Exploring Lactobacillus plantarum genome diversity by using microarrays

NARCIS (Netherlands)

Molenaar, D.; Bringel, F.; Schuren, F.H.; Vos, de W.M.; Siezen, R.J.; Kleerebezem, M.

2005-01-01

Lactobacillus plantarum is a versatile and flexible species that is encountered in a variety of niches and can utilize a broad range of fermentable carbon sources. To assess if this versatility is linked to a variable gene pool, microarrays containing a subset of small genomic fragments of L.

Detection of Alicyclobacillus species in fruit juice using a random genomic DNA microarray chip.

Science.gov (United States)

Jang, Jun Hyeong; Kim, Sun-Joong; Yoon, Bo Hyun; Ryu, Jee-Hoon; Gu, Man Bock; Chang, Hyo-Ihl

2011-06-01

This study describes a method using a DNA microarray chip to rapidly and simultaneously detect Alicyclobacillus species in orange juice based on the hybridization of genomic DNA with random probes. Three food spoilage bacteria were used in this study: Alicyclobacillus acidocaldarius, Alicyclobacillus acidoterrestris, and Alicyclobacillus cycloheptanicus. The three Alicyclobacillus species were adjusted to 2 × 10(3) CFU/ml and inoculated into pasteurized 100% pure orange juice. Cy5-dCTP labeling was used for reference signals, and Cy3-dCTP was labeled for target genomic DNA. The molar ratio of 1:1 of Cy3-dCTP and Cy5-dCTP was used. DNA microarray chips were fabricated using randomly fragmented DNA of Alicyclobacillus spp. and were hybridized with genomic DNA extracted from Bacillus spp. Genomic DNA extracted from Alicyclobacillus spp. showed a significantly higher hybridization rate compared with DNA of Bacillus spp., thereby distinguishing Alicyclobacillus spp. from Bacillus spp. The results showed that the microarray DNA chip containing randomly fragmented genomic DNA was specific and clearly identified specific food spoilage bacteria. This microarray system is a good tool for rapid and specific detection of thermophilic spoilage bacteria, mainly Alicyclobacillus spp., and is useful and applicable to the fruit juice industry.

High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations

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Magness Charles L

2007-01-01

Full Text Available Abstract Background Until recently, few genomic reagents specific for non-human primate research have been available. To address this need, we have constructed a macaque-specific high-density oligonucleotide microarray by using highly fragmented low-pass sequence contigs from the rhesus genome project together with the detailed sequence and exon structure of the human genome. Using this method, we designed oligonucleotide probes to over 17,000 distinct rhesus/human gene orthologs and increased by four-fold the number of available genes relative to our first-generation expressed sequence tag (EST-derived array. Results We constructed a database containing 248,000 exon sequences from 23,000 human RefSeq genes and compared each human exon with its best matching sequence in the January 2005 version of the rhesus genome project list of 486,000 DNA contigs. Best matching rhesus exon sequences for each of the 23,000 human genes were then concatenated in the proper order and orientation to produce a rhesus "virtual transcriptome." Microarray probes were designed, one per gene, to the region closest to the 3' untranslated region (UTR of each rhesus virtual transcript. Each probe was compared to a composite rhesus/human transcript database to test for cross-hybridization potential yielding a final probe set representing 18,296 rhesus/human gene orthologs, including transcript variants, and over 17,000 distinct genes. We hybridized mRNA from rhesus brain and spleen to both the EST- and genome-derived microarrays. Besides four-fold greater gene coverage, the genome-derived array also showed greater mean signal intensities for genes present on both arrays. Genome-derived probes showed 99.4% identity when compared to 4,767 rhesus GenBank sequence tag site (STS sequences indicating that early stage low-pass versions of complex genomes are of sufficient quality to yield valuable functional genomic information when combined with finished genome information from

ChIP on SNP-chip for genome-wide analysis of human histone H4 hyperacetylation

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Porter Christopher J

2007-09-01

Full Text Available Abstract Background SNP microarrays are designed to genotype Single Nucleotide Polymorphisms (SNPs. These microarrays report hybridization of DNA fragments and therefore can be used for the purpose of detecting genomic fragments. Results Here, we demonstrate that a SNP microarray can be effectively used in this way to perform chromatin immunoprecipitation (ChIP on chip as an alternative to tiling microarrays. We illustrate this novel application by mapping whole genome histone H4 hyperacetylation in human myoblasts and myotubes. We detect clusters of hyperacetylated histone H4, often spanning across up to 300 kilobases of genomic sequence. Using complementary genome-wide analyses of gene expression by DNA microarray we demonstrate that these clusters of hyperacetylated histone H4 tend to be associated with expressed genes. Conclusion The use of a SNP array for a ChIP-on-chip application (ChIP on SNP-chip will be of great value to laboratories whose interest is the determination of general rules regarding the relationship of specific chromatin modifications to transcriptional status throughout the genome and to examine the asymmetric modification of chromatin at heterozygous loci.

Experimental annotation of the human genome using microarray technology.

Science.gov (United States)

Shoemaker, D D; Schadt, E E; Armour, C D; He, Y D; Garrett-Engele, P; McDonagh, P D; Loerch, P M; Leonardson, A; Lum, P Y; Cavet, G; Wu, L F; Altschuler, S J; Edwards, S; King, J; Tsang, J S; Schimmack, G; Schelter, J M; Koch, J; Ziman, M; Marton, M J; Li, B; Cundiff, P; Ward, T; Castle, J; Krolewski, M; Meyer, M R; Mao, M; Burchard, J; Kidd, M J; Dai, H; Phillips, J W; Linsley, P S; Stoughton, R; Scherer, S; Boguski, M S

2001-02-15

The most important product of the sequencing of a genome is a complete, accurate catalogue of genes and their products, primarily messenger RNA transcripts and their cognate proteins. Such a catalogue cannot be constructed by computational annotation alone; it requires experimental validation on a genome scale. Using 'exon' and 'tiling' arrays fabricated by ink-jet oligonucleotide synthesis, we devised an experimental approach to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons. These methods can provide more accurate gene numbers and allow the detection of mRNA splice variants and identification of the tissue- and disease-specific conditions under which genes are expressed. We apply our technique to chromosome 22q under 69 experimental condition pairs, and to the entire human genome under two experimental conditions. We discuss implications for more comprehensive, consistent and reliable genome annotation, more efficient, full-length complementary DNA cloning strategies and application to complex diseases.

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

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Moreau Yves

2005-05-01

Full Text Available Abstract Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH. One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http://medgen.ugent.be/arrayCGHbase/.

A salmonid EST genomic study: genes, duplications, phylogeny and microarrays

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Brahmbhatt Sonal

2008-11-01

Full Text Available Abstract Background Salmonids are of interest because of their relatively recent genome duplication, and their extensive use in wild fisheries and aquaculture. A comprehensive gene list and a comparison of genes in some of the different species provide valuable genomic information for one of the most widely studied groups of fish. Results 298,304 expressed sequence tags (ESTs from Atlantic salmon (69% of the total, 11,664 chinook, 10,813 sockeye, 10,051 brook trout, 10,975 grayling, 8,630 lake whitefish, and 3,624 northern pike ESTs were obtained in this study and have been deposited into the public databases. Contigs were built and putative full-length Atlantic salmon clones have been identified. A database containing ESTs, assemblies, consensus sequences, open reading frames, gene predictions and putative annotation is available. The overall similarity between Atlantic salmon ESTs and those of rainbow trout, chinook, sockeye, brook trout, grayling, lake whitefish, northern pike and rainbow smelt is 93.4, 94.2, 94.6, 94.4, 92.5, 91.7, 89.6, and 86.2% respectively. An analysis of 78 transcript sets show Salmo as a sister group to Oncorhynchus and Salvelinus within Salmoninae, and Thymallinae as a sister group to Salmoninae and Coregoninae within Salmonidae. Extensive gene duplication is consistent with a genome duplication in the common ancestor of salmonids. Using all of the available EST data, a new expanded salmonid cDNA microarray of 32,000 features was created. Cross-species hybridizations to this cDNA microarray indicate that this resource will be useful for studies of all 68 salmonid species. Conclusion An extensive collection and analysis of salmonid RNA putative transcripts indicate that Pacific salmon, Atlantic salmon and charr are 94–96% similar while the more distant whitefish, grayling, pike and smelt are 93, 92, 89 and 86% similar to salmon. The salmonid transcriptome reveals a complex history of gene duplication that is

NMD Microarray Analysis for Rapid Genome-Wide Screen of Mutated Genes in Cancer

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Maija Wolf

2005-01-01

Full Text Available Gene mutations play a critical role in cancer development and progression, and their identification offers possibilities for accurate diagnostics and therapeutic targeting. Finding genes undergoing mutations is challenging and slow, even in the post-genomic era. A new approach was recently developed by Noensie and Dietz to prioritize and focus the search, making use of nonsense-mediated mRNA decay (NMD inhibition and microarray analysis (NMD microarrays in the identification of transcripts containing nonsense mutations. We combined NMD microarrays with array-based CGH (comparative genomic hybridization in order to identify inactivation of tumor suppressor genes in cancer. Such a “mutatomics” screening of prostate cancer cell lines led to the identification of inactivating mutations in the EPHB2 gene. Up to 8% of metastatic uncultured prostate cancers also showed mutations of this gene whose loss of function may confer loss of tissue architecture. NMD microarray analysis could turn out to be a powerful research method to identify novel mutated genes in cancer cell lines, providing targets that could then be further investigated for their clinical relevance and therapeutic potential.

Chromosomal Localization of DNA Amplifications in Neuroblastoma Tumors Using cDNA Microarray Comparative Genomic Hybridization

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Ben Beheshti

2003-01-01

Full Text Available Conventional comparative genomic hybridization (CGH profiling of neuroblastomas has identified many genomic aberrations, although the limited resolution has precluded a precise localization of sequences of interest within amplicons. To map high copy number genomic gains in clinically matched stage IV neuroblastomas, CGH analysis using a 19,200-feature cDNA microarray was used. A dedicated (freely available algorithm was developed for rapid in silico determination of chromosomal localizations of microarray cDNA targets, and for generation of an ideogram-type profile of copy number changes. Using these methodologies, novel gene amplifications undetectable by chromosome CGH were identified, and larger MYCN amplicon sizes (in one tumor up to 6 Mb than those previously reported in neuroblastoma were identified. The genes HPCAL1, LPIN1/KIAA0188, NAG, and NSE1/LOC151354 were found to be coamplified with MYCN. To determine whether stage IV primary tumors could be further subclassified based on their genomic copy number profiles, hierarchical clustering was performed. Cluster analysis of microarray CGH data identified three groups: 1 no amplifications evident, 2 a small MYCN amplicon as the only detectable imbalance, and 3 a large MYCN amplicon with additional gene amplifications. Application of CGH to cDNA microarray targets will help to determine both the variation of amplicon size and help better define amplification-dependent and independent pathways of progression in neuroblastoma.

Tiling array-CGH for the assessment of genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs

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Ringnér Markus

2008-07-01

Full Text Available Abstract Background Today, no objective criteria exist to differentiate between individual primary tumors and intra- or intermammary dissemination respectively, in patients diagnosed with two or more synchronous breast cancers. To elucidate whether these tumors most likely arise through clonal expansion, or whether they represent individual primary tumors is of tumor biological interest and may have clinical implications. In this respect, high resolution genomic profiling may provide a more reliable approach than conventional histopathological and tumor biological factors. Methods 32 K tiling microarray-based comparative genomic hybridization (aCGH was used to explore the genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs, and was compared with histopathological and tumor biological parameters. Results Based on global copy number profiles and unsupervised hierarchical clustering, five of ten (p = 1.9 × 10-5 unilateral tumor pairs displayed similar genomic profiles within the pair, while only one of eight bilateral tumor pairs (p = 0.29 displayed pair-wise genomic similarities. DNA index, histological type and presence of vessel invasion correlated with the genomic analyses. Conclusion Synchronous unilateral tumor pairs are often genomically similar, while synchronous bilateral tumors most often represent individual primary tumors. However, two independent unilateral primary tumors can develop synchronously and contralateral tumor spread can occur. The presence of an intraductal component is not informative when establishing the independence of two tumors, while vessel invasion, the presence of which was found in clustering tumor pairs but not in tumor pairs that did not cluster together, supports the clustering outcome. Our data suggest that genomically similar unilateral tumor pairs may represent a more aggressive disease that requires the addition of more severe treatment modalities, and

Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis

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Chavez Adela

2008-07-01

Full Text Available Abstract Background Anaplasma phagocytophilum (Ap is an obligate intracellular bacterium and the agent of human granulocytic anaplasmosis, an emerging tick-borne disease. Ap alternately infects ticks and mammals and a variety of cell types within each. Understanding the biology behind such versatile cellular parasitism may be derived through the use of tiling microarrays to establish high resolution, genome-wide transcription profiles of the organism as it infects cell lines representative of its life cycle (tick; ISE6 and pathogenesis (human; HL-60 and HMEC-1. Results Detailed, host cell specific transcriptional behavior was revealed. There was extensive differential Ap gene transcription between the tick (ISE6 and the human (HL-60 and HMEC-1 cell lines, with far fewer differentially transcribed genes between the human cell lines, and all disproportionately represented by membrane or surface proteins. There were Ap genes exclusively transcribed in each cell line, apparent human- and tick-specific operons and paralogs, and anti-sense transcripts that suggest novel expression regulation processes. Seven virB2 paralogs (of the bacterial type IV secretion system showed human or tick cell dependent transcription. Previously unrecognized genes and coding sequences were identified, as were the expressed p44/msp2 (major surface proteins paralogs (of 114 total, through elevated signal produced to the unique hypervariable region of each – 2/114 in HL-60, 3/114 in HMEC-1, and none in ISE6. Conclusion Using these methods, whole genome transcription profiles can likely be generated for Ap, as well as other obligate intracellular organisms, in any host cells and for all stages of the cell infection process. Visual representation of comprehensive transcription data alongside an annotated map of the genome renders complex transcription into discernable patterns.

Microarray-based genomic surveying of gene polymorphisms in Chlamydia trachomatis

OpenAIRE

Brunelle, Brian W; Nicholson, Tracy L; Stephens, Richard S

2004-01-01

By comparing two fully sequenced genomes of Chlamydia trachomatis using competitive hybridization on DNA microarrays, a logarithmic correlation was demonstrated between the signal ratio of the arrays and the 75-99% range of nucleotide identities of the genes. Variable genes within 14 uncharacterized strains of C. trachomatis were identified by array analysis and verified by DNA sequencing. These genes may be crucial for understanding chlamydial virulence and pathogenesis.

SCK-CEN Genomic Platform: the microarray technology

International Nuclear Information System (INIS)

Benotmane, R.

2006-01-01

The human body contains approximately 10 14 cells, wherein each one is a nucleus. The nucleus contains 2x23 chromosomes, or two complete sets of the human genome, one set coming from the mother and the other from the father. In principle each set includes 30.000-40.000 genes. If the genome was a book, it would be twenty-three chapters, called chromosomes,each chapter with several thousand stories, called genes. Each story made up of paragraphs, called exons and introns. Each paragraph made up of 3 letter words, called codons. Each word is written with letters called bases (AGCT). But the whole is written in a single very long sentence, which is the DNA molecule or deoxy nucleic acid. The usual state of DNA is two complementary strands intertwined forming a double helix. In the cell, DNA is duplicated during each cell division to ensure the transmission of the genome to the daughter cells. For expression, the DNA is transcribed to messenger RNA. The RNA is edited and finally translated to a protein, each three bases coding for one amino acid. When the whole message is translated, the chain of amino acids folds itself up into a distinctive shape that depends on its sequence. Proteins are the effectors of the genes, and are responsible for all metabolic, hormonal and enzymatic reactions in the cells. The expressed RNA determines the amount of proteins to be produced and subsequently the desired effect (strong or weak) in the cell. The microarray technology aims at quantifying the amount of RNA present in the cell from each expressed gene, and at evaluating the changes of these amounts after exposure of the cell to toxic chemicals, ionising radiation or other stress components. The global picture of expressed genes helps to understand the affected genetic pathways in the cell at the molecular level. The microarray technology is used in the Radiobiology and Microbiology topics to study the effect of ionising radiation on human cells and mouse tissue, as well as the

Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments

Science.gov (United States)

Jourdren, Laurent; Duclos, Aurélie; Brion, Christian; Portnoy, Thomas; Mathis, Hugues; Margeot, Antoine; Le Crom, Stéphane

2010-01-01

Despite the development of new high-throughput sequencing techniques, microarrays are still attractive tools to study small genome organisms, thanks to sample multiplexing and high-feature densities. However, the oligonucleotide design remains a delicate step for most users. A vast array of software is available to deal with this problem, but each program is developed with its own strategy, which makes the choice of the best solution difficult. Here we describe Teolenn, a universal probe design workflow developed with a flexible and customizable module organization allowing fixed or variable length oligonucleotide generation. In addition, our software is able to supply quality scores for each of the designed probes. In order to assess the relevance of these scores, we performed a real hybridization using a tiling array designed against the Trichoderma reesei fungus genome. We show that our scoring pipeline correlates with signal quality for 97.2% of all the designed probes, allowing for a posteriori comparisons between quality scores and signal intensities. This result is useful in discarding any bad scoring probes during the design step in order to get high-quality microarrays. Teolenn is available at http://transcriptome.ens.fr/teolenn/. PMID:20176570

Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient.

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Yao, Jianchao; Chang, Chunqi; Salmi, Mari L; Hung, Yeung Sam; Loraine, Ann; Roux, Stanley J

2008-06-18

Currently, clustering with some form of correlation coefficient as the gene similarity metric has become a popular method for profiling genomic data. The Pearson correlation coefficient and the standard deviation (SD)-weighted correlation coefficient are the two most widely-used correlations as the similarity metrics in clustering microarray data. However, these two correlations are not optimal for analyzing replicated microarray data generated by most laboratories. An effective correlation coefficient is needed to provide statistically sufficient analysis of replicated microarray data. In this study, we describe a novel correlation coefficient, shrinkage correlation coefficient (SCC), that fully exploits the similarity between the replicated microarray experimental samples. The methodology considers both the number of replicates and the variance within each experimental group in clustering expression data, and provides a robust statistical estimation of the error of replicated microarray data. The value of SCC is revealed by its comparison with two other correlation coefficients that are currently the most widely-used (Pearson correlation coefficient and SD-weighted correlation coefficient) using statistical measures on both synthetic expression data as well as real gene expression data from Saccharomyces cerevisiae. Two leading clustering methods, hierarchical and k-means clustering were applied for the comparison. The comparison indicated that using SCC achieves better clustering performance. Applying SCC-based hierarchical clustering to the replicated microarray data obtained from germinating spores of the fern Ceratopteris richardii, we discovered two clusters of genes with shared expression patterns during spore germination. Functional analysis suggested that some of the genetic mechanisms that control germination in such diverse plant lineages as mosses and angiosperms are also conserved among ferns. This study shows that SCC is an alternative to the Pearson

Genome rearrangements detected by SNP microarrays in individuals with intellectual disability referred with possible Williams syndrome.

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Ariel M Pani

2010-08-01

Full Text Available Intellectual disability (ID affects 2-3% of the population and may occur with or without multiple congenital anomalies (MCA or other medical conditions. Established genetic syndromes and visible chromosome abnormalities account for a substantial percentage of ID diagnoses, although for approximately 50% the molecular etiology is unknown. Individuals with features suggestive of various syndromes but lacking their associated genetic anomalies pose a formidable clinical challenge. With the advent of microarray techniques, submicroscopic genome alterations not associated with known syndromes are emerging as a significant cause of ID and MCA.High-density SNP microarrays were used to determine genome wide copy number in 42 individuals: 7 with confirmed alterations in the WS region but atypical clinical phenotypes, 31 with ID and/or MCA, and 4 controls. One individual from the first group had the most telomeric gene in the WS critical region deleted along with 2 Mb of flanking sequence. A second person had the classic WS deletion and a rearrangement on chromosome 5p within the Cri du Chat syndrome (OMIM:123450 region. Six individuals from the ID/MCA group had large rearrangements (3 deletions, 3 duplications, one of whom had a large inversion associated with a deletion that was not detected by the SNP arrays.Combining SNP microarray analyses and qPCR allowed us to clone and sequence 21 deletion breakpoints in individuals with atypical deletions in the WS region and/or ID or MCA. Comparison of these breakpoints to databases of genomic variation revealed that 52% occurred in regions harboring structural variants in the general population. For two probands the genomic alterations were flanked by segmental duplications, which frequently mediate recurrent genome rearrangements; these may represent new genomic disorders. While SNP arrays and related technologies can identify potentially pathogenic deletions and duplications, obtaining sequence information

Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system

NARCIS (Netherlands)

Hsiao, Nai-hua; Kirby, Ralph

DNA/DNA microarray hybridization was used to compare the genome content of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens with that of Streptomyces coelicolor A3(2). The array data showed an about 93% agreement with the genome sequence data

Generation of EST and Microarray Resources for Functional Genomic Studies on Chicken Intestinal Health

NARCIS (Netherlands)

Hemert, van S.; Ebbelaar, B.H.; Smits, M.A.; Rebel, J.M.J.

2003-01-01

Expressed sequenced tags (ESTs) and microarray resources have a great impact on the ability to study host response in mice and humans. Unfortunately, these resources are not yet available for domestic farm animals. The aim of this study was to provide genomic resources to study chicken intestinal

Genome-wide identification of estrogen receptor alpha-binding sites in mouse liver

DEFF Research Database (Denmark)

Gao, Hui; Fält, Susann; Sandelin, Albin

2007-01-01

We report the genome-wide identification of estrogen receptor alpha (ERalpha)-binding regions in mouse liver using a combination of chromatin immunoprecipitation and tiled microarrays that cover all nonrepetitive sequences in the mouse genome. This analysis identified 5568 ERalpha-binding regions...... genes. The majority of ERalpha-binding regions lie in regions that are evolutionarily conserved between human and mouse. Motif-finding algorithms identified the estrogen response element, and variants thereof, together with binding sites for activator protein 1, basic-helix-loop-helix proteins, ETS...... signaling in mouse liver, by characterizing the first step in this signaling cascade, the binding of ERalpha to DNA in intact chromatin....

Comparative genomics of Helicobacter pylori strains of China associated with different clinical outcome.

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Yuanhai You

Full Text Available In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90,000 probes covering six sequenced Helicobacter pylori (H. pylori genomes was designed. This microarray was used to compare the genomic profiles of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation was found among these strains, an additional 76 H. pylori strains associated with different clinical outcomes were isolated from various provinces of China. These strains were tested by polymerase chain reaction to demonstrate this distinction. We identified several highly variable regions in strains associated with gastritis, gastric ulceration, and gastric cancer. These regions are associated with genes involved in the bacterial type I, type II, and type III R-M systems. They were also associated with the virB gene, which lies on the well-studied cag pathogenic island. While previous studies have reported on the diverse genetic characterization of this pathogenic island, in this study, we find that it is conserved in all strains tested by microarray. Moreover, a number of genes involved in the type IV secretion system, which is related to horizontal DNA transfer between H. pylori strains, were identified in the comparative analysis of the strain-specific genes. These findings may provide insight into new biomarkers for the prediction of gastric diseases.

Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC and its application for DNA methylation analysis

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Ottaviani Diego

2008-05-01

Full Text Available Abstract Background The major histocompatibility complex (MHC is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome. Methods To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP, methylated DNA immunoprecipitation (MeDIP, array comparative genomic hybridization (aCGH and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls. Results Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs. Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation. Conclusion A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics.

Detection of genomic deletions in rice using oligonucleotide microarrays

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Bordeos Alicia

2009-03-01

Full Text Available Abstract Background The induction of genomic deletions by physical- or chemical- agents is an easy and inexpensive means to generate a genome-saturating collection of mutations. Different mutagens can be selected to ensure a mutant collection with a range of deletion sizes. This would allow identification of mutations in single genes or, alternatively, a deleted group of genes that might collectively govern a trait (e.g., quantitative trait loci, QTL. However, deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify. Here, we present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment. Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions. Results We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip® allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to ~500 kb and were predicted on all 12 rice chromosomes. The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype. Finally, the positions of mutations in 14 mutants were aligned onto the rice pseudomolecules in a user-friendly genome browser to allow for rapid identification of untagged mutations http://irfgc.irri.org/cgi-bin/gbrowse/IR64_deletion_mutants/. Conclusion We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice. The density and distribution of deletions suggests the feasibility of a

Cohen syndrome diagnosed using microarray comparative genomic hibridization

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Saldarriaga-Gil, Wilmar

2017-10-01

Full Text Available Cohen syndrome (CS is an uncommon autosomal recessive genetic disorder attributed to damage on VPS13B gene, locus 8q22-q23. Characteristic phenotype consists of intellectual disability, microcephaly, facial dysmorphism, ophthalmic abnormalities, truncal obesity and hipotony. Worldwide, around 150 cases have been published, mostly in Finish patients. We report the case of a 3 year-old male, with short height, craniosynostosis, facial dysmorphism, hipotony, and developmental delay. He was diagnosed with Cohen syndrome using Microarray Comparative Genomic Hibridization (aCGH that showed homozygous deletion of 0.153 Mb on 8q22.2 including VPS13B gene, OMIM #216550. With this report we contribute to enlarge epidemiological databases on an uncommon genetic disorder. Besides, we illustrate on the contribution of aCGH to the etiological diagnosis of patients with unexplained intellectual disability, delayed psychomotor development, language difficulties, autism and multiple congenital anomalies.

DNA microarrays of baculovirus genomes: differential expression of viral genes in two susceptible insect cell lines.

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Yamagishi, J; Isobe, R; Takebuchi, T; Bando, H

2003-03-01

We describe, for the first time, the generation of a viral DNA chip for simultaneous expression measurements of nearly all known open reading frames (ORFs) in the best-studied members of the family Baculoviridae, Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and Bombyx mori nucleopolyhedrovirus (BmNPV). In this study, a viral DNA chip (Ac-BmNPV chip) was fabricated and used to characterize the viral gene expression profile for AcMNPV in different cell types. The viral chip is composed of microarrays of viral DNA prepared by robotic deposition of PCR-amplified viral DNA fragments on glass for ORFs in the NPV genome. Viral gene expression was monitored by hybridization to the DNA fragment microarrays with fluorescently labeled cDNAs prepared from infected Spodoptera frugiperda, Sf9 cells and Trichoplusia ni, TnHigh-Five cells, the latter a major producer of baculovirus and recombinant proteins. A comparison of expression profiles of known ORFs in AcMNPV elucidated six genes (ORF150, p10, pk2, and three late gene expression factor genes lef-3, p35 and lef- 6) the expression of each of which was regulated differently in the two cell lines. Most of these genes are known to be closely involved in the viral life cycle such as in DNA replication, late gene expression and the release of polyhedra from infected cells. These results imply that the differential expression of these viral genes accounts for the differences in viral replication between these two cell lines. Thus, these fabricated microarrays of NPV DNA which allow a rapid analysis of gene expression at the viral genome level should greatly speed the functional analysis of large genomes of NPV.

Comparison of gene coverage of mouse oligonucleotide microarray platforms

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Medrano Juan F

2006-03-01

Full Text Available Abstract Background The increasing use of DNA microarrays for genetical genomics studies generates a need for platforms with complete coverage of the genome. We have compared the effective gene coverage in the mouse genome of different commercial and noncommercial oligonucleotide microarray platforms by performing an in-house gene annotation of probes. We only used information about probes that is available from vendors and followed a process that any researcher may take to find the gene targeted by a given probe. In order to make consistent comparisons between platforms, probes in each microarray were annotated with an Entrez Gene id and the chromosomal position for each gene was obtained from the UCSC Genome Browser Database. Gene coverage was estimated as the percentage of Entrez Genes with a unique position in the UCSC Genome database that is tested by a given microarray platform. Results A MySQL relational database was created to store the mapping information for 25,416 mouse genes and for the probes in five microarray platforms (gene coverage level in parenthesis: Affymetrix430 2.0 (75.6%, ABI Genome Survey (81.24%, Agilent (79.33%, Codelink (78.09%, Sentrix (90.47%; and four array-ready oligosets: Sigma (47.95%, Operon v.3 (69.89%, Operon v.4 (84.03%, and MEEBO (84.03%. The differences in coverage between platforms were highly conserved across chromosomes. Differences in the number of redundant and unspecific probes were also found among arrays. The database can be queried to compare specific genomic regions using a web interface. The software used to create, update and query the database is freely available as a toolbox named ArrayGene. Conclusion The software developed here allows researchers to create updated custom databases by using public or proprietary information on genes for any organisms. ArrayGene allows easy comparisons of gene coverage between microarray platforms for any region of the genome. The comparison presented here

An estimation of the prevalence of genomic disorders using chromosomal microarray data.

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Gillentine, Madelyn A; Lupo, Philip J; Stankiewicz, Pawel; Schaaf, Christian P

2018-04-24

Multiple genomic disorders result from recurrent deletions or duplications between low copy repeat (LCR) clusters, mediated by nonallelic homologous recombination. These copy number variants (CNVs) often exhibit variable expressivity and/or incomplete penetrance. However, the population prevalence of many genomic disorders has not been estimated accurately. A subset of genomic disorders similarly characterized by CNVs between LCRs have been studied epidemiologically, including Williams-Beuren syndrome (7q11.23), Smith-Magenis syndrome (17p11.2), velocardiofacial syndrome (22q11.21), Prader-Willi/Angelman syndromes (15q11.2q12), 17q12 deletion syndrome, and Charcot-Marie-Tooth neuropathy type 1/hereditary neuropathy with liability to pressure palsy (PMP22, 17q11.2). We have generated a method to estimate prevalence of highly penetrant genomic disorders by (1) leveraging epidemiological data for genomic disorders with previously reported prevalence estimates, (2) obtaining chromosomal microarray data on genomic disorders from a large medical genetics clinic; and (3) utilizing these in a linear regression model to determine the prevalence of this syndromic copy number change among the general population. Using our algorithm, the prevalence for five clinically relevant recurrent genomic disorders: 1q21.1 microdeletion (1/6882 live births) and microduplication syndromes (1/6309), 15q13.3 microdeletion syndrome (1/5525), and 16p11.2 microdeletion (1/3021) and microduplication syndromes (1/4216), were determined. These findings will inform epidemiological strategies for evaluating those conditions, and our method may be useful to evaluate the prevalence of other highly penetrant genomic disorders.

Sparse representation and Bayesian detection of genome copy number alterations from microarray data.

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Pique-Regi, Roger; Monso-Varona, Jordi; Ortega, Antonio; Seeger, Robert C; Triche, Timothy J; Asgharzadeh, Shahab

2008-02-01

Genomic instability in cancer leads to abnormal genome copy number alterations (CNA) that are associated with the development and behavior of tumors. Advances in microarray technology have allowed for greater resolution in detection of DNA copy number changes (amplifications or deletions) across the genome. However, the increase in number of measured signals and accompanying noise from the array probes present a challenge in accurate and fast identification of breakpoints that define CNA. This article proposes a novel detection technique that exploits the use of piece wise constant (PWC) vectors to represent genome copy number and sparse Bayesian learning (SBL) to detect CNA breakpoints. First, a compact linear algebra representation for the genome copy number is developed from normalized probe intensities. Second, SBL is applied and optimized to infer locations where copy number changes occur. Third, a backward elimination (BE) procedure is used to rank the inferred breakpoints; and a cut-off point can be efficiently adjusted in this procedure to control for the false discovery rate (FDR). The performance of our algorithm is evaluated using simulated and real genome datasets and compared to other existing techniques. Our approach achieves the highest accuracy and lowest FDR while improving computational speed by several orders of magnitude. The proposed algorithm has been developed into a free standing software application (GADA, Genome Alteration Detection Algorithm). http://biron.usc.edu/~piquereg/GADA

Microarray analysis of serum mRNA in patients with head and neck squamous cell carcinoma at whole-genome scale

Czech Academy of Sciences Publication Activity Database

Čapková, M.; Šáchová, Jana; Strnad, Hynek; Kolář, Michal; Hroudová, Miluše; Chovanec, M.; Čada, Z.; Štefl, M.; Valach, J.; Kastner, J.; Smetana, K. Jr.; Plzák, J.

-, April 23 (2014) ISSN 2314-6141 R&D Projects: GA MZd(CZ) NT13488 Institutional support: RVO:68378050 Keywords : Microarray Analysis * Head and Neck Squamous Cell Carcinoma * whole-genome scale Subject RIV: EB - Genetics ; Molecular Biology

Probing genomic diversity and evolution of Streptococcus suis serotype 2 by NimbleGen tiling arrays

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Liao Hui

2011-05-01

Full Text Available Abstract Background Our previous studies revealed that a new disease form of streptococcal toxic shock syndrome (STSS is associated with specific Streptococcus suis serotype 2 (SS2 strains. To achieve a better understanding of the pathogenicity and evolution of SS2 at the whole-genome level, comparative genomic analysis of 18 SS2 strains, selected on the basis of virulence and geographic origin, was performed using NimbleGen tiling arrays. Results Our results demonstrate that SS2 isolates have highly divergent genomes. The 89K pathogenicity island (PAI, which has been previously recognized as unique to the Chinese epidemic strains causing STSS, was partially included in some other virulent and avirulent strains. The ABC-type transport systems, encoded by 89K, were hypothesized to greatly contribute to the catastrophic features of STSS. Moreover, we identified many polymorphisms in genes encoding candidate or known virulence factors, such as PlcR, lipase, sortases, the pilus-associated proteins, and the response regulator RevS and CtsR. On the basis of analysis of regions of differences (RDs across the entire genome for the 18 selected SS2 strains, a model of microevolution for these strains is proposed, which provides clues into Streptococcus pathogenicity and evolution. Conclusions Our deep comparative genomic analysis of the 89K PAI present in the genome of SS2 strains revealed details into how some virulent strains acquired genes that may contribute to STSS, which may lead to better environmental monitoring of epidemic SS2 strains.

Microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness

Energy Technology Data Exchange (ETDEWEB)

Wu, L.; Liu, X.; Fields, M.W.; Thompson, D.K.; Bagwell, C.E.; Tiedje, J. M.; Hazen, T.C.; Zhou, J.

2008-01-15

The definition and delineation of microbial species are of great importance and challenge due to the extent of evolution and diversity. Whole-genome DNA-DNA hybridization is the cornerstone for defining procaryotic species relatedness, but obtaining pairwise DNA-DNA reassociation values for a comprehensive phylogenetic analysis of procaryotes is tedious and time consuming. A previously described microarray format containing whole-genomic DNA (the community genome array or CGA) was rigorously evaluated as a high-throughput alternative to the traditional DNA-DNA reassociation approach for delineating procaryotic species relationships. DNA similarities for multiple bacterial strains obtained with the CGA-based hybridization were comparable to those obtained with various traditional whole-genome hybridization methods (r=0.87, P<0.01). Significant linear relationships were also observed between the CGA-based genome similarities and those derived from small subunit (SSU) rRNA gene sequences (r=0.79, P<0.0001), gyrB sequences (r=0.95, P<0.0001) or REP- and BOX-PCR fingerprinting profiles (r=0.82, P<0.0001). The CGA hybridization-revealed species relationships in several representative genera, including Pseudomonas, Azoarcus and Shewanella, were largely congruent with previous classifications based on various conventional whole-genome DNA-DNA reassociation, SSU rRNA and/or gyrB analyses. These results suggest that CGA-based DNA-DNA hybridization could serve as a powerful, high-throughput format for determining species relatedness among microorganisms.

A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence.

Science.gov (United States)

Drost, Derek R; Novaes, Evandro; Boaventura-Novaes, Carolina; Benedict, Catherine I; Brown, Ryan S; Yin, Tongming; Tuskan, Gerald A; Kirst, Matias

2009-06-01

Microarrays have demonstrated significant power for genome-wide analyses of gene expression, and recently have also revolutionized the genetic analysis of segregating populations by genotyping thousands of loci in a single assay. Although microarray-based genotyping approaches have been successfully applied in yeast and several inbred plant species, their power has not been proven in an outcrossing species with extensive genetic diversity. Here we have developed methods for high-throughput microarray-based genotyping in such species using a pseudo-backcross progeny of 154 individuals of Populus trichocarpa and P. deltoides analyzed with long-oligonucleotide in situ-synthesized microarray probes. Our analysis resulted in high-confidence genotypes for 719 single-feature polymorphism (SFP) and 1014 gene expression marker (GEM) candidates. Using these genotypes and an established microsatellite (SSR) framework map, we produced a high-density genetic map comprising over 600 SFPs, GEMs and SSRs. The abundance of gene-based markers allowed us to localize over 35 million base pairs of previously unplaced whole-genome shotgun (WGS) scaffold sequence to putative locations in the genome of P. trichocarpa. A high proportion of sampled scaffolds could be verified for their placement with independently mapped SSRs, demonstrating the previously un-utilized power that high-density genotyping can provide in the context of map-based WGS sequence reassembly. Our results provide a substantial contribution to the continued improvement of the Populus genome assembly, while demonstrating the feasibility of microarray-based genotyping in a highly heterozygous population. The strategies presented are applicable to genetic mapping efforts in all plant species with similarly high levels of genetic diversity.

Interim report on updated microarray probes for the LLNL Burkholderia pseudomallei SNP array

Energy Technology Data Exchange (ETDEWEB)

Gardner, S; Jaing, C

2012-03-27

The overall goal of this project is to forensically characterize 100 unknown Burkholderia isolates in the US-Australia collaboration. We will identify genome-wide single nucleotide polymorphisms (SNPs) from B. pseudomallei and near neighbor species including B. mallei, B. thailandensis and B. oklahomensis. We will design microarray probes to detect these SNP markers and analyze 100 Burkholderia genomic DNAs extracted from environmental, clinical and near neighbor isolates from Australian collaborators on the Burkholderia SNP microarray. We will analyze the microarray genotyping results to characterize the genetic diversity of these new isolates and triage the samples for whole genome sequencing. In this interim report, we described the SNP analysis and the microarray probe design for the Burkholderia SNP microarray.

Application of Microarray-Based Comparative Genomic Hybridization in Prenatal and Postnatal Settings: Three Case Reports

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Jing Liu

2011-01-01

Full Text Available Microarray-based comparative genomic hybridization (array CGH is a newly emerged molecular cytogenetic technique for rapid evaluation of the entire genome with sub-megabase resolution. It allows for the comprehensive investigation of thousands and millions of genomic loci at once and therefore enables the efficient detection of DNA copy number variations (a.k.a, cryptic genomic imbalances. The development and the clinical application of array CGH have revolutionized the diagnostic process in patients and has provided a clue to many unidentified or unexplained diseases which are suspected to have a genetic cause. In this paper, we present three clinical cases in both prenatal and postnatal settings. Among all, array CGH played a major discovery role to reveal the cryptic and/or complex nature of chromosome arrangements. By identifying the genetic causes responsible for the clinical observation in patients, array CGH has provided accurate diagnosis and appropriate clinical management in a timely and efficient manner.

Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes.

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Casey R Richardson

2010-05-01

Full Text Available MicroRNAs (miRNAs and trans-acting small-interfering RNAs (tasi-RNAs are small (20-22 nt long RNAs (smRNAs generated from hairpin secondary structures or antisense transcripts, respectively, that regulate gene expression by Watson-Crick pairing to a target mRNA and altering expression by mechanisms related to RNA interference. The high sequence homology of plant miRNAs to their targets has been the mainstay of miRNA prediction algorithms, which are limited in their predictive power for other kingdoms because miRNA complementarity is less conserved yet transitive processes (production of antisense smRNAs are active in eukaryotes. We hypothesize that antisense transcription and associated smRNAs are biomarkers which can be computationally modeled for gene discovery.We explored rice (Oryza sativa sense and antisense gene expression in publicly available whole genome tiling array transcriptome data and sequenced smRNA libraries (as well as C. elegans and found evidence of transitivity of MIRNA genes similar to that found in Arabidopsis. Statistical analysis of antisense transcript abundances, presence of antisense ESTs, and association with smRNAs suggests several hundred Arabidopsis 'orphan' hypothetical genes are non-coding RNAs. Consistent with this hypothesis, we found novel Arabidopsis homologues of some MIRNA genes on the antisense strand of previously annotated protein-coding genes. A Support Vector Machine (SVM was applied using thermodynamic energy of binding plus novel expression features of sense/antisense transcription topology and siRNA abundances to build a prediction model of miRNA targets. The SVM when trained on targets could predict the "ancient" (deeply conserved class of validated Arabidopsis MIRNA genes with an accuracy of 84%, and 76% for "new" rapidly-evolving MIRNA genes.Antisense and smRNA expression features and computational methods may identify novel MIRNA genes and other non-coding RNAs in plants and potentially other

Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays

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Gray Joanna

2010-11-01

Full Text Available Abstract Background We report an attempt to extend the previously successful approach of combining SNP (single nucleotide polymorphism microarrays and DNA pooling (SNP-MaP employing high-density microarrays. Whereas earlier studies employed a range of Affymetrix SNP microarrays comprising from 10 K to 500 K SNPs, this most recent investigation used the 6.0 chip which displays 906,600 SNP probes and 946,000 probes for the interrogation of CNVs (copy number variations. The genotyping assay using the Affymetrix SNP 6.0 array is highly demanding on sample quality due to the small feature size, low redundancy, and lack of mismatch probes. Findings In the first study published so far using this microarray on pooled DNA, we found that pooled cheek swab DNA could not accurately predict real allele frequencies of the samples that comprised the pools. In contrast, the allele frequency estimates using blood DNA pools were reasonable, although inferior compared to those obtained with previously employed Affymetrix microarrays. However, it might be possible to improve performance by developing improved analysis methods. Conclusions Despite the decreasing costs of genome-wide individual genotyping, the pooling approach may have applications in very large-scale case-control association studies. In such cases, our study suggests that high-quality DNA preparations and lower density platforms should be preferred.

Principles of gene microarray data analysis.

Science.gov (United States)

Mocellin, Simone; Rossi, Carlo Riccardo

2007-01-01

The development of several gene expression profiling methods, such as comparative genomic hybridization (CGH), differential display, serial analysis of gene expression (SAGE), and gene microarray, together with the sequencing of the human genome, has provided an opportunity to monitor and investigate the complex cascade of molecular events leading to tumor development and progression. The availability of such large amounts of information has shifted the attention of scientists towards a nonreductionist approach to biological phenomena. High throughput technologies can be used to follow changing patterns of gene expression over time. Among them, gene microarray has become prominent because it is easier to use, does not require large-scale DNA sequencing, and allows for the parallel quantification of thousands of genes from multiple samples. Gene microarray technology is rapidly spreading worldwide and has the potential to drastically change the therapeutic approach to patients affected with tumor. Therefore, it is of paramount importance for both researchers and clinicians to know the principles underlying the analysis of the huge amount of data generated with microarray technology.

Development and Use of Integrated Microarray-Based Genomic Technologies for Assessing Microbial Community Composition and Dynamics

Energy Technology Data Exchange (ETDEWEB)

J. Zhou; S.-K. Rhee; C. Schadt; T. Gentry; Z. He; X. Li; X. Liu; J. Liebich; S.C. Chong; L. Wu

2004-03-17

To effectively monitor microbial populations involved in various important processes, a 50-mer-based oligonucleotide microarray was developed based on known genes and pathways involved in: biodegradation, metal resistance and reduction, denitrification, nitrification, nitrogen fixation, methane oxidation, methanogenesis, carbon polymer decomposition, and sulfate reduction. This array contains approximately 2000 unique and group-specific probes with <85% similarity to their non-target sequences. Based on artificial probes, our results showed that at hybridization conditions of 50 C and 50% formamide, the 50-mer microarray hybridization can differentiate sequences having <88% similarity. Specificity tests with representative pure cultures indicated that the designed probes on the arrays appeared to be specific to their corresponding target genes. Detection limits were about 5-10ng genomic DNA in the absence of background DNA, and 50-100ng ({approx}1.3{sup o} 10{sup 7} cells) in the presence background DNA. Strong linear relationships between signal intensity and target DNA and RNA concentration were observed (r{sup 2} = 0.95-0.99). Application of this microarray to naphthalene-amended enrichments and soil microcosms demonstrated that composition of the microflora varied depending on incubation conditions. While the naphthalene-degrading genes from Rhodococcus-type microorganisms were dominant in enrichments, the genes involved in naphthalene degradation from Gram-negative microorganisms such as Ralstonia, Comamonas, and Burkholderia were most abundant in the soil microcosms (as well as those for polyaromatic hydrocarbon and nitrotoluene degradation). Although naphthalene degradation is widely known and studied in Pseudomonas, Pseudomonas genes were not detected in either system. Real-time PCR analysis of 4 representative genes was consistent with microarray-based quantification (r{sup 2} = 0.95). Currently, we are also applying this microarray to the study of several

Programmable DNA tile self-assembly using a hierarchical sub-tile strategy.

Science.gov (United States)

Shi, Xiaolong; Lu, Wei; Wang, Zhiyu; Pan, Linqiang; Cui, Guangzhao; Xu, Jin; LaBean, Thomas H

2014-02-21

DNA tile based self-assembly provides a bottom-up approach to construct desired nanostructures. DNA tiles have been directly constructed from ssDNA and readily self-assembled into 2D lattices and 3D superstructures. However, for more complex lattice designs including algorithmic assemblies requiring larger tile sets, a more modular approach could prove useful. This paper reports a new DNA 'sub-tile' strategy to easily create whole families of programmable tiles. Here, we demonstrate the stability and flexibility of our sub-tile structures by constructing 3-, 4- and 6-arm DNA tiles that are subsequently assembled into 2D lattices and 3D nanotubes according to a hierarchical design. Assembly of sub-tiles, tiles, and superstructures was analyzed using polyacrylamide gel electrophoresis and atomic force microscopy. DNA tile self-assembly methods provide a bottom-up approach to create desired nanostructures; the sub-tile strategy adds a useful new layer to this technique. Complex units can be made from simple parts. The sub-tile approach enables the rapid redesign and prototyping of complex DNA tile sets and tiles with asymmetric designs.

Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridization

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Oikawa Masahiro

2011-12-01

Full Text Available Abstract Background It has been postulated that ionizing radiation induces breast cancers among atomic bomb (A-bomb survivors. We have reported a higher incidence of HER2 and C-MYC oncogene amplification in breast cancers from A-bomb survivors. The purpose of this study was to clarify the effect of A-bomb radiation exposure on genomic instability (GIN, which is an important hallmark of carcinogenesis, in archival formalin-fixed paraffin-embedded (FFPE tissues of breast cancer by using microarray-comparative genomic hybridization (aCGH. Methods Tumor DNA was extracted from FFPE tissues of invasive ductal cancers from 15 survivors who were exposed at 1.5 km or less from the hypocenter and 13 calendar year-matched non-exposed patients followed by aCGH analysis using a high-density oligonucleotide microarray. The total length of copy number aberrations (CNA was used as an indicator of GIN, and correlation with clinicopathological factors were statistically tested. Results The mean of the derivative log ratio spread (DLRSpread, which estimates the noise by calculating the spread of log ratio differences between consecutive probes for all chromosomes, was 0.54 (range, 0.26 to 1.05. The concordance of results between aCGH and fluorescence in situ hybridization (FISH for HER2 gene amplification was 88%. The incidence of HER2 amplification and histological grade was significantly higher in the A-bomb survivors than control group (P = 0.04, respectively. The total length of CNA tended to be larger in the A-bomb survivors (P = 0.15. Correlation analysis of CNA and clinicopathological factors revealed that DLRSpread was negatively correlated with that significantly (P = 0.034, r = -0.40. Multivariate analysis with covariance revealed that the exposure to A-bomb was a significant (P = 0.005 independent factor which was associated with larger total length of CNA of breast cancers. Conclusions Thus, archival FFPE tissues from A-bomb survivors are useful for

Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridization

International Nuclear Information System (INIS)

Oikawa, Masahiro; Yoshiura, Koh-ichiro; Kondo, Hisayoshi; Miura, Shiro; Nagayasu, Takeshi; Nakashima, Masahiro

2011-01-01

It has been postulated that ionizing radiation induces breast cancers among atomic bomb (A-bomb) survivors. We have reported a higher incidence of HER2 and C-MYC oncogene amplification in breast cancers from A-bomb survivors. The purpose of this study was to clarify the effect of A-bomb radiation exposure on genomic instability (GIN), which is an important hallmark of carcinogenesis, in archival formalin-fixed paraffin-embedded (FFPE) tissues of breast cancer by using microarray-comparative genomic hybridization (aCGH). Tumor DNA was extracted from FFPE tissues of invasive ductal cancers from 15 survivors who were exposed at 1.5 km or less from the hypocenter and 13 calendar year-matched non-exposed patients followed by aCGH analysis using a high-density oligonucleotide microarray. The total length of copy number aberrations (CNA) was used as an indicator of GIN, and correlation with clinicopathological factors were statistically tested. The mean of the derivative log ratio spread (DLRSpread), which estimates the noise by calculating the spread of log ratio differences between consecutive probes for all chromosomes, was 0.54 (range, 0.26 to 1.05). The concordance of results between aCGH and fluorescence in situ hybridization (FISH) for HER2 gene amplification was 88%. The incidence of HER2 amplification and histological grade was significantly higher in the A-bomb survivors than control group (P = 0.04, respectively). The total length of CNA tended to be larger in the A-bomb survivors (P = 0.15). Correlation analysis of CNA and clinicopathological factors revealed that DLRSpread was negatively correlated with that significantly (P = 0.034, r = -0.40). Multivariate analysis with covariance revealed that the exposure to A-bomb was a significant (P = 0.005) independent factor which was associated with larger total length of CNA of breast cancers. Thus, archival FFPE tissues from A-bomb survivors are useful for genome-wide aCGH analysis. Our results suggested that A

Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridization.

Science.gov (United States)

Oikawa, Masahiro; Yoshiura, Koh-ichiro; Kondo, Hisayoshi; Miura, Shiro; Nagayasu, Takeshi; Nakashima, Masahiro

2011-12-07

It has been postulated that ionizing radiation induces breast cancers among atomic bomb (A-bomb) survivors. We have reported a higher incidence of HER2 and C-MYC oncogene amplification in breast cancers from A-bomb survivors. The purpose of this study was to clarify the effect of A-bomb radiation exposure on genomic instability (GIN), which is an important hallmark of carcinogenesis, in archival formalin-fixed paraffin-embedded (FFPE) tissues of breast cancer by using microarray-comparative genomic hybridization (aCGH). Tumor DNA was extracted from FFPE tissues of invasive ductal cancers from 15 survivors who were exposed at 1.5 km or less from the hypocenter and 13 calendar year-matched non-exposed patients followed by aCGH analysis using a high-density oligonucleotide microarray. The total length of copy number aberrations (CNA) was used as an indicator of GIN, and correlation with clinicopathological factors were statistically tested. The mean of the derivative log ratio spread (DLRSpread), which estimates the noise by calculating the spread of log ratio differences between consecutive probes for all chromosomes, was 0.54 (range, 0.26 to 1.05). The concordance of results between aCGH and fluorescence in situ hybridization (FISH) for HER2 gene amplification was 88%. The incidence of HER2 amplification and histological grade was significantly higher in the A-bomb survivors than control group (P = 0.04, respectively). The total length of CNA tended to be larger in the A-bomb survivors (P = 0.15). Correlation analysis of CNA and clinicopathological factors revealed that DLRSpread was negatively correlated with that significantly (P = 0.034, r = -0.40). Multivariate analysis with covariance revealed that the exposure to A-bomb was a significant (P = 0.005) independent factor which was associated with larger total length of CNA of breast cancers. Thus, archival FFPE tissues from A-bomb survivors are useful for genome-wide aCGH analysis. Our results suggested that A

Facilitating functional annotation of chicken microarray data

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Gresham Cathy R

2009-10-01

Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and

biomvRhsmm: Genomic Segmentation with Hidden Semi-Markov Model

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Yang Du

2014-01-01

Full Text Available High-throughput technologies like tiling array and next-generation sequencing (NGS generate continuous homogeneous segments or signal peaks in the genome that represent transcripts and transcript variants (transcript mapping and quantification, regions of deletion and amplification (copy number variation, or regions characterized by particular common features like chromatin state or DNA methylation ratio (epigenetic modifications. However, the volume and output of data produced by these technologies present challenges in analysis. Here, a hidden semi-Markov model (HSMM is implemented and tailored to handle multiple genomic profile, to better facilitate genome annotation by assisting in the detection of transcripts, regulatory regions, and copy number variation by holistic microarray or NGS. With support for various data distributions, instead of limiting itself to one specific application, the proposed hidden semi-Markov model is designed to allow modeling options to accommodate different types of genomic data and to serve as a general segmentation engine. By incorporating genomic positions into the sojourn distribution of HSMM, with optional prior learning using annotation or previous studies, the modeling output is more biologically sensible. The proposed model has been compared with several other state-of-the-art segmentation models through simulation benchmarking, which shows that our efficient implementation achieves comparable or better sensitivity and specificity in genomic segmentation.

Programmable DNA tile self-assembly using a hierarchical sub-tile strategy

International Nuclear Information System (INIS)

Shi, Xiaolong; Lu, Wei; Wang, Zhiyu; Pan, Linqiang; Cui, Guangzhao; Xu, Jin; LaBean, Thomas H

2014-01-01

DNA tile based self-assembly provides a bottom-up approach to construct desired nanostructures. DNA tiles have been directly constructed from ssDNA and readily self-assembled into 2D lattices and 3D superstructures. However, for more complex lattice designs including algorithmic assemblies requiring larger tile sets, a more modular approach could prove useful. This paper reports a new DNA ‘sub-tile’ strategy to easily create whole families of programmable tiles. Here, we demonstrate the stability and flexibility of our sub-tile structures by constructing 3-, 4- and 6-arm DNA tiles that are subsequently assembled into 2D lattices and 3D nanotubes according to a hierarchical design. Assembly of sub-tiles, tiles, and superstructures was analyzed using polyacrylamide gel electrophoresis and atomic force microscopy. DNA tile self-assembly methods provide a bottom-up approach to create desired nanostructures; the sub-tile strategy adds a useful new layer to this technique. Complex units can be made from simple parts. The sub-tile approach enables the rapid redesign and prototyping of complex DNA tile sets and tiles with asymmetric designs. (paper)

MARS: Microarray analysis, retrieval, and storage system

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Scheideler Marcel

2005-04-01

Full Text Available Abstract Background Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. Results MARS (Microarray Analysis and Retrieval System provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS, a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. Conclusion We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at http://genome.tugraz.at.

The EADGENE Microarray Data Analysis Workshop

DEFF Research Database (Denmark)

de Koning, Dirk-Jan; Jaffrézic, Florence; Lund, Mogens Sandø

2007-01-01

Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from...... 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays...... statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful...

Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA

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Chan Alan

2006-06-01

Full Text Available Abstract Background Current methods for measurement of copy number do not combine all the desirable qualities of convenience, throughput, economy, accuracy and resolution. In this study, to improve the throughput associated with Multiplex Amplifiable Probe Hybridisation (MAPH we aimed to develop a modification based on the 3-Dimensional, Flow-Through Microarray Platform from PamGene International. In this new method, electrophoretic analysis of amplified products is replaced with photometric analysis of a probed oligonucleotide array. Copy number analysis of hybridised probes is based on a dual-label approach by comparing the intensity of Cy3-labelled MAPH probes amplified from test samples co-hybridised with similarly amplified Cy5-labelled reference MAPH probes. The key feature of using a hybridisation-based end point with MAPH is that discrimination of amplified probes is based on sequence and not fragment length. Results In this study we showed that microarray MAPH measurement of PMP22 gene dosage correlates well with PMP22 gene dosage determined by capillary MAPH and that copy number was accurately reported in analyses of DNA from 38 individuals, 12 of which were known to have Charcot-Marie-Tooth disease type 1A (CMT1A. Conclusion Measurement of microarray-based endpoints for MAPH appears to be of comparable accuracy to electrophoretic methods, and holds the prospect of fully exploiting the potential multiplicity of MAPH. The technology has the potential to simplify copy number assays for genes with a large number of exons, or of expanded sets of probes from dispersed genomic locations.

Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA.

Science.gov (United States)

Gibbons, Brian; Datta, Parikkhit; Wu, Ying; Chan, Alan; Al Armour, John

2006-06-30

Current methods for measurement of copy number do not combine all the desirable qualities of convenience, throughput, economy, accuracy and resolution. In this study, to improve the throughput associated with Multiplex Amplifiable Probe Hybridisation (MAPH) we aimed to develop a modification based on the 3-Dimensional, Flow-Through Microarray Platform from PamGene International. In this new method, electrophoretic analysis of amplified products is replaced with photometric analysis of a probed oligonucleotide array. Copy number analysis of hybridised probes is based on a dual-label approach by comparing the intensity of Cy3-labelled MAPH probes amplified from test samples co-hybridised with similarly amplified Cy5-labelled reference MAPH probes. The key feature of using a hybridisation-based end point with MAPH is that discrimination of amplified probes is based on sequence and not fragment length. In this study we showed that microarray MAPH measurement of PMP22 gene dosage correlates well with PMP22 gene dosage determined by capillary MAPH and that copy number was accurately reported in analyses of DNA from 38 individuals, 12 of which were known to have Charcot-Marie-Tooth disease type 1A (CMT1A). Measurement of microarray-based endpoints for MAPH appears to be of comparable accuracy to electrophoretic methods, and holds the prospect of fully exploiting the potential multiplicity of MAPH. The technology has the potential to simplify copy number assays for genes with a large number of exons, or of expanded sets of probes from dispersed genomic locations.

Hierarchical Self Assembly of Patterns from the Robinson Tilings: DNA Tile Design in an Enhanced Tile Assembly Model.

Science.gov (United States)

Padilla, Jennifer E; Liu, Wenyan; Seeman, Nadrian C

2012-06-01

We introduce a hierarchical self assembly algorithm that produces the quasiperiodic patterns found in the Robinson tilings and suggest a practical implementation of this algorithm using DNA origami tiles. We modify the abstract Tile Assembly Model, (aTAM), to include active signaling and glue activation in response to signals to coordinate the hierarchical assembly of Robinson patterns of arbitrary size from a small set of tiles according to the tile substitution algorithm that generates them. Enabling coordinated hierarchical assembly in the aTAM makes possible the efficient encoding of the recursive process of tile substitution.

The Level-1 Tile-Muon Trigger in the Tile Calorimeter Upgrade Program

CERN Document Server

Ryzhov, Andrey; The ATLAS collaboration

2016-01-01

The Tile Calorimeter (TileCal) is the central hadronic calorimeter of the ATLAS experiment at the Large Hadron Collider (LHC). The TileCal provides highly-segmented energy measurements for incident particles. Information from TileCal's last radial layer can assist in muon tagging using Level-1 muon trigger. It can help in the rejection of fake muon triggers arising from background radiation (slow charged particles - protons) without degrading the efficiency of the trigger. The TileCal main activity for Phase-0 upgrade ATLAS program (2013-2014) was the activation of the TileCal third layer signal for assisting the muon trigger at 1.0<|η|<1.3 (Tile-Muon Trigger). This report describes the Tile-Muon Trigger at TileCal upgrade activities, focusing on the new on-detector electronics such as Tile Muon Digitizer Board (TMDB) to provide (receive and digitize) the signal from eight TileCal modules to three Level-1 muon endcap sector logic blocks.

Homogeneous versus heterogeneous probes for microbial ecological microarrays.

Science.gov (United States)

Bae, Jin-Woo; Park, Yong-Ha

2006-07-01

Microbial ecological microarrays have been developed for investigating the composition and functions of microorganism communities in environmental niches. These arrays include microbial identification microarrays, which use oligonucleotides, gene fragments or microbial genomes as probes. In this article, the advantages and disadvantages of each type of probe are reviewed. Oligonucleotide probes are currently useful for probing uncultivated bacteria that are not amenable to gene fragment probing, whereas the functional gene fragments amplified randomly from microbial genomes require phylogenetic and hierarchical categorization before use as microbial identification probes, despite their high resolution for both specificity and sensitivity. Until more bacteria are sequenced and gene fragment probes are thoroughly validated, heterogeneous bacterial genome probes will provide a simple, sensitive and quantitative tool for exploring the ecosystem structure.

The Level-1 Tile-Muon Trigger in the Tile Calorimeter upgrade program

International Nuclear Information System (INIS)

Ryzhov, A.

2016-01-01

The Tile Calorimeter (TileCal) is the central hadronic calorimeter of the ATLAS experiment at the Large Hadron Collider (LHC). TileCal provides highly-segmented energy measurements for incident particles. Information from TileCal's outermost radial layer can assist in muon tagging in the Level-1 Muon Trigger by rejecting fake muon triggers due to slow charged particles (typically protons) without degrading the efficiency of the trigger. The main activity of the Tile-Muon Trigger in the ATLAS Phase-0 upgrade program was to install and to activate the TileCal signal processor module for providing trigger inputs to the Level-1 Muon Trigger. This report describes the Tile-Muon Trigger, focusing on the new detector electronics such as the Tile Muon Digitizer Board (TMDB) that receives, digitizes and then provides the signal from eight TileCal modules to three Level-1 muon endcap Sector-Logic Boards.

The Importance of Normalization on Large and Heterogeneous Microarray Datasets

Science.gov (United States)

DNA microarray technology is a powerful functional genomics tool increasingly used for investigating global gene expression in environmental studies. Microarrays can also be used in identifying biological networks, as they give insight on the complex gene-to-gene interactions, ne...

Triangular spiral tilings

International Nuclear Information System (INIS)

Sushida, Takamichi; Hizume, Akio; Yamagishi, Yoshikazu

2012-01-01

The topology of spiral tilings is intimately related to phyllotaxis theory and continued fractions. A quadrilateral spiral tiling is determined by a suitable chosen triple (ζ, m, n), where ζ element of D/R, and m and n are relatively prime integers. We give a simple characterization when (ζ, m, n) produce a triangular spiral tiling. When m and n are fixed, the admissible generators ζ form a curve in the unit disk. The family of triangular spiral tilings with opposed parastichy pairs (m, n) is parameterized by the divergence angle arg (ζ), while triangular spiral tilings with non-opposed parastichy pairs are parameterized by the plastochrone ratio 1/|ζ|. The generators for triangular spiral tilings with opposed parastichy pairs are not dense in the complex parameter space, while those with non-opposed parastichy pairs are dense. The proofs will be given in a general setting of spiral multiple tilings. We present paper-folding (origami) sheets that build spiral towers whose top-down views are triangular tilings. (paper)

Topology of tiling spaces

CERN Document Server

Sadun, Lorenzo

2008-01-01

Aperiodic tilings are interesting to mathematicians and scientists for both theoretical and practical reasons. The serious study of aperiodic tilings began as a solution to a problem in logic. Simpler aperiodic tilings eventually revealed hidden "symmetries" that were previously considered impossible, while the tilings themselves were quite striking. The discovery of quasicrystals showed that such aperiodicity actually occurs in nature and led to advances in materials science. Many properties of aperiodic tilings can be discerned by studying one tiling at a time. However, by studying families of tilings, further properties are revealed. This broader study naturally leads to the topology of tiling spaces. This book is an introduction to the topology of tiling spaces, with a target audience of graduate students who wish to learn about the interface of topology with aperiodic order. It isn't a comprehensive and cross-referenced tome about everything having to do with tilings, which would be too big, too hard to ...

DNA Microarrays in Comparative Genomics and Transcriptomics

DEFF Research Database (Denmark)

Willenbrock, Hanni

2007-01-01

at identifying the exact breakpoints where DNA has been gained or lost. In this thesis, three popular methods are compared and a realistic simulation model is presented for generating artificial data with known breakpoints and known DNA copy number. By using simulated data, we obtain a realistic evaluation......During the past few years, innovations in the DNA sequencing technology has led to an explosion in available DNA sequence information. This has revolutionized biological research and promoted the development of high throughput analysis methods that can take advantage of the vast amount of sequence...... data. For this, the DNA microarray technology has gained enormous popularity due to its ability to measure the presence or the activity of thousands of genes simultaneously. Microarrays for high throughput data analyses are not limited to a few organisms but may be applied to everything from bacteria...

Shared probe design and existing microarray reanalysis using PICKY

Directory of Open Access Journals (Sweden)

Chou Hui-Hsien

2010-04-01

Full Text Available Abstract Background Large genomes contain families of highly similar genes that cannot be individually identified by microarray probes. This limitation is due to thermodynamic restrictions and cannot be resolved by any computational method. Since gene annotations are updated more frequently than microarrays, another common issue facing microarray users is that existing microarrays must be routinely reanalyzed to determine probes that are still useful with respect to the updated annotations. Results PICKY 2.0 can design shared probes for sets of genes that cannot be individually identified using unique probes. PICKY 2.0 uses novel algorithms to track sharable regions among genes and to strictly distinguish them from other highly similar but nontarget regions during thermodynamic comparisons. Therefore, PICKY does not sacrifice the quality of shared probes when choosing them. The latest PICKY 2.1 includes the new capability to reanalyze existing microarray probes against updated gene sets to determine probes that are still valid to use. In addition, more precise nonlinear salt effect estimates and other improvements are added, making PICKY 2.1 more versatile to microarray users. Conclusions Shared probes allow expressed gene family members to be detected; this capability is generally more desirable than not knowing anything about these genes. Shared probes also enable the design of cross-genome microarrays, which facilitate multiple species identification in environmental samples. The new nonlinear salt effect calculation significantly increases the precision of probes at a lower buffer salt concentration, and the probe reanalysis function improves existing microarray result interpretations.

Recycling Roof Tile Waste Material for Wall Cover Tiles

Directory of Open Access Journals (Sweden)

Ambar Mulyono

2014-02-01

Full Text Available Prior research on roof tile waste treatment has attempted to find the appropriate technology to reuse old roof tile waste by  create  wall  cladding  materials  from  it.  Through  exploration  and  experimentation,  a  treatment  method  has  been discovered  to  transform  the  tile  fragments  into  artificial  stone  that  resembles  the  shape  of  coral.  This  baked  clay artificial stone material is then processed as a decorative element for vertical surfaces that are not load-bearing, such as on the interior and exterior walls of a building. Before applying the fragments as wall tiles, several steps must be taken: 1  Blunting,  which  changes  the  look  of  tile  fragments  using  a  machine  created  specifically  to  blunt  the  roof-tile fragment  edges,  2  Closing  the  pores  of  the  blunted  fragments  as  a  finishing  step  that  can  be  done  with  a  transparent coat or a solid color of paint, 3 Planting the transformed roof-tile fragments on a prepared tile body made of concrete. In this study, the second phase is done using the method of ceramics glazing at a temperature of 700 °C. The finishing step is the strength of this product because it produces a rich color artificial pebble.

Applications of nanotechnology, next generation sequencing and microarrays in biomedical research.

Science.gov (United States)

Elingaramil, Sauli; Li, Xiaolong; He, Nongyue

2013-07-01

Next-generation sequencing technologies, microarrays and advances in bio nanotechnology have had an enormous impact on research within a short time frame. This impact appears certain to increase further as many biomedical institutions are now acquiring these prevailing new technologies. Beyond conventional sampling of genome content, wide-ranging applications are rapidly evolving for next-generation sequencing, microarrays and nanotechnology. To date, these technologies have been applied in a variety of contexts, including whole-genome sequencing, targeted re sequencing and discovery of transcription factor binding sites, noncoding RNA expression profiling and molecular diagnostics. This paper thus discusses current applications of nanotechnology, next-generation sequencing technologies and microarrays in biomedical research and highlights the transforming potential these technologies offer.

Wang Tiles in Computer Graphics

CERN Document Server

Lagae, Ares

2009-01-01

Many complex signals in computer graphics, such as point distributions and textures, cannot be efficiently synthesized and stored. This book presents tile-based methods based on Wang tiles and corner tiles to solve both these problems. Instead of synthesizing a complex signal when needed, the signal is synthesized beforehand over a small set of Wang tiles or corner tiles. Arbitrary large amounts of that signal can then efficiently be generated when needed by generating a stochastic tiling, and storing only a small set of tiles reduces storage requirements. A tile-based method for generating a

Miles of tiles

CERN Document Server

Radin, Charles

1999-01-01

"In this book, we try to display the value (and joy!) of starting from a mathematically amorphous problem and combining ideas from diverse sources to produce new and significant mathematics--mathematics unforeseen from the motivating problem ..." --from the Preface The common thread throughout this book is aperiodic tilings; the best-known example is the "kite and dart" tiling. This tiling has been widely discussed, particularly since 1984 when it was adopted to model quasicrystals. The presentation uses many different areas of mathematics and physics to analyze the new features of such tilings. Although many people are aware of the existence of aperiodic tilings, and maybe even their origin in a question in logic, not everyone is familiar with their subtleties and the underlying rich mathematical theory. For the interested reader, this book fills that gap. Understanding this new type of tiling requires an unusual variety of specialties, including ergodic theory, functional analysis, group theory and ring the...

A Java-based tool for the design of classification microarrays.

Science.gov (United States)

Meng, Da; Broschat, Shira L; Call, Douglas R

2008-08-04

Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed microarrays, which are composed of DNA from more than one organism, are more effective than conventional microarrays composed of DNA from a single organism. Selection of probes is a key factor in designing successful mixed microarrays because redundant sequences are inefficient and limited representation of diversity can restrict application of the microarray. We have developed a Java-based software tool, called PLASMID, for use in selecting the minimum set of probe sequences needed to classify different groups of plasmids or bacteria. The software program was successfully applied to several different sets of data. The utility of PLASMID was illustrated using existing mixed-plasmid microarray data as well as data from a virtual mixed-genome microarray constructed from different strains of Streptococcus. Moreover, use of data from expression microarray experiments demonstrated the generality of PLASMID. In this paper we describe a new software tool for selecting a set of probes for a classification microarray. While the tool was developed for the design of mixed microarrays-and mixed-plasmid microarrays in particular-it can also be used to design expression arrays. The user can choose from several clustering methods (including hierarchical, non-hierarchical, and a model-based genetic algorithm), several probe ranking methods, and several different display methods. A novel approach is used for probe redundancy reduction, and probe selection is accomplished via stepwise discriminant analysis. Data can be entered in different formats (including Excel and comma-delimited text), and dendrogram, heat map, and scatter plot images can be saved in several different formats (including jpeg and tiff). Weights generated using stepwise discriminant analysis can be stored for

Methylation-Sensitive Amplification Length Polymorphism (MS-AFLP) Microarrays for Epigenetic Analysis of Human Genomes.

Science.gov (United States)

Alonso, Sergio; Suzuki, Koichi; Yamamoto, Fumiichiro; Perucho, Manuel

2018-01-01

Somatic, and in a minor scale also germ line, epigenetic aberrations are fundamental to carcinogenesis, cancer progression, and tumor phenotype. DNA methylation is the most extensively studied and arguably the best understood epigenetic mechanisms that become altered in cancer. Both somatic loss of methylation (hypomethylation) and gain of methylation (hypermethylation) are found in the genome of malignant cells. In general, the cancer cell epigenome is globally hypomethylated, while some regions-typically gene-associated CpG islands-become hypermethylated. Given the profound impact that DNA methylation exerts on the transcriptional profile and genomic stability of cancer cells, its characterization is essential to fully understand the complexity of cancer biology, improve tumor classification, and ultimately advance cancer patient management and treatment. A plethora of methods have been devised to analyze and quantify DNA methylation alterations. Several of the early-developed methods relied on the use of methylation-sensitive restriction enzymes, whose activity depends on the methylation status of their recognition sequences. Among these techniques, methylation-sensitive amplification length polymorphism (MS-AFLP) was developed in the early 2000s, and successfully adapted from its original gel electrophoresis fingerprinting format to a microarray format that notably increased its throughput and allowed the quantification of the methylation changes. This array-based platform interrogates over 9500 independent loci putatively amplified by the MS-AFLP technique, corresponding to the NotI sites mapped throughout the human genome.

Extended -Regular Sequence for Automated Analysis of Microarray Images

Directory of Open Access Journals (Sweden)

Jin Hee-Jeong

2006-01-01

Full Text Available Microarray study enables us to obtain hundreds of thousands of expressions of genes or genotypes at once, and it is an indispensable technology for genome research. The first step is the analysis of scanned microarray images. This is the most important procedure for obtaining biologically reliable data. Currently most microarray image processing systems require burdensome manual block/spot indexing work. Since the amount of experimental data is increasing very quickly, automated microarray image analysis software becomes important. In this paper, we propose two automated methods for analyzing microarray images. First, we propose the extended -regular sequence to index blocks and spots, which enables a novel automatic gridding procedure. Second, we provide a methodology, hierarchical metagrid alignment, to allow reliable and efficient batch processing for a set of microarray images. Experimental results show that the proposed methods are more reliable and convenient than the commercial tools.

Fractal analysis of mandibular trabecular bone: optimal tile sizes for the tile counting method.

Science.gov (United States)

Huh, Kyung-Hoe; Baik, Jee-Seon; Yi, Won-Jin; Heo, Min-Suk; Lee, Sam-Sun; Choi, Soon-Chul; Lee, Sun-Bok; Lee, Seung-Pyo

2011-06-01

This study was performed to determine the optimal tile size for the fractal dimension of the mandibular trabecular bone using a tile counting method. Digital intraoral radiographic images were obtained at the mandibular angle, molar, premolar, and incisor regions of 29 human dry mandibles. After preprocessing, the parameters representing morphometric characteristics of the trabecular bone were calculated. The fractal dimensions of the processed images were analyzed in various tile sizes by the tile counting method. The optimal range of tile size was 0.132 mm to 0.396 mm for the fractal dimension using the tile counting method. The sizes were closely related to the morphometric parameters. The fractal dimension of mandibular trabecular bone, as calculated with the tile counting method, can be best characterized with a range of tile sizes from 0.132 to 0.396 mm.

A Java-based tool for the design of classification microarrays

Directory of Open Access Journals (Sweden)

Broschat Shira L

2008-08-01

Full Text Available Abstract Background Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed microarrays, which are composed of DNA from more than one organism, are more effective than conventional microarrays composed of DNA from a single organism. Selection of probes is a key factor in designing successful mixed microarrays because redundant sequences are inefficient and limited representation of diversity can restrict application of the microarray. We have developed a Java-based software tool, called PLASMID, for use in selecting the minimum set of probe sequences needed to classify different groups of plasmids or bacteria. Results The software program was successfully applied to several different sets of data. The utility of PLASMID was illustrated using existing mixed-plasmid microarray data as well as data from a virtual mixed-genome microarray constructed from different strains of Streptococcus. Moreover, use of data from expression microarray experiments demonstrated the generality of PLASMID. Conclusion In this paper we describe a new software tool for selecting a set of probes for a classification microarray. While the tool was developed for the design of mixed microarrays–and mixed-plasmid microarrays in particular–it can also be used to design expression arrays. The user can choose from several clustering methods (including hierarchical, non-hierarchical, and a model-based genetic algorithm, several probe ranking methods, and several different display methods. A novel approach is used for probe redundancy reduction, and probe selection is accomplished via stepwise discriminant analysis. Data can be entered in different formats (including Excel and comma-delimited text, and dendrogram, heat map, and scatter plot images can be saved in several different formats (including jpeg and tiff. Weights

Performance of the Tile PreProcessor Demonstrator for the ATLAS Tile Calorimeter Phase II Upgrade

OpenAIRE

Carrio Argos, Fernando; Valero, Alberto

2015-01-01

The Tile Calorimeter PreProcessor (TilePPr) demonstrator is a high performance double AMC board based on FPGA resources and QSFP modules. This board has been designed in the framework of the ATLAS Tile Calorimeter (TileCal) Demonstrator Project for the Phase II Upgrade as the first stage of the back-end electronics. The TilePPr demonstrator has been conceived for receiving and processing the data coming from the front-end electronics of the TileCal Demonstrator module, as well as for configur...

OPTIMIZATION-BASED APPROACH TO TILING OF FINITE AREAS WITH ARBITRARY SETS OF WANG TILES

Directory of Open Access Journals (Sweden)

Marek Tyburec

2017-11-01

Full Text Available Wang tiles proved to be a convenient tool for the design of aperiodic tilings in computer graphics and in materials engineering. While there are several algorithms for generation of finite-sized tilings, they exploit the specific structure of individual tile sets, which prevents their general usage. In this contribution, we reformulate the NP-complete tiling generation problem as a binary linear program, together with its linear and semidefinite relaxations suitable for the branch and bound method. Finally, we assess the performance of the established formulations on generations of several aperiodic tilings reported in the literature, and conclude that the linear relaxation is better suited for the problem.

Comparison of medieval decorated floor-tiles with clay and tile fragments from the kilns at Bistrup

International Nuclear Information System (INIS)

Als Hansen, B.; Aaman Soerensen, M.; McKerrell, H.; Mejdahl, V.

1977-01-01

In 1976 two tile kilns with numerous wasters of ornamented tiles were excavated at Bistrup near Roskilde. Identical ornaments had earlier been found on floor-tiles from seven sites, mainly churches, in north and east Zealand. The question arose whether some of these tiles were made locally or whether all tiles carrying this particular ornamentation were made at Bistrup. Preliminary results obtained from a comparison of the tiles with material from Bistrup means of neutron activation analysis indicate that not all tiles were made at Bistrup. (author)

A microarray analysis of the rice transcriptome and its comparison to Arabidopsis

DEFF Research Database (Denmark)

Ma, Ligeng; Chen, Chen; Liu, Xigang

2005-01-01

Arabidopsis and rice are the only two model plants whose finished phase genome sequence has been completed. Here we report the construction of an oligomer microarray based on the presently known and predicted gene models in the rice genome. This microarray was used to analyze the transcriptional...... with similar genome-wide surveys of the Arabidopsis transcriptome, our results indicate that similar proportions of the two genomes are expressed in their corresponding organ types. A large percentage of the rice gene models that lack significant Arabidopsis homologs are expressed. Furthermore, the expression...... patterns of rice and Arabidopsis best-matched homologous genes in distinct functional groups indicate dramatic differences in their degree of conservation between the two species. Thus, this initial comparative analysis reveals some basic similarities and differences between the Arabidopsis and rice...

Bacterial identification and subtyping using DNA microarray and DNA sequencing.

Science.gov (United States)

Al-Khaldi, Sufian F; Mossoba, Magdi M; Allard, Marc M; Lienau, E Kurt; Brown, Eric D

2012-01-01

The era of fast and accurate discovery of biological sequence motifs in prokaryotic and eukaryotic cells is here. The co-evolution of direct genome sequencing and DNA microarray strategies not only will identify, isotype, and serotype pathogenic bacteria, but also it will aid in the discovery of new gene functions by detecting gene expressions in different diseases and environmental conditions. Microarray bacterial identification has made great advances in working with pure and mixed bacterial samples. The technological advances have moved beyond bacterial gene expression to include bacterial identification and isotyping. Application of new tools such as mid-infrared chemical imaging improves detection of hybridization in DNA microarrays. The research in this field is promising and future work will reveal the potential of infrared technology in bacterial identification. On the other hand, DNA sequencing by using 454 pyrosequencing is so cost effective that the promise of $1,000 per bacterial genome sequence is becoming a reality. Pyrosequencing technology is a simple to use technique that can produce accurate and quantitative analysis of DNA sequences with a great speed. The deposition of massive amounts of bacterial genomic information in databanks is creating fingerprint phylogenetic analysis that will ultimately replace several technologies such as Pulsed Field Gel Electrophoresis. In this chapter, we will review (1) the use of DNA microarray using fluorescence and infrared imaging detection for identification of pathogenic bacteria, and (2) use of pyrosequencing in DNA cluster analysis to fingerprint bacterial phylogenetic trees.

Tile Patterns with Logo--Part I: Laying Tile with Logo.

Science.gov (United States)

Clason, Robert G.

1990-01-01

Described is a method for drawing periodic tile patterns using LOGO. Squares, triangles, hexagons, shape filling, and random tile laying are included. These activities incorporate problem solving, programing methods, and the geometry of angles and polygons. (KR)

The Utility of Chromosomal Microarray Analysis in Developmental and Behavioral Pediatrics

Science.gov (United States)

Beaudet, Arthur L.

2013-01-01

Chromosomal microarray analysis (CMA) has emerged as a powerful new tool to identify genomic abnormalities associated with a wide range of developmental disabilities including congenital malformations, cognitive impairment, and behavioral abnormalities. CMA includes array comparative genomic hybridization (CGH) and single nucleotide polymorphism…

Preliminary report for analysis of genome wide mutations from four ciprofloxacin resistant B. anthracis Sterne isolates generated by Illumina, 454 sequencing and microarrays for DHS

Energy Technology Data Exchange (ETDEWEB)

Jaing, Crystal [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vergez, Lisa [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Hinckley, Aubree [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Thissen, James [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gardner, Shea [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); McLoughlin, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Jackson, Paul [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ellingson, Sally [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hauser, Loren [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Brettin, Tom [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Fofanov, Viacheslav [Eureka Genomics, Hercules, CA (United States); Koshinsky, Heather [Eureka Genomics, Hercules, CA (United States); Fofanov, Yuriy [Univ. of Houston, TX (United States)

2011-06-21

The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, Taqman PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. As the result of a different DHS project, we have selected for and isolated a large number of ciprofloxacin resistant B. anthracis Sterne isolates. These isolates vary in the concentrations of ciprofloxacin that they can tolerate, suggesting multiple mutations in the samples. In collaboration with University of Houston, Eureka Genomics and Oak Ridge National Laboratory, we analyzed the ciprofloxacin resistant B. anthracis Sterne isolates by microarray hybridization, Illumina and Roche 454 sequencing to understand the error rates and sensitivity of the different methods. The report provides an assessment of the results and a complete set of all protocols used and all data generated along with information to interpret the protocols and data sets.

The JET belt limiter tiles

International Nuclear Information System (INIS)

Deksnis, E.

1988-09-01

The belt limiter system, comprising two full toroidal rings of limiter tiles, was installed in JET in 1987. In consists of water-cooled fins with the limiter material in form of tile inbetween. The tiles are designed to absorb heat fluxes during irradiation without the surface temperature exceeding 2000 0 C and to radiate this heat between pulses to the water cooled sink whose temperature is lower than that of the vacuum vessel. An important feature of the design is to maximise the area of the radiating surface facing the water cooled fin. This leads to a tile depth much greater than the width of the tile facing the heat flux. Limiter tiles intercept particles flowing out of the plasma through the area between the two belt limiter rings and through remaining surface area of the plasma column. Power deposition to a limiter tile depends strongly on the shape of the plasma, the edge plasma properties as well as on the surface profile of the tiles. This paper will discuss the methodology that was followed in producing an optimized surface profile of the tiles. This shaped profile has the feature that the resulting power deposition profile is roughly similar for a wide range of plasma parameters. (author)

Microarray analysis in the archaeon Halobacterium salinarum strain R1.

Directory of Open Access Journals (Sweden)

Jens Twellmeyer

Full Text Available BACKGROUND: Phototrophy of the extremely halophilic archaeon Halobacterium salinarum was explored for decades. The research was mainly focused on the expression of bacteriorhodopsin and its functional properties. In contrast, less is known about genome wide transcriptional changes and their impact on the physiological adaptation to phototrophy. The tool of choice to record transcriptional profiles is the DNA microarray technique. However, the technique is still rarely used for transcriptome analysis in archaea. METHODOLOGY/PRINCIPAL FINDINGS: We developed a whole-genome DNA microarray based on our sequence data of the Hbt. salinarum strain R1 genome. The potential of our tool is exemplified by the comparison of cells growing under aerobic and phototrophic conditions, respectively. We processed the raw fluorescence data by several stringent filtering steps and a subsequent MAANOVA analysis. The study revealed a lot of transcriptional differences between the two cell states. We found that the transcriptional changes were relatively weak, though significant. Finally, the DNA microarray data were independently verified by a real-time PCR analysis. CONCLUSION/SIGNIFICANCE: This is the first DNA microarray analysis of Hbt. salinarum cells that were actually grown under phototrophic conditions. By comparing the transcriptomics data with current knowledge we could show that our DNA microarray tool is well applicable for transcriptome analysis in the extremely halophilic archaeon Hbt. salinarum. The reliability of our tool is based on both the high-quality array of DNA probes and the stringent data handling including MAANOVA analysis. Among the regulated genes more than 50% had unknown functions. This underlines the fact that haloarchaeal phototrophy is still far away from being completely understood. Hence, the data recorded in this study will be subject to future systems biology analysis.

Microarray-based genotyping of Salmonella: Inter-laboratory evaluation of reproducibility and standardization potential

DEFF Research Database (Denmark)

Grønlund, Hugo Ahlm; Riber, Leise; Vigre, Håkan

2011-01-01

Bacterial food-borne infections in humans caused by Salmonella spp. are considered a crucial food safety issue. Therefore, it is important for the risk assessments of Salmonella to consider the genomic variationamong different isolates in order to control pathogen-induced infections. Microarray...... critical methodology parameters that differed between the two labs were identified. These related to printing facilities, choice of hybridization buffer,wash buffers used following the hybridization and choice of procedure for purifying genomic DNA. Critical parameters were randomized in a four......DNA and different wash buffers. However, less agreement (Kappa=0.2–0.6) between microarray results were observed when using different hybridization buffers, indicating this parameter as being highly criticalwhen transferring a standard microarray assay between laboratories. In conclusion, this study indicates...

Brane tilings and their applications

International Nuclear Information System (INIS)

Yamazaki, M.

2008-01-01

We review recent developments in the theory of brane tilings and four-dimensional N=1 supersymmetric quiver gauge theories. This review consists of two parts. In part I, we describe foundations of brane tilings, emphasizing the physical interpretation of brane tilings as fivebrane systems. In part II, we discuss application of brane tilings to AdS/CFT correspondence and homological mirror symmetry. More topics, such as orientifold of brane tilings, phenomenological model building, similarities with BPS solitons in supersymmetric gauge theories, are also briefly discussed. (Abstract Copyright [2008], Wiley Periodicals, Inc.)

Integrated olfactory receptor and microarray gene expression databases

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Crasto Chiquito J

2007-06-01

Full Text Available Abstract Background Gene expression patterns of olfactory receptors (ORs are an important component of the signal encoding mechanism in the olfactory system since they determine the interactions between odorant ligands and sensory neurons. We have developed the Olfactory Receptor Microarray Database (ORMD to house OR gene expression data. ORMD is integrated with the Olfactory Receptor Database (ORDB, which is a key repository of OR gene information. Both databases aim to aid experimental research related to olfaction. Description ORMD is a Web-accessible database that provides a secure data repository for OR microarray experiments. It contains both publicly available and private data; accessing the latter requires authenticated login. The ORMD is designed to allow users to not only deposit gene expression data but also manage their projects/experiments. For example, contributors can choose whether to make their datasets public. For each experiment, users can download the raw data files and view and export the gene expression data. For each OR gene being probed in a microarray experiment, a hyperlink to that gene in ORDB provides access to genomic and proteomic information related to the corresponding olfactory receptor. Individual ORs archived in ORDB are also linked to ORMD, allowing users access to the related microarray gene expression data. Conclusion ORMD serves as a data repository and project management system. It facilitates the study of microarray experiments of gene expression in the olfactory system. In conjunction with ORDB, ORMD integrates gene expression data with the genomic and functional data of ORs, and is thus a useful resource for both olfactory researchers and the public.

Clinical significance of rare copy number variations in epilepsy: a case-control survey using microarray-based comparative genomic hybridization.

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Striano, Pasquale; Coppola, Antonietta; Paravidino, Roberta; Malacarne, Michela; Gimelli, Stefania; Robbiano, Angela; Traverso, Monica; Pezzella, Marianna; Belcastro, Vincenzo; Bianchi, Amedeo; Elia, Maurizio; Falace, Antonio; Gazzerro, Elisabetta; Ferlazzo, Edoardo; Freri, Elena; Galasso, Roberta; Gobbi, Giuseppe; Molinatto, Cristina; Cavani, Simona; Zuffardi, Orsetta; Striano, Salvatore; Ferrero, Giovanni Battista; Silengo, Margherita; Cavaliere, Maria Luigia; Benelli, Matteo; Magi, Alberto; Piccione, Maria; Dagna Bricarelli, Franca; Coviello, Domenico A; Fichera, Marco; Minetti, Carlo; Zara, Federico

2012-03-01

To perform an extensive search for genomic rearrangements by microarray-based comparative genomic hybridization in patients with epilepsy. Prospective cohort study. Epilepsy centers in Italy. Two hundred seventy-nine patients with unexplained epilepsy, 265 individuals with nonsyndromic mental retardation but no epilepsy, and 246 healthy control subjects were screened by microarray-based comparative genomic hybridization. Identification of copy number variations (CNVs) and gene enrichment. Rare CNVs occurred in 26 patients (9.3%) and 16 healthy control subjects (6.5%) (P = .26). The CNVs identified in patients were larger (P = .03) and showed higher gene content (P = .02) than those in control subjects. The CNVs larger than 1 megabase (P = .002) and including more than 10 genes (P = .005) occurred more frequently in patients than in control subjects. Nine patients (34.6%) among those harboring rare CNVs showed rearrangements associated with emerging microdeletion or microduplication syndromes. Mental retardation and neuropsychiatric features were associated with rare CNVs (P = .004), whereas epilepsy type was not. The CNV rate in patients with epilepsy and mental retardation or neuropsychiatric features is not different from that observed in patients with mental retardation only. Moreover, significant enrichment of genes involved in ion transport was observed within CNVs identified in patients with epilepsy. Patients with epilepsy show a significantly increased burden of large, rare, gene-rich CNVs, particularly when associated with mental retardation and neuropsychiatric features. The limited overlap between CNVs observed in the epilepsy group and those observed in the group with mental retardation only as well as the involvement of specific (ion channel) genes indicate a specific association between the identified CNVs and epilepsy. Screening for CNVs should be performed for diagnostic purposes preferentially in patients with epilepsy and mental retardation or

Multi-platform whole-genome microarray analyses refine the epigenetic signature of breast cancer metastasis with gene expression and copy number.

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Joseph Andrews

2010-01-01

Full Text Available We have previously identified genome-wide DNA methylation changes in a cell line model of breast cancer metastasis. These complex epigenetic changes that we observed, along with concurrent karyotype analyses, have led us to hypothesize that complex genomic alterations in cancer cells (deletions, translocations and ploidy are superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes observed in breast cancer metastasis.We undertook simultaneous high-resolution, whole-genome analyses of MDA-MB-468GFP and MDA-MB-468GFP-LN human breast cancer cell lines (an isogenic, paired lymphatic metastasis cell line model using Affymetrix gene expression (U133, promoter (1.0R, and SNP/CNV (SNP 6.0 microarray platforms to correlate data from gene expression, epigenetic (DNA methylation, and combination copy number variant/single nucleotide polymorphism microarrays. Using Partek Software and Ingenuity Pathway Analysis we integrated datasets from these three platforms and detected multiple hypomethylation and hypermethylation events. Many of these epigenetic alterations correlated with gene expression changes. In addition, gene dosage events correlated with the karyotypic differences observed between the cell lines and were reflected in specific promoter methylation patterns. Gene subsets were identified that correlated hyper (and hypo methylation with the loss (or gain of gene expression and in parallel, with gene dosage losses and gains, respectively. Individual gene targets from these subsets were also validated for their methylation, expression and copy number status, and susceptible gene pathways were identified that may indicate how selective advantage drives the processes of tumourigenesis and metastasis.Our approach allows more precisely profiling of functionally relevant epigenetic signatures that are associated with cancer progression and metastasis.

TiArA: a virtual appliance for the analysis of Tiling Array data.

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Jason A Greenbaum

2010-04-01

Full Text Available Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis.Tiling Array Analyzer (TiArA is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range.TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian package or a virtual appliance at http://purl.org/NET/tiara.

Tile drainage as karst: Conduit flow and diffuse flow in a tile-drained watershed

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Schilling, K.E.; Helmers, M.

2008-01-01

The similarity of tiled-drained watersheds to karst drainage basins can be used to improve understanding of watershed-scale nutrient losses from subsurface tile drainage networks. In this study, short-term variations in discharge and chemistry were examined from a tile outlet collecting subsurface tile flow from a 963 ha agricultural watershed. Study objectives were to apply analytical techniques from karst springs to tile discharge to evaluate water sources and estimate the loads of agricultural pollutants discharged from the tile with conduit, intermediate and diffuse flow regimes. A two-member mixing model using nitrate, chloride and specific conductance was used to distinguish rainwater versus groundwater inputs. Results indicated that groundwater comprised 75% of the discharge for a three-day storm period and rainwater was primarily concentrated during the hydrograph peak. A contrasting pattern of solute concentrations and export loads was observed in tile flow. During base flow periods, tile flow consisted of diffuse flow from groundwater sources and contained elevated levels of nitrate, chloride and specific conductance. During storm events, suspended solids and pollutants adhered to soil surfaces (phosphorus, ammonium and organic nitrogen) were concentrated and discharged during the rapid, conduit flow portion of the hydrograph. During a three-day period, conduit flow occurred for 5.6% of the time but accounted for 16.5% of the total flow. Nitrate and chloride were delivered primarily with diffuse flow (more than 70%), whereas 80-94% of total suspended sediment, phosphorus and ammonium were exported with conduit and intermediate flow regimes. Understanding the water sources contributing to tile drainage and the manner by which pollutant discharge occurs from these systems (conduit, intermediate or diffuse flow) may be useful for designing, implementing and evaluating non-point source reduction strategies in tile-drained landscapes. ?? 2007 Elsevier B.V. All

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

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2012-01-01

Background The combination of chromatin immunoprecipitation with two-channel microarray technology enables genome-wide mapping of binding sites of DNA-interacting proteins (ChIP-on-chip) or sites with methylated CpG di-nucleotides (DNA methylation microarray). These powerful tools are the gateway to understanding gene transcription regulation. Since the goals of such studies, the sample preparation procedures, the microarray content and study design are all different from transcriptomics microarrays, the data pre-processing strategies traditionally applied to transcriptomics microarrays may not be appropriate. Particularly, the main challenge of the normalization of "regulation microarrays" is (i) to make the data of individual microarrays quantitatively comparable and (ii) to keep the signals of the enriched probes, representing DNA sequences from the precipitate, as distinguishable as possible from the signals of the un-enriched probes, representing DNA sequences largely absent from the precipitate. Results We compare several widely used normalization approaches (VSN, LOWESS, quantile, T-quantile, Tukey's biweight scaling, Peng's method) applied to a selection of regulation microarray datasets, ranging from DNA methylation to transcription factor binding and histone modification studies. Through comparison of the data distributions of control probes and gene promoter probes before and after normalization, and assessment of the power to identify known enriched genomic regions after normalization, we demonstrate that there are clear differences in performance between normalization procedures. Conclusion T-quantile normalization applied separately on the channels and Tukey's biweight scaling outperform other methods in terms of the conservation of enriched and un-enriched signal separation, as well as in identification of genomic regions known to be enriched. T-quantile normalization is preferable as it additionally improves comparability between microarrays. In

Broad spectrum microarray for fingerprint-based bacterial species identification

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Frey Jürg E

2010-02-01

Full Text Available Abstract Background Microarrays are powerful tools for DNA-based molecular diagnostics and identification of pathogens. Most target a limited range of organisms and are based on only one or a very few genes for specific identification. Such microarrays are limited to organisms for which specific probes are available, and often have difficulty discriminating closely related taxa. We have developed an alternative broad-spectrum microarray that employs hybridisation fingerprints generated by high-density anonymous markers distributed over the entire genome for identification based on comparison to a reference database. Results A high-density microarray carrying 95,000 unique 13-mer probes was designed. Optimized methods were developed to deliver reproducible hybridisation patterns that enabled confident discrimination of bacteria at the species, subspecies, and strain levels. High correlation coefficients were achieved between replicates. A sub-selection of 12,071 probes, determined by ANOVA and class prediction analysis, enabled the discrimination of all samples in our panel. Mismatch probe hybridisation was observed but was found to have no effect on the discriminatory capacity of our system. Conclusions These results indicate the potential of our genome chip for reliable identification of a wide range of bacterial taxa at the subspecies level without laborious prior sequencing and probe design. With its high resolution capacity, our proof-of-principle chip demonstrates great potential as a tool for molecular diagnostics of broad taxonomic groups.

Kinetics of DNA tile dimerization.

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Jiang, Shuoxing; Yan, Hao; Liu, Yan

2014-06-24

Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.

A comparative analysis of DNA barcode microarray feature size

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Smith Andrew M

2009-10-01

Full Text Available Abstract Background Microarrays are an invaluable tool in many modern genomic studies. It is generally perceived that decreasing the size of microarray features leads to arrays with higher resolution (due to greater feature density, but this increase in resolution can compromise sensitivity. Results We demonstrate that barcode microarrays with smaller features are equally capable of detecting variation in DNA barcode intensity when compared to larger feature sizes within a specific microarray platform. The barcodes used in this study are the well-characterized set derived from the Yeast KnockOut (YKO collection used for screens of pooled yeast (Saccharomyces cerevisiae deletion mutants. We treated these pools with the glycosylation inhibitor tunicamycin as a test compound. Three generations of barcode microarrays at 30, 8 and 5 μm features sizes independently identified the primary target of tunicamycin to be ALG7. Conclusion We show that the data obtained with 5 μm feature size is of comparable quality to the 30 μm size and propose that further shrinking of features could yield barcode microarrays with equal or greater resolving power and, more importantly, higher density.

Expanding probe repertoire and improving reproducibility in human genomic hybridization

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Dorman, Stephanie N.; Shirley, Ben C.; Knoll, Joan H. M.; Rogan, Peter K.

2013-01-01

Diagnostic DNA hybridization relies on probes composed of single copy (sc) genomic sequences. Sc sequences in probe design ensure high specificity and avoid cross-hybridization to other regions of the genome, which could lead to ambiguous results that are difficult to interpret. We examine how the distribution and composition of repetitive sequences in the genome affects sc probe performance. A divide and conquer algorithm was implemented to design sc probes. With this approach, sc probes can include divergent repetitive elements, which hybridize to unique genomic targets under higher stringency experimental conditions. Genome-wide custom probe sets were created for fluorescent in situ hybridization (FISH) and microarray genomic hybridization. The scFISH probes were developed for detection of copy number changes within small tumour suppressor genes and oncogenes. The microarrays demonstrated increased reproducibility by eliminating cross-hybridization to repetitive sequences adjacent to probe targets. The genome-wide microarrays exhibited lower median coefficients of variation (17.8%) for two HapMap family trios. The coefficients of variations of commercial probes within 300 nt of a repetitive element were 48.3% higher than the nearest custom probe. Furthermore, the custom microarray called a chromosome 15q11.2q13 deletion more consistently. This method for sc probe design increases probe coverage for FISH and lowers variability in genomic microarrays. PMID:23376933

Case of 7p22.1 Microduplication Detected by Whole Genome Microarray (REVEAL) in Workup of Child Diagnosed with Autism

OpenAIRE

Goitia, Veronica; Oquendo, Marcial; Stratton, Robert

2015-01-01

Introduction. More than 60 cases of 7p22 duplications and deletions have been reported with over 16 of them occurring without concomitant chromosomal abnormalities. Patient and Methods. We report a 29-month-old male diagnosed with autism. Whole genome chromosome SNP microarray (REVEAL) demonstrated a 1.3?Mb interstitial duplication of 7p22.1 ->p22.1 arr 7p22.1 (5,436,367?6,762,394), the second smallest interstitial 7p duplication reported to date. This interval included 14 OMIM annotated gene...

Tile-Packing Tomography Is NP-hard

DEFF Research Database (Denmark)

Chrobak, Marek; Dürr, Christoph; Guíñez, Flavio

2010-01-01

Discrete tomography deals with reconstructing finite spatial objects from their projections. The objects we study in this paper are called tilings or tile-packings, and they consist of a number of disjoint copies of a fixed tile, where a tile is defined as a connected set of grid points. A row...

Geometrical tile design for complex neighborhoods.

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Czeizler, Eugen; Kari, Lila

2009-01-01

Recent research has showed that tile systems are one of the most suitable theoretical frameworks for the spatial study and modeling of self-assembly processes, such as the formation of DNA and protein oligomeric structures. A Wang tile is a unit square, with glues on its edges, attaching to other tiles and forming larger and larger structures. Although quite intuitive, the idea of glues placed on the edges of a tile is not always natural for simulating the interactions occurring in some real systems. For example, when considering protein self-assembly, the shape of a protein is the main determinant of its functions and its interactions with other proteins. Our goal is to use geometric tiles, i.e., square tiles with geometrical protrusions on their edges, for simulating tiled paths (zippers) with complex neighborhoods, by ribbons of geometric tiles with simple, local neighborhoods. This paper is a step toward solving the general case of an arbitrary neighborhood, by proposing geometric tile designs that solve the case of a "tall" von Neumann neighborhood, the case of the f-shaped neighborhood, and the case of a 3 x 5 "filled" rectangular neighborhood. The techniques can be combined and generalized to solve the problem in the case of any neighborhood, centered at the tile of reference, and included in a 3 x (2k + 1) rectangle.

Increasing the specificity and function of DNA microarrays by processing arrays at different stringencies

DEFF Research Database (Denmark)

Dufva, Martin; Petersen, Jesper; Poulsen, Lena

2009-01-01

DNA microarrays have for a decade been the only platform for genome-wide analysis and have provided a wealth of information about living organisms. DNA microarrays are processed today under one condition only, which puts large demands on assay development because all probes on the array need to f...

Development of a Feature and Template-Assisted Assembler and Application to the Analysis of a Foot-and-Mouth Disease Virus Genotyping Microarray.

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Roger W Barrette

Full Text Available Several RT-PCR and genome sequencing strategies exist for the resolution of Foot-and-Mouth Disease virus (FMDV. While these approaches are relatively straightforward, they can be vulnerable to failure due to the unpredictable nature of FMDV genome sequence variations. Sequence independent single primer amplification (SISPA followed by genotyping microarray offers an attractive unbiased approach to FMDV characterization. Here we describe a custom FMDV microarray and a companion feature and template-assisted assembler software (FAT-assembler capable of resolving virus genome sequence using a moderate number of conserved microarray features. The results demonstrate that this approach may be used to rapidly characterize naturally occurring FMDV as well as an engineered chimeric strain of FMDV. The FAT-assembler, while applied to resolving FMDV genomes, represents a new bioinformatics approach that should be broadly applicable to interpreting microarray genotyping data for other viruses or target organisms.

Integration of microarray analysis into the clinical diagnosis of hematological malignancies: How much can we improve cytogenetic testing?

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Peterson, Jess F.; Aggarwal, Nidhi; Smith, Clayton A.; Gollin, Susanne M.; Surti, Urvashi; Rajkovic, Aleksandar; Swerdlow, Steven H.; Yatsenko, Svetlana A.

2015-01-01

Purpose To evaluate the clinical utility, diagnostic yield and rationale of integrating microarray analysis in the clinical diagnosis of hematological malignancies in comparison with classical chromosome karyotyping/fluorescence in situ hybridization (FISH). Methods G-banded chromosome analysis, FISH and microarray studies using customized CGH and CGH+SNP designs were performed on 27 samples from patients with hematological malignancies. A comprehensive comparison of the results obtained by three methods was conducted to evaluate benefits and limitations of these techniques for clinical diagnosis. Results Overall, 89.7% of chromosomal abnormalities identified by karyotyping/FISH studies were also detectable by microarray. Among 183 acquired copy number alterations (CNAs) identified by microarray, 94 were additional findings revealed in 14 cases (52%), and at least 30% of CNAs were in genomic regions of diagnostic/prognostic significance. Approximately 30% of novel alterations detected by microarray were >20 Mb in size. Balanced abnormalities were not detected by microarray; however, of the 19 apparently “balanced” rearrangements, 55% (6/11) of recurrent and 13% (1/8) of non-recurrent translocations had alterations at the breakpoints discovered by microarray. Conclusion Microarray technology enables accurate, cost-effective and time-efficient whole-genome analysis at a resolution significantly higher than that of conventional karyotyping and FISH. Array-CGH showed advantage in identification of cryptic imbalances and detection of clonal aberrations in population of non-dividing cancer cells and samples with poor chromosome morphology. The integration of microarray analysis into the cytogenetic diagnosis of hematologic malignancies has the potential to improve patient management by providing clinicians with additional disease specific and potentially clinically actionable genomic alterations. PMID:26299921

Bacillus subtilis genome diversity.

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Earl, Ashlee M; Losick, Richard; Kolter, Roberto

2007-02-01

Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.

Comparison of Comparative Genomic Hybridization Technologies across Microarray Platforms

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In the 2007 Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) project, we analyzed HL-60 DNA with five platforms: Agilent, Affymetrix 500K, Affymetrix U133 Plus 2.0, Illumina, and RPCI 19K BAC arrays. Copy number variation (CNV) was analyzed ...

Transcriptional landscape estimation from tiling array data using a model of signal shift and drift

DEFF Research Database (Denmark)

Rasmussen, Simon; Jarmer, Hanne Østergaard; Nicolas, P

2009-01-01

MOTIVATION: High-density oligonucleotide tiling array technology holds the promise of a better description of the complexity and the dynamics of transcriptional landscapes. In organisms such as bacteria and yeasts, transcription can be measured on a genome-wide scale with a resolution >25 bp...

Different responsiveness to a high-fat/cholesterol diet in two inbred mice and underlying genetic factors: a whole genome microarray analysis

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Jin Gang

2009-10-01

Full Text Available Abstract Background To investigate different responses to a high-fat/cholesterol diet and uncover their underlying genetic factors between C57BL/6J (B6 and DBA/2J (D2 inbred mice. Methods B6 and D2 mice were fed a high-fat/cholesterol diet for a series of time-points. Serum and bile lipid profiles, bile acid yields, hepatic apoptosis, gallstones and atherosclerosis formation were measured. Furthermore, a whole genome microarray was performed to screen hepatic genes expression profile. Quantitative real-time PCR, western blot and TUNEL assay were conducted to validate microarray data. Results After fed the high-fat/cholesterol diet, serum and bile total cholesterol, serum cholesterol esters, HDL cholesterol and Non-HDL cholesterol levels were altered in B6 but not significantly changed in D2; meanwhile, biliary bile acid was decreased in B6 but increased in D2. At the same time, hepatic apoptosis, gallstones and atherosclerotic lesions occurred in B6 but not in D2. The hepatic microarray analysis revealed distinctly different genes expression patterns between B6 and D2 mice. Their functional pathway groups included lipid metabolism, oxidative stress, immune/inflammation response and apoptosis. Quantitative real time PCR, TUNEL assay and western-blot results were consistent with microarray analysis. Conclusion Different genes expression patterns between B6 and D2 mice might provide a genetic basis for their distinctive responses to a high-fat/cholesterol diet, and give us an opportunity to identify novel pharmaceutical targets in related diseases in the future.

Improvement in the amine glass platform by bubbling method for a DNA microarray

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Jee SH

2015-10-01

Full Text Available Seung Hyun Jee,1 Jong Won Kim,2 Ji Hyeong Lee,2 Young Soo Yoon11Department of Chemical and Biological Engineering, Gachon University, Seongnam, Gyeonggi, Republic of Korea; 2Genomics Clinical Research Institute, LabGenomics Co., Ltd., Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of KoreaAbstract: A glass platform with high sensitivity for sexually transmitted diseases microarray is described here. An amino-silane-based self-assembled monolayer was coated on the surface of a glass platform using a novel bubbling method. The optimized surface of the glass platform had highly uniform surface modifications using this method, as well as improved hybridization properties with capture probes in the DNA microarray. On the basis of these results, the improved glass platform serves as a highly reliable and optimal material for the DNA microarray. Moreover, in this study, we demonstrated that our glass platform, manufactured by utilizing the bubbling method, had higher uniformity, shorter processing time, lower background signal, and higher spot signal than the platforms manufactured by the general dipping method. The DNA microarray manufactured with a glass platform prepared using bubbling method can be used as a clinical diagnostic tool. Keywords: DNA microarray, glass platform, bubbling method, self-assambled monolayer

Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.

Science.gov (United States)

Fernandez, Paula; Soria, Marcelo; Blesa, David; DiRienzo, Julio; Moschen, Sebastian; Rivarola, Maximo; Clavijo, Bernardo Jose; Gonzalez, Sergio; Peluffo, Lucila; Príncipi, Dario; Dosio, Guillermo; Aguirrezabal, Luis; García-García, Francisco; Conesa, Ana; Hopp, Esteban; Dopazo, Joaquín; Heinz, Ruth Amelia; Paniego, Norma

2012-01-01

Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (psunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

Analysis of human HPRT- deletion mutants by the microarray-CGH (comparative genomic hybridization)

International Nuclear Information System (INIS)

Kodaira, M.; Sasaki, K.; Tagawa, H.; Omine, H.; Kushiro, J.; Takahashi, N.; Katayama, H.

2003-01-01

We are trying to evaluate genetic effects of radiation on human using mutation frequency as an indicator. For the efficient detection of mutations, it is important to understand the mechanism and the characteristics of radiation-induced mutations. We have started the analysis of hypoxanthine-guanine phosphoribosyl transferase (HPRT) mutants induced by X-ray in order to clarify the deletion size and the mutation-distribution. We analyzed 39 human X-ray induced HPRT-deletion mutants by using the microarray-CGH. The array for this analysis contains 57 BAC clones covering as much as possible of the 4Mb of the 5' side and 10Mb of the 3' side of the HPRT gene based on the NCBI genome database. DNA from parent strain and each HPRT-mutant strain are labeled with Cy5 and Cy3 respectively, and were mixed and hybridized on the array. Fluorescent intensity ratio of the obtained spots was analyzed using software we developed to identify clones corresponding to the deletion region. The deletion in these strains ranged up to 3.5 Mb on the 5' side and 6 Mb on the 3' side of the HPRT gene. Deletions in 13 strains ended around BAC clones located at about 3 Mb on the 5' side. On the 3' side, deletions extended up to the specific clones located at 1.5 Mb in 11 strains. The mutations seem to be complex on the 3' end of deletion; some accompanied duplications with deletions and others could not be explained by one mutation event. We need to confirm these results, taking into account the experimental reproducibility and the accuracy of the published genetic map. The results of the research using the microarray-CGH help us to search the regions where deletions are easily induced and to identify the factors affecting the range of deletions

Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays.

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Christine M Costello

2005-08-01

Full Text Available BACKGROUND: The differential pathophysiologic mechanisms that trigger and maintain the two forms of inflammatory bowel disease (IBD, Crohn disease (CD, and ulcerative colitis (UC are only partially understood. cDNA microarrays can be used to decipher gene regulation events at a genome-wide level and to identify novel unknown genes that might be involved in perpetuating inflammatory disease progression. METHODS AND FINDINGS: High-density cDNA microarrays representing 33,792 UniGene clusters were prepared. Biopsies were taken from the sigmoid colon of normal controls (n = 11, CD patients (n = 10 and UC patients (n = 10. 33P-radiolabeled cDNA from purified poly(A+ RNA extracted from biopsies (unpooled was hybridized to the arrays. We identified 500 and 272 transcripts differentially regulated in CD and UC, respectively. Interesting hits were independently verified by real-time PCR in a second sample of 100 individuals, and immunohistochemistry was used for exemplary localization. The main findings point to novel molecules important in abnormal immune regulation and the highly disturbed cell biology of colonic epithelial cells in IBD pathogenesis, e.g., CYLD (cylindromatosis, turban tumor syndrome and CDH11 (cadherin 11, type 2. By the nature of the array setup, many of the genes identified were to our knowledge previously uncharacterized, and prediction of the putative function of a subsection of these genes indicate that some could be involved in early events in disease pathophysiology. CONCLUSION: A comprehensive set of candidate genes not previously associated with IBD was revealed, which underlines the polygenic and complex nature of the disease. It points out substantial differences in pathophysiology between CD and UC. The multiple unknown genes identified may stimulate new research in the fields of barrier mechanisms and cell signalling in the context of IBD, and ultimately new therapeutic approaches.

Tritium in the DIII-D carbon tiles

International Nuclear Information System (INIS)

Taylor, P.L.; Kellman, A.G.; Lee, R.L.

1993-06-01

The amount of tritium in the carbon tiles used as a first wall in the DIII-D tokamak was measured recently when the tiles were removed and cleaned. The measurements were made as part of the task of developing the appropriate safety procedures for processing of the tiles. The surface tritium concentration on the carbon tiles was surveyed and the total tritium released from tile samples was measured in test bakes. The total tritium in all the carbon tiles at the time the tiles were removed for cleaning is estimated to be 15 mCi and the fraction of tritium retained in the tiles from DIII-D operations has a lower bound of 10%. The tritium was found to be concentrated in a narrow surface layer on the plasma facing side of the tile, was fully released when baked to 1,000 degree C, and was released in the form of tritiated gas (DT) as opposed to tritiated water (DTO) when baked

A DNA microarray-based methylation-sensitive (MS)-AFLP hybridization method for genetic and epigenetic analyses.

Science.gov (United States)

Yamamoto, F; Yamamoto, M

2004-07-01

We previously developed a PCR-based DNA fingerprinting technique named the Methylation Sensitive (MS)-AFLP method, which permits comparative genome-wide scanning of methylation status with a manageable number of fingerprinting experiments. The technique uses the methylation sensitive restriction enzyme NotI in the context of the existing Amplified Fragment Length Polymorphism (AFLP) method. Here we report the successful conversion of this gel electrophoresis-based DNA fingerprinting technique into a DNA microarray hybridization technique (DNA Microarray MS-AFLP). By performing a total of 30 (15 x 2 reciprocal labeling) DNA Microarray MS-AFLP hybridization experiments on genomic DNA from two breast and three prostate cancer cell lines in all pairwise combinations, and Southern hybridization experiments using more than 100 different probes, we have demonstrated that the DNA Microarray MS-AFLP is a reliable method for genetic and epigenetic analyses. No statistically significant differences were observed in the number of differences between the breast-prostate hybridization experiments and the breast-breast or prostate-prostate comparisons.

Implementing an online tool for genome-wide validation of survival-associated biomarkers in ovarian-cancer using microarray data from 1287 patients

DEFF Research Database (Denmark)

Győrffy, Balázs; Lánczky, András; Szállási, Zoltán

2012-01-01

was set up using gene expression data and survival information of 1287 ovarian cancer patients downloaded from Gene Expression Omnibus and The Cancer Genome Atlas (Affymetrix HG-U133A, HG-U133A 2.0, and HG-U133 Plus 2.0 microarrays). After quality control and normalization, only probes present on all......). A Kaplan–Meier survival plot was generated and significance was computed. The tool can be accessed online at www.kmplot.com/ovar. We used this integrative data analysis tool to validate the prognostic power of 37 biomarkers identified in the literature. Of these, CA125 (MUC16; P=3.7x10–5, hazard ratio (HR...... biomarker validation platform that mines all available microarray data to assess the prognostic power of 22 277 genes in 1287 ovarian cancer patients. We specifically used this tool to evaluate the effect of 37 previously published biomarkers on ovarian cancer prognosis....

Evaluation of toxicity of the mycotoxin citrinin using yeast ORF DNA microarray and Oligo DNA microarray

Directory of Open Access Journals (Sweden)

Nobumasa Hitoshi

2007-04-01

Full Text Available Abstract Background Mycotoxins are fungal secondary metabolites commonly present in feed and food, and are widely regarded as hazardous contaminants. Citrinin, one of the very well known mycotoxins that was first isolated from Penicillium citrinum, is produced by more than 10 kinds of fungi, and is possibly spread all over the world. However, the information on the action mechanism of the toxin is limited. Thus, we investigated the citrinin-induced genomic response for evaluating its toxicity. Results Citrinin inhibited growth of yeast cells at a concentration higher than 100 ppm. We monitored the citrinin-induced mRNA expression profiles in yeast using the ORF DNA microarray and Oligo DNA microarray, and the expression profiles were compared with those of the other stress-inducing agents. Results obtained from both microarray experiments clustered together, but were different from those of the mycotoxin patulin. The oxidative stress response genes – AADs, FLR1, OYE3, GRE2, and MET17 – were significantly induced. In the functional category, expression of genes involved in "metabolism", "cell rescue, defense and virulence", and "energy" were significantly activated. In the category of "metabolism", genes involved in the glutathione synthesis pathway were activated, and in the category of "cell rescue, defense and virulence", the ABC transporter genes were induced. To alleviate the induced stress, these cells might pump out the citrinin after modification with glutathione. While, the citrinin treatment did not induce the genes involved in the DNA repair. Conclusion Results from both microarray studies suggest that citrinin treatment induced oxidative stress in yeast cells. The genotoxicity was less severe than the patulin, suggesting that citrinin is less toxic than patulin. The reproducibility of the expression profiles was much better with the Oligo DNA microarray. However, the Oligo DNA microarray did not completely overcome cross

Design of a 2 x 2 scintillating tile package for the SDC barrel electromagnetic tile/fiber calorimeter

International Nuclear Information System (INIS)

Hara, K.; Maekoba, H.; Minato, H.; Miyamoto, Y.; Nakano, I.; Okabe, M.; Seiya, Y.; Takano, T.; Takikawa, K.; Yasuoka, K.

1996-01-01

We describe R and D results on optical properties of a scintillating tile/fiber system for the SDC barrel electromagnetic calorimeter. The tile/fiber system uses a wavelength shifting fiber to read out the signal of a scintillating plate (tile) and a clear fiber to transmit the signal to a phototube. In the SDC calorimeter design, four of tile/fiber systems are grouped as a 2 x 2 tile package so that the gap width between and the location of the tiles in the absorber slot can be controlled. Optical properties of the tile package such as the light yield, its uniformity, and cross talk were measured in a test bench with a β-ray source and in a 2-GeV/c π + test beam. The performance as an electromagnetic calorimeter was evaluated by a GEANT simulation using the measured response map. We discuss a method of correction for the calorimeter non-uniformity. (orig.)

Evaluation of a gene information summarization system by users during the analysis process of microarray datasets

Directory of Open Access Journals (Sweden)

Cohen Aaron

2009-02-01

Full Text Available Abstract Background Summarization of gene information in the literature has the potential to help genomics researchers translate basic research into clinical benefits. Gene expression microarrays have been used to study biomarkers for disease and discover novel types of therapeutics and the task of finding information in journal articles on sets of genes is common for translational researchers working with microarray data. However, manually searching and scanning the literature references returned from PubMed is a time-consuming task for scientists. We built and evaluated an automatic summarizer of information on genes studied in microarray experiments. The Gene Information Clustering and Summarization System (GICSS is a system that integrates two related steps of the microarray data analysis process: functional gene clustering and gene information gathering. The system evaluation was conducted during the process of genomic researchers analyzing their own experimental microarray datasets. Results The clusters generated by GICSS were validated by scientists during their microarray analysis process. In addition, presenting sentences in the abstract provided significantly more important information to the users than just showing the title in the default PubMed format. Conclusion The evaluation results suggest that GICSS can be useful for researchers in genomic area. In addition, the hybrid evaluation method, partway between intrinsic and extrinsic system evaluation, may enable researchers to gauge the true usefulness of the tool for the scientists in their natural analysis workflow and also elicit suggestions for future enhancements. Availability GICSS can be accessed online at: http://ir.ohsu.edu/jianji/index.html

Composite treatment of ceramic tile armor

Science.gov (United States)

Hansen, James G. R. [Oak Ridge, TN; Frame, Barbara J [Oak Ridge, TN

2010-12-14

An improved ceramic tile armor has a core of boron nitride and a polymer matrix composite (PMC) facing of carbon fibers fused directly to the impact face of the tile. A polyethylene fiber composite backing and spall cover are preferred. The carbon fiber layers are cured directly onto the tile, not adhered using a separate adhesive so that they are integral with the tile, not a separate layer.

Predicting tile drainage discharge

DEFF Research Database (Denmark)

Iversen, Bo Vangsø; Kjærgaard, Charlotte; Petersen, Rasmus Jes

used in the analysis. For the dynamic modelling, a simple linear reservoir model was used where different outlets in the model represented tile drain as well as groundwater discharge outputs. This modelling was based on daily measured tile drain discharge values. The statistical predictive model...... was based on a polynomial regression predicting yearly tile drain discharge values using site specific parameters such as soil type, catchment topography, etc. as predictors. Values of calibrated model parameters from the dynamic modelling were compared to the same site specific parameter as used...

Microstructural characterization of ceramic floor tiles with the incorporation of wastes from ceramic tile industries

Directory of Open Access Journals (Sweden)

Carmeane Effting

2010-09-01

Full Text Available Ceramic floor tiles are widely used in buildings. In places where people are bare feet, the thermal sensation of cold or hot depends on the environmental conditions and material properties including its microstructure and crustiness surface. The introduction of the crustiness surface on the ceramic floor tiles interfere in the contact temperature and also it can be an strategy to obtain ceramic tiles more comfortable. In this work, porous ceramic tiles were obtained by pressing an industrial atomized ceramic powder incorporated with refractory raw material (residue from porcelainized stoneware tile polishing and changing firing temperature. Raw materials and obtained compacted samples were evaluated by chemical analysis, scanning electron microscopy (SEM, energy-dispersive spectrometry (EDS, thermogravimetric analysis (TGA, and differential thermal analysis (DTA. Thermal (thermal conductivity and effusivity and physical (porosity measurements were also evaluated.

Quality control in tile production

Science.gov (United States)

Kalviainen, Heikki A.; Kukkonen, Saku; Hyvarinen, Timo S.; Parkkinen, Jussi P. S.

1998-10-01

This work studies visual quality control in ceramics industry. In tile manufacturing, it is important that in each set of tiles, every single tile looks similar. For example, the tiles should have similar color and texture. Our goal is to design a machine vision system that can estimate the sufficient similarity or same appearance to the human eye. Currently, the estimation is usually done by human vision. Differing from other approaches our aim is to use accurate spectral representation of color, and we are comparing spectral features to the RGB color features. A laboratory system for color measurement is built. Experimentations with five classes of brown tiles are presented. We use chromaticity RGB features and several spectral features for classification with the k-NN classifier and with a neural network, called Self-Organizing Map. We can classify many of the tiles but there are several problems that need further investigations: larger training and test sets are needed, illuminations effects must be studied further, and more suitable spectral features are needed with more sophisticated classifiers. It is also interesting to develop further the neural approach.

Replication dynamics of the yeast genome.

Science.gov (United States)

Raghuraman, M K; Winzeler, E A; Collingwood, D; Hunt, S; Wodicka, L; Conway, A; Lockhart, D J; Davis, R W; Brewer, B J; Fangman, W L

2001-10-05

Oligonucleotide microarrays were used to map the detailed topography of chromosome replication in the budding yeast Saccharomyces cerevisiae. The times of replication of thousands of sites across the genome were determined by hybridizing replicated and unreplicated DNAs, isolated at different times in S phase, to the microarrays. Origin activations take place continuously throughout S phase but with most firings near mid-S phase. Rates of replication fork movement vary greatly from region to region in the genome. The two ends of each of the 16 chromosomes are highly correlated in their times of replication. This microarray approach is readily applicable to other organisms, including humans.

Emerging use of gene expression microarrays in plant physiology.

Science.gov (United States)

Wullschleger, Stan D; Difazio, Stephen P

2003-01-01

Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.

Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships.

Science.gov (United States)

Seok, Junhee; Kaushal, Amit; Davis, Ronald W; Xiao, Wenzhong

2010-01-18

The large amount of high-throughput genomic data has facilitated the discovery of the regulatory relationships between transcription factors and their target genes. While early methods for discovery of transcriptional regulation relationships from microarray data often focused on the high-throughput experimental data alone, more recent approaches have explored the integration of external knowledge bases of gene interactions. In this work, we develop an algorithm that provides improved performance in the prediction of transcriptional regulatory relationships by supplementing the analysis of microarray data with a new method of integrating information from an existing knowledge base. Using a well-known dataset of yeast microarrays and the Yeast Proteome Database, a comprehensive collection of known information of yeast genes, we show that knowledge-based predictions demonstrate better sensitivity and specificity in inferring new transcriptional interactions than predictions from microarray data alone. We also show that comprehensive, direct and high-quality knowledge bases provide better prediction performance. Comparison of our results with ChIP-chip data and growth fitness data suggests that our predicted genome-wide regulatory pairs in yeast are reasonable candidates for follow-up biological verification. High quality, comprehensive, and direct knowledge bases, when combined with appropriate bioinformatic algorithms, can significantly improve the discovery of gene regulatory relationships from high throughput gene expression data.

Improvement of PVC floor tiles by gamma radiation

International Nuclear Information System (INIS)

Plessis, T.A. du; Badenhorst, F.

1988-01-01

Gamma radiation presents a unique method of transforming highly plasticized PVC floor tiles, manufactured at high speed through injection moulding, into a high quality floor covering at a cost at least 30% less than similarly rated rubber tiles. A specially formulated PVC compound was developed in collaboration with a leading manufacturer of floor tiles. These tiles are gamma crosslinked in its shipping cartons to form a dimensionally stable product which is highly fire resistant and inert to most chemicals and solvents. These crosslinked tiles are more flexible than the highly filled conventional PVC floor tiles, scratch resistant and have a longer lifespan and increased colour fastness. These tiles are also less expensive to install than conventional rubber tiles. (author)

Carbohydrate microarrays

DEFF Research Database (Denmark)

Park, Sungjin; Gildersleeve, Jeffrey C; Blixt, Klas Ola

2012-01-01

In the last decade, carbohydrate microarrays have been core technologies for analyzing carbohydrate-mediated recognition events in a high-throughput fashion. A number of methods have been exploited for immobilizing glycans on the solid surface in a microarray format. This microarray...... of substrate specificities of glycosyltransferases. This review covers the construction of carbohydrate microarrays, detection methods of carbohydrate microarrays and their applications in biological and biomedical research....

Investigating critical success factors in tile industry

Directory of Open Access Journals (Sweden)

Davood Salmani

2014-04-01

Full Text Available This paper presents an empirical investigation to determine critical success factors influencing the success of tile industry in Iran. The study designs a questionnaire in Likert scale, distributes it among some experts in tile industry. Using Pearson correlation test, the study has detected that there was a positive and meaningful relationship between marketing planning and the success of tile industry (r = 0.312 Sig. = 0.001. However, there is not any meaningful relationship between low cost production and success of tile industry (r = 0.13 Sig. = 0.12 and, there is a positive and meaningful relationship between organizational capabilities and success of tile industry (r = 0.635 Sig. = 0.000. Finally, our investigation states that technology and distributing systems also influence on the success of tile industry, positively. The study has also used five regression analyses where the success of tile industry was the dependent variable and marketing planning, low cost production and organizational capabilities are independent variables and the results have confirmed some positive and meaningful relationship between the successes of tile industry with all independent variables.

Physical principles for DNA tile self-assembly.

Science.gov (United States)

Evans, Constantine G; Winfree, Erik

2017-06-19

DNA tiles provide a promising technique for assembling structures with nanoscale resolution through self-assembly by basic interactions rather than top-down assembly of individual structures. Tile systems can be programmed to grow based on logical rules, allowing for a small number of tile types to assemble large, complex assemblies that can retain nanoscale resolution. Such algorithmic systems can even assemble different structures using the same tiles, based on inputs that seed the growth. While programming and theoretical analysis of tile self-assembly often makes use of abstract logical models of growth, experimentally implemented systems are governed by nanoscale physical processes that can lead to very different behavior, more accurately modeled by taking into account the thermodynamics and kinetics of tile attachment and detachment in solution. This review discusses the relationships between more abstract and more physically realistic tile assembly models. A central concern is how consideration of model differences enables the design of tile systems that robustly exhibit the desired abstract behavior in realistic physical models and in experimental implementations. Conversely, we identify situations where self-assembly in abstract models can not be well-approximated by physically realistic models, putting constraints on physical relevance of the abstract models. To facilitate the discussion, we introduce a unified model of tile self-assembly that clarifies the relationships between several well-studied models in the literature. Throughout, we highlight open questions regarding the physical principles for DNA tile self-assembly.

Microarray-based comparative genomic profiling of reference strains and selected Canadian field isolates of Actinobacillus pleuropneumoniae

Directory of Open Access Journals (Sweden)

MacInnes Janet I

2009-02-01

Full Text Available Abstract Background Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, is a highly contagious respiratory pathogen that causes severe losses to the swine industry worldwide. Current commercially-available vaccines are of limited value because they do not induce cross-serovar immunity and do not prevent development of the carrier state. Microarray-based comparative genomic hybridizations (M-CGH were used to estimate whole genomic diversity of representative Actinobacillus pleuropneumoniae strains. Our goal was to identify conserved genes, especially those predicted to encode outer membrane proteins and lipoproteins because of their potential for the development of more effective vaccines. Results Using hierarchical clustering, our M-CGH results showed that the majority of the genes in the genome of the serovar 5 A. pleuropneumoniae L20 strain were conserved in the reference strains of all 15 serovars and in representative field isolates. Fifty-eight conserved genes predicted to encode for outer membrane proteins or lipoproteins were identified. As well, there were several clusters of diverged or absent genes including those associated with capsule biosynthesis, toxin production as well as genes typically associated with mobile elements. Conclusion Although A. pleuropneumoniae strains are essentially clonal, M-CGH analysis of the reference strains of the fifteen serovars and representative field isolates revealed several classes of genes that were divergent or absent. Not surprisingly, these included genes associated with capsule biosynthesis as the capsule is associated with sero-specificity. Several of the conserved genes were identified as candidates for vaccine development, and we conclude that M-CGH is a valuable tool for reverse vaccinology.

Shedding genomic light on Aristotle's lantern.

Science.gov (United States)

Sodergren, Erica; Shen, Yufeng; Song, Xingzhi; Zhang, Lan; Gibbs, Richard A; Weinstock, George M

2006-12-01

Sea urchins have proved fascinating to biologists since the time of Aristotle who compared the appearance of their bony mouth structure to a lantern in The History of Animals. Throughout modern times it has been a model system for research in developmental biology. Now, the genome of the sea urchin Strongylocentrotus purpuratus is the first echinoderm genome to be sequenced. A high quality draft sequence assembly was produced using the Atlas assembler to combine whole genome shotgun sequences with sequences from a collection of BACs selected to form a minimal tiling path along the genome. A formidable challenge was presented by the high degree of heterozygosity between the two haplotypes of the selected male representative of this marine organism. This was overcome by use of the BAC tiling path backbone, in which each BAC represents a single haplotype, as well as by improvements in the Atlas software. Another innovation introduced in this project was the sequencing of pools of tiling path BACs rather than individual BAC sequencing. The Clone-Array Pooled Shotgun Strategy greatly reduced the cost and time devoted to preparing shotgun libraries from BAC clones. The genome sequence was analyzed with several gene prediction methods to produce a comprehensive gene list that was then manually refined and annotated by a volunteer team of sea urchin experts. This latter annotation community edited over 9000 gene models and uncovered many unexpected aspects of the sea urchin genetic content impacting transcriptional regulation, immunology, sensory perception, and an organism's development. Analysis of the basic deuterostome genetic complement supports the sea urchin's role as a model system for deuterostome and, by extension, chordate development.

Visualization for genomics: the Microbial Genome Viewer.

Science.gov (United States)

Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

2004-07-22

A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

Transcriptome analysis of exosome-compromised human cells using high-density tiling arrays

DEFF Research Database (Denmark)

Jensen, Torben Heick

The extent of RNA degradation in the nucleus has traditionally been underestimated. However, all major RNA species are synthesized, processed and can be degraded in this compartment and consequently an enormous amount of nucleosides are turned over and recycled. The RNA exosome, a multisubunit co......) tiling array that covers discrete regions from different chromosomes to represent a range of gene content and exonic/nonexonic conservation grades of the human genome....

ATLAS Rewards Russian Supplier for Scintillating Tile Production

CERN Multimedia

2001-01-01

At a ceremony held at CERN on 30 July, the ATLAS collaboration awarded Russian firm SIA Luch from Podolsk in the Moscow region an ATLAS Suppliers Award. This follows delivery by the company of the final batch of scintillating tiles for the collaboration's Tile Calorimeter some six months ahead of schedule.   Representatives of Russian firm Luch Podolsk received the ATLAS Suppliers Award in the collaboration's Tile Calorimeter instrumentation plant at CERN on 30 July. In front of one Tile Calorimeter module instrumented by scintillating tiles are (left to right) IHEP physicists Evgueni Startchenko and Andrei Karioukhine, Luch Podolsk representatives Igor Karetnikov and Yuri Zaitsev, Tile Calorimeter Project Leader Rupert Leitner, ATLAS spokesperson Peter Jenni, and CERN Tile Calorimeter group leader Ana Henriques-Correia. Scintillating tiles form the active part of the ATLAS hadronic Tile Calorimeter, which will measure the energy and direction of particles produced in LHC collisions. They are emb...

Emerging Use of Gene Expression Microarrays in Plant Physiology

Directory of Open Access Journals (Sweden)

Stephen P. Difazio

2006-04-01

Full Text Available Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology were selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.

Computational genomics of hyperthermophiles

NARCIS (Netherlands)

Werken, van de H.J.G.

2008-01-01

With the ever increasing number of completely sequenced prokaryotic genomes and the subsequent use of functional genomics tools, e.g. DNA microarray and proteomics, computational data analysis and the integration of microbial and molecular data is inevitable. This thesis describes the computational

ATLAS rewards Russian supplier for scintillating tile production

CERN Multimedia

Patrice Loïez

2001-01-01

The ATLAS collaboration has awarded Russian firm SIA Luch from Podolsk in the Moscow region an ATLAS Supplier Award. This follows delivery by the company of the final batch of scintillating tiles for the collaboration's tile calorimeter some six months ahead of schedule. Representatives of the firm are seen here receiving the award at a ceremony held in the collaboration's tile calorimeter instrumentation plant at CERN on 30 July. In front of one tile calorimeter module instrumented by scintillating tiles are (left to right) IHEP physicists Evgueni Startchenko and Andrei Karioukhine, Luch Podolsk representatives Igor Karetnikov and Yuri Zaitsev, tile calorimeter project leader Rupert Leitner, ATLAS spokesperson Peter Jenni, and CERN tile calorimeter group leader Ana Henriques-Correia.

Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms

Directory of Open Access Journals (Sweden)

Trent Harold F

2005-03-01

Full Text Available Abstract Background The Marine Genomics project is a functional genomics initiative developed to provide a pipeline for the curation of Expressed Sequence Tags (ESTs and gene expression microarray data for marine organisms. It provides a unique clearing-house for marine specific EST and microarray data and is currently available at http://www.marinegenomics.org. Description The Marine Genomics pipeline automates the processing, maintenance, storage and analysis of EST and microarray data for an increasing number of marine species. It currently contains 19 species databases (over 46,000 EST sequences that are maintained by registered users from local and remote locations in Europe and South America in addition to the USA. A collection of analysis tools are implemented. These include a pipeline upload tool for EST FASTA file, sequence trace file and microarray data, an annotative text search, automated sequence trimming, sequence quality control (QA/QC editing, sequence BLAST capabilities and a tool for interactive submission to GenBank. Another feature of this resource is the integration with a scientific computing analysis environment implemented by MATLAB. Conclusion The conglomeration of multiple marine organisms with integrated analysis tools enables users to focus on the comprehensive descriptions of transcriptomic responses to typical marine stresses. This cross species data comparison and integration enables users to contain their research within a marine-oriented data management and analysis environment.

Comparison of performance of tile drainage routines in SWAT 2009 and 2012 in an extensively tile-drained watershed in the Midwest

Science.gov (United States)

Guo, Tian; Gitau, Margaret; Merwade, Venkatesh; Arnold, Jeffrey; Srinivasan, Raghavan; Hirschi, Michael; Engel, Bernard

2018-01-01

Subsurface tile drainage systems are widely used in agricultural watersheds in the Midwestern US and enable the Midwest area to become highly productive agricultural lands, but can also create environmental problems, for example nitrate-N contamination associated with drainage waters. The Soil and Water Assessment Tool (SWAT) has been used to model watersheds with tile drainage. SWAT2012 revisions 615 and 645 provide new tile drainage routines. However, few studies have used these revisions to study tile drainage impacts at both field and watershed scales. Moreover, SWAT2012 revision 645 improved the soil moisture based curve number calculation method, which has not been fully tested. This study used long-term (1991-2003) field site and river station data from the Little Vermilion River (LVR) watershed to evaluate performance of tile drainage routines in SWAT2009 revision 528 (the old routine) and SWAT2012 revisions 615 and 645 (the new routine). Both the old and new routines provided reasonable but unsatisfactory (NSE runoff. The calibrated monthly tile flow, surface flow, nitrate-N in tile and surface flow, sediment and annual corn and soybean yield results from SWAT with the old and new tile drainage routines were compared with observed values. Generally, the new routine provided acceptable simulated tile flow (NSE = 0.48-0.65) and nitrate in tile flow (NSE = 0.48-0.68) for field sites with random pattern tile and constant tile spacing, while the old routine simulated tile flow and nitrate in tile flow results for the field site with constant tile spacing were unacceptable (NSE = 0.00-0.32 and -0.29-0.06, respectively). The new modified curve number calculation method in revision 645 (NSE = 0.50-0.81) better simulated surface runoff than revision 615 (NSE = -0.11-0.49). The calibration provided reasonable parameter sets for the old and new routines in the LVR watershed, and the validation results showed that the new routine has the potential to accurately

Electrokinetic desalination of glazed ceramic tiles

DEFF Research Database (Denmark)

Ottosen, Lisbeth M.; Ferreira, Celia; Christensen, Iben Vernegren

2010-01-01

Electrokinetic desalination is a method where an applied electric DC field is the driving force for removal of salts from porous building materials. In the present paper, the method is tested in laboratory scale for desalination of single ceramic tiles. In a model system, where a tile...... was contaminated with NaCl during submersion and subsequently desalinated by the method, the desalination was completed in that the high and problematic initial Cl(-) concentration was reduced to an unproblematic concentration. Further conductivity measurements showed a very low conductivity in the tile after...... treatment, indicating that supply of ions from the poultice at the electrodes into the tile was limited. Electroosmotic transport of water was seen when low ionic content was reached. Experiments were also conducted with XVIII-century tiles, which had been removed from Palacio Centeno (Lisbon) during...

Construction of a cDNA microarray derived from the ascidian Ciona intestinalis.

Science.gov (United States)

Azumi, Kaoru; Takahashi, Hiroki; Miki, Yasufumi; Fujie, Manabu; Usami, Takeshi; Ishikawa, Hisayoshi; Kitayama, Atsusi; Satou, Yutaka; Ueno, Naoto; Satoh, Nori

2003-10-01

A cDNA microarray was constructed from a basal chordate, the ascidian Ciona intestinalis. The draft genome of Ciona has been read and inferred to contain approximately 16,000 protein-coding genes, and cDNAs for transcripts of 13,464 genes have been characterized and compiled as the "Ciona intestinalis Gene Collection Release I". In the present study, we constructed a cDNA microarray of these 13,464 Ciona genes. A preliminary experiment with Cy3- and Cy5-labeled probes showed extensive differential gene expression between fertilized eggs and larvae. In addition, there was a good correlation between results obtained by the present microarray analysis and those from previous EST analyses. This first microarray of a large collection of Ciona intestinalis cDNA clones should facilitate the analysis of global gene expression and gene networks during the embryogenesis of basal chordates.

Evaluation of tile layer productivity in construction project

Science.gov (United States)

Aziz, Hamidi Abdul; Hassan, Siti Hafizan; Rosly, Noorsyalili; Ul-Saufie, Ahmad Zia

2017-10-01

Construction is a key sector of the national economy for countries all over the world. Until today, construction industries are still facing lots of problems concerning the low productivity, poor safety and insufficient quality. Labour productivity is one of the factors that will give impact to the quality of projects. This study is focusing on evaluating the tile layer productivity in the area of Seberang Perai, Penang. The objective of this study is to determine the relationship of age and experience of tile layers with their productivity and to evaluate the effect of nationality to tile layers productivity. Interview and site observation of tile layers has been conducted to obtain the data of age, experience and nationality of tile layers. Site observation is made to obtain the number of tiles installed for every tile layer for the duration of 1 hour, and the data were analysed by using Statistical Package for Social Science (IBM SPSS Statistic 23) software. As a result, there is a moderate linear relationship between age and experience of tile layers with their productivity. The age of 30 and the experience of 4 years give the highest productivity. It also can be concluded that the tile layers from Indonesia tend to have higher productivity compared to tile layers from Myanmar.

Mining meiosis and gametogenesis with DNA microarrays.

Science.gov (United States)

Schlecht, Ulrich; Primig, Michael

2003-04-01

Gametogenesis is a key developmental process that involves complex transcriptional regulation of numerous genes including many that are conserved between unicellular eukaryotes and mammals. Recent expression-profiling experiments using microarrays have provided insight into the co-ordinated transcription of several hundred genes during mitotic growth and meiotic development in budding and fission yeast. Furthermore, microarray-based studies have identified numerous loci that are regulated during the cell cycle or expressed in a germ-cell specific manner in eukaryotic model systems like Caenorhabditis elegans, Mus musculus as well as Homo sapiens. The unprecedented amount of information produced by post-genome biology has spawned novel approaches to organizing biological knowledge using currently available information technology. This review outlines experiments that contribute to an emerging comprehensive picture of the molecular machinery governing sexual reproduction in eukaryotes.

Porcelain tiles by the dry route

International Nuclear Information System (INIS)

Melchiades, F. G.; Daros, M. T.; Boschi, A. O.

2010-01-01

In Brazil, the second largest tile producer of the world, at present, 70% of the tiles are produced by the dry route. One of the main reasons that lead to this development is the fact that the dry route uses approximately 30% less thermal energy them the traditional wet route. The increasing world concern with the environment and the recognition of the central role played by the water also has pointed towards privileging dry processes. In this context the objective of the present work is to study the feasibility of producing high quality porcelain tiles by the dry route. A brief comparison of the dry and wet route, in standard conditions industrially used today to produce tiles that are not porcelain tiles, shows that there are two major differences: the particle sizes obtained by the wet route are usually considerably finer and the capability of mixing the different minerals, the intimacy of the mixture, is also usually better in the wet route. The present work studied the relative importance of these differences and looked for raw materials and operational conditions that would result in better performance and glazed porcelain tiles of good quality. (Author) 7 refs.

Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L. gene expression oligonucleotide microarray.

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Paula Fernandez

Full Text Available Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de. The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons. The resulting Sunflower Unigen Resource (SUR version 1.0 was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01 allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

Fibrous-Ceramic/Aerogel Composite Insulating Tiles

Science.gov (United States)

White, Susan M.; Rasky, Daniel J.

2004-01-01

Fibrous-ceramic/aerogel composite tiles have been invented to afford combinations of thermal-insulation and mechanical properties superior to those attainable by making tiles of fibrous ceramics alone or aerogels alone. These lightweight tiles can be tailored to a variety of applications that range from insulating cryogenic tanks to protecting spacecraft against re-entry heating. The advantages and disadvantages of fibrous ceramics and aerogels can be summarized as follows: Tiles made of ceramic fibers are known for mechanical strength, toughness, and machinability. Fibrous ceramic tiles are highly effective as thermal insulators in a vacuum. However, undesirably, the porosity of these materials makes them permeable by gases, so that in the presence of air or other gases, convection and gas-phase conduction contribute to the effective thermal conductivity of the tiles. Other disadvantages of the porosity and permeability of fibrous ceramic tiles arise because gases (e.g., water vapor or cryogenic gases) can condense in pores. This condensation contributes to weight, and in the case of cryogenic systems, the heat of condensation undesirably adds to the heat flowing to the objects that one seeks to keep cold. Moreover, there is a risk of explosion associated with vaporization of previously condensed gas upon reheating. Aerogels offer low permeability, low density, and low thermal conductivity, but are mechanically fragile. The basic idea of the present invention is to exploit the best features of fibrous ceramic tiles and aerogels. In a composite tile according to the invention, the fibrous ceramic serves as a matrix that mechanically supports the aerogel, while the aerogel serves as a low-conductivity, low-permeability filling that closes what would otherwise be the open pores of the fibrous ceramic. Because the aerogel eliminates or at least suppresses permeation by gas, gas-phase conduction, and convection, the thermal conductivity of such a composite even at

A novel multifunctional oligonucleotide microarray for Toxoplasma gondii

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Chen Feng

2010-10-01

Full Text Available Abstract Background Microarrays are invaluable tools for genome interrogation, SNP detection, and expression analysis, among other applications. Such broad capabilities would be of value to many pathogen research communities, although the development and use of genome-scale microarrays is often a costly undertaking. Therefore, effective methods for reducing unnecessary probes while maintaining or expanding functionality would be relevant to many investigators. Results Taking advantage of available genome sequences and annotation for Toxoplasma gondii (a pathogenic parasite responsible for illness in immunocompromised individuals and Plasmodium falciparum (a related parasite responsible for severe human malaria, we designed a single oligonucleotide microarray capable of supporting a wide range of applications at relatively low cost, including genome-wide expression profiling for Toxoplasma, and single-nucleotide polymorphism (SNP-based genotyping of both T. gondii and P. falciparum. Expression profiling of the three clonotypic lineages dominating T. gondii populations in North America and Europe provides a first comprehensive view of the parasite transcriptome, revealing that ~49% of all annotated genes are expressed in parasite tachyzoites (the acutely lytic stage responsible for pathogenesis and 26% of genes are differentially expressed among strains. A novel design utilizing few probes provided high confidence genotyping, used here to resolve recombination points in the clonal progeny of sexual crosses. Recent sequencing of additional T. gondii isolates identifies >620 K new SNPs, including ~11 K that intersect with expression profiling probes, yielding additional markers for genotyping studies, and further validating the utility of a combined expression profiling/genotyping array design. Additional applications facilitating SNP and transcript discovery, alternative statistical methods for quantifying gene expression, etc. are also pursued at

The ATLAS Tile Calorimeter

CERN Document Server

Henriques Correia, Ana Maria

2015-01-01

TileCal is the Hadronic calorimeter covering the most central region of the ATLAS experiment at the LHC. It uses iron plates as absorber and plastic scintillating tiles as the active material. Scintillation light produced in the tiles is transmitted by wavelength shifting fibres to photomultiplier tubes (PMTs). The resulting electronic signals from the approximately 10000 PMTs are measured and digitised every 25 ns before being transferred to off-detector data-acquisition systems. This contribution will review in a first part the performances of the calorimeter during run 1, obtained from calibration data, and from studies of the response of particles from collisions. In a second part it will present the solutions being investigated for the ongoing and future upgrades of the calorimeter electronics.

The ATLAS Tile Calorimeter

International Nuclear Information System (INIS)

Henriques, A.

2015-01-01

TileCal is the Hadronic calorimeter covering the most central region of the ATLAS experiment at the LHC. It uses iron plates as absorber and plastic scintillating tiles as the active material. Scintillation light produced in the tiles is transmitted by wavelength shifting fibres to photomultiplier tubes (PMTs). The resulting electronic signals from the approximately 10000 PMTs are measured and digitised every 25 ns before being transferred to off-detector data-acquisition systems. This contribution will review in a first part the performances of the calorimeter during run 1, obtained from calibration data, and from studies of the response of particles from collisions. In a second part it will present the solutions being investigated for the ongoing and future upgrades of the calorimeter electronics. (authors)

Advanced Data Mining of Leukemia Cells Micro-Arrays

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Richard S. Segall

2009-12-01

Full Text Available This paper provides continuation and extensions of previous research by Segall and Pierce (2009a that discussed data mining for micro-array databases of Leukemia cells for primarily self-organized maps (SOM. As Segall and Pierce (2009a and Segall and Pierce (2009b the results of applying data mining are shown and discussed for the data categories of microarray databases of HL60, Jurkat, NB4 and U937 Leukemia cells that are also described in this article. First, a background section is provided on the work of others pertaining to the applications of data mining to micro-array databases of Leukemia cells and micro-array databases in general. As noted in predecessor article by Segall and Pierce (2009a, micro-array databases are one of the most popular functional genomics tools in use today. This research in this paper is intended to use advanced data mining technologies for better interpretations and knowledge discovery as generated by the patterns of gene expressions of HL60, Jurkat, NB4 and U937 Leukemia cells. The advanced data mining performed entailed using other data mining tools such as cubic clustering criterion, variable importance rankings, decision trees, and more detailed examinations of data mining statistics and study of other self-organized maps (SOM clustering regions of workspace as generated by SAS Enterprise Miner version 4. Conclusions and future directions of the research are also presented.

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

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Hedegaard Jakob

2009-07-01

Full Text Available Abstract Background The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria. Results Several conceptually different analytical approaches, using both commercial and public available software, were applied by the participating groups. The following tools were used: Ingenuity Pathway Analysis, MAPPFinder, LIMMA, GOstats, GOEAST, GOTM, Globaltest, TopGO, ArrayUnlock, Pathway Studio, GIST and AnnotationDbi. The main focus of the approaches was to utilise the relation between probes/genes and their gene ontology and pathways to interpret the affected probes/genes. The lack of a well-annotated chicken genome did though limit the possibilities to fully explore the tools. The main results from these analyses showed that the biological interpretation is highly dependent on the statistical method used but that some common biological conclusions could be reached. Conclusion It is highly recommended to test different analytical methods on the same data set and compare the results to obtain a reliable biological interpretation of the affected genes in a DNA microarray experiment.

Performance of the ATLAS Tile calorimeter

CERN Document Server

Bertoli, Gabriele; The ATLAS collaboration

2015-01-01

The Tile Calorimeter (TileCal) of the ATLAS experiment at the LHC is the central hadronic calorimeter designed for energy reconstruction of hadrons, jets, tau­particles and missing transverse energy. TileCal is a scintillator­steel sampling calorimeter and it covers the region of pseudorapidity < 1.7. The scintillation light produced in the tiles is transmitted by wavelength shifting fibers to photomultiplier tubes (PMTs). The analog signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The TileCal front­end electronics read out the signals produced by about 10000 channels measuring energies ranging from ~30 MeV to ~2 TeV. The read­out system is responsible for reconstructing the data in real­time. The digitized signals are reconstructed with the Optimal Filtering algorithm, which computes for each channel the signal amplitude, time and quality factor at the required high rate. Each stage of the signal production from scintillation light to the signal reconstruc...

Tiling arbitrarily nested loops by means of the transitive

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Bielecki Włodzimierz

2016-12-01

Full Text Available A novel approach to generation of tiled code for arbitrarily nested loops is presented. It is derived via a combination of the polyhedral and iteration space slicing frameworks. Instead of program transformations represented by a set of affine functions, one for each statement, it uses the transitive closure of a loop nest dependence graph to carry out corrections of original rectangular tiles so that all dependences of the original loop nest are preserved under the lexicographic order of target tiles. Parallel tiled code can be generated on the basis of valid serial tiled code by means of applying affine transformations or transitive closure using on input an inter-tile dependence graph whose vertices are represented by target tiles while edges connect dependent target tiles. We demonstrate how a relation describing such a graph can be formed. The main merit of the presented approach in comparison with the well-known ones is that it does not require full permutability of loops to generate both serial and parallel tiled codes; this increases the scope of loop nests to be tiled.

Advanced spot quality analysis in two-colour microarray experiments

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Vetter Guillaume

2008-09-01

Full Text Available Abstract Background Image analysis of microarrays and, in particular, spot quantification and spot quality control, is one of the most important steps in statistical analysis of microarray data. Recent methods of spot quality control are still in early age of development, often leading to underestimation of true positive microarray features and, consequently, to loss of important biological information. Therefore, improving and standardizing the statistical approaches of spot quality control are essential to facilitate the overall analysis of microarray data and subsequent extraction of biological information. Findings We evaluated the performance of two image analysis packages MAIA and GenePix (GP using two complementary experimental approaches with a focus on the statistical analysis of spot quality factors. First, we developed control microarrays with a priori known fluorescence ratios to verify the accuracy and precision of the ratio estimation of signal intensities. Next, we developed advanced semi-automatic protocols of spot quality evaluation in MAIA and GP and compared their performance with available facilities of spot quantitative filtering in GP. We evaluated these algorithms for standardised spot quality analysis in a whole-genome microarray experiment assessing well-characterised transcriptional modifications induced by the transcription regulator SNAI1. Using a set of RT-PCR or qRT-PCR validated microarray data, we found that the semi-automatic protocol of spot quality control we developed with MAIA allowed recovering approximately 13% more spots and 38% more differentially expressed genes (at FDR = 5% than GP with default spot filtering conditions. Conclusion Careful control of spot quality characteristics with advanced spot quality evaluation can significantly increase the amount of confident and accurate data resulting in more meaningful biological conclusions.

Performance of the ATLAS hadronic Tile calorimeter

CERN Document Server

Bartos, Pavol; The ATLAS collaboration

2016-01-01

Performance of the ATLAS hadronic Tile calorimeter The Tile Calorimeter (TileCal) of the ATLAS experiment at the LHC is the central hadronic calorimeter designed for energy reconstruction of hadrons, jets, tau-particles and missing transverse energy. TileCal is a scintillator-steel sampling calorimeter and it covers the region of pseudorapidity < 1.7. The scintillation light produced in the scintillator tiles is transmitted by wavelength shifting fibers to photomultiplier tubes (PMTs). The analog signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The TileCal frontend electronics reads out the signals produced by about 10000 channels measuring energies ranging from ~30 MeV to ~2 TeV. Each stage of the signal production from scintillation light to the signal reconstruction is monitored and calibrated. The performance of the calorimeter have been studied in-situ employing cosmic ray muons and a large sample of proton-proton collisions acquired during the operations o...

Development of a fluorescence-activated cell sorting method coupled with whole genome amplification to analyze minority and trace Dehalococcoides genomes in microbial communities.

Science.gov (United States)

Lee, Patrick K H; Men, Yujie; Wang, Shanquan; He, Jianzhong; Alvarez-Cohen, Lisa

2015-02-03

Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. mccartyi microarray for comparative genomics against four sequenced strains. First, FACS was successfully applied to a D. mccartyi isolate as positive control, and then microarray results verified that WGA from 10(6) cells or ∼1 ng of genomic DNA yielded high-quality coverage detecting nearly all genes across the genome. As expected, some inter- and intrasample variability in WGA was observed, but these biases were minimized by performing multiple parallel amplifications. Subsequent application of the FACS and WGA protocols to two enrichment cultures containing ∼10% and ∼1% D. mccartyi cells successfully enabled genomic analysis. As proof of concept, this study demonstrates that coupling FACS with WGA and microarrays is a promising tool to expedite genomic characterization of target strains in environmental communities where the relative concentrations are low.

Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources

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van Hijum Sacha AFT

2008-10-01

Full Text Available Abstract Background Despite a plethora of functional genomic efforts, the function of many genes in sequenced genomes remains unknown. The increasing amount of microarray data for many species allows employing the guilt-by-association principle to predict function on a large scale: genes exhibiting similar expression patterns are more likely to participate in shared biological processes. Results We developed Prosecutor, an application that enables researchers to rapidly infer gene function based on available gene expression data and functional annotations. Our parameter-free functional prediction method uses a sensitive algorithm to achieve a high association rate of linking genes with unknown function to annotated genes. Furthermore, Prosecutor utilizes additional biological information such as genomic context and known regulatory mechanisms that are specific for prokaryotes. We analyzed publicly available transcriptome data sets and used literature sources to validate putative functions suggested by Prosecutor. We supply the complete results of our analysis for 11 prokaryotic organisms on a dedicated website. Conclusion The Prosecutor software and supplementary datasets available at http://www.prosecutor.nl allow researchers working on any of the analyzed organisms to quickly identify the putative functions of their genes of interest. A de novo analysis allows new organisms to be studied.

A Fisheye Viewer for microarray-based gene expression data.

Science.gov (United States)

Wu, Min; Thao, Cheng; Mu, Xiangming; Munson, Ethan V

2006-10-13

Microarray has been widely used to measure the relative amounts of every mRNA transcript from the genome in a single scan. Biologists have been accustomed to reading their experimental data directly from tables. However, microarray data are quite large and are stored in a series of files in a machine-readable format, so direct reading of the full data set is not feasible. The challenge is to design a user interface that allows biologists to usefully view large tables of raw microarray-based gene expression data. This paper presents one such interface--an electronic table (E-table) that uses fisheye distortion technology. The Fisheye Viewer for microarray-based gene expression data has been successfully developed to view MIAME data stored in the MAGE-ML format. The viewer can be downloaded from the project web site http://polaris.imt.uwm.edu:7777/fisheye/. The fisheye viewer was implemented in Java so that it could run on multiple platforms. We implemented the E-table by adapting JTable, a default table implementation in the Java Swing user interface library. Fisheye views use variable magnification to balance magnification for easy viewing and compression for maximizing the amount of data on the screen. This Fisheye Viewer is a lightweight but useful tool for biologists to quickly overview the raw microarray-based gene expression data in an E-table.

TileDCS web system

International Nuclear Information System (INIS)

Maidantchik, C; Ferreira, F; Grael, F

2010-01-01

The web system described here provides features to monitor the ATLAS Detector Control System (DCS) acquired data. The DCS is responsible for overseeing the coherent and safe operation of the ATLAS experiment hardware. In the context of the Hadronic Tile Calorimeter Detector (TileCal), it controls the power supplies of the readout electronics acquiring voltages, currents, temperatures and coolant pressure measurements. The physics data taking requires the stable operation of the power sources. The TileDCS Web System retrieves automatically data and extracts the statistics for given periods of time. The mean and standard deviation outcomes are stored as XML files and are compared to preset thresholds. Further, a graphical representation of the TileCal cylinders indicates the state of the supply system of each detector drawer. Colors are designated for each kind of state. In this way problems are easier to find and the collaboration members can focus on them. The user selects a module and the system presents detailed information. It is possible to verify the statistics and generate charts of the parameters over the time. The TileDCS Web System also presents information about the power supplies latest status. One wedge is colored green whenever the system is on. Otherwise it is colored red. Furthermore, it is possible to perform customized analysis. It provides search interfaces where the user can set the module, parameters, and the time period of interest. The system also produces the output of the retrieved data as charts, XML files, CSV and ROOT files according to the user's choice.

ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.

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Gary Hon

2008-10-01

Full Text Available Computational methods to identify functional genomic elements using genetic information have been very successful in determining gene structure and in identifying a handful of cis-regulatory elements. But the vast majority of regulatory elements have yet to be discovered, and it has become increasingly apparent that their discovery will not come from using genetic information alone. Recently, high-throughput technologies have enabled the creation of information-rich epigenetic maps, most notably for histone modifications. However, tools that search for functional elements using this epigenetic information have been lacking. Here, we describe an unsupervised learning method called ChromaSig to find, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data. Applying this algorithm to nine chromatin marks across a 1% sampling of the human genome in HeLa cells, we recover eight clusters of distinct chromatin signatures, five of which correspond to known patterns associated with transcriptional promoters and enhancers. Interestingly, we observe that the distinct chromatin signatures found at enhancers mark distinct functional classes of enhancers in terms of transcription factor and coactivator binding. In addition, we identify three clusters of novel chromatin signatures that contain evolutionarily conserved sequences and potential cis-regulatory elements. Applying ChromaSig to a panel of 21 chromatin marks mapped genomewide by ChIP-Seq reveals 16 classes of genomic elements marked by distinct chromatin signatures. Interestingly, four classes containing enrichment for repressive histone modifications appear to be locally heterochromatic sites and are enriched in quickly evolving regions of the genome. The utility of this approach in uncovering novel, functionally significant genomic elements will aid future efforts of genome annotation via chromatin modifications.

Screening for viral extraneous agents in live-attenuated avian vaccines by using a microbial microarray and sequencing

DEFF Research Database (Denmark)

Olesen, Majken Lindholm; Jørgensen, Lotte Leick; Blixenkrone-Møller, Merete

2018-01-01

The absence of extraneous agents (EA) in the raw material used for production and in finished products is one of the principal safety elements related to all medicinal products of biological origin, such as live-attenuated vaccines. The aim of this study was to investigate the applicability...... of the Lawrence Livermore Microbial detection array version 2 (LLMDAv2) combined with whole genome amplification and sequencing for screening for viral EAs in live-attenuated vaccines and specific pathogen-free (SPF) eggs.We detected positive microarray signals for avian endogenous retrovirus EAV-HP and several...... viruses belonging to the Alpharetrovirus genus in all analyzed vaccines and SPF eggs. We used a microarray probe mapping approach to evaluate the presence of intact retroviral genomes, which in addition to PCR analysis revealed that several of the positive microarray signals were most likely due to cross...

Development of a novel multiplex DNA microarray for Fusarium graminearum and analysis of azole fungicide responses

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Deising Holger B

2011-01-01

Full Text Available Abstract Background The toxigenic fungal plant pathogen Fusarium graminearum compromises wheat production worldwide. Azole fungicides play a prominent role in controlling this pathogen. Sequencing of its genome stimulated the development of high-throughput technologies to study mechanisms of coping with fungicide stress and adaptation to fungicides at a previously unprecedented precision. DNA-microarrays have been used to analyze genome-wide gene expression patterns and uncovered complex transcriptional responses. A recently developed one-color multiplex array format allowed flexible, effective, and parallel examinations of eight RNA samples. Results We took advantage of the 8 × 15 k Agilent format to design, evaluate, and apply a novel microarray covering the whole F. graminearum genome to analyze transcriptional responses to azole fungicide treatment. Comparative statistical analysis of expression profiles uncovered 1058 genes that were significantly differentially expressed after azole-treatment. Quantitative RT-PCR analysis for 31 selected genes indicated high conformity to results from the microarray hybridization. Among the 596 genes with significantly increased transcript levels, analyses using GeneOntology and FunCat annotations detected the ergosterol-biosynthesis pathway genes as the category most significantly responding, confirming the mode-of-action of azole fungicides. Cyp51A, which is one of the three F. graminearum paralogs of Cyp51 encoding the target of azoles, was the most consistently differentially expressed gene of the entire study. A molecular phylogeny analyzing the relationships of the three CYP51 proteins in the context of 38 fungal genomes belonging to the Pezizomycotina indicated that CYP51C (FGSG_11024 groups with a new clade of CYP51 proteins. The transcriptional profiles for genes encoding ABC transporters and transcription factors suggested several involved in mechanisms alleviating the impact of the fungicide

Comparison of performance of tile drainage routines in SWAT 2009 and 2012 in an extensively tile-drained watershed in the Midwest

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T. Guo

2018-01-01

Full Text Available Subsurface tile drainage systems are widely used in agricultural watersheds in the Midwestern US and enable the Midwest area to become highly productive agricultural lands, but can also create environmental problems, for example nitrate-N contamination associated with drainage waters. The Soil and Water Assessment Tool (SWAT has been used to model watersheds with tile drainage. SWAT2012 revisions 615 and 645 provide new tile drainage routines. However, few studies have used these revisions to study tile drainage impacts at both field and watershed scales. Moreover, SWAT2012 revision 645 improved the soil moisture based curve number calculation method, which has not been fully tested. This study used long-term (1991–2003 field site and river station data from the Little Vermilion River (LVR watershed to evaluate performance of tile drainage routines in SWAT2009 revision 528 (the old routine and SWAT2012 revisions 615 and 645 (the new routine. Both the old and new routines provided reasonable but unsatisfactory (NSE  <  0.5 uncalibrated flow and nitrate loss results for a mildly sloped watershed with low runoff. The calibrated monthly tile flow, surface flow, nitrate-N in tile and surface flow, sediment and annual corn and soybean yield results from SWAT with the old and new tile drainage routines were compared with observed values. Generally, the new routine provided acceptable simulated tile flow (NSE  =  0.48–0.65 and nitrate in tile flow (NSE  =  0.48–0.68 for field sites with random pattern tile and constant tile spacing, while the old routine simulated tile flow and nitrate in tile flow results for the field site with constant tile spacing were unacceptable (NSE  =  0.00–0.32 and −0.29–0.06, respectively. The new modified curve number calculation method in revision 645 (NSE  =  0.50–0.81 better simulated surface runoff than revision 615 (NSE  =  −0.11–0.49. The calibration

Transcriptome sequencing of the Microarray Quality Control (MAQC RNA reference samples using next generation sequencing

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Thierry-Mieg Danielle

2009-06-01

Full Text Available Abstract Background Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC reference RNA samples using Roche's 454 Genome Sequencer FLX. Results We generated more that 3.6 million sequence reads of average length 250 bp for the MAQC A and B samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values ≤ 10-20. We measured gene expression levels in the A and B samples by counting the numbers of reads that mapped to individual RefSeq genes in multiple sequencing runs to evaluate the MAQC quality metrics for reproducibility, sensitivity, specificity, and accuracy and compared the results with DNA microarrays and Quantitative RT-PCR (QRTPCR from the MAQC studies. In addition, 88% of the reads were successfully aligned directly to the human genome using the AceView alignment programs with an average 90% sequence similarity to identify 137,899 unique exon junctions, including 22,193 new exon junctions not yet contained in the RefSeq database. Conclusion Using the MAQC metrics for evaluating the performance of gene expression platforms, the ExpressSeq results for gene expression levels showed excellent reproducibility, sensitivity, and specificity that improved systematically with increasing shotgun sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRTPCR. In addition, a careful mapping of the reads to the genome using the AceView alignment programs shed new light on the complexity of the human transcriptome including the discovery of thousands of new splice variants.

A comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray

Directory of Open Access Journals (Sweden)

Fairbanks Benjamin D

2006-04-01

Full Text Available Abstract Background DNA microarrays have proven powerful for functional genomics studies. Several technologies exist for the generation of whole-genome arrays. It is well documented that 25mer probes directed against different regions of the same gene produce variable signal intensity values. However, the extent to which this is true for probes of greater length (60mers is not well characterized. Moreover, this information has not previously been reported for whole-genome arrays designed against bacteria, whose genomes may differ substantially in characteristics directly affecting microarray performance. Results We report here an analysis of alternative 60mer probe designs for an in-situ synthesized oligonucleotide array for the GC rich, β-proteobacterium Burkholderia cenocepacia. Probes were designed using the ArrayOligoSel3.5 software package and whole-genome microarrays synthesized by Agilent, Inc. using their in-situ, ink-jet technology platform. We first validated the quality of the microarrays as demonstrated by an average signal to noise ratio of >1000. Next, we determined that the variance of replicate probes (1178 total probes examined of identical sequence was 3.8% whereas the variance of alternative probes (558 total alternative probes examined designs was 9.5%. We determined that depending upon the definition, about 2.4% of replicate and 7.8% of alternative probes produced outlier conclusions. Finally, we determined none of the probe design subscores (GC content, internal repeat, binding energy and self annealment produced by ArrayOligoSel3.5 were predictive or probes that produced outlier signals. Conclusion Our analysis demonstrated that the use of multiple probes per target sequence is not essential for in-situ synthesized 60mer oligonucleotide arrays designed against bacteria. Although probes producing outlier signals were identified, the use of ratios results in less than 10% of such outlier conclusions. We also determined that

Unexpected structural complexity of supernumerary marker chromosomes characterized by microarray comparative genomic hybridization

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Hing Anne V

2008-04-01

Full Text Available Abstract Background Supernumerary marker chromosomes (SMCs are structurally abnormal extra chromosomes that cannot be unambiguously identified by conventional banding techniques. In the past, SMCs have been characterized using a variety of different molecular cytogenetic techniques. Although these techniques can sometimes identify the chromosome of origin of SMCs, they are cumbersome to perform and are not available in many clinical cytogenetic laboratories. Furthermore, they cannot precisely determine the region or breakpoints of the chromosome(s involved. In this study, we describe four patients who possess one or more SMCs (a total of eight SMCs in all four patients that were characterized by microarray comparative genomic hybridization (array CGH. Results In at least one SMC from all four patients, array CGH uncovered unexpected complexity, in the form of complex rearrangements, that could have gone undetected using other molecular cytogenetic techniques. Although array CGH accurately defined the chromosome content of all but two minute SMCs, fluorescence in situ hybridization was necessary to determine the structure of the markers. Conclusion The increasing use of array CGH in clinical cytogenetic laboratories will provide an efficient method for more comprehensive characterization of SMCs. Improved SMC characterization, facilitated by array CGH, will allow for more accurate SMC/phenotype correlation.

The Plasmodium falciparum Sexual Development Transcriptome: A Microarray Analysis using Ontology-Based Pattern Identification

National Research Council Canada - National Science Library

Young, Jason A; Fivelman, Quinton L; Blair, Peter L; de la Vega, Patricia; Le Roch, Karine G; Zhou, Yingyao; Carucci, Daniel J; Baker, David A; Winzeler, Elizabeth A

2005-01-01

... a full-genome high-density oligonucleotide microarray. The interpretation of this transcriptional data was aided by applying a novel knowledge-based data-mining algorithm termed ontology-based pattern identification (OPI...

Computerized Machine for Cutting Space Shuttle Thermal Tiles

Science.gov (United States)

Ramirez, Luis E.; Reuter, Lisa A.

2009-01-01

A report presents the concept of a machine aboard the space shuttle that would cut oversized thermal-tile blanks to precise sizes and shapes needed to replace tiles that were damaged or lost during ascent to orbit. The machine would include a computer-controlled jigsaw enclosed in a clear acrylic shell that would prevent escape of cutting debris. A vacuum motor would collect the debris into a reservoir and would hold a tile blank securely in place. A database stored in the computer would contain the unique shape and dimensions of every tile. Once a broken or missing tile was identified, its identification number would be entered into the computer, wherein the cutting pattern associated with that number would be retrieved from the database. A tile blank would be locked into a crib in the machine, the shell would be closed (proximity sensors would prevent activation of the machine while the shell was open), and a "cut" command would be sent from the computer. A blade would be moved around the crib like a plotter, cutting the tile to the required size and shape. Once the tile was cut, an astronaut would take a space walk for installation.

Geopolymers as potential repair material in tiles conservation

Science.gov (United States)

Geraldes, Catarina F. M.; Lima, Augusta M.; Delgado-Rodrigues, José; Mimoso, João Manuel; Pereira, Sílvia R. M.

2016-03-01

The restoration materials currently used to fill gaps in historical architectural tiles (e.g. lime or organic resin pastes) usually show serious drawbacks in terms of compatibility, effectiveness or durability. The existing solutions do not fully protect Portuguese faïence tiles ( azulejos) in outdoor conditions and frequently result in further deterioration. Geopolymers can be a potential solution for tile lacunae infill, given the chemical-mineralogical similitude to the ceramic body, and also the durability and versatile range of physical properties that can be obtained through the manipulation of their formulation and curing conditions. This work presents and discusses the viability of the use of geopolymeric pastes to fill lacunae in tiles or to act as "cold" cast ceramic tile surrogates reproducing missing tile fragments. The formulation of geopolymers, namely the type of activators, the alumino-silicate source, the quantity of water required for adequate workability and curing conditions, was studied. The need for post-curing desalination was also considered envisaging their application in the restoration of outdoor historical architectural tiles frequently exposed to adverse environmental conditions. The possible advantages and disadvantages of the use of geopolymers in the conservation of tiles are also discussed. The results obtained reveal that geopolymers pastes are a promising material for the restoration of tiles, when compared to other solutions currently in use.

Impact of genomics on microbial food safety

NARCIS (Netherlands)

Abee, T.; Schaik, van W.; Siezen, R.J.

2004-01-01

Genome sequences are now available for many of the microbes that cause food-borne diseases. The information contained in pathogen genome sequences, together with the development of themed and whole-genome DNA microarrays and improved proteomics techniques, might provide tools for the rapid detection

Seamless stitching of tile scan microscope images.

Science.gov (United States)

Legesse, F B; Chernavskaia, O; Heuke, S; Bocklitz, T; Meyer, T; Popp, J; Heintzmann, R

2015-06-01

For diagnostic purposes, optical imaging techniques need to obtain high-resolution images of extended biological specimens in reasonable time. The field of view of an objective lens, however, is often smaller than the sample size. To image the whole sample, laser scanning microscopes acquire tile scans that are stitched into larger mosaics. The appearance of such image mosaics is affected by visible edge artefacts that arise from various optical aberrations which manifest in grey level jumps across tile boundaries. In this contribution, a technique for stitching tiles into a seamless mosaic is presented. The stitching algorithm operates by equilibrating neighbouring edges and forcing the brightness at corners to a common value. The corrected image mosaics appear to be free from stitching artefacts and are, therefore, suited for further image analysis procedures. The contribution presents a novel method to seamlessly stitch tiles captured by a laser scanning microscope into a large mosaic. The motivation for the work is the failure of currently existing methods for stitching nonlinear, multimodal images captured by our microscopic setups. Our method eliminates the visible edge artefacts that appear between neighbouring tiles by taking into account the overall illumination differences among tiles in such mosaics. The algorithm first corrects the nonuniform brightness that exists within each of the tiles. It then compensates for grey level differences across tile boundaries by equilibrating neighbouring edges and forcing the brightness at the corners to a common value. After these artefacts have been removed further image analysis procedures can be applied on the microscopic images. Even though the solution presented here is tailored for the aforementioned specific case, it could be easily adapted to other contexts where image tiles are assembled into mosaics such as in astronomical or satellite photos. © 2015 The Authors Journal of Microscopy © 2015 Royal

Solving Vertex Cover Problem Using DNA Tile Assembly Model

Directory of Open Access Journals (Sweden)

Zhihua Chen

2013-01-01

Full Text Available DNA tile assembly models are a class of mathematically distributed and parallel biocomputing models in DNA tiles. In previous works, tile assembly models have been proved be Turing-universal; that is, the system can do what Turing machine can do. In this paper, we use tile systems to solve computational hard problem. Mathematically, we construct three tile subsystems, which can be combined together to solve vertex cover problem. As a result, each of the proposed tile subsystems consists of Θ(1 types of tiles, and the assembly process is executed in a parallel way (like DNA’s biological function in cells; thus the systems can generate the solution of the problem in linear time with respect to the size of the graph.

2-D tiles declustering method based on virtual devices

Science.gov (United States)

Li, Zhongmin; Gao, Lu

2009-10-01

Generally, 2-D spatial data are divided as a series of tiles according to the plane grid. To satisfy the effect of vision, the tiles in the query window including the view point would be displayed quickly at the screen. Aiming at the performance difference of real storage devices, we propose a 2-D tiles declustering method based on virtual device. Firstly, we construct a group of virtual devices which have same storage performance and non-limited capacity, then distribute the tiles into M virtual devices according to the query window of 2-D tiles. Secondly, we equably map the tiles in M virtual devices into M equidistant intervals in [0, 1) using pseudo-random number generator. Finally, we devide [0, 1) into M intervals according to the tiles distribution percentage of every real storage device, and distribute the tiles in each interval in the corresponding real storage device. We have designed and realized a prototype GlobeSIGht, and give some related test results. The results show that the average response time of each tile in the query window including the view point using 2-D tiles declustering method based on virtual device is more efficient than using other methods.

Performance of the ATLAS hadronic Tile calorimeter

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00304670; The ATLAS collaboration

2016-01-01

The Tile Calorimeter (TileCal) of the ATLAS experiment at the LHC is the central hadronic calorimeter designed for energy reconstruction of hadrons, jets, tau-particles and missing transverse energy. TileCal is a scintillator-steel sampling calorimeter and it covers the region of pseudorapidity < 1.7. The scintillation light produced in the scintillator tiles is transmitted to photomultiplier tubes (PMTs). Signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. Each stage of the signal production from scintillation light to the signal reconstruction is monitored and calibrated. Results on the calorimeter operation and performance are presented, including the calibration, stability, absolute energy scale, uniformity and time resolution. These results show that the TileCal performance is within the design requirements and has given essential contribution to reconstructed objects and physics results.

Gene selection for microarray data classification via subspace learning and manifold regularization.

Science.gov (United States)

Tang, Chang; Cao, Lijuan; Zheng, Xiao; Wang, Minhui

2017-12-19

With the rapid development of DNA microarray technology, large amount of genomic data has been generated. Classification of these microarray data is a challenge task since gene expression data are often with thousands of genes but a small number of samples. In this paper, an effective gene selection method is proposed to select the best subset of genes for microarray data with the irrelevant and redundant genes removed. Compared with original data, the selected gene subset can benefit the classification task. We formulate the gene selection task as a manifold regularized subspace learning problem. In detail, a projection matrix is used to project the original high dimensional microarray data into a lower dimensional subspace, with the constraint that the original genes can be well represented by the selected genes. Meanwhile, the local manifold structure of original data is preserved by a Laplacian graph regularization term on the low-dimensional data space. The projection matrix can serve as an importance indicator of different genes. An iterative update algorithm is developed for solving the problem. Experimental results on six publicly available microarray datasets and one clinical dataset demonstrate that the proposed method performs better when compared with other state-of-the-art methods in terms of microarray data classification. Graphical Abstract The graphical abstract of this work.

Modular robotic tiles: experiments for children with autism

DEFF Research Database (Denmark)

Lund, Henrik Hautop; Dam Pedersen, Martin; Beck, Richard

2009-01-01

rehabilitation), and with the proper radio communication mechanism they may give unique possibilities for documentation of the physical activity (e.g., therapeutic treatment). A major point of concern in modular robotics is the connection mechanism, so we investigated different solutions for the connection......We developed a modular robotic tile and a system composed of a number of these modular robotic tiles. The system composed of the modular robotic tiles engages the user in physical activities, e.g., physiotherapy, sports, fitness, and entertainment. The modular robotic tiles motivate the user...... to perform physical activities by providing immediate feedback based upon their physical interaction with the system. With the modular robotic tiles, the user is able to make new physical set-ups within less than a minute. The tiles are applicable for different forms of physical activities (e.g., therapeutic...

Introductory Tiling Theory for Computer Graphics

CERN Document Server

Kaplan, Craig

2009-01-01

Tiling theory is an elegant branch of mathematics that has applications in several areas of computer science. The most immediate application area is graphics, where tiling theory has been used in the contexts of texture generation, sampling theory, remeshing, and of course the generation of decorative patterns. The combination of a solid theoretical base (complete with tantalizing open problems), practical algorithmic techniques, and exciting applications make tiling theory a worthwhile area of study for practitioners and students in computer science. This synthesis lecture introduces the math

The transcriptionally active regions in the genome of Bacillus subtilis

DEFF Research Database (Denmark)

Rasmussen, Simon; Nielsen, Henrik Bjørn; Jarmer, Hanne Østergaard

2009-01-01

The majority of all genes have so far been identified and annotated systematically through in silico gene finding. Here we report the finding of 3662 strand-specific transcriptionally active regions (TARs) in the genome of Bacillus subtilis by the use of tiling arrays. We have measured the genome...

Employing image processing techniques for cancer detection using microarray images.

Science.gov (United States)

Dehghan Khalilabad, Nastaran; Hassanpour, Hamid

2017-02-01

Microarray technology is a powerful genomic tool for simultaneously studying and analyzing the behavior of thousands of genes. The analysis of images obtained from this technology plays a critical role in the detection and treatment of diseases. The aim of the current study is to develop an automated system for analyzing data from microarray images in order to detect cancerous cases. The proposed system consists of three main phases, namely image processing, data mining, and the detection of the disease. The image processing phase performs operations such as refining image rotation, gridding (locating genes) and extracting raw data from images the data mining includes normalizing the extracted data and selecting the more effective genes. Finally, via the extracted data, cancerous cell is recognized. To evaluate the performance of the proposed system, microarray database is employed which includes Breast cancer, Myeloid Leukemia and Lymphomas from the Stanford Microarray Database. The results indicate that the proposed system is able to identify the type of cancer from the data set with an accuracy of 95.45%, 94.11%, and 100%, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

A fisheye viewer for microarray-based gene expression data

Directory of Open Access Journals (Sweden)

Munson Ethan V

2006-10-01

Full Text Available Abstract Background Microarray has been widely used to measure the relative amounts of every mRNA transcript from the genome in a single scan. Biologists have been accustomed to reading their experimental data directly from tables. However, microarray data are quite large and are stored in a series of files in a machine-readable format, so direct reading of the full data set is not feasible. The challenge is to design a user interface that allows biologists to usefully view large tables of raw microarray-based gene expression data. This paper presents one such interface – an electronic table (E-table that uses fisheye distortion technology. Results The Fisheye Viewer for microarray-based gene expression data has been successfully developed to view MIAME data stored in the MAGE-ML format. The viewer can be downloaded from the project web site http://polaris.imt.uwm.edu:7777/fisheye/. The fisheye viewer was implemented in Java so that it could run on multiple platforms. We implemented the E-table by adapting JTable, a default table implementation in the Java Swing user interface library. Fisheye views use variable magnification to balance magnification for easy viewing and compression for maximizing the amount of data on the screen. Conclusion This Fisheye Viewer is a lightweight but useful tool for biologists to quickly overview the raw microarray-based gene expression data in an E-table.

Glazed Tiles as Floor Finish in Nigeria

Directory of Open Access Journals (Sweden)

Toyin Emmanuel AKINDE

2013-09-01

Full Text Available Tile is no doubt rich in antiquity; its primordial  show, came as mosaic with primary prospect in sacred floor finish before its oblivion, courtesy of, later consciousness towards wall finish in banquets, kitchens, toilets, restaurants and even bars. Today, its renaissance as floor finish is apparent in private and public architectural structures with prevalence in residential, recreational, commercial, governmental and other spaces. In Nigeria, the use of glazed tiles as floor finish became apparent, supposedly in mid-twentieth century; and has since, witnessed ever increasing demands from all sundry; a development that is nascent and has necessitated its mass  production locally with pockets of firms in the country. The latter however, is a resultant response to taste cum glazed tiles affordability, whose divergent sophistication in design, colour, size and shape is believed preferred to terrazzo, carpet and floor flex tile. Accessible as glazed tile and production is, in recent times; its dearth of a holistic literature in Nigeria is obvious. In the light of the latter, this paper examine glazed tiles as floor finish in Nigeria, its advent, usage, production, challenge, benefit and prospect with the hope of opening further frontier in discipline specifics.

Detection of beta radiation emitted from painted tiles

International Nuclear Information System (INIS)

Caldas, L.V.E.

1987-01-01

At the Krafwerk Union (KWU), Erlangen, Germany, it was confirmed that some types of painted tiles of italian origin were radioactive. In this Work, performed at Institut fur Strahlenschutz, GSF, Germany, ultrathin 60μm) thermoluminescent samples of CaSO 4 :Tm were used for the determination of absorved dose rates in air (at the tile surface and at distance of 5cm from it) and of transmission factors for different tissue equivalent material thicknesses. For comparison the absorved dose rates in air from cement walls without tile revestment and with simple tile revestment (tiles without painted ornaments) were also determined. In these cases the results were the same as those obtained normally from building materials. (Author) [pt

Tile Drainage Expansion Detection using Satellite Soil Moisture Dynamics

Science.gov (United States)

Jacobs, J. M.; Cho, E.; Jia, X.

2017-12-01

In the past two decades, tile drainage installation has accelerated throughout the Red River of the North Basin (RRB) in parts of western Minnesota, eastern North Dakota, and a small area of northeastern South Dakota, because the flat topography and low-permeability soils in this region necessitated the removal of excess water to improve crop production. Interestingly, streamflow in the Red River has markedly increased and six of 13 major floods during the past century have occurred since the late 1990s. It has been suggested that the increase in RRB flooding could be due to change in agricultural practices, including extensive tile drainage installation. Reliable information on existing and future tile drainage installation is greatly needed to capture the rapid extension of tile drainage systems and to locate tile drainage systems in the north central U.S. including the RRB region. However, there are few reliable data of tile drainage installation records, except tile drainage permit records in the Bois de Sioux watershed (a sub-basin in southern part of the RRB where permits are required for tile drainage installation). This study presents a tile drainage expansion detection method based on a physical principle that the soil-drying rate may increase with increasing tile drainage for a given area. In order to capture the rate of change in soil drying rate with time over entire RRB (101,500 km2), two satellite-based microwave soil moisture records from the Advanced Microwave Scanning Radiometer for Earth Observing System (AMSR-E) and AMSR2 were used during 2002 to 2016. In this study, a sub-watershed level (HUC10) potential tile drainage growth map was developed and the results show good agreement with tile drainage permit records of six sub-watersheds in the Bois de Sioux watershed. Future analyses will include improvement of the potential tile drainage map through additional information using optical- and thermal-based sensor products and evaluation of its

Beautiful Math, Part 5: Colorful Archimedean Tilings from Dynamical Systems.

Science.gov (United States)

Ouyang, Peichang; Zhao, Weiguo; Huang, Xuan

2015-01-01

The art of tiling originated very early in the history of civilization. Almost every known human society has made use of tilings in some form or another. In particular, tilings using only regular polygons have great visual appeal. Decorated regular tilings with continuous and symmetrical patterns were widely used in decoration field, such as mosaics, pavements, and brick walls. In science, these tilings provide inspiration for synthetic organic chemistry. Building on previous CG&A “Beautiful Math” articles, the authors propose an invariant mapping method to create colorful patterns on Archimedean tilings (1-uniform tilings). The resulting patterns simultaneously have global crystallographic symmetry and local cyclic or dihedral symmetry.

Development and assessment of microarray-based DNA fingerprinting in Eucalyptus grandis.

Science.gov (United States)

Lezar, Sabine; Myburg, A A; Berger, D K; Wingfield, M J; Wingfield, B D

2004-11-01

Development of improved Eucalyptus genotypes involves the routine identification of breeding stock and superior clones. Currently, microsatellites and random amplified polymorphic DNA markers are the most widely used DNA-based techniques for fingerprinting of these trees. While these techniques have provided rapid and powerful fingerprinting assays, they are constrained by their reliance on gel or capillary electrophoresis, and therefore, relatively low throughput of fragment analysis. In contrast, recently developed microarray technology holds the promise of parallel analysis of thousands of markers in plant genomes. The aim of this study was to develop a DNA fingerprinting chip for Eucalyptus grandis and to investigate its usefulness for fingerprinting of eucalypt trees. A prototype chip was prepared using a partial genomic library from total genomic DNA of 23 E. grandis trees, of which 22 were full siblings. A total of 384 cloned genomic fragments were individually amplified and arrayed onto glass slides. DNA fingerprints were obtained for 17 individuals by hybridizing labeled genome representations of the individual trees to the 384-element chip. Polymorphic DNA fragments were identified by evaluating the binary distribution of their background-corrected signal intensities across full-sib individuals. Among 384 DNA fragments on the chip, 104 (27%) were found to be polymorphic. Hybridization of these polymorphic fragments was highly repeatable (R2>0.91) within the E. grandis individuals, and they allowed us to identify all 17 full-sib individuals. Our results suggest that DNA microarrays can be used to effectively fingerprint large numbers of closely related Eucalyptus trees.

Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs.

Science.gov (United States)

Jouffe, Vincent; Rowe, Suzanne; Liaubet, Laurence; Buitenhuis, Bart; Hornshøj, Henrik; SanCristobal, Magali; Mormède, Pierre; de Koning, D J

2009-07-16

Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH). Different approaches to localize the differentially expressed (DE) genes to the pig genome showed different levels of success and a clear lack of concordance for some genes between the various approaches. For a focused analysis on 12 genes, overlapping QTL from the public domain were presented. Also, differentially expressed genes underlying QTL for ACTH response were described. Using the latest version of the draft sequence, the differentially expressed genes were mapped to the pig genome. This enabled co-location of DE genes and previously studied QTL regions, but the draft genome sequence is still incomplete and will contain many errors. A further step to explore links between DE genes and QTL at the pathway level was largely unsuccessful due to the lack of annotation of the pig genome. This could be improved by further comparative mapping analyses but this would be time consuming. This paper provides a case study for the integration of QTL data and microarray data for a species with limited genome sequence information and annotation. The results illustrate the challenges that must be addressed but also provide a roadmap for future work that is applicable to other non-model species.

Performance of the ATLAS hadronic Tile calorimeter

CERN Document Server

Van Daalen, Tal Roelof; The ATLAS collaboration

2018-01-01

Performance of the ATLAS hadronic Tile calorimeter The Tile Calorimeter (TileCal) of the ATLAS experiment at the LHC is the central hadronic calorimeter designed for the reconstruction of hadrons, jets, tau-particles and missing transverse energy. TileCal is a scintillator-steel sampling calorimeter and it covers the region of pseudorapidity < 1.7. The scintillation light produced in the scintillator tiles is transmitted by wavelength shifting fibers to photomultiplier tubes (PMTs). The analog signals from the PMTs are amplified, shaped and digitized every 25 ns by sampling the signal. About 10000 channels of the front-end electronics measure the signals of the calorimeter with energies ranging from ~30 MeV to ~2 TeV. Each step of the signal reconstruction from scintillation light to the digital pulse reconstruction is monitored and calibrated. The performance of the calorimeter has been studied in-situ employing cosmic ray muons and a large sample of proton-proton collisions acquired during the operations...

Performance of the ATLAS hadronic Tile calorimeter

CERN Document Server

Mlynarikova, Michaela; The ATLAS collaboration

2017-01-01

The ATLAS Tile Calorimeter (TileCal) of the ATLAS experiment at the LHC is the central hadronic calorimeter designed for reconstruction of hadrons, jets, tau-particles and missing transverse energy. TileCal is a scintillator-steel sampling calorimeter and it covers the region of pseudorapidity < 1.7. The scintillation light produced in the scintillator tiles is transmitted by wavelength shifting fibers to photomultiplier tubes (PMTs). The analog signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The TileCal frontend electronics reads out the signals produced by about 10000 channels measuring energies ranging from ~30 MeV to ~2 TeV. Each stage of the signal production from scintillation light to the signal reconstruction is monitored and calibrated. The performance of the calorimeter has been studied in-situ employing cosmic ray muons and a large sample of proton-proton collisions acquired during the operations of the LHC. Prompt isolated muons of high momentum fro...

Performance of the ATLAS hadronic Tile calorimeter

CERN Document Server

Mlynarikova, Michaela; The ATLAS collaboration

2017-01-01

The Tile Calorimeter (TileCal) of the ATLAS experiment at the LHC is the central hadronic calorimeter designed for reconstruction of hadrons, jets, tau-particles and missing transverse energy. TileCal is a scintillator-steel sampling calorimeter and it covers the region of pseudorapidity < 1.7. The scintillation light produced in the scintillator tiles is transmitted by wavelength shifting fibers to photomultiplier tubes (PMTs). The analog signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The TileCal frontend electronics reads out the signals produced by about 10000 channels measuring energies ranging from ~30 MeV to ~2 TeV. Each stage of the signal production from scintillation light to the signal reconstruction is monitored and calibrated. The performance of the calorimeter has been studied in-situ employing cosmic ray muons and a large sample of proton-proton collisions acquired during the operations of the LHC. Prompt isolated muons of high momentum from elec...

Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans

OpenAIRE

Jayapal, Karthik P; Lian, Wei; Glod, Frank; Sherman, David H; Hu, Wei-Shou

2007-01-01

Abstract Background The genomes of Streptomyces coelicolor and Streptomyces lividans bear a considerable degree of synteny. While S. coelicolor is the model streptomycete for studying antibiotic synthesis and differentiation, S. lividans is almost exclusively considered as the preferred host, among actinomycetes, for cloning and expression of exogenous DNA. We used whole genome microarrays as a comparative genomics tool for identifying the subtle differences between these two chromosomes. Res...

Drosophila duplication hotspots are associated with late-replicating regions of the genome.

Directory of Open Access Journals (Sweden)

Margarida Cardoso-Moreira

2011-11-01

Full Text Available Duplications play a significant role in both extremes of the phenotypic spectrum of newly arising mutations: they can have severe deleterious effects (e.g. duplications underlie a variety of diseases but can also be highly advantageous. The phenotypic potential of newly arisen duplications has stimulated wide interest in both the mutational and selective processes shaping these variants in the genome. Here we take advantage of the Drosophila simulans-Drosophila melanogaster genetic system to further our understanding of both processes. Regarding mutational processes, the study of two closely related species allows investigation of the potential existence of shared duplication hotspots, and the similarities and differences between the two genomes can be used to dissect its underlying causes. Regarding selection, the difference in the effective population size between the two species can be leveraged to ask questions about the strength of selection acting on different classes of duplications. In this study, we conducted a survey of duplication polymorphisms in 14 different lines of D. simulans using tiling microarrays and combined it with an analogous survey for the D. melanogaster genome. By integrating the two datasets, we identified duplication hotspots conserved between the two species. However, unlike the duplication hotspots identified in mammalian genomes, Drosophila duplication hotspots are not associated with sequences of high sequence identity capable of mediating non-allelic homologous recombination. Instead, Drosophila duplication hotspots are associated with late-replicating regions of the genome, suggesting a link between DNA replication and duplication rates. We also found evidence supporting a higher effectiveness of selection on duplications in D. simulans than in D. melanogaster. This is also true for duplications segregating at high frequency, where we find evidence in D. simulans that a sizeable fraction of these mutations is

AMDA: an R package for the automated microarray data analysis

Directory of Open Access Journals (Sweden)

Foti Maria

2006-07-01

Full Text Available Abstract Background Microarrays are routinely used to assess mRNA transcript levels on a genome-wide scale. Large amount of microarray datasets are now available in several databases, and new experiments are constantly being performed. In spite of this fact, few and limited tools exist for quickly and easily analyzing the results. Microarray analysis can be challenging for researchers without the necessary training and it can be time-consuming for service providers with many users. Results To address these problems we have developed an automated microarray data analysis (AMDA software, which provides scientists with an easy and integrated system for the analysis of Affymetrix microarray experiments. AMDA is free and it is available as an R package. It is based on the Bioconductor project that provides a number of powerful bioinformatics and microarray analysis tools. This automated pipeline integrates different functions available in the R and Bioconductor projects with newly developed functions. AMDA covers all of the steps, performing a full data analysis, including image analysis, quality controls, normalization, selection of differentially expressed genes, clustering, correspondence analysis and functional evaluation. Finally a LaTEX document is dynamically generated depending on the performed analysis steps. The generated report contains comments and analysis results as well as the references to several files for a deeper investigation. Conclusion AMDA is freely available as an R package under the GPL license. The package as well as an example analysis report can be downloaded in the Services/Bioinformatics section of the Genopolis http://www.genopolis.it/

Detection of beta radiation emitted from painted tiles

International Nuclear Information System (INIS)

Caldas, L.V.E.

1988-06-01

At the Kraftwerk Union (KWU), Erlangen, Federal Republic of Germany, it was confirmed that some types of painted tiles of italian origin were radioactive. In this work, performed at Institut fur Strahlenschutz, GSF, Munich, Germany, ultra-thin (60μm) thermoluminescent samples of CaSO 4 :Tm were used for the determination of absorved dose rates in air (at the tile surface and at the distance of 5 cm from it) and of transmission factors for different tissue equivalent material thicknesses. For comparison the absorved dose rates in air from cement walls without tile revestment and with simple tile revestment (tiles without painted ornaments) were also determined. In these cases the results were the same as those obtained normally from building materials. (author) [pt

Performance of the ATLAS Tile Calorimeter

CERN Document Server

Heelan, Louise; The ATLAS collaboration

2015-01-01

The ATLAS Tile hadronic calorimeter (TileCal) provides highly-segmented energy measurements of incoming particles. It is a key detector for the measurement of hadrons, jets, tau leptons and missing transverse energy. It is also useful for identification and reconstruction of muons due to good signal to noise ratio. The calorimeter consists of thin steel plates and 460,000 scintillating tiles configured into 5000 cells, each viewed by two photomultipliers. The calorimeter response and its readout electronics is monitored to better than 1% using radioactive source, laser and charge injection systems. The calibration and performance of the calorimeter have been established through test beam measurements, cosmic ray muons and the large sample of proton-proton collisions acquired in 2011 and 2012. Results on the calorimeter performance are presented, including the absolute energy scale, timing, noise and associated stabilities. The results demonstrate that the Tile Calorimeter has performed well within the design ...

Xylella fastidiosa gene expression analysis by DNA microarrays

OpenAIRE

Travensolo,Regiane F.; Carareto-Alves,Lucia M.; Costa,Maria V.C.G.; Lopes,Tiago J.S.; Carrilho,Emanuel; Lemos,Eliana G.M.

2009-01-01

Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A total of 2,600 primer pairs were synthesized and then used to generate fragments using the PCR technique. The arrays were hybridized against cDNAs labeled during reverse transcrip...

Tiling by rectangles and alternating current

KAUST Repository

Prasolov, M. V.; Skopenkov, Mikhail

2011-01-01

This paper is on tilings of polygons by rectangles. A celebrated physical interpretation of such tilings by R.L. Brooks, C.A.B. Smith, A.H. Stone and W.T. Tutte uses direct-current circuits. The new approach of this paper is an application

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

DEFF Research Database (Denmark)

Hedegaard, Jakob; Arce, Christina; Bicciato, Silvio

2009-01-01

The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microa...... a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria...

The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database

Energy Technology Data Exchange (ETDEWEB)

Tagmount, Abderrahmane; Wang, Mei; Lindquist, Erika; Tanaka, Yoshihiro; Teranishi, Kristen S.; Sunagawa, Shinichi; Wong, Mike; Stillman, Jonathon H.

2010-01-27

Background: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. Methodology/Principal Findings: A set of ~;;30K unique sequences (UniSeqs) representing ~;;19K clusters were generated from ~;;98K high quality ESTs from a set of tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66percent of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases.Conclusions/Significance: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in

Mounting LHCb hadron calorimeter scintillating tiles

CERN Multimedia

Maximilien Brice

2004-01-01

Scintillating tiles are carefully mounted in the hadronic calorimeter for the LHCb detector. These calorimeters measure the energy of particles that interact via the strong force, called hadrons. The detectors are made in a sandwich-like structure where these scintillator tiles are placed between metal sheets.

Construction of an Ostrea edulis database from genomic and expressed sequence tags (ESTs) obtained from Bonamia ostreae infected haemocytes: Development of an immune-enriched oligo-microarray.

Science.gov (United States)

Pardo, Belén G; Álvarez-Dios, José Antonio; Cao, Asunción; Ramilo, Andrea; Gómez-Tato, Antonio; Planas, Josep V; Villalba, Antonio; Martínez, Paulino

2016-12-01

The flat oyster, Ostrea edulis, is one of the main farmed oysters, not only in Europe but also in the United States and Canada. Bonamiosis due to the parasite Bonamia ostreae has been associated with high mortality episodes in this species. This parasite is an intracellular protozoan that infects haemocytes, the main cells involved in oyster defence. Due to the economical and ecological importance of flat oyster, genomic data are badly needed for genetic improvement of the species, but they are still very scarce. The objective of this study is to develop a sequence database, OedulisDB, with new genomic and transcriptomic resources, providing new data and convenient tools to improve our knowledge of the oyster's immune mechanisms. Transcriptomic and genomic sequences were obtained using 454 pyrosequencing and compiled into an O. edulis database, OedulisDB, consisting of two sets of 10,318 and 7159 unique sequences that represent the oyster's genome (WG) and de novo haemocyte transcriptome (HT), respectively. The flat oyster transcriptome was obtained from two strains (naïve and tolerant) challenged with B. ostreae, and from their corresponding non-challenged controls. Approximately 78.5% of 5619 HT unique sequences were successfully annotated by Blast search using public databases. A total of 984 sequences were identified as being related to immune response and several key immune genes were identified for the first time in flat oyster. Additionally, transcriptome information was used to design and validate the first oligo-microarray in flat oyster enriched with immune sequences from haemocytes. Our transcriptomic and genomic sequencing and subsequent annotation have largely increased the scarce resources available for this economically important species and have enabled us to develop an OedulisDB database and accompanying tools for gene expression analysis. This study represents the first attempt to characterize in depth the O. edulis haemocyte transcriptome in

Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

KAUST Repository

Boopathi, Pon Arunachalam

2016-10-09

High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.

Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

KAUST Repository

Boopathi, Pon Arunachalam; Subudhi, Amit; Middha, Sheetal; Acharya, Jyoti; Mugasimangalam, Raja Chinnadurai; Kochar, Sanjay Kumar; Kochar, Dhanpat Kumar; Das, Ashis

2016-01-01

High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.

Performance of the ATLAS Tile Calorimeter

CERN Document Server

Hrynevich, Aliaksei; The ATLAS collaboration

2017-01-01

The Tile Calorimeter (TileCal) is the central scintillator-steel sampling hadronic calorimeter of the ATLAS experiment at the LHC. Jointly with other calorimeters it is designed for energy reconstruction of hadrons, jets, tau-particles and missing transverse energy. The scintillation light produced in the scintillator tiles is transmitted by wavelength shifting fibers to photomultiplier tubes (PMTs). The analog signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The TileCal frontend electronics reads out the signals produced by about 10000 channels measuring energies ranging from ~30 MeV to ~2 TeV. Each stage of the signal production from scintillation light to the signal reconstruction is monitored and calibrated. The performance of the calorimeter has been established with cosmic ray muons and the large sample of the proton-proton collisions. The response of high momentum isolated muons is used to study the energy response at the electromagnetic scale, isolated hadr...

Evaluation of the hooghoudt and kirkham tile drain equations in the soil and water assessment tool to simulate tile flow and nitrate-nitrogen.

Science.gov (United States)

Moriasi, Daniel N; Gowda, Prasanna H; Arnold, Jeffrey G; Mulla, David J; Ale, Srinivasulu; Steiner, Jean L; Tomer, Mark D

2013-11-01

Subsurface tile drains in agricultural systems of the midwestern United States are a major contributor of nitrate-N (NO-N) loadings to hypoxic conditions in the Gulf of Mexico. Hydrologic and water quality models, such as the Soil and Water Assessment Tool, are widely used to simulate tile drainage systems. The Hooghoudt and Kirkham tile drain equations in the Soil and Water Assessment Tool have not been rigorously tested for predicting tile flow and the corresponding NO-N losses. In this study, long-term (1983-1996) monitoring plot data from southern Minnesota were used to evaluate the SWAT version 2009 revision 531 (hereafter referred to as SWAT) model for accurately estimating subsurface tile drain flows and associated NO-N losses. A retention parameter adjustment factor was incorporated to account for the effects of tile drainage and slope changes on the computation of surface runoff using the curve number method (hereafter referred to as Revised SWAT). The SWAT and Revised SWAT models were calibrated and validated for tile flow and associated NO-N losses. Results indicated that, on average, Revised SWAT predicted monthly tile flow and associated NO-N losses better than SWAT by 48 and 28%, respectively. For the calibration period, the Revised SWAT model simulated tile flow and NO-N losses within 4 and 1% of the observed data, respectively. For the validation period, it simulated tile flow and NO-N losses within 8 and 2%, respectively, of the observed values. Therefore, the Revised SWAT model is expected to provide more accurate simulation of the effectiveness of tile drainage and NO-N management practices. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

The ATLAS Tile Calorimeter DCS for Run 2

CERN Document Server

Pedro Martins, Filipe Manuel; The ATLAS collaboration

2016-01-01

TileCal is one of the ATLAS sub-detectors operating at the Large Hadron Collider (LHC), which is taking data since 2010. The Detector Control System (DCS) was developed to ensure the coherent and safe operation of the whole ATLAS detector. Seventy thousand (70000) parameters are used for control and monitoring purposes of TileCal, requiring an automated system. The TileCal DCS is mainly responsible for the control and monitoring of the high and low voltage systems but it also supervises the detector infrastructure (cooling and racks), calibration systems, data acquisition and safety. During the first period of data taking (Run 1, 2010-12) the TileCal DCS allowed a smooth detector operation and should continue to do so for the second period (Run 2) that started in 2015. The TileCal DCS was updated in order to cope with the hardware and software requirements for Run 2 operation. These updates followed the general ATLAS guidelines on the software and hardware upgrade but also the new requirements from the TileCa...

Understanding the Elementary Steps in DNA Tile-Based Self-Assembly.

Science.gov (United States)

Jiang, Shuoxing; Hong, Fan; Hu, Huiyu; Yan, Hao; Liu, Yan

2017-09-26

Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed "multi-tile" arrays in real time and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios. With more sticky ends, tile attachment becomes more thermostable with an approximately linear decrease in the free energy change (more negative). The total binding free energy of sticky ends is partially compromised by a sequence-independent energy penalty when tile attachment forms a constrained configuration: "loop". The minimal loop is a 2 × 2 tetramer (Loop4). The energy penalty of loops of 4, 6, and 8 tiles was analyzed with the independent loop model assuming no interloop tension, which is generalizable to arbitrary tile configurations. More sticky ends also contribute to a faster on-rate under isothermal conditions when nucleation is the rate-limiting step. Incorrect sticky end contributes to neither the thermostability nor the kinetics. The thermodynamic and kinetic parameters of DNA tile attachment elucidated here will contribute to the future improvement and optimization of tile assembly modeling, precise control of experimental conditions, and structural design for error-free self-assembly.

The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella

Directory of Open Access Journals (Sweden)

Sun Meisheng

2006-08-01

Full Text Available Abstract Background Compelling evidence indicates that Shigella species, the etiologic agents of bacillary dysentery, as well as enteroinvasive Escherichia coli, are derived from multiple origins of Escherichia coli and form a single pathovar. To further understand the genome diversity and virulence evolution of Shigella, comparative genomic hybridization microarray analysis was employed to compare the gene content of E. coli K-12 with those of 43 Shigella strains from all lineages. Results For the 43 strains subjected to CGH microarray analyses, the common backbone of the Shigella genome was estimated to contain more than 1,900 open reading frames (ORFs, with a mean number of 726 undetectable ORFs. The mosaic distribution of absent regions indicated that insertions and/or deletions have led to the highly diversified genomes of pathogenic strains. Conclusion These results support the hypothesis that by gain and loss of functions, Shigella species became successful human pathogens through convergent evolution from diverse genomic backgrounds. Moreover, we also found many specific differences between different lineages, providing a window into understanding bacterial speciation and taxonomic relationships.

Genome-Wide Screening of Genes Showing Altered Expression in Liver Metastases of Human Colorectal Cancers by cDNA Microarray

Directory of Open Access Journals (Sweden)

Rempei Yanagawa

2001-01-01

Full Text Available In spite of intensive and increasingly successful attempts to determine the multiple steps involved in colorectal carcinogenesis, the mechanisms responsible for metastasis of colorectal tumors to the liver remain to be clarified. To identify genes that are candidates for involvement in the metastatic process, we analyzed genome-wide expression profiles of 10 primary colorectal cancers and their corresponding metastatic lesions by means of a cDNA microarray consisting of 9121 human genes. This analysis identified 40 genes whose expression was commonly upregulated in metastatic lesions, and 7 that were commonly downregulated. The upregulated genes encoded proteins involved in cell adhesion, or remodeling of the actin cytoskeleton. Investigation of the functions of more of the altered genes should improve our understanding of metastasis and may identify diagnostic markers and/or novel molecular targets for prevention or therapy of metastatic lesions.

Large-Aperture Grating Tiling by Interferometry for Petawatt Chirped-Pulse--Amplification Systems

International Nuclear Information System (INIS)

Qiao, J.; Kalb, A.; Guardalben, M.J.; King, G.; Canning. D.; Kelly, J.H.

2007-01-01

A tiled-grating assembly with three large-scale gratings is developed with real-time interferometric tiling control for the OMEGA EP Laser Facility. An automatic tiling method is achieved and used to tile a three-tile grating assembly with the overall wavefront reconstructed. Tiling parameters sensitivity and focal-spot degradation from all combined tiling errors are analyzed for a pulse compressor composed of four such assemblies

Electro-desalination of glazed tile panels - discussion of possibilities

DEFF Research Database (Denmark)

Dias-Ferreira, Célia; Ottosen, Lisbeth M.; Ribeiro, Alexandra B.

2016-01-01

. In the few experiments conducted on tiles with attached mortar, the mortar was desalinated to a higher degree than the biscuit and successful desalination of the biscuit through the mortar requires further research. In-situ pilot scale tests were performed on highly salt-contaminated walls without tiles...... by placing electrodes at the same side of the wall. Thus it may be possible to desalinate tile panels, without any physical damage of the fragile glaze, by placing electrodes on the back of the wall or by removing some tiles, placing electrodes in their spaces, and extracting the salts from there before...... the tiles are placed back again....

Moving Toward Integrating Gene Expression Profiling into High-throughput Testing:A Gene Expression Biomarker Accurately Predicts Estrogen Receptor α Modulation in a Microarray Compendium

Science.gov (United States)

Microarray profiling of chemical-induced effects is being increasingly used in medium and high-throughput formats. In this study, we describe computational methods to identify molecular targets from whole-genome microarray data using as an example the estrogen receptor α (ERα), ...

Analysis of Chromothripsis by Combined FISH and Microarray Analysis.

Science.gov (United States)

MacKinnon, Ruth N

2018-01-01

Fluorescence in situ hybridization (FISH) to metaphase chromosomes, in conjunction with SNP array, array CGH, or whole genome sequencing, can help determine the organization of abnormal genomes after chromothripsis and other types of complex genome rearrangement. DNA microarrays can identify the changes in copy number, but they do not give information on the organization of the abnormal chromosomes, balanced rearrangements, or abnormalities of the centromeres and other regions comprised of highly repetitive DNA. Many of these details can be determined by the strategic use of metaphase FISH. FISH is a single-cell technique, so it can identify low-frequency chromosome abnormalities, and it can determine which chromosome abnormalities occur in the same or different clonal populations. These are important considerations in cancer. Metaphase chromosomes are intact, so information about abnormalities of the chromosome homologues is preserved. Here we describe strategies for working out the organization of highly rearranged genomes by combining SNP array data with various metaphase FISH methods. This approach can also be used to address some of the uncertainties arising from whole genome or mate-pair sequencing data.

Instrumented module of the ATLAS tile calorimeter

CERN Multimedia

Laurent Guiraud

1998-01-01

The ATLAS tile calorimeter consists of steel absorber plates interspersed with plastic scintillator tiles. Interactions of high-energy hadrons in the plates transform the incident energy into a 'hadronic shower'. When shower particles traverse the scintillating tiles, the latter emit an amount of light proportional to the incident energy. This light is transmitted along readout fibres to a photomultiplier, where a detectable electrical signal is produced. These pictures show one of 64 modules or 'wedges' of the barrel part of the tile calorimeter, which are arranged to form a cylinder around the beam axis. The wedge has been instrumented with scintillators and readout fibres. Photos 03, 06: Checking the routing of the readout fibres into the girder that houses the photomultipliers. Photo 04: A view of the fibre bundles inside the girder.

Optical design and studies of a tiled single grating pulse compressor for enhanced parametric space and compensation of tiling errors

Science.gov (United States)

Daiya, D.; Patidar, R. K.; Sharma, J.; Joshi, A. S.; Naik, P. A.; Gupta, P. D.

2017-04-01

A new optical design of tiled single grating pulse compressor has been proposed, set-up and studied. The parametric space, i.e. the laser beam diameters that can be accommodated in the pulse compressor for the given range of compression lengths, has been calculated and shown to have up to two fold enhancement in comparison to our earlier proposed optical designs. The new optical design of the tiled single grating pulse compressor has an additional advantage of self compensation of various tiling errors like longitudinal and lateral piston, tip and groove density mismatch, compared to the earlier designs. Experiments have been carried out for temporal compression of 650 ps positively chirped laser pulses, at central wavelength 1054 nm, down to 235 fs in the tiled grating pulse compressor set up with the proposed design. Further, far field studies have been performed to show the desired compensation of the tiling errors takes place in the new compressor.

Performance of the ATLAS Tile Calorimeter

Science.gov (United States)

Hrynevich, A.

2017-06-01

The Tile Calorimeter (TileCal) is the central scintillator-steel sampling hadronic calorimeter of the ATLAS experiment at the LHC . Jointly with other calorimeters it is designed for energy reconstruction of hadrons, jets, tau-particles and missing transverse energy. The scintillation light produced in the scintillator tiles is transmitted by wavelength shifting fibers to photomultiplier tubes (PMTs). The analog signals from the PMTs are amplified, shaped and digitized by sampling the signal every 25 ns. The TileCal frontend electronics reads out the signals produced by about 10000 channels measuring energies ranging from ~30 MeV to ~2 TeV . Each stage of the signal production from scintillation light to the signal reconstruction is monitored and calibrated. The performance of the calorimeter has been established with cosmic ray muons and the large sample of the proton-proton collisions. The response of high momentum isolated muons is used to study the energy response at the electromagnetic scale, isolated hadrons are used as a probe of the hadronic response and its modelling by the Monte Carlo simulations. The calorimeter time resolution is studied with multijet events. Results on the calorimeter operation and performance are presented, including the calibration, stability, absolute energy scale, uniformity and time resolution. These results show that the TileCal performance is within the design requirements and has given essential contribution to reconstructed objects and physics results.

ALT-II armor tile design for upgraded TEXTOR operation

International Nuclear Information System (INIS)

Newberry, B.L.; McGrath, R.T.; Watson, R.D.; Kohlhaas, W.; Finken, K.H.

1994-01-01

The upgrade of the TEXTOR tokamak at KFA Juelich was recently completed. This upgrade extended the TEXTOR pulse length from 5 seconds to 10 seconds. The auxiliary heating was increased to a total of 8.0 MW through a combination of neutral beam injection and radio frequency heating. Originally, the inertially cooled armor tiles of the full toroidal belt Advanced Limiter Test -- II (ALT-II) were designed for a 5-second operation with total heating of 6.0 MW. The upgrade of TEXTOR will increase the energy deposited per pulse onto the ALT-II by about 300%. Consequently, the graphite armor tiles for the ALT-II had to be redesigned to avoid excessively high graphite armor surface temperatures that would lead to unacceptable contamination of the plasma. This redesign took the form of two major changes in the ALT-II armor tile geometry. The first design change was an increase of the armor tile thermal mass, primarily by increasing the radial thickness of each tile from 17 mm to 20 mm. This increase in the radial tile dimension reduces the overall pumping efficiency of the ALT-II pump limiter by about 30%. The reduction in exhaust efficiency is unfortunate, but could be avoided only by active cooling of the ALT-II armor tiles. The active cooling option was too complicated and expensive to be considered at this time. The second design change involved redefining the plasma facing surface of each armor tile in order to fully utilize the entire surface area. The incident charged particle heat flux was distributed uniformly over the armor tile surfaces by carefully matching the radial, poloidal and toroidal curvature of each tile to the plasma flow in the TEXTOR boundary layer. This geometry redefinition complicates the manufacturing of the armor tiles, but results in significant thermal performance gains. In addition to these geometry upgrades, several material options were analyzed and evaluated

Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays: Implications for transcriptomics studies

NARCIS (Netherlands)

Ballerstedt, H.; Volkers, R.J.M.; Mars, A.E.; Hallsworth, J.E.; Santos, V.A.M.D.; Puchalka, J.; Duuren, J. van; Eggink, G.; Timmis, K.N.; Bont, J.A.M. de; Wery, J.

2007-01-01

Pseudomonas putida KT2440 is the only fully sequenced P. putida strain. Thus, for transcriptomics and proteomics studies with other P. putida strains, the P. putida KT2440 genomic database serves as standard reference. The utility of KT2440 whole-genome, high-density oligonucleotide microarrays for

NANO-SIZED PIGMENT APPLICATIONS IN İZNİK TILES

Directory of Open Access Journals (Sweden)

Esin GÜNAY

2012-12-01

Full Text Available Traditional İznik tiles are known as “unproducable” due to its high quartz content. İznik tiles contain four different layers as “body, engobe (slip, decors and glaze” and each one has some different starting materials. Recent studies have showed that the production techniques and the particle size of pigments are important parameters in development of colours. TUBITAK MRC and İznik Foundation carried out an experimental work to improve and understand the effects of nanotechnology application to İznik tiles. High quartz content was kept as it is and pigments were applied in decorationas nano-sized pigments.İznik tiles were produced and comparison was carried out between traditional and modern İznik tiles in colour and brightness. Characterization techniques were used in order to understand andcompare the results and also the effects of nano-sized pigments to İznik tiles.

Data Quality system of the ATLAS hadronic Tile calorimeter

International Nuclear Information System (INIS)

Nemecek, Stanislav

2012-01-01

The Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of the ATLAS experiment. It is subdivided into a large central barrel and two smaller lateral extended barrels. Each barrel consists of 64 wedges, made of iron plates and scintillating tiles. Two edges of each scintillating tile are air-coupled to wave-length shifting (WLS) fibres which collect the scintillating light and transmit it to photo-multipliers. The total number of channels is about 10000. An essential part of the TileCal detector is the Data Quality (DQ) system. The DQ system is designed to check the status of the electronic channels. It is designed to provide information at two levels - online and offline. The online TileCal DQ system monitors continuously the data while they are recorded and provides a fast feedback. The offline DQ system allows a detailed study, if needed it provides corrections to be applied to the recorded data and it allows to validate the data for physics analysis. In addition to the check of physics data the TileCal DQ systems also operate with calibration data. The TileCal calibration system provides well defined signals and the response to the calibration signals allows checking the behaviour of the electronic channels in detail. The Monitoring and Calibration Web System supports data quality analyses at the level of channels. All online, offline and calibration versions of the TileCal DQ system also provide automatic tests, the results of which allow fast and robust feedback.

Interpretation of Genomic Data Questions and Answers

Science.gov (United States)

Simon, Richard

2008-01-01

Using a question and answer format we describe important aspects of using genomic technologies in cancer research. The main challenges are not managing the mass of data, but rather the design, analysis and accurate reporting of studies that result in increased biological knowledge and medical utility. Many analysis issues address the use of expression microarrays but are also applicable to other whole genome assays. Microarray based clinical investigations have generated both unrealistic hyperbole and excessive skepticism. Genomic technologies are tremendously powerful and will play instrumental roles in elucidating the mechanisms of oncogenesis and in devlopingan era of predictive medicine in which treatments are tailored to individual tumors. Achieving these goals involves challenges in re-thinking many paradigms for the conduct of basic and clinical cancer research and for the organization of interdisciplinary collaboration. PMID:18582627

MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands

OpenAIRE

Ou, Hong-Yu; He, Xinyi; Harrison, Ewan M.; Kulasekara, Bridget R.; Thani, Ali Bin; Kadioglu, Aras; Lory, Stephen; Hinton, Jay C. D.; Barer, Michael R.; Deng, Zixin; Rajakumar, Kumar

2007-01-01

MobilomeFINDER (http://mml.sjtu.edu.cn/MobilomeFINDER) is an interactive online tool that facilitates bacterial genomic island or ‘mobile genome’ (mobilome) discovery; it integrates the ArrayOme and tRNAcc software packages. ArrayOme utilizes a microarray-derived comparative genomic hybridization input data set to generate ‘inferred contigs’ produced by merging adjacent genes classified as ‘present’. Collectively these ‘fragments’ represent a hypothetical ‘microarray-visualized genome (MVG)’....

Two heuristic approaches to describe periodicities in genomic microarrays

Directory of Open Access Journals (Sweden)

Jörg Aßmus

2009-09-01

Full Text Available In the first part we discuss the filtering of panels of time series based on singular value decomposition. The discussion is based on an approach where this filtering is used to normalize microarray data. We point out effects on the periodicity and phases for time series panels. In the second part we investigate time dependent periodic panels with different phases. We align the time series in the panel and discuss the periodogram of the aligned time series with the purpose of describing the periodic structure of the panel. The method is quite powerful assuming known phases in the model, but it deteriorates rapidly for noisy data.  

Visual Comparison of Multiple Gene Expression Datasets in a Genomic Context

Directory of Open Access Journals (Sweden)

Borowski Krzysztof

2008-06-01

Full Text Available The need for novel methods of visualizing microarray data is growing. New perspectives are beneficial to finding patterns in expression data. The Bluejay genome browser provides an integrative way of visualizing gene expression datasets in a genomic context. We have now developed the functionality to display multiple microarray datasets simultaneously in Bluejay, in order to provide researchers with a comprehensive view of their datasets linked to a graphical representation of gene function. This will enable biologists to obtain valuable insights on expression patterns, by allowing them to analyze the expression values in relation to the gene locations as well as to compare expression profiles of related genomes or of di erent experiments for the same genome.

Upgrade of the ATLAS Tile Calorimeter

CERN Document Server

Reed, Robert; The ATLAS collaboration

2014-01-01

The Tile Calorimeter (TileCal) is the main hadronic calorimeter covering the central region of the ATLAS experiment at LHC. TileCal readout consists of about 10000 channels. The bulk of its upgrade will occur for the High Luminosity LHC operation (Phase 2 around 2023) where the peak luminosity will increase 5x compared to the design luminosity (10^{34} cm^{-2}s^{-1}) but with maintained energy (i.e. 7+7 TeV). The TileCal upgrade aims to replace the majority of the on- and off-detector electronics so that all calorimeter signals can be digitized and directly sent to the off-detector electronics in the counting room. This will reduce pile-up problems and allow more complex trigger algorithms. To achieve the required reliability, redundancy has been introduced at different levels. Three different options are presently being investigated for the front-end electronic upgrade. Extensive test beam studies will determine which option will be selected. 10 Gbps optical links are used to read out all digitized data to t...

Upgrade of the ATLAS Tile Calorimeter

CERN Document Server

Moreno, P; The ATLAS collaboration

2016-01-01

The Tile Calorimeter (TileCal) is the central hadronic calorimeter covering the central region of the ATLAS experiment at LHC. The TileCal readout consists of about 10000 channels. The bulk of its upgrade will occur for the High Luminosity LHC phase (Phase 2) where the peak luminosity will increase 5$\\times$ compared to the design luminosity ($10^{34} cm^{-2}s^{-1}$) but with maintained energy (i.e. 7+7 TeV). The TileCal upgrade aims at replacing the majority of the on- and off-detector electronics to the extent that all calorimeter signals will be digitized and sent to the off-detector electronics in the counting room. To achieve the required reliability, redundancy has been introduced at different levels. Three different options are presently being investigated for the front-end electronic upgrade. Extensive test beam studies will determine which option will be selected. 10 Gbps optical links are used to read out all digitized data to the counting room while 5 Gbps down-links are used for synchronization, c...

Upgrading the ATLAS Tile Calorimeter Electronics

CERN Document Server

Popeneciu, G; The ATLAS collaboration

2014-01-01

The Tile Calorimeter (TileCal) is the central hadronic calorimeter of the ATLAS experiment at LHC. Around 2023, after the upgrade of the LHC (High Luminosity LHC, phase 2) the peak luminosity will increase by a factor of 5 compared to the design value (1034 cm-2 s-1), thus requiring an upgrade of the TileCal readout electronics. Except the 9852 photomultipliers (PMTs), most of the on- and off-detector electronics will be replaced, with the aim of digitizing all PMT pulses at 40 MHz at the front-end level and sending them with 10 Gbps optical links to the back-end electronics. Moreover, to increase reliability, redundancy will be introduced at different levels. Three different options are currently being investigated for the front-end electronics and extensive test beam studies are planned to select the best option. One demonstrator prototype module is also planned to be inserted in TileCal in 2014 that will include hybrid electronic components able to probe the new design, but still compatible with the presen...

Photovoltaic roofing tile systems

Science.gov (United States)

Melchior, B.

The integration of photovoltaic (PV) systems in architecture is discussed. A PV-solar roofing tile system with polymer concrete base; PV-roofing tile with elastomer frame profiles and aluminum profile frames; contact technique; and solar cell modules measuring technique are described. Field tests at several places were conducted on the solar generator, electric current behavior, battery station, electric installation, power conditioner, solar measuring system with magnetic bubble memory technique, data transmission via telephone modems, and data processing system. The very favorable response to the PV-compact system proves the commercial possibilities of photovoltaic integration in architecture.

Electrochemical desalination of historic Portuguese tiles

DEFF Research Database (Denmark)

Ottosen, Lisbeth M.; Dias-Ferreira, Celia; Ribeiro, Alexandra B.

2015-01-01

Soluble salts cause severe decay of historic Portuguese tiles. Treatment options for removal of the salts to stop the decay are few. The present paper deals with development of a method for electrochemical desalination, where an electric DC field is applied to the tiles. Laboratory experiments were...... the electrochemical treatment. The removal rate was similar for the two anions so the chloride concentration reached the lowest concentration level first. At this point the electric resistance increased, but the removal of nitrate continued unaffected till similar low concentration. The sulfate concentration...... was successful. Based on the obtained results an important step is taken towards development of an electrochemical technique for desalination of tile panels....

Upgrading the Atlas Tile Calorimeter Electronics

CERN Document Server

Popeneciu, G; The ATLAS collaboration

2014-01-01

Tile Calorimeter is the central hadronic calorimeter of the ATLAS experiment at LHC. Around 2024, after the upgrade of the LHC the peak luminosity will increase by a factor of 5 compared to the design value, thus requiring an upgrade of the Tile Calorimeter readout electronics. Except the photomultipliers tubes (PMTs), most of the on- and off-detector electronics will be replaced, with the aim of digitizing all PMT pulses at the front-end level and sending them with 10 Gb/s optical links to the back-end electronics. One demonstrator prototype module is planned to be inserted in Tile Calorimeter in 2015 that will include hybrid electronic components able to probe the new design.

Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes

Energy Technology Data Exchange (ETDEWEB)

McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.; Kuehl, Jennifer V.; Boore, Jeffrey L.; dePamphilis, Claude W.

2005-08-26

Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However, for some organisms it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.

The unique genomic properties of sex-biased genes: Insights from avian microarray data

Directory of Open Access Journals (Sweden)

Webster Matthew T

2008-03-01

Full Text Available Abstract Background In order to develop a framework for the analysis of sex-biased genes, we present a characterization of microarray data comparing male and female gene expression in 18 day chicken embryos for brain, gonad, and heart tissue. Results From the 15982 significantly expressed coding regions that have been assigned to either the autosomes or the Z chromosome (12979 in brain, 13301 in gonad, and 12372 in heart, roughly 18% were significantly sex-biased in any one tissue, though only 4 gene targets were biased in all tissues. The gonad was the most sex-biased tissue, followed by the brain. Sex-biased autosomal genes tended to be expressed at lower levels and in fewer tissues than unbiased gene targets, and autosomal somatic sex-biased genes had more expression noise than similar unbiased genes. Sex-biased genes linked to the Z-chromosome showed reduced expression in females, but not in males, when compared to unbiased Z-linked genes, and sex-biased Z-linked genes were also expressed in fewer tissues than unbiased Z coding regions. Third position GC content, and codon usage bias showed some sex-biased effects, primarily for autosomal genes expressed in the gonad. Finally, there were several over-represented Gene Ontology terms in the sex-biased gene sets. Conclusion On the whole, this analysis suggests that sex-biased genes have unique genomic and organismal properties that delineate them from genes that are expressed equally in males and females.

Genome-wide mapping of boundary element-associated factor (BEAF) binding sites in Drosophila melanogaster links BEAF to transcription.

Science.gov (United States)

Jiang, Nan; Emberly, Eldon; Cuvier, Olivier; Hart, Craig M

2009-07-01

Insulator elements play a role in gene regulation that is potentially linked to nuclear organization. Boundary element-associated factors (BEAFs) 32A and 32B associate with hundreds of sites on Drosophila polytene chromosomes. We hybridized DNA isolated by chromatin immunoprecipitation to genome tiling microarrays to construct a genome-wide map of BEAF binding locations. A distinct difference in the association of 32A and 32B with chromatin was noted. We identified 1,820 BEAF peaks and found that more than 85% were less than 300 bp from transcription start sites. Half are between head-to-head gene pairs. BEAF-associated genes are transcriptionally active as judged by the presence of RNA polymerase II, dimethylated histone H3 K4, and the alternative histone H3.3. Forty percent of these genes are also associated with the polymerase negative elongation factor NELF. Like NELF-associated genes, most BEAF-associated genes are highly expressed. Using quantitative reverse transcription-PCR, we found that the expression levels of most BEAF-associated genes decrease in embryos and cultured cells lacking BEAF. These results provide an unexpected link between BEAF and transcription, suggesting that BEAF plays a role in maintaining most associated promoter regions in an environment that facilitates high transcription levels.

The Mu3e Tile Detector

Energy Technology Data Exchange (ETDEWEB)

Eckert, Hans Patrick

2015-05-06

The Mu3e experiment is designed to search for the lepton flavour violating decay μ→e{sup +}e{sup +}e{sup -} with a sensitivity of one in 10{sup 16} decays. An observation of such a decay would be a clear sign of physics beyond the Standard Model. Achieving the targeted sensitivity requires a high precision detector with excellent momentum, vertex and time resolution. The Mu3e Tile Detector is a highly granular sub-detector system based on scintillator tiles with Silicon Photomultiplier (SiPM) readout, and aims at measuring the timing of the muon decay products with a resolution of better than 100 ps. This thesis describes the development of the Tile Detector concept and demonstrates the feasibility of the elaborated design. In this context, a comprehensive simulation framework has been developed, in order to study and optimise the detector performance. The central component of this framework is a detailed simulation of the SiPM response. The simulation model has been validated in several measurements and shows good agreement with the data. Furthermore, a 16-channel prototype of a Tile Detector module has been constructed and operated in an electron beam. In the beam tests, a time resolution up to 56 ps has been achieved, which surpasses the design goal. The simulation and measurement results demonstrate the feasibility of the developed Tile Detector design and show that the required detector performance can be achieved.

The optical instrumentation of the ATLAS Tile Calorimeter

Energy Technology Data Exchange (ETDEWEB)

Abdallah, J [IFIC, Centro Mixto Universidad de Valencia-CSIC, E46100 Burjassot, Valencia (Spain); Adragna, P; Bosi, F [Pisa University and INFN, Pisa (Italy); Alexa, C; Boldea, V [National Institute of Physics and Nuclear Engineering, Bucharest (Romania); Alves, R [LIP and FCTUC Univ. of Coimbra (Portugal); Amaral, P; Andresen, X [CERN, Geneva (Switzerland); Ananiev, A [LIP and IDMEC-IST, Lisbon (Portugal); Anderson, K [University of Chicago, Chicago, Illinois 60637 (United States); Antonaki, A [University of Athens, Athens (Greece); Batusov, V [JINR, Dubna (Russian Federation); Bednar, P [Comenius University, Bratislava (Slovakia); Bergeaas, E; Bohm, C [Stockholm University, Stockholm (Sweden); Biscarat, C [LPC Clermont-Ferrand, Universite Blaise Pascal / CNRS-IN2P3, Clermont-Ferrand (France); Blanch, O; Blanchot, G; Bosman, M [Institut de Fisica d' Altes Energies, Universitat Autonoma de Barcelona, Barcelona (Spain); Bromberg, C [Michigan State University, East Lansing, Michigan 48824 (United States); others, and

2013-01-15

The Tile Calorimeter, covering the central region of the ATLAS experiment up to pseudorapidities of {+-}1.7, is a sampling device built with scintillating tiles that alternate with iron plates. The light is collected in wave-length shifting (WLS) fibers and is read out with photomultipliers. In the characteristic geometry of this calorimeter the tiles lie in planes perpendicular to the beams, resulting in a very simple and modular mechanical and optical layout. This paper focuses on the procedures applied in the optical instrumentation of the calorimeter, which involved the assembly of about 460,000 scintillator tiles and 550,000 WLS fibers. The outcome is a hadronic calorimeter that meets the ATLAS performance requirements, as shown in this paper.

The Diagnostic Yield of Array Comparative Genomic Hybridization Is High Regardless of Severity of Intellectual Disability/Developmental Delay in Children.

Science.gov (United States)

D'Arrigo, Stefano; Gavazzi, Francesco; Alfei, Enrico; Zuffardi, Orsetta; Montomoli, Cristina; Corso, Barbara; Buzzi, Erika; Sciacca, Francesca L; Bulgheroni, Sara; Riva, Daria; Pantaleoni, Chiara

2016-05-01

Microarray-based comparative genomic hybridization is a method of molecular analysis that identifies chromosomal anomalies (or copy number variants) that correlate with clinical phenotypes. The aim of the present study was to apply a clinical score previously designated by de Vries to 329 patients with intellectual disability/developmental disorder (intellectual disability/developmental delay) referred to our tertiary center and to see whether the clinical factors are associated with a positive outcome of aCGH analyses. Another goal was to test the association between a positive microarray-based comparative genomic hybridization result and the severity of intellectual disability/developmental delay. Microarray-based comparative genomic hybridization identified structural chromosomal alterations responsible for the intellectual disability/developmental delay phenotype in 16% of our sample. Our study showed that causative copy number variants are frequently found even in cases of mild intellectual disability (30.77%). We want to emphasize the need to conduct microarray-based comparative genomic hybridization on all individuals with intellectual disability/developmental delay, regardless of the severity, because the degree of intellectual disability/developmental delay does not predict the diagnostic yield of microarray-based comparative genomic hybridization. © The Author(s) 2015.

Acidic preparations of lysed platelets upregulate proliferative pathways in osteoblast-like cells as demonstrated by genome-wide microarray analysis.

Science.gov (United States)

Wahlström, Ola; Linder, Cecilia Halling; Ansell, Anna; Kalén, Anders; Söderström, Mats; Magnusson, Per

2011-01-01

Platelets contain numerous growth factors essential for wound and fracture healing. We investigated the gene expression in human osteoblast-like cells stimulated with lysed platelets prepared in acidic, neutral, or alkaline buffers. Lysed platelets prepared in buffers at pH 5.4, 7.4, and 7.9, were added after neutralization to hFOB 1.19 cells. Genome-wide microarray analysis was performed using the Affymetrix GeneChip 7G Scanner. Biometric, cluster, and pathway analyses were performed with GeneSpring GX. Biometric analyses demonstrated that 53 genes were differentially regulated (p ≤ 0.005, ≥2-fold increase). Pathway analysis revealed 10 significant pathways of which eight are common ones regulating bone formation and cancer growth. Eleven genes were selected for quantitative real-time polymerase chain reaction (PCR) based on the microarray analysis of the lysed platelets prepared in the pH 5.4 experiments. In conclusion, acidic preparations of lysed platelet concentrates release factors essential for cell proliferation and particularly cell metabolism under hypoxic conditions. The genetic response from these factors was dominated by genes associated with the same pathways observed in bone formation and cancer growth. Activation of TGF-β in the acidic preparation could be a stimulatory key factor of cell proliferation. These results support the hypothesis that acidification of platelets modifies the stimulatory response of mesenchymal cells in vitro, which is analogous with the observed milieu of a low pH present in wound and fracture sites, as well as in growing tumors.

Some comments on pinwheel tilings and their diffraction

Energy Technology Data Exchange (ETDEWEB)

Grimm, Uwe [Department of Mathematics and Statistics, Open University, Walton Hall, Milton Keynes MK7 6AA (United Kingdom); Deng Xinghua, E-mail: u.g.grimm@open.ac.uk [University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1 (Canada)

2011-03-01

The pinwheel tiling is the paradigm for a substitution tiling with circular symmetry, in the sense that the corresponding autocorrelation is circularly symmetric. As a consequence, its diffraction measure is also circularly symmetric, so the pinwheel diffraction consists of sharp rings and, possibly, a continuous component with circular symmetry. We consider some combinatorial properties of the tiles and their orientations, and a numerical approach to the diffraction of weighted pinwheel point sets.

Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.

Science.gov (United States)

Guzzi, Pietro Hiram; Cannataro, Mario

2013-08-01

A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power

Modular Interactive Tiles for Rehabilitation – Evidence and Effect

DEFF Research Database (Denmark)

Lund, Henrik Hautop

2010-01-01

years) in daily use in a hospital rehabilitation unit e.g. for cardiac patients. Also, the tiles were tested for performing physical rehabilitation of stroke patients both in hospital, rehabilitation centre and in their private home. In all test cases qualitative feedback indicate that the patients find......We developed modular interactive tiles to be used for playful physiotherapy, which is supposed to motivate patients to engage in and perform physical rehabilitation exercises. We report on evidence for elderly training. We tested the modular interactive tiles for an extensive period of time (4...... the playful use of modular interactive tiles engaging and motivating for them to perform the rehabilitation. Also, test data suggest that some playful exercises on the tiles demand an average heart rate of 75% and 86% of the maximum heart rate....

Status of the ATLAS hadronic tile calorimeter

International Nuclear Information System (INIS)

Leitner, R.

2005-01-01

Short status of the Tile Calorimeter project is given. Major achievements in the mechanical construction of the detector modules, their instrumentation, cylinders assembly, as well as the principles of the detector front-end electronics, are described. The ideas of Tile Calorimeter module calibration are presented

Complete gene expression profiling of Saccharopolyspora erythraea using GeneChip DNA microarrays

Directory of Open Access Journals (Sweden)

Bordoni Roberta

2007-11-01

Full Text Available Abstract Background The Saccharopolyspora erythraea genome sequence, recently published, presents considerable divergence from those of streptomycetes in gene organization and function, confirming the remarkable potential of S. erythraea for producing many other secondary metabolites in addition to erythromycin. In order to investigate, at whole transcriptome level, how S. erythraea genes are modulated, a DNA microarray was specifically designed and constructed on the S. erythraea strain NRRL 2338 genome sequence, and the expression profiles of 6494 ORFs were monitored during growth in complex liquid medium. Results The transcriptional analysis identified a set of 404 genes, whose transcriptional signals vary during growth and characterize three distinct phases: a rapid growth until 32 h (Phase A; a growth slowdown until 52 h (Phase B; and another rapid growth phase from 56 h to 72 h (Phase C before the cells enter the stationary phase. A non-parametric statistical method, that identifies chromosomal regions with transcriptional imbalances, determined regional organization of transcription along the chromosome, highlighting differences between core and non-core regions, and strand specific patterns of expression. Microarray data were used to characterize the temporal behaviour of major functional classes and of all the gene clusters for secondary metabolism. The results confirmed that the ery cluster is up-regulated during Phase A and identified six additional clusters (for terpenes and non-ribosomal peptides that are clearly regulated in later phases. Conclusion The use of a S. erythraea DNA microarray improved specificity and sensitivity of gene expression analysis, allowing a global and at the same time detailed picture of how S. erythraea genes are modulated. This work underlines the importance of using DNA microarrays, coupled with an exhaustive statistical and bioinformatic analysis of the results, to understand the transcriptional

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE.

Science.gov (United States)

Rao, Archana N; Grainger, David W

2014-04-01

Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

Science.gov (United States)

Rao, Archana N.; Grainger, David W.

2014-01-01

Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA’s persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools. PMID:24765522

Gamma radiation scanning of nuclear waste storage tile holes

International Nuclear Information System (INIS)

Das, A.; Yue, S.; Sur, B.; Johnston, J.; Gaudet, M.; Wright, M.; Burton, N.

2010-01-01

Nuclear waste management facilities at Chalk River Laboratories use below-ground 'tile holes' to store solid waste from various activities such as medical radioisotope production. A silicon PIN (p-type-intrinsic-n-type semiconductor) diode based gamma radiation scanning system has been developed and used to profile the gamma radiation fields along the depth of waste storage tile holes by deploying the sensor into verification tubes adjacent to the tile holes themselves. The radiation field measurements were consistent with expected radiation fields in the tile holes based on administrative knowledge of the radioactive contents and their corresponding decay rates. Such measurements allow non-invasive verification of tile hole contents and provide input to the assessment of radiological risk associated with removal of the waste. Using this detector system, radioactive waste that has decayed to very low levels may be identified based on the radiation profile. This information will support planning for possible transfer of this waste to a licensed waste storage facility designed for low level waste, thus freeing storage space for possible tile hole re-use for more highly radioactive waste. (author)

Construction of 2D quasi-periodic Rauzy tiling by similarity transformation

International Nuclear Information System (INIS)

Zhuravlev, V. G.; Maleev, A. V.

2009-01-01

A new approach to constructing self-similar fractal tilings is proposed based on the construction of semigroups generated by a finite set of similarity transformations. The Rauzy tiling-a 2D analog of 1D Fibonacci tiling generated by the golden mean-is used as an example to illustrate this approach. It is shown that the Rauzy torus development and the elementary fractal boundary of Rauzy tiling can be constructed in the form of a set of centers of similarity semigroups generated by two and three similarity transformations, respectively. A centrosymmetric tiling, locally dual to the Rauzy tiling, is constructed for the first time and its parameterization is developed.

The optical instrumentation of the ATLAS Tile Calorimeter

International Nuclear Information System (INIS)

Abdallah, J; Adragna, P; Bosi, F; Alexa, C; Boldea, V; Alves, R; Amaral, P; Andresen, X; Ananiev, A; Anderson, K; Antonaki, A; Batusov, V; Bednar, P; Bergeaas, E; Bohm, C; Biscarat, C; Blanch, O; Blanchot, G; Bosman, M; Bromberg, C

2013-01-01

The Tile Calorimeter, covering the central region of the ATLAS experiment up to pseudorapidities of ±1.7, is a sampling device built with scintillating tiles that alternate with iron plates. The light is collected in wave-length shifting (WLS) fibers and is read out with photomultipliers. In the characteristic geometry of this calorimeter the tiles lie in planes perpendicular to the beams, resulting in a very simple and modular mechanical and optical layout. This paper focuses on the procedures applied in the optical instrumentation of the calorimeter, which involved the assembly of about 460,000 scintillator tiles and 550,000 WLS fibers. The outcome is a hadronic calorimeter that meets the ATLAS performance requirements, as shown in this paper.

Spectral response data for development of cool coloured tile coverings

Science.gov (United States)

Libbra, Antonio; Tarozzi, Luca; Muscio, Alberto; Corticelli, Mauro A.

2011-03-01

Most ancient or traditional buildings in Italy show steep-slope roofs covered by red clay tiles. As the rooms immediately below the roof are often inhabited in historical or densely urbanized centres, the combination of low solar reflectance of tile coverings and low thermal inertia of either wooden roof structures or sub-tile insulation panels makes summer overheating a major problem. The problem can be mitigated by using tiles coated with cool colours, that is colours with the same spectral response of clay tiles in the visible, but highly reflecting in the near infrared range, which includes more than half of solar radiation. Cool colours can yield the same visible aspect of common building surfaces, but higher solar reflectance. Studies aimed at developing cool colour tile coverings for traditional Italian buildings have been started. A few coating solutions with the typical red terracotta colour have been produced and tested in the laboratory, using easily available materials. The spectral response and the solar reflectance have been measured and compared with that of standard tiles.

Hydrogen isotopes retention in divertor tiles of DIII-D tokamak

International Nuclear Information System (INIS)

Skorodumov, B.G.; Buzhinskij, O.I.; West, W.P.; Ulanov, V.G.

1996-01-01

The absolute concentration of hydrogen isotopes in graphite divertor tiles coated with boron carbide after the exposure in DIII-D during 16 operational weeks of the 1993 campaign was obtained using the 14 MeV neutron-induced recoil detection (NERD) method. It is shown that the absolute concentration of H in tile's surface layers correlates with thickness of the deposited layers. The graphite tile without boron carbide coating had a H concentration similar to that of the tile with the thickest deposited layer. Deuterium and tritium were not detected in any of the investigated tiles. The proposed method can be used for the determination of the thickness of coatings without sample destruction. Thus, the thickness of boron carbide coatings on the tiles obtained with this method varied from 80 to 115 μm, which corresponded well to electron microscope data. (orig.)

The Sad Case of the Columbine Tiles.

Science.gov (United States)

Dowling-Sendor, Benjamin

2003-01-01

Analyzes free-speech challenge to school district's guidelines for acceptable expressions on ceramic tiles painted by Columbine High School students to express their feelings about the massacre. Tenth Circuit found that tile painting constituted school-sponsored speech and thus district had the constitutional authority under "Hazelwood School…

ATLAS Tile calorimeter calibration and monitoring systems

CERN Document Server

Marjanovic, Marija; The ATLAS collaboration

2018-01-01

The ATLAS Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of the ATLAS experiment. This sampling calorimeter uses steel plates as absorber and scintillating tiles as active medium. The light produced by the passage of charged particles is transmitted by wavelength shifting fibers to photo-multiplier tubes (PMTs), located in the outer part of the calorimeter. The readout is segmented into about 5000 cells, each one being read out by two PMTs in parallel. To calibrate and monitor the stability and performance of the full readout chain during the data taking, a set of calibration sub-systems is used. The TileCal calibration system comprises Cesium radioactive sources, laser, charge injection elements, and an integrator based readout system. Combined information from all systems allows to monitor and to equalize the calorimeter response at each stage of the signal evolution, from scintillation light to digitization. Calibration runs are monitored from a data quality perspective and u...

ATLAS Tile calorimeter calibration and monitoring systems

CERN Document Server

Boumediene, Djamel Eddine; The ATLAS collaboration

2017-01-01

The ATLAS Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of the ATLAS experiment and provides important information for reconstruction of hadrons, jets, hadronic decays of tau leptons and missing transverse energy. This sampling calorimeter uses steel plates as absorber and scintillating tiles as active medium. The light produced by the passage of charged particles is transmitted by wavelength shifting fibres to photomultiplier tubes (PMTs). PMT signals are then digitized at 40 MHz and stored on detector and are only transferred off detector once the first level trigger acceptance has been confirmed. The readout is segmented into about 5000 cells (longitudinally and transversally), each of them being read out by two PMTs in parallel. To calibrate and monitor the stability and performance of each part of the readout chain, a set of calibration systems is used. The TileCal calibration system comprises Cesium radioactive sources, laser, charge injection elements and an integrator b...

Upgrade of the ATLAS Tile Calorimeter Electronics

CERN Document Server

Carrio, F

2015-01-01

The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the central region of the ATLAS experiment at LHC. The TileCal readout consists of about 10000 channels. The bulk of its upgrade will occur for the High Luminosity LHC phase (P hase - II ) where the pea k luminosity will increase 5 times compared to the design luminosity (10 34 cm −2 s −1 ) but with maintained energy (i.e. 7+7 TeV). An additional increase of the average luminosity with a factor of 2 can be achieved by luminosity levelling. This upgrade is expe cted to happen around 202 4 . The TileCal upgrade aims at replacing the majority of the on - and off - detector electronics to the extent that all calorimeter signals will be digitized and sent to the off - detector electronics in the counting room. To achieve th e required reliability, redundancy has been introduced at different levels. Three different options are presently being investiga...

ATLAS Tile calorimeter calibration and monitoring systems

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00445232; The ATLAS collaboration

2016-01-01

The ATLAS Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of the ATLAS experiment and provides important information for reconstruction of hadrons, jets, hadronic decays of tau leptons and missing transverse energy. This sampling calorimeter uses steel plates as absorber and scintillating tiles as active medium. The light produced by the passage of charged particles is transmitted by wavelength shifting fibres to photomultiplier tubes (PMTs), located on the outside of the calorimeter. The readout is segmented into about 5000 cells (longitudinally and transversally), each of them being read out by two PMTs in parallel. To calibrate and monitor the stability and performance of each part of the readout chain during the data taking, a set of calibration systems is used. The TileCal calibration system comprises Cesium radioactive sources, laser and charge injection elements and it allows to monitor and equalize the calorimeter response at each stage of the signal production, from scin...

ATLAS Tile calorimeter calibration and monitoring systems

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00445232; The ATLAS collaboration

2017-01-01

The ATLAS Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of the ATLAS experiment and provides important information for reconstruction of hadrons, jets, hadronic decays of tau leptons and missing transverse energy. This sampling calorimeter uses steel plates as absorber and scintillating tiles as active medium. The light produced by the passage of charged particles is transmitted by wavelength shifting fibres to photomultiplier tubes (PMTs), located on the outside of the calorimeter. The readout is segmented into about 5000 cells (longitudinally and transversally), each of them being read out by two PMTs in parallel. To calibrate and monitor the stability and performance of each part of the readout chain during the data taking, a set of calibration systems is used. The TileCal calibration system comprises cesium radioactive sources, Laser and charge injection elements, and allows for monitoring and equalization of the calorimeter response at each stage of the signal production, ...

The ATLAS Tile Calorimeter DCS for Run 2

CERN Document Server

Pedro Martins, Filipe Manuel; The ATLAS collaboration

2016-01-01

TileCal is one of the ATLAS subdetectors operating at the Large Hadron Collider (LHC), which is taking data since 2010. Seventy thousand (70000) parameters are used for control and monitoring purposes, requiring an automated system. The Detector Control System (DCS) was developed to ensure the coherent and safe operation of the whole ATLAS detector. The TileCal DCS is mainly responsible for the control and monitoring of the high and low voltage systems but it also supervises the detector infrastructure (cooling and racks), calibration systems, data acquisition and safety. During the first period of data taking (Run 1, 2010-12) the TileCal DCS allowed a smooth detector operation and should continue to do so for the second period (Run 2) that started in 2015. The TileCal DCS was updated in order to cope with the hardware and software requirements for Run 2 operation. These updates followed the general ATLAS guidelines on the software and hardware upgrade but also the new requirements from the TileCal detector. ...

Analysis of phage Mu DNA transposition by whole-genome Escherichia coli tiling arrays reveals a complex relationship to distribution of target selection protein B, transcription and chromosome architectural elements.

Science.gov (United States)

Ge, Jun; Lou, Zheng; Cui, Hong; Shang, Lei; Harshey, Rasika M

2011-09-01

Of all known transposable elements, phage Mu exhibits the highest transposition efficiency and the lowest target specificity. In vitro, MuB protein is responsible for target choice. In this work, we provide a comprehensive assessment of the genome-wide distribution of MuB and its relationship to Mu target selection using high-resolution Escherichia coli tiling DNA arrays. We have also assessed how MuB binding and Mu transposition are influenced by chromosome-organizing elements such as AT-rich DNA signatures, or the binding of the nucleoid-associated protein Fis, or processes such as transcription. The results confirm and extend previous biochemical and lower resolution in vivo data. Despite the generally random nature of Mu transposition and MuB binding, there were hot and cold insertion sites and MuB binding sites in the genome, and differences between the hottest and coldest sites were large. The new data also suggest that MuB distribution and subsequent Mu integration is responsive to DNA sequences that contribute to the structural organization of the chromosome.

40 CFR 427.70 - Applicability; description of the asbestos floor tile subcategory.

Science.gov (United States)

2010-07-01

... asbestos floor tile subcategory. 427.70 Section 427.70 Protection of Environment ENVIRONMENTAL PROTECTION... Asbestos Floor Tile Subcategory § 427.70 Applicability; description of the asbestos floor tile subcategory... manufacture of asbestos floor tile. ...

Optimization of the JET Beryllium tile profile for power handling

International Nuclear Information System (INIS)

Nunes, I.; Vries, P. de; Lomas, P.J.; Loarte, A.

2006-01-01

The primary objective of the ITER-like wall project is to install a beryllium main wall and a tungsten divertor. From the point of view of plasma operations, the power handling properties of the new Be tiles may affect the operational space. The tiles design has to be such that it allows routine plasma operation for ITER relevant scenarios, i.e., 3-5 MA ELMy H-modes with high power input (P in > 30 MW) for lengths of time of ∼ 10 s. Due to the constrains imposed by heat conductivity, eddy current and stress torques on a Be tile, a single Be tile must be an assembly of castellated slices [Thompson V. et al, this conference]. From the point of view of plasma operations, the power handling properties of the new Be tiles can restrict the operational space of JET, if considerable melting of the tiles is to be avoided. This paper describes the power handling studies for the beryllium wall tiles and the optimisation of their design to achieve the operation goal described above. The melting temperature for Be is 1289 o C, corresponding to a energy limit of 60 MJ/m 2 for 10 s [Thompson V. et al, this conference]. For low field line angles, the power density on the toroidally facing surfaces is several times higher than the power density on the tile face requiring these to be shadowed. Furthermore the poloidally facing surfaces also have to be shadowed from assembly to assembly due to the large gap between assemblies. The tiles have been designed taking into account these limits and with a geometrical design such as to avoid exposed surfaces at high angles to the magnetic field being melted due to the expected loads. This has been achieved after detailed studies of the power handling of the various limiters and protections, including the effect of the curvature of the flux surfaces, shadowing and tolerance to misalignment. The surface of the tiles is defined such that, when possible, there is an even distribution of power density over the entire tile surface, and that

Investigation of Parameters that Affect the Success Rate of Microarray-Based Allele-Specific Hybridization Assays

DEFF Research Database (Denmark)

Poulsen, Lena; Søe, Martin Jensen; Moller, Lisbeth Birk

2011-01-01

Background: The development of microarray-based genetic tests for diseases that are caused by known mutations is becoming increasingly important. The key obstacle to developing functional genotyping assays is that such mutations need to be genotyped regardless of their location in genomic regions...

Spatial chaos of Wang tiles with two symbols

Science.gov (United States)

Chen, Jin-Yu; Chen, Yu-Jie; Hu, Wen-Guei; Lin, Song-Sun

2016-02-01

This investigation completely classifies the spatial chaos problem in plane edge coloring (Wang tiles) with two symbols. For a set of Wang tiles B , spatial chaos occurs when the spatial entropy h ( B ) is positive. B is called a minimal cycle generator if P ( B ) ≠ 0̸ and P ( B ' ) = 0̸ whenever B ' ⫋ B , where P ( B ) is the set of all periodic patterns on ℤ2 generated by B . Given a set of Wang tiles B , write B = C 1 ∪ C 2 ∪ ⋯ ∪ C k ∪ N , where Cj, 1 ≤ j ≤ k, are minimal cycle generators and B contains no minimal cycle generator except those contained in C1∪C2∪⋯∪Ck. Then, the positivity of spatial entropy h ( B ) is completely determined by C1∪C2∪⋯∪Ck. Furthermore, there are 39 equivalence classes of marginal positive-entropy sets of Wang tiles and 18 equivalence classes of saturated zero-entropy sets of Wang tiles. For a set of Wang tiles B , h ( B ) is positive if and only if B contains a MPE set, and h ( B ) is zero if and only if B is a subset of a SZE set.

Bio deterioration behaviour in different colour roofing tiles (red and straw coloured)

International Nuclear Information System (INIS)

Guzulla, M. F.; Sanchez, E.; Gonzalez, J. M.; Orduna, M.

2014-01-01

Bio colonization of building materials is a critical problem for the durability of constructions. Industrial experience shows that straw coloured roofing tiles are more prone to colonization than red roofing tiles, even having similar characteristics. The aim of this work is to explain the difference of bio colonization between different colour roofing tiles. The chemical composition of the surface of straw coloured and red roofing tiles, the phase composition and the microstructure of the roofing tiles were determined by WD-XRF, XRD and SEM-EDX, respectively. The pore size distribution was carried out by Hg porosimetry. The solubility was studied by determining the soluble salts (Ca, Mg, Na, K, Cl and SO 4 2-) by ICP-OES and ionic chromatography. Roofing tile bio receptivity was evaluated by determining fluorescence intensity using a pulse amplitude- modulated (PAM) fluoro meter, and cyanobacteria Oscillator sp. The results obtained show higher concentration of calcium and sulphur in straw coloured roofing tiles surface, and higher solubility than red roofing tiles. Moreover, according to the results obtained in bio receptivity assays, straw coloured roofing tiles are more prone to colonization than red roofing tiles, so, there is a relationship between surface properties of roofing tiles and bio colonization, as it is observed in industrial products. (Author)

Fiber-tile optical studies at Argonne

International Nuclear Information System (INIS)

Underwood, D.G.; Morgan, D.J.; Proudfoot, J.

1991-01-01

In support of a fiber-tile calorimeter for SDC, we have done studies on a number of topics. The most basic problems were light output and uniformity of response. Using a small electron beam, we have studied fiber placement, tile preparation, wrapping and masking, fiber splicing, fiber routing, phototube response, and some degradation factors. We found two configurations which produced more light output than the others and reasonably uniform response. We have chosen one of these to go into production for the EM test module on the basis of fiber routing for ease of assembly of the calorimeter. We have also applied some of the tools we developed to CDF end plug tile uniformity, shower max testing and development for a couple of detectors, and development of better techniques for radiation damage studies. 18 figs

Remotely replaceable Tokamak plasma limiter tiles

International Nuclear Information System (INIS)

Remy, G.

1989-01-01

U-shaped limiter tiles placed end-to-end over a pair of parallel runners secured to a wall have two rods which engage L-shaped slots in the runners. The short receiving legs of the L-shaped slots are perpendicular to the wall and open away from the wall, while long retaining legs are parallel to and adjacent the wall. A sliding bar between the runners has grooves with clips to retain the rods pressed into receiving legs of the L-shaped slots in the runners. Sliding the bar in the direction of retaining legs of the L-shaped slots latches the tiles in place over the runners. Resilient contact strips between the parallel arms of the U-shaped tiles and the wall assure thermal and electrical contact with the wall

Tuning iteration space slicing based tiled multi-core code implementing Nussinov's RNA folding.

Science.gov (United States)

Palkowski, Marek; Bielecki, Wlodzimierz

2018-01-15

RNA folding is an ongoing compute-intensive task of bioinformatics. Parallelization and improving code locality for this kind of algorithms is one of the most relevant areas in computational biology. Fortunately, RNA secondary structure approaches, such as Nussinov's recurrence, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. This allows us to apply powerful polyhedral compilation techniques based on the transitive closure of dependence graphs to generate parallel tiled code implementing Nussinov's RNA folding. Such techniques are within the iteration space slicing framework - the transitive dependences are applied to the statement instances of interest to produce valid tiles. The main problem at generating parallel tiled code is defining a proper tile size and tile dimension which impact parallelism degree and code locality. To choose the best tile size and tile dimension, we first construct parallel parametric tiled code (parameters are variables defining tile size). With this purpose, we first generate two nonparametric tiled codes with different fixed tile sizes but with the same code structure and then derive a general affine model, which describes all integer factors available in expressions of those codes. Using this model and known integer factors present in the mentioned expressions (they define the left-hand side of the model), we find unknown integers in this model for each integer factor available in the same fixed tiled code position and replace in this code expressions, including integer factors, with those including parameters. Then we use this parallel parametric tiled code to implement the well-known tile size selection (TSS) technique, which allows us to discover in a given search space the best tile size and tile dimension maximizing target code performance. For a given search space, the presented approach allows us to choose the best tile size and tile dimension in

Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources

Directory of Open Access Journals (Sweden)

Waugh Robbie

2010-12-01

Full Text Available Abstract Background Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a wheat chromosome (3B. However gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B. Results Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridised to a barley Agilent 15K expression microarray. This led to the fine mapping of 738 barley orthologous genes on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3 H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B. Conclusion Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.

Thermal-stress analysis and testing of DIII-D armor tiles

International Nuclear Information System (INIS)

Baxi, C.B.; Anderson, P.M.; Reis, E.E.; Smith, J.P.; Smith, P.D.; Croesmann, C.; Watkins, J.; Whitley, J.

1987-10-01

It is planned to install about 1500 new armor tiles in the DIII-D tokamak. The armor tiles currently installed in DIII-D are made by brazing Poco AXF-5Q graphite onto Inconel X-750 stock. A small percentage of these have failed by breakage of graphite. These failures were believed to be related to significant residual stress remaining in graphite after brazing. Hence, an effort was undertaken to improve the design with all-graphite tiles. Three criteria must be satisfied by the armor tiles and the hardware used to attach the tiles to the vessel walls: tiles should not structurally fail, peak tile temperature must be less than 2500 K, and peak vessel stresses must be below acceptable levels. A number of alternate design concepts were first analyzed with the two-dimensional finite element codes TOPAZ2D and NIKE2D. Promising designs were optimized for best parameters such as thicknesses, etc. The two best designs were further analyzed for thermal stresses with the three-dimensional codes P/THERMAL and P/STRESS. Prototype tiles of a number of materials were fabricated by GA and tested at the Plasma Materials Test Facility of the Sandia National Laboratory at Albuquerque. The tests simulated the heat flux and cooling conditions in DIII-D. This paper describes the 2-D and 3-D thermal stress analyses, the test results and logic which led to the selected design of the DIII-D armor tiles. 5 refs., 7 figs., 3 tabs

Seeded Bayesian Networks: Constructing genetic networks from microarray data

Directory of Open Access Journals (Sweden)

Quackenbush John

2008-07-01

Full Text Available Abstract Background DNA microarrays and other genomics-inspired technologies provide large datasets that often include hidden patterns of correlation between genes reflecting the complex processes that underlie cellular metabolism and physiology. The challenge in analyzing large-scale expression data has been to extract biologically meaningful inferences regarding these processes – often represented as networks – in an environment where the datasets are often imperfect and biological noise can obscure the actual signal. Although many techniques have been developed in an attempt to address these issues, to date their ability to extract meaningful and predictive network relationships has been limited. Here we describe a method that draws on prior information about gene-gene interactions to infer biologically relevant pathways from microarray data. Our approach consists of using preliminary networks derived from the literature and/or protein-protein interaction data as seeds for a Bayesian network analysis of microarray results. Results Through a bootstrap analysis of gene expression data derived from a number of leukemia studies, we demonstrate that seeded Bayesian Networks have the ability to identify high-confidence gene-gene interactions which can then be validated by comparison to other sources of pathway data. Conclusion The use of network seeds greatly improves the ability of Bayesian Network analysis to learn gene interaction networks from gene expression data. We demonstrate that the use of seeds derived from the biomedical literature or high-throughput protein-protein interaction data, or the combination, provides improvement over a standard Bayesian Network analysis, allowing networks involving dynamic processes to be deduced from the static snapshots of biological systems that represent the most common source of microarray data. Software implementing these methods has been included in the widely used TM4 microarray analysis package.

Real-time biscuit tile image segmentation method based on edge detection.

Science.gov (United States)

Matić, Tomislav; Aleksi, Ivan; Hocenski, Željko; Kraus, Dieter

2018-05-01

In this paper we propose a novel real-time Biscuit Tile Segmentation (BTS) method for images from ceramic tile production line. BTS method is based on signal change detection and contour tracing with a main goal of separating tile pixels from background in images captured on the production line. Usually, human operators are visually inspecting and classifying produced ceramic tiles. Computer vision and image processing techniques can automate visual inspection process if they fulfill real-time requirements. Important step in this process is a real-time tile pixels segmentation. BTS method is implemented for parallel execution on a GPU device to satisfy the real-time constraints of tile production line. BTS method outperforms 2D threshold-based methods, 1D edge detection methods and contour-based methods. Proposed BTS method is in use in the biscuit tile production line. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Highly Symmetric and Congruently Tiled Meshes for Shells and Domes

Science.gov (United States)

Rasheed, Muhibur; Bajaj, Chandrajit

2016-01-01

We describe the generation of all possible shell and dome shapes that can be uniquely meshed (tiled) using a single type of mesh face (tile), and following a single meshing (tiling) rule that governs the mesh (tile) arrangement with maximal vertex, edge and face symmetries. Such tiling arrangements or congruently tiled meshed shapes, are frequently found in chemical forms (fullerenes or Bucky balls, crystals, quasi-crystals, virus nano shells or capsids), and synthetic shapes (cages, sports domes, modern architectural facades). Congruently tiled meshes are both aesthetic and complete, as they support maximal mesh symmetries with minimal complexity and possess simple generation rules. Here, we generate congruent tilings and meshed shape layouts that satisfy these optimality conditions. Further, the congruent meshes are uniquely mappable to an almost regular 3D polyhedron (or its dual polyhedron) and which exhibits face-transitive (and edge-transitive) congruency with at most two types of vertices (each type transitive to the other). The family of all such congruently meshed polyhedra create a new class of meshed shapes, beyond the well-studied regular, semi-regular and quasi-regular classes, and their duals (platonic, Catalan and Johnson). While our new mesh class is infinite, we prove that there exists a unique mesh parametrization, where each member of the class can be represented by two integer lattice variables, and moreover efficiently constructable. PMID:27563368

Recent advances of genomic testing in perinatal medicine.

Science.gov (United States)

Peters, David G; Yatsenko, Svetlana A; Surti, Urvashi; Rajkovic, Aleksandar

2015-02-01

Rapid progress in genomic medicine in recent years has made it possible to diagnose subtle genetic abnormalities in a clinical setting on routine basis. This has allowed for detailed genotype-phenotype correlations and the identification of the genetic basis of many congenital anomalies. In addition to the availability of chromosomal microarray analysis, exome and whole-genome sequencing on pre- and postnatal samples of cell-free DNA has revolutionized the field of prenatal diagnosis. Incorporation of these technologies in perinatal pathology is bound to play a major role in coming years. In this communication, we briefly present the current experience with use of classical chromosome analysis, fluorescence in situ hybridization, and microarray testing, development of whole-genome analysis by next-generation sequencing technology, offer a detailed review of the history and current status of non-invasive prenatal testing using cell-free DNA, and discuss the advents of these new genomic technologies in perinatal medicine. Copyright © 2014 Elsevier Inc. All rights reserved.

Self Cleanable Tile Grout

Directory of Open Access Journals (Sweden)

Mehmet CANBAZ

2016-03-01

Full Text Available In this study, In this study, self-cleaning tile grout and white cement specimens are produced and the effect of self-cleaning mechanism of TiO2 is tested. Effects of TiO2 amount and TiO2 type are tested and compared. Anatase form and rutile TiO2 additive are used in the study. In addition, effects of silicate additives on the self-cleaning mechanism is determined. Studies are conducted with respect to Italian UNI code. This study presents a method for solving rust between the tiles of ceramic wet floor coverings with photocatalysis method and then removing the dirt with secondary effects such as water, wind etc.

Coal fly ash utilization: Low temperature sintering of wall tiles

International Nuclear Information System (INIS)

Chandra, Navin; Sharma, Priya; Pashkov, G.L.; Voskresenskaya, E.N.; Amritphale, S.S.; Baghel, Narendra S.

2008-01-01

We present here a study of the sintering of fly ash and its mixture with low alkali pyrophyllite in the presence of sodium hexa meta phosphate (SHMP), a complex activator of sintering, for the purpose of wall tile manufacturing. The sintering of fly ash with SHMP in the temperature range 925-1050 deg. C produces tiles with low impact strength; however, the incremental addition of low alkali pyrophyllite improves impact strength. The impact strength of composites with ≥40% (w/w) pyrophyllite in the fly ash-pyrophyllite mix satisfies the acceptable limit (19.6 J/m) set by the Indian Standards Institute for wall tiles. Increasing the pyrophyllite content results in an increase in the apparent density of tiles, while shrinkage and water absorption decrease. The strength of fly ash tiles is attributed to the formation of a silicophosphate phase; in pyrophyllite rich tiles, it is attributed to the formation of a tridymite-structured T-AlPO 4 phase. Scanning electron micrographs show that the reinforcing rod shaped T-AlPO 4 crystals become more prominent as the pyrophyllite content increases in the sintered tiles

Dynamic, electronically switchable surfaces for membrane protein microarrays.

Science.gov (United States)

Tang, C S; Dusseiller, M; Makohliso, S; Heuschkel, M; Sharma, S; Keller, B; Vörös, J

2006-02-01

Microarray technology is a powerful tool that provides a high throughput of bioanalytical information within a single experiment. These miniaturized and parallelized binding assays are highly sensitive and have found widespread popularity especially during the genomic era. However, as drug diagnostics studies are often targeted at membrane proteins, the current arraying technologies are ill-equipped to handle the fragile nature of the protein molecules. In addition, to understand the complex structure and functions of proteins, different strategies to immobilize the probe molecules selectively onto a platform for protein microarray are required. We propose a novel approach to create a (membrane) protein microarray by using an indium tin oxide (ITO) microelectrode array with an electronic multiplexing capability. A polycationic, protein- and vesicle-resistant copolymer, poly(l-lysine)-grafted-poly(ethylene glycol) (PLL-g-PEG), is exposed to and adsorbed uniformly onto the microelectrode array, as a passivating adlayer. An electronic stimulation is then applied onto the individual ITO microelectrodes resulting in the localized release of the polymer thus revealing a bare ITO surface. Different polymer and biological moieties are specifically immobilized onto the activated ITO microelectrodes while the other regions remain protein-resistant as they are unaffected by the induced electrical potential. The desorption process of the PLL-g-PEG is observed to be highly selective, rapid, and reversible without compromising on the integrity and performance of the conductive ITO microelectrodes. As such, we have successfully created a stable and heterogeneous microarray of biomolecules by using selective electronic addressing on ITO microelectrodes. Both pharmaceutical diagnostics and biomedical technology are expected to benefit directly from this unique method.

Comparison of performance of tile drainage routines in SWAT 2009 and 2012 in an extensively tile-drained watershed in Midwest

Science.gov (United States)

Subsurface tile drainage systems are widely used in agricultural watersheds in the Midwestern U.S. Tile drainage systems enable the Midwest area to become highly productive agricultural lands, but can also create environmental problems, for example nitrate-N contamination associated with drainage w...

Healing assessment of tile sets for error tolerance in DNA self-assembly.

Science.gov (United States)

Hashempour, M; Mashreghian Arani, Z; Lombardi, F

2008-12-01

An assessment of the effectiveness of healing for error tolerance in DNA self-assembly tile sets for algorithmic/nano-manufacturing applications is presented. Initially, the conditions for correct binding of a tile to an existing aggregate are analysed using a Markovian approach; based on this analysis, it is proved that correct aggregation (as identified with a so-called ideal tile set) is not always met for the existing tile sets for nano-manufacturing. A metric for assessing tile sets for healing by utilising punctures is proposed. Tile sets are investigated and assessed with respect to features such as error (mismatched tile) movement, punctured area and bond types. Subsequently, it is shown that the proposed metric can comprehensively assess the healing effectiveness of a puncture type for a tile set and its capability to attain error tolerance for the desired pattern. Extensive simulation results are provided.

MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies

Directory of Open Access Journals (Sweden)

Beaudoing Emmanuel

2006-09-01

Full Text Available Abstract Background High throughput gene expression profiling (GEP is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option. GEP technology is a fast moving target, with new approaches constantly broadening the field diversity. This technology heterogeneity, compounded by the informatics complexity of GEP databases, means that software developments have so far focused on mainstream techniques, leaving less typical yet established techniques such as Nylon microarrays at best partially supported. Results MAF (MicroArray Facility is the laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it can support the widely used glass microarrays and oligo-chips, MAF was designed with the specific idiosyncrasies of Nylon based microarrays in mind. Notably single channel radioactive probes, microarray stripping and reuse, vector control hybridizations and spike-in controls are all natively supported by the software suite. MicroArray Facility is MIAME supportive and dynamically provides feedback on missing annotations to help users estimate effective MIAME compliance. Genomic data such as clone identifiers and gene symbols are also directly annotated by MAF software using standard public resources. The MAGE-ML data format is implemented for full data export. Journalized database operations (audit tracking, data anonymization, material traceability and user/project level confidentiality policies are also managed by MAF. Conclusion MicroArray Facility is a complete data management system for microarray producers and end-users. Particular care has been devoted to adequately model Nylon based microarrays. The MAF system, developed and implemented in both private and academic environments, has proved a robust solution for

Development, installation, and initial operation of DIII-D graphite armor tiles

International Nuclear Information System (INIS)

Anderson, P.M.; Baxi, C.B.; Reis, E.E.; Smith, J.P.; Smith, P.D.

1988-04-01

An upgrade of the DIII-D vacuum vessel protection system has been completed. The ceiling, floor, and inner wall have been armored to enable operation of CIT-relevant doublenull diverted plasmas and to enable the use of the inner wall as a limiting surface. The all- graphite tiles replace the earlier partial coverage armor configuration which consisted of a combination of Inconel tiles and graphite brazed to Inconel tiles. A new all-graphite design concept was chosen for cost and reliability reasons. The 10 minute duration between plasma discharges required the tiles to be cooled by conduction to the water-cooled vessel wall. Using two and three- dimensional analyses, the tile design was optimized to minimize thermal stresses with uniform thermal loading on the plasma-facing surface. Minimizing the stresses around the tile hold-down feature and eliminating stress concentrators were emphasized in the design. The design of the tile fastener system resulted in sufficient hold-down forces for good thermal conductance to the vessel and for securing the tile against eddy current forces. The tiles are made of graphite, and a program to select a suitable grade of graphite was undertaken. Initially, graphites were compared based on published technical data. Graphite samples were then tested for thermal shock capacity in an electron beam test facility at the Sandia National Laboratory (SNLA) in Albuquerque, New Mexico, USA. 4 refs., 6 figs

Functional genomics of tomato

Indian Academy of Sciences (India)

2014-10-20

Oct 20, 2014 ... 1Repository of Tomato Genomics Resources, Department of Plant Sciences, School .... Due to its position at the crossroads of Sanger's sequencing .... replacement for the microarray-based expression profiling. .... during RNA fragmentation step prior to library construction, ...... tomato pollen as a test case.

Functional genomics in forage and turf - present status and future ...

African Journals Online (AJOL)

The combination of bioinformatics and genomics will enhance our understanding ... This review focuses on recent advances and applications of functional genomics for large-scale EST projects, global gene expression analyses, proteomics, and ... ESTs, microarray, proteomics, metabolomics, Medicago truncatula, legume.

LASER monitoring system for the ATLAS Tile Calorimeter

International Nuclear Information System (INIS)

Viret, S.

2010-01-01

The ATLAS detector at the Large Hadron Collider (LHC) at CERN uses a scintillator-iron technique for its hadronic Tile Calorimeter (TileCal). Scintillating light is readout via 9852 photomultiplier tubes (PMTs). Calibration and monitoring of these PMTs are made using a LASER based system. Short light pulses are sent simultaneously into all the TileCal photomultiplier's tubes (PMTs) during ATLAS physics runs, thus providing essential information for ATLAS data quality and monitoring analyses. The experimental setup developed for this purpose is described as well as preliminary results obtained during ATLAS commissioning phase in 2008.

Upgrade of the ATLAS Tile Calorimeter Electronics

CERN Document Server

Moreno, P; The ATLAS collaboration

2014-01-01

The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the central region of the ATLAS experiment at LHC. The TileCal readout consists of about 10000 channels. The bulk of its upgrade will occur for the High Luminosity LHC phase (phase 2) where the peak luminosity will increase 5x compared to the design luminosity (10^34 cm−2s−1) but with maintained energy (i.e. 7+7 TeV). An additional increase of the average luminosity with a factor of 2 can be achieved by luminosity leveling. This upgrade is expected to happen around 2023. The TileCal upgrade aims at replacing the majority of the on- and off-detector electronics to the extent that all calorimeter signals will be digitized and sent to the off-detector electronics in the counting room. To achieve the required reliability, redundancy has been introduced at different levels. Three different options are presently being investigated for the front-end electronic upgrade. Extensive test beam studies will determine which option will be selected. 10 ...

Radioactivity level in Chinese building ceramic tile

International Nuclear Information System (INIS)

Xinwei, L.

2004-01-01

The activity concentrations of 226 Ra, 232 Th and 40 K have been determined by gamma ray spectrometry. The concentrations of 226 Ra, 232 Th and 40 K range from 158.3 to 1087.6, 91.7 to 1218.4, and 473.8 to 1031.3 Bq kg -1 for glaze, and from 63.5 to 131.4, 55.4 to 106.5, and 386.7 to 866.8 Bq kg -1 for ceramic tile, respectively. The measured activity concentrations for these radionuclides were compared with the reported data of other countries and with the typical world values. The radium equivalent activities (Ra eq ), external hazard index (H ex ) and internal hazard index (H in ) associated with the radionuclides were calculated. The Ra eq values of all ceramic tiles are lower than the limit of 370 Bq kg -1 . The values of Hex and H in calculated according to the Chinese criterion for ceramic tiles are less than unity. The Ra eq value for the glaze of glazed tile collected from some areas are >370 Bq kg -1 . (authors)

The construction and use of bacterial DNA microarrays based on an optimized two-stage PCR strategy

Directory of Open Access Journals (Sweden)

Pesta David

2003-06-01

Full Text Available Abstract Background DNA microarrays are a powerful tool with important applications such as global gene expression profiling. Construction of bacterial DNA microarrays from genomic sequence data using a two-stage PCR amplification approach for the production of arrayed DNA is attractive because it allows, in principal, the continued re-amplification of DNA fragments and facilitates further utilization of the DNA fragments for additional uses (e.g. over-expression of protein. We describe the successful construction and use of DNA microarrays by the two-stage amplification approach and discuss the technical challenges that were met and resolved during the project. Results Chimeric primers that contained both gene-specific and shared, universal sequence allowed the two-stage amplification of the 3,168 genes identified on the genome of Synechocystis sp. PCC6803, an important prokaryotic model organism for the study of oxygenic photosynthesis. The gene-specific component of the primer was of variable length to maintain uniform annealing temperatures during the 1st round of PCR synthesis, and situated to preserve full-length ORFs. Genes were truncated at 2 kb for efficient amplification, so that about 92% of the PCR fragments were full-length genes. The two-stage amplification had the additional advantage of normalizing the yield of PCR products and this improved the uniformity of DNA features robotically deposited onto the microarray surface. We also describe the techniques utilized to optimize hybridization conditions and signal-to-noise ratio of the transcription profile. The inter-lab transportability was demonstrated by the virtual error-free amplification of the entire genome complement of 3,168 genes using the universal primers in partner labs. The printed slides have been successfully used to identify differentially expressed genes in response to a number of environmental conditions, including salt stress. Conclusions The technique detailed

Genome-derived vaccines.

Science.gov (United States)

De Groot, Anne S; Rappuoli, Rino

2004-02-01

Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

Automating dChip: toward reproducible sharing of microarray data analysis

Directory of Open Access Journals (Sweden)

Li Cheng

2008-05-01

Full Text Available Abstract Background During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, challenges arise when dChip users want to analyze large number of arrays automatically and share data analysis procedures and parameters. Improvement is also needed when the dChip user support team tries to identify the causes of reported analysis errors or bugs from users. Results We report here implementation and application of the dChip automation module. Through this module, dChip automation files can be created to include menu steps, parameters, and data viewpoints to run automatically. A data-packaging function allows convenient transfer from one user to another of the dChip software, microarray data, and analysis procedures, so that the second user can reproduce the entire analysis session of the first user. An analysis report file can also be generated during an automated run, including analysis logs, user comments, and viewpoint screenshots. Conclusion The dChip automation module is a step toward reproducible research, and it can prompt a more convenient and reproducible mechanism for sharing microarray software, data, and analysis procedures and results. Automation data packages can also be used as publication supplements. Similar automation mechanisms could be valuable to the research community if implemented in other genomics and bioinformatics software packages.

Development and application of a microarray meter tool to optimize microarray experiments

Directory of Open Access Journals (Sweden)

Rouse Richard JD

2008-07-01

Full Text Available Abstract Background Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these parameters and a careful evaluation of emerging slide chemistries are a prerequisite to any large scale array fabrication effort. We have developed a 'microarray meter' tool which assesses the inherent variations associated with microarray measurement prior to embarking on large scale projects. Findings The microarray meter consists of nucleic acid targets (reference and dynamic range control and probe components. Different plate designs containing identical probe material were formulated to accommodate different robotic and pin designs. We examined the variability in probe quality and quantity (as judged by the amount of DNA printed and remaining post-hybridization using three robots equipped with capillary printing pins. Discussion The generation of microarray data with minimal variation requires consistent quality control of the (DNA microarray manufacturing and experimental processes. Spot reproducibility is a measure primarily of the variations associated with printing. The microarray meter assesses array quality by measuring the DNA content for every feature. It provides a post-hybridization analysis of array quality by scoring probe performance using three metrics, a a measure of variability in the signal intensities, b a measure of the signal dynamic range and c a measure of variability of the spot morphologies.

An Effective NoSQL-Based Vector Map Tile Management Approach

Directory of Open Access Journals (Sweden)

Lin Wan

2016-11-01

Full Text Available Within a digital map service environment, the rapid growth of Spatial Big-Data is driving new requirements for effective mechanisms for massive online vector map tile processing. The emergence of Not Only SQL (NoSQL databases has resulted in a new data storage and management model for scalable spatial data deployments and fast tracking. They better suit the scenario of high-volume, low-latency network map services than traditional standalone high-performance computer (HPC or relational databases. In this paper, we propose a flexible storage framework that provides feasible methods for tiled map data parallel clipping and retrieval operations within a distributed NoSQL database environment. We illustrate the parallel vector tile generation and querying algorithms with the MapReduce programming model. Three different processing approaches, including local caching, distributed file storage, and the NoSQL-based method, are compared by analyzing the concurrent load and calculation time. An online geological vector tile map service prototype was developed to embed our processing framework in the China Geological Survey Information Grid. Experimental results show that our NoSQL-based parallel tile management framework can support applications that process huge volumes of vector tile data and improve performance of the tiled map service.

Contributions of systematic tile drainage to watershed-scale phosphorus transport.

Science.gov (United States)

King, Kevin W; Williams, Mark R; Fausey, Norman R

2015-03-01

Phosphorus (P) transport from agricultural fields continues to be a focal point for addressing harmful algal blooms and nuisance algae in freshwater systems throughout the world. In humid, poorly drained regions, attention has turned to P delivery through subsurface tile drainage. However, research on the contributions of tile drainage to watershed-scale P losses is limited. The objective of this study was to evaluate long-term P movement through tile drainage and its manifestation at the watershed outlet. Discharge data and associated P concentrations were collected for 8 yr (2005-2012) from six tile drains and from the watershed outlet of a headwater watershed within the Upper Big Walnut Creek watershed in central Ohio. Results showed that tile drainage accounted for 47% of the discharge, 48% of the dissolved P, and 40% of the total P exported from the watershed. Average annual total P loss from the watershed was 0.98 kg ha, and annual total P loss from the six tile drains was 0.48 kg ha. Phosphorus loads in tile and watershed discharge tended to be greater in the winter, spring, and fall, whereas P concentrations were greatest in the summer. Over the 8-yr study, P transported in tile drains represented 90% of all measured concentrations exceeded recommended levels (0.03 mg L) for minimizing harmful algal blooms and nuisance algae. Thus, the results of this study show that in systematically tile-drained headwater watersheds, the amount of P delivered to surface waters via tile drains cannot be dismissed. Given the amount of P loss relative to typical application rates, development and implementation of best management practices (BMPs) must jointly consider economic and environmental benefits. Specifically, implementation of BMPs should focus on late fall, winter, and early spring seasons when most P loading occurs. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays.

Directory of Open Access Journals (Sweden)

Michael A Cook

Full Text Available BACKGROUND: Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20-60 base unique sequence tags, or "barcodes", associated with each strain or clone in a collection. However, costs of current methods for microarray construction, whether by in situ oligonucleotide synthesis or ex situ coupling of modified oligonucleotides to the slide surface are often prohibitive to large-scale analyses. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that unmodified 20mer oligonucleotide probes printed on conventional surfaces show comparable hybridization signals to covalently linked 5'-amino-modified probes. As a test case, we undertook systematic cell size analysis of the budding yeast Saccharomyces cerevisiae genome-wide deletion collection by size separation of the deletion pool followed by determination of strain abundance in size fractions by barcode arrays. We demonstrate that the properties of a 13K unique feature spotted 20 mer oligonucleotide barcode microarray compare favorably with an analogous covalently-linked oligonucleotide array. Further, cell size profiles obtained with the size selection/barcode array approach recapitulate previous cell size measurements of individual deletion strains. Finally, through atomic force microscopy (AFM, we characterize the mechanism of hybridization to unmodified barcode probes on the slide surface. CONCLUSIONS/SIGNIFICANCE: These studies push the lower limit of probe size in genome-scale unmodified oligonucleotide microarray construction and demonstrate a versatile, cost-effective and reliable method for molecular barcode analysis.

Array comparative genomic hybridization and cytogenetic analysis in pediatric acute leukemias

Science.gov (United States)

Dawson, A.J.; Yanofsky, R.; Vallente, R.; Bal, S.; Schroedter, I.; Liang, L.; Mai, S.

2011-01-01

Most patients with acute lymphocytic leukemia (all) are reported to have acquired chromosomal abnormalities in their leukemic bone marrow cells. Many established chromosome rearrangements have been described, and their associations with specific clinical, biologic, and prognostic features are well defined. However, approximately 30% of pediatric and 50% of adult patients with all do not have cytogenetic abnormalities of clinical significance. Despite significant improvements in outcome for pediatric all, therapy fails in approximately 25% of patients, and these failures often occur unpredictably in patients with a favorable prognosis and “good” cytogenetics at diagnosis. It is well known that karyotype analysis in hematologic malignancies, although genome-wide, is limited because of altered cell kinetics (mitotic rate), a propensity of leukemic blasts to undergo apoptosis in culture, overgrowth by normal cells, and chromosomes of poor quality in the abnormal clone. Array comparative genomic hybridization (acgh—“microarray”) has a greatly increased genomic resolution over classical cytogenetics. Cytogenetic microarray, which uses genomic dna, is a powerful tool in the analysis of unbalanced chromosome rearrangements, such as copy number gains and losses, and it is the method of choice when the mitotic index is low and the quality of metaphases is suboptimal. The copy number profile obtained by microarray is often called a “molecular karyotype.” In the present study, microarray was applied to 9 retrospective cases of pediatric all either with initial high-risk features or with at least 1 relapse. The conventional karyotype was compared to the “molecular karyotype” to assess abnormalities as interpreted by classical cytogenetics. Not only were previously undetected chromosome losses and gains identified by microarray, but several karyotypes interpreted by classical cytogenetics were shown to be discordant with the microarray results. The

TileCal TDAQ/DCS communication

CERN Document Server

Solans, C; Arabidze, G; Carneiro Ferreira, B; Sotto-Maior Peralva, B

2007-01-01

This document describes the communication between the TDAQ and DCS systems of the Hadronic Tile Calorimeter detector of the ATLAS experiment, currently under commissioning phase at CERN. It is a further step on the TDAQ and DCS communication for TileCal operation. The aim of the implementation is to increase the robustness and understanding of the detector from the two systems involved. The basic principle observed is that the two systems operate independently in parallel. Hence, the knowledge of the status of the whole detector from each of the two systems is required for further analysis of the archived data.

Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.

Science.gov (United States)

Dai, Yilin; Guo, Ling; Li, Meng; Chen, Yi-Bu

2012-06-08

Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have implemented a comprehensive strategy to address the accuracy and reliability issue of microarray data analysis due to the well known probe design problems associated with many widely used microarray chips. There is also a lack of tools that would expedite the functional analysis of microarray results. We present Microarray Я US, an R-based graphical user interface that implements over a dozen popular Bioconductor packages to offer researchers a streamlined workflow for routine differential microarray expression data analysis without the need to learn R language. In order to enable a more accurate analysis and interpretation of microarray data, we incorporated the latest custom probe re-definition and re-annotation for Affymetrix and Illumina chips. A versatile microarray results output utility tool was also implemented for easy and fast generation of input files for over 20 of the most widely used functional analysis software programs. Coupled with a well-designed user interface, Microarray Я US leverages cutting edge Bioconductor packages for researchers with no knowledge in R language. It also enables a more reliable and accurate microarray data analysis and expedites downstream functional analysis of microarray results.

METHOD FOR EVALUATING MOLD GROWTH ON CEILING TILE

Science.gov (United States)

A method to extract mold spores from porous ceiling tiles was developed using a masticator blender. Ceiling tiles were inoculated and analyzed using four species of mold. Statistical analysis comparing results obtained by masticator extraction and the swab method was performed. T...

Characterization of an Ionization Readout Tile for nEXO

Science.gov (United States)

Jewell, M.; Schubert, A.; Cen, W. R.; Dalmasson, J.; DeVoe, R.; Fabris, L.; Gratta, G.; Jamil, A.; Li, G.; Odian, A.; Patel, M.; Pocar, A.; Qiu, D.; Wang, Q.; Wen, L. J.; Albert, J. B.; Anton, G.; Arnquist, I. J.; Badhrees, I.; Barbeau, P.; Beck, D.; Belov, V.; Bourque, F.; Brodsky, J. P.; Brown, E.; Brunner, T.; Burenkov, A.; Cao, G. F.; Cao, L.; Chambers, C.; Charlebois, S. A.; Chiu, M.; Cleveland, B.; Coon, M.; Craycraft, A.; Cree, W.; Côté, M.; Daniels, T.; Daugherty, S. J.; Daughhetee, J.; Delaquis, S.; Der Mesrobian-Kabakian, A.; Didberidze, T.; Dilling, J.; Ding, Y. Y.; Dolinski, M. J.; Dragone, A.; Fairbank, W.; Farine, J.; Feyzbakhsh, S.; Fontaine, R.; Fudenberg, D.; Giacomini, G.; Gornea, R.; Hansen, E. V.; Harris, D.; Hasan, M.; Heffner, M.; Hoppe, E. W.; House, A.; Hufschmidt, P.; Hughes, M.; Hößl, J.; Ito, Y.; Iverson, A.; Jiang, X. S.; Johnston, S.; Karelin, A.; Kaufman, L. J.; Koffas, T.; Kravitz, S.; Krücken, R.; Kuchenkov, A.; Kumar, K. S.; Lan, Y.; Leonard, D. S.; Li, S.; Li, Z.; Licciardi, C.; Lin, Y. H.; MacLellan, R.; Michel, T.; Mong, B.; Moore, D.; Murray, K.; Newby, R. J.; Ning, Z.; Njoya, O.; Nolet, F.; Odgers, K.; Oriunno, M.; Orrell, J. L.; Ostrovskiy, I.; Overman, C. T.; Ortega, G. S.; Parent, S.; Piepke, A.; Pratte, J.-F.; Radeka, V.; Raguzin, E.; Rao, T.; Rescia, S.; Retiere, F.; Robinson, A.; Rossignol, T.; Rowson, P. C.; Roy, N.; Saldanha, R.; Sangiorgio, S.; Schmidt, S.; Schneider, J.; Sinclair, D.; Skarpaas, K.; Soma, A. K.; St-Hilaire, G.; Stekhanov, V.; Stiegler, T.; Sun, X. L.; Tarka, M.; Todd, J.; Tolba, T.; Tsang, R.; Tsang, T.; Vachon, F.; Veeraraghavan, V.; Visser, G.; Vuilleumier, J.-L.; Wagenpfeil, M.; Weber, M.; Wei, W.; Wichoski, U.; Wrede, G.; Wu, S. X.; Wu, W. H.; Yang, L.; Yen, Y.-R.; Zeldovich, O.; Zhang, X.; Zhao, J.; Zhou, Y.; Ziegler, T.

2018-01-01

A new design for the anode of a time projection chamber, consisting of a charge-detecting "tile", is investigated for use in large scale liquid xenon detectors. The tile is produced by depositing 60 orthogonal metal charge-collecting strips, 3 mm wide, on a 10 cm × 10 cm fused-silica wafer. These charge tiles may be employed by large detectors, such as the proposed tonne-scale nEXO experiment to search for neutrinoless double-beta decay. Modular by design, an array of tiles can cover a sizable area. The width of each strip is small compared to the size of the tile, so a Frisch grid is not required. A grid-less, tiled anode design is beneficial for an experiment such as nEXO, where a wire tensioning support structure and Frisch grid might contribute radioactive backgrounds and would have to be designed to accommodate cycling to cryogenic temperatures. The segmented anode also reduces some degeneracies in signal reconstruction that arise in large-area crossed-wire time projection chambers. A prototype tile was tested in a cell containing liquid xenon. Very good agreement is achieved between the measured ionization spectrum of a 207Bi source and simulations that include the microphysics of recombination in xenon and a detailed modeling of the electrostatic field of the detector. An energy resolution σ/E=5.5% is observed at 570 keV, comparable to the best intrinsic ionization-only resolution reported in literature for liquid xenon at 936 V/cm.

ALT-II armor tile design for upgraded TEXTOR operation

International Nuclear Information System (INIS)

Newberry, B.L.; McGrath, R.T.; Watson, R.D.

1994-01-01

The upgrade of the TEXTOR tokamak at KFA Julich will be completed in the spring of 1994. The upgrade will extend the TEXTOR pulse length from 5 seconds to 10 seconds. The auxiliary heating systems are also scheduled to be upgraded so that eventually a total of 8.0 MW auxiliary heating will be available through a combination of neutral beam injection and radio frequency heating. Originally, the inertially cooled armor tiles on the full toroidal belt Advanced Limiter Test - II (ALT-II) were designed for 5-second operation with a total heating power of 6.0 MW. The upgrade of TEXTOR will increase the energy deposited per pulse onto ALT-II by more than 300%. Consequently, the graphite armor tiles for ALT-II had to be redesigned in order to increase their thermal inertia and, thereby, avoid excessively high graphite armor surface temperatures that would lead to unacceptable contamination of the plasma. The armor tile thermal inertia had been increase primarily by expanding the radial thickness of the tiles from 17 mm to 20 mm. This increase in radial tile dimension will reduce the overall pumping efficiency of the ALT-II pump limiter by about 30%. The final armor tile design was a compromise between increasing the power handling capability and reducing the particle exhaust efficiency of ALT-II. The reduction in exhaust efficiency is unfortunate, but could only be avoided by active cooling of the ALT-II armor tiles. The active cooling option was too complicated and expensive to be considered at this time

Run 1 Performance of the ATLAS Tile Calorimeter

CERN Document Server

Heelan, Louise; The ATLAS collaboration

2014-01-01

The ATLAS Tile hadronic calorimeter (TileCal) provides highly-segmented energy measurements of incoming particles. It is a key detector for the measurement of hadrons, jets, tau leptons and missing transverse energy. It is also useful for identification and reconstruction of muons due to good signal to noise ratio. The calorimeter consists of thin steel plates and 460,000 scintillating tiles configured into 5000 cells, each viewed by two photomultipliers. The calorimeter response and its readout electronics is monitored to better than 1% using radioactive source, laser and charge injection systems. The calibration and performance of the calorimeter have been established through test beam measurements, cosmic ray muons and the large sample of proton-proton collisions acquired in 2011 and 2012. Results on the calorimeter performance are presented, including the absolute energy scale, timing, noise and associated stabilities. The results demonstrate that the Tile Calorimeter has performed well within the design ...

Microarray BASICA: Background Adjustment, Segmentation, Image Compression and Analysis of Microarray Images

Directory of Open Access Journals (Sweden)

Jianping Hua

2004-01-01

Full Text Available This paper presents microarray BASICA: an integrated image processing tool for background adjustment, segmentation, image compression, and analysis of cDNA microarray images. BASICA uses a fast Mann-Whitney test-based algorithm to segment cDNA microarray images, and performs postprocessing to eliminate the segmentation irregularities. The segmentation results, along with the foreground and background intensities obtained with the background adjustment, are then used for independent compression of the foreground and background. We introduce a new distortion measurement for cDNA microarray image compression and devise a coding scheme by modifying the embedded block coding with optimized truncation (EBCOT algorithm (Taubman, 2000 to achieve optimal rate-distortion performance in lossy coding while still maintaining outstanding lossless compression performance. Experimental results show that the bit rate required to ensure sufficiently accurate gene expression measurement varies and depends on the quality of cDNA microarray images. For homogeneously hybridized cDNA microarray images, BASICA is able to provide from a bit rate as low as 5 bpp the gene expression data that are 99% in agreement with those of the original 32 bpp images.

Frost damage of roof tiles: A study on moisture boundary conditions

OpenAIRE

Iba, Chiemi; Ueda, Ayumi; Hokoi, Shuichi

2015-01-01

Freeze-thaw cycles are the most serious cause of roof tile deterioration; thus, it is important to know the temperature and moisture distributions in tile materials for protection against frost damage. This study focused on moisture boundary conditions for air layers under the tile. Temperature and humidity were measured using model structures with different types of roof tiles. The results showed that the temperatures around the roof were strongly influenced by solar and longwave radiation, ...

A flexible whole-genome microarray for transcriptomics in three-spine stickleback (Gasterosteus aculeatus

Directory of Open Access Journals (Sweden)

Primmer Craig R

2009-09-01

Full Text Available Abstract Background The use of microarray technology for describing changes in mRNA expression to address ecological and evolutionary questions is becoming increasingly popular. Since three-spine stickleback are an important ecological and evolutionary model-species as well as an emerging model for eco-toxicology, the ability to have a functional and flexible microarray platform for transcriptome studies will greatly enhance the research potential in these areas. Results We designed 43,392 unique oligonucleotide probes representing 19,274 genes (93% of the estimated total gene number, and tested the hybridization performance of both DNA and RNA from different populations to determine the efficacy of probe design for transcriptome analysis using the Agilent array platform. The majority of probes were functional as evidenced by the DNA hybridization success, and 30,946 probes (14,615 genes had a signal that was significantly above background for RNA isolated from liver tissue. Genes identified as being expressed in liver tissue were grouped into functional categories for each of the three Gene Ontology groups: biological process, molecular function, and cellular component. As expected, the highest proportions of functional categories belonged to those associated with metabolic functions: metabolic process, binding, catabolism, and organelles. Conclusion The probe and microarray design presented here provides an important step facilitating transcriptomics research for this important research organism by providing a set of over 43,000 probes whose hybridization success and specificity to liver expression has been demonstrated. Probes can easily be added or removed from the current design to tailor the array to specific experiments and additional flexibility lies in the ability to perform either one-color or two-color hybridizations.

Supplementing High-Density SNP Microarrays for Additional Coverage of Disease-Related Genes: Addiction as a Paradigm

Energy Technology Data Exchange (ETDEWEB)

SacconePhD, Scott F [Washington University, St. Louis; Chesler, Elissa J [ORNL; Bierut, Laura J [Washington University, St. Louis; Kalivas, Peter J [Medical College of South Carolina, Charleston; Lerman, Caryn [University of Pennsylvania; Saccone, Nancy L [Washington University, St. Louis; Uhl, George R [Johns Hopkins University; Li, Chuan-Yun [Peking University; Philip, Vivek M [ORNL; Edenberg, Howard [Indiana University; Sherry, Steven [National Center for Biotechnology Information; Feolo, Michael [National Center for Biotechnology Information; Moyzis, Robert K [Johns Hopkins University; Rutter, Joni L [National Institute of Drug Abuse

2009-01-01

Commercial SNP microarrays now provide comprehensive and affordable coverage of the human genome. However, some diseases have biologically relevant genomic regions that may require additional coverage. Addiction, for example, is thought to be influenced by complex interactions among many relevant genes and pathways. We have assembled a list of 486 biologically relevant genes nominated by a panel of experts on addiction. We then added 424 genes that showed evidence of association with addiction phenotypes through mouse QTL mappings and gene co-expression analysis. We demonstrate that there are a substantial number of SNPs in these genes that are not well represented by commercial SNP platforms. We address this problem by introducing a publicly available SNP database for addiction. The database is annotated using numeric prioritization scores indicating the extent of biological relevance. The scores incorporate a number of factors such as SNP/gene functional properties (including synonymy and promoter regions), data from mouse systems genetics and measures of human/mouse evolutionary conservation. We then used HapMap genotyping data to determine if a SNP is tagged by a commercial microarray through linkage disequilibrium. This combination of biological prioritization scores and LD tagging annotation will enable addiction researchers to supplement commercial SNP microarrays to ensure comprehensive coverage of biologically relevant regions.

Plasma surface interactions at the JET X-point tiles

International Nuclear Information System (INIS)

Martinelli, A.P.; Behrisch, R.; Coad, J.P.; Kock, L. de

1989-01-01

Operation with a magnetic divertor, which leads to a zero poloidal field inside the volume of the discharge vessel (the X-point) has led to substantial improvements in confinement time in JET. In this mode the diverted plasma is conducted to a large number of graphite tiles (X-point tiles) near the top of the vessel. The power handling capability of these tiles limits the maximum additional heating power to the discharge. The study of the surface modifications of the X-point tiles of JET is therefore of interest both to correlate the magnetic configuration and plasma particle and energy fluxes with the surface modifications, and also to get information about the erosion and deposition at these wall areas. (author) 5 refs., 4 figs

Direct calibration of PICKY-designed microarrays

Directory of Open Access Journals (Sweden)

Ronald Pamela C

2009-10-01

Full Text Available Abstract Background Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples. Results Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by PICKY, an oligo microarray design software tool, and to test a direct microarray calibration method based on the PICKY-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website http://www.complex.iastate.edu under the PICKY Download area. Conclusion PICKY-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by PICKY. In addition, other microarrays can be reanalyzed by PICKY to obtain the thermodynamically closest nontarget information for calibration.

DNA microarray technique for detecting food-borne pathogens

Directory of Open Access Journals (Sweden)

Xing GAO

2012-08-01

Full Text Available Objective To study the application of DNA microarray technique for screening and identifying multiple food-borne pathogens. Methods The oligonucleotide probes were designed by Clustal X and Oligo 6.0 at the conserved regions of specific genes of multiple food-borne pathogens, and then were validated by bioinformatic analyses. The 5' end of each probe was modified by amino-group and 10 Poly-T, and the optimized probes were synthesized and spotted on aldehyde-coated slides. The bacteria DNA template incubated with Klenow enzyme was amplified by arbitrarily primed PCR, and PCR products incorporated into Aminoallyl-dUTP were coupled with fluorescent dye. After hybridization of the purified PCR products with DNA microarray, the hybridization image and fluorescence intensity analysis was acquired by ScanArray and GenePix Pro 5.1 software. A series of detection conditions such as arbitrarily primed PCR and microarray hybridization were optimized. The specificity of this approach was evaluated by 16 different bacteria DNA, and the sensitivity and reproducibility were verified by 4 food-borne pathogens DNA. The samples of multiple bacteria DNA and simulated water samples of Shigella dysenteriae were detected. Results Nine different food-borne bacteria were successfully discriminated under the same condition. The sensitivity of genomic DNA was 102 －103pg/ μl, and the coefficient of variation (CV of the reproducibility of assay was less than 15%. The corresponding specific hybridization maps of the multiple bacteria DNA samples were obtained, and the detection limit of simulated water sample of Shigella dysenteriae was 3.54×105cfu/ml. Conclusions The DNA microarray detection system based on arbitrarily primed PCR can be employed for effective detection of multiple food-borne pathogens, and this assay may offer a new method for high-throughput platform for detecting bacteria.

An automated data management/analysis system for space shuttle orbiter tiles. [stress analysis

Science.gov (United States)

Giles, G. L.; Ballas, M.

1982-01-01

An engineering data management system was combined with a nonlinear stress analysis program to provide a capability for analyzing a large number of tiles on the space shuttle orbiter. Tile geometry data and all data necessary of define the tile loads environment accessed automatically as needed for the analysis of a particular tile or a set of tiles. User documentation provided includes: (1) description of computer programs and data files contained in the system; (2) definitions of all engineering data stored in the data base; (3) characteristics of the tile anaytical model; (4) instructions for preparation of user input; and (5) a sample problem to illustrate use of the system. Description of data, computer programs, and analytical models of the tile are sufficiently detailed to guide extension of the system to include additional zones of tiles and/or additional types of analyses

Nondeterministic self-assembly of two tile types on a lattice.

Science.gov (United States)

Tesoro, S; Ahnert, S E

2016-04-01

Self-assembly is ubiquitous in nature, particularly in biology, where it underlies the formation of protein quaternary structure and protein aggregation. Quaternary structure assembles deterministically and performs a wide range of important functions in the cell, whereas protein aggregation is the hallmark of a number of diseases and represents a nondeterministic self-assembly process. Here we build on previous work on a lattice model of deterministic self-assembly to investigate nondeterministic self-assembly of single lattice tiles and mixtures of two tiles at varying relative concentrations. Despite limiting the simplicity of the model to two interface types, which results in 13 topologically distinct single tiles and 106 topologically distinct sets of two tiles, we observe a wide variety of concentration-dependent behaviors. Several two-tile sets display critical behaviors in the form of a sharp transition from bound to unbound structures as the relative concentration of one tile to another increases. Other sets exhibit gradual monotonic changes in structural density, or nonmonotonic changes, while again others show no concentration dependence at all. We catalog this extensive range of behaviors and present a model that provides a reasonably good estimate of the critical concentrations for a subset of the critical transitions. In addition, we show that the structures resulting from these tile sets are fractal, with one of two different fractal dimensions.

Design and Applications of Rapid Image Tile Producing Software Based on Mosaic Dataset

Science.gov (United States)

Zha, Z.; Huang, W.; Wang, C.; Tang, D.; Zhu, L.

2018-04-01

Map tile technology is widely used in web geographic information services. How to efficiently produce map tiles is key technology for rapid service of images on web. In this paper, a rapid producing software for image tile data based on mosaic dataset is designed, meanwhile, the flow of tile producing is given. Key technologies such as cluster processing, map representation, tile checking, tile conversion and compression in memory are discussed. Accomplished by software development and tested by actual image data, the results show that this software has a high degree of automation, would be able to effectively reducing the number of IO and improve the tile producing efficiency. Moreover, the manual operations would be reduced significantly.

DESIGN AND APPLICATIONS OF RAPID IMAGE TILE PRODUCING SOFTWARE BASED ON MOSAIC DATASET

Directory of Open Access Journals (Sweden)

Z. Zha

2018-04-01

Full Text Available Map tile technology is widely used in web geographic information services. How to efficiently produce map tiles is key technology for rapid service of images on web. In this paper, a rapid producing software for image tile data based on mosaic dataset is designed, meanwhile, the flow of tile producing is given. Key technologies such as cluster processing, map representation, tile checking, tile conversion and compression in memory are discussed. Accomplished by software development and tested by actual image data, the results show that this software has a high degree of automation, would be able to effectively reducing the number of IO and improve the tile producing efficiency. Moreover, the manual operations would be reduced significantly.

Calibration and monitoring of the ATLAS Tile calorimeter

CERN Document Server

Boumediene, Djamel Eddine; The ATLAS collaboration

2017-01-01

The ATLAS Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of the ATLAS experiment and provides important information for reconstruction of hadrons, jets, hadronic decays of tau leptons and missing transverse energy. This sampling calorimeter uses steel plates as absorber and scintillating tiles as active medium. The light produced by the passage of charged particles is transmitted by wavelength shifting fibres to photomultiplier tubes (PMTs). PMT signals are then digitized at 40~MHz and stored on detector and are only transferred off detector once the first level trigger acceptance has been confirmed. The readout is segmented into about 5000 cells (longitudinally and transversally), each of them being read out by two PMTs in parallel. To calibrate and monitor the stability and performance of each part of the readout chain, a set of calibration systems is used. The TileCal calibration system comprises Cesium radioactive sources, laser, charge injection elements and an integrator b...

ATLAS Tile calorimeter calibration and monitoring systems

Science.gov (United States)

Chomont, Arthur; ATLAS Collaboration

2017-11-01

The ATLAS Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of the ATLAS experiment and provides important information for reconstruction of hadrons, jets, hadronic decays of tau leptons and missing transverse energy. This sampling calorimeter uses steel plates as absorber and scintillating tiles as active medium. The light produced by the passage of charged particles is transmitted by wavelength shifting fibres to photomultiplier tubes (PMTs), located on the outside of the calorimeter. The readout is segmented into about 5000 cells (longitudinally and transversally), each of them being read out by two PMTs in parallel. To calibrate and monitor the stability and performance of each part of the readout chain during the data taking, a set of calibration systems is used. The TileCal calibration system comprises cesium radioactive sources, Laser and charge injection elements, and allows for monitoring and equalization of the calorimeter response at each stage of the signal production, from scintillation light to digitization. Based on LHC Run 1 experience, several calibration systems were improved for Run 2. The lessons learned, the modifications, and the current LHC Run 2 performance are discussed.

Thermoluminescence study of materials (natural minerals) used in ceramic tiles industry

Energy Technology Data Exchange (ETDEWEB)

Murthy, K V R, E-mail: drmurthykvr@yahoo.com [Display Materials Laboratory Applied Physics Department Faculty of Technology and Engineering M.S. University of Baroda, Baroda-390 001 (India)

2009-07-15

Mother earth is giving many materials in the natural form as well as in mineral form. Among them the marbles, granites and other variety of slabs for house hold flooring purposes. The people demand for variety of flooring materials leads to develop various types of ceramic tile. In India ceramic tiles industry is one of the fast growing one. More than two hundred units are manufacturing the ceramic tiles situated around Morbi, Rajkot, Gujarat, India. The basic raw materials required for manufacturing the various types of ceramic tiles are natural minerals. The following are the minerals used to manufacture the ceramic tiles i.e. quartz, feldspar, zircon, china clay, talc, grok, Aluminum oxide etc.,

Thermoluminescence study of materials (natural minerals) used in ceramic tiles industry

International Nuclear Information System (INIS)

Murthy, K V R

2009-01-01

Mother earth is giving many materials in the natural form as well as in mineral form. Among them the marbles, granites and other variety of slabs for house hold flooring purposes. The people demand for variety of flooring materials leads to develop various types of ceramic tile. In India ceramic tiles industry is one of the fast growing one. More than two hundred units are manufacturing the ceramic tiles situated around Morbi, Rajkot, Gujarat, India. The basic raw materials required for manufacturing the various types of ceramic tiles are natural minerals. The following are the minerals used to manufacture the ceramic tiles i.e. quartz, feldspar, zircon, china clay, talc, grok, Aluminum oxide etc.,

Ecology and genomics of Bacillus subtilis.

Science.gov (United States)

Earl, Ashlee M; Losick, Richard; Kolter, Roberto

2008-06-01

Bacillus subtilis is a remarkably diverse bacterial species that is capable of growth within many environments. Recent microarray-based comparative genomic analyses have revealed that members of this species also exhibit considerable genomic diversity. The identification of strain-specific genes might explain how B. subtilis has become so broadly adapted. The goal of identifying ecologically adaptive genes could soon be realized with the imminent release of several new B. subtilis genome sequences. As we embark upon this exciting new era of B. subtilis comparative genomics we review what is currently known about the ecology and evolution of this species.

Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray

DEFF Research Database (Denmark)

Willenbrock, Hanni; Hallin, Peter Fischer; Wassenaar, Trudy

2007-01-01

of the same species are rapidly becoming available, allowing for the definition and characterization of a whole species as a population of genomes - the 'pan-genome'. Results: Using 32 Escherichia coli and Shigella genome sequences we estimate the pan- and core genome of the species. We designed a high...

GROWTH EVALUATION OF FUNGI (PENICILLIUM AND ASPERGILLUS SPP.) ON CEILING TILES

Science.gov (United States)

The paper gives results of an evaluation of the potential for fungal growth on four different ceiling tiles in static chambers. It was found that even new ceiling tiles supported fungal growth under favorable conditions. Used ceiling tiles appeared to be more susceptible to funga...

Upgrading the ATLAS Tile Calorimeter electronics

CERN Document Server

Oreglia, M; The ATLAS collaboration

2013-01-01

The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the most central region of the ATLAS experiment at LHC. The TileCal readout consists of about 10000 channels. The main upgrade will occur for the High Luminosity LHC phase (phase 2) which is scheduled around 2022. The upgrade aims at replacing the majority of the on- and off- detector electronics so that all calorimeter signals are directly digitized and sent to the off-detector electronics in the counting room. An ambitious upgrade development program is pursued studying different electronics options. Three different options are presently being investigated for the front-end electronic upgrade. Which one to use will be decided after extensive test beam studies. High speed optical links are used to read out all digitized data to the counting room. For the off-detector electronics a new back-end architecture is being developed, including the initial trigger processing and pipeline memories. A demonstrator prototype read-out for a slice of the ...

Upgrading the ATLAS Tile Calorimeter electronics

CERN Document Server

Carrio, F; The ATLAS collaboration

2013-01-01

The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the most central region of the ATLAS experiment at LHC. The TileCal readout consists of about 10000 channels. Its main upgrade will occur for the High Luminosity LHC phase (phase 2) where the luminosity will have increased 5-fold compared to the design luminosity (1034 cm−2s−1) but with maintained energy (i.e. 7+7 TeV). An additional luminosity increase by a factor of 2 can be achieved by luminosity leveling. This upgrade will probably happen around 2022. The upgrade aims at replacing the majority of the on- and off- detector electronics so that all calorimeter signals are directly digitized and sent to the off-detector electronics in the counting room. To achieve the required reliability, redundancy has been introduced at different levels. An ambitious upgrade development program is pursued studying different electronics options. Three different options are presently being investigated for the front-end electronic upgrade. Which one to u...

Hybridization chain reaction amplification for highly sensitive fluorescence detection of DNA with dextran coated microarrays.

Science.gov (United States)

Chao, Jie; Li, Zhenhua; Li, Jing; Peng, Hongzhen; Su, Shao; Li, Qian; Zhu, Changfeng; Zuo, Xiaolei; Song, Shiping; Wang, Lianhui; Wang, Lihua

2016-07-15

Microarrays of biomolecules hold great promise in the fields of genomics, proteomics, and clinical assays on account of their remarkably parallel and high-throughput assay capability. However, the fluorescence detection used in most conventional DNA microarrays is still limited by sensitivity. In this study, we have demonstrated a novel universal and highly sensitive platform for fluorescent detection of sequence specific DNA at the femtomolar level by combining dextran-coated microarrays with hybridization chain reaction (HCR) signal amplification. Three-dimensional dextran matrix was covalently coated on glass surface as the scaffold to immobilize DNA recognition probes to increase the surface binding capacity and accessibility. DNA nanowire tentacles were formed on the matrix surface for efficient signal amplification by capturing multiple fluorescent molecules in a highly ordered way. By quantifying microscopic fluorescent signals, the synergetic effects of dextran and HCR greatly improved sensitivity of DNA microarrays, with a detection limit of 10fM (1×10(5) molecules). This detection assay could recognize one-base mismatch with fluorescence signals dropped down to ~20%. This cost-effective microarray platform also worked well with samples in serum and thus shows great potential for clinical diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

Principal minors and rhombus tilings

International Nuclear Information System (INIS)

Kenyon, Richard; Pemantle, Robin

2014-01-01

The algebraic relations between the principal minors of a generic n × n matrix are somewhat mysterious, see e.g. Lin and Sturmfels (2009 J. Algebra 322 4121–31). We show, however, that by adding in certain almost principal minors, the ideal of relations is generated by translations of a single relation, the so-called hexahedron relation, which is a composition of six cluster mutations. We give in particular a Laurent-polynomial parameterization of the space of n × n matrices, whose parameters consist of certain principal and almost principal minors. The parameters naturally live on vertices and faces of the tiles in a rhombus tiling of a convex 2n-gon. A matrix is associated to an equivalence class of tilings, all related to each other by Yang–Baxter-like transformations. By specializing the initial data we can similarly parameterize the space of Hermitian symmetric matrices over R,C or H the quaternions. Moreover by further specialization we can parametrize the space of positive definite matrices over these rings. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Cluster algebras mathematical physics’. (paper)

Quantitative inference of dynamic regulatory pathways via microarray data

Directory of Open Access Journals (Sweden)

Chen Bor-Sen

2005-03-01

Full Text Available Abstract Background The cellular signaling pathway (network is one of the main topics of organismic investigations. The intracellular interactions between genes in a signaling pathway are considered as the foundation of functional genomics. Thus, what genes and how much they influence each other through transcriptional binding or physical interactions are essential problems. Under the synchronous measures of gene expression via a microarray chip, an amount of dynamic information is embedded and remains to be discovered. Using a systematically dynamic modeling approach, we explore the causal relationship among genes in cellular signaling pathways from the system biology approach. Results In this study, a second-order dynamic model is developed to describe the regulatory mechanism of a target gene from the upstream causality point of view. From the expression profile and dynamic model of a target gene, we can estimate its upstream regulatory function. According to this upstream regulatory function, we would deduce the upstream regulatory genes with their regulatory abilities and activation delays, and then link up a regulatory pathway. Iteratively, these regulatory genes are considered as target genes to trace back their upstream regulatory genes. Then we could construct the regulatory pathway (or network to the genome wide. In short, we can infer the genetic regulatory pathways from gene-expression profiles quantitatively, which can confirm some doubted paths or seek some unknown paths in a regulatory pathway (network. Finally, the proposed approach is validated by randomly reshuffling the time order of microarray data. Conclusion We focus our algorithm on the inference of regulatory abilities of the identified causal genes, and how much delay before they regulate the downstream genes. With this information, a regulatory pathway would be built up using microarray data. In the present study, two signaling pathways, i.e. circadian regulatory

A Global User-Driven Model for Tile Prefetching in Web Geographical Information Systems.

Science.gov (United States)

Pan, Shaoming; Chong, Yanwen; Zhang, Hang; Tan, Xicheng

2017-01-01

A web geographical information system is a typical service-intensive application. Tile prefetching and cache replacement can improve cache hit ratios by proactively fetching tiles from storage and replacing the appropriate tiles from the high-speed cache buffer without waiting for a client's requests, which reduces disk latency and improves system access performance. Most popular prefetching strategies consider only the relative tile popularities to predict which tile should be prefetched or consider only a single individual user's access behavior to determine which neighbor tiles need to be prefetched. Some studies show that comprehensively considering all users' access behaviors and all tiles' relationships in the prediction process can achieve more significant improvements. Thus, this work proposes a new global user-driven model for tile prefetching and cache replacement. First, based on all users' access behaviors, a type of expression method for tile correlation is designed and implemented. Then, a conditional prefetching probability can be computed based on the proposed correlation expression mode. Thus, some tiles to be prefetched can be found by computing and comparing the conditional prefetching probability from the uncached tiles set and, similarly, some replacement tiles can be found in the cache buffer according to multi-step prefetching. Finally, some experiments are provided comparing the proposed model with other global user-driven models, other single user-driven models, and other client-side prefetching strategies. The results show that the proposed model can achieve a prefetching hit rate in approximately 10.6% ~ 110.5% higher than the compared methods.

Tiling as a Durable Abstraction for Parallelism and Data Locality

Energy Technology Data Exchange (ETDEWEB)

Unat, Didem [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Chan, Cy P. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Zhang, Weiqun [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bell, John [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Shalf, John [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2013-11-18

Tiling is a useful loop transformation for expressing parallelism and data locality. Automated tiling transformations that preserve data-locality are increasingly important due to hardware trends towards massive parallelism and the increasing costs of data movement relative to the cost of computing. We propose TiDA as a durable tiling abstraction that centralizes parameterized tiling information within array data types with minimal changes to the source code. The data layout information can be used by the compiler and runtime to automatically manage parallelism, optimize data locality, and schedule tasks intelligently. In this study, we present the design features and early interface of TiDA along with some preliminary results.

An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays

Directory of Open Access Journals (Sweden)

Laurenzi Ian J

2009-12-01

Full Text Available Abstract Background Although oligonucleotide microarray technology is ubiquitous in genomic research, reproducibility and standardization of expression measurements still concern many researchers. Cross-hybridization between microarray probes and non-target ssDNA has been implicated as a primary factor in sensitivity and selectivity loss. Since hybridization is a chemical process, it may be modeled at a population-level using a combination of material balance equations and thermodynamics. However, the hybridization reaction network may be exceptionally large for commercial arrays, which often possess at least one reporter per transcript. Quantification of the kinetics and equilibrium of exceptionally large chemical systems of this type is numerically infeasible with customary approaches. Results In this paper, we present a robust and computationally efficient algorithm for the simulation of hybridization processes underlying microarray assays. Our method may be utilized to identify the extent to which nucleic acid targets (e.g. cDNA will cross-hybridize with probes, and by extension, characterize probe robustnessusing the information specified by MAGE-TAB. Using this algorithm, we characterize cross-hybridization in a modified commercial microarray assay. Conclusions By integrating stochastic simulation with thermodynamic prediction tools for DNA hybridization, one may robustly and rapidly characterize of the selectivity of a proposed microarray design at the probe and "system" levels. Our code is available at http://www.laurenzi.net.

The Development of Protein Microarrays and Their Applications in DNA-Protein and Protein-Protein Interaction Analyses of Arabidopsis Transcription Factors

Science.gov (United States)

Gong, Wei; He, Kun; Covington, Mike; Dinesh-Kumar, S. P.; Snyder, Michael; Harmer, Stacey L.; Zhu, Yu-Xian; Deng, Xing Wang

2009-01-01

We used our collection of Arabidopsis transcription factor (TF) ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and protein-protein interaction analyses. For protein-DNA interaction studies, we examined AP2/ERF family TFs and their cognate cis-elements. By careful comparison of the DNA-binding specificity of 13 TFs on the protein microarray with previous non-microarray data, we showed that protein microarrays provide an efficient and high throughput tool for genome-wide analysis of TF-DNA interactions. This microarray protein-DNA interaction analysis allowed us to derive a comprehensive view of DNA-binding profiles of AP2/ERF family proteins in Arabidopsis. It also revealed four TFs that bound the EE (evening element) and had the expected phased gene expression under clock-regulation, thus providing a basis for further functional analysis of their roles in clock regulation of gene expression. We also developed procedures for detecting protein interactions using this TF protein microarray and discovered four novel partners that interact with HY5, which can be validated by yeast two-hybrid assays. Thus, plant TF protein microarrays offer an attractive high-throughput alternative to traditional techniques for TF functional characterization on a global scale. PMID:19802365

Research about the number of D-points of -tiling in given ellipse

Directory of Open Access Journals (Sweden)

Xianglin WEI

2017-04-01

Full Text Available An Archimedean tiling is a tiling of the plane by one type of regular polygon or several types of regular polygons, and every vertex of the tiling has the same vertex characteristics. There are 11 Archimedean tiling, and this paper studies -tiling, which is an Archimedean tiling generated by squares and regular octagons in the plane, and every vertex is associated with one square and two octagons. This paper studies the number of vertices contained in an ellipse in -tiling. Through analysing the sequence of vertices lying on half chord in the ellipse, and using the method of the geometry of number and congruence in number theory, it presents an algorithm about the value of the number of vertices contained in the ellipse, and obtains a formula of limit about the number of vertices and the square of short semi-axis of the ellipse. It is proved that the value of limit is connected with the area of the corresponding central polygon. The algorithm and the formula of limit are very useful for the study of related problems in other Archimedean tilings.

ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development.

Science.gov (United States)

Alba, Rob; Fei, Zhangjun; Payton, Paxton; Liu, Yang; Moore, Shanna L; Debbie, Paul; Cohn, Jonathan; D'Ascenzo, Mark; Gordon, Jeffrey S; Rose, Jocelyn K C; Martin, Gregory; Tanksley, Steven D; Bouzayen, Mondher; Jahn, Molly M; Giovannoni, Jim

2004-09-01

Gene expression profiling holds tremendous promise for dissecting the regulatory mechanisms and transcriptional networks that underlie biological processes. Here we provide details of approaches used by others and ourselves for gene expression profiling in plants with emphasis on cDNA microarrays and discussion of both experimental design and downstream analysis. We focus on methods and techniques emphasizing fabrication of cDNA microarrays, fluorescent labeling, cDNA hybridization, experimental design, and data processing. We include specific examples that demonstrate how this technology can be used to further our understanding of plant physiology and development (specifically fruit development and ripening) and for comparative genomics by comparing transcriptome activity in tomato and pepper fruit.

Radioactive sources for ATLAS hadron tile calorimeter calibration

International Nuclear Information System (INIS)

Budagov, Yu.; Cavalli-Sforza, M.; Ivanyushenkov, Yu.

1997-01-01

The main requirements for radioactive sources applied in the TileCal calibration systems are formulated; technology of the sources production developed in the Laboratory of Nuclear Problems, JINR is described. Design and characteristics of the prototype sources manufactured in Dubna and tested on ATLAS TileCal module 0 are presented

MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands

Science.gov (United States)

Ou, Hong-Yu; He, Xinyi; Harrison, Ewan M.; Kulasekara, Bridget R.; Thani, Ali Bin; Kadioglu, Aras; Lory, Stephen; Hinton, Jay C. D.; Barer, Michael R.; Rajakumar, Kumar

2007-01-01

MobilomeFINDER (http://mml.sjtu.edu.cn/MobilomeFINDER) is an interactive online tool that facilitates bacterial genomic island or ‘mobile genome’ (mobilome) discovery; it integrates the ArrayOme and tRNAcc software packages. ArrayOme utilizes a microarray-derived comparative genomic hybridization input data set to generate ‘inferred contigs’ produced by merging adjacent genes classified as ‘present’. Collectively these ‘fragments’ represent a hypothetical ‘microarray-visualized genome (MVG)’. ArrayOme permits recognition of discordances between physical genome and MVG sizes, thereby enabling identification of strains rich in microarray-elusive novel genes. Individual tRNAcc tools facilitate automated identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites and other integration hotspots in closely related sequenced genomes. Accessory tools facilitate design of hotspot-flanking primers for in silico and/or wet-science-based interrogation of cognate loci in unsequenced strains and analysis of islands for features suggestive of foreign origins; island-specific and genome-contextual features are tabulated and represented in schematic and graphical forms. To date we have used MobilomeFINDER to analyse several Enterobacteriaceae, Pseudomonas aeruginosa and Streptococcus suis genomes. MobilomeFINDER enables high-throughput island identification and characterization through increased exploitation of emerging sequence data and PCR-based profiling of unsequenced test strains; subsequent targeted yeast recombination-based capture permits full-length sequencing and detailed functional studies of novel genomic islands. PMID:17537813

The Production and Qualification of Scintillator Tiles for the ATLAS Hadronic Calorimeter

CERN Document Server

Abdallah, J; Alexa, C; Alves, R; Amaral, P; Ananiev, A; Anderson, K; Andresen, X; Antonaki, A; Batusov, V; Bednar, P; Bergeaas, E; Biscarat, C; Blanch, O; Blanchot, G; Bohm, C; Boldea, V; Bosi, F; Bosman, M; Bromberg, C; Budagov, Yu; Calvet, D; Cardeira, C; Carli, T; Carvalho, J; Cascella, M; Castillo, M V; Costello, J; Cavalli-Sforza, M; Cavasinni, V; Cerqueira, A S; Clément, C; Cobal, M; Cogswell, F; Constantinescu, S; Costanzo, D; Da Silva, P; David, M; Davidek, T; Dawson, J; De, K; Del Prete, T; Diakov, E; Di Girolamo, B; Dita, S; Dolejsi, J; Dolezal, Z; Dotti, A; Downing, R; Drake, G; Efthymiopoulos, I; Errede, D; Errede, S; Farbin, A; Fassouliotis, D; Feng, E; Fenyuk, A; Ferdi, C; Ferreira, B C; Ferrer, A; Flaminio, V; Flix, J; Francavilla, P; Fullana, E; Garde, V; Gellerstedt, K; Giakoumopoulou, V; Giangiobbe, V; Gildemeister, O; Gilewsky, V; Giokaris, N; Gollub, N; Gomes, A; González, V; Gouveia, J; Grenier, P; Gris, P; Guarino, V; Guicheney, C; Sen-Gupta, A; Hakobyan, H; Haney, M; Hellman, S; Henriques, A; Higón, E; Hill, N; Holmgren, S; Hruska, I; Hurwitz, M; Huston, J; Jen-La Plante, I; Jon-And, K; Junk, T; Karyukhin, A; Khubua, J; Klereborn, J; Konsnantinov, V; Kopikov, S; Korolkov, I; Krivkova, P; Kulchitskii, Yu A; Kurochkin, Yu; Kuzhir, P; Lapin, V; LeCompte, T; Lefèvre, R; Leitner, R; Li, J; Liablin, M; Lokajícek, M; Lomakin, Y; Lourtie, P; Lovas, L; Lupi, A; Maidantchik, C; Maio, A; Maliukov, S; Manousakis, A; Marques, C; Marroquim, F; Martin, F; Mazzoni, E; Merritt, F S; Myagkov, A; Miller, R; Minashvili, I; Miralles, L; Montarou, G; Némécek, S; Nessi, M; Nikitine, I; Nodulman, L; Norniella, O; Onofre, A; Oreglia, M; Palan, B; Pallin, D; Pantea, D; Pereira, A; Pilcher, J E; Pina, J; Pinhão, J; Pod, E; Podlyski, F; Portell, X; Poveda, J; Pribyl, a L; Price, L E; Proudfoot, J; Ramalho, M; Ramstedt, M; Raposeiro, L; Reis, J; Richards, R; Roda, C; Romanov, V; Rosnet, P; Roy, P; Ruiz, A; Rumiantsau, V; Rusakovich, N; Sada Costa, J; Salto, O; Salvachúa, B; Sanchis, E; Sanders, H; Santoni, C; Santos, J; Saraiva, J G; Sarri, F; Says, L P; Schlager, G; Schlereth, J L; Seixas, J M; Selldén, B; Shalanda, N; Shevtsov, P; Shochet, M; Silva, J; Simaitis, V; Simonyan, M; Sisakian, A; Sjölin, J; Solans, C; Solodkov, A; Solovyanov, O; Sosebee, M; Spanó, F; Speckmeyer, P; Stanek, R; Starchenko, E; Starovoitov, P; Suk, M; Sykora, I; Tang, F; Tas, P; Teuscher, R; Tischenko, M; Tokar, S; Topilin, N; Torres, J; Underwood, D; Usai, G; Valero, A; Valkár, S; Valls, J A; Vartapetian, A; Vazeille, F; Vellidis, C; Ventura, F; Vichou, I; Vivarelli, I; Volpi, M; White, A; Zaitsev, A; Zaytsev, Yu; Zenin, A; Zenis, T; Zenonos, Z; Zenz, S; Zilka, B

2007-01-01

The production of the scintillator tiles for the ATLAS Tile Calorimeter is presented. In addition to the manufacture and production, the properties of the tiles will be presented including light yield, uniformity and stability.

Unraveling the rat blood genome-wide transcriptome after oral administration of lavender oil by a two-color dye-swap DNA microarray approach

Directory of Open Access Journals (Sweden)

Motohide Hori

2016-06-01

Full Text Available Lavender oil (LO is a commonly used essential oil in aromatherapy as non-traditional medicine. With an aim to demonstrate LO effects on the body, we have recently established an animal model investigating the influence of orally administered LO in rat tissues, genome-wide. In this brief, we investigate the effect of LO ingestion in the blood of rat. Rats were administered LO at usual therapeutic dose (5 mg/kg in humans, and following collection of the venous blood from the heart and extraction of total RNA, the differentially expressed genes were screened using a 4 × 44-K whole-genome rat chip (Agilent microarray platform; Agilent Technologies, Palo Alto, CA, USA in conjunction with a two-color dye-swap approach. A total of 834 differentially expressed genes in the blood were identified: 362 up-regulated and 472 down-regulated. These genes were functionally categorized using bioinformatics tools. The gene expression inventory of rat blood transcriptome under LO, a first report, has been deposited into the Gene Expression Omnibus (GEO: GSE67499. The data will be a valuable resource in examining the effects of natural products, and which could also serve as a human model for further functional analysis and investigation.

Genomic interrogation of mechanism(s) underlying cellular responses to toxicants

International Nuclear Information System (INIS)

Amin, Rupesh P.; Hamadeh, Hisham K.; Bushel, Pierre R.; Bennett, Lee; Afshari, Cynthia A.; Paules, Richard S.

2002-01-01

Assessment of the impact of xenobiotic exposure on human health and disease progression is complex. Knowledge of mode(s) of action, including mechanism(s) contributing to toxicity and disease progression, is valuable for evaluating compounds. Toxicogenomics, the subdiscipline which merges genomics with toxicology, holds the promise to contributing significantly toward the goal of elucidating mechanism(s) by studying genome-wide effects of xenobiotics. Global gene expression profiling, revolutionized by microarray technology and a crucial aspect of a toxicogenomic study, allows measuring transcriptional modulation of thousands of genes following exposure to a xenobiotic. We use our results from previous studies on compounds representing two different classes of xenobiotics (barbiturate and peroxisome proliferator) to discuss the application of computational approaches for analyzing microarray data to elucidate mechanism(s) underlying cellular responses to toxicants. In particular, our laboratory demonstrated that chemical-specific patterns of gene expression can be revealed using cDNA microarrays. Transcript profiling provides discrimination between classes of toxicants, as well as, genome-wide insight into mechanism(s) of toxicity and disease progression. Ultimately, the expectation is that novel approaches for predicting xenobiotic toxicity in humans will emerge from such information

Genomics approaches in the understanding of Entamoeba ...

African Journals Online (AJOL)

STORAGESEVER

2009-04-20

Apr 20, 2009 ... Here, we reviewed recent advances in the efforts to understand ... expression regulation in E. histolytica by using genomic approaches based on microarray technology ... tic abscesses that result in approximately 70,000 -.

On the algebraic characterization of aperiodic tilings related to ADE-root systems

International Nuclear Information System (INIS)

Kellendonk, J.

1992-09-01

The algebraic characterization of sets of locally equivalent aperiodic tilings, being examples of quantum spaces, is conducted for a certain type of tilings in a manner proposed by A. Connes. These 2-dimensional tilings are obtained by application of the strip method to the root lattice of an ADE-Coxeter group. The plane along which the strip is constructed is determined by the canonical Coxeter element leading to the result that a 2- dimensional tiling decomposes into a cartesian product of two 1- dimensional tilings. The properties of the tilings are investigated, including selfsimilarity, and the determination of the relevant algebraic is considered, namely the ordered K 0 -group of an algebra naturaly assigned to the quantum space. The result also yields an application of the 2-dimensional abstract gap labelling theorem. (orig.)

Divertor tungsten tiles erosion in the region of the castellated gaps

Energy Technology Data Exchange (ETDEWEB)

Hu, Wanpeng, E-mail: wangdez@dlut.edu.cn; Sang, Chaofeng; Sun, Zhenyue; Wang, Dezhen

2016-11-01

Highlights: • Simulation of the tungsten tiles erosion by different impurities in the divertor gap region is done by using a 2d3v Particle-In-Cell code. • High-Z impurity causes the largest erosion rate on W tile. • The peak physical sputtering erosion rate locates at the plasma-facing corners. - Abstract: Erosion of tungsten (W) is a very important issue for the future fusion device. The castellated divertor makes it more complicated due to complex geometry of the gap between the tiles. In this work, the plasma behaviors and resulting W tile erosion in the divertor tile gap region are studied by using a two dimension-in-space and three dimension-in-velocity (2d3 v) Particle-In-Cell (PIC) code. Deuterium ions (D{sup +}) and electrons are traced self-consistently in the simulation to provide the plasma background. Since there are lots of impurities, which may make a great impact on the tile erosion, in the divertor region to radiate the power, the erosion of W tile by different species are thus considered. The contributions of deuterium and impurities: Li, C, Ne, and Ar, to the W erosion, are studied under EAST conditions to show a straightforward insight. It is observed that the physical sputtering of W tile by impurities is much higher than that by the D ions, and the peak erosion region locates at the plasma-facing corners.

Stoneware tile manufacturing using rice straw ash as feldspar replacement

International Nuclear Information System (INIS)

Alvaro Guzman, A.; John Torres, L.; Martha Cedeno, V.; Silvio Delvasto, A.; Vicente Amigo, B.; Enrique Sanchez, V.

2013-01-01

In this research are presented the results of using rice straw ash (RSA) in low proportions as substitute of feldspar for manufacturing stoneware tiles. Specimens of semidry triaxial mixtures, where feldspar was substituted for different percentages (25 % and 50 %) of RSA, were prepared by uniaxial pressing, followed by drying and sintering. Physical and mechanical properties of sintered bodies were evaluated. Porcelain stoneware tile specimens C0 and CF25 reached bending strength and water absorption values were in accordance with standard ISO 13006 (Annex G, BIa) ( ≥ 35 MPa and ≤ 0.5 %, respectively). However, in porcelain stoneware tile specimens CF50 due to bloating phenomenon was not possible obtain commercial tiles in accordance with standard ISO 13006. By using Scanning Electron Microscopy (SEM) needles of primary and secondary mullite were identified in a vitreous phase; and by using X-Ray Diffraction (XRD) mullite and quartz phases were identified. It was concluded that feldspar can be substituted positively by RSA in stoneware tile pastes. (Author)

Valorization of rice straw waste: production of porcelain tiles

Directory of Open Access Journals (Sweden)

Álvaro Guzmán A

2015-12-01

Full Text Available Abstract The rice industry generates huge amounts of rice straw ashes (RSA. This paper presents the results of an experimental research work about the incorporation of RSA waste as a new alternative raw material for production of porcelain tiles. The RSA replaces, partially or completely, the non-plastic raw materials (quartz (feldspathic sand in this research and feldspar, that together with the clays, constitute the major constituents of formulations of porcelain tiles. A standard industrial composition (0% RSA and two more compositions in which feldspar and feldspathic sand were replaced with two percentages of RSA (12.5% RSA and 60% RSA were formulated, keeping the clay content constant. The mixtures were processed, reproducing industrial porcelain tile manufacturing conditions by the dry route and fired at peak temperatures varying from 1140-1260 ºC. The results showed that additions of 12.5% RSA in replacement of feldspar and feldspathic sand allowed producing porcelain tiles that did not display marked changes in processing behaviour, in addition to obtain a microstructure and the typical mineralogical phases of porcelain tile. Thus, an alternative use of an agricultural waste material is proposed, which can be translated into economic and environmental benefits.

Producing superhydrophobic roof tiles

International Nuclear Information System (INIS)

Carrascosa, Luis A M; Facio, Dario S; Mosquera, Maria J

2016-01-01

Superhydrophobic materials can find promising applications in the field of building. However, their application has been very limited because the synthesis routes involve tedious processes, preventing large-scale application. A second drawback is related to their short-term life under outdoor conditions. A simple and low-cost synthesis route for producing superhydrophobic surfaces on building materials is developed and their effectiveness and their durability on clay roof tiles are evaluated. Specifically, an organic–inorganic hybrid gel containing silica nanoparticles is produced. The nanoparticles create a densely packed coating on the roof tile surface in which air is trapped. This roughness produces a Cassie–Baxter regime, promoting superhydrophobicity. A surfactant, n-octylamine, was also added to the starting sol to catalyze the sol–gel process and to coarsen the pore structure of the gel network, preventing cracking. The application of ultrasound obviates the need to use volatile organic compounds in the synthesis, thereby making a ‘green’ product. It was also demonstrated that a co-condensation process effective between the organic and inorganic species is crucial to obtain durable and effective coatings. After an aging test, high hydrophobicity was maintained and water absorption was completely prevented for the roof tile samples under study. However, a transition from a Cassie–Baxter to a Wenzel state regime was observed as a consequence of the increase in the distance between the roughness pitches produced by the aging of the coating. (paper)

Automatic generation of aesthetic patterns on fractal tilings by means of dynamical systems

International Nuclear Information System (INIS)

Chung, K.W.; Ma, H.M.

2005-01-01

A fractal tiling or f-tiling is a tiling which possesses self-similarity and the boundary of which is a fractal. In this paper, we investigate the classification of fractal tilings with kite-shaped and dart-shaped prototiles from which three new f-tilings are found. Invariant mappings are constructed for the creation of aesthetic patterns on such tilings. A modified convergence time scheme is described, which reflects the rate of convergence of various orbits and at the same time, enhances the artistic appeal of a generated image. A scheme based on the frequency of visit at a pixel is used to generate chaotic attractors

Usefulness of the SNP microarray technology to identify rare mutations in the case of perinatal death

DEFF Research Database (Denmark)

Hoeffding, L. K.; Kock, K. F.; Johnsen, Iben Birgit Gade

2015-01-01

The single nucleotide polymorphism (SNP) microarray technology has emerged as a powerful tool to screen the whole genome for sub-microscopic duplications and deletions that are not detectable by traditional cytogenetic analysis. Case: We report a case of a female twin born at 27th week of gestation...

The design of central column protection tiles for the TCV tokamak

International Nuclear Information System (INIS)

Pitts, R.A.; Chavan, R.; Moret, J.M.

1999-01-01

The large variety of plasma shapes produced in the TCV tokamak places unique demands on the plasma facing surfaces. In particular, the central column graphite armour tiles are solicited during the creation of all TCV plasmas and function as power handling surfaces for both limited and diverted discharges. The higher power flux densities accompanying the addition of electron cyclotron heating systems have necessitated a new, optimized, design for these tiles. The optimization process and the subsequent new tile design are described. A basic 'two point' model of the scrape-off layer plasma in conjunction with TCV equilibrium reconstructions and a simplified representation of the local magnetic field line geometry are used to impose simulated power flux densities onto a parametric toroidal tile contour. The thermo-mechanical response of the tile is then investigated via full 3-D finite element simulations accounting for the non-linear temperature dependence of the graphite thermal diffusivity and radiation from the tile surface. The final design choice is a compromise between the requirements for adequate power handling for a range of magnetic configurations, the need to protect against tile edge misalignment in the presence of grazing field line angles of incidence and the space restrictions imposed by vacuum vessel design. (author)

Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution

DEFF Research Database (Denmark)

Novak, Jaroslav P; Kim, Seon-Young; Xu, Jun

2006-01-01

BACKGROUND: DNA microarrays are a powerful technology that can provide a wealth of gene expression data for disease studies, drug development, and a wide scope of other investigations. Because of the large volume and inherent variability of DNA microarray data, many new statistical methods have...

Batched Tile Low-Rank GEMM on GPUs

KAUST Repository

Charara, Ali

2018-02-01

Dense General Matrix-Matrix (GEMM) multiplication is a core operation of the Basic Linear Algebra Subroutines (BLAS) library, and therefore, often resides at the bottom of the traditional software stack for most of the scientific applications. In fact, chip manufacturers give a special attention to the GEMM kernel implementation since this is exactly where most of the high-performance software libraries extract the hardware performance. With the emergence of big data applications involving large data-sparse, hierarchically low-rank matrices, the off-diagonal tiles can be compressed to reduce the algorithmic complexity and the memory footprint. The resulting tile low-rank (TLR) data format is composed of small data structures, which retains the most significant information for each tile. However, to operate on low-rank tiles, a new GEMM operation and its corresponding API have to be designed on GPUs so that it can exploit the data sparsity structure of the matrix while leveraging the underlying TLR compression format. The main idea consists in aggregating all operations onto a single kernel launch to compensate for their low arithmetic intensities and to mitigate the data transfer overhead on GPUs. The new TLR GEMM kernel outperforms the cuBLAS dense batched GEMM by more than an order of magnitude and creates new opportunities for TLR advance algorithms.

ATLAS TileCal submodule B-field measurement

International Nuclear Information System (INIS)

Budagov, Yu.A.; Fedorenko, S.B.; Kalinichenko, V.V.; Lomakin, Yu.F.; Vorozhtsov, S.B.; Nessi, M.

1997-01-01

The work was done to cross check of the previous measurement done at CERN and to simulate the magnetic structure in the vicinity of the symmetry plane of the TileCal. To perform magnetic measurements for submodule the magnet E2 was chosen. The magnetometer used in the magnetic test of the submodule consists of Hall current supply and Hall voltage measuring device. The indium antimonide Hall probe used in this measurement is a model PKhE 606. Experimental set-up provides a true measurement accuracy of order ± 1%. External magnetic field measurements were conducted at the outer surface of the submodule. Two levels of the external field were applied: 108 Gs and 400 Gs. The result of this measurement in general confirms the data, obtained at CERN, but the shielding capability of the submodule under consideration was ∼ 20% higher than there. The field at the tile location is < 150 Gs up to the external field level 500 Gs and the tile field grows much less than the external field level in this range. The data obtained in this measurement could be used as a benchmark when producing a computer model of the TileCal magnetic field distribution

Synthesizing genome-wide association studies and expression microarray reveals novel genes that act in the human growth plate to modulate height.

Science.gov (United States)

Lui, Julian C; Nilsson, Ola; Chan, Yingleong; Palmer, Cameron D; Andrade, Anenisia C; Hirschhorn, Joel N; Baron, Jeffrey

2012-12-01

Previous meta-analysis of genome-wide association (GWA) studies has identified 180 loci that influence adult height. However, each GWA locus typically comprises a set of contiguous genes, only one of which presumably modulates height. We reasoned that many of the causative genes within these loci influence height because they are expressed in and function in the growth plate, a cartilaginous structure that causes bone elongation and thus determines stature. Therefore, we used expression microarray studies of mouse and rat growth plate, human disease databases and a mouse knockout phenotype database to identify genes within the GWAS loci that are likely required for normal growth plate function. Each of these approaches identified significantly more genes within the GWA height loci than at random genomic locations (P analysis strongly implicates 78 genes in growth plate function, including multiple genes that participate in PTHrP-IHH, BMP and CNP signaling, and many genes that have not previously been implicated in the growth plate. Thus, this analysis reveals a large number of novel genes that regulate human growth plate chondrogenesis and thereby contribute to the normal variations in human adult height. The analytic approach developed for this study may be applied to GWA studies for other common polygenic traits and diseases, thus providing a new general strategy to identify causative genes within GWA loci and to translate genetic associations into mechanistic biological insights.

Development of Clay Tile Coatings for Steep-Sloped Cool Roofs

Directory of Open Access Journals (Sweden)

Lucia Brinchi

2013-07-01

Full Text Available Most of the pitched roofs of existing buildings in Europe are covered by non-white roofing products, e.g., clay tiles. Typical, cost effective, cool roof solutions are not applicable to these buildings due to important constraints deriving from: (i the owners of homes with roofs visible from the ground level; (ii the regulation about the preservation of the historic architecture and the minimization of the visual environment impact, in particular in historic centers. In this perspective, the present paper deals with the development of high reflective coatings with the purpose to elaborate “cool” tiles with the same visual appearance of traditional tiles for application to historic buildings. Integrated experimental analyses of reflectance, emittance, and superficial temperature were carried out. Deep analysis of the reflectance spectra is undertaken to evaluate the effect of different mineral pigments, binders, and an engobe basecoat. Two tile typologies are investigated: substrate-basecoat-topcoat three-layer tile and substrate-topcoat two-layer tile. The main results show that the developed coatings are able to increase the overall solar reflectance by more than 20% with acceptable visual appearance, suitable for application in historic buildings. Additionally, the effect of a substrate engobe layer allows some further contribution to the increase of the overall reflectance characteristics.

ATLAS TileCal LVPS Upgrade Hardware and Testing

CERN Document Server

Hibbard, Michael James; The ATLAS collaboration; Hadavand, Haleh Khani

2018-01-01

UTA (University of Texas at Arlington) has been designing and producing new testing stations to ensure the reliability and quality of new TileLVPS (Low Voltage Power Supplies), also produced at UTA, which will power the next generation of upgraded hardware in the TileCal (Tile Calorimeter) system of ATLAS at CERN. UTA has produced two new types of testing stations, which build upon the previous generation of testing stations used in the initial production of the TileCal system. The first station is the Initial Test Station, and quickly quantifies a multitude of performance metrics of a LVPS. We have developed our own PC based program which graphically display and records onto file these metrics. A few notable metrics we are measuring are the system clock and its jitter. Excessive clock jitter in LVPS can affect system stability and derate the working range of the system duty cycle. This station also verifies protection circuitry of LVPS, which protects it from over temperature, current and voltage. The second...

The ATLAS Tile Calorimeter Performance at LHC

CERN Document Server

Molander, S; The ATLAS collaboration

2013-01-01

The Tile Calorimeter (TileCal) is the central section of the hadronic calorimeter of the ATLAS experiment at LHC. The TileCal pays a major role in detecting hadrons, jets, hadronic decays of tau leptons and measuring the missing transverse energy. Due to the very good signal to noise ratio it assists the muon spectrometer in the identification and reconstruction of muons, which are also a tool for the in situ energy scale validation. The results presented here stem from the data collection in dedicated calibration runs, in cosmic rays data-taking and in LHC collisions along 3 years of operation. The uniformity, stability and precision of the energy scale, the time measurement capabilities and the robustness of the performance against pile-up are exposed through the usage of hadronic and muon final states and confirm the design expectations.

Flat tile armour cooled by hypervapotron tube: a possible technology for ITER

International Nuclear Information System (INIS)

Schlosser, J.; Escourbiac, F.; Bayetti, P.; Missirlian, M.; Mitteau, R.; Schedler, B.; Bobin-Vastra, I.

2003-01-01

Carbon fibre composite (CFC) flat tile armours for actively cooled plasma facing components (PFC's) are an important challenge for controlled fusion machine. Flat tile concepts, water cooled by tubes, were studied, developed, tested and finally experienced with success in Tore Supra. The components were designed for 10 MW/m 2 and mock-ups were successfully fatigue tested at 15 MW/m 2 , 1000 cycles. For ITER, a tube-in-tile concept was developed and mock-ups sustained up to 25 MW/m 2 for 1000 cycles without failure. Recently flat tile armored mock-ups cooled by Hypervapotron tube successfully sustained a cascade failure test under a mean heat flux of 10 MW/m 2 but with a doubling of the heat flux on some tiles to simulate missing tiles (500 cycles). This encouraging results lead to reconsider the limits for flat tile concept when cooled by Hypervapotron tube. New tests are now scheduled to investigate these limits notably in regards to the ITER requirements. The concept could also be experimented in Tore Supra by installing a new limiter into the machine. (authors)

Deposition of deuterium and metals on divertor tiles in the DIII-D tokamak

International Nuclear Information System (INIS)

Walsh, D.S.; Doyle, B.L.; Jackson, G.L.

1991-01-01

Hydrogen recycling and impurity influx are important issues in obtaining high confinement discharges in the D3-D tokamak. To reduce metallic impurities in D3-D, 40% of the wall area, including the highest heat flux zones, have been covered with graphite tiles. However erosion, redeposition and hydrogen retention in the tiles, as well as metal transport from the remaining Inconel walls can lead to enhanced recycling and impurity influx. Hydrogen and metal retention in divertor floor tiles have been measured using external ion beam analysis techniques following four campaigns where tiles were exposed to several thousand tokamak discharges. The areal density of deuterium retained following exposure to tokamak plasmas was measured with external nuclear reaction analysis. External proton-induced x-ray emission analysis was used to measure the areal densities of metallic impurities deposited upon the divertor tiles either by sputtering of metallic components during discharges or as contamination during tile fabrication. Measurements for both deuterium and metallic impurities were taken on both the tile surfaces which face the operating plasma and the surfaces on the side of the tiles which form the small gaps separating each of the tiles in the divertor. The highest areal densities of both deuterium and metals were found on the plasma-facing surface near the inner strike point region of each set of divertor tiles. Significant deposits, extending as fast a 1 cm from the plasma-facing and containing up to forty percent of the total divertor deposition, were also observed on the gap-forming surfaces of the tiles

Detecting Subsurface Agricultural Tile Drainage using GIS and Remote Sensing Technique

Science.gov (United States)

Budhathoki, M.; Gokkaya, K.; Tank, J. L.; Christopher, S. F.; Hanrahan, B.

2015-12-01

Subsurface tile drainage is a common practice in many of the row crop dominated agricultural lands in the Upper Midwest, which increases yield by making the soil more productive. It is reported that nearly half of all cropland in Indiana benefits from some sort of artificial drainage. However, subsurface tile has a significant negative impact on surface water quality by providing a fast means of transport for nutrients from fertilizers. Therefore, generating spatial data of tile drainage in the field is important and useful for agricultural landscape and hydrological studies. Subsurface tile drains in Indiana's croplands are not widely mapped. In this study, we will delineate subsurface tile drainage in agricultural land in Shatto Ditch watershed, located in Kosciusko County, Indiana. We will use geo-spatial methodology, which was purposed by earlier researchers to detect tile drainage. We will use aerial color-infrared and satellite imagery along with Light Detection and Ranging (LiDAR) data. In order to map tile lines with possible accuracy, we will use GIS-based analysis in combination with remotely sensed data. This research will be comprised of three stages: 1) masking out the potential drainage area using a decision tree rule based on land cover information, soil drainage category, surface slope, and satellite image differencing technique, 2) delineate tile lines using image processing techniques, and 3) check the accuracy of mapped tile lines with ground control points. To our knowledge, this study will be the first to check the accuracy of mapping with ground truth data. Based on the accuracy of results, we will extend the methodology to greater spatial scales. The results are expected to contribute to better characterizing and controlling water pollution sources in Indiana, which is a major environmental problem.

Consolidation and upgrades of the ATLAS Tile Calorimeter

CERN Document Server

Cerda Alberich, Leonor; The ATLAS collaboration

2017-01-01

This is a presentation of the status of the ATLAS Tile Calorimeter during the EYETS and before starting 2017 data-taking. Updates on the upgrade of the readout system such as doubling the RODs output links and the number of processing units (PUs) are being worked on at the moment as well as items concerning the maintenance of the detector which involves issues such as cooling leaks and consolidation of the Low Voltage Power Supplies, which are being replaced if necessary. Other updates include works on the Tile calibration, in particular on the Cesium system. In addition, the whole Tile readout electronics is being replaced for Phase-II and it is being tested in Test Beam area.

Fibre optic microarrays.

Science.gov (United States)

Walt, David R

2010-01-01

This tutorial review describes how fibre optic microarrays can be used to create a variety of sensing and measurement systems. This review covers the basics of optical fibres and arrays, the different microarray architectures, and describes a multitude of applications. Such arrays enable multiplexed sensing for a variety of analytes including nucleic acids, vapours, and biomolecules. Polymer-coated fibre arrays can be used for measuring microscopic chemical phenomena, such as corrosion and localized release of biochemicals from cells. In addition, these microarrays can serve as a substrate for fundamental studies of single molecules and single cells. The review covers topics of interest to chemists, biologists, materials scientists, and engineers.

Foam-on-Tile Damage Model

Science.gov (United States)

Koharchik, Michael; Murphy, Lindsay; Parker, Paul

2012-01-01

An impact model was developed to predict how three specific foam types would damage the Space Shuttle Orbiter insulating tiles. The inputs needed for the model are the foam type, the foam mass, the foam impact velocity, the foam impact incident angle, the type being impacted, and whether the tile is new or aged (has flown at least one mission). The model will determine if the foam impact will cause damage to the tile. If it can cause damage, the model will output the damage cavity dimensions (length, depth, entry angle, exit angle, and sidewall angles). It makes the calculations as soon as the inputs are entered (less than 1 second). The model allows for the rapid calculation of numerous scenarios in a short time. The model was developed from engineering principles coupled with significant impact testing (over 800 foam impact tests). This model is applicable to masses ranging from 0.0002 up to 0.4 pound (0.09 up to 181 g). A prior tool performed a similar function, but was limited to the assessment of a small range of masses and did not have the large test database for verification. In addition, the prior model did not provide outputs of the cavity damage length, entry angle, exit angle, or sidewall angles.

Quasiperiodic canonical-cell tiling with pseudo icosahedral symmetry

Science.gov (United States)

Fujita, Nobuhisa

2017-10-01

Icosahedral quasicrystals and their approximants are generally described as packing of icosahedral clusters. Experimental studies show that clusters in various approximants are orderly arranged, such that their centers are located at the nodes (or vertices) of a periodic tiling composed of four basic polyhedra called the canonical cells. This so called canonical-cell geometry is likely to serve as a common framework for modeling how clusters are arranged in approximants, while its applicability seems to extend naturally to icosahedral quasicrystals. To date, however, it has not been proved yet if the canonical cells can tile the space quasiperiodically, though we usually believe that clusters in icosahedral quasicrystals are arranged such that quasiperiodic long-range order as well as icosahedral point symmetry is maintained. In this paper, we report for the first time an iterative geometrical transformation of the canonical cells defining a so-called substitution rule, which we can use to generate a class of quasiperiodic canonical-cell tilings. Every single step of the transformation proceeds as follows: each cell is first enlarged by a magnification ratio of τ3 (τ = golden mean) and then subdivided into cells of the original size. Here, cells with an identical shape can be subdivided in several distinct manners depending on how their adjacent neighbors are arranged, and sixteen types of cells are identified in terms of unique subdivision. This class of quasiperiodic canonical-cell tilings presents the first realization of three-dimensional quasiperiodic tilings with fractal atomic surfaces. There are four distinct atomic surfaces associated with four sub-modules of the primitive icosahedral module, where a representative of the four submodules corresponds to the Σ = 4 coincidence site module of the icosahedral module. It follows that the present quasiperiodic tilings involve a kind of superlattice ordering that manifests itself in satellite peaks in the

Upgrading the ATLAS Tile Calorimeter electronics

CERN Document Server

Souza, J; The ATLAS collaboration

2014-01-01

The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the central region of the ATLAS experiment at LHC. The TileCal readout consists of about 10000 channels. Its main upgrade will occur for the High Luminosity LHC phase (phase 2) where the peak luminosity will increase 5-fold compared to the design luminosity (10exp34 cm−2s−1) but with maintained energy (i.e. 7+7 TeV). An additional increase of the average luminosity with a factor of 2 can be achieved by luminosity leveling. This upgrade will probably happen around 2023. The upgrade aims at replacing the majority of the on- and off-detector electronics so that all calorimeter signals are directly digitized and sent to the off-detector electronics in the counting room. To achieve the required reliability, redundancy has been introduced at different levels. The smallest independent on-detector electronics module has been reduced from 45 channels to 6, greatly reducing the consequences of a failure in the on-detector electronics. The size of t...

Small regions of overlapping deletions on 6q26 in human astrocytic tumours identified using chromosome 6 tile path array CGH

Science.gov (United States)

Ichimura, Koichi; Mungall, Andrew J; Fiegler, Heike; Pearson, Danita M.; Dunham, Ian; Carter, Nigel P; Collins, V. Peter

2009-01-01

Deletions of chromosome 6 are a common abnormality in diverse human malignancies including astrocytic tumours, suggesting the presence of tumour suppressor genes (TSG). In order to help identify candidate TSGs, we have constructed a chromosome 6 tile path microarray. The array contains 1780 clones (778 PACs and 1002 BACs) that cover 98.3% of the published chromosome 6 sequences. A total of 104 adult astrocytic tumours (10 diffuse astrocytomas, 30 anaplastic astrocytomas (AA), 64 glioblastomas (GB)) were analysed using this array. Single copy number change was successfully detected and the result was in general concordant with a microsatellite analysis. The pattern of copy number change was complex with multiple interstitial deletions/gains. However, a predominance of telomeric 6q deletions was seen. Two small common and overlapping regions of deletion at 6q26 were identified. One was 1002 kb in size and contained PACRG and QKI, while the second was 199 kb and harbours a single gene, ARID1B. The data show that the chromosome 6 tile path array is useful in mapping copy number changes with high resolution and accuracy. We confirmed the high frequency of chromosome 6 deletions in AA and GB, and identified two novel commonly deleted regions that may harbour TSGs. PMID:16205629

Gene expression profiling to characterize sediment toxicity – a pilot study using Caenorhabditis elegans whole genome microarrays

Directory of Open Access Journals (Sweden)

Reifferscheid Georg

2009-04-01

Full Text Available Abstract Background Traditionally, toxicity of river sediments is assessed using whole sediment tests with benthic organisms. The challenge, however, is the differentiation between multiple effects caused by complex contaminant mixtures and the unspecific toxicity endpoints such as survival, growth or reproduction. The use of gene expression profiling facilitates the identification of transcriptional changes at the molecular level that are specific to the bio-available fraction of pollutants. Results In this pilot study, we exposed the nematode Caenorhabditis elegans to three sediments of German rivers with varying (low, medium and high levels of heavy metal and organic contamination. Beside chemical analysis, three standard bioassays were performed: reproduction of C. elegans, genotoxicity (Comet assay and endocrine disruption (YES test. Gene expression was profiled using a whole genome DNA-microarray approach to identify overrepresented functional gene categories and derived cellular processes. Disaccharide and glycogen metabolism were found to be affected, whereas further functional pathways, such as oxidative phosphorylation, ribosome biogenesis, metabolism of xenobiotics, aging and several developmental processes were found to be differentially regulated only in response to the most contaminated sediment. Conclusion This study demonstrates how ecotoxicogenomics can identify transcriptional responses in complex mixture scenarios to distinguish different samples of river sediments.

Terahertz NDE application for corrosion detection and evaluation under Shuttle tiles

Science.gov (United States)

Anastasi, Robert F.; Madaras, Eric I.; Seebo, Jeffrey P.; Smith, Stephen W.; Lomness, Janice K.; Hintze, Paul E.; Kammerer, Catherine C.; Winfree, William P.; Russell, Richard W.

2007-04-01

Pulsed Terahertz NDE is being examined as a method to inspect for possible corrosion under Space Shuttle Tiles. Other methods such as ultrasonics, infrared, eddy current and microwave technologies have demonstrable shortcomings for tile NDE. This work applies Terahertz NDE, in the frequency range between 50 GHz and 1 THz, for the inspection of manufactured corrosion samples. The samples consist of induced corrosion spots that range in diameter (2.54 to 15.2 mm) and depth (0.036 to 0.787 mm) in an aluminum substrate material covered with tiles. Results of these measurements are presented for known corrosion flaws both covered and uncovered and for blind tests with unknown corrosion flaws covered with attached tiles. The Terahertz NDE system is shown to detect all artificially manufactured corrosion regions under a Shuttle tile with a depth greater than 0.13 mm.

Genomic diversity of Escherichia isolates from diverse habitats.

Directory of Open Access Journals (Sweden)

Seungdae Oh

Full Text Available Our understanding of the Escherichia genus is heavily biased toward pathogenic or commensal isolates from human or animal hosts. Recent studies have recovered Escherichia isolates that persist, and even grow, outside these hosts. Although the environmental isolates are typically phylogenetically distinct, they are highly related to and phenotypically indistinguishable from their human counterparts, including for the coliform test. To gain insights into the genomic diversity of Escherichia isolates from diverse habitats, including freshwater, soil, animal, and human sources, we carried out comparative DNA-DNA hybridizations using a multi-genome E. coli DNA microarray. The microarray was validated based on hybridizations with selected strains whose genome sequences were available and used to assess the frequency of microarray false positive and negative signals. Our results showed that human fecal isolates share two sets of genes (n>90 that are rarely found among environmental isolates, including genes presumably important for evading host immune mechanisms (e.g., a multi-drug transporter for acids and antimicrobials and adhering to epithelial cells (e.g., hemolysin E and fimbrial-like adhesin protein. These results imply that environmental isolates are characterized by decreased ability to colonize host cells relative to human isolates. Our study also provides gene markers that can distinguish human isolates from those of warm-blooded animal and environmental origins, and thus can be used to more reliably assess fecal contamination in natural ecosystems.

Genome plasticity of Vibrio parahaemolyticus: microevolution of the 'pandemic group'

Directory of Open Access Journals (Sweden)

Liu Xiumei

2008-11-01

Full Text Available Abstract Background Outbreak of V. parahaemolyticus infections occurred since 1996 was linked to a proposed clonal complex, the pandemic group. The whole genome sequence provides an unprecedented opportunity for dissecting genome plasticity and phylogeny of the populations of V. parahaemolyticus. In the present work, a whole-genome cDNA microarray was constructed to compare the genomic contents of a collection of 174 strains of V. parahaemolyticus. Results Genes that present variably in the genome accounted for about 22% of the whole gene pool on the genome. The phylogenetic analysis of microarray data generated a minimum spanning tree that depicted the phylogenetic structure of the 174 strains. Strains were assigned into five complexes (C1 to C5, and those in each complex were related genetically and phylogenetically. C3 and C4 represented highly virulent clinical clones. C2 and C3 constituted two different clonal complexes 'old-O3:K6 clone' and 'pandemic clone', respectively. C3 included all the 39 pandemic strains tested (trh-, tdh+ and GS-PCR+, while C2 contained 12 pre-1996 'old' O3:K6 strains (trh+, tdh- and GS-PCR- tested herein. The pandemic clone (post-1996 'new' O3:K6 and its derivates O4:K68, O1:K25, O1:KUT and O6:K18 might be emerged from the old-O3:K6 clone, which was promoted by acquisition of toxRS/new sequence and genomic islands. A phylogenetic intermediate O3:K6 clade (trh-, tdh- and GS-PCR+ was identified between the pandemic and old-O3:K6 clones. Conclusion A comprehensive overview of genomic contents in a large collection of global isolates from the microarray-based comparative genomic hybridization data enabled us to construct a phylogenetic structure of V. parahaemolyticus and an evolutionary history of the pandemic group (clone of this pathogen.

Deposition of deuterium and metals on divertor tiles in the DIII--D tokamak

International Nuclear Information System (INIS)

Walsh, D.S.; Doyle, B.L.; Jackson, G.L.

1992-01-01

Hydrogen recycling and impurity influx are important issues in obtaining high confinement discharges in the DIII--D tokamak. To reduce metallic impurities in DIII--D, 40% of the wall area, including the highest heat flux zones, have been covered with graphite tiles. However, erosion, redeposition, and hydrogen retention in the tiles, as well as metal transport from the remaining Inconel walls, can lead to enhanced recycling and impurity influx. Hydrogen and metal retention in divertor floor tiles have been measured using external ion beam analysis techniques following four campaigns where tiles were exposed to several thousand tokamak discharges. The areal density of deuterium retained following exposure to tokamak plasmas was measured with external nuclear reaction analysis. External proton-induced x-ray emission analysis was used to measure the areal densities of metallic impurities deposited upon the divertor tiles either by sputtering of metallic components during discharges or as contamination during tile fabrication. Measurements for both deuterium and metallic impurities were taken on both the tile surfaces which face the operating plasma and the surfaces on the sides of the tiles which form the small gaps separating each of the tiles in the divertor. The highest areal densities of both deuterium (from 2 to 8 x 10 18 atoms/cm 2 ) and metals (from 0.2 to 1 x 10 18 atoms/cm 2 ) were found on the plasma-facing surface near the inner strike point region of each set of divertor tiles. Significant deposits, extending as far as 1 cm from the plasma-facing surface and containing up to 40% of the total divertor deposition, were also observed on the gap-forming surfaces of the tiles

Kinetic calculation of plasma deposition in castellated tile gaps

International Nuclear Information System (INIS)

Dejarnac, R.; Gunn, J.P.

2007-01-01

Plasma-facing divertors and limiters are armoured with castellated tiles to withstand intense heat fluxes. Recent experimental studies show that a non-negligible amount of deuterium is deposited in the gaps between tiles. We present here a numerical study of plasma deposition in this critical region. For this purpose we have developed a particle-in-cell code with realistic boundary conditions determined from kinetic calculations. We find a strong asymmetry of plasma deposition into the gaps. A significant fraction of the plasma influx is expelled from the gap to be deposited on the leading edge of the downstream tile

MASHUP SCHEME DESIGN OF MAP TILES USING LIGHTWEIGHT OPEN SOURCE WEBGIS PLATFORM

Directory of Open Access Journals (Sweden)

T. Hu

2018-04-01

Full Text Available To address the difficulty involved when using existing commercial Geographic Information System platforms to integrate multi-source image data fusion, this research proposes the loading of multi-source local tile data based on CesiumJS and examines the tile data organization mechanisms and spatial reference differences of the CesiumJS platform, as well as various tile data sources, such as Google maps, Map World, and Bing maps. Two types of tile data loading schemes have been designed for the mashup of tiles, the single data source loading scheme and the multi-data source loading scheme. The multi-sources of digital map tiles used in this paper cover two different but mainstream spatial references, the WGS84 coordinate system and the Web Mercator coordinate system. According to the experimental results, the single data source loading scheme and the multi-data source loading scheme with the same spatial coordinate system showed favorable visualization effects; however, the multi-data source loading scheme was prone to lead to tile image deformation when loading multi-source tile data with different spatial references. The resulting method provides a low cost and highly flexible solution for small and medium-scale GIS programs and has a certain potential for practical application values. The problem of deformation during the transition of different spatial references is an important topic for further research.

Reuse of solid petroleum waste in the manufacture of porcelain stoneware tile.

Science.gov (United States)

Pinheiro, B C A; Holanda, J N F

2013-03-30

This study investigates the incorporation of solid petroleum waste as raw material into a porcelain stoneware tile body, in replacement to natural kaolin material by up to 5 wt.%. Tile formulations containing solid petroleum waste were pressed and fired at 1240 °C by using a fast-firing cycle. The tile pieces were tested to determine their properties (linear shrinkage, water absorption, apparent density, and flexural strength), sintered microstructure, and leaching toxicity. The results therefore indicated that the growing addition of solid petroleum waste into tile formulations leads to a decrease of linear shrinkage, apparent density, and flexural strength, and to an increase of water absorption of the produced tile materials. It was also found that the replacement of kaolin with solid petroleum waste, in the range up to 2.5 wt.%, allows the production of porcelain stoneware tile (group BIa, ISO 13006 standard). All concentrations of Ag, As, Ba, Cd, Cr (total), Hg, and Pb of the fired porcelain stoneware tile pieces in the leachate comply with the current regulatory limits. These results indicate that the solid petroleum waste could be used for high-quality porcelain stoneware tile production, thus giving rise to a new possibility for an environmentally friendly management of this abundant waste. Copyright © 2013 Elsevier Ltd. All rights reserved.

Preparation of porcelain tile granulates by more environmentally sustainable processes

Energy Technology Data Exchange (ETDEWEB)

Gil, C.; Silvestre, D.; Piquer, J.; Garcia-Ten, J.; Quereda, E.; Vicente, M. J.

2012-07-01

This study examines the feasibility of manufacturing glazed porcelain tiles with a more environmentally friendly manufacturing process, by reducing water and thermal energy consumption. The process studied in this paper is dry milling in a pendulum mill, with subsequent granulation (in order to obtain a press powder with similar flow ability to that of spray dried powders). The different morphology of the new granulate with respect to the standard spray-dried granulate modifies the microstructure of the green compacts and thus, their behaviour and fired tile properties. In order to obtain porcelain tiles with the required properties (water absorption, mechanical strength,) changes have been made in the raw materials mixture and in the processing variables. Finally, porcelain tiles measuring 50x50 cm have been manufactured at industrial scale with the new granulate using a conventional firing cycle, obtaining quality levels identical to those provided by the spray-dried granulate. These results open the possibility of preparing porcelain tile body compositions through a manufacturing process alternative to the standard one, more environmentally friendly and with lower costs. (Author)

Design issues in toxicogenomics using DNA microarray experiment

International Nuclear Information System (INIS)

Lee, Kyoung-Mu; Kim, Ju-Han; Kang, Daehee

2005-01-01

The methods of toxicogenomics might be classified into omics study (e.g., genomics, proteomics, and metabolomics) and population study focusing on risk assessment and gene-environment interaction. In omics study, microarray is the most popular approach. Genes falling into several categories (e.g., xenobiotics metabolism, cell cycle control, DNA repair etc.) can be selected up to 20,000 according to a priori hypothesis. The appropriate type of samples and species should be selected in advance. Multiple doses and varied exposure durations are suggested to identify those genes clearly linked to toxic response. Microarray experiments can be affected by numerous nuisance variables including experimental designs, sample extraction, type of scanners, etc. The number of slides might be determined from the magnitude and variance of expression change, false-positive rate, and desired power. Instead, pooling samples is an alternative. Online databases on chemicals with known exposure-disease outcomes and genetic information can aid the interpretation of the normalized results. Gene function can be inferred from microarray data analyzed by bioinformatics methods such as cluster analysis. The population study often adopts hospital-based or nested case-control design. Biases in subject selection and exposure assessment should be minimized, and confounding bias should also be controlled for in stratified or multiple regression analysis. Optimal sample sizes are dependent on the statistical test for gene-to-environment or gene-to-gene interaction. The design issues addressed in this mini-review are crucial in conducting toxicogenomics study. In addition, integrative approach of exposure assessment, epidemiology, and clinical trial is required

Research on Reasons for Repeated Falling of Tiles in Internal Walls of Construction

Science.gov (United States)

Xu, LiBin; Chen, Shangwei; He, Xinzhou; Zhu, Guoliang

2018-03-01

In view of the quality problem of repeated falling of facing tiles in some construction, the essay had a comparative trial in laboratory on cement mortar which is often used to paste tiles, special tile mortar and dry-hang glue, and measured durability of tile adhesive mortar through freezing and thawing tests. The test results indicated that ordinary cement mortar cannot meet standards due to reasons like big shrinkage and low adhesive. In addition, the ten times of freezing and thawing tests indicated that ordinary cement mortar would directly shell and do not have an adhesive force, and moreover, adhesive force of special tile mortar would reduce. Thus, for tiles of large size which are used for walls, dry-hang techniques are recommended to be used.

Clonal diversity analysis using SNP microarray: a new prognostic tool for chronic lymphocytic leukemia.

Science.gov (United States)

Zhang, Linsheng; Znoyko, Iya; Costa, Luciano J; Conlin, Laura K; Daber, Robert D; Self, Sally E; Wolff, Daynna J

2011-12-01

Chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease. The methods currently used for monitoring CLL and determining conditions for treatment are limited in their ability to predict disease progression, patient survival, and response to therapy. Although clonal diversity and the acquisition of new chromosomal abnormalities during the disease course (clonal evolution) have been associated with disease progression, their prognostic potential has been underappreciated because cytogenetic and fluorescence in situ hybridization (FISH) studies have a restricted ability to detect genomic abnormalities and clonal evolution. We hypothesized that whole genome analysis using high resolution single nucleotide polymorphism (SNP) microarrays would be useful to detect diversity and infer clonal evolution to offer prognostic information. In this study, we used the Infinium Omni1 BeadChip (Illumina, San Diego, CA) array for the analysis of genetic variation and percent mosaicism in 25 non-selected CLL patients to explore the prognostic value of the assessment of clonal diversity in patients with CLL. We calculated the percentage of mosaicism for each abnormality by applying a mathematical algorithm to the genotype frequency data and by manual determination using the Simulated DNA Copy Number (SiDCoN) tool, which was developed from a computer model of mosaicism. At least one genetic abnormality was identified in each case, and the SNP data was 98% concordant with FISH results. Clonal diversity, defined as the presence of two or more genetic abnormalities with differing percentages of mosaicism, was observed in 12 patients (48%), and the diversity correlated with the disease stage. Clonal diversity was present in most cases of advanced disease (Rai stages III and IV) or those with previous treatment, whereas 9 of 13 patients without detected clonal diversity were asymptomatic or clinically stable. In conclusion, SNP microarray studies with simultaneous evaluation

Military Curriculum Materials for Vocational and Technical Education. Builders School, Ceramic Tile Setting 3-9.

Science.gov (United States)

Ohio State Univ., Columbus. National Center for Research in Vocational Education.

This course, for individualized or group instruction on ceramic tile setting, was developed from military sources for use in vocational education. The course provides students with skills in mortar preparation, surface preparation, tile layout planning, tile setting, tile cutting, and the grouting of tile joints. Both theory and shop assignments…

Direct Mutagenesis of Thousands of Genomic Targets using Microarray-derived Oligonucleotides

DEFF Research Database (Denmark)

Bonde, Mads; Kosuri, Sriram; Genee, Hans Jasper

2015-01-01

Multiplex Automated Genome Engineering (MAGE) allows simultaneous mutagenesis of multiple target sites in bacterial genomes using short oligonucleotides. However, large-scale mutagenesis requires hundreds to thousands of unique oligos, which are costly to synthesize and impossible to scale-up by ...

Flat tile armour cooled by hypervapotron tube: a possible technology for ITER

Energy Technology Data Exchange (ETDEWEB)

Schlosser, J.; Escourbiac, F.; Bayetti, P.; Missirlian, M.; Mitteau, R. [Association Euratom-CEA Cadarache, 13 - Saint-Paul-lez-Durance (France). Dept. de Recherches sur la Fusion Controlee; Merola, M. [European Fusion Development Agreement - Close Support Unit (EFDA), Garching (Germany); Schedler, B. [Plansee Aktiengesellschaft, Technology Center, Reutte/Tirol (Austria); Bobin-Vastra, I. [FRAMATOME-ANP, Centre Technique, 71 - Le Creusot (France)

2003-07-01

Carbon fibre composite (CFC) flat tile armours for actively cooled plasma facing components (PFC's) are an important challenge for controlled fusion machine. Flat tile concepts, water cooled by tubes, were studied, developed, tested and finally experienced with success in Tore Supra. The components were designed for 10 MW/m{sup 2} and mock-ups were successfully fatigue tested at 15 MW/m{sup 2}, 1000 cycles. For ITER, a tube-in-tile concept was developed and mock-ups sustained up to 25 MW/m{sup 2} for 1000 cycles without failure. Recently flat tile armored mock-ups cooled by Hypervapotron tube successfully sustained a cascade failure test under a mean heat flux of 10 MW/m{sup 2} but with a doubling of the heat flux on some tiles to simulate missing tiles (500 cycles). This encouraging results lead to reconsider the limits for flat tile concept when cooled by Hypervapotron tube. New tests are now scheduled to investigate these limits notably in regards to the ITER requirements. The concept could also be experimented in Tore Supra by installing a new limiter into the machine. (authors)

Flat Tile Armour Cooled by Hypervapotron Tube: a Possible Technology for ITER

Science.gov (United States)

Schlosser, J.; Escourbiac, F.; Merola, M.; Schedler, B.; Bayetti, P.; Missirlian, M.; Mitteau, R.; Robin-Vastra, I.

Carbon fibre composite (CFC) flat tile armours for actively cooled plasma facing components (PFC’s) are an important challenge for controlled fusion machines. Flat tile concepts, water cooled by tubes, were studied, developed, tested and finally operated with success in Tore Supra. The components were designed for 10 MW/m2 and mock-ups were successfully fatigue tested at 15 MW/m2, 1000 cycles. For ITER, a tube-in-tile concept was developed and mock-ups sustained up to 25 MW/m2 for 1000 cycles without failure. Recently flat tile armoured mock-ups cooled by a hypervapotron tube successfully sustained a cascade failure test under a mean heat flux of 10 MW/m2 but with a doubling of the heat flux on some tiles to simulate missing tiles (500 cycles). This encouraging results lead to reconsider the limits for flat tile concept when cooled by hypervapotron (HV) tube. New tests are now scheduled to investigate these limits in regard to the ITER requirements. Experimental evidence of the concept could be gained in Tore Supra by installing a new limiter into the machine.

Flat Tile Armour Cooled by Hypervapotron Tube: a Possible Technology for ITER

Energy Technology Data Exchange (ETDEWEB)

Schlosser, J.; Escourbiac, F.; Bayetti, P.; Missirlian, M.; Mitteau, R. [Association Euratom CEA, DSM/DRFC/SIPP, St Paul lez Durance (France); Merola, M. [EFDA Close Support Unit, Garching (Germany); Schedler, B. [Plansee Aktiengesellschaft, Reutte (Austria). Technology Center; Bobin-Vastra, I. [Framatome-ANP, Le Creusot (France). Centre Technique

2004-08-01

Carbon fibre composite (CFC) flat tile armours for actively cooled plasma facing components (PFC's) are an important challenge for controlled fusion machines. Flat tile concepts, water cooled by tubes, were studied, developed, tested and finally operated with success in Tore Supra. The components were designed for 10MW/m{sup 2} and mock-ups were successfully fatigue tested at 15MW/m{sup 2}; 1000 cycles. For ITER, a tube-in-tile concept was developed and mock-ups sustained up to 25MW/m{sup 2} for 1000 cycles without failure. Recently flat tile armoured mock-ups cooled by a hypervapotron tube successfully sustained a cascade failure test under a mean heat flux of 10MW/m{sup 2} but with a doubling of the heat flux on some tiles to simulate missing tiles (500 cycles). This encouraging results lead to reconsider the limits for flat tile concept when cooled by hypervapotron (HV) tube. New tests are now scheduled to investigate these limits in regard to the ITER requirements. Experimental evidence of the concept could be gained in Tore Supra by installing a new limiter into the machine.

Evaluation of gene importance in microarray data based upon probability of selection

Directory of Open Access Journals (Sweden)

Fu Li M

2005-03-01

Full Text Available Abstract Background Microarray devices permit a genome-scale evaluation of gene function. This technology has catalyzed biomedical research and development in recent years. As many important diseases can be traced down to the gene level, a long-standing research problem is to identify specific gene expression patterns linking to metabolic characteristics that contribute to disease development and progression. The microarray approach offers an expedited solution to this problem. However, it has posed a challenging issue to recognize disease-related genes expression patterns embedded in the microarray data. In selecting a small set of biologically significant genes for classifier design, the nature of high data dimensionality inherent in this problem creates substantial amount of uncertainty. Results Here we present a model for probability analysis of selected genes in order to determine their importance. Our contribution is that we show how to derive the P value of each selected gene in multiple gene selection trials based on different combinations of data samples and how to conduct a reliability analysis accordingly. The importance of a gene is indicated by its associated P value in that a smaller value implies higher information content from information theory. On the microarray data concerning the subtype classification of small round blue cell tumors, we demonstrate that the method is capable of finding the smallest set of genes (19 genes with optimal classification performance, compared with results reported in the literature. Conclusion In classifier design based on microarray data, the probability value derived from gene selection based on multiple combinations of data samples enables an effective mechanism for reducing the tendency of fitting local data particularities.

Porcelain tiles by the dry route

Directory of Open Access Journals (Sweden)

Boschi, A. O.

2010-10-01

Full Text Available In Brazil, the second largest tile producer of the world, at present, 70% of the tiles are produced by the dry route. One of the main reasons that lead to this development is the fact that the dry route uses approximately 30% less thermal energy them the traditional wet route. The increasing world concern with the environment and the recognition of the central role played by the water also has pointed towards privileging dry processes. In this context the objective of the present work is to study the feasibility of producing high quality porcelain tiles by the dry route. A brief comparison of the dry and wet route, in standard conditions industrially used today to produce tiles that are not porcelain tiles, shows that there are two major differences: the particle sizes obtained by the wet route are usually considerably finer and the capability of mixing the different minerals, the intimacy of the mixture, is also usually better in the wet route. The present work studied the relative importance of these differences and looked for raw materials and operational conditions that would result in better performance and glazed porcelain tiles of good quality.

En Brasil, en este momento segundo productor mundial, el 70% de los pavimentos cerámicos se obtiene por vía seca. Una de las razones fundamentales se debe a que esta vía supone un consumo energético inferior, en un 30%, a la via húmeda tradicional. La creciente preocupación mundial sobre los problemas medioambientales y el reconocimiento del papel central que juega el agua en este proceso han favorecido el desarrollo de la vía seca. En este contexto, el objetivo del presente trabajo es estudiar la viabilidad de la producción de pavimentos porcelánicos de alta calidad por vía seca. Una breve comparación entre ambas vías, en las condiciones standard de producción vigentes para producciones que no son de porcelánico, indican que existen dos diferencias substanciales; el tamaño de

Tile-based parallel coordinates and its application in financial visualization

Science.gov (United States)

Alsakran, Jamal; Zhao, Ye; Zhao, Xinlei

2010-01-01

Parallel coordinates technique has been widely used in information visualization applications and it has achieved great success in visualizing multivariate data and perceiving their trends. Nevertheless, visual clutter usually weakens or even diminishes its ability when the data size increases. In this paper, we first propose a tile-based parallel coordinates, where the plotting area is divided into rectangular tiles. Each tile stores an intersection density that counts the total number of polylines intersecting with that tile. Consequently, the intersection density is mapped to optical attributes, such as color and opacity, by interactive transfer functions. The method visualizes the polylines efficiently and informatively in accordance with the density distribution, and thus, reduces visual cluttering and promotes knowledge discovery. The interactivity of our method allows the user to instantaneously manipulate the tiles distribution and the transfer functions. Specifically, the classic parallel coordinates rendering is a special case of our method when each tile represents only one pixel. A case study on a real world data set, U.S. stock mutual fund data of year 2006, is presented to show the capability of our method in visually analyzing financial data. The presented visual analysis is conducted by an expert in the domain of finance. Our method gains the support from professionals in the finance field, they embrace it as a potential investment analysis tool for mutual fund managers, financial planners, and investors.

Characterization of ancient ceramic tiles using XRF = = = =

International Nuclear Information System (INIS)

Ben Abdelwahed, Haifa

2002-01-01

The measurement of energies and intensities of fluorescent X-rays emitted from a given material when atoms are bombarded with suitable projectiles like electrons, protons, particles or photons has been successfully used for non-destructive elemental analysis in many applications, especially in the analysis of ceramic glasses. Use of radioisotopes as a source of excitation radiation in combination with high resolution semiconductor detectors in x-ray fluorescence has found wide applications in elemental analysis. A radioisotope excited X-ray fluorescence spectrometer consisting of a standard 5.45mm Si(Li) detector having a resolution of 200 eV at 5.9 keV coupled to a TRUMP-8K multichannel analyzer has been used. Tow sources of annular geometry using 10 mCi 109Cd and 10 mCi 55Fe together with PC AXIL software have been used for this study of tile-pavement glasses of ''Ksar Said'' in Tunisia. Analytical data shows that those tile pavement witch are broken in the 19th century from France (Marseille) have not the same composition of Tunisian tile pavement. Referring to our data, The kind of that analyzed glasses is of alkaline lead. we found also, through this study, the elemental compositions of different pigments (green, blue, brownish, yellow, white and red) used to color that tile-pavement glasses. (author). 21 refs

Similarity of eigenstates in generalized labyrinth tilings

International Nuclear Information System (INIS)

Thiem, Stefanie; Schreiber, Michael

2010-01-01

The eigenstates of d-dimensional quasicrystalline models with a separable Hamiltonian are studied within the tight-binding model. The approach is based on mathematical sequences, constructed by an inflation rule P = {w → s,s → sws b-1 } describing the weak/strong couplings of atoms in a quasiperiodic chain. Higher-dimensional quasiperiodic tilings are constructed as a direct product of these chains and their eigenstates can be directly calculated by multiplying the energies E or wave functions ψ of the chain, respectively. Applying this construction rule, the grid in d dimensions splits into 2 d-1 different tilings, for which we investigated the characteristics of the wave functions. For the standard two-dimensional labyrinth tiling constructed from the octonacci sequence (b = 2) the lattice breaks up into two identical lattices, which consequently yield the same eigenstates. While this is not the case for b ≠ 2, our numerical results show that the wave functions of the different grids become increasingly similar for large system sizes. This can be explained by the fact that the structure of the 2 d-1 grids mainly differs at the boundaries and thus for large systems the eigenstates approach each other. This property allows us to analytically derive properties of the higher-dimensional generalized labyrinth tilings from the one-dimensional results. In particular participation numbers and corresponding scaling exponents have been determined.

Evaluation of Salt Removal from Azulejo Tiles and Mortars using Electrodesalination

DEFF Research Database (Denmark)

Ferreira, Célia Maria Dias; Ottosen, Lisbeth M.; Christensen, Iben Vernegren

2011-01-01

Azulejo tiles are part of the Portuguese cultural heritage and are worldwide appreciated. The durability of this building material is affected by the accumulation of salts, causing fractures and peeling of the glazing and ultimately leading to the degradation of the tile panels and the irremediable...... loss of historic value. In this work preliminary studies with single tiles presenting an underlying layer of mortar have been conducted to assess the amount of salts that can be removed from the building material using a new technique called “electrodesalination”, in which the salt’s ions...... are transported out from the tiles by applying an electric current on the backside. Results shown here include an assessment of how much of the salts did come out in comparison to what was originally there, and additionally if the electrodesalination succeeded in removing salts down to a point where the tile...

Detritiation of tiles from tokamaks by laser cleaning

International Nuclear Information System (INIS)

Coad, J. Paul; Widdowson, Anna; Farcage, Daniel; Semerok, Alexander; Thro, P.-Y.; Likonen, Jari; Renvall, Tommi

2007-01-01

Laser ablation has been used to clean surfaces or to decontaminate hot cells by removing paint, and has been tested on deposited carbon layers from the TEXTOR tokamak. This paper reports on successful trials in the Beryllium Handling Facility of a pulsed laser cleaning system to remove H-isotope containing carbon deposits on tiles from the JET tokamak. The laser beam is rastered over the surface of the tiles to remove the deposit. Two types of JET carbon-fibre composite (CFC) tiles were treated. The first was covered with carbon-based deposits up to 300 μm thick with high H-isotope content, the other was covered with a mixed Be/C film ∼ 50 microns thick. One scan of the laser was sufficient to completely change the appearance and expose the fibre planes. From cross-sectional micrographs, it was found that overall three scans provided the most effective settings for complete film removal. An area 250 cm 2 of the second tile was cleaned in 20 minutes, clearly demonstrating the efficiency of laser cleaning for the removal of tokamak deposits such as likely to occur in ITER. (authors)

Measurement of Tritium Surface Distribution on TFTR Bumper Limiter Tiles

International Nuclear Information System (INIS)

Sugiyama, K.; Tanabe, T.; Skinner, C.H.; Gentile, C.A.

2004-01-01

The tritium surface distribution on graphite tiles used in the Tokamak Fusion Test Reactor (TFTR) bumper limiter and exposed to TFTR deuterium-tritium (D-T) discharges from 1993 to 1997 was measured by the Tritium Imaging Plate Technique (TIPT). The TFTR bumper limiter shows both re-/co-deposition and erosion. The tritium images for all tiles measured are strongly correlated with erosion and deposition patterns, and long-term tritium retention was found in the re-/co-depositions and flakes. The CFC tiles located at erosion dominated areas clearly showed their woven structure in their tritium images owing to different erosion yields between fibers and matrix. Significantly high tritium retention was observed on all sides of the erosion tiles, indicating carbon transport via repetition of local erosion/deposition cycles

Genomic analysis of Fusarium verticillioides.

Science.gov (United States)

Brown, D W; Butchko, R A E; Proctor, R H

2008-09-01

Fusarium verticillioides (teleomorph Gibberella moniliformis) can be either an endophyte of maize, causing no visible disease, or a pathogen-causing disease of ears, stalks, roots and seedlings. At any stage, this fungus can synthesize fumonisins, a family of mycotoxins structurally similar to the sphingolipid sphinganine. Ingestion of fumonisin-contaminated maize has been associated with a number of animal diseases, including cancer in rodents, and exposure has been correlated with human oesophageal cancer in some regions of the world, and some evidence suggests that fumonisins are a risk factor for neural tube defects. A primary goal of the authors' laboratory is to eliminate fumonisin contamination of maize and maize products. Understanding how and why these toxins are made and the F. verticillioides-maize disease process will allow one to develop novel strategies to limit tissue destruction (rot) and fumonisin production. To meet this goal, genomic sequence data, expressed sequence tags (ESTs) and microarrays are being used to identify F. verticillioides genes involved in the biosynthesis of toxins and plant pathogenesis. This paper describes the current status of F. verticillioides genomic resources and three approaches being used to mine microarray data from a wild-type strain cultured in liquid fumonisin production medium for 12, 24, 48, 72, 96 and 120h. Taken together, these approaches demonstrate the power of microarray technology to provide information on different biological processes.

Multisegment one-step RT-PCR fluorescent labeling of influenza A virus genome for use in diagnostic microarray applications

Energy Technology Data Exchange (ETDEWEB)

Vasin, A V; Plotnikova, M A; Klotchenko, S A; Elpaeva, E A; Komissarov, A B; Egorov, V V; Kiselev, O I [Research Institute of Influenza of the Ministry of Health and Social Development of the Russian Federation, 15/17 Prof. Popova St., St. Petersburg (Russian Federation); Sandybaev, N T; Chervyakova, O V; Strochkov, V M; Taylakova, E T; Koshemetov, J K; Mamadaliev, S M, E-mail: vasin@influenza.spb.ru [Research Institute for Biological Safety Problems of the RK NBC/SC ME and S RK, Gvardeiskiy (Kazakhstan)

2011-04-01

Microarray technology is one of the most challenging methods of influenza A virus subtyping, which is based on the antigenic properties of viral surface glycoproteins - hemagglutinin and neuraminidase. On the example of biochip for detection of influenza A/H5N1 virus we showed the possibility of using multisegment RTPCR method for amplification of fluorescently labeled cDNA of all possible influenza A virus subtypes with a single pair of primers in influenza diagnostic microarrays.

SPECTRAL SETS AND TILES IN CARTESIAN PRODUCTS OVER ...

Indian Academy of Sciences (India)

41

Spectral set conjecture: A Borel set Ω ⊂ Rd of positive and finite. Lebesgue measure is a spectral set if and only if it ... Ω ⊂ G of positive and finite Haar measure is a spectral set if and only if it is a translational tile. ... Key words and phrases. p-adic number field, Cartesian product, tile, spectral set. This work was supported by ...

Inference of sigma factor controlled networks by using numerical modeling applied to microarray time series data of the germinating prokaryote.

Science.gov (United States)

Strakova, Eva; Zikova, Alice; Vohradsky, Jiri

2014-01-01

A computational model of gene expression was applied to a novel test set of microarray time series measurements to reveal regulatory interactions between transcriptional regulators represented by 45 sigma factors and the genes expressed during germination of a prokaryote Streptomyces coelicolor. Using microarrays, the first 5.5 h of the process was recorded in 13 time points, which provided a database of gene expression time series on genome-wide scale. The computational modeling of the kinetic relations between the sigma factors, individual genes and genes clustered according to the similarity of their expression kinetics identified kinetically plausible sigma factor-controlled networks. Using genome sequence annotations, functional groups of genes that were predominantly controlled by specific sigma factors were identified. Using external binding data complementing the modeling approach, specific genes involved in the control of the studied process were identified and their function suggested.

Extended DNA Tile Actuators

DEFF Research Database (Denmark)

Kristiansen, Martin; Kryger, Mille; Zhang, Zhao

2012-01-01

A dynamic linear DNA tile actuator is expanded to three new structures of higher complexity. The original DNA actuator was constructed from a central roller strand which hybridizes with two piston strands by forming two half-crossover junctions. A linear expansion of the actuator is obtained...

Multi-application inter-tile synchronization on ultra-high-resolution display walls

KAUST Repository

Nam, Sungwon

2010-01-01

Ultra-high-resolution tiled-display walls are typically driven by a cluster of computers. Each computer may drive one or more displays. Synchronization between the computers is necessary to ensure that animated imagery displayed on the wall appears seamless. Most tiled-display middleware systems are designed around the assumption that only a single application instance is running in the tiled display at a time. Therefore synchronization can be achieved with a simple solution such as a networked barrier. When a tiled display has to support multiple applications at the same time, however, the simple networked barrier approach does not scale. In this paper we propose and experimentally validate two synchronization algorithms to achieve low-latency, intertile synchronization for multiple applications with independently varying frame rates. The two-phase algorithm is more generally applicable to various highresolution tiled display systems. The one-phase algorithm provides superior results but requires support for the Network Time Protocol and is more CPU-intensive. Copyright 2010 ACM.

ATLAS Tile Calorimeter time calibration, monitoring and performance

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00075913; The ATLAS collaboration

2016-01-01

The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the central region of the ATLAS experiment at the LHC. This sampling device is made of plastic scintillating tiles alternated with iron plates and its response is calibrated to electromagnetic scale by means of several dedicated calibration systems. The accurate time calibration is important for the energy reconstruction, non-collision background removal as well as for specific physics analyses. The initial time calibration with so-called splash events and subsequent fine-tuning with collision data are presented. The monitoring of the time calibration with laser system and physics collision data is discussed as well as the corrections for sudden changes performed still before the recorded data are processed for physics analyses. Finally, the time resolution as measured with jets and isolated muons particles is presented.

Reconnecting tile drainage to riparian buffer hydrology for enhanced nitrate removal.

Science.gov (United States)

Jaynes, D B; Isenhart, T M

2014-03-01

Riparian buffers are a proven practice for removing NO from overland flow and shallow groundwater. However, in landscapes with artificial subsurface (tile) drainage, most of the subsurface flow leaving fields is passed through the buffers in drainage pipes, leaving little opportunity for NO removal. We investigated the feasibility of re-routing a fraction of field tile drainage as subsurface flow through a riparian buffer for increasing NO removal. We intercepted an existing field tile outlet draining a 10.1-ha area of a row-cropped field in central Iowa and re-routed a fraction of the discharge as subsurface flow along 335 m of an existing riparian buffer. Tile drainage from the field was infiltrated through a perforated pipe installed 75 cm below the surface by maintaining a constant head in the pipe at a control box installed in-line with the existing field outlet. During 2 yr, >18,000 m (55%) of the total flow from the tile outlet was redirected as infiltration within the riparian buffer. The redirected water seeped through the 60-m-wide buffer, raising the water table approximately 35 cm. The redirected tile flow contained 228 kg of NO. On the basis of the strong decrease in NO concentrations within the shallow groundwater across the buffer, we hypothesize that the NO did not enter the stream but was removed within the buffer by plant uptake, microbial immobilization, or denitrification. Redirecting tile drainage as subsurface flow through a riparian buffer increased its NO removal benefit and is a promising management practice to improve surface water quality within tile-drained landscapes. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

R and D and maintenance on graphite tile of divertor region at EAST

International Nuclear Information System (INIS)

Ji, X.; Song, Y.T.; Wu, S.T.; Hao, J.; Du, S.; Peng, Y.; Cao, L.; Wang, S.

2012-01-01

Highlights: ► Find out the reason of damage of graphite tile. ► Simulation the halo current. ► Stress analysis of graphite tile by ANSYS. ► Do the experiments to test the strength of graphite tile. ► Do the optimization and maintenance of graphite tile. - Abstract: EAST, with full superconducting magnetic coils, had been designed and constructed to address the scientific and engineering issues under steady state operation. The in-vessel components are full graphite tiles as first wall had been operated successfully. In the experiment campaign of 2010, the H mode operation and 1 MA operation have been gotten on EAST. However, in some case, some of the graphite tiles of divertor region are damaged with the plasma parameter enhanced. As most of the damaged graphite tiles are in the divertor region, they are probably damaged by the electro-magnetic force of the halo current when the VDEs occur. The force of the halo current is re-estimated. The structure analysis has been done by the ANSYS software. From the analysis result. It can be obtained that the stress is larger than the allowable stress when the halo current on the graphite tile is larger than 2.7 kA. The tensile testing of the graphite also has been done. As the result, the graphite tiles are damaged when the forces are up to 2400 N. To deal with the problem, two proposes are accepted. In the one hand, the new type graphite material is used, whose tensile strength is up to 45 MPa. In the other hand, the structure of the graphite tiles is optimized.

Color features for quality control in ceramic tile industry

Science.gov (United States)

Kukkonen, Saku; Kaelviaeinen, Heikki; Parkkinen, Jussi P.

2001-02-01

We study visual quality control in the ceramics industry. In the manufacturing, it is important that in each set of tiles, every single tile looks similar. Currently, the estimation is usually done by human vision. Our goal is to design a machine vision system that can estimate the sufficient similarity, or same appearance, to the human eye. Our main approach is to use accurate spectral representation of color, and compare spectral features to the RGB color features. A laboratory system for color measurements is built. Experimentations with five classes of brown tiles are presented and discussed. In addition to the k-nearest neighbor (k-NN) classifier, a neural network called the self-organizing map (SOM) is used to provide understanding of the spectral features. Every single spectrum in each tile of a training set is used as input to a 2D SOM. The SOM is analyzed to understand how spectra are clustered. As a result, tiles are classified using a trained 2D SOM. It is also of interest to know whether the order of spectral colors can be determined. In our approach, all spectra are clustered in a 1D SOM, and each pixel spectrum) is presented by pseudocolors according to the trained nodes. Finally, the results are compared to experiments with human vision.

Leaching of dissolved phosphorus from tile-drained agricultural areas.

Science.gov (United States)

Andersen, H E; Windolf, J; Kronvang, B

2016-01-01

We investigated leaching of dissolved phosphorus (P) from 45 tile-drains representing animal husbandry farms in all regions of Denmark. Leaching of P via tile-drains exhibits a high degree of spatial heterogeneity with a low concentration in the majority of tile-drains and few tile-drains (15% in our investigation) having high to very high concentration of dissolved P. The share of dissolved organic P (DOP) was high (up to 96%). Leaching of DOP has hitherto been a somewhat overlooked P loss pathway in Danish soils and the mechanisms of mobilization and transport of DOP needs more investigation. We found a high correlation between Olsen-P and water extractable P. Water extractable P is regarded as an indicator of risk of loss of dissolved P. Our findings indicate that Olsen-P, which is measured routinely in Danish agricultural soils, may be a useful proxy for the P leaching potential of soils. However, we found no straight-forward correlation between leaching potential of the top soil layer (expressed as either degree of P saturation, Olsen-P or water extractable P) and the measured concentration of dissolved P in the tile-drain. This underlines that not only the source of P but also the P loss pathway must be taken into account when evaluating the risk of P loss.

Design study of an armor tile handling manipulator for the Fusion Experimental Reactor

International Nuclear Information System (INIS)

Shibanuma, K.; Honda, T.; Satoh, K.; Terakado, T.; Kondoh, M.; Sasaki, N.; Munakata, T.; Murakami, S.

1991-01-01

A conceptual design of the Fusion Experimental Reactor (FER), which is a D-T burning reactor following on JT-60 in Japan, has been developed by Japan Atomic Energy Research Institute (JAERI). In FER, a rail-mounted vehicle concept is planned to be adopted for in-vessel maintenance, such as maintenance of divertor plates and armor tiles. Advantages of this concept are the high stiffness of the rail as a base structure for maintenance and the high mobility of the vehicle along the rail. Twin armor tile handling manipulators installed on both sides of the vehicle have been designed. The respective manipulators for armor tile handling have 8 degrees of freedom in order to have access to any place of the first wall and to go through the horizontal port by operating manipulator joints. If the two types of manipulators for divertor plates and armor tiles are installed on the vehicle and the divertor handling manipulator carries a case filled with armor tiles, the replacement time of armor tiles will be reduced. In FER, moreover, maintenance of armor tiles, which is a scheduled maintenance, is planned to be carried out by the autonomous control using position sensors etc. In order to accumulate the data base for the development of the autonomous control of the manipulator in armor tile maintenance, the present paper describes basic mechanical characteristics (stress, deflection and natural frequency) of the armor tile handling manipulator calculated by static stress and dynamic eigenvalue analyses. (orig.)

Study of the pressing operation of large-sized tiles using X-ray absorption

International Nuclear Information System (INIS)

Amoros, J. L.; Mallol, G.; Llorens, D.; Boix, J.; Arnau, J. M.; Feliu, C.; Cerisuelo, J. A.; Gargallo, J. J.

2010-01-01

An apparatus for X-Ray non destructive inspection of bulk density distribution in large ceramic tiles has been designed, built and patented. This technique has many advantages compared with other methods: it allows tile bulk density distribution to be mapped and is neither destructive nor toxic, provided the X-ray tube and detector area are shielded to prevent leakage. In the present study, this technique, whose technical feasibility and accuracy had been verified in previous studies, has been used to scan ceramic tiles formed under different industrial conditions, modifying press working parameters. The use of high-precision laser telemeters allows tile thicknesses to be mapped, facilitating the interpretation of manufacturing defects produced in pressing, which cannot be interpreted by just measuring bulk density. The bulk density distributions obtained in the same unfired and fired tiles are also compared, a possibility afforded only by this measurement method, since it is non-destructive. The comparison of both unfired and fired tile bulk density distributions allows the influence of the pressing and firing stages on tile end porosity to be individually identified. (Author) 12 refs.

Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level.

Science.gov (United States)

Evans, Constantine G; Hariadi, Rizal F; Winfree, Erik

2012-06-27

While the theoretical implications of models of DNA tile self-assembly have been extensively researched and such models have been used to design DNA tile systems for use in experiments, there has been little research testing the fundamental assumptions of those models. In this paper, we use direct observation of individual tile attachments and detachments of two DNA tile systems on a mica surface imaged with an atomic force microscope (AFM) to compile statistics of tile attachments and detachments. We show that these statistics fit the widely used kinetic Tile Assembly Model and demonstrate AFM movies as a viable technique for directly investigating DNA tile systems during growth rather than after assembly.

Replicate high-density rat genome oligonucleotide microarrays reveal hundreds of regulated genes in the dorsal root ganglion after peripheral nerve injury.

Directory of Open Access Journals (Sweden)

Mannion James W

2002-10-01

Full Text Available Abstract Background Rat oligonucleotide microarrays were used to detect changes in gene expression in the dorsal root ganglion (DRG 3 days following sciatic nerve transection (axotomy. Two comparisons were made using two sets of triplicate microarrays, naïve versus naïve and naïve versus axotomy. Results Microarray variability was assessed using the naïve versus naïve comparison. These results support use of a P 1.5-fold expression change and P 1.5-fold and P in situ hybridization verified the expression of 24 transcripts. These data showed an 83% concordance rate with the arrays; most mismatches represent genes with low expression levels reflecting limits of array sensitivity. A significant correlation was found between actual mRNA differences and relative changes between microarrays (r2 = 0.8567. Temporal patterns of individual genes regulation varied. Conclusions We identify parameters for microarray analysis which reduce error while identifying many putatively regulated genes. Functional classification of these genes suggest reorganization of cell structural components, activation of genes expressed by immune and inflammatory cells and down-regulation of genes involved in neurotransmission.

The ATLAS Tile Calorimeter Phase-II Upgrade Demonstrator Data Acquisition and Software

CERN Document Server

Little, Jared David; The ATLAS collaboration

2018-01-01

The LHC plans a series of upgrades culminating in the High Luminosity LHC (HL-LHC) which will have an average luminosity 5-7 times larger than the design LHC value. The electronics of the hadronic Tile Calorimeter (TileCal) will undergo a substantial upgrade to accommodate to the HL-LHC parameters. In particular, TileCal will undergo a major replacement of its on- and off-detector electronics. The photomultiplier signals will be digitized and transferred off-detector to the TileCal PreProcessors (TilePPr) for every bunch crossing, requiring a data bandwidth of 40 Tbps. The TilePPr will reconstruct, store and send the calorimeter signals to first level of trigger at a rate of 40 MHz. This will provide better precision of the calorimeter signals used by the trigger system and will allow the development of more complex trigger algorithms. In parallel, the data samples will be stored in pipeline memories and the data of the events selected by the ATLAS central trigger system and transferred to the ATLAS global Da...

Gene Expression Profiling and Identification of Resistance Genes to Aspergillus flavus Infection in Peanut through EST and Microarray Strategies

Directory of Open Access Journals (Sweden)

Baozhu Guo

2011-06-01

Full Text Available Aspergillus flavus and A. parasiticus infect peanut seeds and produce aflatoxins, which are associated with various diseases in domestic animals and humans throughout the world. The most cost-effective strategy to minimize aflatoxin contamination involves the development of peanut cultivars that are resistant to fungal infection and/or aflatoxin production. To identify peanut Aspergillus-interactive and peanut Aspergillus-resistance genes, we carried out a large scale peanut Expressed Sequence Tag (EST project which we used to construct a peanut glass slide oligonucleotide microarray. The fabricated microarray represents over 40% of the protein coding genes in the peanut genome. For expression profiling, resistant and susceptible peanut cultivars were infected with a mixture of Aspergillus flavus and parasiticus spores. The subsequent microarray analysis identified 62 genes in resistant cultivars that were up-expressed in response to Aspergillus infection. In addition, we identified 22 putative Aspergillus-resistance genes that were constitutively up-expressed in the resistant cultivar in comparison to the susceptible cultivar. Some of these genes were homologous to peanut, corn, and soybean genes that were previously shown to confer resistance to fungal infection. This study is a first step towards a comprehensive genome-scale platform for developing Aspergillus-resistant peanut cultivars through targeted marker-assisted breeding and genetic engineering.

Characterization of particulate and dissolved phosphorus in tile and nearby riverine systems

Science.gov (United States)

Jiang, X.; Arai, Y.; David, M.; Gentry, L.

2017-12-01

In the Midwestern U.S., the drainage of agricultural land is predominantly managed by the tile drain system because of its poorly drain properties of clay rich indigenous soils. An accelerated subsurface flow of phosphorus (P) has recently been documented as a primary P transport path in contrast to the typical surface runoff events observed in the Eastern U.S. Recent studies suggested the important role of particulate P (PP) load in agricultural tile drainage water during high flow events. It was hypothesized that PP in the tile water is transported to riverine system contributing to the negative environmental impacts in the Midwestern U.S. In this study, correlation assessment of physicochemical properties of PP in agricultural tile drainage and nearby river samples after a storm event was conducted using a combination of 31P-nuclear magnetic resonance spectroscopy, P K-edge X-ray absorption near edge structure spectroscopy, X-ray diffraction, zetasizer, and transmission electron microscopy. Results show that significantly more colloidal (i.e. 1 nm- 2 µm) and silt-sized (i.e. > 2 µm) particles as well as higher dissolved total P (DTP) and dissolved reactive P (DRP) concentrations existed in river samples than tile samples. Tile and river samples showed similar zeta potential in each particle-size fraction and similar element distributions on colloidal fraction. However, colloidal P concentration and distribution are slightly different between tile and river samples: more colloidal total P and organic P existed in tile colloids than river colloids. The results of P speciation and mineralogical assessment will also be discussed.

Self assembly of rectangular shapes on concentration programming and probabilistic tile assembly models.

Science.gov (United States)

Kundeti, Vamsi; Rajasekaran, Sanguthevar

2012-06-01

Efficient tile sets for self assembling rectilinear shapes is of critical importance in algorithmic self assembly. A lower bound on the tile complexity of any deterministic self assembly system for an n × n square is [Formula: see text] (inferred from the Kolmogrov complexity). Deterministic self assembly systems with an optimal tile complexity have been designed for squares and related shapes in the past. However designing [Formula: see text] unique tiles specific to a shape is still an intensive task in the laboratory. On the other hand copies of a tile can be made rapidly using PCR (polymerase chain reaction) experiments. This led to the study of self assembly on tile concentration programming models. We present two major results in this paper on the concentration programming model. First we show how to self assemble rectangles with a fixed aspect ratio ( α:β ), with high probability, using Θ( α + β ) tiles. This result is much stronger than the existing results by Kao et al. (Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008) and Doty (Randomized self-assembly for exact shapes. In: proceedings of the 50th annual IEEE symposium on foundations of computer science (FOCS), IEEE, Atlanta. pp 85-94, 2009)-which can only self assembly squares and rely on tiles which perform binary arithmetic. On the other hand, our result is based on a technique called staircase sampling . This technique eliminates the need for sub-tiles which perform binary arithmetic, reduces the constant in the asymptotic bound, and eliminates the need for approximate frames (Kao et al. Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008). Our second result applies staircase sampling on the equimolar concentration programming model (The tile complexity of linear assemblies. In: proceedings of the 36th international colloquium automata, languages and programming: Part I on ICALP '09, Springer-Verlag, pp 235

Genomics of Salmonella Species

Science.gov (United States)

Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

Development of remote replacement system for armor tiles of first wall of FER

International Nuclear Information System (INIS)

Adachi, Junichi; Yoshizawa, Shunji; Nakano, Yasuo; Kuboyama, Takashi; Shibanuma, Kiyoshi; Kakudate, Satoshi; Oka, Kiyoshi.

1993-01-01

A remote system has been developed to replace automatically armor tiles of first walls with a single manipulator arm for the Fusion Experimental Reactor (FER). The system is composed of a manipulator arm and an end-effector (a tile replacement hand), which have a gripper of the tiles, a nutrunner to rotate attatching bolts of them and a vision sensor to measure positions of them. The system can replace the tiles by means of a visual feedback system using vision sensor, even if the positions of the tiles would have changed. As a result of tests, it has been proved that the end-effector is useful and the control system is practicable. (author)

Differential gene expression from genome-wide microarray analyses distinguishes Lohmann Selected Leghorn and Lohmann Brown layers.

Directory of Open Access Journals (Sweden)

Christin Habig

Full Text Available The Lohmann Selected Leghorn (LSL and Lohmann Brown (LB layer lines have been selected for high egg production since more than 50 years and belong to the worldwide leading commercial layer lines. The objectives of the present study were to characterize the molecular processes that are different among these two layer lines using whole genome RNA expression profiles. The hens were kept in the newly developed small group housing system Eurovent German with two different group sizes. Differential expression was observed for 6,276 microarray probes (FDR adjusted P-value <0.05 among the two layer lines LSL and LB. A 2-fold or greater change in gene expression was identified on 151 probe sets. In LSL, 72 of the 151 probe sets were up- and 79 of them were down-regulated. Gene ontology (GO enrichment analysis accounting for biological processes evinced 18 GO-terms for the 72 probe sets with higher expression in LSL, especially those taking part in immune system processes and membrane organization. A total of 32 enriched GO-terms were determined among the 79 down-regulated probe sets of LSL. Particularly, these terms included phosphorus metabolic processes and signaling pathways. In conclusion, the phenotypic differences among the two layer lines LSL and LB are clearly reflected in their gene expression profiles of the cerebrum. These novel findings provide clues for genes involved in economically important line characteristics of commercial laying hens.

Analysis and design of the beryllium tiles for the JET ITER-like wall project

International Nuclear Information System (INIS)

Thompson, V.; Krivchenkov, Y.; Riccardo, V.; Vizvary, Z.

2007-01-01

Work is in progress to completely replace, in 2008/9, the existing JET CFC tiles with a configuration of plasma facing materials consistent with the ITER design. The ITER-like wall (ILW) will be created with a combination of beryllium (Be), tungsten (W), W-coated CFC and Be-coated inconel tiles, with the material depending on the local anticipated heat flux and geometry. Over 4000 tiles will be replaced and the ILW will accommodate additional heating up to at least 50 MW for 10 s. One of the objectives is to maintain or improve the existing CFC tile power handling performance which has been achieved in most cases by hiding bolt holes, optimising tile size and profile and introducing castellations on plasma facing surfaces. This paper describes the generic problems associated with the Be tiles (power handling capacity and disruption induced eddy currents) and illustrates the solution selected for the inner wall guard limiter (IWGL) where the present CFC tiles will be replaced with Be

Analysis of genomic imbalances and gene expression changes in transformed follicular lymphoma (FL)

DEFF Research Database (Denmark)

Obel, G.; Farinha, P.; Lam, W.

2005-01-01

American patients with transformed FL. Methods: High-resolution BAC-array comparative genomic hybridisation (CGH) was used to detect genomic imbalances. Gene expression profiling was performed using cDNA microarrays (Affymetrix). Results: Of 9 biopsy pairs identified so far, analysis results of the first 4...

Upgrade of the ATLAS Tile Calorimeter for the High Luminosity LHC

CERN Document Server

Scuri, Fabrizio; The ATLAS collaboration

2018-01-01

The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the central region of the ATLAS experiment. TileCal is a sampling calorimeter with steel as absorber and scintillators as active medium. The scintillators are read-out by wavelength shifting fibers coupled to photomultiplier tubes (PMTs). The analogue signals from the PMTs are amplified, shaped, digitized by sampling the signal every 25 ns and stored on detector until a trigger decision is received. The High-Luminosity phase of LHC (HL-LHC) expected to begin in year 2026 requires new electronics to meet the requirements of a 1 MHz trigger, higher ambient radiation, and for better performance under high pileup. Both the on- and off-detector TileCal electronics will be replaced during the shutdown of 2024-2025. PMT signals from every TileCal cell will be digitized and sent directly to the back-end electronics, where the signals are reconstructed, stored, and sent to the first level of trigger at a rate of 40 MHz. This will provide better precis...

On residual gas analysis during high temperature baking of graphite tiles

International Nuclear Information System (INIS)

Prakash, A A; Chaudhuri, P; Khirwadkar, S; Reddy, D Chenna; Saxena, Y C; Chauhan, N; Raole, P M

2008-01-01

Steady-state Super-conducting Tokamak-1 (SST-1) is a medium size tokamak with major radius of 1.1 m and minor radius of 0.20 m. It is designed for plasma discharge duration of 1000 seconds to obtain fully steady-state plasma operation. Plasma Facing Components (PFC), consisting of divertors, passive stabilizers, baffles and poloidal limiters are also designed to be UHV compatible for steady state operation. All PFC are made up of graphite tiles mechanically attached to the copper alloy substrate. Graphite is one of the preferred first wall armour material in present day tokamaks. High thermal shock resistance and low atomic number of carbon are the most important properties of graphite for this application. High temperature vacuum baking of graphite tiles is the standard process to remove the impurities. Residual Gas Analyzer (RGA) has been used for qualitative and quantitative measurements of released gases from graphite tiles during baking. Surface Analysis of graphite tiles has also been done before and after baking. This paper describes the residual gas analysis during baking and surface analysis of graphite tiles

On residual gas analysis during high temperature baking of graphite tiles

Energy Technology Data Exchange (ETDEWEB)

Prakash, A A; Chaudhuri, P; Khirwadkar, S; Reddy, D Chenna; Saxena, Y C [Institute for Plasma Research, Bhat, Gandhinagar - 382 428 (India); Chauhan, N; Raole, P M [Facilitation Center for Industrial Plasma Technologies, IPR, Gandhinagar (India)], E-mail: arun@ipr.res.in

2008-05-01

Steady-state Super-conducting Tokamak-1 (SST-1) is a medium size tokamak with major radius of 1.1 m and minor radius of 0.20 m. It is designed for plasma discharge duration of 1000 seconds to obtain fully steady-state plasma operation. Plasma Facing Components (PFC), consisting of divertors, passive stabilizers, baffles and poloidal limiters are also designed to be UHV compatible for steady state operation. All PFC are made up of graphite tiles mechanically attached to the copper alloy substrate. Graphite is one of the preferred first wall armour material in present day tokamaks. High thermal shock resistance and low atomic number of carbon are the most important properties of graphite for this application. High temperature vacuum baking of graphite tiles is the standard process to remove the impurities. Residual Gas Analyzer (RGA) has been used for qualitative and quantitative measurements of released gases from graphite tiles during baking. Surface Analysis of graphite tiles has also been done before and after baking. This paper describes the residual gas analysis during baking and surface analysis of graphite tiles.

Noise dependence with pile-up in the ATLAS Tile calorimeter

CERN Document Server

Araque Espinosa, Juan Pedro; The ATLAS collaboration

2015-01-01

The Tile Calorimeter, TileCal, is the central hadronic calorimeter of the ATLAS experiment and comprises alternating layers of steel (as absorber material) and plastic (as active material), known as tiles. Between 2009 and 2012, the LHC has performed better than expected producing proton-proton collisions at a very high rate. Under these challenging conditions not only the energy from an interesting event will be measured but also a component coming from other collisions. This component is referred to as pile-up noise. Studies carried out to better understand how pile-up affects calorimeter noise under different circumstances are described.

Direct Atomic Force Microscopy Observation of DNA Tile Crystal Growth at the Single-Molecule Level

OpenAIRE

Evans, Constantine G.; Hariadi, Rizal F.; Winfree, Erik

2012-01-01

While the theoretical implications of models of DNA tile self-assembly have been extensively researched and such models have been used to design DNA tile systems for use in experiments, there has been little research testing the fundamental assumptions of those models. In this paper, we use direct observation of individual tile attachments and detachments of two DNA tile systems on a mica surface imaged with an atomic force microscope (AFM) to compile statistics of tile attachments and detach...

Data Mining Supercomputing with SAS JMP® Genomics

Directory of Open Access Journals (Sweden)

Richard S. Segall

2011-02-01

Full Text Available JMP® Genomics is statistical discovery software that can uncover meaningful patterns in high-throughput genomics and proteomics data. JMP® Genomics is designed for biologists, biostatisticians, statistical geneticists, and those engaged in analyzing the vast stores of data that are common in genomic research (SAS, 2009. Data mining was performed using JMP® Genomics on the two collections of microarray databases available from National Center for Biotechnology Information (NCBI for lung cancer and breast cancer. The Gene Expression Omnibus (GEO of NCBI serves as a public repository for a wide range of highthroughput experimental data, including the two collections of lung cancer and breast cancer that were used for this research. The results for applying data mining using software JMP® Genomics are shown in this paper with numerous screen shots.

Chemical functionalization of ceramic tile surfaces by silane coupling agents: polymer modified mortar adhesion mechanism implications

Directory of Open Access Journals (Sweden)

Alexandra Ancelmo Piscitelli Mansur

2008-09-01

Full Text Available Adhesion between tiles and mortars are crucial to the stability of ceramic tile systems. From the chemical point of view, weak forces such as van der Waals forces and hydrophilic interactions are expected to be developed preferably at the tiles and polymer modified Portland cement mortar interface. The main goal of this paper was to use organosilanes as primers to modify ceramic tile hydrophilic properties to improve adhesion between ceramic tiles and polymer modified mortars. Glass tile surfaces were treated with several silane derivatives bearing specific functionalities. Contact angle measurements and Fourier Transform Infrared Spectroscopy (FTIR were used for evaluating the chemical changes on the tile surface. In addition, pull-off tests were conducted to assess the effect on adhesion properties between tile and poly(ethylene-co-vinyl acetate, EVA, modified mortar. The bond strength results have clearly shown the improvement of adherence at the tile-polymer modified mortar interface, reflecting the overall balance of silane, cement and polymer interactions.

The epigenetic landscape of latent Kaposi sarcoma-associated herpesvirus genomes.

Directory of Open Access Journals (Sweden)

Thomas Günther

Full Text Available Herpesvirus latency is generally thought to be governed by epigenetic modifications, but the dynamics of viral chromatin at early timepoints of latent infection are poorly understood. Here, we report a comprehensive spatial and temporal analysis of DNA methylation and histone modifications during latent infection with Kaposi Sarcoma-associated herpesvirus (KSHV, the etiologic agent of Kaposi Sarcoma and primary effusion lymphoma (PEL. By use of high resolution tiling microarrays in conjunction with immunoprecipitation of methylated DNA (MeDIP or modified histones (chromatin IP, ChIP, our study revealed highly distinct landscapes of epigenetic modifications associated with latent KSHV infection in several tumor-derived cell lines as well as de novo infected endothelial cells. We find that KSHV genomes are subject to profound methylation at CpG dinucleotides, leading to the establishment of characteristic global DNA methylation patterns. However, such patterns evolve slowly and thus are unlikely to control early latency. In contrast, we observed that latency-specific histone modification patterns were rapidly established upon a de novo infection. Our analysis furthermore demonstrates that such patterns are not characterized by the absence of activating histone modifications, as H3K9/K14-ac and H3K4-me3 marks were prominently detected at several loci, including the promoter of the lytic cycle transactivator Rta. While these regions were furthermore largely devoid of the constitutive heterochromatin marker H3K9-me3, we observed rapid and widespread deposition of H3K27-me3 across latent KSHV genomes, a bivalent modification which is able to repress transcription in spite of the simultaneous presence of activating marks. Our findings suggest that the modification patterns identified here induce a poised state of repression during viral latency, which can be rapidly reversed once the lytic cycle is induced.

ZODET: software for the identification, analysis and visualisation of outlier genes in microarray expression data.

Directory of Open Access Journals (Sweden)

Daniel L Roden

Full Text Available Complex human diseases can show significant heterogeneity between patients with the same phenotypic disorder. An outlier detection strategy was developed to identify variants at the level of gene transcription that are of potential biological and phenotypic importance. Here we describe a graphical software package (z-score outlier detection (ZODET that enables identification and visualisation of gross abnormalities in gene expression (outliers in individuals, using whole genome microarray data. Mean and standard deviation of expression in a healthy control cohort is used to detect both over and under-expressed probes in individual test subjects. We compared the potential of ZODET to detect outlier genes in gene expression datasets with a previously described statistical method, gene tissue index (GTI, using a simulated expression dataset and a publicly available monocyte-derived macrophage microarray dataset. Taken together, these results support ZODET as a novel approach to identify outlier genes of potential pathogenic relevance in complex human diseases. The algorithm is implemented using R packages and Java.The software is freely available from http://www.ucl.ac.uk/medicine/molecular-medicine/publications/microarray-outlier-analysis.

Evaluation of chronic lymphocytic leukemia by BAC-based microarray analysis

Directory of Open Access Journals (Sweden)

McDaniel Lisa D

2011-02-01

Full Text Available Abstract Background Chronic lymphocytic leukemia (CLL is a highly variable disease with life expectancies ranging from months to decades. Cytogenetic findings play an integral role in defining the prognostic significance and treatment for individual patients. Results We have evaluated 25 clinical cases from a tertiary cancer center that have an established diagnosis of CLL and for which there was prior cytogenetic and/or fluorescence in situ hybridization (FISH data. We performed microarray-based comparative genomic hybridization (aCGH using a bacterial artificial chromosome (BAC-based microarray designed for the detection of known constitutional genetic syndromes. In 15 of the 25 cases, aCGH detected all copy number imbalances identified by prior cytogenetic and/or FISH studies. For the majority of those not detected, the aberrations were present at low levels of mosaicism. Furthermore, for 15 of the 25 cases, additional abnormalities were detected. Four of those cases had deletions that mapped to intervals implicated in inherited predisposition to CLL. For most cases, aCGH was able to detect abnormalities present in as few as 10% of cells. Although changes in ploidy are not easily discernable by aCGH, results for two cases illustrate the detection of additional copy gains and losses present within a mosaic tetraploid cell population. Conclusions Our results illustrate the successful evaluation of CLL using a microarray optimized for the interrogation of inherited disorders and the identification of alterations with possible relevance to CLL susceptibility.

Characterization of adjacent breast tumors using oligonucleotide microarrays

International Nuclear Information System (INIS)

Unger, Meredith A; Rishi, Mazhar; Clemmer, Virginia B; Hartman, Jennifer L; Keiper, Elizabeth A; Greshock, Joel D; Chodosh, Lewis A; Liebman, Michael N; Weber, Barbara L

2001-01-01

Current methodology often cannot distinguish second primary breast cancers from multifocal disease, a potentially important distinction for clinical management. In the present study we evaluated the use of oligonucleotide-based microarray analysis in determining the clonality of tumors by comparing gene expression profiles. Total RNA was extracted from two tumors with no apparent physical connection that were located in the right breast of an 87-year-old woman diagnosed with invasive ductal carcinoma (IDC). The RNA was hybridized to the Affymetrix Human Genome U95A Gene Chip ® (12,500 known human genes) and analyzed using the Gene Chip Analysis Suite ® 3.3 (Affymetrix, Inc, Santa Clara, CA, USA) and JMPIN ® 3.2.6 (SAS Institute, Inc, Cary, NC, USA). Gene expression profiles of tumors from five additional patients were compared in order to evaluate the heterogeneity in gene expression between tumors with similar clinical characteristics. The adjacent breast tumors had a pairwise correlation coefficient of 0.987, and were essentially indistinguishable by microarray analysis. Analysis of gene expression profiles from different individuals, however, generated a pairwise correlation coefficient of 0.710. Transcriptional profiling may be a useful diagnostic tool for determining tumor clonality and heterogeneity, and may ultimately impact on therapeutic decision making

Study of the effect of nano surface morphology on the stain-resistant property of ceramic tiles

International Nuclear Information System (INIS)

Pan, S P; Hung, J K; Liu, Y T

2014-01-01

In this study, six types of commercially available ceramic tiles, including nano-structured ceramic tiles and regular ceramic tiles, were selected to investigate the effect of surface morphology on their stain-resistant property. The stain-resistant efficiencies of various ceramic tiles with nano-size surface were measured in order to determine the appropriate method for testing ceramic tiles with nano-structure surface

Coverage percentage and raman measurement of cross-tile and scaffold cross-tile based DNA nanostructures.

Science.gov (United States)

Gnapareddy, Bramaramba; Ahn, Sang Jung; Dugasani, Sreekantha Reddy; Kim, Jang Ah; Amin, Rashid; Mitta, Sekhar Babu; Vellampatti, Srivithya; Kim, Byeonghoon; Kulkarni, Atul; Kim, Taesung; Yun, Kyusik; LaBean, Thomas H; Park, Sung Ha

2015-11-01

We present two free-solution annealed DNA nanostructures consisting of either cross-tile CT1 or CT2. The proposed nanostructures exhibit two distinct structural morphologies, with one-dimensional (1D) nanotubes for CT1 and 2D nanolattices for CT2. When we perform mica-assisted growth annealing with CT1, a dramatic dimensional change occurs where the 1D nanotubes transform into 2D nanolattices due to the presence of the substrate. We assessed the coverage percentage of the 2D nanolattices grown on the mica substrate with CT1 and CT2 as a function of the concentration of the DNA monomer. Furthermore, we fabricated a scaffold cross-tile (SCT), which is a new design of a modified cross-tile that consists of four four-arm junctions with a square aspect ratio. For SCT, eight oligonucleotides are designed in such a way that adjacent strands with sticky ends can produce continuous arms in both the horizontal and vertical directions. The SCT was fabricated via free-solution annealing, and self-assembled SCT produces 2D nanolattices with periodic square cavities. All structures were observed via atomic force microscopy. Finally, we fabricated divalent nickel ion (Ni(2+))- and trivalent dysprosium ion (Dy(3+))-modified 2D nanolattices constructed with CT2 on a quartz substrate, and the ion coordinations were examined via Raman spectroscopy. Copyright © 2015 Elsevier B.V. All rights reserved.

CFD analysis and experimental comparison of novel roof tile shapes

Directory of Open Access Journals (Sweden)

Michele Bottarelli

2017-06-01

Using an experimental rig, the air pressure difference and the volumetric flow rate between tiles have been measured for an existing Portoghese tile design over a range of pressures. Then, in order to understand the air flows under different conditions, a three-dimensional computational fluid dynamics (CFD model has been implemented to recreate the full geometry of the rig. The model was calibrated against the aforementioned experimental results, and run with boundary conditions simulating different wind directions. Even in the low velocities typical of average local wind patterns, the fluid dynamic problem remains complex because of the geometry of the gaps between the tiles. However, it has been possible to assess the coefficient of local head loss and then apply it in an analytical relationship between pressure drop and flow rate, taking into account the open area. The results have shown how the wind direction affects the air permeability and, therefore, important insights have been gathered for the design of novel tiles.

Upgrade of the ATLAS Tile Calorimeter Electronics

International Nuclear Information System (INIS)

Carrió, F

2015-01-01

The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the central region of the ATLAS experiment at LHC. The TileCal readout consists of about 10000 channels. The bulk of its upgrade will occur for the High Luminosity LHC phase (Phase-II) where the peak luminosity will increase 5 times compared to the design luminosity (10 34 cm −2 s −1 ) but with maintained energy (i.e. 7+7 TeV). An additional increase of the average luminosity with a factor of 2 can be achieved by luminosity levelling. This upgrade is expected to happen around 2024. The TileCal upgrade aims at replacing the majority of the on- and off- detector electronics to the extent that all calorimeter signals will be digitized and sent to the off-detector electronics in the counting room. To achieve the required reliability, redundancy has been introduced at different levels. Three different options are presently being investigated for the front-end electronic upgrade. Extensive test beam studies will determine which option will be selected. 10 Gbps optical links are used to read out all digitized data to the counting room while 5 Gbps down-links are used for synchronization, configuration and detector control. For the off-detector electronics a pre-processor (sROD) is being developed, which takes care of the initial trigger processing while temporarily storing the main data flow in pipeline and derandomizer memories. One demonstrator prototype module with the new calorimeter module electronics, but still compatible with the present system, is planned to be inserted in ATLAS this year

GIBS Web Map Tile Service (WMTS)

Data.gov (United States)

National Aeronautics and Space Administration — The WMTS implementation standard provides a standards-based solution for serviing digital maps using predefined image tiles. Through the constructs of the...

Comprehensive nitrogen budgets for controlled tile drainage fields in eastern ontario, Canada.

Science.gov (United States)

Sunohara, M D; Craiovan, E; Topp, E; Gottschall, N; Drury, C F; Lapen, D R

2014-03-01

Excessive N loading from subsurface tile drainage has been linked to water quality degradation. Controlled tile drainage (CTD) has the potential to reduce N losses via tile drainage and boost crop yields. While CTD can reduce N loss from tile drainage, it may increase losses through other pathways. A multiple-year field-scale accounting of major N inputs and outputs during the cropping season was conducted on freely drained and controlled tile drained agricultural fields under corn ( L.)-soybean [ (L.) Merr.] production systems in eastern Ontario, Canada. Greater predicted gaseous N emissions for corn and soybean and greater observed lateral seepage N losses were observed for corn and soybean fields under CTD relative to free-draining fields. However, observed N losses from tile were significantly lower for CTD fields, in relation to freely drained fields. Changes in residual soil N were essentially equivalent between drainage treatments, while mass balance residual terms were systematically negative (slightly more so for CTD). Increases in plant N uptake associated with CTD were observed, probably resulting in higher grain yields for corn and soybean. This study illustrates the benefits of CTD in decreasing subsurface tile drainage N losses and boosting crop yields, while demonstrating the potential for CTD to increase N losses via other pathways related to gaseous emissions and groundwater seepage. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

A portable high-power diode laser-based single-stage ceramic tile grout sealing system

Science.gov (United States)

Lawrence, J.; Schmidt, M. J. J.; Li, L.; Edwards, R. E.; Gale, A. W.

2002-02-01

By means of a 60 W high-power diode laser (HPDL) and a specially developed grout material the void between adjoining ceramic tiles has been successfully sealed. A single-stage process has been developed which uses a crushed ceramic tile mix to act as a tough, inexpensive bulk substrate and a glazed enamel surface to provide an impervious surface glaze. The single-stage ceramic tile grout sealing process yielded seals produced in normal atmospheric conditions that displayed no discernible cracks and porosities. The single-stage grout is simple to formulate and easy to apply. Tiles were successfully sealed with power densities as low as 200 kW/ mm2 and at rates of up to 600 mm/ min. Bonding of the enamel to the crushed ceramic tile mix was identified as being primarily due to van der Waals forces and, on a very small scale, some of the crushed ceramic tile mix material dissolving into the glaze. In terms of mechanical, physical and chemical characteristics, the single-stage ceramic tile grout was found to be far superior to the conventional epoxy tile grout and, in many instances, matched and occasionally surpassed that of the ceramic tiles themselves. What is more, the development of a hand-held HPDL beam delivery unit and the related procedures necessary to lead to the commercialisation of the single-stage ceramic tile grout sealing process are presented. Further, an appraisal of the potential hazards associated with the use of the HPDL in an industrial environment and the solutions implemented to ensure that the system complies with the relevant safety standards are given.

Clock Distribution and Readout Architecture for the ATLAS Tile Calorimeter at the HL-LHC

CERN Document Server

Carrio Argos, Fernando; The ATLAS collaboration

2018-01-01

The Tile Calorimeter (TileCal) is one detector of the ATLAS experiment at the Large Hadron Collider (LHC). TileCal is a sampling calorimeter made of steel plates and plastic scintillators which are readout using approximately 10,000 PhotoMultipliers Tubes (PMTs). In 2024, the LHC will undergo a series of upgrades towards a High Luminosity LHC (HL-LHC) to deliver up to 7.5 times the current nominal instantaneous luminosity. The ATLAS Tile Phase II Upgrade will accommodate detector and data acquisition system to the HL-LHC requirements. The detector electronics will be redesigned using a new clock distribution and readout architecture with a full-digital trigger system. After the Long Shutdown 3 (2024-2026), the on-detector electronics will transfer digitized data for every bunch crossing (~25 ns) to the Tile PreProcessors (TilePPr) in the counting rooms with a total data bandwidth of 40 Tbps. The TilePPrs will store the detector data in pipeline memories to cope with the new ATLAS DAQ architecture requirements...

Quality of Experience for Large Ultra-High-Resolution Tiled Displays with Synchronization Mismatch

Directory of Open Access Journals (Sweden)

Deshpande Sachin

2011-01-01

Full Text Available This paper relates to quality of experience when viewing images, video, or other content on large ultra-high-resolution displays made from individual display tiles. We define experiments to measure vernier acuity caused by synchronization mismatch for moving images. The experiments are used to obtain synchronization mismatch acuity threshold as a function of object velocity and as a function of occlusion or gap width. Our main motivation for measuring the synchronization mismatch vernier acuity is its relevance in the application of tiled display systems, which create a single contiguous image using individual discrete panels arranged in a matrix with each panel utilizing a distributed synchronization algorithm to display parts of the overall image. We also propose a subjective assessment method for perception evaluation of synchronization mismatch for large ultra-high-resolution tiled displays. For this, we design a synchronization mismatch measurement test video set for various tile configurations for various interpanel synchronization mismatch values. The proposed method for synchronization mismatch perception can evaluate tiled displays with or without tile bezels. The results from this work can help during design of low-cost tiled display systems, which utilize distributed synchronization mechanisms for a contiguous or bezeled image display.

Effects of occupational exposures and smoking on lung function in tile factory workers.

Science.gov (United States)

Jaakkola, Maritta S; Sripaiboonkij, Penpatra; Jaakkola, Jouni J K

2011-02-01

The aims of this study were to investigate the relations of occupational exposures in tile industry to lung function and to evaluate potential interaction between smoking and tile dust exposure containing silica. A cross-sectional study of 232 workers (response rate 100%) in a tile factory and 76 office workers (response rate 73%) from four factories in Thailand was conducted in 2006-2007. Participants answered a questionnaire and performed spirometry. Factory workers had lower spirometric functions than office workers, especially those with high dust exposure. There was a dose-response relation between duration of dust exposure and FEV1 and FVC, the adjusted effect of ≥ 21 years of exposure on FEV1 being -240 ml (-100 to -380) and on FVC -300 ml (-140 to -460). The adverse effect of dust on lung function was larger in current smokers suggesting synergism between smoking and tile dust exposure. This study provides evidence that long-term exposure to dust in tile industry is related to lung function reduction. There was a suggestion of synergistic effect between dust exposure and smoking. Tile factories should consider measures to reduce dust exposure and arrange spirometry surveillance for workers with such exposure. Smoking cessation should be promoted to prevent harmful effects of occupational tile dust exposure.

Upgrade of the ATLAS hadronic Tile calorimeter for the High luminosity LHC

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00236332; The ATLAS collaboration

2016-01-01

The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the central region of the ATLAS detector at the LHC. It is a sampling calorimeter consisting of alternating thin steel plates and scintillating tiles. Wavelength shifting fibers coupled to the tiles collect the produced light and are read out by photomultiplier tubes. An analog sum of the processed signal of several photomultipliers serves as input to the first level of trigger. Photomultiplier signals are then digitized and stored on detector and are only transferred off detector once the first trigger acceptance has been confirmed. The Large Hadron Collider (LHC) has envisaged a series of upgrades towards a High Luminosity LHC (HL-LHC) delivering five times the LHC nominal instantaneous luminosity. The ATLAS Phase II upgrade, in 2024, will accommodate the detector and data acquisition system for the HL-LHC. In particular, TileCal will undergo a major replacement of its on- and off-detector electronics. All signals will be digitized and then...

Upgrade of the ATLAS hadronic Tile calorimeter for the High luminosity LHC

CERN Document Server

Mlynarikova, Michaela; The ATLAS collaboration

2017-01-01

The Tile Calorimeter (TileCal) is the hadronic calorimeter covering the central region of the ATLAS detector at the LHC. It is a sampling calorimeter consisting of alternating thin steel plates and scintillating tiles. Wavelength shifting fibers coupled to the tiles collect the produced light and are read out by photomultiplier tubes. Currently, an analog sum of the processed signal of several photomultipliers serves as input to the first level of trigger. Photomultiplier signals are then digitized and stored on detector and are only transferred off detector once the first trigger acceptance has been confirmed. The Large Hadron Collider (LHC) has envisaged a series of upgrades towards a High Luminosity LHC (HL-LHC) delivering five times the LHC nominal instantaneous luminosity. The ATLAS Phase II upgrade, in 2024, will accommodate the detector and data acquisition system for the HL-LHC. In particular, TileCal will undergo a major replacement of its on- and off-detector electronics. All signals will be digitiz...

Tests with beam setup of the TileCal Phase-II upgrade electronics

CERN Document Server

Hlaluku, Dingane Reward; The ATLAS collaboration

2017-01-01

The LHC has planned a series of upgrades culminating in the High Luminosity LHC (HL-LHC) which will have an average luminosity 5-7 times larger than the nominal Run-2 value. The ATLAS Tile Calorimeter (TileCal) will undergo an upgrade to accommodate to the HL-LHC parameters. The TileCal electronics both on- and off-detector will be completely redesigned and a new readout architecture will be adopted. The photomultiplier signals will be digitised and transferred to the TileCal PreProcessors (PPr) located off-detector for every bunch crossing. Then, the PPr will provide preprocessed digital data to the first level trigger with improved spatial granularity and energy resolution with respect to the current analog trigger signals. We plan to insert one TileCal module instrumented with the new electronics in the real detector to evaluate and qualify the new readout and trigger concepts in the overall ATLAS data acquisition system. This new drawer, so-called Hybrid Demonstrator, must provide analog trigger signal fo...

Retention of Hydrogen Isotopes in Divertor Tiles Used in JT-60U

International Nuclear Information System (INIS)

Hirohata, Y.; Shibahara, T.; Tanabe, T.; Oya, Y.; Arai, T.; Gotoh, Y.; Masaki, K.; Yagyu, J.; Oyaidzu, M.; Okuno, K.; Nishikawa, M.; Miya, N.

2005-01-01

Retention characteristics of deuterium and hydrogen retained in graphite tiles placed in the divertor region of JT-60U were investigated by thermal desorption spectroscopy (TDS). The deuterium retained in the near surface of all graphite tiles was mostly replaced by hydrogen due to exposure to hydrogen plasma at the final stage operations, resulting in main deuterium retention in the deeper region. The dominant species desorbed from the divertor tiles were H 2 , HD, D 2 and CH 4 . The smallest retention of hydrogen isotopes (H+D) was observed in the outer divertor tile which was eroded with maximum of 20 μm depth. The amount of H+D retained in the inner divertor tiles covered by the re-deposited layers increased with the thickness of the re-deposited layers. Hydrogen isotopes concentration ((H+D)/C) in the re-deposited layers was ∼0.02, which was much smaller than those observed in JET and other devices

Tile drainage phosphorus loss with long-term consistent cropping systems and fertilization.