the resulting particle cascade produces a pressure pulse that has a bipolar temporal structure and propagates within a flat disk-like volume. A telescope that consists of thousands of acoustic sensors deployed in the deep sea can monitor hundreds of cubic kilometres of water looking for these signals and discriminating them from acoustic noise. To study the feasibility of the technique it is critical to have a calibrator able to mimic the neutrino “signature” that can be operated from a vessel. Due to the axial-symmetry of the signal, their very directive short bipolar shape and the constraints of operating at sea, the development of such a calibrator is very challenging. Once the possibility of using the acoustic parametric technique for this aim was validated with the first compact array calibrator prototype, in this paper we describe the new design for such a calibrator composed of an array of piezo ceramic tube transducers emitting in axial direction.

  5. A compact array calibrator to study the feasibility of acoustic neutrino detection

    Science.gov (United States)

    Ardid, M.; Camarena, F.; Felis, I.; Herrero, A.; Llorens, C. D.; Martínez-Mora, J.; Saldaña, M.

    2016-04-01

    Underwater acoustic detection of ultra-high-energy neutrinos was proposed already in 1950s: when a neutrino interacts with a nucleus in water, the resulting particle cascade produces a pressure pulse that has a bipolar temporal structure and propagates within a flat disk-like volume. A telescope that consists of thousands of acoustic sensors deployed in the deep sea can monitor hundreds of cubic kilometres of water looking for these signals and discriminating them from acoustic noise. To study the feasibility of the technique it is critical to have a calibrator able to mimic the neutrino "signature" that can be operated from a vessel. Due to the axial-symmetry of the signal, their very directive short bipolar shape and the constraints of operating at sea, the development of such a calibrator is very challenging. Once the possibility of using the acoustic parametric technique for this aim was validated with the first compact array calibrator prototype, in this paper we describe the new design for such a calibrator composed of an array of piezo ceramic tube transducers emitting in axial direction.

  6. Attenuation study for Tibet Water Cherenkov Muon Detector Array-A

    CERN Document Server

    Gou, Quanbu; Liu, Cheng; Feng, Zhaoyang; Qian, Xiangli; Hou, Zhengtao

    2011-01-01

    The attenuation study of the long cable used in Tibet Water Cherenkov Muon Detector Array-A, called Tibet MD-A (one of 12 Tibet MD detectors), under the 37000 m2 Tibet air shower array, is reported. The cable frequency response is measured by using the sinusoidal signals, with which the influence of the cable on the pulse rise time is obtained. For the reason that the commercial 20 inch PMT (R3600_06) has a waterproof connection with the signal cable, one end of the signal cable is permanently connected to the PMT. Terminal reflection method is tested and used for measuring the signal attenuation. During the measurement, a practical way to eliminate the uncertainty caused by the baseline of the signal is achieved. To check the terminal reflection method, comparison measurement between it and QDC data taking method are carried out by using open-ended cables. The confirmed terminal reflection method is a fast and convenient method being suitable to online measure the signal attenuation for Tibet MD-A. The measu...

  7. Formation and manipulation of regular metallic nanoparticle arrays on bacterial surface layers: an advanced TEM study

    Science.gov (United States)

    Mertig, M.; Wahl, R.; Lehmann, M.; Simon, P.; Pompe, W.

    The template-directed formation of regular nanoparticle arrays on two-dimensional crystalline protein layers after their treatment with metal salt complexes was studied by transmission electron microscopy. For these investigations, bacterial surface layers (S layers), recrystallized in vitro into sheets and tube-shaped protein crystals with typical dimensions in the micrometer range, were used as the template. As identified by electron holography and scanning force microscopy, the S-layer tubes form alternating double layers when deposited onto a solid substrate surface. Two distinct pathways for the metal particle formation at the templates have been found: the site-specific growth of metal clusters by chemical reduction of the metal salt complexes, and the electron-beam induced growth of nanoparticles in the transmission electron microscope. Both mechanisms lead to regular arrays with particle densities > 6×1011cm-2. Nanoparticle formation by electron exposure takes exclusively place in the flat-lying double-layered protein tubes, where a sufficient amount of metal complexes can be accumulated during sample preparation.

  8. Theoretical study of two-element array of equilateral triangular patch microstrip antenna on ferrite substrate

    Indian Academy of Sciences (India)

    K K Verma; K R Soni

    2005-09-01

    The radiation characteristics of a two-element array of equilateral triangular patch microstrip antenna on a ferrite substrate are studied theoretically by considering the presence of bias magnetic field in the direction of propagation of electromagnetic waves. It is found that the natural modes of propagation in the direction of magnetic field are left- and right-circularly polarized waves and these modes have different propagation constants. In loss-less isotropic warm plasma, this array antenna geometry excites both electromagnetic (EM) and electroacoustic plasma (P) waves in addition to a nonradiating surface wave. In the absence of an external magnetic field, the EM- and P-waves can be decoupled into two independent modes, the electroacoustic mode is longitudinal while the electromagnetic mode is transverse. The far-zone EM-mode and P-mode radiation fields are derived using vector wave function techniques and pattern multiplication approaches. The results are obtained in both plasma medium and free space. Some important antenna parameters such as radiation conductance, directivity and quality factor are plotted for different values of plasma-to-source frequency.

  9. A scintillating bolometer array for double beta decay studies: The LUCIFER experiment

    Energy Technology Data Exchange (ETDEWEB)

    Gironi, L., E-mail: luca.gironi@mib.infn.it [Università degli Studi di Milano-Bicocca, Milano (Italy); INFN – Sezione di Milano-Bicocca, Milano (Italy)

    2016-07-11

    The main goal of the LUCIFER experiment is to study the neutrinoless double beta decay, a rare process allowed if neutrinos are Majorana particles. Although aiming at a discovery, in the case of insufficient sensitivity the LUCIFER technique will be the demonstrator for a higher mass experiment able to probe the entire inverted hierarchy region of the neutrino mass. In order to achieve this challenging result, high resolution detectors with active background discrimination capability are required. This very interesting possibility can be largely fulfilled by scintillating bolometers thanks to the simultaneous read-out of heat and light emitted by the interactions in the detector or by pulse shape analysis. - Highlights: • The LUCIFER technique will be the demonstrator for a higher mass experiment. • Scintillating bolometers allow high energy resolution and background discrimination. • The first choice for the LUCIFER tower are ZnSe crystals. • The LUCIFER setup will consist of an array of 30 individual single module detectors. • An array of ZnMoO4 crystals allowed the bolometric observation of the 2vDBD of {sup 100}Mo.

  10. A Triboelectric Sensor Array for Electrostatic Studies on the Lunar Surface

    Science.gov (United States)

    Johansen, Michael R.; Mackey, Paul J.; Calle, C. I.

    2015-01-01

    The moons electrostatic environment requires careful consideration in the development of future lunar landers. Electrostatically charged dust was well documented during the Apollo missions to cause thermal control, mechanical, and visibility issues. The fine dust particles that make up the surface are electrostatically charged as a result of numerous charging mechanisms. The relatively dry conditions on the moon creates a prime tribocharging environment during surface operations. The photoelectric effect is dominant for lunar day static charging, while plasma electrons are the main contributor for lunar night electrostatic effects. Electrostatic charging is also dependent on solar intensity, Earth-moon relative positions, and cosmic ray flux. This leads to a very complex and dynamic electrostatic environment that must be studied for the success of long term lunar missions.In order to better understand the electrostatic environment of planetary bodies, Kennedy Space Center, in previous collaboration with the Jet Propulsion Laboratory, has developed an electrostatic sensor suite. One of the instruments included in this package is the triboelectric sensor array. It is comprised of strategically selected materials that span the triboelectric series and that also have previous spaceflight history. In this presentation, we discuss detailed testing with the triboelectric sensor array performed at Kennedy Space Center. We will discuss potential benefits and use cases of this low mass, low cost sensor package, both for science and for mission success.

  11. New Diversity Arrays Technology (DArT) markers for tetraploid oat (Avena magna Murphy et Terrell) provide the first complete oat linkage map and markers linked to domestication genes from hexaploid A. sativa L.

    Science.gov (United States)

    Oliver, R E; Jellen, E N; Ladizinsky, G; Korol, A B; Kilian, A; Beard, J L; Dumlupinar, Z; Wisniewski-Morehead, N H; Svedin, E; Coon, M; Redman, R R; Maughan, P J; Obert, D E; Jackson, E W

    2011-11-01

    Nutritional benefits of cultivated oat (Avena sativa L., 2n = 6x = 42, AACCDD) are well recognized; however, seed protein levels are modest and resources for genetic improvement are scarce. The wild tetraploid, A. magna Murphy et Terrell (syn A. maroccana Gdgr., 2n = 4x = 28, CCDD), which contains approximately 31% seed protein, was hybridized with cultivated oat to produce a domesticated A. magna. Wild and cultivated accessions were crossed to generate a recombinant inbred line (RIL) population. Although these materials could be used to develop domesticated, high-protein oat, mapping and quantitative trait loci introgression is hindered by a near absence of genetic markers. Objectives of this study were to develop high-throughput, A. magna-specific markers; generate a genetic linkage map based on the A. magna RIL population; and map genes controlling oat domestication. A Diversity Arrays Technology (DArT) array derived from 10 A. magna genotypes was used to generate 2,688 genome-specific probes. These, with 12,672 additional oat clones, produced 2,349 polymorphic markers, including 498 (21.2%) from A. magna arrays and 1,851 (78.8%) from other Avena libraries. Linkage analysis included 974 DArT markers, 26 microsatellites, 13 SNPs, and 4 phenotypic markers, and resulted in a 14-linkage-group map. Marker-to-marker correlation coefficient analysis allowed classification of shared markers as unique or redundant, and putative linkage-group-to-genome anchoring. Results of this study provide for the first time a collection of high-throughput tetraploid oat markers and a comprehensive map of the genome, providing insights to the genome ancestry of oat and affording a resource for study of oat domestication, gene transfer, and comparative genomics.

  12. Study of the magnetization behavior of ferromagnetic nanowire array: Existence of growth defects revealed by micromagnetic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen Vien, G., E-mail: gilles.nguyen@univ-brest.fr [Laboratoire de Magnétisme de Bretagne, EA 4522, Université de Bretagne Occidentale, CS 93837, 29238 Brest-Cedex 3 (France); Rioual, S. [Laboratoire de Magnétisme de Bretagne, EA 4522, Université de Bretagne Occidentale, CS 93837, 29238 Brest-Cedex 3 (France); Gloaguen, F. [Chimie, Electrochimie Moléculaires et Chimie Analytique, UMR CNRS 6521, Université de Bretagne Occidentale, CS 93837, 29238 Brest-Cedex 3 (France); Rouvellou, B.; Lescop, B. [Laboratoire de Magnétisme de Bretagne, EA 4522, Université de Bretagne Occidentale, CS 93837, 29238 Brest-Cedex 3 (France)

    2016-03-01

    High aspect ratio nanowires were electrodeposited in nanoporous anodic alumina template by a potentiostatic method. The angular dependence of the coercive field and remanence magnetization extracted from magnetometry measurements are compared with micromagnetic simulations. Inclusion of magnetostatic interactions between Ni nanowires in simulations is required to explain some of the properties of the magnetization reversal. However, it is not sufficient to reproduce fully the angular dependence of the coercive field. Due to the polycrystalline nature of nanowires and thus to the presence of grain boundaries, defects are included in simulations. A good agreement between theory and experiment is then clearly highlighted, in particular in the nanowire easy axis direction. The achieved results allow a description of several experimental data published in the literature and consequently to get a better understanding of reversal mechanisms that operate in such nanowire arrays. A complementary study of composite nanowire array is successfully performed to prove the adequacy of the simulations method to describe the magnetic properties of nanowire array. - Highlights: • High axial squareness nanowire array are synthetized by a potentiostatic method. • Nanowires are modeled as non-ideal magnetic particles. • Segmentation of nanowire is required to describe the angular dependence of coercivity. • Respective role of magnetostatic coupling and nanowire segmentation in nanowire array are studied. • Micromagnetic simulations lead to quantitative agreement for well-defined composite nanowire array.

  13. Scalar localization by cone-beam computed tomography of cochlear implant carriers: a comparative study between straight and periomodiolar precurved electrode arrays.

    Science.gov (United States)

    Boyer, Eric; Karkas, Alexandre; Attye, Arnaud; Lefournier, Virginie; Escude, Bernard; Schmerber, Sebastien

    2015-03-01

    To compare the incidence of dislocation of precurved versus straight flexible cochlear implant electrode arrays using cone-beam computed tomography (CBCT) image analyses. Consecutive nonrandomized case-comparison study. Tertiary referral center. Analyses of patients' CBCT images after cochlear implant surgery. Precurved and straight flexible electrode arrays from two different manufacturers were implanted. A round window insertion was performed in most cases. Two cases necessitated a cochleostomy. The patients' CBCT images were reconstructed in the coronal oblique, sagittal oblique, and axial oblique section. The insertion depth angle and the incidence of dislocation from the scala tympani to the scala vestibuli were determined. The CBCT images and the incidence of dislocation were analyzed in 54 patients (61 electrode arrays). Thirty-one patients were implanted with a precurved perimodiolar electrode array and 30 patients with a straight flexible electrode array. A total of nine (15%) scalar dislocations were observed in both groups. Eight (26%) scalar dislocations were observed in the precurved array group and one (3%) in the straight array group. Dislocation occurred at an insertion depth angle between 170 and 190 degrees in the precurved array group and at approximately 370 degrees in the straight array group. With precurved arrays, dislocation usually occurs in the ascending part of the basal turn of the cochlea. With straight flexible electrode arrays, the incidence of dislocation was lower, and it seems that straight flexible arrays have a higher chance of a confined position within the scala tympani than perimodiolar precurved arrays.

  14. A gene-based information gain method for detecting gene-gene interactions in case-control studies.

    Science.gov (United States)

    Li, Jin; Huang, Dongli; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Zhang, Ruijie; Jiang, Yongshuai; Lv, Hongchao; Wang, Limei

    2015-11-01

    Currently, most methods for detecting gene-gene interactions (GGIs) in genome-wide association studies are divided into SNP-based methods and gene-based methods. Generally, the gene-based methods can be more powerful than SNP-based methods. Some gene-based entropy methods can only capture the linear relationship between genes. We therefore proposed a nonparametric gene-based information gain method (GBIGM) that can capture both linear relationship and nonlinear correlation between genes. Through simulation with different odds ratio, sample size and prevalence rate, GBIGM was shown to be valid and more powerful than classic KCCU method and SNP-based entropy method. In the analysis of data from 17 genes on rheumatoid arthritis, GBIGM was more effective than the other two methods as it obtains fewer significant results, which was important for biological verification. Therefore, GBIGM is a suitable and powerful tool for detecting GGIs in case-control studies.

  15. The KCNE genes in hypertrophic cardiomyopathy: a candidate gene study

    DEFF Research Database (Denmark)

    Hedley, Paula L; Haundrup, Ole; Andersen, Paal S

    2011-01-01

    The gene family KCNE1-5, which encode modulating β-subunits of several repolarising K+-ion channels, has been associated with genetic cardiac diseases such as long QT syndrome, atrial fibrillation and Brugada syndrome. The minK peptide, encoded by KCNE1, is attached to the Z-disc of the sarcomere...... as well as the T-tubules of the sarcolemma. It has been suggested that minK forms part of an "electro-mechanical feed-back" which links cardiomyocyte stretching to changes in ion channel function. We examined whether mutations in KCNE genes were associated with hypertrophic cardiomyopathy (HCM), a genetic...

  16. Study of cross-shaped ultrasonic array sensor applied to partial discharge location in transformer oil.

    Science.gov (United States)

    Li, Jisheng; Xin, Xiaohu; Luo, Yongfen; Ji, Haiying; Li, Yanming; Deng, Junbo

    2013-11-01

    A conformal combined sensor is designed and it is used in Partial Discharge (PD) location experiments in transformer oil. The sensor includes a cross-shaped ultrasonic phased array of 13 elements and an ultra-high-frequency (UHF) electromagnetic rectangle array of 2 × 2 elements. Virtual expansion with high order cumulants, the ultrasonic array can achieve the effect of array with 61 elements. This greatly improves the aperture and direction sharpness of original array and reduces the cost of follow-up hardware. With the cross-shaped ultrasonic array, the results of PD location experiments are precise and the maximum error of the direction of arrival (DOA) is less than 5°.

  17. Dehydroepiandrosterone affects the expression of multiple genes in rat liver including 11 beta-hydroxysteroid dehydrogenase type 1: a cDNA array analysis.

    Science.gov (United States)

    Gu, Shi; Ripp, Sharon L; Prough, Russell A; Geoghegan, Thomas E

    2003-03-01

    Dehydroepiandrosterone (DHEA) is a C-19 adrenal steroid precursor to the gonadal steroids. In humans, circulating levels of DHEA, as its sulfated conjugate, are high at puberty and throughout early adulthood but decline with age. Dietary supplementation to maintain high levels of DHEA purportedly has beneficial effects on cognitive memory, the immune system, and fat and carbohydrate metabolism. In rodents, DHEA is a peroxisome proliferator that induces genes for the classical peroxisomal and microsomal enzymes associated with this response. These effects are mediated through activation of peroxisome proliferator-activated receptor alpha (PPAR alpha). However, DHEA can affect the expression of genes independently of PPAR alpha, including the gene for the major inducible drug and xenobiotic metabolizing enzyme, cytochrome P450 3A23. To elucidate the biochemistry associated with DHEA treatment, we employed a cDNA gene expression array using liver RNA from rats treated with DHEA or the classic peroxisome proliferator nafenopin. Principal components analysis identified 30 to 35 genes whose expression was affected by DHEA and/or nafenopin. Some were genes previously identified as PPAR-responsive genes. Changes in expression of several affected genes were verified by quantitative reverse transcriptase-polymerase chain reaction. These included aquaporin 3, which was induced by DHEA and to a lesser extent nafenopin, nuclear tyrosine phosphatase, which was induced by both agents, and 11 beta-hydroxysteroid dehydrogenase 1, which was decreased by treatment with DHEA in a dose-dependent fashion. Regulation of 11 beta-hydroxysteroid dehydrogenase 1 expression is important since the enzyme is believed to amplify local glucocorticoid signaling, and its repression may cause some of the metabolic effects associated with DHEA.

  18. The KCNE genes in hypertrophic cardiomyopathy: a candidate gene study

    Directory of Open Access Journals (Sweden)

    Moolman-Smook Johanna C

    2011-10-01

    Full Text Available Abstract Background The gene family KCNE1-5, which encode modulating β-subunits of several repolarising K+-ion channels, has been associated with genetic cardiac diseases such as long QT syndrome, atrial fibrillation and Brugada syndrome. The minK peptide, encoded by KCNE1, is attached to the Z-disc of the sarcomere as well as the T-tubules of the sarcolemma. It has been suggested that minK forms part of an "electro-mechanical feed-back" which links cardiomyocyte stretching to changes in ion channel function. We examined whether mutations in KCNE genes were associated with hypertrophic cardiomyopathy (HCM, a genetic disease associated with an improper hypertrophic response. Results The coding regions of KCNE1, KCNE2, KCNE3, KCNE4, and KCNE5 were examined, by direct DNA sequencing, in a cohort of 93 unrelated HCM probands and 188 blood donor controls. Fifteen genetic variants, four previously unknown, were identified in the HCM probands. Eight variants were non-synonymous and one was located in the 3'UTR-region of KCNE4. No disease-causing mutations were found and no significant difference in the frequency of genetic variants was found between HCM probands and controls. Two variants of likely functional significance were found in controls only. Conclusions Mutations in KCNE genes are not a common cause of HCM and polymorphisms in these genes do not seem to be associated with a propensity to develop arrhythmia

  19. Novel Hamamatsu Multi-Pixel Photon Counter (MPPC) array studies for the GlueX experiment: New results

    Science.gov (United States)

    Soto, Orlando; Rojas, Rimsky; Kuleshov, Sergey; Hakobyan, Hayk; Toro, Alam; Brooks, William K.; Rios, Rene

    2014-03-01

    The novel Hamamatsu Multi-Pixel Photon Counter (MPPC) S12045(X) is an array of 16 individual 3×3 mm2 MPPC devices each with 3600 Geiger-mode Avalanche Photodiode pixels of 50×50 μm2. Each MPPC in the array operates at a reverse bias of approximately 70 V. This paper summarizes our characterization of MPPC arrays used in the GlueX experiment in Hall D at Thomas Jefferson National Accelerator Facility (Jefferson Lab). We studied the main features of each of the 16 MPPC array channels for 2800 MPPC arrays at several different temperatures. Two measurement stations were built to extract gain, breakdown voltage, photon detection efficiency, optical crosstalk and dark rate for each of the 44 800 MPPC array channels at each temperature setting. The hardware and the data analysis are described, and new analytical expressions for the mean number of photoelectrons and optical crosstalk are presented, as well as systematic trends of the performance parameters.

  20. Novel Hamamatsu Multi-Pixel Photon Counter (MPPC) array studies for the GlueX experiment: New results

    Energy Technology Data Exchange (ETDEWEB)

    Soto, Orlando; Rojas, Rimsky; Kuleshov, Sergey; Hakobyan, Hayk, E-mail: hayk.hakobyan@usm.cl; Toro, Alam; Brooks, William K.; Rios, Rene

    2014-03-01

    The novel Hamamatsu Multi-Pixel Photon Counter (MPPC) S12045(X) is an array of 16 individual 3×3 mm{sup 2} MPPC devices each with 3600 Geiger-mode Avalanche Photodiode pixels of 50×50 μm{sup 2}. Each MPPC in the array operates at a reverse bias of approximately 70 V. This paper summarizes our characterization of MPPC arrays used in the GlueX experiment in Hall D at Thomas Jefferson National Accelerator Facility (Jefferson Lab). We studied the main features of each of the 16 MPPC array channels for 2800 MPPC arrays at several different temperatures. Two measurement stations were built to extract gain, breakdown voltage, photon detection efficiency, optical crosstalk and dark rate for each of the 44 800 MPPC array channels at each temperature setting. The hardware and the data analysis are described, and new analytical expressions for the mean number of photoelectrons and optical crosstalk are presented, as well as systematic trends of the performance parameters.

  1. High-resolution SNP array analysis of patients with developmental disorder and normal array CGH results

    Directory of Open Access Journals (Sweden)

    Siggberg Linda

    2012-09-01

    Full Text Available Abstract Background Diagnostic analysis of patients with developmental disorders has improved over recent years largely due to the use of microarray technology. Array methods that facilitate copy number analysis have enabled the diagnosis of up to 20% more patients with previously normal karyotyping results. A substantial number of patients remain undiagnosed, however. Methods and Results Using the Genome-Wide Human SNP array 6.0, we analyzed 35 patients with a developmental disorder of unknown cause and normal array comparative genomic hybridization (array CGH results, in order to characterize previously undefined genomic aberrations. We detected no seemingly pathogenic copy number aberrations. Most of the vast amount of data produced by the array was polymorphic and non-informative. Filtering of this data, based on copy number variant (CNV population frequencies as well as phenotypically relevant genes, enabled pinpointing regions of allelic homozygosity that included candidate genes correlating to the phenotypic features in four patients, but results could not be confirmed. Conclusions In this study, the use of an ultra high-resolution SNP array did not contribute to further diagnose patients with developmental disorders of unknown cause. The statistical power of these results is limited by the small size of the patient cohort, and interpretation of these negative results can only be applied to the patients studied here. We present the results of our study and the recurrence of clustered allelic homozygosity present in this material, as detected by the SNP 6.0 array.

  2. Field study of cyclic hypoxic effects on gene expression in grass shrimp hepatopancreas.

    Science.gov (United States)

    Li, Tiandao; Brouwer, Marius

    2013-12-01

    Grass shrimp, Palaemonetes pugio, are widely used for ecological and toxicological research. They commonly experience cyclic hypoxia in their natural habitats. The response of grass shrimp to laboratory-controlled cyclic hypoxia has been studied in detail, but little is known about how field acclimatized grass shrimp regulate the gene expression and response to cyclic hypoxia. In this study we examined morphometric parameters, relative fecundity and gene expression of grass shrimp collected from two areas in Weeks Bay (Mobile, Alabama). One is a traditionally normoxic location (WBM), and the other is a traditionally cyclic hypoxic location (WC). In the week preceding grass shrimp collection dissolved oxygen (DO) at the field sites was measured continuously. DO was shrimp were significantly greater than weight and length of WC shrimp. WBM shrimp had more eggs than WC shrimp, but the difference was not significant. Shrimp from WC had a significant higher number of parasites than those from WBM. A cDNA microarray was utilized to investigate the changes in gene expression in grass shrimp hepatopancreas. Five genes, previously identified as hypoxia/cyclic hypoxia-responsive genes in laboratory exposure studies, were significantly up-regulated in WC shrimp relative to WBM. A total of 5 genes were significantly down-regulated in the field study. Only one of those genes, vitellogenin, has been previously found in chronic and cyclic hypoxic studies. Up and down-regulation of 7 selected genes was confirmed by qPCR. The overall pattern of gene expression in wild shrimp from cyclic DO sites in Weeks Bay showed only weak correlations with gene expression in shrimp from chronic and cyclic hypoxic laboratory studies. It appears therefore that transcriptome profiles of laboratory acclimated animals are of limited utility for understanding responses in field acclimatized animals that are exposed to a broader array of environmental variables.

  3. Global nutrient profiling by Phenotype MicroArrays: a tool complementing genomic and proteomic studies in conidial fungi*

    Science.gov (United States)

    Atanasova, Lea; Druzhinina, Irina S.

    2010-01-01

    Conidial fungi or molds and mildews are widely used in modern biotechnology as producers of antibiotics and other secondary metabolites, industrially important enzymes, chemicals and food. They are also important pathogens of animals including humans and agricultural crops. These various applications and extremely versatile natural phenotypes have led to the constantly growing list of complete genomes which are now available. Functional genomics and proteomics widely exploit the genomic information to study the cell-wide impact of altered genes on the phenotype of an organism and its function. This allows for global analysis of the information flow from DNA to RNA to protein, but it is usually not sufficient for the description of the global phenotype of an organism. More recently, Phenotype MicroArray (PM) technology has been introduced as a tool to characterize the metabolism of a (wild) fungal strain or a mutant. In this article, we review the background of PM applications for fungi and the methodic requirements to obtain reliable results. We also report examples of the versatility of this tool. PMID:20205302

  4. A study of bacterial gene regulatory mechanisms

    DEFF Research Database (Denmark)

    Hansen, Sabine

    regulator studied accurately reproduced the experimental data. Simulations of system dynamics reveals that even two step regulatory cascades significantly increase response times compared to direct allosteric regulation of a transcription factor. It is observed that while many system behaviors...... of GRNs this thesis also provided the first evidence of the sensor histidine kinase VC1831 being an additional player in the Vibrio cholerae quorum sensing (QS) GRN. Bacteria use a process of cell-cell communication called QS which enable the bacterial cells to collectively control their gene expression...

  5. The Use of High-Density SNP Array to Map Homozygosity in Consanguineous Families to Efficiently Identify Candidate Genes: Application to Woodhouse-Sakati Syndrome

    Directory of Open Access Journals (Sweden)

    Molly B. Sheridan

    2015-01-01

    Full Text Available Two consanguineous Qatari siblings presented for evaluation: a 17-4/12-year-old male with hypogonadotropic hypogonadism, alopecia, intellectual disability, and microcephaly and his 19-year-old sister with primary amenorrhea, alopecia, and normal cognition. Both required hormone treatment to produce secondary sex characteristics and pubertal development beyond Tanner 1. SNP array analysis of both probands was performed to detect shared regions of homozygosity which may harbor homozygous mutations in a gene causing their common features of abnormal pubertal development, alopecia, and variable cognitive delay. Our patients shared multiple homozygous genomic regions; ten shared regions were >1 Mb in length and constituted 0.99% of the genome. DCAF17, encoding a transmembrane nuclear protein of uncertain function, was the only gene identified in a homozygous region known to cause hypogonadotropic hypogonadism. DCAF17 mutations are associated with Woodhouse-Sakati syndrome, a rare disorder characterized by alopecia, hypogonadotropic hypogonadism, sensorineural hearing loss, diabetes mellitus, and extrapyramidal movements. Sequencing of the coding exons and flanking intronic regions of DCAF17 in the proband revealed homozygosity for a previously described founder mutation (c.436delC. Targeted DCAF17 sequencing of his affected sibling revealed the same homozygous mutation. This family illustrates the utility of SNP array testing in consanguineous families to efficiently and inexpensively identify regions of genomic homozygosity in which genetic candidates for recessive conditions can be identified.

  6. Study of multiwavelength DFB semiconductor laser array with asymmetric structures based on sampling technique.

    Science.gov (United States)

    Shi, Yuechun; Cao, Baoli; Li, Lianyan; Tang, Song; Zheng, Junshou; Zhang, Peng; Chen, Ting; Liu, Shengchun

    2014-10-10

    Multiwavelength distributed feedback (DFB) semiconductor laser arrays (MLA) with asymmetric structures are studied in this paper. Thanks to the sampling technique, the asymmetric structures, including asymmetric phase shift and asymmetric coupling coefficient, can be achieved by common holographic exposure. Therefore, the cost of fabrication is remarkably reduced. In addition, due to the large scale of the sampling pattern, the wavelength precision of these kinds of MLA can be simultaneously improved. As an example, we designed and fabricated an asymmetrically phase-shifted MLA with 10 wavelengths for the first time. Compared with the common phase-shifted DFB laser, slope efficiency is significantly improved and single longitudinal mode is still guaranteed. Besides, relatively high wavelength precision is also obtained. The proposed MLA configurations may significantly benefit multiwavelength emitters for future photonic integration.

  7. Array configuration studies for the SKA -- Implementation of figures of merit based on SDR

    CERN Document Server

    Lal, Dharam V

    2007-01-01

    The Square Kilometre Array is going to become operational at the time when several new large optical, X-ray and Gamma-ray telescopes are expected to be working. The main drive for building the SKA is a significant improvement of sensitivity that would widen the general scope of the centimetre-wavelength radio science. To this end, a thorough design studies should be made, in order to ensure that the SKA becomes a competitive counterpart of the facilities at other wavebands. To quantify imaging performance of the SKA configurations, we are implementing figures of merit based on spatial dynamic range (SDR). This work is focused on extensive numerical tests of the analytical, SDR--based figures of merit derived in the SKA Memo 38 (A. Lobanov). Here, we present our preliminary results.

  8. Statistical magnetometry on isolated NiCo nanowires and nanowire arrays: a comparative study

    Science.gov (United States)

    Sergelius, Philip; Garcia Fernandez, Javier; Martens, Stefan; Zocher, Michael; Böhnert, Tim; Vega Martinez, Victor; de la Prida, Victor Manuel; Görlitz, Detlef; Nielsch, Kornelius

    2016-04-01

    The first-order reversal curve (FORC) method can be used to extract information about the interaction and switching field distribution of ferromagnetic nanowire arrays, yet it remains challenging to acquire reliable values. Within ordered pores of anodic alumina templates we electrochemically synthesize eight different Ni x Co1-x samples with x varying between 0.05 and 1. FORC diagrams are acquired using vibrating sample magnetometry. By dissolving the template and using the magneto-optical Kerr effect, we measure the hysteresis loops of up to 100 different and isolated nanowires for each sample to gain precise information about the intrinsic switching field distribution. Values of the interaction field are extracted from a deshearing of the major hysteresis loop. We present a comparative study between all methods in order to evaluate and reinforce current FORC theory with experimental findings.

  9. DLTS Study of RIE-Induced Deep Levels in Si Using p+n Diode Arrays

    Science.gov (United States)

    Watanabe, Miyoko Oku; Taguchi, Minoru; Kanzaki, Koichi; Zohta, Yasuhito

    1983-02-01

    Deep levels in Si induced by reactive ion etching (RIE) of SiO2 film have been studied by DLTS. In order to detect the RIE-induced damage existing near the surface region, special device structures consisting of p+n diode arrays are used. It is found that the dominant deep levels produced by RIE are four hole traps. One level at Ev+0.40 eV exhibits the Poole-Frenkel effect, from which it is identified as an acceptor. Another level at Ev+0.46 eV is deduced to be an interstitial iron level from the emission rate. There is a strong decrease in the deep level concentrations upon annealing above 500°C. However, the deep levels do not completely disappear upon annealing at high temperatures. The deep level concentrations correlate well with the current-voltage characteristics of the devices.

  10. Photo-enhanced field emission study of TiO{sub 2} nanotubes array

    Energy Technology Data Exchange (ETDEWEB)

    Chavan, Padmakar G.; Shende, Sugat V.; Joag, Dilip S. [Center for Advanced Studies in Materials Science and Condensed Matter Physics, Department of Physics, University of Pune, Pune 411007 (India); More, Mahendra A., E-mail: mam@physics.unipune.ac.in [Center for Advanced Studies in Materials Science and Condensed Matter Physics, Department of Physics, University of Pune, Pune 411007 (India)

    2011-05-15

    Aligned TiO{sub 2} nanotubes were synthesized by simple anodization of the Ti foil surface. The as-anodized product is further characterized by SEM, XRD, and PL. The tube inner diameter is found to be {approx}60-80 nm with the average wall thickness {approx}30 nm and areal density {approx}15x10{sup 6}/ cm{sup 2}. FE studies of the aligned TiO{sub 2} nanotubes are carried out at base pressure of {approx}1x10{sup -8} mbar. The turn-on field observed for an emission current density of {approx}10 {mu}A/cm{sup 2} is found to be {approx}1.7 V/{mu}m and current density of {approx}44 {mu}A/cm{sup 2} is obtained at an applied field of {approx}2.3 V/{mu}m. Photo-enhanced FE study is carried out by shining visible and UV light on the cathode. The aligned TiO{sub 2} nanotubes show sensitivity to both the light sources. The FE current shows fast switching response to the visible light. The increment in the preset current upon UV illumination can be attributed to the band edge excitation of the electrons. The free excitons associated with band gap of the TiO{sub 2} nanotubes array may be responsible for the visible light sensitivity. TiO{sub 2} nanotubes are also grown on the Ti wire and exhibit similar photo-enhanced behavior. The FE and photo-enhanced FE properties demonstrate the applicability of the aligned TiO{sub 2} nanotubes in the FE based micro/nanoelectronic devices. -- Research Highlights: {yields} TiO{sub 2} nanotubes array is easily synthesized by simple anodization method. {yields} Field emission results are found to be superior. {yields} Good correlation is found between photoluminescence, photo-enhanced field emission, and photoconductivity of the TiO{sub 2}.

  11. Feasibility of the use of combinatorial chemokine arrays to study blood and CSF in multiple sclerosis.

    Directory of Open Access Journals (Sweden)

    Keith R Edwards

    Full Text Available Meningeal inflammation, including the presence of semi-organized tertiary lymphoid tissue, has been associated with cortical pathology at autopsy in secondary progressive multiple sclerosis (SPMS. Accessible and robust biochemical markers of cortical inflammation for use in SPMS clinical trials are needed. Increased levels of chemokines in the cerebrospinal fluid (CSF can report on inflammatory processes occurring in the cerebral cortex of MS patients. A multiplexed chemokine array that included BAFF, a high sensitivity CXCL13 assay and composite chemokine scores were developed to explore differences in lymphoid (CXCL12, CXCL13, CCL19 and CCL21 and inflammatory (CCL2, CXCL9, CXCL10 and CXCL11 chemokines in a small pilot study. Paired CSF and serum samples were obtained from healthy controls (n=12, relapsing-remitting MS (RRMS (n=21 and SPMS (N=12. A subset of the RRMS patients (n = 9 was assessed upon disease exacerbation and 1 month later following iv methylprednisone. SPMS patients were sampled twice to ascertain stability. Both lymphoid and inflammatory chemokines were elevated in RRMS and SPMS with the highest levels found in the active RRMS group. Inflammatory and lymphoid chemokine signatures were defined and generally correlated with each other. This small exploratory clinical study shows the feasibility of measuring complex and potentially more robust chemokine signatures in the CSF of MS patients during clinical trials. No differences were found between stable RRMS and SPMS. Future trials with larger patient cohorts with this chemokine array are needed to further characterize the differences, or the lack thereof, between stable RRMS and SPMS.

  12. Design Studies for a VUV--Soft X-ray Free-Electron Laser Array

    Energy Technology Data Exchange (ETDEWEB)

    Corlett, J.; Baptiste, K.; Byrd, J.M.; Denes, P.; Falcone, R.; Kirz, J.; McCurdy, W.; Padmore, H.; Penn, G.; Qiang, J.; Robin, D.; Sannibale, F.; Schoenlein, R.; Staples, J.; Steier, C.; Venturnini, M.; Wan, W.; Wells, R.; Wilcox, R.; Zholents, A.

    2009-08-04

    Several recent reports have identified the scientific requirements for a future soft X-ray light source [1, 2, 3, 4, 5], and a high-repetition-rate free-electron laser (FEL) facility responsive to them is being studied at Lawrence Berkeley National Laboratory (LBNL) [6]. The facility is based on a continuous-wave (CW) superconducting linear accelerator with beam supplied by a high-brightness, high-repetition-rate photocathode electron gun operating in CW mode, and on an array of FELs to which the accelerated beam is distributed, each operating at high repetition rate and with even pulse spacing. Dependent on the experimental requirements, the individualFELs may be configured for either self-amplified spontaneous emission (SASE), seeded highgain harmonic generation (HGHG), echo-enabled harmonic generation (EEHG), or oscillator mode of operation, and will produce high peak and average brightness x-rays with a flexible pulse format ranging from sub-femtoseconds to hundreds of femtoseconds. This new light source would serve a broad community of scientists in many areas of research, similar to existing utilization of storage ring based light sources. To reduce technical risks and constructioncosts, accelerator research, development, and design studies at LBNL target the most critical components and systems of the facility. We are developing a high-repetition-rate low-emittance electron gun, high quantum efficiency photocathodes, and have embarked on design and optimization of the electron beam accelerator, FEL switchyard, and array of FELs. We continue our work on precision timing and synchronization systems critical for time-resolved experiments using pump-probe techniques.

  13. Nanoindentation study of the mechanical behavior of TiO{sub 2} nanotube arrays

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Y. N.; Wang, M. C.; Oloyede, A.; Bell, J. M.; Yan, C., E-mail: c2.yan@qut.edu.au [School of Chemistry, Physics and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology (QUT), Brisbane, Queensland 4001 (Australia); Liu, M. N. [i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Science, Suzhou (China)

    2015-10-14

    Titanium dioxide (TiO{sub 2}) nanotube arrays are attracting increasing attention for use in solar cells, lithium-ion batteries, and biomedical implants. To take full advantage of their unique physical properties, such arrays need to maintain adequate mechanical integrity in applications. However, the mechanical performance of TiO{sub 2} nanotube arrays is not well understood. In this work, we investigate the deformation and failure of TiO{sub 2} nanotube arrays using the nanoindentation technique. We found that the load–displacement response of the arrays strongly depends on the indentation depth and indenter shape. Substrate-independent elastic modulus and hardness can be obtained when the indentation depth is less than 2.5% of the array height. The deformation mechanisms of TiO{sub 2} nanotube arrays by Berkovich and conical indenters are closely associated with the densification of TiO{sub 2} nanotubes under compression. A theoretical model for deformation of the arrays under a large-radius conical indenter is also proposed.

  14. Coupling multielectrode array recordings with silver labeling of recording sites to study cervical spinal network connectivity.

    Science.gov (United States)

    Streeter, K A; Sunshine, M D; Patel, S R; Liddell, S S; Denholtz, L E; Reier, P J; Fuller, D D; Baekey, D M

    2017-03-01

    Midcervical spinal interneurons form a complex and diffuse network and may be involved in modulating phrenic motor output. The intent of the current work was to enable a better understanding of midcervical "network-level" connectivity by pairing the neurophysiological multielectrode array (MEA) data with histological verification of the recording locations. We first developed a method to deliver 100-nA currents to electroplate silver onto and subsequently deposit silver from electrode tips after obtaining midcervical (C3-C5) recordings using an MEA in anesthetized and ventilated adult rats. Spinal tissue was then fixed, harvested, and histologically processed to "develop" the deposited silver. Histological studies verified that the silver deposition method discretely labeled (50-μm resolution) spinal recording locations between laminae IV and X in cervical segments C3-C5. Using correlative techniques, we next tested the hypothesis that midcervical neuronal discharge patterns are temporally linked. Cross-correlation histograms produced few positive peaks (5.3%) in the range of 0-0.4 ms, but 21.4% of neuronal pairs had correlogram peaks with a lag of ≥0.6 ms. These results are consistent with synchronous discharge involving mono- and polysynaptic connections among midcervical neurons. We conclude that there is a high degree of synaptic connectivity in the midcervical spinal cord and that the silver-labeling method can reliably mark metal electrode recording sites and "map" interneuron populations, thereby providing a low-cost and effective tool for use in MEA experiments. We suggest that this method will be useful for further exploration of midcervical network connectivity.NEW & NOTEWORTHY We describe a method that reliably identifies the locations of multielectrode array (MEA) recording sites while preserving the surrounding tissue for immunohistochemistry. To our knowledge, this is the first cost-effective method to identify the anatomic locations of neuronal

  15. Gene-environment interaction effects on lung function- a genome-wide association study within the Framingham heart study

    Science.gov (United States)

    2013-01-01

    Background Previous studies in occupational exposure and lung function have focused only on the main effect of occupational exposure or genetics on lung function. Some disease-susceptible genes may be missed due to their low marginal effects, despite potential involvement in the disease process through interactions with the environment. Through comprehensive genome-wide gene-environment interaction studies, we can uncover these susceptibility genes. Our objective in this study was to explore gene by occupational exposure interaction effects on lung function using both the individual SNPs approach and the genetic network approach. Methods The study population comprised the Offspring Cohort and the Third Generation from the Framingham Heart Study. We used forced expiratory volume in one second (FEV1) and ratio of FEV1 to forced vital capacity (FVC) as outcomes. Occupational exposures were classified using a population-specific job exposure matrix. We performed genome-wide gene-environment interaction analysis, using the Affymetrix 550 K mapping array for genotyping. A linear regression-based generalized estimating equation was applied to account for within-family relatedness. Network analysis was conducted using results from single-nucleotide polymorphism (SNP)-level analyses and from gene expression study results. Results There were 4,785 participants in total. SNP-level analysis and network analysis identified SNP rs9931086 (Pinteraction =1.16 × 10-7) in gene SLC38A8, which may significantly modify the effects of occupational exposure on FEV1. Genes identified from the network analysis included CTLA-4, HDAC, and PPAR-alpha. Conclusions Our study implies that SNP rs9931086 in SLC38A8 and genes CTLA-4, HDAC, and PPAR-alpha, which are related to inflammatory processes, may modify the effect of occupational exposure on lung function. PMID:24289273

  16. Options Studied for Managing Space Station Solar Array Electrical Hazards for Sequential Shunt Unit Replacement

    Science.gov (United States)

    Delleur, Ann M.; Kerslake, Thomas W.; Levy, Robert K.

    2004-01-01

    The U.S. solar array strings on the International Space Station are connected to a sequential shunt unit (SSU). The job of the SSU is to shunt, or short, the excess current from the solar array, such that just enough current is provided downstream to maintain the 160-V bus voltage while meeting the power load demand and recharging the batteries. Should an SSU fail on-orbit, it would be removed and replaced with the on-orbit spare during an astronaut space walk or extravehicular activity (EVA) (see the photograph). However, removing an SSU during an orbit Sun period with input solar array power connectors fully energized could result in substantial hardware damage and/or safety risk to the EVA astronaut. The open-circuit voltage of cold solar-array strings can exceed 320 V, and warm solar-array strings could feed a short circuit with a total current level exceeding 240 A.

  17. Integrating murine gene expression studies to understand obstructive lung disease due to chronic inhaled endotoxin.

    Directory of Open Access Journals (Sweden)

    Peggy S Lai

    Full Text Available RATIONALE: Endotoxin is a near ubiquitous environmental exposure that that has been associated with both asthma and chronic obstructive pulmonary disease (COPD. These obstructive lung diseases have a complex pathophysiology, making them difficult to study comprehensively in the context of endotoxin. Genome-wide gene expression studies have been used to identify a molecular snapshot of the response to environmental exposures. Identification of differentially expressed genes shared across all published murine models of chronic inhaled endotoxin will provide insight into the biology underlying endotoxin-associated lung disease. METHODS: We identified three published murine models with gene expression profiling after repeated low-dose inhaled endotoxin. All array data from these experiments were re-analyzed, annotated consistently, and tested for shared genes found to be differentially expressed. Additional functional comparison was conducted by testing for significant enrichment of differentially expressed genes in known pathways. The importance of this gene signature in smoking-related lung disease was assessed using hierarchical clustering in an independent experiment where mice were exposed to endotoxin, smoke, and endotoxin plus smoke. RESULTS: A 101-gene signature was detected in three murine models, more than expected by chance. The three model systems exhibit additional similarity beyond shared genes when compared at the pathway level, with increasing enrichment of inflammatory pathways associated with longer duration of endotoxin exposure. Genes and pathways important in both asthma and COPD were shared across all endotoxin models. Mice exposed to endotoxin, smoke, and smoke plus endotoxin were accurately classified with the endotoxin gene signature. CONCLUSIONS: Despite the differences in laboratory, duration of exposure, and strain of mouse used in three experimental models of chronic inhaled endotoxin, surprising similarities in gene

  18. Leader genes in osteogenesis: a theoretical study.

    Science.gov (United States)

    Orlando, Bruno; Giacomelli, Luca; Ricci, Massimiliano; Barone, Antonio; Covani, Ugo

    2013-01-01

    Little is still known about the molecular mechanisms involved in the process of osteogenesis. In this paper, the leader genes approach, a new bioinformatics method which has already been experimentally validated, is adopted in order to identify the genes involved in human osteogenesis. Interactions among genes are then calculated and genes are ranked according to their relative importance in this process. In total, 167 genes were identified as being involved in osteogenesis. Genes were divided into 4 groups, according to their main function in the osteogenic processes: skeletal development; cell adhesion and proliferation; ossification; and calcium ion binding. Seven genes were consistently identified as leader genes (i.e. the genes with the greatest importance in osteogenesis), while 14 were found to have slightly less importance (class B genes). It was interesting to notice that the larger part of leader and class B genes belonged to the cell adhesion and proliferation or to the ossification sub-groups. This finding suggested that these two particular sub-processes could play a more important role in osteogenesis. Moreover, among the 7 leader genes, it is interesting to notice that RUNX2, BMP2, SPARC, PTH play a direct role in bone formation, while the 3 other leader genes (VEGF, IL6, FGF2) seem to be more connected with an angiogenetic process. Twenty-nine genes have no known interactions (orphan genes). From these results, it may be possible to plan an ad hoc experimentation, for instance by microarray analyses, focused on leader, class B and orphan genes, with the aim to shed new light on the molecular mechanisms underlying osteogenesis.

  19. Targeted array comparative genomic hybridization--a new diagnostic tool for the detection of large copy number variations in nemaline myopathy-causing genes.

    Science.gov (United States)

    Kiiski, K; Laari, L; Lehtokari, V-L; Lunkka-Hytönen, M; Angelini, C; Petty, R; Hackman, P; Wallgren-Pettersson, C; Pelin, K

    2013-01-01

    Nemaline myopathy (NM) constitutes a heterogeneous group of congenital myopathies. Mutations in the nebulin gene (NEB) are the main cause of recessively inherited NM. NEB is one of the most largest genes in human. To date, 68 NEB mutations, mainly small deletions or point mutations have been published. The only large mutation characterized is the 2.5 kb deletion of exon 55 in the Ashkenazi Jewish population. To investigate any copy number variations in this enormous gene, we designed a novel custom comparative genomic hybridization microarray, NM-CGH, targeted towards the seven known genes causative for NM. During the validation of the NM-CGH array we identified two novel deletions in two different families. The first is the largest deletion characterized in NEB to date, (∼53 kb) encompassing 24 exons. The second deletion (1 kb) covers two exons. In both families, the copy number change was the second mutation to be characterized and shown to have been inherited from one of the healthy carrier parents. In addition to these novel mutations, copy number variation was identified in four samples in three families in the triplicate region of NEB. We conclude that this method appears promising for the detection of copy number variations in NEB. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. Cell behavior observation and gene expression analysis of melanoma associated with stromal fibroblasts in a three-dimensional magnetic cell culture array.

    Science.gov (United States)

    Okochi, Mina; Matsumura, Taku; Yamamoto, And Shuhei; Nakayama, Eiichi; Jimbow, Kowichi; Honda, Hiroyuki

    2013-01-01

    A three-dimensional (3D) multicellular tumor spheroid culture array has been fabricated using a magnetic force-based cell patterning method, analyzing the effect of stromal fibroblast on the invasive capacity of melanoma. Formation of spheroids was observed when array-like multicellular patterns of melanoma were developed using a pin-holder device made of magnetic soft iron and an external magnet, which enables the assembly of the magnetically labeled cells on the collagen gel-coated surface as array-like cell patterns. The interaction of fibroblast on the invasion of melanoma was investigated using three types of cell interaction models: (i) fibroblasts were magnetically labeled and patterned together in array with melanoma spheroids (direct-interaction model), (ii) fibroblasts coexisting in the upper collagen gel (indirect-interaction model) of melanoma spheroids, and (iii) fibroblast-sheets coexisting under melanoma spheroids (fibroblast-sheet model). The fibroblast-sheet model has largely increased the invasive capacity of melanoma, and the promotion of adhesion, migration, and invasion were also observed. In the fibroblast-sheet model, the expression of IL-8 and MMP-2 increased by 24-fold and 2-fold, respectively, in real time RT-PCR compared to the absence of fibroblasts. The results presented in this study demonstrate the importance of fibroblast interaction to invasive capacity of melanoma in the 3D in vitro bioengineered tumor microenvironment.

  1. Improved focalization of electrical microstimulation using microelectrode arrays: a modeling study.

    Directory of Open Access Journals (Sweden)

    Sébastien Joucla

    Full Text Available Extracellular electrical stimulation (EES of the central nervous system (CNS has been used empirically for decades, with both fundamental and clinical goals. Currently, microelectrode arrays (MEAs offer new possibilities for CNS microstimulation. However, although focal CNS activation is of critical importance to achieve efficient stimulation strategies, the precise spatial extent of EES remains poorly understood. The aim of the present work is twofold. First, we validate a finite element model to compute accurately the electrical potential field generated throughout the extracellular medium by an EES delivered with MEAs. This model uses Robin boundary conditions that take into account the surface conductance of electrode/medium interfaces. Using this model, we determine how the potential field is influenced by the stimulation and ground electrode impedances, and by the electrical conductivity of the neural tissue. We confirm that current-controlled stimulations should be preferred to voltage-controlled stimulations in order to control the amplitude of the potential field. Second, we evaluate the focality of the potential field and threshold-distance curves for different electrode configurations. We propose a new configuration to improve the focality, using a ground surface surrounding all the electrodes of the array. We show that the lower the impedance of this surface, the more focal the stimulation. In conclusion, this study proposes new boundary conditions for the design of precise computational models of extracellular stimulation, and a new electrode configuration that can be easily incorporated into future MEA devices, either in vitro or in vivo, for a better spatial control of CNS microstimulation.

  2. Demonstration of diet-induced decoupling of fatty acid and cholesterol synthesis by combining gene expression array and 2H2O quantification.

    Science.gov (United States)

    Jensen, Kristian K; Previs, Stephen F; Zhu, Lei; Herath, Kithsiri; Wang, Sheng-Ping; Bhat, Gowri; Hu, Guanghui; Miller, Paul L; McLaren, David G; Shin, Myung K; Vogt, Thomas F; Wang, Liangsu; Wong, Kenny K; Roddy, Thomas P; Johns, Douglas G; Hubbard, Brian K

    2012-01-15

    The liver is a crossroad for metabolism of lipid and carbohydrates, with acetyl-CoA serving as an important metabolic intermediate and a precursor for fatty acid and cholesterol biosynthesis pathways. A better understanding of the regulation of these pathways requires an experimental approach that provides both quantitative metabolic flux measurements and mechanistic insight. Under conditions of high carbohydrate availability, excess carbon is converted into free fatty acids and triglyceride for storage, but it is not clear how excessive carbohydrate availability affects cholesterol biosynthesis. To address this, C57BL/6J mice were fed either a low-fat, high-carbohydrate diet or a high-fat, carbohydrate-free diet. At the end of the dietary intervention, the two groups received (2)H(2)O to trace de novo fatty acid and cholesterol synthesis, and livers were collected for gene expression analysis. Expression of lipid and glucose metabolism genes was determined using a custom-designed pathway focused PCR-based gene expression array. The expression analysis showed downregulation of cholesterol biosynthesis genes and upregulation of fatty acid synthesis genes in mice receiving the high-carbohydrate diet compared with the carbohydrate-free diet. In support of these findings, (2)H(2)O tracer data showed that fatty acid synthesis was increased 10-fold and cholesterol synthesis was reduced by 1.6-fold in mice fed the respective diets. In conclusion, by applying gene expression analysis and tracer methodology, we show that fatty acid and cholesterol synthesis are differentially regulated when the carbohydrate intake in mice is altered.

  3. LegumeIP 2.0--a platform for the study of gene function and genome evolution in legumes.

    Science.gov (United States)

    Li, Jun; Dai, Xinbin; Zhuang, Zhaohong; Zhao, Patrick X

    2016-01-04

    The LegumeIP 2.0 database hosts large-scale genomics and transcriptomics data and provides integrative bioinformatics tools for the study of gene function and evolution in legumes. Our recent updates in LegumeIP 2.0 include gene and protein sequences, gene models and annotations, syntenic regions, protein families and phylogenetic trees for six legume species: Medicago truncatula, Glycine max (soybean), Lotus japonicus, Phaseolus vulgaris (common bean), Cicer arietinum (chickpea) and Cajanus cajan (pigeon pea) and two outgroup reference species: Arabidopsis thaliana and Poplar trichocarpa. Moreover, the LegumeIP 2.0 features the following new data resources and bioinformatics tools: (i) an integrative gene expression atlas for four model legumes that include 550 array hybridizations from M. truncatula, 962 gene expression profiles of G. max, 276 array hybridizations from L. japonicas and 56 RNA-Seq-based gene expression profiles for C. arietinum. These datasets were manually curated and hierarchically organized based on Experimental Ontology and Plant Ontology so that users can browse, search, and retrieve data for their selected experiments. (ii) New functions/analytical tools to query, mine and visualize large-scale gene sequences, annotations and transcriptome profiles. Users may select a subset of expression experiments and visualize and compare expression profiles for multiple genes. The LegumeIP 2.0 database is freely available to the public at http://plantgrn.noble.org/LegumeIP/.

  4. Identification of Hematopoietic Stem Cell Engraftment Genes in Gene Therapy Studies.

    Science.gov (United States)

    Powers, John M; Trobridge, Grant D

    2013-09-01

    Hematopoietic stem cell (HSC) therapy using replication-incompetent retroviral vectors is a promising approach to provide life-long correction for genetic defects. HSC gene therapy clinical studies have resulted in functional cures for several diseases, but in some studies clonal expansion or leukemia has occurred. This is due to the dyregulation of endogenous host gene expression from vector provirus insertional mutagenesis. Insertional mutagenesis screens using replicating retroviruses have been used extensively to identify genes that influence oncogenesis. However, retroviral mutagenesis screens can also be used to determine the role of genes in biological processes such as stem cell engraftment. The aim of this review is to describe the potential for vector insertion site data from gene therapy studies to provide novel insights into mechanisms of HSC engraftment. In HSC gene therapy studies dysregulation of host genes by replication-incompetent vector proviruses may lead to enrichment of repopulating clones with vector integrants near genes that influence engraftment. Thus, data from HSC gene therapy studies can be used to identify novel candidate engraftment genes. As HSC gene therapy use continues to expand, the vector insertion site data collected will be of great interest to help identify novel engraftment genes and may ultimately lead to new therapies to improve engraftment.

  5. Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis

    Science.gov (United States)

    Zhang, Zhang; Liu, Jingxing; Wu, Jiayan; Yu, Jun

    2013-01-01

    The regulation of gene expression is essential for eukaryotes, as it drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types in multicellular organisms. RNA-Sequencing (RNA-Seq) provides researchers with a powerful toolbox for characterization and quantification of transcriptome. Many different human tissue/cell transcriptome datasets coming from RNA-Seq technology are available on public data resource. The fundamental issue here is how to develop an effective analysis method to estimate expression pattern similarities between different tumor tissues and their corresponding normal tissues. We define the gene expression pattern from three directions: 1) expression breadth, which reflects gene expression on/off status, and mainly concerns ubiquitously expressed genes; 2) low/high or constant/variable expression genes, based on gene expression level and variation; and 3) the regulation of gene expression at the gene structure level. The cluster analysis indicates that gene expression pattern is higher related to physiological condition rather than tissue spatial distance. Two sets of human housekeeping (HK) genes are defined according to cell/tissue types, respectively. To characterize the gene expression pattern in gene expression level and variation, we firstly apply improved K-means algorithm and a gene expression variance model. We find that cancer-associated HK genes (a HK gene is specific in cancer group, while not in normal group) are expressed higher and more variable in cancer condition than in normal condition. Cancer-associated HK genes prefer to AT-rich genes, and they are enriched in cell cycle regulation related functions and constitute some cancer signatures. The expression of large genes is also avoided in cancer group. These studies will help us understand which cell type-specific patterns of gene expression differ among different cell types, and particularly for cancer. PMID:23382867

  6. Clustered array of ochratoxin A biosynthetic genes in Aspergillus steynii and their expression patterns in permissive conditions.

    Science.gov (United States)

    Gil-Serna, Jessica; Vázquez, Covadonga; González-Jaén, María Teresa; Patiño, Belén

    2015-12-01

    Aspergillus steynii is probably the most relevant species of section Circumdati producing ochratoxin A (OTA). This mycotoxin contaminates a wide number of commodities and it is highly toxic for humans and animals. Little is known on the biosynthetic genes and their regulation in Aspergillus species. In this work, we identified and analysed three contiguous genes in A. steynii using 5'-RACE and genome walking approaches which predicted a cytochrome P450 monooxygenase (p450ste), a non-ribosomal peptide synthetase (nrpsste) and a polyketide synthase (pksste). These three genes were contiguous within a 20742 bp long genomic DNA fragment. Their corresponding cDNA were sequenced and their expression was analysed in three A. steynii strains using real time RT-PCR specific assays in permissive conditions in in vitro cultures. OTA was also analysed in these cultures. Comparative analyses of predicted genomic, cDNA and amino acid sequences were performed with sequences of similar gene functions. All the results obtained in these analyses were consistent and point out the involvement of these three genes in OTA biosynthesis by A. steynii and showed a co-ordinated expression pattern. This is the first time that a clustered organization OTA biosynthetic genes has been reported in Aspergillus genus. The results also suggested that this situation might be common in Aspergillus OTA-producing species and distinct to the one described for Penicillium species.

  7. Optimization of PV array inclination in India using ANN estimator: Method comparison study

    Indian Academy of Sciences (India)

    T V Dixit; Anamika Yadav; S Gupta

    2015-08-01

    The network of solar power plants in distributed power system (in India) is growing exponentially. Since tilt angle affects the energy collection by solar panels, the conduction of experiments to find optimum tilt angle is expensive and time consuming in each location. Although different non-linear, empirical models have been proposed by different researchers in India, they have too many constraints and needs complex and rigorous computational effort each time. In this paper, a data driven approach such as ANN estimator has been proposed to estimate (opt) at which solar energy collection of Photo-Voltaic Array (PVA) will be maximum at selected cities of India. The latitude () elevation (L) from sea level and monthly mean hourly and daily global solar irradiance (g) of location are taken into account for this study. The ANN estimator takes g, and L of site as inputs which are easily available and estimate optimum tilt angle almost instantaneously while testing. The proposed ANN estimator results are compared with analytical results. To validate the performance of ANN estimator results, statistical analysis study is carried out. Where, two statistical approaches such as descriptive method and Altman–Bland methods are applied. The ANA estimator results are found much close to ANA results at 95% confidence interval under statistical study.

  8. A parametric study of ultrasonic beam profiles for a linear phased array transducer.

    Science.gov (United States)

    Lee, J H; Choi, S W

    2000-01-01

    A numerical simulation model is presented to investigate the influences of design parameters of linear phased array transducers on beam focusing and steering performance. The characteristic of ultrasonic beam profiles has been simulated on the basis of the Huygen's superposition principle. For the simulation, a linear phased array is considered as the composition of finite number of elements separated by equidistance. Individual elements are considered as two-dimensional point sources. The waves generated from piezoelectric elements are considered as simplified transient ultrasonic waves that are constructed with the cosine function enveloped with a Hanning window. The characteristic of ultrasonic wave propagation into a medium from the phased array transducer is described. The effects of the number, the interelement spacing, steering angle, the focal length, and frequency bandwidth of the piezoelectric elements on beam directivity and ultrasonic pressure field in a linear phased array transducer are systematically discussed.

  9. Arc arrays: studies of high resolution techniques for multibeam bathymetric applications

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, B.; Schenke, H.W.

    arrayof 15 degrees arc. The superiorityof the high resolution methods is seen by examining the patterns of the 15 degrees arc array under multiple source/interference conditions, i.e. the situation for rough terrain or artefactcreating conditions...

  10. Field Emission Study of Carbon Nanotubes: High Current Density from Nanotube Bundle Arrays

    Science.gov (United States)

    Bronikowski, Micheal J.; Manohara, Harish M.; Siegel, Peter H.; Hunt, Brian D.

    2004-01-01

    We have investigated the field emission behavior of lithographically patterned bundles of multiwalled carbon nanotubes arranged in a variety of array geometries. Such arrays of nanotube bundles are found to perform significantly better in field emission than arrays of isolated nanotubes or dense, continuous mats of nanotubes, with the field emission performance depending on the bundle diameter and inter-bundle spacing. Arrays of 2-micrometers diameter nanotube bundles spaced 5 micrometers apart (edge-to-edge spacing) produced the largest emission densities, routinely giving 1.5 to 1.8 A/cm(sup 2) at approximately 4 V/micrometer electric field, and greater than 6 A/cm(sup 2) at 20 V/micrometers.

  11. Experimental study on high-voltage solar array sustained arc discharge induced by high charging

    Institute of Scientific and Technical Information of China (English)

    LI Kai; XIE ErQing; WANG Li; LIU YanXia; YANG Yang; SUN YanZheng; CUI XinYu; MAI ShengLi

    2007-01-01

    It has been reported that sustained arc discharge induced by electrostatic discharge (ESD) could cause permanent damage to high-power and high-voltage solar array of spacecrafts. The paper focuses on ESD simulating experiments on Si and GaAs samples, and induces sustained arc discharge. The physical mechanism of sustained arc discharge is discussed by comparing the charging/discharging phenomena between Si and GaAs samples. The experiments show that sustained arc discharge can produce a permanent short-circuit channel between solar cell strings through which the solar array's photovoltaic power may flow out sustainedly. The analyses show that sustained arc discharge strongly depends on solar array structure, solar array operating voltage, ESD characteristics and cell materials.

  12. Detection of fast radio transients with multiple stations: a case study using the Very Long Baseline Array

    CERN Document Server

    Thompson, David R; Brisken, Walter; Deller, Adam T; Majid, Walid A; Tingay, Steven J; Wayth, Randall B

    2011-01-01

    Recent investigations reveal an important new class of transient radio phenomena that occur on sub-millisecond timescales. Often transient surveys' data volumes are too large to archive exhaustively. Instead, an on-line automatic system must excise impulsive interference and detect candidate events in real-time. This work presents a case study using data from multiple geographically distributed stations to perform simultaneous interference excision and transient detection. We present several algorithms that incorporate dedispersed data from multiple sites, and report experiments with a commensal real-time transient detection system on the Very Long Baseline Array (VLBA). We test the system using observations of pulsar B0329+54. The multiple-station algorithms enhanced sensitivity for detection of individual pulses. These strategies could improve detection performance for a future generation of geographically distributed arrays such as the Australian Square Kilometre Array Pathfinder and the Square Kilometre A...

  13. Study of performance of small gamma camera consisting of crystal pixel array and position sensitive photomultiplier tube

    Institute of Scientific and Technical Information of China (English)

    ZHU Jie; LIU Shi-Tao; LEI Xiao-Wen; YAN Tian-Xin; XU Zi-Zong; WANG Zhao-Min

    2005-01-01

    The performance of gamma camera with NaI(T1) array coupled with position sensitive photomultiplier tube (PSPMT) R2486 has been studied. The pixel size of NaI(T1) crystal is 2mm×2mm and the overall dimension of the array is 48.2mm×48.2mm×5mm. There are 484 pixels in a 22×22 matrix. Because each pixel can produce a much focused light spot and restrict the spread of photons, position resolution of the gamma camera is mainly determined by pixel size. It is shown that crystal array pixel can reduce shrinkage effect and improve intrinsic position resolution greatly via restricting the spread of photons. Experimental results demonstrate that its position resolution and linearity are much improved comparing with the gamma camera using planar crystals coupled with PSPMT.

  14. Linkage and candidate gene studies of autism spectrum disorders in European populations

    Science.gov (United States)

    Holt, Richard; Barnby, Gabrielle; Maestrini, Elena; Bacchelli, Elena; Brocklebank, Denise; Sousa, Inês; Mulder, Erik J; Kantojärvi, Katri; Järvelä, Irma; Klauck, Sabine M; Poustka, Fritz; Bailey, Anthony J; Monaco, Anthony P

    2010-01-01

    Over the past decade, research on the genetic variants underlying susceptibility to autism and autism spectrum disorders (ASDs) has focused on linkage and candidate gene studies. This research has implicated various chromosomal loci and genes. Candidate gene studies have proven to be particularly intractable, with many studies failing to replicate previously reported associations. In this paper, we investigate previously implicated genomic regions for a role in ASD susceptibility, using four cohorts of European ancestry. Initially, a 384 SNP Illumina GoldenGate array was used to examine linkage at six previously implicated loci. We identify linkage approaching genome-wide suggestive levels on chromosome 2 (rs2885116, MLOD=1.89). Association analysis showed significant associations in MKL2 with ASD (rs756472, P=4.31 × 10−5) and between SND1 and strict autism (rs1881084, P=7.76 × 10−5) in the Finnish and Northern Dutch populations, respectively. Subsequently, we used a second 384 SNP Illumina GoldenGate array to examine the association in seven candidate genes, and evidence for association was found in RELN (rs362780, P=0.00165). Further increasing the sample size strengthened the association with RELN (rs362780, P=0.001) and produced a second significant result in GRIK2 (rs2518261, P=0.008). Our results strengthen the case for a more detailed study of the role of RELN and GRIK2 in autism susceptibility, as well as identifying two new potential candidate genes, MKL2 and SND1. PMID:20442744

  15. a Study Into the Effects of AN Austenitic Weld on Ultrasonic Array Imaging Performance

    Science.gov (United States)

    Hunter, A. J.; Drinkwater, B. W.; Zhang, J.; Wilcox, P. D.

    2011-06-01

    An industrial application of ultrasonic array imaging is the inspection of austenitic welds with high inhomogeneity and anisotropy. These result in attenuation and perturbation of the signals that adversely affects imaging performance. Here, the effects of perturbations introduced by an austenitic weld on array imaging performance are investigated experimentally. It is shown that three major factors contribute to the degradation of image quality: timing errors, phase errors, and multi-path propagation and scattering.

  16. Status and perspective of FARCOS: A new correlator array for nuclear reaction studies

    Directory of Open Access Journals (Sweden)

    Pagano E.V.

    2016-01-01

    Full Text Available The experimental investigation of Heavy Ion reactions at Fermi energies requires an accurate measurement of observables, such as linear momentum and energy of the detected particles. In order to address this problem, dedicated and flexible correlator arrays are useful tools to be coupled with 4π detectors. One of these arrays is FARCOS, presently under construction at the INFN Sezione di Catania and Laboratori Nazionali del Sud (LNS.

  17. Status and perspective of FARCOS: A new correlator array for nuclear reaction studies

    Science.gov (United States)

    Pagano, E. V.; Acosta, L.; Auditore, L.; Boiano, C.; Cardella, G.; Castoldi, A.; D'Andrea, M.; Dell'aquila, D.; De Filippo, E.; De Luca, S.; Fichera, F.; Francalanza, L.; Giudice, N.; Gnoffo, B.; Grimaldi, A.; Guazzoni, C.; Lanzalone, G.; Lombardo, I.; Minniti, T.; Norella, S.; Pagano, A.; Papa, M.; Pirrone, S.; Politi, G.; Porto, F.; Quattrocchi, L.; Rizzo, F.; Russotto, P.; Saccá, G.; Trifirò, A.; Trimarchi, M.; Verde, G.; Vigilante, M.

    2016-05-01

    The experimental investigation of Heavy Ion reactions at Fermi energies requires an accurate measurement of observables, such as linear momentum and energy of the detected particles. In order to address this problem, dedicated and flexible correlator arrays are useful tools to be coupled with 4π detectors. One of these arrays is FARCOS, presently under construction at the INFN Sezione di Catania and Laboratori Nazionali del Sud (LNS).

  18. Searching for novel modes of toxic actions of oil spill using E. coli live cell array reporter system - A Hebei Spirit oil spill study.

    Science.gov (United States)

    Jung, Dawoon; Guan, Miao; Lee, Sangwoo; Kim, Cheolmin; Shin, Hyesoo; Hong, Seongjin; Yim, Un Hyuk; Shim, Won Joon; Giesy, John P; Khim, Jong Seong; Zhang, Xiaowei; Choi, Kyungho

    2017-02-01

    Oil is a complex mixture of numerous compounds. Therefore, oil spills near shore can cause various adverse effects on coastal ecosystems. However, most toxicological assessments conducted on oil spill sites have focused on limited modes of toxic actions. In the present study, we utilized the Escherichia coli (E. coli) live cell array system (LCA) to identify novel modes of toxicities of the oil spill-affected sediments. For this purpose, sediment samples were collected from an area heavily polluted by Hebei Spirit oil spill (HSOS) incident of 2007. A total of 93 E. coli reporter genes were used to study responses to the chemicals in the mixture. E. coli K12 strains were exposed to extracts of oil or the sediment, and changes in gene expression were measured. Exposure to extracts of crude and weathered oil resulted in decreased expression in ∼30% of tested genes. However, changes in expression observed after exposure to sediment extracts varied. Sediment extracts containing large concentrations of polycyclic aromatic hydrocarbons (PAH) caused down-regulation of >70% of the genes, while extracts containing lesser total concentrations of PAHs exhibited different trends: genes involved in drug resistance were generally up-regulated, while genes responsive to DNA damage were up-regulated in only two extracts. Results suggest that oil pollution can modulate several toxic response pathways related to DNA repair and antibiotic responses. Results from LCA obtained from the sediment and oil samples were different from those observed in the H4IIE-luc assay. Toxicological implications of such observations deserve further examination. Overall, LCA is a promising tool for screening samples and identifying potential modes of toxicities of environmental samples associated with oil spills.

  19. Study on Millimeter-Wave Vivaldi Rectenna and Arrays with High Conversion Efficiency

    Directory of Open Access Journals (Sweden)

    Guan-Nan Tan

    2016-01-01

    Full Text Available A novel Vivaldi rectenna operated at 35 GHz with high millimeter wave to direct current (MMW-to-DC conversion efficiency is presented and the arrays are investigated. The measured conversion efficiency is 51.6% at 35 GHz and the efficiency higher than 30% is from 33.2 GHz to 36.6 GHz when the input MMW power is 79.4 mW. The receiving Vivaldi antenna loaded with metamaterial units has a high gain of 10.4 dBi at 35 GHz. A SIW- (substrate integrated waveguide- to-microstrip transition is designed not only to integrate the antenna with the rectifying circuit directly but also to provide the DC bypass for the rectifying circuit. When the power density is 8.7 mW/cm2, the received MMW power of the antenna is 5.6 mW, and the maximum conversion efficiency of the rectenna element is 31.5%. The output DC voltage of the element is nearly the same as that of the parallel array and is about half of the series array. The DC power obtained by the 1 × 2 rectenna arrays is about two times as much as that of the element. The conversion efficiencies of the arrays are very close to that of the element. Large scale arrays could be expended for collecting more DC power.

  20. Nuclear structure studies at Saha Institute of Nuclear Physics using gamma detector arrays

    Indian Academy of Sciences (India)

    P Banerjee

    2001-07-01

    In-beam gamma-ray spectroscopy, carried out at the Saha Institute of Nuclear Physics in the recent past, using heavy-ion projectiles from the pelletron accelerator centres in the country and multi-detector arrays have yielded significant data on the structure of a large number of nuclei spanning different mass regions. The experiments included the study of two-fold -coincidence events for establishing decay schemes, directional correlation of oriented nuclei (DCO) for help in spin assignments and Doppler shift attenuation for lifetime information. The studies have led to the observation of rotational sequences of states in nuclei near closed shell in the mass = 110 region, vibrational spectra in nuclei with ∼ 60, interplay between single-particle and collective modes of excitation in the doubly-odd bromine isotopes, decoupled bands with large quadrupole deformation in 77Br, shape transition with rotational frequency within a band in 138Pm and octupole collectivity in 153Eu. Particle-rotor-model and cranked-shell-model calculations have been carried out to provide an understanding of the underlying nuclear structure

  1. Performance Study of Cryogenically Treated HSS Drills in Drillilg Gray Cast Iron Using Orthogonal Array Technique

    Directory of Open Access Journals (Sweden)

    B.R. Ramji

    2010-08-01

    Full Text Available The objective of this research was to study the performance of cryogenically treated HSS drills for drilling gray cast iron. Drilling experiments were conducted with cutting speeds: 560, 710, 900, 1120 rpm, feeds: 0.05, 0.08, 0.12, 0.19 mm/rev and a constant drill diameter: 8 mm. The cryogenic treatment cycle consisted of cooling the test samples from room temperature to cryogenic temperature of -178.9ºC in 3 h, soaking at cryogenic temperature for 24 h and w arming to room temperature in about 5 h. The thrust force and torque were measured using drill tool dynamometer. The surface roughness (Ra, Rz, Rq and R t of the drilled specimens were measured using talysurf. The experimental lay-out was designed using Taguchi’s Orthogonal Array technique. Signal-to-Noise Ratio analysis was performed to identify the effect of the parameters on the response variables. The treated drills were found superior to the non-treated in all the test conditions in terms of lesser thrust force, torque and also superior surface roughness of the specimens. The tool wear was studied using SEM.

  2. A Deuterated Neutron Detector Array For Nuclear (Astro)Physics Studies

    Science.gov (United States)

    Almaraz-Calderon, Sergio; Asher, B. W.; Barber, P.; Hanselman, K.; Perello, J. F.

    2016-09-01

    The properties of neutron-rich nuclei are at the forefront of research in nuclear structure, nuclear reactions and nuclear astrophysics. The advent of intense rare isotope beams (RIBs) has opened a new door for studies of systems with very short half-lives and possible fascinating properties. Neutron spectroscopic techniques become increasingly relevant when these neutron rich nuclei are used in a variety of experiments. At Florida State University, we are developing a neutron detector array that will allow us to perform high-resolution neutron spectroscopic studies with stable and radioactive beams. The neutron detection system consists of 16 deuterated organic liquid scintillation detectors with fast response and pulse-shape discrimination capabilities. In addition to these properties, there is the potential to use the structure in the pulse-height spectra to extract the energy of the neutrons and thus produce directly excitation spectra. This type of detector uses deuterated benzene (C6D6) as the liquid scintillation medium. The asymmetric nature of the scattering between a neutron and a deuterium in the center of mass produces a pulse-height spectrum from the deuterated scintillator which contains useful information on the initial energy of the neutron. Work supported in part by the State of Florida and NSF Grant No. 1401574.

  3. Ground state study of the thin ferromagnetic nano-islands for artificial spin ice arrays

    Energy Technology Data Exchange (ETDEWEB)

    Vieira Júnior, D. S., E-mail: damiao.vieira@ifsudestemg.edu.br [Departamento Acadêmico de Matemática, Física e Estatística, Instituto Federal de Educação, Ciência e Tecnologia do Sudeste de Minas Gerais - Câmpus Rio Pomba, Rio Pomba, Minas Gerais 36180-000 (Brazil); Departamento de Física, Laboratório de Simulação Computacional, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais 36036-330 (Brazil); Leonel, S. A., E-mail: sidiney@fisica.ufjf.br; Dias, R. A., E-mail: radias@fisica.ufjf.br; Toscano, D., E-mail: danilotoscano@fisica.ufjf.br; Coura, P. Z., E-mail: pablo@fisica.ufjf.br; Sato, F., E-mail: sjfsato@fisica.ufjf.br [Departamento de Física, Laboratório de Simulação Computacional, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais 36036-330 (Brazil)

    2014-09-07

    In this work, we used numerical simulations to study the magnetic ground state of the thin elongated (elliptical) ferromagnetic nano-islands made of Permalloy. In these systems, the effects of demagnetization of dipolar source generate a strong magnetic anisotropy due to particle shape, defining two fundamental magnetic ground state configurations—vortex or type C. To describe the system, we considered a model Hamiltonian in which the magnetic moments interact through exchange and dipolar potentials. We studied the competition between the vortex states and aligned states—type C—as a function of the shape of each elliptical nano-islands and constructed a phase diagram vortex—type C state. Our results show that it is possible to obtain the elongated nano-islands in the C-state with aspect ratios less than 2, which is interesting from the technological point of view because it will be possible to use smaller islands in spin ice arrays. Generally, the experimental spin ice arrangements are made with quite elongated particles with aspect ratio approximately 3 to ensure the C-state.

  4. Chemiluminescent detection of sequential DNA hybridizations to high-density, filter-arrayed cDNA libraries: a subtraction method for novel gene discovery.

    Science.gov (United States)

    Guiliano, D; Ganatra, M; Ware, J; Parrot, J; Daub, J; Moran, L; Brennecke, H; Foster, J M; Supali, T; Blaxter, M; Scott, A L; Williams, S A; Slatko, B E

    1999-07-01

    A chemiluminescent approach for sequential DNA hybridizations to high-density filter arrays of cDNAs, using a biotin-based random priming method followed by a streptavidin/alkaline phosphatase/CDP-Star detection protocol, is presented. The method has been applied to the Brugia malayi genome project, wherein cDNA libraries, cosmid and bacterial artificial chromosome (BAC) libraries have been gridded at high density onto nylon filters for subsequent analysis by hybridization. Individual probes and pools of rRNA probes, ribosomal protein probes and expressed sequence tag probes show correct specificity and high signal-to-noise ratios even after ten rounds of hybridization, detection, stripping of the probes from the membranes and rehybridization with additional probe sets. This approach provides a subtraction method that leads to a reduction in redundant DNA sequencing, thus increasing the rate of novel gene discovery. The method is also applicable for detecting target sequences, which are present in one or only a few copies per cell; it has proven useful for physical mapping of BAC and cosmid high-density filter arrays, wherein multiple probes have been hybridized at one time (multiplexed) and subsequently "deplexed" into individual components for specific probe localizations.

  5. Experimental study of implosion dynamics of multi-material nested wire-arrays on S-300 pulsed power generator

    NARCIS (Netherlands)

    Chernenko, AS; Smirnov, VP; Kingsep, AS; Kalinin, YG; Bakshaev, YL; Bartov, AV; Blinov, PI; Danko, SA; Dubas, LG; Korelskii, AV; Korolev, VD; Mizhiritsky, [No Value; Shaskov, AY; Ustroev, GI; Li, ZH; Hua, XS; Feng, SP; Guo, C; Jiang, SL; Ning, C; Peng, XJ; Song, FJ; Xu, RK; Xu, ZP; Yan, CL; Yang, JL; Yang, LB; Cai, HC

    2004-01-01

    On "S-300" generator (700 W, 4 MA, 70 ns) at the Kurchatov Institute, the experimental studies with multi-material wire array units are carried on aimed at creating the powerful X-ray source. The development of new diagnostic methods would definitely contribute to attain new data, which could help i

  6. Reference genes for gene expression studies in wheat flag leaves grown under different farming conditions

    Directory of Open Access Journals (Sweden)

    Cordeiro Raposo Fernando

    2011-09-01

    Full Text Available Abstract Background Internal control genes with highly uniform expression throughout the experimental conditions are required for accurate gene expression analysis as no universal reference genes exists. In this study, the expression stability of 24 candidate genes from Triticum aestivum cv. Cubus flag leaves grown under organic and conventional farming systems was evaluated in two locations in order to select suitable genes that can be used for normalization of real-time quantitative reverse-transcription PCR (RT-qPCR reactions. The genes were selected among the most common used reference genes as well as genes encoding proteins involved in several metabolic pathways. Findings Individual genes displayed different expression rates across all samples assayed. Applying geNorm, a set of three potential reference genes were suitable for normalization of RT-qPCR reactions in winter wheat flag leaves cv. Cubus: TaFNRII (ferredoxin-NADP(H oxidoreductase; AJ457980.1, ACT2 (actin 2; TC234027, and rrn26 (a putative homologue to RNA 26S gene; AL827977.1. In addition of these three genes that were also top-ranked by NormFinder, two extra genes: CYP18-2 (Cyclophilin A, AY456122.1 and TaWIN1 (14-3-3 like protein, AB042193 were most consistently stably expressed. Furthermore, we showed that TaFNRII, ACT2, and CYP18-2 are suitable for gene expression normalization in other two winter wheat varieties (Tommi and Centenaire grown under three treatments (organic, conventional and no nitrogen and a different environment than the one tested with cv. Cubus. Conclusions This study provides a new set of reference genes which should improve the accuracy of gene expression analyses when using wheat flag leaves as those related to the improvement of nitrogen use efficiency for cereal production.

  7. Study on Fabrication and UV Photoelectric Property of TiO2 Nanotube Array Electrodes.

    Science.gov (United States)

    Fu, Yao; Duan, Xiao-Long; Xing, Ming-Ming; Luo, Xi-Xian; Zhang, Ying-Hui; Liu, Wang

    2016-04-01

    Highly ordered TiO2 nanotube array electrodes were successfully fabricated by a two-step anodization method on Ti sheet substrates in an electrolyte composed of ammonium fluoride, deionized water, and glycol. The tube wall was smooth, and the average internal and external diameters, wall thickness, and tube length achieved were 80 nm, 90 nm, 10 nm, and 9 µm, respectively. X-ray diffraction and field emission scanning electron microscopy results revealed that the TiO2 nanotube arrays presented an amorphous structure. When calcined at 300 °C, the arrays crystallized into the anatase phase, and the crystallization degree of the oxide layer increased as the temperature rose. Calcinating at 400 °C did not obviously disrupt the porous structure of the highly ordered arrays. However, higher temperature enlarged the diameter of the nanotube array and roughened the tube wall. When the temperature reached 600 °C, the nanotube mouth broke because of the excessive stress, causing the oxide layer's thinness and nanotube mouth clogging. The photoelectric test showed that the electrode presented obvious photoresponse under 300-400 nm UV excitation (maximized at 360 nm). The degree of crystallization and the micro-structure of the oxide layer can significantly affect the photoelectric properties of the electrode. After calcination at 400 °C, the TiO2 nanotube arrays, with highly ordered tubular structure directly connected to the Ti substrate, can ensure the rapid transportation of photo-induced electrons to the Ti substrate, while the high crystallinity of the arrays can help reduce the defect density of the nanotube and extend the lifetime of the photo-induced carriers. The electrode showed the best photoelectric property, and the photocurrent intensity was maximized (29.6 µA). However, the calcination process with over-temperature resulted in substantial loss of the TiO2 oxide layer, mouth clogging, and a severe decline in the photoelectric properties.

  8. Genome Array on Differentially Expressed Genes of Skin Tissue in Cashmere Goat at Early Anagen of Cashmere Growth Cycle Using DNA Microarray

    Institute of Scientific and Technical Information of China (English)

    DI Jiang; Marzeya Yasen; XU Xin-ming; Lazate Ainiwaer; ZHANG Yan-hua; TIAN Ke-chuan; YU Li-juan; WU Wei-wei; Hanikezi Tulafu; FU Xue-feng

    2014-01-01

    In order to study the molecular mechanism involved in cashmere regeneration, this study investigated the gene expression proifle of skin tissue at various stages of the cashmere growth cycle and screen differentially expressed genes at proangen in 10 cashmere goats at 2 years of age using agilent sheep oligo microarray. Signiifcance analysis of microarray (SAM) methods was used to identify the differentially expressed genes, Hierarchical clustering was performed to clarify these genes in association with different cashmere growth stages, and GO (Gene ontology) and the pathway analyses were con-ducted by a free web-based Molecular Annotation System3.0 (MAS 3.0). Approximately 10 200 probe sets were detected in skin tissue of 2-yr-old cashmere goat. After SAM analysis of the microarray data, totally 417 genes were shown to be differentially expressed at different cashmere growth stages, and 24 genes are signiifcantly up-regulated (21) or down-regulated (3) at proangen concurrently compared to angen and telogen. Hierarchical clustering analysis clearly distinguished the differentially expressed genes of each stage. GO analysis indicated that these altered genes at proangen were predominantly involved in collagen ifbril organization, integrin-mediated signaling pathway, cell-matrix adhesion, cell adhesion, transforming growth factor-β (TGF-β) receptor signaling pathway, regulation of cell growth. Kyoto encyclopedia of genes and genomes (KEGG) analysis showed that the signiifcant pathways involved mainly included focal adhesion and extracellular matrixc (ECM)-receptor interaction. Some important genes involved in these biological processes, such as COL1A1, COL1A2, COL3A1, SPARC, CYR61 and CTGF, were related to tissue remolding and repairing and detected by more than one probe with similar expression trends at different stages of cashmere growth cycle. The different expression of these genes may contribute to understanding the molecular mechanism of cashmere

  9. Selection of reliable reference genes for gene expression studies in peach using real-time PCR

    Directory of Open Access Journals (Sweden)

    Zhou Jun

    2009-07-01

    Full Text Available Abstract Background RT-qPCR is a preferred method for rapid and reliable quantification of gene expression studies. Appropriate application of RT-qPCR in such studies requires the use of reference gene(s as an internal control to normalize mRNA levels between different samples for an exact comparison of gene expression level. However, recent studies have shown that no single reference gene is universal for all experiments. Thus, the identification of high quality reference gene(s is of paramount importance for the interpretation of data generated by RT-qPCR. Only a few studies on reference genes have been done in plants and none in peach (Prunus persica L. Batsch. Therefore, the present study was conducted to identify suitable reference gene(s for normalization of gene expression in peach. Results In this work, eleven reference genes were investigated in different peach samples using RT-qPCR with SYBR green. These genes are: actin 2/7 (ACT, cyclophilin (CYP2, RNA polymerase II (RP II, phospholipase A2 (PLA2, ribosomal protein L13 (RPL13, glyceraldehyde-3-phosphate dehydrogenase (GAPDH, 18S ribosomal RNA (18S rRNA, tubblin beta (TUB, tubblin alpha (TUA, translation elongation factor 2 (TEF2 and ubiquitin 10 (UBQ10. All eleven reference genes displayed a wide range of Cq values in all samples, indicating that they expressed variably. The stability of these genes except for RPL13 was determined by three different descriptive statistics, geNorm, NormFinder and BestKeeper, which produced highly comparable results. Conclusion Our study demonstrates that expression stability varied greatly between genes studied in peach. Based on the results from geNorm, NormFinder and BestKeeper analyses, for all the sample pools analyzed, TEF2, UBQ10 and RP II were found to be the most suitable reference genes with a very high statistical reliability, and TEF2 and RP II for the other sample series, while 18S rRNA, RPL13 and PLA2 were unsuitable as internal controls

  10. Performance study of an OFDM visible light communication system based on white LED array

    Science.gov (United States)

    Tian, Chong-Wen; Li, Yan-Ting; Ye, Wei-Lin; Quan, Xiang-Yin; Song, Zhanwei; Zheng, Chuan-Tao

    2011-11-01

    By introducing orthogonal frequency division multiplexing (OFDM) technology, a visible light communication (VLC) system using a 5×5 white LED array is studied in this paper. The OFDM transmitter and receiver are modeled through MATLAB/Simulink tool. The electrical-optical-electrical (EOE) response of the VLC channel, which is also the response of the detector, is derived based on Lambert's lighting model. Then the modeling on the overall OFDM/VLC system is established by combining the above three models together. The effects of the factors which include the digital modulation, Reed-Solomon (RS) coding, pilot form, pilot ratio (PR) and communication distance on the bit error rate (BER) of the system are discussed. The results show that through the use of RS coding, block pilot, quadrate phase shift keying (QPSK) modulation and a suitable pilot ratio about 1/3, under the communication rate about 550 kbit/s, the BER can be dropped to below 10-5, and the communication distance can reach 0.9 m.

  11. Feasibility study of a unilateral RF array coil for MR-scintimammography

    Science.gov (United States)

    Ha, Seunghoon; Hamamura, Mark J.; Roeck, Werner W.; Hugg, James; Wagenaar, Douglas J.; Meier, Dirk; Patt, Bradley E.; Nalcioglu, Orhan

    2011-11-01

    Despite its high sensitivity, the variable specificity of magnetic resonance imaging (MRI) in breast cancer diagnosis can lead to unnecessary biopsies and over-treatment. Scintimammography (SMM) could potentially supplement MRI to improve the diagnostic specificity. The synergistic combination of MRI and SMM (MRSMM) could result in both high sensitivity from MRI and high specificity from SMM. Development of such a dual-modality system requires the integration of a radio frequency (RF) coil and radiation detector in a strong magnetic field without significant mutual interference. In this study, we developed and tested a unilateral breast array coil specialized for MRSMM imaging. The electromagnetic field, specific absorption ratio and RF coil parameters with cadmium-zinc-telluride detectors encapsulated in specialized RF and gamma-ray shielding mounted within the RF coil were investigated through simulation and experimental measurements. Simultaneous MR and SMM images of a breast phantom were also acquired using the integrated MRSMM system. This work, we feel, represents an important step toward the fabrication of a working MRSMM system.

  12. Performance study of an OFDM visible light communication system based on white LED array

    Institute of Scientific and Technical Information of China (English)

    TIAN Chong-wen; LI Yan-ting; YE Wei-lin; QUAN Xiang-yin; SONG Zhan-wei; ZHENG Chuan-tao

    2011-01-01

    By introducing orthogonaI frequency division multiplexing (OFDM) technology,a visible light communication (VLC) system using a 5×5 white LED array is studied in this paper.The OFDM transmitter and receiver are modeled through MATLAB/Simulink tool.The electrical optical-electrical (EOE) response of the VLC channel,which is also the response of the detector,is derived based on Lambert's lighting model.Then the modeling on the overall OFDM/VLC system is established by combining the above three models together.The effects of the factors which include the digital modulation,Reed-Solomon (RS) coding,pilot form,pilot ratio (PR) and communication distance on the bit error rate (BER) of the system are discussed.The results show that through the use of RS coding,block pilot,quadrate phase shift keying (QPSK) modulation and a suitable pilot ratio about 1/3,under the communication rate about 550 kbit/s,the BER can be dropped to below 10s,and the communication distance can reach 0.9 m.

  13. Study on Dynamic Compression Properties of K9 Glass with Doppler Pins Array Measurements

    Science.gov (United States)

    Changming, Hu; Xiang, Wang; Lingcang, Cai; Cangli, Liu

    2009-06-01

    K9 glass is one of archetypal brittle materials for studies of dynamic fracture, failure wave, and so on. This paper presented the dynamic compression properties of K9 glass under uniaxial strain condition. Experimental sample is K9 glass with internal pre-existed defects, and the shape of pre-existed defects is disc with less than 0.5 mm diameter. All tests were conducted by power gun with 37 mm diameter chamber. Doppler Pins array with high space-time resolutions, which consists of sixteen pins in range of 2 mm line length, were applied to measure the particle velocity histories in different positions at the sample rear surface, and the space-resolution is 127 μm, Experimental results show failure waves initiate at internal micro-surfaces of the sample under shock loading, and the dynamic stress concentration is likely attributed to be a physical mechanism of the initiation of the failure wave. These defects that by the controlled laser irradiation in advance are some internal micro-surfaces. Meanwhile, the experimental results show that internal micro-surfaces of the sample have influence on the elastic precursor wave decay.

  14. Feasibility study of a unilateral RF array coil for MR-scintimammography

    Energy Technology Data Exchange (ETDEWEB)

    Ha, Seunghoon; Hamamura, Mark J; Roeck, Werner W; Nalcioglu, Orhan [Tu and Yuen Center for Functional Onco-Imaging, University of California, Irvine, CA (United States); Hugg, James; Wagenaar, Douglas J; Patt, Bradley E [Gamma Medica, Inc. (Clinical Division), Northridge, CA (United States); Meier, Dirk, E-mail: seunghoh@uci.edu [Gamma Medica, Inc. (Industrial Division), Fornebu (Norway)

    2011-11-07

    Despite its high sensitivity, the variable specificity of magnetic resonance imaging (MRI) in breast cancer diagnosis can lead to unnecessary biopsies and over-treatment. Scintimammography (SMM) could potentially supplement MRI to improve the diagnostic specificity. The synergistic combination of MRI and SMM (MRSMM) could result in both high sensitivity from MRI and high specificity from SMM. Development of such a dual-modality system requires the integration of a radio frequency (RF) coil and radiation detector in a strong magnetic field without significant mutual interference. In this study, we developed and tested a unilateral breast array coil specialized for MRSMM imaging. The electromagnetic field, specific absorption ratio and RF coil parameters with cadmium-zinc-telluride detectors encapsulated in specialized RF and gamma-ray shielding mounted within the RF coil were investigated through simulation and experimental measurements. Simultaneous MR and SMM images of a breast phantom were also acquired using the integrated MRSMM system. This work, we feel, represents an important step toward the fabrication of a working MRSMM system.

  15. Microplate array diagonal gel electrophoresis for cohort studies of microsatellite loci.

    Science.gov (United States)

    Chen, Xiao-he; O'Dell, Sandra D; Day, Ian N M

    2002-05-01

    After PCR amplification, we have achieved precise sizing of trinucleotide and tetranucleotide microsatellite alleles on 96-well open-faced polyacrylamide microplate array diagonal gel electrophoresis (MADGE) gels: two tetranucleotide repeats, HUMTHOI (five alleles 248-263 bp) and DYS390 (eight alleles 200-228 bp), and DYS392, a trinucleotide repeat (eight alleles 210-231 bp). A gel matrix of Duracryl, a high mechanical strength polyacrylamide derivative, and appropriate ionic conditions provide the 1.3%-1.5% band resolution required. No end-labeling of primers is needed, as the sensitive Vistra Green intercalating dye is used for the visualization of bands. Co-run markers bracketing the PCR fragments ensure accurate sizing without inter-lane variability. Electrophoresis of multiple gels in a thermostatically controlled tank allows up to 1000 samples to be run in 90 min. Gel images were analyzed using a Fluorlmager 595 fluorescent scanning system, and alleles were identified using Phoretix software for band migration measurement and Microsoft Excel to compute fragment sizes. Estimated sizes were interpolated precisely to achieve accurate binning. Microsatellite-MADGE represents a utilitarian methodfor high-throughput genotyping in cohort studies, using standard laboratory equipment.

  16. Comparative genomic hybridization array study and its utility in detection of constitutional and acquired anomalies.

    Science.gov (United States)

    Andrieux, Joris; Sheth, Frenny

    2009-10-01

    The last decade has witnessed an upsurge in the knowledge of cytogenetic disorders and putting the old technology in a new basket with molecular genetics. As conventional cytogenetic can detect the genetic alteration of 10-15 Mb, many of the micro-deletions and micro-duplications are missed. However, with the advent of technology of fluorescence in situ hybridization (FISH), the resolution of genetic aberrations can reach to 3-5 Mb, nonetheless the anomalies smaller than the above, need further precision which has been achieved using comparative genomic hybridization array (CGH-array). Introduction of array-CGH has brought higher sensitivity with automated DNA fragment analyzer and DNA chip for submicroscopic chromosomal anomalies that are missed till date in many of the acquired and constitutional genetic disorders. The resolution of the technology varies from several Kb to 1 Mb depending upon the type of array selected. With the recent improvement in the array-CGH technology, a link between cytogenetic and molecular biology has been established without replacing conventional cytogenetic technique. The wider accessibility of the technology shall certainly provide a clue to the many unidentified/unexplained genetic disorders which shall prove to be a boon to the clinicians.

  17. Study on simulation and experiment of array micro Faraday cup ion detector for FAIMS

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    An array micro Faraday cup ion detector for FAIMS (High-field Asymmetric Waveform Ion Mobility Spectrometry) was introduced, with which the size of the FAIMS system was reduced. With simple structure, good stability, low noise, large measurements range, this detector can work under the condition of atmospheric pressure. The array micro Faraday cup was composed of gate electrode, sensitive electrode and shielding electrode. The sensitive electrode was made of tens of crossing silicon columns with diameter of 200 μm. It was fabricated through typical MEMS technology, which was compatible completely with plane FAIMS. It was shown from FLUENT simulation result that the resistance to gas motion was low and the flow field distribution was helpful for full absorption of the ion in this array design. Through electricity simulation, the method to reduce interference on the detection signal of the micro Faraday cup was given out. Connecting with KEITHLEY 237 ampere meter, the noise level of the array micro Faraday cup was lower than 0.5 pA. The output signal of the acetone sample measured by experiment was about 210 pA. Through contrast experiment, the design parameter of the micro Faraday cup was obtained primarily. This array micro Faraday cup can meet the requirements of the FAIMS system.

  18. Assessment of Suitable Reference Genes for Quantitative Gene Expression Studies in Melon Fruits.

    Science.gov (United States)

    Kong, Qiusheng; Gao, Lingyun; Cao, Lei; Liu, Yue; Saba, Hameed; Huang, Yuan; Bie, Zhilong

    2016-01-01

    Melon (Cucumis melo L.) is an attractive model plant for investigating fruit development because of its morphological, physiological, and biochemical diversity. Quantification of gene expression by quantitative reverse transcription polymerase chain reaction (qRT-PCR) with stably expressed reference genes for normalization can effectively elucidate the biological functions of genes that regulate fruit development. However, the reference genes for data normalization in melon fruits have not yet been systematically validated. This study aims to assess the suitability of 20 genes for their potential use as reference genes in melon fruits. Expression variations of these genes were measured in 24 samples that represented different developmental stages of fertilized and parthenocarpic melon fruits by qRT-PCR analysis. GeNorm identified ribosomal protein L (CmRPL) and cytosolic ribosomal protein S15 (CmRPS15) as the best pair of reference genes, and as many as five genes including CmRPL, CmRPS15, TIP41-like family protein (CmTIP41), cyclophilin ROC7 (CmCYP7), and ADP ribosylation factor 1 (CmADP) were required for more reliable normalization. NormFinder ranked CmRPS15 as the best single reference gene, and RAN GTPase gene family (CmRAN) and TATA-box binding protein (CmTBP2) as the best combination of reference genes in melon fruits. Their effectiveness was further validated by parallel analyses on the activities of soluble acid invertase and sucrose phosphate synthase, and expression profiles of their respective encoding genes CmAIN2 and CmSPS1, as well as sucrose contents during melon fruit ripening. The validated reference genes will help to improve the accuracy of gene expression studies in melon fruits.

  19. Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR

    Directory of Open Access Journals (Sweden)

    Xiang Fengning

    2008-11-01

    Full Text Available Abstract Background The wild grass species Brachypodium distachyon (Brachypodium hereafter is emerging as a new model system for grass crop genomics research and biofuel grass biology. A draft nuclear genome sequence is expected to be publicly available in the near future; an explosion of gene expression studies will undoubtedly follow. Therefore, stable reference genes are necessary to normalize the gene expression data. Results A systematic exploration of suitable reference genes in Brachypodium is presented here. Nine reference gene candidates were chosen, and their gene sequences were obtained from the Brachypodium expressed sequence tag (EST databases. Their expression levels were examined by quantitative real-time PCR (qRT-PCR using 21 different Brachypodium plant samples, including those from different plant tissues and grown under various growth conditions. Effects of plant growth hormones were also visualized in the assays. The expression stability of the candidate genes was evaluated using two analysis software packages, geNorm and NormFinder. In conclusion, the ubiquitin-conjugating enzyme 18 gene (UBC18 was validated as a suitable reference gene across all the plant samples examined. While the expression of the polyubiquitin genes (Ubi4 and Ubi10 was most stable in different plant tissues and growth hormone-treated plant samples, the expression of the S-adenosylmethionine decarboxylase gene (SamDC ranked was most stable in plants grown under various environmental stresses. Conclusion This study identified the reference genes that are most suitable for normalizing the gene expression data in Brachypodium. These reference genes will be particularly useful when stress-responsive genes are analyzed in order to produce transgenic plants that exhibit enhanced stress resistance.

  20. Assessment of Suitable Reference Genes for Quantitative Gene Expression Studies in Melon Fruits

    Science.gov (United States)

    Kong, Qiusheng; Gao, Lingyun; Cao, Lei; Liu, Yue; Saba, Hameed; Huang, Yuan; Bie, Zhilong

    2016-01-01

    Melon (Cucumis melo L.) is an attractive model plant for investigating fruit development because of its morphological, physiological, and biochemical diversity. Quantification of gene expression by quantitative reverse transcription polymerase chain reaction (qRT-PCR) with stably expressed reference genes for normalization can effectively elucidate the biological functions of genes that regulate fruit development. However, the reference genes for data normalization in melon fruits have not yet been systematically validated. This study aims to assess the suitability of 20 genes for their potential use as reference genes in melon fruits. Expression variations of these genes were measured in 24 samples that represented different developmental stages of fertilized and parthenocarpic melon fruits by qRT-PCR analysis. GeNorm identified ribosomal protein L (CmRPL) and cytosolic ribosomal protein S15 (CmRPS15) as the best pair of reference genes, and as many as five genes including CmRPL, CmRPS15, TIP41-like family protein (CmTIP41), cyclophilin ROC7 (CmCYP7), and ADP ribosylation factor 1 (CmADP) were required for more reliable normalization. NormFinder ranked CmRPS15 as the best single reference gene, and RAN GTPase gene family (CmRAN) and TATA-box binding protein (CmTBP2) as the best combination of reference genes in melon fruits. Their effectiveness was further validated by parallel analyses on the activities of soluble acid invertase and sucrose phosphate synthase, and expression profiles of their respective encoding genes CmAIN2 and CmSPS1, as well as sucrose contents during melon fruit ripening. The validated reference genes will help to improve the accuracy of gene expression studies in melon fruits. PMID:27536316

  1. Rotatable Small Permanent Magnet Array for Ultra-Low Field Nuclear Magnetic Resonance Instrumentation: A Concept Study.

    Directory of Open Access Journals (Sweden)

    Michael W Vogel

    Full Text Available We studied the feasibility of generating the variable magnetic fields required for ultra-low field nuclear magnetic resonance relaxometry with dynamically adjustable permanent magnets. Our motivation was to substitute traditional electromagnets by distributed permanent magnets, increasing system portability.The finite element method (COMSOL® was employed for the numerical study of a small permanent magnet array to calculate achievable magnetic field strength, homogeneity, switching time and magnetic forces. A manually operated prototype was simulated and constructed to validate the numerical approach and to verify the generated magnetic field.A concentric small permanent magnet array can be used to generate strong sample pre-polarisation and variable measurement fields for ultra-low field relaxometry via simple prescribed magnet rotations. Using the array, it is possible to achieve a pre-polarisation field strength above 100 mT and variable measurement fields ranging from 20-50 μT with 200 ppm absolute field homogeneity within a field-of-view of 5 x 5 x 5 cubic centimetres.A dynamic small permanent magnet array can generate multiple highly homogeneous magnetic fields required in ultra-low field nuclear magnetic resonance (NMR and magnetic resonance imaging (MRI instruments. This design can significantly reduce the volume and energy requirements of traditional systems based on electromagnets, improving portability considerably.

  2. Characterization of mammary epithelial cell line HC11 using the NIA 15k gene array reveals potential regulators of the undifferentiated and differentiated phenotypes.

    Science.gov (United States)

    Perotti, C; Wiedl, T; Florin, L; Reuter, H; Moffat, S; Silbermann, M; Hahn, M; Angel, P; Shemanko, C S

    2009-12-01

    Differentiation of undifferentiated mammary epithelial stem and/or progenitor cells results in the production of luminal-ductal and myoepithelial cells in the young animal and upon pregnancy, the production of luminal alveolar cells. A few key regulators of differentiation have been identified, though it is not known yet how these proteins function together to achieve their well-orchestrated products. In an effort to identify regulators of early differentiation, we screened the NIA 15k gene array of 15,247 developmentally expressed genes using mouse mammary epithelial HC11 cells as a model of differentiation. We have confirmed a number of genes preferentially expressed in the undifferentiated cells (Lgals1, Ran, Jam-A and Bmpr1a) and in those induced to undergo differentiation (Id1, Nfkbiz, Trib1, Rps21, Ier3). Using antibodies to the proteins encoded by Lgals1, and Jam-A, we confirmed that their proteins levels were higher in the undifferentiated cells. Although the amounts of bone morphogenetic protein receptor-1A (BMPR1A) protein were present at all stages, we found the activity of its downstream signal transduction pathway, as measured by the presence of phosphorylated-SMAD1, -SMAD5, and -SMAD8, is elevated in undifferentiated cells and decreases in fully differentiated cells. This evidence supports that the BMPR1A pathway functions primarily in undifferentiated mammary epithelial cells. We have identified a number of genes, of known and unknown function, that are candidates for the maintenance of the undifferentiated phenotype and for early regulators of mammary alveolar cell differentiation.

  3. Comparison of Frequency-Domain Array Methods for Studying Earthquake Rupture Process

    Science.gov (United States)

    Sheng, Y.; Yin, J.; Yao, H.

    2014-12-01

    Seismic array methods, in both time- and frequency- domains, have been widely used to study the rupture process and energy radiation of earthquakes. With better spatial resolution, the high-resolution frequency-domain methods, such as Multiple Signal Classification (MUSIC) (Schimdt, 1986; Meng et al., 2011) and the recently developed Compressive Sensing (CS) technique (Yao et al., 2011, 2013), are revealing new features of earthquake rupture processes. We have performed various tests on the methods of MUSIC, CS, minimum-variance distortionless response (MVDR) Beamforming and conventional Beamforming in order to better understand the advantages and features of these methods for studying earthquake rupture processes. We use the ricker wavelet to synthesize seismograms and use these frequency-domain techniques to relocate the synthetic sources we set, for instance, two sources separated in space but, their waveforms completely overlapping in the time domain. We also test the effects of the sliding window scheme on the recovery of a series of input sources, in particular, some artifacts that are caused by the sliding window scheme. Based on our tests, we find that CS, which is developed from the theory of sparsity inversion, has relatively high spatial resolution than the other frequency-domain methods and has better performance at lower frequencies. In high-frequency bands, MUSIC, as well as MVDR Beamforming, is more stable, especially in the multi-source situation. Meanwhile, CS tends to produce more artifacts when data have poor signal-to-noise ratio. Although these techniques can distinctly improve the spatial resolution, they still produce some artifacts along with the sliding of the time window. Furthermore, we propose a new method, which combines both the time-domain and frequency-domain techniques, to suppress these artifacts and obtain more reliable earthquake rupture images. Finally, we apply this new technique to study the 2013 Okhotsk deep mega earthquake

  4. ArrayExplorer, a program in Visual Basic for robust and accurate filter cDNA array analysis.

    Science.gov (United States)

    Patriotis, P C; Querec, T D; Gruver, B N; Brown, T R; Patriotis, C

    2001-10-01

    Determining the dynamics in the global regulation of gene expression holds the promise of bringing a better understanding of the processes that govern physiological cell growth regulation and its disruption during the development of disease. The advent for cDNA arrays has created the possibility for the parallel analysis of expression of thousands of genes in a given cell population, simultaneously. The level of expression of a given set of genes within the studied tissue corresponds to the intensity of a labeled cDNA probe synthesized from the studied tissue RNA and bound specifically to the cDNAs of the genes spotted on the array. The accurate extraction of gene expression intensity values is essential for further data analysis and the interpretation of the obtained results. Here, we describe a new array image-processing software developed in Microsoft Visual Basic, the ArrayExplorer, which provides a user-friendly, multiple-window interface and a number of automatic and manual features that facilitate a reliable, robust, and accurate extraction of gene intensity values from filter-array images.

  5. Identification of disrupted AUTS2 and EPHA6 genes by array painting in a patient carrying a de novo balanced translocation t(3;7) with intellectual disability and neurodevelopment disorder.

    Science.gov (United States)

    Schneider, Anouck; Puechberty, Jacques; Ng, Bee Ling; Coubes, Christine; Gatinois, Vincent; Tournaire, Magali; Girard, Manon; Dumont, Bruno; Bouret, Pauline; Magnetto, Julia; Baghdadli, Amaria; Pellestor, Franck; Geneviève, David

    2015-12-01

    Intellectual disability (ID) is a frequent feature but is highly clinically and genetically heterogeneous. The establishment of the precise diagnosis in patients with ID is challenging due to this heterogeneity but crucial for genetic counseling and appropriate care for the patients. Among the etiologies of patients with ID, apparently balanced de novo rearrangements represent 0.6%. Several mechanisms explain the ID in patients with apparently balanced de novo rearrangement. Among them, disruption of a disease gene at the breakpoint, is frequently evoked. In this context, technologies recently developed are used to characterize precisely such chromosomal rearrangements. Here, we report the case of a boy with ID, facial features and autistic behavior who is carrying a de novo balanced reciprocal translocation t(3;7)(q11.2;q11.22)dn. Using microarray analysis, array painting (AP) technology combined with molecular study, we have identified the interruption of the autism susceptibility candidate 2 gene (AUTS2) and EPH receptor A6 gene (EPHA6). We consider that the disruption of AUTS2 explains the phenotype of the patient; the exact role of EPHA6 in human pathology is not well defined. Based on the observation of recurrent germinal and somatic translocations involving AUTS2 and the molecular environment content, we put forward the hypothesis that the likely chromosomal mechanism responsible for the translocation could be due either to replicative stress or to recombination-based mechanisms.

  6. Validation of housekeeping genes for studying differential gene expression in the bovine myometrium.

    Science.gov (United States)

    Rekawiecki, Robert; Kowalik, Magdalena K; Kotwica, Jan

    2013-12-01

    The aim of this study was to determine the steady-state expression of 13 selected housekeeping genes in the myometrium of cyclic and pregnant cows. Cells taken from bovine myometrium on days 1-5, 6-10, 11-16 and 17-20 of the oestrous cycle and in weeks 3-5, 6-8 and 9-12 of pregnancy were used. Reverse transcribed RNA was amplified in real-time PCR using designed primers. Reaction efficiency was determined with the Linreg programme. The geNorm and NormFinder programmes were used to select the best housekeeping genes. They calculate the expression stability factor for each used housekeeping gene with the smallest value for most stably expressed genes. According to geNorm, the most stable housekeeping genes in the myometrium were C2orf29, TPB and TUBB2B, while the least stably expressed genes were 18S RNA, HPRT1 and GAPDH. NormFinder identified the best genes in the myometrium as C2orf29, MRPL12 and TBP, while the worst genes were 18S RNA, B2M and SF3A1. Differences in stability factors between the two programmes may also indicate that the physiological status of the female, e.g. pregnancy, affects the stability of expression of housekeeping genes. The different expression stability of housekeeping genes did not affect progesterone receptor expression but it could be important if small differences in gene expression were measured between studies.

  7. Identification of reference genes in human myelomonocytic cells for gene expression studies in altered gravity.

    Science.gov (United States)

    Thiel, Cora S; Hauschild, Swantje; Tauber, Svantje; Paulsen, Katrin; Raig, Christiane; Raem, Arnold; Biskup, Josefine; Gutewort, Annett; Hürlimann, Eva; Unverdorben, Felix; Buttron, Isabell; Lauber, Beatrice; Philpot, Claudia; Lier, Hartwin; Engelmann, Frank; Layer, Liliana E; Ullrich, Oliver

    2015-01-01

    Gene expression studies are indispensable for investigation and elucidation of molecular mechanisms. For the process of normalization, reference genes ("housekeeping genes") are essential to verify gene expression analysis. Thus, it is assumed that these reference genes demonstrate similar expression levels over all experimental conditions. However, common recommendations about reference genes were established during 1 g conditions and therefore their applicability in studies with altered gravity has not been demonstrated yet. The microarray technology is frequently used to generate expression profiles under defined conditions and to determine the relative difference in expression levels between two or more different states. In our study, we searched for potential reference genes with stable expression during different gravitational conditions (microgravity, normogravity, and hypergravity) which are additionally not altered in different hardware systems. We were able to identify eight genes (ALB, B4GALT6, GAPDH, HMBS, YWHAZ, ABCA5, ABCA9, and ABCC1) which demonstrated no altered gene expression levels in all tested conditions and therefore represent good candidates for the standardization of gene expression studies in altered gravity.

  8. Facile synthesis and magnetic study of Ni@polyamide 66 coaxial nanotube arrays

    Science.gov (United States)

    Li, Xiaoru; Yang, Chao; Han, Ping; Zhao, Qingpei; Song, Guojun

    2016-12-01

    Ni@polyamide 66 (PA66) core/shell coaxial double-layer nanotube arrays have been prepared in the nanopores of anodic aluminum oxide templates (AAO). The shell of PA66 nanotubes were formed first and then served as templates to deposit Ni nanotubes used as the core. The morphology, structures of the obtained arrays were examined by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The formation of this unique coaxial nanotube structure was confirmed by SEM and TEM images and X-ray diffraction (XRD). We further explored the magnetic properties of the obtained coaxial nanotube arrays with vibrating sample magnetometer (VSM) and found that Ni@PA66 coaxial nanotubes exhibited higher remanence ratio than that of Ni nanotubes. These Ni@PA66 coaxial nanotubes are promising to be used as templates to fill in other materials.

  9. Study of 2D DOA Estimation for Uniform Circular Array in Wireless Location System

    Directory of Open Access Journals (Sweden)

    Ping TAN

    2010-12-01

    Full Text Available in this paper, the use of a uniform circular antenna arrays (UCA for high resolution of two dimensional (2D direction of arrivals (DOAs estimation in wireless location system is investigated. Performance of 2D DOA estimation based on the real-valued unitary transformation MUSIC algorithm for UCA is presented, especially focusing on DOA estimation of multiple correlated signals. The determination of the number of incident signals on an antenna array is addressed in the condition of colored noise and coherent signal sources. Selected method for estimating the number of these sources is formulated based on the modified eigenvectors of the covariance matrix of the received signal at the antenna array. The calibration procedure is also presented for UCA especially. Simulation results are presented to confirm the performance analysis of algorithm, then the validations of Unitary Transformation MUSIC algorithm are performed based on the measurement data in a wireless location system.

  10. Experimental study on high-voltage solar array sustained arc discharge induced by high charging

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    It has been reported that sustained arc discharge induced by electrostatic discharge (ESD) could cause permanent damage to high-power and high-voltage solar array of spacecrafts. The paper focuses on ESD simulating experiments on Si and GaAs samples, and induces sustained arc discharge. The physical mechanism of sustained arc discharge is discussed by comparing the charging/discharging phenomena between Si and GaAs samples. The experiments show that sustained arc discharge can produce a permanent short-circuit channel between solar cell strings through which the solar array’s photovoltaic power may flow out sustainedly. The analyses show that sustained arc discharge strongly depends on solar array structure, solar array operating voltage, ESD characteristics and cell materials.

  11. Tube array heat transfer in fluidized beds; a study of particle size effects

    Energy Technology Data Exchange (ETDEWEB)

    Chung, T.Y.; Welty, J.R. (Oregon State Univ., Corvallis, OR (USA). Dept. of Mechanical Engineering)

    1989-07-01

    Experiments were performed with an array of horizontal tubes, arranged in a regular equilateral triangular pattern, immersed in a fluidized bed operating at 812 {Kappa}. Data are reported for heat transfer between the bed and a centrally-located tube in the array. Both total and radiative heat transfer rates were measured for superficial velocities spanning the range from packed bed conditions to over twice the minimum fluidization velocity. Results are presented for five different-size particles. Local heat transfer values, measured around the tube periphery, and integrated averages are reported for all test conditions. Comparisons are also made between the heat transfer behavior of a tube in an array and that for a single tube in a hot fluidized bed under the same overall operating conditions. The results of this comparison suggests that the two mechanisms, gas convection and radiation, are competing effects.

  12. Application of gene array chip in diagnosis of cytogenetics of recurrent spontaneous abortion%基因芯片技术在复发性流产遗传学诊断中的应用

    Institute of Scientific and Technical Information of China (English)

    沈国松; 张甦; 何平亚

    2013-01-01

    目的 探讨基因芯片单核苷酸多态性阵列(SNP-array)技术在复发性流产遗传学诊断中的应用价值.方法 选择2012年1-10月在浙江省湖州市妇幼保健院产前诊断中心就诊的、曾有自然流产≥2次、本次妊娠又发生自然流产的患者26例(RSA组),对流产物分别应用绒毛染色体核型分析技术和SNP-array技术进行分析;同时选取20例早孕期人工流产妇女作为对照组.结果 绒毛染色体核型分析获得结果19例,检测成功率为73% (19/26),发现染色体异常10例,异常检出率为10/19;SNP-array技术检测获得结果26例,检测成功率为100%,发现全基因组拷贝数异常15例,异常检出率为58% (15/26).对照组胚胎绒毛染色体核型分析获得结果16例,检测成功率为16/20,均未发现染色体核型异常;SNP-array技术检测获得结果20例,检测成功率为20/20,均未发现全基因组拷贝数异常.结论 SNP-array技术具有分辨率高、准确性好等优点,是自然流产特别是复发性流产遗传学诊断的有力工具.%Objective To investigate clinical value of single nucleotide polymorphism array (SNParray) gene chip technique in diagnosis of genetics of recurrent spontaneous abortion (RSA).Methods From January to October 2012,the 26 patients with more than twice of spontaneous abortion in Huzhou Maternal and Child Health Care Hospital were enrolled in this study(RSA group).Meanwhile 20 cases with induced abortion were taken as control group.All aborted tissues were analyzed with conventional cytogenetic karyotyping and SNP-array,respectively.Results Chorionic villus chromosomal examination was successfully done in 19 cases (73%,19/26),which 10 cases were found with chromosomal anomaly,the overall detection rate is 10/19.However,SNP-array analysis was successfully performed in all 26 cases.The overall rate of detection was 100%,and abnormalities were found in 15 cases,which reached the detection rate was 58% (15

  13. The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits

    DEFF Research Database (Denmark)

    Voight, Benjamin F; Kang, Hyun Min; Ding, Jun;

    2012-01-01

    of loci with promising but not yet compelling association evidence. To establish association at additional loci and to characterize the genome-wide significant loci by fine-mapping, we designed the "Metabochip," a custom genotyping array that assays nearly 200,000 SNP markers. Here, we describe...... dramatic cost efficiencies compared to designing single-trait follow-up reagents, and provides the opportunity to compare results across a range of related traits. The metabochip and similar custom genotyping arrays offer a powerful and cost-effective approach to follow-up large-scale genotyping...

  14. Study on data acquisition circuit used in SSPA linear array detector X-ray detection

    CERN Document Server

    Wei Biao; Che Zhen Ping

    2002-01-01

    After SSPA used as X-ray array detector is developed, the authors take a research on the data acquisition circuit applied to the detector. The experiment designed has verified the feasibility of application of this array detector and its data acquisition circuit to X-ray computed tomography (X-CT). The preliminary test results indicate that the method of the X-ray detection is feasible for industry X-CT nondestructive testing, which brings about advantage for detecting and measuring with high resolution, good efficiency and low cost

  15. Transparently wrap-gated semiconductor nanowire arrays for studies of gate-controlled photoluminescence

    Energy Technology Data Exchange (ETDEWEB)

    Nylund, Gustav; Storm, Kristian; Torstensson, Henrik; Wallentin, Jesper; Borgström, Magnus T.; Hessman, Dan; Samuelson, Lars [Solid State Physics, Nanometer Structure Consortium, Lund University, Box 118, S-221 00 Lund (Sweden)

    2013-12-04

    We present a technique to measure gate-controlled photoluminescence (PL) on arrays of semiconductor nanowire (NW) capacitors using a transparent film of Indium-Tin-Oxide (ITO) wrapping around the nanowires as the gate electrode. By tuning the wrap-gate voltage, it is possible to increase the PL peak intensity of an array of undoped InP NWs by more than an order of magnitude. The fine structure of the PL spectrum reveals three subpeaks whose relative peak intensities change with gate voltage. We interpret this as gate-controlled state-filling of luminescing quantum dot segments formed by zincblende stacking faults in the mainly wurtzite NW crystal structure.

  16. Gene and pathway level analyses of germline DNA-repair gene variants and prostate cancer susceptibility using the iCOGS-genotyping array

    DEFF Research Database (Denmark)

    Saunders, Edward J; Dadaev, Tokhir; Leongamornlert, Daniel A

    2016-01-01

    BACKGROUND: Germline mutations within DNA-repair genes are implicated in susceptibility to multiple forms of cancer. For prostate cancer (PrCa), rare mutations in BRCA2 and BRCA1 give rise to moderately elevated risk, whereas two of B100 common, low-penetrance PrCa susceptibility variants identif...

  17. A large-eddy simulation study of wake propagation and power production in an array of tidal-current turbines.

    Science.gov (United States)

    Churchfield, Matthew J; Li, Ye; Moriarty, Patrick J

    2013-02-28

    This paper presents our initial work in performing large-eddy simulations of tidal turbine array flows. First, a horizontally periodic precursor simulation is performed to create turbulent flow data. Then those data are used as inflow into a tidal turbine array two rows deep and infinitely wide. The turbines are modelled using rotating actuator lines, and the finite-volume method is used to solve the governing equations. In studying the wakes created by the turbines, we observed that the vertical shear of the inflow combined with wake rotation causes lateral wake asymmetry. Also, various turbine configurations are simulated, and the total power production relative to isolated turbines is examined. We found that staggering consecutive rows of turbines in the simulated configurations allows the greatest efficiency using the least downstream row spacing. Counter-rotating consecutive downstream turbines in a non-staggered array shows a small benefit. This work has identified areas for improvement. For example, using a larger precursor domain would better capture elongated turbulent structures, and including salinity and temperature equations would account for density stratification and its effect on turbulence. Additionally, the wall shear stress modelling could be improved, and more array configurations could be examined.

  18. Twenty-channel bolometer array for studying impurity radiation and transport in the TCS field-reversed configuration

    Science.gov (United States)

    Kostora, M. R.; Hsu, S. C.; Wurden, G. A.

    2006-10-01

    A bolometer array diagnostic has been developed for the University of Washington Translation, Confinement, and Sustainment (TCS) field-reversed configuration (FRC) experiment in order to measure radially resolved total radiated power per unit length of the FRC. This will provide radiation energy loss information, useful in power balance and impurity studies. The 20-element photodiode bolometer will be mounted at the midplane of the TCS cylindrical vacuum chamber to view the rotating magnetic field (RMF) generated FRC plasma. Key features of this new bolometer array are (1) extensive electrical shielding against the RMF, (2) robust electrical isolation, (3) trans-impedance amplifiers using a microcoax interface at the array and a fiber optic interface to the screen room, and (4) a custom glass-on-metal socket for the 20-element photodiode chip to ensure high vacuum compatibility. The bolometer array can be retracted behind a gate valve using a stepper motor to protect it during vacuum chamber bakeout. The slit assembly housing is interchangeable to provide flexibility for the viewing sightlines.

  19. Large-Eddy Simulation Study of Wake Propagation and Power Production in an Array of Tidal-Current Turbines: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Churchfield, M. J.; Li, Y.; Moriarty, P. J.

    2012-07-01

    This paper presents our initial work in performing large-eddy simulations of tidal turbine array flows. First, a horizontally-periodic precursor simulation is performed to create turbulent flow data. Then that data is used as inflow into a tidal turbine array two rows deep and infinitely wide. The turbines are modeled using rotating actuator lines, and the finite-volume method is used to solve the governing equations. In studying the wakes created by the turbines, we observed that the vertical shear of the inflow combined with wake rotation causes lateral wake asymmetry. Also, various turbine configurations are simulated, and the total power production relative to isolated turbines is examined. Staggering consecutive rows of turbines in the simulated configurations allows the greatest efficiency using the least downstream row spacing. Counter-rotating consecutive downstream turbines in a non-staggered array shows a small benefit. This work has identified areas for improvement, such as the use of a larger precursor domain to better capture elongated turbulent structures, the inclusion of salinity and temperature equations to account for density stratification and its effect on turbulence, improved wall shear stress modelling, and the examination of more array configurations.

  20. Large-Eddy Simulation Study of Wake Propagation and Power Production in an Array of Tidal-Current Turbines: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Churchfield, M. J.; Li, Y.; Moriarty, P. J.

    2011-07-01

    This paper presents our initial work in performing large-eddy simulations of tidal turbine array flows. First, a horizontally-periodic precursor simulation is performed to create turbulent flow data. Then that data is used to determine the inflow into a tidal turbine array two rows deep and infinitely wide. The turbines are modeled using rotating actuator lines, and the finite-volume method is used to solve the governing equations. In studying the wakes created by the turbines, we observed that the vertical shear of the inflow combined with wake rotation causes lateral wake asymmetry. Also, various turbine configurations are simulated, and the total power production relative to isolated turbines is examined. Staggering consecutive rows of turbines in the simulated configurations allows the greatest efficiency using the least downstream row spacing. Counter-rotating consecutive downstream turbines in a non-staggered array shows a small benefit. This work has identified areas for improvement, such as the use of a larger precursor domain to better capture elongated turbulent structures, the inclusion of salinity and temperature equations to account for density stratification and its effect on turbulence, improved wall shear stress modeling, and the examination of more array configurations.

  1. On the Statics for Micro-Array Data Analysis

    Science.gov (United States)

    Urushibara, Tomoko; Akasaka, Shizu; Ito, Makiko; Suzuki, Tomonori; Miyazaki, Satoru

    2010-01-01

    Recently after human genome sequence has been determined almost perfectly, more and more researchers have been studying genes in detail. Therefore, we are sure that accumulated gene information for human will be getting more important in the near future to develop customized medicine and to make gene interactions clear. Among plenty of information, micro array might be one of the most important analysis method for genes because it is the technique that can get big amount of the gene expressions data from one time experiment and also can be used for DNA isolation. To get the novel knowledge from micro array data, we need to enrich statistical tools for its data analysis. So far, many mathematical theories and definition have been proposing. However, many of those proposals are tested with strict conditions or customized to data for specific species. In this paper, we reviewed existing typical statistical methods for micro array analysis and discussed the repeatability of the analysis, construction the guideline with more general procedure. First we analyzed the micro array data for TG rats, with statistical methods of family-wise error rate (FWER) control approach and False Discovery Rate (FDR) control approach. As existing report, no significantly different gene could be detected with FWER control approach. On the other hand, we could find several genes significantly with FDR control approach even q=0.5. To find out the reliability of FDR control approach with micro array conditions, we have analyzed 2 more pieces of data from Gene Expression Omnibus (GEO) public database on the web site with SAM in addition to FWER and FDR control approaches. We could find a certain number of significantly different genes with BH method and SAM in the case of q=0.05. However, we have to note that the number and kinds of detected genes are different when we compare our result with the one from the published paper. Even if the same approach is used to analyze the same micro array

  2. Reaction selectivity studies on nanolithographically-fabricated platinum model catalyst arrays

    Energy Technology Data Exchange (ETDEWEB)

    Grunes, Jeffrey Benjamin

    2004-05-15

    In an effort to understand the molecular ingredients of catalytic activity and selectivity toward the end of tuning a catalyst for 100% selectivity, advanced nanolithography techniques were developed and utilized to fabricate well-ordered two-dimensional model catalyst arrays of metal nanostructures on an oxide support for the investigation of reaction selectivity. In-situ and ex-situ surface science techniques were coupled with catalytic reaction data to characterize the molecular structure of the catalyst systems and gain insight into hydrocarbon conversion in heterogeneous catalysis. Through systematic variation of catalyst parameters (size, spacing, structure, and oxide support) and catalytic reaction conditions (hydrocarbon chain length, temperature, pressures, and gas composition), the data presented in this dissertation demonstrate the ability to direct a reaction by rationally adjusting, through precise control, the design of the catalyst system. Electron beam lithography (EBL) was employed to create platinum nanoparticles on an alumina (Al{sub 2}O{sub 3}) support. The Pt nanoparticle spacing (100-150-nm interparticle distance) was varied in these samples, and they were characterized using x-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and atomic force microscopy (AFM), both before and after reactions. The TEM studies showed the 28-nm Pt nanoparticles with 100 and 150-nm interparticle spacing on alumina to be polycrystalline in nature, with crystalline sizes of 3-5 nm. The nanoparticle crystallites increased significantly after heat treatment. The nanoparticles were still mostly polycrystalline in nature, with 2-3 domains. The 28-nm Pt nanoparticles deposited on alumina were removed by the AFM tip in contact mode with a normal force of approximately 30 nN. After heat treatment at 500 C in vacuum for 3 hours, the AFM tip, even at 4000 nN, could not remove the platinum nanoparticles. The

  3. Reaction selectivity studies on nanolithographically-fabricated platinum model catalyst arrays

    Energy Technology Data Exchange (ETDEWEB)

    Grunes, Jeffrey Benjamin [Univ. of California, Berkeley, CA (United States)

    2004-05-01

    In an effort to understand the molecular ingredients of catalytic activity and selectivity toward the end of tuning a catalyst for 100% selectivity, advanced nanolithography techniques were developed and utilized to fabricate well-ordered two-dimensional model catalyst arrays of metal nanostructures on an oxide support for the investigation of reaction selectivity. In-situ and ex-situ surface science techniques were coupled with catalytic reaction data to characterize the molecular structure of the catalyst systems and gain insight into hydrocarbon conversion in heterogeneous catalysis. Through systematic variation of catalyst parameters (size, spacing, structure, and oxide support) and catalytic reaction conditions (hydrocarbon chain length, temperature, pressures, and gas composition), the data presented in this dissertation demonstrate the ability to direct a reaction by rationally adjusting, through precise control, the design of the catalyst system. Electron beam lithography (EBL) was employed to create platinum nanoparticles on an alumina (Al2O3) support. The Pt nanoparticle spacing (100-150-nm interparticle distance) was varied in these samples, and they were characterized using x-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and atomic force microscopy (AFM), both before and after reactions. The TEM studies showed the 28-nm Pt nanoparticles with 100 and 150-nm interparticle spacing on alumina to be polycrystalline in nature, with crystalline sizes of 3-5 nm. The nanoparticle crystallites increased significantly after heat treatment. The nanoparticles were still mostly polycrystalline in nature, with 2-3 domains. The 28-nm Pt nanoparticles deposited on alumina were removed by the AFM tip in contact mode with a normal force of approximately 30 nN. After heat treatment at 500 C in vacuum for 3 hours, the AFM tip, even at 4000 nN, could not remove the platinum

  4. Genome-wide association study identifies candidate genes for starch content regulation in maize kernels

    Directory of Open Access Journals (Sweden)

    Na Liu

    2016-07-01

    Full Text Available Kernel starch content is an important trait in maize (Zea mays L. as it accounts for 65% to 75% of the dry kernel weight and positively correlates with seed yield. A number of starch synthesis-related genes have been identified in maize in recent years. However, many loci underlying variation in starch content among maize inbred lines still remain to be identified. The current study is a genome-wide association study that used a set of 263 maize inbred lines. In this panel, the average kernel starch content was 66.99%, ranging from 60.60% to 71.58% over the three study years. These inbred lines were genotyped with the SNP50 BeadChip maize array, which is comprised of 56,110 evenly spaced, random SNPs. Population structure was controlled by a mixed linear model (MLM as implemented in the software package TASSEL. After the statistical analyses, four SNPs were identified as significantly associated with starch content (P ≤ 0.0001, among which one each are located on chromosomes 1 and 5 and two are on chromosome 2. Furthermore, 77 candidate genes associated with starch synthesis were found within the 100-kb intervals containing these four QTLs, and four highly associated genes were within 20-kb intervals of the associated SNPs. Among the four genes, Glucose-1-phosphate adenylyltransferase (APS1; Gene ID GRMZM2G163437 is known as an important regulator of kernel starch content. The identified SNPs, QTLs, and candidate genes may not only be readily used for germplasm improvement by marker-assisted selection in breeding, but can also elucidate the genetic basis of starch content. Further studies on these identified candidate genes may help determine the molecular mechanisms regulating kernel starch content in maize and other important cereal crops.

  5. Evaluation of reference genes for gene expression studies in human brown adipose tissue.

    Science.gov (United States)

    Taube, Magdalena; Andersson-Assarsson, Johanna C; Lindberg, Kristin; Pereira, Maria J; Gäbel, Markus; Svensson, Maria K; Eriksson, Jan W; Svensson, Per-Arne

    2015-01-01

    Human brown adipose tissue (BAT) has during the last 5 year been subjected to an increasing research interest, due to its putative function as a target for future obesity treatments. The most commonly used method for molecular studies of human BAT is the quantitative polymerase chain reaction (qPCR). This method requires normalization to a reference gene (genes with uniform expression under different experimental conditions, e.g. similar expression levels between human BAT and WAT), but so far no evaluation of reference genes for human BAT has been performed. Two different microarray datasets with samples containing human BAT were used to search for genes with low variability in expression levels. Seven genes (FAM96B, GNB1, GNB2, HUWE1, PSMB2, RING1 and TPT1) identified by microarray analysis, and 8 commonly used reference genes (18S, B2M, GAPDH, LRP10, PPIA, RPLP0, UBC, and YWHAZ) were selected and further analyzed by quantitative PCR in both BAT containing perirenal adipose tissue and subcutaneous adipose tissue. Results were analyzed using 2 different algorithms (Normfinder and geNorm). Most of the commonly used reference genes displayed acceptably low variability (geNorm M-values genes identified by microarray displayed an even lower variability (M-values genes for qPCR analysis of human BAT and we recommend that they are included in future gene expression studies of human BAT.

  6. A new study of muons in air showers by NBU air shower array

    Science.gov (United States)

    Chaudhuri, N.; Mukherjee, N.; Sarkar, S.; Basak, D. K.; Ghosh, B.

    1985-01-01

    The North Bengal University (NBU) air shower array has been in operation in conjunction with two muon magnetic spectrographs. The array incorporates 21 particle density sampling detectors around the magnetic spectrographs covering an area of 900 sq m. The layout of the array is based on the arrangement of detectors in a square symmetry. The array set up on the ground level is around a 10 m high magnetic spectrograph housing. This magnetic spectrograph housing limits the zenith angular acceptance of the incident showers to a few degrees. Three hundred muons in the fitted showers of size range 10 to the 4th power to 10 to the 5th power particles have so far been scanned and the momenta determined in the momentum range 2 - 440 GeV/c. More than 1500 recorded showers are now in the process of scanning and fitting. A lateral distribution of muons of energy greater than 300 MeV in the shower size range 10 to the 5th power to 7 x 10 to the 5th power has been obtained.

  7. Report for simultaneous, multiple independently steered beam study for Airborne Electronically Steerable Phased Array (AESPA) program

    Science.gov (United States)

    1978-01-01

    Design concepts of an array for the formation of multiple, simultaneous, independently pointed beams for satellite communication links were investigated through tradeoffs of various approaches which were conceived as possible solutions to the problem. After the preferred approach was selected, a more detailed design was configured and is presented as a candidate system that should be given further consideration for development leading to a preliminary design. This array uses an attenuator and a phase shifter with every element. The aperture excitation necessary to form the four beams is calculated and then placed across the array using these devices. Pattern analysis was performed for two beam and four beam cases with numerous patterns being presented. Parameter evaluation shown includes pointing accuracy and beam shape, sidelobe characteristics, gain control, and beam normalization. It was demonstrated that a 4 bit phase shifter and a 6 bit, 30 dB attenuator were sufficient to achieve adequate pattern performances. The phase amplitude steered multibeam array offers the flexibility of 1 to 4 beams with an increase in gain of 6 dB if only one beam is selected.

  8. Microwave Synthesized ZnO Nanorod Arrays for UV Sensors: A Seed Layer Annealing Temperature Study

    Directory of Open Access Journals (Sweden)

    Ana Pimentel

    2016-04-01

    Full Text Available The present work reports the influence of zinc oxide (ZnO seed layer annealing temperature on structural, optical and electrical properties of ZnO nanorod arrays, synthesized by hydrothermal method assisted by microwave radiation, to be used as UV sensors. The ZnO seed layer was produced using the spin-coating method and several annealing temperatures, ranging from 100 to 500 °C, have been tested. X-ray diffraction (XRD, scanning electron microscopy (SEM, atomic force microscopy (AFM and spectrophotometry measurements have been used to investigate the structure, morphology, and optical properties variations of the produced ZnO nanorod arrays regarding the seed layer annealing temperatures employed. After the growth of ZnO nanorod arrays, the whole structure was tested as UV sensors, showing an increase in the sensitivity with the increase of seed layer annealing temperature. The UV sensor response of ZnO nanorod arrays produced with the seed layer annealed temperature of 500 °C was 50 times superior to the ones produced with a seed layer annealed at 100 °C.

  9. Studying DAC capacitor-array degradation in charge-redistribution SAR ADCs

    NARCIS (Netherlands)

    Khan, M.A.; Kerkhoff, Hans G.

    2014-01-01

    In this paper, system-level behavioural models are used to simulate the aging-related degradation effects in the DAC capacitor array of a charge-redistribution successive approximation register (SAR) ADC because of the large calculation time of transistor-level aging simulators. A performance-analys

  10. Studying DAC capacitor-array degradation in charge-redistribution SAR ADCs

    NARCIS (Netherlands)

    Khan, Muhammad Aamir; Kerkhoff, Hans G.

    2014-01-01

    In this paper, system-level behavioural models are used to simulate the aging-related degradation effects in the DAC capacitor array of a charge-redistribution successive approximation register (SAR) ADC because of the large calculation time of transistor-level aging simulators. A performance-analys

  11. The water Cherenkov detector array for studies of cosmic rays at the University of Puebla

    Science.gov (United States)

    Cotzomi, J.; Moreno, E.; Murrieta, T.; Palma, B.; Pérez, E.; Salazar, H.; Villaseñor, L.

    2005-11-01

    We describe the design and performance of a hybrid extensive air shower detector array built on the Campus of the University of Puebla ( 19∘N, 90∘W, 800 g/cm2) to measure the energy, arrival direction and composition of primary cosmic rays with energies around 1 PeV, i.e., around the knee of the cosmic ray spectrum. The array consists of 3 water Cherenkov detectors of 1.86 m2 cross-section and 12 liquid scintillator detectors of 1 m2 distributed in a square grid with a detector spacing of 20 m over an area of 4000 m2. We discuss the calibration and stability of the array for both sets of detectors and report on preliminary measurements and reconstruction of the lateral distributions for the electromagnetic (EM) and muonic components of extensive air showers. We also discuss how the hybrid character of the array can be used to measure mass composition of the primary cosmic rays by estimating the relative contents of muons with respect to the EM component of extensive air showers. This facility is also used to train students interested in the field of cosmic rays.

  12. Hybrid Extensive Air Shower Detector Array at the University of Puebla to Study Cosmic Rays

    Science.gov (United States)

    Martínez, O.; Pérez, E.; Salazar, H.; Villaseñor, L.

    We describe the design of an extensive air shower detector array built in the Campus of the University of Puebla (located at 19°N, 90°W, 800 gcm -2) to measure the energy and arrival direction of primary cosmic rays with energies around 1015 eV. The array consists of 18 liquid scintillator detectors (12 in the first stage) and 6 water Cherenkov detectors (one of 10 m 2 cross section and five smaller ones of 1.86 m 2 cross section), distributed in a square grid with a detector spacing of 20 m over an area of 4000 m 2. In this paper we discuss the calibration and stability of the array, and discuss the capability of hybrid arrays, such as this one consisting of water Cherenkov and liquid scintillator detectors, to allow a separation of the electromagnetic and muon components of extensive air showers. This separation plays an important role in the determination of the mass and identity of the primary cosmic ray. This facility is also used to train students interested in the field of cosmic rays.

  13. Feasibility study of a 110 watt per kilogram lightweight solar array system

    Science.gov (United States)

    Shepard, N. F.; Stahle, C. V.; Schneider, A.; Hanson, K. L.

    1972-01-01

    An investigation of the feasibility of a solar array panel subsystem which will produce 10,000 watts of electrical output at 1 A.U. with an overall beginning-of-life power-to-weight ratio of at least 110 watt/kg is reported. A description of the current baseline configuration which meets these requirements is presented. A parametric analysis of the single boom, two blanket planar solar array system was performed to arrive at the optimum system aspect ratio. A novel concept for the stiffening of a lightweight solar array by canting the solar cell blankets at a small angle to take advantage of the inherent in-plane stiffness to increase the symmetric out-of-plane frequency is introduced along with a preliminary analysis of the stiffening effect. A comparison of welded and soldered solar cell interconnections leads to the conclusion that welding is required on this ultralightweight solar array. The use of a boron/aluminum composite material in a BI-STEM type deployable boom is investigated as a possible advancement in the state-of-the-art.

  14. Identification of Reference Genes in Human Myelomonocytic Cells for Gene Expression Studies in Altered Gravity

    Directory of Open Access Journals (Sweden)

    Cora S. Thiel

    2015-01-01

    Full Text Available Gene expression studies are indispensable for investigation and elucidation of molecular mechanisms. For the process of normalization, reference genes (“housekeeping genes” are essential to verify gene expression analysis. Thus, it is assumed that these reference genes demonstrate similar expression levels over all experimental conditions. However, common recommendations about reference genes were established during 1 g conditions and therefore their applicability in studies with altered gravity has not been demonstrated yet. The microarray technology is frequently used to generate expression profiles under defined conditions and to determine the relative difference in expression levels between two or more different states. In our study, we searched for potential reference genes with stable expression during different gravitational conditions (microgravity, normogravity, and hypergravity which are additionally not altered in different hardware systems. We were able to identify eight genes (ALB, B4GALT6, GAPDH, HMBS, YWHAZ, ABCA5, ABCA9, and ABCC1 which demonstrated no altered gene expression levels in all tested conditions and therefore represent good candidates for the standardization of gene expression studies in altered gravity.

  15. Using a sensitivity study to facilitate the design of a multi-electrode array to measure six cardiac conductivity values.

    Science.gov (United States)

    Johnston, Barbara M

    2013-07-01

    When using the bidomain model to model the electrical activity of the heart, there are potentially six cardiac conductivity values involved: conductivity values in directions along and normal to the cardiac fibres with a sheet, as well as a conductivity value in the normal direction between the sheets, and these occur for both the extracellular and intracellular domains in the model. To date it has been common to assume that the two normal direction conductivity values are the same. However, recent work has demonstrated that six cardiac conductivity values, rather than four, are necessary for accurate modelling, which can then facilitate understanding of cardiovascular disease. To design a method to determine these conductivities, it is also necessary to design a suitable multi-electrode array, which can be used, in conjunction with an inversion technique, to retrieve conductivity values from measurements of potential made on the array. This work uses the results of a study, into the sensitivity of the measuring potentials to variability in the input conductivities, to facilitate the design of an array that could be used to retrieve six cardiac conductivity values, as well as fibre rotation angle. It is found that if an electrode in the array has a much lower value of potential than the other electrodes, then it tends to be much more sensitive to the input conductivities than the other electrodes. It also appears that inclusion of this type of electrode in the set of measuring electrodes is essential for accurately retrieving conductivity values. This technique is used to identify electrodes to be included in the array and using the final design it is demonstrated, using synthetic values of potential, that the six cardiac conductivity values, and the fibre rotation angle, can be retrieved very accurately.

  16. Large plasmids of Escherichia coli and Salmonella encode highly diverse arrays of accessory genes on common replicon families.

    Science.gov (United States)

    Williams, Laura E; Wireman, Joy; Hilliard, Valda C; Summers, Anne O

    2013-01-01

    Plasmids are important in evolution and adaptation of host bacteria, yet we lack a comprehensive picture of their own natural variation. We used replicon typing and RFLP analysis to assess diversity and distribution of plasmids in the ECOR, SARA, SARB and SARC reference collections of Escherichia coli and Salmonella. Plasmids, especially large (≥30 kb) plasmids, are abundant in these collections. Host species and genotype clearly impact plasmid prevalence; plasmids are more abundant in ECOR than SAR, but, within ECOR, subgroup B2 strains have the fewest large plasmids. The majority of large plasmids have unique RFLP patterns, suggesting high variation, even within dominant replicon families IncF and IncI1. We found only four conserved plasmid types within ECOR, none of which are widely distributed. Within SAR, conserved plasmid types are primarily serovar-specific, including a pSLT-like plasmid in 13 Typhimurium strains. Conservation of pSLT contrasts with variability of other plasmids, suggesting evolution of serovar-specific virulence plasmids is distinct from that of most enterobacterial plasmids. We sequenced a conserved serovar Heidelberg plasmid but did not detect virulence or antibiotic resistance genes. Our data illustrate the high degree of natural variation in large plasmids of E. coli and Salmonella, even among plasmids sharing backbone genes.

  17. Characterization of 11p14-p12 deletion in WAGR syndrome by array CGH for identifying genes contributing to mental retardation and autism.

    Science.gov (United States)

    Xu, S; Han, J C; Morales, A; Menzie, C M; Williams, K; Fan, Y-S

    2008-01-01

    WAGR (Wilms tumor, Aniridia, Genitourinary malformations and mental Retardation) syndrome is a rare genomic disorder caused by deletion of the 11p14-p12 chromosome region. The majority of WAGR patients have mental retardation and behavioral problems, and more than 20% of the patients also have features of autism. While the Wilms tumor/genitourinary anomalies and aniridia are caused by deletion of WT1 and PAX6 respectively, the genomic cause of mental retardation and autism in WAGR syndrome remains unknown. Using oligonucleotide arrays, we have characterized the 11p14-p12 deletions in 31 patients and identified all the genes involved in each deletion. The deletions had sizes ranging from 4.9 to 23 Mb that encompass 18-62 genes (40 on average). In addition to WT1 and PAX6, all the patients had deletion of PRRG4 (transmembrane gamma-carboxyglutamic acid protein 4). The majority of them had deletion of BDNF (brain-derived neurotrophic factor) and SLC1A2 [solute carrier family 1 (glial high affinity glutamate transporter) member 2]. Deletion of BDNF and SLC1A2 occurred in patients with autism more frequently than in those without autism. Literature review on the functions of the genes suggests that haploinsufficiency of SLC1A2, PRRG4, and BDNF may contribute to mental retardation and behavioral problems. In particular, BDNF may modulate the risk of autism in WAGR patients as suggested by its link with Rett syndrome as a target of MECP2. We observed that all the de novo deletions occurred in the chromosome 11 inherited from the father in the families genotyped, implying a predisposition for de novo mutations occurring in spermatogenesis and possible involvement of imprinting in cognitive impairment in WAGR patients. Copyright 2008 S. Karger AG, Basel.

  18. Validation of reference genes for gene expression studies in the emerald ash borer (Agrilus planipennis)

    Institute of Scientific and Technical Information of China (English)

    Swapna Priya Rajarapu; Praveen Mamidala; Omprakash Mittapalli

    2012-01-01

    The Emerald ash borer (EAB,Agrilus planipennis Fairmaire) an exotic invasive insect pest has killed millions of ash trees (Fraxinus spp.) across North America and threatens billions more.We validated six A.planipennis reference genes (actin,ACT; beta tubulin,β- TUB; glyceraldehyde-3-phosphate dehydrogenase,GAPDH; ribosomal protein,RPL7; translation elongation factor 1α,TEF-1α; and ubiquitin,UBQ) using geNorm,Normfinder and BestKeeper for accurate determination of target messenger RNA levels in gene expression studies.The stability of the six reference genes was evaluated in different larval tissues,developmental stages and two treatments ofA.planipennis using quantitative real-time polymerase chain reaction.Although there was no consistent ranking observed among the reference genes across the samples,the overall analysis revealed TEF-1α as the most stable reference gene.GAPDH and ACT showed least stability for all the samples studied.We conclude that TEF-1α is the most appropriate reference gene for gene expression studies inA.planipennis.Results obtained can be applicable for transcript profiling in other invasive insect pests.Further,these validated reference genes could also serve as the basis for selection of candidate reference genes in any given insect system post-validation.

  19. Selection and validation of reference genes for quantitative gene expression studies in Erythroxylum coca.

    Science.gov (United States)

    Docimo, Teresa; Schmidt, Gregor W; Luck, Katrin; Delaney, Sven K; D'Auria, John C

    2013-01-01

    Real-time quantitative PCR is a powerful technique for the investigation of comparative gene expression, but its accuracy and reliability depend on the reference genes used as internal standards. Only genes that show a high level of expression stability are suitable for use as reference genes, and these must be identified on a case-by-case basis. Erythroxylum coca produces and accumulates high amounts of the pharmacologically active tropane alkaloid cocaine (especially in the leaves), and is an emerging model for the investigation of tropane alkaloid biosynthesis. The identification of stable internal reference genes for this species is important for its development as a model species, and would enable comparative analysis of candidate biosynthetic genes in the different tissues of the coca plant. In this study, we evaluated the expression stability of nine candidate reference genes in E. coca ( Ec6409, Ec10131, Ec11142, Actin, APT2, EF1α, TPB1, Pex4, Pp2aa3). The expression of these genes was measured in seven tissues (flowers, stems, roots and four developmental leaf stages) and the stability of expression was assessed using three algorithms (geNorm, NormFinder and BestKeeper). From our results we conclude that Ec10131 and TPB1 are the most appropriate internal reference genes in leaves (where the majority of cocaine is produced), while Ec10131 and Ec6409 are the most suitable internal reference genes across all of the tissues tested.

  20. Efficacy of Hummel (Modified Schlumberger Arrays of Vertical Electrical Sounding in Groundwater Exploration: Case Study of Parts of Ibadan Metropolis, Southwestern Nigeria

    Directory of Open Access Journals (Sweden)

    Micheal Oladunjoye

    2015-01-01

    Full Text Available This research compared the interpretation results of the Vertical Electrical Sounding data acquired using the conventional Schlumberger and modified Schlumberger arrays with a view to assessing the effectiveness of the modified Schlumberger arrays of vertical electrical sounding as an alternative to the conventional Schlumberger array at sites with space constraint during groundwater exploration. A total of thirty-seven (37 sounding locations were occupied and one hundred (100 sounding data for both conventional Schlumberger and modified Schlumberger arrays were collected across different rock units within Ibadan metropolis, south-western Nigeria, with electrode spacing (AB/2 ranging from 1 to 75 m. The field data were interpreted qualitatively by curve matching and computer iterative methods. Also, statistical analysis of subsurface units and the coefficient of correlation “R” of the statistical plots of the field data shows the relationship between the different arrays. The raw data plot of the different arrays shows significant similarities while statistical analysis of the geo-electric parameters obtained from the different arrays across varied lithologic units show that strong relationships exist between the different field methods. The coefficient of correlation R with values ranging from 0.7 to 0.99 implies that a good similarity exists between the different field methods employed in this study. Hence, modified Schlumberger arrays can be said to be a good alternative to the conventional Schlumberger array for groundwater exploration especially in urban settings where space constraint is a major challenge.

  1. Paralogous Genes as a Tool to Study the Regulation of Gene Expression

    DEFF Research Database (Denmark)

    Hoffmann, Robert D

    The genomes of plants are marked by reoccurring events of whole-genome duplication. These events are major contributors to speciation and provide the genetic material for organisms to evolve ever greater complexity. Duplicated genes, referred to as paralogs, may be retained because they acquired...... new functions, or their gene products are in a dosage balance. Regulatory DNA elements - some of which are conserved across species and hence called conserved non-coding sequences (CNSs) - that control expression of duplicated genes are thus under similar purifying selection. In the present study, I...... have performed in-depth analyses of paralogous genes in Arabidopsis thaliana, their expression profile, their sequence conservation, and their functions, in order to investigate the relationship between gene expression and retention of paralogous genes. Paralogs with lower expression than...

  2. Microchannel arrays with improved accessibility and use for cell studies and emulsification

    Science.gov (United States)

    Kikuchi, Yuji; Kikuchi, Hiroko E.; Kuboki, Yoshinori; Nakajima, Mitsutoshi

    2000-03-01

    Arrays of microgrooves (groove width; 2, 3, 4, 5, 6, 7, 8, 10, 12, and 14 micrometer, groove interval; width x3, x10, and x20, one size and interval per chip) each connecting a center well and a side edge of a silicon substrate were created by photolithography and anisotropic wet etching. A penetrating hole was made by sand blast at the substrate center for the access to the center well. By tightly covering the substrate surface with a glass plate, the microgroove arrays were converted to microchannel arrays having one ends open at the side edges of the substrate. These microchannel arrays were used for cell trapping for microinjection and also used for emulsification. Poplar (Populus alba) protoplasts were used for the test of cell trapping. Cells showed a very large variation in size and irregularity in shape, and, furthermore, the protoplast preparation contained a number of cell membrane fragments and chloroplasts. Despite the cell size and shape variations and obstruction by the admixtures, many cells could be trapped by aspiration at the channel ends because of their openness to the outside free space and also their large multiplicity in parallel. The free space outside the side of the substrate allowed a free manipulation of a glass micropipette under microscopic observation using transmitted illumination. The microscopic observation direction nearly perpendicular to the movement directions of the micropipette further allowed the movement of the pipette tip nearly always in focus. These led to an easy pointing and puncturing. In addition, the cell trapping points in a line made successive approach to adjacent cells easier. Soybean oil containing 1.5 wt% polyoxyethylene(20)sorbitan monoolete as a surfactant was forced to flow into physiological saline filling the outside of the substrate through the microchannels. Regularly sized oil particles were created by this process with a variation coefficient (S.D./mean) 16% of their diameter. This variation, which is

  3. Correlation of gene expression and contaminat concentrations in wild largescale suckers: a field-based study

    Science.gov (United States)

    Christiansen, Helena E.; Mehinto, Alvine C.; Yu, Fahong; Perry, Russell W.; Denslow, Nancy D.; Maule, Alec G.; Mesa, Matthew G.

    2014-01-01

    Toxic compounds such as organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether flame retardants (PBDEs) have been detected in fish, birds, and aquatic mammals that live in the Columbia River or use food resources from within the river. We developed a custom microarray for largescale suckers (Catostomus macrocheilus) and used it to investigate the molecular effects of contaminant exposure on wild fish in the Columbia River. Using Significance Analysis of Microarrays (SAM) we identified 72 probes representing 69 unique genes with expression patterns that correlated with hepatic tissue levels of OCs, PCBs, or PBDEs. These genes were involved in many biological processes previously shown to respond to contaminant exposure, including drug and lipid metabolism, apoptosis, cellular transport, oxidative stress, and cellular chaperone function. The relation between gene expression and contaminant concentration suggests that these genes may respond to environmental contaminant exposure and are promising candidates for further field and laboratory studies to develop biomarkers for monitoring exposure of wild fish to contaminant mixtures found in the Columbia River Basin. The array developed in this study could also be a useful tool for studies involving endangered sucker species and other sucker species used in contaminant research.

  4. Study of magnetoelastic and magnetocrystalline anisotropies in Co{sub x}Ni{sub 1−x} nanowire arrays

    Energy Technology Data Exchange (ETDEWEB)

    Moskaltsova, Anastasiia, E-mail: amoskaltsova@inesc-mn.pt [National Technical University Kharkiv Polytechnic Institute, 21, Frunze Str., 61002 Kharkiv (Ukraine); INESC-MN, Rua Alves Redol, 9-1, 1000-029 Lisbon (Portugal); Proenca, Mariana P. [IFIMUP and IN Institute of Nanoscience and Nanotechnology and Dep. Física e Astronomia, Univ. Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); Nedukh, Sergey V. [O. Ya. Usikov Institute for Radiophysics and Electronics of the National Academy of Sciences of Ukraine, 12, Proskura str., 61085 Kharkov (Ukraine); Sousa, Célia T. [IFIMUP and IN Institute of Nanoscience and Nanotechnology and Dep. Física e Astronomia, Univ. Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); Vakula, Arthur [O. Ya. Usikov Institute for Radiophysics and Electronics of the National Academy of Sciences of Ukraine, 12, Proskura str., 61085 Kharkov (Ukraine); Kakazei, Gleb N. [IFIMUP and IN Institute of Nanoscience and Nanotechnology and Dep. Física e Astronomia, Univ. Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); Institute of Magnetism National Academy of Sciences of Ukraine, 36b Vernadskogo Blvd., 03142 Kiev (Ukraine); Tarapov, Sergey I. [O. Ya. Usikov Institute for Radiophysics and Electronics of the National Academy of Sciences of Ukraine, 12, Proskura str., 61085 Kharkov (Ukraine); Araujo, Joao P. [IFIMUP and IN Institute of Nanoscience and Nanotechnology and Dep. Física e Astronomia, Univ. Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal)

    2015-01-15

    Highly ordered Co{sub x}Ni{sub 1−x} nanowire (NW) arrays were electrodeposited inside nanoporous anodic aluminum oxide membranes. The control of the applied potential during the electrodeposition process allowed us to easily tune the Co% in the alloy. Systematic studies on the morphological and crystallographic properties together with static and dynamic magnetic characterizations were performed. In this work we focus on the study of the dynamic magnetic properties of CoNi NW arrays using the ferromagnetic resonance method at both room (RT) and low (LT) temperatures. The careful comparison analysis performed between the magnetic anisotropy fields obtained at RT and LT, allowed us to extract for the first time the magnetocrystalline anisotropy effect of the Co component and, most importantly, the magnetoelastic anisotropy effect of Ni. - Highlights: • Ordered hexagonal arrays of Co{sub x}Ni{sub 1−x} nanowires were grown by DC electrodeposition. • The Co:Ni ratio in the nanowires was tuned by varying the deposition potential. • We studied magnetic anisotropies using ferromagnetic resonance method. • The experiments were performed at room and low temperatures. • We extracted the magnetoelastic contribution of Ni in the fabricated nanowires.

  5. 12-Channel Peltier array temperature control unit for single molecule enzymology studies using capillary electrophoresis.

    Science.gov (United States)

    Craig, Douglas B; Reinfelds, Gundars; Henderson, Anna

    2014-08-01

    Capillary electrophoresis has been used to demonstrate that individual molecules of a given enzyme support different catalytic rates. In order to determine how rate varies with temperature, and determine activation energies for individual β-galactosidase molecules, a 12-channel Peltier array temperature control device was constructed where the temperature of each cell was separately controlled. This array was used to control the temperature of the central 30 cm of a 50 cm long capillary, producing a temperature gradient along its length. Continuous flow single β-galactosidase molecule assays were performed allowing measurement of the catalytic rates at different temperatures. Arrhenius plots were produced and the distribution of activation energies for individual β-galactosidase molecules was found to be 56 ± 10 kJ/mol with a range of 34-72 kJ/mol.

  6. Feasibility study of flexible phased array ultrasonic technology using irregular surface specimen

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Seung Pyo; Moon, Yong Sik; Jung, Nam Du [NDE Performance Demonstration Team, Korea Hydro and Nuclear Power, Central Research Institute, Daejeon (Korea, Republic of)

    2015-02-15

    Nuclear power plant contain many dissimilar metal welds that connect carbon steel components with stainless steel pipes using alloy 600 welding materials. Primary water stress corrosion cracks at dissimilar metal welds have been continuously reported around the world. In periodic integrity evaluations, dissimilar metal welds are examined using a generic ultrasonic testing procedure, KPD-UT-10. In this procedure, the gap between the probe and examination surface is limited to 1/32 inch (0.8 mm). It is not easy to test some dissimilar metal welds in Korean plants applying ordinary technology because of their tapered shapes and irregular surface conditions. This paper introduces a method for applying a flexible phased array technology to improve the reliability of ultrasonic testing results for various shapes and surface conditions. The artificial flaws in specimens with irregular surfaces were completely detected using the flexible phased array ultrasonic technology. Therefore, it can be said that the technology is applicable to field examination.

  7. Porous silicon nanowire arrays decorated by Ag nanoparticles for surface enhanced Raman scattering study

    Science.gov (United States)

    Su, L.; Xu, H. J.; Chan, Y. F.; Sun, X. M.

    2012-02-01

    A large scale and highly ordered Ag nanoparticle-decorated porous silicon nanowire array was fabricated for a uniform and reproducible surface-enhanced Raman scattering (SERS) substrate. The overall process for the proposed structure is simple and reliable with the use of only chemical etching and metal reduction processes. The SERS sensitivity of the novel substrate as low as 10-16 M for rhodamine 6G (R6G) and the Raman enhancement factor as high as 10^14 were obtained. The excellent SERS performances were mainly attributed to the strong local electromagnetic effect which is associated with the formation of large-quantity Ag nanoparticles on porous silicon nanowire array and the existence of semiconductor silicon nanowires. Significantly, the quadratic relation between the logarithmic concentrations and the logarithmic integrated Raman peak intensities provided quantitative detection of R6G. Our results open new possibilities for applying SERS to trace detection of low-concentration biomolecules.

  8. A Case Study of Some Issues in the Optimization of Fortran 90 Array Notation

    Directory of Open Access Journals (Sweden)

    John D. McCalpin

    1996-01-01

    Full Text Available Some issues in the relationship of coding style and compiler optimization are discussed with regard to Fortran 90 array notation. A review of several important Fortran 90 array constructs and their performance on vector and scalar hardware sets the stage for a more detailed example based on the kernel of a finite difference computational fluid dynamics model, specifically the nonlinear shallow water equations. Special attention is paid to the optimization of memory use and memory traffic. It is shown that the style of coding interacts with the rules of Fortran 90 and the current state of the art of Fortran 90 compilers to produce a fairly wide range of performance levels. Although performance degradations are typically small, a few cases of more serious loss of effciency are identified and discussed.

  9. Monte Carlo Performance Studies of Candidate Sites for the Cherenkov Telescope Array

    CERN Document Server

    Maier, G; Bernlöhr, K; Bregeon, J; Di Pierro, F; Hassan, T; Jogler, T; Hinton, J; Moralejo, A; Wood, M

    2015-01-01

    The Cherenkov Telescope Array (CTA) is the next-generation gamma-ray observatory with sensitivity in the energy range from 20 GeV to beyond 300 TeV. CTA is proposed to consist of two arrays of 40-100 imaging atmospheric Cherenkov telescopes, with one site located in each of the Northern and Southern Hemispheres. The evaluation process for the candidate sites for CTA is supported by detailed Monte Carlo simulations, which take different attributes like site altitude and geomagnetic field configuration into account. In this contribution we present the comparison of the sensitivity and performance of the different CTA site candidates for the measurement of very-high energy gamma rays.

  10. Parameter study of global and cluster synchronization in arrays of dry friction oscillators

    Science.gov (United States)

    Marszal, Michał; Stefański, Andrzej

    2017-04-01

    We investigate synchronization thresholds in arrays of identical classic stick-slip dry friction oscillators connected in a nearest neighbor fashion in closed and open ring network. Friction force is modeled by smoothened Stribeck model. Arrays of different length are checked in two parameter space (i.e., coupling coefficient vs. excitation frequency) for complete synchronization as well as cluster synchronization. Synchronization thresholds obtained by brute force numerical integration are compared with possible synchronization regions using the concept called master stability function in the form of two-oscillator reference probe. The results show existence of both complete synchronization and cluster synchronization regions in the investigated systems and confirm that two-oscillator probe can be applied for prediction of synchronization thresholds in systems with stick-slip phenomenon.

  11. A study of angle dependent surface plasmon polaritons in nano-hole array structures

    Energy Technology Data Exchange (ETDEWEB)

    Balakrishnan, Shankar [Department of Physics and Astronomy, University of Western Ontario, London, Ontario N6A 3K7 (Canada); Lawson Health Research Institute, St. Joseph' s Health Care, London, Ontario N6A 4V2 (Canada); Najiminaini, Mohamadreza; Carson, Jeffrey J. L. [Lawson Health Research Institute, St. Joseph' s Health Care, London, Ontario N6A 4V2 (Canada); Department of Medical Biophysics, University of Western Ontario, London, Ontario N6A 3K7 (Canada); Singh, Mahi R. [Department of Physics and Astronomy, University of Western Ontario, London, Ontario N6A 3K7 (Canada)

    2016-07-21

    We report that the light-matter interaction in metallic nano-hole array structures possess a subwavelength hole radius and periodicity. The transmission coefficient for nano-hole array structures was measured for different angles of incidence of light. Each measured transmission spectrum had several peaks due to surface plasmon polaritons. A theory of the transmission coefficient was developed based on the quantum density matrix method. It was found that the location of the surface plasmon polariton and the heights of the spectral peaks were dependent on the angle of incidence of light. Good agreement was observed between the experimental and theoretical results. This property of these structures has opened up new possibilities for sensing applications.

  12. Discovering Study-Specific Gene Regulatory Networks

    OpenAIRE

    2014-01-01

    This article has been made available through the Brunel Open Access Publishing Fund. This article has been made available through the Brunel Open Access Publishing Fund. Microarrays are commonly used in biology because of their ability to simultaneously measure thousands of genes under different conditions. Due to their structure, typically containing a high amount of variables but far fewer samples, scalable network analysis techniques are often employed. In particular, consensus appro...

  13. Feasibility Study for a Dual Field of View-Single Detector Array Infrared System.

    Science.gov (United States)

    1974-06-01

    the background is shown in Figure 2-8. In this system the field stop is scare I with a vertical slit and essentially all the energy falling on the...cylindrical mirror will be o focused as a vertical iine on the detector array. Several of the previous problems have been solved in this system. The...patterns Limillid only by DAC, AD,,.J Access y u, limited by speed. anid Display Mtsaitor strict possible formats. xalbe Modification of timing salto

  14. Study of dc micro-discharge arrays made in silicon using CMOS compatible technology

    Science.gov (United States)

    Kulsreshath, M. K.; Schwaederle, L.; Overzet, L. J.; Lefaucheux, P.; Ladroue, J.; Tillocher, T.; Aubry, O.; Woytasik, M.; Schelcher, G.; Dussart, R.

    2012-07-01

    In this paper we present the fabrication technology used to make micro-discharge ‘reactors’ on a silicon (Si) substrate. For the fabrication of these reactors we have used Si wafers with 4 inch diameter and standard cleanroom facilities. The fabrication technology used is compatible with standard CMOS device fabrication and the fabricated micro-discharge reactors can be used to produce dc discharges. These micro-discharges operate at near atmospheric pressure. They were given ring-shaped anodes separated from the cathode by a SiO2 dielectric with a thickness of approximately 5-6 µm rather than the much more common ˜100 µm. The micro-discharge reactors can consist of either a single hole or multiple holes and we have built devices with holes from 25 to 150 µm in diameter. The micro-discharge measurements were obtained for helium and argon dc plasmas between 100 and 1000 Torr. We used a single ballast resistor to produce micro-discharges in multi-hole array. This resistor also acted to limit the discharge power. An average current density of 0.8 A cm-2 was calculated for the 1024 holes array with 100 µm diameter holes. In addition, we will report on stability of micro-discharges depending on the cavity configuration of the micro-reactors and the ignition trends for the micro-discharge arrays. Finally, we discuss the life time of micro-discharge arrays as well as the factors affecting them (cathode sputtering, thermally affected zones, etc).

  15. Process Study of Oceanic Responses to Typhoons Using Arrays of EM-APEX Floats and Moorings

    Science.gov (United States)

    2015-03-01

    Arrays of EM-APEX Floats and Moorings Ren-Chieh Lien Applied Physics Laboratory University of Washington 1013 NE 40th Street Seattle, Washington...Long-term observations of atmospheric forcing and upper oceanic conditions were made by moorings in the western Pacific Ocean, in collaboration with...of ITOP), subsurface temperature measurements on the moorings were transmitted via Iridium satellite, and one upward-looking 75-kHz Long Ranger ADCP

  16. Studying the Origin of the Kuroshio with an Array of ADCP-CTD Moorings

    Science.gov (United States)

    2014-09-30

    ADCP-CTD Moorings Ren-Chieh Lien Applied Physics Laboratory University of Washington 1013 NE 40th Street Seattle, Washington 98105 Phone: (206...APPROACH An array of six subsurface moorings was deployed in June 2012 northeast of the Philippines, where the strong Kuroshio enters Luzon Strait...All moorings were recovered in June 2013. Each mooring had an Acoustic Doppler Current Profiler (ADCP) to measure the velocity field in the upper

  17. A Feasibility Study for a Versatile Deep Sea, Multileg, Stable, Cable Array.

    Science.gov (United States)

    1981-03-01

    candidate materials were investigated: HY80 steel , 7075T6 aluminum, and 32 lb/cu.ft syntactic foam. Using these commonly available materials, the size, air...provide mooring materials which are non-corrosible and weigh only one-seventh the weight of a comparable steel cable in water. 2.0 ARRAY REQUIREMENTS The...strength of copper will necessitate a high strength/modulus material be incorporated into the construction. Normally steel wires are laid in two or more

  18. Computational gene network study on antibiotic resistance genes of Acinetobacter baumannii.

    Science.gov (United States)

    Anitha, P; Anbarasu, Anand; Ramaiah, Sudha

    2014-05-01

    Multi Drug Resistance (MDR) in Acinetobacter baumannii is one of the major threats for emerging nosocomial infections in hospital environment. Multidrug-resistance in A. baumannii may be due to the implementation of multi-combination resistance mechanisms such as β-lactamase synthesis, Penicillin-Binding Proteins (PBPs) changes, alteration in porin proteins and in efflux pumps against various existing classes of antibiotics. Multiple antibiotic resistance genes are involved in MDR. These resistance genes are transferred through plasmids, which are responsible for the dissemination of antibiotic resistance among Acinetobacter spp. In addition, these resistance genes may also have a tendency to interact with each other or with their gene products. Therefore, it becomes necessary to understand the impact of these interactions in antibiotic resistance mechanism. Hence, our study focuses on protein and gene network analysis on various resistance genes, to elucidate the role of the interacting proteins and to study their functional contribution towards antibiotic resistance. From the search tool for the retrieval of interacting gene/protein (STRING), a total of 168 functional partners for 15 resistance genes were extracted based on the confidence scoring system. The network study was then followed up with functional clustering of associated partners using molecular complex detection (MCODE). Later, we selected eight efficient clusters based on score. Interestingly, the associated protein we identified from the network possessed greater functional similarity with known resistance genes. This network-based approach on resistance genes of A. baumannii could help in identifying new genes/proteins and provide clues on their association in antibiotic resistance.

  19. Suitability of endogenous reference genes for gene expression studies with human intraocular endothelial cells

    Directory of Open Access Journals (Sweden)

    Wei Ruoxin

    2013-02-01

    Full Text Available Abstract Background The use of quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR has become widely applied as a method to measure transcript abundance. In order to be reflective of biological processes during health and disease this method is dependent on normalisation of data against stable endogenous controls. However, these genes can vary in their stability in different cell types. The importance of reference gene validation for a particular cell type is now well recognised and is an important step in any gene expression study. Results Cultured primary human choroidal and retinal endothelial cells were treated with the immunostimulant polyinosinic: polycytidylic acid or untreated. qRT-PCR was used to quantify the expression levels of 10 commonly used endogenous control genes, TBP, HPRT1, GAPDH, GUSB, PPIA, RPLP0, B2M, 18S rRNA, PGK1 and ACTB. Three different mathematical algorithms, GeNorm, NormFinder, and BestKeeper were used to analyse gene stability to give the most representative validation. In choroidal endothelial cells the most stable genes were ranked as HPRT1 and GUSB by GeNorm and NormFinder and HPRT1 and PPIA by BestKeeper. In retinal endothelial cells the most stable genes ranked were TBP and PGK1 by GeNorm and NormFinder and HPRT1 by BestKeeper. The least stable gene for both cell types was 18S with all 3 algorithms. Conclusions We have identified the most stable endogenous control genes in intraocular endothelial cells. It is suggested future qRT-PCR studies using these cells would benefit from adopting the genes identified in this study as the most appropriate endogenous control genes.

  20. Geant4 simulation study of Indian National Gamma Array at TIFR

    Science.gov (United States)

    Saha, S.; Palit, R.; Sethi, J.; Biswas, S.; Singh, P.

    2016-03-01

    A Geant4 simulation code for the Indian National Gamma Array (INGA) consisting of 24 Compton suppressed clover high purity germanium (HPGe) detectors has been developed. The calculated properties in the energy range that is of interest for nuclear γ-ray spectroscopy are spectral distributions for various standard radioactive sources, intrinsic peak efficiencies and peak-to-total (P/T) ratios in various configurations such as singles, add-back and Compton suppressed mode. The principle of operation of the detectors in add-back and Compton suppression mode have been reproduced in the simulation. The reliability of the calculation is checked by comparison with the experimental data for various γ-ray energies up to 5 MeV. The comparison between simulation results and experimental data demonstrate the need of incorporating the exact geometry of the clover detectors, Anti-Compton Shield and other surrounding materials in the array to explain the detector response to the γ-ray. Several experimental effects are also investigated. These include the geometrical correction to angular distribution, crosstalk probability and the impact of heavy metal collimators between the target and the array on the P/T ratio.

  1. Studies of Air Showers above 10^18 eV with the CHICOS Array

    CERN Document Server

    Lynn, T W; Carlson, B E; Jillings, C J; Larson, M B; McKeown, R D; Hill, J E; Falkowski, B J; Seki, R; Sepikas, J; Yodh, G B; Wells, D; Chan, K C

    2005-01-01

    CHICOS (California HIgh school Cosmic ray ObServatory) is presently an array of more than 140 detectors distributed over a large area (~400 km^2) of southern California, and will consist of 180 detectors at 90 locations in the near future. These sites, located at area schools, are equipped with computerized data acquisition and automatic nightly data transfer (via internet) to our Caltech lab. The installed sites make up the largest currently operating ground array for ultra-high energy cosmic ray research in the northern hemisphere. The goal of CHICOS is to provide data related to the flux and distribution of arrival directions for ultra-high energy cosmic rays. We have performed detailed Monte-Carlo calculations to determine the density and arrival-time distribution of charged particles in extensive air showers for the CHICOS array. Calculations were performed for proton primaries with energies 10^18 to 10^21 eV and zenith angles out to 50 degrees. We have developed novel parameterizations for both distribu...

  2. The study of structural color filter based on periodic nanohole arrays for bio-detection

    Science.gov (United States)

    Kim, Seunguk; Shin, Jeonghee; Yoo, Seungjun; Kim, Samhwan; Jeon, Byoungok; Moon, Cheil; Jang, Jae-Eun

    2015-07-01

    A nanostructure which induces localized surface plasmon resonance (LSPR) can be utilized in visible light and near infrared (NIR) regions and it shows promising features as a bio-detector because LSPR state is changed easily by different bio-related materials. Owing to transparent property of many biomolecules as well as diluted states in base solutions, it is hard to distinguish each other by eye or microscope analysis. However, difference in molecular structure and composition makes difference in optical characteristics such as a refractive index or a dielectric constant. Therefore, our LSPR-based nanohole array structure which has high sensitivity to detect small changes in optical characteristics can be a great candidate for a bio detector. Here, we fabricated structural color filters (SCFs) to detect wavelength shifts for several biomolecules and optimized the nanohole array structures for high sensitivity. Periodic nanohole arrays were designed to present resonance peaks in visible light region for optical analysis and fabricated in Au or Al thin film layer. The spectral shifts were detected caused by biomolecules.

  3. Facile synthesis and magnetic study of Ni@polyamide 66 coaxial nanotube arrays

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xiaoru, E-mail: lixiaoruqdu@126.com; Yang, Chao; Han, Ping; Zhao, Qingpei; Song, Guojun, E-mail: songguojunqdu@126.com

    2016-12-01

    Ni@polyamide 66 (PA66) core/shell coaxial double-layer nanotube arrays have been prepared in the nanopores of anodic aluminum oxide templates (AAO). The shell of PA66 nanotubes were formed first and then served as templates to deposit Ni nanotubes used as the core. The morphology, structures of the obtained arrays were examined by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The formation of this unique coaxial nanotube structure was confirmed by SEM and TEM images and X-ray diffraction (XRD). We further explored the magnetic properties of the obtained coaxial nanotube arrays with vibrating sample magnetometer (VSM) and found that Ni@PA66 coaxial nanotubes exhibited higher remanence ratio than that of Ni nanotubes. These Ni@PA66 coaxial nanotubes are promising to be used as templates to fill in other materials. - Highlights: • Ni@PA66 coaxial nanotubes are prepared successfully with PA66 nanotubes obtained first and then Ni nanotubes were deposited in PA66 nanotubes. • The magnetic property of Ni@PA66 coaxial nanotubes is better than that of Ni nanotubes. • Ni@PA66 coaxial nanotubes can be used as templates to fill in other materials.

  4. Study on the Behavior of Solar Array Deployment with Root Hinge Drive Assembly

    Institute of Scientific and Technical Information of China (English)

    DING Xilun; LI Xin; XU Kun; YANG Qiaolong; PU Hailing

    2012-01-01

    In this paper,a method of using a root hinge drive assembly (RHDA) to control the solar array deployment is provided and a multi-DOF mechanism dynamic model of the system is established.In this way,the root hinge torque can be calculated iteratively.Then taking the predicted torque as a reference,a RHDA is designed for a large multiple-stage packaging and deployable solar array system.The control effect of the drive assembly is validated by ground tests.The test results indicate that the solar arrays can be deployed smoothly,and the deployment velocities are restricted by the drive assembly as expected.During the tests,the RHDA output speed and output torque are obtained.In order to examine the impact force when the yoke is lock-up with a hard stop,dynamics simulations are performed according to the actual behavior.The simulation result indicates that the designed RHDA reduces the impact force significantly and improves the lock-up reliability effectively.

  5. Development of a novel ozone- and photo-stable HyPer5 red fluorescent dye for array CGH and microarray gene expression analysis with consistent performance irrespective of environmental conditions

    Directory of Open Access Journals (Sweden)

    Kille Peter

    2008-11-01

    Full Text Available Abstract Background Array-based comparative genomic hybridization (CGH and gene expression profiling have become vital techniques for identifying molecular defects underlying genetic diseases. Regardless of the microarray platform, cyanine dyes (Cy3 and Cy5 are one of the most widely used fluorescent dye pairs for microarray analysis owing to their brightness and ease of incorporation, enabling high level of assay sensitivity. However, combining both dyes on arrays can become problematic during summer months when ozone levels rise to near 25 parts per billion (ppb. Under such conditions, Cy5 is known to rapidly degrade leading to loss of signal from either "homebrew" or commercial arrays. Cy5 can also suffer disproportionately from dye photobleaching resulting in distortion of (Cy5/Cy3 ratios used in copy number analysis. Our laboratory has been active in fluorescent dye research to find a suitable alternative to Cy5 that is stable to ozone and resistant to photo-bleaching. Here, we report on the development of such a dye, called HyPer5, and describe its' exceptional ozone and photostable properties on microarrays. Results Our results show HyPer5 signal to be stable to high ozone levels. Repeated exposure of mouse arrays hybridized with HyPer5-labeled cDNA to 300 ppb ozone at 5, 10 and 15 minute intervals resulted in no signal loss from the dye. In comparison, Cy5 arrays showed a dramatic 80% decrease in total signal during the same interval. Photobleaching experiments show HyPer5 to be resistant to light induced damage with 3- fold improvement in dye stability over Cy5. In high resolution array CGH experiments, HyPer5 is demonstrated to detect chromosomal aberrations at loci 2p21-16.3 and 15q26.3-26.2 from three patient sample using bacterial artificial chromosome (BAC arrays. The photostability of HyPer5 is further documented by repeat array scanning without loss of detection. Additionally, HyPer5 arrays are shown to preserve sensitivity and

  6. Human reporter genes: potential use in clinical studies

    Energy Technology Data Exchange (ETDEWEB)

    Serganova, Inna [Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021 (United States); Ponomarev, Vladimir [Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021 (United States); Blasberg, Ronald [Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021 (United States); Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021 (United States)], E-mail: blasberg@neuro1.mskcc.org

    2007-10-15

    The clinical application of positron-emission-tomography-based reporter gene imaging will expand over the next several years. The translation of reporter gene imaging technology into clinical applications is the focus of this review, with emphasis on the development and use of human reporter genes. Human reporter genes will play an increasingly more important role in this development, and it is likely that one or more reporter systems (human gene and complimentary radiopharmaceutical) will take leading roles. Three classes of human reporter genes are discussed and compared: receptors, transporters and enzymes. Examples of highly expressed cell membrane receptors include specific membrane somatostatin receptors (hSSTrs). The transporter group includes the sodium iodide symporter (hNIS) and the norepinephrine transporter (hNET). The endogenous enzyme classification includes human mitochondrial thymidine kinase 2 (hTK2). In addition, we also discuss the nonhuman dopamine 2 receptor and two viral reporter genes, the wild-type herpes simplex virus 1 thymidine kinase (HSV1-tk) gene and the HSV1-tk mutant (HSV1-sr39tk). Initial applications of reporter gene imaging in patients will be developed within two different clinical disciplines: (a) gene therapy and (b) adoptive cell-based therapies. These studies will benefit from the availability of efficient human reporter systems that can provide critical monitoring information for adenoviral-based, retroviral-based and lenteviral-based gene therapies, oncolytic bacterial and viral therapies, and adoptive cell-based therapies. Translational applications of noninvasive in vivo reporter gene imaging are likely to include: (a) quantitative monitoring of gene therapy vectors for targeting and transduction efficacy in clinical protocols by imaging the location, extent and duration of transgene expression; (b) monitoring of cell trafficking, targeting, replication and activation in adoptive T-cell and stem/progenitor cell therapies

  7. Enhancement of the Yakutsk array by atmospheric Cherenkov telescopes to study cosmic rays above $10^{15}$ eV

    CERN Document Server

    Ivanov, A A; Petrov, Z E; Pravdin, M I; Sleptsov, I Ye

    2010-01-01

    The aim of the Yakutsk array enhancement project is to create an instrument to study the highest-energy galactic cosmic rays (CRs) -- their sources, energy spectrum, and mass composition. Additionally, there will be unique capabilities for investigations in the transition region between galactic and extragalactic components of CRs. Using the well-developed imaging atmospheric Cherenkov telescope technique adapted to the energy region $E>10^{15}$ eV, we plan to measure the longitudinal structure parameters of the shower, e.g., angular and temporal distributions of the Cherenkov signal related to $X_{max}$ and the mass composition of CRs. The main advantages of the Yakutsk array, such as its multi-component measurements of extensive air showers, and model-independent CR energy estimation based on Cherenkov light measurements, will be inherited by the instrument to be created.

  8. Suitability of commonly used housekeeping genes in gene expression studies for space radiation research

    Science.gov (United States)

    Arenz, A.; Stojicic, N.; Lau, P.; Hellweg, C. E.; Baumstark-Khan, C.

    Research on the effects of ionizing radiation exposure involves the use of real-time reverse transcription polymerase chain reaction (qRT-PCR) for measuring changes in gene expression. Several variables need to be controlled for gene expression analysis, such as different amounts of starting material between the samples, variations in enzymatic efficiencies of the reverse transcription step, and differences in RNA integrity. Normalization of the obtained data to an invariant endogenous control gene (reference gene) is the elementary step in relative quantification strategy. There is a strong correlation between the quality of the normalized data and the stability of the reference gene itself. This is especially relevant when the samples have been obtained after exposure to radiation qualities inducing different amounts and kinds of damage, leading to effects on cell cycle delays or even on cell cycle blocks. In order to determine suitable reference genes as internal controls in qRT-PCR assays after exposure to ionizing radiation, we studied the gene expression levels of nine commonly used reference genes which are constitutively expressed in A549 lung cancer cells. Expression levels obtained for ACTB, B2M, GAPDH, PBGD, 18S rRNA, G6PDH, HPRT, UBC, TFRC and SDHA were determined after exposure to 2 and 6 Gy X-radiation. Gene expression data for Growth arrest and damage-inducible gene 45 (GADD45α) and Cyclin-dependent kinase inhibitor 1A (CDKN1A/p21CIP1) were selected to elucidate the influence of normalization by using appropriate and inappropriate internal control genes. According to these results, we strongly recommend the use of a panel of reference genes instead of only one.

  9. Serial Analysis of Gene Expression: Applications in Human Studies

    OpenAIRE

    2004-01-01

    Serial analysis of gene expression (SAGE) is a powerful tool, which provides quantitative and comprehensive expression profile of genes in a given cell population. It works by isolating short fragments of genetic information from the expressed genes that are present in the cell being studied. These short sequences, called SAGE tags, are linked together for efficient sequencing. The frequency of each SAGE tag in the cloned multimers directly reflects the transcript abundance. Therefore, SAGE r...

  10. Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies.

    Science.gov (United States)

    Pearce, Dominic A; Arthur, Laura M; Turnbull, Arran K; Renshaw, Lorna; Sabine, Vicky S; Thomas, Jeremy S; Bartlett, John M S; Dixon, J Michael; Sims, Andrew H

    2016-07-07

    Patient-matched transcriptomic studies using tumour samples before and after treatment allow inter-patient heterogeneity to be controlled, but tend not to include an untreated comparison. Here, Illumina BeadArray technology was used to measure dynamic changes in gene expression from thirty-seven paired diagnostic core and surgically excised breast cancer biopsies obtained from women receiving no treatment prior to surgery, to determine the impact of sampling method and tumour heterogeneity. Despite a lack of treatment and perhaps surprisingly, consistent changes in gene expression were identified during the diagnosis-surgery interval (48 up, 2 down; Siggenes FDR 0.05) in a manner independent of both subtype and sampling-interval length. Instead, tumour sampling method was seen to directly impact gene expression, with similar effects additionally identified in six published breast cancer datasets. In contrast with previous findings, our data does not support the concept of a significant wounding or immune response following biopsy in the absence of treatment and instead implicates a hypoxic response following the surgical biopsy. Whilst sampling-related gene expression changes are evident in treated samples, they are secondary to those associated with response to treatment. Nonetheless, sampling method remains a potential confounding factor for neoadjuvant study design.

  11. Screening for the Most Suitable Reference Genes for Gene Expression Studies in Equine Milk Somatic Cells.

    Directory of Open Access Journals (Sweden)

    Jakub Cieslak

    Full Text Available Apart from the well-known role of somatic cell count as a parameter reflecting the inflammatory status of the mammary gland, the composition of cells isolated from milk is considered as a valuable material for gene expression studies in mammals. Due to its unique composition, in recent years an increasing interest in mare's milk consumption has been observed. Thus, investigating the genetic background of horse's milk variability presents and interesting study model. Relying on 39 milk samples collected from mares representing three breeds (Polish Primitive Horse, Polish Cold-blooded Horse, Polish Warmblood Horse we aimed to investigate the utility of equine milk somatic cells as a source of mRNA and to screen the best reference genes for RT-qPCR using geNorm and NormFinder algorithms. The results showed that despite relatively low somatic cell counts in mare's milk, the amount and the quality of the extracted RNA are sufficient for gene expression studies. The analysis of the utility of 7 potential reference genes for RT-qPCR experiments for the normalization of equine milk somatic cells revealed some differences between the outcomes of the applied algorithms, although in both cases the KRT8 and TOP2B genes were pointed as the most stable. Analysis by geNorm showed that the combination of 4 reference genes (ACTB, GAPDH, TOP2B and KRT8 is required for apropriate RT-qPCR experiments normalization, whereas NormFinder algorithm pointed the combination of KRT8 and RPS9 genes as the most suitable. The trial study of the relative transcript abundance of the beta-casein gene with the use of various types and numbers of internal control genes confirmed once again that the selection of proper reference gene combinations is crucial for the final results of each real-time PCR experiment.

  12. Gene Transfer & Hybridization Studies in Hyperthermophilic Species

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, Karen E.

    2005-10-14

    A. ABSTRACT The importance of lateral gene transfer (LGT) in the evolution of microbial species has become increasingly evident with each completed microbial genome sequence. Most significantly, the genome of Thermotoga maritima MSB8, a hyperthermophilic bacterium isolated by Karl Stetter and workers from Vulcano Italy in 1986, and sequenced at The Institute for Genomic Research (TIGR) in Rockville Maryland in 1999, revealed extensive LGT between % . this bacterium and members of the archaeal domain (in particular Archaeoglobus fulgidus, and Pyracoccus frcriosus species). Based on whole genome comparisons, it was estimated that 24% of the genetic information in this organism was acquired by genetic exchange with archaeal species, Independent analyses including periodicity analysis of the T. maritimu genomic DNA sequence, phylogenetic reconstruction based on genes that appear archaeal-like, and codon and amino acid usage, have provided additional evidence for LGT between T. maritima and the archaea. More recently, DiRuggiero and workers have identified a very recent LGT event between two genera of hyperthermophilic archaea, where a nearly identical DNA fragment of 16 kb in length flanked by insertion sequence (IS) elements, exists. Undoubtedly, additional examples of LGT will be identified as more microbial genomes are completed. For the present moment however, the genome sequence of T. maritima and other hyperthermophiles including P. furiosus, Pyrococcus horikoshii, Pyrococcus abyssi, A. fulgidus, and Aquifex aeolicus, have significantly increased out awareness of evolution being a web of life rather than a tree of life, as suggested by single gene phylogenies. In this proposal, we will aim to determine the extent of LGT across the hyperthemophiles, employing iY maritima as the model organism. A variety of biochemical techniques and phylogenetic reconstructions will allow for a detailed and thorough characterization of the extent of LGT in this species. The

  13. NuChart: an R package to study gene spatial neighbourhoods with multi-omics annotations.

    Directory of Open Access Journals (Sweden)

    Ivan Merelli

    Full Text Availabl